Do Croatian open access journals support ethical research? Content analysis of instructions to authors

Introduction

The aim of our study was to investigate the extent to which Instructions to authors of the Croatian open access (OA) journals are addressing ethical issues. Do biomedical journals differ from the journals from other disciplines in that respect? Our hypothesis was that biomedical journals maintain much higher publication ethics standards.

Materials and methods

This study looked at 197 Croatian OA journals Instructions to authors to address the following groups of ethical issues: general terms; guidelines and recommendations; research approval and registration; funding and conflict of interest; peer review; redundant publications, misconduct and retraction; copyright; timeliness; authorship; and data accessibility. We further compared a subset of 159 non-biomedical journals with a subset of 38 biomedical journals. Content analysis was used to discern the ethical issues representation in the instructions to authors.

Results

The groups of biomedical and non-biomedical journals were similar in terms of originality (χ² = 2.183, P = 0.140), peer review process (χ² = 0.296, P = 0.586), patent/grant statement (χ² = 2.184, P = 0.141), and timeliness of publication (χ² = 0.369, P = 0.544). We identified significant differences among categories including ethical issues typical for the field of biomedicine, like patients (χ² = 47.111, P < 0.001), and use of experimental animals (χ² = 42.543, P < 0.001). Biomedical journals also rely on international editorial guidelines formulated by relevant professional organizations heavily, compared with non-biomedical journals (χ² = 42.666, P < 0.001).

Conclusion

Low representation or absence of some key ethical issues in author guidelines calls for more attention to the structure and the content of Instructions to authors in Croatian OA journals.Key words: instructions to authors, publication ethics, publication standards, open access, OA, research integrity     

Discriminative sentence compression with conditional random fields

The paper focuses on a particular approach to automatic sentence compression which makes use of a discriminative sequence classifier known as Conditional Random Fields (CRF). We devise several features for CRF that allow it to incorporate information on nonlinear relations among words. Along with that, we address the issue of data paucity by collecting data from RSS feeds available on the Internet, and turning them into training data for use with CRF, drawing on techniques from biology and information retrieval. We also discuss a recursive application of CRF on the syntactic structure of a sentence as a way of improving the readability of the compression it generates. Experiments found that our approach works reasonably well compared to the state-of-the-art system [Knight, K., & Marcu, D. (2002). Summarization beyond sentence extraction: A probabilistic approach to sentence compression. Artificial Intelligence 139, 91–107.].     

Flow of DNA solutions in a microfluidic gradual contraction

The flow of λ-DNA solutions in a gradual micro-contraction was investigated using direct measurement techniques. The effects on DNA transport in microscale flows are significant because the flow behavior is influenced by macromolecular conformations, both viscous and elastic forces dominate inertial forces at this length scale, and the fully extended length of the molecule approaches the characteristic channel length w_c (L/w_c ∼ 0.13). This study examines the flow of semi-dilute and entangled DNA solutions in a gradual planar micro-contraction for low Reynolds numbers (3.7 × 10⁻⁶< Re < 3.1 × 10⁻¹) and high Weissenberg numbers (0.4 < Wi < 446). The semi-dilute DNA solutions have modest elasticity number, El = Wi/Re = 55, and do not exhibit viscoelastic behavior. For the entangled DNA solutions, we access high elasticity numbers (7.9 × 10³< El < 6.0 × 10⁵). Video microscopy and streak images of entangled DNA solution flow reveal highly elastic behavior evidenced by the presence of large, stable vortices symmetric about the centerline and upstream of the channel entrance. Micro-particle image velocimetry measurements are used to obtain high resolution, quantitative velocity measurements of the vortex growth in this micro-contraction flow. These direct measurements provide a deeper understanding of the underlying physics of macromolecular transport in microfluidic flow, which will enable the realization of enhanced designs of lab-on-a-chip systems.     

Polyphosphonium-based ion bipolar junction transistors

Advancements in the field of electronics during the past few decades have inspired the use of transistors in a diversity of research fields, including biology and medicine. However, signals in living organisms are not only carried by electrons but also through fluxes of ions and biomolecules. Thus, in order to implement the transistor functionality to control biological signals, devices that can modulate currents of ions and biomolecules, i.e., ionic transistors and diodes, are needed. One successful approach for modulation of ionic currents is to use oppositely charged ion-selective membranes to form so called ion bipolar junction transistors (IBJTs). Unfortunately, overall IBJT device performance has been hindered due to the typical low mobility of ions, large geometries of the ion bipolar junction materials, and the possibility of electric field enhanced (EFE) water dissociation in the junction. Here, we introduce a novel polyphosphonium-based anion-selective material into npn-type IBJTs. The new material does not show EFE water dissociation and therefore allows for a reduction of junction length down to 2 μm, which significantly improves the switching performance of the ion transistor to 2 s. The presented improvement in speed as well the simplified design will be useful for future development of advanced iontronic circuits employing IBJTs, for example, addressable drug-delivery devices.There has been a recent interest in developing diodes^1–4 and transistors^4–8 that conduct and modulate ion currents. Such non-linear iontronic components are, for example, interesting as they allow further control of ions in, for instance, electrophoretic drug delivery devices. A range of microfabricated diodes,^9–11 transistors,^12,13 and circuits^9,14 has been constructed using ion-selective membranes. These membranes contain fixed charges of either polarity, compensated by mobile ions of opposite charge (counter-ions). When immersed in an electrolyte, counter-ions can move through the membrane, while ions with the same charge as the fixed charges (co-ions) are repelled. This renders the membrane selective for the counter-ion and can therefore be considered as p- or n-type ion conductors. By combining two membranes of opposite polarity, a bipolar membrane (BM) configuration is obtained¹⁵ (Figure 1(a)). The BM junction can be biased by an ion current in the reverse and forward directions, respectively.^16,17 This modulates the ion concentration inside the BM, and thus the ionic conductivity, which then results in an current rectification.^2,18 In the three-terminal ion bipolar junction transistor¹² (IBJT), an ion-selective base (B) is connected to oppositely selective emitter (E) and collector (C), forming two BM configurations (EB and BC) (Figure 1(b)). pnp- and npn-IBJTs have been constructed¹⁴ from photolithography patterned poly(styrene sulfonate) (PSS, p-selective) and quaternized poly(vinylbenzyl chloride) (n-selective) as emitter, collector, and base. In these devices, a neutral poly(ethylene glycol) (PEG) electrolyte is typically inserted into the junction to separate the base from the emitter and collector,¹² in order to avoid¹⁹ electric field enhanced (EFE) water dissociation¹⁶ (Figure 1(a)). EFE water dissociation is typically observed in BMs²⁰ and produces water ions inside the BM under reverse bias, which prevents proper IBJT operation. In PEG-IBJTs, the current between the emitter and collector (I_C) is thus modulated by controlling the ion concentration inside the PEG-junction.²¹ Ions are injected or extracted into the junction depending on the bias of the base (V_EB). In a npn-IBJT, a positive bias is typically applied between emitter and collector (V_EC), thus allowing anions to migrate from the emitter to the collector. In the cut-off mode (Figure 1(c)), a negative bias V_EB is applied, resulting in reverse bias of both EB and BC. Cations in the junction will migrate into the base, while anions will primarily migrate into the collector, due to the higher collector bias. This base current (I_B) will extract ions from the junction, which decreases the ionic conductivity in the junction resulting in a low I_C. Eventually, the resistive characteristics for ion charge transport, between the emitter and collector, will be entirely dominated by the junction. This gives that most of the applied V_EC is consumed across the junction with only a minimal voltage potential drop across the emitter and base terminals.Open in a separate windowFIG. 1.(a) The modes of operation for a BM; forward bias (high conduction and ion accumulation), reverse bias (low conduction and ion depletion), and EFE water dissociation (high conduction, formation of ions). (b) Illustrations of an npn-IBJT, with anion-selective emitter (E) and collector (C) forming a junction with a cation-selective base (B). (c) In cut-off mode, the base and collector extract ions from the junction, prohibiting co-ion migration through the base. (d) In active mode, the forward biased EB injects ions into the base, thus allowing anions from the emitter to migrate as co-ions through the base into the collector.In the active-mode of the npn-IBJT (Figure 1(d)), the V_EB bias at the base is reversed (i.e., now positive). This causes injection of cations, from the base, and anions, from the emitter, into the junction. As the ion concentration increases, anions from the emitter can start to drift across the junction to the collector, thus a high I_C is obtained. The high concentration of ions inside the junction is reflected in a low resistive value for ion transport. This now causes the voltage to drop over the emitter and collector terminals, thus lowering the EB forward bias and the injection of ions from the base. At the collector-junction interface, the extraction of anions produces an ion depletion zone and a corresponding voltage drop. Thus, in the active-mode, the applied V_EC is primarily consumed across the emitter and collector terminals and also at the collector-junction interface.The switching speed of an IBJT should be strongly correlated to the distance separating the emitter and collector,¹⁴ as this length determines the volume that needs to be filled or emptied with ions causing modulation of ions in the junction. To achieve a fast-switching IBJT, the junction volume, i.e., the collector-emitter separation, should be as small as possible. However, EFE water dissociation must be avoided since this process ruin the IBJT operation. EFE water dissociation is, in part, driven by the appearance of a large potential drop across a small distance, as occurring at the interface of a BM under reverse bias, producing a high electric field that accelerates the forward reaction rate of water auto-dissociation.¹⁶ Miniaturization of the collector-emitter distance is therefore problematic, as the separation inside the EB and BC BMs evidently also mush shrink, resulting in higher reverse bias electric fields across the BMs and thus promoting EFE water dissociation. The problem of EFE water dissociation in an IBJT primarily manifests itself in the cut-off mode, as water ions are generated in the reversed biased EB and BC BMs. These ions produce an elevated cut-off I_C, and hence deteriorate the IBJTs on–off performance. Here, we report an IBJT, in which the EFE water dissociation is avoided by the use of a novel polyphosphonium-based anion-selective material, which previously has been shown to prevent EFE water dissociation in BM diodes.¹¹ This allows the collector and emitter to directly contact the base without an intermediate PEG-layer. Without the need for a PEG-separator inside the BMs, the collector-emitter distance is reduced to only 2 μm.Polyphosphonium-based npn-IBJTs were produced following the same manufacturing protocol as was reported for polyphosphonium-based ion diodes.¹¹ Conjugated polymer electrodes and cation-selective base was patterned from ∼200 nm thick poly(3,4-ethylenedioxythiophene):polystyrene sulfonate film on polyethylene terephthalate-sheets using photolithography and dry-etching. The base was rendered electronically insulating by chemical overoxidation via exposure to sodium hypochlorite through a mask. A 2 μm thick SU8-layer was patterned on-top of this configuration, with an opening defining the actual junction. 1 μm thick polyphosphonium-based anion-selective emitter and collector were deposited and patterned using photolithography and dry-etching, to overlap with the base at the opening of the SU8. Finally, a second 10 μm thick layer of SU8 was used to seal the junction. The membranes were hydrated by incubation in dH2O for 24 h before any measurements were carried out. Aqueous 0.1M NaCl electrolytes were used during the measurement. All electrical measurements were performed using a Keithley 2602 source meter.The switching characteristics of the npn-IBJT were obtained by applying V_EC of 10 V and alternating V_EB at ±3 V for various duration of time, see Figure ​Figure2.2. A periodic 5 s switching with 8 Hz measurement rate was used to record the dynamics of the turn-on/off characteristics of the device. When V_EB switches from −3 to +3 V, there is a quick increase in the I_B, as ions from the base and emitter migrate into the emitter/base junction. After a delay of ∼0.25 s, I_C starts to increase due to the increased ion concentration in the emitter/base junction and the subsequent diffusion of anions into the base. As the I_C increases, the I_B decreases as the voltage drop between the emitter and base decreases, and after ∼2 s I_C reaches 90% of the steady state on-current level. For longer on-switching times, the I_B and I_C stay stable over 30 s, after which a small increase is observed. This current-drift in both I_B and I_C is likely due to the contribution of co-ion migration. As cations from the base migrate into the emitter as co-ions, the conductivity in the emitter increases, leading to an increased I_C value. This increases the ion concentration at the base, which gives less selective ion injection and thus more cation injection from the base, i.e., a higher I_B.Open in a separate windowFIG. 2.Emitter-collector current response as the IBJT is switched between cut-off (V_EB = −3 V) and active mode (V_EB = 3 V) for V_EC = 10 V, at 5 s and 120 s periods.As V_EB is switched back to −3 V, there is a sharp negative peak in I_E as ions are extracted from the junction, which occur mainly through the base (cations) and collector (anions) terminals. As the ion concentration in the base drops, I_C decreases. The transistor turns off to 10% of the value of the steady state on-current within ∼2 s, regardless of the duration of the on-state. The constant turn-off time indicates that ions are not accumulating to a significant extent inside the junction during the on-steady state but are instead constantly transported out of the junction. When all co-ions have been extracted from the junction, the Donnan exclusion prevents subsequent injection of anions into the base, and I_C is therefore low. The on/off ratio of I_C reaches above 100.A transfer curve was obtained by scanning V_EB between −3 and +3 V while keeping V_EC at 10 V (Figure 3(a)). As expected, both I_C and I_B remain low for negative V_EB. In this range, both EB and BC are biased in reverse direction. As V_EB turns positive, the EB configuration is switched into forward bias and ions are injected into the junction. This leads to a linear increase in I_C vs. V_EB. For the reverse scan, a minor hysteresis is observed for both the I_C and I_B scans, again probably due to the contribution of co-ion migration due to long time operation of the device.Open in a separate windowFIG. 3.Transfer and output curves. (a) The transfer curve is low for negative V_EB and increases linearly for positive V_EB with approximately zero threshold. (b) The output curves show I_C saturating with respect of V_EC for positive V_EB.The transistor output characteristics were obtained by scanning V_EC at different V_EB values (Figure 3(b)). The saturation regime, i.e., the bias mode was both EB and BC are in forward bias, was avoided as this has negative impact on the stability of the device. As reported for previous IBJT devices, the output characteristics show a clear saturation behaviour of I_C across the entire range of V_EC. Further, the I_C increases linearly with V_EB. The increase of both I_C and I_B when operating for extended periods of time in the active mode is again attributed to the addition and inclusion of co-ions in the junction. The current gain (I_C/I_B) at V_EC = 10 V decreases with V_EB and reaches 43.9, 17.9, and 10.7 for V_EB = 1 V, 2 V, and 3 V, respectively. For higher base bias voltages, the ion concentration increases in the junction and thus the injection selectivity decreases.In comparison with previously reported IBJTs,^12,14,21 the lack of a neutral electrolyte layer in the junction has an overall positive effect on the device characteristics. Main performance improvements are found in a decrease in the turn-on time from 9 s (for npn-IBJT²¹) to 2 s, for devices with comparable junction widths and heights. The main contribution to the improved switching speed is likely the decreased length between the emitter and collector. Interestingly, simulations have shown that an extended space charge region (ESCR), for a PEG-IBJT in cut-off mode, can extend several micrometers away from the collector.²² Thus, a PEG-IBJT with an emitter-collector separation of single micrometers should show an increased cut-off current due to the ESCR overlapping in the junction. However, by omitting the PEG in the junction, the ESCR is reduced due to screening from the fixed charges in the BM layers. This enables the IBJT, reported here, to operate with retained low cut-off currents. On-off ratios and ion current gains are approximately equal to previous IBJTs,^12,14,21 at above 100 and 10, respectively. The on–off ratio and ion current gain are more dependent on the selectivity of the membranes and the charge of the junction.Further, the need to separate the layers in a PEG-IBJT puts high demands on the patterning resolution and alignment accuracy to reduce the separation between emitter/collector and base. As polyphosphonium allows the IBJT to be built without separation of layers, miniaturization of the junction is relatively easier to obtain. The switching speed can potentially be further improved by retaining the base material between the emitter and collector (see Figure 1(b)), thus allowing for a more direct pathway for I_C. This design would, however, require a much more accurate layer alignment or that the base patterned on top of the emitter and collector layers. In general, such modifications of device geometry are simpler to accomplish with the non-EFE water dissociating polyphosphonium as fewer active layers are used, suggesting a further use of polyphosphonium to improve switching speed and miniaturization of IBJTs. Such further advancement in IBJT performance would be welcomed, for example, in the continued work towards complex ionic circuits¹⁴ to regulate signalling in bioelectronics and in drug delivery applications, in which generation of dynamic and complex gradients, at high spatial resolution, is of generic interest.     

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C > T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by >94% of Tibetans but absent or in low frequencies (<3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10⁻⁵), red blood cell count (p = 5.72 × 10⁻⁷) and hematocrit (p = 2.57 × 10⁻⁶). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.     

Influence of buoyancy-driven flow on mass transfer in a two-stream microfluidic channel: Introduction of cryoprotective agents into cell suspensions

A variety of methods have been used to introduce chemicals into a stream or to mix two or more streams of different compositions using microfluidic devices. In the following paper, the introduction of cryoprotective agents (CPAs) used during cryopreservation of cells in order to protect them from freezing injuries and increase viability post thaw is described. Dimethylsulphoxide (DMSO) is the most commonly used CPA. We aim to optimize the operating conditions of a two-stream microfluidic device to introduce a 10% vol/vol solution of DMSO into a cell suspension. Transport behavior of DMSO between two streams in the device has been experimentally characterized for a spectrum of flow conditions (0.7 < Re < 10), varying initial donor stream concentrations, (1% vol/vol < C_o < 15% vol/vol) and different flow rate fractions (0.23 < f_q < 0.77). The outlet cell stream concentration is analyzed for two different flow configurations: one with the cell stream flowing on top of the DMSO-rich donor stream, and the other with the cell stream flowing beneath the heavy DMSO-laden stream. We establish a transition from a diffusive mode of mass transfer to gravity-influenced convective currents for Atwood numbers (A_t) in the range of (1.7 × 10⁻³ < A_t < 3.1 × 10⁻³) for the latter configuration. Flow visualization with cells further our understanding of the effect of A_t on the nature of mass transport. Cell motion studies performed with Jurkat cells confirm a high cell recovery from the device while underscoring the need to collect both the streams at the outlet of the device and suggesting flow conditions that will help us achieve the target DMSO outlet concentration for clinical scale flow rates of the cell suspension.     

Human activities aggravate nitrogen-deposition pollution to inland water over China

In the past three decades, China has built more than 87 000 dams with a storage capacity of ≈6560 km³ and the total surface area of inland water has increased by 6672 km². Leaching of N from fertilized soils to rivers is the main source of N pollution in China, but the exposure of a growing inland water area to direct atmospheric N deposition and N leaching caused by N deposition on the terrestrial ecosystem, together with increased N deposition and decreased N flow, also tends to raise N concentrations in most inland waters. The contribution of this previously ignored source of  N deposition to freshwaters is estimated in this study, as well as mitigation strategies. The results show that the annual amounts of N depositions ranged from 4.9 to 16.6 kg · ha⁻¹ · yr⁻¹ in the 1990s to exceeding 20 kg · ha⁻¹ · yr⁻¹ in the 2010s over most of regions in China, so the total mass of ΔN (the net contribution of N deposition to the increase in N concentration) for lakes, rivers and reservoirs change from 122.26 Gg N · yr⁻¹ in the 1990s to 237.75 Gg N · yr⁻¹ in the 2010s. It is suggested that reducing the N deposition from various sources, shortening the water-retention time in dams and decreasing the degree of regulation for rivers are three main measures for preventing a continuous increase in the N-deposition pollution to inland water in China.     

Molecular grafting towards high-fraction active nanodots implanted in N-doped carbon for sodium dual-ion batteries

Sodium-based dual-ion batteries (Na-DIBs) show a promising potential for large-scale energy storage applications due to the merits of environmental friendliness and low cost. However, Na-DIBs are generally subject to poor rate capability and cycling stability for the lack of suitable anodes to accommodate large Na⁺ ions. Herein, we propose a molecular grafting strategy to in situ synthesize tin pyrophosphate nanodots implanted in N-doped carbon matrix (SnP₂O₇@N-C), which exhibits a high fraction of active SnP₂O₇ up to 95.6 wt% and a low content of N-doped carbon (4.4 wt%) as the conductive framework. As a result, this anode delivers a high specific capacity ∼400 mAh g⁻¹ at 0.1 A g⁻¹, excellent rate capability up to 5.0 A g⁻¹ and excellent cycling stability with a capacity retention of 92% after 1200 cycles under a current density of 1.5 A g⁻¹. Further, pairing this anode with an environmentally friendly KS6 graphite cathode yields a SnP₂O₇@N-C||KS6 Na-DIB, exhibiting an excellent rate capability up to 30 C, good fast-charge/slow-discharge performance and long-term cycling life with a capacity retention of ∼96% after 1000 cycles at 20 C. This study provides a feasible strategy to develop high-performance anodes with high-fraction active materials for Na-based energy storage applications.     

Evaluation of the BD Vacutainer? RST blood collection tube for routine chemistry analytes: clinical significance of differences and stability study

Introduction:

Preanalytical variables account for most of laboratory errors. There is a wide range of factors that affect the reliability of laboratory report. Most convenient sample type for routine laboratory analysis is serum. BD Vacutainer^® Rapid Serum Tube (RST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) blood collection tube provides rapid clotting time allowing fast serum separation. Our aim was to evaluate the comparability of routine chemistry parameters in BD Vacutainer^® RST blood collection tube in reference with the BD Vacutainer^® Serum Separating Tubes II Advance Tube (SST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA).

Materials and methods:

Blood specimens were collected from 90 participants for evaluation on its results, clotting time and stability study of six routine biochemistry parameters: glucose (Glu), aspartate aminotransferase (AST), alanine aminotransferase (ALT), calcium (Ca), lactate dehidrogenase (LD) and potassium (K) measured with Olympus AU2700 analyzer (Beckman Coulter, Tokyo, Japan). The significance of the differences between samples was assessed by paired t-test or Wilcoxon Matched-Pairs Rank test after checking for normality.

Results:

Clotting process was significantly shorter in the RSTs compared to SSTs (2.49 min vs. 19.47 min, respectively; P < 0.001). There was a statistically significant difference between the RST and SST II tubes for glucose, calcium and LD (P < 0.001). Differences for glucose and LD were also clinically significant. Analyte stability studies showed that all analytes were stable for 24 h at 4 °C.

Conclusions:

Most results (except LD and glucose) from RST are comparable with those from SST. In addition, RST tube provides shorter clotting time.     

Correlation of Microalbuminuria with Estimated GFR (eGFR) by Cockcroft–Gault and MDRD Formula in Type 2 Diabetics and Hypertensives

Increase in urine albumin excretion rate (AER) precede a fall in glomerular filtration rate in patients developing diabetic chronic kidney disease (CKD). Our results have shown that 7 (50 %) of diabetic and hypertensive individuals with decreased GFR do not have increased AER. In this cross-sectional study, we measured AER of 75 patients with type 2 diabetes and hypertension by immunoturbidimetric method. We correlated the results with eGFR values obtained by Cockcroft–Gault and MDRD method. The method used was not a compensated method. We measured serum creatinine by modified Jaffe’s kinetic method in autoanalyzer XL-600. Analysis of data showed positive correlation between eGFR and microalbuminuria by both the methods with eGFR <60 mL/min/1.73 m². Pearson’s correlation co-efficient (r) was 0.9 (p = 0.0001) by Cockcroft–Gault formula and 0.69 (p = 0.0063) by MDRD formula. Our results concluded that there was positive correlation between AER and eGFR <60 mL/min/1.73 m². We have recognized that these two parameters provide a complimentary benefit in management of cases with CKD.     

Precision measurement of the Newtonian gravitational constant

The Newtonian gravitational constant G, which is one of the most important fundamental physical constants in nature, plays a significant role in the fields of theoretical physics, geophysics, astrophysics and astronomy. Although G was the first physical constant to be introduced in the history of science, it is considered to be one of the most difficult to measure accurately so far. Over the past two decades, eleven precision measurements of the gravitational constant have been performed, and the latest recommended value for G published by the Committee on Data for Science and Technology (CODATA) is (6.674 08 ± 0.000 31) × 10⁻¹¹ m³ kg⁻¹ s⁻² with a relative uncertainty of 47 parts per million. This uncertainty is the smallest compared with previous CODATA recommended values of G; however, it remains a relatively large uncertainty among other fundamental physical constants. In this paper we briefly review the history of the G measurement, and introduce eleven values of G adopted in CODATA 2014 after 2000 and our latest two values published in 2018 using two independent methods.     

Quantifying the volume of single cells continuously using a microfluidic pressure-driven trap with media exchange

We demonstrate a microfluidic device capable of tracking the volume of individual cells by integrating an on-chip volume sensor with pressure-activated cell trapping capabilities. The device creates a dynamic trap by operating in feedback; a cell is periodically redirected back and forth through a microfluidic volume sensor (Coulter principle). Sieve valves are positioned on both ends of the sensing channel, creating a physical barrier which enables media to be quickly exchanged while keeping a cell firmly in place. The volume of individual Saccharomyces cerevisiae cells was tracked over entire growth cycles, and the ability to quickly exchange media was demonstrated.Measuring cell growth is of primary interest to researchers who seek to study the effects of drugs, nutrients, disease, and environmental stress. This has traditionally been accomplished by monitoring the optical transmittance of large ensembles of cells and applying the Beer-Lambert Law.^1,2 Such population-scale measurements provide important culture statistics, but averaging obscures the behaviour of individual cells. In addition, these techniques often require cell synchronicity in order to correlate growth with specific points in the cell cycle, but synchronicity typically decays rapidly in many cell lines including Saccharomyces cerevisiae (yeast) cultures.³ Researchers have thus adopted methods that study the growth of individual cells. Quantifying cellular growth is especially challenging since proliferating cells such as yeast or Escherichia coli are irregularly shaped, and will only increase in size by a factor of two.⁴ Growth will affect the mass, volume, and density of the cell; having access to each of these characteristics is important in obtaining a complete picture of this process. Time-lapse fluorescence microscopy can provide valuable information as to the cell cycle progression of individual cells,⁵ but 2D optics requires geometric assumptions, and, thus, can provide an incomplete picture of growth.^6,7Microfluidic lab-on-chip devices with integrated sensors can provide high-resolution growth tracking of individual cells, either through mass, volume, or density monitoring.^4,7,8 Recently, a microfluidic mass sensor was used to track the buoyant mass of individual cells using a suspended microchannel resonator (SMR).^4,9 Monitoring growth can also be accomplished by tracking volume using microfluidic volume sensors⁷ operating on the Coulter principle.¹⁰ Trapping can be achieved by either (1) cycling the target back and forth through the sensor (pressure-driven⁴ and electrokinetic⁷) or (2) holding a cell in place (posts,¹¹ chevron structure,¹² and E-Field¹³). The former, dynamic approach, allows a single cell to be sampled periodically by reversing flow directions after a cell is detected. Simple in its implementation, this technique also has the ability to compensate for a drifting baseline current resulting from parasitic ionic changes within the sensing channel or other sources of noise. On the other hand, static traps allow cells to be held in place while the buffer is rapidly exchanged.¹² The ability to dynamically change cellular growth conditions during an experiment can lead to significant insight into the behaviour of cells in environments of varying salinity,¹⁴ oxidative,^15,16 or osmotic conditions,¹⁷ as well as the effect of nutrients¹⁸ and drugs.¹⁹In this work, we propose a device capable of tracking growth using high-resolution volume measurements, combining the best attributes of both types of measurement systems; continuous baseline correction and the ability to rapidly exchange cell media. This is accomplished by using a pressure-driven, feedback-based dynamic trap, whereby a cell is cycled back and forth through the sensor within a microfluidic channel. On-chip sieve valves positioned at both ends of the sensing channel are able to selectively capture a cell while the solution is being replaced. As proof of principle, the volume of several individual yeast cells was monitored over the course of their respective growth cycles, and the ability to quantify growth response to media exchange was demonstrated.Devices were fabricated using multilayered soft lithography with polydimethylsiloxane (PDMS) molding.²⁰ The completed device is pictured in Figure 1(a); full fabrication protocols are presented as supplementary material.²¹ To maximize measurement sensitivity, it is optimal to choose a channel width and height slightly larger than the dimensions of the target cell.²² However, yeast cells are asymmetrically shaped and tend to tumble as they traverse the sensor. Preliminary testing suggested this effect could be mitigated by having cells flow along trajectories far from the electrodes (through buoyancy), where electric field is more uniform. Thus, a channel height of 20 μm was chosen as a compromise. Channel height increases to 28 μm in the wider part of the central and bypass channels, a result of using a mold made out of reflowed photoresist.²³ Channel width was set at 25 μm through the sensor, and widens to 80 μm at the sieve valves to facilitate valve actuation, which requires a high width to height ratio.²⁰ The fluidic layer is integrated in a 35 μm thick PDMS spin-coated layer, above which sits a 50 μm tall valve channel in a 4 mm PDMS layer. Tubing connects I1 and I2 to a common inlet vial, V1 and V2 to vials filled with deionised water and O1 and O2 connect to empty vials (not pictured). Inlet pressures I1 and I2, and valve pressures V1 and V2 are controlled with manual regulators (SMC IR2000-N02-R and SMC IR2010-N02-R); outlet pressures are computer-controlled (SMC ITV-1011). This pressure scheme is detailed elsewhere.²⁴ Current pulses caused by transiting particles/cells (Figure 1(d)) were acquired by applying a 50 kHz, 220 mV AC voltage between a pair of electrodes and measuring the drawn current. This frequency is sufficiently elevated to avoid the electrical double layer capacitance at the electrode-electrolyte interface,²⁵ but low enough to avoid sensitivity to cell impedance or substrate.²⁶ The electrical setup used for these experiments has been described previously.^24,27 A temperature controller maintains the device at 30 °C.Open in a separate windowFIG. 1.(a) Micrograph of the microfluidic device. Two parallel bypass channels are connected by a sensing channel with sensing electrodes. Pressure is applied at inlets (I1, I2) and outlets (O1, O2) to control flow conditions. Valves (V1, V2) are positioned over each end of the sensing channel. Food coloring is used to highlight the valve (red) and fluidic layers (blue). (b) Flow mode: valves are unpressurized, and cells flow freely through the device. (c) Trapping mode: valves are pressurized to capture a cell within the central channel. Pressure-driven flow cycles the cell back and forth across the sensor. (d)Typical current pulses measured for a yeast cell.The cell capture, media exchange, and detection process occurs as follows. A cell suspension is loaded into the bypass channel and made to flow through the central sensing channel by imposing a pressure gradient (Figure 1(b)). Cells flowing through the sensor are observed optically; once a cell of interest is observed (a cell without a bud), valves are sealed (V1 = V2 = 35 psi). This stops all flow through the sensor, and enables bypass channels to be flushed and replaced with fresh media. After 2 min, valve channels are pressurized to 24 psi where they compress the channel to a sufficient height to physically restrict the passage of yeast cells, while allowing the media to flow through the central channel (Figure 1(c)). The pressure gradient between bypasses causes the media in the central channel to be flushed out, while the target cell is physically trapped. Replacing the media in the central channel takes 2 min. At this stage, a pressure-driven feedback-based dynamic trap can be initiated. In this dynamic trap mode, the pressure settings at O1 and O2 are adjusted to redirect the cell back and forth through the sensor, based on current pulses measured from cells transiting through the sensor. Through custom LabView® software, these outlet pressure settings are feedback-adjusted to maintain a speed of 250 μm/s in both directions at a detection frequency of 30 cells/min (Figure 1(d)). To minimize the effects of channel stretching/shrinking, the sum of pressures at O1 and O2 is held constant. This precaution was taken since the sensing channel structured within the flexible PDMS polymer will alter its geometry based on internal pressure.²⁸ The short central channel ensures steady nutrient replenishment from the bypasses. For example, a glucose molecule takes ∼4 min to diffuse from the bypass to the electrodes. In practice, Taylor-Aris dispersion will reduce this replenishment time considerably. Based on video analysis, 25% of the central channel''s media is replenished every pressure reversal (video presented as supplementary material²¹). Polystyrene microspheres of 3.9 ± 0.3 μm, 5.6 ± 0.2 μm, and 8.3 ± 0.7 μm (NIST size standards) were used to calibrate the sensor, and obtain the current pulse-to-volume calibration for every solution (supplementary material²¹). The validity of this calibration method is discussed elsewhere.²⁹ Care was taken to limit trajectory-based variations in signal: the device is positioned with electrodes at the top of the sensing channel, and with the negatively buoyant cells/particles flowing along the bottom. Based on previous experimental and theory work, we found that signal amplitude can vary as much as 3.5 fold for different heights.²⁷ The effect of trajectory on current pulse amplitude has also been reported elsewhere.^30,31 In this work, buoyancy is used to ensure that the cell flows along a trajectory at the same distance from the electrodes for every measurement.Saccharomyces cerevisiae (BY4743 Mat a/alpha, genotype: his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 LYS2/lys2Δ0 met15Δ0/MET15 ura3Δ0/ura3Δ0 ade2::LEU2/ade2::URA3) was cultured to exponential phase at 30 °C in an incubator/shaker in yeast bacto-peptone (YPD) with 2% w/v glucose, supplemented with 0.2 M NaCl, 0.05% bovine serum albumin (BSA) and 42 mg/l adenine. Sodium chloride was added to enable the current pulse measurement, at a concentration where cells are viable;³² BSA was used to prevent cell agglomeration; adenine was supplemented since this particular yeast mutant does not produce its own supply. A cell suspension was introduced into the device, from which a cell at the early stages of its cell cycle was captured, and dynamically trapped for 100 min. Three typical cell growth results are shown in Figure 2(a). Since the culture was not synchronized, this leads to variability between “initial” cell volumes: there is a 27% difference in initial volume between the cells identified by red squares and green triangles. This is caused by (1) optical limits, whereby cells chosen for study are not all at the exact same cell cycle stage and (2) differences in the age of the mother cell: the more buds a mother cell has produced, the larger it becomes.³³ On average, captured yeast cell demonstrated a doubling time consistent with growth rates under ideal incubator/shaker conditions; nutrient depletion, electric field, and shear stresses are not affecting growth. Optical inspection of budding cells confirms that most growth is occurring at the daughter cell, as expected.³³ An elevated signal-to-noise ratio allows for high resolution volumetric measurements (4 μm³); cell asymmetry⁷ and trajectory variability^27,30,31 lead to a relative standard deviation of 6% for cells and 4% for microspheres of similar size. While mass or protein synthesis methods have indicated linear³⁴ or exponential^4,6,35,36 growth curves, volume-based methods have suggested sigmoidal patterns.^7,37 Prior to daughter cell emergence, and later in the cycle as the daughter cell emerges, volumetric growth rate declines.³⁸ In this work, it is difficult to ascertain with mathematical rigor the shape of the growth profile; however, for each cell, volume increases steadily throughout the growth cycle before declining near the end of the cycle.Open in a separate windowFIG. 2.(a) Growth curves for 3 cells trapped in succession. Simultaneous optical and electrical measurements allow cell cycle stage to be correlated with volume. Pictures of cell corresponding to the red squares are presented in 15 min increments. A cell is cycled through the sensor every 2 s. For clarity, each data point for yeast volume represents the average of data points over a period of 5 min, with standard deviation. (b) Demonstration of an interrupted growth cycle, where YPD + 0.2 M NaCl was replaced with 0.2 M NaCl at 40 min, and then again returned to YPD + 0.2 M NaCl at 80 min. The media exchange process takes 4 min.To demonstrate our ability to easily exchange media while maintaining a trap, the solution was exchanged 40 min into a yeast growth cycle; culture media was replaced with a pure saline solution 0.2 M NaCl + 0.05% BSA, and then replaced again with culture media at 80 min (Figure 2(b)). Cell growth is halted temporarily while in saline solution, before resuming normal growth thereafter. The cell cycle time is extended by this period. The cell volume drifts downward after the initial solution change at 40 min. Though this drift lies within our uncertainty bounds, cellular responses to osmotic shock on similar timescales have been documented elsewhere.³⁹ This result demonstrates an ability to quickly exchange cell media, and observe cellular response.In conclusion, we have demonstrated a microfluidic device capable of maintaining a dynamic, pressure-driven cell trap, which can monitor cellular volume over the cell cycle. Concurrent optical microscopy allows for real-time visual inspection of the cells. In addition, sieve valve integration provides for the exchange of media or the addition of drugs. Such a platform could also be key in cancer cell cytotoxicity assays,⁴⁰ where growth response to anticancer drugs could be monitored.     

Black silicon as a platform for bacterial detection

Surface-enhanced Raman scattering (SERS) shows promise for identifying single bacteria, but the short range nature of the effect makes it most sensitive to the cell membrane, which provides limited information for species-level identification. Here, we show that a substrate based on black silicon can be used to impale bacteria on nanoscale SERS-active spikes, thereby producing spectra that convey information about the internal composition of the bacterial capsule. This approach holds great potential for the development of microfluidic devices for the removal and identification of single bacteria in important clinical diagnostics and environmental monitoring applications.Plasma etching of silicon can be used to produce inexpensive, large surface area, nano-textured surfaces known as black silicon. Recently, it has been shown that black silicon nano-needles can impale bacteria¹ and that it can be used as a sensor in microfluidic devices.² When coated by a plasmonic metal, such as gold, the nano-textured surface of black silicon is ideal for use as a surface-enhanced Raman scattering (SERS) sensing platform.³ This work aims to investigate whether gold-coated black silicon nano-needles can be used to both impale bacteria and identify them by SERS. This combination of properties would promote the development of microfluidic devices for the removal and monitoring of bacteria in a wide range of medical, environmental, and industrial applications.⁴Black silicon was fabricated by a reactive ion etching technique,⁵ resulting in pyramidal-shaped spikes of height 185 ± 30 nm, full width at half height of 54 ± 10 nm, and 10 ± 2.4 nm radius of curvature at the tip. Samples were then magnetron sputter coated with 200 nm of gold, as this coating thickness was found to provide a suitable compromise between SERS enhancement and impalement efficiency. E. coli (ATCC 25922) from −80 °C stock was isolated on a nutrient agar plate (Difco nutrient broth, Becton Dickinson) for approximately 12 h. A single E. coli colony was then inoculated from the plate into 20 ml of nutrient broth media and incubated overnight at 37 °C with orbital shaking at 200 rpm. The total biomass of overnight culture was adjusted to an optical density of 0.3 at λ = 600 nm by adding fresh sterile nutrient broth (Cary 50 spectrophotometer, Agilent). The E. coli planktonic cells were washed three times by centrifugation at 12 000 rpm (Centrifuge 5804 R, Eppendorf) for 2 min. The washed cells were then re-suspended in a low strength minimum medium (Dulbecco A, phosphate buffered saline). A volume of 100 μl of solution was pipetted onto substrates and left to incubate for 1 h on the bench. Separate sets of samples were created for scanning electron microscope (SEM) imaging, live/dead staining, and SERS. Three sets were needed as each of these measurements altered the samples and left them unsuitable for further analysis.The first set of samples was washed three times with milliQ water after incubation, allowed to dry and then immediately sputter coated with gold using the Emitech K975x (operating current 35 mA, sputter time 32 s, stage rotation 138 rpm, and vacuum of 1 × 10⁻² mbar). SEM imaging was performed with a Zeiss Supra 40VP in high vacuum mode with a working distance of 5 mm and an accelerating voltage of 3 kV. Figure ​Figure11 shows an example of the different levels of impalement that occurred on the black silicon surface. All cells showed signs of damage, but in some cases, the damage was limited to the perimeter of the cell and the main body appeared whole. In other cases, the entire cell had collapsed onto the spikes.Open in a separate windowFIG. 1.A typical SEM image showing E. coli cells with different levels of impalement on gold-coated black silicon.The second set of samples was used for live/dead staining (Invitrogen BacLight Bacterial Viability Kit L7012) with 3.34 mM SYTO 9 (green fluorescence) and 20 mM propidium iodide (red fluorescence). Equal volumes of both dyes were mixed thoroughly in a tube and added to the sample in a ratio of 3 μl of mixed dye to 1 ml of bacterial suspension. After mixing, a volume of 100 μl of the solution was pipetted onto the substrates, which were then incubated at room temperature in the dark for 15 min, before the staining solution was removed by pipetting. The substrates were then washed three times with milliQ water and mounted on a microscope slide for fluorescence imaging. The substrates were not allowed to dry and were stored in phosphate buffered saline at 4 °C when not in use. An epifluorescence microscope (Olympus IX71) with a mercury lamp source and a 60× water immersion objective was used to collect live/dead images from the substrates. Two filter blocks were used to collect the images: U-MNIBA2 blue excitation narrow band delivered green emission (live) and U-MWIG2 green excitation wide band provided red emission (dead).The live/dead image in Figure ​Figure22 shows a mix of both live and dead cells on the black silicon sample. The prevalence of live cells could be due to the incomplete impalement seen under SEM for some cells. It can also be explained by the sample still being wet during live/dead staining. The cells are dried prior to imaging in the SEM and this could weaken the cell wall and allow capillary forces to draw the cells onto the spikes for impalement. This hypothesis is supported by the large number of cells on the stained sample and the presence of cell groupings and cells imaged during mid-division. If the cells were immediately impaled, then such activity would not have been visible and a greater proportion of red cells would be expected.Open in a separate windowFIG. 2.Epifluorescence image showing live (green) and dead (red) E. coli cells after incubation on gold-coated black silicon.The third set of samples was washed three times with milliQ water after incubation and allowed to dry prior to spectral analysis. SERS spectra were collected with a Renishaw inVia Raman spectrometer operating at 785 nm with a 1200 l/mm grating. Power at the sample was 150 mW focused with a 100 × /0.85 NA objective to obtain a diffraction limited laser spot. The resulting spot size (≤2 μm in diameter) is well matched to the size of the bacterial cells. Spectra were collected with three accumulations of 10 s. Data were background subtracted⁶ and normalised to unity for ease of plotting. A great deal of variability was observed in the resulting spectra, as shown in Figure ​Figure33.Open in a separate windowFIG. 3.SERS spectra of E. coli after incubation on a gold-coated black silicon substrate. The spectrum numbers represent single cells at different locations and different levels of impalement.It should be noted that E. coli SERS is known to produce a high level of variability,^7–12 depending on the experimental setup.¹³ However, the variability seen in the SERS spectra of Fig. ​Fig.33 is unusual for measurements performed under consistent experimental conditions. This increased level of variability may be related to the different levels of impalement seen in Fig. ​Fig.1,1, which results in the probing of different internal components. SERS is a surface sensitive technique, with the signal primarily arising within 2 nm of the metal surface.¹⁴ Note that unlike apertureless nanoprobes¹⁵ or conical plasmonic nanotips,¹⁶ the SERS signal in black silicon arises primarily from “hot spots” between the spikes, where the plasmon resonance field is particularly strong.¹⁷ Therefore, depending on the depth and location of impalement, different biomolecules are expected to be excited by this novel substrate.Some peaks occur in the same position for multiple spectra (e.g., peak positions 420, 893, 1001, 1285, and 1307 cm⁻¹), but there are also a lot of unique peaks. The vertical lines in Fig. ​Fig.33 indicate peaks which have appeared in the literature for SERS of E. coli.^7–12 Spectrum 3 has a high proportion of peaks matching published values. This is also the case for spectrum 5, which shares a few peak positions with spectrum 3. Preliminary peak allocations have identified carbohydrates¹¹ (420 cm⁻¹), tyrosine¹¹ (650 cm⁻¹), adenine^10,11 (706 and 735 cm⁻¹), hypoxanthine⁷ (722 and1373 cm⁻¹), phenylalanine⁹ (1001 cm⁻¹), amide III (Ref. ¹⁰) (1285 cm⁻¹), CH₂ deformation¹² (1556 cm⁻¹), and C=C¹⁰ (1587 cm⁻¹).Given the varying levels of impalement observed in the SEM, it appears that the spike shape and Au coating should be further optimized to ensure that the entire cell is consistently pierced and the internal biomolecules are more comprehensively probed. In this way, it may be possible to obtain a more reproducible SERS spectrum of the internal biomolecular constituents of single bacterial cells, thereby providing rapid identification for medical and environmental diagnostic applications. Given that SERS is insensitive to water,⁴ future work should aim to achieve impalement in an aqueous environment, so that the full capability of microfluidics can be used to separate and concentrate suspended bacteria before presenting them to the substrate for rapid analysis.⁴ This suggests a broad range of potential applications in the detection, monitoring, and control of bacterial contamination.     

Diffraction-limited ultrasensitive molecular nano-arrays with singular nano-cone scattering

Large-library fluorescent molecular arrays remain limited in sensitivity (1 × 10⁶ molecules) and dynamic range due to background auto-fluorescence and scattering noise within a large (20–100 μm) fluorescent spot. We report an easily fabricated silica nano-cone array platform, with a detection limit of 100 molecules and a dynamic range that spans 6 decades, due to point (10 nm to 1 μm) illumination of preferentially absorbed tagged targets by singular scattering off wedged cones. Its fluorescent spot reaches diffraction-limited submicron dimensions, which are 10⁴ times smaller in area than conventional microarrays, with comparable reduction in detection limit and amplification of dynamic range.Commercially available fluorescent micro-arrays based on target labeling, northern blot, or enzyme-linked immunosorbent assay (ELISA) are limited to a detection threshold of 1 to 10 × 10⁶ molecules per fluorescent spot,^{1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23} thus requiring cell culturing or Polymerase Chain Reaction (PCR) amplification for many applications. The low sensitivity is often due to broad illumination, which creates auto-fluorescence noise. Even if point illumination and pin-hole filtering of non-focal plane noise are implemented in a confocal setup, the large and non-uniform fluorescent spots create scattering noise over each 20–100 μm element, which degrades the detection limit.⁴ Smaller spots can, in theory, be introduced by nano-sprays and nano-imprinting. However, directing the targets to such small areas then becomes problematic. Real-time PCR is, in principle, capable of detecting a single molecule but is limited in its target number⁵ and is hence slow/expensive for large-library assays. A large-library platform with much better detection limit than the current fluorescent microarrays would transform many screening assays. Ideally, this platform would not use the confocal configuration. Instead, it would direct the target molecules to a submicron spot and illuminate them with a nearby point source that does not require scanning.A promising platform is the optical fiber bundle array,⁶ with more than 10⁴ fibers and targets, in principle. With its endoscopic configuration, these fiber bundles are most convenient for in situ and real-time biosensing modalities in microfluidic biochips and microfluidic 3-D cell cultures. Consequently, the optical sensing is typically carried out in the transmission mode, with the optical signals transmitted through the optical fibers to a detector. Microwell arrays at the distal end of imaging fiber, with molecular targets captured and transported to the microwells by microbeads, are the most popular among these optical fiber arrays. Although detection limit better than 1 × 10⁶ molecules per bead has been reported, the bar-coded beads limit the target number of this platform.^{7, 8}Our previous work^{9, 10} has shown that plasmonics at nanotips can enhance local electric field by three orders of magnitude. However, conduction loss and quenching of fluorescence^{11, 12} by the metal substrates limit the use of plasmonic enhanced fluorescence for large-library assays. Only nano-molar sensitivity has been demonstrated using plasmonics from metal coated nanocone tips.^{13, 14} In this paper, we will extend the conical fiber array platform not by tip plasmonics but by another optical phenomenon with induced dipoles: singular scattering off dielectric wedges and tips.¹⁵ Instead of the surface plasmon resonance on metallic nanostructures,¹⁶ field focusing at the cone tip by the dielectric media (the silica fiber) is used to produce a localized and singularly large scattering intensity at the tip. Singular scattering from a wedge or a cone has been known for decades.^{17, 18} It is only recently that numerical simulation¹⁹ has revealed that field focusing by this singular scattering can effect a five-order intensity enhancement that is frequency independent. This intense tip scattering produces a local light source at the tip that does not suffer from conduction loss. Unlike plasmonic metal nanostructures, the dielectric tip would also not quench the fluorescent reporters excited by the light source. In fact, it will help scatter the fluorescent signal, with Rayleigh scattering intensity scaling with respect to wavelength. We hence utilize this phenomenon for diffraction-limit fluorescent sensing/imaging for the first time here.The local light source due to tip scattering minimizes background auto-fluorescence and scattering noise, provided the target molecules preferentially diffuse towards the dielectric vertices. If the targets do not preferentially hybridize with probes at the vertices, there would be significant target loss, with a concomitant loss in sensitivity, because the vertex regions are just a small fraction of the total area. Fortunately, like electromagnetic radiation at the electrostatic limit of the Maxwell equations for sharp (sub-wavelength) vertices,²⁰ the steady-state diffusion of molecules also obey the Laplace equation and so do the DC or AC electric potentials that drive electrophoresis and dielectrophoresis of the molecules.²¹ Hence, the diffusive, electrophoretic, and dielectrophoretic fluxes of target molecules are also singularly large at the vertices and there will be preferential hybridization there until the tip is saturated. Previously, we have demonstrated preferential diffusive transport of colloids to channel corners²² and dieletrophoretic trapping of bacteria²³ and DNA molecules²⁴ around sharp nanostructures like carbon nanotubes. Hence, dielectric nanotips fabricated by low-cost techniques can potentially provide the smallest fluorescent spot, which can preferentially capture target molecules and whose fluorescent image is limited in size only by the diffraction limit, without a confocal configuration.Although the scattering singularity is stronger at the conic tip, the total increase in scattering area of this singularity of measure zero is not as high as that of a sharp wedge, thus rendering the signal relatively weak. We hence employ a well-defined multi-wedged silica cone fabricated by wet-etching, with the wedges introduced by non-uniform stress formed during the fiber assembly process, to produce maximum scattering at the tip where three to four wedges converge (see inset of Fig. ​Fig.1A).1A). Using the reflection mode to fully exploit this singular scattering to excite fluorescent reporters at the tip and transmit the resulting signal, we report a nanocone array that can detect down to 100 molecules per cone tip with a large dynamic range from femtomolar to nanomolar concentrations. Although quantification for a single target is reported in this preliminary report, multi-target assays can readily be developed.Open in a separate windowFigure 1(A) A SEM image of the silica cone array where the single cone inset image shows three wedges converging into a 10 nm junction at the tip. (B) The optical setup of measurement. (C) The diffraction-limited fluorescent spot images.Amine-modified 35-base oligo-probes were functionalized onto both unetched silica fibers (as a control) and etched conic silica tips. The sample of 35-base ssDNA targets (corresponding to a primer for a segment of the Serotype 2 dengue genome) with a 5′ tagged Cy3 fluorophore was inserted into a microfluidic chip housing the fiber bundle (Fig. ​(Fig.1B)1B) and left overnight (see the supplementary material²⁵ for exact sequence). After a standard rinsing protocol, fluorescent images were taken with an Olympus IX-71 fluorescent microscope for target concentrations ranging from 1 fM to 1 nM. A typical fluorescent image after hybridization is shown in Fig. ​Fig.1c,1c, where each micron-sized bright spot corresponds to a single tip in the cone array. The intensity profile shown in the supplementary material²⁵ indicates a fluorescent spot smaller than 1 μm, indicating that the fluorescent light source is sub-wavelength and the resolution is close to diffraction limit. The size of this bright spot at the conic tip does not vary much with respect to the concentration but its intensity does, as shown in Fig. ​Fig.2A.2A. It was found that for flat fibers, only concentrations higher than 1 nM produced significant signals above the background. However, for etched conic fibers, 10 fM is clearly distinguishable from the background, which indicates that an improvement of sensitivity up to five orders can be realized by simply etching the flat surface into cone arrays. It also suggests very little target loss due to preferential hybridization onto the cone at sub-nM concentrations. We estimated the number of molecules per cone from the total number of molecules in target solution divided by the number of pixels on each fiber (10⁴), which suggests less than 100 molecules per cone for a 10 fM bulk concentration, four orders better than any existing technology.Open in a separate windowFigure 2(A) Fluorescent intensity of etched conic fiber and unetched fiber for different concentrations of target molecules from 1 fM to 1 nM. (B) Fluorescent intensity increases linearly with exposure time. Non-target molecules with 1 μM concentration do not produce significant signal compared to lower concentrations of target molecules such as 1 nM and 10 nM (see the supplementary material²⁵ for details of image analysis).Selectivity of the platform was also examined. Fig. ​Fig.2B2B presents the fluorescent intensity of the tips for non-target (1 μM) and target (1 nM and 10 nM) at different exposure times, which shows that fluorescent intensity increases linearly with exposure time. Beyond 5 s, saturation of images prevents further increase in the signal. For non-target, the intensity is much lower than 1 nM Target and 10 nM Target, which means non-target do not bind to the probes at the wedged tip as effectively as target molecules. Non-specific binding can be further removed by using more stringent buffers and higher flow rates.²⁶ This platform can be extended to detect 70 000 targets, in theory, by functionalizing different probes onto each cones using localized photochemistry via masking, micro-mirror directed illumination, or direct laser writing. Extension to ELISA type protein assays is also straight forward. Integration of a transmission-mode optical fiber endoscope into a microfluidic biochip and into a 3-D cell culture for real-time monitoring of multiple molecular targets at near-single molecule resolution is currently underway.     

Continuous separation of blood cells in spiral microfluidic devices

Blood cell sorting is critical to sample preparation for both clinical diagnosis and therapeutic research. The spiral inertial microfluidic devices can achieve label-free, continuous separation of cell mixtures with high throughput and efficiency. The devices utilize hydrodynamic forces acting on cells within laminar flow, coupled with rotational Dean drag due to curvilinear microchannel geometry. Here, we report on optimized Archimedean spiral devices to achieve cell separation in less than 8 cm of downstream focusing length. These improved devices are small in size (<1 in.²), exhibit high separation efficiency (∼95%), and high throughput with rates up to 1 × 10⁶ cells per minute. These device concepts offer a path towards possible development of a lab-on-chip for point-of-care blood analysis with high efficiency, low cost, and reduced analysis time.     

Dielectrophoresis based discrimination of human embryonic stem cells from differentiating derivatives

Assessment of the dielectrophoresis (DEP) cross-over frequency (f_xo), cell diameter, and derivative membrane capacitance (C_m) values for a group of undifferentiated human embryonic stem cell (hESC) lines (H1, H9, RCM1, RH1), and for a transgenic subclone of H1 (T8) revealed that hESC lines could not be discriminated on their mean f_xo and C_m values, the latter of which ranged from 14 to 20 mF/m². Differentiation of H1 and H9 to a mesenchymal stem cell-like phenotype resulted in similar significant increases in mean C_m values to 41–49 mF/m² in both lines (p < 0.0001). BMP4-induced differentiation of RCM1 to a trophoblast cell-like phenotype also resulted in a distinct and significant increase in mean C_m value to 28 mF/m² (p < 0.0001). The progressive transition to a higher membrane capacitance was also evident after each passage of cell culture as H9 cells transitioned to a mesenchymal stem cell-like state induced by growth on a substrate of hyaluronan. These findings confirm the existence of distinctive parameters between undifferentiated and differentiating cells on which future application of dielectrophoresis in the context of hESC manufacturing can be based.     

Polyphosphonium‐based bipolar membranes for rectification of ionic currents

Bipolar membranes (BMs) have interesting applications within the field of bioelectronics, as they may be used to create non-linear ionic components (e.g., ion diodes and transistors), thereby extending the functionality of, otherwise linear, electrophoretic drug delivery devices. However, BM based diodes suffer from a number of limitations, such as narrow voltage operation range and/or high hysteresis. In this work, we circumvent these problems by using a novel polyphosphonium-based BM, which is shown to exhibit improved diode characteristics. We believe that this new type of BM diode will be useful for creating complex addressable ionic circuits for delivery of charged biomolecules.Combined electronic and ionic conduction makes organic electronic materials well suited for bioelectronics applications as a technological mean of translating electronic addressing signals into delivery of chemicals and ions.¹ For complex regulation of functions in cells and tissues, a chemical circuit technology is necessary in order to generate complex and dynamic signal gradients with high spatiotemporal resolution. One approach to achieve a chemical circuit technology is to use bipolar membranes (BMs), which can be used to create the ionic equivalents of diodes^{2, 3, 4, 5} and transistors.^{6, 7, 8} A BM consists of a stack of a cation- and an anion-selective membrane, and functions similar to the semiconductor PN-junction, i.e., it offers ionic current rectification^{9, 10} (Figure ​(Figure1a).1a). The high fixed charge concentration in a BM configuration make them more suited in bioelectronic applications as compared to other non-linear ionic devices, such as diodes constructed from surface charged nanopores¹¹ or nanochannels,¹² as the latter devices typically suffers from reduced performance at elevated electrolyte concentration (i.e., at physiological conditions) due to reduced Debye screening length.¹³ However, a unique property of most BMs, as compared to the electronic PN-junction and other ionic diodes, is the electric field enhanced (EFE) water dissociation effect.^{10, 14} This occurs above a threshold reverse bias voltage, typically around −1 V, as the high electric field across the ion-depleted BM interface accelerates the forward reaction rate of the dissociation of water into H⁺ and OH⁻ ions. As these ions migrate out from the BM, there will be an increase in the reverse bias current. The EFE water dissociation is a very interesting effect and is commonly used in industrial electrodialysis applications,¹⁵ where highly efficient water dissociating BMs are being researched.¹⁶ Also, BMs have also been utilized to generate H⁺ and OH⁻ ions in lab-on-a-chip applications.^{2, 17} However, the EFE water dissociation effect diminishes the diode property of BMs when operated outside the ±1 V window, which is unwanted in, for instance, chemical circuits and addressing matrices for delivery of complex gradients of chemical species. The effect can be suppressed by incorporating a neutral electrolyte inside the BM,^{10, 18} for instance, poly(ethylene glycol) (PEG).^{2, 6, 7} However, as previously reported,² the PEG volume will introduce hysteresis when switching from forward to reverse bias, due to its ability to store large amounts of charges. This was circumvented by ensuring that only H⁺ and OH⁻ are present in the diode, which recombines into water within the PEG volume. Such diodes are well suited as integrated components in chemical circuits for pH-regulation, due to the in situ formed H⁺ and OH⁻, but are less attractive if, for instance, other ions, e.g., biomolecules, are to be processed or delivered in and from the circuit. Furthermore, a PEG electrolyte introduces additional patterning layers, making device downscaling more challenging. This is undesired when designing complex, miniaturized, and large-scale ionic circuits. Thus, there is an interest in BM diodes that intrinsically do not exhibit any EFE water dissociation, are easy to miniaturize, and that turn off at relatively high speeds. It has been suggested that tertiary amines in the BM interface are important for efficient EFE water dissociation,^{19, 20, 21} as they function as a weak base and can therefore catalyze dissociation of water by accepting a proton. For example, anion-selective membranes that have undergone complete methylation, converting all tertiary amines to quaternary amines, shows no EFE water dissociation,¹⁹ although this effect was not permanent, as the quaternization was reversed upon application of a current. Similar results were found for anion-selective membranes containing alkali-metal complexing crown ethers as fixed charges.²¹ Also, EFE water dissociation was not observed or reduced in BMs with poor ion selectivity, for example, in BMs with low fixed-charge concentration⁵ or with predominantly secondary and tertiary amines in the anion-selective membrane,²² as the increased co-ion transport reduces the electric field at the BM interface. However, due to decreased ion selectivity, these membranes show reduced rectification. In this work, we present a non-amine based BM diode that avoids EFE water dissociation, enables easy miniaturization, and provides fast turn-off speeds and high rectification.Open in a separate windowFigure 1(a) Ionic current rectification in a BM. In forward bias, mobile ions migrate towards the interface of the BM. The changing ion selectivity causes ion accumulation, resulting in high ion concentration and high conductivity. At high ion concentration, the selectivity of the membranes fails (Donnan exclusion failure), and ions start to pass the BM. In reverse bias, the mobile ions migrate away from the BM, eventually giving a zone with low ion concentration and low conductivity. Reverse bias can cause EFE water dissociation, producing H⁺ and OH^- ions. (b) Chemical structures of PSS, qPVBC, and PVBPPh₃. (c) The device used to characterize the BMs and the BM1A, BM2A, and BM1P designs. The BM interfaces are 50 × 50 μm.An anion-selective phosphonium-based polycation (poly(vinylbenzyl chloride) (PVBC) quaternized by triphenylphospine, PVBPPh₃) was synthesized and compared to the ammonium-based polycation (PVBC quaternized by dimethylbenzylamine, qPVBC) previously used in BM diodes² and transistors,^{7, 8} when included in BM diode structures together with polystyrenesulfonate (PSS) as the cation-selective material (Figure ​(Figure1b).1b). Three types of BM diodes were fabricated using standard photolithography patterning (Figure ​(Figure1c),1c), either with qPVBC (BM1A and BM2A) or PVBPPh₃ (BM1P) as polycation and either with (BM2A) or without PEG (BM1A and BM1P). Poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) electrodes covered with aqueous electrolytes were used to convert electronic input signals into ionic currents through the BMs, according to the redox reaction PEDOT⁺:PSS⁻ + M⁺ + e⁻ ↔ PEDOT⁰ + M⁺:PSS⁻.The rectifying behavior of the diodes was evaluated using linear sweep voltammetry (Figure ​(Figure2).2). The BM1A diode exhibited an increase in the reverse bias current for voltages lower than −1 V, a typical signature of EFE water dissociation,^{10, 14} which decreased the current rectification at ±4 V to 6.14. No such deviation in the reverse bias current was observed for BM2A and BM1P, which showed rectification ratios of 751 and 196, respectively. In fact, for BM1P, no evident EFE water dissociation was observed even at −40 V (see inset of Figure ​Figure2).2). Thus, the PVBPPh₃ polycation allows BM diodes to operate at voltages beyond the ±1 V window with maintained high ion current rectification.Open in a separate windowFigure 2Linear sweep voltammetry from −4 to +4 V (25 mV/s) for the BM diodes. The inset shows BM1P scanning from −40 V to +4 V (250 mV/s).The dynamic performance of the diodes was tested by applying a square wave pulse from reverse bias to a forward bias voltage of 4 V with 5–90 s pulse duration (Figure ​(Figure3).3). To access the amount of charge injected and extracted during the forward bias and subsequent turn off, the current through the device was integrated. For BM2A, we observed that the fall time increased with the duration of the forward bias pulse. This hysteresis is due to the efficient storage of ions in the large PEG volume, with no ions crossing the BM due to Donnan exclusion failure.² As a result, during the initial period of the return to reverse bias, a large amount of charge needs to be extracted in order to deplete the BM. After a 90 s pulse, 90.6% of the injected charge during the forward bias was extracted before turn-off. This may be contrasted with BM1P, where the fall time is hardly affected by the pulse duration, and the extracted/injected ratio is only 15.4% for a 90 s pulse. For this type of BM, the interface quickly becomes saturated with ions during forward bias, leading to Donnan exclusion failure and transport of ions across the BM.⁴ Thus, less charge needs to be extracted to deplete the BM, allowing for faster fall times and significantly reduced hysteresis.Open in a separate windowFigure 3Switching characteristics (5, 10, 20, 30, 60, or 90 s pulse) and ion accumulation (at 90 s pulse) of the BM2A and BM1P diodes. BM1A showed similar characteristics as BM1P when switched at ±1V (see supplementary material).²⁴Since the neutral electrolyte is no longer required to obtain high ion current rectification over a wide potential range, the size of the BM can be miniaturized. This translates into higher component density when integrating the BM diode into ionic/chemical circuits. A miniaturized BM1P diode was constructed, where the interface of the BM was shrunk from 50 μm to 10 μm. The 10 μm device showed similar IV and switching characteristics as before (Figure ​(Figure4),4), but with higher ion current rectification ratio (over 800) and decreased rise/fall times (corresponding to 90%/–10% of forward bias steady state) from 10 s/12.5 s to 4 s/4 s. Since the overlap area is smaller, a probable reason for the faster switching times is the reduced amount of ions needed to saturate and deplete the BM interface. In comparison to our previous reported low hysteresis BM diode,² this miniaturized polyphosphonium-based devices shows the same rise and fall times but increased rectification ratio.Open in a separate windowFigure 4(a) Linear sweep voltammetry and (b) switching performance of a BM1P diode with narrow junction.In summary, by using polyphosphonium instead of polyammonium as the polycation in BM ion diodes the EFE water dissociation can be entirely suppressed over a large operational voltage window, supporting the theory that a weak base, such as a tertiary amine, is needed for efficient EFE water dissociation.^{17, 18} As no additional neutral layer at the BM interface is needed, ion diodes that operate outside the usual EFE water dissociation window of ±1 V can be constructed using less active layers, fewer processing steps and with relaxed alignment requirement as compared to polyammonium-based devices. This enables the fabrication of ion rectification devices with an active interface as low as 10 μm. Furthermore, the exclusion of a neutral layer improves the overall dynamic performance of the BM ion diode significantly, as there is less hysteresis due to ion accumulation. Previously, the hysteresis of BM ion diodes has been mitigated by designing the diode so that only H⁺ and OH⁻ enters the BM, which then recombines into water.² Such diodes also show high ion current rectification ratio and switching speed but are more complex to manufacture, and their application in organic bioelectronic systems is limited due to the H⁺/OH⁻ production. By instead using the polyphosphonium-based BM diode, reported here, we foresee ionic, complex, and miniaturized circuits that can include charged biomolecules as the signal carrier to regulate functions and the physiology in cell systems, such as in biomolecule and drug delivery applications, and also in lab-on-a-chip applications.     

Effect of L-carnitine Supplementation on Nutritional Status and Physical Performance Under Calorie Restriction

L-carnitine is popular as a potential ergogenic aid because of its role in the conversion of fat into energy. The present study was undertaken to investigate the effect of short term supplementation of L-carnitine on metabolic markers and physical efficiency tests under short term calorie restriction. Male albino rats were divided into four groups (n = 12 in each)—control, calorie restricted (CR for 5 days, 25 % of basal food intake), L-carnitine supplemented (CAR, given orally for 5 days at a dose of 100 mg/kg), CR with L-carnitine supplementation (CR + CAR). Food intake and body weight of the rats were measured along with biochemical variables like blood glucose, tissue glycogen, plasma and muscle protein and enzymatic activities of CPT-1 (carnitine palmitoyl transferase-1) and AMP kinase. Results demonstrated that L-carnitine caused marked increase in muscle glycogen, plasma protein, CPT-1 activity and swim time of rats (P < 0.05) on short term supplementation. In addition to the substantive effects caused by CR alone, L-carnitine under CR significantly affected muscle glycogen, plasma protein, CPT-1 activity and AMP kinase (P < 0.05). Short term CR along with L-carnitine also resulted in increased swim time of rats than control, CR and L-carnitine treated rats (P < 0.05). The present study was an attempt towards developing an approach for better adherence to dietary restriction regimen, with the use of L-carnitine.     

A nonchlorinated solvent-processed polymer semiconductor for high-performance ambipolar transistors

Ambipolar polymer semiconductors are potentially serviceable for logic circuits, light-emitting field-effect transistors (LFETs) and polymer solar cells (PSCs). Although several high-performance ambipolar polymers have been developed, their optoelectronic devices are generally processed from toxic chlorinated solvents. To achieve the commercial applications of organic FETs (OFETs), the polymers should be processed from nonchlorinated solvents, instead of chlorinated solvents. However, most conjugated polymers show poor solubility in nonchlorinated solvents. It is of great importance to develop ambipolar polymers that can be processed from nonchlorinated solvents. Here, we develop a nonchlorinated solvent processed polymer named poly[7-fluoro-N, N^′-di(4-decyltetradecyl)-7^′-azaisoindigo-6^′,6^″-(thieno[3,2-b]thiophene-2,5-diyl)-7‴-fluoro-N^″, N‴-di(4-decyltetradecyl)-7^″-azaisoindigo-6,6‴-([2,2^″-bithiophene]-5,5^″-diyl)] (PITTI-BT) by designing a monomer with a large molar mass. The polymer displays good solubility in p-xylene (PX). Well-aligned films of PITTI-BT are achieved by an off-center spin-coating (SC) method. Based on the high-quality films, the OFETs fabricated from PX solution achieve record ambipolar performance with hole and electron mobilities of 3.06 and 2.81 cm² V⁻¹ s⁻¹, respectively. The combination of nonchlorinated solvents and good alignment process offers an effective and eco-friendly approach to obtain high-performance ambipolar transistors.