Miracle-dz/UniFAR-FTUs huggingface dataset:
Exogenous glutathione improves intracellular glutathione synthesis via the γ‐glutamyl cycle in bovine zygotes and cleavage embryos

Excess reactive oxygen species (ROS) generated in embryos during in vitro culture damage cellular macromolecules and embryo development. Glutathione (GSH) scavenges ROS and optimizes the culture system. However, how exogenous GSH influences intracellular GSH and improves the embryo developmental rate is poorly understood. In this study, GSH or GSX (a stable GSH isotope) was added to the culture media of bovine in vitro fertilization embryos for 7 days. The cleavage rate, blastocyst rate, and total cell number of blastocysts were calculated. Similarly to GSH, GSX increased the in vitro development rate and embryo quality. We measured intracellular ROS, GSX, and GSH for 0–32‐hr postinsemination (hpi) in embryos (including zygotes at G1, S, and G2 phases and cleaved embryos) cultured in medium containing GSX. Intracellular ROS significantly decreased with increasing intracellular GSH in S‐stage zygotes (18 hpi) and cleaved embryos (32 hpi). γ‐Glutamyltranspeptidase ( GGT) and glutathione synthetase ( GSS) messenger RNA expression increased in zygotes (18 hpi) and cleaved embryos treated with GSH, consistent with the tendency of overall GSH content. GGT activity increased significantly in 18 hpi zygotes. GGT and GCL enzyme inhibition with acivicin and buthionine sulfoximine, respectively, decreased cleavage rate, blastocyst rate, total cell number, and GSH and GSX content. All results indicated that exogenous GSH affects intracellular GSH levels through the γ‐glutamyl cycle and improves early embryo development, enhancing our understanding of the redox regulation effects and transport of GSH during embryo culture in vitro.
Cytotoxicity and Survival Fitness of Invasive covS Mutant of Group A Streptococcus in Phagocytic Cells

Group A streptococci (GAS) with spontaneous mutations in the CovR/CovS regulatory system are more invasive and related to severe manifestations. GAS can replicate inside phagocytic cells; therefore, phagocytic cells could serve as the niche to select invasive covS mutants. Nonetheless, the encapsulated covS mutant is resistant to phagocytosis. The fate of intracellular covS mutant in phagocytic cells and whether the intracellular covS mutant contributes to invasive infections are unclear. In this study, capsule-deficient (cap-) strains were utilized to study how intracellular bacteria interacted with phagocytic cells. Results from the competitive infection model showed that the cap- covS mutant had better survival fitness than the cap- wild-type strain in the PMA-activated U937 cells. In addition, the cap- covS mutant caused more cell damages than the cap- wild-type strain and encapsulated covS mutant. Furthermore, treatments with infected cells with clindamycin to inhibit the intracellular bacteria growth was more effective to reduce bacterial toxicity than utilized penicillin to kill the extracellular bacteria. These results not only suggest that the covS mutant could be selected from the intracellular niche of phagocytic cells but also indicating that inactivating or killing intracellular GAS may be critical to prevent invasive infection.
Bleeding Detection in Wireless Capsule Endoscopy Image Video Using Superpixel-Color Histogram and a Subspace KNN Classifier

Wireless Capsule Endoscopy (WCE) has become increasingly popular in clinical gastrointestinal (GI) disease diagnosis, benefiting from its painless and noninvasive examination. However, reviewing a large number of images is time-consuming for doctors, thus a computer-aided diagnosis (CAD) system is in high demand. In this paper, we present an automatic bleeding detection algorithm that consists of three stages. The first stage is the preprocessing, including key frame extraction and edge removal. In the second stage, we discriminate the bleeding frames using a novel superpixelcolor histogram (SPCH) feature based on the principle color spectrum, and then the decision is made by a subspace KNN classifier. Thirdly, we further segment the bleeding regions by extracting a 9-D color feature vector from the multiple color spaces at the superpixel level. Experimental results with an accuracy of 0.9922 illustrate that our proposed method outperforms the state-of-the-art methods in GI bleeding detection with low computational costs.
Comprehensive Thermal SPICE Modeling of FinFETs and BEOL with Layout Flexibility Considering Frequency Dependent Thermal Time Constant, 3D Heat Flows, Boundary/Alloy Scattering, and Interfacial Thermal Resistance with Circuit Level Reliability Evaluation

Thermal SPICE modeling with distributed R<inf>th</inf>-C<inf>th</inf> network is proposed to provide more accurate AC self-heating (SH) results than two τ<inf>c</inf> and one τ<inf>c</inf> models. The thermal time constant of the hotspot (τhotspot) in FinFETs is frequency dependent, not a constant. The severe SH by boundary/alloy scattering and interfacial thermal resistance (ITR) is included in our SPICE. The modularized components of fins, metals, and IMDs provide device and routing flexibility, without additional FEM simulation. ITR of Si<inf>80</inf>Ge<inf>20</inf>/Si<inf>1-</inf>xGe<inf>x</inf> is calculated by AMM model as the lower bound for SiGe FinFETs. The intrinsic electromigration (EM) improvement of Co interconnect (5X) is countervailed (5X→2.44X) by the increasing T<inf>metal</inf> due to the low thermal conductivity of Co. Different V2 placements on the power line of a ring oscillator (RO) are proposed to lower both the T<inf>j</inf> (FinFET) and T<inf>metal</inf>. The predicted EM MTTF of Co interconnect with the additional heat dissipation by V2 insertion is ~5.65X of W/Cu interconnect.
Optimal Application of Fractional Flow Reserve to Assess Serial Coronary Artery Disease: A 3D‐Printed Experimental Study With Clinical Validation

Background Assessing the physiological significance of stenoses with coexistent serial disease is prone to error. We aimed to use 3‐dimensional‐printing to characterize serial stenosis interplay and to derive and validate a mathematical solution to predict true stenosis significance in serial disease. Methods and Results Fifty‐two 3‐dimensional‐printed serial disease phantoms were physiologically assessed by pressure‐wire pullback (ΔFFR app) and compared with phantoms with the stenosis in isolation (ΔFFR true). Mathematical models to minimize error in predicting FFR true, the FFR in the vessel where the stenosis is present in isolation, were subsequently developed using 32 phantoms and validated in another 20 and also a clinical cohort of 30 patients with serial disease. ΔFFR app underestimated ΔFFR true in 88% of phantoms, with underestimation proportional to total FFR. Discrepancy as a proportion of ΔFFR true was 17.1% (absolute difference 0.036±0.048), which improved to 2.9% (0.006±0.023) using our model. In the clinical cohort, discrepancy was 38.5% (0.05±0.04) with 13.3% of stenoses misclassified (using FFR <0.8 threshold). Using mathematical correction, this improved to 15.4% (0.02±0.03), with the proportion of misclassified stenoses falling to 6.7%. Conclusions Individual stenoses are considerably underestimated in serial disease, proportional to total FFR. We have shown within in vitro and clinical cohorts that this error is significantly improved using a mathematical correction model, incorporating routinely available pressure‐wire pullback data.
On the Fly Reporting of Human Body Movement based on Kinect v2

Human gait analysis is of utmost importance in understanding several aspects of human movement. In clinical practice, characterizing movement in order to obtain accurate and reliable information is a major challenge, and physicians usually rely on direct observation in order to evaluate a patient’s motor abilities. In this contribution, a system that can objectively analyze the patients gait and generate an on the fly, targeted and optimized gait analysis report is presented. It is an extension to an existing system that could be used without interfering with the healthcare environment, which did not provide any on the fly feedback to physicians. Patient data are acquired using Kinect v2, followed by data processing, gait specific feature extraction, ending with the generation of a quantitative on the fly report. To the best of our knowledge, the complete system fills the gap as a proper gait analysis system, i.e., a low-cost tool that can be applied without interfering with the healthcare environment, provide quantitative gait information and on the fly feedback to physicians through a motion quantification report that can be useful in multiple areas.
Energy-Efficient Neural Network Acceleration in the Presence of Bit-Level Memory Errors

As a result of the increasing demand for deep neural network (DNN)-based services, efforts to develop hardware accelerators for DNNs are growing rapidly. However, while highly efficient accelerators on convolutional DNNs (Conv-DNNs) have been developed, less progress has been made with regards to fully-connected DNNs. Based on analysis of bit-level SRAM errors, we propose memory adaptive training with in-situ canaries (MATIC), a methodology that enables aggressive voltage scaling of accelerator weight memories to improve the energy-efficiency of DNN accelerators. To enable accurate operation with voltage overscaling, MATIC combines characteristics of SRAM bit failures with the error resilience of neural networks in a memory-adaptive training (MAT) process. Furthermore, PVT-related voltage margins are eliminated using bit-cells from synaptic weights as in-situ canaries to track runtime environmental variation. Demonstrated on a low-power DNN accelerator fabricated in 65 nm CMOS, MATIC enables up to <inline-formula> <tex-math notation="LaTeX">$3.3\times $ </tex-math></inline-formula> energy reduction versus the nominal voltage, or <inline-formula> <tex-math notation="LaTeX">$18.6\times $ </tex-math></inline-formula> application error reduction. We also perform a simulation study that extends MAT to Conv-DNNs, and characterize the accuracy impact of bit failure statistics. Finally, we develop a weight refinement algorithm to improve the performance of MAT, and show that it improves absolute accuracy by 0.8–1.3% or reduces training time by 5–<inline-formula> <tex-math notation="LaTeX">$10\times $ </tex-math></inline-formula>.
Multi-Carrier Differential Chaos Shift Keying System With Subcarriers Allocation for Noise Reduction

In this brief, a multi-carrier differential chaos shift keying system capable of mitigating channel noise is proposed. In this system, subcarriers are allocated to the reference and data signals in an optimal way, while noise reduction is achieved through reference diversity. To verify its performance, the bit error rate of the proposed system over multipath Rayleigh fading channels is derived, together with a detailed discussion about the determination of the optimal number of reference-carrying subcarriers. Extensive simulations are carried out for performance evaluation, which are further compared to other state-of-the-art systems. Results confirm the superior bit error rate performance of the proposed system, which has only small loss in energy and spectral efficiencies.
Case series on acute HCV in HIV-negative men in regular clinical practice: a call for action.

BACKGROUND The evidence that HIV treatment as prevention (TasP) and HIV pre-exposure prophylaxis (PrEP) reduces the risk of HIV transmission is overwhelming. But as PrEP and TasP can lead to increased sexual mixing between HIV positive and negative men who have sex with men (MSM), sexually transmitted infections such as acute hepatitis C (HCV), which were thought to be limited to HIV-infected MSM, could become more frequent in HIV uninfected MSM as well. The objective of this study was to describe a series of cases of sexually transmitted HCV infections in HIV-uninfected MSM in the Netherlands and Belgium. METHODS Through the Dutch Acute HCV in HIV Study (a Dutch-Belgian prospective multicentre study on the treatment of acute HCV infection, NCT02600325) and the Be-PrEP-ared study (a PrEP project in Antwerp, EudraCT2015-000054-37) several acute HCV infections were detected in HIV-negative men. RESULTS A newly acquired HCV infection was diagnosed in ten HIV-negative MSM. HCV was diagnosed at a sexually transmitted infection (STI) clinic (n = 2), by their general practitioner (n = 2), by their HIV physician (n = 1) or at a PrEP clinic (n = 5). Ten patients reported unprotected anal intercourse and four had a concomitant STI at the time of HCV diagnosis. Six patients reported using drugs during sex. CONCLUSIONS Our observation calls for a larger nationwide epidemiological study on the prevalence, incidence and risk factors of HCV infection in HIV-uninfected MSM. In the changing landscape of TasP and PrEP, reliable and up-to-date epidemiological data on HCV among HIV-uninfected MSM are needed and will help in developing evidence-based testing policies.
CUNI x-ling: Parsing Under-Resourced Languages in CoNLL 2018 UD Shared Task

This is a system description paper for the CUNI x-ling submission to the CoNLL 2018 UD Shared Task. We focused on parsing under-resourced languages, with no or little training data available. We employed a wide range of approaches, including simple word-based treebank translation, combination of delexicalized parsers, and exploitation of available morphological dictionaries, with a dedicated setup tailored to each of the languages. In the official evaluation, our submission was identified as the clear winner of the Low-resource languages category.
Is the alcohol industry doing well by ‘doing good’? Findings from a content analysis of the alcohol industry’s actions to reduce harmful drinking

Objectives The aims of this study were to: (1) describe alcohol industry corporate social responsibility (CSR) actions conducted across six global geographic regions; (2) identify the benefits accruing to the industry (‘doing well’); and (3) estimate the public health impact of the actions (‘doing good’). Setting Actions from six global geographic regions. Participants A web-based compendium of 3551 industry actions, representing the efforts of the alcohol industry to reduce harmful alcohol use, was issued in 2012. The compendium consisted of short descriptions of each action, plus other information about the sponsorship, content and evaluation of the activities. Public health professionals (n=19) rated a sample (n=1046) of the actions using a reliable content rating procedure. Outcome measures WHO Global strategy target area, estimated population reach, risk of harm, advertising potential, policy impact potential and other aspects of the activity. Results The industry actions were conducted disproportionately in regions with high-income countries (Europe and North America), with lower proportions in Latin America, Africa and Asia. Only 27% conformed to recommended WHO target areas for global action to reduce the harmful use of alcohol. The overwhelming majority (96.8%) of industry actions lacked scientific support (p<0.01) and 11.0% had the potential for doing harm. The benefits accruing to the industry (‘doing well’) included brand marketing and the use of CSR to manage risk and achieve strategic goals. Conclusion Alcohol industry CSR activities are unlikely to reduce harmful alcohol use but they do provide commercial strategic advantage while at the same time appearing to have a public health purpose.
Feasibility of an Interactive Voice Response System for Daily Monitoring of Illicit Opioid Use During Buprenorphine Treatment

In-person retrospective timeline follow-back (TLFB) interviews are a well-established method for collecting self-reports of drug use from patients. However, this method can require significant staff and patient time. In the context of a randomized clinical trial evaluating interim buprenorphine dosing, we examined the feasibility of an interactive voice response (IVR) system for daily monitoring of illicit opioid use during buprenorphine treatment, with a focus on the agreement of illicit opioid use self-report data collected from the concurrent IVR methodology versus retrospective TLFB interviews. Participants (n = 24) received buprenorphine maintenance for 12 weeks and completed nightly IVR calls in which they reported illicit opioid use in the prior 24 hrs. At approximately weekly visits, they provided in-person TLFB reports of illicit opioid use. Levels of data collection were high for both IVR and TLFB methodologies (94.2% vs. 98.5%, respectively) and did not differ. Overall agreement between the 2 methods was high (97%), whereas Cohen’s kappa was moderate (k = 0.60). When self-report data were compared with urinalysis results for illicit opioid use, IVR and TLFB approaches both showed high specificity (∼99%), although sensitivity was greater for the TLFB method (48% and 69% for IVR and TLFB, respectively; p = .003). These pilot data suggest that an automated IVR approach may offer an efficient alternative for monitoring self-reported opioid use, especially in rural or resource-constrained settings. Additional efforts to understand and improve IVR sensitivity are warranted.
Bioactive Constituents of Lamium album L. as Inhibitors of Cytokine Secretion in Human Neutrophils

The traditional role of Lamium album L. (white dead nettle, Lamiaceae) in providing relief from pain in rheumatism as well as vaginal and cervical inflammation was described. The aim of the study was to screen for the anti-inflammatory bioactivity of compounds isolated from aqueous-methanolic extract of Lamium album herb in human neutrophils (PMNs). The effect of the compounds on the inhibition of selected inflammatory markers released by neutrophils, such as cytokines (IL-8, TNF-α), was studied. The molecular masses and the purity of compounds were determined using high-performance liquid chromatography coupled with diode array detection and mass spectrometry (HPLC-DAD-MSn). The level of cytokines production after incubation with the compounds (1–25 µM) was measured by ELISA. Two derivatives of quercetin, not previously described, were isolated in this study. Phenylpropanoids (verbascoside and phlinoside D), as well as iridoids (lamalbid, and shanzhiside methyl ester), and flavonoids revealed to be more significant inhibitors of IL-8 secretion than TNF-α. The compounds at a concentration of 25 µM, except for shanzhiside methyl ester (6), inhibited secretion of IL-8 in the range from 29.1 to 50.0%. In conclusion, L. album might be a valuable source of bioactive compounds and may provide constituents to limit noninfectious inflammation associated with the aforementioned diseases.
Local Evaluation of Variation in Pulse Wave Velocity over the Cardiac Cycle using Single-Element Ultrasound Transducer

A method and system for single-site measurement of local pulse wave velocity (PWV) and its variation over the cardiac cycle are presented. The proposed system employs a single-element ultrasound transducer and associated custom technology to record arterial diameter and wall thickness waveforms in real-time. Simultaneously acquired blood pressure, diameter and wall thickness parameters were used to evaluate diastolic local PWV (CD) and systolic local PWV (Cs) from an arterial site of interest. The developed prototype system was validated on a cohort of 15 subjects (age $=43\pm 12$ years) that includes normotensives and hypertensives. Cs and CD measurements were obtained from the left carotid artery. A significant difference between carotid Cs and CD $(\Delta \mathrm{C})$ was observed in all recruited subjects (group average $\Delta \mathrm{C} = 0.92\pm 0.76\mathrm{m}/\mathrm{s})$, illustrating the arterial pressure dependency of local PWV. The absolute values of Cs and CD were within a range of 3.39 m/s to 7.5 m/s and 3.12 m/s to 5.82 m/s respectively. Normotensive versus hypertensive group-wise analysis was performed to investigate the degree of variation in the carotid local PWV over a cardiac cycle among different BP categories. Study results demonstrated that the proposed approach has a potential to provide valuable surrogate markers for cardiovascular risk assessment.
Sex‐Biased Dispersal Obscures Species Boundaries in Integrative Species Delimitation Approaches

Abstract Accurate delimitation of species is crucial for a stable taxonomy, which provides the foundation for the study of evolutionary biology, ecology, and essentially all biological disciplines. Several approaches toward impartial and repeatable taxonomic practices are available but all existing methods have potentially unacceptable shortcomings. In particular, problems can arise when the underlying model assumptions are violated, for instance, in the presence of reduced gene flow. This is observed in the context of sex‐biased dispersal, which is a common but underappreciated feature in many groups of organisms. Previously, simulations have indicated that sex‐biased dispersal may lead to erroneous estimations of the true species numbers. However, this phenomenon has never been examined using empirical data. We evaluate the bias introduced by extreme female philopatry on a range of de novo [GMYC, PTP, ABGD, statistical parsimony, trinomial distribution of triplets model (tr2)] and validation (STACEY, iBPP) approaches to species delimitation in the scarab beetle genus Pachypus. Since female philopatry exhibited in this genus in particular can affect mitochondrial gene flow, we compared the results from analyses of single loci, mitochondrial loci, nuclear loci and combined data, as well as the performance of morphometric data as a secondary data source in a fully integrative Bayesian framework. Large overestimation of species numbers was observed across all analyses of combined and mitochondrial DNA data sets, suggesting specimens from nearly every sampling location as separate species. The use of nuclear data resulted in more reasonable estimations of species boundaries, which were largely supported by morphometrics of linear measurements, while geometric morphometrics of body outlines resulted in stronger splitting. Simulations of population divergence with migration, corresponding to the biology of Pachypus, showed that female philopatry strongly increases reciprocal monophyly of mitochondrial markers and may substantially contribute to over‐splitting in species delimitation. Robust results recovered using nuclear DNA and morphological data nevertheless enabled us to reach novel conclusions about species boundaries in Pachypus. Our findings suggest that mitochondrial DNA will be less suited to species delimitation in many cases, in particular in the presence of sex‐biased dispersal.