Miracle-dz/UniFAR-FTUs huggingface dataset:
Obinutuzumab induces superior B-cell cytotoxicity to rituximab in rheumatoid arthritis and systemic lupus erythematosus patient samples

Abstract Objective. A proportion of RA and SLE patients treated with standard doses of rituximab (RTX) display inefficient B cell deletion and poor clinical responses that can be augmented by delivering higher doses, indicating that standard-dose RTX is a sub-optimal therapy in these patients. This study aimed to investigate whether better responses could be achieved with mechanistically different anti-CD20 mAbs. Methods. We compared RTX with obinutuzumab (OBZ), a new-generation, glycoengineered type II anti-CD20 mAb, in a series of in vitro assays measuring B cell cytotoxicity in RA and SLE patient samples. Results. We found that OBZ was at least 2-fold more efficient than RTX at inducing B-cell cytotoxicity in in vitro whole blood assays. Dissecting this difference, we found that RTX elicited more potent complement-dependent cellular cytotoxicity than OBZ. In contrast, OBZ was more effective at evoking Fc gamma receptor-mediated effector mechanisms, including activation of NK cells and neutrophils, probably due to stronger interaction with Fc gamma receptors and the ability of OBZ to remain at the cell surface following CD20 engagement, whereas RTX became internalized. OBZ was also more efficient at inducing direct cell death. This was true for all CD19+ B cells as a whole and in naïve (IgD+CD27−) and switched (IgD−CD27+) memory B cells specifically, a higher frequency of which is associated with poor clinical response after RTX. Conclusion. Taken together, these data provide a mechanistic basis for resistance to rituximab-induced B-cell depletion, and for considering obinutuzumab as an alternative B-cell depleting agent in RA and SLE.
The Effect of Applied Voltage and Anodisation Time on Anodized Aluminum Oxide Nanostructures

The use of anodized aluminum oxide (AAO) is vastly being explored in recent years. The application includes molecular separation, sensing, energy storage and template synthesis for various nanostructures. The reason AAO is preferred was because of the ability to control the nanopore structure by manipulating some factors during the anodisation process. This study will investigate the exploitation of voltage and anodisation time during the anodisation process and the effect it has on the nanopore structure of the AAO by examining the structure under Field Emission Scanning Electron Microscope (FE-SEM). The experiment was carried out by anodizing aluminum foil in 0.3 M oxalic acid as electrolyte under the constant temperature of 5 °C. The applied voltage was varied from 40, 60 and 100 V with different anodisation time. The outcome of this study demonstrates that applied voltage has a proportional relationship with the developed pore size. Increasing the applied voltage from 40 to 100 V had increased the pore size of the AAO from 38 nm to 186 nm, respectively. Aluminium oxide anodized at 60 V demonstrates pore size in the range of 76 nm. Prolong anodisation time had improved the pore morphology of anodized aluminium oxide in the case of 40 V, however, the pore wall starts to collapse when anodisation time is more than 4 minutes at 100 V.
A Novel Approach to Video Detection for Background Updating and Target Tracking

A novel approach to video detection, synchronous detection lines method, is firstly proposed in this paper. It is actually a way to divide the pixel sets of the video images. Then, an algorithm of three-layer probability model based on synchronous detection lines is presented to solve the problems of background updating and target tracking. The results of a practical system show that this approach has better effect to solve the problems of background updating and target tracking.
PulmOnary vein isolation With vs. without continued antiarrhythmic Drug trEatment in subjects with Recurrent Atrial Fibrillation (POWDER AF): results from a multicentre randomized trial

Aims Catheter ablation is indicated in patients with symptomatic paroxysmal atrial fibrillation (AF) resistant to antiarrhythmic drug therapy (ADT). We investigated whether continued use of previously ineffective ADT beyond the post-ablation blanking period reduces recurrence of atrial tachyarrhythmia within the 1st year after ablation. Methods and results This was a multicentre, randomized controlled study in patients undergoing contact force-guided pulmonary vein isolation (PVI) for paroxysmal AF in whom previously ineffective ADT was continued during a blanking period of 3 months. If free of AF at the end of the blanking period, patients were randomly assigned in the ratio of 1:1 to continue ADT (ADT ON group, n = 77) or discontinue ADT (ADT OFF group, n = 76). Patients were followed up until 1 year after PVI, with clinical visits, Holter monitoring, and quality-of-life (QOL) questionnaires at 6 and 12 months post-procedure. Analysis of the primary endpoint (any documented atrial tachyarrhythmia lasting >30 s) was performed according to the modified intention-to-treat principle. Secondary endpoints included repeat ablation, unscheduled visits, and QOL score. Baseline clinical characteristics and initial ablation procedure characteristics were comparable between both groups. Three patients were lost to follow-up in each arm. The primary endpoint was observed in 2 of 74 (2.7%) patients in the ADT ON group vs. 16 of 73 (21.9%) patients in the ADT OFF group (P < 0.001). The ADT ON group had a lower rate of repeat ablation [1.4% vs. 19.2%, hazard ratio (HR) = 0.053; 95% confidence interval (CI) 0.007-0.399; P < 0.01) and less unscheduled arrhythmia-related health care visits (2.7% vs. 20.5%, HR = 0.055, 95% CI 0.007-0.410; P < 0.01). Quality-of-life scores were similar in both groups. Conclusion In patients free of AF at the end of 3 months of post-ablation blanking period, continued use of previously ineffective ADT significantly reduces the recurrence of atrial tachyarrhythmia in the 1st year after PVI.
Evidence for formation of DNA repair centers and dose-response nonlinearity in human cells

The concept of DNA “repair centers” and the meaning of radiation-induced foci (RIF) in human cells have remained controversial. RIFs are characterized by the local recruitment of DNA damage sensing proteins such as p53 binding protein (53BP1). Here, we provide strong evidence for the existence of repair centers. We used live imaging and mathematical fitting of RIF kinetics to show that RIF induction rate increases with increasing radiation dose, whereas the rate at which RIFs disappear decreases. We show that multiple DNA double-strand breaks (DSBs) 1 to 2 μm apart can rapidly cluster into repair centers. Correcting mathematically for the dose dependence of induction/resolution rates, we observe an absolute RIF yield that is surprisingly much smaller at higher doses: 15 RIF/Gy after 2 Gy exposure compared to approximately 64 RIF/Gy after 0.1 Gy. Cumulative RIF counts from time lapse of 53BP1-GFP in human breast cells confirmed these results. The standard model currently in use applies a linear scale, extrapolating cancer risk from high doses to low doses of ionizing radiation. However, our discovery of DSB clustering over such large distances casts considerable doubts on the general assumption that risk to ionizing radiation is proportional to dose, and instead provides a mechanism that could more accurately address risk dose dependency of ionizing radiation.
Meropenem/vaborbactam fixed combination for the treatment of patients with complicated urinary tract infections.

On August 29, 2017, the United States Food and Drug Administration (FDA) approved meropenem/ vaborbactam fixed combination for the treatment of adults with complicated urinary tract infections (cUTI). The decision was based on substantial preclinical and clinical data, including two recent trials involving hundreds of adults with cUTI. Meropenem/ vaborbactam represents a powerful new treatment option to address antibiotic-resistant pathogens, including Klebsiella pneumoniae carbapenemase-producing bacteria. In this paper, we examine the work that led to FDA approval, with special emphasis on molecular pharmacology, pharmacokinetics, metabolism, efficacy and drug safety. We also look ahead, to explore how this promising new antimicrobial agent might be used in the near future to confront other drug-resistant infections.
Depletion of the Insulator Protein CTCF Results in Herpes Simplex Virus 1 Reactivation In Vivo

ABSTRACT Herpes simplex virus 1 (HSV-1) establishes a lifelong latent infection in host peripheral neurons, including the neurons of the trigeminal ganglia (TG). HSV-1 can reactivate from neurons to cause recurrent infection. During latency, the insulator protein CTCF occupies DNA binding sites on the HSV-1 genome, and these sites have been previously characterized as functional enhancer-blocking insulators. Previously, CTCF was found to be dissociated from wild-type virus postreactivation but not in mutants that do not reactivate, indicating that CTCF eviction may also be an important component of reactivation. To further elucidate the role of CTCF in reactivation of HSV-1, we used recombinant adeno-associated virus (rAAV) vectors to deliver a small interfering RNA targeting CTCF to peripheral neurons latent with HSV-1 in rabbit TG. Our data show that CTCF depletion resulted in long-term and persistent shedding of infectious virus in the cornea and increased ICP0 expression in the ganglia, indicating that CTCF depletion facilitates HSV-1 reactivation. IMPORTANCE Increasing evidence has shown that the insulator protein CTCF regulates gene expression of DNA viruses, including the gammaherpesviruses. While CTCF occupation and insulator function control gene expression in DNA viruses, CTCF eviction has been correlated to increased lytic gene expression and the dissolution of transcriptional domains. Our previous data have shown that in the alphaherpesvirus HSV-1, CTCF was found to be dissociated from the HSV-1 genome postreactivation, further indicating a global role for CTCF eviction in the transition from latency to reactivation in HSV-1 genomes. Using an rAAV8, we targeted HSV-1-infected peripheral neurons for CTCF depletion to show that CTCF depletion precedes the shedding of infectious virus and increased lytic gene expression in vivo, providing the first evidence that CTCF depletion facilitates HSV-1 reactivation.
Stochastic Mirror Descent in Variationally Coherent Optimization Problems

In this paper, we examine a class of non-convex stochastic optimization problems which we call variationally coherent, and which properly includes pseudo-/quasiconvex and star-convex optimization problems. To solve such problems, we focus on the widely used stochastic mirror descent (SMD) family of algorithms (which contains stochastic gradient descent as a special case), and we show that the last iterate of SMD converges to the problem’s solution set with probability 1. This result contributes to the landscape of non-convex stochastic optimization by clarifying that neither pseudo-/quasi-convexity nor star-convexity is essential for (almost sure) global convergence; rather, variational coherence, a much weaker requirement, suffices. Characterization of convergence rates for the subclass of strongly variationally coherent optimization problems as well as simulation results are also presented.
A Study on the Benefit of TCP Packet Prioritisation

This paper studies and analyses the benefits of favoring the transferor packets of a TCP flow over a best-effort network. Specifically, we aim at studying whether we could improve the pace of short data request, such as HTTP request, by giving a high priority to that are not previously enqueued inside a core router.Following the idea that long-lived TCP flows greatly increase the routing queue delay, the motivation of this work is to minimise the impact in terms of delay, introduced by long-lived TCP flows over shot TCP flows. Thus, this forwarding scheme avoids to delay packets that do not belong to a flow already enqueued inside a router in order to avoid delay penalty to short flow. We define metrics to study the bhaviour of such forwarding scheme and run several experiments over a complex and realistic topology. The results obtained present interesting and unexpected property of this forwarding scheme where not only short TCP flows take benefit of such routing mechanism.
Ten simple rules for making research software more robust

Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.
ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research

Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades. Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening. The performance of molecular docking is highly dependent on the protein structures selected. It is especially challenging for large-scale target prediction research when multiple structures are available for a single target. Therefore, we have established ProSelection, a docking preferred-protein selection algorithm, in order to generate the proper structure subset(s). By the ProSelection algorithm, protein structures of "weak selectors" are filtered out whereas structures of "strong selectors" are kept. Specifically, the structure which has a good statistical performance of distinguishing active ligands from inactive ligands is defined as a strong selector. In this study, 249 protein structures of 14 autophagy-related targets are investigated. Surflex-dock was used as the docking engine to distinguish active and inactive compounds against these protein structures. Both t test and Mann-Whitney U test were used to distinguish the strong from the weak selectors based on the normality of the docking score distribution. The suggested docking score threshold for active ligands (SDA) was generated for each strong selector structure according to the receiver operating characteristic (ROC) curve. The performance of ProSelection was further validated by predicting the potential off-targets of 43 U.S. Federal Drug Administration approved small molecule antineoplastic drugs. Overall, ProSelection will accelerate the computational work in protein structure selection and could be a useful tool for molecular docking, target prediction, and protein-chemical database establishment research.
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases

Motivation Rapid and low cost sequencing of genomes enabled widespread use of genomic data in research studies and personalized customer applications, where genomic data is shared in public databases. Although the identities of the participants are anonymized in these databases, sensitive information about individuals can still be inferred. One such information is kinship. Results We define two routes kinship privacy can leak and propose a technique to protect kinship privacy against these risks while maximizing the utility of shared data. The method involves systematic identification of minimal portions of genomic data to mask as new participants are added to the database. Choosing the proper positions to hide is cast as an optimization problem in which the number of positions to mask is minimized subject to privacy constraints that ensure the familial relationships are not revealed.We evaluate the proposed technique on real genomic data. Results indicate that concurrent sharing of data pertaining to a parent and an offspring results in high risks of kinship privacy, whereas the sharing data from further relatives together is often safer. We also show arrival order of family members have a high impact on the level of privacy risks and on the utility of sharing data. Availability Available at: https://github.com/tastanlab/Kinship-Privacy. Contact erman@cs.bilkent. edu.tr or oznur.tastan@cs.bilkent. edu.tr. Supplementary information Supplementary data are available at Bioinformatics online.
Ethogram of Immature Green Turtles: Behavioral Strategies for Somatic Growth in Large Marine Herbivores

Animals are assumed to obtain/conserve energy effectively to maximise their fitness, which manifests itself in a variety of behavioral strategies. For marine animals, however, these behavioral strategies are generally unknown due to the lack of high-resolution monitoring techniques in marine habitats. As large marine herbivores, immature green turtles do not need to allocate energy to reproduction but are at risk of shark predation, although it is a rare occurrence. They are therefore assumed to select/use feeding and resting sites that maximise their fitness in terms of somatic growth, while avoiding predation. We investigated fine-scale behavioral patterns (feeding, resting and other behaviors), microhabitat use and time spent on each behavior for eight immature green turtles using data loggers including: depth, global positioning system, head acceleration, speed and video sensors. Immature green turtles at Iriomote Island, Japan, spent an average of 4.8 h feeding on seagrass each day, with two peaks, between 5∶00 and 9∶00, and between 17∶00 and 20∶00. This feeding pattern appeared to be restricted by gut capacity, and thus maximised energy acquisition. Meanwhile, most of the remaining time was spent resting at locations close to feeding grounds, which allowed turtles to conserve energy spent travelling and reduced the duration of periods exposed to predation. These behavioral patterns and time allocations allow immature green turtles to effectively obtain/conserve energy for growth, thus maximising their fitness.
Resistance Training Augments Cerebral Blood Flow Pulsatility: Cross-Sectional Study

BACKGROUND Increased central arterial stiffness and/or decreased compliance reduces buffer function and increases cerebral blood flow (CBF) pulsatility, which leads to increased cerebral microvascular damage, resulting in the augmentation of the risk of cerebrovascular diseases. Resistance-trained men showed higher central arterial stiffness and lower arterial compliance than age-matched, sedentary men. This study examined the effect of increased central arterial stiffness and/or decreased arterial compliance on CBF pulsatility. METHODS The study participants included 31 young healthy men (15 resistance-trained men, aged 21 ± 1 years; and 16 controls, aged 23 ± 1 years). β-Stiffness index and arterial compliance were measured in the right carotid artery as index of central arterial stiffness and compliance, respectively. The pulsatility index (PI) was measured in the middle cerebral artery as index of CBF pulsatility. RESULTS β-Stiffness index and PI were significantly higher in the resistance-trained group than in the control group (β-stiffness index: 5.3 ± 0.3 vs. 3.5 ± 0.3 a.u., P < 0.05, PI: 0.80 ± 0.02 vs. 0.70 ± 0.02, P < 0.05). The resistance-trained group showed significantly lower arterial compliance than the control group (0.16 ± 0.01 vs. 0.23 ± 0.01 mm2/mm Hg, P < 0.05). Positive and negative correlations were observed between β-stiffness index and PI (r = 0.39, P < 0.05), and between arterial compliance and PI (r = -0.59, P < 0.05), respectively. CONCLUSIONS The resistance-trained group showed higher central arterial stiffness and PI and lower arterial compliance. Central arterial stiffness and arterial compliance were associated with PI. Increased arterial stiffness and decreased arterial compliance with resistance training impair buffer function, resulting in increased CBF pulsatility. CLINICAL TRIAL REGISTRATION Trial Number UMIN000023816 URL: http://www.umin. ac.jp/icdr/index.html Official scientific title of the study: effect of increase arterial stiffness by resistance training on cerebral hemodynamic.
Long-term effects of beta-blocker use on lung function in Japanese patients with chronic obstructive pulmonary disease

Background Some recent studies have suggested that beta-blocker use in patients with chronic obstructive pulmonary disease (COPD) is associated with a reduction in the frequency of acute exacerbations. However, the long-term effects of beta-blocker use on lung function of COPD patients have hardly been evaluated. Patients and methods We retrospectively reviewed 31 Japanese COPD patients taking beta-blockers for >1 year and 72 patients not taking them. The association between beta-blocker use and the annual change in forced expiratory volume in 1 second (FEV1) was assessed. Results At baseline, patient demographic characteristics were as follows: 97 males (mean age 67.0±8.2 years); 32 current smokers; and Global Initiative for Chronic Obstructive Lung disease (GOLD) stages I: n=26, II: n=52, III: n=19, and IV: n=6. Patients taking beta-blockers exhibited a significantly lower forced vital capacity (FVC), FEV1, and %FVC, and a more advanced GOLD stage. The mean duration of beta-blocker administration was 2.8±1.7 years. There were no differences in the annual change in FEV1 between patients who did and did not use beta-blockers (−7.6±93.5 mL/year vs −4.7±118.9 mL/year, P=0.671). After controlling for relevant confounders in multivariate analyses, it was found that beta-blocker use was not significantly associated with the annual decline in FEV1 (β=−0.019; 95% confidence interval: −0.073 to 0.036; P=0.503). Conclusion Long-term beta-blocker use in Japanese COPD patients might not affect the FEV1, one of the most important parameters of lung function in COPD patients.