Miracle-dz/UniFAR-FTUs huggingface dataset:
wCQ: A Fast Wait-Free Queue with Bounded Memory Usage

The concurrency literature presents a number of approaches for building non-blocking, FIFO, multiple-producer and multiple-consumer (MPMC) queues. However, only a fraction of them have high performance. In addition, many queue designs, such as LCRQ, trade memory usage for better performance. The recently proposed SCQ design achieves both memory efficiency as well as excellent performance. Unfortunately, both LCRQ and SCQ are only lock-free. On the other hand, existing wait-free queues are either not very performant or suffer from potentially unbounded memory usage. Strictly described, the latter queues, such as Yang & Mellor-Crummey's (YMC) queue, forfeit wait-freedom as they are blocking when memory is exhausted. We present a wait-free queue, called wCQ. wCQ is based on SCQ and uses its own variation of fast-path-slow-path methodology to attain wait-freedom and bound memory usage. Our experimental studies on x86 and PowerPC architectures validate wCQ's great performance and memory efficiency. They also show that wCQ's performance is often on par with the best known concurrent queue designs.
Survey Propagation: A Resource Allocation Solution for Large Wireless Networks

The ever-increasing number of nodes in current and future wireless communication networks brings unprecedented challenges for the allocation of the available communication resources. This is caused by the combinatorial nature of the resource allocation problems, which limits the performance of stateof-the-art techniques when the network size increases. In this paper, we take a new direction and investigate how methods from statistical physics can be used to address resource allocation problems in large networks. To this aim, we propose a novel model of the wireless network based on a type of disordered physical systems called spin glasses. We show that resource allocation problems have the same structure as the problem of finding specific configurations in spin glasses. Based on this parallel, we investigate the use of the Survey Propagation method from statistical physics in the solution of resource allocation problems in wireless networks. Through numerical simulations we show that the proposed statistical-physics-based resource allocation algorithm is a promising tool for the efficient allocation of communication resources in large wireless communications networks. Given a fixed number of resources, we are able to serve a larger number of nodes, compared to state-of-the-art reference schemes, without introducing more interference into the system.
Interviewer Effects in Live Video and Prerecorded Video Interviewing

Abstract Live video (LV) communication tools (e.g., Zoom) have the potential to provide survey researchers with many of the benefits of in-person interviewing, while also greatly reducing data collection costs, given that interviewers do not need to travel and make in-person visits to sampled households. The COVID-19 pandemic has exposed the vulnerability of in-person data collection to public health crises, forcing survey researchers to explore remote data collection modes—such as LV interviewing—that seem likely to yield high-quality data without in-person interaction. Given the potential benefits of these technologies, the operational and methodological aspects of video interviewing have started to receive research attention from survey methodologists. Although it is remote, video interviewing still involves respondent–interviewer interaction that introduces the possibility of interviewer effects. No research to date has evaluated this potential threat to the quality of the data collected in video interviews. This research note presents an evaluation of interviewer effects in a recent experimental study of alternative approaches to video interviewing including both LV interviewing and the use of prerecorded videos of the same interviewers asking questions embedded in a web survey (“prerecorded video” interviewing). We find little evidence of significant interviewer effects when using these two approaches, which is a promising result. We also find that when interviewer effects were present, they tended to be slightly larger in the LV approach as would be expected in light of its being an interactive approach. We conclude with a discussion of the implications of these findings for future research using video interviewing.
CircleBase: an integrated resource and analysis platform for human eccDNAs

Abstract Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human

Abstract Transcription factors (TFs) play key roles in biological processes and are usually used as cell markers. The emerging importance of TFs and related markers in identifying specific cell types in human diseases increases the need for a comprehensive collection of human TFs and related markers sets. Here, we developed the TF-Marker database (TF-Marker, http://bio.liclab.net/TF-Marker/), aiming to provide cell/tissue-specific TFs and related markers for human. By manually curating thousands of published literature, 5905 entries including information about TFs and related markers were classified into five types according to their functions: (i) TF: TFs which regulate expression of the markers; (ii) T Marker: markers which are regulated by the TF; (iii) I Marker: markers which influence the activity of TFs; (iv) TFMarker: TFs which play roles as markers and (v) TF Pmarker: TFs which play roles as potential markers. The 5905 entries of TF-Marker include 1316 TFs, 1092 T Markers, 473 I Markers, 1600 TFMarkers and 1424 TF Pmarkers, involving 383 cell types and 95 tissue types in human. TF-Marker further provides a user-friendly interface to browse, query and visualize the detailed information about TFs and related markers. We believe TF-Marker will become a valuable resource to understand the regulation patterns of different tissues and cells.
Web interface for 3D visualization and analysis of SARS-CoV-2—human mimicry and interactions

Abstract Summary We present a web-based server for navigating and visualizing possible interactions between SARS-CoV-2 and human host proteins. The interactions are obtained from HMI_Pred which relies on the rationale that virus proteins mimic host proteins. The structural alignment of the viral protein with one side of the human protein-protein interface determines the mimicry. The mimicked human proteins and predicted interactions, and the binding sites are presented. The user can choose one of the 18 SARS-CoV-2 protein structures and visualize the potential 3D complexes it forms with human proteins. The mimicked interface is also provided. The user can superimpose two interacting human proteins in order to see whether they bind to the same site or different sites on the viral protein. The server also tabulates all available mimicked interactions together with their match scores and number of aligned residues. This is the first server listing and cataloging all interactions between SARS-CoV-2 and human protein structures, enabled by our innovative interface mimicry strategy. Availability The server is available at https://interactome.ku. edu.tr/sars/.
DICAM, a molecular passport for TH17 cell entry into the brain

Description DICAM, a trafficking molecule preferentially expressed by TH17 cells, may be a therapeutic target for treating neuroinflammation (Charabati et al.). DICAM, a trafficking molecule preferentially expressed by TH17 cells, may be a therapeutic target for treating neuroinflammation (Charabati et al.).
Knee joint biomechanics during gait improve from 3 to 6 months after anterior cruciate ligament reconstruction

Gait alterations after anterior cruciate ligament reconstruction (ACLR) are commonly reported and have been linked to posttraumatic osteoarthritis development. While knee gait alterations have been studied at several time points after ACLR, little is known about how these biomechanical variables change earlier than 6 months after surgery, nor is much known about how they differ over the entire stance phase of gait. The purpose of this study was to examine knee gait biomechanical variables over their entire movement pattern through stance at both 3 and 6 months after ACLR and to study the progression of interlimb asymmetry between the two postoperative time points. Thirty‐five individuals underwent motion analysis during overground walking 3 (3.2 ± 0.5) and 6 (6.4 ± 0.7) months after ACLR. Knee biomechanical variables were compared between limbs and across time points through 100% of stance using statistical parametric mapping; this included a 2 × 2 (Limb × Time) repeated measures analysis of variance and two‐tailed t‐tests. Smaller knee joint angles, moments, extensor forces, and medial compartment forces were present in the involved versus uninvolved limb. Interlimb asymmetries were present at both time points but were less prevalent at 6 months. The uninvolved limb's biomechanical variables stayed relatively consistent over time, while the involved limb's trended toward that of the uninvolved limb. Statement of Clinical Significance: Interventions to correct asymmetrical gait patterns after ACLR may need to occur early after surgery and may need to focus on multiple parts of stance phase.
14 GHz Schottky Diodes Using a p‐Doped Organic Polymer

The low carrier mobility of organic semiconductors and the high parasitic resistance and capacitance often encountered in conventional organic Schottky diodes hinder their deployment in emerging radio frequency (RF) electronics. Here, these limitations are overcome by combining self‐aligned asymmetric nanogap electrodes (≈25 nm) produced by adhesion lithography, with a high mobility organic semiconductor, and RF Schottky diodes able to operate in the 5G frequency spectrum are demonstrated. C16IDT‐BT is used, as the high hole mobility polymer, and the impact of p‐doping on the diode performance is studied. Pristine C16IDT‐BT‐based diodes exhibit maximum intrinsic and extrinsic cutoff frequencies (fC) of >100 and 6 GHz, respectively. This extraordinary performance is attributed to the planar nature of the nanogap channel and the diode's small junction capacitance (<2 pF). Doping of C16IDT‐BT with the molecular p‐dopant C60F48 improves the diode's performance further by reducing the series resistance resulting to intrinsic and extrinsic fC of >100 and ≈14 GHz respectively, while the DC output voltage of an RF rectifier circuit increases by a tenfold. Our work highlights the importance of the planar nanogap architecture and paves the way for the use of organic Schottky diodes in large‐area RF electronics of the future.
Complete Genome Sequence of Hafnia paralvei Isolate AVS0177, Harboring mcr-9 on a Plasmid

Here, we report the complete genome sequence of a Hafnia paralvei strain isolated from a lake in Switzerland in 2020. The genome consists of a 4.7-Mbp chromosome, a large plasmid (213 kb) harboring mcr-9, and a small plasmid (6 kb). ABSTRACT Here, we report the complete genome sequence of a Hafnia paralvei strain isolated from a lake in Switzerland in 2020. The genome consists of a 4.7-Mbp chromosome, a large plasmid (213 kb) harboring mcr-9, and a small plasmid (6 kb).
Discontinuous gas exchange in Madagascan hissing cockroaches is not a consequence of hysteresis around a fixed PCO2 threshold.

It has been hypothesised that insects display discontinuous gas-exchange cycles (DGCs) due to hysteresis in their ventilatory control, where CO2-sensitive respiratory chemoreceptors respond to changes in hemolymph PCO2 only after some delay. If correct, DGCs would be a manifestation of an unstable feedback loop between chemoreceptors and ventilation causing PCO2 to oscillate around some fixed threshold value: PCO2 above this ventilatory threshold would stimulate excessive hyperventilation, driving PCO2 below the threshold and causing a subsequent apnoea. This hypothesis was tested by implanting micro-optodes into the hemocoel of Madagascar hissing cockroaches and measuring hemolymph PO2 and PCO2 simultaneously during continuous and discontinuous gas exchange. The mean hemolymph PCO2 of 1.9 kPa measured during continuous gas exchange was assumed to represent the threshold level stimulating ventilation, and this was compared with PCO2 levels recorded during DGCs elicited by decapitation. Cockroaches were also exposed to hypoxic (PO2 10 kPa) and hypercapnic (PCO2 2 kPa) gas mixtures to manipulate hemolymph PO2 and PCO2. Decapitated cockroaches maintained DGCs even when their hemolymph PCO2 was forced above or below the putative ∼2 kPa ventilation threshold, demonstrating that the characteristic oscillation between apnoea and gas exchange is not driven by a lag between changing hemolymph PCO2 and a PCO2 chemoreceptor with a fixed ventilatory threshold. However, it was observed that the gas exchange periods within the DGC were altered to enhance O2 uptake and CO2 release during hypoxia and hypercapnia exposure. This indicates that while respiratory chemoreceptors do modulate ventilatory activity in response to hemolymph gas levels, their role in initiating or terminating the gas exchange periods within the DGC remains unclear.
Joint engagement in the home environment is frequent, multimodal, timely, and structured.

Infants develop in a social context, surrounded by knowledgeable caregivers who scaffold learning through shared engagement with objects. However, researchers have typically examined joint engagement in structured tasks, where caregivers sit near infants and display frequent, prompt, and multimodal behaviors around the objects of infant action. Which features of joint engagement generalize to the real-world? Despite the importance of joint engagement for infant learning, critical assumptions around joint engagement in everyday interaction remain unexamined. We investigated behavioral and temporal features of joint engagement in the home environment, where objects for play abound and dyad proximity fluctuates. Infant manual actions, mother manual and verbal behaviors, and dyad proximity were coded frame-by-frame from 2-h naturalistic recordings of 13- to 23-month-old infants and their mothers (N = 38). Infants experienced rich, highly structured, multimodal mother input around the objects of their actions. Specifically, joint engagement occurred within seconds of infant action and was amplified in the context of interpersonal proximity. Findings validate laboratory-based research on characteristics of joint engagement while highlighting unique properties around the role of mother-infant proximity and temporal structuring of caregiver input over extended time frames. Implications for the social contexts that support infant learning and development are discussed.
Increased heroin intake and relapse vulnerability in intermittent relative to continuous self‐administration: Sex differences in rats

Studies using intermittent‐access drug self‐administration show increased motivation to take and seek cocaine and fentanyl, relative to continuous access. In this study, we examined the effects of intermittent‐ and continuous‐access self‐administration on heroin intake, patterns of self‐administration and cue‐induced heroin‐seeking, after forced or voluntary abstinence, in male and female rats. We also modelled brain levels of heroin and its active metabolites.
Liver Transplantation in Hepatocellular Carcinoma: Experiences from the Shiraz Transplant Center.

Background Studies evaluating liver transplantation (LT) in hepatocellular carcinoma (HCC) in the Middle East have been scarce, mainly due to intricacy of this type of surgery. Objective In here we report our experiences with LT among patients with HCC cirrhosis.Methods: All patients who underwent LT with primary diagnosis of HCC older than 18 years old, during 2004 to 2019, were initially included in our study. Results Overall, 124 patients entered our study, among which majority were males (86.3%). Mean (SD) age of patients was 53.1±10.6 years old. Most common underlying liver diseases were HBV (55.6%) and HCV infections (12.1%). Mean MELD score of patients was 18±5.5. Child-Pugh score of most patients was class B (50%). Mean (SD) duration of hospitalization was 12.1±3.5 days. Patients were followed for a median of 32 (9, 62) months. The most common causes of death were recurrence of HCC (47.7%) and sepsis (34.1%). Median (IQR) duration to recurrence and death were 18 (4, 34) months and 17.5 (5.7, 44.5) months, respectively. One-year survival (89%, 86.4%, and 63.2%, respectively) (p=0.011) and one-year DFS (89%, 86.4%, and 57.9%, respectively) (p=0.001) was significant different between those who were selected based on the Milan, UCSF and extended criteria. Conclusion Our study provides valuable experiences on LT and HCC from one of the largest LT centers in the world. Accordingly, we found that the Milan criterion provides the best survival compared to the UCSF and our extended criteria for patient selection.
CXCR4 promotes the growth and metastasis of esophageal squamous cell carcinoma as a critical downstream mediator of HIF‐1α

C–X–C motif chemokine receptor 4 (CXCR4) belongs to the CXC chemokine receptor family, which mediates the metastasis of tumor cells and promotes the malignant development of cancers. However, its biological role and regulatory mechanism in esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we found that CXCR4 expression was associated with lymph node metastasis and a poor prognosis. In vitro and in vivo studies demonstrated that CXCR4 overexpression promoted ESCC cell proliferation, migration, invasion, and survival, whereas silencing CXCR4 induced the opposite effects. Mechanically, HIF‐1α transcriptionally regulates CXCR4 expression by binding to a hypoxia response element in its promoter. HIF‐1α‐induced ESCC cell migration and invasion were reversed by CXCR4 knockdown or treatment with MSX‐122, a CXCR4 antagonist. Collectively, these data revealed that the HIF‐1α/CXCR4 axis plays key roles in ESCC growth and metastasis and indicated CXCR4 as a potential target for ESCC treatment.
Effects of Computer-Based Cognitive Rehabilitation on Attention, Executive Functions, and Quality of Life in Patients with Parkinson’s Disease: A Randomized, Controlled, Single-Blinded Pilot Study

Background: Cognitive decline in Parkinson’s disease (PD) has become increasingly recognized in recent years, and there is a need to identify methods for cognitive rehabilitation in PD patients. Objective: The aim of this study was to explore the feasibility and effects of 2 different computer-based cognitive rehabilitation (CBCR) interventions on attention, executive functions, and quality of life (QoL) in PD patients. Methods: Thirty nondemented PD patients were randomly assigned to one of 3 groups: one passive control group and 2 intervention groups with 2 different CBCR programmes. The intervention period was 8 weeks with follow-up visits in clinic every second week. Before and after the intervention period, patients were tested with a neuropsychological battery of attention, executive functions, and QoL. Results: Twenty-four patients completed the study. Patients in one of the CBCR groups experienced a significant within-group increase on the primary measures of attention, executive functions, and QoL. However, this effect was not significant between groups. No significant differences were observed for the other CBCR group or the control group. Conclusions: CBCR is a feasible intervention for cognitive rehabilitation in nondemented PD patients. The effects of training were modest and should be further explored in larger clinical trials. Some CBCR programmes might be more effective than others for PD patients. The protocol for this study was published prospectively at ClinicalTrials.gov on September 18, 2017 with ID: NCT03285347.
Preliminary study of active earth pressure under nonlimit state

A reasonable and simple method is proposed to calculate the active earth pressure on rigid retaining wall under nonlimit state. Based on the unloading stress-strain relationship obtained from the unloading stress path experiment reflecting the stress-strain characters of soil in the active area behind the wall, the relationship between the friction angle and wall movement is established under nonlimit state. The sliding wedge, behind the retaining wall of not reaching the limit displacement, can be divided into numerous differential slices paralleling to the sliding plane. Then, with the force analysis of these differential slices and the relationship mentioned above, equations can be set up and the inclination of the sliding plane is also derived. Thereby, the calculation formula of the nonlimit active earth pressure is obtained. Subsequently, compared with one model test, the value of the calculated earth pressure has a satisfying agreement with the observed at the upper two-third of wall height and a certain deviation at the lower one-third of wall surface. The results show that the proposed method can provide a good prediction of active earth pressures for walls under nonlimit state and has some theoretical significance and engineering reference value.