bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sub-nanosecond synchronization implementation in pure Xilinx Kintex-7 FPGA
Authors: Ye Y. , Li H. , Li J. , Gong G. 
Published: November 2021

Abstract
White Rabbit (WR) provides high-performance synchronization
with sub-nanosecond accuracy and picoseconds precision, and it has
been included in the new High Accuracy Default PTP Profile in the
IEEE 1588-2019. As an open-source project, WR Precision Time
Protocol (WR-PTP) core has been implemented in different FPGA
platforms with dedicated clock circuits. This paper presents a novel
approach to achieve the WR function in Xilinx Kintex-7 FPGA
depending on the on-chip resource. This approach could achieve
sub-nanosecond accuracy and tens of picoseconds precision,
simplifying WR devices' hardware design and making it possible to
port the WR PTP core to many mature hardware platforms.
Homogeneity of the photocathode in the Hamamatsu R15458-02 Photomultiplier Tube
Authors: Unland Elorrieta M.A. , Busse R.S. , Classen L. , Kappes A. 
Published: November 2021

Abstract
It is common practice to test the optical properties of
photomultiplier tubes (PMTs) by illuminating the entire photocathode
region from the front at once and measuring the average
performance. However, for optimal utilisation of the PMT performance
in experiments, especially in the single-photon region, it is
essential to also know the systematic variations across the
photocathode, which requires measurements with focused light sources
that illuminate only small regions of the PMT. We present a detailed
uniformity characterisation of the gain, transit time, transit time
spread, and pulse shape of the 80 mm Hamamatsu R15458-02 PMT. We
find that the parameters exhibit asymmetry along one axis, likely
caused by the position and geometry of the dynode system. For all
parameters except the transit time, the observed variations are
small given the intrinsic variation of the parameters. For positions
with shifted transit time we observe on average underamplified
pulses which can potentially be exploited to improve the pulse
reconstruction.
Scintillating thermal neutron detectors for cosmic ray soil moisture monitoring
Authors: Stowell P. , Fargher S. , Steer C. , Thompson L.F. 
Published: November 2021

Abstract
Cosmic Ray Neutron Sensing (CRNS) is a powerful technique
that allows non-invasive monitoring of soil moisture on length
scales well matched for agricultural applications. One factor
limiting the use of the technique within industrial agriculture
settings is the high initial cost of Helium-3 or BF3 tubes typically
used for ground level neutron monitoring. This paper discusses the
use of Geant4 to design and optimise an alternative scintillator
based epi-thermal neutron detector that may be applicable for
challenges where cost is a higher driving factor than temporal
resolution.
Unprecedented acceleration of winter discharge of Upper Yenisei River inferred from tree rings
Authors: Panyushkina Irina P , Meko David M , Shiklomanov Alexander , Thaxton Richard D , Myglan Vladimir , Barinov Valentin V , Taynik Anna V 
Published: November 2021

AbstractThe Yenisei River is the largest contributor of freshwater and energy fluxes among all rivers draining to the Arctic Ocean. Modeling long-term variability of Eurasian runoff to the Arctic Ocean is complicated by the considerable variability of river discharge in time and space, and the monitoring constraints imposed by a sparse gauged-flow network and paucity of satellite data. We quantify tree growth response to river discharge at the upper reaches of the Yenisei River in Tuva, South Siberia. Two regression models built from eight tree-ring width chronologies ofLarix sibiricaare applied to reconstruct winter (Nov–Apr) discharge for the period 1784–1997 (214 years), and annual (Oct–Sept) discharge for the period 1701–2000 (300 years). The Nov–Apr model explains 52% of the discharge variance whereas Oct–Sept explains 26% for the calibration intervals 1927–1997 and 1927–2000, respectively. This new hydrological archive doubles the length of the instrumental discharge record at the Kyzyl gauge and resets the temporal background of discharge variability back to 1784. The reconstruction finds a remarkable 80% upsurge in winter flow over the last 25 years, which is unprecedented in the last 214 years. In contrast, annual discharge fluctuated normally for this system, with only a 7% increase over the last 25 years. Water balance modeling with CRU data manifests a significant discrepancy between decadal variability of the gauged flow and climate data after 1960. We discuss the impact on the baseflow rate change of both the accelerating permafrost warming in the discontinuous zone of South Siberia and widespread forest fires. The winter discharge accounts for only one third of the annual flow, yet the persistent 25 year upsurge is alarming. This trend is likely caused by Arctic Amplification, which can be further magnified by increased winter flow delivering significantly more fresh water to the Kara Sea during the cold season.
Bone Mineral Density, Bone Microarchitecture and Vertebral Fractures in Male Patients with Alcohol Use Disorders
Authors: Balhara Yatan Pal Singh , Narang Parul , Saha Soma , Kandasamy Devasenathipathy , Chattopadhyay Naibedya , Goswami Ravinder 
Published: November 2021

Abstract

Aim
To investigate abnormalities in bone mineral density, trabecular bone score and vertebral fractures in male patients with alcohol use disorder to understand the impact on bone health.

Methods
The study subjects included 134 male patients. Controls were 134 age matched healthy males. Assessments were made of the bone mineral density (BMD), trabecular bone score (TBS) and vertebral morphometry (VFA) for vertebral fractures. Biochemical measurements included serum total T4, thyroid stimulating hormone (TSH), parathyroid hormone (PTH) and 25- Hydroxyvitamin D 25(OH) D.

Results
The mean BMD at total forearm, proximal forearm (or distal 1/3) and mid forearm was significantly higher in the alcohol use disorders (AUD) group than the controls (P &lt; 0.01). Around 15% of patients with AUD had VFs compared with 9.0% of the healthy controls (P = 0.19). For each kg/m2 gain in body mass index (BMI), lumbar spine and total hip BMD increased by 0.009 and 0.014 g/cm2, respectively. Lumbar and hip BMD decreased by 0.002 and 0.003 g/cm2 per year increase in duration of alcohol used. For every 5 years increase in age of the patients the odds of having VFs increased by 39% (odds ratio 1.393 [95% confidence interval = 1.031–1.881, P = 0.03]).

Conclusion
The findings of the current study suggest that persons with AUD in third and fourth decades of life, with BMI in normal range and with alcohol use disorder duration of around one decade might have no major alteration in BMD and TBS. Impact of alcohol use in this population was manifest by marginal increase in the prevalence of mild grade of vertebral fractures, mostly in the thoracic region.
SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging
Authors: Luo Qinhuan , Yu Yongzhen , Lan Xun 
Published: November 2021

Abstract
High-throughput single-cell RNA-seq data have provided unprecedented opportunities for deciphering the regulatory interactions among genes. However, such interactions are complex and often nonlinear or nonmonotonic, which makes their inference using linear models challenging. We present SIGNET, a deep learning-based framework for capturing complex regulatory relationships between genes under the assumption that the expression levels of transcription factors participating in gene regulation are strong predictors of the expression of their target genes. Evaluations based on a variety of real and simulated scRNA-seq datasets showed that SIGNET is more sensitive to ChIP-seq validated regulatory interactions in different types of cells, particularly rare cells. Therefore, this process is more effective for various downstream analyses, such as cell clustering and gene regulatory network inference. We demonstrated that SIGNET is a useful tool for identifying important regulatory modules driving various biological processes.
trfermikit: a tool to discover VNTR-associated deletions
Authors: McHale Peter , Quinlan Aaron R 
Published: November 2021

AbstractSummaryWe present trfermikit, a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. In such regions, it achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta and complements it by recovering a significant number of deletions that Manta missed. trfermikit is based upon the fermikit pipeline, which performs read assembly, maps the assembly to the reference genome and calls variants from the alignment.Availability and implementationhttps://github.com/petermchale/trfermikit.Supplementary informationSupplementary data are available at Bioinformatics online.
Make Interactive Complex Heatmaps in R
Authors: Gu Zuguang , Hübschmann Daniel 
Published: November 2021

Abstract

Summary
Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In this work, we introduce a new R package InteractiveComplexHeatmap that brings interactivity to the widely used ComplexHeatmap package. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one additional line of code. InteractiveComplexHeatmap also provides flexible functionalities for integrating interactive heatmap widgets to build more complex and customized Shiny web applications.

Availability and implementation
The InteractiveComplexHeatmap package and documentations are freely available from the Bioconductor project: https://bioconductor.org/packages/InteractiveComplexHeatmap/. A complete and printer-friendly version of the documentation can also be found in Supplementary File S1.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Multilevel Investigation of the Association between Collective Psychological Ownership as Psychosocial Resources and Social Workers’ Turnover Intention
Authors: Su Xuebing , Wong Victor , Liang Kun 
Published: November 2021

Abstract
Using a multilevel approach and a nationally representative sample of 5,478 social workers from 813 social service organisations in China, this study investigated the association between collective psychological ownership (CPO), an emerging construct of psychosocial resources characterised by sharedness, and social workers’ turnover intention by controlling for psychological demands (i.e. emotional exhaustion and role ambiguity) and psychological resources (i.e. self-perceived autonomy, self-perceived and composite person–organisation value congruence, and self-perceived and composite social support). The results showed that CPO conceptualised as both individual- and organisational-level psychosocial resources were negatively associated with social workers’ turnover intention. The findings of the study will draw implications for keeping social workers and other helping professionals in their organisations by practicing co-workers’ shared agency and joint actions defined in terms of collective decision-making and hardship endurance.
Spike firing attenuation of serotonin neurons in learned helplessness rats is reversed by ketamine
Authors: Hashimoto Kouichi , Yamawaki Yosuke , Yamaoka Kenji , Yoshida Takayuki , Okada Kana , Tan Wanqin , Yamasaki Miwako , Matsumoto-Makidono Yoshiko , Kubo Reika , Nakayama Hisako , Kataoka Tsutomu , Kanematsu Takashi , Watanabe Masahiko , Okamoto Yasumasa , Morinobu Shigeru , Aizawa Hidenori , Yamawaki Shigeto 
Published: November 2021

Abstract
Animals suffering from uncontrollable stress sometimes show low effort to escape stress (learned helplessness). Changes in serotonin (5-hydroxytryptamine) signalling are thought to underlie this behaviour. Although the release of 5-hydroxytryptamine is triggered by the action potential firing of dorsal raphe nuclei 5-hydroxytryptamine neurons, the electrophysiological changes induced by uncontrollable stress are largely unclear. Herein, we examined electrophysiological differences among 5-hydroxytryptamine neurons in naïve rats, learned helplessness rats and rats resistant to inescapable stress (non-learned helplessness). Five-week-old male Sprague Dawley rats were exposed to inescapable foot shocks. After an avoidance test session, rats were classified as learned helplessness or non-learned helplessness. Activity-dependent 5-hydroxytryptamine release induced by the administration of high-potassium solution was slower in free-moving learned helplessness rats. Subthreshold electrophysiological properties of 5-hydroxytryptamine neurons were identical among the three rat groups, but the depolarization-induced spike firing was significantly attenuated in learned helplessness rats. To clarify the underlying mechanisms, potassium (K+) channels regulating the spike firing were initially examined using naïve rats. K+ channels sensitive to 500 μM tetraethylammonium caused rapid repolarization of the action potential and the small conductance calcium-activated K+ channels produced afterhyperpolarization. Additionally, dendrotoxin-I, a blocker of Kv1.1 (encoded by Kcna1), Kv1.2 (encoded by Kcna2) and Kv1.6 (encoded by Kcna6) voltage-dependent K+ channels, weakly enhanced the spike firing frequency during depolarizing current injections without changes in individual spike waveforms in naïve rats. We found that dendrotoxin-I significantly enhanced the spike firing of 5-hydroxytryptamine neurons in learned helplessness rats. Consequently, the difference in spike firing among the three rat groups was abolished in the presence of dendrotoxin-I. These results suggest that the upregulation of dendrotoxin-I-sensitive Kv1 channels underlies the firing attenuation of 5-hydroxytryptamine neurons in learned helplessness rats. We also found that the antidepressant ketamine facilitated the spike firing of 5-hydroxytryptamine neurons and abolished the firing difference between learned helplessness and non-learned helplessness by suppressing dendrotoxin-I-sensitive Kv1 channels. The dendrotoxin-I-sensitive Kv1 channel may be a potential target for developing drugs to control activity of 5-hydroxytryptamine neurons.
The effect of micro-osteoperforations on orthodontic space closure investigated over 12 weeks: a split-mouth, randomized controlled clinical trial
Authors: Li Jiaojiao , Papadopoulou Alexandra K , Gandedkar Narayan , Dalci Kerem , Darendeliler Mehmet Ali , Dalci Oyku 
Published: November 2021

SummaryObjectivesTo evaluate the effects of minimally invasive micro-osteoperforations (MOPs) on orthodontic tooth movement and pain.DesignProspective, split-mouth, randomized controlled trial.SettingSingle-centre, university hospital.MethodsTwenty subjects requiring maxillary first premolar extractions were included. Right and left sides of the maxilla were randomly allocated into experimental and controls. Space closure was initiated following alignment on 0.20″ stainless steel archwires, using 150 g force, applied by coil springs on power arms. Nance-TPA was used for anchorage. On the experimental side, two 5 mm deep MOPs in vertical alignment on distal aspect of the maxillary canine mid-root region were performed prior to space closure.OutcomesThe primary outcome was the amount of tooth movement during space closure, measured every 4 weeks for 12 weeks (T1, T2, and T3). Secondary outcome was the pain levels related to MOP, measured using Visual Analogue Scale (VAS) questionnaires. Significance was set at P &lt; 0.01.RandomizationRandomization was generated using a randomization table, and allocation was concealed in sequentially numbered, opaque, sealed envelopes.BlindingBlinding was not possible during the experiment but assessor was blinded during outcome assessment.ResultsAll subjects completed the study, with tooth movement measurements available for all 20 patients for T0–T2. In three patients, space was closed on one side at T2. The average tooth movement between sides at three intervals (T0–T1, T1–T2, and T2–T3) were not significantly different. Overall difference following 12 weeks (T0–T3) was 0.69 mm higher on the experimental side (P &lt; 0.001). No harms were observed.LimitationsShort-term study, cast measurements done with digital callipers.ConclusionThis 12-week randomized split-mouth controlled clinical trial showed two MOPs that are 5 mm deep, applied once prior to space closure, did not create clinically significant increase in maxillary premolar space closure.ProtocolThe protocol was not published before trial commencement.RegistrationTrial was not registered.FundingThe Australian Society of Orthodontists Foundation for Research and Education.
Startlingly strong shape anisotropy of AC magnetic susceptibility due to eddy currents
Authors: Ježek Josef , Hrouda František 
Published: November 2021

SUMMARY
In order to better understand the anisotropy of AC magnetic susceptibility due to eddy currents (EC susceptibility) in rocks and minerals, we investigated the anisotropy of both in-phase (ipAMS) and out-of-phase (opAMS) magnetic susceptibility. Copper cylinders were chosen as experimental material because copper is diamagnetic, internally isotropic magnetically, and its out-of-phase magnetic susceptibility is no doubt due to eddy currents. Results of laboratory measurements were successfully compared to theoretical models. Both the in-phase and out-of-phase EC susceptibility components are strongly frequency dependent. The principal directions of both ipAMS and opAMS are closely related to the shapes of the copper bodies. While the degree of AMS of elongated cylinders asymptotically approaches 2, which is the value for infinite cylinder, it can be two orders higher in strongly flattened cylinders of the same volume. Analysis of directional susceptibilities has shown that EC susceptibility is well described by the tensor of second rank. These results are useful for the structural interpretation of the opAMS of rocks and ores whose opAMS is due to eddy currents (in electrically conductive minerals, such as graphite, and galena).
Development and simulation testing for a new approach to density dependence in species distribution models
Authors: Thorson James T 
Published: November 2021

Abstract
Density dependence is included in many population–dynamics models, but few options exist within species distribution models (SDMs). One option for density-dependence in SDMs proceeds by including an independent time-series of population abundance as covariate using a spatially varying coefficient (SVC). We extend this via three alternative approaches that replace the independent time-series with information available within the SDM. We recommend the “intermediate complexity” approach that estimates a SVC responding to median abundance in each time; this SVC indicates whether a given location has a smaller- or greater-than-average sensitivity to changes in median abundance. We next develop a reaction–advection–diffusive simulation model, wherein individuals avoid habitats that exceed a threshold in local density. This movement model results in an estimated SVC that is negatively correlated with the average spatial distribution. Finally, we show that a SVC can be identified using bottom trawl data for four species in the eastern Bering Sea from 1982 to 2019. We conclude that the common “basin-model” for animal movement results in an ecological teleconnection, wherein population depletion or recovery at one locations will affect resulting dynamics at geographically distant habitats, and that this form of density dependence can be detected using SDMs.
Cooperative decisions of competitive supply chains considering carbon trading mechanism
Authors: Li Hui , Li Rou , Shang Meng , Liu Yu , Su Dandan 
Published: November 2021

Abstract
Carbon emissions trading policy is a market mechanism which promotes global greenhouse gas emissions reduction and reduces global carbon dioxide emissions. The emissions reduction in the supply chain operation has become a hot issue in supply chain management. Thus, this paper studies the optimal cap setting and pricing in chain-to-chain system under carbon emissions trading mechanism. Based on the double decentralized scenario, the five different cooperation models are established by introducing the structural cooperation and the contractual cooperation (the wholesale price contract) of supply chains. The optimal solutions of these models are obtained through the Stackelberg game and Nash game. The results show that the bargaining power of the supply chains is changed by the asymmetric competition structure. Besides, the government should emphasize the influencing factors change of the cap in the process of setting carbon emissions cap.
Early Immunogenicity and Safety of the Third Dose of BNT162b2 Messenger RNA Coronavirus Disease 2019 Vaccine Among Adults Older Than 60 Years: Real-World Experience
Authors: Gilboa Mayan , Mandelboim Michal , Indenbaum Victoria , Lustig Yaniv , Cohen Carmit , Rahav Galia , Asraf Keren , Amit Sharon , Jaber Hanaa , Nemet Ital , Kliker Limor , Bar-Haim Erez , Mendelson Ella , Doolman Ram , Rubin Carmit , Regev-Yochay Gili , Kreiss Yitshak 
Published: November 2021

Abstract

Background
Despite high vaccine coverage, an increase in breakthrough coronavirus disease 2019 (COVID-19) infections, prompted administration of a third BNT162b2 dose to people aged &gt;60 years in Israel since July 2021. Here, we report real-world immunogenicity following third dose.

Methods
Overall, 208 healthcare workers aged &gt;60 years were included. Paired pre– and post–second and/or third dose immunoglobulin G (IgG) and neutralizing antibody titers were compared. A subpopulation of low responders to the second dose was also tested for T-cell activation. For 25 paired serum samples, we tested neutralization of wild-type vs neutralization of Delta and Lambda variants, pre– and post–third dose. Active surveillance of vaccine adverse events was conducted through surveys.

Results
A pronounced immune response was observed following the third dose, including a 33-fold and 51-fold increase in IgG and neutralizing antibody, respectively. The neutralizing antibody levels post–third dose were 9.34 times higher than post–second dose (geometric mean titer, 2598 [95% confidence interval {CI}, 2085–3237] vs 207 [95% CI, 126–339]). Nine previously low responders had a significant antibody increase post–third dose, and 7 of 9 showed increase in T-cell activation. Additionally, sera obtained post–third dose highly and comparably neutralized the wild-type and Delta and Lambda variants. Of 1056 responders to the adverse-event survey, none had serious events.

Conclusions
We demonstrate a rapid and broad immune response to the third BNT162b2 dose in individuals &gt;60 years of age.