bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnus induced diode effect for skyrmions in channels with periodic potentials
Authors: Bellizotti Souza J C , Vizarim N P , Reichhardt C J O , Reichhardt C , Venegas P A 
Published: October 2022

Abstract
Using a particle based model, we investigate the skyrmion dynamical behavior in a channel where the upper wall contains divots of one depth and the lower wall contains divots of a different depth. Under an applied driving force, skyrmions in the channels move with a finite skyrmion Hall angle that deflects them toward the upper wall for −x direction driving and the lower wall for +x direction driving. When the upper divots have zero height, the skyrmions are deflected against the flat upper wall for −x direction driving and the skyrmion velocity depends linearly on the drive. For +x direction driving, the skyrmions are pushed against the lower divots and become trapped, giving reduced velocities and a nonlinear velocity-force response. When there are shallow divots on the upper wall and deep divots on the lower wall, skyrmions get trapped for both driving directions; however, due to the divot depth difference, skyrmions move more easily under −x direction driving, and become strongly trapped for +x direction driving. The preferred −x direction motion produces what we call a Magnus diode effect since it vanishes in the limit of zero Magnus force, unlike the diode effects observed for asymmetric sawtooth potentials. We show that the transport curves can exhibit a series of jumps or dips, negative differential conductivity, and reentrant pinning due to collective trapping events. We also discuss how our results relate to recent continuum modeling on a similar skyrmion diode system.
Extended stability of vasopressin 0.2 unit/mL in PVC containers
Authors: Bae Hyunbeom , Weaver Eric , Ellis Steffani , Murray Jason 
Published: October 2022

AbstractPurposeVasopressin is used to maintain blood pressure in vasodilatory shock. Vasopressin is diluted from concentrated vials prior to administration as a continuous infusion. This study evaluates the physical and chemical stability changes of vasopressin diluted to 0.2 units/mL with 0.9% sodium chloride injection in polyvinyl chloride (PVC) bags stored under refrigeration.MethodsVasopressin Injection, USP, 20 unit/mL solution was diluted to 0.2 unit/mL with 0.9% sodium chloride injection, and stability changes were evaluated over 10 days via mass spectrometry on days 0, 7, and 10.ResultsSolutions of vasopressin 0.2 unit/mL in 0.9% sodium chloride injection in PVC bags were physically stable and showed less than 10% degradation over 10 days of refrigerated storage.ConclusionVasopressin 0.2 unit/mL may be given a beyond-use date (BUD) of 10 days based on United States Pharmacopeia BUD recommendations, with this study showing less than 10% degradation over 10 days of refrigerated storage.
Situationism and trait-eliciting situations
Authors: Piovarchy Adam 
Published: October 2022

Abstract
Doris, in his 2002 book Lack of Character and 2005 paper ‘Replies: evidence and sensibility’, famously argues that we lack the kinds of global character traits posited by theories of virtue, because the situationist experiments demonstrate that people do not display trait-relevant behaviour in trait-relevant situations above chance. This paper argues that some notable situationist experiments are not trait-relevant situations. By analysing which factors improve or reduce participants’ chances of success (e.g. stress, lack of familiarity, ambiguity), and observing that these factors decrease agents’ capacity to recognize and respond to a variety of reasons in a variety of settings, the best explanation of many subjects’ failure to do the right thing is that they are affected by factors that are capacity-compromising. This matters, because settings in which agents have a reduced capacity to avoid wrongdoing are typically not apt tests of an agent’s character traits.
Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous–Palaeogene (K/Pg) transition
Authors: Zecca Giovanni , Panzeri Davide , Grassi Fabrizio 
Published: October 2022

AbstractBackground and AimsAlthough plastid genes are widely used in phylogenetic studies, signals of positive selection have been scarcely investigated in the grape family. The plastomes from 91 accessions of Vitaceae were examined to understand the extent to which positive selection is present and to identify which genes are involved. Moreover, the changes through time of genes under episodic positive selection were investigated and the hypothesis of an adaptive process following the Cretaceous–Palaeogene (K/Pg) transition about 66 million years ago was tested.MethodsDifferent codon-substitution models were used to assess pervasive and episodic positive selection events on 70 candidate plastid genes. Divergence times between lineages were estimated and stochastic character mapping analysis was used to simulate variation over time of the genes found to be under episodic positive selection.Key ResultsA total of 20 plastid genes (29 %) showed positive selection. Among them, 14 genes showed pervasive signatures of positive selection and nine genes showed episodic signatures of positive selection. In particular, four of the nine genes (psbK, rpl20, rpoB, rps11) exhibited a similar pattern showing an increase in the rate of variation close to the K/Pg transition.ConclusionMultiple analyses have shown that the grape family has experienced ancient and recent positive selection events and that the targeted genes are involved in essential functions such as photosynthesis, self-replication and metabolism. Our results are consistent with the idea that the K/Pg transition has favoured an increased rate of change in some genes. Intense environmental perturbations have influenced the rapid diversification of certain lineages, and new mutations arising on some plastid genes may have been fixed by natural selection over the course of many generations.
Interactive effect between tree ageing and trunk-boring pest reduces hydraulics and carbon metabolism inHippophae rhamnoides
Authors: Wang Lin , Li Junpeng , Wang Yang , Xue Hao , Dai Yongxin , Han Youzhi 
Published: October 2022

AbstractSea-buckthorn (Hippophae rhamnoides) is widely distributed across the Eurasian continent. Recently sea-buckthorn has shown premature ageing and decline when confronted with water deficiency and Holcocerus hippophaecolus damage in northwest China and the Loess Plateau region. However, the physiological process of sea-buckthorn senescence in response to drought and pest damage is still unknown. In this study, 4-year-old (4y), 15-year-old normal growth (15yN) and 15-year-old seriously moth-damaged sea-buckthorn plants (15yH) were used as the research objects. The growth of branches and roots, branch water potential and percentage loss of conductivity (PLC), branch vulnerability to embolism (quantified by P50, xylem water potential at 50 % of PLC), branch xylem parenchyma cell viability, photosynthesis and the non-structural carbohydrate (NSC) content in branches and roots in dry and wet seasons were measured. The results showed that the length, basal diameter of 1-year-old branches and the leaf area of 4y trees were significantly larger than that of 15yN and 15yH trees, and the fine root density of 15yH trees was significantly lower than that of 15yN trees in all measured areas. The branch-specific hydraulic conductivity of 15yN and 15yH trees was only 50.2 % and 12.3 % of that of 4y trees, and the P50 of 4y, 15yH and 15yN trees was −3.69 MPa, −2.71 MPa and −1.15 MPa, respectively. The midday water potential and photosynthetic rate were highest in 4y trees, followed by 15yN and then 15yH trees in both the dry season and wet seasons, while branch PLC declined in the opposite direction (15yH trees highest, 4y trees lowest). The degree of PLC repair within a day was highest in 4y trees, followed by 15yN and then 15yH trees, and the viability of xylem cells was consistent with this pattern. The branch xylem starch and NSC content of 4y and 15yN trees were significantly higher than that of 15yH trees in the dry season, and the root starch and NSC content of 4y trees were significantly higher than that of 15yH trees in the two seasons. The above results suggest that the hydraulic properties of the normal elderly and seriously pest-damaged sea-buckthorn were significantly worse than in juvenile plants. Narrower early wood width and vessel density, high embolism vulnerability and weak embolism repair capacity led to the decline in water-conducting ability, and similarly further affected photosynthesis and the root NSC content. The decline in xylem parenchyma cell viability was the main reason for the limited embolism repair in the branches.
Variations in fungal and bacterial microbiome and chemical composition among fermenting Kishu-Narezushi batches
Authors: Kubo Miki , Niwa Ryo , Ohno Tomoki , Iwahashi Hitoshi 
Published: October 2022

ABSTRACT
Kishu-Narezushi is a spontaneously fermented food comprising fish, rice, and salt. During spontaneous fermentation, the microbiome may differ among batches, even when manufactured in the same way. In addition, analyses of changes in the chemical composition of the product are important for clarifying flavor characteristics. We collected basic information on the microbiome and chemical composition of Kishu-Narezushi using multiple batches of fermentation and evaluated whether the microbiome was homogeneous. The fungal microbiome of Kishu-Narezushi was dominated by Saccharomycetales and Trichosporonales. The bacterial microbiome was diverse, although seven specific genera of lactic acid bacteria were identified. Glutamic acid, histidine, and serine levels decreased after ∼10 days of fermentation. Succinic acid, characteristic of Kishu-Narezushi, accumulated upon the consumption of glutamic acid. Though the microbiome was diverse, the chemical composition was similar among the batches.
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome
Authors: Wang Ye , Chen Li 
Published: October 2022

AbstractMotivationUnderstanding the functional consequence of genetic variants, especially the non-coding ones, is important but particularly challenging. Genome-wide association studies (GWAS) or quantitative trait locus analyses may be subject to limited statistical power and linkage disequilibrium, and thus are less optimal to pinpoint the causal variants. Moreover, most existing machine-learning approaches, which exploit the functional annotations to interpret and prioritize putative causal variants, cannot accommodate the heterogeneity of personal genetic variations and traits in a population study, targeting a specific disease.ResultsBy leveraging paired whole-genome sequencing data and epigenetic functional assays in a population study, we propose a multi-modal deep learning framework to predict genome-wide quantitative epigenetic signals by considering both personal genetic variations and traits. The proposed approach can further evaluate the functional consequence of non-coding variants on an individual level by quantifying the allelic difference of predicted epigenetic signals. By applying the approach to the ROSMAP cohort studying Alzheimer’s disease (AD), we demonstrate that the proposed approach can accurately predict quantitative genome-wide epigenetic signals and in key genomic regions of AD causal genes, learn canonical motifs reported to regulate gene expression of AD causal genes, improve the partitioning heritability analysis and prioritize putative causal variants in a GWAS risk locus. Finally, we release the proposed deep learning model as a stand-alone Python toolkit and a web server.Availability and implementationhttps://github.com/lichen-lab/DeepPerVar.Supplementary informationSupplementary data are available at Bioinformatics online.
Fritz Müller: 200 years of a pioneer evolutionist
Authors: Araujo Leonardo Augusto Luvison 
Published: October 2022

Abstract
Fritz Müller is known for explaining the evolutionary consequences of what is now called Müllerian mimicry, but his scientific contributions encompass a wide range of organisms and both ecological and evolutionary processes. His originality is seen in aspects as different as the discovery of the mutualistic nature of ant–fungus symbiosis, pioneering research in evolutionary developmental biology and the first mathematical treatment in a Darwinian framework. From his intimate knowledge of the natural history of Brazil and original observations of morphology and development, Müller provided evidence supporting natural selection. From the 20th century onwards, however, his scientific legacy has been re-examined only for single topics. To celebrate the bicentenary of his birth in 2022, this article briefly discusses his importance for current ecological and evolutionary knowledge.
In Living Color: Pigment-Based Microbial Ecology At the Mineral–Air Interface
Authors: Villa Federica , Wu Ying-Li , Zerboni Andrea , Cappitelli Francesca 
Published: October 2022

AbstractPigment-based color is one of the most important phenotypic traits of biofilms at the mineral–air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral–air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities’ structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.
Focused ultrasound using a novel targeting method four-tract tractography for magnetic resonance–guided high-intensity focused ultrasound targeting
Authors: Feltrin Fabricio S , Chopra Rajiv , Pouratian Nader , Elkurd Mazen , El-Nazer Rasheda , Lanford Lauren , Dauer William , Shah Bhavya R 
Published: October 2022

AbstractMagnetic resonance–guided high-intensity focused ultrasound thalamotomy is a Food and Drug Administration–approved treatment for essential tremor. The target, the ventral intermediate nucleus of the thalamus, is not visualized on standard, anatomic MRI sequences. Several recent reports have used diffusion tensor imaging to target the dentato-rubro-thalamic-tract. There is considerable variability in fibre tracking algorithms and what fibres are tracked. Targeting discrete white matter tracts with magnetic resonance–guided high-intensity focused ultrasound is an emerging precision medicine technique that has the promise to improve patient outcomes and reduce treatment times. We provide a technical overview and clinical benefits of our novel, easily implemented advanced tractography method: four-tract tractography. Our method is novel because it targets both the decussating and non-decussating dentato-rubro-thalamic-tracts while avoiding the medial lemniscus and corticospinal tracts. Our method utilizes Food and Drug Administration-approved software and is easily implementable into existing workflows. Initial experience using this approach suggests that it improves patient outcomes by reducing the incidence of adverse effects.
Shorter Linkable Ring Signature Based on Middle-Product Learning with Errors Problem
Authors: Lin Hao , Sun Shi-Feng , Wang Mingqiang , Liu Joseph K , Wang Weijia 
Published: October 2022

Abstract
DualRing is a novel generic construction introduced by Yuen et al. (CRYPTO’21), which can transform a special kind of (Type-T*) canonical identification scheme to a ring signature scheme. Compared with the classical approaches, this method can get a shorter signature. In this paper, we construct a new middle-product learning with errors (MPLWE)-based ring signature scheme by using this framework. Specifically, we propose a new MPLWE-based identification scheme, which is compatible with the DualRing, then we obtain a ring signature scheme by using DualRing framework. We also show how to achieve linkability from this ring signature by using a collision resistant hash function. In the end, we provide available parameter options for our (linkable) ring signature scheme. Under these parameters, the signature size of our linkable ring signature is $2-40 \times $ shorter (depending on the ring size) than the previous MPLWE-based scheme by Das et al. (Africacrypt’19).
Multicentre Real-world Experience of Upadacitinib in the Treatment of Crohn’s Disease
Authors: Chugh Rishika , Braga-Neto Manuel B , Fredrick Thomas W , Ramos Guilherme P , Terdiman Jonathan , El-Nachef Najwa , Loftus Edward V , Mahadevan Uma , Kane Sunanda V 
Published: October 2022

Abstract

Background
Upadacitinib is a selective Janus kinase inhibitor approved for the management of ulcerative colitis and is under evaluation for the management of Crohn’s disease [CD] in Phase 3 clinical trials.

Aims
Our goal was to describe our real-world experience with upadacitinib in CD.

Methods
This is a two-centre retrospective cohort study of adult patients with moderate to severe CD on upadacitinib. The primary outcome was clinical response and remission as determined by stool frequency and abdominal pain scores. Secondary endpoints included endoscopic response and remission as determined by change in Simple Endoscopic Score for CD. Outcomes were assessed at 3 months after starting upadacitinib and at the patient’s most recent follow-up. We further evaluated adverse events and dose-related response.

Results
A total of 45 CD patients received upadacitinib and were included in the safety analysis. Thirty-six patients received upadacitinib for CD, whereas nine received it for inflammatory arthritis [n = 8] or pyoderma [n = 1]. Thirty-three patients received upadacitinib for 3 months or longer and were included in the efficacy analysis. At the 3-month follow-up, 21 patients achieved clinical response [63.6%] and nine achieved clinical remission [27.2%]. At time of last follow-up, 23 patients had clinical response [69.7%], ten achieved clinical remission [30.3%] and four [28.6%] achieved endoscopic remission. Adverse events occurred in 12 patients [26.7%]. Two patients had a serious adverse event [4.5%] without associated mortality.

Conclusion
In this real-world cohort of highly refractory CD patients, upadacitinib was effective in inducing remission and had an acceptable safety profile.
Placebo Response Rates in Randomized Controlled Trials for Perianal Crohn’s Disease: A Systematic Review and Meta-Analysis
Authors: Sharma Tanmay , Ma Christopher , Sedano Rocio , Hanzel Jurij , McDonald Cassandra , Hogan Malcolm , Kochhar Gursimran S , Narula Neeraj , Peyrin-Biroulet Laurent , Danese Silvio , MacDonald John K , Jairath Vipul 
Published: October 2022

Abstract

Background and Aims
Perianal fistulizing disease is a common complication of Crohn’s disease [CD], for which new therapies are urgently needed. To assist the design of clinical trials for novel therapeutics, we conducted a systematic review and meta-analysis of randomised controlled trials [RCTs] to quantify placebo rates and identify factors influencing them in perianal CD [pCD].

Methods
We searched MEDLINE, Embase and CENTRAL from inception to June 2021. Eligible studies were placebo-controlled trials of pharmacological interventions for pCD. Placebo fistula response and remission rates for induction and maintenance trials were extracted and pooled using a random-effects model. Mixed-effects meta-regression was used to evaluate the impact of patient and study-level characteristics on point estimates.

Results
In 17 RCTs [13 induction, five maintenance] the pooled placebo fistula response and remission rate for induction trials was 25% (95% confidence interval [CI] 17–36%) and 17% [95% CI 11–25%], respectively. For maintenance trials, the pooled placebo fistula response and remission rate was 23% [95% CI 17–32%] and 19% [95% CI 14–25%], respectively. Trials enrolling patients with less disease activity and a higher proportion with ileal predominant disease were associated with significantly higher placebo response rates. Trials originating in Europe [compared to North America], therapies requiring perianal injection and a longer timepoint to measure remission were associated with higher placebo remission rates.

Conclusions
Placebo response and remission rates in pCD trials are influenced by patient and disease-related factors, as well as the type of intervention being studied. These contemporary rates will inform trial design for novel therapeutics.
Disease Activity and Health-related Quality of Life Relationships with Work Productivity in Patients with Ulcerative Colitis in OCTAVE Induction 1 and 2 and OCTAVE Sustain
Authors: Targownik Laura , Dubinsky Marla C , Steinwurz Flavio , Bushmakin Andrew G , Cappelleri Joseph C , Tai Elaine , Gardiner Sean , Hur Peter , Panés Julian 
Published: October 2022

Abstract

Background
Tofacitinib is an oral small molecule Janus kinase inhibitor for the treatment of ulcerative colitis [UC]. We evaluated the relationship between Mayo/Inflammatory Bowel Disease Questionnaire [IBDQ] scores and Work Productivity and Activity Impairment-UC [WPAI-UC] components in patients with UC.

Methods
All available pooled data from three Phase 3 tofacitinib studies [OCTAVE Induction 1 and 2 and OCTAVE Sustain] were included. Relationships were estimated using repeated measures regression models with Mayo score/subscores or IBDQ total/domain scores as a separate anchor predictor and WPAI-UC components as the outcome.

Results
Evidence for linear relationships was confirmed between Mayo/IBDQ scores and WPAI-UC components. Robust relationships between total Mayo score/IBDQ total score and WPAI-UC presenteeism, work productivity loss, and activity impairment were observed; relationships with absenteeism were weak. Total Mayo scores of 0 and 12 corresponded, on average, to WPAI-UC component scores of &lt; 15% and ≥ 60%, respectively, and IBDQ total scores of 224 and 32 corresponded, on average, to WPAI-UC component scores of &lt; 6% and ≥ 90%, respectively. Presenteeism, work productivity loss, and activity impairment [all 0–100%], respectively, improved on average by 14.7, 13.6, and 16.4 percentage points for every 3-point improvement in total Mayo score, and by 8.1, 7.9, and 8.8 percentage points for every 16-point improvement in IBDQ total score.

Conclusion
Robust relationships between Mayo/IBDQ scores with WPAI-UC presenteeism, work productivity loss, and activity impairment suggest that patient productivity and non-work activities are strongly associated with disease activity and HRQoL. The weak relationships with absenteeism suggest that patients attend work regardless of their disease activity/poor HRQoL.
ClinicalTrials.gov: NCT01465763;NCT01458951;NCT01458574.