bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land–atmosphere–ocean coupling associated with the Tibetan Plateau and its climate impacts
Authors: Liu Yimin , Lu Mengmeng , Yang Haijun , Duan Anmin , He Bian , Yang Song , Wu Guoxiong 
Published: February 2020

Abstract
This paper reviews recent advances regarding land–atmosphere–ocean coupling associated with the Tibetan Plateau (TP) and its climatic impacts. Thermal forcing over the TP interacts strongly with that over the Iranian Plateau, forming a coupled heating system that elevates the tropopause, generates a monsoonal meridional circulation over South Asia and creates conditions of large-scale ascent favorable for Asian summer monsoon development. TP heating leads to intensification and westward extension (northward movement) of the South Asian High (Atlantic Intertropical Convergence Zone), and exerts strong impacts on upstream climate variations from North Atlantic to West Asia. It also affects oceanic circulation and buoyancy fields via atmospheric stationary wave trains and air–sea interaction processes, contributing to formation of the Atlantic Meridional Overturning Circulation. The TP thermal state and atmospheric–oceanic conditions are highly interactive and Asian summer monsoon variability is controlled synergistically by internal TP variability and external forcing factors.
Factor Xa Inhibition Reduces Coagulation Activity but Not Inflammation Among People With HIV: A Randomized Clinical Trial
Authors: Baker Jason V , Wolfson Julian , Peterson Tess , Mooberry Micah , Gissel Matthew , Mystakelis Harry , Henderson Michael W , Garcia-Myers Kelly , Rhame Frank S , Schacker Timothy W , Brummel-Ziedins Kathleen E , Sereti Irini , Key Nigel S , Tracy Russell P 
Published: February 2020

Abstract

Background
Coagulation activity among persons with HIV is associated with end-organ disease risk, but the pathogenesis is not well characterized. We tested a hypothesis that hypercoagulation contributes to disease risk, in part, via upregulation of inflammation.

Methods
Treatment effects of edoxaban (30 mg), a direct factor Xa inhibitor, vs placebo were investigated in a randomized, double-blind crossover trial among participants with HIV and viral suppression and D-dimer levels ≥100 ng/mL. During each 4-month crossover period, blood measures of coagulation, inflammation, and immune activation were assessed. Analyses of change on edoxaban vs change on placebo used linear mixed models.

Results
Forty-four participants were randomized, and 40 completed at least 1 visit during each study period. The mean age was 49 years, and the CD4+ count was 739 cells/mm3. Edoxaban treatment led to declines in D-dimer (44%) and thrombin-antithrombin complex (26%) but did not lower inflammatory or immune activation measures. More bruising or bleeding events occurred during edoxaban (n = 28) than during placebo or no drug periods (n = 15).

Conclusions
The direct factor Xa inhibitor edoxaban led to a substantial reduction in coagulation but no effect on inflammation or immune activation. These results do not support that hypercoagulation contributes to ongoing inflammation during chronic antiretroviral therapy–treated HIV disease.
Independent Validation in a Large Privately Insured Population of the Risk Index for Serious Prescription Opioid–Induced Respiratory Depression or Overdose
Authors: Metcalfe Leanne , Murrelle E Lenn , Vu Lan , Joyce Andrew R , Averhart Preston Veronica , Maryon Thomas , McDanald Conway , Yoo Phillip 
Published: February 2020

Abstract

Objective
To assess the generalizability of the overdose or serious opioid-induced respiratory depression risk index (VHA-RIOSORD), created by Zedler et al., using claims data from a large private insurer.

Design
A retrospective nested case–control analysis of health care claims data.

Subjects
Commercially insured individuals with a claim for an opioid prescription between October 1, 2014, and September 30, 2016 (N = 1,431,737).

Methods
An overdose or serious opioid–induced respiratory depression (OSORD) occurred in 1,097 patients. Ten controls were selected per case (N = 10,970). Items and the assignment of point values to predictors were consistent with those determined by Zedler et al. Modeling of risk index scores produced predicted probabilities of OSORD; risk classes were defined by the predicted probability distribution.

Results
All 15 items of the VHA-RIOSORD were used to determine a member’s risk of OSORD. The average predicted probability of experiencing OSORD ranged from 3% in the lowest risk decile to 90% in the highest, with excellent agreement between predicted and observed incidence across risk classes. The model’s C-statistic was 0.88.

Conclusions
Consistent with the findings of its developers, the VHA-RIOSORD performed well in identifying members of a large private insurance company who were medical users of prescription opioids at elevated risk of overdose or life-threatening respiratory depression, those most likely to benefit from preventive interventions.
Modelling the epidemic trend of the 2019-nCOV outbreak in Hubei Province, China
Authors: Ai Lizhe 
Published: February 2020

AbstractAs of 8am 30th January (Beijing Time) 2020, Approximate 8000 cases across the world have been confirmed. It’s necessary to simulate epidemic trend of the 2019-nCOV outbreak in Hubei Province, the hardest-hit area. By SEIR simulation, the predicted epidemic peak in Hubei will be within 28th January 2020 to 7th February 2020, up to 7000-9000 infectious cases in total. The estimate above was based on some assumptions and limitations exited.
Skill-specific changes in cortical preparatory activity during motor learning
Authors: Sun Xulu , O’Shea Daniel J. , Golub Matthew D. , Trautmann Eric M. , Vyas Saurabh , Ryu Stephen I. , Shenoy Krishna V. 
Published: February 2020

AbstractAnimals have a remarkable capacity to learn new motor skills, but it remains an open question as to how learning changes neural population dynamics underlying movement1. Specifically, we asked whether changes in neural population dynamics relate purely to newly learned movements or if additional patterns are generated that facilitate learning without matching motor output. We trained rhesus monkeys to learn a curl force field2task that elicited new arm-movement kinetics for some but not all reach directions3,4. We found that along certain neural dimensions, preparatory activity in motor cortex reassociated existing activity patterns with new movements. These systematic changes were observed only for learning-altered reaches. Surprisingly, we also found prominent shifts of preparatory activity along a nearly orthogonal neural dimension. These changes in preparatory activity were observed uniformly for all reaches including those unaltered by learning. This uniform shift during learning implies formation of new neural activity patterns, which was not observed in other short-term learning contexts5–8. During a washout period when the curl field was removed, movement kinetics gradually reverted, but the learning-induced uniform shift of preparatory activity persisted and a second, orthogonal uniform shift occurred. This persistent shift may retain a motor memory of the learned field9–11, consistent with faster relearning of the same curl field observed behaviorally and neurally. When multiple different curl fields were learned sequentially, we found distinct uniform shifts, each reflecting the identity of the field applied and potentially separating the associated motor memories12,13. The neural geometry of these shifts in preparatory activity could serve to organize skill-specific changes in movement production, facilitating the acquisition and retention of a broad motor repertoire.
HIV-1 Viremia Not Suppressible By Antiretroviral Therapy Can Originate from Large T-Cell Clones Producing Infectious Virus
Authors: Halvas Elias K. , Joseph Kevin W. , Brandt Leah D. , Guo Shuang , Sobolewski Michele D. , Jacobs Jana L. , Tumiotto Camille , Bui John K. , Cyktor Joshua C. , Keele Brandon F. , Morse Gene D. , Bale Michael J. , Kearney Mary F. , Coffin John M. , Rausch Jason W. , Wu Xiaolin , Hughes Stephen H. , Mellors John W. 
Published: February 2020

AbstractBACKGROUNDHIV-1 viremia that is not suppressed by combination antiretroviral therapy (ART) is generally attributed to incomplete medication adherence and/or drug resistance. We evaluated individuals referred for non-suppressible viremia (plasma HIV-1 RNA above 40 copies/ml) who reported adherence to ART and did not show drug resistance to their current regimen.METHODSSamples were collected from at least two time points from eight donors who had non-suppressible viremia for more than six months on ART. Single templates of HIV-1 RNA obtained from plasma and viral outgrowth of cultured cells and from proviral DNA were PCR-amplified and sequenced for evidence of clones of cells that produced infectious viruses. Clones were identified by host-proviral integration site analysis.RESULTSHIV-1 genomic RNAs with identical sequences were identified in plasma samples from all eight donors. The identical viral RNA sequences did not change over time and lacked resistance to the ART regimen. In four of the donors, viral RNA sequences obtained from plasma matched those sequences from viral outgrowth cultures, indicating that the viruses were replication-competent. Integration sites for infectious proviruses from those four donors were mapped to introns of theMATR3,ZNF268,ZNF721/ABCA11P, andABCA11Pgenes. The sizes of the clones were from 50 million to 350 million cells.CONCLUSIONClones of HIV-1-infected cells producing virus can cause failure of ART to suppress viremia despite medication adherence and absence of drug resistance. The mechanisms involved in clonal expansion and persistence need to be defined to eliminate viremia and the HIV-1 reservoir.
The immune response and microbiota profiles during co-infection withP. vivaxand soil-transmitted helminths
Authors: Easton Alice V. , Raciny-Aleman Mayra , Liu Victor , Ruan Erica , Yasnot Maria Fernanda , Rodriguez Ana , Loke P’ng 
Published: February 2020

AbstractCo-infection with soil-transmitted helminths (STH) andPlasmodiumspp. parasites is a common occurrence in tropical low-income countries, but the consequences of this interaction remain poorly understood. Here, we performed a multi-omic analysis on peripheral blood and fecal samples from 130 individuals in Tierralta, Córdoba, Colombia who were infected withP. vivaxalone (n = 33), co-infected withP. vivaxand STH (n = 27), infected with STH alone (n = 39) or were infected with neitherP. vivaxnor STH (n = 31). In addition to Complete Blood Count (CBC) with differential, transcriptional profiling of peripheral blood samples was performed by RNA-Seq, fecal microbial communities were determined by 16S ribosomal RNA gene sequencing and circulating cytokine levels were measured by bead-based immunoassays. Differences in blood cell counts were driven primarily byP. vivaxinfection, including an increased percentage of neutrophils that was associated with a transcriptional signature of neutrophil activation in the blood.P. vivaxinfection was also associated with increased levels of IL-6, IL-8 and IL-10, and these cytokine levels were not affected by STH co-infection. Surprisingly,P. vivaxinfection was more strongly associated with changes in the microbiome than STH infection. Children infected withP. vivaxexhibited elevatedBacteroidesand reducedPrevotellaandClostridiaceae, but these differences were not observed in individuals co-infected with STH. We also observed thatP. vivaxparasitemia was higher in the STH-infected population. When we used machine learning to identify the most important predictors ofP. vivaxparasite burden from all measured variables, bacterial taxa were the strongest predictors of parasitemia levels. In contrast, circulating TGF-β was the strongest predictor ofT. trichiuraegg burden. This study provides unexpected evidence that the gut microbiota may have a stronger link withP. vivaxthan with STH infection.
aiMeRA: A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk
Authors: Jimenez-Dominguez Gabriel , Ravel Patrice , Jalaguier Stéphan , Cavaillès Vincent , Colinge Jacques 
Published: February 2020

AbstractModular response analysis (MRA) is a widely used modeling technique to uncover coupling strengths in molecular networks under a steady-state condition by means of perturbation experiments. We propose an extension of this methodology to search genomic data for new associations with a network modeled by MRA and to improve the predictive accuracy of MRA models. These extensions are illustrated by exploring the cross talk between estrogen and retinoic acid receptors, two nuclear receptors implicated in several hormone-driven cancers such as breast. We also present a novel, rigorous and elegant mathematical derivation of MRA equations, which is the foundation of this work and of an R package that is freely available athttps://github.com/bioinfo-ircm/aiMeRA/. This mathematical analysis should facilitate MRA understanding by newcomers.Author summaryEstrogen and retinoic acid receptors play an important role in several hormone-driven cancers and share co-regulators and co-repressors that modulate their transcription factor activity. The literature shows evidence for crosstalk between these two receptors and suggests that spatial competition on the promoters could be a mechanism. We used MRA to explore the possibility that key co-repressors, i.e., NRIP1 (RIP140) and LCoR could also mediate crosstalk by exploiting new quantitative (qPCR) and RNA sequencing data. The transcription factor role of the receptors and the availability of genome-wide data enabled us to explore extensions of the MRA methodology to explore genome-wide data setsa posteriori, searching for genes associated with a molecular network that was sampled by perturbation experiments. Despite nearly two decades of use, we felt that MRA lacked a systematic mathematical derivation. We present here an elegant and rather simple analysis that should greatly facilitate newcomers’ understanding of MRA details. Moreover, an easy-to-use R package is released that should make MRA accessible to biology labs without mathematical expertise. Quantitative data are embedded in the R package and RNA sequencing data are available from GEO.
Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird
Authors: Bowler Diana E. , Kvasnes Mikkel A. J. , Pedersen Hans C. , Sandercock Brett K. , Nilsen Erlend B. 
Published: February 2020

AbstractAccording to classic theory, species’ population dynamics and distributions are less influenced by species interactions under harsh climatic conditions compared to under more benign climatic conditions. In alpine and boreal ecosystems in Fennoscandia, the cyclic dynamics of rodents strongly affect many other species, including ground-nesting birds such as ptarmigan. According to the ‘alternative prey hypothesis’ (APH), the densities of ground-nesting birds and rodents are positively associated due to predator-prey dynamics and prey-switching. However, it remains unclear how the strength of these predator-mediated interactions change along a climatic harshness gradient in comparison with the effects of climatic variation. We built a hierarchical Bayesian model to estimate the sensitivity of ptarmigan populations to interannual variation in climate and rodent occurrence across Norway during 2007–2017. Ptarmigan abundance was positively linked with rodent occurrence, consistent with the APH. Moreover, we found that rodent dynamics had stronger effects on ptarmigan in colder regions. Our study highlights how species interactions play an important role for the population dynamics of species at higher latitudes and suggests that they can become even more important in the most climatically harsh regions.
Rapid evolution of coordinated and collective movement in response to artificial selection
Authors: Kotrschal Alexander , Szorkovszky Alexander , Herbert-Read James , Bloch Natasha I. , Romenskyy Maksym , Buechel Séverine Denise , Eslava Ada Fontrodona , Sánchez Alòs Laura , Zeng Hongli , Le Foll Audrey , Braux Ganaël , Pelckmans Kristiaan , Mank Judith E. , Sumpter David , Kolm Niclas 
Published: February 2020

AbstractCollective motion occurs when individuals use social interaction rules to respond to the movements and positions of their neighbors. How readily these social decisions are shaped by selection remains unknown. Through artificial selection on fish (guppies,Poecilia reticulata) for increased social coordination (group polarization), we demonstrate that social interaction rules can evolve remarkably fast. Within just three generations, groups of polarization selected females showed a 15% increase in polarization, coupled with increased cohesiveness, compared to fish from control lines. They did not differ in physical swimming ability or exploratory behavior. However, polarization selected fish adopted faster speeds, particularly in social contexts, and showed stronger alignment and attraction responses to multiple neighbors. Our results demonstrate that animals’ social interactions can rapidly evolve under strong selection, and reveal which social interaction rules change when collective behavior evolves.
Single-cell transcriptome analyses recapitulate the cellular and developmental responses to abiotic stresses in rice
Authors: Wang Yu , Huan Qing , Chu Xiao , Li Ke , Qian Wenfeng 
Published: February 2020

ABSTRACTThe metabolism and reproduction of plants depend on the division of labors among cells. However, cells with various functions are often studied as a bulk where their specificities were diluted. Here, we apply single-cell RNA sequencing to the aerial part of rice seedlings growing in various environments. We capture the transcriptomes of thousands of cells, identify all major cell types, and reconstruct their developmental trajectories. We find that abiotic stresses not only affect gene expression in a cell-type-specific manner but also have impacts on the physical size of cells and the composition of cell populations. We validate some of these conclusions with microscopy and provide developmental mechanisms with computational analyses. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas in rice and an illustration of exploiting such resource to drive discoveries in plant biology.
The functional foundations of episodic memory remain stable throughout the lifespan
Authors: Vidal-Piñeiro D. , Sneve MH. , Amlien IK. , Grydeland H. , Mowinckel AM. , Roe J.M. , Sørensen Ø. , Nyberg LH. , Walhovd KB. , Fjell AM. 
Published: February 2020

AbstractIt is suggested that the functional mechanisms behind specific forms of cognition, particularly episodic memory, may be dynamic over the lifespan and that cognitive preservation or decay in older age thus relies on age-specific mechanisms such as compensatory processes. Here instead, we tested whether the functional foundations of successful episodic memory encoding adhere to a principle of lifespan continuity, shaped by developmental, structural and evolutionary influences. We identified the generic lifespan patterns of memory encoding function across the brain (n = 540; age range = 6 – 82 years). The lifespan trajectories of brain activity were organized in a topologically meaningful manner and aligned to fundamental aspects of brain organization, such as large-scale connectivity hierarchies and evolutionary cortical expansion gradients. None of the normative trajectories of encoding function was solely determined by late-life patterns of activity, but rather showed continuities across development and adulthood. Inter-individual differences in activity in age-sensitive regions were predicted by general cognitive abilities and variation in grey matter structure, which are core variables of cognitive and structural change throughout the lifespan. Altogether, the results provide evidence for the lifelong continuity of the functional foundations of episodic memory which are bounded by both brain architecture and core mechanisms of cognitive and structural change over life. We provide novel support for a perspective on memory aging in which maintenance and decay of episodic memory in older age needs to be understood from a comprehensive life-long perspective rather than as a late-life phenomenon only.Significance statementIt is suggested that cognitive function in older age largely relies on late-life specific mechanisms such as compensatory processes. In contrast, here we tested whether and to what degree brain activity during episodic memory encoding adheres to fundamental principles of life-long brain organization and continuity. The results revealed that generic lifespan trajectories of memory encoding function were not specific to late-life. Instead, the age-trajectories showed a continuity through life, were related to fundamental features of brain structure and cognition and to functional and evolutionary hierarchies. We argue that rather than focusing on older-age specific mechanisms, a framework that takes lifespan mechanisms of cognition and brain anatomy into account is necessary to understand episodic memory vulnerability in older age.
In vivo assessment of mechanisms underlying the neurovascular basis of postictal amnesia
Authors: Farrell Jordan S. , Colangeli Roberto , Dudok Barna , Wolff Marshal D. , Nguyen Sarah L. , Jackson Jesse , Dickson Clayton T. , Soltesz Ivan , Teskey G. Campbell 
Published: February 2020

AbstractLong-lasting confusion and memory difficulties during the postictal state remain a major unmet problem in epilepsy that lacks pathophysiological explanation and treatment. We previously identified that long-lasting periods of severe postictal hypoperfusion/hypoxia, not seizuresper se, are associated with memory impairment after temporal lobe seizures. While this observation suggests a key pathophysiological role for insufficient energy delivery, it is unclear how the networks that underlie episodic memory respond to vascular constraints that ultimately give rise to amnesia. Here, we focused on cellular/network level analyses in the CA1 of hippocampusin vivoto determine if neural activity, network oscillations, synaptic transmission, and/or synaptic plasticity are impaired following kindled seizures. Importantly, the induction of severe postictal hypoperfusion/hypoxia was prevented in animals treated by a COX-2 inhibitor, which experimentally separated seizures from their vascular consequences. We observed complete activation of CA1 pyramidal neurons during brief seizures, followed by a short period of reduced activity and flattening of the local field potential that resolved within minutes. During the postictal state, constituting tens of minutes to hours, we observed no changes in neural activity, network oscillations, and synaptic transmission. However, long-term potentiation of the temporoammonic pathway to CA1 was impaired in the postictal period, but only when severe local hypoxia occurred. Lastly, we tested the ability of rats to perform object-context discrimination, which has been proposed to require temporoammonic input to differentiate between sensory experience and the stored representation of the expected object-context pairing. Deficits in this task following seizures were reversed by COX-2 inhibition, which prevented severe postictal hypoxia. These results support a key role for hypoperfusion/hypoxia in postictal memory impairments and identify that many aspects of hippocampal network function are resilient during severe hypoxia except for long-term synaptic plasticity.