bluuebunny/crossref_metadata_2025_split huggingface dataset:
yacrd and fpa: upstream tools for long-read genome assembly
Authors: Marijon Pierre , Chikhi Rayan , Varré Jean-Stéphane 
Published: April 2020

Abstract

Motivation
Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.

Results
We introduce two tools: yacrd for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative.

Availability and implementation
https://github.com/natir/yacrd and https://github.com/natir/fpa.

Supplementary information
Supplementary data are available at Bioinformatics online.
Temporal changes in the corpus luteum during early pregnancy reveal regulation of pathways that enhance steroidogenesis and suppress luteolytic mechanisms†
Authors: Hughes C H K , Inskeep E K , Pate J L 
Published: April 2020

AbstractAlthough rescue of the corpus luteum (CL) is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored. CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Next-generation sequencing was used to profile mRNA abundance during this time, while tandem mass spectrometry and nanostring technology were used to profile proteins and miRNA, respectively. A total of 1157 mRNA were differentially abundant, while 27 miRNA changed, and 29 proteins tended to change. mRNA that increased were regulators of interferon signaling and DNA repair, while those that decreased were associated with luteolytic processes, such as calcium signaling and matrix metallopeptidase (MMP) signaling, indicating inhibition of these processes. One of these, MMP12, was regulated by prostaglandin F2A in vitro. mRNA that were maximally abundant on day 20 were primarily associated with immune processes. Two of these, C-C motif chemokine ligand 1 and NFKB inhibitor alpha, were regulated by interferon tau in vitro. MiRNA that increased were predicted to inhibit phosphatidylinositol signaling, while those that decreased may be negative regulators of steroidogenesis. One protein that was greater on day 20 than on day 14 was aldehyde dehydrogenase 1 family member A1 (ALDH1A1), which synthesizes retinoic acid. Pharmacological inhibition of this enzyme, or of retinoic acid receptor signaling, led to suppression of progesterone production in vitro. Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.
The role of the inferior parietal lobule in writer’s cramp
Authors: Merchant Shabbir Hussain I , Frangos Eleni , Parker Jacob , Bradson Megan , Wu Tianxia , Vial-Undurraga Felipe , Leodori Giorgio , Bushnell M C , Horovitz Silvina G , Hallett Mark , Popa Traian 
Published: April 2020

AbstractHumans have a distinguishing ability for fine motor control that is subserved by a highly evolved cortico-motor neuronal network. The acquisition of a particular motor skill involves a long series of practice movements, trial and error, adjustment and refinement. At the cortical level, this acquisition begins in the parieto-temporal sensory regions and is subsequently consolidated and stratified in the premotor-motor cortex. Task-specific dystonia can be viewed as a corruption or loss of motor control confined to a single motor skill. Using a multimodal experimental approach combining neuroimaging and non-invasive brain stimulation, we explored interactions between the principal nodes of the fine motor control network in patients with writer’s cramp and healthy matched controls. Patients and healthy volunteers underwent clinical assessment, diffusion-weighted MRI for tractography, and functional MRI during a finger tapping task. Activation maps from the task-functional MRI scans were used for target selection and neuro-navigation of the transcranial magnetic stimulation. Single- and double-pulse TMS evaluation included measurement of the input-output recruitment curve, cortical silent period, and amplitude of the motor evoked potentials conditioned by cortico-cortical interactions between premotor ventral (PMv)-motor cortex (M1), anterior inferior parietal lobule (aIPL)-M1, and dorsal inferior parietal lobule (dIPL)-M1 before and after inducing a long term depression-like plastic change to dIPL node with continuous theta-burst transcranial magnetic stimulation in a randomized, sham-controlled design. Baseline dIPL-M1 and aIPL-M1 cortico-cortical interactions were facilitatory and inhibitory, respectively, in healthy volunteers, whereas the interactions were converse and significantly different in writer’s cramp. Baseline PMv-M1 interactions were inhibitory and similar between the groups. The dIPL-PMv resting state functional connectivity was increased in patients compared to controls, but no differences in structural connectivity between the nodes were observed. Cortical silent period was significantly prolonged in writer’s cramp. Making a long term depression-like plastic change to dIPL node transformed the aIPL-M1 interaction to inhibitory (similar to healthy volunteers) and cancelled the PMv-M1 inhibition only in the writer’s cramp group. These findings suggest that the parietal multimodal sensory association region could have an aberrant downstream influence on the fine motor control network in writer’s cramp, which could be artificially restored to its normal function.
Enhancer Locus in ch14q23.1 Modulates Brain Asymmetric Temporal Regions Involved in Language Processing
Authors: Le Guen Yann , Leroy François , Philippe Cathy ,   IMAGEN Consortium, Mangin Jean-François , Dehaene-Lambertz Ghislaine , Frouin Vincent 
Published: April 2020

Abstract
Identifying the genes that contribute to the variability in brain regions involved in language processing may shed light on the evolution of brain structures essential to the emergence of language in Homo sapiens. The superior temporal asymmetrical pit (STAP), which is not observed in chimpanzees, represents an ideal phenotype to investigate the genetic variations that support human communication. The left STAP depth was significantly associated with a predicted enhancer annotation located in the 14q23.1 locus, between DACT1 and KIAA0586, in the UK Biobank British discovery sample (N = 16 515). This association was replicated in the IMAGEN cohort (N = 1726) and the UK Biobank non-British validation sample (N = 2161). This genomic region was also associated to a lesser extent with the right STAP depth and the formation of sulcal interruptions, “plis de passage,” in the bilateral STAP but not with other structural brain MRI phenotypes, highlighting its notable association with the superior temporal regions. Diffusion MRI emphasized an association with the fractional anisotropy of the left auditory fibers of the corpus callosum and with networks involved in linguistic processing in resting-state functional MRI. Overall, this evidence demonstrates a specific relationship between this locus and the establishment of the superior temporal regions that support human communication.
National Trends in Antibiotic Use in Australian Residential Aged Care Facilities, 2005–2016
Authors: Sluggett Janet K , Moldovan Max , Lynn David J , Papanicolas Lito E , Crotty Maria , Whitehead Craig , Wesselingh Steve L , Rogers Geraint B , Inacio Maria C 
Published: April 2020

Abstract

Background
Understanding current patterns of antibiotic use in residential aged care facilities (RACFs) is essential to inform stewardship activities, but limited utilization data exist. This study examined changes in prevalence and consumption of antibiotics in Australian RACFs between 2005–2006 and 2015–2016.

Methods
This population-based, repeated cross-sectional analysis included all long-term permanent residents of Australian RACFs between July 2005 and June 2016 who were aged ≥ 65 years. The yearly prevalence rate of antibiotic use and number of defined daily doses (DDDs) of systemic antibiotics per 1000 resident-days were determined annually from linked pharmaceutical claims data. Trends were assessed using ordinary least squares regression.

Results
This study included 502 752 residents from 3218 RACFs, with 424.9 million resident-days analyzed. Antibiotics were dispensed on 5 608 126 occasions during the study period, of which 88% were for oral use. Cefalexin, amoxicillin-clavulanic acid, and trimethoprim were the most commonly dispensed antibiotics. The annual prevalence of antibiotic use increased from 63.8% (95% confidence interval [CI], 63.3%–64.4%) to 70.3% (95% CI, 69.9%–70.7%) between 2005–2006 and 2015–2016 (0.8% average annual increase, P &lt; .001). There was a 39% relative increase in total consumption of systemic antibiotics, with utilization increasing from 67.6 to 93.8 DDDs/1000 resident-days during the study period (average annual increase of 2.8 DDDs/1000 resident-days, P &lt; .001).

Conclusions
This nationwide study showed substantial increases in both prevalence of use and total consumption of antibiotics in Australian RACFs between 2005 and 2016. The increasingly widespread use of antibiotics in Australian RACFs is concerning and points to a need for enhanced efforts to optimize antibiotic use in this setting.
Importance of Inclusion of Pregnant and Breastfeeding Women in COVID-19 Therapeutic Trials
Authors: LaCourse Sylvia , John-Stewart Grace , Adams Waldorf Kristina M 
Published: April 2020

Abstract
Investigators are employing unprecedented innovation in the design of clinical trials to rapidly and rigorously assess potentially promising therapies for coronavirus disease 2019 (COVID-19); this is in stark contrast to the continued near-universal regressive practice of exclusion of pregnant and breastfeeding women from these trials. The few trials that allow their inclusion focus on postexposure prophylaxis or outpatient treatment of milder disease, limiting the options available to pregnant women with severe COVID-19 to compassionate use of remdesivir, or off-label drug use of hydroxychloroquine or other therapies. These restrictions were put in place despite experience with these drugs in pregnant women. In this Viewpoint, we call attention to the need and urgency to engage pregnant women in COVID-19 treatment trials now in order to develop data-driven recommendations regarding the risks and benefits of therapies in this unique but not uncommon population.
Sequential Analysis of Viral Load in a Neonate and Her Mother Infected With Severe Acute Respiratory Syndrome Coronavirus 2
Authors: Han Mi Seon , Seong Moon-Woo , Heo Eun Young , Park Ji Hong , Kim Namhee , Shin Sue , Cho Sung Im , Park Sung Sup , Choi Eun Hwa 
Published: April 2020

AbstractWe report changes in viral load over time in a 27-day-old neonate with coronavirus disease 2019 who presented with fever, cough, and vomiting. Severe acute respiratory syndrome coronavirus 2 RNA was detected in the nasopharynx, oropharynx, stool, saliva, plasma, and urine. The highest viral RNA copies in nasopharynx decreased over time while viral load in stool remained high.
Race, Interdependence and Healing in Toni Morrison’s God Help the Child
Authors: Gallego Mar 
Published: April 2020

Abstract
In Toni Morrison’s works, traumatized characters are victimized by the damaging, racist dominant ideology that still codifies black bodies as the non-human “Other” due to the long-lasting effects of slavery and diasporic dispersal. These individual and collective traumas seemingly hinder their articulation of healthy forms of subject formation and community-building efforts. My contention is that in God Help the Child (2015) Morrison explores the ramifications of early trauma in her characters’ lives but also, more importantly, an array of resistance strategies, which facilitate healing, within an ethics of interdependence. Hence, Morrison critiques fundamental inequities in American society and around the world, by paying attention to the intersections of race, gender, and age discourses.
Adverse Employment Histories, Later Health Functioning and National Labor Market Policies: European Findings Based on Life-History Data From SHARE and ELSA
Authors: Wahrendorf Morten , Hoven Hanno , Deindl Christian , Lunau Thorsten , Zaninotto Paola 
Published: April 2020

Abstract

Objectives
We investigate associations between adverse employment histories over an extended time period and health functioning in later life, and explore whether national labor market policies moderate the association.

Methods
We use harmonized life-history data from the Gateway to Global Aging Data on two European studies (SHARE and ELSA) linked to health beyond age 50 (men = 11,621; women = 10,999). Adverse employment histories consist of precarious, discontinued, and disadvantaged careers between age 25 and 50, and we use depressive symptoms, grip strength, and verbal memory as outcomes.

Results
Adverse employment histories between age 25 and 50 are associated with poor health functioning later in life, particularly repeated periods of unemployment, involuntary job losses, weak labor market ties, and disadvantaged occupational positions. Associations remain consistent after adjusting for age, partnership history, education and employment situation, and after excluding those with poor health prior to or during working life. We find no variations of the associations by national labor market policies.

Discussion
Our study calls for increased intervention efforts to improve working conditions at early career stages. Despite the importance in shaping employment histories, the role of national policies in modifying the impact of employment on health is less clear.
Large Extracellular Cord Formation in a Zebrafish Model of Mycobacterium kansasii Infection
Authors: Johansen Matt D , Kremer Laurent 
Published: April 2020

Abstract
Mycobacterium kansasii is a slow-growing nontuberculous mycobacteria responsible for coinfections particularly in patients with human immunodeficiency virus. To date, our knowledge of M. kansasii infection has been hampered owing to the lack of an effective animal model to study pathogenesis. In the current study, we showed that the zebrafish embryo is permissive to M. kansasii infection, resulting in chronic infection and formation of granulomas. On macrophage depletion, we identified M. kansasii forms extracellular cords, resulting in acute infection and rapid larval death. These findings highlight the feasibility of zebrafish for studying M. kansasii pathogenesis and for the first time identify extracellular cords in this species.
Antibiotic use and deprivation: an analysis of Welsh primary care antibiotic prescribing data by socioeconomic status
Authors: Adekanmbi Victor , Jones Hywel , Farewell Daniel , Francis Nick A 
Published: April 2020

Abstract

Objectives
To examine the association between socioeconomic status (SES) and antibiotic prescribing, controlling for the presence of common chronic conditions and other potential confounders and variation amongst GP practices and clusters.

Methods
This was an electronic cohort study using linked GP and Welsh Index of Multiple Deprivation (WIMD) data. The setting was GP practices contributing to the Secure Anonymised Information Linkage (SAIL) Databank 2013–17. The study involved 2.9 million patients nested within 339 GP practices, nested within 67 GP clusters.

Results
Approximately 9 million oral antibiotics were prescribed between 2013 and 2017. Antibiotic prescribing rates were associated with WIMD quintile, with more deprived populations receiving more antibiotics. This association persisted after controlling for patient demographics, smoking, chronic conditions and clustering by GP practice and cluster, with those in the most deprived quintile receiving 18% more antibiotic prescriptions than those in the least deprived quintile (incidence rate ratio = 1.18; 95% CI = 1.181–1.187). We found substantial unexplained variation in antibiotic prescribing rates between GP practices [intra-cluster correlation (ICC) = 47.31%] and GP clusters (ICC = 12.88%) in the null model, which reduced to ICCs of 3.50% and 0.85% for GP practices and GP clusters, respectively, in the final adjusted model.

Conclusions
Antibiotic prescribing in primary care is increased in areas of greater SES deprivation and this is not explained by differences in the presence of common chronic conditions or smoking status. Substantial unexplained variation in prescribing supports the need for ongoing antimicrobial stewardship initiatives.
Population pharmacokinetics of ceftazidime in critically ill children: impact of cystic fibrosis
Authors: Bui S , Facchin A , Ha P , Bouchet S , Leroux S , Nacka F , Fayon M , Jacqz-Aigrain E ,   network of Paediatric Clinical Investigation Centres, M Fayon Bordeaux , E Jacqz-Aigrain Paris , J Kanold Clermont-Ferrand , H Chevassus Montpellier , R Hankard Tours , B Kassai Lyon , Marc Bardou Dijon 
Published: April 2020

Abstract

Background
Pharmacokinetics data on ceftazidime are sparse for the paediatric population, particularly for children with cystic fibrosis (CF) or severe infections.

Objectives
To characterize the population pharmacokinetics of ceftazidime in critically ill children, identify covariates that affect drug disposition and evaluate the current dosing regimens.

Methods
The study was registered with Clinicaltrials.gov (NCT01344512). Children receiving ceftazidime were selected in 13 French hospitals. Plasma concentrations were determined by UPLC-MS/MS. Population pharmacokinetic analyses were performed using NONMEN software.

Results
One hundred and eight patients, aged 28 days to 12 years, with CF (n = 32), haematology and/or oncology disorders (n = 47) or severe infection (n = 29) were included. Ceftazidime was administered by continuous or intermittent infusions; 271 samples were available for analysis. A two-compartment model with first-order elimination and allometric scaling was developed and covariate analysis showed that ceftazidime pharmacokinetics were also significantly affected by CLCR and CF. Ceftazidime clearance was 82% higher in CF than in non-CF patients. Monte Carlo simulations showed that the percentage of target attainment (PTA) for the target of T&gt;MIC = 65% was (i) lower in CF than in non-CF children with intermittent infusions and (ii) higher with continuous than intermittent infusion in all children.

Conclusions
The population pharmacokinetics model for ceftazidime in children was influenced by body weight, CLCR and CF. A higher PTA was obtained with continuous versus intermittent infusions. Further studies should explore the benefits of continuous versus intermittent infusion of ceftazidime, including current versus increased doses in CF children.
Agency Insight from Portugal’s Autoridade da Concorrência
Authors: Matos Rosa Margarida 
Published: April 2020

Abstract
2020 will be a landmark year for reasons that had not been anticipated. But it is also a critical year for the implementation, by national legislators in the European Union, of the ECN+ Directive. This will grant competition agencies stronger means of enforcement and will consecrate independence of enforcement decisions based on the pursuit of consumer welfare protection. Another developing topic in 2020 is industrial policy in the EU and its coexistence with competition policy. While the EU needs to remain pragmatic, it need not — must not, I would argue - lose its distinctive economic features.
Separation of RRR-α-Tocopherol by Chiral Chromatography
Authors: Gill Brendon D , Indyk Harvey E 
Published: April 2020

Abstract

Background
α-Tocopherol can exist as eight possible stereoisomers due to the presence of three chiral carbons. Regulations and industry guidelines necessitate that dietary vitamin E intakes be based on the vitamin E activity of RRR-α-tocopherol. Food products fortified with synthetic all-rac-α-tocopherol or all-rac-α-tocopheryl acetate during manufacturing will require chiral separation of the α-tocopherol stereoisomers for accurate estimation of vitamin E activity.

Objective
The development of an HPLC method utilizing a chiral column for the chromatographic separation of RRR-α-tocopherol from other α-tocopherol stereoisomers.

Method
Normal phase liquid chromatographic separation using a polysaccharide-based chiral column with fluorescence detection of α-tocopherol stereoisomers.

Results
The described chromatographic method achieves baseline resolution of RRR-α-tocopherol from its stereoisomers. Method selectivity, precision, and robustness were evaluated and acceptable performance was achieved.

Conclusions
The chromatographic method was found to be suitable for application where both RRR-α-tocopherol content and total α-tocopherol content are required for routine compliance testing.

Highlights
A robust and precise chomatographic method for the baseline resolution of RRR-α-tocopherol from its stereoisomers was acheived.
The Singaporean natural gas hub: reassembling global production networks and markets in Asia
Authors: Dodge Alexander 
Published: April 2020

AbstractRecently, economic geographers have sought to account for how regional and national initiatives shape the strategic decisions of actors in global production networks (GPNs). In this article, I intend to discuss the political and institutional dynamics by which GPNs evolve, and the capacity of states to shape emerging organizational and spatial arrangements in dynamic GPNs. Building on assemblage thinking, I conceptualize these political and institutional dynamics as the unbundling of legal, regulatory and institutional components of nation-state authorities that govern GPNs, and the subsequent reassembling of these components through emerging interactions with finance, technology and new forms of private authority. These emerging global assemblages are both partially embedded in global cities and stretch across and within the borders of nation-states. Building on this conceptual framework, this article explains how the exclusive nation-state authorities that traditionally governed liquefied natural gas (LNG) trade and markets are becoming unbundled. The article focuses on the initiatives of public and private actors in Singapore who are attempting to shape evolutionary dynamics in GPNs by establishing a hub for LNG trading and speculative financing in Asia. The article finds that Singapore’s capacity to shape LNG production networks is dependent upon the capacity of public and private actors in Singapore to establish cross-border connectivity to markets in Southeast Asia.