bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peering Through the Glass Ceiling: A Mixed Methods Study of Faculty Perceptions of Gender Barriers to Academic Advancement in Infectious Diseases
Authors: Manne-Goehler Jennifer , Krakower Douglas , Marcelin Jasmine , Salles Arghavan , del Rio Carlos , Stead Wendy 
Published: April 2020

Abstract

Background
The drivers of the gap in advancement between men and women faculty in academic Infectious Diseases (ID) remain poorly understood. This study sought to identify key barriers to academic advancement among faculty in ID and offer policy suggestions to narrow this gap.

Methods
During the 2019 IDWeek, we conducted focus groups with women faculty members at all ranks and men Full Professors, then we administered a brief survey regarding work-related barriers to advancement to the Infectious Disease Society of America (IDSA) membership. We report themes from the 4 focus group discussions that are most closely linked to policy changes and descriptive analyses of the complementary survey domains.

Results
Policy change suggestions fell into 3 major categories: (1) Policy changes for IDSA to implement; (2) Future IDWeek Program Recommendations; and (3) Policy Changes for IDSA to Endorse as Best Practices for ID Divisions. Among 790 faculty respondents, fewer women reported that their institutional promotion process was transparent and women Full Professors were significantly more likely to have been sponsored.

Conclusions
Sponsorship and informed advising about institutional promotions tracks may help to narrow the advancement gap. The Infectious Disease Society of America should consider ambitious policy changes within the society and setting expectations for best practices among ID divisions across the United States.
Molecular epidemiology of imipenem resistance in invasive Haemophilus influenzae infections in Germany in 2016
Authors: Lâm Thiên-Trí , Nürnberg Sebastian , Claus Heike , Vogel Ulrich 
Published: April 2020

Abstract

Background
The carbapenems imipenem and meropenem play an important role in the empirical anti-infective treatment of critically ill patients. Carbapenem resistance in Haemophilus influenzae (Hi) has rarely been reported.

Objectives
We provide prevalence data for resistance to carbapenems from laboratory surveillance of invasive Hi infections in Germany in 2016.

Methods
Phenotypic susceptibility testing against ampicillin, amoxicillin/clavulanate, cefotaxime and imipenem was carried out on 474 isolates from blood and CSF. The isolates were collected as part of the national laboratory surveillance programme. Imipenem-resistant strains were further tested for meropenem susceptibility. Molecular analysis was done by ftsI sequencing to detect mutations in PBP3, by acrR sequencing to detect alterations in the regulatory protein of the AcrAB-TolC efflux pump and by MLST.

Results
No resistance to meropenem was detected. Cefotaxime resistance was rare (n = 3; 0.6%). Imipenem resistance was found in 64 strains (13.5%) using gradient agar diffusion and was confirmed in 26 isolates by broth microdilution (5.5%). Imipenem resistance occurred predominantly in Hi that were β-lactamase negative but ampicillin resistant and in those that were β-lactamase positive but nevertheless amoxicillin/clavulanate resistant. This finding suggested a β-lactamase-independent mechanism. Accordingly, sequence analysis of PBP3 identified previously described mutations. MLST of the imipenem-resistant strains, which were all non-typeable Hi, revealed a high diversity.

Conclusions
We conclude that imipenem, but not meropenem, resistance is frequent in Hi. It is likely to be supported by PBP3 mutations.
Community antibiotic prescribing for children in France from 2015 to 2017: a cross-sectional national study
Authors: Trinh Nhung T H , Cohen Robert , Lemaitre Magali , Chahwakilian Pierre , Coulthard Gregory , Bruckner Tim A , Milic Dejan , Levy Corinne , Chalumeau Martin , Cohen Jérémie F 
Published: April 2020

Abstract

Objectives
To assess recent community antibiotic prescribing for French children and identify areas of potential improvement.

Methods
We analysed 221 768 paediatric (&lt;15 years) visits in a national sample of 680 French GPs and 70 community paediatricians (IQVIA’s EPPM database), from March 2015 to February 2017, excluding well-child visits. We calculated antibiotic prescription rates per 100 visits, separately for GPs and paediatricians. For respiratory tract infections (RTIs), we described broad-spectrum antibiotic use and duration of treatment. We used Poisson regression to identify factors associated with antibiotic prescribing.

Results
GPs prescribed more antibiotics than paediatricians [prescription rate 26.1 (95% CI 25.9–26.3) versus 21.6 (95% CI 21.0–22.2) per 100 visits, respectively; P &lt; 0.0001]. RTIs accounted for more than 80% of antibiotic prescriptions, with presumed viral RTIs being responsible for 40.8% and 23.6% of all antibiotic prescriptions by GPs and paediatricians, respectively. For RTIs, antibiotic prescription rates per 100 visits were: otitis, 68.1 and 79.8; pharyngitis, 67.3 and 53.3; sinusitis, 67.9 and 77.3; pneumonia, 80.0 and 99.2; bronchitis, 65.2 and 47.3; common cold, 21.7 and 11.6; bronchiolitis 31.6 and 20.1; and other presumed viral RTIs, 24.1 and 11.0, for GPs and paediatricians, respectively. For RTIs, GPs prescribed more broad-spectrum antibiotics [49.8% (95% CI 49.3–50.3) versus 35.6% (95% CI 34.1–37.1), P &lt; 0.0001] and antibiotic courses of similar duration (P = 0.21). After adjustment for diagnosis, antibiotic prescription rates were not associated with season and patient age, but were significantly higher among GPs aged ≥50 years.

Conclusions
Future antibiotic stewardship campaigns should target presumed viral RTIs, broad-spectrum antibiotic use and GPs aged ≥50 years.
Collecting Deer Keds (Diptera: Hippoboscidae: Lipoptena Nitzsch, 1818 and Neolipoptena Bequaert, 1942) and Ticks (Acari: Ixodidae) From Hunter-Harvested Deer and Other Cervids
Authors: Poh Karen C , Skvarla Michael , Evans Jesse R , Machtinger Erika T 
Published: April 2020

AbstractDeer keds (Diptera: Hippoboscidae: Lipoptena Nitzsch, 1818 and Neolipoptena Bequaert, 1942) are blood-feeding ectoparasites that primarily attack cervids and occasionally bite humans, while ticks may be found on cervids, but are more generalized in host choice. Recent detection of pathogens such as Anaplasma and Borrelia in deer keds and historical infections of tick-borne diseases provides reason to investigate these ectoparasites as vectors. However, previous methods employed to sample deer keds and ticks vary, making it difficult to standardize and compare ectoparasite burdens on cervids. Therefore, we propose a standardized protocol to collect deer keds and ticks from hunter-harvested deer, which combines previous methods of sampling, including timing of collections, dividing sections of the deer, and materials used in the collection process. We tested a three-section and a five-section sampling scheme in 2018 and 2019, respectively, and found that dividing the deer body into five sections provided more specificity in identifying where deer keds and ticks may be found on deer. Data from 2018 suggested that deer keds and ticks were found on all three sections (head, anterior, posterior), while data from 2019 suggested that more Ixodes scapularis were found on the head and deer keds were found on all body sections (head, dorsal anterior, dorsal posterior, ventral anterior, and ventral posterior). The protocol provides an efficient way to sample deer for deer keds and ticks and allows researchers to compare ectoparasite burdens across geographical regions. Furthermore, this protocol can be used to collect other ectoparasites from deer or other cervids.
The evolutionary origins of auxin transport: what we know and what we need to know
Authors: Vosolsobě Stanislav , Skokan Roman , Petrášek Jan 
Published: April 2020

Abstract
Auxin, represented by indole-3-acetic acid (IAA), has for a long time been studied mainly with respect to the development of land plants, and recent evidence confirms that canonical nuclear auxin signaling is a land plant apomorphy. Increasing sequential and physiological data show that the presence of auxin transport machinery pre-dates the emergence of canonical signaling. In this review, we summarize the present state of knowledge regarding the origins of auxin transport in the green lineage (Viridiplantae), integrating both data from wet lab experiments and sequence evidence on the presence of PIN-FORMED (PIN), PIN-LIKES (PILS), and AUXIN RESISTANT 1/LIKE-AUX1 (AUX1/LAX) homologs. We discuss a high divergence of auxin carrier homologs among algal lineages and emphasize the urgent need for the establishment of good molecular biology models from within the streptophyte green algae. We further postulate and discuss two hypotheses for the ancestral role of auxin in the green lineage. First, auxin was present as a by-product of cell metabolism and the evolution of its transport was stimulated by the need for IAA sequestration and cell detoxification. Second, auxin was primarily a signaling compound, possibly of bacterial origin, and its activity in the pre-plant green algae was a consequence of long-term co-existence with bacteria in shared ecological consortia.
Interacting galaxies in the IllustrisTNG simulations - I: Triggered star formation in a cosmological context
Authors: Patton David R , Wilson Kieran D , Metrow Colin J , Ellison Sara L , Torrey Paul , Brown Westley , Hani Maan H , McAlpine Stuart , Moreno Jorge , Woo Joanna 
Published: April 2020

ABSTRACT
We use the IllustrisTNG cosmological hydrodynamical simulations to investigate how the specific star formation rates (sSFRs) of massive galaxies (M* &gt; 1010 M⊙) depend on the distance to their closest companions. We estimate sSFR enhancements by comparing with control samples that are matched in redshift, stellar mass, local density, and isolation, and we restrict our analysis to pairs with stellar mass ratios of 0.1 to 10. At small separations (∼15 kpc), the mean sSFR is enhanced by a factor of 2.0 ± 0.1 in the flagship (110.7 Mpc)3 simulation (TNG100-1). Statistically significant enhancements extend out to 3D separations of 280 kpc in the (302.6 Mpc)3 simulation (TNG300-1). We find similar trends in the EAGLE and Illustris simulations, although their sSFR enhancements are lower than those in TNG100-1 by about a factor of two. Enhancements in IllustrisTNG galaxies are seen throughout the redshift range explored (0 ≤ $z$ &lt; 1), with the strength of the enhancements decreasing with increasing redshift for galaxies with close companions. In order to more closely compare with observational results, we separately consider 2D projected distances between galaxies in IllustrisTNG. We detect significant sSFR enhancements out to projected separations of 260 kpc in TNG300-1, with projection effects diluting the size of the enhancements by about 20 per cent below 50 kpc. We find similar sSFR enhancements in TNG100-1 and Sloan Digital Sky Survey galaxies, with enhancements extending out to projected separations of about 150 kpc for star-forming galaxies at $z$ &lt; 0.2. Finally, by summing over all separations, we estimate that the presence of closest companions boosts the average sSFR of massive galaxies in TNG100-1 by 14.5 per cent.
A closer look at the spur, blob, wiggle, and gaps in GD-1
Authors: de Boer T J L , Erkal D , Gieles M 
Published: April 2020

ABSTRACT
The GD-1 stream is one of the longest and coldest stellar streams discovered to date, and one of the best objects for constraining the dark matter properties of the Milky Way. Using data from Gaia DR2, we study the proper motions (PMs), distance, morphology, and density of the stream to uncover small-scale perturbations. The PM cleaned data show a clear distance gradient across the stream, ranging from 7 to 12 kpc. However, unlike earlier studies that found a continuous gradient, we uncover a distance minimum at φ1 ≈ −40 deg, after which the distance increases again. We can reliably trace the stream between −85 &lt; φ1 &lt;15 deg, showing an even further extent to GD-1 beyond the earlier extension of Price-Whelan and Bonaca. We constrain the stream track and density using a Boolean matched filter approach and find three large under densities and significant residuals in the stream track lining up with these gaps. The gaps are located at φ1 = −36, −20, and −3 deg, with the gap at −3 deg being surrounded by a clear sinusoidal wiggle. We argue that this wiggle is due to a perturbation since it has the wrong orientation to come from a progenitor. We compute a total initial stellar mass of the stream segment of 1.58 ± 0.07 × 104 M⊙. With the extended view of the spur in this work, we argue that the spur may be unrelated to the adjacent gap in the stream. Finally, we show that an interaction with the Sagittarius dwarf can create features similar to the spur.
Shock breakouts from red supergiants: analytical and numerical predictions
Authors: Kozyreva Alexandra , Nakar Ehud , Waldman Roni , Blinnikov Sergei , Baklanov Petr 
Published: April 2020

ABSTRACT
The signal from a shock breakout (SBO) is the first signature of a supernova explosion, apart from gravitational waves and neutrinos. Observational properties of SBOs, such as bolometric luminosity and colour temperature, are connected with the parameters of the supernova progenitor and explosion. The detection of SBOs or the cooling of SBOs will constrain the progenitor and explosion models of collapsing stars. Since the recent launch of the eROSITA on the SPECTRUM-RG spacecraft, the detection rate for SBOs is a few events per year. In the current study, we examine the analytical formulae derived by Shussman, Waldman & Nakar  (arXiv:1610.05323). We use four red supergiant models from their study, while running explosions with the radiation hydrodynamics code stella. We conclude that there is a good agreement between analytical and numerical approaches for bolometric luminosity and colour temperature during SBOs. The analytical formulae for the SBO signal based on the global supernova parameters can be used instead of running time-consuming numerical simulations. We define the spectral range in which analytical formulae for SBO spectra are valid. We provide an improved analytical expression for the SBO spectral energy distribution. We confirm that the colour temperature is dependent on radius derived by analytical studies and we suggest using early time observations to confine the progenitor radius. Additionally, we show the prediction for the SBO signal from red supergiants as seen by eROSITA.
Neutrinos and gravitational waves from magnetized neutrino-dominated accretion discs with magnetic coupling
Authors: Song Cui-Ying , Liu Tong , Wei Yun-Feng 
Published: April 2020

ABSTRACT
Gamma-ray bursts (GRBs) might be powered by black hole (BH) hyperaccretion systems via the Blandford–Znajek (BZ) mechanism or neutrino annihilation from neutrino-dominated accretion flows (NDAFs). Magnetic coupling (MC) between the inner disc and BH can transfer angular momentum and energy from the fast-rotating BH to the disc. The neutrino luminosity and neutrino annihilation luminosity are both efficiently enhanced by the MC process. In this paper, we study the structure, luminosity, MeV neutrinos, and gravitational waves (GWs) of magnetized NDAFs (MNDAFs) under the assumption that both the BZ and MC mechanisms are present. The results indict that the BZ mechanism will compete with the neutrino annihilation luminosity to trigger jets under the different partitions of the two magnetic mechanisms. The typical neutrino luminosity and annihilation luminosity of MNDAFs are definitely higher than those of NDAFs. The typical peak energy of neutrino spectra of MNDAFs is higher than that of NDAFs, but similar to those of core-collapse supernovae. Moreover, if the MC process is dominant, then the GWs originating from the anisotropic neutrino emission will be stronger particularly for discs with high accretion rates.
PAM recognition by miniature CRISPR–Cas12f nucleases triggers programmable double-stranded DNA target cleavage
Authors: Karvelis Tautvydas , Bigelyte Greta , Young Joshua K , Hou Zhenglin , Zedaveinyte Rimante , Budre Karolina , Paulraj Sushmitha , Djukanovic Vesna , Gasior Stephen , Silanskas Arunas , Venclovas Česlovas , Siksnys Virginijus 
Published: April 2020

Abstract
In recent years, CRISPR-associated (Cas) nucleases have revolutionized the genome editing field. Being guided by an RNA to cleave double-stranded (ds) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer unprecedented flexibility, however, more compact versions would simplify delivery and extend application. Here, we present a collection of 10 exceptionally compact (422–603 amino acids) CRISPR–Cas12f nucleases that recognize and cleave dsDNA in a PAM dependent manner. Categorized as class 2 type V-F, they originate from the previously identified Cas14 family and distantly related type V-U3 Cas proteins found in bacteria. Using biochemical methods, we demonstrate that a 5′ T- or C-rich PAM sequence triggers dsDNA target cleavage. Based on this discovery, we evaluated whether they can protect against invading dsDNA in Escherichia coli and find that some but not all can. Altogether, our findings show that miniature Cas12f nucleases can protect against invading dsDNA like much larger class 2 CRISPR effectors and have the potential to be harnessed as programmable nucleases for genome editing.
Weak interactions in higher-order chromatin organization
Authors: Kantidze Omar L , Razin Sergey V 
Published: April 2020

AbstractThe detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein–protein and protein–DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.
Population Health, Prevention, Health Promotion, and Wellness Competencies in Physical Therapist Professional Education: Results of a Modified Delphi Study
Authors: Magnusson Dawn M , Rethorn Zachary D , Bradford Elissa H , Maxwell Jessica , Ingman Mary Sue , Davenport Todd E , Bezner Janet R 
Published: April 2020

AbstractObjectivePhysical therapists are well positioned to meet societal needs and reduce the global burden of noncommunicable diseases through the integration of evidence-based population health, prevention, health promotion, and wellness (PHPW) activities into practice. Little guidance exists regarding the specific PHPW competencies that entry-level clinicians ought to possess. The objective of this study was to establish consensus-based entry-level PHPW competencies for graduates of US-based physical therapist education programs.MethodsIn a 3-round modified Delphi study, a panel of experts (N = 37) informed the development of PHPW competencies for physical therapist professional education. The experts, including physical therapists representing diverse practice settings and geographical regions, assessed the relevance and clarity of 34 original competencies. Two criteria were used to establish consensus: a median score of 4 (very relevant) on a 5-point Likert scale, and 80% of participants perceiving the competency as very or extremely relevant.ResultsTwenty-five competencies achieved final consensus in 3 broad domains: preventive services and health promotion (n = 18), foundations of population health (n = 4), and health systems and policy (n = 3).ConclusionsAdoption of the 25 accepted competencies would promote consistency across physical therapist education programs and help guide physical therapist educators as they seek to integrate PHPW content into professional curricula.ImpactThis is the first study to establish consensus-based competencies in the areas of PHPW for physical therapist professional education in the United States. These competencies ought to guide educators who are considering including or expanding PHPW content in their curricula. Development of such competencies is critical as we seek to contribute to the amelioration of chronic disease and transform society to improve the human experience.
DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Authors: Bouwmeester Robbin , Gabriels Ralf , Hulstaert Niels , Martens Lennart , Degroeve Sven 
Published: April 2020

AbstractThe inclusion of peptide retention time prediction promises to remove peptide identification ambiguity in complex LC-MS identification workflows. However, due to the way peptides are encoded in current prediction models, accurate retention times cannot be predicted for modified peptides. This is especially problematic for fledgling open modification searches, which will benefit from accurate retention time prediction for modified peptides to reduce identification ambiguity. We here therefore present DeepLC, a novel deep learning peptide retention time predictor utilizing a new peptide encoding based on atomic composition that allows the retention time of (previously unseen) modified peptides to be predicted accurately. We show that DeepLC performs similarly to current state-of-the-art approaches for unmodified peptides, and, more importantly, accurately predicts retention times for modifications not seen during training. Moreover, we show that DeepLC’s ability to predict retention times for any modification enables potentially incorrect identifications to be flagged in an open modification search of CD8-positive T-cell proteome data. DeepLC is available under the permissive Apache 2.0 open source license and comes with a user-friendly graphical user interface, as well as a Python package on PyPI, Bioconda, and BioContainers for effortless workflow integration.
Science Map of the Highly Tweeted Endodontic Articles
Authors: Kolahi Jafar , Khazaei Saber , Iranmanesh Pedram 
Published: April 2020

AbstractIntroductionTo identify active journals, authors, institutions and hot topics in the field of Endodontics within the Twittersphere.MethodsOn December 23, 2019, the Altmetric database was searched using the titles of 11 endodontic journals. The bibliometric data of the top 5% of endodontic articles with the highest tweets number were extracted from the Web of Science and analyzed.ResultsOverall, 3,918 tweets (from 3,881 individual posts) related to endodontic articles from seven journals were identified, which were mostly from the U.S. The Journal of Endodontics received the most tweets. Systematic review and apical periodontitis were the most popular keywords. At the author level, Dummer PMH and Patel S and at institution level King’s College London and Cardiff University, had the largest number of popular articles in the Twittersphere. The number of tweets was not correlated with citations (r=0.007, P=0.929). No statistically significant differences were found between open access (n=41, Mean=11.19) and non-open access (n=136, Mean=9.38) articles regarding the number of tweets (P=0.648).ConclusionsIn the ‘Twittersphere’, the overall activity of endodontic journals and associations were low. They could be more active and increase their visibility and social impact by immediately sharing research outcomes and communicating with peers, practitioners, and patients.