bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae
Authors: Comandatore Francesco , Sassera Davide , Bayliss Sion C , Scaltriti Erika , Gaiarsa Stefano , Cao Xiaoli , Gales Ana C , Saito Ryoichi , Pongolini Stefano , Brisse Sylvain , Feil Edward J , Bandi Claudio 
Published: October 2019

AbstractKlebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens worldwide, able to cause multiorgan infections and hospital outbreaks. One of the most widely disseminated lineage of Kp is the clonal group 258 (CG258), which includes the highly resistant “high-risk” sequence types ST258 and ST11. Genomic investigations revealed that very large recombination events have occurred during the emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hypervirulent or resistant clones remains unclear. Here, we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100 kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which have been involved by recombination events with different frequencies. Our results also indicate that certain lineages are more likely to act as donors to CG258. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion.
Asymptotically conical Calabi-Yau metrics with cone singularities along a compact divisor
Authors: de Borbon Martin , Spotti Cristiano 
Published: October 2019

AbstractWe construct Asymptotically Locally Euclidean (ALE) and, more generally, asymptotically conical Calabi–Yau metrics with cone singularities along a compact simple normal crossing divisor. In particular, this includes the case of the minimal resolution of 2D quotient singularities for any finite subgroup $\Gamma \subset U(2)$ acting freely on the three-sphere, hence generalizing Kronheimer’s construction of smooth ALE gravitational instantons.
Effect of Antimalarial Drugs on the Immune Response to Intramuscular Rabies Vaccination Using a Postexposure Prophylaxis Regimen
Authors: Endy Timothy P , Keiser Paul B , Cibula Don , Abbott Mark , Ware Lisa , Thomas Stephen J , Polhemus Mark E 
Published: October 2019

Abstract

Background
Chloroquine can impair the immune responses to intradermal rabies vaccination. Current guidelines recommend an extra intramuscular dose be given for postexposure prophylaxis in previously unvaccinated persons taking any antimalarial drug.

Methods
We conducted a randomized, open-label, single-site study in 103 previously unvaccinated healthy adults age ≥18 to ≤60 years old to evaluate the effects of chloroquine, atovaquone/proguanil (Malarone), and doxycycline on the antibody response to a purified chick embryo cell vaccine, given on a postexposure prophylaxis schedule. All treatment groups received antimalarials 14 days prior to and during vaccination.

Results
All subjects achieved accepted neutralizing antibody titers of ≥0.5 IU/mL following the second rabies vaccination dose and maintained this protection through the duration of the study. We observed a reduction in rabies antibody geometric mean titer in the chloroquine versus control groups 28 days after vaccination: 2.3 versus 6.87 IU/mL, respectively (P &lt; .001, t test). A significant difference was not observed for those taking Malarone or doxycycline.

Conclusions
We conclude that there is no reduction of rabies antibody response in subjects taking Malarone or doxycycline, but a significant reduction in those taking chloroquine; however, accepted antibody levels were achieved for all 3 antimalarials.

Clinical Trials Registration
NCT02564471.
Characterizing the impact of health literacy, computer ability, patient demographics, and portal usage on patient satisfaction with a patient portal
Authors: Wong Joseph Isaac Salientes , Steitz Bryan D , Rosenbloom Samuel Trent 
Published: October 2019

AbstractObjectiveWe sought to measure patient portal satisfaction with patient portals and characterize its relationship to attitude towards computers, health literacy, portal usage, and patient demographics.Materials and MethodsWe invited 13 040 patients from an academic medical center to complete a survey measuring satisfaction, perceived control over computers, and health literacy using validated instruments (End User Computing Satisfaction, Computer Attitude Measure, and Brief Health Literacy Screen). We extracted portal usage and demographic information from the medical center data warehouse.ResultsA total of 6026 (46.2%) patients completed the survey. The median (IQR) scores for satisfaction, computer control, and health literacy were 87% (20%), 86% (22%), and 95% (15%), respectively. The normalized mean (SD) usage of messaging, lab, appointment, medication, and immunization functions were 6.6 (2.6), 4.6 (2.4), 3.1 (1.7), 1.5 (1.2), and 0.88 (0.91) times, respectively. Logistic regression yielded significant odds ratios [99% CI] for computer control (3.6 [2.5–5.2]), health literacy (12 [6.9–23]), and immunization function usage (0.84 [0.73–0.96]).DiscussionRespondents were highly satisfied and had high degrees of computer control and health literacy. Statistical analysis revealed that higher computer control and health literacy predicted higher satisfaction, whereas usage of the immunization function predicted lower satisfaction. Overall, the analytical model had low predictive capability, suggesting that we failed to capture the main drivers of satisfaction, or there was inadequate variation in satisfaction to delineate its contributing factors.ConclusionThis study provides insight into patient satisfaction with and usage of a patient portal. These data can guide the development of the patient portal, with the ultimate goal of increasing functionality and usability to enhance the patient experience.
Alice Stopford Green and Vernon Lee: Salon Culture and Intellectual Exchange
Authors: Ní Bheacháin Caoilfhionn , Mitchell Angus 
Published: October 2019

Abstract
Archival evidence of the connection between Alice Stopford Green (1847–1929) and Vernon Lee (1856–1935) is restricted to a handful of letters and a few scattered references in ancillary documents. Extant correspondence provides a glimpse into the conversation and concerns of these two important European intellectuals, demonstrating their nascent interest in questions of social justice. Using network theory as a lens, this essay traces the contours of this connection, initiated during a formative period for both in the fertile context of the salons and dining rooms of London in the 1880s. This connection demonstrates the importance of social networks for women writers, artists, intellectuals and activists during the fin de siècle. By exploring the limited archival remnants of this friendship, this study highlights the Irish and European dimensions of Victorian metropolitan culture. It was because of salon culture that women with strikingly different backgrounds and sensibilities could connect and explore ideas of mutual concern, with reverberations for their political positioning and activism in subsequent decades.
Radiative pulsar magnetospheres: aligned rotator
Authors: Pétri J 
Published: October 2019

ABSTRACT
Force-free neutron star magnetospheres are nowadays well known and found through numerical simulations. Even extension to general relativity has recently been achieved. However, those solutions are by definition dissipationless, meaning that the star is unable to accelerate particles and let them radiate any photon. Interestingly, the force-free model has no free parameter however it must be superseded by a dissipative mechanism within the plasma. In this Letter, we investigate the magnetosphere electrodynamics for particles moving in the radiation reaction regime, using the limit where acceleration is fully balanced by radiation, also called Aristotelian dynamics. An Ohm’s law is derived, from which the dissipation rate is controlled by a one parameter family of solutions depending on the pair multiplicity κ. The spatial extension of the dissipation zone is found self-consistently from the simulations. We show that the radiative magnetosphere of an aligned rotator tends to the force-free regime whenever the pair multiplicity becomes moderately large, κ ≫ 1. However, for low multiplicity, a substantial fraction of the spin-down energy goes into particle acceleration and radiation in addition to the Poynting flux, the latter remaining only dominant for large multiplicities. We show that the work done on the plasma occurs predominantly in the equatorial current sheet right outside the light-cylinder.
UCSC Genome Browser enters 20th year
Authors: Lee Christopher M , Barber Galt P , Casper Jonathan , Clawson Hiram , Diekhans Mark , Gonzalez Jairo Navarro , Hinrichs Angie S , Lee Brian T , Nassar Luis R , Powell Conner C , Raney Brian J , Rosenbloom Kate R , Schmelter Daniel , Speir Matthew L , Zweig Ann S , Haussler David , Haeussler Maximilian , Kuhn Robert M , Kent W James 
Published: October 2019

Abstract
The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a ‘lollipop’ plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.
A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS
Authors: Yang Yidai , Joshi Monika , Takahashi Yoh-hei , Ning Zhibin , Qu Qianhui , Brunzelle Joseph S , Skiniotis Georgios , Figeys Daniel , Shilatifard Ali , Couture Jean-François 
Published: October 2019

Abstract
COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS’s subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.
The Vaginal Microbiome as a Predictor for Outcome of In Vitro Fertilization With or Without Intracytoplasmic Sperm Injection: A Prospective Study
Authors: Koedooder R. , Singer M. , Schoenmakers S. , Savelkoul P. H. M. , Morré S. A. , de Jonge J. D. , Poort L. , Cuypers W. J. S. S. , Beckers N. G. M. , Broekmans F. J. M. , Cohlen B. J. , den Hartog J. E. , Fleischer K. , Lambalk C. B. , Smeenk J. M. J. S. , Budding A. E. , Laven J. S. E. 
Published: October 2019

(Abstracted from Human Reproduction 2019;34(6):1042–1054)
Nearly one third of all subfertility causes remain unexplained. In addition, assisted-reproductive technologies (ARTs) such as IVF-ICSI are invasive and only 25% to 35% of women become pregnant after the first embryo transfer (ET).
Massachusetts’ Parental Consent Law and Procedural Timing Among Adolescents Undergoing Abortion
Authors: Janiak Elizabeth , Fulcher Isabel R. , Cottrill Alischer A. , Tantoco Nicole , Mason Ashley H. , Fortin Jennifer , Sabino Jamie , Goldberg Alisa B. 
Published: October 2019

(Abstracted from Obstet Gynecol 2019;133:978–986)
Thirty-seven states mandate parental consent or notification before providing abortion care to minors. In Massachusetts' parental consent law, a minor (17 years old or younger) requires parental approval before a legal abortion is permitted, but parental involvement can be bypassed through some mechanism, such as a petition to a judge (“judicial bypass”).
Clinical Utility of Expanded Carrier Screening: Results-Guided Actionability and Outcomes
Authors: Johansen Taber Katherine A. , Beauchamp Kyle A. , Lazarin Gabriel A. , Muzzey Dale , Arjunan Aishwarya , Goldberg James D. 
Published: October 2019

(Abstracted from Genet Med 2019;21(5):1041–1048)
One in 300 pregnancies is impacted by a recessive or X-linked condition. Universal screening is recommended by guidelines for 2 of these conditions (cystic fibrosis and spinal muscular atrophy), but this misses approximately 70% of carriers of other diseases and fails to detect somewhere between 13% and 94% of pregnancies affected with severe conditions, depending on race/ethnicity.
Analgesic and Respiratory Depressant Effects of R-dihydroetorphine
Authors: Olofsen Erik , Boom Merel , Sarton Elise , van Velzen Monique , Baily Paul , Smith Kevin J. , Oksche Alexander , Dahan Albert , Niesters Marieke 
Published: October 2019

Abstract

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New

Background
There is an ongoing need for potent opioids with less adverse effects than commonly used opioids. R-dihydroetorphine is a full opioid receptor agonist with relatively high affinity at the μ-, δ- and κ-opioid receptors and low affinity at the nociception/orphanin FQ receptor. The authors quantified its antinociceptive and respiratory effects in healthy volunteers. The authors hypothesized that given its receptor profile, R-dihydroetorphine will exhibit an apparent plateau in respiratory depression, but not in antinociception.

Methods
The authors performed a population pharmacokinetic–pharmacodynamic study (Eudract registration No. 2009-010880-17). Four intravenous R-dihydroetorphine doses were studied: 12.5, 75, 125, and 150 ng/kg (infused more than 10 min) in 4 of 4, 6 of 6, 6 of 6, and 4 of 4 male subjects in pain and respiratory studies, respectively. The authors measured isohypercapnic ventilation, pain threshold, and tolerance responses to electrical noxious stimulation and arterial blood samples for pharmacokinetic analysis.

Results
R-dihydroetorphine displayed a dose-dependent increase in peak plasma concentrations at the end of the infusion. Concentration-effect relationships differed significantly between endpoints. R-dihydroetorphine produced respiratory depression best described by a sigmoid EMAX-model. A 50% reduction in ventilation in between baseline and minimum ventilation was observed at an R-dihydroetorphine concentration of 17 ± 4 pg/ml (median ± standard error of the estimate). The maximum reduction in ventilation observed was at 33% of baseline. In contrast, over the dose range studied, R-dihydroetorphine produced dose-dependent analgesia best described by a linear model. A 50% increase in stimulus intensity was observed at 34 ± 11 pg/ml.

Conclusions
Over the dose range studied, R-dihydroetorphine exhibited a plateau in respiratory depression, but not in analgesia. Whether these experimental advantages extrapolate to the clinical setting and whether analgesia has no plateau at higher concentrations than investigated requires further studies.
Central nervous system vasculitis: advances in diagnosis
Authors: Hajj-Ali Rula A. , Calabrese Leonard H. 
Published: October 2019

Purpose of review
The main purpose of this review is to present advances in diagnostics of central nervous system vasculitis (CNS-V).

Recent findings
Progress in molecular technologies and neuroimaging have added formidably to our knowledge of CNS-V. Next-generation sequencing has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases, making this test attractive and capable of avoiding brain biopsy in cases where CNS infections are suspected. Further the continuum of neuroimaging progress has advanced our ability to diagnose CNS-V. Our capability to visualize the vessel wall have added a great value in differentiating inflammatory from noninflammatory vasculopathies. New genetic variations are being exposed with exome and genome sequences which will aid future diagnosis.

Summary
We have witnessed tremendous advances in CNS-V mainly by our ability to rule out mimics. Progress in molecular technologies, neuroimaging and genetic studies will continue to enhance the field further.
Impact of Surrounding Canal Size on Time to Union After Intramedullary Nailing of Femur Fractures: Are 10-mm Nails All We Need?
Authors: Yoon Richard S. , Adams Donald M. , Seigerman Daniel A. , Lim Philip K. , Donegan Derek J. , Liporace Frank A. 
Published: October 2019

Objective:
To determine whether intramedullary nail (IMN) size and its relation to the canal diameter [nail-canal (NC) diameter] impacts the union rate or time to union in the treatment of femoral shaft fractures.

Design:
Retrospective review.

Setting:
Two Level 1 and 1 Level 2 trauma centers.

Patients:
Two hundred eighty-seven patients met the criteria and were included in the study.

Intervention:
Patients were treated with either an antegrade or retrograde IMN. Comparisons were first performed comparing 10- versus 11- versus 13-mm nails. Patients were then divided into 3 groups based on the difference between the size of the femoral canal at the isthmus and the IMN (NC diameter). Group 1: <1.0 mm, group 2: >1.0 and <2.0 mm, and group 3: >2.0 mm.

Main Outcome Measurements:
Nonunion rates, mean time to union.

Results:
Two hundred eighty-seven patients with a minimum of 12-month follow-up, who were treated with size with IMN for femoral shaft fractures, were assessed for fracture characteristics, time to union, and union rate. When comparing IMN size, no statistical difference was found when comparing time to union or overall union rate. When comparing NC diameter, no significant difference was found in union rate and time to union when comparing between the groups.

Conclusion:
Similar rate of union and time to union were exhibited regardless of nail size or NC diameter. This can correlate to the standard utilization of a reamed, titanium 10-mm IMN with 5.0-mm interlocking screws in the treatment of femoral shaft fractures, offering potentially less reaming, shorter operative times, and removing unnecessary stock from inventory.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Prostate cancer screening in Portugal: prevalence and perception of potential benefits and adverse effects
Authors: Braga Raquel , Costa Ana Rute , Pina Francisco , Moura-Ferreira Pedro , Lunet Nuno 
Published: October 2019

Introduction:
Opportunistic screening for prostate cancer has been widely used, though organized programs are not recommended. We aimed to estimate the prevalence of prostate cancer screening and the perception of potential benefits and harms of screening, among the Portuguese general population.

Methods:
A representative sample of Portuguese-speaking inhabitants in mainland Portugal was selected, using a stratified probabilistic sampling procedure; men above 40 were considered for analysis (n = 414). Data on sociodemographic characteristics, lifetime use and usual frequency of prostate cancer screening (prostate-specific antigen test or digital rectal examination) and perception of potential benefits and adverse effects of cancer screening were assessed using face-to-face interviews, by structured questionnaire.

Results:
The proportion of participants who reported having been submitted to prostate cancer screening at least once in their lifetime was 44.2% (95% confidence interval: 37.5–51.0; 13.8% only digital rectal examination, 12.2% only prostate-specific antigen test, and 18.2% digital rectal examination and prostate-specific antigen test). As potential benefits of cancer screening, the options “knowledge of not having the disease”, “earlier detection” and “more effective treatment” were selected by 55.8%, 12.9% and 31.3% of the participants, respectively. Regarding potential adverse effects, the most and least frequently identified were ‘anxiety while waiting for the results’ (55.1%) and ‘false negatives’ (38.0%), respectively.

Conclusions:
Almost half of the men between 40 and 79 years old declared that they have been screened for prostate cancer. Nearly one-third of the participants considered that reassurance of a negative result was the main potential benefit of screening, whereas most failed to identify the most frequent adverse effects.
Increased detection of suspected atrial fibrillation in elderly and female hypertensive patients through home blood pressure monitoring: the HOME-AF study
Authors: Savvari Paraskevi , Triantafyllidi Helen , Skiadas John , Kalogeropoulos Petros , Menegas Damianos , Manolis Athanasios , Papoulidis Neofitos , Andrikopoulos George , Tsioufis Konstantinos 
Published: October 2019

Background:
Episodes of suspected atrial fibrillation are particularly frequent in essential hypertension. This study aimed to investigate the incidence of new suspected atrial fibrillation cases detected through home blood pressure (BP) screening among hypertensive patients. Association of new suspected atrial fibrillation cases with arterial hypertension (AH) phenotypes and the CHA2DS2-VASc score was also investigated.

Methods:
The prospective study recruited hypertensive patients at least 50 years old from private and hospital hypertensive clinics. An ECG was performed during the first visit. Microlife BP A6 PC was used to measure office and home BP for at least 3 and preferably 7 consecutive days.

Results:
A total of 2408 AH patients were recruited. Suspected atrial fibrillation was detected by BP monitor in 12.5% of patients. CHA2DS2-VASc was greater in hypertensive patients with suspected atrial fibrillation detection, as compared with all other hypertensive patients (3.3 ± 1.4 vs. 2.8 ± 1.4, P < 0.0001). Suspected atrial fibrillation detection was associated with advanced age (≥ 75 years, P < 0.0001) and female sex (P = 0.01). A nonsignificant association between suspected atrial fibrillation detection and history of chronic heart failure/left ventricular dysfunction was observed (P = 0.06). In the multivariate analysis, age and sex were the only independent risk factors with patients at least 75 years old having more than twice the risk of suspected atrial fibrillation compared with patients less than 64 years old. No differences between new suspected atrial fibrillation cases and AH phenotype (white coat/uncontrolled/masked hypertension) were identified.

Conclusion:
In our cohort of hypertensive patients, suspected atrial fibrillation was common particularly among elderly and female patients. These results underline the need for early suspected atrial fibrillation detection to minimize the increased thromboembolic risk associated with hypertension.