bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmission Dynamics and Microevolution of Neisseria meningitidis During Carriage and Invasive Disease in High School Students in Georgia and Maryland, 2006–2007
Authors: Mustapha Mustapha M , Marsh Jane W , Shutt Kathleen A , Schlackman Jessica , Ezeonwuka Chinelo , Farley Monica M , Stephens David S , Wang Xin , Van Tyne Daria , Harrison Lee H 
Published: October 2020

Abstract

Background
The mechanisms by which Neisseria meningitidis cause persistent human carriage and transition from carriage to invasive disease have not been fully elucidated.

Methods
Georgia and Maryland high school students were sampled for pharyngeal carriage of N. meningitidis during the 2006–2007 school year. A total of 321 isolates from 188 carriers and all 67 invasive disease isolates collected during the same time and from the same geographic region underwent whole-genome sequencing. Core-genome multilocus sequence typing was used to compare allelic profiles, and direct read mapping was used to study strain evolution.

Results
Among 188 N. meningitidis culture–positive students, 98 (52.1%) were N. meningitidis culture positive at 2 or 3 samplings. Most students who were positive at &gt;1 sampling (98%) had persistence of a single strain. More than a third of students carried isolates that were highly genetically related to isolates from other students in the same school, and occasional transmission within the same county was also evident. The major pilin subunit gene, pilE, was the most variable gene, and no carrier had identical pilE sequences at different time points.

Conclusion
We found strong evidence of local meningococcal transmission at both the school and county levels. Allelic variation within genes encoding bacterial surface structures, particularly pilE, was common.
Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital
Authors: Gomez-Simmonds Angela , Annavajhala Medini K , McConville Thomas H , Dietz Donald E , Shoucri Sherif M , Laracy Justin C , Rozenberg Felix D , Nelson Brian , Greendyke William G , Furuya E Yoko , Whittier Susan , Uhlemann Anne-Catrin 
Published: October 2020

Abstract

Background
Patients with COVID-19 may be at increased risk for secondary bacterial infections with MDR pathogens, including carbapenemase-producing Enterobacterales (CPE).

Objectives
We sought to rapidly investigate the clinical characteristics, population structure and mechanisms of resistance of CPE causing secondary infections in patients with COVID-19.

Methods
We retrospectively identified CPE clinical isolates collected from patients testing positive for SARS-CoV-2 between March and April 2020 at our medical centre in New York City. Available isolates underwent nanopore sequencing for rapid genotyping, antibiotic resistance gene detection and phylogenetic analysis.

Results
We identified 31 CPE isolates from 13 patients, including 27 Klebsiella pneumoniae and 4 Enterobacter cloacae complex isolates. Most patients (11/13) had a positive respiratory culture and 7/13 developed bacteraemia; treatment failure was common. Twenty isolates were available for WGS. Most K. pneumoniae (16/17) belonged to ST258 and encoded KPC (15 KPC-2; 1 KPC-3); one ST70 isolate encoded KPC-2. E. cloacae isolates belonged to ST270 and encoded NDM-1. Nanopore sequencing enabled identification of at least four distinct ST258 lineages in COVID-19 patients, which were validated by Illumina sequencing data.

Conclusions
While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic. Increased surveillance and antimicrobial stewardship efforts, as well as identification of optimal treatment approaches for CPE, will be needed to mitigate their future impact.
Towards clinical data-driven eligibility criteria optimization for interventional COVID-19 clinical trials
Authors: Kim Jae Hyun , Ta Casey N , Liu Cong , Sung Cynthia , Butler Alex M , Stewart Latoya A , Ena Lyudmila , Rogers James R , Lee Junghwan , Ostropolets Anna , Ryan Patrick B , Liu Hao , Lee Shing M , Elkind Mitchell S V , Weng Chunhua 
Published: October 2020

Abstract

Objective
This research aims to evaluate the impact of eligibility criteria on recruitment and observable clinical outcomes of COVID-19 clinical trials using electronic health record (EHR) data.

Materials and Methods
On June 18, 2020, we identified frequently used eligibility criteria from all the interventional COVID-19 trials in ClinicalTrials.gov (n = 288), including age, pregnancy, oxygen saturation, alanine/aspartate aminotransferase, platelets, and estimated glomerular filtration rate. We applied the frequently used criteria to the EHR data of COVID-19 patients in Columbia University Irving Medical Center (CUIMC) (March 2020–June 2020) and evaluated their impact on patient accrual and the occurrence of a composite endpoint of mechanical ventilation, tracheostomy, and in-hospital death.

Results
There were 3251 patients diagnosed with COVID-19 from the CUIMC EHR included in the analysis. The median follow-up period was 10 days (interquartile range 4–28 days). The composite events occurred in 18.1% (n = 587) of the COVID-19 cohort during the follow-up. In a hypothetical trial with common eligibility criteria, 33.6% (690/2051) were eligible among patients with evaluable data and 22.2% (153/690) had the composite event.

Discussion
By adjusting the thresholds of common eligibility criteria based on the characteristics of COVID-19 patients, we could observe more composite events from fewer patients.

Conclusions
This research demonstrated the potential of using the EHR data of COVID-19 patients to inform the selection of eligibility criteria and their thresholds, supporting data-driven optimization of participant selection towards improved statistical power of COVID-19 trials.
House Fly (Diptera: Muscidae): Biology, Pest Status, Current Management Prospects, and Research Needs
Authors: Geden C J , Nayduch D , Scott J G , Burgess E R , Gerry A C , Kaufman P E , Thomson J , Pickens V , Machtinger E T 
Published: October 2020

AbstractThe house fly, Musca domestica L. (Diptera: Muscidae), is a global pest of humans and animals that carries scores of pathogens and costs up to $1 billion per year in the United States alone. Information is reviewed on recognition, distribution, biology, dispersal, and associations with microbes. Particular challenges of managing flies in different animal systems are discussed for swine, poultry, dairy cattle, beef feedlot, and equine operations. Effective fly management requires diligent monitoring and integration of cultural control, especially manure management, with mechanical control, traps, conservation or augmentative biological control, and judicious use of insecticides. House fly is notorious for developing insecticide resistance and its resistance status is summarized as of August 2020. Several critical research needs are identified. Monitoring systems and nuisance/action thresholds need improvement. Faster-killing strains and better formulations are needed to integrate pathogens into Integrated Pest management (IPM) programs. The use of parasitoids remains an inexact science with many questions remaining about species selection and release rates. New attractants are needed for use in traps and attract-and-infect/kill strategies. Screening of new active ingredients for toxicity should continue, including a rigorous assessment of essential oils and other botanicals. Rising global temperatures may affect the balance of the fly with natural enemies. An understanding of the fly microbiome may reveal unknown vulnerabilities, and much remains to be learned about how flies acquire, retain, and transmit human and animal pathogens. System-specific research is also needed to tailor fly IPM programs to individual animal systems, especially in organic and free-range animal production.
Validity of measuring psoas muscle mass index for assessing sarcopenia in patients with gynecological cancer
Authors: Yamada Ryutaro , Todo Yukiharu , Kurosu Hiroyuki , Minowa Kaoru , Tsuruta Tomohiko , Minobe Shinichiro , Matsumiya Hiroko , Kato Hidenori , Mori Yoichi , Osanai Toshihisa 
Published: October 2020

Abstract

Objective
The current study evaluated the performance of psoas muscle mass measurement for detecting low skeletal muscle mass quantity.

Methods
A sample of 82 consecutive patients with gynecological cancers was examined using computed tomography and dual energy X-ray absorptiometric scan before treatment. Skeletal muscle mass index was measured by dual energy X-ray absorptiometric scan and its cut-off value was set at 5.40 kg/m2 for detecting low skeletal muscle mass. Psoas muscle mass index was manually measured with cross-sectional computed tomography imaging at the level of L3 by six evaluators.

Results
Low skeletal muscle mass index was identified in 23 (28.0%) patients. Two-way analysis of variance confirmed a significant main effect of skeletal muscle mass index on mean psoas muscle mass index values (P &lt; 0.0001). A receiver operating characteristic curve obtained from a total of 492 psoas muscle mass index data points gathered from six evaluators produced an area under the curve value of 0.697 (95% confidence interval 0.649–0.744) and a cut-off value of 3.52 cm2/m2, with sensitivity of 79.0% and specificity of 59.6%. Using the cut-off value, the kappa coefficient for evaluating diagnostic agreement between skeletal muscle mass index (low vs. normal) and psoas muscle mass index (low vs. normal) was 0.308 (95% confidence interval 0.225–0.392), suggesting poor agreement. Fleiss’ kappa produced a coefficient of 0.418 (95% confidence interval 0.362–0.473), suggesting moderate agreement.

Conclusions
Although relevance between skeletal muscle mass index and psoas muscle mass index was confirmed, intensity of relevance between them was weak. Psoas muscle mass index measurement should be subordinated to skeletal muscle mass index measurement for detection of low skeletal muscle mass.
Patient-Reported Outcomes in Clinical Trials Leading to Cancer Immunotherapy Drug Approvals From 2011 to 2018: A Systematic Review
Authors: Safa Houssein , Tamil Monica , Spiess Philippe E , Manley Brandon , Pow-Sang Julio , Gilbert Scott M , Safa Firas , Gonzalez Brian D , Oswald Laura B , Semaan Adele , Diab Adi , Chahoud Jad 
Published: October 2020

Abstract

Background
Patient-reported outcomes (PROs) promote patient centeredness in clinical trials; however, in the field of rapidly emerging and clinically impressive immunotherapy, data on PROs are limited.

Methods
We systematically identified all immunotherapy approvals from 2011 through 2018 and assessed the analytic tools and reporting quality of associated PRO reports. For randomized clinical trials (RCTs), we developed a novel 24-point scoring scale: the PRO Endpoints Analysis Score based on 24 criteria derived from the recommendations of the Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints Data Consortium.

Results
We assessed 44 trial publications supporting 42 immunotherapy approvals. PROs were published for 21 of the 44 (47.7%) trial publications. Twenty-three trials (52.3%) were RCTs and 21 (47.7%) pertained to single-arm trials. The median time between primary clinical outcomes publications and their corresponding secondary PRO publications was 19 months (interquartile range = 9-29 months). Of the 21 PRO reports, 4 (19.0%) reported a specific hypothesis, and most (85.7%) used descriptive statistics. Three (3 of 21 [14.3%]) studies performed a control for type I error. As for RCTs, 14 of 23 (60.9%) published PRO data, including 13 (56.5%) that published a secondary dedicated manuscript. One-half of these 14 trials scored less than 13 points on the 24-point PRO Endpoints Analysis Score. The mean score was 12.71 (range = 5-17, SD = 3.71), and none met all the recommendations of the Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints Data Consortium.

Conclusions
Suboptimal reporting of PROs occurs regularly in cancer immunotherapy trials. Increased efforts are needed to maximize the value of these data in cancer immunotherapy development and approval.
PRKCA D463H Mutation in Chordoid Glioma of the Third Ventricle: A Cohort of 16 Cases, Including Two Cases Harboring BRAFV600E Mutation
Authors: Yao Kun , Duan Zejun , Du Zunguo , Fan Xiaolong , Qu Yanming , Zhang Mingshan , Wang Yin , Liu Hailong , Sun Lingyan , Qi Xueling 
Published: October 2020

Abstract
Chordoid gliomas (CG) of the third ventricle are characterized by chordoid and glial features, but the extent of histological variations across CG is not fully understood. Herein, we report 16 consecutive cases of CG. All 16 patients had histories of headache and vision loss; their median age was 41.7 years at the surgery. Histological examination revealed typical features of CG, including cords of epithelioid cells within the mucinous stroma and lymphoplasmacytic infiltration. Two cases exhibited atypical histological features including histiocyte-like cells. PRKCA mutation was found in 14 cases, including the 2 with histiocytic features. BRAFV600E mutation was found only in the 2 cases with histiocytic features. The patients underwent gross total tumor resection without radiotherapy or chemotherapy. Three patients died between 1 and 4 months postsurgery. Only one had a recurrence. Eleven were alive at the most recent follow-up (range: 2–58 months). These data indicate that PRKCA mutation was a good diagnostic marker for CG and additionally suggest that histiocyte-like features can be present in CG in association with BRAF mutations.
On the compressive nature of turbulence driven by ionizing feedback in the pillars of the Carina Nebula
Authors: Menon Shyam H , Federrath Christoph , Klaassen Pamela , Kuiper Rolf , Reiter Megan 
Published: October 2020

ABSTRACT
The ionizing radiation of massive stars sculpts the surrounding neutral gas into pillar-like structures. Direct signatures of star formation through outflows and jets are observed in these structures, typically at their tips. Recent numerical simulations have suggested that this star formation could potentially be triggered by photoionizing radiation, driving compressive modes of turbulence in the pillars. In this study, we use recent high-resolution ALMA observations of 12CO, 13CO, and C18O, J = 2 − 1 emission to test this hypothesis for pillars in the Carina Nebula. We analyse column density and intensity-weighted velocity maps, and subtract any large-scale bulk motions in the plane of the sky to isolate the turbulent motions. We then reconstruct the dominant turbulence driving mode in the pillars, by computing the turbulence driving parameter b, characterized by the relation $\sigma _{\rho /\rho _0} = b \mathcal {M}$ between the standard deviation of the density contrast $\sigma _{\rho /\rho _0}$ (with gas density ρ and its average ρ0) and the turbulent Mach number $\mathcal {M}$. We find values of b ∼ 0.7–1.0 for most of the pillars, suggesting that predominantly compressive modes of turbulence are driven in the pillars by the ionizing radiation from nearby massive stars. We find that this range of b values can produce star formation rates in the pillars that are a factor ∼3 greater than with b ∼ 0.5, a typical average value of b for spiral-arm molecular clouds. Our results provide further evidence for the potential triggering of star formation in pillars through compressive turbulent motions.
Inferring the dark matter velocity anisotropy to the cluster edge
Authors: Svensmark Jacob , Hansen Steen H , Martizzi Davide , Moore Ben , Tessier Romaine 
Published: October 2020

ABSTRACTDark matter (DM) dominates the properties of large cosmological structures such as galaxy clusters, and the mass profiles of the DM have been inferred for these equilibrated structures for years by using cluster X-ray surface brightnesses and temperatures. A new method has been proposed, which should allow us to infer a dynamical property of the DM, namely the velocity anisotropy. For the gas, a similar velocity anisotropy is zero due to frequent collisions; however, the collisionless nature of DM allows it to be non-trivial. Numerical simulations have for years found non-zero and radially varying DM velocity anisotropies. Here we employ the method proposed by Hansen & Piffaretti, and developed by Høst et al. to infer the DM velocity anisotropy in the bright galaxy cluster Perseus, to near five times the radii previously obtained. We find the DM velocity anisotropy to be consistent with the results of numerical simulations, however, still with large error bars. At half the virial radius, we find the DM velocity anisotropy to be non-zero at 1.7$\, \sigma$, lending support to the collisionless nature of DM.
Implications of baryon–dark matter interaction on IGM temperature and tSZ effect with magnetic field
Authors: Pandey Arun Kumar , Malik Sunil , Seshadri T R 
Published: October 2020

ABSTRACT
We show that the combined effect of cosmic magnetic field and a possible non-standard interaction between baryons and dark matter (DM) has interesting consequences on the thermal Sunyaev−Zel’dovich (tSZ) effect depending on the temperature and the ionization state of the intergalactic medium. The drag force between the baryons and DM due to the relative velocity between them, and their temperature difference results in heat transfer between these two species. At the same time, the ambipolar diffusion and the decaying magnetic turbulence tends to heat up the baryons. This interplay of these two processes give rise to different evolution histories of the thermal and ionization state of the universe and hence influences the cosmic microwave background (CMB) spectrum at small scales through the tSZ effect. In this work, we have computed the evolution of the temperature, ionization fraction, and the y-parameter of the CMB for different strengths of the magnetic field and the interaction cross-section. We note that the y-parameter can be significantly enhanced with the inclusion of magnetic field and baryon–DM interaction as compared to the case when these are absent. The enhancement depends on the strength of the magnetic field.
Brightest cluster galaxies: the centre can(not?) hold
Authors: De Propris Roberto , West Michael J , Andrade-Santos Felipe , Ragone-Figueroa Cinthia , Rasia Elena , Forman William , Jones Christine , Kipper Rain , Borgani Stefano , Lambas Diego García , Romashkova Elena A , Patra Kishore C 
Published: October 2020

ABSTRACT
We explore the persistence of the alignment of brightest cluster galaxies (BCGs) with their local environment. We find that a significant fraction of BCGs do not coincide with the centroid of the X-ray gas distribution and/or show peculiar velocities (they are not at rest with respect to the cluster mean). Despite this, we find that BCGs are generally aligned with the cluster mass distribution even when they have significant offsets from the X-ray centre and significant peculiar velocities. The large offsets are not consistent with simple theoretical models. To account for these observations BCGs must undergo mergers preferentially along their major axis, the main infall direction. Such BCGs may be oscillating within the cluster potential after having been displaced by mergers or collisions, or the dark matter halo itself may not yet be relaxed.
A new estimator of resolved molecular gas in nearby galaxies
Authors: Chown Ryan , Li Cheng , Parker Laura , Wilson Christine D , Li Niu , Gao Yang 
Published: October 2020

ABSTRACT
A relationship between dust-reprocessed light from recent star formation and the amount of star-forming gas in a galaxy produces a correlation between Wide-field Infrared Survey Explorer (WISE) 12 μm emission and CO line emission. Here, we explore this correlation on kiloparsec scales with CO(1–0) maps from EDGE–CALIFA matched in resolution to WISE 12 μm images. We find strong CO-12 μm correlations within each galaxy and we show that the scatter in the global CO-12 μm correlation is largely driven by differences from galaxy to galaxy. The correlation is stronger than that between star formation rate and H2 surface densities [Σ(H2)]. We explore multivariable regression to predict Σ(H2) in star-forming pixels using the WISE 12 μm data combined with global and resolved galaxy properties, and provide the fit parameters for the best estimators. We find that Σ(H2) estimators that include $\Sigma (\mathrm{12\:\mu m})$ are able to predict Σ(H2) more accurately than estimators that include resolved optical properties instead of $\Sigma (\mathrm{12\:\mu m})$. These results suggest that 12 μm emission and H2 as traced by CO emission are physically connected at kiloparsec scales. This may be due to a connection between polycyclic aromatic hydrocarbon emission and the presence of H2. The best single-property estimator is $\log \frac{\Sigma (\mathrm{H_2})}{\mathrm{M_\odot \:pc^{-2}}} = (0.48 \pm 0.01) + (0.71 \pm 0.01)\log \frac{\Sigma (\mathrm{12\:\mu m})}{\mathrm{L_\odot \:pc^{-2}}}$. This correlation can be used to efficiently estimate Σ(H2) down to at least 1 M⊙ pc−2 in star-forming regions within nearby galaxies.
Stellar velocity dispersion and dynamical mass of the ultra diffuse galaxy NGC 5846_UDG1 from the keck cosmic web imager
Authors: Forbes Duncan A , Gannon Jonah S , Romanowsky Aaron J , Alabi Adebusola , Brodie Jean P , Couch Warrick J , Ferré-Mateu Anna 
Published: October 2020

ABSTRACTThe ultra diffuse galaxy in the NGC 5846 group (NGC 5846_UDG1) was shown to have a large number of globular cluster (GC) candidates from deep imaging as part of the VEGAS survey. Recently, Müller et al. published a velocity dispersion, based on a dozen of its GCs. Within their quoted uncertainties, the resulting dynamical mass allowed for either a dark matter free or a dark-matter-dominated galaxy. Here, we present spectra from KCWI that reconfirms membership of the NGC 5846 group and reveals a stellar velocity dispersion for UDG1 of σGC = 17 ± 2 km s−1. Our dynamical mass, with a reduced uncertainty, indicates a very high contribution of dark matter within the effective radius. We also derive an enclosed mass from the locations and motions of the GCs using the tracer mass estimator, finding a similar mass inferred from our stellar velocity dispersion. We find no evidence that the galaxy is rotating and is thus likely pressure supported. The number of confirmed GCs, and the total number inferred for the system (∼45), suggests a total halo mass of ∼2 × 1011 M⊙. A cored mass profile is favoured when compared to our dynamical mass. Given its stellar mass of 1.1 × 108 M⊙, NGC 5846_UDG1 appears to be an ultra diffuse galaxy with a dwarf-like stellar mass and an overly massive halo.