bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tale of two sites – II. Inferring the properties of minihalo-hosted galaxies with upcoming 21-cm interferometers
Authors: Qin Yuxiang , Mesinger Andrei , Greig Bradley , Park Jaehong 
Published: October 2020

ABSTRACT
The first generation of galaxies is expected to form in minihaloes, accreting gas through H2 cooling, and possessing unique properties. Although unlikely to be directly detected in UV/infrared surveys, the radiation from these molecular-cooling galaxies (MCGs) could leave an imprint in the 21-cm signal from the Cosmic Dawn. Here, we quantify their detectability with upcoming radio interferometers. We generate mock 21-cm power spectra using a model for both MCGs as well as more massive, atomic-cooling galaxies, allowing both populations to have different properties and scaling relations. The galaxy parameters are chosen so as to be consistent with: (i) high-redshift UV luminosity functions; (ii) the upper limit on the neutral fraction from QSO spectra; (iii) the Thomson scattering optical depth to the CMB; and (iv) the timing of the recent putative EDGES detection. The latter implies a significant contribution of MCGs to the Cosmic Dawn, if confirmed to be cosmological. We then perform Bayesian inference on two models including and ignoring MCG contributions. Comparing their Bayesian evidences, we find a strong preference for the model including MCGs, despite the fact that it has more free parameters. This suggests that if MCGs indeed play a significant role in the Cosmic Dawn, it should be possible to infer their properties from upcoming 21-cm power spectra. Our study illustrates how these observations can discriminate among uncertain galaxy formation models with varying complexities, by maximizing the Bayesian evidence.
G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
Authors: Belmonte-Reche Efres , Morales Juan Carlos 
Published: October 2020

Abstract
We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.
Novel in vitro assays to detect circulating permeability factor(s) in idiopathic focal segmental glomerulosclerosis
Authors: den Braanker Dirk J W , Maas Rutger J , Deegens Jeroen K , Yanginlar Cansu , Wetzels Jack F M , van der Vlag Johan , Nijenhuis Tom 
Published: October 2020

Abstract

Background
Many patients with idiopathic focal segmental glomerulosclerosis (FSGS) develop recurrence of proteinuria after kidney transplantation (TX). Although several circulating permeability factors (CPFs) responsible for recurrence have been suggested, there is no consensus. To facilitate CPF identification and predict recurrence after TX, there is a need for robust methods that demonstrate the presence of CPFs.

Methods
Cultured human podocytes (hPods) and human and mouse glomerular endothelial cells (ciGEnC, mGEnC) were exposed to plasmas of FSGS patients with presumed CPFs, and of (disease) controls. A visual scoring assay and flow cytometry analysis of side scatter were used to measured changes in cellular granularity after exposure to plasma.

Results
Nine out of 13 active disease plasmas of 10 FSGS patients with presumed CPFs induced granularity in hPod in a dose- and time-dependent manner. Corresponding remission plasmas induced no or less granularity in hPod. Similar results were obtained with ciGEnC and mGEnC, although induced granularity was less compared with hPod. Notably, foetal calf serum, healthy plasma and a remission plasma partially blocked FSGS plasma-induced hPod granularity.

Conclusions
We developed a novel assay in which active disease, presumably CPF-containing, FSGS plasmas induced granularity in cultured hPod. Our results may indicate the presence of CPF inhibitor(s) in healthy and remission plasma. We suggest the presence of a delicate balance between CPF and a CPF inhibitory factor, which is disturbed in patients with active disease. Our novel assays can be applied in future research to identify CPF and CPF inhibitors, and possibly to predict recurrence after TX.
Temporal controls on crown nonstructural carbohydrates in southwestern US tree species
Authors: Peltier Drew M P , Guo Jessica , Nguyen Phiyen , Bangs Michael , Gear Linnea , Wilson Michelle , Jefferys Stacy , Samuels-Crow Kimberly , Yocom Larissa L , Liu Yao , Fell Michael K , Auty David , Schwalm Christopher , Anderegg William R L , Koch George W , Litvak Marcy E , Ogle Kiona 
Published: October 2020

Abstract
In trees, large uncertainties remain in how nonstructural carbohydrates (NSCs) respond to variation in water availability in natural, intact ecosystems. Variation in NSC pools reflects temporal fluctuations in supply and demand, as well as physiological coordination across tree organs in ways that differ across species and NSC fractions (e.g., soluble sugars vs starch). Using landscape-scale crown (leaves and twigs) NSC concentration measurements in three foundation tree species (Populus tremuloides, Pinus edulis, Juniperus osteosperma), we evaluated in situ, seasonal variation in NSC responses to moisture stress on three timescales: short-term (via predawn water potential), seasonal (via leaf δ13C) and annual (via current year’s ring width index). Crown NSC responses to moisture stress appeared to depend on hydraulic strategy, where J. osteosperma appears to regulate osmotic potentials (via higher sugar concentrations), P. edulis NSC responses suggest respiratory depletion and P. tremuloides responses were consistent with direct sink limitations. We also show that overly simplistic models can mask seasonal and tissue variation in NSC responses, as well as strong interactions among moisture stress at different timescales. In general, our results suggest large seasonal variation in crown NSC concentrations reflecting the multiple cofunctions of NSCs in plant tissues, including storage, growth and osmotic regulation of hydraulically vulnerable leaves. We emphasize that crown NSC pool size cannot be viewed as a simple physiological metric of stress; in situ NSC dynamics are complex, varying temporally, across species, among NSC fractions and among tissue types.
Risk factors and clinical course of children with cystic fibrosis colonized with Staphylococcus aureus
Authors: Ghimire Jagat Jeevan , Gulla Krishna Mohan , Jat Kana Ram , Sankar Jhuma , Lodha Rakesh , Kabra S K 
Published: October 2020

Abstract

Background
The literature is limited on staphylococcal infection in children with cystic fibrosis (CF) from tropical countries. We aimed to study the risk factors and clinical course of children with CF infected with Staphylococcus aureus.

Methods
In this chart review we compared demographic, clinical and spirometry characteristics in CF children with S. aureus alone (group A), both S. aureus and Pseudomonas aeruginosa (group B) and P. aeruginosa alone (group C) colonization.

Results
We included 79 cases (group A, 22; group B, 19; group C, 38). There was no difference in age of onset of symptoms, age of diagnosis, age of first isolation and spirometry parameters before colonization between the groups. The median duration of follow-up was shorter in group A. After colonization, children in group A and group B had significantly lower mean Shwachman and Kulczycki (SK) scores (44.7±5.4 and 40.8±5.8, respectively) compared with group C (49.9±6.8). Pulmonary exacerbations and hospitalizations were significantly greater in the combined group. After colonization, group A had a significant deterioration in SK score and forced vital capacity (FVC).

Conclusions
S. aureus colonization, especially in combination with P. aeruginosa, in children with CF was associated with worsening of FVC and clinical severity score and increased pulmonary exacerbations.
Aerosol Retention Characteristics of Barrier Devices
Authors: Fidler Richard L. , Niedek Christopher R. , Teng Justin J. , Sturgeon Mary E. , Zhang Qi , Robinowitz David L. , Hirsch Jan 
Published: October 2020

Background
Disease severity in coronavirus disease 2019 (COVID-19) may be associated with inoculation dose. This has triggered interest in intubation barrier devices to block droplet exposure; however, aerosol protection with these devices is not known. This study hypothesized that barrier devices reduce aerosol outside of the barrier.

Methods
Aerosol containment in closed, semiclosed, semiopen, and open barrier devices was investigated: (1) “glove box” sealed with gloves and caudal drape, (2) “drape tent” with a drape placed over a frame, (3) “slit box” with armholes and caudal end covered by vinyl slit diaphragms, (4) original “aerosol box,” (5) collapsible “interlocking box,” (6) “simple drape” over the patient, and (7) “no barrier.” Containment was investigated by (1) vapor instillation at manikin’s right arm with video-assisted visual evaluation and (2) submicrometer ammonium sulfate aerosol particles ejected through the manikin’s mouth with ventilation and coughs. Samples were taken from standardized locations inside and around the barriers using a particle counter and a mass spectrometer. Aerosol evacuation from the devices was measured using standard hospital suction, a surgical smoke evacuator, and a Shop-Vac.

Results
Vapor experiments demonstrated leakage via arm holes and edges. Only closed and semiclosed devices and the aerosol box reduced aerosol particle counts (median [25th, 75th percentile]) at the operator’s mouth compared to no barrier (combined median 29 [−11, 56], n = 5 vs. 157 [151, 166], n = 5). The other barrier devices provided less reduction in particle counts (133 [128, 137], n = 5). Aerosol evacuation to baseline required 15 min with standard suction and the Shop-Vac and 5 min with a smoke evacuator.

Conclusions
Barrier devices may reduce exposure to droplets and aerosol. With meticulous tucking, the glove box and drape tent can retain aerosol during airway management. Devices that are not fully enclosed may direct aerosol toward the laryngoscopist. Aerosol evacuation reduces aerosol content inside fully enclosed devices. Barrier devices must be used in conjunction with body-worn personal protective equipment.

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Examining the burden of opioid prescribing for non-cancer pain considering socio-economic differences, in Wales. A retrospective database study examining trends between 2005 – 2015
Authors: Davies Emma , Sewell Bernadette , Jones Mari , Phillips Ceri , Rance Jaynie 
Published: October 2020

AbstractObjectivesTo use a proxy-measure of oral morphine equivalent dose (OMED) to determine trends in opioid burden in people with non-cancer pain and explore differences related to deprivation status.Design, setting and participantsRetrospective cohort study using cross-sectional and longitudinal trend analyses of opioid prescribing data from 78% of Welsh Primary Care General Practices, whose data is shared with the Secure Anonymised Information Linkage (SAIL) databank. Anonymised data for the period 2005 to 2015, for people aged 18 or over, without a recorded cancer diagnosis and who received at least one prescription for an opioid medicine was included.Primary and Secondary outcomesA proxy-measure of oral morphine equivalence dose (OMED) was used to describe trends in opioid burden over the study period. OMED burden was stratified by 8 drug groups and deprivation, based on the quintile measures of the Welsh Index of Multiple Deprivation 2011 (WIMD2011).ResultsIn the 11 years examined, 22 641 424 prescriptions for opioids were issued from 345 primary care general practices in Wales. Daily OMED per 1000 population increased by 94.7% (from 16 266 mg to 31 665 mg). Twenty-eight percent of opioid prescribing occurred in the most deprived quintile. More than 100 000 000mg more OMED was prescribed in the most deprived areas of Wales, compared to the least deprived. Codeine prescribing accounted for 35% of the OMED burden in Wales over the study period.ConclusionsWhilst opioid prescription numbers increased 44% between 2005 and 2015, the OMED burden nearly doubled, with a disproportionate OMED load in the most deprived communities in Wales. Using OMED provides an insightful representation of opioid burden, more so than prescription numbers alone. Socio-economic differences are likely to affect pain presentation, access to support services and increase the likelihood of receiving an opioid prescription.Strengths and limitations of this studyThis study forms part of the first large-scale examination of opioid prescribing in Wales and is the first to use oral morphine equivalent dose as an outcome measure.Access to anonymously linked data allows more detailed examination of demographic influences on opioid prescribing.The study used a proxy-measure for oral morphine equivalent dose due to unavailability of anonymously linked prescription dispensing data.Disproportionate levels of prescribing in particular populations have been reported in many countries; further research should seek to understand the reasons for the differences and develop means to address any inequality noted.
Digital Imaging and Vision Analysis in Science Project improves the self-efficacy and skill of undergraduate students in computational work
Authors: Brooks Tessa Durham , Burks Raychelle , Doyle Erin , Meysenburg Mark , Frey Tim 
Published: October 2020

AbstractIn many areas of science, the ability to use computers to process, analyze, and visualize large data sets has become essential. The mismatch between the ability to generate large data sets and the computing skill to analyze them is arguably the most striking within the life sciences. The Digital Image and Vision Applications in Science (DIVAS) project describes a scaffolded series of interventions implemented over the span of a year to build the coding and computing skill of undergraduate students majoring primarily in the natural sciences. The program is designed as a community of practice, providing support within a network of learners. The program focus, images as data, provides a compelling ‘hook’ for participating scholars. Scholars begin the program with a one-credit spring semester seminar where they are exposed to image analysis. The program continues in the summer with a one-week, intensive Python and image processing workshop. From there, scholars tackle image analysis problems using a pair programming approach and finish the summer with independent research. Finally, scholars participate in a follow-up seminar the following spring and help onramp the next cohort of incoming scholars. We observed promising growth in participant self-efficacy in computing that was maintained throughout the project as well as significant growth in key computational skills. DIVAS program funding was able to support seventeen DIVAS over three years, with 76% of DIVAS scholars identifying as women and 14% of scholars being members of an underrepresented minority group. Most scholars (82%) entered the program as freshmen, with 89% of DIVAS scholars retained for the duration of the program and 100% of scholars remaining a STEM major one year after completing the program. The outcomes of the DIVAS project support the efficacy of building computational skill through repeated exposure of scholars to relevant applications over an extended period within a community of practice.
Retrospective assessment of SARS-COV2 circulation in two hospital nurseries hosting healthcare workers’ children during lockdown in one of the most affected French areas
Authors: Penot Pauline , Delaval Anne , L’Hour Fabienne , Grenier Angélique , Harich Raya 
Published: October 2020

AbstractBackgroundEvidence as to whether childcare and school closure limits the spread of SARS-CoV-2 virus is limited, especially because the role of children in SARS-CoV2 transmission remains unclear.MethodsBetween May 29 and July 2, 2020, a retrospective cohort study was conducted among two populations: requisitioned health-care workers and requisitioned staff from hospitals childcare centers, to investigate the virus circulation during lockdown, in a French area of high transmission.ResultsThe infection attack rate was 6/52 (11.6%) and 8/46 (17.4%) among health-care workers and childcare staff, respectively. An early epidemic occurred among Montreuil s hospital childcare staff, but the parents were not affected (p=0.029). Among Aulnay-sous-bois childcare center, three staff members were infected but none of them was in charge of a child whose parents were infected. Also among the parents of the children they cared for, none developed antibodies. Out of 14 infections, 12 were reliable to a source of transmission, mostly among colleagues.Discussion-conclusionThe assessment of viral circulation among healthcare workers and childcare staff suggests that the children did not contribute to SARS-CoV-2 spread in our setting.
Symptom based and transmission-prevention based testing in long-term care facilities: Symptomatology, clinical course and mortality for residents with COVID-19
Authors: Paap Kelly C. , van Loon Anouk M. , van Rijs Sarian M. , Helmich Esther , Buurman Bianca M. , Smalbrugge Martin , Hertogh Cees M.P.M. 
Published: October 2020

AbstractObjectivesInitially, for preventing COVID-19 transmission in long-term care facilities (LTCF) primarily rely on presence of core symptoms (fever, cough, dyspnea), but LTCF residents may also show an atypical course of a SARS-CoV-2 infection. We described the clinical presentation and course of COVID-19 in LTCF residents who were tested either because of presence of core symptoms (S-based) or because of transmission prevention (TP-based)DesignRetrospective cohort study.Setting and participantsAmsta (Amsterdam, The Netherlands), is a 1185-bed LTCF. All LTCF residents who underwent SARS-CoV-2 RT-PCR testing between March 16, 2020 and May 31, 2020 were included (n = 380).MeasuresClinical symptoms, temperature and oxygen saturation were extracted from medical records, 7 days before testing up to 14 days after testing.ResultsSARS-CoV-2 was confirmed in 81 (21%) residents. Of these 81, 36 (44%) residents were tested S-based and 45 (56%) residents were tested TP-based. Yet, CT-values did not differ between the groups. In the 7 days prior to the test the most common symptoms in both groups were: falling (32%), somnolence (25%) and fatigue (21%). Two days before the test, we observed a stronger decrease in oxygen saturation and an increase in temperature for the S-based group compared to the T-based group that remained up to 10 days after testing. Residents with in the S-based group were 2.5 times more likely to decease within 30 days than residents in the TP-based group (HR, 2.56; 95% 1.3 to 5.2). Even though, 73% of the T-based group did eventually developed core symptoms.Conclusion and implicationsMany LTCF residents with a positive PCR did not have core symptoms when tested but had other signs/symptoms in the week before the positive test. Testing policies should therefore be adjusted to prevent transmission. Daily measures of temperature and oxygen saturation can contribute to earlier detection.
A distributed learning strategy improves performance and retention of skills in neonatal resuscitation: A simulation-based randomized controlled trial
Authors: Nambyiah Pratheeban , Boet Sylvain , Moore Gregory , Boyle Riley , Aylward Deborah , Jakubow Andre , Lam Sandy , Abdulla Karim , Bould M. Dylan 
Published: October 2020

AbstractSkill retention after neonatal resuscitation training is poor. A distributed learning strategy – where learning is spread over multiple sessions – can improve retention of declarative memory (facts & knowledge). Session timings are critical – maximal retention occurs when a refresher session is scheduled at 10-30% of the time between initial training and test. We hypothesized this also holds true for neonatal resuscitation, a complex skill set requiring both declarative and procedural memory. We conducted a prospective, single-blinded randomized-controlled trial. University of Ottawa residents were recruited to training in neonatal resuscitation, with a high-fidelity simulated pre-test, immediate post-tests, and a retention test at 4 months. After training, they were randomized to either a refresher session at 3 weeks (18% of interval) or at 2 months (50%). Technical and non-technical skills were scored using validated checklists, knowledge with standardized questions. There was no difference between groups prior to the retention test. The early refresher group demonstrated significantly improved technical (mean ± 95% CI: 22.4 ± 1.3 v 18.2 ± 2.5, p = 0.02) and non-technical (31.0 ± 0.9 v 25.6 ± 3.1, p = 0.03) skill scores in the retention post-test compared to the late group. No difference was seen with knowledge scores. We conclude that both technical and non-technical aspects of neonatal resuscitation performance can benefit from an early refresher session. Session timings are critical and should be tailored to the desired length of skill retention. Findings may be generalizable to other interventions that depend on mixed types of memory.