bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis and prediction of human R-loop binding proteins
Authors: Kumar Arun , Fournier Louis-Alexandre , Stirling Peter C 
Published: June 2022

Abstract
In the past decade, there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair, and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins, we mined published proteomic studies and distilled 10 features that were enriched in R-loop binding proteins compared with the rest of the proteome. Applying an easy-ensemble machine learning approach, we used these R-loop binding protein-specific features along with their amino acid composition to create random forest classifiers that predict the likelihood of a protein to bind to R-loops. Known R-loop regulating pathways such as splicing, DNA damage repair and chromatin remodeling are highly enriched in our datasets, and we validate 2 new R-loop binding proteins LIG1 and FXR1 in human cells. Together these datasets provide a reference to pursue analyses of novel R-loop regulatory proteins.
Loss of BAF (mSWI/SNF) chromatin-remodeling ATPase Brg1 causes multiple malformations of cortical development in mice
Authors: Jin Yecheng , Gao Xiaotong , Lu Miaoqing , Chen Ge , Yang Xiaofan , Ren Naixia , Song Yuning , Hou Congzhe , Li Jiangxia , Liu Qiji , Gao Jiangang 
Published: June 2022

Abstract
Mutations in genes encoding subunits of the BAF (BRG1/BRM-associated factor) complex cause various neurodevelopmental diseases. However, the underlying pathophysiology remains largely unknown. Here, we analyzed the function of Brahma-related gene 1 (Brg1), a core ATPase of BAF complexes, in the developing cerebral cortex. Loss of Brg1 causes several morphological defects resembling human malformations of cortical developments (MCDs), including microcephaly, cortical dysplasia, cobblestone lissencephaly and periventricular heterotopia. We demonstrated that neural progenitor cell renewal, neuronal differentiation, neuronal migration, apoptotic cell death, pial basement membrane and apical junctional complexes, which are associated with MCD formation, were impaired after Brg1 deletion. Furthermore, transcriptome profiling indicated that a large number of genes were deregulated. The deregulated genes were closely related to MCD formation, and most of these genes were bound by Brg1. Cumulatively, our study indicates an essential role of Brg1 in cortical development and provides a new possible pathogenesis underlying Brg1-based BAF complex-related neurodevelopmental disorders.
The Squamate Clitoris: A Review and Directions for Future Research
Authors: Folwell Megan , Sanders Kate , Crowe-Riddell Jenna 
Published: June 2022

Abstract
The clitoris is a part of the genitalia of female amniotes that typically functions to stimulate sensory arousal. It usually consists of a small organ that is dimorphic and homologous to the penis. The developing amniote embryo forms a genital tubule, then sex hormones initiate a developmental cascade to form either a penis or clitoris. In squamates (lizards and snakes), the genital tubule develops into a paired hemiphallus structure called the “hemiclitores” in the female and the “hemipenes” in the male. The complex evolution of squamate hemipenes has been extensively researched since early discoveries in the 1800s and this has uncovered a huge diversity in hemipenis size, shape, and ornamentation (e.g., protrusions of spines, hooks, chalices, and cups). In contrast, the squamate hemiclitoris has been conspicuously under-investigated, and the studies that describe this anatomy are fraught with inconsistences. This paper aims to clarify the current state of knowledge of the squamate hemiclitoris, providing a foundation for further research on its morphology and functional role. We show that while several studies have described the gross anatomy of hemiclitores in lizards, comparative information is entirely lacking for snakes. Several papers cite earlier authors as having reported discoveries of the snake hemiclitores in vipers and colubrid snakes. However, our examination of this reveals only erroneous reports of hemiclitores in snakes and shows that these stem from misinterpretations of the true anatomy or species involved. An especially problematic source of confusion is the presence of intersex individuals in some snake populations; these form reproductively functional ovaries and a single hemipenis, with the latter sometimes mistaken for a hemiclitoris. (The intersex hemipenis is usually smaller and less spinous than the male hemipenis.) Further research is recommended to identify the defining anatomical features of the squamate hemiclitores. Such studies will form a vital basis of future comparative analyzes of variation in female genitalia in squamates and other amniotes.
Evaluation of the Salmonella CANARY® Zephyr Assay for the Detection of Salmonella enterica on Environmental Surfaces: AOAC Performance Tested MethodSM 042201
Authors: Wang Yangyang , Wright Samantha , Rodriguez Maria , Young Deevyne , Maltbie Alexandra , Lehett J J , Flannery Andrew R 
Published: June 2022

Abstract

Background
The Salmonella CANARY® Zephyr assay is designed to provide rapid and reliable detection of Salmonella enterica from various types of environmental surfaces, including stainless steel, silicone rubber, high-density polyethylene (HDPE), and glazed ceramic. The assay is using cell- and immuno-based CANARY technology and tested on Smiths Detection’s Zephyr platform.

Objective
The objective of this validation study was to evaluate the Salmonella CANARY Zephyr assay for its inclusivity/exclusivity, matrix study for 4 claimed environmental surfaces, consistency/stability, and robustness.

Methods
The Salmonella CANARY Zephyr assay was compared to the U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM) Chapter 5 “Salmonella” using an unpaired study design for environmental surfaces including stainless steel, silicone rubber, HDPE, and glazed ceramic (1” × 1” test area).

Results
For the inclusivity and exclusivity evaluation, the Salmonella CANARY Zephyr assay correctly identified 101 out of 102 target organism isolates (with one strain of S. enterica subsp. indica not detected) and excluded all 33 non-target strains that were analyzed. For the matrix study, the Salmonella CANARY Zephyr assay demonstrated no statistically significant differences between presumptive and confirmed results or between candidate and reference method results. Probability of detection analysis of the Salmonella CANARY Zephyr method on robustness and product consistency/stability (lot-to-lot) study demonstrated no statistically significant differences.

Conclusion
The Salmonella CANARY Zephyr assay is an effective method for the detection of Salmonella enterica from various environmental surfaces including stainless steel, silicone rubber, HDPE, and glazed ceramic.

Highlight
The Salmonella CANARY Zephyr assay allows for rapid and sensitive detection of Salmonella enterica on environmental surfaces. It only takes less than 5 min to prepare the sample and 1 min for instrument running/reading.
Analysis of Bovine Lactoferrin in Infant Formula and Adult Nutritional Products by Optical Biosensor Immunoassay: First Action 2021.07
Authors: Gill Brendon D , Kobayashi Tadashi , Wood Jackie E , Indyk Harvey E 
Published: June 2022

Abstract

Background
Bovine lactoferrin is increasingly being used as an ingredient in infant formula manufacture to enhance nutritional efficacy through the provision of immunoprotective, growth, and antimicrobial factors to the neonate.

Objective
To evaluate the analytical performance of an optical biosensor immunoassay for compliance with the method performance requirements described in SMPR 2020.005.

Method
Following dilution of the sample in buffer, an automated, label-free, real-time optical biosensor immunoassay was used in a direct assay format to quantitate bovine lactoferrin by its interaction with an immobilized anti-lactoferrin antibody. Quantitation was accomplished by the external standard technique with interpolation from a 4-parameter calibration regression.

Results
The analytical range (0–200 mg/hg), method detection limit (0.8 mg/hg), recovery (96.1–109.2%), and repeatability (1.0–5.3%) complied with the requirements given in the lactoferrin SMPR. The method was shown to be specific for native, intact lactoferrin; thermally denatured lactoferrin generated no measurable binding response.

Conclusion
The method described is suitable for the quantification of intact, undenatured lactoferrin in milk products, infant formulas (bovine milk protein-based, soy protein-based, and amino acid-based), and adult nutritionals and has been demonstrated to meet the performance requirements defined in SMPR 2020.005.

Highlights
A single-laboratory validation (SLV) of an automated biosensor immunoassay for the determination of intact, undenatured lactoferrin is described.
Burns During Coronavirus Disease 19 Lockdown: a Multi-Center Retrospective Study in Israel
Authors: Kruchevsky Dani , Levanon Shir , Givon Adi , Bodas Moran ,   Israeli Trauma Group, Acker Asaf , Aviran Nimrod , Bahouth Hany , Bar Alon , Becker Alexander , Braslavsky Alexander , Fadeev Dmitry , Goldstein Adam Lee , Grevtsev Ilia , Jeroukhimov Igor , Kedar Asaf , Korin Alexander , Qarawany Milad , Schwarz Alon , Shomar Wael , Soffer Dror , Stein Michael , Venturero Moris , Weiss Michael , Yaslowitz Ori , Zoarets Itay , Ramon Yitzchak , Ullmann Yehuda , Zeltzer Assaf A 
Published: June 2022

Abstract
The coronavirus disease 2019 (COVID-19) pandemic forced many countries into lockdowns to limit the spread of infection. Israel’s containment measures included school closures, mobility restrictions, and workforce reductions. Our study evaluated the effect of COVID-19 on the occurrence and patterns of burn injuries. The study data was obtained via retrospective chart review of burn patients treated between March 15, 2020 and April 30, 2020, namely the period of strict national lockdown. This data was compared against data from paralleling periods between 2017 and 2019. A total of 686 patients were treated for burn injuries in the two study periods. Age group analysis revealed an increased ratio of pediatric patients aged 0–3 years during the lockdown (55.91% vs 40.79%, P = .002). In contrast, there were fewer patients presenting with burn injuries in the 7–16 and 17–29 age groups (9.66% vs 3.15%, P = .017; 16.46% vs 7.09%, P = .007, respectively). During both study periods, scald injuries were the most common burn etiology and burn injuries occurred most often at home. This predominance was further pronounced during the lockdown (71.65% vs 58.68%, P = .007; 90.55% vs 74.60%, P = .0001, respectively). The lockdown period underlined the danger faced by pediatric patients in their household environment. This danger was possibly compounded by an improper level of adult supervision as parents transitioned to remote work. These findings can educate us about factors that render burn injuries more likely not only during lockdowns, but also during regular times, thus shaping the development of burn prevention practices.
Sensitivity Training for Mothers With Premature Infants: A Randomized Controlled Trial
Authors: Yu Nicky Ka Ki , Shum Kathy Kar-man , Lam Yuen Yu , Kwan Queenie Kwok Loi , Ng Sylvia Yin Ping , Chan Natalie Tsz Ting 
Published: June 2022

Abstract

Objective
This single-blind parallel design randomized controlled trial evaluated the feasibility and effectiveness of a modified version of the Mother–Infant Transaction Program (MITP) in enhancing Chinese mothers’ sensitivity towards their premature infants’ physiological and social cues.

Methods
Sixty mothers of hospitalized premature infants (mean gestational age = 32.1 weeks; SD = 2.8) were randomly assigned to either the MITP group or the treatment-as-usual control group. The intervention group (n = 30) received four sessions of parental sensitivity training adapted from the MITP, delivered by clinical psychologists before the infants were discharged. The control group (n = 30) received standard care provided by the hospitals. Each dyad was assessed at baseline (Time 1), immediately after intervention (Time 2), and when the infants were at the gestation-corrected ages of 3, 6, 9, and 12 months (Times 3–6). Maternal sensitivity, mother–infant interaction quality, parenting stress, postpartum depression, and mother’s perception of infant’s temperament were measured at Times 1–4, whereas infants’ weight gain and developmental performance were assessed at Times 3–6.

Results
The MITP group showed significantly higher maternal sensitivity and better mother–infant interaction quality after completing the training. They also reported less parenting stress and postnatal depression than the control group at Time 2 and subsequent follow-ups. The intervention significantly predicted better weight gain and developmental outcomes in infants across Times 3–6, mediated by maternal wellbeing and interaction quality.

Conclusion
Our results demonstrated the feasibility and effectiveness of this adapted sensitivity training among Chinese mothers with premature infants. [ClinicalTrials.gov NCT04383340]
Handlebar hernia–unusual complication from blunt trauma
Authors: Vieira Bruno , Melo Ana , Gomes Carina , Lajut Leandro , Ribeiro Artur , Fernandes Urânia , Guidi Gonçalo , Leal Clara , Pinto-de-Sousa João 
Published: June 2022

AbstractHandlebar hernia is a rare entity, mainly resulting from blunt abdominal trauma with a sudden deceleration mechanism. Diagnosis of handlebar at admission may be difficult because the rupture of abdominal wall layers often is not clinically recognized in the emergency department, which requires a high degree of suspicion to identify theses lesions. It is very important to rule out the presence of intra-abdominal injuries, and in adults, surgical repair is needed. Herein, the case of an adult man who presented to the emergency department with blunt abdominal trauma caused by a motorcycle handlebar is described.
Interactions Between Natural Selection and Recombination Shape the Genomic Landscape of Introgression
Authors: Duranton Maud , Pool John E 
Published: June 2022

Abstract
Hybridization between lineages that have not reached complete reproductive isolation appears more and more like a common phenomenon. Indeed, speciation genomic studies have now extensively shown that many species’ genomes have hybrid ancestry. However, genomic patterns of introgression are often heterogeneous across the genome. In many organisms, a positive correlation between introgression levels and recombination rate has been observed. It is usually explained by the purging of deleterious introgressed material due to incompatibilities. However, the opposite relationship was observed in a North American population of Drosophila melanogaster with admixed European and African ancestry. In order to explore how directional and epistatic selection can impact the relationship between introgression and recombination, we performed forward simulations of whole D. melanogaster genomes reflecting the North American population’s history. Our results revealed that the simplest models of positive selection often yield negative correlations between introgression and recombination such as the one observed in D. melanogaster. We also confirmed that incompatibilities tend to produce positive introgression–recombination correlations. And yet, we identify parameter space under each model where the predicted correlation is reversed. These findings deepen our understanding of the evolutionary forces that may shape patterns of ancestry across genomes, and they strengthen the foundation for future studies aimed at estimating genome-wide parameters of selection in admixed populations.
Identification of Streptomyces spp. in a Clinical Sample: Always Contamination? Results of a French Retrospective Study
Authors: Gras Emmanuelle , Bergeron Emmanuelle , Puges Mathilde , Ducours Maïlys , Leleux Charlotte , Amoureux Lucie , Jean Baptiste , Bendjelloul Imane , Camelena François , Chenouard Rachel , Mahieu Rafael , Lemenand Olivier , Toro Alexandre , Lecoustumier Alain , Lortholary Olivier , Rodriguez Nava Véronica , Lebeaux David ,   for the French Streptomyces Study Group
Published: June 2022

Abstract

Background
Streptomyces are environmental gram-positive bacilli that can cause ubiquitous mycetoma and, more rarely, invasive infections. We describe the clinical relevance of Streptomyces spp. identified in human samples and characteristics of patients with invasive Streptomyces infections.

Methods
We conducted a retrospective (2006–2017) study of Streptomyces isolates identified in clinical samples in French microbiology laboratories. Streptomyces genus was confirmed by a specific 16S rRNA polymerase chain reaction, and antibiotic susceptibility testing was performed by disk diffusion and trimethoprim-sulfamethoxazole minimum inhibitory concentration (E-test) if resistance was suspected. Patient characteristics, treatments, and outcomes were collected. Invasive infection was defined as a positive culture from a sterile site with signs of infection but without cutaneous inoculation.

Results
Of 137 Streptomyces isolates, all were susceptible to amikacin (113/113) and linezolid (112/112), and 92.9% to imipenem (105/113). Using disk diffusion, 50.9% (57/112) of isolates were susceptible to trimethoprim-sulfamethoxazole, but most of the apparently resistant isolates (25/36, 69.4%) tested by E-test were ultimately classified as susceptible. Clinical data were obtained for 63/137 (45.9%) isolates: 30 (47.6%) invasive infections, 8 (12.7%) primary cutaneous infections, 22 (34.9%) contaminations, 3 (4.7%) respiratory colonization. Patients with invasive infection were more frequently receiving corticosteroids than patients without invasive infection (11/30, 36.7%, vs 2/25, 8.0%; P = .03), and at 6-month follow-up, 14 of them were cured, 3 had relapsed, 4 were dead, and 9 were lost to follow-up.

Conclusions
Half of the clinical samples that grew Streptomyces were from patients with invasive infection. In that case, antimicrobial therapy should include 1 or 2 antibiotics among linezolid, amikacin, or imipenem.
Temporal changes in coronary artery function and flow velocity reserve in mice exposed to chronic intermittent hypoxia
Authors: Badran Mohammad , Bender Shawn B , Khalyfa Abdelnaby , Padilla Jaume , Martinez-Lemus Luis A , Gozal David 
Published: June 2022

Abstract

Study Objectives
Obstructive sleep apnea (OSA) is a chronic condition characterized by intermittent hypoxia (IH) that is implicated in an increased risk of cardiovascular disease (i.e., coronary heart disease, CHD) and associated with increased overall and cardiac-specific mortality. Accordingly, we tested the hypothesis that experimental IH progressively impairs coronary vascular function and in vivo coronary flow reserve.

Methods
Male C57BL/6J mice (8-week-old) were exposed to IH (FiO2 21% 90 s–6% 90 s) or room air (RA; 21%) 12 h/day during the light cycle for 2, 6, 16, and 28 weeks. Coronary artery flow velocity reserve (CFVR) was measured at each time point using a Doppler system. After euthanasia, coronary arteries were micro-dissected and mounted on wire myograph to assess reactivity to acetylcholine (ACh) and sodium nitroprusside (SNP).

Results
Endothelium-dependent coronary relaxation to ACh was preserved after 2 weeks of IH (80.6 ± 7.8%) compared to RA (87.8 ± 7.8%, p = 0.23), but was significantly impaired after 6 weeks of IH (58.7 ± 16.2%, p = 0.02). Compared to ACh responses at 6 weeks, endothelial dysfunction was more pronounced in mice exposed to 16 weeks (48.2 ± 5.3%) but did not worsen following 28 weeks of IH (44.8 ± 11.6%). A 2-week normoxic recovery after a 6-week IH exposure reversed the ACh abnormalities. CFVR was significantly reduced after 6 (p = 0.0006) and 28 weeks (p &lt; 0.0001) of IH when compared to controls.

Conclusion
Chronic IH emulating the hypoxia-re-oxygenation cycles of moderate-to-severe OSA promotes coronary artery endothelial dysfunction and CFVR reductions in mice, which progressively worsen until reaching asymptote between 16 and 28 weeks. Normoxic recovery after 6 weeks exposure reverses the vascular abnormalities.
The space-time profiles of sleep spindles and their coordination with slow oscillations on the electrode manifold
Authors: Malerba Paola , Whitehurst Lauren , Mednick Sara C 
Published: June 2022

Abstract
Sleep spindles are important for sleep quality and cognitive functions, with their coordination with slow oscillations (SOs) potentially organizing cross-region reactivation of memory traces. Here, we describe the organization of spindles on the electrode manifold and their relation to SOs. We analyzed the sleep night EEG of 34 subjects and detected spindles and SOs separately at each electrode. We compared spindle properties (frequency, duration, and amplitude) in slow wave sleep (SWS) and Stage 2 sleep (S2); and in spindles that coordinate with SOs or are uncoupled. We identified different topographical spindle types using clustering analysis that grouped together spindles co-detected across electrodes within a short delay (±300 ms). We then analyzed the properties of spindles of each type, and coordination to SOs. We found that SWS spindles are shorter than S2 spindles, and spindles at frontal electrodes have higher frequencies in S2 compared to SWS. Furthermore, S2 spindles closely following an SO (about 10% of all spindles) show faster frequency, shorter duration, and larger amplitude than uncoupled ones. Clustering identified Global, Local, Posterior, Frontal-Right and Left spindle types. At centro-parietal locations, Posterior spindles show faster frequencies compared to other types. Furthermore, the infrequent SO-spindle complexes are preferentially recruiting Global SO waves coupled with fast Posterior spindles. Our results suggest a non-uniform participation of spindles to complexes, especially evident in S2. This suggests the possibility that different mechanisms could initiate an SO-spindle complex compared to SOs and spindles separately. This has implications for understanding the role of SOs-spindle complexes in memory reactivation.