bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heart rate variability as a potential biomarker of pediatric obstructive sleep apnea resolution
Authors: Martín-Montero Adrián , Gutiérrez-Tobal Gonzalo C , Kheirandish-Gozal Leila , Vaquerizo-Villar Fernando , Álvarez Daniel , del Campo Félix , Gozal David , Hornero Roberto 
Published: September 2021

AbstractStudy ObjectivesPediatric obstructive sleep apnea (OSA) affects cardiac autonomic regulation, altering heart rate variability (HRV). Although changes in classical HRV parameters occur after OSA treatment, they have not been evaluated as reporters of OSA resolution. Specific frequency bands (named BW1, BW2, and BWRes) have been recently identified in OSA. We hypothesized that changes with treatment in these spectral bands can reliably identify changes in OSA severity and reflect OSA resolution.MethodsFour hundred and four OSA children (5–9.9 years) from the prospective Childhood Adenotonsillectomy Trial were included; 206 underwent early adenotonsillectomy (eAT), while 198 underwent watchful waiting with supportive care (WWSC). HRV changes from baseline to follow-up were computed for classical and OSA-related frequency bands. Causal mediation analysis was conducted to evaluate how treatment influences HRV through mediators such as OSA resolution and changes in disease severity. Disease resolution was initially assessed by considering only obstructive events, and was followed by adding central apneas to the analyses.ResultsTreatment, regardless of eAT or WWSC, affects HRV activity, mainly in the specific frequency band BW2 (0.028–0.074 Hz). Furthermore, only changes in BW2 were specifically attributable to all OSA resolution mediators. HRV activity in BW2 also showed statistically significant differences between resolved and non-resolved OSA.ConclusionsOSA treatment affects HRV activity in terms of change in severity and disease resolution, especially in OSA-related BW2 frequency band. This band allowed to differentiate HRV activity between children with and without resolution, so we propose BW2 as potential biomarker of pediatric OSA resolution.Clinical Trial RegistrationChildhood Adenotonsillectomy Trial, NCT00560859, https://sleepdata.org/datasets/chat.
Genome-wide identification of lncRNAs, miRNAs, mRNAs and their regulatory networks involved in tapping panel dryness in rubber tree (Hevea brasiliensis)
Authors: Liu Hui , Hu Yiyu , Yuan Kun , Feng Chengtian , He Qiguang , Sun Liang , Wang Zhenhui 
Published: September 2021

Abstract
Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis Muell. Arg.) is largely unknown. Here, the whole transcriptome analyses of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNAs (DEMs), genes (DEGs) and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs and 1574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. Kyoto Encyclopedia of Genes and Genomes analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were downregulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and 2 and 44 DELs were predicted as precursors and endogenous target mimics of 2 and 6 DEMs, respectively. Based on these, the DEL–DEM–DEG regulatory network involved in TPD was constructed, and 13 hub DELs, 3 hub DEMs and 2 hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of long ncRNAs, miRNAs and genes involved in TPD in rubber tree.
The Use of Medical Scribes in Primary Care Settings
Authors: Ziemann Margaret , Erikson Clese , Krips Maddie 
Published: September 2021

Background:
Clerical burdens have strained primary care providers already facing a shifting health care landscape and workforce shortages. These pressures may cause burnout and job dissatisfaction, with negative implications for patient care. Medical scribes, who perform real-time electronic health record documentation, have been posited as a solution to relieve clerical burdens, thus improving provider satisfaction and other outcomes.

Objective:
The purpose of this study is to identify and synthesize the published research on medical scribe utilization in primary care and safety net settings.

Research Design:
We conducted a review of the literature to identify outcomes studies published between 2010 and 2020 assessing medical scribe utilization in primary care settings. Searches were conducted in PubMed and supplemented by a review of the gray literature. Articles for inclusion were reviewed by the study authors and synthesized based on study characteristics, medical scribe tasks, and reported outcomes.

Results:
We identified 21 publications for inclusion, including 5 that examined scribes in health care safety net settings. Scribe utilization was consistently reported as being associated with improved productivity and efficiency, provider experience, and documentation quality. Findings for patient experience were mixed.

Conclusions:
Published studies indicate scribe utilization in primary care may improve productivity, clinic and provider efficiencies, and provider experience without diminishing the patient experience. Further large-scale research is needed to validate the reliability of study findings and assess additional outcomes, including how scribes enhance providers’ ability to advance health equity.
Disparities in heart and lung transplantation
Authors: Tsuang Wayne , Khedraki Rola , Hsich Eileen 
Published: September 2021

Purpose of review
Cardiothoracic transplantation is the definitive therapy for end-stage heart and lung disease. In service to this population, disparities in access and care must be simultaneously understood and addressed.

Recent findings
There are sex, race, geographic, age, and underlying disease disparities in both heart and lung transplantation. Women have reduced waitlist survival but improved posttransplant survival when compared with men for both heart and lung transplantation. Black patients have worse outcome compared with other races postheart transplant. Geographic disparities impact the likelihood of receiving heart or lung transplant and the growing number of patients with advanced age seeking transplant complicates discussions on survival benefit. Finally, underlying disease has affected outcomes for both heart and lung transplant and now are incorporated into the allocation system.

Summary
Though heart and lung transplantation have several existing disparities, it remains to be seen how advancements in medical technology, changes in donor organ allocation policies, and growing experience in patient selection will impact these concerns.
SARS-CoV-2 mRNA Vaccination-Associated Myocarditis in Children Ages 12-17: A Stratified National Database Analysis
Authors: Høeg Tracy Beth , Krug Allison , Stevenson Josh , Mandrola John 
Published: September 2021

ABSTRACTObjectivesEstablishing the rate of post-vaccination cardiac myocarditis in the 12-15 and 16-17-year-old population in the context of their COVID-19 hospitalization risk is critical for developing a vaccination recommendation framework that balances harms with benefits for this patient demographic.Design, Setting and ParticipantsUsing the Vaccine Adverse Event Reporting System (VAERS), this retrospective epidemiological assessment reviewed reports filed between January 1, 2021, and June 18, 2021, among adolescents ages 12-17 who received mRNA vaccination against COVID-19. Symptom search criteria included the words chest pain, myocarditis, pericarditis and myopericarditis to identify children with evidence of cardiac injury. The word troponin was a required element in the laboratory findings. Inclusion criteria were aligned with the CDC working case definition for probable myocarditis. Stratified cardiac adverse event (CAE) rates were reported for age, sex and vaccination dose number. A harm-benefit analysis was conducted using existing literature on COVID-19-related hospitalization risks in this demographic.Main outcome measures1) Stratified rates of mRNA vaccine-related myocarditis in adolescents age 12-15 and 16-17; and 2) harm-benefit analysis of vaccine-related CAEs in relation to COVID-19 hospitalization risk.ResultsA total of 253 CAEs were identified. Rates per million following dose 2 among males were 162.2 (ages 12-15) and 93.0 (ages 16-17); among females, rates were 13.0 and 12.5 per million, respectively. For boys 12-15 without medical comorbidities receiving their second mRNA vaccination dose, the rate of CAE is 2.6 to 4.3 times higher than their 120-day COVID-19 hospitalization risk even at times of peak incidence such as during the delta wave (7-day hospitalizations 2.1/100k population). For boys 16-17 without medical comorbidities, the rate of CAE is 1.5 to 2.5 times higher at times of high weekly COVID-19 hospitalization.ConclusionsPost-vaccination CAE rate was highest in young boys aged 12-15 following dose two. For boys 12-17 without medical comorbidities, the likelihood of post vaccination dose two CAE is 162.2 and 93.0/million respectively. This incidence exceeds their expected 120-day COVID-19 hospitalization rate at both moderate and high COVID-19 hospitalization incidence. Further research into the severity and long-term sequelae of post-vaccination CAE is warranted. Quantification of the benefits of the second vaccination dose and vaccination in addition to natural immunity in this demographic may be indicated to minimize harm.
RNA-Seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification
Authors: Díaz-Silva Mónica , Maldonado Jonathan , Veloso Pamela , Delgado Nicol , Silva Herman , Gallardo José A. 
Published: September 2021

ABSTRACTBackgroundSalicornia neei is a halophyte plant that has been proposed for use in the phytoremediation of the saline wastewater generated by land-based aquaculture, which usually contains elevated concentrations of ammonium resulting from protein metabolism. To identify the molecular mechanisms related to ammonium response, we analyzed the transcriptome of S. neei in response to growth in saline water containing 3 mM ammonium and the Michaelis–Menten ammonium removal biokinetics.ResultsThe RNA sequencing generated a total of 14,680,108 paired-end reads from the control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,020 transcripts and a reference transcriptome with an N50 of 683 bp.A total of 45,327 genes were annotated, representing 51.2% of the contig predicted from de novo assembly. As regards DEGs, a total of 9,140 genes were differentially expressed in response to ammonium in saline water; of these, 7,396 could be annotated against functional databases. The upregulated genes were mainly involved in cell wall biosynthesis, transmembrane transport and antiporter activities, including biological KEGG pathways linked to the biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, and nitrogen metabolism. In addiction, a set of 72 genes was directly involved in ammonium metabolism, including glutamine synthetase 1 (GLN1), glutamate synthase 1 (GLT1), and ferredoxin-dependent glutamate synthase chloroplastic (Fd-GOGAT). Finally, we observed that the ammonium uptake rate increased with increasing ammonium concentrations, and tended toward saturation in the range of 3 to 4 mM.ConclusionOur results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. neei when exposed to ammonium and saline water. The present transcriptome profiling method could be useful when investigating the response of halophyte plants to saline wastewater from land-based aquaculture.
Dynamic analysis and control of a rice-pest system under transcritical bifurcations
Authors: Mandal Sajib , Oberst Sebastian , Biswas Md. Haider Ali , Islam Md. Sirajul 
Published: September 2021

AbstractCultural methods were widely applied at an early stage of agricultural pest management but then replaced over time through pesticides with adverse effects on crop quality and the environment due to extensive and long-term use. In this study, we have reformulated a rice-pest-control model by first modelling a rice-pest system rigorously to then extend it to become an optimal control problem. We consider both, cultural methods and pesticides, and minimize thereby the density of agricultural pests, to increase the production of rice and to reduce gross annual losses. Pesticides have been applied only in an emergency scenario, which reduces environmental pollution and damage to nearby ecosystems. For the emergency case, we have developed a decision model to mitigate potential risks. The formulated models are verified by stability analysis at equilibrium points and investigated through transcritical bifurcations. Moreover, we have extensively confirmed our main results by numerical investigations and discussed the biological implications in more detail.
eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction
Authors: Wade Abdou Rahmane , Duruflé Harold , Sanchez Leopoldo , Segura Vincent 
Published: September 2021

AbstractMulti-omics represent a promising link between phenotypes and genome variation. Few studies yet address their integration to understand genetic architecture and improve predictability. Our study used 241 poplar genotypes, phenotyped in two common gardens, with their xylem and cambium RNA sequenced at one site, yielding large phenotypic, genomic and transcriptomic datasets. For each trait, prediction models were built with genotypic or transcriptomic data and compared to concatenation integrating both omics. The advantage of integration varied across traits and, to understand such differences, we made an eQTL analysis to characterize the interplay between the genome and the transcriptome and classify the predicting features into CIS or TRANS relationships. A strong and significant negative correlation was found between the change in predictability and the change in predictor importance for eQTLs (both TRANS and CIS effects) and CIS regulated transcripts, and mostly for traits showing beneficial integration and evaluated in the site of transcriptomic sampling. Consequently, beneficial integration happens when redundancy of predictors is decreased, leaving the stage to other less prominent but complementary predictors. An additional GO enrichment analysis appeared to corroborate such statistical output. To our knowledge, this is a novel finding delineating a promising way to explore data integration.One-sentence summarySuccessful multi-omics integration when predicting phenotypes makes redundant the predictors that are linked to ubiquitous connections between the omics, according to biological and statistical approaches
Evidence for a selective link between cooperation and individual recognition
Authors: Tumulty James P. , Miller Sara E. , Van Belleghem Steven M. , Weller Hannah I. , Jernigan Christopher M. , Vincent Sierra , Staudenraus Regan J. , Legan Andrew W. , Polnaszek Timothy J. , Uy Floria M. K. , Walton Alexander , Sheehan Michael J. 
Published: September 2021

AbstractThe ability to recognize and discriminate among others is a frequent assumption of models of the evolution of cooperative behavior. At the same time, cooperative behavior has been proposed as a selective agent favoring the evolution of individual recognition abilities. While theory predicts that recognition and cooperation may co-evolve, data linking recognition abilities and cooperative behavior with fitness or evidence of selection are elusive. Here, we provide evidence of a fitness link between individual recognition and cooperation in the paper waspPolistes fuscatus. Nest founding females in northern populations frequently form cooperative multiple foundress nests and possess highly variable facial patterns that mediate individual recognition. We describe a dearth of cooperative nesting, low phenotypic diversity, and a lack of individual recognition in southern populations. In a common garden experiment, northern co-foundress associations successfully reared offspring while all cooperative southern groups failed to rear any offspring, suggesting a fitness link between individual recognition and successful cooperation. Consistent with a selective link between individual recognition and cooperation, we find that rates of cooperative co-nesting correlate with identity-signaling color pattern diversity across the species’ range. Moreover, genomic evidence of recent positive selection on cognition loci likely to mediate individual recognition is substantially stronger in northern compared to southernP. fuscatuspopulations. Collectively, these data suggest that individual recognition and cooperative nesting behavior have co-evolved inP. fuscatusbecause recognition helps mediate conflict among co-nesting foundresses. This work provides evidence of a specific cognitive phenotype under selection because of social interactions, supporting the idea that social behavior can be a key driver of cognitive evolution.
Depside and depsidone synthesis in lichenized fungi comes into focus through a genome-wide comparison of the olivetoric and physodic acid chemotype of Pseudevernia furfuracea
Authors: Singh Garima , Armaleo Daniele , Grande Francesco Dal , Schmitt Imke 
Published: September 2021

ABSTRACTPrimary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are Non-Reducing Polyketide Synthases (NR-PKSs), and cytochrome P450s (CytP450). However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acyl synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for the synthesis of olivetoric and physodic acid, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for olivetoric and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for physodic and olivetoric acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.
Intersegmental coordination of the central pattern generator via interleaved electrical and chemical synapses in zebrafish spinal cord
Authors: Kim Lae Un , Riecke Hermann 
Published: September 2021

AbstractA significant component of the repetitive dynamics during locomotion in vertebrates is generated within the spinal cord. The legged locomotion of mammals is most likely controled by a hierarchical, multi-layer spinal network structure, while the axial circuitry generating the undulatory swimming motion of animals like lamprey is thought to have only a single layer in each segment. Recent experiments have suggested a hybrid network structure in zebrafish larvae in which two types of excitatory interneurons (V2a-I and V2a-II) both make first-order connections to the brain and last-order connections to the motor pool. These neurons are connected by electrical and chemical synapses across segments. Through computational modeling and an asymptotic perturbation approach we show that this interleaved interaction between the two neuron populations allows the spinal network to quickly establish the correct activation sequence of the segments when starting from random initial conditions and to reduce the dependence of the intersegmental phase difference (ISPD) of the oscillations on the swimming frequency. The latter reduces the frequency dependence of the waveform of the swimming motion. In the model the reduced frequency dependence is largely due to the different impact of chemical and electrical synapses on the ISPD and to the significant spike-frequency adaptation that has been observed experimentally in V2a-II neurons, but not in V2a-I neurons. Our model makes experimentally testable predictions and points to a benefit of the hybrid structure for undulatory locomotion that may not be relevant for legged locomotion.
Atria: An Ultra-fast and Accurate Trimmer for Adapter and Quality Trimming
Authors: Chuan Jiacheng , Zhou Aiguo , Hale Lawrence Richard , He Miao , Li Xiang 
Published: September 2021

AbstractBackgroundAs Next Generation Sequencing takes a dominant role in terms of output capacity and sequence length, adapters attached to the reads and low-quality bases hinder the performance of downstream analysis directly and implicitly, such as producing false-positive single nucleotide polymorphisms (SNP), and generating fragmented assemblies. A fast trimming algorithm is in demand to remove adapters precisely, especially in read tails with relatively low quality.FindingsWe present a trimming program named Atria. Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (O(n)time withO(1)space). Atria also implements multi-threading in both sequence processing and file compression and supports single-end reads.ConclusionsAtria performs favorably in various trimming and runtime benchmarks of both simulated and real data with other cutting-edge trimmers. We also provide an ultra-fast and lightweight byte-based matching algorithm. The algorithm can be used in a broad range of short-sequence matching applications, such as primer search and seed scanning before alignment.Availability & ImplementationThe Atria executables, source code, and benchmark scripts are available athttps://github.com/cihga39871/Atriaunder the MIT license.