bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the viral load expelled in saliva droplets carrying SARS-CoV-2
Authors: Calles A , Morán-López J L 
Published: August 2021

Abstract
One of the most likely routes of transmission of COVID-19 is through the saliva droplets that are produced while speaking, coughing or sneezing by infected people. The expelled droplets, measuring between 0.4 and 450 μm, follow trajectories determined, mainly, by the gravitational, and air frictional forces. We solve numerically the equations of motion in which the linear and quadratic velocity terms in the drag force are considered. In order to model the virus load expelled during respiratory events, we assume log-log Gaussian distributions, with peaks around 10 μm, and analyze four size ranges: the aerosol (0.4–5 μm), the small (5.1–10 μm), the middle (10.1–100 μm), and big (100.1–450 μm) droplet size regimes. In the aerosol regime, the frictional forces quickly stop the droplets in their horizontal movement and they fall extremely slowly pulled down by the gravitational force. The residence time, in a calm environment, goes from 3.83 days to 33.3 min. More massive droplets take shorter times and hit the ground meters away from the source. By assuming a constant density of virions per milliliter, we estimate the expelled amount into the environment. The middle and small size droplets contain the highest amount but since the aerosol droplets remain in the air such a long time, they represent also a high risk for infection. We emphasize the importance of face protection to minimize COVID-19, transmission.
The fushi tarazu zebra element is not required for Drosophila viability or fertility
Authors: Graham Patricia L , Fischer Matthew D , Giri Abhigya , Pick Leslie 
Published: August 2021

Abstract
Expression of genes in precisely controlled spatiotemporal patterns is essential for embryonic development. Much of our understanding of mechanisms regulating gene expression comes from the study of cis-regulatory elements (CREs) that direct expression of reporter genes in transgenic organisms. This reporter-transgene approach identifies genomic regions sufficient to drive expression but fails to provide information about quantitative and qualitative contributions to endogenous expression, although such conclusions are often inferred. Here we evaluated the endogenous function of a classic Drosophila CRE, the fushi tarazu (ftz) zebra element. ftz is a pair-rule segmentation gene expressed in seven stripes during embryogenesis, necessary for formation of alternate body segments. Reporter transgenes identified the promoter-proximal zebra element as a major driver of the seven ftz stripes. We generated a precise genomic deletion of the zebra element (ftzΔZ) to assess its role in the context of native chromatin and neighboring CREs, expecting large decreases in ftz seven-stripe expression. However, significant reduction in expression was found for only one stripe, ftz stripe 4, expressed at ∼25% of wild type levels in ftzΔZ homozygotes. Defects in corresponding regions of ftzΔZ mutants suggest this level of expression borders the threshold required to promote morphological segmentation. Further, we established true-breeding lines of homozygous ftzΔZ flies, demonstrating that the body segments missing in the mutants are not required for viability or fertility. These results highlight the different types of conclusions drawn from different experimental designs and emphasize the importance of examining transcriptional regulatory mechanisms in the context of the native genomic environment.
Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries
Authors: Telzrow Calla L , Zwack Paul J , Esher Righi Shannon , Dietrich Fred S , Chan Cliburn , Owzar Kouros , Alspaugh J Andrew , Granek Joshua A 
Published: August 2021

Abstract
RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing must be performed to compensate for the sequencing reads wasted on rRNA. The ideal RNA enrichment method removes all rRNA without affecting other RNA in the sample. We tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We find that the RNase H depletion method is more efficient in depleting rRNA and more specific in recapitulating non-rRNA levels present in unenriched controls than the commonly-used Poly(A) isolation method. The RNase H depletion method is also more effective than the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding RNA levels present in unenriched controls, while the Ribo-Zero depletion method more closely recapitulates annotated non-coding RNA (ncRNA) levels. Finally, we leverage these data to accurately map the C. neoformans mitochondrial rRNA genes, and also demonstrate that RNA-Seq data generated with the RNase H and Ribo-Zero depletion methods can be used to explore novel C. neoformans long non-coding RNA genes.
Insm1, Neurod1, and Pax6 promote murine pancreatic endocrine cell development through overlapping yet distinct RNA transcription and splicing programs
Authors: Dudek Karrie D , Osipovich Anna B , Cartailler Jean-Philippe , Gu Guoquing , Magnuson Mark A 
Published: August 2021

Abstract
Insm1, Neurod1, and Pax6 are essential for the formation and function of pancreatic endocrine cells. Here, we report comparative immunohistochemical, transcriptomic, functional enrichment, and RNA splicing analyses of these genes using gene knock-out mice. Quantitative immunohistochemical analysis confirmed that elimination of each of these three factors variably impairs the proliferation, survival, and differentiation of endocrine cells. Transcriptomic analysis revealed that each factor contributes uniquely to the transcriptome although their effects were overlapping. Functional enrichment analysis revealed that genes downregulated by the elimination of Insm1, Neurod1, and Pax6 are commonly involved in mRNA metabolism, chromatin organization, secretion, and cell cycle regulation, and upregulated genes are associated with protein degradation, autophagy, and apoptotic process. Elimination of Insm1, Neurod1, and Pax6 impaired expression of many RNA-binding proteins thereby altering RNA splicing events, including for Syt14 and Snap25, two genes required for insulin secretion. All three factors are necessary for normal splicing of Syt14, and both Insm1 and Pax6 are necessary for the processing of Snap25. Collectively, these data provide new insights into how Insm1, Neurod1, and Pax6 contribute to the formation of functional pancreatic endocrine cells.
Societies to genes: can we get there from here?
Authors: Page Robert E 
Published: August 2021

Abstract
Understanding the organization and evolution of social complexity is a major task because it requires building an understanding of mechanisms operating at different levels of biological organization from genes to social interactions. I discuss here, a unique forward genetic approach spanning more than 30 years beginning with human-assisted colony-level selection for a single social trait, the amount of pollen honey bees (Apis mellifera L.) store. The goal was to understand a complex social trait from the social phenotype to genes responsible for observed trait variation. The approach combined the results of colony-level selection with detailed studies of individual behavior and physiology resulting in a mapped, integrated phenotypic architecture composed of correlative relationships between traits spanning anatomy, physiology, sensory response systems, and individual behavior that affect individual foraging decisions. Colony-level selection reverse engineered the architecture of an integrated phenotype of individuals resulting in changes in the social trait. Quantitative trait locus (QTL) studies combined with an exceptionally high recombination rate (60 kb/cM), and a phenotypic map, provided a genotype–phenotype map of high complexity demonstrating broad QTL pleiotropy, epistasis, and epistatic pleiotropy suggesting that gene pleiotropy or tight linkage of genes within QTL integrated the phenotype. Gene expression and knockdown of identified positional candidates revealed genes affecting foraging behavior and confirmed one pleiotropic gene, a tyramine receptor, as a target for colony-level selection that was under selection in two different tissues in two different life stages. The approach presented here has resulted in a comprehensive understanding of the structure and evolution of honey bee social organization.
Plasmatic Hippuric Acid as a Hallmark of Frailty in an Italian Cohort: The Mediation Effect of Fruit–Vegetable Intake
Authors: Brunelli Laura , Davin Annalisa , Sestito Giovanna , Mimmi Maria Chiara , De Simone Giulia , Balducci Claudia , Pansarasa Orietta , Forloni Gianluigi , Cereda Cristina , Pastorelli Roberta , Guaita Antonio 
Published: August 2021

Abstract
Frailty syndrome is an age-related condition involving a loss of resilience, susceptibility to adverse health outcomes, and poor quality of life. This study was conducted in the framework of InveCe.Ab, an ongoing longitudinal population-based study. Plasma from 130 older individuals (older adults aged 76–78 years) was analyzed and validated (on 303 participants) using mass spectrometry-based metabolomics approaches. Equivalence tests showed that metabolites from the central cellular metabolic pathways were equivalent in frail and fit participants. Hippuric acid was the only cometabolite that distinguished fit from frail older adults. Logistic regression analysis indicated that high hippuric acid levels are significantly associated with a reduction of the risk of frailty after 4 years. Mediation analysis using a Frailty Index, hippuric acid, and fruit–vegetable intake supported the role of fruit–vegetable consumption in the hippuric acid relationship with the Frailty Index. These data point to low plasma hippuric acid as a plausible hallmark of frailty status, associated with lower fruit–vegetable intakes.
ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
Authors: Gaggion Nicolás , Ariel Federico , Daric Vladimir , Lambert Éric , Legendre Simon , Roulé Thomas , Camoirano Alejandra , Milone Diego H , Crespi Martin , Blein Thomas , Ferrante Enzo 
Published: August 2021

Abstract

Background
Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system that combines 3D-printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium.

Results
We developed a novel deep learning–based root extraction method that leverages the latest advances in convolutional neural networks for image segmentation and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals.

Conclusions
Our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies, as well as the screening of clock-related mutants, revealing novel root traits.
Arabidopsis SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2 inhibit WRKY75 function in abscisic acid-mediated leaf senescence and seed germination
Authors: Zhang Haiyan , Zhang Liping , Ji Yunrui , Jing Yifen , Li Lanxin , Chen Yanli , Wang Ruling , Zhang Huimin , Yu Diqiu , Chen Ligang 
Published: August 2021

Abstract
The plant-specific VQ gene family participates in diverse physiological processes but little information is available on their role in leaf senescence. Here, we show that the VQ motif-containing proteins, Arabidopsis SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2 are negative regulators of abscisic acid (ABA)-mediated leaf senescence. Loss of SIB1 and SIB2 function resulted in increased sensitivity of ABA-induced leaf senescence. In contrast, overexpression of SIB1 significantly delayed this process. Moreover, biochemical studies revealed that SIBs interact with WRKY75 transcription factor. Loss of WRKY75 function decreased sensitivity to ABA-induced leaf senescence, while overexpression of WRKY75 significantly accelerated this process. Chromatin immunoprecipitation assays revealed that WRKY75 directly binds to the promoters of GOLDEN 2-LIKE1(GLK1) and GLK2, to repress their expression. SIBs repress the transcriptional function of WRKY75 and negatively regulate ABA-induced leaf senescence in a WRKY75-dependent manner. In contrast, WRKY75 positively modulates ABA-mediated leaf senescence in a GLK-dependent manner. In addition, SIBs inhibit WRKY75 function in ABA-mediated seed germination. These results demonstrate that SIBs can form a complex with WRKY75 to regulate ABA-mediated leaf senescence and seed germination.
A randomized iterative approach to optimizing an online substance use intervention for collegiate athletes
Authors: Rulison Kelly L , Milroy Jeffrey J , Wyrick David L 
Published: August 2021

Lay Summary
Rates of drug use among collegiate athletes are high, yet there are few evidence-based interventions for this population, and the few existing interventions only address alcohol use. In addition, alcohol and drug use interventions targeting college students are not always as effective or efficient as they could be. Our goal was to strengthen modules from myPlaybook, an online drug use intervention for collegiate athletes as a way to optimize the full intervention package. We conducted three intervention trials. Each trial occurred in separate academic years and included 2,000–3,000 athletes from 40 to 50 colleges and universities. We randomly assigned athletes to receive one or more intervention modules that target known risk factors for drug use (i.e., social norms, expectancies about the effects of drug use, harm prevention strategies, and life skills). We used the results about the effects of each module to improve the module prior to the next trial. After these trials, the revised modules targeting social norms and expectancies about drug use had meaningful effects, increasing the likelihood that the full myPlaybook intervention will lead to clinical reductions in drug use among collegiate athletes.
A Review of the Design and Implementation of a Hybrid Cardiac Rehabilitation Program
Authors: Keteyian Steven J. , Ades Philip A. , Beatty Alexis L. , Gavic-Ott Anne , Hines Stephen , Lui Karen , Schopfer David W. , Thomas Randal J. , Sperling Laurence S. 
Published: August 2021

Purpose:
This review describes the considerations for the design and implementation of a hybrid cardiac rehabilitation (HYCR) program, a patient-individualized combination of facility-based cardiac rehabilitation (FBCR) with virtual cardiac rehabilitation (CR) and/or remote CR.

Review Methods:
To help meet the goal of the Millions Hearts Initiative to increase CR participation to 70% by 2022, a targeted review of the literature was conducted to identify studies pertinent to the practical design and implementation of an HYCR program. Areas focused upon included the current use of HYCR, exercise programming considerations (eligibility and safety, exercise prescription, and patient monitoring), program assessments and outcomes, patient education, step-by-step instructions for billing and insurance reimbursement, patient and provider engagement strategies, and special considerations.

Summary:
A FBCR is the first choice for patient participation in CR, as it is supported by an extensive evidence base demonstrating effectiveness in decreasing cardiac and overall mortality, as well as improving functional capacity and quality of life. However, to attain the CR participation rate goal of 70% set by the Million Hearts Initiative, CR programming will need to be expanded beyond the confines of FBCR. In particular, HYCR programs will be necessary to supplement FBCR and will be particularly useful for the many patients with geographic or work-related barriers to participation in an FBCR program. Research is ongoing and needed to develop optimal programming for HYCR.
Impact of DBP on all-cause and cardiovascular mortality: results from the National Health and Nutrition Examination survey, 1999–2014
Authors: Bae Eunjin , Rocco Michael V. , Lee Jeonghwan , Park Jae Yoon , Kim Yong Chul , Yoo Kyung Don , Kim Eun Young , Park Dong Jun , Lim Chun Soo , Kim Yon Su , Lee Jung Pyo 
Published: August 2021

Introduction:
Hypertension is common and has a significant effect on cardiovascular morbidity and death. However, despite the development of several guidelines to manage SBP, there is little research or guidance on the evaluation and management of DBP or isolated diastolic hypertension (IDH).

Method:
To determine the association of DBP with all-cause and cardiovascular mortality, we used NHANES data from 1999 to 2014 and included adults aged at least 18 years. The relationship between DBP, IDH and all-cause, cardiovascular mortality was evaluated.

Results:
Of the 35 109 participants, all-cause death occurred in 10.6%, and cardiovascular death occurred in 2.1% over a median follow-up of 7.2 years. Multivariate Cox regression analysis revealed that the risk of all-cause mortality was significantly higher in the lowest (≤56.9 mmHg) DBP groups than in the reference group (DBP 74–76.9 mmHg). However, the risk of cardiovascular mortality was significantly higher in the lowest and highest (≥83 mmHg) DBP group than in the reference group. The risk of all-cause mortality was higher for most groups with SBP at least 140 mmHg than for the reference group with DBP 74–76.9 mmHg and SBP 100–139.9 mmHg. Both the 2018 ESC/NICE and the 2017 AHA/ACC-defined IDH was not significantly associated with all-cause mortality.

Conclusion:
DBP and all-cause mortality had an inverse relationship, whereas DBP and cardiovascular mortality had a U-shaped relationship, with the DBP reference group having the lowest risk for all-cause and cardiovascular mortality. There was no significant relationship between IDH and death.
Ethnic differences and heritability of blood pressure circadian rhythm in African and European American youth and young adults
Authors: Xu Yanyan , Su Shaoyong , Brown Michelle , Snieder Harold , Harshfield Gregory , Wang Xiaoling 
Published: August 2021

Background: The aim of this study was to investigate whether blood pressure (BP) circadian rhythm in African Americans differed from that in European Americans. We further examined the genetic and/or environmental sources of variances of the BP circadian rhythm parameters and the extent to which they depend on ethnicity or sex.
Method: Quantification of BP circadian rhythm was obtained using Fourier transformation from the ambulatory BP monitoring data of 760 individuals (mean age, 17.2 ± 3.3; 322 twin pairs and 116 singletons; 351 African Americans).
Results: BP circadian rhythm showed a clear difference by ethnic group with African Americans having a lower amplitude (P = 1.5e–08), a lower percentage rhythm (P = 2.8e–11), a higher MESOR (P = 2.5e–05) and being more likely not to display circadian rhythm (P = 0.002) or not in phase (P = 0.003). Familial aggregation was identified for amplitude, percentage rhythm and acrophase with genetic factors and common environmental factors together accounting for 23 to 33% of the total variance of these BP circadian rhythm parameters. Unique environmental factors were the largest contributor explaining up to 67--77% of the total variance of these parameters. No sex or ethnicity difference in the variance components of BP circadian rhythm was observed.
Conclusion: This study suggests that ethnic differences in BP circadian rhythm already exist in youth with African Americans having a dampened circadian rhythm and better BP circadian rhythm may be achieved by changes in environmental factors.
New approach to quantifying acute stress in cataract surgeons to investigate the relationship between surgeon experience and intraoperative stress
Authors: Cap Veronika , Palkovits Stefan , Bijak Manfred , Ruiss Manuel , Schmoll Martin , Findl Oliver 
Published: August 2021

Purpose:
To quantify intraoperative stress levels in cataract surgeons and investigate the relationship between intraoperative stress and surgeon experience.

Setting:
Department of Ophthalmology, Hanusch Krankenhaus, Vienna, Austria.

Design:
Prospective, observational case series.

Methods:
5 ophthalmologists with surgery experiences of 70 to 15 000 previous surgeries volunteered for this study. Surgeons' heart rate (HR) and heart rate variability (HRV) were measured during a total of 45 cataract surgeries. HR and HRV values were normalized to the minimal HR and maximal HRV of an overnight baseline measurement. The resulting normalized HR measure and HRV stress index are stress dependent and comparable between subjects. No case selection was performed.

Results:
Less experienced surgeons showed higher HRV stress indices; differences between the surgeons with less than 180 and 500 surgeries and the 2 with 600 and 1500 surgeries, respectively, were statistically significant (α = 0.05). No statistically significant difference in stress indices was found between surgeons with 1500 and 15 000 surgeries, suggesting that there may be a plateau effect after 1500 surgeries. HRV stress indices and case times were negatively correlated with the logarithm of experience in the number of previously performed surgeries (r
2 = 0.67 and 0.52). No significant stress buildup over multiple successive surgeries was found (α = 0.05).

Conclusions:
The new HRV stress index is a simple but powerful tool for quantifying intraoperative stress in cataract surgeons. Decreases in stress with increasing experience are congruent with previous works on general surgeons' stress and follow a similar timeline as previously published, proficiency-based learning curves for cataract surgery.