bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occupational respiratory allergy to reactive dyes
Authors: Muñoz Xavier , Clofent David , Cruz María-Jesús 
Published: December 2022

Purpose of review
Reactive dyes have been shown to cause respiratory sensitization in workers with occupational exposure. The present review analyzes the current knowledge of the role of reactive dyes in promoting occupational respiratory allergy. We discuss the current classification of reactive dyes as well as the potential development of occupational respiratory diseases after exposure to these substances.

Recent findings
Few descriptions of the role of reactive dyes in the development of occupational allergy have been published in recent years. Several reactive dyes are considered causes of occupational asthma (OA), mainly in workers in textile industries. Positive skin tests and the presence of specific serum IgE antibodies to reactive dyes suggest that respiratory symptoms provoked by reactive dyes may be immunoglobulin E (IgE)-mediated reactions. It was suggested that airborne dye molecules may act as haptens and induce IgE-mediated hypersensitivity reactions.

Summary
Reactive dyes are widely used in the textile industry, owing to their ability to produce strong covalent bonds to textile fibers. These substances have been identified as potential respiratory sensitizers causing OA and occupational rhinitis. The clinical presentation and phenotype of patients with OA due to reactive dyes is very similar to those presented by patients with OA to high molecular weight agents. The extensive use of reactive dyes in industry means that it is particularly important to describe their implications for health, which in fact are probably underestimated.
Accelerated Partial Breast Irradiation
Authors: Meattini Icro , Kim Kyubo , Livi Lorenzo 
Published: December 2022

Accelerated partial breast irradiation Florence phase 3 trial is a single-center study comparing intensity-modulated based accelerated partial breast irradiation (PBI, 30 Gy in 5 fractions) and whole breast irradiation (50 Gy in 25 fractions) followed by a tumor bed boost (10 Gy in 5 fractions). This easy-to-deliver PBI approach showed excellent long-term disease control with favorable safety and cosmetic outcome profiles. A plateau has been probably reached concerning the reduction of the number of fractions in the postoperative PBI setting. A 5-fraction schedule is the standard regimen and probably the appropriate compromise in terms of efficacy, safety, and quality of life, also considering the negative results of most intraoperative single-fraction PBI trials. A new frontier is now open on the potential benefit of preoperative PBI delivery, although concerns remain on the optimal dose, fractionation, and technique. Hereby we report the accelerated PBI Florence phase 3 trial experience and future perspectives.
Haematopoietic stem cell quiescence exposed using mitochondrial membrane potential
Authors: Ghaffari Saghi 
Published: December 2022

Purpose of review
Quiescence is a fundamental property of haematopoietic stem cells (HSCs). Despite the importance of quiescence in predicting the potency of HSCs, tools that measure routinely the degree of quiescence or select for quiescent HSCs have been lacking. This Commentary discusses recent findings that address this fundamental gap in the HSC toolbox.

Recent findings
Highly purified, phenotypically-defined HSCs are heterogeneous in their mitochondrial membrane potential (MMP). The lowest MMP subsets are enriched in greatly quiescent HSCs with the highest potency within the purified HSC population. MMP provides an intrinsic probe to select HSC subsets with unique cell cycle properties and distinct stem cell potential. Using this approach, new and unanticipated metabolic properties of quiescent HSCs’ exit have been discovered. This methodology may improve the mechanistic understanding, of HSCs’ exit from and entry to, quiescence.

Summary
Selecting HSCs using MMP is likely to lead to discoveries of new HSC properties, may improve the ex vivo maintenance of HSCs and has implications for the clinic, including for improving HSC transplantations.
Characteristics of Reported Gonorrhea Diagnoses During The COVID-19 Pandemic Compared With Pre–COVID-19 Pandemic, Baltimore City, Maryland
Authors: Coen Michelle E. , Williford Sarah L. , Muvva Ravikiran , Genberg Becky , Greenbaum Adena , Schumacher Christina M. 
Published: December 2022

Background
Sexual health service disruptions due to COVID-19 mitigation measures may have decreased gonorrhea screening and biased case-ascertainment toward symptomatic individuals. We assessed changes in reported symptoms and other characteristics among reported gonorrhea cases during pandemic versus prepandemic periods in 1 city with persistent gonorrhea transmission.

Methods
Enhanced surveillance data collected on a random sample of gonorrhea cases reported to the Baltimore City Health Department between March 2018 and September 2021 was used. Logistic regression assessed differences in case characteristics by diagnosis period (during pandemic: March 2020–September 2021; prepandemic: March 2018–September 2019).

Results
Analyses included 2750 (1090 during pandemic, 1660 prepandemic) gonorrhea cases, representing 11,904 reported cases. During pandemic versus prepandemic, proportionally fewer cases were reported by sexual health clinics (8.8% vs 23.2%), and more frequently reported by emergency departments/urgent care centers (23.3% vs 11.9%). Adjusting for diagnosing provider, fewer cases who were men with urethral infections (adjusted odds ratio [aOR], 0.65; 95% confidence interval [CI], 0.55–0.77), aged <18 years (aOR, 0.64; 95% CI, 0.47–0.89), and women (aOR, 0.84; 95% CI, 0.71–0.99) were reported, and cases with insurance (aOR, 1.85; 95% CI, 1.40–2.45), living with human immunodeficiency virus (aOR, 1.43; 95% CI, 1.12–1.83), or recent (≤12 months) gonorrhea history (aOR, 1.25; 95% CI, 1.02–1.53) were more frequently reported during pandemic versus prepandemic. Reported symptoms and same-day/empiric treatment did not differ across periods.

Conclusions
We observed no changes in reported symptoms among cases diagnosed during pandemic versus prepandemic. Increased frequency of reported diagnoses who were insured, living with human immunodeficiency virus, or with recent gonorrhea history are suggestive of differences in care access and care-seeking behaviors among populations with high gonorrhea transmission during the pandemic.
Organ Dysfunction Among Children Meeting Brain Death Criteria: Implications for Organ Donation*
Authors: Nickerson Taylor E. , Lovett Marlina E. , O’Brien Nicole F. 
Published: December 2022

OBJECTIVES:
Over 70% of pediatric organ donors are declared deceased by brain death (BD) criteria. Patients with these devastating neurologic injuries often have accompanying multiple organ dysfunction. This study was performed to characterize organ dysfunction in children who met BD criteria and were able to donate their organs compared with those deemed medically ineligible.

DESIGN:
Retrospective cohort study.

SETTING:
PICU at a quaternary care children’s hospital.

PATIENTS:
Patients with International Classification of Diseases, 9th Edition codes corresponding to BD between 2012 and 2018 were included.

MEASUREMENTS AND MAIN RESULTS:
Demographics, comorbidities, Pediatric Risk of Mortality (PRISM)–III, and injury mechanisms were derived from the medical record. Organ dysfunction was quantified by evaluating peak daily organ-specific variables. Fifty-eight patients, from newborn to 22 years old, were included with a median PRISM-III of 34 (interquartile range [IQR], 26–36), and all met criteria for multiple organ dysfunction syndrome (MODS). Thirty-four of 58 BD children (59%) donated at least one organ. Of the donors (not mutually exclusive proportions), 10 of 34 donated lungs, with a peak oxygenation index of 11 (IQR, 8–23); 24 of 34 donated their heart (with peak Vasoactive Inotrope Score 23 [IQR, 18–33]); 31 of 34 donated kidneys, of whom 16 of 31 (52%) had evidence of acute kidney injury; and 28 of 34 patients donated their liver, with peak alanine transferase (ALT) of 104 U/L (IQR, 44–268 U/L) and aspartate aminotransferase (AST) of 165 U/L (IQR, 94–434 U/L). Organ dysfunction was similar between heart and lung donors and respective medically ineligible nondonors. Those deemed medically ineligible to donate their liver had higher peak ALT 1,518 U/L (IQR, 986–1,748 U/L) (p = 0.01) and AST 2,200 U/L (IQR, 1,453–2,405 U/L) (p = 0.01) compared with liver donors.

CONCLUSIONS:
In our single-center experience, all children with BD had MODS, yet more than one-half were still able to donate organs. Future research should further evaluate transplant outcomes of dysfunctional organs prior to standardizing donation eligibility criteria.
Professionals Perception of a Strategy to Avoid Interruptions During Medication Handling
Authors: Castro-Rodríguez Cristina , De Lucas-Volle Sara , González-Roca Isora , Diaz-Redondo Alicia , Mora-Capín Andrea , Marañón Rafael 
Published: December 2022

Introduction
The use of vests for handling medication (prescription, preparation, and dispensing) in the emergency department is a strategy designed to increase patient safety by reducing interruptions and, consequently, medication errors. In this study, we aim to assess how professionals perceive the use of vests in a pediatric emergency department of a tertiary hospital.

Material and Methods
A cross-sectional survey was conducted among pediatric emergency physicians and nurses in October and November 2019. We analyzed the results of a 19-item survey on the perception of vests as a tool for reducing interruptions and medication errors.

Results
In this study, 91 surveys were delivered and 89 (97.8%) were completed. One hundred percent of the professionals were aware of the vests. Nurses reported the following reasons for not using the vest: high workload (25%) and preparation of nebulized and oral medications (25%). One hundred percent of doctors asked for the vest because of forgetfulness. Thirty-five physicians (81.4%) and 17 nurses (85.0%) said that wearing the vest, they were rarely or never interrupted. Eighty-two respondents (93.2%) agreed that vests are an effective strategy for minimizing medication errors.

Conclusions
Although medical professionals consider vests to be a useful strategy to prevent interruptions and reduce medication errors, adherence to the protocol is low, so a promotion strategy is needed to encourage professionals to use the vests.
Discovering Social Determinants of Health from Case Reports using Natural Language Processing: Algorithmic Development and Validation
Authors: Raza Shaina , Dolatabadi Elham , Ondrusek Nancy , Rosella Laura , Schwartz Brian 
Published: December 2022

AbstractBackgroundSocial determinants of health are non-medical factors that influence health outcomes (SDOH). There is a wealth of SDOH information available in electronic health records, clinical reports, and social media data, usually in free text format. Extracting key information from free text poses a significant challenge and necessitates the use of natural language processing (NLP) techniques to extract key information.ObjectiveThe objective of this research is to advance the automatic extraction of SDOH from clinical texts.Setting and DataThe case reports of COVID-19 patients from the published literature are curated to create a corpus. A portion of the data is annotated by experts to create ground truth labels, and semi-supervised learning method is used for corpus re-annotation.MethodsAn NLP framework is developed and tested to extract SDOH from the free texts. A two-way evaluation method is used to assess the quantity and quality of the methods.ResultsThe proposed NER implementation achieves an accuracy (F1-score) of 92.98% on our test set and generalizes well on benchmark data. A careful analysis of case examples demonstrates the superiority of the proposed approach in correctly classifying the named entities.ConclusionsNLP can be used to extract key information, such as SDOH factors from free texts. A more accurate understanding of SDOH is needed to further improve healthcare outcomes.
A high throughput splicing assay to investigate the effect of variants of unknown significance on exon inclusion
Authors: Scott Hilary A. , Place Emily M. , Harper Evelyn , Mehrotra Sudeep ,   Broad CMG, Huckfeldt Rachel , Comander Jason , Pierce Eric A. , Bujakowska Kinga M. 
Published: December 2022

AbstractPurposeInconclusive interpretation of pathogenicity of variants is a common problem in Mendelian disease diagnostics. We hypothesized that some variants of unknown significance (VUS) may lead to aberrant pre-mRNA splicing. To address this we have developed a high throughput splicing assay (HTSA) than can be utilized to test the effects of 1000s of variants on exon recognition.Methods2296 reference, control and variant sequences from 380 exons of 89 genes associated with inherited retinal degenerations (IRDs) were cloned as a pool into a split-GFP HTSA construct and expressed in landing pad RCA7 HEK293T cells. Exon inclusion led to disruption of GFP and exon skipping led to GFP reconstitution, enabling to separate GFP+ve and GFP-ve cells by fluorescence activated cell sorting. After deep sequencing-based quantification of studied sequences in each cell pool, exon inclusion index (EII) was determined, where EII = GFP-ve oligo count/total oligo count.ResultsHTSA showed high reproducibility when compared between different biological replicates (tetrachoric correlation coefficient r2= 0.83). Reference exon sequences showed a high level of exon recognition (median EII = 0.88) which was significantly reduced by mutations to the essential splice sites (donor site variants: median EII=0.06; acceptor site variants: median EII=0.48). Of the 748 studied VUSs, 47 variants led to decreased exon inclusion (ΔEII ≤ −0.3) with 11 variants showing a strong effect (ΔEII ≤ −0,6). Using the HTSA data we were able to provide a likely genetic diagnosis to five IRD cases.ConclusionHTSA offers a robust method to study the effects of VUSs on exon recognition allowing to provide new diagnoses for patients with Mendelian disorders.
Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches
Authors: Kazmi Aleeza , Kazim Muhammad , Aslam Faisal , Kazmi Syeda Mahreen-ul-Hassan , Wahab Abdul , Mikhlef Rafid Magid , Khizar Chandni , Kazmi Abeer , Wazir Nadeem Ullah , Mainali Ram Parsad 
Published: December 2022

ABSTRACTProtein is the building block for all organisms. Protein structure prediction is always a complicated task in the field of proteomics. DNA and protein databases can find the primary sequence of the peptide chain and even similar sequences in different proteins. Mainly, there are two methodologies based on the presence or absence of a template for Protein structure prediction. Template-based structure prediction (threading and homology modeling) and Template-free structure prediction (ab initio). Numerous web-based servers that either use templates or do not can help us forecast the structure of proteins. In this current study, ORF7a, a transmembrane protein of the SARS-coronavirus, is predicted using Phyre2, IntFOLD, and Robetta. The protein sequence is straightforwardly entered into the sequence bar on all three web servers. Their findings provided information on the domain, the region with the disorder, the global and local quality score, the predicted structure, and the estimated error plot. Our study presents the structural details of the SARS-CoV protein ORF7a. This immunomodulatory component binds to immune cells and induces severe inflammatory reactions.
Disability disparities in STEM: Gaps in salaries and representation for doctorate recipients with disabilities in the U.S., 2019
Authors: Castro Franz , Stuart Elizabeth , Deal Jennifer , Varadaraj Varshini , Swenor Bonnielin K. 
Published: December 2022

AbstractIntroductionThere is paucity of data examining disparities in salary and representation for disabled scientists, which is needed to advance inclusion and equity for people with disabilities in Science, Technology, Engineering and Mathematics (STEM).MethodsAnalyses used cross-sectional data from the 2019 Survey of Doctorate Recipients. We compared salaries between doctorate recipients with and without disabilities who were currently employed in STEM (N = 704,013), but who were otherwise similar on socioeconomic, degree and job-related characteristics, using propensity score weighting to carry out balanced comparisons, and further examined these differences in salary in the subset of doctorate recipients working in STEM at academic institutions (N = 219,413). In the subset of participants working in academia, we examined whether the representation of people with disabilities differed across categories of academic career milestones using chi-square tests (α = 0.05).ResultsDoctorate recipients working in STEM with early onset disabilities (identified <25 years of age) earned $10,580 less per year than non-disabled workers, and in the subset of academic workers this difference was larger (-$14,360). Salaries appeared lower for people with late onset disabilities as compared to those without, although these differences did not reach statistical significance. We observed an underrepresentation of academics with disabilities at higher faculty ranks (p<0.0001), among Deans/Presidents (p<0.0001) and among those with tenure (p: 0.0004).ConclusionThese findings support a need to expand efforts to foster inclusion, provide equal opportunities for career advancement, and improve working conditions for people with disabilities in STEM.
The alarm pheromone and alarm response of the clonal raider ant
Authors: Lopes Lindsey E. , Frank Erik T. , Kárpáti Zsolt , Schmitt Thomas , Kronauer Daniel J. C. 
Published: December 2022

AbstractAnts communicate via an arsenal of different pheromones produced in a variety of exocrine glands. For example, ants release alarm pheromones in response to danger to alert their nestmates and to trigger behavioral alarm responses. Here we characterize the alarm pheromone and the alarm response of the clonal raider antOoceraea biroi, a species that is amenable to laboratory studies but for which no pheromones have been identified. During an alarm response, ants quickly become unsettled, leave their nest pile, and are sometimes initially attracted to the source of alarm, but ultimately move away from it. We find that the alarm pheromone is released from the head of the ant and identify the putative alarm pheromone as a blend of two compounds found in the head, 4-methyl-3-heptanone and 4-methyl-3-heptanol. These compounds are sufficient to induce alarm behavior alone and in combination. They elicit similar, though slightly different behavioral features of the alarm response, with 4-methyl-3-heptanone being immediately repulsive and 4-methyl-3-heptanol being initially attractive before causing ants to move away. The behavioral response to these compounds in combination is dose-dependent, with ants becoming unsettled and attracted to the source of alarm pheromone at low concentrations and repulsed at high concentrations. While 4-methyl-3-heptanone and 4-methyl-3-heptanol are known alarm pheromones in other more distantly related ant species, this is the first report of the chemical identity of a pheromone inO. biroi, and the first alarm pheromone identified in the genusOoceraea. Identification of a pheromone that triggers a robust, consistent, and conserved behavior, like the alarm pheromone, provides an avenue to dissect the behavioral and neuronal mechanisms underpinning chemical communication.
Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors
Authors: Hippen Ariel A. , Omran Dalia K. , Weber Lukas M. , Jung Euihye , Drapkin Ronny , Doherty Jennifer A. , Hicks Stephanie C. , Greene Casey S. 
Published: December 2022

AbstractBackgroundSingle-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary population-scale analytical strategy. Many algorithms can deconvolve these tumors using single-cell profiles to infer their composition. While experimental choices do not change the true underlying composition of the tumor, they can affect the measurements produced by the assay.ResultsWe generated a dataset of high-grade serous ovarian tumors with paired expression profiles from using multiple strategies to examine the extent to which experimental factors impact the results of downstream tumor deconvolution methods. We find that pooling samples for single-cell sequencing and subsequent demultiplexing has a minimal effect. We identify dissociation-induced differences that affect cell composition, leading to changes that may compromise the assumptions underlying some deconvolution algorithms. We also observe differences across mRNA enrichment methods that introduce additional discrepancies between the two data types. We also find that experimental factors change cell composition estimates and that the impact differs by method.ConclusionsPrevious benchmarks of deconvolution methods have largely ignored experimental factors. We find that methods vary in their robustness to experimental factors. We provide recommendations for methods developers seeking to produce the next generation of deconvolution approaches and for scientists designing experiments using deconvolution to study tumor heterogeneity.
Deregulation of Y-linked protamine-like genes in sex chromosome-biased spermatid demise
Authors: Park Jun I. , Bell George W. , Yamashita Yukiko M. 
Published: December 2022

AbstractMeiotic drive is a phenomenon wherein a genetic element achieves a higher rate of transmission than dictated by Mendelian segregation (1-3). One proposed mechanism for meiotic drivers to achieve biased transmission is by sabotaging essential processes of gametogenesis (e.g. spermatogenesis), leading to demise of gametes that contain their opponents (1). Studies inD. simulanshave recently found that a set of meiotic driver genes contain a sequence homologous to protamines (4, 5), critical proteins that package sperm chromatin (6-8). However, the underlying mechanisms of drive and the relevance of protamine-like sequences in meiotic drive remain unknown. While studying the function of Modulo, the homolog of Nucleolin inDrosophila melanogaster(9, 10), we unexpectedly discovered Y-linked protamine genes function as a meiotic driver: we found thatmodulomutant’s known sterility is caused by deregulation of the autosomal protamine-like gene (Mst77F) and its Y chromosome-linked homolog (Mst77Y). Modulo regulates these genes at the step of polyadenylation of the transcripts. We show thatMst77Ylikely acts as a dominant-negative form ofMst77F, interfering with the process of histone-to-protamine transition, leading to nuclear decompaction. Overexpression ofMst77Yin a wild-type background is sufficient to cause nuclear decompaction and results in the biased demise of X chromosome-bearing sperm. We propose that dominant-negative protamine variants may be a common strategy found in male meiotic drive and may explain known rapid divergence of protamine genes.Significance statementProtamines are small, highly positively charged proteins that are required for packaging DNA to produce mature sperm with highly-condensed nuclei capable of fertilization. Even small changes in the dosage of protamines in humans is associated with infertility. Yet, despite their essential function, protamines are rapidly evolving. It has been speculated that protamines’ rapid divergence may be explained by their potential participation in genomic conflict. Our work implicates the involvement of Y chromosome-linked multicopy protamine-like genes in meiotic drive inDrosophila melanogaster. Our results suggest that dominant negative protamines can sabotage the process of nuclear compaction during spermiogenesis, revealing a potential cellular mechanism of sperm killing in meiotic drive.