bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 2021 PhD Board-Certified Clinical Chemist Compensation Survey
Authors: Patel Khushbu , El-Khoury Joe M , Kataria Yachana , Wheeler Sarah , Hackenmueller Sarah A 
Published: August 2021

Abstract

Introduction
Doctoral-level clinical chemists work in various settings including academia, healthcare systems, reference laboratories, and industry. Information regarding compensation and benefits for PhD board-certified clinical chemists is limited. The American Association for Clinical Chemistry’s (AACC) Society for Young Clinical Laboratorians (SYCL) Core Committee completed a compensation survey in February 2021 and compared that to previous survey results.

Methods
The 2021 salary survey was made available to all doctoral-level AACC members working in the United States and Canada. Respondents provided information on type of degree and board certification, years of experience, employment sector, geographic location, and gender. The survey collected confidential self-reported data from 208 respondents, with 187 (90%) respondents residing in the United States.

Results
The 25th percentile, median and 75th percentile total compensation range for 113 PhDrespondents who are certified by the American Board of Clinical Chemistry (ABCC) and residing in the United States was $150 000 to $159 000, $180 000 to $189 000, and $230 000 to $239 000, respectively. Most of the respondents worked in either an academic, hospital, or healthcare system setting, with 47% of respondents working at academic medical centers.

Conclusions
In this 2021 compensation survey, we continue to see an upward trend in compensation ranges for board certified PhD clinical chemists. This report is important in allowing individuals to actively advocate with prospective and current employers for equal and fair compensation as well as other benefits that impact career development and growth.
A predictive model for next cycle start date that accounts for adherence in menstrual self-tracking
Authors: Li Kathy , Urteaga Iñigo , Shea Amanda , Vitzthum Virginia J , Wiggins Chris H , Elhadad Noémie 
Published: August 2021

Abstract

Objective
The study sought to build predictive models of next menstrual cycle start date based on mobile health self-tracked cycle data. Because app users may skip tracking, disentangling physiological patterns of menstruation from tracking behaviors is necessary for the development of predictive models.

Materials and Methods
We use data from a popular menstrual tracker (186 000 menstruators with over 2 million tracked cycles) to learn a predictive model, which (1) accounts explicitly for self-tracking adherence; (2) updates predictions as a given cycle evolves, allowing for interpretable insight into how these predictions change over time; and (3) enables modeling of an individual's cycle length history while incorporating population-level information.

Results
Compared with 5 baselines (mean, median, convolutional neural network, recurrent neural network, and long short-term memory network), the model yields better predictions and consistently outperforms them as the cycle evolves. The model also provides predictions of skipped tracking probabilities.

Discussion
Mobile health apps such as menstrual trackers provide a rich source of self-tracked observations, but these data have questionable reliability, as they hinge on user adherence to the app. By taking a machine learning approach to modeling self-tracked cycle lengths, we can separate true cycle behavior from user adherence, allowing for more informed predictions and insights into the underlying observed data structure.

Conclusions
Disentangling physiological patterns of menstruation from adherence allows for accurate and informative predictions of menstrual cycle start date and is necessary for mobile tracking apps. The proposed predictive model can support app users in being more aware of their self-tracking behavior and in better understanding their cycle dynamics.
Functional analyses of plasmodium ferredoxin Asp97Tyr mutant related to artemisinin resistance of human malaria parasites
Authors: Kimata-Ariga Yoko , Morihisa Rena 
Published: August 2021

Abstract
Mutation of Asp97Tyr in the C-terminal region of ferredoxin (PfFd) in the apicoplast of malaria parasites was recently reported to be strongly related to the parasite’s resistance to the frontline antimalarial drug, artemisinin. We previously showed that the aromatic amino acid in the C-terminal region of PfFd is important for the interaction with its electron transfer partner, Fd-NADP+ reductase (PfFNR). Here, the importance of the aromatic–aromatic interaction between PfFd and PfFNR was shown using the kinetic analysis of the electron transfer reaction of site-directed mutants of PfFNR with PfFd. Mutation of Asp97Tyr of PfFd was further shown to increase the affinity with PfFNR by the measurements of the dissociation constant (Kd) using tryptophan fluorescence titration and the Michaelis constant (Km) in the kinetic analysis with PfFNRs. Diaphorase activity of PfFNR was inhibited by D97Y PfFd at lower concentration as compared to wild-type PfFd. Ascorbate radical scavenging activity of PfFd and electron transfer activity to a heterogeneous Fd-dependent enzyme was lower with D97Y PfFd than that of wild-type PfFd. These results showed that D97Y mutant of PfFd binds to PfFNR tighter than wild-type PfFd, and thus may suppress the function of PfFNR which could be associated with the action of artemisinin.
Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Amphipoda: Haustoriidae)
Authors: Hancock Zachary B , Hardin Faith O , Murthy Archana , Hillhouse Andrew , Johnston J Spencer 
Published: August 2021

Abstract
Dramatic genome size variation exists across the Tree of Life. Some crustacean groups, such as amphipods, have genome sizes that correlate with body size, temperature, and water depth, indicating that genome sizes may be constrained due to physiological pressures. This may indicate that a general “genome-temperature-size” rule exists in ectotherms, in which body-size and latitude may be predictive of genome size. We examined the relationship between genome size, repetitive content, and environmental variables on a clade of sand-burrowing amphipods (Haustoriidae) that are distributed across the Gulf of Mexico and the North Atlantic. We uncovered a 6-fold genome size variation within Haustoriidae, a substantial amount considering this clade is less than 7 million years old. Unlike previous studies, we find no correlation between genome size and latitude, but do uncover a significant relationship between genome size and body length. Further, we find that the proportion of repetitive content predicts genome size, and that the largest genomes appear to be driven by expansions of LINE elements. We also found evidence of genomic purging and body size reduction in two lineages that have independently colonized warm brackish waters, possibly indicating a strong physiological constraint of transitioning from surf-swept beaches to protected bays.
The sexual spore pigment asperthecin is required for normal ascospore production and protection from UV light in Aspergillus nidulans
Authors: Palmer Jonathan M , Wiemann Philipp , Greco Claudio , Chiang Yi Ming , Wang Clay C C , Lindner Daniel L , Keller Nancy P 
Published: August 2021

Abstract
Many fungi develop both asexual and sexual spores that serve as propagules for dissemination and/or recombination of genetic traits. Asexual spores are often heavily pigmented and this pigmentation provides protection from UV light. However, little is known about any purpose pigmentation that may serve for sexual spores. The model Ascomycete Aspergillus nidulans produces both green pigmented asexual spores (conidia) and red pigmented sexual spores (ascospores). Here we find that the previously characterized red pigment, asperthecin, is the A. nidulans ascospore pigment. The asperthecin biosynthetic gene cluster is composed of three genes: aptA, aptB, and aptC, where deletion of either aptA (encoding a polyketide synthase) or aptB (encoding a thioesterase) yields small, mishappen hyaline ascospores; while deletion of aptC (encoding a monooxygenase) yields morphologically normal but purple ascospores. ∆aptA and ∆aptB but not ∆aptC or wild type ascospores are extremely sensitive to UV light. We find that two historical ascospore color mutants, clA6 and clB1, possess mutations in aptA and aptB sequences, respectively.
Adolescents’ Experiences of Idiopathic Scoliosis in the Presurgical Period: A Qualitative Study
Authors: Motyer Gillian S , Kiely Patrick J , Fitzgerald Amanda 
Published: August 2021

Abstract

Objective
Adolescent idiopathic scoliosis (AIS) is a sideways curvature of the spine that can progress severely during adolescent development and require surgical intervention. This qualitative study was conducted to explore the psychosocial experiences of adolescents with idiopathic scoliosis during the presurgical stage of treatment.

Methods
Fourteen adolescents with moderate-to-severe AIS aged 12–17 years participated in semistructured interviews and data were analyzed using inductive reflexive thematic analysis.

Results
Four key themes were generated from the analysis. “Proceeding with Caution” described adolescents’ adaptation to the physical impact of their AIS, while “Am I Different?” encompassed adolescents’ perceptions of their changing appearance and visibility of their condition. “An Emotional Journey” captured the rollercoaster of emotions from shock at diagnosis to the daunting realization of the severity of their condition, while knowing others with AIS could ease the emotional burden. Finally, adolescents’ concerns and expectations about their prospective surgery were captured by the theme “No Pain, No Gain”, whereby they were often keen to put surgery behind them.

Conclusions
Understanding and addressing adolescents’ psychosocial support needs as they manage the challenges associated with idiopathic scoliosis is a key component of promoting better outcomes among this patient group. Clinical implications and opportunities for support provision are discussed.
Antigen Test Performance Among Children and Adults at a SARS-CoV-2 Community Testing Site
Authors: Ford Laura , Whaley Melissa J , Shah Melisa M , Salvatore Phillip P , Segaloff Hannah E , Delaney Augustina , Currie Dustin W , Boyle-Estheimer Lauren , O’Hegarty Michelle , Morgan Clint N , Meece Jennifer , Ivacic Lynn , Thornburg Natalie J , Tamin Azaibi , Harcourt Jennifer L , Folster Jennifer M , Medrzycki Magdalena , Jain Shilpi , Wong Phili , Goffard Kimberly , Gieryn Douglas , Kahrs Juliana , Langolf Kimberly , Zochert Tara , Tate Jacqueline E , Hsu Christopher H , Kirking Hannah L 
Published: August 2021

Abstract

Background
Performance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture.

Methods
Two anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals ≥5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR-positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (&lt;18 years) and adults.

Results
About 1 in 10 included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR-positive. Cycle threshold values were similar among RT-PCR-positive specimens from children and adults (22.5 vs 21.3, P = .46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, P = .39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive values were 100% (27/27) and 94.9% (188/198), respectively. Virus was isolated from 51.4% (19/37) of RT-PCR-positive pediatric specimens; all 19 had positive antigen test results.

Conclusions
With lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus.
Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria
Authors: Cavassim Maria Izabel A , Andersen Stig U , Bataillon Thomas , Schierup Mikkel Heide 
Published: August 2021

Abstract
Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.
Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function
Authors: Janko Karel , Bartoš Oldřich , Kočí Jan , Roslein Jan , Drdová Edita Janková , Kotusz Jan , Eisner Jan , Mokrejš Martin , Štefková-Kašparová Eva 
Published: August 2021

AbstractHybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways.To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one.This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism’s ploidy level, as well as functional properties and parental ancestry of the genomic region.
MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases
Authors: Ratnaike Thiloka E , Greene Daniel , Wei Wei , Sanchis-Juan Alba , Schon Katherine R , van den Ameele Jelle , Raymond Lucy , Horvath Rita , Turro Ernest , Chinnery Patrick F 
Published: August 2021

AbstractDiagnosing mitochondrial disorders remains challenging. This is partly because the clinical phenotypes of patients overlap with those of other sporadic and inherited disorders. Although the widespread availability of genetic testing has increased the rate of diagnosis, the combination of phenotypic and genetic heterogeneity still makes it difficult to reach a timely molecular diagnosis with confidence. An objective, systematic method for describing the phenotypic spectra for each variant provides a potential solution to this problem. We curated the clinical phenotypes of 6688 published individuals with 89 pathogenic mitochondrial DNA (mtDNA) mutations, collating 26 348 human phenotype ontology (HPO) terms to establish the MitoPhen database. This enabled a hypothesis-free definition of mtDNA clinical syndromes, an overview of heteroplasmy-phenotype relationships, the identification of under-recognized phenotypes, and provides a publicly available reference dataset for objective clinical comparison with new patients using the HPO. Studying 77 patients with independently confirmed positive mtDNA diagnoses and 1083 confirmed rare disease cases with a non-mitochondrial nuclear genetic diagnosis, we show that HPO-based phenotype similarity scores can distinguish these two classes of rare disease patients with a false discovery rate &lt;10% at a sensitivity of 80%. Enriching the MitoPhen database with more patients will improve predictions for increasingly rare variants.
Transitioning to molecular diagnostics in pediatric high-grade glioma: experiences with the 2016 WHO classification of CNS tumors
Authors: Baugh Joshua N , Gielen Gerrit H , van Vuurden Dannis G , Veldhuijzen van Zanten Sophie E M , Hargrave Darren , Massimino Maura , Biassoni Veronica , Morales la Madrid Andres , Karremann Michael , Wiese Maria , Thomale Ulrich , Janssens Geert O , von Bueren André O , Perwein Thomas , Hoving Eelco W , Pietsch Torsten , Andreiuolo Felipe , Kramm Christof M 
Published: August 2021

Abstract

Background
Pediatric neuro-oncology was profoundly changed in the wake of the 2016 revision of the WHO Classification of Tumors of the Central Nervous System. Practitioners were challenged to quickly adapt to a system of tumor classification redefined by molecular diagnostics.

Methods
We designed a 22-question survey studying the impact of the revised WHO classification on pediatric high-grade glioma. The survey collected basic demographics, general attitudes, issues encountered, and opinions on pediatric subtypes. Participant answers were analyzed along socioeconomic lines utilizing the human development index (HDI) of the United Nations and membership in the group of seven (G7) world economic forum.

Results
Four hundred and sixty-five participants from 53 countries were included, 187 pediatric neurooncologists (40%), 160 neuropathologists (34%), and 118 other experts (26%). When asked about pediatric high-grade glioma entities, participants from very high development countries preferred treating a patient based on genetic findings. Participants from high and medium development countries indicated using traditional histology and tumor location as mainstays for therapeutic decisions. Non-G7 countries tended to regard the introduction of molecularly characterized tumor entities as a problem for daily routine due to lack of resources.

Conclusions
Our findings demonstrate an overall greater reliance and favorability to molecular diagnostics among very high development countries. A disparity in resources and access to molecular diagnostics has left some centers unable to classify pediatric high-grade glioma per the WHO classification. The forthcoming edition should strain to abate disparities in molecular diagnostic availability and work toward universal adaptation.
Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan
Authors: Furukawa Koichi , Tjan Lidya Handayani , Sutandhio Silvia , Kurahashi Yukiya , Iwata Sachiyo , Tohma Yoshiki , Sano Shigeru , Nakamura Sachiko , Nishimura Mitsuhiro , Arii Jun , Kiriu Tatsunori , Yamamoto Masatsugu , Nagano Tatsuya , Nishimura Yoshihiro , Mori Yasuko 
Published: August 2021

Abstract

Background
As of March 2021, Japan is facing a fourth wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To prevent further spread of infection, sera cross-neutralizing activity of patients previously infected with conventional SARS-CoV-2 against novel variants is important but has not been firmly established.

Methods
We investigated the neutralizing potency of 81 coronavirus disease 2019 (COVID-19) patients’ sera from the first to fourth waves of the pandemic against SARS-CoV-2 D614G, B.1.1.7, P.1, and B.1.351 variants using their authentic viruses.

Results
Most sera had neutralizing activity against all variants, showing similar activity against B.1.1.7 and D614G, but lower activity especially against B.1.351. In the fourth wave, sera-neutralizing activity against B.1.1.7 was significantly higher than that against any other variants, including D614G. The sera-neutralizing activity in less severe patients was lower than that of more severe patients for all variants.

Conclusions
The cross-neutralizing activity of convalescent sera was effective against all variants but was potentially weaker for B.1.351. The high neutralizing activity specific to B.1.1.7 in the fourth wave suggests that mutations in the virus might cause conformational change of its spike protein, which affects immune recognition of D614G. Our results indicate that individuals who recover from COVID-19 could be protected from the severity caused by infection with newly emerging variants.
A Fistful of Dollars: Financial Incentives, Peer Information, and Retirement Savings
Authors: Bauer Rob , Eberhardt Inka , Smeets Paul 
Published: August 2021

Abstract
To understand what motivates individuals to look at their pension situation and make adequate savings decisions, we conduct two field experiments with 226,946 and 257,433 pension fund participants. We find peer-information statements do not increase the rate at which individuals check their pension information, but lottery-type financial incentives do. Offering a few large prizes rather than many small prizes is most effective. However, the uptake of pension information does not lead to improved pension knowledge nor to increased self-reported savings three weeks after our intervention.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.