bluuebunny/crossref_metadata_2025_split huggingface dataset:
A capture methyl-seq protocol with improved efficiency and cost-effectiveness using pre-pooling and enzymatic conversion
Authors: Hasegawa Keita , Nakabayashi Kazuhiko , Ishiwata Keisuke , Kasuga Yoshifumi , Hata Kenichiro , Tanaka Mamoru 
Published: July 2023

Abstract
Objective
The opportunities for sequencing-based methylome analysis of clinical samples are increasing. To reduce its cost and the amount of genomic DNA required for library preparation, we aimed to establish a capture methyl-seq protocol, which adopts pre-pooling of multiple libraries before hybridization capture and TET2/APOBEC-mediated conversion of unmethylated cytosine to thymine.

Results
We compared a publicly available dataset generated by the standard Agilent protocol of SureSelect XT Human Methyl-Seq Kit and our dataset obtained by our modified protocol, EMCap, that adopted sample pre-pooling and enzymatic conversion. We confirmed that the quality of DNA methylation data was comparable between the two datasets. As our protocol, EMCap, is more cost-effective and reduces the amount of input genomic DNA, it would serve as a better choice for clinical methylome sequencing.
Pyrosequencing analysis for rapid and accurate detection of clarithromycin resistance-associated mutations in Iranian Helicobacter pylori isolates
Authors: Alavifard Helia , Nabavi-Rad Ali , Baghaei Kaveh , Sadeghi Amir , Yadegar Abbas , Zali Mohammad Reza 
Published: July 2023

Abstract
Background
Treatment of Helicobacter pylori (H. pylori) infection has become challenging following the development of primary antibiotic resistance. A primary therapeutic regimen for H. pylori eradication includes clarithromycin; however, the presence of point mutations within the 23S rRNA sequence of H. pylori contributes to clarithromycin resistance and eradication failure. Thus, we aimed to develop a rapid and precise method to determine clarithromycin resistance-related point mutations using the pyrosequencing method.

Methods and results
H. pylori was isolated from 82 gastric biopsy samples and minimal inhibitory concentration (MIC) was evaluated using the agar dilution method. Clarithromycin resistance-associated point mutations were detected by Sanger sequencing, from which 11 isolates were chosen for pyrosequencing. Our results demonstrated a 43.9% (36/82) prevalence in resistance to clarithromycin. The A2143G mutation was detected in 8.3% (4/48) of H. pylori isolates followed by A2142G (6.2%), C2195T (4.1%), T2182C (4.1%), and C2288T (2%). Although the C2195T mutation was only detected by Sanger sequencing, the overall results from pyrosequencing and Sanger sequencing platforms were comparable.

Conclusions
Pyrosequencing could be used as a rapid and practical platform in clinical laboratories to determine the susceptibility profile of H. pylori isolates. This might pave the way for efficient H. pylori eradication upon detection.
Prenatal delta-9-tetrahydrocannabinol exposure is associated with changes in rhesus macaque DNA methylation enriched for autism genes
Authors: Shorey-Kendrick Lyndsey E. , Roberts Victoria H. J. , D’Mello Rahul J. , Sullivan Elinor L. , Murphy Susan K. , Mccarty Owen J. T. , Schust Danny J. , Hedges Jason C. , Mitchell A. J. , Terrobias Jose Juanito D. , Easley Charles A. , Spindel Eliot R. , Lo Jamie O. 
Published: July 2023

AbstractBackgroundWith the growing availability of cannabis and the popularization of additional routes of cannabis use beyond smoking, including edibles, the prevalence of cannabis use in pregnancy is rapidly increasing. However, the potential effects of prenatal cannabis use on fetal developmental programming remain unknown.ResultsWe designed this study to determine whether the use of edible cannabis during pregnancy is deleterious to the fetal and placental epigenome. Pregnant rhesus macaques consumed a daily edible containing either delta-9-tetrahydrocannabinol (THC) (2.5 mg/7 kg/day) or placebo. DNA methylation was measured in 5 tissues collected at cesarean delivery (placenta, lung, cerebellum, prefrontal cortex, and right ventricle of the heart) using the Illumina MethylationEPIC platform and filtering for probes previously validated in rhesus macaque. In utero exposure to THC was associated with differential methylation at 581 CpGs, with 573 (98%) identified in placenta. Loci differentially methylated with THC were enriched for candidate autism spectrum disorder (ASD) genes from the Simons Foundation Autism Research Initiative (SFARI) database in all tissues. The placenta demonstrated greatest SFARI gene enrichment, including genes differentially methylated in placentas from a prospective ASD study.ConclusionsOverall, our findings reveal that prenatal THC exposure alters placental and fetal DNA methylation at genes involved in neurobehavioral development that may influence longer-term offspring outcomes. The data from this study add to the limited existing literature to help guide patient counseling and public health polices focused on prenatal cannabis use in the future.
Projection of hydrological responses to changing future climate of Upper Awash Basin using QSWAT model
Authors: Gebremichael Haftu Brhane , Raba Gelana Amente , Beketie Kassahun Ture , Feyisa Gudina Legese , Anose Fikru Abiko 
Published: July 2023

Abstract
Background
Projecting future streamflow variation or the hydrological impact of climate change plays a pivotal role in the sustainable implication of planning water resources management. Therefore, this study predicts the potential of climate change’s impact on hydrological components in the Upper Awash Basin (UAB). The study applied a statistical downscaling model (SDSM) to generate future high-resolution climate data from the climate model output of the Canadian Second Generation Earth System Model (CanESM2) and the National Centers for Environmental Prediction (NCEP) under the representative concentration pathways (RCP4.5 and RCP8.5) scenarios. To analyze the trend of future rainfall and temperature, non-parametric Mann-Kendall, Modified Mann-Kendall tests, Sen’s slope estimator, and changing point (Pettit) tests were used. The output of downscaled climate data is used as input to a calibrated and validated Soil and Water Assessment Tool (QSWAT) model to assess the impact of future climate change on UAB hydrology.

Results
The results show that annual rainfall and temperature are significantly increased (p < 0.05) in the UAB under RCP4.5 and 8.5 for the model ensemble mean for both short- and long-term scenarios. The change in the rainfall, the maximum and minimum temperature is mostly visible in the second period (the 2060s). Climate change is likely to cause persistent decreases in surface runoff (SUR_Q) and increases in actual evapotranspiration (ET) under all climate scenarios in the three periods. Reduction in SUR_Q despite an increase in rainfall could be due to an increment in both temperature and ET. The study also identified inconsistent seasonal changes in projected future precipitation that considerably impact overall climatic conditions.

Conclusions
This research is essential to develop an interdisciplinary approach that integrates environmental policies for the coherent use and management of water resources for future climate change and ecological protection in the basin, including other similar basins.
Firearm locking device preferences among firearm owners in the USA: a systematic review
Authors: Buck-Atkinson Jessica , McCarthy Megan , Stanley Ian H. , Harnke Ben , Anestis Michael D. , Bryan Craig. J. , Baker Justin C. , Betz Marian E. 
Published: July 2023

Abstract
Background
Preventing firearm-involved injuries is a critical public health priority. Firearm locking devices can prevent firearm injuries, such as suicide and unintentional shootings, as well as theft. Various firearm locking devices exist; however, little is known about firearm owners’ preferred locking devices for secure firearm storage. In this systematic review, we examined existing literature on preferred locking devices for secure storage of personal firearms among United States (US) firearm owners with the purpose of understanding practical implications and needs for future research.

Methods
We searched 8 major databases, as well as the grey literature, for English-language sources published on or before January 24, 2023, that empirically examined firearm locking device preferences. Following PRISMA guidelines, coders independently screened and reviewed 797 sources using pre-determined criteria. Overall, 38 records met inclusion criteria and were included in this review.

Results
The majority of studies measure and report on participant use of various types of locking devices, but few go on to measure preference between device options and the attributes and features that may contribute to an individual’s preference. Included studies suggest that a preference for larger devices, such as lockboxes and gun safes, may exist among US firearm owners.

Conclusions
Review of included studies suggests that current prevention efforts may not be aligned with firearm owners’ preferences. Additionally, findings from this systematic review emphasize the need for additional methodological rigorous research to understand firearm locking device preferences. Expanded knowledge in this area will result in actionable data and foundational best practices for programming that encourages behavior change concerning secure storage of personal firearms to prevent injury and death.
Identification of the barriers and enablers for receiving a speaking up message: a content analysis approach
Authors: Barlow Melanie , Morse Kate J. , Watson Bernadette , Maccallum Fiona 
Published: July 2023

AbstractBackgroundWithin healthcare, the barriers and enablers that influence clinicians’ ability to speak up are well researched. However, despite the receiver of the message being identified as a key barrier to a speaker voicing a concern, there have been very few receiver-focused studies. As a result, little is known about the barriers and enablers that influence message reception. Understanding these can help inform speaking up training and ultimately enhance patient safety through more effective clinical communication.ObjectivesTo identify enabling or inhibiting factors that influence the receiver’s reception and response to a speaking up message, and if the identified barriers and enablers are related to speaker or receiver characteristics.Design and methodsTwenty-two interdisciplinary simulations were video recorded and transcribed. Simulation participants formed the patient discharge team and were receivers of a speaking up message, delivered by a nurse at the patient’s bedside. How the message was delivered (verbose or abrupt wording), was manipulated and counterbalanced across the simulations. Within the post simulation debriefs, barriers and enablers of being a receiver of a message were explored using content analysis.Setting/participantsThis study took place in a large Australian tertiary healthcare setting. Participants were qualified clinicians of varying disciplines and specialties.ResultsA total of 261 barriers and 285 enablers were coded. Results showed that how the message was delivered (differing tone, phases, and manner) influenced what receivers identified as barriers and enablers. Additionally, the receiver’s own cognitive processes, such as making positive attributions of the speaker and attempting to build rapport and collegiality, better enabled message reception and response. Receiver behaviour was negatively impacted by listening to fix, rather than understand, and not knowing in the moment how to manage their own reactions and appropriately frame a response.ConclusionThe debriefings identified key barriers and enablers to receiving a speaking up message that differ from those previously identified for senders of the speaking up message. Current speaking up programs are predominately speaker centric. This study identified that both speaker and receiver behaviour influenced message reception. Therefore, training must place equal attention on both the speaker and receiver and be inclusive of experiential conversational rehearsal of both positive and challenging encounters.
Bat roosting strategies and torpor expression in a wildfire-affected landscape during summer
Authors: Doty Anna C. , Crawford Reed D. , Blakey Rachel V. 
Published: July 2023

Abstract
Background
Climate change has caused several alterations in the frequency, intensity, and severity of wildfires globally, particularly in the western United States. Wildfire can dramatically change the microclimate experienced by animals who inhabit fire-prone areas, with implications for energy expenditure, particularly for heterothermic species. Heterothermic mammals manage energy expenditure by selecting optimal microclimates and regulating their body temperature. Because bats frequently use torpor, they are a useful model organism to understand how wildfires affect heterothermic mammal communities. In 2020, Sequoia and Kings Canyon National Parks were subjected to a severe wildfire that spanned 3636 ha within the boundaries of the park. We tracked eight California myotis (Myotis californicus) captured in Sequoia National Park to 22 roost sites in a gradient of burn severities in the summer from June–August 2021. We also quantified the torpor expression of bats on this post-burn landscape by measuring the roosting skin temperature of four M. californicus captured in a fire-affected site using temperature-sensitive radio telemetry.

Results
M. californicus showed preference for taller and larger diameter trees with more exfoliating bark, although they did not show preference for whether individual trees were burned or unburned. At the roost habitat-scale, 21 out of 22 M. californicus roosts were within or < 5 m from the burn mosaic, despite availability of unburned landscape. M. californicus most frequently roosted in low-severity burned areas, as opposed to unburned or severely burned areas. Additionally, bats avoided areas without a canopy and used areas with taller trees in proportion to their availability. Myotis californicus used torpor during the coolest periods of the morning before sunrise and regularly used torpor in low-severity burn area roosts.

Conclusions
This research indicates that while fire may be beneficial to some bat species, those that are clutter-tolerant could be negatively affected by severe wildfires that cause major reductions in vegetative complexity. Bats in our study appear to use both habitat selection and torpor to manage their energy and water budgets. Protecting large diameter trees with exfoliating bark, like those used by bats in our study, could be key to promoting the persistence of M. californicus on this landscape as severe wildfire may reduce these roosts. In addition, restoring historical mixed-severity fire regimes, thereby creating a fire mosaic containing low severity burned areas, may be critical for maintaining both roosting and foraging habitat suitable for our study species in the fire-adapted coniferous forests of North America’s Sierra Nevada.
Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps
Authors: Zhang Yong-Jie , Fan Xiang-Ping , Li Jia-Ni , Zhang Shu 
Published: July 2023

AbstractCordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.
A survey of the workplace experiences of police force employees who are autistic and/or have attention deficit hyperactivity disorder
Authors: Tromans Samuel J. , Drewett Alison , Lee Paul H. , O'Reilly Michelle 
Published: July 2023

Background
There has been little focus on autism and attention-deficit hyperactivity disorder (ADHD) in occupational groups, particularly in high-demand roles such as the police.

Aims
To describe the characteristics and experiences of UK-based police force employees who are autistic and/or have ADHD, including the benefits and challenges their conditions bring to their occupation, their need for reasonable adjustments, and their co-occurring mental illnesses.

Method
An online survey was developed, containing both quantitative and qualitative elements. Survey invitations were disseminated through the National Police Autism Association. The survey was open from 23 April to 23 July 2022.

Results
A total of 117 participants participated in the survey, including 66 who were autistic and 51 with ADHD. Participants who were autistic and/or had ADHD widely reported both benefits and challenges related to their condition(s) in policing work. Both the autistic and ADHD groups widely reported having requested workplace adjustments related to their condition(s), although these were frequently not made. Anxiety (n = 57; 49%) and depression (n = 40; 36%) were both highly prevalent among the participants.
The qualitative findings identified four themes: (a) motivations for taking on this career, (b) rewards of the role, (c) challenges of the job and (d) challenges regarding career progression.

Conclusions
Police force employees who are autistic and/or have ADHD reported that their conditions provided both benefits and challenges with respect to policing work, and that they had requested related workplace adjustments, although such adjustments frequently do not take place. Healthcare professionals need to recognise the importance of workplace considerations and advocacy for people who are autistic and/or have ADHD.
Hybridity and the Domestication of Wildness: Creating the Paco-vicuña in Early Nineteenth-Century Peru
Authors: Stephenson Marcia 
Published: July 2023

AbstractOn August 29, 1846, Peruvian president Ramón Castilla issued a decree honoring Juan Pablo Cabrera, an interim priest from the Macusani district of Puno. The decree recognized the priest's long-standing endeavor to cross the wild vicuña with the domesticated alpaca. The exquisite quality of the fiber and the tractable nature of this new hybrid animal gave rise to the hope that it might become a valuable resource, and therefore Peru was indebted to the priest and his service on behalf of the young republic. This essay examines Cabrera's venture, the creation of the paco-vicuña, and its emergence onto the national and international scene in the 1840s. Cabrera's paco-vicuña endeavor highlights the importance of local ventures, knowledge, and expertise, and shows how these were deeply entangled in contemporary intellectual and political projects, especially those concerning mestizaje and nation formation, as well as international scientific and economic interests of the time.
Eligibility for obesity management in Peru: Analysis of National Health Surveys from 2014 to 2022
Authors: Bernabe-Ortiz Antonio , Carrillo-Larco Rodrigo M. 
Published: July 2023

Background: The prevalence of overweight and obesity has increased fastest in low- and middle-income countries in the last decades. Together with this rising prevalence, pharmacological and surgical interventions for obesity have emerged. How many people need these treatments is unknown. We quantified the prevalence of people in need of pharmacological and surgical treatment for obesity in Peru between 2014 and 2022. Methods: Repeated cross-sectional analysis of national health surveys in Peru was conducted. Eligibility for pharmacological treatment for obesity was: body mass index (BMI) ≥30 kg/m2 or BMI ≥27 kg/m2 alongside type 2 diabetes or hypertension (self-reported). Eligibility for bariatric surgery were BMI ≥40 kg/m2 or BMI between 35 to 39.9 kg/m2 linked to weight-related health problems. We used Poisson regressions to identify associated factors with eligibility for obesity management. Results: Across years, 260,131 people (mean age 44.0 and 54.5% were women) were studied, 66,629 (27.7%; 95% CI: 27.4% - 28.1%) were eligible for obesity medication, and 5,263 (2.5%; 95% CI: 2.4% - 2.6%) were eligible for bariatric surgery. Female sex, older age, higher socioeconomic level and study year were associated with higher probability of eligibility for both obesity medication and bariatric surgery. Conclusions: Eligibility for obesity management has increased over time in Peru. There is a need to strengthen policies to tackle overweight and obesity in Peru, acknowledging that some individuals may benefit from pharmacological and surgical interventions.
The Impact of a Supreme Court Decision on the Preferences of Americans Regarding Abortion Policy
Authors: Thomadsen Raphael , Zeithammer Robert , Yao Song 
Published: July 2023

We examine the effect of a U.S. Supreme Court decision regarding abortion laws on Americans’ preferences for political candidates. The decision was leaked in advance of the official announcement, and we track the evolution of political preferences from before to after the leak and, eventually, to after the formal announcement. The abortion issue was already very important to voters before the leak, but the Court’s decision did not simply make it more important for everyone. We find that the decision decreased the importance weight of abortion for Republicans, while increasing it for independents/nonvoters. Further, the decision increased Republican support for candidates who want to ban abortions although this effect is diminished for candidates that oppose exceptions for rape, incest, or the mother’s health. Nonaffiliated voters move sharply away from candidates who want to ban abortions without exceptions. The decision also resulted in a lasting polarization along gender lines whereby men became more likely to vote for a candidate that supports a ban on abortion, while women are less likely to support candidates that ban abortions. This paper was accepted by David Simchi-Levi, marketing. Supplemental Material: The data files are available at https://doi.org/10.1287/mnsc.2023.4802 .