bluuebunny/crossref_metadata_2025_split huggingface dataset:
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap
Authors: Lapp Zena , Abel Lucy , Mangeni Judith , Obala Andrew A. , O'Meara Wendy P. , Taylor Steve M. , Markwalter Christine F. 
Published: December 2023

Abstract

Measuring vector–human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector‐borne diseases. One approach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs). Existing methods for matching STR profiles in bloodmeals to the people bitten preclude the ability to match most incomplete profiles and multisource bloodmeals to bitten individuals.

We developed bistro, an R package that implements three pre‐existing STR matching methods as well as the package's namesake, bistro, a new algorithm described here. bistro employs forensic analysis methods to calculate likelihood ratios and match human STR profiles in bloodmeals to people using a dynamic threshold. We evaluated the algorithm's accuracy and compared it to existing matching approaches using a publicly available panel of 188 single‐source and 100 multisource samples containing DNA from 50 known human sources. Then, we applied it to match 777 newly field‐collected mosquito bloodmeals to a database of 645 people.

The R package implements four STR matching algorithms in user‐friendly functions with clear documentation. bistro correctly matched 99% (187/188) of profiles in single‐source samples, and 62% (224/359) of profiles from multisource samples, resulting in a sensitivity of 0.75 (vs. <0.51 for other algorithms). The specificity of bistro was 0.9998 (vs. 1 for other algorithms). Furthermore, bistro identified 79% (720/906) of all possible matches for field‐derived mosquitoes, yielding 1.4× more matches than existing algorithms.

bistro identifies more correct bloodmeal–human matches than existing approaches, enabling more accurate and robust analyses of vector–human contact in natural settings. The bistro R package and corresponding documentation allow for straightforward uptake of this algorithm by others.
Review article: Advances in the management of lower gastrointestinal bleeding
Authors: Alali Ali A. , Almadi Majid A. , Barkun Alan N. 
Published: December 2023

SummaryBackgroundLower gastrointestinal bleeding (LGIB) is a common emergency with substantial associated morbidity and mortality. Elective colonoscopy plays an essential role in management, with an even more important role for radiology in the acute setting. Recent advances in the management of patients with LGIB warrant review as the management has recently evolved.AimsTo provide a comprehensive and updated overview of advances in the approach to patients with LGIBMethodsWe performed a comprehensive literature search to examine the current data for this narrative review supplemented by expert opinion.ResultsThe incidence of LGIB is increasing worldwide, partly related to an ageing population and the increasing use of antithrombotics. Diverticulosis continues to be the most common aetiology of LGIB. Pre‐endoscopic risk stratification tools, especially the Oakland score, can aid appropriate patient triage. Adequate resuscitation continues to form the basis of management, while appropriate management of antithrombotics is crucial to balance the risk of worsening bleeding against increased cardiovascular risk. Radiological imaging plays an essential role in the diagnosis and treatment of acute LGIB, especially among unstable patients. Colonoscopy remains the gold‐standard test for the elective management of stable patients.ConclusionsThe management of LGIB has evolved significantly in recent years, with a shift towards radiological interventions for unstable patients while reserving elective colonoscopy for stable patients. A multidisciplinary approach is essential to optimise the outcomes of patients with LGIB.
Drivers of variation in postpartum opioid prescribing across hospitals participating in a statewide maternity care quality collaborative
Authors: Peahl Alex F. , Low Lisa Kane , Langen Elizabeth S. , Moniz Michelle H. , Aaron Bryan , Hu Hsou Mei , Waljee Jennifer , Townsel Courtney 
Published: December 2023

AbstractBackgroundWe describe variation in postpartum opioid prescribing across a statewide quality collaborative and assess the proportion due to practitioner and hospital characteristics.MethodsWe assessed postpartum prescribing data from nulliparous, term, singleton, vertex births between January 2020 and June 2021 included in the clinical registry of a statewide obstetric quality collaborative funded by Blue Cross Blue Shield of Michigan. Data were summarized using descriptive statistics. Mixed effect logistic regression and linear models adjusted for patient characteristics and assessed practitioner‐ and hospital‐level predictors of receiving a postpartum opioid prescription and prescription size. Relative contributions of practitioner and hospital characteristics were assessed using the intraclass correlation coefficient.ResultsOf 40,589 patients birthing at 68 hospitals, 3.0% (872/29,412) received an opioid prescription after vaginal birth and 87.8% (9812/11,177) received one after cesarean birth, with high variation across hospitals. In adjusted models, the strongest patient‐level predictors of receiving a prescription were cesarean birth (aOR 899.1, 95% CI 752.8–1066.7) and third−/fourth‐degree perineal laceration (aOR 25.7, 95% CI 17.4–37.9). Receiving care from a certified nurse‐midwife (aOR 0.63, 95% CI 0.48–0.82) or family medicine physician (aOR 0.60, 95%CI 0.39–0.91) was associated with lower prescribing rates. Hospital‐level predictors included receiving care at hospitals with <500 annual births (aOR 4.07, 95% CI 1.61–15.0). A positive safety culture was associated with lower prescribing rates (aOR 0.37, 95% CI 0.15–0.88). Much of the variation in postpartum prescribing was attributable to practitioners and hospitals (prescription receipt: practitioners 25.1%, hospitals 12.1%; prescription size: practitioners 5.4%, hospitals: 52.2%).DiscussionVariation in postpartum opioid prescribing after birth is high and driven largely by practitioner‐ and hospital‐level factors. Opioid stewardship efforts targeted at both the practitioner and hospital level may be effective for reducing opioid prescribing harms.
Anti‐PL‐7, anti‐Ro/SSA, anti‐Mi‐2, and anti‐TIF1‐γ correlate with specific patterns of histopathologic features in dermatomyositis: An analysis of 39 skin biopsy specimens from 25 patients
Authors: Bennett Raven , Bradley Katherine , Stevanovic Mirjana , McFadden Jason R. , Chaudhari Advaita S. , Ramos‐Rodriguez Alvaro J. , Yan Shaofeng , Momtahen Shabnam , LeBlanc Robert E. , Cloutier Jeffrey M. , Salem Iman , Grand David G. , Hodson Emma L. , Sriharan Aravindhan 
Published: December 2023

AbstractBackgroundIn dermatomyositis (DM), myositis‐specific and myositis‐associated antibodies have been correlated with clinical features. It is unknown if histopathologic findings in lesional skin biopsies correlate with serologic subtypes of DM.MethodsA retrospective chart review of patients with DM was performed. Patients with myositis antibodies and DM lesional skin biopsies were included in the study. Skin biopsies were reviewed by blinded dermatopathologists for 20 histopathologic features.ResultsThere was a statistically significant (p < 0.05) association between anti‐PL‐7 serology and decreased degree of vacuolar degeneration, necrotic keratinocytes, and thickening of the epidermal basement membrane. Anti‐aminoacyl tRNA synthetase (anti‐ARS) antibodies had the same significant negative association with degree of vacuolar degeneration, necrotic keratinocytes, and thickening of the epidermal basement membrane. A similar pattern was seen with an anti‐cytoplasmic serology; where there was a significant association with an increased degree of vacuolar degeneration and necrotic keratinocytes, and a nonsignificant trend of minimally thickened epidermal basement membrane. There was a statistically significant association between anti‐Ro/SSA serology and increased degree of vacuolar degeneration. Anti‐TIF1‐γ serology was significantly associated with the increased presence of necrotic keratinocytes and pigment incontinence, and displayed a pattern of increased neutrophils. There was a significant association between anti‐Mi‐2 antibodies and pigment incontinence, as well as between myositis‐specific antibodies and pigment incontinence. A statistically significant positive association was found between nuclear antibodies and degree of vacuolar degeneration, thickened epidermal basement membrane, pigment incontinence, and epidermal atrophy.ConclusionIn patients with DM, some specific serotypes, including anti‐PL‐7, anti‐Ro/SSA, anti‐Mi‐2, and anti‐TIF1‐γ, may have characteristic histopathologic features.
The Coastal Carbon Library and Atlas: Open source soil data and tools supporting blue carbon research and policy
Authors: Holmquist James R. , Klinges David , Lonneman Michael , Wolfe Jaxine , Boyd Brandon , Eagle Meagan , Sanderman Jonathan , Todd‐Brown Kathe , Belshe E. Fay , Brown Lauren N. , Chapman Samantha , Corstanje Ron , Janousek Christopher , Morris James T. , Noe Gregory , Rovai André , Spivak Amanda , Vahsen Megan , Windham‐Myers Lisamarie , Kroeger Kevin , Megonigal J. Patrick 
Published: December 2023

AbstractQuantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous ‘blue carbon’ studies have generated, or benefitted from, synthetic datasets. However, the community those efforts inspired does not have a centralized, standardized database of disaggregated data used to estimate carbon stocks and fluxes. In this paper, we describe a data structure designed to standardize data reporting, maximize reuse, and maintain a chain of credit from synthesis to original source. We introduce version 1.0.0. of the Coastal Carbon Library, a global database of 6723 soil profiles representing blue carbon‐storing systems including marshes, mangroves, tidal freshwater forests, and seagrasses. We also present the Coastal Carbon Atlas, an R‐shiny application that can be used to visualize, query, and download portions of the Coastal Carbon Library. The majority (4815) of entries in the database can be used for carbon stock assessments without the need for interpolating missing soil variables, 533 are available for estimating carbon burial rate, and 326 are useful for fitting dynamic soil formation models. Organic matter density significantly varied by habitat with tidal freshwater forests having the highest density, and seagrasses having the lowest. Future work could involve expansion of the synthesis to include more deep stock assessments, increasing the representation of data outside of the U.S., and increasing the amount of data available for mangroves and seagrasses, especially carbon burial rate data. We present proposed best practices for blue carbon data including an emphasis on disaggregation, data publication, dataset documentation, and use of standardized vocabulary and templates whenever appropriate. To conclude, the Coastal Carbon Library and Atlas serve as a general example of a grassroots F.A.I.R. (Findable, Accessible, Interoperable, and Reusable) data effort demonstrating how data producers can coordinate to develop tools relevant to policy and decision‐making.
Metastatic potentials classified with hypoxia‐inducible factor 1 downstream genes in pan‐cancer cell lines
Authors: Nakamichi Kazuya , Yamamoto Yusuke , Semba Kentaro , Nakayama Jun 
Published: December 2023

AbstractHypoxia‐inducible factor 1 (HIF1) is a transcription factor that is stabilized under hypoxia conditions via post‐translational modifications. HIF1 regulates tumor malignancy and metastasis by gene transcriptions, such as Warburg effect and angiogenesis‐related genes, in cancer cells. However, the HIF1 downstream genes show varied expressional patterns in different cancer types. Herein, we performed the hierarchical clustering based on the HIF1 downstream gene expression patterns using 1406 cancer cell lines crossing 30 types of cancer to understand the relationship between HIF1 downstream genes and the metastatic potential of cancer cell lines. Two types of cancers, including bone and breast cancers, were classified based on HIF1 downstream genes with significantly altered metastatic potentials. Furthermore, different HIF1 downstream gene subsets were extracted to discriminate each subtype for these cancer types. HIF1 downstream subtyping classification will help to understand the novel insight into tumor malignancy and metastasis in each cancer type.
Refractory alopecia areata with single hairs imitating frontal fibrosing alopecia: a prospective observational study
Authors: Qiao Rui , Zhu Jiaping , Liu Yi , Zhao Xiaohui , Nie Jin , Lan Xuemei , Li Yufen , Jiang Yiqun 
Published: December 2023

AbstractBackgroundLonely hair sign is considered as a clue to the diagnosis of frontal fibrosing alopecia (FFA).ObjectiveTo report an undescribed variant of alopecia areata (AA) with which the patient developed single hairs and other features similar to FFA and to determine the underlying mechanism.MethodsWe conducted a prospective observational study in patients who presented with receding hairline and single hairs, evaluating the clinical, trichoscopic, and histological features and their correlation. Immunochemistry studies were performed to describe the microenvironment.ResultsEighteen patients were enrolled in the study. Despite the similarity to FFA clinically, these patients showed different histopathology which revealed a normal number of pilosebaceous units, one anagen hair in one or more pilosebaceous units, and others in telogen stage, consistent with single hairs under the naked eye or under trichoscopy. The severity of the hair loss assessed by SALT was no more than 50, but the response to conventional therapy was poor.ConclusionsThis study reports a unique variant of AA. The pathological basis is an increase in the telogen hair follicles, with one anagen hair in one or more pilosebaceous units. Minimal inflammation consisting of CD3+ T lymphocytes and mast cells was demonstrated in the microenvironment.
Australian clinicians' perceptions of patients with very high risk of fracture
Authors: Girgis Christian M. , Choi Yoonah , Ebeling Peter R. 
Published: December 2023

AbstractBackgroundInternational osteoporosis guidelines have recommended treatment approaches based on fracture risk stratification, in particular, anabolic therapy for patients with very high risk (VHR) of fragility fracture.AimTo summarise Australian clinicians' perceptions of patients at VHR of fracture.MethodsAustralian clinicians invited to educational webinars on anabolic treatments for osteoporosis were surveyed in March and April 2021 about a typical patient they had most recently seen and identified as at VHR of fracture.ResultsOf the 268 clinician attendees who were invited to complete the post‐webinar surveys, 67 (25%) responded and permitted the publication of aggregated data. A typical patient perceived to have a VHR of fracture was a woman in her 80's, living at home, who had been diagnosed with osteoporosis between 5 and 10 years ago, and received treatment for 1–5 years' duration, most commonly denosumab. The patient frequently had a T‐score below −3.0 SD (standard deviation), multiple fragility fractures and most commonly suffered a vertebral fracture in the past 12 months, whereas on an adequate regimen of osteoporosis medication. There was a mismatch between the patient being eligible for anabolic therapy (64.2%) and actually having been prescribed an anabolic treatment in the past (20.9%).ConclusionsAustralian clinicians' perceptions of patients with a VHR of fracture and the use of anabolic agents appear to be heavily influenced by local reimbursement criteria. The mismatch between patients deemed eligible for reimbursed anabolic therapy and those prescribed an anabolic agent suggests treatment inertia.
Pre‐service teacher knowledge of children's literature and attitudes to Reading for Pleasure: an international comparative study
Authors: Farrar Jennifer , Simpson Alyson 
Published: December 2023

AbstractReading for Pleasure (RfP) acknowledges the importance of reader engagement and the role of the teacher as a reader of children's literature. The foundational work of the Teachers as Readers (TARs) programme successfully illustrated the impact of RfP activities on student learning. Previous studies of teachers' reader identities have shown a strong need for professional learning to boost teachers' confidence with children's literature. However, less emphasis has been placed on the adoption of RfP pedagogy within initial teacher education (ITE) to develop pre‐service teachers' (PST) knowledge of children's literature, as well as their understanding of teachers as reading role models for future students. This paper analyses data from research into RfP undertaken in two ITE programmes for primary teachers informed by contrasting policies in Scotland and Australia. Though both countries aim to improve school student literacy success, the curriculum mandates differ, shaping the potential pathways available in ITE courses. It is within this context that we report on 3 years of data on PST reader knowledge collected from 300 students using survey tools adopted from the original TARs study. Emerging findings provide evidence that teacher educators need to act as circuit breakers to alter PST attitudes to reading.
Smart dynamic evacuation planning and online management using vehicular communication system
Authors: Idoudi Hassan , Ameli Mostafa , Nguyen Van Phu Cyril , Zargayouna Mahdi , Rachedi Abderrezak 
Published: December 2023

AbstractDuring disasters, swiftly and efficiently evacuating populations in hazardous situations is crucial to minimize losses. This study proposes a novel framework to address dynamic population evacuation (DPE) problems, which includes planning and online evacuation management phases facilitated by vehicular communication. In the planning phase, a shelter allocation problem (SAP) is solved dynamically for destination choice and a dynamic traffic assignment (DTA) for path choice toward the chosen destinations to obtain an initial evacuation plan. The initial plan is then enhanced by employing a vehicular ad hoc network (VANET) within the vehicular edge computing (VEC) architecture. This enhancement enables communication among evacuees, allowing them to revise their vehicle's route choice and planned destination. These revisions take into account the changing risk and traffic conditions. The proposed online DPE framework is applied to the real evacuation scenario of Mill Valley City, CA. The proposed model is evaluated with different VANET architectures, including vehicular cloud computing (VCC) and VEC. The results show that the VEC framework outperforms other configurations and improves the evacuation process compared to the scenario with an initial plan by more than 30% in network clearance time. Additionally, a performance analysis is carried out for evacuation scenarios with different penetration rates of connected vehicles in VANET.
Skin cancer prevention in extreme sports: Intervention in a 24‐h race
Authors: Martínez Alba Rodríguez , Pardal Carmen Vaz , Arjona José Aguilera , Ruiz Francisco Rivas , Molinero Diego Doncel , Paulano Manuel Ruiz , Subert Andras , Manzanedo Jose Vicente Gutiérrez , Cambil Martín Jacobo , de Gálvez Aranda Maria Victoria , López Leocricia Jiménez , Sánchez Nuria Blázquez , de Troya Martín Magdalena 
Published: December 2023

AbstractIntroductionExcessive sun exposure and sunburns are the main preventable causes of skin cancer. The growing popularity of outdoor sports in developed countries has motivated the objective of this work to study the risk of photoexposure and the skin cancer prevention needs of athletes in an extreme race and evaluate an intervention targeted at this population.MethodsAn observational study was conducted during the XXIII edition of the 101 km de Ronda race, which consisted of trail running and mountain biking categories. Environmental and personal dosimetry, monitoring of meteorological conditions, evaluation of the athletes' photoprotection and skin examination habits, a dermatological checkup, and a satisfaction questionnaire were performed.ResultsThe ultra‐endurance race was carried out under adverse conditions (maximum ultraviolet index (UVI) = 9.2, temperatures above 30°C, and relative humidity >35%). The mean effective erythema dose received by race athletes (n = 11) was 2959.2 ± 404.2 J/m2, equivalent to 29.6 standard erythema doses (SED). The CHACES questionnaire (n = 1145) showed a sunburn rate of 58% and poor protective habits: 62.9% of athletes do not usually use sunscreen and 67.2% do not self‐examine their skin. Actinic keratoses (4.7%) and suspicious skin cancer lesions (4.2%) were found in dermatologic screening exams (n = 170). On the satisfaction questionnaire (n = 111), this intervention was rated as excellent (95.5%).ConclusionThis research highlights the extreme risk of photoexposure that athletes are subjected to during ultra‐endurance competitions. In the same way, it shows the need to carry out interventions aimed at the acquisition of healthy photoprotection habits and skin surveillance in this target group.
Phylogeny and taxonomy of five species associated with apricot canker in Beijing, China
Authors: Bai Yukun , Pan Meng , Lin Lu , Fan Xinlei 
Published: December 2023

AbstractApricot (Prunus armeniaca) is an economically important fruit tree in Beijing, China. However, canker diseases have become one of the main threats to apricot production. In the present study, a field survey was conducted in apricot orchards in Beijing and the disease incidence of apricots was surveyed (75.7%). Thirty fungal strains were isolated from branches of apricots. Five species were identified through multilocus phylogenetic (rDNA internal transcribed spacer [ITS], large subunit [LSU] and tef1‐a for Botryosphaeriales; ITS, act, rpb2, tef1‐a and tub2 for Cytospora) and morphological analyses, including two new species (Cytospora huairouensis and C. prunina) and three known species (C. leucostoma, Diplodia gallae and Phaeobotryon rhois). C. leucostoma and P. rhois were identified as the causal agents of canker of apricot by pathogenicity tests conducted on 3‐year‐old plants in the greenhouse. The current study contributed to a theoretical basis for predicting the potential risk of apricot canker in Beijing, China.
Employment transitions and COVID‐19 containment measures: Evidence from a developing country
Authors: Oyenubi Adeola 
Published: December 2023

AbstractContainment measures implemented to curb the spread of coronavirus (COVID‐19) disrupted labour markets across the world. While several studies focus on the impact of containment measures on job losses, this paper documents the effect of containment measures (specifically variation in the strictness of these measures) on employment patterns or transitions. COVID disruption can be viewed as multiple shocks to the labour market (as against a single shock). This is important because labour income is a key driver of aggregate inequality in developing countries, and such disruption has a knock‐on effect on the achievement of the Sustainable Development Goals. Therefore, we estimate the causal relationship between coronavirus containment measures and employment dynamics in South Africa. Exploiting the timing of interviews and within individual variation, we find that containment measures impact employment transitions. Specifically, stricter containment measures have a positive effect on the transition into unemployment, and the converse is true for the transition into employment. The implication of this causal relationship for development, ongoing management of COVID‐19 and future pandemics is discussed.