bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnomycological study on wild mushrooms in Pu’er Prefecture, Southwest Yunnan, China
Authors: Wang Ran , Herrera Mariana , Xu Wenjun , Zhang Peng , Moreno Jesús Pérez , Colinas Carlos , Yu Fuqiang 
Published: August 2022

Abstract
Background
Yunnan is rich in fungal diversity and cultural diversity, but there are few researches on ethnomycology. In addition, extensive utilization of wild edible fungi (WEF), especially the ectomycorrhizal fungi, threatens the fungal diversity. Hence, this study aims to contribute to the ethnomycological knowledge in Pu’er Prefecture, Yunnan, China, including information on the fungal taxa presented in markets and natural habitats, with emphasis in ectomycorrhizal fungi (EMF).

Methods
Semi-structured interviews with mushroom vendors in markets and with mushroom collectors in natural habitats were conducted. Information related to local names, habitat, fruiting time, species identification, price, cooking methods and preservation methods of wild edible mushrooms were recorded. Wild edible fungi were collected from forests, and morphological and molecular techniques were used to identify fungal species.

Results
A total of 11 markets were visited during this study. The 101 species collected in the markets belonged to 22 families and 39 genera, and about 76% of them were EMF. A wealth of ethnomycological knowledge was recorded, and we found that participants in the 45–65 age group were able to judge mushroom species more accurately. Additionally, men usually had a deepest mushroom knowledge than women. A total of 283 species, varieties and undescribed species were collected from natural habitats, and about 70% of them were EMF. Mushroom species and recorded amounts showed correspondence between markets and the natural habitats on different months.

Conclusion
The present study shows that Pu’er Prefecture is rich in local mycological knowledge and fungal diversity. However, it is necessary to continue the research of ethnomycological studies and to design and conduct dissemination of local knowledge in order to preserve it, since it currently remains mainly among the elderly population.
REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
Authors: Dolzhenko Egor , Weisburd Ben , Ibañez Kristina , Rajan-Babu Indhu-Shree , Anyansi Christine , Bennett Mark F. , Billingsley Kimberley , Carroll Ashley , Clamons Samuel , Danzi Matt C. , Deshpande Viraj , Ding Jinhui , Fazal Sarah , Halman Andreas , Jadhav Bharati , Qiu Yunjiang , Richmond Phillip A. , Saunders Christopher T. , Scheffler Konrad , van Vugt Joke J. F. A. , Zwamborn Ramona R. A. J. ,   Genomics England Research Consortium, Chong Samuel S. , Friedman Jan M. , Tucci Arianna , Rehm Heidi L. , Eberle Michael A. 
Published: August 2022

AbstractBackgroundExpansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads.ResultsWe implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions and FlipBook, a companion image viewer designed for manual curation of large collections of REViewer images. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in short tandem repeat research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically relevant repeat interruptions by comparing visual assessment results of 44FMR1repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR.ConclusionsRead pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer and FlipBook to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions. REViewer and FlipBook are available under open-source licenses athttps://github.com/illumina/REViewerandhttps://github.com/broadinstitute/flipbookrespectively.
Minimum acceptable diet and associated factors among children aged 6–23 months during fasting days of orthodox Christian mothers in Gondar city, North West Ethiopia
Authors: Birhanu Haregewoin , Gonete Kedir Abdela , Hunegnaw Melkamu Tamir , Aragaw Fantu Mamo 
Published: August 2022

Abstract
Background
Nutritional improvement through appropriate feeding practices is critical for young children's healthy growth and development. Even if children are exempted from fasting, their diets are influenced by the widespread fasting practices of their Orthodox Christian mothers. However, scientific evidence on a minimum acceptable diet (MAD) among children aged 6–23 months during the fasting period was limited. Therefore, this study aimed to assess the minimum acceptable diet and associated factors among children aged 6–23 months during the fasting period among Orthodox Christian mothers in Gondar city, Northwest Ethiopia.

Method
A community-based cross-sectional study was conducted during the fasting season (Lent) from March 8, 20,121 to April 8, 2021. A total of 738 Orthodox Christian mothers with their children were selected by multistage sampling. A structured questionnaire was used to collect data among mothers to assess children’s MAD status. The degree of association between independent and dependent variables was assessed by using an odds ratio with a 95% confidence interval. Those variables with a p-value of less than 0.05 in the multivariable analysis were considered as a significant factor for MAD among children aged 6–23 months. Data were presented using texts, tables and figures.

Results
The overall prevalence of MAD among children aged 6–23 months was 19.4% (95% CI: 16.40%-22.20). Having household wealth index of rich and middle (AOR = 4.39, 95% CI: 2.26,8.50) and (AOR = 3.25, 95% CI: 1.69,6.22), respectively, children aged from 12–17 months (AOR = 2.66, 95% CI: 1.43,4.92) and 18–23 months (AOR = 5.39, 95% CI: 2.93,9.95) respectively, Children who lived with a family member who consumed any time without keeping the fasting time(AOR = 1.79, 95% CI: 1.13,2.83) and mothers of young children who were married (AOR = 4.13, 95% CI: 1.29,13.23) have significant association with MAD.

Conclusion
The practice of minimum acceptable diet was inadequate. Age of child, wealth status, marital status, and presence of family member who fed without keeping fasting time were significantly associated factors for MAD among children aged 6–23 months. Advocacy for appropriate feeding practice and meeting the MAD for children aged 6–23 months during the fasting period should also be strengthened targeting the unmarried women and those with poor households and giving awareness for mothers in collaboration with the respective religious leaders is highly recommended.
Corpus-based analysis of near-synonymous verbs
Authors: Alanazi Zaha 
Published: August 2022

AbstractDespite having different semantic profiles, near synonyms are usually presented in dictionaries as being contextually interchangeable, which may lead EFL learners to assume their contextual interchangeability. Nevertheless, there is a scarcity of studies on how near synonyms are similar or different in their semantic and grammatical preferences. To enrich the literature on near synonyms’ semantic and grammatical profiles, this study explores the collocational behaviors and the semantic preferences of the near-synonymous verbs (affectvs.impact). Sketch Engine was used to examine lexical collocates, the colligational profile and the semantic prosody of the two verbs. The findings revealed fine-grained contextual differences in their collocational, grammatical, and semantic preferences. Applications of the findings for English language teaching will be discussed a long with recommendations for future research.
Cost-Related Medication Nonadherence and Patient Cost Responsibility for Rural and Urban Cancer Survivors
Authors: Williams Courtney P. , Davidoff Amy , Halpern Michael T. , Mollica Michelle , Castro Kathleen , Allaire Benjamin , de Moor Janet S. 
Published: August 2022

PURPOSE: The relationship between out-of-pocket spending and cost-related medication nonadherence among older rural- and urban-dwelling cancer survivors is not well understood. METHODS: This retrospective cohort study used the Surveillance, Epidemiology, and End Results Program, Medicare claims, and the Consumer Assessment of Healthcare Providers and Systems survey linked data resource linked data (2007-2015) to investigate the relationship between cancer survivors' cost responsibility in the year before and after report of delaying or not filling a prescription medication because of cost in the past 6 months (cost-related medication nonadherence). Secondary exposures and outcomes included Medicare spending and utilization. Generalized linear models assessed bidirectional relationships between cost-related medication nonadherence, spending, and utilization. Effects of residence were assessed via interaction terms. RESULTS: Of 6,591 older cancer survivors, 13% reported cost-related medication nonadherence. Survivors were a median 8 years (interquartile range, 4.5-12.5 years) from their cancer diagnosis, 15% were dually Medicare/Medicaid-eligible, and prostate (40%) and breast (32%) cancer survivors were most prevalent. With every $500 USD increase in patient cost responsibility, risk of cost-related medication nonadherence increased by 3% (risk ratio, 1.03; 95% CI, 1.02 to 1.04). After report of cost-related medication nonadherence, patient cost responsibility was 22% higher (95% CI, 1.11 to 1.32) compared with those not reporting nonadherence, amounting to $523 USD (95% CI, $430 USD to $630 USD). Medicare spending and utilization were also higher before and after report of cost-related nonadherence versus none. For survivors residing in rural (18%) and urban (82%) areas, residence did not modify adherence or cost outcomes. CONCLUSION: A bidirectional relationship exists between patient cost responsibility and cost-related medication nonadherence. Interventions reducing urban- and rural-dwelling survivor health care costs and cost-related adherence barriers are needed.
Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 and Subsequent Mortality in a Multisite Cohort of Patients With Cancer in the CancerLinQ Discovery Database
Authors: Ray Emily M. , Riffon Mark F. , Kakamada Sirisha , Miller Robert S. , Potter Danielle 
Published: August 2022

PURPOSE: Understanding risks for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent mortality among patients with cancer may help inform treatment decisions during the COVID-19 pandemic. METHODS: CancerLinQ is an electronic health record database from US oncology practices. We identified a cohort of patients with malignancy and 2+ encounters at CancerLinQ practices in the 12 months before the study period (January 1, 2020-January 31, 2021). We identified a SARS-CoV-2 subcohort as having a positive SARS-CoV-2 test or International Classification of Diseases, 10th Revision, code. We examined predictors of SARS-CoV-2 infection and mortality including sex, race, ethnicity, age, malignancy type, and prior therapy. Unadjusted and adjusted incidence rate ratios (aIRRs) and 95% CIs were estimated from Poisson regression models for SARS-CoV-2 infections and mortality. RESULTS: The cancer cohort included 629,128 patients, and the SARS-CoV-2 subcohort included 12,300 patients. Higher incidence of SARS-CoV-2 was seen among patients who were male (incidence rate ratio [IRR], 1.14; 95% CI, 1.10 to 1.18), Black (IRR, 1.48; 95% CI, 1.41 to 1.56), Hispanic (IRR, 2.02; 95% CI, 1.91 to 2.14), age < 50 years (IRR, 1.34; 95% CI, 1.26 to 1.42), with hematologic malignancies (IRR, 1.07; 95% CI, 1.02 to 1.12), and with recent chemotherapy (IRR, 1.30, 95% CI, 1.22 to 1.40). In the adjusted analysis, higher incidence was seen in patients who were male (aIRR, 1.17; 95% CI, 1.13 to 1.21), Hispanic (aIRR, 2.01; 95% CI, 1.88 to 2.14), and with recent chemotherapy (aIRR, 1.17; 95% CI, 1.09 to 1.25). There were 182 all-cause deaths within the SARS-CoV-2 subcohort. Higher mortality was seen among patients who were male (IRR, 1.39; 95% CI, 1.04 to 1.86), unknown race (IRR, 2.64; 95% CI, 1.42 to 4.91), other/unknown ethnicity (IRR, 1.99; 95% CI, 1.20 to 3.29), age 60-69 years (IRR, 2.76; 95% CI, 1.23 to 6.19), age 70-79 years (IRR, 5.28; 95% CI, 2.42 to 11.5), age 80+ years (IRR, 7.31; 95% CI, 3.31 to 16.1), or with recent chemotherapy (IRR, 1.52, 95% CI, 1.01 to 2.29). In the adjusted analysis, higher mortality was seen with increased age and receipt of chemotherapy. CONCLUSION: Patients with increased risk of SARS-CoV-2 infection must balance the competing risks of their cancer diagnosis/treatment and SARS-CoV-2 infection.
Multicenter Analysis of Cardiometabolic-related Diagnoses in Transgender and Gender-Diverse Youth: A PEDSnet Study
Authors: Valentine Anna , Davis Shanlee , Furniss Anna , Dowshen Nadia , Kazak Anne E , Lewis Christopher , Loeb Danielle F , Nahata Leena , Pyle Laura , Schilling Lisa M , Sequeira Gina M , Nokoff Natalie 
Published: August 2022

Abstract

Context
Studies on cardiometabolic health in transgender and gender-diverse youth (TGDY) are limited to small cohorts.

Objective
This work aimed to determine the odds of cardiometabolic-related diagnoses in TGDY compared to matched controls in a cross-sectional analysis, using a large, multisite database (PEDSnet).

Methods
Electronic health record data (2009-2019) were used to determine odds of cardiometabolic-related outcomes based on diagnosis, anthropometric, and laboratory data using logistic regression among TGDY youth vs controls. The association of gender-affirming hormone therapy (GAHT) with these outcomes was examined separately among TGDY. TGDY (n = 4172) were extracted from 6 PEDSnet sites and propensity-score matched on 8 variables to controls (n = 16 648). Main outcomes measures included odds of having cardiometabolic-related diagnoses among TGDY compared to matched controls, and among TGDY prescribed GAHT compared to those not prescribed GAHT.

Results
In adjusted analyses, TGDY had higher odds of overweight/obesity (1.2; 95% CI, 1.1-1.3) than controls. TGDY with a testosterone prescription alone or in combination with a gonadotropin-releasing hormone agonist (GnRHa) had higher odds of dyslipidemia (1.7; 95% CI, 1.3-2.3 and 3.7; 95% CI, 2.1-6.7, respectively) and liver dysfunction (1.5; 95% CI, 1.1-1.9 and 2.5; 95% CI, 1.4-4.3) than TGDY not prescribed GAHT. TGDY with a testosterone prescription alone had higher odds of overweight/obesity (1.8; 95% CI, 1.5-2.1) and hypertension (1.6 95% CI, 1.2-2.2) than those not prescribed testosterone. Estradiol and GnRHa alone were not associated with greater odds of cardiometabolic-related diagnoses.

Conclusion
TGDY have increased odds of overweight/obesity compared to matched controls. Screening and tailored weight management, sensitive to the needs of TGDY, are needed.
Comparative Effectiveness of Management by Surgical Resection vs Observation for Cerebral Cavernous Malformations: A Matched Propensity Score Analysis
Authors: Han Rowland H. , Johnson Gabrielle W. , Coxon Andrew T. , Gupta Vivek P. , Richards Matthew J. , Lancia Samantha , Salter Amber , Miller-Thomas Michelle M. , Dacey Ralph G. , Zipfel Gregory J. , Osbun Joshua W. 
Published: August 2022

BACKGROUND:
Despite increasing incidental identification of cerebral cavernous malformations (CCMs), uncertainty remains about how to best manage CCM patients.

OBJECTIVE:
To compare the outcomes of patients with surgically resected vs observed CCMs after adjusting for indication bias through propensity score matching.

METHODS:
Single-center retrospective chart review was performed on individuals treated for CCMs between 1995 and 2016 at Washington University and Barnes-Jewish Hospital. Participants underwent surgical resection (n = 54) or were observed without surgery (n = 203). Propensity score matching was used to match observed to surgical cases on characteristics at first observation or initial surgery. Time to first focal neurological deficit and mortality postinitial visit or postsurgery was estimated using a Cox proportional hazards model with robust sandwich estimators. Differences in the presence of specific follow-up symptoms were estimated using exact logistic regression.

RESULTS:
After propensity score matching, 34 matched pairs were created. The median (IQR) follow-up duration was 1.5 (0, 5) years for surgical cases and 3 (0, 5) years for observed cases. After matching, no significant differences were found for time to first focal neurological deficit (P = .37, hazard ratio [HR]: 0.76, 95% CI: 0.41, 1.39) or mortality (P = .91, HR: 0.85, 95% CI: 0.06, 12.24). No significant differences were found between the groups for seizure (P = .15, odds ratio: 0.33, 95% CI: 0.06, 1.34) or hemorrhage (P = 1.00, odds ratio 1.00, 95% CI: 0.07, 13.80).

CONCLUSION:
In this propensity scored–matched analysis, there were no significant differences between surgical or observed cases in time to focal neurological deficit, mortality, recurrent hemorrhage, or seizure.
Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants
Authors: Houston Douglas W. , Elliott Karen L. , Coppenrath Kelsey , Wlizla Marcin , Horb Marko E. 
Published: August 2022

ABSTRACT
Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions (e.g. amphibian dorsal morula, mammalian anterior visceral endoderm) require stabilised nuclear β-catenin, but the role of localised Wnt ligand signalling activity in their establishment remains unclear. In Xenopus, dorsal β-catenin is initiated by vegetal microtubule-mediated symmetry breaking in the fertilised egg, known as ‘cortical rotation’. Localised wnt11b mRNA and ligand-independent activators of β-catenin have been implicated in dorsal β-catenin activation, but the extent to which each contributes to axis formation in this paradigm remains unclear. Here, we describe a CRISPR-mediated maternal-effect mutation in Xenopus laevis wnt11b.L. We find that wnt11b is maternally required for robust dorsal axis formation and for timely gastrulation, and zygotically for left-right asymmetry. Importantly, we show that vegetal microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs. In addition, we show that activated Wnt coreceptor Lrp6 and Dishevelled lack behaviour consistent with roles in early β-catenin stabilisation, and that neither is regulated by Wnt11b. This work thus implicates Wnt11b in the distribution of putative dorsal determinants rather than in comprising the determinants themselves.
This article has an associated ‘The people behind the papers’ interview.
RRIMS: Radiation Risk In Mammography Screening – a novel model for predicting the lifetime dose and risk of radiation-induced breast cancer from the first screening visit
Authors: Hooshmand Sahand , Reed Warren M , Suleiman Mo'ayyad E , Brennan Patrick C 
Published: August 2022

Objectives:
Radiation Risk In Mammography Screening (RRIMS) builds on the prototype, formerly known as Breast-iRRISC, to develop a model that aims to establish a dose and risk profile for females by calculating their lifetime mean glandular dose (MGD) for each age of screening between 40 and 75 years, using only the information from her first screening visit. This is then used to allocate her to a dose category and estimate the lifetime risk of radiation-induced breast cancer incidence and mortality for a population of females in that category.

Methods:
This model training was developed using a large dataset of Hologic images containing a total of 20,232 images from 5,076 visits from 4,154 females. The female’s breast characteristics and exposure parameters were extracted from the images to calculate the female’s MGD throughout a lifetime of screening from just her first screening visit, using modelling of various parameters and their change through time.

Results:
This development has ultimately provided a model that uses the female’s first screening visit to calculate the received MGD for all ages of potential screening. This has enabled the allocation of females to either a low-, medium-, or high-dose category, ultimately followed by the lifetime effective risk (LER) estimation for any screening attendance pattern. A female in the low-dose category undergoing biennial screening from 50 to 74 years would expect a risk of radiation-induced breast cancer incidence and mortality of 8.64 and 2.61 cases per 100,000 females, respectively. Similarly, a female in the medium- or high-dose category undergoing the same regimen would expect an incidence and mortality risk of 11.76 and 3.55, and 15.08 and 4.55 cases per 100,000 females, respectively.

Conclusions:
This novel approach of establishing a female’s dose profile and lifetime risk from a single visit will further assist females in their informed consent on breast screening attendance and help inform policy-makers when exploring the benefits and drawbacks of various screening patterns and frequencies.

Advances in knowledge:
RRIMS is a novel tool that enables the assessment of a female’s lifetime dose and risk profile using only the information from her first screening visit.