bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health impacts of smoke exposure in South America: increased risk for populations in the Amazonian Indigenous territories
Authors: Bonilla E X , Mickley L J , Raheja G , Eastham S D , Buonocore J J , Alencar A , Verchot L , Westervelt D M , Castro M C 
Published: May 2023

Abstract
Smoke particulate matter emitted by fires in the Amazon Basin poses a threat to human health. Past research on this threat has mainly focused on the health impacts on countries as a whole or has relied on hospital admission data to quantify the health response. Such analyses do not capture the impact on people living in Indigenous territories close to the fires and who often lack access to medical care and may not show up at hospitals. Here we quantify the premature mortality due to smoke exposure of people living in Indigenous territories across the Amazon Basin. We use the atmospheric chemistry transport model GEOS-Chem to simulate PM2.5 from fires and other sources, and we apply a recently updated concentration dose-response function. We estimate that smoke from fires in South America accounted for ∼12 000 premature deaths each year from 2014–2019 across the continent, with about ∼230 of these deaths occurring in Indigenous lands. Put another way, smoke exposure accounts for 2 premature deaths per 100 000 people per year across South America, but 4 premature deaths per 100 000 people in the Indigenous territories. Bolivia and Brazil represent hotspots of smoke exposure and deaths in Indigenous territories in these countries are 9 and 12 per 100 000 people, respectively. Our analysis shows that smoke PM2.5 from fires has a detrimental effect on human health across South America, with a disproportionate impact on people living in Indigenous territories.
Characterizing the distribution of alterations in mesothelioma and their correlation to morphology
Authors: Chen-Yost Heather I-Hsuan , Tjota Melissa Y , Gao Guimin , Mitchell Owen , Kindler Hedy , Segal Jeremy , Husain Aliya N , Mueller Jeffrey , Schulte Jefree J 
Published: May 2023

Abstract

Objectives
Mesothelioma is a lethal disease that arises from the serosal lining of organ cavities. Several recurrent alterations have been observed in pleural and peritoneal ­mesotheliomas, including in BAP1, NF2, and CDKN2A. Although specific histopathologic parameters have been correlated with prognosis, it is not as well known whether genetic alterations correlate with histologic findings.

Methods
We reviewed 131 mesotheliomas that had undergone next-generation sequencing (NGS) at our institutions after pathologic diagnosis. There were 109 epithelioid mesotheliomas, 18 biphasic mesotheliomas, and 4 sarcomatoid mesotheliomas. All our biphasic and sarcomatoid cases arose in the pleura. Of the epithelioid mesotheliomas, 73 were from the pleura and 36 were from the peritoneum. On average, patients were 66 years of age (range, 26-90 years) and predominantly male (92 men, 39 women).

Results
The most common alterations identified were in BAP1, CDKN2A, NF2, and TP53. Twelve mesotheliomas did not show a pathogenic alteration on NGS. For epithelioid mesotheliomas in the pleura, the presence of an alteration in BAP1 correlated with low nuclear grade (P = .04), but no correlation was found in the peritoneum (P = .62). Similarly, there was no correlation between the amount of solid architecture in epithelioid mesotheliomas and any alterations in the pleura (P = .55) or peritoneum (P = .13). For biphasic mesotheliomas, cases with either no alteration detected or with an alteration in BAP1 were more likely to be epithelioid predominant (&gt;50% of the tumor, P = .0001), and biphasic mesotheliomas with other alterations detected and no alteration in BAP1 were more likely to be sarcomatoid predominant (&gt;50% of the tumor, P = .0001).

Conclusions
This study demonstrates a significant association between morphologic features associated with a better prognosis and an alteration in BAP1.
Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning
Authors: Acera Mateos Pablo , Zhou You , Zarnack Kathi , Eyras Eduardo 
Published: May 2023

Abstract
The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. In recent years, the development of new high-throughput experimental and computational techniques has been a key driving force in discovering the properties of RNA modifications. Machine learning applications, such as for classification, clustering or de novo identification, have been critical in these advances. Nonetheless, various challenges remain before the full potential of machine learning for epitranscriptomics can be leveraged. In this review, we provide a comprehensive survey of machine learning methods to detect RNA modifications using diverse input data sources. We describe strategies to train and test machine learning methods and to encode and interpret features that are relevant for epitranscriptomics. Finally, we identify some of the current challenges and open questions about RNA modification analysis, including the ambiguity in predicting RNA modifications in transcript isoforms or in single nucleotides, or the lack of complete ground truth sets to test RNA modifications. We believe this review will inspire and benefit the rapidly developing field of epitranscriptomics in addressing the current limitations through the effective use of machine learning.
InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop
Authors: Zhang Feng , Jiao Huiyuan , Wang Yihao , Yang Chen , Li Linying , Wang Zhiming , Tong Ran , Zhou Junmei , Shen Jianfeng , Li Lingjie 
Published: May 2023

Abstract
Deciphering cell-type-specific 3D structures of chromatin is challenging. Here, we present InferLoop, a novel method for inferring the strength of chromatin interaction using single-cell chromatin accessibility data. The workflow of InferLoop is, first, to conduct signal enhancement by grouping nearby cells into bins, and then, for each bin, leverage accessibility signals for loop signals using a newly constructed metric that is similar to the perturbation of the Pearson correlation coefficient. In this study, we have described three application scenarios of InferLoop, including the inference of cell-type-specific loop signals, the prediction of gene expression levels and the interpretation of intergenic loci. The effectiveness and superiority of InferLoop over other methods in those three scenarios are rigorously validated by using the single-cell 3D genome structure data of human brain cortex and human blood, the single-cell multi-omics data of human blood and mouse brain cortex, and the intergenic loci in the GWAS Catalog database as well as the GTEx database, respectively. In addition, InferLoop can be applied to predict loop signals of individual spots using the spatial chromatin accessibility data of mouse embryo. InferLoop is available at https://github.com/jumphone/inferloop.
Translational informatics for human microbiota: data resources, models and applications
Authors: Shen Ke , Din Ahmad Ud , Sinha Baivab , Zhou Yi , Qian Fuliang , Shen Bairong 
Published: May 2023

Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
Diabetes, brain health, and treatment gains in post-stroke aphasia
Authors: Roth Rebecca , Busby Natalie , Wilmskoetter Janina , Schwen Blackett Deena , Gleichgerrcht Ezequiel , Johnson Lisa , Rorden Chris , Newman-Norlund Roger , Hillis Argye E , den Ouden Dirk B , Fridriksson Julius , Bonilha Leonardo 
Published: May 2023

Abstract
In post-stroke aphasia, language improvements following speech therapy are variable and can only be partially explained by the lesion. Brain tissue integrity beyond the lesion (brain health) may influence language recovery and can be impacted by cardiovascular risk factors, notably diabetes. We examined the impact of diabetes on structural network integrity and language recovery. Seventy-eight participants with chronic post-stroke aphasia underwent six weeks of semantic and phonological language therapy. To quantify structural network integrity, we evaluated the ratio of long-to-short-range white matter fibers within each participant’s whole brain connectome, as long-range fibers are more susceptible to vascular injury and have been linked to high level cognitive processing. We found that diabetes moderated the relationship between structural network integrity and naming improvement at 1 month post treatment. For participants without diabetes (n = 59), there was a positive relationship between structural network integrity and naming improvement (t = 2.19, p = 0.032). Among individuals with diabetes (n = 19), there were fewer treatment gains and virtually no association between structural network integrity and naming improvement. Our results indicate that structural network integrity is associated with treatment gains in aphasia for those without diabetes. These results highlight the importance of post-stroke structural white matter architectural integrity in aphasia recovery.
A Genomic Perspective on the Near-term Impact of Doxycycline Post-exposure Prophylaxis on Neisseria gonorrhoeae Antimicrobial Resistance
Authors: Mortimer Tatum D , Grad Yonatan H 
Published: May 2023

Abstract
Pre-existing tetracycline resistance in Neisseria gonorrhoeae limits the effectiveness of post-exposure prophylaxis (PEP) with doxycycline against gonorrhea, and selection for tetracycline resistance may influence prevalence of multi-drug resistant strains. Using genomic and antimicrobial susceptibility data from N. gonorrhoeae, we assessed the near-term impact of doxycycline PEP on N. gonorrhoeae resistance.
Executive Function in Deaf Native Signing Children
Authors: Kotowicz Justyna , Woll Bencie , Herman Rosalind 
Published: May 2023

Abstract
The aim of this study is twofold: To examine if deafness is invariably associated with deficits in executive function (EF) and to investigate the relationship between sign language proficiency and EF in deaf children of deaf parents with early exposure to a sign language. It is also the first study of EF in children acquiring Polish Sign Language. Even though the mothers of the deaf children (N = 20) had lower levels of education compared with the mothers of a hearing control group, the children performed similarly to their hearing peers (N = 20) on a variety of EF task-based assessments. Only in the Go/No-go task were weaker inhibition skills observed in younger deaf children (6–9 years) compared with hearing peers, and this difference was not seen in older children (10–12 years). Hence, deafness does not necessarily impair EF; however, attentional and inhibition abilities may be acquired via a different route in deaf children. Sign language receptive skills predicted EF in deaf children. In conclusion, we highlight the importance of deaf parenting building the scaffolding for EF in deaf children.
A Kiss of Deep Homology: Partial Convergence in the Genomic Basis of Hypertrophied Lips in Cichlid Fish and Human Cleft Lip
Authors: Masonick Paul , Meyer Axel , Darrin Hulsey Christopher 
Published: May 2023

AbstractThe genomic loci generating both adaptive and maladaptive variation could be surprisingly predictable in deeply homologous vertebrate structures like the lips. Variation in highly conserved vertebrate traits such as the jaws and teeth in organisms as evolutionarily disparate as teleost fishes and mammals is known to be structured by the same genes. Likewise, hypertrophied lips that have evolved repeatedly in Neotropical and African cichlid fish lineages could share unexpectedly similar genetic bases themselves and even provide surprising insight into the loci underlying human craniofacial anomalies. To isolate the genomic regions underlying adaptive divergence in hypertrophied lips, we first employed genome-wide associations (GWAs) in several species of African cichlids from Lake Malawi. Then, we tested if these GWA regions were shared through hybridization with another Lake Malawi cichlid lineage that has evolved hypertrophied lips seemingly in parallel. Overall, introgression among hypertrophied lip lineages appeared limited. Among our Malawi GWA regions, one contained the gene kcnj2 that has been implicated in the convergently evolved hypertrophied lips in Central American Midas cichlids that diverged from the Malawi radiation over 50 million years ago. The Malawi hypertrophied lip GWA regions also contained several additional genes that cause human lip–associated birth defects. Cichlid fishes are becoming prominent examples of replicated genomic architecture underlying trait convergence and are increasingly providing insight into human craniofacial anomalies such as a cleft lip.
Retirement planning and types of healthy lifestyle after retirement: a Nationwide Survey in Taiwan
Authors: Huang Nuan-Ching , Kuo Pin-Han , Hsu Wan-Chen , Hu Susan C 
Published: May 2023

Abstract
Limited research has examined the components of retirement planning and the effects on retirees’ health behaviors. This study aims to explore whether retirement planning is associated with different types of healthy lifestyles after retirement. We conducted a nationwide Health and Retirement Survey in Taiwan and analyzed the data from 2015 to 2016. A total of 3128 retirees aged 50–74 years were included in the analysis. Twenty items on retirement planning from five categories were administered, and 20 health-related behaviors were used for measuring healthy lifestyles. Results showed that five types of healthy lifestyles were found from the 20 health behaviors by factor analysis. After controlling for all covariates, various components of retirement planning were associated with different types of lifestyles. Retirees having any item of retirement planning would significantly increase the score of ‘healthy living’. Those with 1–2 items were also associated with the total score and the type of ‘no unhealthy food’. However, those with ≥ 6 items were the only group positively related to the type of ‘regular health checkups’ but negatively to the type of ‘good medication’. In conclusion, retirement planning offers a ‘window of opportunity’ for promoting healthy lifestyles after retirement. Pre-retirement planning should be advocated in the workplace to improve health-related behaviors, especially for those upcoming retired workers. In addition, a friendly environment and continuous programs should also be incorporated for better retirement life.
CsXDH1 gene promotes caffeine catabolism induced by continuous strong light in tea plant
Authors: Tang Qianhui , Liu Keyi , Yue Chuan , Luo Liyong , Zeng Liang , Wu Zhijun 
Published: May 2023

Abstract
Tea plant (Camellia sinensis) is an important cash crop with extensive adaptability in the world. However, complex environmental factors force a large variation of tea quality-related components. Caffeine is essential for the formation of bitter and fresh flavors in tea, and is the main compound of tea that improves human alertness. Continuous strong light stimulation was observed to cause caffeine reduction in tea leaves, but the mechanism is not clear. In this study, the response of tea plant to light intensity was analysed mainly by multi-omics association, antisense oligodeoxynucleotide (asODN) silencing technique, and in vitro enzyme activity assay. The results revealed multiple strategies for light intensity adaptation in tea plant, among which the regulation of chloroplasts, photosynthesis, porphyrin metabolism, and resistance to oxidative stress were prominent. Caffeine catabolism was enhanced in continuous strong light, which may be a light-adapted strategy due to strict regulation by xanthine dehydrogenase (XDH). asODN silencing and enzymatic activity assays confirmed that CsXDH1 is a protein induced by light intensity to catalyze the substrate xanthine. CsXDH1 asODN silencing resulted in significant up-regulation of both caffeine and theobromine in in vitro enzyme activity assay, but not in vivo. CsXDH1 may act as a coordinator in light intensity adaptation, thus disrupting this balance of caffeine catabolism.
Conventional outcome reporting per IVF cycle/embryo transfer may systematically underestimate chances of success for women undergoing ART: relevant biases in registries, epidemiological studies, and guidelines
Authors: Griesinger Georg , Larsson Per 
Published: May 2023

Abstract
Pre-conception counselling and management of expectations about chance of success of IVF/ICSI treatments is an integral part of fertility care. Registry data are usually used to inform patients about expected success rates of IVF/ICSI treatment, as these data should best represent real-world populations and clinical practice. In registries, the success rate of IVF/ICSI treatments is conventionally reported per treatment cycle or per embryo transfer and estimated from data for which several treatment attempts per subject have been pooled (e.g. repetitive IVF/ICSI attempts or repetitive attempts of cryotransfer). This, however, may underestimate the true mean chance of success per treatment attempt, because treatment attempts of women with a poor prognosis will usually be over-represented in a pool of treatment cycle data compared to treatment events of women with a good prognosis. Of note, this phenomenon is also a source of potential bias when comparing outcomes between fresh transfers and cryotransfers, since women can undergo a maximum of only one fresh transfer after each IVF/ICSI treatment, but potentially several cryotransfers. Herein, we use a trial dataset from 619 women, who underwent one cycle of ovarian stimulation and ICSI, a Day 5 fresh transfer and/or subsequent cryotransfers (follow-up of all cryotransfers up to 1 year after the start of stimulation), to exemplify the underestimation of the live birth rate, when not accounting for repeated transfers in the same woman. Using mixed-effect logistic regression modelling, we show that the mean live birth rate per transfer per woman in cryocycles is underestimated by the factor 0.69 (e.g. live birth rate per cryotransfer of 36% after adjustment versus 25% unadjusted). We conclude that the average chance of success of treatment cycles of women of a given age, treated in a given centre, etc., when conventionally calculated per cycle or per embryo transfer from a pool of treatment events, do not apply to an individual woman. We suggest that patients are, especially at the outset of treatment, systematically confronted with mean estimates of success per attempt that are too low. Live birth rates per transfer from datasets encompassing multiple transfers from single individuals could be more accurately reported using statistical models accounting for the correlation between cycle outcomes within women.
178 Academic Quadrathlon as an In-Service Training Tool
Authors: Mason Katie , Fancher Malerie , Ivey Jennie L , Strickland Lew G , Rowan Troy N , Eckelkamp Elizabeth , Rhinehart Justin D , Shanks Jessica , Fisher Aaron , Tabler Tom , Zoca Saulo , Main Sawyer 
Published: May 2023

Abstract
The Animal Science Extension team at the University of Tennessee Institute of Agriculture provides a yearly joint in-service training for county agents. In previous years, in-service trainings were held on a regional basis, with one one-day training in each region of the state for a total of 3 trainings. In 2021, the Animal Science team took a difference approach by offering a centrally located, conference style in-service training that lasted for 3 days. There were separate tracks for 4-H and Agriculture and Natural Resources (ANR) with concurrent sessions, and a few combined sessions with general program updates. A range of topics were covered in species-specific sessions, covering beef, dairy, small ruminant, equine, and poultry. On day 3, to increase agent interaction during the in-service training, the Animal Science Extension team created a mini-academic quadrathlon (AQ) to test the agents in a friendly competition. The AQ had species-specific hands-on lab sections and a quiz bowl competition. Teams were created by Specialists to ensure that each team comprised agents with varying levels of knowledge and experience. In December 2021, fifty-two agents participated in the training. An evaluation was administered at the end of the training to gauge effectiveness of each session. Of the 28 respondents, 15 were ANR agents, 7 were 4-H agents, 5 were ANR/4-H agents, and 1 was an area specialist. When asked to give an overall rating for the quiz bowl session of AQ on scale of 1 to 5, with 1 being poor and 5 being excellent, 71% of respondent responded “5: excellent.” When asked the same for hands-on lab portions of AQ, 95% of agents responded “5: excellent.” Selected comments regarding the AQ during in-service training included: “Day 3 by far was the most fun I have had at an in-service. I loved it.” and “I thought the stations and quiz bowl was a great way to tie in everything that was covered in the first two days. Fun and educational!” Specialists concluded that the AQ was a highly effective way to deliver in-service training to agents in an exciting way. Due to the success of the program, the 2022 in-service training taking place in December, will follow the same format.