bluuebunny/crossref_metadata_2025_split huggingface dataset:
Halvade somatic: Somatic variant calling with Apache Spark
Authors: Decap Dries , de Schaetzen van Brienen Louise , Larmuseau Maarten , Costanza Pascal , Herzeel Charlotte , Wuyts Roel , Marchal Kathleen , Fostier Jan 
Published: January 2022

Abstract

Background
The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired. In turn, this leads to large volumes of raw sequencing data to process and hence, large computational requirements. For example, calling the somatic variants according to the GATK best practices guidelines requires days of computing time for a typical whole-genome sequencing sample.

Findings
We introduce Halvade Somatic, a framework for somatic variant calling from DNA sequencing data that takes advantage of multi-node and/or multi-core compute platforms to reduce runtime. It relies on Apache Spark to provide scalable I/O and to create and manage data streams that are processed on different CPU cores in parallel. Halvade Somatic contains all required steps to process the tumor and matched normal sample according to the GATK best practices recommendations: read alignment (BWA), sorting of reads, preprocessing steps such as marking duplicate reads and base quality score recalibration (GATK), and, finally, calling the somatic variants (Mutect2). Our approach reduces the runtime on a single 36-core node to 19.5 h compared to a runtime of 84.5 h for the original pipeline, a speedup of 4.3 times. Runtime can be further decreased by scaling to multiple nodes, e.g., we observe a runtime of 1.36 h using 16 nodes, an additional speedup of 14.4 times. Halvade Somatic supports variant calling from both whole-genome sequencing and whole-exome sequencing data and also supports Strelka2 as an alternative or complementary variant calling tool. We provide a Docker image to facilitate single-node deployment. Halvade Somatic can be executed on a variety of compute platforms, including Amazon EC2 and Google Cloud.

Conclusions
To our knowledge, Halvade Somatic is the first somatic variant calling pipeline that leverages Big Data processing platforms and provides reliable, scalable performance. Source code is freely available.
High Degree of Practice Variability in Colonic Dysplasia Surveillance for Patients With Inflammatory Bowel Disease
Authors: Lewis James D , Cross Raymond K , Long Millie , Singh Siddharth , Herfarth Hans , Weiss Alexandra , Buchner Anna 
Published: January 2022

Lay Summary
Dysplasia surveillance practice varies widely among high-volume inflammatory bowel disease providers. We surveyed high-volume inflammatory bowel disease providers about practice patterns to detect dysplasia. Regular use of dye-based chromoendoscopy was reported by 20%, virtual chromoendoscopy by 27%, and random biopsies by 58%.
Service quality in outpatient teaching hospital pharmacies based on the SERVQUAL model: An assessment in the south of Iran
Authors: Kashfi Seyyed Mansour , Karimian Elham , Ravangard Ramin , Mehralian Gholamhossein , Bastani Peivand 
Published: January 2022

Abstract

Objectives
The present study assessed the quality of services in the outpatient teaching hospital pharmacies affiliated to Shiraz University of Medical Sciences, Iran, in 2019 according to the SERVQUAL model to identify areas for improvement.

Methods
The research was cross-sectional, descriptive and analytical. Patients referred to the outpatient teaching hospital pharmacies affiliated to Shiraz University of Medical Sciences formed the study population. The sample size was 300 people chosen through the stratified sampling method proportional to the size as well as the convenience sampling method. The modified SERVQUAL questionnaire developed by Mohammadi et al. (in Eftekhar Ardabili H, Akbari Haghighi F, Mahmoudi M, Poorreza A. Evaluation of service quality based on the patients’ expectations and perceptions in Zanjan hospitals. J Sch Public Health Inst Public Health Res. 2003;2:71-84) was used for data collection. Data analysis was performed by SPSS 24.0 using statistical tests of paired t-test, independent t-test and ANOVA. A P-value of &lt;0.05 showed statistical significance. Moreover, EXCEL 2013 was used to draw the graphs.

Key findings
The results showed that the participants had higher expectations regarding the quality of pharmacy services in all six dimensions compared to their perceptions (negative gaps) and the difference was statistically significant (P &lt;0.05). The largest gap was in the ‘access’ dimension (G = −0.44 ± 1.15) and the smallest one was in the ‘reliability’ dimension (G = −0.21 ± 1.30). Also, the mean of overall quality gap, among the patients’ demographic characteristics, had a significant relationship only with having supplementary health insurance coverage (P = 0.03).

Conclusions
It seems that hospital managers and technical managers of pharmacies should make several interventions in the field of staff empowerment and training empathy and teamwork skills. Also, strengthening the system of receiving quick and easy feedback from patients and paying attention to the voice of customers can pave the way for hospital managers and technical managers of pharmacies to enhance the service quality with subsequence reduction of the existing gaps.
Incidence of Malignancies Among Patients With Chronic Hepatitis B in US Health Care Organizations, 2006–2018
Authors: Spradling Philip R , Xing Jian , Zhong Yuna , Rupp Loralee B , Moorman Anne C , Lu Mei , Teshale Eyasu H , Schmidt Mark A , Daida Yihe G , Boscarino Joseph A , Gordon Stuart C 
Published: January 2022

Abstract
Hepatitis B virus (HBV) infection causes hepatocellular carcinoma but its association with other cancers is not well established. We compared age-adjusted incidence of primary cancers among 5773 HBV-infected persons with US cancer registries during 2006–2018. Compared with the US population, substantially higher incidence among HBV-infected persons was observed for hepatocellular carcinoma (standardized rate ratio [SRR], 30.79), gastric (SRR, 7.95), neuroendocrine (SRR, 5.88), cholangiocarcinoma (SRR, 4.62), and ovarian (SRR, 3.72) cancers, and non-Hodgkin lymphoma (SRR, 2.52). Clinicians should be aware of a heightened potential for certain nonhepatic malignancies among hepatitis B patients, as earlier diagnosis favors improved survival.
A time-resolved experimental–mathematical model for predicting the response of glioma cells to single-dose radiation therapy
Authors: Liu Junyan , Hormuth David A , Davis Tessa , Yang Jianchen , McKenna Matthew T , Jarrett Angela M , Enderling Heiko , Brock Amy , Yankeelov Thomas E 
Published: January 2022

Abstract

Purpose
To develop and validate a mechanism-based, mathematical model that characterizes 9L and C6 glioma cells’ temporal response to single-dose radiation therapy in vitro by explicitly incorporating time-dependent biological interactions with radiation.

Methods
We employed time-resolved microscopy to track the confluence of 9L and C6 glioma cells receiving radiation doses of 0, 2, 4, 6, 8, 10, 12, 14 or 16 Gy. DNA repair kinetics are measured by γH2AX expression via flow cytometry. The microscopy data (814 replicates for 9L, 540 replicates for C6 at various seeding densities receiving doses above) were divided into training (75%) and validation (25%) sets. A mechanistic model was developed, and model parameters were calibrated to the training data. The model was then used to predict the temporal dynamics of the validation set given the known initial confluences and doses. The predictions were compared to the corresponding dynamic microscopy data.

Results
For 9L, we obtained an average (± standard deviation, SD) Pearson correlation coefficient between the predicted and measured confluence of 0.87 ± 0.16, and an average (±SD) concordance correlation coefficient of 0.72 ± 0.28. For C6, we obtained an average (±SD) Pearson correlation coefficient of 0.90 ± 0.17, and an average (±SD) concordance correlation coefficient of 0.71 ± 0.24.

Conclusion
The proposed model can effectively predict the temporal development of 9L and C6 glioma cells in response to a range of single-fraction radiation doses. By developing a mechanism-based, mathematical model that can be populated with time-resolved data, we provide an experimental–mathematical framework that allows for quantitative investigation of cells’ temporal response to radiation. Our approach provides two key advances: (i) a time-resolved, dynamic death rate with a clear biological interpretation, and (ii) accurate predictions over a wide range of cell seeding densities and radiation doses.
Vγ5Vδ1 TCR signaling is required to different extents for embryonic versus postnatal development of DETCs
Authors: Sudo Koichi , Todoroki Takero , Ka Yuyo , Takahara Kazuhiko 
Published: January 2022

Abstractγδ T cells expressing Vγ5Vδ1 TCR originally develop in the embryonic thymus and migrate to the epidermis, forming dendritic epidermal T cells (DETCs) throughout life. It is thought that a TCR signal is essential for their development; e.g., lack of TCR signal-transducer ZAP70 significantly decreases DETC numbers. On the other hand, lack of ZAP70 does not affect Vγ5Vδ1+ T cells in the embryonic thymus; thus, the involvement of TCR signaling remains elusive. Here, we used SKG mice with attenuated TCR signaling rather than gene-knockout mice. In SKG mice, Vγ5+ T cells showed a marked decrease [10% of wild-type (WT)] in adult epidermis; however, there was just a moderate decrease (50% of WT) in the embryonic thymus. In early postnatal epidermis in SKG mice, substantial numbers of Vγ5+ T cells were observed (50% of WT). Their activation markers including CD122, a component of the IL-15 receptor indispensable for DETC proliferation, were comparable to those of WT. However, the Vγ5+ T cells in SKG mice did not proliferate and form DETCs thereafter. Furthermore, in SKG/+ mice, the number of thymic Vγ5Vδ1+ T cells increased, compared to SKG mice; however, the number of DETCs remained significantly lower than in WT, similar to SKG mice. Our results suggest that signaling via Vγ5Vδ1 TCR is indispensable for DETC development, with distinct contributions to embryonic development and postnatal proliferation.
BCS impact report: winter 2021
Authors: Penketh Claire 
Published: January 2022

Abstract
BCS members speak out about Green IT, the future of AI — and a global social media outage. Senior Media Offcer Claire Penketh reports.
As part of its Open Technology for Sustainability Day at COP26, Claire Penketh also spoke to Amanda Brock, CEO of OpenUK about how rethinking tech could help save the planet.
Genomic analyses of Staphylococcus aureus isolated from yaks in Ganzi Tibetan Autonomous Prefecture, China
Authors: Zou Geng , Matuszewska Marta , Bai Fenglan , Wang Suya , Wang Shuang , Li Huaixia , Ke Yan , Tang Cheng , Li Jinquan , Tang Junni , Zhou Rui 
Published: January 2022

Abstract

Objectives
To investigate the transmission and origination of MRSA in livestock with limited antimicrobial use. Yak (Bos grunniens) herds in Ganzi Tibetan Autonomous Prefecture, China were chosen for sampling.

Methods
The yaks from all 18 districts of Ganzi were sampled (anal swabs, n = 657; nasal swabs, n = 634). Based on the WGS data of 83 Staphylococcus aureus isolates, the novel structure of the yak S. aureus population was described. Phylogenetic analyses were utilized for determining the origin of the MRSA lineage in yaks.

Results
The yak S. aureus population consisted of 11 STs, 6 of which were previously undescribed, with ST6267 being the predominant novel ST. These isolates were generally susceptible to most of the tested antibiotics and lacked the associated antimicrobial resistance genes (ARGs) but showed high penicillin MIC values (MIC90 = 32 mg/L), which were consistent with the high positivity rate for blaZ (61/83). The MRSA identified in yaks were all ST59 and most likely of human origin. The yak ST59 MRSA each carried the human immune evasion cluster (IEC) while lacking the ARGs that are identified in the majority of reported Chinese human ST59 MRSA isolates [erm(B), ant6-Ia and aph(3″)-III].

Conclusions
The yak herds living on the Qinghai–Tibet Plateau are important livestock and follow the traditional free-grazing farming model. We surveyed the yak S. aureus population and found that all the yak MRSA isolates belonged to the lineage that might originate from the prevalent community-acquired MRSA ST59 in China. From a ‘One Health’ perspective, the transmission of human MRSA to farming animals with limited antimicrobial exposure highlights the multiple roles of animals in the expansion of MRSA.
Sleep apnea phenotyping and relationship to disease in a large clinical biobank
Authors: Cade Brian E , Hassan Syed Moin , Dashti Hassan S , Kiernan Melissa , Pavlova Milena K , Redline Susan , Karlson Elizabeth W 
Published: January 2022

Abstract

Objective
Sleep apnea is associated with a broad range of pathophysiology. While electronic health record (EHR) information has the potential for revealing relationships between sleep apnea and associated risk factors and outcomes, practical challenges hinder its use. Our objectives were to develop a sleep apnea phenotyping algorithm that improves the precision of EHR case/control information using natural language processing (NLP); identify novel associations between sleep apnea and comorbidities in a large clinical biobank; and investigate the relationship between polysomnography statistics and comorbid disease using NLP phenotyping.

Materials and Methods
We performed clinical chart reviews on 300 participants putatively diagnosed with sleep apnea and applied International Classification of Sleep Disorders criteria to classify true cases and noncases. We evaluated 2 NLP and diagnosis code-only methods for their abilities to maximize phenotyping precision. The lead algorithm was used to identify incident and cross-sectional associations between sleep apnea and common comorbidities using 4876 NLP-defined sleep apnea cases and 3× matched controls.

Results
The optimal NLP phenotyping strategy had improved model precision (≥0.943) compared to the use of one diagnosis code (≤0.733). Of the tested diseases, 170 disorders had significant incidence odds ratios (ORs) between cases and controls, 8 of which were confirmed using polysomnography (n = 4544), and 281 disorders had significant prevalence OR between sleep apnea cases versus controls, 41 of which were confirmed using polysomnography data.

Discussion and Conclusion
An NLP-informed algorithm can improve the accuracy of case-control sleep apnea ascertainment and thus improve the performance of phenome-wide, genetic, and other EHR analyses of a highly prevalent disorder.
The Original Scientific Description of the Lone Star Tick (Amblyomma americanum, Acari: Ixodidae) and Implications for the Species’ Past and Future Geographic Distributions
Authors: Rochlin Ilia , Egizi Andrea , Lindström Anders 
Published: January 2022

AbstractAmblyomma americanum L. is an important vector in North America originally described by Linnaeus based on Pehr Kalm’s 1754 report. While Kalm’s ‘Travels into North America’ is well known, his 1754 report remains obscure. Some authors were skeptical that Kalm referred to A. americanum because he encountered them at sites farther north outside of the species’ range. However, the details in 1754 report leave no doubt that Kalm described lone star ticks. In this historical review, we provide support for Kalm’s identification using a modern translation of his 1754 report and other sources. We also delineate distributional changes of lone star ticks from the pre-colonization era to the present and interpret them in the context of large-scale anthropogenic changes in the landscape. In this framework, the lone star tick’s current northward expansion is a recolonization of their former range. Extensive deforestation and extirpation of their principal host species, white-tailed deer, led to A. americanum’s disappearance from the northern parts of its range by the 20th century. Subsequent recolonization by second-growth forest and increases in white-tailed deer populations by the mid-20th century is now allowing A. americanum to reclaim its former range. These changes in the land appear to be the driving force behind A. americanum’s present expansion. Understanding this species’ history and the factors contributing to its current expansion will enable better predictions about its future distribution and potential to transmit human pathogens.
Diversity of Mosquitoes (Diptera: Culicidae) in the Bom Retiro Private Natural Heritage Reserve, Rio de Janeiro State, Brazil
Authors: Bastos Amanda Queiroz , de Mello Cecilia Ferreira , dos Santos Silva Júlia , Gil-Santana Hélcio Reinaldo , Silva Shayenne Olsson Freitas , Alencar Jeronimo 
Published: January 2022

Abstract
This study registers the diversity of Culicidae in the Bom Retiro Private Natural Heritage Reserve (RPPNBR), Rio de Janeiro state, Brazil, based on the collection of the immature stages in natural and artificial larval habitats. Larvae and pupae were collected monthly at two sites of the RPPNBR from May 2014 to July 2015 using dippers and aquatic pipettes. The diversity of the mosquito community was described using the Shannon–Wiener Diversity Index (H′), as well as diversity, richness, and dominance of species found in different larval habitats (lake, bamboos, bromeliads, and artificial vessels). The Mann–Whitney test was used to calculate differences between the two natural and artificial habitats. Overall, 15,659 specimens belonging to 25 species, ten genera, and two subfamilies were collected. The most abundant species collected at sites that were reforested recently were Culex pleuristriatus Theobald, 1903, Limatus durhamii (Theobald, 1901), Aedes albopictus (Skuse, 1895), Culex neglectus (Lutz, 1904), and Culex retrosus (Lane & Whitman, 1951). In a forest preserved site, the most abundant species were Cx. neglectus, Culex iridescens (Lutz, 1905), Sabethes identicus (Dyar & Knab, 1907), Wyeomyia arthrostigma (Lutz, 1905), and Li. durhamii. With respect to larval habitats, 0.1% of the specimens were collected along the edge of a lake, 5.5% in bamboos, 35.9% in bromeliads, and 58.4% in artificial containers. Only 5.5% of the specimens were collected in the forest preserved site, with the remaining samples from the site with altered vegetation. A greater species richness and diversity were found in forest-altered sites compared to the forest preserved site. Several species were collected in the water accumulated in the nylon lids of plastic water tanks. Such vessels can promote an increase in mosquito population density in the environment surrounding the study area.
Trends in the Incidence of Human Papillomavirus-Associated Cancers by County-Level Income and Smoking Prevalence in the United States, 2000-2018
Authors: Lin Yueh-Yun , Damgacioglu Haluk , Suk Ryan , Wu Chi-Fang , Zhu Yenan , Ortiz Ana P , Hara Sehej Kaur , Sonawane Kalyani , Deshmukh Ashish A 
Published: January 2022

Abstract
Human papillomavirus (HPV)-associated cancer burden is rising in the United States. Trends in the incidence by county-level income and smoking prevalence remain undescribed. We used the Surveillance, Epidemiology, and End Results 21 database to ascertain HPV-associated cancers during 2000-2018. Trends were estimated by county-level income and smoking prevalence quartiles. Anal and vulvar cancer incidence among women and anal cancer incidence among men increased markedly in the lowest-income counties, whereas the increases were slower in the highest-income counties (eg, for vulvar cancer, incidence increased 1.9% per year, 95% confidence interval [CI] = 0.9% to 2.9%, in the lowest-income counties vs 0.8% per year, 95% CI = 0.6% to 1.1%, in the highest-income counties). In recent years, cervical cancer incidence plateaued (0.0% per year [95% CI = −0.5% to 0.5%]) in the highest-income counties; in the lowest-income counties, the annual percentage change was 1.6% per year (95% CI = −0.7% to 4.0%). Counties with high smoking prevalence had marked increases in incidence compared with their counterparts (eg, anal cancer among men increased 4.4% per year [95% CI = 2.7% to 6.0%] for those living in counties with the highest smoking prevalence vs 1.2% per year [95% CI = 0.7% to 1.7%] for those living in counties with the lowest smoking prevalence). Improved and targeted prevention is needed to combat the widening disparities.
The Effects of Tobacco Coverage in the Public Communication Environment on Young People’s Decisions to Smoke Combustible Cigarettes
Authors: Hornik Robert , Binns Steven , Emery Sherry , Epstein Veronica Maidel , Jeong Michelle , Kim Kwanho , Kim Yoonsang , Kranzler Elissa C , Jesch Emma , Lee Stella Juhyun , Levin Allyson V , Liu Jiaying , O’Donnell Matthew B , Siegel Leeann , Tran Hy , Williams Sharon , Yang Qinghua , Gibson Laura A 
Published: January 2022

Abstract
In today’s complex media environment, does media coverage influence youth and young adults’ (YYA) tobacco use and intentions? We conceptualize the “public communication environment” and effect mediators, then ask whether over time variation in exogenously measured tobacco media coverage from mass and social media sources predicts daily YYA cigarette smoking intentions measured in a rolling nationally representative phone survey (N = 11,847 on 1,147 days between May 2014 and June 2017). Past week anti-tobacco and pro-tobacco content from Twitter, newspapers, broadcast news, Associated Press, and web blogs made coherent scales (thetas = 0.77 and 0.79). Opportunities for exposure to anti-tobacco content in the past week predicted lower intentions to smoke (Odds ratio [OR] = 0.95, p &lt; .05, 95% confidence interval [CI] = 0.91–1.00). The effect was stronger among current smokers than among nonsmokers (interaction OR = 0.88, p &lt; .05, 95% CI = 0.77–1.00). These findings support specific effects of anti-tobacco media coverage and illustrate a productive general approach to conceptualizing and assessing effects in the complex media environment.
The response of soil respiration to different N compounds addition in a saline–alkaline grassland of northern China
Authors: Diao Huajie , Chen Xiaopeng , Wang Ge , Ning Qiushi , Hu Shuya , Sun Wei , Dong Kuanhu , Wang Changhui 
Published: January 2022

AbstractThe increase in atmospheric nitrogen (N) deposition has profound effects on soil respiration (SR). However, the responses of SR to the addition of different N compounds, particularly in saline–alkaline grasslands remain unclear. A 3-year controlled field experiment was conducted to investigate the responses of SR to different N compounds (NH4NO3, (NH4)2SO4 and NH4HCO3) during the growing seasons in a saline–alkaline grassland located in the agro-pastoral ecotone of northern China. Our results demonstrated that SR showed a bimodal pattern and a significant interannual difference that was regulated by air or soil temperature and precipitation. Nitrogen addition had a significant effect on SR, and the effect of N addition on SR varied yearly, which was related to seasonal precipitation. The mean SR across 3 years (2017–2019) was increased by 19.9%, 13.0% and 16.6% with the addition of NH4NO3, (NH4)2SO4 and NH4HCO3, respectively. The highest effect of NH4NO3 addition on SR across 3 years was ascribed to the highest aboveground net primary production, belowground net primary production (BNPP) and soil NO3− concentrations. SR (C loss) was significantly increased while plant productivity (C input) did not significantly change under NH4HCO3 addition, indicating a decrease in C sequestration. In addition, BNPP was the main direct factor influencing SR in this saline–alkaline grassland, and soil salinization (e.g. soil base cations and pH) indirectly affected SR through soil microorganisms. Notably, NH4NO3 addition overestimated the response of SR to N addition, and different N compounds should be considered, especially in saline–alkaline grassland.