bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antifungal Activity and Biological Characteristics of the Novel Fungicide Quinofumelin AgainstSclerotinia sclerotiorum
Authors: Tao Xian , Zhao Huahua , Xu Haorong , Li Zhongke , Wang Jianxin , Song Xiushi , Zhou Mingguo , Duan Yabing 
Published: January 2021

Sclerotinia sclerotiorum is a devastating plant pathogen with a broad host range and worldwide distribution. The application of chemical fungicides is a primary strategy for controlling this pathogen. However, under the high selective pressure of chemical fungicides, fungicide resistance has emerged and gradually increased, resulting in the failure to control S. sclerotiorum in the field. Quinofumelin is a novel quinoline fungicide, but its antifungal activities against plant pathogens have been rarely reported. Here, we determined the antifungal activity of quinofumelin against S. sclerotiorum in vitro and in planta. The median effect concentration (EC50) values ranged from 0.0004 to 0.0059 µg ml−1with a mean EC50of 0.0017 ± 0.0009 µg ml−1and were normally distributed (P = 0.402). In addition, no cross resistance was observed between quinofumelin and other fungicides, dimethachlone, boscalid, or carbendazim, which are commonly used to manage S. sclerotiorum. Quinofumelin did not affect glycerol and oxalic acid production of either carbendazim-sensitive or -resistant isolates. Moreover, quinofumelin exhibited excellent protective, curative, and translaminar activity against S. sclerotiorum on oilseed rape leaves. Protective activity was higher than curative activity. Interestingly, quinofumelin inhibited the formation of the infection cushion in S. sclerotiorum, which may contribute to the control efficacy of quinofumelin against S. sclerotiorum in the field. Our findings indicate that quinofumelin has excellent control efficacy against S. sclerotiorum in vitro and in planta as compared with extensively used fungicides and could be used to manage carbendazim- and dimethachlone-resistance in S. sclerotiorum in the field.
Current prevalence of self-monitoring of blood pressure during pregnancy: the BUMP Survey
Authors: Tucker Katherine L. , Hodgkinson James , Wilson Hannah M. , Crawford Carole , Stevens Richard , Lay-Flurrie Sarah , Dale Madeleine , Astbury Nerys , Chappell Lucy C. , McManus Richard J. 
Published: January 2021

Objective:
To understand the current prevalence of, and attitudes to, self-monitoring of blood pressure (BP) during pregnancy.

Methods:
Five thousand, five hundred and fifty-five pregnant women from antenatal clinics in 16 hospitals in England were invited to complete a survey.

Main outcome measures:
The primary outcome was the proportion of women currently BP self-monitoring. Secondary outcomes included self-monitoring schedules and women's interactions with clinicians regarding self-monitoring. Population characteristics including risk factors for preeclampsia, ethnicity and deprivation level were considered.

Results:
Completed surveys were received and analysed from 5181 pregnant women (93% response rate). Comparison to hospital demographic data suggests that respondents were representative of the UK population. Nine hundred and eighty-three of 5181 (19%) women were currently self-monitoring their BP, constituting 189 of 389 (49%) hypertensive women and 794 of 4792 (17%) normotensive women. However, only 482 of 983 (49%) reported ever sharing this information with antenatal care teams. Of those who self-monitored, 68% (668/983) were able to provide a previous BP reading, compared with 1% (67/5181) of those who did not self-monitor.

Conclusion:
Many women are now choosing to self-monitor their BP during pregnancy and clinicians should enquire about this proactively and consider providing better information on BP monitoring. Those who self-monitor appear to have better knowledge about their blood pressure. If these findings were replicated nationwide, around 125 000 pregnant women would be currently self-monitoring BP in the UK, yet only half of these women may communicate their readings to their antenatal care teams, suggesting a missed opportunity for enhanced care. Current trials will make the place of self-monitoring in pregnancy clearer.
The Impact of COVID‐19 on Job Prospects and Educational Training for Pediatric Gastroenterology Fellows
Authors: Irastorza Laura E. , Hopson Puanani , Ta Allison , Kemme Sarah , Mallon Daniel , Lee Christine K. 
Published: January 2021

ABSTRACTObjectives:The COVID‐19 pandemic has significantly affected graduate medical education with redistribution of trainees, altered clinical care, and decreased research. For graduating trainees, there remains concern that financial stability of health systems will affect the availability of new positions and hiring practices. This survey aims to evaluate the pandemic's impact from pediatric gastroenterology fellows’ perspectives.Methods:An anonymous survey was distributed by e‐mail from June 11 to July 1, 2020 to all North American pediatric gastroenterology and advanced training fellows. The survey was tailored for the fellows’ year of training including questions on education, clinical experience, research, and job outlook.Results:Of the 434 pediatric gastroenterology fellows, 145 completed the survey. Of all respondents, negative impact was reported in 52% on clinical training, 46% research projects, and 41% procedural confidence. A majority (93%) of third‐year respondents had a job contract signed at the time of the survey; however, 18% of those contracts were subsequently altered with 5 respondents having job contracts rescinded due to hiring freezes. Fifty‐four percent of first‐ and second‐year fellow respondents reported concern regarding finding a job with the majority being second‐year fellows (78%).Conclusions:The COVID‐19 pandemic continues to affect the medical system and healthcare professionals. This survey identified significant impact on job acquisition for graduating pediatric gastroenterology fellows and other critical components of training, which are likely applicable to other pediatric trainees. The survey results raise questions about potential strategies to improve medical education and job search success for graduating trainees.
Prevalence and Trends in HIV Infection and Testing Among Adults in the United States: The National Health and Nutrition Examination Surveys, 1999–2018
Authors: McQuillan Geraldine M. , Kruszon-Moran Deanna , Masciotra Silvina , Gu Qiuping , Storandt Renee 
Published: January 2021

Background:
HIV antibody testing has been included in the National Health and Nutrition Examination Survey, for ages 18–49 since 1999 and for ages 18–59 years since 2009 enabling estimation of trends in HIV prevalence as part of national surveillance in the U.S. household population. Self-reported HIV testing and antiretroviral use was also included in the survey since 1999.

Setting:
A continuous household-based probability sample of the U.S. population.

Methods:
From 1999 to 2018, 29,020 participants age 18–49 years were tested for HIV antibody and 34,092 participants age 18–59 years were asked about self-report of any previous HIV testing.

Results:
HIV prevalence was 0.41% among those aged 18–59 in 2009–2018 with a nonsignificant trend over time among those aged 18–49 years from 1999–2002 to 2015–2018. However, significant declines in prevalence were seen among those aged 18–39 years (0.37%–0.11%), women (0.22%–0.06%) and non-Hispanic black persons (2.14%–0.80%). Participants aged 18–39 years self-reported a decline in HIV testing, whereas those aged 40–49 and 50–59 years, non-Hispanic black persons and women reported an increase in getting a HIV test. Prevalence of infection and self-reported history of HIV testing varied by demographic and risk groups. HIV testing among HIV-positive persons was 83.9%. Antiretroviral therapy among those HIV-positive was under 50%.

Conclusion:
Although total HIV prevalence and previous self-reported HIV testing remained stable for the last 20 years, there were significant declines in age and demographic subgroups. Prevalence for both outcomes varied by demographic and risk variables.
Entirely Robot-assisted Total Colectomy/Total Proctocolectomy Compared With a Laparoscopic Approach
Authors: Kim Jin Cheon , Lee Jong Lyul , Yoon Yong Sik , Kim Hyung Min , Kim Chan Wook , Park In Ja , Aldilaijan Abdulmohsin Fawzi , Lim Seok-Byung 
Published: January 2021

Purpose:
Previous robot-assisted total colectomy/total proctocolectomy (TC/TPC) has been mostly confined to completion proctectomy combined with open or laparoscopic colon dissection. This study describes an integrative method of entirely robot-assisted maintaining anatomical dissection with single docking and one-off arm placement.

Materials and Methods:
Twenty patients who underwent robot-assisted TC/TPC and 36 who underwent laparoscopic procedures at the Asan Medical Center (Seoul, Korea) were enrolled.

Results:
Mean operation time was ∼1 hour longer in the robot-assisted than in the laparoscopic group (P=0.003), due primarily to the extra time required for instrument installation and more frequent transient ileal diversion. Three patients (8%) in the laparoscopic group required conversion to open surgery, compared with none in the robot-assisted group. Rates of postoperative adverse events did not differ in the 2 groups (P=0.063). Short (8 cm) ileal pouches were applied to all patients who underwent robot-assisted TPC/ileal-pouch anal anastomosis, but to one patient who underwent laparoscopic surgery. There were no discrepancies of mean daily bowel movement between patients with short and long ileal pouches 6 months after surgery (P=0.694), showing 5 times per day (range: 1 to 10).

Conclusion:
The advantages of the boom system and motion-sensitive table were successfully utilized to integrate anatomical dissection with the multiquadrant procedures of TC/TPC, with none of these patients requiring conversion to open surgery. Refinement of these techniques may overcome some of the technical and time-related and cost-related concerns of the robotic approach.
Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation
Authors: Yeung Arnold YS , Roewer-Despres Francois , Rosella Laura , Rudzicz Frank 
Published: January 2021

AbstractBackgroundNational governments have implemented non-pharmaceutical interventions to control and mitigate against the COVID-19 pandemic. A deep understanding of these interventions is required.ObjectiveWe investigate the prediction of future daily national Confirmed Infection Growths – the percentage change in total cumulative cases across 14 days – using metrics representative of non-pharmaceutical interventions and cultural dimensions of each country.MethodsWe combine the OxCGRT dataset, Hofstede’s cultural dimensions, and COVID-19 daily reported infection case numbers to train and evaluate five non-time series machine learning models in predicting Confirmed Infection Growth. We use three validation methods – in-distribution, out-of-distribution, and country-based cross-validation – for evaluation, each applicable to a different use case of the models.ResultsOur results demonstrate high R2 values between the labels and predictions for the in-distribution, out-of-distribution, and country-based cross-validation methods (0.959, 0.513, and 0.574 respectively) using random forest and AdaBoost regression. While these models may be used to predict the Confirmed Infection Growth, the differing accuracies obtained from the three tasks suggest a strong influence of the use case.ConclusionsThis work provides new considerations in using machine learning techniques with non-pharmaceutical interventions and cultural dimensions data for predicting the national growth of confirmed infections of COVID-19.
Population dynamics of multi-host communities attacked by a common parasitoid
Authors: Singh Abhyudai 
Published: January 2021

AbstractWe model population dynamics of two host species attacked by a common parasitoid using a discrete-time formalism that captures their population densities from year to year. It is well known starting from the seminal work of Nicholson and Bailey that a constant parasitoid attack rate leads to an unstable host-parasitoid interaction. However, a Type III functional response, where the parasitoid attack rate accelerates with increasing host density stabilizes the population dynamics. We first consider a scenario where both host species are attacked by a parasitoid with the same Type III functional response. Our results show that sufficient fast acceleration of the parasitoid attack rate stabilizes the population dynamics of all three species. For two symmetric host species, the extent of acceleration needed to stabilize the three-species equilibrium is exactly the same as that needed for a single host-parasitoid interaction. However, asymmetry can lead to scenarios where the removal of a host species from a stable interaction destabilizes the interaction between the remaining host species and the parasitoid. Next, we consider a situation where one of the host species is attacked at a constant rate (i.e., Type I functional response), and the other species is attacked via a Type III functional response. We identify parameter regimes where a Type III functional response to just one of the host species stabilizes the three species interaction. In summary, our results show that a generalist parasitoid with a Type III functional response to one or many host species can play a key role in stabilizing population dynamics of host-parasitoid communities in apparent competition.
Pre-Settlement Forests of Southwest Washington: Witness Statements
Authors: Schroeder Tom 
Published: January 2021

AbstractIn the mid-nineteenth century overland immigration into western Washington State passed through lands bracketed by the lower Columbia River and the Pacific Ocean. Witness trees from the region’s first GLO surveys (General Land Office), which preceded settlement, are used to reconstruct the composition, character, and distribution of the region’s natural forests. As such, this investigation augments a similar study of early forests around Puget Sound, situated immediately to the north (Schroeder, 2019). A retrospective species map is constructed from locational information from more than thirty-five thousand witness trees; accompanying tree diameters elucidate size differences by species and geographic locales. Three principal forest types were noted: western hemlock in the rainy western hills, with some Sitka spruce near the coast; Douglas-fir with woodland tree species in the rain-shadowed central plains; and hemlock/Douglas-fir/redcedar mixtures on the lower flanks of the Cascade Range. Although the majority of trees were small or medium in size, a significant fraction was large. All forest types displayed significant amounts of old growth, as judged by screening witness trees against a quantitative model. Mensuration exercises estimate that the region’s pre-settlement tree population approached one-half billion specimens with a timber volume of nearly 50 billion cubic feet.
Predicting chemotherapy response using a variational autoencoder approach
Authors: Wei Qi , Ramsey Stephen A. 
Published: January 2021

AbstractMotivationMultiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clinically annotated for response to chemotherapy. The paucity of labeled examples and high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemotherapy drug response for five cancer types: colon adenocarcinoma, pancreatic adenocarcinoma, bladder carcinoma, sarcoma, and breast invasive carcinoma.ResultsWe found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to-chemotherapy, the unsupervised VAE encoding of the tumor’s gene expression profile leads to better area under the receiver operating characteristic curve (AUROC) classification performance than either the original gene expression profile or the PCA principal components of the gene expression profile, in four out of five cancer types that we tested.Availabilitygithub.com/ATHED/VAE_for_chemotherapy_drug_response_predictionContactramseyst@oregonstate.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Sexual dimorphism in mastoid process volumes measured from 3D models of dry crania from medieval Croatia
Authors: Petaros Anja , Sholts Sabrina B. , Čavka Mislav , Slaus Mario , Wärmländer Sebastian K.T.S. 
Published: January 2021

ABSTRACT3D analysis of skeletal volumes has become an important field in digital anthropology studies. The volume of the mastoid process has been proposed to display significant sexual dimorphism, but it has a complex shape and to date no study has quantified the full mastoid volume for sex estimation purposes. In this study we compared three different ways to isolate the volume of the mastoid process from digital 3D models of dry crania, and then evaluated the performance of the three different volume definitions for sex estimation purposes. A total of 170 crania (86 male, 84 females) excavated from five medieval Croatian sites were CT-scanned and used to produce 3D stereolitographic models. The three different isolation techniques were based on various anatomical landmarks and planes, as well as the anatomy of the mastoid process itself. Measurements of the three different mastoid volumes yielded different accuracies and precisions. Interestingly, anatomical structures were sometimes more useful than classical landmarks as demarcators of mastoid volume. For all three volume definitions, male mastoid volumes were significantly larger than female volumes, in both relative and absolute numbers. Sex estimation based on mastoid volume showed a slightly higher precision and better accuracy (71 % correct classifications) than visual scoring techniques (67 %) and linear distance measurements (69 %) of the mastoid process. Sex estimation based on cranial size performed even better (78 %), and multifactorial analysis (skull size + mastoid volume) reached up to 81% accuracy. These results show that measurements of the mastoid volume represent a promising metric to be used in multifactorial approaches for sex estimation of human remains.
Learning association for single-cell transcriptomics by integrating profiling of gene expression and alternative polyadenylation
Authors: Ji Guoli , Xuan Wujing , Zhuang Yibo , Ye Lishan , Zhu Sheng , Ye Wenbin , Wang Xi , Wu Xiaohui 
Published: January 2021

AbstractSingle-cell RNA-sequencing (scRNA-seq) has enabled transcriptome-wide profiling of gene expressions in individual cells. A myriad of computational methods have been proposed to learn cell-cell similarities and/or cluster cells, however, high variability and dropout rate inherent in scRNA-seq confounds reliable quantification of cell-cell associations based on the gene expression profile alone. Lately bioinformatics studies have emerged to capture key transcriptome information on alternative polyadenylation (APA) from standard scRNA-seq and revealed APA dynamics among cell types, suggesting the possibility of discerning cell identities with the APA profile. Complementary information at both layers of APA isoforms and genes creates great potential to develop cost-efficient approaches to dissect cell types based on multiple modalities derived from existing scRNA-seq data without changing experimental technologies. We proposed a toolkit called scLAPA forlearning association forsingle-cell transcriptomics by combing single-cell profiling of gene expression andalternativepolyadenylation derived from the same scRNA-seq data. We compared scLAPA with seven similarity metrics and five clustering methods using diverse scRNA-seq datasets. Comparative results showed that scLAPA is more effective and robust for learning cell-cell similarities and clustering cell types than competing methods. Moreover, with scLAPA we found two hidden subpopulations of peripheral blood mononuclear cells that were undetectable using the gene expression data alone. As a comprehensive toolkit, scLAPA provides a unique strategy to learn cell-cell associations, improve cell type clustering and discover novel cell types by augmentation of gene expression profiles with polyadenylation information, which can be incorporated in most existing scRNA-seq pipelines. scLAPA is available athttps://github.com/BMILAB/scLAPA.
Crystal structure of the classical MHC-I molecule: insights into the MHC-I system in antiviral diseases in dogs
Authors: Sun Yujiao , Ma Lizhen , Li Shen , Wang Yawen , Xiao Ruiqi , Yang Junqi , Xia Chun 
Published: January 2021

AbstractOnly one classical MHC-I locus (aka DLA-88) evolved in dogs, and thus far, a total of 76 DLA-88 alleles can be divided into two categories. The first category consists of 60 alleles, and the second category consists of 16 alleles. The main difference between the two categories is the insertion of an amino acid in the α2 region of DLA-88 alleles. To elucidate the structure of the first category, in this study, the crystal structure of pDLA-88*001:01 was determined for the first time. The 3D structure and topological characteristics of the ABG of pDLA-88*001:01 with a CDV peptide were analyzed. The viral presentation profile and the binding motif of viruses presented by pDLA-88*001:01 were determined. Most importantly, there were no amino acid insertions in the α2 region of the first category, which changed the conformation of the D pocket and the docking of the TCR. The results suggest obvious differences between the two categories. Because of the variation in the α2 region, pDLA-88*001:01 showed distinctive features in the two categories. Due to the peptide-binding motif of pDLA-88*001:01, more than 320 high-affinity viral peptides were predicted from dog H7N9, CPV, CMV, CMV, and CDV strains. The results reveal that there are two kinds of structural MHC-I systems in dogs that are responsible for CTL immunity against viral diseases. The results provide knowledge for designing viral epitope vaccines in canines.ImportanceDLA plays an important role in the acquired immunity of organism. In previous study, the pMHC-I structure of dog was analyzed with DLA-88 self-peptide. In this study, we screened several viral peptides which can bind to DLA-88 and resolved the structure of the DLA-88 complex binding the CDV peptide. This study enriches the study of canine MHC-I molecular-presenting polypeptide-activated TCR, which is of great significance for the study of canine cellular immunity and anti-viral vaccine development.