bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genetic basis of natural antibody titers of young healthy pigs and relationships with disease resilience
Authors: Chen Yulu , Tibbs-Cortes Laura E. , Ashley Carolyn , Putz Austin M. , Lim Kyu-Sang , Dyck Michael K. , Fortin Frederic , Plastow Graham S. , Dekkers Jack C. M. , Harding John C. S. ,   PigGen Canada, Canada Pig Gen 
Published: October 2020

AbstractBackgroundDisease resilience is the ability to maintain performance under pathogen exposure but is difficult to select for because breeding populations are raised under high health. Selection for resilience requires a trait that is heritable, easy to measure on healthy animals, and genetically correlated with resilience. Natural antibodies (NAb) are important parts of the innate immune system and are found to be heritable and associated with disease susceptibility in dairy cattle and poultry. Our objective was to investigate NAb and total IgG in blood of healthy, young pigs as potential indicator traits for disease resilience.ResultsData were from Yorkshire x Landrace pigs, with IgG and IgM NAb (four antigens) and total IgG measured by ELISA in blood plasma collected ~ 1 week after weaning, prior to their exposure to a natural polymicrobial challenge. Heritability estimates were lower for IgG NAb (0.12 to 0.24,+ 0.05) and for total IgG (0.19 + 0.05) than for IgM NAb (0.33 to 0.53,+ 0.07) but maternal effects were larger for IgG NAb (0.41 to 0.52,+ 0.03) and for total IgG (0.19 + 0.05) than for IgM NAb (0.00 to 0.10,+ 0.04). Phenotypically, IgM NAb titers were moderately correlated with each other (average 0.60), as were IgG NAb titers (average 0.42), but correlations between IgM and IgG NAb titers were weak (average 0.09). Phenotypic correlations of total IgG were moderate with NAb IgG (average 0.46) but weak with NAb IgM (average 0.01). Estimates of genetic correlations among NAb showed similar patterns but with small SE, with estimates averaging 0.76 among IgG NAb, 0.63 among IgM NAb, 0.17 between IgG and IgM NAb, 0.64 between total IgG and IgG NAb, and 0.13 between total IgG and IgM NAb. Phenotypically, pigs that survived had slightly higher levels of NAb and total IgG than pigs that died. Genetically, higher levels of NAb tended to be associated with greater disease resilience based on lower mortality and fewer parenteral antibiotic treatments. Genome-wide association analyses for NAb titers identified several genomic regions, with several candidate genes for immune response.ConclusionsLevels of NAb in blood of healthy young piglets are heritable and potential genetic indicators of resilience to polymicrobial disease.
Multi-scale supervised clustering-based feature selection for tumor classification and identification of biomarkers and targets on genomic data
Authors: Xu Da , Zhang Jialin , Xu Hanxiao , Zhang Yusen , Chen Wei , Gao Rui , Dehmer Matthias 
Published: October 2020

Abstract
Background
The small number of samples and the curse of dimensionality hamper the better application of deep learning techniques for disease classification. Additionally, the performance of clustering-based feature selection algorithms is still far from being satisfactory due to their limitation in using unsupervised learning methods. To enhance interpretability and overcome this problem, we developed a novel feature selection algorithm. In the meantime, complex genomic data brought great challenges for the identification of biomarkers and therapeutic targets. The current some feature selection methods have the problem of low sensitivity and specificity in this field.

Results
In this article, we designed a multi-scale clustering-based feature selection algorithm named MCBFS which simultaneously performs feature selection and model learning for genomic data analysis. The experimental results demonstrated that MCBFS is robust and effective by comparing it with seven benchmark and six state-of-the-art supervised methods on eight data sets. The visualization results and the statistical test showed that MCBFS can capture the informative genes and improve the interpretability and visualization of tumor gene expression and single-cell sequencing data. Additionally, we developed a general framework named McbfsNW using gene expression data and protein interaction data to identify robust biomarkers and therapeutic targets for diagnosis and therapy of diseases. The framework incorporates the MCBFS algorithm, network recognition ensemble algorithm and feature selection wrapper. McbfsNW has been applied to the lung adenocarcinoma (LUAD) data sets. The preliminary results demonstrated that higher prediction results can be attained by identified biomarkers on the independent LUAD data set, and we also structured a drug-target network which may be good for LUAD therapy.

Conclusions
The proposed novel feature selection method is robust and effective for gene selection, classification, and visualization. The framework McbfsNW is practical and helpful for the identification of biomarkers and targets on genomic data. It is believed that the same methods and principles are extensible and applicable to other different kinds of data sets.
Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars
Authors: Ding Haisheng , Liu Min , Zhou Changfan , You Xiangbin , Su Tao , Yang Youbing , Xu Dequan 
Published: October 2020

Abstract
Background
MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis.

Results
In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p.

Conclusions
This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.
New contributions to two ciliate genera (Ciliophora, Heterotrichea) based on morphological and molecular analyses, with description of a new Gruberia species
Authors: Chi Yong , Li Yuqing , Zhang Qianqian , Ma Mingzhen , Warren Alan , Chen Xiangrui , Song Weibo 
Published: October 2020

Abstract
Background
Heterotrichous ciliates are common members of microeukaryote communities which play important roles in both the transfer of material and the flow of energy in aquatic food webs. This group has been known for over two centuries due to their large body size and cosmopolitan distribution. Nevertheless, species identification and phylogenetic relationships of heterotrichs remain challenging due to the lack of accurate morphological information and insufficient molecular data.

Results
The morphology and phylogeny of two heterotrichous ciliates, namely Gruberia foissneri spec. nov. and Linostomella vorticella (Ehrenberg, 1833) Aescht in Foissner et al., 1999, were studied using rigorous methods (living morphology, stained preparations, and small subunit rDNA sequence data). Gruberia foissneri spec. nov. is morphologically very similar to G. uninucleata Kahl, 1932, however, it can be distinguished from the latter by having more ciliary rows (about 32 vs. about 20) and macronuclear shape (sausage-shaped vs. ellipsoid). Based on a combination of previous and present studies, an improved diagnosis of L. vorticella is supplied and several taxonomic anomalies are clarified. In addition, phylogenetic analyses based on SSU rDNA sequence data support the generic assignment of these two species.

Conclusions
Modern ciliate taxonomy should be performed by means of detailed living observation, stained preparations and molecular information. For those species that have been reported in previous studies, it is necessary to provide as much useful information as possible using state-of-the-art methods in order to resolve taxonomic anomalies.
Isolation and effect of Trichoderma citrinoviride Snef1910 for the biological control of root-knot nematode, Meloidogyne incognita
Authors: Fan Haiyan , Yao Meiling , Wang Haiming , Zhao Di , Zhu Xiaofeng , Wang Yuanyuan , Liu Xiaoyu , Duan Yuxi , Chen Lijie 
Published: October 2020

Abstract
Background
Root-knot nematode is one of the most significant diseases of vegetable crops in the world. Biological control with microbial antagonists has been emerged as a promising and eco-friendly treatment to control pathogens. The aim of this study was to screen and identify novel biocontrol agents against root-knot nematode, Meloidogyne incognita.

Results
A total of 890 fungal isolates were obtained from rhizosphere soil of different crops and screened by nematicidal activity assays. Snef1910 strain showed high virulence against second stage juveniles (J2s) of M. incognita and identified as Trichoderma citrinoviride by morphology analysis and biomolecular assay. Furthermore, T. citrinoviride Snef1910 significantly inhibited egg hatching with the hatching inhibition percentages of 90.27, 77.50, and 67.06% at 48, 72, and 96 h after the treatment, respectively. The results of pot experiment showed that the metabolites of T. citrinoviride Snef1910 significantly decreased the number of root galls, J2s, and nematode egg masses and J2s population density in soil and significantly promoted the growth of tomato plants. In the field experiment, the biocontrol application showed that the control efficacy of T. citrinoviride Snef1910 against root-knot nematode was more than 50%. Meanwhile, T. citrinoviride Snef1910 increased the tomato plant biomass.

Conclusions
T. citrinoviride strain Snef1910 could be used as a potential biological control agent against root-knot nematode, M. incognita.
Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut
Authors: Yuan Cuiling , Li Chunjuan , Lu Xiaodong , Zhao Xiaobo , Yan Caixia , Wang Juan , Sun Quanxi , Shan Shihua 
Published: October 2020

Abstract
Background
Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut.

Results
We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results.

Conclusion
Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.
Familial dilated cardiomyopathy caused by a novel variant in the Lamin A/C gene: a case report
Authors: Huang Jing , Wan Qing , Zou Yu , Wang Lijie , Pan Yesheng 
Published: October 2020

Abstract
Background
Familial dilated cardiomyopathy (FDCM) is most commonly inherited as an autosomal dominant trait. The Lamin A/C (LMNA) gene variants have been identified to be associated with DCM, conductive system disorders, type 2 Emery-Dreifuss muscular dystrophy and several other disorders. Here, we reported a novel variant in the LMNA gene that might be related to FDCM.

Case presentation
A 30-year-old young man was hospitalized for chest tightness, extreme fatigue, palpitation and impaired activity tolerance. He had clinical characteristics including cardiac dilatation, atrial tachyarrhythmia, severe conductive system disorders, and dyskinesia of both upper limbs and the neck. Genetic sequence analysis indicated that the patient carried a novel c.1325 T>C heterozygous LMNA gene variant. Catheter ablation and cardiac resynchronization therapy with pacing function (CRT-P) were performed to treat the arrhythmia.

Conclusion
The variant c.1325 T>C is a novel variant in the LMNA gene that has not been previously reported. Young patients with DCM, conductive system disorders and skeletal myopathy should be alert to the possibility of LMNA gene variant. Cardiac resynchronization therapy (CRT) may be a reasonable choice for patient carrying a LMNA gene variant with third-degree atrioventricular block even if the left ventricular ejection fraction is preserved in order to prevent the deterioration of cardiac function caused by right ventricular pacing dependency.
Identifying the fundamental structures and processes of care contributing to emergency general surgery quality using a mixed-methods Donabedian approach
Authors: Santry Heena P. , Strassels Scott A. , Ingraham Angela M. , Oslock Wendelyn M. , Ricci Kevin B. , Paredes Anghela Z. , Heh Victor K. , Baselice Holly E. , Rushing Amy P. , Diaz Adrian , Daniel Vijaya T. , Ayturk M. Didem , Kiefe Catarina I. 
Published: October 2020

Abstract
Background
Acute Care Surgery (ACS) was developed as a structured, team-based approach to providing round-the-clock emergency general surgery (EGS) care for adult patients needing treatment for diseases such as cholecystitis, gastrointestinal perforation, and necrotizing fasciitis. Lacking any prior evidence on optimizing outcomes for EGS patients, current implementation of ACS models has been idiosyncratic. We sought to use a Donabedian approach to elucidate potential EGS structures and processes that might be associated with improved outcomes as an initial step in designing the optimal model of ACS care for EGS patients.

Methods
We developed and implemented a national survey of hospital-level EGS structures and processes by surveying surgeons or chief medical officers regarding hospital-level structures and processes that directly or indirectly impacted EGS care delivery in 2015. These responses were then anonymously linked to 2015 data from the American Hospital Association (AHA) annual survey, Medicare Provider Analysis and Review claims (MedPAR), 17 State Inpatient Databases (SIDs) using AHA unique identifiers (AHAID). This allowed us to combine hospital-level data, as reported in our survey or to the AHA, to patient-level data in an effort to further examine the role of EGS structures and processes on EGS outcomes. We describe the multi-step, iterative process utilizing the Donabedian framework for quality measurement that serves as a foundation for later work in this project.

Results
Hospitals that responded to the survey were primarily non-governmental and located in urban settings. A plurality of respondent hospitals had fewer than 100 inpatient beds. A minority of the hospitals had medical school affiliations.

Discussion
Our results will enable us to develop a measure of preparedness for delivering EGS care in the US, provide guidance for regionalized care models for EGS care, tiering of ACS programs based on the robustness of their EGS structures and processes and the quality of their outcomes, and formulate triage guidelines based on patient risk factors and severity of EGS disease.

Conclusions
Our work provides a template for team science applicable to research efforts combining primary data collection (i.e., that derived from our survey) with existing national data sources (i.e., SIDs and MedPAR).
Fishbone foreign body ingestion in duodenal papilla: a cause of abdominal pain resembling gastric ulcer
Authors: Yi Lizhi , Cheng Zhengyu , Zhou Yafei , Wang Qin , Liu Yangyang , Liu Ke , Wang Tao , Zhong Xianfei 
Published: October 2020

Abstract
Background
Foreign body ingestion is a common clinical problem. The upper esophagus is the most common site of foreign body, accounting for more than 75% of all cases, but cases with a foreign body in the duodenal papilla or common bile duct are rarely reported.

Case presentation
Herein, we report a rare case that a patient’s abdominal pain resembling gastric ulcer was caused by a 3 cm long fishbone inserted into the duodenal papilla.

Conclusion
Fishbone inserted into the duodenal papilla can cause an abdominal pain resembling gastric ulcer. Endoscopy is useful for the diagnosis and treatment of fishbone ingestion in clinical.
Is kidney function associated with cognition and mood in late life?
Authors: Tap Lisanne , Corsonello Andrea , Formiga Francesc , Moreno-Gonzalez Rafael , Ärnlöv Johan , Carlsson Axel C. , Roller-Wirnsberger Regina , Wirnsberger Gerhard , Ziere Gijsbertus , Freiberger Ellen , Sieber Cornel , Kostka Tomasz , Guligowska Agnieszka , Gil Pedro , Martinez Sara Lainez , Artzi-Medvedik Rada , Yehoshua Ilan , Fabbietti Paolo , Lattanzio Fabrizia , Mattace-Raso Francesco ,   on behalf of SCOPE investigators, Corsonello Andrea , Bustacchini Silvia , Bolognini Silvia , D’Ascoli Paola , Moresi Raffaella , Di Stefano Giuseppina , Giammarchi Cinzia , Bonfigli Anna Rita , Galeazzi Roberta , Lenci Federica , Bella Stefano Della , Bordoni Enrico , Provinciali Mauro , Giacconi Robertina , Giuli Cinzia , Postacchini Demetrio , Garasto Sabrina , Cozza Annalisa , Guarasci Francesco , D’Alia Sonia , Firmani Romano , Nacciariti Moreno , Di Rosa Mirko 
Published: October 2020

Abstract
Background
Chronic kidney disease (CKD), cognitive impairment and depression share common risk factors. Previous studies did not investigate the possible association between kidney function and cognitive and mood disorders in older persons in a broad range of kidney function. The present study explored associations between kidney function, cognition and mood in outpatients of 75 years and over.

Methods
Baseline data of 2252 participants of the SCOPE study, an international multicenter cohort observational study,were used in which community-dwelling persons of 75 years and over were enrolled to screen for CKD Kidney function was estimated with the BIS1-eGFR equation, cognition was assessed with the Mini-Mental State Examination (MMSE) and mood with the Geriatric Depression Scale 15 items (GDS-15). Characteristics were compared across stages of CKD. Mean eGFR values were also compared across categories of MMSE (< 24, 24–26, ≥27) and between groups with high and low score on the GDS-15 (> 5/≤5).

Results
In total, 63% of the population had an eGFR < 60 mL/min. In advanced stages of CKD, participants were older and more often men than in earlier stages (p < 0.001). Cardiovascular diseases and diabetes mellitus were more often found in those in advanced stages of CKD (p < 0.001), and also cumulative comorbidity scores were higher than in those in earlier stages (p < 0.001). Median MMSE was 29 in CKD stage 1–2 and 3, and 30 in CKD stage 4, whereas median GDS-15 score was 2 in all stages of CKD. Mean values of eGFR did not differ across categories of MMSE or between groups with high and low score on the GDS-15. Stratification for albuminuria did not change these results.

Conclusions
Older persons in more advanced stages of CKD did not have lower cognitive scores or higher rates of depressive symptoms than older persons in earlier stages. Future longitudinal studies might give information on the possible effect of kidney function on cognition and mood in late life.

Trial registration
This study was registered prospectively on 25th February 2016 at clinicaltrials.gov (NCT02691546).
Kaumātua Mana Motuhake Pōi: a study protocol for enhancing wellbeing, social connectedness and cultural identity for Māori elders
Authors: Hokowhitu Brendan , Oetzel John G. , Simpson Mary Louisa , Nock Sophie , Reddy Rangimahora , Meha Pare , Johnston Kirsten , Jackson Anne-Marie , Erueti Bevan , Rewi Poia , Warbrick Isaac , Cameron Michael P. , Zhang Yingsha , Ruru Stacey 
Published: October 2020

AbstractBackgroundThe Aotearoa New Zealand population is ageing accompanied by health and social challenges including significant inequities that exist between Māori and non-Māori around poor ageing and health. Although historically kaumātua (elder Māori) faced a dominant society that failed to realise their full potential as they age, Māori culture has remained steadfast in upholding elders as cultural/community anchors. Yet, many of today’s kaumātua have experienced ‘cultural dissonance’ as the result of a hegemonic dominant culture subjugating an Indigenous culture, leading to generations of Indigenous peoples compelled or forced to dissociate with their culture. The present research project, Kaumātua Mana Motuhake Pōī (KMMP) comprises two interrelated projects that foreground dimensions of wellbeing within a holistic Te Ao Māori (Māori epistemology) view of wellbeing. Project 1 involves a tuakana-teina/peer educator model approach focused on increasing service access and utilisation to support kaumātua with the greatest health and social needs. Project 2 focuses on physical activity and cultural knowledge exchange (including te reo Māori--Māori language) through intergenerational models of learning.MethodsBoth projects have a consistent research design and common set of methods that coalesce around the emphasis on kaupapa kaumatua; research projects led by kaumātua and kaumātua providers that advance better life outcomes for kaumātua and their communities. The research design for each project is a mixed-methods, pre-test and two post-test, staggered design with 2–3 providers receiving the approach first and then 2–3 receiving it on a delayed basis. A pre-test (baseline) of all participants will be completed. The approach will then be implemented with the first providers. There will then be a follow-up data collection for all participants (post-test 1). The second providers will then implement the approach, which will be followed by a final data collection for all participants (post-test 2).DiscussionTwo specific outcomes are anticipated from this research; firstly, it is hoped that the research methodology provides a framework for how government agencies, researchers and relevant sector stakeholders can work with Māori communities. Secondly, the two individual projects will each produce a tangible approach that, it is anticipated, will be cost effective in enhancing kaumātua hauora and mana motuhake.Trial registrationAustralia New Zealand Clinical Trial Registry (ACTRN12620000316909).Registered6 March 2020.