bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological analysis of 67 local COVID-19 clusters in Sichuan Province, China
Authors: Mao Suling , Huang Ting , Yuan Heng , Li Min , Huang Xiaomei , Yang Changxiao , Zhou Xingyu , Cheng Xiuwei , Su Qian , Wu Xianping 
Published: May 2020

Abstract
Background This study was intended to investigate the epidemiological characteristics of COVID-19 clusters and the severity distribution of clinical symptoms of involved cases in Sichuan Province, so as to provide information support for the development and adjustment of strategies for the prevention and control of local clusters.Methods The epidemiological characteristics of 67 local clusters of COVID-19 cases in Sichuan Province reported as of March 17, 2020 were described and analyzed. Information about all COVID-19 clusters and involved cases was acquired from the China Information System for Disease Control and Prevention and analyzed with the epidemiological investigation results taken into account.Results The clusters were temporally and regionally concentrated. Clusters caused by imported cases from Wuhan and other provinces except Wuhan accounted for 73.13%; familial clusters accounted for 68.66%; the average attack rate was 8.54%, and the average secondary attack rate was 6.11%; the median incubation period was 8.5 d;a total of 28 cases met the criteria for incubation period determination, and in the 28 cases, the incubation period was > 14 d in 21.43% (6/28). a total of 226 confirmed cases were reported in the 67 clusters. Ten cases were exposed before the confirmed cases they contacted with developed clinical symptoms, and the possibility of exposure to other infection sources was ruled out; two clusters were caused by asymptomatic carriers; confirmed cases mainly presented with fever, respiratory and systemic symptoms; a gradual decline in the severity of clinical symptoms was noted with the increase of the case generation.Conclusions Population movement and gathering restrictions and strict close contact management measures will significantly contribute to the identification and control of cases. Transmission during the incubation period and asymptomatic infections have been noted. Studies on the pathogenicity and transmissibility in these populations and on COVID-19 antibody levels and protective effects in healthy people and cases are required.
Uterine Transcriptome Analysis Reveals Mechanism Underlying the Ultrastructure Differences of Eggshell in Young and Aged Laying Hens
Authors: Feng Jia , Zhang Hai-jun , Wu Shu-geng , Qi Guang-hai , Wang J. 
Published: May 2020

Abstract
Background: Lower eggshell quality in the late laying period leads to economic loss. It is a major threat to the quality and safety of egg products. Age-related variations in ultrastructure were thought to induce this deterioration. Eggshell mineralization is a highly complex process under precise regulation of genes and biological pathways in uterus of laying hens. Herein, we evaluated the physical, mechanical and ultrastructure properties of eggshell and conducted RNA sequencing to learn the transcriptomic differences in uterus between laying hens in the peak (young hens) and late phase (aged hens) of production.Results: The declined breaking strength and fracture toughness of eggshell were observed in aged hen group compared to those in young hen group, accompanied with ultrastructure variations including the increased thickness of mammillary layer and the decreased incidence of early fusion. During the initial stage of eggshell formation, a total of 183 differentially expressed genes (DEGs; 125 upregulated and 58 downregulated) were identified in uterus of laying hens in the late phase in relative to those at peak production. The DEGs annotated to Gene Ontology terms related to antigen processing and presentation were downregulated in aged hens compared to young hens. The contents of proinflammatory cytokine IL-1β in uterus were higher in aged hens relative to those in young hens. Besides, the genes of some matrix proteins potentially involved in eggshell mineralization, such as ovalbumin, versican and glypican 3, were also differentially expressed between two groups.Conclusions: Altered gene expression of matrix proteins along with the compromised immune function in uterus of laying hens in the late phase of production may conduce to age-related impairments of eggshell ultrastructure and mechanical properties. The current study enhances our understanding of the age-related deteriorations in eggshell ultrastructure and provides potential targets for improvement of eggshell quality in the late laying period.
The trend of morbidity and mortality of Coronavirus disease 2019 under the first-level public health emergency response in China
Authors: Xu Jingya , Lin Xiling , Pan Xiaowen , Huang Xin , Chen Ying , Zhou Enjie , Wu Zhaoyuan , Zou Yuxuan , Xu Feng , Ren Yuezhong , Shan Peng-Fei 
Published: May 2020

Abstract
Background The ongoing outbreak of Coronavirus disease 2019 (COVID-19) has led to declaration of public health emergency of international concern by World Health Organization and the first-level public health emergency response in China. We aimed to share the Joint Prevention and Control Mechanism taken in Mainland China and evaluate the effectiveness.Methods A powerful Joint Prevention and Control Mechanism was adopted to fight against COVID-19 in Mainland China. Data were collected from the daily epidemic reports released by the national and provincial health commissions of China from January 21 to April 6, 2020. Global data were collected from daily situation reports by World Health Organization.Results As of April 6, 2020, there were 81,740 confirmed COVID-19 cases (32 new) in Mainland China. The case fatality ratio was 4.74% and 0.85% in and outside Hubei respectively. It is gratifying to see that there were up to 22 provinces reporting zero new infections, but it can’t be ignored that there were 1,196,651 confirmed cases (68,700 new) reported in over 221 countries and territories outside China and the total death number were 69,274, nowadays China is facing great challenges of imported cases.Conclusions Great achievements have been made in controlling the spread of COVID-19 in Mainland China, but it is still a major challenge worldwide. The comprehensive and powerful control measures taken by Mainland China have proved to be effective and might be applicable to other regions.
A SNP-Based Linkage Map and QTL Identification for Resistance to Yam Anthracnose Disease (YAD) in Water Yam (Dioscorea alata)
Authors: Darkwa Kwabena , AGRE Paterne , Olasanmi Bunmi , Kolade Olufisayo , Mournet Pierre , Lopez-Montes Antonio , Dekoeyer David , Adebola Patrick , Kumar Lava P. , Asiedu Robert , Asfaw Asrat 
Published: May 2020

Abstract
Background: Yam anthracnose disease (YAD) caused by Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Development of resistant cultivars have been a prime target for sustainable management of anthracnose in water yam. Molecular breeding tools are required to expedite the development of improved yam varieties. QTL analysis using high density genetic maps serve as a powerful tool to discover key locations of quantitave traits. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata.Results: In this study, two contrasting parents for yam anthracnose disease reaction and their 204 full- sib offspring were used to develop a high-density genetic linkage map with 3,257 SNP markers by the GBS technique. The total length of the consensus map was 1460.94 cM with an average of 163 markers per chromosome. Four QTLs were detected for anthracnose disease resistance in 4 locations on 3 chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 10 to 13%. Plant defense response genes including GDSL-like Lipase/Acylhydrolase, Protein kinase domain and F-box protein were also detected within the QTL regions. Conclusion: The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers and putative genes identified herewith form a relevant resource to apply marker-assisted selection as alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.
Frequent birth-and-death events throughout perforin-1 evolution
Authors: Araujo-Voces Miguel , Quesada Victor 
Published: May 2020

Abstract
Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci with important variations in the number of copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.
Ultrasonographic diagnosis, classification, and treatment of cervical lymphatic malformation in paediatric patients: a retrospective study
Authors: Li Jiaoling , Zhong Wei , Geng Xiuping , Liu Xiaofang , Zhang Xiangxiang , Wang Yurun , Li Haibo 
Published: May 2020

Abstract
Background: To explore the imaging features, key diagnostic points, classification, treatment, and prognosis of cervical lymphatic malformation. Methods: Overall, 320 patients diagnosed with cervical lymphatic malformation were retrospectively analysed in our hospital between 1 January 2014 and 31 December 2017. Imaging modalities included colour Doppler ultrasound, magnetic resonance imaging, and contrast-enhanced computed tomography. Cervical lymphatic malformations were classified by cyst diameter. Treatments included interventional therapy, surgery, and expectant treatment. Results: Cervical lymphatic malformation was identified in 320 of 1,192 patients with lymphatic malformation, the sensitivity of ultrasonographic diagnosis was 99.38% (318/320). Cervical lymphatic malformation was classified as mixed, macrocystic, and microcystic in 184 (57.5%), 117 (36.56%), and 19 (5.94%) patients, respectively. Sixty-four (20%), ten (3.12%), seven (2.19%), and three (0.94%) patients experienced intracystic haemorrhage, infection, concurrent intracystic haemorrhage and infection, and calcification, respectively. Among 260 (81.25%) patients who underwent interventional sclerotherapy, 163 (50.94%) received it once and 96 (30%) received it two or more times. Twenty-eight (8.75%), five (1.56%), and 27 (8.44%) patients underwent surgical resection, interventional sclerotherapy plus surgery, and expectant management, respectively. Conclusions: Ultrasonography is useful for diagnosing definitely cervical lymphatic malformation. Interventional therapy is the first choice for children with confirmed cervical lymphatic malformation.
Comparison of ‘Mental Training’ and Physical Practice in the Mediation of a Structured Facial Examination
Authors: Nelskamp Arne , Schnurr Benedikt , Sterz Jasmina , Lorenz Jonas , Sader Robert , Rüsseler Miriam , Seifert Lukas Benedikt 
Published: May 2020

Abstract
Background: The correct performance of a structured facial examination presents a fundamental clinical skill to detect facial pathologies. However, many students are not adequately prepared in this basic clinical skill. Many argue that the traditional ‘See One, Do One’ approach is not sufficient to fully master a clinical skill. ‘Mental Training’ has successfully been used to train psychomotor and technical skills in sports and other surgical fields, but its use in Oral and Maxillofacial Surgery is not described. We conducted a fully randomized experiment to determine if ‘Mental Training’ was effective in teaching a structured facial examination.Methods: 67 students were randomly assigned to a ‘Mental Training’ and ‘See One, Do One’ group. Both groups received standardized video instruction on how to perform a structured facial examination. The ‘See One, Do One’ group then received 60 minutes of guided physical practice while the ‘Mental Training’ group actively developed a detailed, stepwise sequence of the performance of a structured facial examination and visualized this sequence subvocally before practicing the skill. Student performance was measured shortly after (T1) and five to ten weeks (T2) after the training by two blinded examiners (E1 and E2) using a validated checklist.Results: Groups did not differ in gender, age or in experience. The ‘Mental Training’ group averaged significantly more points in T1 (pE1 = 0.00012; pE2 = 0.004) and T2 (pE1 = 0.04; pE2 = 0.008) than the ‘See One, Do One’ group. The intragroup comparison showed a significant (pE1 = 0.0002; pE2 = 0.06) increase in knowledge in the ‘See One, Do One’ group, while the ‘Mental Training’ group maintained an already high level of knowledge between T1 and T2. Gender analysis showed a significant difference in favor of female students at T1 for Rater 1 (pE1 = 0.03).Discussion: ‘Mental Training’ is an efficient tool to teach and maintain basic clinical skills. In this study ‘Mental Training’ was shown to be superior to the commonly used ‘See One, Do One’ approach in learning how to perform a structured facial examination and should therefore be considered more often to teach basic surgical skills.
Patient Perceptions of Students in a Longitudinal Clerkship in Taiwan: A Qualitative Study
Authors: Chang Yaw-Wen , Hirsh David A. , Fang Wen-Hui , Li Honghe , Tzeng Wen-Chii , Kao Senyeong 
Published: May 2020

Abstract
Background:Patient-centered care is a core component of medical professionalism. East Asian cultures hold different conceptualizations of medical professionalism than Western cultures. To support patient-centered care, education leaders in Taiwan restructured clinical education and implemented the first longitudinal integrated clerkship (LIC) in East Asia. We aimed to investigate patients’ perceptions of longitudinal relationships with the LIC students within Taiwan’s Confucian cultural and social context.Methods:We invited patients or their family members who were cared for longitudinally by a LIC student to participate in the study. Participating patients or their family members undertook semi-structured interviews. We analyzed data qualitatively using a general inductive approach to identify themes in the patients’ descriptions of their experiences interacting with the LIC students.Results:Twenty-five patients and family members participated in interviews: 16 patients and 9 family members. Qualitative analysis of interview transcripts identified three themes from patients’ experience receiving care from their LIC students: care facilitation, companionship, and empathy. To provide care facilitation, LIC students served as a bridge between the physicians and patients. Students served patients by reminding, consulting, tracking disease progression, and researching solutions for problems. To provide companionship, students accompanied patients interpersonally like a friend or confidant who listens and provides a presence for patients. To provide empathy, patients reported that students showed sincere concern for patients’ experience, feelings, and mood.Conclusion: In our study, Taiwanese patients’ perspectives of LIC students suggested the value of care facilitation, companionship, and empathy. We discuss these themes within the context of Confucian culture and the Taiwanese context of care.
Clinical and echocardiographic management of patients with Chronic Heart Failure and Type 2 Diabetes Mellitus: the SCODIAC Follow up Study
Authors: Luca Mariarosaria De , Bosso Giorgio , Valvano Antonio , Guardasole Vincenzo , Botta Amodio , Carbone Vincenzo , Carella Giovanni , Buono Andrea Del , Giovanni Giuseppe Di , Fimiani Biagio , Guarnaccia Franco , Lapice Emanuela , Martedì Emilia , Memoli Giuseppe , Oliva Domenica , Romano Geremia , Cittadini Antonio , Zito Giovanni Battista , Oliviero Ugo 
Published: May 2020

Abstract
Background

SCODIAC study revealed an increasing use of SGLT2 inhibitors in 123 patients affected with Heart Failure (HF) and Type 2 Diabetes Mellitus (T2DM), referred to Cardiologists and Diabetologists of the pertaining healthcare districts. SCODIAC Follow Up, the second phase of the program, has been carried out to determine diagnostic and therapeutic pathways in a larger group of HF diabetic patients and to verify whether the use of innovative antidiabetic therapies could modify echocardiographic parameters and influence cardiological therapy.
Methods

406 patients affected with HF and T2DM, referred to Cardiologists and Diabetologists of pertaining healthcare districts in Campania, and followed for at least one year between 2018 and 2019, were enrolled in this retrospective study and divided in Group A, composed of 136 HF diabetic patients with preserved Ejection Fraction (HF-pEF) (> 45%) and Group B, formed of 270 HF diabetic patients with reduced EF (HF-rEF) (≤ 45%). All patients had performed periodic clinical evaluations and an echocardiographic exam every 12 months. Anthropometric parameters, HF etiology, co-morbidities, complications and ongoing therapies were collected.
Results

The clinical and laboratory parameters and the treatments adopted were assessed at beginning and after 12 months of treatment. The antidiabetic therapies resulted modified after one year with a greater use of GLP1 AR, gliptins and SGLT2i. Cardiological therapy resulted also modified with a greater use of ARNI and a reduction of ACE inhibitors and ARBs in HF-rEF patients. At the end of the study echocardiography E velocity, A velocity and E/E’ ratio resulted markedly reduced in 25 HF-pEF patients and in 60 HF-rEF patients treated with SGLT2i, in respect to both the whole sample of subjects at beginning and the other diabetic patients, while LAVi resulted reduced only in HF-pEF patients and EF increased only in HF-rEF patients.
Conclusions

The approach to the patients with HF and T2DM must necessarily take place in the healthcare districts and be multidisciplinary and integrated in order to tailor therapy to the characteristics of the patient. SGLT2i could improve left ventricular function in HF-rEF patients and modify cardiological therapeutic approach, almost in this setting of patients.
Trial registration:

The protocol was approved by the University of Naples Federico II Ethics Committee and registered at ClinicalTrial.gov (CT04375943). The principles outlined in the Declaration of Helsinki were followed.
T-CNV: a robust tool for detecting and visualizing copy number variants in targeted sequencing data.
Authors: ye liu , yangming wu , zexin zheng , tianliangwen zhou 
Published: May 2020

Abstract
Background Copy number variants (CNVs) are widespread among human genes, causing Mendelian or sporadic traits, or associating with complex diseases. Several tools have been developed for CNV assessment based on next generation sequencing (NGS) data using Read-depth (RD) strategy. However, maintaining high level of sensitivity and specificity is always challenging. Here, we present a novel, powerful, user-friendly and open accessed tool, T-CNV for CNV detection and visualization in targeted NGS panel.Results T-CNV consists of primary CNV detection and CNV candidates confirmation steps. After computing log2 values of normalized read depth ratio of tumor and normal/control sample, T-CNV confirms each possible CNV candidates by bins method, Gaussian Mixture Model (GMM) clustering approach and window-sliding method. We benchmarked its capacity with MLPA-validated dataset. Compared to three other advanced tools, T-CNV presents excellent performance with 95.42% sensitivity, 99.93% specificity and 93.63% positive predict value in MLPA-validated dataset, while achieving satisfactory performance in simulation study (sensitivity 65.95%, positive predict value 88.71% at coverage 100X).Conclusions T-CNV is a novel and robust tool for CNV detection and visualization in targeted NGS panel consisting of determination of possible CNV candidates and further confirmation by three different methods. It’s publicly available at https://github.com/Top-Gene/T-CNV.
Skin Transcriptome Analysis Identifies the Key Genes Underlying Fur Development in Chinese Tan Sheep in the Birth and Er-mao Periods
Authors: Li ya chao , Hui Ma Yue , Ma Qin , Ding Wei , Chen Yong Hong , Zhang Meng , Luo Fang , Chen Li Yao , He Dong Qian , Wang Jun Kui , Jiang Lin , Li Ying Kang , Tao Jin Zhong 
Published: May 2020

Abstract
BackgroundHairfollicle development in Tan sheepdiffers significantly between the birth and Er-mao periods, but the underlying molecular mechanism is still unclear.MethodsWe profiled the skin transcriptomes of Tan sheepinthe birth and Er-mao periods via RNA-seq technology. TheTan sheep examined consisted ofthree sheep inthe birth period and threesheep inthe Er-mao period. ResultsA total of 364 differentially expressed genes (DEGs) in the skin of Tan sheepbetweenthe birth period and the Er-mao period were identified, among which 168 were upregulated and 196 were downregulated. Interestingly, the FOS proto-oncogene(FOS)(fold change=22.67, P value=2.15*10^-44)was the most significantly differentially expressed gene. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the FOS gene was significantly enriched in the signaling pathway related to hair follicle development. Immunohistochemical analysis showed that the FOS gene was expressed in the skin of Chinese Tan sheep at the birth and Er-mao periods,with abnormally high expression in the Er-mao period. Conclusions Our findings suggest that the FOS gene promotes hair follicle development in Tan sheep.