bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of climatic factors on the seasonal fluctuation of human brucellosis in Yulin, Northern China
Authors: Liu Kun , Yang Zurong , Liang Weifeng , Guo Tianci , Long Yong , Shao Zhongjun 
Published: December 2019

Abstract
Background: Brucellosis is a serious public health problem primarily affecting livestock workers. The strong seasonality of the disease indicates that climatic factors may play important roles in the transmission of the disease. However, the associations between climatic variability and human brucellosis are still poorly understood. Methods: Data for a 14-year series of human brucellosis cases and seven climatic factors were collected in Yulin City from 2005 to 2018, one of the most endemic areas in northern China. Using cross-correlation analysis, the Granger causality test, and a distributed lag non-linear model (DLNM), we assessed the quantitative relationships and exposure-lag-response effects between monthly climatic factors and human brucellosis.Results: A total of 7,103 cases of human brucellosis were reported from 2005 to 2018 in Yulin City with a distinct peak between April and July each year. Seasonal fluctuations in the transmission of human brucellosis were significantly affected by temperature, sunshine duration, and evaporation. The effects of climatic factors were non-linear over the 6-month period, and higher values of these factors usually increased disease incidence. The maximum separate relative risk (RR) was 1.36 (95% confidence interval [CI], 1.03–1.81) at a temperature of 17.4 °C, 1.12 (95% CI, 1.03–1.22) with 311 hours of sunshine, and 1.18 (95% CI, 0.94–1.48) with 314 mm of evaporation. In addition, the effects of these three climatic factors were cumulative, with the highest RRs of 2.27 (95% CI, 1.09–4.57), 1.54 (95% CI, 1.10–2.18), and 1.27 (95% CI, 0.73–2.14), respectively. Conclusions: In Yulin, northern China, variations in climatic factors, especially temperature, sunshine duration, and evaporation, contributed significantly to seasonal fluctuations of human brucellosis within 6 months. The key determinants of brucellosis transmission and the identified complex associations are useful references for developing strategies to reduce the disease burden.
Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants
Authors: Leman Raphael , Tubeuf Hélène , Raad Sabine , Tournier Isabelle , Derambure Céline , Lanos Raphaël , Gaildrat Pascaline , Castelain Gaia , Hauchard Julie , Killian Audrey , Baert-Desurmont Stéphanie , Legros Angelina , Goardon Nicolas , Quesnelle Céline , Ricou Agathe , Castera Laurent , Vaur Dominique , Gac Gérald Le , Ka Chandran , Fichou Yann , Bonnet-Dorion Françoise , Sevenet Nicolas , Guillaud-Bataille Marine , Boutry-Kryza Nadia , Schultz Ines , Caux-Moncoutier Virginie , Rossing Maria , Walker Logan C , Spurdle Amanda B , Houdayer Claude , Martins Alexandra , Krieger Sophie 
Published: December 2019

Abstract
Background: Branch points (BPs) map within short motifs upstream of acceptor splice sites (3’ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3’ss.
Results: We used a large set of constitutive and alternative human 3’ss collected from Ensembl (n = 264,787 3’ss) and from in-house RNAseq experiments (n = 51,986 3’ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3’ss (99.48 % and 65.84 % accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17 %.
Conclusions: Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3’ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.
Keywords: Branch Point, Prediction, RNA, Benchmark, HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR, RNABPS, Variants
Superiority of mucosal incision-assisted biopsy over ultrasound-guided fine needle aspiration biopsy to diagnose small gastric subepithelial lesions:A propencity score matching analysis
Authors: Minoda Yosuke , Chinen Takatoshi , Osoegawa Takashi , Itaba Soichi , Haraguchi Kazuhiro , Akiho Hirotada , Aso Akira , Sumida Yorinobu , Komori Keishi , Ogino Haruei , Ihara Eikichi , Ogawa Yoshihiro 
Published: December 2019

Abstract
Background Gastric subepithelial lesions, including gastrointestinal stromal tumors, are often found during routine gastroscopy. While endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNAB) has been the gold standard for diagnosing gastric subepithelial lesions, alternative open biopsy procedures, such as mucosal incision-assisted biopsy (MIAB) has been reported useful. The aim of this study is to evaluate the efficacy of MIAB for the diagnosis of gastric SELs compared with EUS-FNAB. Methods We retrospectively analyzed medical records of 177 consecutive patients with gastric SELs who underwent either MIAB or EUS-FNAB at five hospitals in Japan between January 2010 and January 2018. Diagnostic yield, procedural time, and adverse event rates for the two procedures were evaluated before and after propensity-score matching. Results No major procedure-related adverse events were observed in either group. Both procedures yielded highly-accurate diagnoses once large enough samples were obtained; however, such successful sampling was more often accomplished by MIAB than by EUS-FNAB, especially for small SELs. As a result, MIAB provided better diagnostic yields for SELs smaller than 20-mm diameter. The diagnostic yields of both procedures were comparable for SELs larger than 20-mm diameter; however, MIAB required significantly longer procedural time (approximately 13 minutes) compared with EUS-FNAB. Conclusions Although MIAB required longer procedural time, it outperformed EUS-FNAB when diagnosing gastric SELs smaller than 20-mm diameter.
Reduced serum levels of pro-inflammatory chemokines in Fragile X Syndrome
Authors: Dijck Anke Van , Barbosa Susana , Bermudez-Martin Patricia , Khalfallah Olfa , Gilet Cyprien , Martinuzzi Emanuela , Elinck Ellen , Kooy R Frank , Glaichenhaus Nicolas , Davidovic Laetitia 
Published: December 2019

Abstract
Background: Fragile X syndrome (FXS) is the most frequent cause of inherited intellectual disability and the most commonly identified monogenic cause of autism. Recent studies have shown that long-term pathological consequences of FXS are not solely confined to the central nervous system (CNS) but rather extend to other physiological dysfunctions in peripheral organs. To gain insights into possible immune dysfunctions in FXS, we profiled a large panel of immune-related biomarkers in the serum of FXS patients and healthy controls. Methods: We have used a sensitive and robust Electro Chemi Luminescence (ECL)-based immunoassay to measure the levels of 52 cytokines in the serum of n=25 FXS patients and n=29 healthy controls. We then used univariate statistics and multivariate analysis, as well as an advanced unsupervised clustering method, to identify combinations of immune-related biomarkers that could discriminate FXS patients from healthy individuals. Results: While the majority of the tested cytokines were present at similar levels in FXS patients and healthy individuals, nine chemokines, CCL2, CCL3, CCL4, CCL11, CCL13, CCL17, CCL22, CCL26 and CXCL10, were present at much lower levels in FXS patients. Using robust regression, we show that six of these biomarkers (CCL2, CCL3, CCL11, CCL22, CCL26 and CXCL10) were negatively associated with FXS diagnosis. Finally, applying the K-sparse unsupervised clustering method to the biomarker dataset allowed for the identification of two subsets of individuals, which essentially matched the FXS and healthy control categories. Conclusions: Our data show that FXS patients exhibit reduced serum levels of several chemokines and may therefore exhibit impaired immune responses. The present study also highlights the power of unsupervised clustering methods to identify combinations of biomarkers for diagnosis and prognosis in medicine.
Are matching patterns of male and female flowers in response to nutrient supply and pollen concentration optimal for fruit and seed growth?
Authors: Gao Lei , Zhai Jun Jie , Yu Guo Zhu , Li Wei Hua , Peng Chang Lian 
Published: December 2019

Abstract
Background: Changes in the proportions of male and female flowers in monoecious plants in response to external environmental conditions are directly related to the reproductive fitness of plants. The monoecious cucumber plant was used in this study to assess the responses of sex differentiation and the breeding process to nutrient supply and the degree of artificial pollination using pollen solutions of different concentrations. Results: We found that the nutrient supply significantly increased the number of female flowers, although the number of female flowers did not increase with the strength of the pollination. The number of male flowers did not decrease even under the low nutrient concentration; consequently, the matching pattern of male and female flowers reflects the response of plants to nutrients and nutrient resources during flowering stage. Pollination treatment affected the fruit growth, seed set, and fruit yield. However, the number of fruit, fruit set percentage, and total seeds per plant did not increase with the pollination level, although individual fruit weight and seed number in one fruit did increase. Conclusions: It is concluded that the response of cucumber flowering to external factors is direct and instantaneous, and this matching pattern of male and female flowers may not be optimal for fruit development and seed formation. Keywords: Cucumber, Plant fitness, Sex differentiation, Monoecious, Pollen resource
Comparative transcriptomic and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids
Authors: Batyrshina Zhaniya S , Yaakov Beery , Shavit Reut , Singh Anuradha , Tzin Vered 
Published: December 2019

Abstract

Background: Young wheat plants are continuously exposed to herbivorous insect attack. To reduce insect damage and maintain their growth, plants evolved different defense mechanisms, including the biosynthesis of deterrent compounds named benzoxazinoids, and/or trichome formation that provides physical barriers. It is unclear whether both of these mechanisms are equally critical in providing an efficient defense for wheat seedlings against aphids—an economically costly pest in cereal production.
Results: In this study, we compared the transcriptome, metabolome, benzoxazinoids, and trichome density of three selected wheat genotypes, with a focus on differences related to defense mechanisms. We chose diverse wheat genotypes: two tetraploid wheat genotypes, domesticated durum ‘Svevo’ and wild emmer ‘Zavitan,’ and one hexaploid bread wheat, ‘Chinese Spring.’ The full transcriptomic analysis revealed a major difference between the three genotypes, while the clustering of significantly different genes suggested a higher similarity between the two domesticated wheats than between either and the wild wheat. A pathway enrichment analysis indicated that the genes associated with primary metabolism, as well as the pathways associated with defense such as phytohormones and specialized metabolites, were different between the three genotypes. Measurement of benzoxazinoid levels at the three time points (11, 15, and 18 days after germination) revealed high levels in the two domesticated genotypes, while in wild emmer wheat, they were below detection level. In contrast to the benzoxazinoid levels, the trichome density was dramatically higher in the wild emmer than in the domesticated wheat. Lastly, we tested the bird cherry-oat aphid’s ( Rhopalosiphum padi ) performance and found that Chinese Spring is more resistant than the tetraploid genotypes.
Conclusions: Our results show that benzoxazinoids play a more significant defensive role than trichomes. Differences between the abundance of defense mechanisms in the wild and domesticated plants were observed in which wild emmer possesses high physical defenses while the domesticated wheat genotypes have high chemical defenses. These findings provide new insights into the defense adaptations of wheat plants against aphids.
A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status.
Authors: Wollenberg Kurt , Harris Michael , Gabrielian Andrei , Ciobanu Nelly , Chesov Dumitru , Long Alyssa , Taaffe Jessica , Hurt Darrell , Rosenthal Alex , Tartakovsky Michael , Crudu Valeriu 
Published: December 2019

Abstract
Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent.Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection.Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections.Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
Information needs and information seeking behaviour of people with dementia and their non-professional caregivers: a scoping review
Authors: Soong Aijia , Au Shu Ting , Kyaw Bhone Myint , Theng Yin Leng , Car Lorainne Tudor 
Published: December 2019

Abstract
Background Patients with dementia often require full-time caregivers especially in the later stages of their condition. Patients and caregivers’ access to reliable information on dementia is essential as it may have an important impact on patient care and quality of life. This study aims to provide an overview of the information needs and information seeking behaviour of dementia patients and their caregivers.Methods We conducted a scoping review of the literature and searched four electronic databases for eligible studies published up to August 2018. Two reviewers independently screened studies and extracted data. Information needs were classified according to emerging themes in the literature, and information seeking behaviour was categorized using Wilson’s model of information behaviour.Results Twenty studies with a total of 4,140 participants, were included in this review. Reported information needs focused on: (i) disease; (ii) patient care provision; (iii) healthcare services; and (iv) caregiver self-care. The most commonly reported information need was on healthcare service-related information. Characteristics found to influence information needs were the severity of dementia as well as patient and caregiver status. Dementia patients and caregivers mainly displayed active searching information seeking behaviour and preferred using electronic sources to obtain health information.Conclusion Current dementia information sources available in English are extensive in the information they offer, but more emphasis needs to be placed on healthcare service-related information. All studies originated from high income countries and focused on information needs of caregiver only. The only variable found to significantly influence information needs was severity of dementia condition. The information needs identified in this review can be used to inform development and design of future dementia resources for patients and their caregivers.
A qualitative analysis of junior doctors’ journeys to preparedness in acute care
Authors: Burridge Samuel , Shanmugalingam Thurkaa , Nawrozzadeh Fatima , Leedham-Green Kathleen , Sharif Amar 
Published: December 2019

Abstract

Background New doctors are expected to assess and manage acutely deteriorating patients from their first days in the hospital. However, current evidence suggests that medical graduates are not prepared for this. We aimed to explore junior doctors’ first experiences with unwell patients and how they developed preparedness over time. Methods We conducted seven semi-structured interviews with doctors in their first postgraduate year. The interview transcripts underwent inductive thematic analysis using consensual qualitative research approaches. Themes identified were categorised into early experiences of unpreparedness, first experiences of genuine preparedness, and making sense of how they became prepared. Reflection on how participants progressed between the two was facilitated through a sorting and ranking exercise. Results Most participants initially felt unprepared when responding to acutely unwell patients. They described feeling overwhelmed, apprehensive and challenged. Two main challenges involved knowing when to escalate, and feeling expected to perform beyond their level of competency. A lack of acute care exposure at medical school was a common thread. All participants felt prepared to respond to unwell patients three to six months after starting work. Hands-on experience, reflection, simulation and multidisciplinary team-working were consistently ranked as the most useful learning experiences. Conclusions Starting work as a doctor is a challenging time and preparedness to manage an acutely deteriorating patient is a common area of concern. As preparedness in acute care ranks poorly compared to other outcomes, we see this as an important area for improvement. Our findings suggest that undergraduates may lack sufficient opportunities for scaffolded decision making in acute care, and that increasing the intensity of clinical shadowing may improve preparedness and should inform future educational interventions.
Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
Authors: Alexandersson Erik , Kushwaha Sandeep , Subedi Aastha , Weighill Deborah , Climer Sharlee , Jacobson Daniel , Andreasson Erik 
Published: December 2019

Abstract
Background Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93-1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding. Results A total of 34 progeny lines from SW93-1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate. Conclusion In our study, we identify 100’s of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.