bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Reference Springs to Describe Expected Flow, Temperature, and Chemistry Conditions for Geologically Related Groups of Springs
Authors: Swanson Susan K. , Graham Grace E. , Hart David J. 
Published: June 2020

ABSTRACT
Reference springs can result in improved conceptual models of groundwater flow and an expanded understanding of the temporal variations in flow, temperature, and chemistry that may be expected for related springs. The reference spring concept is patterned off of the common practice of establishing reference sites to establish benchmark ecological conditions. We use the term “reference spring” to indicate a spring that is minimally disturbed and representative of a geologically related group of springs. Seven reference springs were selected from six previously defined groups that represent over 400 springs in Wisconsin, United States. Geologic cross-sections were constructed for each reference spring site, and springs were monitored for flow, spring-water temperature, and chemistry for up to 4 years, revealing new relationships within and between groups. Examples include: a range of temperature conditions that can be related to the depth of groundwater circulation for springs discharging from layered bedrock uplands, and differences in thermal patterns and specific conductance that can be related to the permeability and solubility of surficial glacial deposits for springs emanating from uneven glacial terrain. The results suggest that establishing reference springs may be a useful approach in other regions where geologically related groups of spring have been identified.
Classificação de Eventos Extremos de Precipitação quanto sua Intensidade, Persistência e Abrangência na Região das ZCAS
Authors: Rodrigues Barcellos Deise , Leal de Quadro Mário Francisco 
Published: June 2020

Eventos extremos de precipitação são de grande relevância na climatologia. Suas estimativas e a abrangência desses eventos, são importantes para o planejamento e desenvolvimento de atividades sujeitas a seus efeitos adversos, além do planejamento para diminuição dos impactos causados pelos desastres naturais que acarretam danos econômicos, ao meio ambiente e a sociedade. Este estudo tem por objetivo analisar e classificar os eventos extremos de precipitação na região das ZCAS. As bases de dados utilizadas neste trabalho são provenientes de reanálise do Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), para os meses de novembro a março, de 1987 a 2016. A utilização de um algoritmo computacional permite a classificação dos eventos em Chuva Intensa Abrangente ou Não Abrangente (CIA/CIN) e Chuva Persistente Abrangente ou Não Abrangente (CPA/CPN), conforme critérios de intensidade, persistência e abrangência. Os resultados encontrados mostram que o algoritmo de rastreamento de CI e CP se mostrou uma ferramenta eficiente para rastrear eventos intensos/extremos de precipitação, além de configurar a CP e a abrangência espacial. Na análise do episódio ocorrido entre os dias 11 e 12 de janeiro de 2011, foi detectado CIA e CPA sobre o Estado do Rio de Janeiro, que contribuiu para a ocorrência de chuvas contínuas, fortes enxurradas e deslizamentos de terra.
Electroencephalogram (EEG) Recording Protocol for Cognitive and Affective Human Neuroscience Research
Authors: Farrens Jaclyn L. , Simmons Aaron M. , Luck Steven J. , Kappenman Emily S. 
Published: June 2020

Abstract
Electroencephalography (EEG) is one of the most widely used techniques to measure human brain activity. EEG recordings provide a direct, high temporal resolution measure of cortical activity from noninvasive scalp electrodes. However, the signals are small relative to the noise, and optimizing the quality of the recorded EEG data can significantly improve the ability to identify signatures of brain processing. This protocol provides a step-by-step guide to recording the EEG from human research participants using strategies optimized for producing the best quality EEG.
An Outbreak of Acute Respiratory Infection at a Training Base in Beijing, China Due to Human Adenovirus Type B55
Authors: Lu Guilan , Peng Xiaomin , Li Renqing , Liu Yimeng , Wu Zhanguo , Wang Xifeng , Zhang Daitao , Zhao Jiachen , Sun Ying , Zhang Li , Yang Peng , Wang Quanyi 
Published: June 2020

Abstract
Background: Twelve students experienced symptoms of acute respiratory infection (ARI) at a training base in Beijing from August 26 to August 30, 2015. We investigated the cause of this ARI outbreak. Methods: In partnership with the local center for disease control, we collected a total of twelve pharyngeal swab specimens as well as demographic information for the affected patients. We used multiplex real-time PCR to screen for sixteen common respiratory viruses in these samples. To isolate HAdV, we inoculated Hep-2 cells with the human adenovirus (HAdV)-positive samples and then carried out sequencing and phylogenetic analysis of the hexon, fiber, and penton genes of the isolated adenoviruses. In addition, we analyzed the entire genome of one strain isolated from the index case to identify single-nucleotide substitutions. Results: We identified ten HAdV-positive students using multiplex real-time PCR. None of the students were co-infected with other viruses. We successfully isolated seven HAdV strains from the pharyngeal swab specimens. The coding sequences of the hexon, fiber, and penton genes of these seven HAdV strains were identical, suggesting that they represented seven strains from a single virus clone. One HAdV isolate obtained from the index case, BJDX-01-2015, was selected for whole genome analysis. From this isolate, we obtained a 34,774-nucleotide sequence. The genome of BJDX-01-2015 clustered with HAdV-B55 in phylogenetic analyses and had 99.97% identity with human adenovirus 55 isolate HAdV-B/CHN/BJ01/2011/55 (GenBank accession no. JX491639). Conclusions: We identified HAdV-B55 as the strain associated with the August 2015 ARI outbreak at a training base in Beijing. This was the first reported outbreak in Beijing due to HAdV-B55. Continuous surveillance of respiratory adenoviruses is urgently needed to understand the epidemiological and evolutionary features of HAdV-B55, and an epidemiological modeling approach may provide further insights into this emerging public health threat. Furthermore, the clinical laboratory data from this outbreak provides important reference for the clinical diagnosis and may ultimately aid in informing the development of strategies to control and prevent respiratory tract infections caused by HAdV-B55.
Association of PIN3 16-bp Duplication Polymorphism of TP53 with Breast Cancer Risk in Mali and A Meta-analysis.
Authors: Diakite Brehima , Kassogue Yaya , Dolo Guimogo , Kassogue Oumar , Keita Mamadou Lassine , Joyce Brian , Neuschler Erin , Wang Jun , Musa Jonah , Traore Cheick Bougari , Kamate Bakarou , Dembele Etienne , Nadifi Sellama , Isichei Mercy , Holl Jane L , Murphy Robert , Doumbia Seydou , Hou Lifang , Maiga Mamoudou 
Published: June 2020

Abstract
Background. Breast cancer, the most common tumor in women in Mali and worldwide has been linked to several risk factors, including genetic factors, such as the PIN3 16-bp duplication polymorphism of TP53. The aim of our study was to evaluate the role of the PIN3 16-bp duplication polymorphism in the susceptibility to breast cancer in the Malian population and to perform a meta-analysis to better understand the correlation with data from other populations.Methods. We analyzed the PIN3 16-bp duplication polymorphism in blood samples of 60 Malian women with breast cancer and 60 healthy Malian women using PCR. In addition, we performed a meta-analysis of case-control study data from international databases, including Pubmed, Harvard University Library, Genetics Medical Literature Database, Genesis Library and Web of Science. Overall, odds ratio (OR) with 95% CI from fixed and random effects models were determined. Inconsistency was used to assess heterogeneity between studies and publication bias was estimated using the funnel plot.Results. In the studied Malian patients, a significant association of PIN3 16-bp duplication polymorphism with breast cancer risk was observed in dominant (A1A2+A2A2 vs. A1A1: OR = 2.26, CI 95% = 1.08-4.73; P = 0.02) and additive (A2 vs. A1: OR =1.87, CI 95% = 1.05-3.33; P = 0.03) models, but not in the recessive model (P = 0.38). In the meta-analysis, nineteen (19) articles were included with a total of 6,018 disease cases and 4,456 controls. Except for the dominant model (P = 0.15), an increased risk of breast cancer was detected with the recessive (OR=1.46, 95% CI = 1.15-1.85; P = 0.002) and additive (OR = 1.11, 95% CI = 1.02-1.19; P = 0.01) models.Conclusion. The case-control study showed that PIN3 16-bp duplication polymorphism of TP53 is a significant risk factor for breast cancer in Malian women. These findings are supported by data from the meta-analysis carried out on different ethnic groups around the world.
Fusion transcript detection using spatial transcriptomics
Authors: Friedrich Stefanie , Sonnhammer Erik LL 
Published: June 2020

Abstract
Background Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in tissue sections due to the lack of full-length transcripts with spatial information. New high-throughput technologies like spatial transcriptomics measure the transcriptome of tissue sections on almost single-cell level. While this technique does not allow for direct detection of fusion transcripts, we show that they can be inferred using the relative poly(A) tail abundance of the involved parental genes. Method We present a new method STfusion, which uses spatial transcriptomics to infer the presence and absence of poly(A) tails. A fusion transcript lacks a poly(A) tail for the 5´ gene and has an elevated number of poly(A) tails for the 3´ gene. Its expression level is defined by the upstream promoter of the 5´ gene. STfusion measures the difference between the observed and expected number of poly(A) tails with a novel C-score. Results We verified the STfusion ability to predict fusion transcripts on HeLa cells with known fusions. STfusion and C-score applied to clinical prostate cancer data revealed the spatial distribution of the cis-SAGe SLC45A3-ELK4 in 12 tissue sections with almost single-cell resolution. The cis-SAGe occurred in disease areas, e.g. inflamed, prostatic intraepithelial neoplastic, or cancerous areas, and occasionally in normal glands. Conclusions STfusion detects fusion transcripts in cancer cell line and clinical tissue data, and distinguishes chimeric transcripts from chimeras caused by trans-splicing events. With STfusion and the use of C-scores, fusion transcripts can be spatially localised in clinical tissue sections on almost single cell level.
Decoding the differentiation of mesenchymal stem cells into mesangial cells at the transcriptomic level
Authors: Wong Chee-Yin , Chang Yao-Ming , Tsai Yu-Shuen , Ng Wailap Victor , Cheong Soon-Keng , Chang Ting-Yu , Chung I-Fang , Lim Yang-Mooi 
Published: June 2020

Abstract
Background: Mesangial cells play an important role in the glomerulus, providing mechanical support to it, and maintaining efficient ultrafiltration of renal plasma. Loss of mesangial cells due to pathologic conditions may lead to impaired renal function. Mesenchymal stem cells (MSC) can differentiate into many cell types, including mesangial cells. However transcriptomic profiling during MSC differentiation into mesangial cells had not been studied yet. The aim of this study is to examine the pattern of transcriptomic changes during MSC differentiation into mesangial cells as well as to understand the involvement of transcription factor (TF) along the differentiation process, and finally to elucidate the relationship among TF-TF and TF-key gene or biomarkers during the differentiation of MSC into mesangial cells.Methods: Differentiation of MSC into mesangial cells was induced by co-culturing with injured mesangial cells. RNA from co-cultured MSC was extracted before running RNA sequencing. Generated RNA-seq data was analysed by two methods simultaneously: 1) Monotonic Feature Selector (MFSelector) to identify the key genes with ascending and descending monotonic patterns, and 2) Time-Ordered Gene Co-expression Network (TO-GCN) to construct a TF co-expression network. Results : MFSelector has identified several monotonic key genes (either ascending or descending). These identified descending monotonic key genes are related to stemness or regulation of cell cycle while ascending monotonic key genes are associated with the functions of mesangial cells. The TFs were arranged in a co-expression network in order of time by TO-GCN analysis. Additionally, not only can TO-GCN analysis classify the differentiation process into three stages: differentiation preparation, differentiation initiation and maturation, but it can also explore TF-TF-key genes regulatory relationships in the muscle contraction process.Conclusions: A systematic analysis for transcriptomic profiling of MSC differentiation into mesangial cells has been established. Key genes or biomarkers, TFs and pathways involved in differentiation of MSC-mesangial cells have been identified and the related biological implications have been discussed. Finally, we further elucidated for the first time the three main stages of mesangial cell differentiation, and the regulatory relationships between TF-TF-key genes existing in the muscle contraction process.
National mapping of soil-transmitted helminth and schistosome infections in Ethiopia
Authors: Leta Gemechu Tadesse , Mekete Kalkidan , Wuletaw Yonas , Gebretsadik Abeba , Sime Heven , Mekasha Sindew , Woyessa Adugna , Shafi Oumer , Vercruysse Jozef , Grimes Jack ET , Gardiner Iain , French Michael , Levecke Bruno , Drake Lesley , Harrison Wendy , Fenwick Alan 
Published: June 2020

Abstract
Background : An accurate understanding of the geographical distributions of both soil-transmitted helminths (STHs; Ascaris lumbricoides , Trichuris trichiura , and the hookworms ( Necator americanus and Ancylostoma duodenale ) and schistosomes (SCH; Schistosoma mansoni and S. haematobium ) is pivotal to be able to effectively design and implement mass drug administration (MDA) programs. The objective of this study was to provide up-to-date data on the distribution of both STH and SCH in Ethiopia to inform the design of the national control program and to be able to efficiently achieve the 75% MDA coverage target set by the WHO. Methods : Between 2013 and 2015, we assessed the distributions of STH and SCH infections in a nationwide survey covering 153,238 school-aged children (aged five to 15 years), from 625 woredas (districts), representing all nine Regional States and two City Administrations of Ethiopia. Nationwide disease maps were developed at the woreda level to enable recommendations on the design of the national MDA program. Results: The prevalence of any STH infection across the study population was 21.7%, with A. lumbricoides (12.8%) being the most prevalent STH, followed by hookworms (7.6%) and T. trichiura (5.9%). The prevalence for any SCH was 4.0% in areas where both SCH species were evaluated. S. mansoni was the most prevalent SCH (3.5% vs. 0.3%). STHs were more prevalent in southwest Ethiopia, whereas SCH was found mostly in the west and northeast of the country. The prevalence of moderate-to-heavy intensity infections was 2.0% for STHs and 1.6% for SCH. For STH, a total of 251 woredas were classified as moderately (178) or highly endemic (73), and therefore qualify for an annual and biannual MDA program, respectively. For SCH, 67 woredas were classified as endemic and 8 as highly endemic, and hence they require every two years and annual MDA program, respectively. Conclusions : The results confirm that Ethiopia is endemic for both STHs and SCH, posing a significant public health problem. Following WHO recommendations on mass drug administration, 18 and 14 million school-aged children are in need of MDA for STHs and SCH respectively based on the number of SACs that live on the eligible geographic areas.
Efficacy and safety of artesunate-amodiaquine and artemether-lumefantrine and prevalence of molecular markers associated with resistance, Guinea: an open-label two-arm randomised controlled trial
Authors: Beavogui Abdoul Habib , Camara Alioune , Delamou Alexandre , Doumbouya Abdoulaye , Kourouma Karifa , Bouedouno Patrice , Guilavogui Timothee , Santos Souza Samaly dos , Kelley Julia , Talundzic Eldin , Fofana Aissata , Plucinski Mateusz M , Diallo Mamadou Saliou 
Published: June 2020

Abstract
Background Anti-malarial resistance is a threat to recent gains in malaria control. This study aimed to assess the efficacy and safety of artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) in the management of uncomplicated malaria and to measure the prevalence of molecular markers of resistance of Plasmodium falciparum in sentinel sites in Maferinyah and Labé Health Districts in Guinea in 2016.Methods This was a two-arm randomised controlled trial of the efficacy of AL and ASAQ among children aged 6-59 months with uncomplicated Plasmodium falciparum malaria in two sites. Children were followed for 28 days to assess clinical and parasitological response. The primary outcome was the Kaplan-Meier estimate of Day 28 (D28) efficacy after correction by microsatellite-genotyping. Pre-treatment (D0) and day of failure samples were assayed for molecular markers of resistance in the pfk13 and pfmdr1 genes.Results A total of 421 participants were included with 211 participants in the Maferinyah site and 210 in Labé. No early treatment failure was observed in any study arms. However, 22 (5.3%) participants developed a late treatment failure (8 in the ASAQ arm and 14 in the AL arm), which were further classified as 2 recrudescences and 20 reinfections. The Kaplan-Meier estimate of the corrected efficacy at D28 was 100% for both AL and ASAQ in Maferinyah site and 99% (95% Confidence Interval: 97.2-100%) for ASAQ and 99% (97.1-100%) for AL in Labé. The majority of successfully analysed D0 (98%, 380/389) and all day of failure (100%, 22/22) samples were wild type for pfk13. All 9 observed pfk13 mutations were polymorphisms not associated with artemisinin resistance. The NFD haplotype was the predominant haplotype in both D0 (197/362, 54%) and day of failure samples (11/18, 61%) successfully analysed for pfmdr1. Conclusion This study observed high efficacy and safety of both ASAQ and AL in Guinea, providing evidence for their continued use to treat uncomplicated malaria. Continued monitoring of ACT efficacy and safety and molecular makers of resistance in Guinea is important to detect emergence of parasite resistance and to inform evidence-based malaria treatment policies.
Expression of Epithelial-Mesenchymal Transition Related Markers in Plasmacytoid Urothelial Carcinoma of the Urinary Bladder
Authors: Nomura Shunichiro , Suzuki Yasutomo , Akatsuka Jun , Endo Yuki , Shimizu Akira , Hamasaki Tsutomu , Kimura Go , Kondo Yukihiro 
Published: June 2020

Abstract
Background: Plasmacytoid urothelial carcinoma (PUC) of the urinary bladder is a variant of urothelial carcinoma that carries a poor prognosis. The epithelial-mesenchymal transition (EMT) has been demonstrated to contribute to tumor progression. As the cause of the increased aggressiveness of PUC is unknown, we investigated PUC and EMT-related marker expression. Methods: A total of 633 bladder carcinoma cases diagnosed from 2006 to 2015 at the Nippon Medical School Hospital were analyzed. Twelve patients were found to have plasmacytoid histology and diagnosed with PUC. Slides were evaluated for percentage of plasmacytoid variant, and stained for E-cadherin, N-cadherin, Vimentin, Fibronectin and Snail expression. Results: The incidence of PUC was 1.9% (12/633). The median patient age at diagnosis was 71 years (range, 60–80 years) and the male-female ratio was 11:1. All but three patients had stage T2b or higher. The median overall survival was 10 months. In 10/12 cases, Snail and N-cadherin were positive. Vimentin was positive in 9/12 cases. Fibronectin was positive in 8/12 cases. While E-cadherin was negative in 10/12 cases. Nine cases showed >10% plasmacytoid component. Eight of the nine patients (88.9%) with >10% plasmacytoid component died.Conclusions: The results indicate that PUC may induce EMT and may be associated with high invasion.
Diagnostic accuracy of perioperative electromyography in the positioning of pedicle screws in adolescent idiopathic scoliosis treatment: a cross-sectional diagnostic study
Authors: Barsotti Carlos Eduardo , Gavassi Bruno Moreira , Prado Francisco Eugenio , Batista Bernardo Nogueira , Pratali Raphael de Resende , Ribeiro Ana Paula , de Oliveira Carlos Eduardo Soares , Ferreira Ricardo Rodrigues 
Published: June 2020

Abstract
Background: To investigate electromyography (EMG) thresholds for predicting pedicle screw positioning during adolescent idiopathic scoliosis (AIS) surgery.Methods: 16 patients were included. Each screw was classified as “at risk for nerve injury” (ARNI) or “no risk for nerve injury” (NRNI) using CT and the diagnostic accuracy of EMG thresholds for predicting screw positions ARNI was investigated.Results: 226 pedicles were analyzed. In the axial plane, 204 (90.3%) screws were considered as NRNI, and 22 (9.7%), as ARNI. In the sagittal plane, 183 (81%) pedicle screws were considered as NRNI, and 43 (19%), as ARNI. We observed a significant association between EMG responses and screw positioning ARNI. A 1-mA decrease in EMG threshold corresponded to a 12% increase in the odds of screw position ARNI (OR=1.12; p<.001). The positive predictive value of EMG for diagnosing ARNI was very low, with the highest 18% corresponding to a cutoff of 25 mA, but the negative predictive value was moderate to high (78%-93%) for every cutoff.Conclusions: EMG had a poor accuracy for predicting screws ARNI but was effective for minimizing false-negative screws ARNI.