bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files
Authors: Rausch Tobias , Fritz Markus Hsi-Yang , Untergasser Andreas , Benes Vladimir 
Published: March 2020

Abstract
Background
DNA sequencing is at the core of many molecular biology laboratories. Despite its long history, there is a lack of user-friendly Sanger sequencing data analysis tools that can be run interactively as a web application or at large-scale in batch from the command-line.

Results
We present Tracy, an efficient and versatile command-line application that enables basecalling, alignment, assembly and deconvolution of sequencing chromatogram files. Its companion web applications make all functionality of Tracy easily accessible using standard web browser technologies and interactive graphical user interfaces. Tracy can be easily integrated in large-scale pipelines and high-throughput settings, and it uses state-of-the-art file formats such as JSON and BCF for reporting chromatogram sequencing results and variant calls. The software is open-source and freely available at https://github.com/gear-genomics/tracy, the companion web applications are hosted at https://www.gear-genomics.com.

Conclusions
Tracy can be routinely applied in large-scale validation efforts conducted in clinical genomics studies as well as for high-throughput genome editing techniques that require a fast and rapid method to confirm discovered variants or engineered mutations. Molecular biologists benefit from the companion web applications that enable installation-free Sanger chromatogram analyses using intuitive, graphical user interfaces.
Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice
Authors: Xia Hui , Yu Shunwu , Kong Deyan , Xiong Jie , Ma Xiaosong , Chen Liang , Luo Lijun 
Published: March 2020

Abstract
Background
Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, development, and reproduction (GDP). This will facilitate our utilization of rice miRNAs in breeding.

Results
In this study, we investigated the time course of miRNA responses to a long-term drought among six rice genotypes by high-throughput sequencing. In total, 354 conserved miRNAs were drought responsive, representing obvious genotype- and stage-dependent patterns. The drought-responsive miRNAs (DRMs) formed complex regulatory network via their coexpression and direct/indirect impacts on the rice transcriptome. Based on correlation analyses, 211 DRMs were predicted to be associated with DT and/or GDP. Noticeably, 14.2% DRMs were inversely correlated with DT and GDP. In addition, 9 pairs of mature miRNAs, each derived from the same pre-miRNAs, were predicted to have opposite roles in regulating DT and GDP. This suggests a potential yield penalty if an inappropriate miRNA/pre-miRNA is utilized. miRNAs have profound impacts on the rice transcriptome reflected by great number of correlated drought-responsive genes. By regulating these genes, a miRNA could activate diverse biological processes and metabolic pathways to adapt to drought and have an influence on its GDP.

Conclusion
Based on the temporal pattern of miRNAs in response to drought, we have described the complex network between DRMs. Potential associations of DRMs with DT and/or GDP were disclosed. This knowledge provides valuable information for a better understanding in the roles of miRNAs play in rice DT and/or GDP, which can facilitate our utilization of miRNA in breeding.
Modified high-throughput Nile red fluorescence assay for the rapid screening of oleaginous yeasts using acetic acid as carbon source
Authors: Miranda Catarina , Bettencourt Sara , Pozdniakova Tatiana , Pereira Joana , Sampaio Paula , Franco-Duarte Ricardo , Pais Célia 
Published: March 2020

Abstract
Background
Over the last years oleaginous yeasts have been studied for several energetic, oleochemical, medical and pharmaceutical purposes. However, only a small number of yeasts are known and have been deeply exploited. The search for new isolates with high oleaginous capacity becomes imperative, as well as the use of alternative and ecological carbon sources for yeast growth.

Results
In the present study a high-throughput screening comprising 366 distinct yeast isolates was performed by applying an optimised protocol based on two approaches: (I) yeast cultivation on solid medium using acetic acid as carbon source, (II) neutral lipid estimation by fluorimetry using the lipophilic dye Nile red.

Conclusions
Results showed that, with the proposed methodology, the oleaginous potential of yeasts with broad taxonomic diversity and variety of growth characteristics was discriminated. Furthermore, this work clearly demonstrated the association of the oleaginous yeast character to the strain level, contrarily to the species-level linkage, as usually stated.
Methylation in HT22 cells and primary hippocampal neurons with and without isoflurane exposure
Authors: Klenke Stefanie , Specking Christian , Stegen Maike , Engler Andrea , Peters Jürgen 
Published: March 2020

Abstract
Background
Epigenetic modulation may play a role in anesthesia related phenotypes, such as cognitive impairment or memory loss, especially with exposure to anesthetics in the vulnerable phase of brain development. While isoflurane anesthesia can evoke neuroinflammation and neuroapoptosis in young animals, we investigated in a permanent hippocampal cell line (HT22) and in primary hippocampal neurons in an a priori in vitro analysis, whether isoflurane exposure 1) evokes DNA methylation changes in genes involved in apoptosis and inflammation, and 2) results observed in a permanent hippocampal cell line are comparable to primary hippocampal neurons. In case of methylation changes in specific genes, (3) mRNA analysis was performed to assess possible effects on gene expression.

Methods
HT22 cells and primary mouse hippocampal neurons were exposed to 3% isoflurane for 4 h and DNA (each 6 single experiments) and RNA (3 single independent experiments) were extracted. Methylation analysis (EpiTect Methyl II PCR Array Systems, Qiagen) included the methylation status of 66 genes involved in apoptosis, cytokine production, inflammatory response, and autoimmunity. Quantitative Real-Time PCR was performed using the Quantitect SYBR Green Kit on a Step One Plus.

Results
Methylation status was markedly different between immortalized HT22 cells and cultured primary hippocampal neurons without isoflurane exposure. Of 66 genes investigated, 29 were methylated to a significantly greater degree in HT22 cells compared to primary hippocampal neurons. In cultured primary hippocampal neurons, in contrast, there was a greater methylation in several genes involved in inflammation, accompanied with significant downregulation of C-X-C motif chemokine 12 with isoflurane exposure (p = 0.023).

Conclusions
We demonstrate marked differences in gene methylation between HT22 cells and cultured primary hippocampal neurons without isoflurane exposure, with a greater methylation of several genes involved in inflammation upon isoflurane exposure and significant downregulation of Cxcl12 mRNA expression in primary hippocampal neurons. Accordingly, further investigations of anesthesia related DNA methylation should be performed with special consideration being given to the choice of cells targeted for such investigations.
Refractoriness to subcutaneous implantable cardioverter defibrillator after frequent therapies for ventricular fibrillation storms in a Brugada syndrome case
Authors: Nakao Yasuhisa , Suenari Kazuyoshi , Yamashiro Kohei , Nakagawa Hiroshi , Shiode Nobuo 
Published: March 2020

Abstract
Background
The subcutaneous implantable cardioverter defibrillator (S-ICD) is an alternative to the transvenous implantable cardioverter defibrillator for the prevention of sudden cardiac death. Here, we report a rare case of refractoriness to an S-ICD after frequent therapies for ventricular fibrillation (VF) storms.

Case presentation
A 24-year-old man underwent a bout of syncope with vomiting and incontinence at home. He was brought to the emergency room and was witnessed to spontaneously go into VF successfully converted by external defibrillation. Previously, he was diagnosed with a type I Brugada electrocardiogram pattern by a pilsicainide administration test in another hospital. Although he had a family history of sudden cardiac death in 3 relatives, including his brother, he was followed closely without any therapies because he had never had an episode of syncope. He was implanted with an S-ICD without any trouble. Seven months later, frequent S-ICD shocks for VF storms occurred. His VF was controlled by using intravenous amiodarone, which was converted to an oral preparation. However, his VF recurred after another 2 months. The analysis of his S-ICD data revealed that 4 consecutive shock deliveries could not terminate his VF and the final shock delivered could fortunately terminate it because of a high defibrillation threshold test (DFT) due to an increasing shock impedance (64 to 90 Ω). First, we performed an epicardial Brugada syndrome ablation and subsequently replaced and repositioned the S-ICD lead from a left to a right parasternal site. After the re-implantation of the S-ICD, the DFT test improved to within normal range. According to the pathological analysis, infiltration of inflammatory cells and extensive fibrosis were confirmed in the subcutaneous tissue around the shock lead and S-ICD body.

Conclusion
Frequent S-ICD shocks for VF storms might cause various pathological changes around the device and lead to a high DFT.
Giant coronary artery fistula complicated with coronary artery aneurysm and acute myocardial infarction: a case report
Authors: Yang Zhuoxuan , Zhang Liang , Gao Jin , Cui Jingang , Yuan Jiansong , Liu Shengwen , Zhou Yue , Qiao Shubin 
Published: March 2020

Abstract
Background
Coronary artery fistula (CAF) is an abnormal connection between a coronary artery and either a cardiac chamber or the great vessels. Although most patients are asymptomatic, potential complications such as heart failure, angina pectoris or acute myocardial infarction can be fatal.

Case presentation
We present here a 62-year-old man diagnosed with giant coronary artery fistula complicated with gross coronary artery aneurysm and acute myocardial infarction. He underwent intravenous thrombolysis treatment at a local hospital, coronary angiography at a regional hospital and complex surgery at a national centre for cardiovascular disease. The patient had no major adverse cardiac events during the 3-year follow-up.

Conclusion
Early diagnosis of CAF patients and an appropriate treatment plan are the key factors for avoiding serious complications. Because of the rare incidence of this disease, it is necessary to discover and discuss management strategies, including medical management, percutaneous interventions or surgical treatment, for a successful outcome.
Analytical methods used in estimating the prevalence of HIV/AIDS from demographic and cross-sectional surveys with missing data: a systematic review
Authors: Mosha Neema R. , Aluko Omololu S. , Todd Jim , Machekano Rhoderick , Young Taryn 
Published: March 2020

AbstractBackgroundSero- prevalence studies often have a problem of missing data. Few studies report the proportion of missing data and even fewer describe the methods used to adjust the results for missing data. The objective of this review was to determine the analytical methods used for analysis in HIV surveys with missing data.MethodsWe searched for population, demographic and cross-sectional surveys of HIV published from January 2000 to April 2018 in Pub Med/Medline, Web of Science core collection, Latin American and Caribbean Sciences Literature, Africa-Wide Information and Scopus, and by reviewing references of included articles. All potential abstracts were imported into Covidence and abstracts screened by two independent reviewers using pre-specified criteria. Disagreements were resolved through discussion. A piloted data extraction tool was used to extract data and assess the risk of bias of the eligible studies. Data were analysed through a quantitative approach; variables were presented and summarised using figures and tables.ResultsA total of 3426 citations where identified, 194 duplicates removed, 3232 screened and 69 full articles were obtained. Twenty-four studies were included. The response rate for an HIV test of the included studies ranged from 32 to 96% with the major reason for the missing data being refusal to consent for an HIV test. Complete case analysis was the primary method of analysis used, multiple imputations 11(46%) was the most advanced method used, followed by the Heckman’s selection model 9(38%). Single Imputation and Instrumental variables method were used in only two studies each, with 13(54%) other different methods used in several studies. Forty-two percent of the studies applied more than two methods in the analysis, with a maximum of 4 methods per study. Only 6(25%) studies conducted a sensitivity analysis, while 11(46%) studies had a significant change of estimates after adjusting for missing data.ConclusionMissing data in survey studies is still a problem in disease estimation. Our review outlined a number of methods that can be used to adjust for missing data on HIV studies; however, more information and awareness are needed to allow informed choices on which method to be applied for the estimates to be more reliable and representative.
Incorporating sampling weights into robust estimation of Cox proportional hazards regression model, with illustration in the Multi-Ethnic Study of Atherosclerosis
Authors: Sitlani Colleen M. , Lumley Thomas , McKnight Barbara , Rice Kenneth M. , Olson Nels C. , Doyle Margaret F. , Huber Sally A. , Tracy Russell P. , Psaty Bruce M. , Delaney Joseph A. C. 
Published: March 2020

AbstractBackgroundCox proportional hazards regression models are used to evaluate associations between exposures of interest and time-to-event outcomes in observational data. When exposures are measured on only a sample of participants, as they are in a case-cohort design, the sampling weights must be incorporated into the regression model to obtain unbiased estimating equations.MethodsRobust Cox methods have been developed to better estimate associations when there are influential outliers in the exposure of interest, but these robust methods do not incorporate sampling weights. In this paper, we extend these robust methods, which already incorporate influence weights, so that they also accommodate sampling weights.ResultsSimulations illustrate that in the presence of influential outliers, the association estimate from the weighted robust method is closer to the true value than the estimate from traditional weighted Cox regression. As expected, in the absence of outliers, the use of robust methods yields a small loss of efficiency. Using data from a case-cohort study that is nested within the Multi-Ethnic Study of Atherosclerosis (MESA) longitudinal cohort study, we illustrate differences between traditional and robust weighted Cox association estimates for the relationships between immune cell traits and risk of stroke.ConclusionsRobust weighted Cox regression methods are a new tool to analyze time-to-event data with sampling, e.g. case-cohort data, when exposures of interest contain outliers.
Incidence and epidemiology of acute kidney injury in a pediatric Malawian trauma cohort: a prospective observational study
Authors: Bjornstad Erica C. , Muronya William , Smith Zachary H. , Gibson Keisha , Mottl Amy K. , Charles Anthony , Marshall Stephen W. , Golightly Yvonne M. , Munthali Charles K. , Gower Emily W. 
Published: March 2020

AbstractBackgroundAcute kidney injury (AKI) is highly associated with mortality risk in children worldwide. Trauma can lead to AKI and is a leading cause of pediatric death in Africa. However, there is no information regarding the epidemiology of pediatric, trauma-associated AKI in Africa.MethodsProspective cohort study of pediatric trauma patients admitted to a tertiary referral hospital in Malawi. Participants enrolled at admission were followed prospectively throughout their hospitalization. AKI was defined by creatinine-only Kidney Disease Improving Global Outcomes criteria. We calculated descriptive statistics and univariate relative risks (RR) for hypothesis-generation of potential risk factors associated with AKI.ResultsWe analyzed data from 114 participants. Depending on baseline creatinine definition, AKI incidence ranged from 4 to 10%. The new Schwartz equation estimated baseline creatinine values best and yielded an AKI incidence of 9.7%. Almost one in ten children died during hospitalization, but those with AKI (n = 4) were at significantly higher risk of death compared to those without AKI (40.0% vs 6.2%; RR 6.5, 95% CI 2.2–19.1). Burn injuries were most commonly associated with AKI (63.6%). Other potential AKI risk factors included multiple injuries, trunk or facial injuries, and recent consumption of herbal remedies.ConclusionsAKI occurs in up to 10% of admitted pediatric trauma patients in Malawi and increases the risk of death 7-fold compared to those without AKI. This large unrecognized burden in trauma requires further investment by researchers, clinicians and policymakers to develop evidenced-based triage, recognition, and management approaches to prevent the associated sequelae and potential mortality from AKI.
Design of a non-interventional post-marketing study to assess the long-term safety and effectiveness of ocrelizumab in German real world multiple sclerosis cohorts – the CONFIDENCE study protocol
Authors: Dirks Petra , Zingler Vera , Leemhuis Jost , Berthold Heike , Hieke-Schulz Stefanie , Wormser David , Ziemssen Tjalf 
Published: March 2020

Abstract
Background
Multiple sclerosis (MS) is a chronic disease that requires lifelong treatment. A highly effective drug not only for relapsing but also for progressive forms of MS with a favorable safety profile is needed to further improve overall patient outcomes. Ocrelizumab, a recombinant humanized monoclonal antibody that selectively targets CD20-expressing B-cells, is the first drug indicated for the treatment of adult patients with relapsing forms of MS (RMS) and primary progressive MS (PPMS). Its safety and effectiveness profile has yet to be studied in a large, real-world setting. CONFIDENCE aims to further characterize the safety profile of ocrelizumab in routine clinical practice. In addition, real-world effectiveness data will be collected to complement the efficacy data documented in the pivotal clinical trials.

Methods
CONFIDENCE is a non-interventional, prospective, multicenter, long-term study collecting primary data from 3000 RMS and PPMS patients newly treated with ocrelizumab and 1500 patients newly treated with other selected MS disease-modifying therapies (DMTs). Treatment must be in accordance with the local label and follow routine practice. Data will be collected at approximately 250 neurological centers and practices across Germany. The recruitment period of 30 months started in April 2018. The observation period per patient is planned 7.5 to 10 years, depending on the date of inclusion, regardless of whether patients discontinue treatment. Visits follow routine practice and will be documented approximately every 6 months. The primary endpoint is the incidence and type of uncommon adverse events and death. Statistical analyses will be mainly descriptive and exploratory.

Discussion
CONFIDENCE is a large, non-interventional, post-authorization safety study that assesses long-term safety and effectiveness of ocrelizumab and other DMTs in a real-world setting. Data collected in CONFIDENCE will also be integrated into studies that have been developed to fulfil international regulatory requirements.
Pregnancy and perinatal outcomes in pregnancies resulting from time interval between a freeze-all cycle and a subsequent frozen-thawed single blastocyst transfer
Authors: Hu Shiqiao , Xu Bei , Long Rui , Jin Lei 
Published: March 2020

Abstract
Background
Adverse obstetric outcomes are correlated with altered circulating hormone levels at the time implantation by the trophectoderm. What’ more, embryo freezing process may also have adverse effect on perinatal outcomes. This study aims to evaluate whether increasing interval time between a freeze-all cycle and a subsequent frozen-thawed single blastocyst transfer could have any effect on pregnancy and perinatal outcomes.

Methods
This was a retrospective cohort study included the first single blastocyst transfer in artificially cycles of all patients who underwent a freeze-all cycle between January 1st, 2016 and September 30th, 2018. All patients were divided into two groups according to the time interval between oocyte retrieval and the day of first frozen-thawed embryo transferred (FET): Group 1 (immediate FET cycles) and Group 2 (delayed FET cycles).

Results
No significant differences were reported between the two groups regarding the rates of clinical pregnancy, live birth, biochemical pregnancy and pregnancy loss even after adjusting for measured confounding. When accounting for perinatal outcomes, gestational age, birth weight, delivery mode, fetus gender, preterm birth, gestational hypertension, GDM, placenta previa, fetal malformation and low birthweight also did not vary significantly between the two groups. Only the incidence of macrosomia was more frequently in the Group 2 compared with the Group 1 (AOR 3.886, 95%CI 1.153–13.103, P = 0.029) after adjusting with a multiple logistic regression model.

Conclusions
We found delayed FET cycles for blastocyst transfer following freeze-all cycles may not improve the pregnancy outcomes. On the contrary, postponement of FET cycles may increase the risk of macrosomia. Therefore, FET cycles for blastocyst transfer should be done immediately to avoid adverse effects of delayed time on perinatal outcomes.
Polyclonal BRCA2 mutations following carboplatin treatment confer resistance to the PARP inhibitor rucaparib in a patient with mCRPC: a case report
Authors: Simmons Andrew D. , Nguyen Minh , Pintus Elias 
Published: March 2020

AbstractBackgroundPoly (ADP-ribose) polymerase (PARP) inhibitors are approved for the treatment of breast cancer susceptibility genes 1 and 2 (BRCA1/2) mutant ovarian and breast cancers, and are now being evaluated in metastatic castration-resistant prostate cancer (mCRPC). Reversion mutations that restoreBRCA1/2function have been shown to be responsible for resistance to platinum-based chemotherapy and PARP inhibitors, however there is no information on the sequential use of these agents in prostate cancer.Case presentationA patient with mCRPC associated with a germlineBRCA2mutation was sequentially treated with carboplatin and the PARP inhibitor rucaparib. Genomic profiling of the available baseline tumor and progression blood samples using next-generation sequencing panel tests identified polyclonalBRCA2reversion mutations post carboplatin treatment but prior to rucaparib treatment. A total of 12 somatic reversion mutations were detected and ranged from small indels to larger deletions of up to 387 amino acids. These alterations are all predicted to restore theBRCA2open reading frame and potentially protein function. The patient received limited benefit while on rucaparib, likely due to these reversion mutations observed prior to treatment.ConclusionsHere we report a case of a patient with prostate cancer who received a platinum agent and PARP inhibitor sequentially and in whom polyclonalBRCA2reversion mutations were identified as the likely mechanism of acquired resistance to carboplatin and primary resistance to PARP inhibition. These findings suggest caution is warranted in sequencing these agents.