bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros (Ebenaceae) in the western Indian Ocean
Authors: Linan Alexander G , Schatz George E , Lowry Porter P , Miller Allison , Edwards Christine E 
Published: June 2019

AbstractUsing analyses that exhaustively sampled Mascarene Diospyros and included representative taxa from Madagascar and other regions, we explored: (1) evolutionary relationships among Diospyros spp. across the WIO and (2) biogeographic connections of Malagasy taxa with those in surrounding regions, particularly focusing on connections with taxa in the Mascarene Islands. We obtained plastid sequence data for 146 Diospyros taxa, including 40 species not previously included in molecular analyses, and conducted Bayesian and maximum-likelihood phylogenetic analyses, divergence-time estimation and ancestral area reconstructions. Diospyros sampled from Madagascar fell into two clades, one of which contains all but two Malagasy species. Biogeographic analyses revealed that many clades probably originated in Madagascar and dispersed to locations in Africa and the Mascarenes, indicating that Madagascar may have acted as an important source of diversity for the region.
Classification of Unmedicated Bipolar Disorder Using Whole-Brain Functional Activity and Connectivity: A Radiomics Analysis
Authors: Wang Ying , Sun Kai , Liu Zhenyu , Chen Guanmao , Jia Yanbin , Zhong Shuming , Pan Jiyang , Huang Li , Tian Jie 
Published: June 2019

AbstractThe aim of this study was to develop and validate a method of disease classification for bipolar disorder (BD) by functional activity and connectivity using radiomics analysis. Ninety patients with unmedicated BD II as well as 117 healthy controls underwent resting-state functional magnetic resonance imaging (rs-fMRI). A total of 4 types of 7018 features were extracted after preprocessing, including mean regional homogeneity (mReHo), mean amplitude of low-frequency fluctuation (mALFF), resting-state functional connectivity (RSFC), and voxel-mirrored homotopic connectivity (VMHC). Then, predictive features were selected by Mann–Whitney U test and removing variables with a high correlation. Least absolute shrinkage and selection operator (LASSO) method was further used to select features. At last, support vector machine (SVM) model was used to estimate the state of each subject based on the selected features after LASSO. Sixty-five features including 54 RSFCs, 7 mALFFs, 1 mReHo, and 3 VMHCs were selected. The accuracy and area under curve (AUC) of the SVM model built based on the 65 features is 87.3% and 0.919 in the training dataset, respectively, and the accuracy and AUC of this model validated in the validation dataset is 80.5% and 0.838, respectively. These findings demonstrate a valid radiomics approach by rs-fMRI can identify BD individuals from healthy controls with a high classification accuracy, providing the potential adjunctive approach to clinical diagnostic systems.
Expression of Bitter Taste Receptors and Solitary Chemosensory Cell Markers in the Human Sinonasal Cavity
Authors: Chen Jingguo , Larson Eric D , Anderson Catherine B , Agarwal Pratima , Frank Daniel N , Kinnamon Sue C , Ramakrishnan Vijay R 
Published: June 2019

Abstract
Some bitter taste receptors (TAS2R gene products) are expressed in the human sinonasal cavity and may function to detect airborne irritants. The expression of all 25 human bitter taste receptors and their location within the upper airway is not yet clear. The aim of this study is to characterize the presence and distribution of TAS2R transcripts and solitary chemosensory cells (SCCs) in different locations of the human sinonasal cavity. Biopsies were obtained from human subjects at up to 4 different sinonasal anatomic sites. PCR, microarray, and qRT-PCR were used to examine gene transcript expression. The 25 human bitter taste receptors as well as the sweet/umami receptor subunit, TAS1R3, and canonical taste signaling effectors are expressed in sinonasal tissue. All 25 human bitter taste receptors are expressed in the human upper airway, and expression of these gene products was higher in the ethmoid sinus than nasal cavity locations. Fluorescent in situ hybridization demonstrates that epithelial TRPM5 and TAS2R38 are expressed in a rare cell population compared with multiciliated cells, and at times, consistent with SCC morphology. Secondary analysis of published human sinus single-cell RNAseq data did not uncover TAS2R or canonical taste transduction transcripts in multiciliated cells. These findings indicate that the sinus has higher expression of SCC markers than the nasal cavity in chronic rhinosinusitis patients, comprising a rare cell type. Biopsies obtained from the ethmoid sinus may serve as the best location for study of human upper airway taste receptors and SCCs.
Trends in Prevalence of Protective Levels of Hepatitis B Surface Antibody Among Adults Aged 18–49 Years With Risk Factors for Hepatitis B Virus Infection—United States, 2003–2014
Authors: King Hope , Xing Jian , Dean Hazel D , Holtzman Deborah 
Published: June 2019

Abstract

Background
Hepatitis B virus (HBV) infection can be prevented through vaccination. However, previous data show that only about 24%–45% of US adults at high risk of HBV infection are protected. Our aims were to assess prevalence and trends in protective levels of hepatitis B surface antibody (anti-HBs) from 2003 to 2014 and explore factors associated with protection among adults at high risk.

Methods
Data were taken from the 2003–2014 National Health and Nutrition Examination surveys. Our sample included adults aged 18-49 years who were tested for HBV and reported at least 1 of the following infection risks: history of sexually transmitted disease, sex with men (for men), infection with human immunodeficiency virus, and injection drug use. We calculated the prevalence of anti-HBs (≥10 mIU/mL), indicative of immunity from vaccination, among respondents for three 4-year time intervals (2003–2006, 2007–2010, and 2011–2014) and applied the Cochran-Mantel-Haenszel test to assess trends. Using multivariable logistic regression, we examined factors associated with positive anti-HBs serology.

Results
The prevalence of positive anti-HBs serology was 23.4%. Prevalence increased from 2003–2006 (16.3%) to 2007–2010 (27.3%), but no change occurred from 2007–2010 (27.3%) to 2011–2014 (28.1%). Among factors predicting positive anti-HBs serology were young age and higher education.

Conclusions
By 2014, less than one-third of adults aged 18-49 years at risk of infection exhibited protective antibodies ≥10 mIU/mL. Because these adults account for a majority of unprotected adults, targeted intervention strategies are essential to achieve the hepatitis B elimination goal.
Concentration of a widespread breeding population in a few critically important nonbreeding areas: Migratory connectivity in the Prothonotary Warbler
Authors: Tonra Christopher M , Hallworth Michael T , Boves Than J , Reese Jessie , Bulluck Lesley P , Johnson Matthew , Viverette Cathy , Percy Katie , Ames Elizabeth M , Matthews Alix , Slevin Morgan C , Wilson R Randy , Johnson Erik I 
Published: June 2019

AbstractOne of the greatest challenges to informed conservation of migratory animals is elucidating spatiotemporal variation in distributions. Without such information, it is impossible to understand full-annual-cycle ecology and effectively implement conservation actions that address where and when populations are most limited. We deployed and recovered light-level geolocators (n = 34) at 6 breeding sites in North America across the breeding range of a declining long-distance migratory bird, the Prothonotary Warbler (Protonotaria citrea). We sought to determine migratory routes, stopover location and duration, and the location of overwintering grounds. We found that the species exhibits a large-scale, east‒west split in migratory routes and weak migratory connectivity across its range. Specifically, almost all individuals, regardless of breeding origin, overlapped in their estimated wintering location in northern Colombia, in an area 20% the size of the breeding range. Additionally, most of the individuals across all breeding locations concentrated in well-defined stopover locations in Central America while en route to Colombia. Although error inherent in light-level geolocation cannot be fully ruled out, surprisingly much of the estimated wintering area included inland areas even though the Prothonotary Warbler is considered a specialist on coastal mangroves in winter. Based on these results, conservation efforts directed at very specific nonbreeding geographical areas will potentially have benefits across most of the breeding population. Our findings highlight the importance of using modern technologies to validate assumptions about little-studied portions of a species’ annual cycle, and the need to distribute sampling across its range.
Multiscale effects of wetland availability and matrix composition on wetland breeding birds in Minnesota, USA
Authors: Saunders Sarah P , Hall Kristin A L , Hill Nina , Michel Nicole L 
Published: June 2019

Abstract
The increasing intensity of wetland stressors in the Upper Midwestern United States hastens the need to understand how matrix composition influences wetland bird occurrence and abundance. The optimal spatial scale for assessing species–habitat relationships is not always apparent, but may affect inference about wetland use and suitability. We developed occupancy and abundance models, accounting for imperfect detection, for 9 wetland bird species breeding in Minnesota. We evaluated land cover associations at 3 spatial scales (12.6 ha, 50.3 ha, and 4,000 ha), quantified species-specific sensitivity to wetland availability and matrix habitat composition (agricultural and developed land covers), and assessed ecoregional variation in occupancy and abundance. Amount of wetland cover was positively associated with occupancy of 89% of species and with abundance of 67% of species, but the spatial scale of support differed among species. American Bittern (Botaurus lentiginosus), Pied-billed Grebe (Podilymbus podiceps), and Wilson’s Snipe (Gallinago delicata) in particular were negatively impacted by anthropogenic land uses within the surrounding matrix, indicating a need to shift wetland conservation planning from the site scale to the landscape scale to capture pertinent drivers of wetland bird habitat use. Mean expected occupancy across all species was greatest in the Prairie Pothole Region (PPR), suggesting that restoration efforts within this ecoregion are likely to maintain wetland bird diversity. However, given the minimal total wetland availability and predominantly agricultural matrix in the PPR, protecting wetlands and upland buffers in the Aspen Parklands or Boreal ecoregions may represent a better investment for agricultural-sensitive species such as American Bittern, Sandhill Crane (Antigone canadensis), and Wilson’s Snipe. Our modeling approach provides a multi-species framework for identifying habitat management priorities; future applications at broader spatial extents can continue to improve wetland bird conservation in a region with high rates of wetland loss and degradation.
Relationship between epicardial adipose tissue and coronary vascular function in patients with suspected coronary artery disease and normal myocardial perfusion imaging
Authors: Nappi Carmela , Ponsiglione Andrea , Acampa Wanda , Gaudieri Valeria , Zampella Emilia , Assante Roberta , Cuocolo Renato , Mannarino Teresa , Dell’Aversana Serena , Petretta Mario , Imbriaco Massimo , Cuocolo Alberto 
Published: June 2019

Abstract

Aims
We evaluated the relationship between epicardial adipose tissue (EAT) and coronary vascular function assessed by rubidium-82 (82Rb) positron emission tomography/computed tomography (PET/CT) in patients with suspected coronary artery disease (CAD).

Methods and results
The study population included 270 patients with suspected CAD and normal myocardial perfusion at stress–rest 82Rb PET/CT. Coronary artery calcium (CAC) score and EAT volume were measured. Absolute myocardial blood flow (MBF) was computed in mL/min/ from the dynamic rest and stress imaging. Myocardial perfusion reserve (MPR) was defined as the ratio of hyperaemic to baseline MBF and it was considered reduced when <2. MPR was normal in 177 (65%) patients and reduced in 93 (35%). Patients with impaired MPR were older (P < 0.001) and had higher CAC score values (P = 0.033), EAT thickness (P = 0.009), and EAT volume (P < 0.001). At univariable logistic regression analysis, age, heart rate reserve (HRR), CAC score, EAT thickness, and EAT volume resulted significant predictors of reduced MPR, but only age (P = 0.002), HRR (P = 0.021), and EAT volume (P = 0.043) were independently associated with reduced MPR, at multivariable analysis. In patients with CAC score 0 (n = 114), a significant relation between EAT volume and MPR (P = 0.014) was observed, while the relationship was not significant (P = 0.21) in patients with CAC score >0 (n = 156).

Conclusion
In patients with suspected CAD and normal myocardial perfusion, EAT volume predicts hyperaemic MBF and reduced MPR, confirming that visceral pericardium fat may influence coronary vascular function. Thus, EAT evaluation has a potential role in the early identification of coronary vascular dysfunction.
The entirely subcutaneous ICDTM system in patients with congenital heart disease: experience from a large single-centre analysis
Authors: Willy Kevin , Reinke Florian , Bögeholz Nils , Köbe Julia , Eckardt Lars , Frommeyer Gerrit 
Published: June 2019

Abstract

Aims
The subcutaneous implantable cardioverter-defibrillator (S-ICDTM) is an important advance in device therapy for the prevention of sudden cardiac death (SCD). Although current guidelines recommend S-ICDTM use, long-term data are still limited, especially in subgroups such as adult patients with congenital heart diseases. This cohort is of high interest because of the difficult anatomic conditions in these patients.

Methods and results
All S-ICDTM patients with an underlying congenital heart disease (CHD) resulting in an indication for ICD implantation (n = 20 patients) in our large-scaled single-centre S-ICDTM registry (n = 249 patients) were included in this study. Baseline characteristics, appropriate and inappropriate shocks, and complications were documented in a mean follow-up of 36 months. Primary prevention of SCD was the indication for implantation of an S-ICDTM in six patients (30%). Of all 20 patients with an overall mean age of 40.5 ± 11.5 years, 12 were male (60%). The mean left ventricular ejection fraction was 46.5 ± 11.3%. Nine episodes of ventricular tachycardia (two monomorphic and seven polymorphic) were adequately terminated in three patients (15%). In two patients, T-Wave-Oversensing resulting in an inappropriate shock was observed, which could be managed by changing the sensing vector or activation of the SMART PASSTM filter. There were no S-ICDTM system-related infections. In one patient, surgical revision was necessary due to a persistent haematoma.

Conclusion
The S-ICDTM seems to be a valuable option for the prevention of SCD in patients with various CHDs and complex anatomical anomalies. The S-ICDTM is safe and works effectively, also in these complex patients. Inadequate shock delivery was rare and could be managed by reprogramming.
Changes over time in attitudes towards the management of older patients with heart failure by general practitioners: a qualitative study
Authors: Moscova Laura , Leblanc Fabien , Cittee Jacques , Le Breton Julien , Vallot Sophie , Fabre Julie , Phan Tan-Trung , Renard Vincent , Ferrat Emilie 
Published: June 2019

AbstractBackgroundUnderdiagnosis and undertreatment of chronic heart failure (CHF) are common in older patients, who are usually treated by general practitioners (GPs). In 2007, the French ICAGE study explored GPs’ attitudes to the management of this condition in older patients.ObjectivesTo explore changes over time in GPs’ attitudes towards the management of CHF in patients aged ≥75 and to identify barriers to optimal management.MethodsIn 2015, we performed a qualitative study of 20 French GPs via semi-structured interviews and a thematic content analysis. The results were compared with the findings of a 2007 study.ResultsIn 2015, the perceived barriers to diagnosis were the same as in 2007. Echocardiography was still the preferred diagnostic method but the GPs relied on the cardiologist to confirm the diagnosis. Many GPs were still unaware of the different types of CHF. In contrast, they reported greater knowledge of decompensation factors and the ultrasound criteria for CHF. They also prescribed a brain natriuretic peptide assay more frequently. Angiotensin-converting enzyme inhibitors and beta blockers were more strongly perceived to be core treatments. Few GPs initiated drug treatments and optimized dosages. Although patient education was never mentioned, the importance of multidisciplinary care was emphasized.ConclusionOur results evidenced a small recent improvement in the management of older patients with CHF. Appropriate guidelines and training for GPs, patient education and multidisciplinary collaboration might further improve the care given to this population.
Influential cited references in FEMS Microbiology Letters: lessons from Reference Publication Year Spectroscopy (RPYS)
Authors: Haunschild Robin , Bauer Johann , Bornmann Lutz 
Published: June 2019

ABSTRACT
The journal FEMS Microbiology Letters covers all aspects of microbiology including virology. On which scientific shoulders do the papers published in this journal stand? Which are the classic papers used by the authors? We aim to answer these questions in this study by applying the Reference Publication Year Spectroscopy (RPYS) analysis to all papers published in this journal between 1977 and 2017. In total, 16 837 publications with 410 586 cited references are analyzed. Mainly, the studies published in the journal FEMS Microbiology Letters draw knowledge from methods developed to quantify or characterize biochemical substances such as proteins, nucleic acids, lipids, or carbohydrates and from improvements of techniques suitable for studies of bacterial genetics. The techniques frequently used for studying the genetic of microorganisms in FEMS Microbiology Letters’ studies were developed using samples prepared from microorganisms. Methods required for the investigation of proteins, carbohydrates, or lipids were mostly transferred from other fields of life science to microbiology.
#EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide
Authors: López-Goñi I , Giner-Lamia J , Álvarez-Ordoñez A , Benitez-Páez Alfonso , Claessen D , Cortesao M , de Toro M , García-Ruano D , Granato E T , Kovács Á T , Romalde J L , Sana T G , Sánchez-Angulo M , Sangari F J , Smits W K , Sturm T , Thomassin J L , Valdehuesa K N G , Zapotoczna M 
Published: June 2019

ABSTRACT
Twitter is one of the most popular social media networks that, in recent years, has been increasingly used by researchers as a platform to share science and discuss ongoing work. Despite its popularity, Twitter is not commonly used as a medium to teach science. Here, we summarize the results of #EUROmicroMOOC: the first worldwide Microbiology Massive Open Online Course taught in English using Twitter. Content analytics indicated that more than 3 million users saw posts with the hashtag #EUROmicroMOOC, which resulted in over 42 million Twitter impressions worldwide. These analyses demonstrate that free Microbiology MOOCs shared on Twitter are valuable educational tools that reach broad audiences throughout the world. We also describe our experience teaching an entire Microbiology course using Twitter and provide recommendations when using social media to communicate science to a broad audience.
TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer
Authors: Singh Amartya , Bhanot Gyan , Khiabanian Hossein 
Published: June 2019

Abstract

Background
Traditional clustering approaches for gene expression data are not well adapted to address the complexity and heterogeneity of tumors, where small sets of genes may be aberrantly co-expressed in specific subsets of tumors. Biclustering algorithms that perform local clustering on subsets of genes and conditions help address this problem. We propose a graph-based Tunable Biclustering Algorithm (TuBA) based on a novel pairwise proximity measure, examining the relationship of samples at the extremes of genes' expression profiles to identify similarly altered signatures.

Results
TuBA's predictions are consistent in 3,940 breast invasive carcinoma samples from 3 independent sources, using different technologies for measuring gene expression (RNA sequencing and Microarray). More than 60% of biclusters identified independently in each dataset had significant agreement in their gene sets, as well as similar clinical implications. Approximately 50% of biclusters were enriched in the estrogen receptor−negative/HER2-negative (or basal-like) subtype, while &gt;50% were associated with transcriptionally active copy number changes. Biclusters representing gene co-expression patterns in stromal tissue were also identified in tumor specimens.

Conclusions
TuBA offers a simple biclustering method that can identify biologically relevant gene co-expression signatures not captured by traditional unsupervised clustering approaches. It complements biclustering approaches that are designed to identify constant or coherent submatrices in gene expression datasets, and outperforms them in identifying a multitude of altered transcriptional profiles that are associated with observed genomic heterogeneity of diseased states in breast cancer, both within and across tumor subtypes, a promising step in understanding disease heterogeneity, and a necessary first step in individualized therapy.
A chromosome-scale genome assembly of cucumber (Cucumis sativus L.)
Authors: Li Qing , Li Hongbo , Huang Wu , Xu Yuanchao , Zhou Qian , Wang Shenhao , Ruan Jue , Huang Sanwen , Zhang Zhonghua 
Published: June 2019

Abstract

Background
Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential.

Findings
We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (~211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants.

Conclusion
This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.