bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections
Authors: Verhagen Lilly M , Rivera-Olivero Ismar A , Clerc Melanie , Chu Mei Ling J N , van Engelsdorp Gastelaars Jody , Kristensen Maartje I , Berbers Guy A M , Hermans Peter W M , de Jonge Marien I , de Waard Jacobus H , Bogaert Debby 
Published: January 2020

Abstract

Background
Recent research suggests that the microbiota affects susceptibility to both respiratory tract infections (RTIs) and gastrointestinal infections (GIIs). In order to optimize global treatment options, it is important to characterize microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high.

Methods
We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks–59 months who were participating in a 13-valent pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing, and regression analysis, we determined whether specific bacteria were associated with RTIs or GIIs and variation in PCV13 response.

Results
Microbiota compositions differed between children with or without RTIs (P = .018) or GIIs (P = .001). Several species were associated with the absence of infections. Some of these health-associated bacteria are also observed in developed regions, such as Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) = 1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06, respectively). Klebsiella spp. presence was associated with both RTIs (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20).

Conclusions
The nasopharyngeal microbiota of rural Venezuelan children included several bacteria that thrive in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with an RTI but also in those with a GII, which suggests a reciprocal interplay between the 2 environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.
Homotypic and Heterotypic Protection and Risk of Reinfection Following Natural Norovirus Infection in a Highly Endemic Setting
Authors: Chhabra Preeti , Rouhani Saba , Browne Hannah , Peñataro Yori Pablo , Siguas Salas Mery , Paredes Olortegui Maribel , Moulton Lawrence H , Kosek Margaret N , Vinjé Jan 
Published: January 2020

Abstract

Background
Norovirus is a leading cause of acute gastroenteritis worldwide, yet there is limited information on homotypic or heterotypic protection following natural infection to guide vaccine development.

Methods
A total of 6020 stools collected from 299 Peruvian children between 2010 and 2014 were tested by norovirus real-time reverse-transcription polymerase chain reaction followed by sequence-based genotyping. Cox proportional hazards models were used to derive adjusted hazard ratios (HRs) of infection among children with vs without prior exposure.

Results
Norovirus was detected in 1288 (21.3%) samples. GII.4 (26%), GII.6 (19%), and GI.3 (9%) viruses accounted for 54% of infections. Homotypic protection for GI.3 (HR, 0.35; P = .015), GI.7 (HR, 0.19; P = .022), GII.4 (HR, 0.39; P &lt; .001), and GII.6 (HR, 0.52; P = .006) infections was observed. Hazard analysis showed that children with prior GII.4 infection exhibited heterotypic protection with a 48% reduction of subsequent GI.3 infection (HR, 0.52; P = .005). Prior exposure to GI.3, GII.2, and GII.17 infections enhanced susceptibility to subsequent infections with several other norovirus genotypes.

Conclusions
Children up to 2 years of age infected with GII.4 noroviruses demonstrated both homotypic and heterotypic protection to reinfection with other genotypes. These data support the need for ongoing vaccine development efforts with GII.4 as the main component and caution the inclusion of genotypes that may enhance susceptibility to infections.
Joubert syndrome diagnosed renally late
Authors: Collard Elizabeth , Byrne Catherine , Georgiou Michalis , Michaelides Michel , Dixit Abhijit 
Published: January 2020

Abstract
Joubert syndrome is a genetically heterogeneous multisystem disorder typically diagnosed in childhood. Nephronophthisis is the most common renal pathology in Joubert syndrome, and renal failure usually occurs in childhood or in young adults. We report a 61-year-old female diagnosed with AHI1-related oculorenal Joubert syndrome, who presented initially with decline in renal function in her 50s. Our report describes exceptionally late presentation of renal disease in Joubert syndrome and highlights the importance of continued renal function monitoring in older adults with Joubert syndrome.
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
Authors: Banchi Elisa , Ametrano Claudio G , Greco Samuele , Stanković David , Muggia Lucia , Pallavicini Alberto 
Published: January 2020

AbstractDNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called ‘better clustering for QIIME’ (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) and PLANiTS (97 550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering.Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.
In vivo relationship between near-infrared spectroscopy-detected lipid-rich plaques and morphological plaque characteristics by optical coherence tomography and intravascular ultrasound: a multimodality intravascular imaging study
Authors: Zanchin Christian , Ueki Yasushi , Losdat Sylvain , Fahrni Gregor , Daemen Joost , Ondracek Anna S , Häner Jonas D , Stortecky Stefan , Otsuka Tatsuhiko , Siontis George C M , Rigamonti Fabio , Radu Maria , Spirk David , Kaiser Christoph , Engstrom Thomas , Lang Irene , Koskinas Konstantinos C , Räber Lorenz 
Published: January 2020

Abstract

Aims
We assessed morphological features of near-infrared spectroscopy (NIRS)-detected lipid-rich plaques (LRPs) by using optical coherence tomography (OCT) and intravascular ultrasound (IVUS).

Methods and results
IVUS-NIRS and OCT were performed in the two non-infarct-related arteries (non-IRAs) in patients undergoing percutaneous coronary intervention for treatment of an acute coronary syndrome. A lesion was defined as the 4 mm segment with the maximum amount of lipid core burden index (maxLCBI4mm) of each LRP detected by NIRS. We divided the lesions into three groups based on the maxLCBI4mm value: &lt;250, 250–399, and ≥400. OCT analysis and IVUS analysis were performed blinded for NIRS. We measured fibrous cap thickness (FCT) by using a semi-automated method. A total of 104 patients underwent multimodality imaging of 209 non-IRAs. NIRS detected 299 LRPs. Of those, 41% showed a maxLCBI4mm &lt;250, 39% a maxLCBI4mm 251–399, and 19% a maxLCBI4mm ≥400. LRPs with a maxLCBI4mm ≥400, as compared with LRPs with a maxLCBI4mm 250–399 and &lt;250, were more frequently thin-cap fibroatheroma (TCFA) (42.1% vs. 5.1% and 0.8%; P &lt; 0.001) with a smaller minimum FCT (80 μm vs. 110 μm and 120 μm; P &lt; 0.001); a higher IVUS-derived percent atheroma volume (53% vs. 53% and 44%; P &lt; 0.001) and a higher remodelling index (1.08 vs. 1.02 and 1.01; P &lt; 0.001). MaxLCBI4mm correlated with OCT-derived FCT (r = 0.404; P &lt; 0.001) and was the best predictor for TCFA with an optimal cut-off value of 401 (area under the curve = 0.882; P &lt; 0.001).

Conclusion
LRPs with increasing maxLCBI4mm exhibit OCT and IVUS features of presumed plaque vulnerability including TCFA morphology, increased plaque burden, and positive remodelling.
Very short vs. long dual antiplatelet therapy after second generation drug-eluting stents in 35 785 patients undergoing percutaneous coronary interventions: a meta-analysis of randomized controlled trials
Authors: Benenati Stefano , Galli Mattia , De Marzo Vincenzo , Pescetelli Fabio , Toma Matteo , Andreotti Felicita , Bona Roberta Della , Canepa Marco , Ameri Pietro , Crea Filippo , Porto Italo 
Published: January 2020

Abstract

Aim
To provide an updated assessment of the efficacy–safety profile of very short (1 or 3 months) dual antiplatelet therapy (DAPT) compared with long (12 months) DAPT in patients undergoing percutaneous coronary interventions (PCIs).

Methods and results
Seven randomized controlled trials (RCTs) comparing very short vs. long DAPT in 35 785 patients undergoing PCI were selected. The primary efficacy endpoint was major adverse cardiovascular events (MACE) and the primary safety endpoint trial-defined major bleeding through at least 1 year. Compared with longer duration, very short DAPT yielded comparable rates of MACE [odds ratio (OR) 0.93, 95% confidence interval (CI) 0.84–1.03, P = 0.19], all-cause mortality (OR 0.92, 95% CI 0.80–1.06, P = 0.25), myocardial infarction (OR 1.01, 95% CI 0.88–1.15, P = 0.91), stroke (OR 1.04, 95% CI 0.72–1.50, P = 0.83), stent thrombosis (OR 1.05, 95% CI 0.80–1.37, P = 0.73), target vessel revascularization (OR 0.99, 95% CI 0.82–1.18, P = 0.89), and comparable net clinical benefit (OR 0.92, 95% CI 0.84–1.01, P = 0.08). Very short DAPT was associated with reduced rates of major bleeding (OR 0.61, 95% CI 0.40–0.94, P = 0.03) or any bleeding (OR 0.65, 95% CI 0.47–0.90, P = 0.009). Subgroup analyses showed consistent results for 1 vs. 3 month DAPT and for aspirin vs. P2Y12 inhibitor monotherapy following very short DAPT.

Conclusions
Compared with long DAPT, very short DAPT did not increase the odds of ischaemic complications, while reducing the odds of major or any bleeding by over 30%.
Molecular identification of bronchopulmonary neuroendocrine tumours and neuroendocrine genotype in lung neoplasia using the NETest liquid biopsy
Authors: Filosso Pier Luigi , Öberg Kjell , Malczewska Anna , Lewczuk Anna , Roffinella Matteo , Aslanian Harry , Bodei Lisa 
Published: January 2020

Abstract

OBJECTIVES
Diagnosing lung neuroendocrine neoplasia (NEN) requires a biopsy or an operation. We evaluated a ‘liquid biopsy’ (NETest) as an in vitro diagnostic tool for identifying NEN and compared it to chromogranin A (CgA).

METHODS
We identified 4 study cohorts: patients with bronchopulmonary carcinoids (n = 99, including 62 typical and 37 atypical carcinoids), lung cancers [n = 101, including 41 adenocarcinomas, 37 squamous carcinomas (SQC), 16 small-cell lung cancers and 7 large-cell neuroendocrine carcinomas]; benign disease (50 idiopathic pulmonary fibrosis) and healthy controls (n = 102). Transcript levels measured quantitatively (activity scores: 0–100) were compared to CgA (enzyme-linked immunosorbent assay; normal &lt; 109 ng/ml) levels.

RESULTS
The results of the NETest were positive (&gt;20) in 94% of patients with bronchopulmonary carcinoid compared to 8% of the controls (Fisher’s exact test; P &lt; 0.001) and were significantly more accurate as a diagnostic test (McNemar’s test; P &lt; 0.001, χ2 = 72) than was CgA (positive: 19% bronchopulmonary carcinoid, 15% controls). Small-cell lung cancers (87%), large-cell neuroendocrine carcinomas (86%), adenocarcinoma (42%) and SQC (35%) were also NETest-positive. Increasing the NETest cut-off score to &gt;40 was useful for detecting all NENs and differentiating these tumours from either controls/benign lung diseases (specificity 97%) or adenocarcinoma/SQC (specificity 94%). CgA was positive in 15–44% irrespective of pathology and had no diagnostic value.

CONCLUSIONS
A gene-based liquid biopsy is an effective and accurate method for diagnosing lung tumours with neuroendocrine gene expression. CgA has no value. An NETest score &gt;40 provides an accurate (94–97%) rule-in for the diagnosis of NEN and a rule-out for benign and other neoplastic diseases. Because neuroendocrine gene expression is associated with a poor prognosis, NETest levels may have utility both in the diagnosis of and the treatment stratification for lung neoplasia.
Mapping pre-dissection aortic wall abnormalities: a multiparametric assessment
Authors: Houben Ignas B , Nama Nitesh , Moll Frans L , van Herwaarden Joost A , Nordsletten David A , Williams David M , Patel Himanshu J , Figueroa C Alberto , Burris Nicholas S 
Published: January 2020

Abstract

OBJECTIVES
Maximal aortic diameter is commonly used to assess aortic risk but poorly predicts the timing and location of dissection events in patients with connective tissue disease who undergo regular imaging surveillance. Hence, we aimed to use available surveillance computed tomography angiography (CTA) scans to investigate the correlation between 3-dimensional (3D) growth and cyclic transmural wall stress with the location of intimal tear formation.

METHODS
Three type B aortic dissection patients with 2 available electrocardiogram (ECG)-gated pre-dissection CTA scans and without surgical repair during the pre-dissection interval were retrospectively identified at our institution. Vascular deformation mapping was used to measure 3D aortic growth between 2 pre-dissection clinical CTA studies. In addition, we performed a computational analysis to estimate cyclic transmural wall stress in patient-specific baseline CTA geometries.

RESULTS
In all 3 connective tissue disease patients, the site of type B aortic intimal tear co-localized with areas of peak 3D aortic wall growth. Aortic growth was detected by clinical radiological assessment in only 1 case. Co-localization of peak transmural stress and the site of intimal tear formation were found in all cases.

CONCLUSIONS
Focal areas of growth and transmural wall stress co-localized with the site of intimal tear formation. These hypothesis-generating results suggest a possible new analytic pathway for a more sophisticated assessment of the factors leading to the initiation of dissection in patients with connective tissue disease. These methods could improve on current risk-stratification techniques.
Prediction of sudden cardiac death in Japanese heart failure patients: international validation of the Seattle Proportional Risk Model
Authors: Fukuoka Ryoma , Kohno Takashi , Kohsaka Shun , Shiraishi Yasuyuki , Sawano Mitsuaki , Abe Takayuki , Nagatomo Yuji , Goda Ayumi , Mizuno Atsushi , Fukuda Keiichi , Shadman Ramin , Dardas Todd F , Levy Wayne C , Yoshikawa Tsutomu 
Published: January 2020

Abstract

Aims
Heart failure (HF) is associated with an increased risk of sudden cardiac death (SCD). This study sought to demonstrate the incidence of SCD within a multicentre Japanese registry of HF patients hospitalized for acute decompensation, and externally validate the Seattle Proportional Risk Model (SPRM).

Methods and results
We consecutively registered 2240 acute HF patients from academic institutions in Tokyo, Japan. The discrimination and calibration of the SPRM were assessed by the c-statistic, Hosmer–Lemeshow statistic, and visual plotting among non-survivors. Patient-level SPRM predictions and implantable cardioverter-defibrillator (ICD) benefit [ICD estimated hazard ratio (HR), derived from the Cox proportional hazards model in the Sudden Cardiac Death in Heart Failure Trial (SCD-HeFT)] was calculated. During the 2-year follow-up, 356 deaths (15.9%) occurred, which included 76 adjudicated SCDs (3.4%) and 280 non-SCDs (12.5%). The SPRM showed acceptable discrimination [c-index = 0.63; 95% confidence interval (CI) 0.56–0.70], similar to that of original SPRM-derivation cohort. The calibration plot showed reasonable conformance. Among HF patients with reduced ejection fraction (EF; &lt; 40%), SPRM showed improved discrimination compared with the ICD eligibility criteria (e.g. New York Heart Association functional Class II–III with EF ≤ 35%): c-index = 0.53 (95% CI 0.42–0.63) vs. 0.65 (95% CI 0.55–0.75) for SPRM. Finally, in the subgroup of 246 patients with both EF ≤ 35% and SPRM-predicted risk of ≥ 42.0% (SCD-HeFT defined ICD benefit threshold), mean ICD estimated HR was 0.70 (30% reduction of all-cause mortality by ICD).

Conclusion
The cumulative incidence of SCD was 3.4% in Japanese HF registry. The SPRM performed reasonably well in Japanese patients and may aid in improving SCD prediction.
Microbial abundance, composition, and function in nectar are shaped by flower visitor identity
Authors: Morris Megan M , Frixione Natalie J , Burkert Alexander C , Dinsdale Elizabeth A , Vannette Rachel L 
Published: January 2020

ABSTRACT
Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.
Differential impact of top-down and bottom-up forces in structuring freshwater bacterial communities
Authors: Pradeep Ram A S , Keshri J , Sime-Ngando T 
Published: January 2020

ABSTRACTLimited data exist on the simultaneous impact of bottom-up (nutrients) and top-down (viruses and heterotrophic nanoflagellates) forces in shaping freshwater bacterial communities. In our laboratory microcosms, nutrient additions (organic and inorganic) and viral reduction approach led to the proliferation of high nucleic acid (HNA) bacterial subpopulation without an increase in phage abundance. High viral-mediated bacterial lysis in the presence of nanoflagellates yielded high proportion of low nucleic acid bacterial subpopulation. 16S rRNA gene sequence analysis indicated that members of classes Proteobacteria and Bacteroidetes evoked differential responses to nutrients and mortality forces, thereby resulting in differences (P &lt; 0.001) in bacterial community composition and diversity, as observed from analysis of similarities and UniFrac analysis. Bacterial species richness (Chao) and diversity (Shannon) index was significantly higher (P &lt; 0.001) in the presence of both the top-down factors and viruses alone, whereas lower host diversity was observed under nutrient relaxation of growth-limiting substrates due to the explosive growth of opportunistic HNA bacterial subpopulation. Our results are in agreement with the theoretical model of ‘killing the winner’, where the availability of growth-limiting substrates can act as a stimulating factor for host community composition while top-down forces can operate in the control of host diversity.
A subcellular proteome atlas of the yeastKomagataella phaffii
Authors: Valli Minoska , Grillitsch Karlheinz , Grünwald-Gruber Clemens , Tatto Nadine E , Hrobath Bernhard , Klug Lisa , Ivashov Vasyl , Hauzmayer Sandra , Koller Martina , Tir Nora , Leisch Friedrich , Gasser Brigitte , Graf Alexandra B , Altmann Friedrich , Daum Günther , Mattanovich Diethard 
Published: January 2020

ABSTRACTThe compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.