bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rs72613567
Authors: Di Sessa Anna , Umano Giuseppina Rosaria , Cirillo Grazia , Marzuillo Pierluigi , Arienzo Maria Rosaria , Pedullà Marcella , Miraglia del Giudice Emanuele 
Published: December 2019

ABSTRACTWe first investigated in obese children the protective role of the hydroxysteroid 17‐beta dehydrogenase 13 (HSD17B13) rs72613567:TA variant in liver damage. Six hundred eighty‐five obese children were genotyped for HSD17B13, patatin‐like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), and membrane bound O‐acyltransferase domain containing 7 (MBOAT7) polymorphisms and underwent anthropometrical, ultrasonographic, and biochemical evaluation. Indirect measurement of liver fibrosis (Pediatric NAFLD Fibrosis Index [PNFI]) was calculated. The population was clustered in 2 genetic risk groups based on the numbers of steatogenic alleles (low: carriers up to 3 risk alleles, high: 4–6 risk alleles). Carriers of the HSD17B13 rare A allele showed lower percentage of hepatic steatosis and both lower serum transaminase and PNFI levels than noncarriers, even after adjustments for confounders. These findings were also confirmed in both risk groups. We demonstrated the protective effect of the rs72613567:TA HSD17B13 variant in reducing liver damage in obese children regardless of genetic predisposition.
Kawasaki at the Extremes of Age
Authors: Rosario Jennifer M. , Patel Faisalmohemed , Levasseur Kelly , Adams Lauren 
Published: December 2019

Abstract
Kawasaki disease is an acute vasculitis syndrome that typically occurs in children aged 1 to 4 years. Because there is no specific diagnostic test for Kawasaki disease, the diagnosis is made clinically based on specific characteristic signs and symptoms. Cases in which patients fall outside of the typical age range are uncommon and often challenging to diagnose because they have atypical presentations. This is especially true in infants, who rarely meet all the clinical criteria required for diagnosis. Patients at the extremes of ages often have a delayed diagnosis, which can lead to worse cardiac outcomes. We describe the cases of a young infant and an older adolescent who present with Kawasaki disease. These cases illustrate the challenge of diagnosing Kawasaki disease in patients beyond the typical age range. Both patients were return visits to the emergency department after inpatient stays. When fever persists longer than 5 days, clinicians must have a high index of suspicion for Kawasaki disease in all pediatric age groups to prevent treatment delay and disease sequelae.
Beware the Innocent Presentation of a Spontaneous Perforated Meckel Diverticulum
Authors: McKelvie Mark , Soares-Oliveira Miguel , Wang-Koh Yuan , Trayers Claire , Aslam Adil 
Published: December 2019

Abstract
Perforation of a Meckel diverticulum in a preterm neonate is very rare. To our knowledge, only 7 cases of spontaneous Meckel perforation in a preterm neonate have previously been described in the literature. The etiology is uncertain. We present the case of a 30-week preterm female twin with a spontaneous Meckel diverticulum perforation discovered on day 3 of life and review the published cases. A possible etiological explanation for this rare entity at this age group is also suggested.
Effect of 5-Line Signs in the Prediction of Staging, Progression, and Prognosis of Peripheral Lung Carcinoma: Preliminary Observation Report
Authors: Yu Anle , Li Qun , He Jinlong , Zhan Yuefu 
Published: December 2019

Background
The single line of the normal interlobar fissure shown on a thin section image can be reconstructed as a 5-line sign on axial maximal intensity projection. The line between the lung nodule and the pleura is called the pleural tail sign on thin image. On the axial maximal intensity projection, it can also be reconstructed as the 5-line sign or fewer than 5 lines.

Objective
This study aimed to observe the effect of 5-line signs in staging, progression, and prognosis of peripheral lung carcinoma.

Materials and Methods
This study included 132 patients with peripheral lung carcinoma. Among these patients, 93 were men and 39 were women, with an age range of 27 to 82 years and a lung nodule range of 0.98 to 8.75 cm. Maximal intensity projection was reconstructed based on 1.0 or 1.25 mm of thin-slice images in multislice spiral computed tomography. Five-line signs on the margin of the nodule (mass) were observed and were classified into grades 1 to 4 according to the sharpness of the 5-line signs.

Results
Multivariate logistic regression analysis showed that the sharpness of the 5-line signs was correlated with N and TNM staging of peripheral lung carcinoma (P = 0.012, P = 0.016). The lower the sharpness of the 5-line signs, the greater the number of cases of progression of the tumor (P < 0.001), and thus the higher the mortality rate and the lower the survival rate (P = 0.001). The sensitivity and specificity of predicting tumor progression were 56.3% and 93.3%, and those of tumor prognosis were 61.1% and 82.4%, respectively.

Conclusions
The sharpness of the 5-line signs has certain effects on the prediction of invasion, progression, and prognosis of lung carcinoma, particularly of small lung cancer (≤3.0 cm).
Investigating a novel commensal strain of Candida famata within Daniorerio
Authors: Jones Daniel , Hagen Ferry , Donaldson Christopher , Rudman Jacob , Canedo Jaime , Johnston Simon 
Published: December 2019

Our understanding of normal immunity to opportunistic fungal infection is limited by a lack of species-specific commensal/host/pathogen models. There are many species of opportunistic fungal pathogens (such as Candida spp. and Cryptococcus spp.) which exist as commensal organisms or are common in our environment. Therefore, we sought to develop a model of commensal opportunistic infection within zebrafish by identification of a normal commensal fungus that could act as an opportunistic pathogen.
Using dissections of D. rerio guts we isolated a monoculture of a commensal yeast. The strain was identified as Candida famata via DNA sequencing and phenotypic analysis (e.g. halotolerance). C. famata was isolated from six individual animals and three strains (DJ1-3) have been deposited in the CBS collection.

C. famata is a common commensal of animals, including humans and is a rare opportunistic pathogen. Our DJ1 strain was thermotolerant and grows at mammalian body temperature. We found it was easily phagocytosed by mouse macrophages, in some cases to the extent of host cell destruction. Infection of zebrafish larval model of opportunistic infection demonstrated C. famata could act as an opportunistic pathogen of its commensal host.
Thus, we have characterised the first commensal fungus to be isolated from zebrafish and demonstrated that it may be a potential opportunistic pathogen, as in humans. The study of C. famata in zebrafish therefore represents an unparalleled opportunity to understand the evolution of fungal immunology and the switch between commensal and pathogen.
Assessing the ecological role of yeasts in the human gut
Authors: Ward Grace , Gibson Glenn , Wijeyesekera Anisha , Sanderson Jeremy , Brostoff Jonathan 
Published: December 2019

Background:
The influence of gut microorganisms in health and disease is well documented, however, the role of yeasts has not been as widely studied as bacteria, despite associations with gastrointestinal disorders, such as Irritable Bowel Syndrome (IBS). For instance, Candida albicans is an opportunistic pathogen that has been linked to gastrointestinal symptoms.

Methods:
Urine, stool and blood samples will be collected from 40 healthy controls, 40 IBS and 40 inflammatory bowel disease (IBD) patients for microbial and metabolic analysis using primarily flow cytometry-fluorescence in situ hybridisation (FC-FISH) and proton nuclear magnetic resonance (1H-NMR) spectroscopy, respectively. Calprotectin and anti-Saccharomyces cerevisiae antibodies (ASCA) levels will assess gastrointestinal inflammation. Statistical analysis will identify yeasts and their metabolites associated with the cohorts of interest.

Preliminary results:
Preliminary tests to assess the presence and functionality of yeasts in healthy and IBS faecal samples using in vitro batch culture fermentation highlighted significant metabolic differences between the phenotypes: Trimethylamine (TMA), short chain fatty acids (SCFA) and ethanol predominantly distinguished in the IBS metabolic profile, compared to gamma-amino-N-butyrate (GABA) in the healthy donor. The addition of C. albicans shifted the healthy phenotype to resemble the IBS donor, whereas nystatin shifted the IBS phenotype towards the healthy metabolic profile.

Conclusion:
This study will further define the preliminary results that indicate the implication of yeasts in IBS pathogenesis. Understanding the role of yeasts within the healthy and diseased human gut is necessary to develop targeted therapies to improve patient’s quality of lives and relieve burdens on the economy and healthcare systems.
Comparative Genomics of the Saccharomyces complex
Authors: Keane Ann-Marie , Elliston Adam , Roberts Ian , Dicks Jo 
Published: December 2019

The Saccharomyces complex is a well-studied group of yeasts of considerable academic and industrial importance. Many species within the complex have no genome sequence publicly available and have yet to be formally compared at the genomic level with related species. We have recently sequenced the genomes of 40 species from 11 clades within the Saccharomyces complex. Considerable genomic diversity was observed in this dataset, including varying predicted genome size (9-22Mbp), coding proportion (42-76%) and gene number (4,194-11,001).
We evaluated the completeness of our gene sets and draft genome assemblies using the BUSCO tool, with a few species found to have a large number of duplicated and missing genes. These same species also had larger than average genome sizes and numbers of genes, which could indicate a duplication or hybridisation event. The total GC content was also found to vary significantly across the dataset, from Hanseniaspora uvarum (31.3%) to Lachancea thermotolerans (46%). GC content in the coding regions versus the whole genome was also observed, which could indicate differences in evolutionary pressures between species according to their environmental niches.
Here, we highlight some of the key differences found within this fascinating dataset, investigating the origins of some of the more extreme results and touching upon the opportunities and challenges they present in investigating the evolution of these yeasts.
Dissecting the role of Peroxiredoxins in regulating conserved ROS-activated kinases
Authors: Galler Martin , Day Alison , Latimer Heather , Vos Harmjan , Quinn Janet , Dansen Tobias , Veal Elizabeth 
Published: December 2019

In order to protect against oxidative damage, cells have evolved a host of ROS-detoxifying enzymes. These include peroxiredoxins, a highly conserved family of thioredoxin peroxidases. Unexpectedly, given their role in lowering H2O2levels, peroxiredoxins have been shown to be required for the activation of conserved stress-activated MAPKs in response to ROS in yeast1 and human2 cells. For example, we have previously shown that the single 2-Cys peroxiredoxin in S. pombe, Tpx1, but not its thioredoxin peroxidase activity, is required for the H2O2-induced activation of the p38/JNK-related MAPK, Sty1. Our findings revealed that Tpx1 forms H2O2-induced disulphide bonds with cysteines in Sty11, which suggested that Tpx1 may directly regulate Sty1 through these complexes. However, the mechanisms by which Tpx1-Sty1 disulphide complexes alter Sty1 function have remained unclear. Sty1, like its mammalian counterparts, has a number of important functions, including roles in coordinating cell growth, division, stress resistance and longevity in response to a variety of nutritional and stress stimuli. Our data suggests that disulphide complexes with Tpx1 are important for a subset of these roles. Intriguingly, our proteomic studies have identified multiple protein kinases that form disulphide complexes with Tpx1, these include kinases with established roles in regulating cell division and ageing. Here, we will present data suggesting that interactions with Tpx1 play important roles in regulating the activities of these kinases.
1. Veal et al. (2004) Molecular Cell, 15(1), pp. 129-139.
2. Jarvis et al. (2012) Free Radical Biology and Medicine, 53(7), pp. 1522-1530.
Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing
Authors: Chen Zhoutao , Pham Long , Wu Tsai-Chin , Mo Guoya , Xia Yu , Chang Peter , Porter Devin , Phan Tan , Che Huu , Tran Hao , Bansal Vikas , Shaffer Justin , Belda-Ferre Pedro , Humphrey Greg , Knight Rob , Pevzner Pavel , Pham Son , Wang Yong , Lei Ming 
Published: December 2019

AbstractLong-range sequencing information is required for haplotype phasing, de novo assembly and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirement. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-Seq™) technology, which enables a low-cost, high-accuracy and high-throughput short-read next generation sequencer to routinely generate over 100 Kb long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcode linked reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate mega-base-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.
CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles
Authors: Zhang Qiong , Luo Mei , Liu Chun-Jie , Guo An-Yuan 
Published: December 2019

AbstractCancer cell lines (CCLs) as important model systems play critical roles in cancer researches. The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphisms, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication,http://bioinfo.life.hust.edu.cn/web/CCLA/) to authenticate 1,291 human CCLs of 28 tissues using gene expression profiles. CCLA curated CCL-specific gene signatures and employed machine learning methods to measure overall similarities and distances between the query sample and each reference CCL. CCLA showed an excellent speed advantage and high accuracy with a top 1 accuracy of 96.58% or 92.15% (top 3 accuracy of 100% or 95.11%) for microarray or RNA-Seq validation data (719 samples, 461 CCLs), respectively. To the best of our knowledge, CCLA is the first approach to authenticate CCLs based on gene expression. Users can freely and conveniently authenticate CCLs using gene expression profiles or NCBI GEO accession on CCLA website.
Plant traits are poor predictors of long-term ecosystem functioning
Authors: van der Plas Fons , Schröder-Georgi Thomas , Weigelt Alexandra , Barry Kathryn , Meyer Sebastian , Alzate Adriana , Barnard Romain L. , Buchmann Nina , de Kroon Hans , Ebeling Anne , Eisenhauer Nico , Engels Christof , Fischer Markus , Gleixner Gerd , Hildebrandt Anke , Koller-France Eva , Leimer Sophia , Milcu Alexandru , Mommer Liesje , Niklaus Pascal A. , Oelmann Yvonne , Roscher Christiane , Scherber Christoph , Scherer-Lorenzen Michael , Scheu Stefan , Schmid Bernhard , Schulze Ernst-Detlef , Temperton Vicky , Tscharntke Teja , Voigt Winfried , Weisser Wolfgang , Wilcke Wolfgang , Wirth Christian 
Published: December 2019

ABSTRACTEarth is home to over 350,000 vascular plant species1that differ in their traits in innumerable ways. Yet, a handful of functional traits can help explaining major differences among species in photosynthetic rate, growth rate, reproductive output and other aspects of plant performance2–6. A key challenge, coined “the Holy Grail” in ecology, is to upscale this understanding in order to predict how natural or anthropogenically driven changes in the identity and diversity of co-occurring plant species drive the functioning of ecosystems7, 8. Here, we analyze the extent to which 42 different ecosystem functions can be predicted by 41 plant traits in 78 experimentally manipulated grassland plots over 10 years. Despite the unprecedented number of traits analyzed, the average percentage of variation in ecosystem functioning that they jointly explained was only moderate (32.6%) within individual years, and even much lower (12.7%) across years. Most other studies linking ecosystem functioning to plant traits analyzed no more than six traits, and when including either only six random or the six most frequently studied traits in our analysis, the average percentage of explained variation in across-year ecosystem functioning dropped to 4.8%. Furthermore, different ecosystem functions were driven by different traits, with on average only 12.2% overlap in significant predictors. Thus, we did not find evidence for the existence of a small set of key traits able to explain variation in multiple ecosystem functions across years. Our results therefore suggest that there are strong limits in the extent to which we can predict the long-term functional consequences of the ongoing, rapid changes in the composition and diversity of plant communities that humanity is currently facing.
S-nitrosylation affects TRAP1 structure and ATPase activity and modulates cell response to apoptotic stimuli
Authors: Faienza Fiorella , Lambrughi Matteo , Rizza Salvatore , Pecorari Chiara , Giglio Paola , Viloria Juan Salamanca , Allega Maria Francesca , Chiappetta Giovanni , Vinh Joëlle , Pacello Francesca , Battistoni Andrea , Rasola Andrea , Papaleo Elena , Filomeni Giuseppe 
Published: December 2019

ABSTRACTThe mitochondrial chaperone TRAP1 has been involved in several mitochondrial functions, and modulation of its expression/activity has been suggested to play a role in the metabolic reprogramming distinctive of cancer cells. TRAP1 posttranslational modifications, i.e. phosphorylation, can modify its capability to bind to different client proteins and modulate its oncogenic activity. Recently, it has been also demonstrated that TRAP1 isS-nitrosylated at Cys501, a redox modification associated with its degradationviathe proteasome. Here we report molecular dynamics simulations of TRAP1, together with analysis of long-range structural communication, providing a model according to which Cys501S-nitrosylation induces conformational changes to distal sites in the structure of the protein. The modification is also predicted to alter open and closing motions for the chaperone function. By means of colorimetric assays and site directed mutagenesis aimed at generating C501S variant, we also experimentally confirmed that selectiveS-nitrosylation of Cys501 decreases ATPase activity of recombinant TRAP1. Coherently, C501S mutant was more active and conferred protection to cell death induced by staurosporine. Overall, our results provide the firstin silico, in vitroand cellular evidence of the relevance of Cys501S-nitrosylation in TRAP1 biology.
Impacts of intraspecific variability and local adaptation on the ecophysiology of mosses: an example withSphagnum magellanicum
Authors: Oke Tobi A. , Turetsky Merritt R. , Weston David J. , Shaw A. Jonathan 
Published: December 2019

AbstractBackgroundBryophytes are a diverse plant group and are functionally different from vascular plants. Yet, plant ecology theories and hypotheses are often presented in an inclusive term. The trait-based approach to ecology is no exception; largely focusing on vascular plant traits and almost exclusively on interspecific traits. Currently, we lack information about the magnitude and the importance of intraspecific variability to the ecophysiology of bryophytes and how these might translate to local adaptation—a prerequisite for adaptive evolution.MethodWe used transplant and factorial experiments involving moisture and light to ask whether variability in traits between morphologically distinct individuals ofSphagnum magellanicumfrom habitat extremes was due to phenotypic plasticity or local adaptation and the implications for the ecophysiology of the species.Key ResultsWe found that the factors that discriminated between the plant origins in the field did not translate to their ecophysiological functioning and the pattern of variability changed with the treatments, which suggests that the trait responses were due largely to phenotypic plasticity. The trait responses suggest that the need for mosses to grow in clumps where they maintain a uniform growth rate may have an overriding effect on responses to environmental heterogeneity, and therefore a constraint for local adaptation.ConclusionThe circumstances under which local adaptation would be beneficial in this plant group is not clear. We conclude that extending the trait-based framework to mosses or making comparisons between mosses and vascular plants under any theoretical framework would only be meaningful to the extent that growth form and dispersal strategies are considered.
Growth-inhibiting activity of citronella essential oil to multiple fungal plant pathogens
Authors: Balendres Mark Angelo O. , Dela Cueva Fe M. 
Published: December 2019

AbstractCymbopogon species are among the most reported essential oils with fungitoxic effect. In this study, mycelial growth of Fusarium oxysporum (banana wilt), Colletotrichum gloeosporioides (mango anthracnose), C. falcatum (sugarcane red rot) and Neopestalotiopsis spp. (mango leaf spot) as influenced by varying concentrations of citronella essential oil (CEO) was assessed in in vitro assays. Following growth inhibition test, spore germination and germ tube elongation of C. gloeosporioides were then examined. Mycelial growth of all test fungal pathogens was strongly inhibited by CEO, but variations were observed among fungal species. This growth inhibition activity was caused by the inhibition of spore germination and germ tube elongation as observed in C. gloeosporioides. The findings of this study show the strong growth-inhibitory activity of CEO to multiple fungal pathogens, indicating CEO’s potential as a chemical control approach against these fungal pathogens. Glasshouse and field experiments would establish CEO as one potential alternative to fungicides.
Phase separation-aided compartmentalization of protein-protein interactions in cells
Authors: Liu Hongrui , Wang Jing , Li Pilong 
Published: December 2019

SummaryProtein-protein interactions (PPIs) are of great significance in many biological activities and diseases. It is essential to distinguish between direct, indirect and false PPIs in order to accurately understand their biological functions. Here we report a method based onphase separation-aidedcompartmentalization ofprotein-protein interactions incells (PACPIC), which is tailored for identification of direct and indirect PPIs in cells, using recruitment as the readout.