bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of five automated white matter hyperintensity segmentation methods in a multicenter dataset
Authors: Heinen Rutger , Steenwijk Martijn D. , Barkhof Frederik , Biesbroek J. Matthijs , van der Flier Wiesje M. , Kuijf Hugo J. , Prins Niels D. , Vrenken Hugo , Biessels Geert Jan , de Bresser Jeroen ,   TRACE-VCI study group, van den Berg E. , Biessels G. J. , Boomsma J. M. F. , Exalto L. G. , Ferro D. A. , Frijns C. J. M. , Groeneveld O. N. , Heinen R. , van Kalsbeek N. M. , Verwer J. H. , de Bresser J. , Kuijf H. J. , Emmelot-Vonk M. E. , Koek H. L. , Benedictus M. R. , Bremer J. , van der Flier W. M. , Leeuwis A. E. , Leijenaar J. , Prins N. D. , Scheltens P. , Tijms B. M. , Barkhof F. , Wattjes M. P. , Teunissen C. E. , Koene T. , Boomsma J. M. F. , Weinstein H. C. , Hamaker M. , Faaij R. , Pleizier M. , Prins M. , Vriens E. 
Published: November 2019

AbstractWhite matter hyperintensities (WMHs) are a common manifestation of cerebral small vessel disease, that is increasingly studied with large, pooled multicenter datasets. This data pooling increases statistical power, but poses challenges for automated WMH segmentation. Although there is extensive literature on the evaluation of automated WMH segmentation methods, such evaluations in a multicenter setting are lacking. We performed WMH segmentations in sixty patients scanned on six different magnetic resonance imaging (MRI) scanners (10 patients per scanner) using five freely available and fully-automated WMH segmentation methods (Cascade, kNN-TTP, Lesion-TOADS, LST-LGA and LST-LPA). Different MRI scanner vendors and field strengths were included. We compared these automated WMH segmentations with manual WMH segmentations as a reference. Performance of each method both within and across scanners was assessed using spatial and volumetric correspondence with the reference segmentations by Dice’s similarity coefficient (DSC) and intra-class correlation coefficient (ICC) respectively. We found the best performance, both within and across scanners, for kNN-TTP, followed by LST-LPA and LST-LGA, with worse performance for Lesion-TOADS and Cascade. Our findings can serve as a guide for choosing a method and also highlight the importance to further improve and evaluate consistency of methods in a multicenter setting.
High-fat diet-mediated dysbiosis exacerbates NSAID-induced small intestinal damage through the induction of interleukin-17A
Authors: Sugimura Naoki , Otani Koji , Watanabe Toshio , Nakatsu Geicho , Shimada Sunao , Fujimoto Kosuke , Nadatani Yuji , Hosomi Shuhei , Tanaka Fumio , Kamata Noriko , Taira Koichi , Nagami Yasuaki , Tanigawa Tetsuya , Uematsu Satoshi , Fujiwara Yasuhiro 
Published: November 2019

AbstractNon-steroidal anti-inflammatory drugs (NSAIDs) cause damage in the small intestine in a bacteria-dependent manner. As high-fat diet (HFD) is a potent inducer of gut dysbiosis, we investigated the effects of HFD on bacterial flora in the small intestine and NSAID-induced enteropathy. 16S rRNA gene analysis revealed that the population of Bifidobacterium spp. significantly decreased by fold change of individual operational taxonomic units in the small intestine of mice fed HFD for 8 weeks. HFD increased intestinal permeability, as indicated by fluorescein isothiocyanate-dextran absorption and serum lipopolysaccharide levels, accompanied by a decrease in the protein expressions of ZO-1 and occludin and elevated mRNA expression of interleukin (IL)-17A in the small intestine. HFD-fed mice exhibited increased susceptibility to indomethacin-induced damage in the small intestine; this phenotype was observed in normal diet-fed mice that received small intestinal microbiota from HFD-fed mice. Administration of neutralizing antibodies against IL-17A to HFD-fed mice reduced intestinal permeability and prevented exacerbation of indomethacin-induced damage. Thus, HFD-induced microbial dysbiosis in small intestine caused microinflammation through the induction of IL-17A and increase in intestinal permeability, resulting in the aggravation of NSAID-induced small intestinal damage.
The morpho-genetic and ecological niche analyses reveal the existence of climatically restricted Cycas zeylanica complex in Sri Lanka
Authors: Mudannayake Asanka , Ranaweera Lahiru , Samaraweera Preminda , Sooriyapathirana Suneth , Perera Anoma 
Published: November 2019

AbstractTaxonomy and phylogenesis of Sri Lankan cycad species of the subsection Rumphiae has not been fully resolved and therefore, we conducted an island-wide survey of cycads of the subsection to assess their morphological or genetic variations while exploring the phylogenetic relationship between Sri Lankan Rumphiae and other world cycad species. Further, we assessed the possible distribution of the species in the region through climatic profiling, using maximum entropy modeling approach. We analyzed 21 variable morphological features in collected specimens and used the polymorphism of trnH-psbA locus to understand the phylogeny. The distance tree drawn from the principal component analysis revealed a significant variation in female reproductive structures. The maximum likelihood tree separated Sri Lankan Cycas zeylanica to a well-supported unigeneric clade (bootstrap = 96, posterior probability = 100) with shallow divergence. Ecological niche modeling supported the existence of Cycas zeylanica in South East Asia and in southern Western Ghats in India in addition to the Wet Zone of Sri Lanka. We rename the taxa as Cycas zeylanica complex based on the observed high morphological diversity of female reproductive structures which might have ascended due to multiple introductions of South East Asian cycads by long distance dispersal of seeds through sea currents.
PGC-1β Induces Susceptibility To Acetaminophen-Driven Acute Liver Failure
Authors: Piccinin Elena , Ducheix Simon , Peres Claudia , Arconzo Maria , Vegliante Maria Carmela , Ferretta Anna , Bellafante Elena , Villani Gaetano , Moschetta Antonio 
Published: November 2019

AbstractAcetaminophen (APAP) is a worldwide commonly used painkiller drug. However, high doses of APAP can lead to acute hepatic failure and, in some cases, death. Previous studies indicated that different factors, including life-style and metabolic diseases, could predispose to the risk of APAP-induced liver failure. However, the molecular process that could favor APAP hepatotoxicity remains understood. Here, we reported that a short-term high fat-enriched diet worsens APAP-induced liver damage, by promoting liver accumulation of lipids that induces the activation of peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1β). Therefore, we challenged mice with hepatic-specific PGC-1β overexpression on a chow diet with a subtoxic dose of APAP and we found that PGC-1β overexpression renders the liver more sensitive to APAP damage, mainly due to intense oxidative stress, finally ending up with liver necrosis and mice death. Overall, our results indicated that during high fat feeding, PGC-1β adversely influences the ability of the liver to overcome APAP toxicity by orchestrating different metabolic pathways that finally lead to fatal outcome.
Fecal microbiome signatures of pancreatic cancer patients
Authors: Half Elizabeth , Keren Nirit , Reshef Leah , Dorfman Tatiana , Lachter Ishai , Kluger Yoram , Reshef Naama , Knobler Hilla , Maor Yaakov , Stein Assaf , Konikoff Fred M. , Gophna Uri 
Published: November 2019

AbstractPancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiota, potentially yielding biomarkers for PC. However, the usefulness of these biomarkers may be limited if they are specific for advanced stages of disease, which may involve comorbidities such as biliary obstruction or diabetes. In this study we analyzed the fecal microbiota of 30 patients with pancreatic adenocarcinoma, 6 patients with pre-cancerous lesions, 13 healthy subjects and 16 with non-alcoholic fatty liver disease, using amplicon sequencing of the bacterial 16S rRNA gene. Fourteen bacterial features discriminated between PC and controls, and several were shared with findings from a recent Chinese cohort. A Random Forest model based on the microbiota classified PC and control samples with an AUC of 82.5%. However, inter-subject variability was high, and only a small part of the PC-associated microbial signals were also observed in patients with pre-cancerous pancreatic lesions, implying that microbiome-based early detection of such lesions will be challenging.
Shrub cover homogenizes small mammals’ activity and perceived predation risk
Authors: Loggins Anne A. , Shrader Adrian M. , Monadjem Ara , McCleery Robert A. 
Published: November 2019

AbstractAltered disturbance regimes, increasing atmospheric CO2, and other processes have increased woody cover and homogenized vegetation in savannas across the planet. African savannas with extensive versus minimal woody cover often have vastly different animal communities. However, we lack a clear mechanistic understanding of why animal communities are changing with vegetation structure. Our goal for this study was to understand how vegetation structure in an African savanna shaped the perceived predation risk of small mammals, hence affecting their activity. Using a reciprocal measure of standard giving-up-densities, amount of food eaten, we found sharp declines in rodents’ perceived predation risk and increased rodent activity underneath shrub cover. This response was consistent across species; however, species showed subtle differences in their responses to grassy vegetation. Our findings suggest that areas of minimal or extensive shrub cover (shrub encroachment) may be homogenizing rodents’ perceptions of predation risk and thus shaping their use of space.
Multiple genome analyses reveal key genes in Vitamin C and Vitamin D synthesis and transport pathways are shared
Authors: Dong Wei , Tian Cheng , Jiao Yan , Blackwell Savannah , Lou Ge , Postlethwaite Arnold , Gu Weikuan , Sun Dianjun 
Published: November 2019

AbstractVitamin C (VC) and vitamin D (VD) have been widely used as the dietary supplements and in treatment of diseases both independently and in combination. Whether there is a connection between their pathways is critical for their therapeutic applications. Using whole-genome expression profiles, we performed multiple measures of associations, networks, eQTL mappings and expressions of key genes of interest in VC and VD functions. Several key genes in their pathways were found to be associated. Gc and Rgn play important roles connecting VC and VD pathways in mice. The r values of expression levels between Gc and Rgn in mouse spleen, liver, lung, and kidney are 0.937, 0.558, 0.901, and 0.617, respectively. The expression QTLs of Gc and Rgn are mapped onto the same locations, i.e., 68–76 MB in chromosome 7 and 26–36 MB in chromosome 9. In humans, there are positive correlations between CYP27B1 and SLC23A1 expression levels in kidney (r = 0.733) and spleen (r = 0.424). SLC23A2 and RXRA are minimally associated in both mouse and human. These data indicate that pathways of VC and VD are not independent but affect each other, and this effect is different between mice and humans during VC and VD synthesis and transportation.
Duration of stunting impacts compensatory growth and carcass quality of farmed milkfish, Chanos chanos (Forsskal, 1775) under field conditions
Authors: Lingam Somu Sunder , Sawant Paramita Banerjee , Chadha Narinder Kumar , Prasad Kurcheti Pani , Muralidhar A. P. , Syamala Karthireddy , Xavier K. A. Martin 
Published: November 2019

AbstractAn 18-months field trial was performed to explore the effect of duration of stunting on growth, digestive enzymes and carcass quality in Chanos chanos. Milkfish fry (weight of 1.25 ± 0.03 g and length of 5.53 ± 0.03 cm) were stocked in earthen ponds of 0.02 ha, in triplicate, for different duration of stunting, viz., 4 months (Treatment-1; T4), 8 months (Treatment-2; T8) and 12 months (Treatment-3; T12) and a normal seed (Control; C) separately. In the stunting phase, fish were stocked at higher stocking density (0.2 million/ha) and fed de-oiled rice bran at sub-optimal level. Post-stunting or re-feeding phase commenced immediately after completion of respective stunting duration and fish were reared for the rest of the period to complete the total rearing period of 18 months. In post-stunting, fish stocking density was adjusted to (5000 pieces/ha) and fed at an optimum level (3%). At the end of stunting phase, the study found a significant reduction in growth, survival, digestive enzymes activity, except protease in the T4 group, and carcass nutrients composition of stunted fish. However, in the initial phase of post-stunting, T8 group exhibited an elevated specific growth rate (5.00 ± 0.092%/day), body weight gain (80.82 ± 1.28 g), amylase (0.585 ± 0.021 U/mg protein), protease (5.48 ± 0.13 U/mg protein), and lipase activity (7.92 ± 0.32 U/mg protein). All stunted fish groups displayed a compensatory growth response in post-stunting, but a complete growth compensation was observed in T8 group, which resulted in better feed conversion ratio (3.03 ± 0.04) feed efficiency ratio (0.33 ± 0.01), protein efficiency ratio (1.91 ± 0.03), survival (91.38 ± 0.07%) and digestive enzyme activities. Similarly, at the end of post-stunting, carcass analysis revealed a complete restoration of nutrients in stunted fish and significantly higher protein content in T8 group. Further, the study found lower meat and higher bone contents in normally reared fish than the post-stunted fish which revealed the carcass quality improvement in post-stunted fish thus indicates superiority of the stunting process over normal rearing. Overall, the study suggests that stunting of milkfish, for 8 months (T8), positively affects its growth, survival, digestive enzyme activities and carcass quality which in turn, shall help to overcome the contemporary challenges in milkfish culture.
PRAS40 suppresses atherogenesis through inhibition of mTORC1-dependent pro-inflammatory signaling in endothelial cells
Authors: Zhang Kevin Sun , Schecker Johannes , Krull Alexandros , Riechert Eva , Jürgensen Lonny , Kamuf-Schenk Verena , Burghaus Jana , Kiper Leon , Cao Ho Thanh , Wöltje Kerstin , Stangl Verena , Katus Hugo A. , Stangl Karl , Völkers Mirko , Althoff Till F. 
Published: November 2019

AbstractEndothelial pro-inflammatory activation plays a pivotal role in atherosclerosis, and many pro-inflammatory and atherogenic signals converge upon mechanistic target of rapamycin (mTOR). Inhibitors of mTOR complex 1 (mTORC1) reduced atherosclerosis in preclinical studies, but side effects including insulin resistance and dyslipidemia limit their clinical use in this context. Therefore, we investigated PRAS40, a cell type-specific endogenous modulator of mTORC1, as alternative target. Indeed, we previously found PRAS40 gene therapy to improve metabolic profile; however, its function in endothelial cells and its role in atherosclerosis remain unknown. Here we show that PRAS40 negatively regulates endothelial mTORC1 and pro-inflammatory signaling. Knockdown of PRAS40 in endothelial cells promoted TNFα-induced mTORC1 signaling, proliferation, upregulation of inflammatory markers and monocyte recruitment. In contrast, PRAS40-overexpression blocked mTORC1 and all measures of pro-inflammatory signaling. These effects were mimicked by pharmacological mTORC1-inhibition with torin1. In an in vivo model of atherogenic remodeling, mice with induced endothelium-specific PRAS40 deficiency showed enhanced endothelial pro-inflammatory activation as well as increased neointimal hyperplasia and atherosclerotic lesion formation. These data indicate that PRAS40 suppresses atherosclerosis via inhibition of endothelial mTORC1-mediated pro-inflammatory signaling. In conjunction with its favourable effects on metabolic homeostasis, this renders PRAS40 a potential target for the treatment of atherosclerosis.
Disrupting coupling within mycobacterial F-ATP synthases subunit ε causes dysregulated energy production and cell wall biosynthesis
Authors: Saw Wuan-Geok , Wu Mu-Lu , Ragunathan Priya , Biuković Goran , Lau Aik-Meng , Shin Joon , Harikishore Amaravadhi , Cheung Chen-Yi , Hards Kiel , Sarathy Jickky Palmae , Bates Roderick W. , Cook Gregory M. , Dick Thomas , Grüber Gerhard 
Published: November 2019

AbstractThe dynamic interaction of the N- and C-terminal domains of mycobacterial F-ATP synthase subunit ε is proposed to contribute to efficient coupling of H+-translocation and ATP synthesis. Here, we investigate crosstalk between both subunit ε domains by introducing chromosomal atpC missense mutations in the C-terminal helix 2 of ε predicted to disrupt inter domain and subunit ε-α crosstalk and therefore coupling. The ε mutant εR105A,R111A,R113A,R115A (ε4A) showed decreased intracellular ATP, slower growth rates and lower molar growth yields on non-fermentable carbon sources. Cellular respiration and metabolism were all accelerated in the mutant strain indicative of dysregulated oxidative phosphorylation. The ε4A mutant exhibited an altered colony morphology and was hypersusceptible to cell wall-acting antimicrobials suggesting defective cell wall biosynthesis. In silico screening identified a novel mycobacterial F-ATP synthase inhibitor disrupting ε’s coupling activity demonstrating the potential to advance this regulation as a new area for mycobacterial F-ATP synthase inhibitor development.
Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers
Authors: Höglund Julia , Rafati Nima , Rask-Andersen Mathias , Enroth Stefan , Karlsson Torgny , Ek Weronica E. , Johansson Åsa 
Published: November 2019

AbstractGenome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.
An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains
Authors: Fratev Filip , Sirimulla Suman 
Published: November 2019

AbstractRecent improvements to the free energy perturbation (FEP) calculations, especially FEP+ , established their utility for pharmaceutical lead optimization. Herein, we propose a modified version of the FEP/REST (i.e., replica exchange with solute tempering) sampling protocol, based on detail studies on several targets by probing a large number of perturbations with different sampling schemes. Improved FEP+ binding affinity predictions for regular flexible-loop motions and considerable structural changes can be obtained by extending the prior to REST (pre-REST) sampling time from 0.24 ns/λ to 5 ns/λ and 2 × 10 ns/λ, respectively. With this new protocol, much more precise ∆∆G values of the individual perturbations, including the sign of the transformations and decreased error were obtained. We extended the REST simulations from 5 ns to 8 ns to achieve reasonable free energy convergence. Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in the ligand binding domain (LBD) has considerably improved the FEP+ results in most of the studied cases. Preliminary molecular dynamics (MD) runs were useful for establishing the correct binding mode of the compounds and thus precise alignment for FEP+ . Our improved protocol may further increase the FEP+ accuracy.
The first comprehensive phylogenetic and biochemical analysis of NADH diphosphatases reveals that the enzyme from Tuber melanosporum is highly active towards NAD+
Authors: García-Saura Antonio Ginés , Zapata-Pérez Rubén , Martínez-Moñino Ana Belén , Hidalgo José Francisco , Morte Asunción , Pérez-Gilabert Manuela , Sánchez-Ferrer Álvaro 
Published: November 2019

AbstractNudix (for nucleoside diphosphatases linked to other moieties, X) hydrolases are a diverse family of proteins capable of cleaving an enormous variety of substrates, ranging from nucleotide sugars to NAD+-capped RNAs. Although all the members of this superfamily share a common conserved catalytic motif, the Nudix box, their substrate specificity lies in specific sequence traits, which give rise to different subfamilies. Among them, NADH pyrophosphatases or diphosphatases (NADDs) are poorly studied and nothing is known about their distribution. To address this, we designed a Prosite-compatible pattern to identify new NADDs sequences. In silico scanning of the UniProtKB database showed that 3% of Nudix proteins were NADDs and displayed 21 different domain architectures, the canonical architecture (NUDIX-like_zf-NADH-PPase_NUDIX) being the most abundant (53%). Interestingly, NADD fungal sequences were prominent among eukaryotes, and were distributed over several Classes, including Pezizomycetes. Unexpectedly, in this last fungal Class, NADDs were found to be present from the most common recent ancestor to Tuberaceae, following a molecular phylogeny distribution similar to that previously described using two thousand single concatenated genes. Finally, when truffle-forming ectomycorrhizal Tuber melanosporum NADD was biochemically characterized, it showed the highest NAD+/NADH catalytic efficiency ratio ever described.