bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of caspase 8 polymorphisms -652 6N InsDel and Asp302His with progression-free survival and tumor infiltrating lymphocytes in early breast cancer
Authors: Kuhlmann Jan Dominik , Bachmann Hagen Sjard , Link Theresa , Wimberger Pauline , Kröber Eric , Thomssen Christoph , Mallé Brahima , Bethmann Daniel , Vetter Martina , Kantelhardt Eva Johanna 
Published: August 2019

AbstractThe caspase 8 variantsCASP8-652 6N InsDel and Asp302His have previously been identified to promote survival of T-lymphocytes and to indicate reduced breast cancer susceptibility. Besides some preliminary findings, prognostic relevance of these polymorphisms in patients with existing breast cancer has not been investigated. Considering an immunomodulatory role of these polymorphisms, we genotyped 785 early breast cancer patients and correlated caspase 8 variants with disease-free survival (DFS) and the presence of tumor infiltrating lymphocytes (TILs). Early breast cancer specimens were collected as part of the multicenter prospective PiA study. Genotyping was performed by pyrosequencing, TILs status was assessed using hematoxylin & eosin staining. TheCASP8-652Del variant was significantly associated with improved DFS in an allele-dose dependent manner (p = 0.027). Homozygosity for the -652Del variant was an independent predictor for improved DFS (HR = 0.36; 95% CI = 0.174–0.726; p = 0.005). In patients with the 302HisHis genotype, there was no event of recurrence during observation time. Combined analysis of diplotypes revealed an influence of both polymorphisms on DFS (p = 0.029). Interestingly, patients with the 302HisHis variant among the unstratified patient cohort (and among the luminal-like subtype, by trend) had tumors with lower lymphocyte infiltration (p = 0.025). We propose a prognostically favorable role of the -652Del and the 302His variant in primary breast cancer and suggest for the first time an association between polymorphisms in apoptosis-related genes and the immunophenotype in breast cancer. Our findings encourage further investigation of caspase 8 polymorphisms as biomarkers for prognostic and immunotherapeutic considerations.
A Langevin equation that governs the irregular stick-slip nano-scale friction
Authors: Jannesar M. , Sadeghi A. , Meyer E. , Jafari G. R. 
Published: August 2019

AbstractFriction force at the nanoscale, as measured from the lateral deflection of the tip of an atomic force microscope, usually shows a regular stick-slip behavior superimposed by a stochastic part (fluctuations). Previous studies showed the overall fluctuations to be correlated and multi-fractal, and thus not describable simply by e.g. a white noise. In the present study, we investigate whether one can extract an equation to describe nano-friction fluctuations directly from experimental data. Analysing the raw data acquired by a silicon tip scanning the NaCl(001) surface (of lattice constant 5.6 Å) at room temperature and in ultra-high vacuum, we found that the fluctuations possess a Markovian behavior for length scales greater than 0.7 Å. Above this characteristic length, the Kramers-Moyal approach applies. However, the fourth-order KM coefficient turns out to be negligible compared to the second order coefficients, such that the KM expansion reduces to the Langevin equation. The drift and diffusion terms of the Langevin equation show linear and quadratic trends with respect to the fluctuations, respectively. The slope 0.61 ± 0.02 of the drift term, being identical to the Hurst exponent, expresses a degree of correlation among the fluctuations. Moreover, the quadratic trend in the diffusion term causes the scaling exponents to become nonlinear, which indicates multifractality in the fluctuations. These findings propose the practical way to correct the prior models that consider the fluctuations as a white noise.
Energy dissipation in functionally two-dimensional phase transforming cellular materials
Authors: Zhang Yunlan , Restrepo David , Velay-Lizancos Mirian , Mankame Nilesh D. , Zavattieri Pablo D. 
Published: August 2019

AbstractPhase Transforming Cellular Materials (PXCMs) are periodic cellular materials whose unit cells exhibit multiple stable or meta-stable configurations. Transitions between the various (meta-) stable configurations at the unit cell level enable these materials to exhibit reusable solid state energy dissipation. This energy dissipation arises from the storage and non-equilibrium release of strain energy accompanying the limit point traversals underlying these transitions. The material deformation is fully recoverable, and thus the material can be reused to absorb and dissipate energy multiple times. In this work, we present two designs for functionally two-dimensional PXCMs: the S-type with four axes of reflectional symmetry based on a square motif and, the T-type with six axes of symmetry based on a triangular motif. We employ experiments and simulations to understand the various mechanisms that are triggered under multiaxial loading conditions. Our numerical and experimental results indicate that these materials exhibit similar solid state energy dissipation for loads applied along the various axes of reflectional symmetry of the material. The specific energy dissipation capacity of the T-type is slightly greater and less sensitive to the loading direction than the S-type under the most of loading directions. However, both types of material are shown to be very effective in dissipating energy.
The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato
Authors: Quispe-Huamanquispe Dora G. , Gheysen Godelieve , Yang Jun , Jarret Robert , Rossel Genoveva , Kreuze Jan F. 
Published: August 2019

AbstractThe discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato occurred before or after its speciation. Therefore, this study aims to evaluate the presence of IbT-DNAs in the genomes of sweetpotato’s wild relatives belonging to the taxonomic group series Batatas. Both IbT-DNA1 and IbT-DNA2 were found in tetraploid I. batatas (L.) Lam. and had highly similar sequences and at the same locus to those found in the cultivated sweetpotato. Moreover, IbT-DNA1 was also found in I. cordatotriloba and I. tenuissima while IbT-DNA2 was detected in I. trifida. This demonstrates that genome integrated IbT-DNAs are not restricted to the cultivated sweetpotato but are also present in tetraploid I. batatas and other related species.
Gene Expression Predicts Histological Severity and Reveals Distinct Molecular Profiles of Nonalcoholic Fatty Liver Disease
Authors: Hoang Stephen A. , Oseini Abdul , Feaver Ryan E. , Cole Banumathi K. , Asgharpour Amon , Vincent Robert , Siddiqui Mohammad , Lawson Mark J. , Day Nathan C. , Taylor Justin M. , Wamhoff Brian R. , Mirshahi Faridoddin , Contos Melissa J. , Idowu Michael , Sanyal Arun J. 
Published: August 2019

AbstractThe heterogeneity of biological processes driving the severity of nonalcoholic fatty liver disease (NAFLD) as reflected in the transcriptome and the relationship between the pathways involved are not well established. Well-defined associations between gene expression profiles and disease progression would benefit efforts to develop novel therapies and to understand disease heterogeneity. We analyzed hepatic gene expression in controls and a cohort with the full histological spectrum of NAFLD. Protein-protein interaction and gene set variation analysis revealed distinct sets of coordinately regulated genes and pathways whose expression progressively change over the course of the disease. The progressive nature of these changes enabled us to develop a framework for calculating a disease progression score for individual genes. We show that, in aggregate, these scores correlate strongly with histological measures of disease progression and can thus themselves serve as a proxy for severity. Furthermore, we demonstrate that the expression levels of a small number of genes (~20) can be used to infer disease severity. Finally, we show that patient subgroups can be distinguished by the relative distribution of gene-level scores in specific gene sets. While future work is required to identify the specific disease characteristics that correspond to patient clusters identified on this basis, this work provides a general framework for the use of high-content molecular profiling to identify NAFLD patient subgroups.
Near-Field Scanning Microwave Microscopy in the Single Photon Regime
Authors: Geaney S. , Cox D. , Hönigl-Decrinis T. , Shaikhaidarov R. , Kubatkin S. E. , Lindström T. , Danilov A. V. , de Graaf S. E. 
Published: August 2019

AbstractThe microwave properties of nano-scale structures are important in a wide variety of applications in quantum technology. Here we describe a low-power cryogenic near-field scanning microwave microscope (NSMM) which maintains nano-scale dielectric contrast down to the single microwave photon regime, up to 109 times lower power than in typical NSMMs. We discuss the remaining challenges towards developing nano-scale NSMM for quantum coherent interaction with two-level systems as an enabling tool for the development of quantum technologies in the microwave regime.
Deep Machine Learning Techniques for the Detection and Classification of Sperm Whale Bioacoustics
Authors: Bermant Peter C. , Bronstein Michael M. , Wood Robert J. , Gero Shane , Gruber David F. 
Published: August 2019

AbstractWe implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract finer-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classification tasks, including (1) “coda type classification” where we obtained 97.5% accuracy in categorizing 23 coda types from a Dominica dataset containing 8,719 codas and 93.6% accuracy in categorizing 43 coda types from an Eastern Tropical Pacific (ETP) dataset with 16,995 codas; (2) “vocal clan classification” where we obtained 95.3% accuracy for two clan classes from Dominica and 93.1% for four ETP clan types; and (3) “individual whale identification” where we obtained 99.4% accuracy using two Dominica sperm whales. These results demonstrate the feasibility of applying ML to sperm whale bioacoustics and establish the validity of constructing neural networks to learn meaningful representations of whale vocalizations.
Time of Day and its Association with Risk of Death and Chance of Discharge in Critically Ill Patients: A Retrospective Study
Authors: Zajic Paul , Bauer Peter , Rhodes Andrew , Moreno Rui , Fellinger Tobias , Metnitz Barbara , Posch Martin , Metnitz Philipp G. H. 
Published: August 2019

AbstractOutcomes following admission to intensive care units (ICU) may vary with time and day. This study investigated associations between time of day and risk of ICU mortality and chance of ICU discharge in acute ICU admissions. Adult patients (age ≥ 18 years) who were admitted to ICUs participating in the Austrian intensive care database due to medical or surgical urgencies and emergencies between January 2012 and December 2016 were included in this retrospective study. Readmissions were excluded. Statistical analysis was conducted using the Fine-and-Gray proportional subdistribution hazards model concerning ICU mortality and ICU discharge within 30 days adjusted for SAPS 3 score. 110,628 admissions were analysed. ICU admission during late night and early morning was associated with increased hazards for ICU mortality; HR: 1.17; 95% CI: 1.08–1.28 for 00:00–03:59, HR: 1.16; 95% CI: 1.05–1.29 for 04:00–07:59. Risk of death in the ICU decreased over the day; lowest HR: 0.475, 95% CI: 0.432–0.522 for 00:00–03:59. Hazards for discharge from the ICU dropped sharply after 16:00; lowest HR: 0.024; 95% CI: 0.019–0.029 for 00:00–03:59. We conclude that there are “time effects” in ICUs. These findings may spark further quality improvement efforts.
Toxoplasma gondii-induced host cellular cell cycle dysregulation is linked to chromosome missegregation and cytokinesis failure in primary endothelial host cells
Authors: Velásquez Zahady D. , Conejeros Iván , Larrazabal Camilo , Kerner Katharina , Hermosilla Carlos , Taubert Anja 
Published: August 2019

AbstractToxoplasma gondii is a zoonotic and intracellular parasite with fast proliferating properties leading to rapid host cell lysis. T. gondii modulates its host cell on numerous functional levels. T. gondii was previously reported to influence host cellular cell cycle and to dampen host cell division. By using primary endothelial host cells, we show for the first time that T. gondii tachyzoite infections led to increased host cell proliferation and to an enhanced number of multi-nucleated host cells. As detected on DNA content level, parasite infections induced a G2/M cell cycle arrest without affecting expression of G2-specific cyclin B1. In line, parasite-driven impairment mainly concerned mitotic phase of host cells by propagating several functional alterations, such as chromosome segregation errors, mitotic spindle alteration and blockage of cytokinesis progression, with the latter most likely being mediated by the downregulation of the Aurora B kinase expression.
High-fat and high-cholesterol diet decreases phosphorylated inositol-requiring kinase-1 and inhibits autophagy process in rat liver
Authors: Naito Hisao , Yoshikawa-Bando Yuki , Yuan Yuan , Hashimoto Sayuki , Kitamori Kazuya , Yatsuya Hiroshi , Nakajima Tamie 
Published: August 2019

AbstractPrecise molecular pathways involved in the progression of non-alcoholic steatohepatitis (NASH) remain to be elucidated. As Mallory–Denk bodies were occasionally observed in the enlarged hepatocytes in NASH model rat (SHRSP5/Dmcr) fed high-fat and high-cholesterol (HFC) diet, we aimed to clarify the roles of autophagy and endoplasmic reticulum (ER) stress in NASH progression. Male SHRSP5/Dmcr were randomly divided into 4 groups. Two groups were fed a control diet; the other two groups were fed a HFC diet for 2 and 8 weeks, respectively. The HFC diet increased the autophagy-related proteins levels and microtubule-associated protein 1 light chain 3-II/I ratio after 2 and 8 weeks, respectively. However, regarding ER stress-related proteins, the HFC diet decreased the levels of phosphorylated (p-) inositol-requiring kinase-1 (p-IRE-1) and p-protein kinase RNA-like ER kinase after 2 weeks. Additionally, the HFC diet increased anti-ubiquitin-positive cells and the level of the autophagy substrate p62, suggesting that the HFC diet induced dysfunction in ubiquitin-dependent protein degradation pathways. In conclusion, the HFC diet arrested the autophagy process in the liver; this was particularly associated with decreases in p-IRE-1 expression.
Dynamic of a Delayed Predator-Prey Model with Application to Network’ Users’ Data Forwarding
Authors: Zhang Yaming , Koura Yaya Hamadou , Su Yanyuan 
Published: August 2019

AbstractIn most situations where entities interact by sharing limited resources, controlling populations’ density is crucial to maintain ecosystem sustainability. This is the case in a predator-prey type interaction when predator survival relies on its ability to harvest and consume resources. In this article, we analyzed a modified predator-prey model based on Rosenzweig-MacArthur characterized by a delayed conversion of prey into resources and applied the proposed model to network users’ data forwarding at a bottleneck node. We discuss system fixed points behaviour and prove that delaying the handling time has a significant impact on the dynamic of interaction and system bifurcates, exhibits chaotic behaviour and is highly responsive to small perturbations.
Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken
Authors: Yamashita Satoshi , Kataoka Kensuke , Yamamoto Hiroto , Kato Tomoko , Hara Satoshi , Yamaguchi Katsushi , Renard-Guillet Claire , Katou Yuki , Shirahige Katsuhiko , Ochi Haruki , Ogino Hajime , Uchida Tokujiro , Inui Masafumi , Takada Shuji , Shigenobu Shuji , Asahara Hiroshi 
Published: August 2019

AbstractSRY (sex-determining region Y)-box 9 (SOX9) is a transcription factor regulating both chondrogenesis and sex determination. Among vertebrates, SOX9’s functions in chondrogenesis are well conserved, while they vary in sex determination. To investigate the conservation of SOX9’s regulatory functions in chondrogenesis and gonad development among species, we performed chromatin immunoprecipitation sequencing (ChIP-seq) using developing limb buds and male gonads from embryos of two vertebrates, mouse and chicken. In both mouse and chicken, SOX9 bound to intronic and distal regions of genes more frequently in limb buds than in male gonads, while SOX9 bound to the proximal upstream regions of genes more frequently in male gonads than in limb buds. In both species, SOX palindromic repeats were identified more frequently in SOX9 binding regions in limb bud genes compared with those in male gonad genes. The conservation of SOX9 binding regions was significantly higher in limb bud genes. In addition, we combined RNA expression analysis (RNA sequencing) with the ChIP-seq results at the same stage in developing chondrocytes and Sertoli cells and determined SOX9 target genes in these cells of the two species and disclosed that SOX9 targets showed high similarity of targets in chondrocytes, but not in Sertoli cells.
Molecular Mechanisms of Natural Carotenoid-based Pigmentation of Queen Loach, Botia dario (Hamilton, 1822) Under Captive Condition
Authors: Tripathy Partha Sarathi , Devi Ningthoujam Chaoba , Parhi Janmejay , Priyadarshi Himanshu , Patel Arun Bhai , Pandey Pramod Kumar , Mandal Sagar Chandra 
Published: August 2019

AbstractThe genetic basis and expression patterns of key genes are important aspects of study to understand the colouration. This trait differs between wild and domesticated fish which is a matter of research. Botia dario is an indigenous fish, having ornamental and aesthetic value, which shows faded appearance in terms of colour in domesticated condition than wild. In the present study the carotenoid-fed B. dario were examined through incorporation of marigold petal meal in the diets at the rate of 5, 10 and 15% w/w along with wild fish. The carotenoid content of tissues that is skin, muscle and intestine along with intensity of colouration increased in a dose dependant manner of carotenoid in the diet. Important carotenoid-based colouration genes that is csf1r, BCDO2, SR-B1, MLN64, STAR5, GSTA2 and PLIN2 were characterized in the fish, to find out their role in fish pigmentation. The significant difference (p < 0.05) in the expression of these genes in different tissues, when compared among carotenoid-fed domesticated and wild fish, revealed the mechanism responsible for faded colouration and also revealed the means to enhance colour in the fish.
Assessing Susceptibility of Debris Flow in Southwest China Using Gradient Boosting Machine
Authors: Di Baofeng , Zhang Hanyue , Liu Yongyao , Li Jierui , Chen Ningsheng , Stamatopoulos Constantine A. , Luo Yuzhou , Zhan Yu 
Published: August 2019

AbstractA gradient boosting machine (GBM) was developed to model the susceptibility of debris flow in Sichuan, Southwest China for risk management. A total of 3839 events of debris flow during 1949–2017 were compiled from the Sichuan Geo-Environment Monitoring program, field surveys, and satellite imagery interpretation. In the cross-validation, the GBM showed better performance, with the prediction accuracy of 82.0% and area under curve of 0.88, than the benchmark models, including the Logistic Regression, the K-Nearest Neighbor, the Support Vector Machine, and the Artificial Neural Network. The elevation range, precipitation, and aridity index played the most important role in determining the susceptibility. In addition, the water erosion intensity, road construction, channel gradient, and human settlement sites also largely contributed to the formation of debris flow. The susceptibility map produced by the GBM shows that the spatial distributions of high-susceptibility watersheds were highly coupled with the locations of the topographical extreme belt, fault zone, seismic belt, and dry valleys. This study provides critical information for risk mitigating and prevention of debris flow.
Dissecting phenotypic responses of the druggable targetome in cancers
Authors: Jeong Euna , Park Choa , Moon Sung Ung , Cho Juyeon , Song Mee , Ryoo Seungeun , Gu Hyejeong , Lee Yejin , Kim Wooyoung , Yoon Sukjoon 
Published: August 2019

AbstractAlthough a large amount of screening data comprising target genes and/or drugs tested against cancer cell line panels are available, different assay conditions and readouts limit the integrated analysis and batch-to-batch comparison of these data. Here, we systematically produced and analyzed the anticancer effect of the druggable targetome to understand the varied phenotypic outcomes of diverse functional classes of target genes. A library of siRNAs targeting ~4,800 druggable genes was screened against cancer cell lines under 2D and/or 3D assay conditions. The anticancer effect was simultaneously measured by quantifying cell proliferation and/or viability. Hit rates varied significantly depending on assay conditions and/or phenotypic readouts. Functional classes of hit genes were correlated with the microenvironment difference between the 2D monolayer cell proliferation and 3D sphere formation assays. Furthermore, multiplexing of cell proliferation and viability measures enabled us to compare the sensitivity and resistance responses to the gene knockdown. Many target genes that inhibited cell proliferation increased the single-cell-level viability of surviving cells, leading to an increase in self-renewal potential. In this study, combinations of parallel 2D/3D assays and multiplexing of cell proliferation and viability measures provided functional insights into the varied phenotypic outcomes of the cancer targetome.