bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae
Authors: Natesuntorn Waranya , Iwami Kotaro , Matsubara Yuki , Sasano Yu , Sugiyama Minetaka , Kaneko Yoshinobu , Harashima Satoshi 
Published: July 2015

AbstractSegmental aneuploidy can play an important role in environmental adaptation. However, study of segmental aneuploids is severely hampered by the difficulty of creating them in a designed fashion. Here, we describe a PCR-mediated chromosome duplication (PCDup) technology that enables the generation of segmental aneuploidy at any desired chromosomal region in Saccharomyces cerevisiae. We constructed multiple strains harboring 100 kb to 200 kb segmental duplications covering the whole of the S. cerevisiae genome. Interestingly, some segmental aneuploidies confer stress tolerance, such as to high temperature, ethanol and strong acids, while others induce cell lethality and stress sensitivity, presumably as result of the simultaneous increases in dosages of multiple genes. We suggest that our PCDup technology will accelerate studies into the phenotypic changes resulting from alteration of gene dosage balance of multiple genes and will provide new insights into the adaptive molecular mechanisms in the genome in segmental aneuploidy-derived human diseases.
HPVbase – a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas
Authors: Kumar Gupta Amit , Kumar Manoj 
Published: July 2015

AbstractHuman papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis.
Biochemical nature of Russell Bodies
Authors: Francesca Mossuto Maria , Ami Diletta , Anelli Tiziana , Fagioli Claudio , Maria Doglia Silvia , Sitia Roberto 
Published: July 2015

AbstractProfessional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.
The role of dynamically induced variability in the recent warming trend slowdown over the Northern Hemisphere
Authors: Guan Xiaodan , Huang Jianping , Guo Ruixia , Lin Pu 
Published: July 2015

AbstractSince the slowing of the trend of increasing surface air temperature (SAT) in the late 1990 s, intense interest and debate have arisen concerning the contribution of human activities to the warming observed in previous decades. Although several explanations have been proposed for the warming-trend slowdown (WTS), none has been generally accepted. We investigate the WTS using a recently developed methodology that can successfully identify and separate the dynamically induced and radiatively forced SAT changes from raw SAT data. The dynamically induced SAT changes exhibited an obvious cooling effect relative to the warming effect of the adjusted SAT in the hiatus process. A correlation analysis suggests that the changes are dominated primarily by the North Atlantic Oscillation (NAO), Pacific Decadal Oscillation (PDO) and Atlantic Multidecadal Oscillation (AMO). Our results confirm that dynamically induced variability caused the WTS. The radiatively forced SAT changes are determined mainly by anthropogenic forcing, indicating the warming influence of greenhouse gases (GHGs), which reached levels of 400 ppm during the hiatus period. Therefore, the global SAT will not remain permanently neutral. The increased radiatively forced SAT will be amplified by increased dynamically induced SAT when the natural mode returns to a warming phase in the next period.
A Sensor Array Using Multi-functional Field-effect Transistors with Ultrahigh Sensitivity and Precision for Bio-monitoring
Authors: Kim Do-Il , Quang Trung Tran , Hwang Byeong-Ung , Kim Jin-Su , Jeon Sanghun , Bae Jihyun , Park Jong-Jin , Lee Nae-Eung 
Published: July 2015

AbstractMechanically adaptive electronic skins (e-skins) emulate tactition and thermoception by cutaneous mechanoreceptors and thermoreceptors in human skin, respectively. When exposed to multiple stimuli including mechanical and thermal stimuli, discerning and quantifying precise sensing signals from sensors embedded in e-skins are critical. In addition, different detection modes for mechanical stimuli, rapidly adapting (RA) and slowly adapting (SA) mechanoreceptors in human skin are simultaneously required. Herein, we demonstrate the fabrication of a highly sensitive, pressure-responsive organic field-effect transistor (OFET) array enabling both RA- and SA- mode detection by adopting easily deformable, mechano-electrically coupled, microstructured ferroelectric gate dielectrics and an organic semiconductor channel. We also demonstrate that the OFET array can separate out thermal stimuli for thermoreception during quantification of SA-type static pressure, by decoupling the input signals of pressure and temperature. Specifically, we adopt piezoelectric-pyroelectric coupling of highly crystalline, microstructured poly(vinylidene fluoride-trifluoroethylene) gate dielectric in OFETs with stimuli to allow monitoring of RA- and SA-mode responses to dynamic and static forcing conditions, respectively. This approach enables us to apply the sensor array to e-skins for bio-monitoring of humans and robotics.
American Water Willow Mediates Survival and Antipredator Behavior of Juvenile Largemouth Bass
Authors: Stahr Kristopher J. , Shoup Daniel E. 
Published: July 2015

AbstractState and federal agencies typically introduce aquatic vegetation to increase the recruitment of sport fishes, particularly Largemouth Bass Micropterus salmoides. However, due to frequent turbidity and water‐level fluctuations, managers in the southern United States are often left to introduce emergent macrophytes instead of submersed macrophytes. Emergent macrophytes have less underwater structural complexity than most submersed macrophytes and therefore may not be as effective in reducing the predation risk of Largemouth Bass. Therefore, the objective of this study was to determine if American water willow Justicia americana, a common emergent macrophyte species introduced in reservoirs, increases the survival of juvenile Largemouth Bass when exposed to predation. Predator–prey interactions between 10 juvenile and 1 adult Largemouth Bass were observed in tanks with natural densities of American water willow and compared with similar trials in vegetation‐free control tanks. Each adult Largemouth Bass was tested once in each treatment (vegetation present or absent). Water willow significantly reduced the capture‐to‐attack ratio of adult Largemouth Bass and decreased the amount of time spent searching and the number of captures, resulting in significantly higher juvenile survival in the vegetated trials. Although water willow provided a similar increase in survival compared with previous studies using submersed macrophytes, the mechanism underlying this change differed, likely resulting from the more rigid stem design of water willow. We conclude water willow is an excellent candidate for establishment in reservoirs because it is easier to establish than many other macrophyte species yet still reduces predation risk on juvenile Largemouth Bass.
Improved Ability to Characterize Recruitment of Gray Snapper in Three Florida Estuaries along the Gulf of Mexico through Targeted Sampling of Polyhaline Seagrass Beds
Authors: Flaherty‐Walia Kerry E. , Switzer Theodore S. , Winner Brent L. , J. Tyler‐Jedlund Amanda , Keenan Sean F. 
Published: July 2015

AbstractEstuarine‐dependent Gray Snapper Lutjanus griseus support extensive recreational fisheries in estuarine and coastal waters throughout the eastern Gulf of Mexico. Multiyear fisheries‐independent monitoring data collected in three Florida estuaries can be used to estimate the strength of juvenile Gray Snapper recruitment, which has been critical to assessments of other fish populations. Earlier evaluation of these data indicated that Gray Snapper inhabit polyhaline seagrass beds, which are underrepresented in ongoing monitoring efforts. During this study, in addition to the routine monitoring of shorelines and channel habitats, sampling of shoal and deepwater polyhaline seagrass habitats was implemented using 183‐m haul seines and 6.1‐m otter trawls. The incorporation of polyhaline seagrass surveys from 2008 through 2011 allowed a more thorough sampling of the Gray Snapper population, resulting in improved catch rates, increased frequency of occurrence, and a substantial reduction of the coefficient of variation for CPUE in most years and estuarine systems. Habitat‐based sampling of polyhaline seagrass habitats also provided additional data for annual abundance indices and therefore improved the ability to characterize the strength of recruitment for Gray Snapper over time. These results demonstrated that periodically reevaluating habitat‐based stratification approaches to estimate fish abundance indices from long‐term surveys can lead to more precise estimates and greater numbers of measured individuals, which are key components of successful monitoring programs.
High-order neural networks and kernel methods for peptide-MHC binding prediction
Authors: Kuksa Pavel P. , Min Martin Renqiang , Dugar Rishabh , Gerstein Mark 
Published: July 2015

Abstract
Motivation: Effective computational methods for peptide-protein binding prediction can greatly help clinical peptide vaccine search and design. However, previous computational methods fail to capture key nonlinear high-order dependencies between different amino acid positions. As a result, they often produce low-quality rankings of strong binding peptides. To solve this problem, we propose nonlinear high-order machine learning methods including high-order neural networks (HONNs) with possible deep extensions and high-order kernel support vector machines to predict major histocompatibility complex-peptide binding.
Results: The proposed high-order methods improve quality of binding predictions over other prediction methods. With the proposed methods, a significant gain of up to 25–40% is observed on the benchmark and reference peptide datasets and tasks. In addition, for the first time, our experiments show that pre-training with high-order semi-restricted Boltzmann machines significantly improves the performance of feed-forward HONNs. Moreover, our experiments show that the proposed shallow HONN outperform the popular pre-trained deep neural network on most tasks, which demonstrates the effectiveness of modelling high-order feature interactions for predicting major histocompatibility complex-peptide binding.
Availability and implementation: There is no associated distributable software.
Contact: renqiang@nec-labs.com or mark.gerstein@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data
Authors: Ryall Karen A. , Shin Jimin , Yoo Minjae , Hinz Trista K. , Kim Jihye , Kang Jaewoo , Heasley Lynn E. , Tan Aik Choon 
Published: July 2015

Abstract
Motivation: Targeted kinase inhibitors have dramatically improved cancer treatment, but kinase dependency for an individual patient or cancer cell can be challenging to predict. Kinase dependency does not always correspond with gene expression and mutation status. High-throughput drug screens are powerful tools for determining kinase dependency, but drug polypharmacology can make results difficult to interpret.
Results: We developed Kinase Addiction Ranker (KAR), an algorithm that integrates high-throughput drug screening data, comprehensive kinase inhibition data and gene expression profiles to identify kinase dependency in cancer cells. We applied KAR to predict kinase dependency of 21 lung cancer cell lines and 151 leukemia patient samples using published datasets. We experimentally validated KAR predictions of FGFR and MTOR dependence in lung cancer cell line H1581, showing synergistic reduction in proliferation after combining ponatinib and AZD8055.
Availability and implementation: KAR can be downloaded as a Python function or a MATLAB script along with example inputs and outputs at: http://tanlab.ucdenver.edu/KAR/.
Contact: aikchoon.tan@ucdenver.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
BackCLIP: a tool to identify common background presence in PAR-CLIP datasets
Authors: Reyes-Herrera P. H. , Speck-Hernandez C. A. , Sierra C. A. , Herrera S. 
Published: July 2015

Abstract
Motivation: PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify the presence of common background in PAR-CLIP datasets is not yet available.
Results: We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common background set has a score that reflects its presence in several PAR-CLIP datasets. We present a tool that uses this score to identify the amount of common backgrounds present in a PAR-CLIP dataset, and we provide the user the option to use or remove it. We used the proposed strategy in 30 PAR-CLIP datasets from nine proteins. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds.
Availability: The tool was implemented in python. The common background set and the supplementary data are available at https://github.com/phrh/BackCLIP.
Contact: phreyes@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Empedobacter stercoris sp. nov., isolated from an input sample of a biogas plant
Authors: Schauss Thorsten , Busse Hans-Jürgen , Golke Jan , Kämpfer Peter , Glaeser Stefanie P. 
Published: July 2015

Two Gram-stain-negative, rod-shaped bacteria, strains 990B6_12ER2AT and 994B6_12ER2A, were isolated during microbiological analysis of a mixed manure sample which was used as input material for a German biogas plant. Phylogenetic identification based on nearly full-length 16S rRNA gene sequences placed the isolates into the family Flavobacteriaceae within the phylum Bacteroidetes. Strains 990B6_12ER2AT and 994B6_12ER2A shared identical 16S rRNA gene sequences and showed highest 16S rRNA gene sequence similarity to the type strains of Empedobacter falsenii (97.3 %) and Empedobacter brevis (96.8 %).
The major cellular fatty acids of strains 990B6_12ER2AT and 994B6_12ER2A were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH.
The polyamine pattern contained predominantly sym-homospermidine and the quinone system was menaquinone MK-6. Major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified polar lipid not containing an amino residue, a phosphate residue or a sugar moiety. In addition, moderate to minor amounts of several unidentified lipids were detected. The DNA G+C content was 31.7 and 29.0 mol%, for strains 990B6_12ER2AT and 994B6_12ER2A, respectively. On the basis of phylogenetic, chemotaxonomic and physiological analysis we propose a novel species of the genus Empedobacter, Empedobacter stercoris sp. nov. (type strain 990B6_12ER2AT = CIP 110833T = LMG 28501T).
Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex
Authors: Radzvilavicius Arunas L. , Blackstone Neil W. 
Published: July 2015

AbstractThe complex eukaryotic cell is a result of an ancient endosymbiosis and one of the major evolutionary transitions. The timing of key eukaryotic innovations relative to the acquisition of mitochondria remains subject to considerable debate, yet the evolutionary process itself might constrain the order of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation were based on the pathways inherited from prokaryotic symbionts and led to metabolic homeostasis in the eukaryotic cell, while later mechanisms (e.g., mitochondrial gene transfer) contributed to the expansion of the eukaryotic genome. Perhaps the greatest opportunity for conflict arose with the emergence of sex involving whole-cell fusion. While early evolution of cell fusion may have affected symbiont acquisition, sex together with the competitive symbiont behaviour would have destabilized the emerging higher-level unit. Cytoplasmic mixing, on the other hand, would have been beneficial for selfish endosymbionts, capable of using their own metabolism to manipulate the life history of the host. Given the results of our mathematical modelling, we argue that sex represents a rather late proto-eukaryotic innovation, allowing for the growth of the chimeric nucleus and contributing to the successful completion of the evolutionary transition.
Ancestral gene synteny reconstruction improves extant species scaffolding
Authors: Anselmetti Yoann , Berry Vincent , Chauve Cedric , Chateau Annie , Tannier Eric , Bérard Sèverine 
Published: July 2015

AbstractWe exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ART-DECOthat constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ART-DECOby simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.
Does Islamic bank financing contribute to economic growth? The Malaysian case
Authors: Hachicha Nejib , Ben Amar Amine 
Published: July 2015

Purpose– The purpose of this paper is to investigate empirically the impact of the Islamic Bank Financing on Malaysia’s economic growth over the period 2000Q1-2011Q4.Design/methodology/approach– A neoclassical production function augmented by some indicators of Islamic bank finance has been the theoretical framework for this paper’s empirical investigation. The unit root tests show that all the variables are integrated of order 1. The test of Johansen and Juselius (1990) has shown the existence of a single cointegrating relationship between the gross domestic product (GDP), the investment, the labor force and the indicator of Islamic bank finance. Hence, an error correction model has been constructed to estimate the economic growth elasticity with respect to the different Islamic bank finance indicators.Findings– The estimated elasticities show that, in the long run, the GDP in Malaysia is not sensitive to the Islamic financing. The estimation of an error correction model shows that the elasticity of the Malaysian output with respect to the different Islamic financing indicators in the short run turn around 0.35. Thus, the effect of the different Islamic finance indicators on the economic growth in the long run is less important than their effect in the short run. This economic result can be explained by the structure of the Islamic bank financing that marginalizes the profit-and-loss sharing (PLS)-based instruments. This turns out to be consistent with the economic reality in Malaysia, as the Islamic banks engage much more in non-participatory activities whose impact is, generally, of short term.Social implications– To improve the efficiency of the Malaysian Islamic banks as financial inter-mediaries that facilitate the capital accumulation and the economic growth, the paper suggests to strengthen the weight of the PLS-based instruments in the loan portfolios of the Malaysian Islamic banks. This may reduce inequalities and improve economic opportunities for people who have a high potential to contribute to the capital accumulation and the creation of the value-added.Originality/value– The contribution of this paper is two-fold. On the one hand, it provides a further contribution to the rare empirical literature relative to the impact of the Islamic finance on growth by determining the elasticity of economic growth with respect to Islamic bank financing in Malaysia. On the other hand, and to the best of the authors’ knowledge, this paper remains the first to correctly resort to the error correction model in determining this elasticity.