bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes
Authors: Yabuki Akinori , Toyofuku Takashi , Takishita Kiyotaka 
Published: January 2014

Abstract
Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.
Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest
Authors: Xiang Xingjia , Shi Yu , Yang Jian , Kong Jianjian , Lin Xiangui , Zhang Huayong , Zeng Jun , Chu Haiyan 
Published: January 2014

AbstractFires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties.
Engineering Topological Surface States and Giant Rashba Spin Splitting in BiTeI/Bi2Te3 Heterostructures
Authors: Zhou Jin-Jian , Feng Wanxiang , Zhang Ying , Yang Shengyuan A. , Yao Yugui 
Published: January 2014

AbstractThe search for strongly inversion asymmetric topological insulators is an active research field because these materials possess distinct properties compared with the inversion symmetric ones. In particular, it is desirable to realize a large Rashba spin-splitting (RSS) in such materials, which combined with the topological surface states (TSS) could lead to useful spintronics applications. In this report, based on first principles calculations, we predict that the heterostructure of BiTeI/Bi2Te3 is a strong topological insulator with a giant RSS. The coexistence of TSS and RSS in the current system is native and stable. More importantly, we find that both the "Equation missing" invariants and the Rashba energy can be controlled by engineering the layer geometries of the heterostructure and the Rashba energy can be made even larger than that of bulk BiTeI. Our work opens a new route for designing topological spintronics devices based on inversion asymmetric heterostructures.
PARP inhibitors for anticancer therapy
Authors: Curtin Nicola 
Published: January 2014

PARP-1 [poly(ADP-ribose) polymerase-1], which plays a key role in DNA repair, was discovered 50 years ago. PARPi (PARP inhibitors), originally made to probe the function of the enzyme, inhibit DNA repair and increase the potency of anticancer cytotoxic agents. PARPi of increasing potency were developed as chemo- and radio-sensitizers and first entered clinical trial in cancer patients in 2003. However, it was the revelation in 2005 that they were synthetically lethal in cells with DNA repair defects, found almost exclusively in some tumours, that led to a major interest in this class of drug. Several PARPi have entered clinical trials and show promising activity in breast, ovarian and other cancers associated with BRCA (breast cancer early-onset) mutations or other defects in homologous recombination DNA repair. It is likely that at least one of these will be licensed soon. The present review describes key events from the discovery to clinical application of PARPi.
Structural organization of signalling to and from IP3 receptors
Authors: Taylor Colin W. , Tovey Stephen C. , Rossi Ana M. , Lopez Sanjurjo Cristina I. , Prole David L. , Rahman Taufiq 
Published: January 2014

In the 30 years since IP3 (inositol 1,4,5-trisphosphate) was first shown to release Ca2+ from intracellular stores, the importance of spatially organized interactions within IP3-regulated signalling pathways has been universally recognized. Recent evidence that addresses three different levels of the structural determinants of IP3-evoked Ca2+ signalling is described in the present review. High-resolution structures of the N-terminal region of the IP3R (IP3 receptor) have established that the two essential phosphate groups of IP3 bind to opposite sides of the IP3-binding site, pulling its two domains together. This conformational change is proposed to disrupt an interaction between adjacent subunits within the tetrameric IP3R that normally holds the channel in a closed state. Similar structural changes are thought to allow gating of ryanodine receptors. cAMP increases the sensitivity of IP3Rs and thereby potentiates the Ca2+ signals evoked by receptors that stimulate IP3 formation. We speculate that both IP3 and cAMP are delivered to IP3Rs within signalling junctions, wherein the associated IP3Rs are exposed to a saturating concentration of either messenger. The concentration-dependent effects of extracellular stimuli come from recruitment of junctions rather than from a graded increase in the activity of individual junctions. IP3Rs within ‘IP3 junctions’ respond directly to receptors that stimulate phospholipase C, whereas extra-junctional IP3Rs are exposed to suboptimal concentrations of IP3 and open only when they are sensitized by cAMP. These results highlight the importance of selective delivery of diffusible messengers to IP3Rs. The spatial organization of IP3Rs also allows them to direct Ca2+ to specific intracellular targets that include other IP3Rs, mitochondria and Ca2+-regulated channels and enzymes. IP3Rs also interact functionally with lysosomes because Ca2+ released by IP3Rs, but not that entering cells via store-operated Ca2+ entry pathways, is selectively accumulated by lysosomes. This Ca2+ uptake shapes the Ca2+ signals evoked by IP3 and it may regulate lysosomal behaviour.
Structure and function of RLIP76 (RalBP1): an intersection point between Ras and Rho signalling
Authors: Mott Helen R. , Owen Darerca 
Published: January 2014

RLIP76 (Ral-interacting protein of 76 kDa) [also known as RalBP1 (Ral-binding protein 1)] is an effector for the Ral family small GTPases. RLIP76 has been implicated in a number of cell processes, including receptor-mediated endocytosis, cell migration, mitochondrial division and metabolite transport. RLIP76 has two recognizable domains in the centre of the protein sequence: a GAP (GTPase-activating protein) domain for the Rho family G-proteins and an RBD (Ral-binding domain). The remainder of RLIP76 has no discernable homology with other proteins. The RBD forms a simple coiled-coil of two α-helices, which interacts with RalB by binding to both of the nucleotide-sensitive ‘switch’ regions. Both of these RLIP76 helices are involved in the interaction with Ral, but the interhelix loop is left free. This is the location of one of the two ATP-binding sites that have been identified in RLIP76 and suggests that Ral interaction would not prevent ATP binding. The structure of the RhoGAP–RBD dyad shows that the two domains are fixed in their orientation by a relatively rigid linker. This domain arrangement allows the two domains to engage Rho family and Ral small G-proteins simultaneously at the membrane. This suggests that RLIP76 is a node for Rho and Ras family signalling.
Dynamics of ezrin and EBP50 in regulating microvilli on the apical aspect of epithelial cells
Authors: Viswanatha Raghuvir , Bretscher Anthony , Garbett Damien 
Published: January 2014

Microvilli are found on the apical surface of epithelial cells. Recent studies on the microvillar proteins ezrin and EBP50 (ezrin/radixin/moesin-binding phosphoprotein of 50 kDa) have revealed both the dynamics and the regulation of microvillar components, and how a dynamic ezrin phosphocycle is necessary to confine microvilli to the apical membrane. In the present review, we first summarize the background to allow us to place these advances in context.
Wideband microstrip rat‐race hybrid with via‐swap phase inverter
Authors: Mung S.W.Y. , Chan W.S. 
Published: January 2014

A via‐swap 180° phase inverter on the slotted ground is presented. The phase inverter with a 90° line replaces the conventional 270° line built into the microstrip rat‐race hybrid. This results in a size reduction and the widening of the bandwidth. The experiments show that the proposed hybrid has a good performance from 1.5 to 2.5 GHz (fo = 2 GHz). The bandwidth is increased from 10 to 50% and a 43% size reduction is obtained compared with the conventional rat‐race hybrid.
Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in
Escherichia coli
Authors: Egloff Pascal , Hillenbrand Matthias , Klenk Christoph , Batyuk Alexander , Heine Philipp , Balada Stefanie , Schlinkmann Karola M. , Scott Daniel J. , Schütz Marco , Plückthun Andreas 
Published: January 2014

Significance
Only a tiny fraction (<2%) of the unique structures in the protein database correspond to membrane proteins, and only a few of these are of eukaryotic origin, representing potential drug targets. The difficulties in structure determination of these proteins are due to two specific complications, which are unique for membrane proteins: first, low expression levels and, second, the necessity for detergent micelles, which are often destabilizing as they mimic the hydrophobic membrane environment only poorly. We prove that directed evolution has the potential to overcome these problems by determining several structures of evolved eukaryotic G protein–coupled receptor variants. High functional expression levels and superior receptor stability in harsh detergents allowed us to gain deeper insights into this important receptor family.
Use of Clove Oil and Eugenol to Anesthetize Fingerling Shabut Barbus grypus
Authors: Öğretmen Fatih , Gölbaşi Selami , Inanan Burak E , Kizak Volkan , Kayim Murathan 
Published: January 2014

Abstract
In this study, the efficacy of four doses of clove oil and eugenol were compared to sedate fingerling Shabut Barbus grypus to various stages of sedation and recovery. The results from the present study indicated that effective concentrations were at 50 μL/L for eugenol (induction time: 58 ± 8 s; recovery time: 199 ± 15 s [mean ± SD]) and clove oil (induction time: 76 ± 6 s; recovery time: 161 ± 34 s). The induction times decreased significantly with the increasing concentrations of clove oil and eugenol, while recovery times increased with increasing concentrations of anesthetic (P &lt; 0.05). Exposure of fish to 75 or 100 μL/L clove oil or to 50, 75, or 100 μL/L eugenol resulted in mean induction times ≤ 1 min. Fish did not become fully sedated within 3 min when treated with 25 μL/L clove oil. Other concentrations of both anesthetics, fish reached to full induction at ≤ 3 min and recovered from anesthesia ≤ 5 min. Our results showed the clove oil and eugenol are effective anesthetics for fingerling Shabut when used at concentrations of 50–100 μL/L.
Effects of Dietary Nutrient Composition on Compensatory Growth of Juvenile Blunt Snout Bream Megalobrama amblycephala
Authors: Lu Kang-Le , Li Xiang-Fei , Wang Li-Na , Zhang Chun-Nuan , Liu Wen-Bin 
Published: January 2014

Abstract
A feeding trial was conducted to evaluate the influences of dietary nutrient composition on the compensatory growth of Blunt Snout Bream Megalobrama amblycephala. Three diets were tested: a control, a high-protein (HP), and a high-protein and carbohydrate (HPC) diet. Each of the three diets was fed to Blunt Snout Bream (initially weight, 24 ± 0.50 g) for 60 d using either satiation feeding (in which fish were fed daily) or restricted feeding (no feeding for 3 d followed by feeding for the next 12 d). The weight gain of fish fed the HP and HPC diets was significantly higher than that of fish fed the control diet. In addition, restricted feeding led to significantly less weight gain than daily feeding with the control and HP diets. However, there was no significant difference between the two feeding regimes in the weight gain of fish fed the HPC diet. The feed conversion ratio of fish fed the control diet was significantly higher than that of fish fed the HP and HPC diets. Moreover, the ratio was significantly lower with restricted feeding than with satiation feeding. Whole-body composition was not significantly different among treatments. Fish subjected to the restricted feeding regime had an elevated hepatosomatic index compared with fish fed to satiation. On the whole, the HPC diet could improve the compensatory growth of fish without altering their whole-body composition, and compensatory growth has the advantage of improving feed efficiency and nutrient retention.
Optimizing Soybean Meal Levels in Alternative Diets for Pond-Raised Hybrid Catfish
Authors: Li Menghe H , Robinson Edwin H , Bosworth Brian G , Oberle Daniel F , Lucas Penelope M 
Published: January 2014

Abstract
We evaluated decreasing soybean meal levels by the use of a combination of cottonseed meal and corn germ meal for pond-raised hybrid catfish (Channel Catfish Ictalurus punctatus×Blue Catfish I. furcatus). Five 28% protein diets containing 40, 30, 25, 20, 15% of soybean meal were formulated based on digestible nutrients and energy to meet or exceed all known nutrient requirements of Channel Catfish. Fingerling hybrid catfish with a mean initial weight of 25.1 g/fish were stocked into 25, earthen ponds (0.04 ha) at a rate of 14,826 fish/ha. Fish were fed once daily to apparent satiation over a 184-d growing season. Reducing soybean meal levels from 40% to 15% in the diet by the use of a combination of cottonseed meal and corn germ meal did not significantly affect total amount of diet fed, gross yield, weight gain, and survival of hybrid catfish by ANOVA or regression analyses. However, feed conversion ratio was significantly higher in fish fed diets containing ≤30% soybean meal than those fed the control diet (40% soybean meal) and feed conversion ratio increased linearly as soybean meal levels decreased. Hybrid catfish fed diets containing 20% and 15% soybean meal had significantly lower carcass yield than fish fed the control diet. Fish fed the diet containing 15% soybean meal also had significantly lower fillet yield. Regression analyses show that both carcass and fillet yields decreased linearly with decreasing soybean meal levels in the diet. No significant differences were observed for fillet protein, fat, and moisture levels among fish fed the diets containing various levels of soybean meal. A 28% protein diet containing 25% soybean meal appears to support maximum growth of hybrid catfish without marked impact on feed conversion ratio and processed yield.
Economic Feasibility of an In-Pond Raceway System for Commercial Catfish Production in West Alabama
Authors: Brown Travis W , Hanson Terrill R , Chappell Jesse A , Boyd Claude E , Wilson Dean S 
Published: January 2014

Abstract
Our objective was to improve profitability of catfish farming by demonstrating methods to achieve high levels of survival, feed performance, and efficiency in a commercial farm setting. During 2007, a commercial-scale in-pond raceway system (IPRS) was constructed in a 6.0-acre earthen pond on a catfish farm in west Alabama. The IPRS consisted of six raceways, each stocked with uniform-sized Channel Catfish Ictalurus punctatus or hybrid catfish (Channel Catfish × Blue Catfish I. furcatus). Co-cultured fish species (Paddlefish Polyodon spathula and Nile Tilapia Oreochromis niloticus) were stocked and harvested in the outside area of the pond containing the IPRS. Results from the 2008 production season were used to project 12 months of production from stocking either Channel Catfish or hybrid catfish in the IPRS. In addition, Channel Catfish production in traditional ponds was monitored from 2005 to 2009 on the same farm (∼430 water-acres). The 8-month IPRS results were compared with (1) the 12-month average production from the traditional farm and (2) the 12-month projected production in the IPRS. Variable and fixed costs to produce catfish were US0.71 and 0.14 per pound, respectively, in the IPRS during the 8-month study; 0.78 and 0.05 per pound for the 12-month average performance of the traditional farm; 0.74 and 0.19 per pound for 12-month projected Channel Catfish production; and 0.64 and 0.11 per pound for 12-month projected hybrid catfish production. Income above variable costs and net returns to land from using the IPRS increased when co-cultured species were included in the economic analysis. Our results showed that the IPRS can be efficient at producing catfish and co-cultured species, although the energy input per pound was greater than that for the traditional farm. Additional studies using the IPRS for fish production are underway to verify our initial research results.
h5vc: scalable nucleotide tallies with HDF5
Authors: Pyl Paul Theodor , Gehring Julian , Fischer Bernd , Huber Wolfgang 
Published: January 2014

AbstractSummary: As applications of genome sequencing, including exomes and whole genomes, are expanding, there is a need for analysis tools that are scalable to large sets of samples and/or ultra-deep coverage. Many current tool chains are based on the widely used file formats BAM and VCF or VCF-derivatives. However, for some desirable analyses, data management with these formats creates substantial implementation overhead, and much time is spent parsing files and collating data. We observe that a tally data structure, i.e. the table of counts of nucleotides × samples × strands × genomic positions, provides a reasonable intermediate level of abstraction for many genomics analyses, including single nucleotide variant (SNV) and InDel calling, copy-number estimation and mutation spectrum analysis. Here we present h5vc, a data structure and associated software for managing tallies. The software contains functionality for creating tallies from BAM files, flexible and scalable data visualization, data quality assessment, computing statistics relevant to variant calling and other applications. Through the simplicity of its API, we envision making low-level analysis of large sets of genome sequencing data accessible to a wider range of researchers.Availability and implementation: The package h5vc for the statistical environment R is available through the Bioconductor project. The HDF5 system is used as the core of our implementation.Contact: pyl@embl.de or whuber@embl.deSupplementary information: Supplementary data are available at Bioinformatics online.
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
Authors: Bollen Sander , Leddin Mathias , Andrade-Navarro Miguel A. , Mah Nancy 
Published: January 2014

AbstractSummary: The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues. It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.Availability and implementation: CAFE is available from https://bitbucket.org/cob87icW6z/cafe/ as both source and compiled packages for Linux and Windows. It is released under the GPL version 3 license. CAFE will also be freely available from Bioconductor.Contact: sander.h.bollen@gmail.com or nancy.mah@mdc-berlin.deSupplementary information: Supplementary data are available at Bioinformatics online.
Reference-free cell mixture adjustments in analysis of DNA methylation data
Authors: Houseman Eugene Andres , Molitor John , Marsit Carmen J. 
Published: January 2014

AbstractMotivation: Recently there has been increasing interest in the effects of cell mixture on the measurement of DNA methylation, specifically the extent to which small perturbations in cell mixture proportions can register as changes in DNA methylation. A recently published set of statistical methods exploits this association to infer changes in cell mixture proportions, and these methods are presently being applied to adjust for cell mixture effect in the context of epigenome-wide association studies. However, these adjustments require the existence of reference datasets, which may be laborious or expensive to collect. For some tissues such as placenta, saliva, adipose or tumor tissue, the relevant underlying cell types may not be known.Results: We propose a method for conducting epigenome-wide association studies analysis when a reference dataset is unavailable, including a bootstrap method for estimating standard errors. We demonstrate via simulation study and several real data analyses that our proposed method can perform as well as or better than methods that make explicit use of reference datasets. In particular, it may adjust for detailed cell type differences that may be unavailable even in existing reference datasets.Availability and implementation: Software is available in the R package RefFreeEWAS. Data for three of four examples were obtained from Gene Expression Omnibus (GEO), accession numbers GSE37008, GSE42861 and GSE30601, while reference data were obtained from GEO accession number GSE39981.Contact: andres.houseman@oregonstate.eduSupplementary information: Supplementary data are available at Bioinformatics online.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Authors: Stamatakis Alexandros 
Published: January 2014

Abstract
Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available.
Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Contact: alexandros.stamatakis@h-its.org
Supplementary information: Supplementary data are available at Bioinformatics online.