bluuebunny/crossref_metadata_2025_split huggingface dataset:
Completing bacterial genome assemblies: strategy and performance comparisons
Authors: Liao Yu-Chieh , Lin Shu-Hung , Lin Hsin-Hung 
Published: March 2015

AbstractDetermining the genomic sequences of microorganisms is the basis and prerequisite for understanding their biology and functional characterization. While the advent of low-cost, extremely high-throughput second-generation sequencing technologies and the parallel development of assembly algorithms have generated rapid and cost-effective genome assemblies, such assemblies are often unfinished, fragmented draft genomes as a result of short read lengths and long repeats present in multiple copies. Third-generation, PacBio sequencing technologies circumvented this problem by greatly increasing read length. Hybrid approaches including ALLPATHS-LG, PacBio corrected reads pipeline, SPAdes and SSPACE-LongRead and non-hybrid approaches—hierarchical genome-assembly process (HGAP) and PacBio corrected reads pipeline via self-correction—have therefore been proposed to utilize the PacBio long reads that can span many thousands of bases to facilitate the assembly of complete microbial genomes. However, standardized procedures that aim at evaluating and comparing these approaches are currently insufficient. To address the issue, we herein provide a comprehensive comparison by collecting datasets for the comparative assessment on the above-mentioned five assemblers. In addition to offering explicit and beneficial recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly.
Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling
Authors: Wang Hua , Fang Yan , Wang Lipeng , Zhu Wenjuan , Ji Haipeng , Wang Haiying , Xu Shiqing , Sima Yanghu 
Published: March 2015

AbstractHeterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, heterosis might be caused by differences in gene expression or modification. Differential gene expression was analyzed in hybrids and parents in Bombyx mori. The results showed that there were significant changes in gene expression in the fat body involving biological regulation, cellular and metabolic processes. Consistent trends in expression patterns covering different hybrid combinations were seen in 74 genes. Moreover, these differential gene expression patterns included overdominance, dominance and additive effects. By correlating these patterns with economic traits, a potential relationship was found. Differential gene expression was seen in different cross combinations and in different sexes. In addition, a regulatory mechanism involving metabolism and ErbB signaling pathways was also found, suggesting that such a network might also be related to heterosis in Bombyx mori. Together, our data provide a comprehensive overview and useful resource for transcriptional analysis of heterosis of Bombyx mori.
Coupled Néel domain wall motion in sandwiched perpendicular magnetic anisotropy nanowires
Authors: Purnama I. , Kerk I. S. , Lim G. J. , Lew W. S. 
Published: March 2015

AbstractThe operating performance of a domain wall-based magnetic device relies on the controlled motion of the domain walls within the ferromagnetic nanowires. Here, we report on the dynamics of coupled Néel domain wall in perpendicular magnetic anisotropy (PMA) nanowires via micromagnetic simulations. The coupled Néel domain wall is obtained in a sandwich structure, where two PMA nanowires that are separated by an insulating layer are stacked vertically. Under the application of high current density, we found that the Walker breakdown phenomenon is suppressed in the sandwich structure. Consequently, the coupled Néel domain wall of the sandwich structure is able to move faster as compared to individual domain walls in a single PMA nanowire.
βA3/A1-crystallin is a critical mediator of STAT3 signaling in optic nerve astrocytes
Authors: Valapala Mallika , Edwards Malia , Hose Stacey , Hu Jianfei , Wawrousek Eric , Lutty Gerard A. , Zigler, J. Samuel , Qian Jiang , Sinha Debasish 
Published: March 2015

AbstractWe have previously reported that in the Nuc1 rat, which has a spontaneous mutation in Cryba1 (the gene encoding βA3/A1-crystallin), astrocytes exhibit decreased Notch signaling, leading to reduced promoter activity for glial fibrillary acidic protein (GFAP). Interestingly, in both Nuc1 astrocytes and in wild type astrocytes following knockdown of Cryba1, vascular endothelial growth factor (VEGF) secretion is decreased. This has led us to explore signaling mediators that could be regulated by βA3/A1-crystallin to modulate both GFAP and VEGF. Several studies have shown that the signal transducer and activator of transcription 3 (STAT3) is involved in the co-regulation of GFAP and VEGF. We show that STAT3 and βA3/A1-crystallin may co-regulate each other in astrocytes. Such co-regulation would create a positive feedback circuit; i.e., in the cytosol of astrocytes, βA3/A1-crystallin is necessary for the phosphorylation of STAT3, which then dimerizes and translocates to the nucleus to form DNA-binding complexes, activating transcription of Cryba1. This stoichiometric co-regulation of STAT3 and Cryba1 could potentiate expression of GFAP and secretion of VEGF, both of which are essential for maintaining astrocyte and blood vessel homeostasis in the retina. Consistent with this idea, Cryba1 knockout mice exhibit an abnormal astrocyte pattern and defective remodeling of retinal vessels.
Improving Prediction of Prostate Cancer Recurrence using Chemical Imaging
Authors: Kwak Jin Tae , Kajdacsy-Balla André , Macias Virgilia , Walsh Michael , Sinha Saurabh , Bhargava Rohit 
Published: March 2015

AbstractPrecise Outcome prediction is crucial to providing optimal cancer care across the spectrum of solid cancers. Clinically-useful tools to predict risk of adverse events (metastases, recurrence), however, remain deficient. Here, we report an approach to predict the risk of prostate cancer recurrence, at the time of initial diagnosis, using a combination of emerging chemical imaging, a diagnostic protocol that focuses simultaneously on the tumor and its microenvironment and data analysis of frequent patterns in molecular expression. Fourier transform infrared (FT-IR) spectroscopic imaging was employed to record the structure and molecular content from tumors prostatectomy. We analyzed data from a patient cohort that is mid-grade dominant – which is the largest cohort of patients in the modern era and in whom prognostic methods are largely ineffective. Our approach outperforms the two widely used tools, Kattan nomogram and CAPRA-S score in a head-to-head comparison for predicting risk of recurrence. Importantly, the approach provides a histologic basis to the prediction that identifies chemical and morphologic features in the tumor microenvironment that is independent of conventional clinical information, opening the door to similar advances in other solid tumors.
Synchrotron x-ray imaging of pulmonary alveoli in respiration in live intact mice
Authors: Chang Soeun , Kwon Namseop , Kim Jinkyung , Kohmura Yoshiki , Ishikawa Tetsuya , Rhee Chin Kook , Je Jung Ho , Tsuda Akira 
Published: March 2015

AbstractDespite nearly a half century of studies, it has not been fully understood how pulmonary alveoli, the elementary gas exchange units in mammalian lungs, inflate and deflate during respiration. Understanding alveolar dynamics is crucial for treating patients with pulmonary diseases. In-vivo, real-time visualization of the alveoli during respiration has been hampered by active lung movement. Previous studies have been therefore limited to alveoli at lung apices or subpleural alveoli under open thorax conditions. Here we report direct and real-time visualization of alveoli of live intact mice during respiration using tracking X-ray microscopy. Our studies, for the first time, determine the alveolar size of normal mice in respiration without positive end expiratory pressure as 58 ± 14 (mean ± s.d.) μm on average, accurately measured in the lung bases as well as the apices. Individual alveoli of normal lungs clearly show heterogeneous inflation from zero to ~25% (6.7 ± 4.7% (mean ± s.d.)) in size. The degree of inflation is higher in the lung bases (8.7 ± 4.3% (mean ± s.d.)) than in the apices (5.7 ± 3.2% (mean ± s.d.)). The fraction of the total tidal volume allocated for alveolar inflation is 34 ± 3.8% (mean ± s.e.m). This study contributes to the better understanding of alveolar dynamics and helps to develop potential treatment options for pulmonary diseases.
Wavelength beam combining of VECSELs using multiplexed volume Bragg gratings in a compound cavity
Authors: Lu C.A. , Newell T.C. , Glebov L. , Balakrishnan G. 
Published: March 2015

A method of wavelength beam combining to enhance the total output brightness of vertical external cavity surface emitting lasers (VECSELs) using multiplexed volume Bragg gratings (MVBGs) is presented. The MVBGs are designed to introduce wavelength‐specific feedback for the 1020 nm near‐infrared wavelength VECSELs to achieve both spectral stabilisation and beam combining effects. In conjunction with the compound cavity arrangement, a combined output of >6 W is achieved with >98% combining efficiency using two VECSELs. The beam combining scheme produces near‐diffraction limited output with enhanced spectral density and wavelength‐stabilised characteristics.
Eight‐wavelength hybrid Si/AlGaInAs/InP microring laser array
Authors: Sui Shao‐Shuai , Tang Ming‐Ying , Huang Yong‐Zhen , Yang Yue‐De , Xiao Jin‐Long , Du Yun 
Published: March 2015

An eight‐wavelength hybrid Si/AlGaInAs/InP microring laser array coupled with an underlying silicon waveguide has been fabricated based on the bonding technique, with the radii varying from 15 to 15.14 μm at a step of 20 nm and with a microring width of 2 μm. Continuous‐wave (CW) electrically injected operation is obtained at 280 K, with threshold currents of about 6 mA, channel spacing of about 2 nm and sidemode‐suppression ratios above 20 dB.
The Impact of Obesity on Perioperative Resource Utilization after Elective Spine Surgery for Degenerative Disease
Authors: Planchard Ryan F. , Higgins Dominique M. , Mallory Grant W. , Puffer Ross C. , Jacob Jeffrey T. , Curry Timothy B. , Kor Daryl J. , Clarke Michelle J. 
Published: March 2015

Study Design Retrospective case series. Objective To determine the effect of obesity on the resource utilization and cost in 3270 consecutive patients undergoing elective noninstrumented decompressive surgeries for degenerative spine disease at Mayo Clinic Rochester between 2005 and 2012. Methods Groups were assessed for baseline differences (age, gender, and American Society of Anesthesiologists [ASA] classification, procedure type, and number of operative levels). Outcome variables included the transfusion requirements during surgery, the total anesthesia and surgical times, intensive care unit (ICU) admissions, standardized costs, as well as the ICU and hospital length of stay (LOS). Regression analysis was used to evaluate for strength of association between obesity and outcome variables. Results Baseline differences between the groups (nonobese: n = 1,853; obese: n = 1,417) were found with respect to age, ASA class, gender, procedure type, and number of operative levels. After correcting for differences, we found significant associations between obesity and surgical ( p < 0.0001) and anesthesia times ( p < 0.0001) and hospital LOS ( p < 0.0001). Additionally, ICU admission rates ( p = 0.02) and requirement for postoperative ventilation ( p = 0.048) were significantly higher in obese patients. Finally, mean difference in total cost ($1,632, p < 0.0001) was significantly higher for the obese cohort. Conclusion Obesity is associated with increased resource utilization and cost in patients undergoing a noninstrumented decompressive surgery for degenerative spine disease.
Modeling memory consolidation during posttraining periods in cerebellovestibular learning
Authors: Yamazaki Tadashi , Nagao Soichi , Lennon William , Tanaka Shigeru 
Published: March 2015

Significance
An efficient way to form a new declarative memory is to repeat a short-term training many times with a rest between the training sessions, because the learned memory is consolidated after training. This suggests that the brain still keeps actively working even after training, but the synaptic dynamics during posttraining periods has been studied rarely. The posttraining memory consolidation is also observed in cerebellar motor learning. To investigate the mechanism, we formulated a simple theoretical model of the cerebellum with a minimal number of elements and learning-related changes in synaptic efficacy at multiple locations. Computer simulations with this model closely reproduced learning behavior for oculomotor reflexes in wild-type mice and explained peculiar learning behavior in genetically manipulated mice.
Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation
Authors: Suzuki Sho W. , Yamamoto Hayashi , Oikawa Yu , Kondo-Kakuta Chika , Kimura Yayoi , Hirano Hisashi , Ohsumi Yoshinori 
Published: March 2015

Significance
Autophagy is a highly conserved degradative process in eukaryotes. In response to starvation, a number of autophagosome-related (Atg) proteins are recruited, and these proteins govern the process of autophagosome formation. Atg9 vesicles are thought to play an essential role in the nucleation step, but it remains unclear how Atg9 vesicles are localized to the site of autophagosome formation. In this study, we found that Atg9 interacts with the HORMA (from Hop1, Rev7, and Mad2) domain of Atg13. Atg13 mutants lacking the Atg9-binding region fail to recruit Atg9 vesicles to the site of autophagosome formation and exhibit severe defects in autophagy. Thus, the HORMA domain of Atg13 facilitates recruitment of Atg9 vesicles during autophagosome formation. Our studies provide a molecular insight into how Atg9 vesicles become part of the autophagosomal membrane.
Coastal Wetland Support of Great Lakes Fisheries: Progress from Concept to Quantification
Authors: Trebitz Anett S. , Hoffman Joel C. 
Published: March 2015

AbstractFishery support is recognized as a valuable ecosystem service provided by aquatic systems, but it is harder to quantify than to describe conceptually. In this paper, we combine data on fish inhabiting Great Lakes coastal wetlands (GLCWs) with information on commercial and recreational harvest and the piscivore forage base to develop quantitative understanding of the multiple species involved in direct and indirect fishery support of this complex fishery. We then examine patterns of species co‐occurrence and life history and relationships to GLCW conditions in order to identify fishery support metrics useful in aggregating species patterns and evaluating management outcomes. Our criteria for wetland prevalence (≥10% occurrence) and fishery importance (≥1% of recreational or commercial harvest in one or more of the Great Lakes or having a major forage fish role) yielded 21 wetland‐using, fishery‐relevant species representing multiple taxonomic groups and life history attributes. Wetland‐using species are estimated to make up half the biomass and 60% of the dollar value of the fish landed commercially and ∼80% of the fish numbers harvested recreationally. All of the GLCWs studied supported species of interest to recreational and commercial fishers but with widely varying composition. A few key habitat characteristics (e.g., vegetation structure) are broadly predictive of the types of sport and panfish present, with more degraded GLCWs generally supporting abundant but lower‐value taxa (rough‐fish species) and less degraded GLCWs supporting fewer but higher‐value taxa (sport and panfish species). No single taxonomic or functional metric seems adequate to capture the diversity of fishery‐relevant species supported by GLCWs; fishery support needs to be understood and managed in a multimetric context.Received May 16, 2014; accepted October 15, 2014
Isolation, identification, and formation conditions of a novel Maillard yellowish pigment, pyrrolothiazolate
Authors: Noda Kyoko , Yamada Shinji , Murata Masatsune 
Published: March 2015

Abstract
We isolated a novel yellow pigment from a model Maillard reaction system containing l-cysteine, l-lysine, and glucose and identified it as 6-hydroxy-3[R],7a[S]-dimethyl-7-oxo-2,3-dihydropyrrolo[2,1-b]thiazole-3-calboxylic acid. This compound was a novel pyrrolothiazole derivative carrying a carboxy group and was named pyrrolothiazolate. This compound showed the absorption maxima at 300 and 360 nm under acidic and neutral conditions, while 320 and 400 nm did under alkaline conditions. Pyrrolothiazolate formed from cysteine and glucose was the major low-molecular-weight Maillard pigment in the reaction mixture, and its formation was stimulated by adding lysine to the reaction cocktail. After heating at 110 °C for 2 h, 1–2 mg/mL of pyrrolothiazolate was formed in a reaction mixture containing 100 mM cysteine, 200 mM lysine, and 300 mM glucose dissolved in 0.5 m acetate buffer (pH 6.0) or 0.5 m phosphate buffer (pH 6.5).
Effects of Fish Oil Sparing on Fillet Fatty Acid Composition in Hybrid Striped Bass Are Influenced by Dietary Levels of Saturated and Unsaturated Fatty Acids
Authors: Trushenski Jesse T , Crouse Curtis C , Rombenso Artur N 
Published: March 2015

Abstract
We assessed the growth performance and fillet fatty acid composition of hybrid Striped Bass (White Bass Morone chrysops × Striped Bass M. saxatilis; initial weight = 29.1 ± 0.2 g [mean ± SE]) fed diets containing only menhaden fish oil (100 FISH); fully hydrogenated saturated fatty acid (SFA)-rich soybean oil (100 SFA SOY); 75:25, 50:50, 25:75, or 0:100 blends of fish oil and standard C18 polyunsaturated fatty acid (C18 PUFA)-rich soybean oil (25 PUFA SOY, 50 PUFA SOY, 75 PUFA SOY, 100 PUFA SOY); or nonhydrogenated monounsaturated fatty acid (MUFA)-rich soybean oil (25 MUFA SOY, 50 MUFA SOY, 75 MUFA SOY, 100 MUFA SOY) for 8 weeks. Feed conversion ratio varied, with the 100 SFA SOY feed yielding a significantly greater value (1.3) than the rest of the feeds (0.9–1.0). Although significant treatment effects were not observed for weight gain, specific growth rate, feed intake, or organosomatic indices, some variation was observed, suggesting some minor (albeit not significant) loss of growth performance among fish fed the 100 SFA SOY and, to a lesser extent, 100 MUFA SOY feeds. Fillets of fish fed diets containing soybean-derived lipids had reduced levels of fish-oil-associated, n-3 long-chain polyunsaturated fatty acids (LC-PUFAs, i.e., 20:5[n-3] and 22:6[n-3]) compared with those fed the 100 FISH feed. Conversely, fillets of fish fed diets containing C18 PUFA-rich soybean oil and nonhydrogenated MUFA-rich soybean oil had higher levels of these fatty acids (i.e., 18:2[n-6] and 18:1[n-9], respectively). Although the 100 SFA SOY diet contained substantially more SFAs (i.e., 18:0) than the other diets, these fatty acids were not proportionally elevated in the fillets. It is possible that blending SFA-rich lipids with ingredients containing some level of unsaturated fatty acids may be a means of addressing digestibility limitations while still mitigating the effects of fish oil sparing on tissue composition.
Comparison of Two Trap Net Sizes for Collecting Walleye Broodstock
Authors: Blackwell Brian G , Kaufman Todd M , Moos Tyrel S , Lucchesi David O 
Published: March 2015

Abstract
Trap nets are commonly used to collect Walleye Sander vitreus broodstock for spawning as part of culture and stocking programs. We compared overnight catch rates of Walleyes captured in two trap net sizes (small [0.9- × 1.5-m frame, 0.9-m-diameter hoop, single throat, 0.9- × 15.2-m lead, 19-mm knotted mesh] and large [1.5- × 1.8-m frame, 1.5-m-diameter hoop, double throated, 1.5- × 30.5-m lead, 19-mm knotless mesh]) to determine the relative efficiency of each size for broodstock collection. Sampling was completed during the spring of 2013 and 2014 soon after ice-out at three waters in South Dakota. In all but two cases, total Walleye CPUE in large trap nets was significantly higher than that in small trap nets. However, length-frequency distributions between the two net sizes generally were similar. The use of large trap nets will result in higher numbers of broodstock collected than with the smaller nets, likely offsetting the additional labor required to deploy and retrieve the larger traps.
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals
Authors: Abascal Federico , Tress Michael L. , Valencia Alfonso 
Published: March 2015

Abstract
Summary: Transposable elements constitute a large fraction of vertebrate genomes and, during evolution, may be co-opted for new functions. Exonization of transposable elements inserted within or close to host genes is one possible way to generate new genes, and alternative splicing of the new exons may represent an intermediate step in this process. The genes TMPO and ZNF451 are present in all vertebrate lineages. Although they are not evolutionarily related, mammalian TMPO and ZNF451 do have something in common—they both code for splice isoforms that contain LAP2alpha domains. We found that these LAP2alpha domains have sequence similarity to repetitive sequences in non-mammalian genomes, which are in turn related to the first ORF from a DIRS1-like retrotransposon. This retrotransposon domestication happened separately and resulted in proteins that combine retrotransposon and host protein domains. The alternative splicing of the retrotransposed sequence allowed the production of both the new and the untouched original isoforms, which may have contributed to the success of the colonization process. The LAP2alpha-specific isoform of TMPO (LAP2α) has been co-opted for important roles in the cell, whereas the ZNF451 LAP2alpha isoform is evolving under strong purifying selection but remains uncharacterized.
Contact: mtress@cnio.es or valencia@cnio.es
Supplementary information: Supplementary data are available at Bioinformatics online.