bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-level genomic variation in natural populations ofLebetimonasfrom an erupting deep-sea volcano
Authors: Meyer Julie L , Huber Julie A 
Published: November 2013

AbstractChemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.
In-line fiber microcantilever vibration sensor
Authors: Lu Ping , Xu Yanping , Baset Farhana , Bao Xiaoyi , Bhardwaj Ravi 
Published: November 2013

We demonstrate a fiber-based vibration sensor that involves an enclosed suspended microcantilever integrated with a readout fiber, providing in-line measurement of frequency and amplitude of vibration. The microcantilever is fabricated from a bend-insensitive fiber by chemical etching and fused to a single-mode fiber. Vibration induced periodic bending of the microcantilever angularly scans the readout fiber core resulting in output power modulation corresponding to certain drive frequencies and voltages of a shaker. Experimental results agree well with the theoretical analysis and demonstrate a continuous vibration frequency range of 5 Hz–10 kHz with a maximum signal-to-noise ratio of 68 dB.
Effect of separate sampling on classification accuracy
Authors: Shahrokh Esfahani Mohammad , Dougherty Edward R. 
Published: November 2013

Abstract
Motivation: Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In this ‘separate sampling’ scenario, the data cannot be used to estimate the class prior probabilities. Moreover, predetermined class sizes can severely degrade classifier performance, even for large samples.
Results: We employ simulations using both synthetic and real data to show the detrimental effect of separate sampling on a variety of classification rules. We establish propositions related to the effect on the expected classifier error owing to a sampling ratio different from the population class ratio. From these we derive a sample-based minimax sampling ratio and provide an algorithm for approximating it from the data. We also extend to arbitrary distributions the classical population-based Anderson linear discriminant analysis minimax sampling ratio derived from the discriminant form of the Bayes classifier.
Availability: All the codes for synthetic data and real data examples are written in MATLAB. A function called mmratio, whose output is an approximation of the minimax sampling ratio of a given dataset, is also written in MATLAB. All the codes are available at: http://gsp.tamu.edu/Publications/supplementary/shahrokh13b.
Contact: edward@ece.tamu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
FastPros: screening of reaction knockout strategies for metabolic engineering
Authors: Ohno Satoshi , Shimizu Hiroshi , Furusawa Chikara 
Published: November 2013

Abstract
Motivation: Although constraint-based flux analysis of knockout strains has facilitated the production of desirable metabolites in microbes, current screening methods have placed a limitation on the number knockouts that can be simultaneously analyzed.
Results: Here, we propose a novel screening method named FastPros. In this method, the potential of a given reaction knockout for production of a specific metabolite is evaluated by shadow pricing of the constraint in the flux balance analysis, which generates a screening score to obtain candidate knockout sets. To evaluate the performance of FastPros, we screened knockout sets to produce each metabolite in the entire Escherichia coli metabolic network. We found that 75% of these metabolites could be produced under biomass maximization conditions by adding up to 25 reaction knockouts. Furthermore, we demonstrated that using FastPros in tandem with another screening method, OptKnock, could further improve target metabolite productivity.
Availability and implementation: Source code is freely available at http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FastPros/, implemented in MATLAB and COBRA toolbox.
Contact: chikara.furusawa@riken.jp or shimizu@ist.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Trans-splicing and RNA editing of LSU rRNA in Diplonema mitochondria
Authors: Valach Matus , Moreira Sandrine , Kiethega Georgette N. , Burger Gertraud 
Published: November 2013

Abstract
Mitochondrial ribosomal RNAs (rRNAs) often display reduced size and deviant secondary structure, and sometimes are fragmented, as are their corresponding genes. Here we report a mitochondrial large subunit rRNA (mt-LSU rRNA) with unprecedented features. In the protist Diplonema, the rnl gene is split into two pieces (modules 1 and 2, 534- and 352-nt long) that are encoded by distinct mitochondrial chromosomes, yet the rRNA is continuous. To reconstruct the post-transcriptional maturation pathway of this rRNA, we have catalogued transcript intermediates by deep RNA sequencing and RT-PCR. Gene modules are transcribed separately. Subsequently, transcripts are end-processed, the module-1 transcript is polyuridylated and the module-2 transcript is polyadenylated. The two modules are joined via trans-splicing that retains at the junction ∼26 uridines, resulting in an extent of insertion RNA editing not observed before in any system. The A-tail of trans-spliced molecules is shorter than that of mono-module 2, and completely absent from mitoribosome-associated mt-LSU rRNA. We also characterize putative antisense transcripts. Antisense-mono-modules corroborate bi-directional transcription of chromosomes. Antisense-mt-LSU rRNA, if functional, has the potential of guiding concomitantly trans-splicing and editing of this rRNA. Together, these findings open a window on the investigation of complex regulatory networks that orchestrate multiple and biochemically diverse post-transcriptional events.
The Effect of Bioprocessing on the Phenolic Acid Composition and Antioxidant Activity of Wheat Bran
Authors: Zhang Lixia , Gao Wenyuan , Chen Xuetao , Wang Haiyang 
Published: November 2013

ABSTRACTIn the present study, bioprocessing with eight microbial strains including Bacillus species, yeasts, and filamentous fungi was evaluated for its potential to improve the phenolic acid composition and antioxidant activity of wheat bran. The soluble free and soluble conjugated fractions of ethanolic extracts of the treated bran samples were compared for their total phenolic contents, phenolic acid composition, and in vitro antioxidant activities. In general, total phenolic content in the soluble free fraction increased significantly, accounting for 241.11 ± 1.25 μg of gallic acid equivalents (GE)/g (Rhizopus oryzae), 230.50 ± 1.05 μg of GE/g (Mucor circinelloides), and 230.19 ± 1.02 μg of GE/g (Saccharomycopsis fibuligera). The phenolic acid composition, especially of the soluble free fraction, was improved most by S. fibuligera (hydroxybenzoic, vanillic, syringic, and trans‐ferulic acids), M. circinelloides (chlorogenic acid), and R. oryzae (protocatechuic, trans‐coumaric, and benzoic acids). Comparatively, bioprocessing exhibited less effectiveness on conjugated phenolic acid composition. Fermented wheat bran displayed enhanced reducing capacity, superoxide anion radical scavenging activity, and 1,1‐diphenyl‐2‐picrylhydrazyl radical scavenging activity in comparison with the nonfermented sample. The antioxidant activity was significantly correlated to the total phenolic content.
Concurrent effects of age class and food distribution on immigration success and population dynamics in a small mammal
Authors: Rémy Alice , Le Galliard Jean‐François , Odden Morten , Andreassen Harry P. 
Published: November 2013

SummaryDuring the settlement stage of dispersal, the outcome of conflicts between residents and immigrants should depend on the social organization of resident populations as well as on individual traits of immigrants, such as their age class, body mass and/or behaviour.We have previously shown that spatial distribution of food influences the social organization of female bank voles (Myodes glareolus). Here, we aimed to determine the relative impact of food distribution and immigrant age class on the success and demographic consequences of female bank vole immigration. We manipulated the spatial distribution of food within populations having either clumped or dispersed food. After a pre‐experimental period, we released either adult immigrants or juvenile immigrants, for which we scored sociability and aggressiveness prior to introduction.We found that immigrant females survived less well and moved more between populations than resident females, which suggest settlement costs. However, settled juvenile immigrants had a higher probability to reproduce than field‐born juveniles.Food distribution had little effects on the settlement success of immigrant females. Survival and settlement probabilities of immigrants were influenced by adult female density in opposite ways for adult and juvenile immigrants, suggesting a strong adult–adult competition. Moreover, females of higher body mass at release had a lower probability to survive, and the breeding probability of settled immigrants increased with their aggressiveness and decreased with their sociability.Prior to the introduction of immigrants, resident females were more aggregated in the clumped food treatment than in the dispersed food treatment, but immigration reversed this relationship. In addition, differences in growth trajectories were seen during the breeding season, with populations reaching higher densities when adult immigrants were introduced in a plot with dispersed food, or when juvenile immigrants were introduced in a plot with clumped food.These results indicate the relative importance of intrinsic and extrinsic factors on immigration success and demographic consequences of dispersal and are of relevance to conservation actions, such as reinforcement of small populations.
GC Analysis of Black Gel Pen Ink Stored under Different Conditions
Authors: Li Biao , Xie Peng , Guo Ying‐min , Fei Qing 
Published: November 2013

AbstractIn many criminal and civil cases in China, the most commonly questioned documents are those written with gel pen ink. An important task for forensic document examiners is to identify whether two or more ink entries in one or more documents were written with the same ink type. The identification of the age of gel ink entries made poses an important and difficult problem for forensic document examiners. In this paper, the volatile components of gel ink were determined and the gel ink was classified by gas chromatography with a flame ionization detector. Calibration curves were created to express the relationship between the content of volatile gel ink components and the age of gel ink entries stored under natural and UV‐induced aging conditions. The correspondence between the natural and UV‐induced aging conditions was also established. The experimental results showed that GC was useful in the analysis of black gel ink and applicable for determining the relative age of gel ink entries under certain conditions.
Infrared Spectra of U.S. Automobile Original Finishes (Post – 1989). VIII: In Situ Identification of Bismuth Vanadate Using Extended Range FT‐IR Spectroscopy, Raman Spectroscopy, and X‐Ray Fluorescence Spectrometry
Authors: Suzuki Edward M. 
Published: November 2013

AbstractChrome Yellow (PbCrO4·xPbSO4) was a common pigment in U.S. automobile OEM finishes for more than three decades, but in the early 1990s its use was discontinued. One of its main replacements was Bismuth Vanadate (BiVO4·nBi2MoO6, n = 0–2), which was commercially introduced in 1985, as this inorganic pigment also produces a very bright hue and has excellent outdoor durability. This paper describes the in situ identification of Bismuth Vanadate in automotive finishes using FT‐IR and dispersive Raman spectroscopy and XRF spectrometry. Some differentiation of commercial formulations of this pigment is possible based on far‐infrared absorptions, Raman data, and elemental analysis. The spectral differences arise from the presence or absence of molybdenum, the use of two crystal polymorphs of BiVO4, and differences in pigment stabilizers. Bismuth Vanadate is usually not used alone, and it is typically found with Isoindoline Yellow, hydrous ferric oxide, rutile, Isoindolinone Yellow 3R, or various combinations of these.
Effect of Temperature on the Visualization by Digital Color Mapping of Latent Fingerprint Deposits on Metal
Authors: Peel Alicia , Bond John W. 
Published: November 2013

AbstractVisualization of fingerprint deposits by digital color mapping of light reflected from the surface of heated brass, copper, aluminum, and tin has been investigated using Adobe® Photoshop®. Metals were heated to a range of temperatures (T) between 50°C and 500°C in 50°C intervals with enhancement being optimal when the metals are heated to 250°C, 350°C, 50°C, and 300°C, respectively, and the hue values adjusted to 247°, 245°, 5°, and 34°, respectively. Fingerprint visualization after color mapping was not degraded by subsequent washing of the metals and color mapping did not compromise the visibility of the fingerprint for all values of T. The optimum value of T for fingerprint visibility is significantly dependent of the standard reduction potential of the metal with Kendall's Tau (τ) = 0.953 (p < 0.001). For brass, this correlation is obtained when considering the standard reduction potential of zinc rather than copper.
Overview of: “Valuing Developmental Crime Prevention”
Authors: Manning Matthew , Smith Christine , Homel Ross 
Published: November 2013

Research SummaryDevelopmental crime prevention programs produce positive returns on investment. Previous studies of such returns have not adequately quantified and weighted impacts across multiple domains of quality of life (e.g., social‐emotional development and family well‐being) or have provided a protocol for deciding between programs that recognizes these multiple domains (i.e., propose a method for the ranking of program alternatives). We adapted a multiple‐criteria decision‐making (MCDM) technique to address these deficiencies. Incorporating subjective decisions (a survey of those individuals who directly affect policy decisions) and objective evidence (the effect sizes from a meta‐analysis of longitudinal intervention outcomes) allowed us to construct a common metric for making structured choices between diverse developmental crime prevention program options. Our results show that a structured preschool program that incorporates family intervention and support was the most preferred option to reduce youth crime.Policy ImplicationsThe adapted MCDM technique employed in this study can be used to evaluate many crime prevention policy options that have effects that are spread across multiple domains and for which objective evidence from past research can usefully be combined with stakeholder judgments to recommend a preferred option.
Multi‐element Fingerprinting as a Tool in Origin Authentication of Four East China Marine Species
Authors: Guo Lipan , Gong Like , Yu Yanlei , Zhang Hong 
Published: November 2013

AbstractThe contents of 25 elements in 4 types of commercial marine species from the East China Sea were determined by inductively coupled plasma mass spectrometry and atomic absorption spectrometry. The elemental composition was used to differentiate marine species according to geographical origin by multivariate statistical analysis. The results showed that principal component analysis could distinguish samples from different areas and reveal the elements which played the most important role in origin diversity. The established models by partial least squares discriminant analysis (PLS‐DA) and by probabilistic neural network (PNN) can both precisely predict the origin of the marine species. Further study indicated that PLS‐DA and PNN were efficacious in regional discrimination. The models from these 2 statistical methods, with an accuracy of 97.92% and 100%, respectively, could both distinguish samples from different areas without the need for species differentiation.
Xanthine Oxidase Inhibitory Activity and Hypouricemic Effect of Aspalathin from Unfermented Rooibos
Authors: Kondo Makoto , Hirano Yoshiaki , Nishio Masahiro , Furuya Yutaka , Nakamura Hiromichi , Watanabe Tsuyoshi 
Published: November 2013

AbstractRooibos is rich in flavonoids such as aspalathin, which is a unique C‐glycosyl dihydrochalcone, that is used as a traditional herbal tea. This study was designed to evaluate the in vitro xanthine oxidase (XOD) inhibitory activity of the aspalathin‐rich fraction (ARF) and purified aspalathin from rooibos. The hypouricemic effects of the ARF and aspalathin on hyperuricemic mice were also assessed. The ARF was prepared from aqueous extract of unfermented rooibos leaves and stems, and it was collected by column chromatography; the aspalathin content in this fraction was 21.4%. The ARF and aspalathin inhibited XOD in a dose‐dependent manner. The concentrations of the ARF and aspalathin required to inhibit XOD at 50% (IC50) were 20.4 μg/mL (4.4 μg/mL aspalathin equivalents) and 4.5 μg/mL, respectively. Lineweaver–Burk plot analysis indicated that aspalathin was a competitive inhibitor of XOD, and the inhibition constant (Ki) was 3.1 μM. In hyperuricemic mice induced by inosine‐5’‐monophosphate, treatment with the ARF and aspalathin significantly suppressed the increased plasma uric acid level in a dose‐dependent manner. The suppressed plasma uric acid level in mice could be attributed to the XOD inhibitory activity of the ARF and aspalathin. Further study is required to determine the effect of aspalathin or its metabolites on XOD activity in vivo.
Group music therapy for severe mental illness: a randomized embedded‐experimental mixed methods study
Authors: Grocke D. , Bloch S. , Castle D. , Thompson G. , Newton R. , Stewart S. , Gold C. 
Published: November 2013

ObjectiveMusic therapy is an innovative approach to support people with severe mental illness (SMI). The aim of the study was to determine whether group music therapy (GMT) positively impacted on quality of life (QoL), social enrichment, self‐esteem, spirituality and psychiatric symptoms of participants with SMI and how they experienced the intervention.MethodThe primary outcome was QoL; secondary measures assessed social enrichment, self‐esteem, spirituality and psychiatric symptoms. The 13‐week intervention comprised singing familiar songs and composing original songs recorded in a professional studio. Qualitative data were generated from focus group interviews and song lyric analysis.ResultsNinety‐nine adults (57 female) were recruited, with an initial cohort (n = 75) randomized to either: weekly GMT followed by standard care (SC) or SC followed by GMT. Crossover occurred after 13 weeks. Measures were conducted at baseline, 13, 26 and 39 weeks. A second cohort (n = 24) could not be randomized and were assigned to GMT followed by SC. Intention‐to‐treat analysis showed a significant difference between GMT and SC on QoL and spirituality. This was robust to different assumptions about missing data (listwise deletion, last observation carried forward or multiple imputation). Per‐protocol analysis suggested greater benefit for those receiving more sessions. Focus group interview and song lyric analyses suggested that GMT was enjoyable; self‐esteem was enhanced; participants appreciated therapists and peers; and although challenges were experienced, the programme was recommended to others.ConclusionGroup music therapy may enhance QoL and spirituality of persons with SMI.
Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units
Authors: Vásquez‐Carrillo C. , Friesen V. , Hall L. , Peery M. Z. 
Published: November 2013

AbstractConserving genetic variation is critical for maintaining the evolutionary potential and viability of a species. Genetic studies seeking to delineate conservation units, however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major histocompatibility complex (MHC) class II B genes was characterized in four populations of marbled murrelets Brachyramphus marmoratus, a threatened species in which little neutral genetic population structure has been detected. High diversity, as well as evidence of balancing selection, was detected in exon 2 of these genes. Genetic population structure based on MHC markers was uncorrelated to genetic structure estimated with neutral markers, suggesting that selection played a more important role in shaping population structure at these markers than genetic drift. A high proportion of alleles and inferred peptides were unique to a single population, with the Aleutian Islands and southeast Alaska having the highest richness of both. Murrelets sampled in Oregon had low MHC exon 2 allele and inferred peptide richness, and were significantly differentiated from individuals sampled in the Aleutian Islands based on the frequency of exon 2 alleles. In addition, murrelets sampled in Oregon were differentiated from murrelets in both the Aleutian Islands and southeast Alaska based on inferred peptide frequencies, suggesting that the Oregon population could be prioritized for conservation measures. More broadly, combining information from neutral and adaptive genetic markers can improve the delineation of conservation units in threatened species.