bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metacognitive training for schizophrenia spectrum patients: a meta-analysis on outcome studies
Authors: van Oosterhout B. , Smit F. , Krabbendam L. , Castelein S. , Staring A. B. P. , van der Gaag M. 
Published: July 2015

Background.Metacognitive training (MCT) for schizophrenia spectrum is widely implemented. It is timely to systematically review the literature and to conduct a meta-analysis.Method.Eligible studies were selected from several sources (databases and expert suggestions). Criteria included comparative studies with a MCT condition measuring positive symptoms and/or delusions and/or data-gathering bias. Three meta-analyses were conducted on data gathering (three studies; 219 participants), delusions (seven studies; 500 participants) and positive symptoms (nine studies; 436 participants). Hedges’gis reported as the effect size of interest. Statistical power was sufficient to detect small to moderate effects.Results.All analyses yielded small non-significant effect sizes (0.26 for positive symptoms; 0.22 for delusions; 0.31 for data-gathering bias). Corrections for publication bias further reduced the effect sizes to 0.21 for positive symptoms and to 0.03 for delusions. In blinded studies, the corrected effect sizes were 0.22 for positive symptoms and 0.03 for delusions. In studies using proper intention-to-treat statistics the effect sizes were 0.10 for positive symptoms and −0.02 for delusions. The moderate to high heterogeneity in most analyses suggests that processes other than MCT alone have an impact on the results.Conclusions.The studies so far do not support a positive effect for MCT on positive symptoms, delusions and data gathering. The methodology of most studies was poor and sensitivity analyses to control for methodological flaws reduced the effect sizes considerably. More rigorous research would be helpful in order to create enough statistical power to detect small effect sizes and to reduce heterogeneity. Limitations and strengths are discussed.
Quantitative X-ray phase-contrast microtomography from a compact laser-driven betatron source
Authors: Wenz J. , Schleede S. , Khrennikov K. , Bech M. , Thibault P. , Heigoldt M. , Pfeiffer F. , Karsch S. 
Published: July 2015

AbstractX-ray phase-contrast imaging has recently led to a revolution in resolving power and tissue contrast in biomedical imaging, microscopy and materials science. The necessary high spatial coherence is currently provided by either large-scale synchrotron facilities with limited beamtime access or by microfocus X-ray tubes with rather limited flux. X-rays radiated by relativistic electrons driven by well-controlled high-power lasers offer a promising route to a proliferation of this powerful imaging technology. A laser-driven plasma wave accelerates and wiggles electrons, giving rise to a brilliant keV X-ray emission. This so-called betatron radiation is emitted in a collimated beam with excellent spatial coherence and remarkable spectral stability. Here we present a phase-contrast microtomogram of a biological sample using betatron X-rays. Comprehensive source characterization enables the reconstruction of absolute electron densities. Our results suggest that laser-based X-ray technology offers the potential for filling the large performance gap between synchrotron- and current X-ray tube-based sources.
Impacts of elevated atmospheric CO2 on nutrient content of important food crops
Authors: Dietterich Lee H. , Zanobetti Antonella , Kloog Itai , Huybers Peter , Leakey Andrew D. B. , Bloom Arnold J. , Carlisle Eli , Fernando Nimesha , Fitzgerald Glenn , Hasegawa Toshihiro , Holbrook N. Michele , Nelson Randall L. , Norton Robert , Ottman Michael J. , Raboy Victor , Sakai Hidemitsu , Sartor Karla A. , Schwartz Joel , Seneweera Saman , Usui Yasuhiro , Yoshinaga Satoshi , Myers Samuel S. 
Published: July 2015

AbstractOne of the many ways that climate change may affect human health is by altering the nutrient content of food crops. However, previous attempts to study the effects of increased atmospheric CO2 on crop nutrition have been limited by small sample sizes and/or artificial growing conditions. Here we present data from a meta-analysis of the nutritional contents of the edible portions of 41 cultivars of six major crop species grown using free-air CO2 enrichment (FACE) technology to expose crops to ambient and elevated CO2 concentrations in otherwise normal field cultivation conditions. This data, collected across three continents, represents over ten times more data on the nutrient content of crops grown in FACE experiments than was previously available. We expect it to be deeply useful to future studies, such as efforts to understand the impacts of elevated atmospheric CO2 on crop macro- and micronutrient concentrations, or attempts to alleviate harmful effects of these changes for the billions of people who depend on these crops for essential nutrients.
Investigation of Ion Channel Activities of Gramicidin A in the Presence of Ionic Liquids Using Model Cell Membranes
Authors: Ryu Hyunil , Lee Hwankyu , Iwata Seigo , Choi Sangbaek , Ki Kim Moon , Kim Young-Rok , Maruta Shinsaku , Min Kim Sun , Jeon Tae-Joon 
Published: July 2015

AbstractIonic liquids (ILs) are considered to be green solvents because of their non-volatility. Although ILs are relatively safe in the atmospheric environment, they may be toxic in other environments. Our previous research showed that the cytotoxicity of ILs to biological organisms is attributable to interference with cell membranes by IL insertion. However, the effects of ILs on ion channels, which play important roles in cell homeostasis, have not been comprehensively studied to date. In this work, we studied the interactions between ILs and lipid bilayer membranes with gramicidin A ion channels. We used two methods, namely electrical and fluorescence measurements of ions that permeate the membrane. The lifetimes of channels were increased by all the ILs tested in this work via stabilizing the compressed structure of the lipid bilayer and the rate of ion flux through gA channels was decreased by changing the membrane surface charge. The former effect, which increased the rate of ion flux, was dominant at high salt concentrations, whereas the latter, which decreased the rate of ion flux, was dominant at low salt concentrations. The effects of ILs increased with increasing concentration and alkyl chain length. The experimental results were further studied using molecular dynamics simulations.
Engineering functionalized multi-phased silicon/silicon oxide nano-biomaterials to passivate the aggressive proliferation of cancer
Authors: Premnath P. , Tan B. , Venkatakrishnan K. 
Published: July 2015

AbstractCurrently, the use of nano silicon in cancer therapy is limited as drug delivery vehicles and markers in imaging, not as manipulative/controlling agents. This is due to limited properties that native states of nano silicon and silicon oxides offers. We introduce nano-functionalized multi-phased silicon/silicon oxide biomaterials synthesized via ultrashort pulsed laser synthesis, with tunable properties that possess inherent cancer controlling properties that can passivate the progression of cancer. This nanostructured biomaterial is composed of individual functionalized nanoparticles made of a homogenous hybrid of multiple phases of silicon and silicon oxide in increasing concentration outwards from the core. The chemical properties of the proposed nanostructure such as number of phases, composition of phases and crystal orientation of each functionalized nanoparticle in the three dimensional nanostructure is defined based on precisely tuned ultrashort pulsed laser-material interaction mechanisms. The amorphous rich phased biomaterial shows a 30 fold (95%) reduction in number of cancer cells compared to bulk silicon in 48 hours. Further, the size of the cancer cells reduces by 76% from 24 to 48 hours. This method exposes untapped properties of combination of multiple phases of silicon oxides and its applications in cancer therapy.
Domain analysis of the Nematostella vectensis SNAIL ortholog reveals unique nucleolar localization that depends on the zinc-finger domains
Authors: Dattoli Ada A. , Hink Mark A. , DuBuc Timothy Q. , Teunisse Bram J. , Goedhart Joachim , Röttinger Eric , Postma Marten 
Published: July 2015

AbstractSNAIL transcriptional factors are key regulators during development and disease. They arose early during evolution and in cnidarians such as Nematostella vectensis, NvSNAILA/B are detected in invaginating tissues during gastrulation. The function of SNAIL proteins is well established in bilaterians but their roles in cnidarians remain unknown. The structure of NvSNAILA and B is similar to the human SNAIL1 and 2, including SNAG and zinc-finger domains. Here, we performed a molecular analysis on localization and mobility of NvSNAILA/B using mammalian cells and Nematostella embryos. NvSNAILA/B display nuclear localization and mobility similar to HsSNAIL1/2. Strikingly, NvSNAILA is highly enriched in the nucleoli and shuttles between the nucleoli and the nucleoplasm. Truncation of the N-terminal SNAG domain, reported to contain Nuclear Localization Signals, markedly reduces nucleolar levels, without effecting nuclear localization or mobility. Truncation of the C-terminal zinc-fingers, involved in DNA binding in higher organisms, significantly affects subcellular localization and mobility. Specifically, the zinc-finger domains are required for nucleolar enrichment of NvSNAILA. Differently from SNAIL transcriptional factors described before, NvSNAILA is specifically enriched in the nucleoli co-localizing with nucleolar markers even after nucleolar disruption. Our findings implicate additional roles for SNAG and zinc-finger domains, suggesting a role for NvSNAILA in the nucleolus.
Performance of genetic risk factors in prediction of trichloroethylene induced hypersensitivity syndrome
Authors: Dai Yufei , Chen Ying , Huang Hanlin , Zhou Wei , Niu Yong , Zhang Mingrong , Bin Ping , Dong Haiyan , Jia Qiang , Huang Jianxun , Yi Juan , Liao Qijun , Li Haishan , Teng Yanxia , Zang Dan , Zhai Qingfeng , Duan Huawei , Shen Juan , He Jiaxi , Meng Tao , Sha Yan , Shen Meili , Ye Meng , Jia Xiaowei , Xiang Yingping , Huang Huiping , Wu Qifeng , Shi Mingming , Huang Xianqing , Yang Huanming , Luo Longhai , Li Sai , Li Lin , Zhao Jinyang , Li Laiyu , Wang Jun , Zheng Yuxin 
Published: July 2015

AbstractTrichloroethylene induced hypersensitivity syndrome is dose-independent and potentially life threatening disease, which has become one of the serious occupational health issues and requires intensive treatment. To discover the genetic risk factors and evaluate the performance of risk prediction model for the disease, we conducted genomewide association study and replication study with total of 174 cases and 1761 trichloroethylene-tolerant controls. Fifty seven SNPs that exceeded the threshold for genome-wide significance (P < 5 × 10−8) were screened to relate with the disease, among which two independent SNPs were identified, that is rs2857281 at MICA (odds ratio, 11.92; Pmeta = 1.33 × 10−37) and rs2523557 between HLA-B and MICA (odds ratio, 7.33; Pmeta = 8.79 × 10−35). The genetic risk score with these two SNPs explains at least 20.9% of the disease variance and up to 32.5-fold variation in inter-individual risk. Combining of two SNPs as predictors for the disease would have accuracy of 80.73%, the area under receiver operator characteristic curves (AUC) scores was 0.82 with sensitivity of 74% and specificity of 85%, which was considered to have excellent discrimination for the disease and could be considered for translational application for screening employees before exposure.
Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation
Authors: Fan Di , Liu Tingting , Li Chaofeng , Jiao Bo , Li Shuang , Hou Yishu , Luo Keming 
Published: July 2015

AbstractRecently, RNA-guided genome editing using the type II clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system has been applied to edit the plant genome in several herbaceous plant species. However, it remains unknown whether this system can be used for genome editing in woody plants. In this study, we describe the genome editing and targeted gene mutation in a woody species, Populus tomentosa Carr. via the CRISPR/Cas9 system. Four guide RNAs (gRNAs) were designed to target with distinct poplar genomic sites of the phytoene desaturase gene 8 (PtoPDS) which are followed by the protospacer-adjacent motif (PAM). After Agrobacterium-mediated transformation, obvious albino phenotype was observed in transgenic poplar plants. By analyzing the RNA-guided genome-editing events, 30 out of 59 PCR clones were homozygous mutants, 2 out of 59 were heterozygous mutants and the mutation efficiency at these target sites was estimated to be 51.7%. Our data demonstrate that the Cas9/sgRNA system can be exploited to precisely edit genomic sequence and effectively create knockout mutations in woody plants.
The Balance of Expression of Dihydroflavonol 4-reductase and Flavonol Synthase Regulates Flavonoid Biosynthesis and Red Foliage Coloration in Crabapples
Authors: Tian Ji , Han Zhen-yun , Zhang Jie , Hu YuJing , Song Tingting , Yao Yuncong 
Published: July 2015

AbstractRed leaf color is an attractive trait of Malus families, including crabapple (Malus spp.); however, little is known about the molecular mechanisms that regulate the coloration. Dihydroflavonols are intermediates in the production of both colored anthocyanins and colorless flavonols and this current study focused on the gene expression balance involved in the relative accumulation of these compounds in crabapple leaves. Levels of anthocyanins and the transcript abundances of the anthocyanin biosynthetic gene, dihydroflavonol 4-reductase (McDFR) and the flavonol biosynthetic gene, flavonol synthase (McFLS), were assessed during the leaf development in two crabapple cultivars, ‘Royalty’ and ‘Flame’. The concentrations of anthocyanins and flavonols correlated with leaf color and we propose that the expression of McDFR and McFLS influences their accumulation. Further studies showed that overexpression of McDFR, or silencing of McFLS, increased anthocyanin production, resulting in red-leaf and red fruit peel phenotypes. Conversely, elevated flavonol production and green phenotypes in crabapple leaves and apple peel were observed when McFLS was overexpressed or McDFR was silenced. These results suggest that the relative activities of McDFR and McFLS are important determinants of the red color of crabapple leaves, via the regulation of the metabolic fate of substrates that these enzymes have in common.
Regulatory B cells preferentially accumulate in tumor-draining lymph nodes and promote tumor growth
Authors: Ganti Sheila N. , Albershardt Tina C. , Iritani Brian M. , Ruddell Alanna 
Published: July 2015

AbstractOur previous studies found that B16-F10 melanoma growth in the rear footpad of immunocompetent mice induces marked B cell accumulation within tumor-draining popliteal lymph nodes (TDLN). This B cell accumulation drives TDLN remodeling that precedes and promotes metastasis, indicating a tumor-promoting role for TDLN B cells. Here we show that phenotypic characterization of lymphocytes in mice bearing B16-F10 melanomas identifies preferential accumulation of T2-MZP B cells in the TDLN. Comparison of non-draining LNs and spleens of tumor-bearing mice with LNs and spleens from naïve mice determined that this pattern of B cell accumulation was restricted to the TDLN. B cell-deficient and immunocompetent mice reconstituted with T2-MZP B cells but not with other B cell subsets displayed accelerated tumor growth, demonstrating that T2-MZP B cells possess regulatory activity in tumor-bearing mice. Unlike splenic regulatory B cells, however, these TDLN B cells did not exhibit increased IL-10 production, nor did they promote Treg generation in the TDLN. These findings demonstrate that tumors initially signal via the lymphatic drainage to stimulate the preferential accumulation of T2-MZP regulatory B cells. This local response may be an early and critical step in generating an immunosuppressive environment to permit tumor growth and metastasis.
MuCor: Mutation Aggregation and Correlation
Authors: Kroll Karl W. , Eisfeld Ann-Katherin , Lozanski Gerard , Bloomfield Clara D. , Byrd John C. , Blachly James S. 
Published: July 2015

AbstractMotivationThere are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting, and summarizing variants and effects across a cohort is often done withad hocscripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many report types. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters, or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls.AvailabilitySource code is freely available athttps://github.com/blachlylabContactjames.blachly@osumc.eduSupplementary dataSupplementary data, including detailed documentation, are available online.
Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population
Authors: Turner Caroline B. , Blount Zachary D. , Lenski Richard E. 
Published: July 2015

AbstractIn a long-term evolution experiment withEscherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit−) ecotypes, with Cit−bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+bacteria. After more than 10,000 generations of coexistence, however, the Cit−lineage went extinct; cells with the Cit−phenotype dropped to levels below detection, and the Cit−clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction event was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ecotype that competitively excluded the Cit−ecotype. We tested this hypothesis by re-evolving the population from one frozen sample taken just prior to the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit−type did not go extinct in any of these replays, and Cit−cells also persisted in a single replicate that was propagated for 3,000 generations. Even more unexpectedly, we showed that the Cit−ecotype could reinvade the Cit+population after its extinction. Taken together, these results indicate that the extinction of the Cit−ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ecotype. The extinction also cannot be explained by demographic stochasticity, as the population size of the Cit−ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.
Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hotspots in mouse
Authors: Boer Esther de , Jasin Maria , Keeney Scott 
Published: July 2015

ABSTRACTMeiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study we analyze the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hotspots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hotspots in oocytes to date. One hotspot, located centrally on chromosome 1, behaved similarly in male and female meiosis: crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hotspot crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further find that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hotspots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency.
Intensity of shock transmission amid US-BRICS markets
Authors: Lakshmi P. , Visalakshmi S. , Shanmugam Kavitha 
Published: July 2015

Purpose
– The purpose of this paper is to analyze the intensity of transmission of shocks from USA to BRICS countries in the long-run and short-run deviations and swiftness of recovery during US subprime mortgage crisis. This analysis enables the authors to explore the evolving patterns of relationships between these markets and examine whether their co-movements altered either in response to international shocks that originated in advanced markets like USA or due to their domestic fluctuations.

Design/methodology/approach
– Employing data of daily stock market indices (open and close) of BRICS countries for the period January 2, 2001 to May 31, 2012, this paper examines the interactions and characteristics of price movements of BRICS with US market by applying co-integration tests, vector error correction model and Granger causality relationship. The daily stock market indices data are derived from respective stock exchange web sites.

Findings
– The results exhibit that both long-run co-integration relationships and short-run Granger causality relationships exist between the stock markets of US-BRICS. Furthermore, this nexus is amplified in the short-run during 2007-2009, when the subprime mortgage financial crisis in the USA cropped up. This finding lends support to the prominence of developed (US) market links in the proliferation of persistent co-movements of BRICS stock markets.

Research limitations/implications
– The findings imply an increasing degree of global market integration due to quick dissemination of global shocks originating from developed market like USA, and swift recovery which can be attributed to the increased resilience, consistent with the moderated level of domestically driven risk in the BRICS markets. In spite of their similarities, long-run and short-run interdependences with the US stock market exhibit differences among the BRICS. This can be attributed to the regional heterogeneity in long-run risk and return co-movements with the USA.

Practical implications
– Changes from the US index easily affect these stock markets in the short-run, which implies that the US index may act as a leading indicator for investing funds in BRICS markets.

Originality/value
– This study would enable the authors to understand whether BRICS economies actually remain resilient to adverse developments in USA and could serve as alternative investment destinations for global portfolio diversification.