bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of adolescent psychopathology: a symptom-level analysis
Authors: Carragher N. , Teesson M. , Sunderland M. , Newton N. C. , Krueger R. F. , Conrod P. J. , Barrett E. L. , Champion K. E. , Nair N. K. , Slade T. 
Published: December 2015

BackgroundMost empirical studies into the covariance structure of psychopathology have been confined to adults. This work is not developmentally informed as the meaning, age-of-onset, persistence and expression of disorders differ across the lifespan. This study investigates the underlying structure of adolescent psychopathology and associations between the psychopathological dimensions and sex and personality risk profiles for substance misuse and mental health problems.MethodThis study analyzed data from 2175 adolescents aged 13.3 years. Five dimensional models were tested using confirmatory factor analysis and the external validity was examined using a multiple-indicators multiple-causes model.ResultsA modified bifactor model, with three correlated specific factors (internalizing, externalizing, thought disorder) and one general psychopathology factor, provided the best fit to the data. Females reported higher mean levels of internalizing, and males reported higher mean levels of externalizing. No significant sex differences emerged in liability to thought disorder or general psychopathology. Liability to internalizing, externalizing, thought disorder and general psychopathology was characterized by a number of differences in personality profiles.ConclusionsThis study is the first to identify a bifactor model including a specific thought disorder factor. The findings highlight the utility of transdiagnostic treatment approaches and the importance of restructuring psychopathology in an empirically based manner.
A biomimetic hybrid nanoplatform for encapsulation and precisely controlled delivery of theranostic agents
Authors: Wang Hai , Agarwal Pranay , Zhao Shuting , Yu Jianhua , Lu Xiongbin , He Xiaoming 
Published: December 2015

AbstractNanoparticles have demonstrated great potential for enhancing drug delivery. However, the low drug encapsulation efficiency at high drug-to-nanoparticle feeding ratios and minimal drug loading content in nanoparticle at any feeding ratios are major hurdles to their widespread applications. Here we report a robust eukaryotic cell-like hybrid nanoplatform (EukaCell) for encapsulation of theranostic agents (doxorubicin and indocyanine green). The EukaCell consists of a phospholipid membrane, a cytoskeleton-like mesoporous silica matrix and a nucleus-like fullerene core. At high drug-to-nanoparticle feeding ratios (for example, 1:0.5), the encapsulation efficiency and loading content can be improved by 58 and 21 times, respectively, compared with conventional silica nanoparticles. Moreover, release of the encapsulated drug can be precisely controlled via dosing near infrared laser irradiation. Ultimately, the ultra-high (up to ∼87%) loading content renders augmented anticancer capacity both in vitro and in vivo. Our EukaCell is valuable for drug delivery to fight against cancer and potentially other diseases.
Comparative proteomic analysis of compartmentalised Ras signalling
Authors: Hernandez-Valladares Maria , Prior Ian A. 
Published: December 2015

AbstractRas proteins are membrane bound signalling hubs that operate from both the cell surface and endomembrane compartments. However, the extent to which intracellular pools of Ras can contribute to cell signalling is debated. To address this, we have performed a global screen of compartmentalised Ras signalling. We find that whilst ER/Golgi- and endosomal-Ras only generate weak outputs, Ras localised to the mitochondria or Golgi significantly and distinctly influence both the abundance and phosphorylation of a wide range of proteins analysed. Our data reveal that ~80% of phosphosites exhibiting large (≥1.5-fold) changes compared to control can be modulated by organellar Ras signalling. The majority of compartmentalised Ras-specific responses are predicted to influence gene expression, RNA splicing and cell proliferation. Our analysis reinforces the concept that compartmentalisation influences Ras signalling and provides detailed insight into the widespread modulation of responses downstream of endomembranous Ras signalling.
Targeting TRPV1 for Body Weight Control using TRPV1−/− Mice and Electroacupuncture
Authors: Choowanthanapakorn Monchanok , Lu Kung-Wen , Yang Jun , Hsieh Ching-Liang , Lin Yi-Wen 
Published: December 2015

AbstractObesity is a global social medical problem resulting in morbidity as high as 20–30%. Here we investigated whether the manipulation of TRPV1 can control mice body weight through electroacupuncture (EA). The results demonstrated that body weight increased with time in the control group (108.19 ± 1.31%, n = 7). The increase of mice body weight was significantly less in the EA group (104.41 ± 0.76%, p < 0.05, compared with the control group, n = 7) but not in the sham EA group (109.1 ± 0.63%, p < 0.05, compared with EA group, n = 7). EA did not decrease the gain of body weight in TRPV1 knock mice (107.94 ± 0.41% and 107.79 ± 1.04% for TRPV1−/− and TRPV1−/− with EA, respectively, p > 0.05). The visceral white adipose tissue (WAT) weight was lower in the EA group at 4 weeks after manipulation. Moreover, the protein levels of TRPV1, pPKA, pPKC and pERK were increased in the dorsal root ganglion (DRG) and spinal cord (SC) after EA treatment but not in the sham EA and TRPV1−/− mice. This study suggests that targeting TRPV1 is beneficial in controlling body weight and TRPV1-associated mechanisms in mice.
Acetylation of glucokinase regulatory protein decreases glucose metabolism by suppressing glucokinase activity
Authors: Park Joo-Man , Kim Tae-Hyun , Jo Seong-Ho , Kim Mi-Young , Ahn Yong-Ho 
Published: December 2015

AbstractGlucokinase (GK), mainly expressed in the liver and pancreatic β-cells, is critical for maintaining glucose homeostasis. GK expression and kinase activity, respectively, are both modulated at the transcriptional and post-translational levels. Post-translationally, GK is regulated by binding the glucokinase regulatory protein (GKRP), resulting in GK retention in the nucleus and its inability to participate in cytosolic glycolysis. Although hepatic GKRP is known to be regulated by allosteric mechanisms, the precise details of modulation of GKRP activity, by post-translational modification, are not well known. Here, we demonstrate that GKRP is acetylated at Lys5 by the acetyltransferase p300. Acetylated GKRP is resistant to degradation by the ubiquitin-dependent proteasome pathway, suggesting that acetylation increases GKRP stability and binding to GK, further inhibiting GK nuclear export. Deacetylation of GKRP is effected by the NAD+-dependent, class III histone deacetylase SIRT2, which is inhibited by nicotinamide. Moreover, the livers of db/db obese, diabetic mice also show elevated GKRP acetylation, suggesting a broader, critical role in regulating blood glucose. Given that acetylated GKRP may affiliate with type-2 diabetes mellitus (T2DM), understanding the mechanism of GKRP acetylation in the liver could reveal novel targets within the GK-GKRP pathway, for treating T2DM and other metabolic pathologies.
Spliced leader RNA trans-splicing discovered in copepods
Authors: Yang Feifei , Xu Donghui , Zhuang Yunyun , Yi Xiaoyan , Huang Yousong , Chen Hongju , Lin Senjie , Campbell David A. , Sturm Nancy R. , Liu Guangxing , Zhang Huan 
Published: December 2015

AbstractCopepods are one of the most abundant metazoans in the marine ecosystem, constituting a critical link in aquatic food webs and contributing significantly to the global carbon budget, yet molecular mechanisms of their gene expression are not well understood. Here we report the detection of spliced leader (SL) trans-splicing in calanoid copepods. We have examined nine species of wild-caught copepods from Jiaozhou Bay, China that represent the major families of the calanoids. All these species contained a common 46-nt SL (CopepodSL). We further determined the size of CopepodSL precursor RNA (slRNA; 108-158 nt) through genomic analysis and 3′-RACE technique, which was confirmed by RNA blot analysis. Structure modeling showed that the copepod slRNA folded into typical slRNA secondary structures. Using a CopepodSL-based primer set, we selectively enriched and sequenced copepod full-length cDNAs, which led to the characterization of copepod transcripts and the cataloging of the complete set of 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for a single copepod species. We uncovered the SL trans-splicing in copepod natural populations and demonstrated that CopepodSL was a sensitive and specific tool for copepod transcriptomic studies at both the individual and population levels and that it would be useful for metatranscriptomic analysis of copepods.
Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment
Authors: Liu Qingyun , Via Laura E. , Luo Tao , Liang Lili , Liu Xin , Wu Sufang , Shen Qingyu , Wei Wang , Ruan Xianglin , Yuan Xing , Zhang Guolong , Barry Clifton E. , Gao Qian 
Published: December 2015

AbstractGenetic heterogeneity of Mycobacterium tuberculosis (MTB) within a patient has caused great concern as it might complicate antibiotic treatment and cause treatment failure. But the extent of genetic heterogeneity has not been described in detail nor has its association with heterogeneous treatment response. During treatment of a subject with MDR-TB, serial computed tomography (CT) scans showed this subject had six anatomically discrete lesions and they responded to treatment with disparate kinetics, suggesting heterogeneous MTB population may exist. To investigate this heterogeneity, we applied deep whole genome sequencing of serial sputum isolates and discovered that the MTB population within this patient contained three dominant sub-clones differing by 10 ~ 14 single nucleotide polymorphisms (SNPs). Differential mutation patterns in known resistance alleles indicated these sub-clones had different drug-resistance patterns, which may explain the heterogeneous treatment responses between lesions. Our results showed clear evidence of branched microevolution of MTB in vivo, which led to a diverse bacterial community. These findings indicated that complex sub-populations of MTB might coexist within patient and contribute to lesions’ disparate responses to antibiotic treatment.
Quantum Zeno and Zeno-like effects in nitrogen vacancy centers
Authors: Qiu Jing , Wang Yang-Yang , Yin Zhang-Qi , Zhang Mei , Ai Qing , Deng Fu-Guo 
Published: December 2015

AbstractWe present a proposal to realize the quantum Zeno effect (QZE) and quantum Zeno-like effect (QZLE) in a proximal 13C nuclear spin by controlling a proximal electron spin of a nitrogen vacancy (NV) center. The measurement is performed by applying a microwave pulse to induce the transition between different electronic spin states. Under the practical experimental conditions, our calculations show that there exist both QZE and QZLE in a 13C nuclear spin in the vicinity of an NV center.
The significant association of Taq1A genotypes in DRD2/ANKK1 with smoking cessation in a large-scale meta-analysis of Caucasian populations
Authors: Ma Y , Wang M , Yuan W , Su K , Li M D 
Published: December 2015

AbstractAlthough a number of studies have analyzed the relation between the DRD2/ANKK1 gene Taq1A polymorphism and smoking cessation, the results remain controversial. The primary objective of the present study was to determine whether this variant indeed has any effect on smoking cessation. The A1-dominant model that considers A1/* (*=A1 or A2) and A2/A2 as two genotypes and compares their frequencies in current and former smokers was applied. A total of 22 studies with 11 075 subjects were included in the meta-analyses. Considering the potential influence of between-study heterogeneity, we conducted stratified meta-analyses with the Comprehensive Meta-Analysis statistical software (version 2.0). Results based on either cross-sectional or longitudinal studies consistently showed a statistically significant association between Taq1A A1/* genotypes and smoking cessation. Further, a more significant association of the variant with smoking cessation was detected when both types of studies were combined. However, there was marginal evidence of heterogeneity among studies (I2=33.9%; P=0.06). By excluding other ethnicities and subjects with cancer, the meta-analysis on the basis of 9487 Caucasians demonstrated that Taq1A A1/* genotypes indeed were significantly associated with smoking cessation under both the fixed- and random-effects models (pooled OR 1.22; 95% CI 1.11–1.34; P=3.9 × 10−5 for both models). No evidence of between-study heterogeneity or publication bias was observed. Thus, we conclude that the polymorphism of Taq1A has an important role in the process of abstaining from smoking, and smokers carrying A2/A2 genotype have a higher likelihood of smoking cessation than those who carry A1/A1 or A1/A2.
Emodin inhibits coxsackievirus B3 replication via multiple signalling cascades leading to suppression of translation
Authors: Zhang Huifang M. , Wang Fengping , Qiu Ye , Ye Xin , Hanson Paul , Shen Hongxing , Yang Decheng 
Published: December 2015

CVB3 (coxsackievirus 3) is a primary causal agent of viral myocarditis. Emodin is a natural compound isolated from certain plant roots. In the present study, we found that emodin inhibited CVB3 replication in vitro and in mice, and now we report an unrecognized mechanism by which emodin inhibits CVB3 replication through suppression of viral protein translation via multiple pathways. On one hand, emodin treatment inhibited Akt/mTOR (mammalian target of rapamycin) signalling and activated 4EBP1 (eukaryotic initiation factor 4R-binding protein 1), leading to suppression of translation initiation of ribosomal protein L32 encoded by a 5′-TOP (terminal oligopyrimidine) mRNA. On the other hand, emodin treatment differentially regulated multiple signal cascades, including Akt/mTORC1/p70S6K (p70 S6 kinase), ERK1/2 (extracellular-signal-regulated kinase 1/2)/p90RSK (p90 ribosomal S6 kinase) and Ca2+/calmodulin, leading to activation of eEF2K (eukaryotic elongation factor 2 kinase) and subsequent inactivation of eEF2 (eukaryotic elongation factor 2), resulting in inhibition of CVB3 VP1 (viral protein 1) synthesis. These data imply that eEF2K is a major factor mediating cross-talk of different arms of signalling cascades in this signal network. This notion was verified by either overexpressing eEF2K or treating the cells with siRNAs or eEF2K inhibitor A484954. We showed further that the emodin-induced decrease in p70S6K phosphorylation plays a dominant positive role in activation of eEF2K and in turn in conferring the antiviral effect of emodin. This finding was further solidified by expressing constitutively active and dominant-negative Akt. Collectively, our data reveal that emodin inhibits viral replication through impairing translational machinery and suppression of viral translation elongation.
Rudimentary empathy in macaques’ social decision-making
Authors: Ballesta Sebastien , Duhamel Jean-René 
Published: December 2015

Significance
We investigated nonhuman primate prosociality within a decision-making behavioral framework. Our results suggest that macaques have a concept of their peers’ well being. The strength and originality of our experimental design is in challenging monkeys with several decisions involving both pleasant and unpleasant outcomes to self and others, thus allowing us to evaluate social motivation in different contexts. Behavioral measures, such as empathic eye blinking and mutual looking, show that the degrees of empathy and of willingness to interact with peers differ among individuals. These differences were mainly consistent with the preexisting social bonds displayed within our group-housed monkeys. Our results thus provide evidence of partner-dependent behavioral mechanisms shaping primates’ social decisions.
How culture gets embrained: Cultural differences in event-related potentials of social norm violations
Authors: Mu Yan , Kitayama Shinobu , Han Shihui , Gelfand Michele J. 
Published: December 2015

Significance
Despite the fact that social norms are a fundamental aspect of human nature, there has been little research on how social norm violations are detected at the neurobiological level. Combining a new social norm violation paradigm with cross-cultural electroencephalography, we show consistent negative deflection of event-related potential around 400 ms (N400) over the central and parietal regions for both Americans and Chinese in detecting norm violations. However, the N400 at the frontal and temporal regions was evident only among Chinese, illustrating culture-specific neural substrates underlying detecting norm violations. Moreover, the frontal N400 was associated with greater cultural superiority and self-control, as well as lower creativity. The findings shed new light on the neurobiology of the detection of social norm violations.
Numb deficiency in cerebellar Purkinje cells impairs synaptic expression of metabotropic glutamate receptor and motor coordination
Authors: Zhou Liang , Yang Dong , Wang De-Juan , Xie Ya-Jun , Zhou Jia-Huan , Zhou Lin , Huang Hao , Han Shuo , Shao Chong-Yu , Li Hua-Shun , Zhu J. Julius , Qiu Meng-Sheng , De Zeeuw Chris I. , Shen Ying 
Published: December 2015

SignificanceProtein Numb controls cell fate by interacting with a number of signaling molecules, critical for maintaining neural stem cells and neuronal development in the central nervous system. However, the function of Numb has not been studied in mature neurons. Here, we found that deletion of Numb in cerebellar Purkinje cells causes deficits in motor learning, which can be ascribed to a reduced level of synaptic metabotropic glutamate 1 receptor (mGlu1). Although Numb deficiency does not alter the expression of mGlu1-associated proteins and activity-dependent plasticity of mGlu1, it inhibits intracellular trafficking of mGlu1. To our knowledge, our work is the first to demonstrate an important function of Numb in mature neurons.
Ventral and dorsal streams for choosing word order during sentence production
Authors: Thothathiri Malathi , Rattinger Michelle 
Published: December 2015

Significance
Languages allow multiple word orders for expressing the same meaning. Prior statistical experience with verbs in less-common sentence structures is known to facilitate subsequent use of those structures. To investigate how this is implemented in the brain, we trained participants in an artificial language and examined how they used that language to describe novel scenarios. Different verbs were associated with different word orders during training. Functional activation and connectivity patterns revealed that the choice of word order was supported by a ventral pathway for verbs that appeared in two competing orders, and dorsal pathways for verbs that appeared exclusively in the less-common order. Thus, the brain accomplishes the same language output via different routes, depending on past experience.
Discontinuous shear thickening in Brownian suspensions by dynamic simulation
Authors: Mari Romain , Seto Ryohei , Morris Jeffrey F. , Denn Morton M. 
Published: December 2015

Significance
Colloidal shear thickening is a phenomenon by which a dense mixture (or suspension) of sub–micrometer-sized particles in a fluid becomes more viscous when strained. It has important (mostly negative) consequences as dense suspensions are found in many industrial processes. Its origin is a long-standing unsolved problem in soft-matter physics. We perform dynamic simulations that show that the shear thickening may be explained as a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Our numerical data quantitatively match previous experimental data.
Accurate continuous geographic assignment from low- to high-density SNP data
Authors: Guillot Gilles , Jónsson Hákon , Hinge Antoine , Manchih Nabil , Orlando Ludovic 
Published: November 2015

Abstract
Motivation: Large-scale genotype datasets can help track the dispersal patterns of epidemiological outbreaks and predict the geographic origins of individuals. Such genetically-based geographic assignments also show a range of possible applications in forensics for profiling both victims and criminals, and in wildlife management, where poaching hotspot areas can be located. They, however, require fast and accurate statistical methods to handle the growing amount of genetic information made available from genotype arrays and next-generation sequencing technologies.
Results: We introduce a novel statistical method for geopositioning individuals of unknown origin from genotypes. Our method is based on a geostatistical model trained with a dataset of georeferenced genotypes. Statistical inference under this model can be implemented within the theoretical framework of Integrated Nested Laplace Approximation, which represents one of the major recent breakthroughs in statistics, as it does not require Monte Carlo simulations. We compare the performance of our method and an alternative method for geospatial inference, SPA in a simulation framework. We highlight the accuracy and limits of continuous spatial assignment methods at various scales by analyzing genotype datasets from a diversity of species, including Florida Scrub-jay birds Aphelocoma coerulescens, Arabidopsis thaliana and humans, representing 41–197,146 SNPs. Our method appears to be best suited for the analysis of medium-sized datasets (a few tens of thousands of loci), such as reduced-representation sequencing data that become increasingly available in ecology.
Availability and implementation: http://www2.imm.dtu.dk/∼gigu/Spasiba/
Contact: gilles.b.guillot@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Comment on: ‘ERGC: an efficient referential genome compression algorithm’
Authors: Deorowicz Sebastian , Grabowski Szymon , Ochoa Idoia , Hernaez Mikel , Weissman Tsachy 
Published: November 2015

Abstract
Motivation: Data compression is crucial in effective handling of genomic data. Among several recently published algorithms, ERGC seems to be surprisingly good, easily beating all of the competitors.
Results: We evaluated ERGC and the previously proposed algorithms GDC and iDoComp, which are the ones used in the original paper for comparison, on a wide data set including 12 assemblies of human genome (instead of only four of them in the original paper). ERGC wins only when one of the genomes (referential or target) contains mixed-cased letters (which is the case for only the two Korean genomes). In all other cases ERGC is on average an order of magnitude worse than GDC and iDoComp.
Contact: sebastian.deorowicz@polsl.pl, iochoa@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.