bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of plant defense responses to herbivores by simultaneous recognition of different herbivore-associated elicitors in rice
Authors: Shinya Tomonori , Hojo Yuko , Desaki Yoshitake , Christeller John T. , Okada Kazunori , Shibuya Naoto , Galis Ivan 
Published: September 2016

AbstractInduced plant defense responses against insect herbivores are triggered by wounding and/or perception of herbivore elicitors from their oral secretions (OS) and/or saliva. In this study, we analyzed OS isolated from two rice chewing herbivores, Mythimna loreyi and Parnara guttata. Both types of crude OS had substantial elicitor activity in rice cell system that allowed rapid detection of early and late defense responses, i.e. accumulation of reactive oxygen species (ROS) and defense secondary metabolites, respectively. While the OS from M. loreyi contained large amounts of previously reported insect elicitors, fatty acid-amino acid conjugates (FACs), the elicitor-active P. guttata’s OS contained no detectable FACs. Subsequently, elicitor activity associated with the high molecular mass fraction in OS of both herbivores was identified and shown to promote ROS and metabolite accumulations in rice cells. Notably, the application of N-linolenoyl-Gln (FAC) alone had only negligible elicitor activity in rice cells; however, the activity of isolated elicitor fraction was substantially promoted by this FAC. Our results reveal that plants integrate various independent signals associated with their insect attackers to modulate their defense responses and reach maximal fitness in nature.
Suppressor of cytokine signaling 3 plays an important role in porcine circovirus type 2 subclinical infection by downregulating proinflammatory responses
Authors: Zhu Xuejiao , Bai Juan , Liu Panrao , Wang Xianwei , Jiang Ping 
Published: September 2016

AbstractPorcine circovirus type 2 (PCV2) causes porcine circovirus-associated diseases and usually evokes a subclinical infection, without any obvious symptoms, in pigs. It remains unclear how PCV2 leads to a subclinical infection. In this study, we found that peripheral blood mononuclear cells (PBMCs) from PCV2-challenged piglets with no significant clinical symptoms exhibited increased expression of suppressor of cytokine signaling (SOCS) 3, but no significant changes in the expression of the proinflammatory cytokines interleukin (IL)-6 and tumor necrosis factor (TNF)-α; this differed from piglets that displayed significant clinical symptoms. IL-6- and TNF-α-mediated signalings were inhibited in PBMCs from subclinical piglets. Elevated SOCS3 levels inhibited IL-6- and TNF-α-mediated NF-kappa-B inhibitor alpha degradation in PBMCs and PK-15 cells. SOCS3 production was also increased in PCV2-infected PK-15 porcine kidney cells and IL-6 and TNF-α production that was induced by PCV2 in PK-15 cells was significantly increased when SOCS3 was silenced by a small interfering RNA. SOCS3 interacted with signal transducer and activator of transcription 3 and TNF-associated receptor-associated factor 2, suggesting mechanisms by which SOCS3 inhibits IL-6 and TNF-α signaling. We conclude that SOCS3 plays an important role in PCV2 subclinical infection by suppressing inflammatory responses in primary immune cells.
Consolidating soil carbon turnover models by improved estimates of belowground carbon input
Authors: Taghizadeh-Toosi Arezoo , Christensen Bent T. , Glendining Margaret , Olesen Jørgen E. 
Published: September 2016

AbstractWorld soil carbon (C) stocks are third only to those in the ocean and earth crust and represent twice the amount currently present in the atmosphere. Therefore, any small change in the amount of soil organic C (SOC) may affect carbon dioxide (CO2) concentrations in the atmosphere. Dynamic models of SOC help reveal the interaction among soil carbon systems, climate and land management and they are also frequently used to help assess SOC dynamics. Those models often use allometric functions to calculate soil C inputs in which the amount of C in both above and below ground crop residues are assumed to be proportional to crop harvest yield. Here we argue that simulating changes in SOC stocks based on C input that are proportional to crop yield is not supported by data from long-term experiments with measured SOC changes. Rather, there is evidence that root C inputs are largely independent of crop yield, but crop specific. We discuss implications of applying fixed belowground C input regardless of crop yield on agricultural greenhouse gas mitigation and accounting.
A new method for identifying causal genes of schizophrenia and anti-tuberculosis drug-induced hepatotoxicity
Authors: Huang Tao , Liu Cheng-Lin , Li Lin-Lin , Cai Mei-Hong , Chen Wen-Zhong , Xu Yi-Feng , O’Reilly Paul F. , Cai Lei , He Lin 
Published: September 2016

AbstractSchizophrenia (SCZ) may cause tuberculosis, the treatments for which can induce anti-tuberculosis drug-induced hepatotoxicity (ATDH) and SCZ-like disorders. To date, the causal genes of both SCZ and ATDH are unknown. To identify them, we proposed a new network-based method by integrating network random walk with restart algorithm, gene set enrichment analysis, and hypergeometric test; using this method, we identified 500 common causal genes. For gene validation, we created a regularly updated online database ATDH-SCZgenes and conducted a systematic meta-analysis of the association of each gene with either disease. Till now, onlyGSTM1andGSTT1have been well studied with respect to both diseases; and a total of 23 high-quality association studies were collected for the current meta-analysis validation. Finally, theGSTM1present genotype was confirmed to be significantly associated with both ATDH [Odds Ratio (OR): 0.71, 95% confidence interval (CI): 0.56–0.90,P = 0.005] and SCZ (OR: 0.78, 95% CI: 0.66–0.92,P = 0.004) according to the random-effect model. Furthermore, these significant results were supported by “moderate” evidence according to the Venice criteria. Our findings indicate thatGSTM1may be a causal gene of both ATDH and SCZ, although further validation pertaining to other genes, such asCYP2E1orDRD2, is necessary.
Inter-hemispheric functional dysconnectivity mediates the association of corpus callosum degeneration with memory impairment in AD and amnestic MCI
Authors: Qiu Yingwei , Liu Siwei , Hilal Saima , Loke Yng Miin , Ikram Mohammad Kamran , Xu Xin , Yeow Tan Boon , Venketasubramanian Narayanaswamy , Chen Christopher Li-Hsian , Zhou Juan 
Published: September 2016

AbstractEvidences suggested that both corpus callosum (CC) degeneration and alternations of homotopic inter-hemispheric functional connectivity (FC) are present in Alzheimer’s disease (AD). However, the associations between region-specific CC degeneration and homotopic inter-hemispheric FC and their relationships with memory deficits in AD remain uncharacterized. We hypothesized that selective CC degeneration is associated with memory impairment in AD and amnestic mild cognitive impairment (aMCI), which is mediated by homotopic inter-hemispheric functional dysconnectivity. Using structural magnetic resonance imaging (MRI) and task-free functional MRI, we assessed the CC volume and inter-hemispheric FC in 66 healthy controls, 41 aMCI and 41 AD. As expected, AD had CC degeneration and attenuated inter-hemispheric homotopic FC. Nevertheless, aMCI had relatively less severe CC degeneration (mainly in mid-anterior, central, and mid-posterior) and no reduction in inter-hemispheric homotopic FC. The degeneration of each CC sub-region was associated with specific inter-hemispheric homotopic functional disconnections in AD and aMCI. More importantly, impairment of inter-hemispheric homotopic FC partially mediated the association between CC (particularly the central and posterior parts) degeneration and memory deficit. Notably, these results remained after controlling for hippocampal volume. Our findings shed light on how CC degeneration and the related inter-hemispheric FC impact memory impairment in early stage of AD.
Li-ion Battery Separators, Mechanical Integrity and Failure Mechanisms Leading to Soft and Hard Internal Shorts
Authors: Zhang Xiaowei , Sahraei Elham , Wang Kai 
Published: September 2016

AbstractSeparator integrity is an important factor in preventing internal short circuit in lithium-ion batteries. Local penetration tests (nail or conical punch) often produce presumably sporadic results, where in exactly similar cell and test set-ups one cell goes to thermal runaway while the other shows minimal reactions. We conducted an experimental study of the separators under mechanical loading, and discovered two distinct deformation and failure mechanisms, which could explain the difference in short circuit characteristics of otherwise similar tests. Additionally, by investigation of failure modes, we provided a hypothesis about the process of formation of local “soft short circuits” in cells with undetectable failure. Finally, we proposed a criterion for predicting onset of soft short from experimental data.
Physapubescin selectively induces apoptosis in VHL-null renal cell carcinoma cells through down-regulation of HIF-2α and inhibits tumor growth
Authors: Chen Lixia , Xia Guiyang , Qiu Feng , Wu Chunli , Denmon Andria P. , Zi Xiaolin 
Published: September 2016

AbstractWe have purified physapubescin, a predominant steroidal lactone, from medicinal plant Physalis pubescens L., commonly named as “hairy groundcherry” in English and “Deng-Long-Cao” in Chinese. Von Hippel-Lindau (VHL)-null 786-O, RCC4 and A498 Renal Cell Carcinoma (RCC) cell lines expressing high levels of Hypoxia Inducible Factor (HIF)-2α are more sensitive to physapubescin-mediated apoptosis and growth inhibitory effect than VHL wild-type Caki-2 and ACHN RCC cell lines. Restoration of VHL in RCC4 cells attenuated the growth inhibitory effect of physapubescin. Physapubescin decreases the expression of HIF-2α and increases the expression of CCAAT/enhancer-binding protein homologus protein (CHOP), which leads to up-regulation of death receptor 5 (DR5), activation of caspase-8 and -3, cleavage of poly (ADP-Ribose) polymerase (PARP) and apoptosis. Under hypoxia conditions, the apoptotic and growth inhibitory effects of physapubescin are further enhanced. Additionally, physapubescin synergizes with TNF-related apoptosis-inducing ligand (TRAIL) for markedly enhanced induction of apoptosis in VHL-null 786-O cells but not in VHL wild-type Caki-2 cells. Physapubescin significantly inhibited in vivo angiogenesis in the 786-O xenograft. Physapubescin as a novel agent for elimination of VHL-null RCC cells via apoptosis is warranted for further investigation.
Performance of Verbal Fluency as an Endophenotype in Patients with Familial versus Sporadic Schizophrenia and Their Parents
Authors: Liang Sugai , Deng Wei , Wang Qiang , Ma Xiaohong , Li Mingli , Brown Matthew R. G. , Hu Xun , Li Xinmin , Greenshaw Andrew J. , Li Tao 
Published: September 2016

AbstractWhat’s the neurocognitive deficit as an endophenotype to familial schizophrenia? Here, we investigate the neurocognitive endophenotype in first-episode patients with familial schizophrenia (FS) and sporadic schizophrenia (SS), and their parents. 98 FS patients and their 105 parents; 190 SS patients and their 207 parents; 195 controls matched with patients, and 190 controls matched with the patients’ parents, were assessed with the short version of the Wechsler Adult Intelligence Scale-Revised in China (WAIS-RC), the immediate and delayed logical memory tests from the Wechsler Memory Scale-Revised in China (WMS-RC), the Verbal Fluency Test (VFT), the Trail Making Test Parts A and B-Modified (TMA, TMB-M), and the Modified Wisconsin Card Sorting Test (WCST-M). The results showed that with age, gender, and education as covariates, after controlling for false discovery rates, the FS group and their parent group performed worse than the SS group and their parent group on VFT. No significant differences were found for other neurocognitive tests between the FS and SS patient groups, and their respective parent groups. Our findings suggest the patients with familial and sporadic schizophrenia and their respective parent groups may have a different genetic predisposition in relation to a cognitive endophenotype.
Invasive stink bug favors naïve plants: Testing the role of plant geographic origin in diverse, managed environments
Authors: Martinson Holly M. , Bergmann Erik J. , Venugopal P. Dilip , Riley Christopher B. , Shrewsbury Paula M. , Raupp Michael J. 
Published: September 2016

AbstractWith the introduction and establishment of exotic species, most ecosystems now contain both native and exotic plants and herbivores. Recent research identifies several factors that govern how specialist herbivores switch host plants upon introduction. Predicting the feeding ecology and impacts of introduced generalist species, however, remains difficult. Here, we examine how plant geographic origin, an indicator of shared co-evolutionary history, influences patterns of host use by a generalist, invasive herbivore, while accounting for variation in plant availability. The brown marmorated stink bug, Halyomorpha halys, is a highly polyphagous Asian herbivore and an economically important invasive pest in North America and Europe. In visual surveys of 220 plant taxa in commercial nurseries in Maryland, USA, H. halys was more abundant on non-Asian plants and selected these over Asian plants. The relationship between the relative use of plants and their availability was strongly positive but depended also on plant origin at two of our three sites, where the higher relative use of non-Asian plants was greatest for highly abundant taxa. These results highlight the importance of considering both plant origin and relative abundance in understanding the selection of host plants by invasive generalist herbivores in diverse, natural and urban forests.
Silencing of SOX12 by shRNA suppresses migration, invasion and proliferation of breast cancer cells
Authors: Ding Hanzhi , Quan Hong , Yan Weiguo , Han Jing 
Published: September 2016

Sex determining region Y-box protein 12 (SOX12) is essential for embryonic development and cell-fate determination. The role of SOX12 in tumorigenesis of breast cancer is not well-understood. Here, we found that SOX12 mRNA expression was up-regulated in human breast cancer tissues. To clarify the roles of SOX12 in breast cancer, we used lentiviral shRNAs to suppress its expression in two breast cancer cells with relatively higher expression of SOX12 (BT474 and MCF-7). Our findings strongly suggested that SOX12 was critical for cell migration and invasion of breast cancer cells. We found that silencing of SOX12 significantly decreased the mRNA and protein levels of MMP9 and Twist, while notably increased E-cadherin. Moreover, SOX12 knockdown significantly inhibited the proliferation of breast cancer cells in vitro and the growth of xenograft tumours in vivo. Flow cytometry analysis revealed that breast cancer cells with SOX12 knockdown showed cell cycle arrest and decreased mRNA and protein levels of proliferating cell nuclear antigen (PCNA), CDK2 and Cyclin D1. Taken together, SOX12 plays an important role in growth inhibition through cell-cycle arrest, as well as migration and invasion of breast cancer cells.
Effects of N-glycosylation of the human cation channel TRPA1 on agonist-sensitivity
Authors: Egan Timothy J. , Acuña Mario A. , Zenobi-Wong Marcy , Zeilhofer Hanns Ulrich , Urech David 
Published: September 2016

Determining the functional significance of post-translational modifications advances our understanding of many broadly-expressed proteins, and particularly ion channels. The enzymes that catalyse these modifications are often expressed in a cell-type specific manner, resulting in considerable structural diversity among post-translationally modified proteins that are expressed across a variety of cell types. TRP channels exhibit notably variable behaviour between cell types in vitro and in vivo, and they are frequently modified with N-glycans that contribute to protein function. TRPA1 possesses two putative N-linked glycosylation sites at Asn747 and Asn753 that have not yet been studied in detail. In the present study, we show that both of these sites can be modified with an N-glycan and that the glycan at position Asn747 modulates agonist-sensitivity of TRPA1 in vitro. Additionally, we found that N-glycosylation also modulates cooperative effects of temperature and the agonist cinnamaldehyde (CA) on TRPA1 channel activation. Collectively, these findings suggest a dynamic role played by the N-glycosylation of human TRPA1. They also provide further evidence of the versatility of N-glycans and will assist in efforts to fully understand the complex regulation of TRPA1 activity.
School tracking, educational mobility and inequality in German secondary education: developments across cohorts
Authors: Schindler Steffen 
Published: September 2016

ABSTRACT
Secondary education is associated with a comparatively high level of inequality in Germany. This has often been attributed to the early ability-based between-school tracking in the German school system. However, as yet there has been no empirical evaluation of the actual impact of initial track placement on social inequality in final school attainment. Since educational reforms in the 1960s increased educational mobility after track placement, it can be expected that initial track allocation has become less important for the process of secondary educational attainment and the inequalities therein. By drawing on longitudinal life-course data for different birth cohorts from the 1930s to the 1980s, this paper analyses temporal developments in the connections between track placement, educational mobility and social inequality in final school outcomes. The analyses reveal that the impact of track placement actually diminished for those cohorts exposed to the reformed school system. Instead, social inequalities in school attainment are increasingly influenced by processes of educational mobility after track allocation. Furthermore, the analyses show that developments in educational mobility have contributed more to declining inequalities in access to upper secondary education than changes of the selectivities in the transition to secondary education.
A unified model based multifactor dimensionality reduction framework for detecting gene–gene interactions
Authors: Yu Wenbao , Lee Seungyeoun , Park Taesung 
Published: September 2016

Abstract

Motivation
Gene–gene interaction (GGI) is one of the most popular approaches for finding and explaining the missing heritability of common complex traits in genome-wide association studies. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGI effects. However, there are several disadvantages of the existing MDR-based approaches, such as the lack of an efficient way of evaluating the significance of multi-locus models and the high computational burden due to intensive permutation. Furthermore, the MDR method does not distinguish marginal effects from pure interaction effects.

Methods
We propose a two-step unified model based MDR approach (UM-MDR), in which, the significance of a multi-locus model, even a high-order model, can be easily obtained through a regression framework with a semi-parametric correction procedure for controlling Type I error rates. In comparison to the conventional permutation approach, the proposed semi-parametric correction procedure avoids heavy computation in order to achieve the significance of a multi-locus model. The proposed UM-MDR approach is flexible in the sense that it is able to incorporate different types of traits and evaluate significances of the existing MDR extensions.

Results
The simulation studies and the analysis of a real example are provided to demonstrate the utility of the proposed method. UM-MDR can achieve at least the same power as MDR for most scenarios, and it outperforms MDR especially when there are some single nucleotide polymorphisms that only have marginal effects, which masks the detection of causal epistasis for the existing MDR approaches.

Conclusions
UM-MDR provides a very good supplement of existing MDR method due to its efficiency in achieving significance for every multi-locus model, its power and its flexibility of handling different types of traits.

Availability and implementation
A R package “umMDR” and other source codes are freely available at http://statgen.snu.ac.kr/software/umMDR/.

Contact
tspark@stats.snu.ac.kr

Supplementary information
Supplementary data are available at Bioinformatics online.
Gene-set association tests for next-generation sequencing data
Authors: Lee Jaehoon , Kim Young Jin , Lee Juyoung ,   T2D-Genes Consortium, Kim Bong-Jo , Lee Seungyeoun , Park Taesung 
Published: September 2016

Abstract

Motivation
Recently, many methods have been developed for conducting rare-variant association studies for sequencing data. These methods have primarily been based on gene-level associations but have not been proven to be as effective as expected. Gene-set-level tests have shown great advantages over gene-level tests in terms of power and robustness, because complex diseases are often caused by multiple genes that comprise of biological gene sets.

Results
Here, we propose several novel gene-set tests that employ rapid and efficient dimensionality reduction. The performance of these tests was investigated using extensive simulations and application to 1058 whole-exome sequences from a Korean population. We identified some known pathways and novel pathways whose rare or common variants are associated with elevated liver enzymes and replicated the results in an independent cohort.

Availability and Implementation
Source R code for our algorithm is freely available at http://statgen.snu.ac.kr/software/QTest.

Contact
tspark@stats.snu.ac.kr

Supplementary information
Supplementary data are available at Bioinformatics online.
Higher order methylation features for clustering and prediction in epigenomic studies
Authors: Kapourani Chantriolnt-Andreas , Sanguinetti Guido 
Published: September 2016

AbstractMotivationDNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the well-understood methylation-switch at CpG islands.ResultsHere, we use probabilistic machine learning to extract higher order features associated with the methylation profile across a defined region. These features quantitate precisely notions of shape of a methylation profile, capturing spatial correlations in DNA methylation across genomic regions. Using these higher order features across promoter-proximal regions, we are able to construct a powerful machine learning predictor of gene expression, significantly improving upon the predictive power of average DNA methylation levels. Furthermore, we can use higher order features to cluster promoter-proximal regions, showing that five major patterns of methylation occur at promoters across different cell lines, and we provide evidence that methylation beyond CpG islands may be related to regulation of gene expression. Our results support previous reports of a functional role of spatial correlations in methylation patterns, and provide a mean to quantitate such features for downstream analyses.Availability and Implementationhttps://github.com/andreaskapou/BPRMethContactG.Sanguinetti@ed.ac.ukSupplementary informationSupplementary data are available at Bioinformatics online.