bluuebunny/crossref_metadata_2025_split huggingface dataset:
An imputation platform to enhance integration of rice genetic resources
Authors: Wang Diane R. , Agosto-Pérez Francisco J. , Chebotarov Dmytro , Shi Yuxin , Marchini Jonathan , Fitzgerald Melissa , McNally Kenneth L. , Alexandrov Nickolai , McCouch Susan R. 
Published: August 2018

AbstractAs sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel. To address these challenges, we develop the Rice Imputation Server, a publicly available web application leveraging genetic information from a globally diverse rice reference panel assembled here. This resource allows researchers to benefit from increased marker density without needing to perform imputation on their own machines. We demonstrate improvements that imputed data provide to rice genome-wide association (GWA) results of grain amylose content and show that the major functional nucleotide polymorphism is tagged only in the imputed data set.
The sulfite oxidase Shopper controls neuronal activity by regulating glutamate homeostasis in Drosophila ensheathing glia
Authors: Otto Nils , Marelja Zvonimir , Schoofs Andreas , Kranenburg Holger , Bittern Jonas , Yildirim Kerem , Berh Dimitri , Bethke Maria , Thomas Silke , Rode Sandra , Risse Benjamin , Jiang Xiaoyi , Pankratz Michael , Leimkühler Silke , Klämbt Christian 
Published: August 2018

AbstractSpecialized glial subtypes provide support to developing and functioning neural networks. Astrocytes modulate information processing by neurotransmitter recycling and release of neuromodulatory substances, whereas ensheathing glial cells have not been associated with neuromodulatory functions yet. To decipher a possible role of ensheathing glia in neuronal information processing, we screened for glial genes required in the Drosophila central nervous system for normal locomotor behavior. Shopper encodes a mitochondrial sulfite oxidase that is specifically required in ensheathing glia to regulate head bending and peristalsis. shopper mutants show elevated sulfite levels affecting the glutamate homeostasis which then act on neuronal network function. Interestingly, human patients lacking the Shopper homolog SUOX develop neurological symptoms, including seizures. Given an enhanced expression of SUOX by oligodendrocytes, our findings might indicate that in both invertebrates and vertebrates more than one glial cell type may be involved in modulating neuronal activity.
In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer
Authors: Zagorac Ivana , Fernandez-Gaitero Sara , Penning Renske , Post Harm , Bueno Maria J. , Mouron Silvana , Manso Luis , Morente Manuel M. , Alonso Soledad , Serra Violeta , Muñoz Javier , Gómez-López Gonzalo , Lopez-Acosta Jose Francisco , Jimenez-Renard Veronica , Gris-Oliver Albert , Al-Shahrour Fatima , Piñeiro-Yañez Elena , Montoya-Suarez Jose Luis , Apala Juan V. , Moreno-Torres Amalia , Colomer Ramon , Dopazo Ana , Heck Albert J. R. , Altelaar Maarten , Quintela-Fandino Miguel 
Published: August 2018

AbstractTriple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, we use high-throughput phosphoproteomics to build a functional TNBC taxonomy. A cluster of 159 phosphosites is upregulated in relapsed cases of a training set (n = 34 patients), with 11 hyperactive kinases accounting for this phosphoprofile. A mass-spectrometry-to-immunohistochemistry translation step, assessing 2 independent validation sets, reveals 6 kinases with preserved independent prognostic value. The kinases split the validation set into two patterns: one without hyperactive kinases being associated with a >90% relapse-free rate, and the other one showing ≥1 hyperactive kinase and being associated with an up to 9.5-fold higher relapse risk. Each kinase pattern encompasses different mutational patterns, simplifying mutation-based taxonomy. Drug regimens designed based on these 6 kinases show promising antitumour activity in TNBC cell lines and patient-derived xenografts. In summary, the present study elucidates phosphosites and kinases implicated in TNBC and suggests a target-based clinical classification system for TNBC.
Systematic mapping of BCL-2 gene dependencies in cancer reveals molecular determinants of BH3 mimetic sensitivity
Authors: Soderquist Ryan S. , Crawford Lorin , Liu Esther , Lu Min , Agarwal Anika , Anderson Gray R. , Lin Kevin H. , Winter Peter S. , Cakir Merve , Wood Kris C. 
Published: August 2018

AbstractWhile inhibitors of BCL-2 family proteins (BH3 mimetics) have shown promise as anti-cancer agents, the various dependencies or co-dependencies of diverse cancers on BCL-2 genes remain poorly understood. Here we develop a drug screening approach to define the sensitivity of cancer cells from ten tissue types to all possible combinations of selective BCL-2, BCL-XL, and MCL-1 inhibitors and discover that most cell lines depend on at least one combination for survival. We demonstrate that expression levels of BCL-2 genes predict single mimetic sensitivity, whereas EMT status predicts synergistic dependence on BCL-XL+MCL-1. Lastly, we use a CRISPR/Cas9 screen to discover that BFL-1 and BCL-w promote resistance to all tested combinations of BCL-2, BCL-XL, and MCL-1 inhibitors. Together, these results provide a roadmap for rationally targeting BCL-2 family dependencies in diverse human cancers and motivate the development of selective BFL-1 and BCL-w inhibitors to overcome intrinsic resistance to BH3 mimetics.
Reconciling persistent and dynamic hypotheses of working memory coding in prefrontal cortex
Authors: Cavanagh Sean E. , Towers John P. , Wallis Joni D. , Hunt Laurence T. , Kennerley Steven W. 
Published: August 2018

AbstractCompeting accounts propose that working memory (WM) is subserved either by persistent activity in single neurons or by dynamic (time-varying) activity across a neural population. Here, we compare these hypotheses across four regions of prefrontal cortex (PFC) in an oculomotor-delayed-response task, where an intervening cue indicated the reward available for a correct saccade. WM representations were strongest in ventrolateral PFC neurons with higher intrinsic temporal stability (time-constant). At the population-level, although a stable mnemonic state was reached during the delay, this tuning geometry was reversed relative to cue-period selectivity, and was disrupted by the reward cue. Single-neuron analysis revealed many neurons switched to coding reward, rather than maintaining task-relevant spatial selectivity until saccade. These results imply WM is fulfilled by dynamic, population-level activity within high time-constant neurons. Rather than persistent activity supporting stable mnemonic representations that bridge subsequent salient stimuli, PFC neurons may stabilise a dynamic population-level process supporting WM.
Melting conditions in the modern Tibetan crust since the Miocene
Authors: Chen Jinyu , Gaillard Fabrice , Villaros Arnaud , Yang Xiaosong , Laumonier Mickael , Jolivet Laurent , Unsworth Martyn , Hashim Leïla , Scaillet Bruno , Richard Guillaume 
Published: August 2018

AbstractAbundant granitic rocks exposed in ancient mountain belts suggest that crustal melting plays a major role in orogenic processes. However, complex field relations and superposition of multiple tectonic events make it difficult to determine the role of melting in orogenesis. In contrast, geophysical measurements image present-day crustal conditions but cannot discriminate between partial melt and aqueous fluids. Here we connect pressure–temperature paths of Himalayan Miocene crustal rocks to the present-day conditions beneath the Tibetan plateau imaged with geophysical data. We use measurements of electrical conductivity to show that 4–16% water-rich melt is required to explain the crustal conductivity in the north-western Himalaya. In southern Tibet, higher melt fractions >30% reflect a crust that is either fluid-enriched (+1% H2O) or hotter (+100 °C) compared to the Miocene crust. These melt fractions are high enough for the partially molten rocks to be significantly weaker than the solid crust.
Mapping the elastic properties of two-dimensional MoS2 via bimodal atomic force microscopy and finite element simulation
Authors: Li Yuhao , Yu Chuanbin , Gan Yingye , Jiang Peng , Yu Junxi , Ou Yun , Zou Dai-Feng , Huang Cheng , Wang Jiahong , Jia Tingting , Luo Qian , Yu Xue-Feng , Zhao Huijuan , Gao Cun-Fa , Li Jiangyu 
Published: August 2018

AbstractElasticity is a fundamental mechanical property of two-dimensional (2D) materials, and is critical for their application as well as for strain engineering. However, accurate measurement of the elastic modulus of 2D materials remains a challenge, and the conventional suspension method suffers from a number of drawbacks. In this work, we demonstrate a method to map the in-plane Young’s modulus of mono- and bi-layer MoS2 on a substrate with high spatial resolution. Bimodal atomic force microscopy is used to accurately map the effective spring constant between the microscope tip and sample, and a finite element method is developed to quantitatively account for the effect of substrate stiffness on deformation. Using these methods, the in-plane Young’s modulus of monolayer MoS2 can be decoupled from the substrate and determined as 265 ± 13 GPa, broadly consistent with previous reports though with substantially smaller uncertainty. It is also found that the elasticity of mono- and bi-layer MoS2 cannot be differentiated, which is confirmed by the first principles calculations. This method provides a convenient, robust and accurate means to map the in-plane Young’s modulus of 2D materials on a substrate.
Microbiota dysbiosis and its pathophysiological significance in bowel obstruction
Authors: Hegde Shrilakshmi , Lin You-Min , Golovko George , Khanipov Kamil , Cong Yingzi , Savidge Tor , Fofanov Yuriy , Shi Xuan-Zheng 
Published: August 2018

AbstractBowel obstruction (OB) causes local and systemic dysfunctions. Here we investigated whether obstruction leads to alterations in microbiota community composition and total abundance, and if so whether these changes contribute to dysfunctions in OB. Partial colon obstruction was maintained in rats for 7 days. The mid colon and its intraluminal feces - proximal to the obstruction - were studied. OB did not cause bacterial overgrowth or mucosa inflammation, but induced profound changes in fecal microbiota composition and diversity. At the phylum level, the 16S rRNA sequencing showed a significant decrease in the relative abundance of Firmicutes with corresponding increases in Proteobacteria and Bacteroidetes in OB compared with sham controls. Daily treatment using broad spectrum antibiotics dramatically reduced total bacterial abundance, but increased the relative presence of Proteobacteria. Antibiotics eliminated viable bacteria in the spleen and liver, but not in the mesentery lymph node in OB. Although antibiotic treatment decreased muscle contractility in sham rats, it had little effect on OB-associated suppression of muscle contractility or inflammatory changes in the muscle layer. In conclusion, obstruction leads to marked dysbiosis in the colon. Antibiotic eradication of microbiota had limited effects on obstruction-associated changes in inflammation, motility, or bacterial translocation.
Genetic polymorphisms of GZMB and vitiligo: A genetic association study based on Chinese Han population
Authors: Xu Meifeng , Liu Yan , Liu Yale , Li Xiaoli , Chen Gang , Dong Wei , Xiao Shengxiang 
Published: August 2018

AbstractVitiligo is a skin disease that affects 1% of the population worldwide. Both environmental and genetic factors contribute to the risk of vitiligo.GZMBencodes the enzyme Granzyme B, which plays an important role in cytotoxic T cell-induced apoptosis, and it has been considered one of the candidate genes for vitiligo because of its connections with human immune system. Overall, 3,120 study subjects with Chinese Han ancestry were recruited, and 15 pre-selected SNPs ofGZMBwere genotyped. Genetic association analyses were performed to evaluate the genetic risk of these SNPs to vitiligo. Further bioinformatic analyses were conducted to examine the potential biological function of targeted SNPs. The SNP rs8192917, a non-synonymous coding SNP, was identified to be significantly associated with the disease status of vitiligo, with OR = 1.39 andP = 1.92 × 10−8. Differences in the association signal can be observed in the stratification analyses of multiple clinical variables. Our positive results provide additional supportive evidence thatGZMBgene is an important locus for vitiligo in Han Chinese population.
A common polymorphism of COMT was associated with symptomatic lumbar disc herniation based on a large sample with Chinese Han ancestry
Authors: Liu Hongliang , Zhao Hongmou , Li Zhong , Xue Hanzhong , Lu Jun , Ma Wei 
Published: August 2018

AbstractLumbar disc herniation (LDH) is a common spine disease characterized by a tear in the disc ring and bulges out at the soft portion. COMT is a protein coding gene located at 22q11.21, and its gene product is a major mammalian enzyme involved in the degradation of catecholamines. A total of 2,678 study subjects with Chinese Han ancestry were recruited and 15 SNPs were selected for genotyping in our study subjects. A synonymous coding SNP, rs4633, was identified to be significantly associated with the disease status of LDH after adjusting for BMI (OR = 0.76, P = 4.83 × 10−5). This SNP was also identified to be significantly associated with COMT gene expression in three types of human tissues. Minor alleles of rs4633 (T) increased the expression of COMT in these 3 tissues. We have identified a significant SNP of COMT, rs4633, which is associated with symptomatic LDH in a large Chinese Han-based sample of the study subjects. This significant finding is further replicated by haplotypic analysis. Evidence from bioinformatics analyses have shown that rs4633 is also significantly associated with the gene expression of COMT. Our findings provide additional supportive evidence for an important role of COMT gene in the symptomatic LDH susceptibility.
Assessing Radiation Hardness of Silicon Photonic Sensors
Authors: Ahmed Zeeshan , Cumberland Lonnie T. , Klimov Nikolai N. , Pazos Ileana M. , Tosh Ronald E. , Fitzgerald Ryan 
Published: August 2018

AbstractIn recent years, silicon photonic platforms have undergone rapid maturation enabling not only optical communication but complex scientific experiments ranging from sensors applications to fundamental physics investigations. There is considerable interest in deploying photonics-based communication and science instruments in harsh environments such as outer space, where radiation damage is a significant concern. In this study, we have examined the impact of cobalt-60 γ-ray radiation up to 1 megagray (MGy) absorbed dose on silicon photonic devices. We do not find any systematic impact of radiation on passivated devices, indicating the durability of passivated silicon devices under harsh conditions.
Non-parametric detection of atmospheric radon concentration anomalies related to earthquakes
Authors: Iwata Daichi , Nagahama Hiroyuki , Muto Jun , Yasuoka Yumi 
Published: August 2018

AbstractAnomalous phenomena related to earthquakes have been studied to aid in the forecasting of large earthquakes. Radon (222Rn) concentration changes are known to be one of those phenomena. Many studies have quantified radon anomalies to identify physical aspects of radon emanations related to earthquakes. Here, we apply singular spectrum transformation, non-parametric analysis to estimate change points in time series, to atmospheric radon concentration. From 10 years of data from continuous observation of the atmospheric radon concentration over northeastern Japan and Hokkaido, we identify anomalies in the atmospheric radon concentration related to the moment releases of large earthquakes. Compared with a conventional model-based method, the singular spectrum transformation method identifies more anomalies. Moreover, we also find that change points in the atmospheric radon concentration prior to the 2011 Tohoku-Oki earthquake (Mw 9.0; 11 Mar. 2011, N38.1°, E142.9°) coincided with periods of other anomalous precursory phenomena. Our results indicate that singular spectrum transformation can be used to detect anomalies in atmospheric radon concentration related to the occurrences of large earthquakes.
Synergistic effect of land-use and vegetation greenness on vulture nestling body condition in arid ecosystems
Authors: Santangeli Andrea , Spiegel Orr , Bridgeford Peter , Girardello Marco 
Published: August 2018

AbstractClimate-driven environmental change and land-use change often interact in their impact on biodiversity, but these interactions have received little scientific attention. Here we study the effects of climate-driven environmental variation (i.e. vegetation greenness) and land-use (protected versus unprotected areas) on body condition of vulture nestlings in savannah landscapes. We combine ringing data on nestling measurements of two vultures (lappet-faced and African white-backed vulture) with land-use and environmental variables. We show that body condition of white-backed vulture nestlings decreased through the study period and was lowest inside protected areas. For the lappet-faced vulture, nestling condition was improved during harsh years with lower than average vegetation greenness assumed to result in increased ungulate mortality, but only within protected areas. Such interaction was not tested for the white-backed vulture due to collinearity. The species-specific effects of land-use and vegetation greenness on nestling condition of the two sympatric vulture species likely stem from their different life-histories, diet preferences and foraging behaviour. While translation of current findings on nestling conditions to their possible influence on population demography and species persistence require further studies, our findings demonstrate how environmental change may trigger selective bottom-up ecosystem responses in arid environments under global change.
The phylogenetic relationships and species richness of host-specific Dactylogyrus parasites shaped by the biogeography of Balkan cyprinids
Authors: Benovics Michal , Desdevises Yves , Vukić Jasna , Šanda Radek , Šimková Andrea 
Published: August 2018

AbstractParasites exhibiting a high degree of host specificity are expected to be intimately associated with their hosts. Therefore, the evolution of host-specific parasites is at least partially shaped by the evolutionary history and distribution of such hosts. Gill ectoparasites of Dactylogyrus (Monogenea) are specific to cyprinid fish. In the present study, we investigated the evolutionary history of 47 Dactylogyrus species from the Balkan Peninsula, the Mediteranean region exhibiting the highest cyprinid diversity in Europe, and from central European cyprinids. Phylogenetic analyses revealed four well-supported clades of endemic and non-endemic Dactylogyrus spp. with four basal taxa. Endemic cyprinids with a limited distribution range were parasitized by endemic Dactylogyrus species, but some of them shared several Dactylogyrus species with central European cyprinids. Species delimitation analyses based on molecular data suggest that Dactylogyrus diversity is higher than that defined from morphology. Some endemic cyprinid species harboured Dactylogyrus species of different origins, this probably resulting from multiple host switching. Our results support the view that the evolution of Dactylogyrus in the Balkans has been influenced not only by the historical dispersion and distribution of their cyprinid hosts, but also by recent contacts of non-native cyprinid species with endemic cyprinid fauna in this region.
Modified RNA triplexes: Thermodynamics, structure and biological potential
Authors: Szabat Marta , Kierzek Elzbieta , Kierzek Ryszard 
Published: August 2018

AbstractThe occurrence of triplexesin vivohas been well documented and is determined by the presence of long homopurine-homopyrimidine tracts. The formation of these structures is the result of conformational changes that occur in the duplex, which allow the binding of a third strand within the major groove of the helix. Formation of these noncanonical forms by introducing synthetic triplex-forming oligonucleotides (TFOs) into the cell may have applications in molecular biology, diagnostics and therapy. This study focused on the formation of RNA triplexes as well as their thermal stability and biological potential in theHeLacell line. Thermodynamics studies revealed that the incorporation of multiple locked nucleic acid (LNA) and 2-thiouridine (2-thioU) residues increased the stability of RNA triplexes. These data suggest that the number and position of the modified nucleotides within TFOs significantly stabilize the formed structures. Moreover, specificity of the interactions between the modified TFOs and the RNA hairpin was characterized using electrophoretic mobility-shift assay (EMSA), and triplex dissociation constants have been also determined. Finally, through quantitative analysis of GFP expression, the triplex structures were shown to regulate GFP gene silencing. Together, our data provide a first glimpse into the thermodynamic, structural and biological properties of LNA- and 2-thioU modified RNA triplexes.
The use of social features in mobile health interventions to promote physical activity: a systematic review
Authors: Tong Huong Ly , Laranjo Liliana 
Published: August 2018

AbstractMobile health (mHealth) technologies have increasingly been used in interventions to promote physical activity (PA), yet, they often have high attrition rates. Integrating social features into mHealth has the potential to engage users; however, little is known about the efficacy and user engagement of such interventions. Thus, the aim of this systematic review was to characterize and evaluate the impact of interventions integrating social features in mHealth interventions to promote PA. During database screening, studies were included if they involved people who were exposed to a mHealth intervention with social features, to promote PA. We conducted a narrative synthesis of included studies and a meta-analysis of randomized controlled trials (RCTs). Nineteen studies were included: 4 RCTs, 10 quasi-experimental, and 5 non-experimental studies. Most experimental studies had retention rates above 80%, except two. Social features were often used to provide social support or comparison. The meta-analysis found a non-significant effect on PA outcomes [standardized difference in means = 0.957, 95% confidence interval −1.09 to 3.00]. Users’ preferences of social features were mixed: some felt more motivated by social support and competition, while others expressed concerns about comparison, indicating that a one-size-fits-all approach is insufficient. In summary, this is an emerging area of research, with limited evidence suggesting that social features may increase user engagement. However, due to the quasi-experimental and multi-component nature of most studies, it is difficult to determine the specific impact of social features, suggesting the need for more robust studies to assess the impact of different intervention components.