bluuebunny/crossref_metadata_2025_split huggingface dataset:
RETRACTED ARTICLE: Culture of previously uncultured members
of the human gut microbiota by culturomics
Authors: Lagier Jean-Christophe , Khelaifia Saber , Alou Maryam Tidjani , Ndongo Sokhna , Dione Niokhor , Hugon Perrine , Caputo Aurelia , Cadoret Frédéric , Traore Sory Ibrahima , Seck El Hadji , Dubourg Gregory , Durand Guillaume , Mourembou Gaël , Guilhot Elodie , Togo Amadou , Bellali Sara , Bachar Dipankar , Cassir Nadim , Bittar Fadi , Delerce Jérémy , Mailhe Morgane , Ricaboni Davide , Bilen Melhem , Dangui Nieko Nicole Prisca Makaya , Dia Badiane Ndeye Mery , Valles Camille , Mouelhi Donia , Diop Khoudia , Million Matthieu , Musso Didier , Abrahão Jônatas , Azhar Esam Ibraheem , Bibi Fehmida , Yasir Muhammad , Diallo Aldiouma , Sokhna Cheikh , Djossou Felix , Vitton Véronique , Robert Catherine , Rolain Jean Marc , La Scola Bernard , Fournier Pierre-Edouard , Levasseur Anthony , Raoult Didier 
Published: November 2016

Abstract
Metagenomics revolutionized the understanding of the relations among
the human microbiome, health and diseases, but generated a countless number of
sequences that have not been assigned to a known
microorganism1. The pure culture of prokaryotes, neglected in
recent decades, remains essential to elucidating the role of these
organisms2. We recently introduced microbial culturomics, a
culturing approach that uses multiple culture conditions and matrix-assisted laser
desorption/ionization–time of flight and 16S rRNA for
identification2. Here, we have selected the best culture conditions
to increase the number of studied samples and have applied new protocols
(fresh-sample inoculation; detection of microcolonies and specific cultures of
Proteobacteria and microaerophilic and halophilic prokaryotes) to address the
weaknesses of the previous studies3–5. We
identified 1,057 prokaryotic species, thereby adding 531 species to the human gut
repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1
archaea not previously isolated in humans, and 197 potentially new species. Genome
sequencing was performed on the new species. By comparing the results of the
metagenomic and culturomic analyses, we show that the use of culturomics allows the
culture of organisms corresponding to sequences previously not assigned. Altogether,
culturomics doubles the number of species isolated at least once from the human
gut.
The role of master clock stability in quantum information processing
Authors: Ball Harrison , Oliver William D , Biercuk Michael J 
Published: November 2016

AbstractExperimentalists seeking to improve the coherent lifetimes of quantum bits have generally focused on mitigating decoherence mechanisms through, for example, improvements to qubit designs and materials, and system isolation from environmental perturbations. In the case of the phase degree of freedom in a quantum superposition, however, the coherence that must be preserved is not solely internal to the qubit, but rather necessarily includes that of the qubit relative to the ‘master clock’ (e.g., a local oscillator) that governs its control system. In this manuscript, we articulate the impact of instabilities in the master clock on qubit phase coherence and provide tools to calculate the contributions to qubit error arising from these processes. We first connect standard oscillator phase-noise metrics to their corresponding qubit dephasing spectral densities. We then use representative lab-grade and performance-grade oscillator specifications to calculate operational fidelity bounds on trapped-ion and superconducting qubits with relatively slow and fast operation times. We discuss the relevance of these bounds for quantum error correction in contemporary experiments and future large-scale quantum information systems, and consider potential means to improve master clock stability.
Spatial and temporal dynamics of multidimensional well-being, livelihoods and ecosystem services in coastal Bangladesh
Authors: Adams Helen , Adger W. Neil , Ahmad Sate , Ahmed Ali , Begum Dilruba , Lázár Attila N. , Matthews Zoe , Rahman Mohammed Mofizur , Streatfield Peter Kim 
Published: November 2016

AbstractPopulations in resource dependent economies gain well-being from the natural environment, in highly spatially and temporally variable patterns. To collect information on this, we designed and implemented a 1586-household quantitative survey in the southwest coastal zone of Bangladesh. Data were collected on material, subjective and health dimensions of well-being in the context of natural resource use, particularly agriculture, aquaculture, mangroves and fisheries. The questionnaire included questions on factors that mediate poverty outcomes: mobility and remittances; loans and micro-credit; environmental perceptions; shocks; and women’s empowerment. The data are stratified by social-ecological system to take into account spatial dynamics and the survey was repeated with the same respondents three times within a year to incorporate seasonal dynamics. The dataset includes blood pressure measurements and height and weight of men, women and children. In addition, the household listing includes basic data on livelihoods and income for approximately 10,000 households. The dataset facilitates interdisciplinary research on spatial and temporal dynamics of well-being in the context of natural resource dependence in low income countries.
A variant reference data set for the Africanized honeybee, Apis mellifera
Authors: Kadri Samir M. , Harpur Brock A. , Orsi Ricardo O. , Zayed Amro 
Published: November 2016

AbstractThe Africanized honeybee (AHB) is a population of Apis mellifera found in the Americas. AHBs originated in 1956 in Rio Clara, Brazil where imported African A. m. scutellata escaped and hybridized with local populations of European A. mellifera. Africanized populations can now be found from Northern Argentina to the Southern United States. AHBs—often referred to as ‘Killer Bees’— are a major concern to the beekeeping industry as well as a model for the evolutionary genetics of colony defence. We performed high coverage pooled-resequencing of 360 diploid workers from 30 Brazilian AHB colonies using Illumina Hi-Seq (150 bp PE). This yielded a high density SNP data set with an average read depth at each site of 20.25 reads. With 3,606,720 SNPs and 155,336 SNPs within 11,365 genes, this data set is the largest genomic resource available for AHBs and will enable high-resolution studies of the population dynamics, evolution, and genetics of this successful biological invader, in addition to facilitating the development of SNP-based tools for identifying AHBs.
Cross-cultural dataset for the evolution of religion and morality project
Authors: Purzycki Benjamin Grant , Apicella Coren , Atkinson Quentin D. , Cohen Emma , McNamara Rita Anne , Willard Aiyana K. , Xygalatas Dimitris , Norenzayan Ara , Henrich Joseph 
Published: November 2016

AbstractA considerable body of research cross-culturally examines the evolution of religious traditions, beliefs and behaviors. The bulk of this research, however, draws from coded qualitative ethnographies rather than from standardized methods specifically designed to measure religious beliefs and behaviors. Psychological data sets that examine religious thought and behavior in controlled conditions tend to be disproportionately sampled from student populations. Some cross-national databases employ standardized methods at the individual level, but are primarily focused on fully market integrated, state-level societies. The Evolution of Religion and Morality Project sought to generate a data set that systematically probed individual level measures sampling across a wider range of human populations. The set includes data from behavioral economic experiments and detailed surveys of demographics, religious beliefs and practices, material security, and intergroup perceptions. This paper describes the methods and variables, briefly introduces the sites and sampling techniques, notes inconsistencies across sites, and provides some basic reporting for the data set.
The role of gibberellins in improving the resistance of tebuconazole-coated maize seeds to chilling stress by microencapsulation
Authors: Yang Lijuan , Yang Daibin , Yan Xiaojing , Cui Li , Wang Zhenying , Yuan Huizhu 
Published: November 2016

AbstractChilling stress during germination often causes severe injury. In the present study, maize seed germination and shoot growth under chilling stress were negatively correlated with the dose of tebuconazole in an exponential manner as predicted by the model Y = A + B × e(−x/k). Microencapsulation was an effective means of eliminating potential phytotoxic risk. The gibberellins (GAs) contents were higher after microencapsulation treatment than after conventional treatment when the dose of tebuconazole was higher than 0.12 g AI (active ingredient) kg−1 seed. Further analysis indicated that microencapsulation can stimulate ent-kaurene oxidase (KO) activity to some extent, whereas GA 3-oxidase (GA3ox) and GA 2-oxidase (GA2ox) activities remained similar to those in the control. Genes encoding GA metabolic enzymes exhibited different expression patterns. Transcript levels of ZmKO1 increased in the microcapsule treatments compared to the control. Even when incorporated into microcapsules, tebuconazole led to the upregulation of ZmGA3ox1 at doses of less than 0.12 g AI kg−1 seed and to the upregulation of ZmGA3ox2 when the dose was higher than 0.12 g AI kg−1 seed. With increasing doses of microencapsulated tebuconazole, the transcript levels of ZmGA2ox4, ZmGA2ox5 and ZmGA2ox6 exhibited upward trends, whereas the transcript levels of ZmGA2ox7 exhibited a downward trend.
Performance Improvement of AlN Crystal Quality Grown on Patterned Si(111) Substrate for Deep UV-LED Applications
Authors: Tran Binh Tinh , Maeda Noritoshi , Jo Masafumi , Inoue Daishi , Kikitsu Tomoka , Hirayama Hideki 
Published: November 2016

AbstractAn AlN template layer is required for growth of AlGaN-based deep ultraviolet light-emitting diodes (UV-LEDs). However, the crystal quality of AlN templates grown on both flat and patterned Si substrates has so far been insufficient for replacing templates grown on sapphire substrates. In this work, we grew a high-quality AlN template on 2 in. micro-circle-patterned Si substrate (mPSiS) with two different sizes and shapes through controlling the bias power of inductively coupled plasma (ICP) etching. The experimental results showed that the best AlN template was obtained on a large pattern size with a bow-angle shape and the template had X-ray rocking curves with full widths at half-maximum of 620 and 1141 arcsec for the (002) and (102) reflection planes. The threading dislocation density near surface of AlN template through transmission electron microscopy (TEM) estimation was in the order of 107 cm−2, which is the lowest dislocation density reported for a Si substrate to our knowledge. A strong single electroluminescence (EL) peak was also obtained for an AlGaN-based deep UV-LED grown on this template, means that it can be used for further developing high-efficiency deep UV-LEDs.
Optogenetic activation of serotonergic terminals facilitates GABAergic inhibitory input to orexin/hypocretin neurons
Authors: Chowdhury Srikanta , Yamanaka Akihiro 
Published: November 2016

AbstractOrexin/hypocretin neurons play a crucial role in the regulation of sleep/wakefulness, primarily in the maintenance of wakefulness. These neurons innervate wide areas of the brain and receive diverse synaptic inputs including those from serotonergic (5-HT) neurons in the raphe nucleus. Previously we showed that pharmacological application of 5-HT directly inhibited orexin neurons via 5-HT1A receptors. However, it was still unclear how 5-HT neurons regulated orexin neurons since 5-HT neurons contain not only 5-HT but also other neurotransmitters. To reveal this, we generated new triple transgenic mice in which orexin neurons express enhanced green fluorescent protein (EGFP) and 5-HT neurons express channelrhodopsin2 (ChR2). Immunohistochemical studies show that nerve endings of ChR2-expressing 5-HT neurons are in close apposition to EGFP-expressing orexin neurons in the lateral hypothalamic area. Using these mice, we could optogenetically activate 5-HT nerve terminals and record postsynaptic effects from orexin neurons. Activation of nerve terminals of 5-HT neurons directly inhibited orexin neurons via the 5HT1A receptor, and also indirectly inhibited orexin neurons by facilitating GABAergic inhibitory inputs without affecting glutamatergic inputs. Increased GABAergic inhibitory inputs in orexin neurons were confirmed by the pharmacological application of 5-HT. These results suggest that orexin neurons are inhibited by 5-HT neurons, primarily via 5-HT, in both direct and indirect manners.
Variant responses of tree seedling to seasonal drought stress along an elevational transect in tropical montane forests
Authors: Song Xiaoyang , Li Jieqiong , Zhang Wenfu , Tang Yong , Sun Zhenhua , Cao Min 
Published: November 2016

AbstractSeasonal drought is a common phenomenon in many forests predominated by monsoon climate. The impact of seasonal drought, however, may vary with elevations, and tree species of forests hence may differ in their response to elevations. In this study, we monitored the seasonal variation of seedling species composition, and their relative growth rate (RGR) along an elevational transect in tropical forests of southwest China for two years. We found tree seedling species richness declined with rising elevation. Seedling abundance and species richness increased significantly from dry season to rainy season. In dry season, RGR declined progressively from low to high elevational bands, while positive RGR occurred in each elevation in rainy season. We grouped seedling species into low and high elevation specialists based on their elevational distributions. Seasonal variance in soil moisture may lead to seasonal dynamics of seedling community in this area. Our results suggest that the observed change in local climate over the last 40 years tends to allow the tree species from high elevation to expand their distribution to the lower elevation, while the ranges of those at low elevations could be compressed or at the risk of extinction.
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks
Authors: Mei Suyu , Zhang Kun 
Published: November 2016

AbstractProtein-protein interaction (PPI) networks are naturally viewed as infrastructure to infer signalling pathways. The descriptors of signal events between two interacting proteins such as upstream/downstream signal flow, activation/inhibition relationship and protein modification are indispensable for inferring signalling pathways from PPI networks. However, such descriptors are not available in most cases as most PPI networks are seldom semantically annotated. In this work, we extend ℓ2-regularized logistic regression to the scenario of multi-label learning for predicting the activation/inhibition relationships in human PPI networks. The phenomenon that both activation and inhibition relationships exist between two interacting proteins is computationally modelled by multi-label learning framework. The problem of GO (gene ontology) sparsity is tackled by introducing the homolog knowledge as independent homolog instances. ℓ2-regularized logistic regression is accordingly adopted here to penalize the homolog noise and to reduce the computational complexity of the double-sized training data. Computational results show that the proposed method achieves satisfactory multi-label learning performance and outperforms the existing phenotype correlation method on the experimental data of Drosophila melanogaster. Several predictions have been validated against recent literature. The predicted activation/inhibition relationships in human PPI networks are provided in the supplementary file for further biomedical research.
Novel CD200 homologues iSEC1 and iSEC2 are gastrointestinal secretory cell-specific ligands of inhibitory receptor CD200R
Authors: Kojima Toshiyuki , Tsuchiya Kiichiro , Ikemizu Shinji , Yoshikawa Soichiro , Yamanishi Yoshinori , Watanabe Mamoru , Karasuyama Hajime 
Published: November 2016

AbstractCD200R is an inhibitory receptor expressed on myeloid cells and some lymphoid cells, and plays important roles in negatively regulating immune responses. CD200 is the only known ligand of CD200R and broadly distributed in a variety of cell types. Here we identified novel CD200 homologues, designated iSEC1 and iSEC2, that are expressed exclusively by secretory cell lineages in the gastrointestinal epithelium while authentic CD200 is expressed by none of epithelial cells including secretory cells. Both iSEC1 and iSEC2 could bind to CD200R but not other members of the CD200R family. Notably, CD200R expression was confined to intraepithelial lymphocytes (IELs) among cells in the gastrointestinal epithelium. Binding of iSEC1 to CD200R on IELs resulted in the suppression of cytokine production and cytolytic activity by activated IELs. Thus, iSEC1 is a previously unappreciated CD200R ligand with restricted expression in gastrointestinal secretory cells and may negatively regulate mucosal immune responses.
Big genomics and clinical data analytics strategies for precision cancer prognosis
Authors: Ow Ghim Siong , Kuznetsov Vladimir A. 
Published: November 2016

AbstractThe field of personalized and precise medicine in the era of big data analytics is growing rapidly. Previously, we proposed our model of patient classification termed Prognostic Signature Vector Matching (PSVM) and identified a 37 variable signature comprising 36 let-7b associated prognostic significant mRNAs and the age risk factor that stratified large high-grade serous ovarian cancer patient cohorts into three survival-significant risk groups. Here, we investigated the predictive performance of PSVM via optimization of the prognostic variable weights, which represent the relative importance of one prognostic variable over the others. In addition, we compared several multivariate prognostic models based on PSVM with classical machine learning techniques such as K-nearest-neighbor, support vector machine, random forest, neural networks and logistic regression. Our results revealed that negative log-rank p-values provides more robust weight values as opposed to the use of other quantities such as hazard ratios, fold change, or a combination of those factors. PSVM, together with the classical machine learning classifiers were combined in an ensemble (multi-test) voting system, which collectively provides a more precise and reproducible patient stratification. The use of the multi-test system approach, rather than the search for the ideal classification/prediction method, might help to address limitations of the individual classification algorithm in specific situation.
Micro-CT evaluation of apical delta morphologies in human teeth
Authors: Gao Xianhua , Tay Franklin R. , Gutmann James L. , Fan Wei , Xu Ting , Fan Bing 
Published: November 2016

AbstractThe apical delta is an intricate system within the root canal and incompletely debridement may affect the long-term prognosis of root canal therapy. The aim of the present study is to investigate the morphologic features of apical deltas in human teeth with micro-computed tomography (micro-CT) using a centreline-fitting algorithm. One hundred and thirty-six apical deltas were detected in 1400 teeth. Molars had more apical deltas (15.8%) than anterior teeth (6.3%). In maxillary molars, the mesiobuccal root had a significantly higher prevalence of apical delta than the palatal root or the distobuccal root. The median vertical distance of the apical delta was 1.87 mm with 13% more than 3 mm. The median diameter and length of the apical delta branches were 132.3 and 934.5 μm. Apical delta branches were not straight with cross-sectional shapes being non-circular. These morphological features of apical delta may complicate debridement of the infected root canal system.
Automatic detection and measurement of viral replication compartments by ellipse adjustment
Authors: Garcés Yasel , Guerrero Adán , Hidalgo Paloma , López Raul Eduardo , Wood Christopher D. , Gonzalez Ramón A. , Rendón-Mancha Juan Manuel 
Published: November 2016

AbstractViruses employ a variety of strategies to hijack cellular activities through the orchestrated recruitment of macromolecules to specific virus-induced cellular micro-environments. Adenoviruses (Ad) and other DNA viruses induce extensive reorganization of the cell nucleus and formation of nuclear Replication Compartments (RCs), where the viral genome is replicated and expressed. In this work an automatic algorithm designed for detection and segmentation of RCs using ellipses is presented. Unlike algorithms available in the literature, this approach is deterministic, automatic, and can adjust multiple RCs using ellipses. The proposed algorithm is non iterative, computationally efficient and is invariant to affine transformations. The method was validated over both synthetic images and more than 400 real images of Ad-infected cells at various timepoints of the viral replication cycle obtaining relevant information about the biogenesis of adenoviral RCs. As proof of concept the algorithm was then used to quantitatively compare RCs in cells infected with the adenovirus wild type or an adenovirus mutant that is null for expression of a viral protein that is known to affect activities associated with RCs that result in deficient viral progeny production.
Axl is required for TGF-β2-induced dormancy of prostate cancer cells in the bone marrow
Authors: Yumoto Kenji , Eber Matthew R. , Wang Jingcheng , Cackowski Frank C. , Decker Ann M. , Lee Eunsohl , Nobre Ana Rita , Aguirre-Ghiso Julio A. , Jung Younghun , Taichman Russell S. 
Published: November 2016

AbstractDisseminated prostate cancer (PCa) cells in the marrow survive for years without evidence of proliferation, while maintaining the capacity to develop into metastatic lesions. These dormant disseminated tumor cells (DTCs) may reside in close proximity to osteoblasts, while expressing high levels of Axl, one of the tyrosine kinase receptors for growth arrest specific 6 (Gas6). Yet how Axl regulates DTC proliferation in marrow remains undefined. Here, we explored the impact of the loss of Axl in PCa cells (PC3 and DU145) on the induction of their dormancy when they are co-cultured with a pre-osteoblastic cell line, MC3T3-E1. MC3T3-E1 cells dramatically decrease the proliferation of PCa cells, however this suppressive effect of osteoblasts is significantly reduced by the reduction of Axl expression in PCa cells. Interestingly, expression of both TGF-β and its receptors were regulated by Axl expression in PCa cells, while specific blockade of TGF-β signaling limited the ability of the osteoblasts to induce dormancy of PCa cells. Finally, we found that both Gas6 and Axl are required for TGF-β2-mediated cell growth suppression. Taken together, these data suggest that a loop between the Gas6/Axl axis and TGF-β2 signaling plays a significant role in the induction of PCa cell dormancy.