bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq
Authors: Castro Joana , França Angela , Bradwell Katie R. , Serrano Myrna G. , Jefferson Kimberly K. , Cerca Nuno 
Published: January 2017

AbstractBacterial vaginosis is the most common gynecological disorder affecting women of reproductive age. Bacterial vaginosis is frequently associated with the development of a Gardnerella vaginalis biofilm. Recent data indicates that G. vaginalis biofilms are more tolerant to antibiotics and are able to incorporate other bacterial vaginosis -associated species, yielding a multi-species biofilm. However, despite its apparent role in bacterial vaginosis, little is known regarding the molecular determinants involved in biofilm formation by G. vaginalis. To gain insight into the role of G. vaginalis in the pathogenesis of bacterial vaginosis, we carried out comparative transcriptomic analysis between planktonic and biofilm phenotypes, using RNA-sequencing. Significant differences were found in the expression levels of 815 genes. A detailed analysis of the results obtained was performed based on direct and functional gene interactions. Similar to other bacterial species, expression of genes involved in antimicrobial resistance were elevated in biofilm cells. In addition, our data indicate that G. vaginalis biofilms assume a characteristic response to stress and starvation conditions. The abundance of transcripts encoding proteins involved in glucose and carbon metabolism was reduced in biofilms. Surprisingly, transcript levels of vaginolysin were reduced in biofilms relative to planktonic cultures. Overall, our data revealed that gene-regulated processes in G. vaginalis biofilms resulted in a protected form of bacterial growth, characterized by low metabolic activity. This phenotype may contribute towards the chronic and recurrent nature of bacterial vaginosis. This suggests that G. vaginalis is capable of drastically adjusting its phenotype through an extensive change of gene expression.
Scalable ion–photon quantum interface based on integrated diffractive mirrors
Authors: Ghadimi Moji , Blūms Valdis , Norton Benjamin G. , Fisher Paul M. , Connell Steven C. , Amini Jason M. , Volin Curtis , Hayden Harley , Pai Chien-Shing , Kielpinski David , Lobino Mirko , Streed Erik W. 
Published: January 2017

AbstractQuantum networking links quantum processors through remote entanglement for distributed quantum information processing and secure long-range communication. Trapped ions are a leading quantum information processing platform, having demonstrated universal small-scale processors and roadmaps for large-scale implementation. Overall rates of ion–photon entanglement generation, essential for remote trapped ion entanglement, are limited by coupling efficiency into single mode fibers and scaling to many ions. Here, we show a microfabricated trap with integrated diffractive mirrors that couples 4.1(6)% of the fluorescence from a174Yb+ion into a single mode fiber, nearly triple the demonstrated bulk optics efficiency. The integrated optic collects 5.8(8)% of theπtransition fluorescence, images the ion with sub-wavelength resolution, and couples 71(5)% of the collected light into the fiber. Our technology is suitable for entangling multiple ions in parallel and overcomes mode quality limitations of existing integrated optical interconnects.
Unravelling socio-motor biomarkers in schizophrenia
Authors: Słowiński Piotr , Alderisio Francesco , Zhai Chao , Shen Yuan , Tino Peter , Bortolon Catherine , Capdevielle Delphine , Cohen Laura , Khoramshahi Mahdi , Billard Aude , Salesse Robin , Gueugnon Mathieu , Marin Ludovic , Bardy Benoit G. , di Bernardo Mario , Raffard Stephane , Tsaneva-Atanasova Krasimira 
Published: January 2017

AbstractWe present novel, low-cost and non-invasive potential diagnostic biomarkers of schizophrenia. They are based on the ‘mirror-game’, a coordination task in which two partners are asked to mimic each other’s hand movements. In particular, we use the patient’s solo movement, recorded in the absence of a partner, and motion recorded during interaction with an artificial agent, a computer avatar or a humanoid robot. In order to discriminate between the patients and controls, we employ statistical learning techniques, which we apply to nonverbal synchrony and neuromotor features derived from the participants’ movement data. The proposed classifier has 93% accuracy and 100% specificity. Our results provide evidence that statistical learning techniques, nonverbal movement coordination and neuromotor characteristics could form the foundation of decision support tools aiding clinicians in cases of diagnostic uncertainty.
Role of KCNB1 in the prognosis of gliomas and autophagy modulation
Authors: Wang Hao-Yuan , Wang Wen , Liu Yan-Wei , Li Ming-Yang , Liang Ting-Yu , Li Ji-Ye , Hu Hui-Min , Lu Yang , Yao Chen , Ye Yong-Yi , Wang Yong-Zhi , Zhang Shi-Zhong 
Published: January 2017

AbstractIncreasing evidence suggests that ion channel genes play an important role in the progression of gliomas. However, the mechanisms by which ion channel genes influence the progression of glioma are not fully understood. We identified KCNB1 as a novel ion gene, associated with malignant progression and favorable overall survival (OS) and progression-free survival (PFS) in glioma patients from three datasets (CGGA, GSE16011 and REMBRANDT). Moreover, we characterized a novel function of autophagy induction accompanied by increased apoptosis and reduced proliferation and invasion of glioma cells for KCNB1. KEGG pathway analysis and in vitro studies suggested that the ERK pathway is involved in KCNB1-mediated regulation of autophagy, which was confirmed by inhibition of KCNB1-induced autophagy by using a selective ERK1/2 inhibitor (U0126) or siERK1/2. In vivo studies showed that KCNB1 induced autophagy while inhibiting tumor growth and increasing survival. Overall, our studies define KCNB1 as a novel prognostic factor for gliomas that exerts its tumor suppressive function through autophagy induction.
A 4-study replication of the moderating effects of greed on socioeconomic status and unethical behaviour
Authors: Balakrishnan Anjana , Palma Paolo A. , Patenaude Joshua , Campbell Lorne 
Published: January 2017

AbstractFour replications of Piff and colleagues’ study examined the moderating effects of greed attitudes on the relationship between socio-economic status (SES) and unethical behaviour (Study 7). In the original study, the researchers found that both greed and SES predicted increased propensity to engage in unethical behavior. Furthermore, this association was moderated such that the effects of SES on unethical behaviour were no longer present in the greed prime condition versus the neutral condition. In replication 1 of the original study main effects of greed attitudes and SES were found, but no interaction was found. Main effects for greed emerged in replications 3 and 4. However no main effects for SES or interactions emerged for replications 2–4. A meta-analysis was conducted with all replications and the original study, and found no moderating effect of greed on the relationship between SES and unethical behavior.
High-throughput screening of inorganic compounds for the discovery of novel dielectric and optical materials
Authors: Petousis Ioannis , Mrdjenovich David , Ballouz Eric , Liu Miao , Winston Donald , Chen Wei , Graf Tanja , Schladt Thomas D. , Persson Kristin A. , Prinz Fritz B. 
Published: January 2017

AbstractDielectrics are an important class of materials that are ubiquitous in modern electronic applications. Even though their properties are important for the performance of devices, the number of compounds with known dielectric constant is on the order of a few hundred. Here, we use Density Functional Perturbation Theory as a way to screen for the dielectric constant and refractive index of materials in a fast and computationally efficient way. Our results constitute the largest dielectric tensors database to date, containing 1,056 compounds. Details regarding the computational methodology and technical validation are presented along with the format of our publicly available data. In addition, we integrate our dataset with the Materials Project allowing users easy access to material properties. Finally, we explain how our dataset and calculation methodology can be used in the search for novel dielectric compounds.
A longitudinal dataset of five years of public activity in the Scratch online community
Authors: Hill Benjamin Mako , Monroy-Hernández Andrés 
Published: January 2017

AbstractScratch is a programming environment and an online community where young people can create, share, learn, and communicate. In collaboration with the Scratch Team at MIT, we created a longitudinal dataset of public activity in the Scratch online community during its first five years (2007–2012). The dataset comprises 32 tables with information on more than 1 million Scratch users, nearly 2 million Scratch projects, more than 10 million comments, more than 30 million visits to Scratch projects, and more. To help researchers understand this dataset, and to establish the validity of the data, we also include the source code of every version of the software that operated the website, as well as the software used to generate this dataset. We believe this is the largest and most comprehensive downloadable dataset of youth programming artifacts and communication.
Effect of LPSO and SFs on microstructure evolution and mechanical properties of Mg-Gd-Y-Zn-Zr alloy
Authors: Xu Chao , Nakata Taiki , Qiao Xiaoguang , Zheng Mingyi , Wu Kun , Kamado Shigeharu 
Published: January 2017

AbstractHigh performance Mg-8.2Gd-3.8Y-1.0Zn-0.4Zr alloy with high strength and excellent ductility has been successfully developed by hot extrusion. The effect of plate-shaped long period stacking ordered (LPSO) phases and solute-segregated stacking faults (SFs) on the dynamically recrystallization (DRX) behavior was analyzed. The plate-shaped LPSO phases stimulate the DRX by particle stimulated nucleation mechanism, leading to higher DRX ratio and weaker basal texture. While for the alloy with dense fine SFs inside the original grains, discontinuous DRX initially occurs at the original grain boundaries, and the DRX is obviously restricted. Consequently, alloy containing dense SFs exhibits higher strength but lower ductility compared with alloy with plated-shaped LPSO phases.
The dynamic behaviors of complementary correlations under decoherence channels
Authors: Du Ming-Ming , Wang Dong , Ye Liu 
Published: January 2017

AbstractComplementary correlations can reveal the genuine quantum correlations present in a composite quantum system. Here, we explore an effective method to identify the entangled Bell diagonal states by means of Pearson correlation, one of the complementary correlations. Then, we extend this method to expose the dynamic behavior of complementary correlations under various kinds of decoherence channels. The sudden death and revival of entanglement can be explained by the idea of Pearson correlation. The threshold that is used to identify entanglement is proposed. Furthermore, we put forward a new method to expound the underlying physical mechanisms for which classical and quantum correlations suffer a sudden change in the decoherence process.
Exciton Emission Intensity Modulation of Monolayer MoS2 via Au Plasmon Coupling
Authors: Mukherjee B. , Kaushik N. , Tripathi Ravi P. N. , Joseph A. M. , Mohapatra P. K. , Dhar S. , Singh B. P. , Kumar G. V. Pavan , Simsek E. , Lodha S. 
Published: January 2017

AbstractModulation of photoluminescence of atomically thin transition metal dichalcogenide two-dimensional materials is critical for their integration in optoelectronic and photonic device applications. By coupling with different plasmonic array geometries, we have shown that the photoluminescence intensity can be enhanced and quenched in comparison with pristine monolayer MoS2. The enhanced exciton emission intensity can be further tuned by varying the angle of polarized incident excitation. Through controlled variation of the structural parameters of the plasmonic array in our experiment, we demonstrate modulation of the photoluminescence intensity from nearly fourfold quenching to approximately threefold enhancement. Our data indicates that the plasmonic resonance couples to optical fields at both, excitation and emission bands, and increases the spontaneous emission rate in a double spacing plasmonic array structure as compared with an equal spacing array structure. Furthermore our experimental results are supported by numerical as well as full electromagnetic wave simulations. This study can facilitate the incorporation of plasmon-enhanced transition metal dichalcogenide structures in photodetector, sensor and light emitter applications.
Analyzing historical land use changes using a Historical Land Use Reconstruction Model: a case study in Zhenlai County, northeastern China
Authors: Yang Yuanyuan , Zhang Shuwen , Liu Yansui , Xing Xiaoshi , de Sherbinin Alex 
Published: January 2017

AbstractHistorical land use information is essential to understanding the impact of anthropogenic modification of land use/cover on the temporal dynamics of environmental and ecological issues. However, due to a lack of spatial explicitness, complete thematic details and the conversion types for historical land use changes, the majority of historical land use reconstructions do not sufficiently meet the requirements for an adequate model. Considering these shortcomings, we explored the possibility of constructing a spatially-explicit modeling framework (HLURM: Historical Land Use Reconstruction Model). Then a three-map comparison method was adopted to validate the projected reconstruction map. The reconstruction suggested that the HLURM model performed well in the spatial reconstruction of various land-use categories, and had a higher figure of merit (48.19%) than models used in other case studies. The largest land use/cover type in the study area was determined to be grassland, followed by arable land and wetland. Using the three-map comparison, we noticed that the major discrepancies in land use changes among the three maps were as a result of inconsistencies in the classification of land-use categories during the study period, rather than as a result of the simulation model.
Identification and Characterization of a Plastidic Adenine Nucleotide Uniporter (OsBT1-3) Required for Chloroplast Development in the Early Leaf Stage of Rice
Authors: Hu Daoheng , Li Yang , Jin Wenbin , Gong Hanyu , He Qiong , Li Yangsheng 
Published: January 2017

AbstractChloroplast development is an important subject in botany. In this study, a rice (Oryza sativa) mutant exhibiting impairment in early chloroplast development (seedling leaf albino (sla)) was isolated from a filial generation via hybridization breeding. The sla mutant seedlings have an aberrant form of chloroplasts, which resulted in albinism at the first and second leaves; however, the leaf sheath was green. The mutant gradually turned green after the two-leaf stage, and the third leaf was a normal shade of green. Map-based cloning indicated that the gene OsBT1-3, which belongs to the mitochondrial carrier family (MCF), is responsible for the sla mutant phenotype. OsBT1-3 expression was high in the young leaves, decreased after the two-leaf stage, and was low in the sheath, and these findings are consistent with the recovery of a number of chloroplasts in the third leaf of sla mutant seedlings. The results also showed that OsBT1-3-yellow fluorescent protein (YFP) was targeted to the chloroplast, and a Western blot assay using a peptide-specific antibody indicated that OsBT1-3 localizes to the chloroplast envelope. We also demonstrated that OsBT1-3 functions as a unidirectional transporter of adenine nucleotides. Based on these findings, OsBT1-3 likely acts as a plastid nucleotide uniporter and is essential for chloroplast development in rice leaves at the young seedling stage.
Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder
Authors: Sun Jiajie , Zeng Bin , Chen Zujing , Yan Shijuan , Huang Wenjie , Sun Baoli , He Qian , Chen Xiaoyang , Chen Ting , Jiang Qingyan , Xi Qianyun , Zhang Yongliang 
Published: January 2017

AbstractMoringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera.
Exploring the dark foldable proteome by considering hydrophobic amino acids topology
Authors: Bitard-Feildel Tristan , Callebaut Isabelle 
Published: January 2017

AbstractThe protein universe corresponds to the set of all proteins found in all organisms. A way to explore it is by taking into account the domain content of the proteins. However, some part of sequences and many entire sequences remain un-annotated despite a converging number of domain families. The un-annotated part of the protein universe is referred to as the dark proteome and remains poorly characterized. In this study, we quantify the amount of foldable domains within the dark proteome by using the hydrophobic cluster analysis methodology. These un-annotated foldable domains were grouped using a combination of remote homology searches and domain annotations, leading to define different levels of darkness. The dark foldable domains were analyzed to understand what make them different from domains stored in databases and thus difficult to annotate. The un-annotated domains of the dark proteome universe display specific features relative to database domains: shorter length, non-canonical content and particular topology in hydrophobic residues, higher propensity for disorder, and a higher energy. These features make them hard to relate to known families. Based on these observations, we emphasize that domain annotation methodologies can still be improved to fully apprehend and decipher the molecular evolution of the protein universe.
Modulation of actin dynamics as potential macrophage subtype-targeting anti-tumour strategy
Authors: Pergola Carlo , Schubert Katrin , Pace Simona , Ziereisen Jana , Nikels Felix , Scherer Olga , Hüttel Stephan , Zahler Stefan , Vollmar Angelika M. , Weinigel Christina , Rummler Silke , Müller Rolf , Raasch Martin , Mosig Alexander , Koeberle Andreas , Werz Oliver 
Published: January 2017

AbstractTumour-associated macrophages mainly comprise immunosuppressive M2 phenotypes that promote tumour progression besides anti-tumoural M1 subsets. Selective depletion or reprogramming of M2 may represent an innovative anti-cancer strategy. The actin cytoskeleton is central for cellular homeostasis and is targeted for anti-cancer chemotherapy. Here, we show that targeting G-actin nucleation using chondramide A (ChA) predominantly depletes human M2 while promoting the tumour-suppressive M1 phenotype. ChA reduced the viability of M2, with minor effects on M1, but increased tumour necrosis factor (TNF)α release from M1. Interestingly, ChA caused rapid disruption of dynamic F-actin filaments and polymerization of G-actin, followed by reduction of cell size, binucleation and cell division, without cellular collapse. In M1, but not in M2, ChA caused marked activation of SAPK/JNK and NFκB, with slight or no effects on Akt, STAT-1/-3, ERK-1/2, and p38 MAPK, seemingly accounting for the better survival of M1 and TNFα secretion. In a microfluidically-supported human tumour biochip model, circulating ChA-treated M1 markedly reduced tumour cell viability through enhanced release of TNFα. Together, ChA may cause an anti-tumoural microenvironment by depletion of M2 and activation of M1, suggesting induction of G-actin nucleation as potential strategy to target tumour-associated macrophages in addition to neoplastic cells.
Rapid Sputum Multiplex Detection of the M. tuberculosis Complex (MTBC) and Resistance Mutations for Eight Antibiotics by Nucleotide MALDI-TOF MS
Authors: Su Kang-Yi , Yan Bo-Shiun , Chiu Hao-Chieh , Yu Chong-Jen , Chang So-Yi , Jou Ruwen , Liu Jia-Long , Hsueh Po-Ren , Yu Sung-Liang 
Published: January 2017

AbstractThe increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) adds further urgency for rapid and multiplex molecular testing to identify the MTB complex and drug susceptibility directly from sputum for disease control. A nucleotide matrix-assisted-laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based assay was developed to identify MTB (MTBID panel) and 45 chromosomal mutations for resistance to eight antibiotics (MTBDR panel). We conducted a 300 case trial from outpatients to evaluate this platform. An MTBID panel specifically identified MTB with as few as 10 chromosome DNA copies. The panel was 100% consistent with an acid-fast stain and culture for MTB, nontuberculous mycobacteria, and non-mycobacteria bacteria. The MTBDR panel was validated using 20 known MDR-MTB isolates. In a 64-case double-blind clinical isolates test, the sensitivity and specificity were 83% and 100%, respectively. In a 300-case raw sputum trial, the MTB identification sensitivity in smear-negative cases using MALDI-TOF MS was better than the COBAS assay (61.9% vs. 46.6%). Importantly, the failure rate of MALDI-TOF MS was better than COBAS (11.3% vs. 26.3%). To the best of our knowledge, the test described herein is the only multiplex test that predicts resistance for up to eight antibiotics with both sensitivity and flexibility.
Critical scattering and incommensurate phase transition in antiferroelectric PbZrO3 under pressure
Authors: Burkovsky R. G. , Bronwald I. , Andronikova D. , Wehinger B. , Krisch M. , Jacobs J. , Gambetti D. , Roleder K. , Majchrowski A. , Filimonov A. V. , Rudskoy A. I. , Vakhrushev S. B. , Tagantsev A. K. 
Published: January 2017

AbstractAntiferroelectric lead zirconate is the key ingredient in modern ferroelectric and piezoelectric functional solid solutions. By itself it offers opportunities in new-type non-volatile memory and energy storage applications. A highly useful and scientifically puzzling feature of this material is the competition between the ferro- and antiferroelectric phases due to their energetic proximity, which leads to a challenge in understanding of the critical phenomena driving the formation of the antiferroelectric structure. We show that application of hydrostatic pressure drastically changes the character of critical lattice dynamics and enables the soft-mode-driven incommensurate phase transition sequence in lead zirconate. In addition to the long known cubic and antiferroelectric phases we identify the new non-modulated phase serving as a bridge between the cubic and the incommensurate phases. The pressure effect on ferroelectric and incommensurate critical dynamics shows that lead zirconate is not a single-instability-driven system.