bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Automated Annotation of Benthic Survey Images Using Wide-band Fluorescence
Authors: Beijbom Oscar , Treibitz Tali , Kline David I. , Eyal Gal , Khen Adi , Neal Benjamin , Loya Yossi , Mitchell B. Greg , Kriegman David 
Published: March 2016

AbstractLarge-scale imaging techniques are used increasingly for ecological surveys. However, manual analysis can be prohibitively expensive, creating a bottleneck between collected images and desired data-products. This bottleneck is particularly severe for benthic surveys, where millions of images are obtained each year. Recent automated annotation methods may provide a solution, but reflectance images do not always contain sufficient information for adequate classification accuracy. In this work, the FluorIS, a low-cost modified consumer camera, was used to capture wide-band wide-field-of-view fluorescence images during a field deployment in Eilat, Israel. The fluorescence images were registered with standard reflectance images, and an automated annotation method based on convolutional neural networks was developed. Our results demonstrate a 22% reduction of classification error-rate when using both images types compared to only using reflectance images. The improvements were large, in particular, for coral reef genera Platygyra, Acropora and Millepora, where classification recall improved by 38%, 33%, and 41%, respectively. We conclude that convolutional neural networks can be used to combine reflectance and fluorescence imagery in order to significantly improve automated annotation accuracy and reduce the manual annotation bottleneck.
An Essential Role for the Transcription Factor Runx1 in T Cell Maturation
Authors: Hsu Fan-Chi , Shapiro Michael J. , Dash Barsha , Chen Chien-Chang , Constans Megan M. , Chung Ji Young , Romero Arocha Sinibaldo R. , Belmonte Paul J. , Chen Meibo W. , McWilliams Douglas C. , Shapiro Virginia Smith 
Published: March 2016

AbstractThe transcription factor Runx1 has essential roles throughout hematopoiesis. Here, we demonstrate that Runx1 is critical for T cell maturation. Peripheral naïve CD4+ T cells from CD4-cre Runx1 cKO mice are phenotypically and functionally immature as shown by decreased production of TNF-α upon TCR stimulation. The loss of peripheral CD4+ T cells in CD4-cre Runx1 cKO mice is not due to defects in homeostasis or decreased expression of IL-7Rα, as transgenic expression of IL-7Rα does not rescue the loss of CD4+ T cells. Rather, immature Runx1-deficient CD4+ T cells are eliminated in the periphery by the activation and fixation of the classical complement pathway. In the thymus, there is a severe block in all aspects of intrathymic T cell maturation, although both positive and negative selection are unaltered. Thus, loss of Runx1 leads to the earliest characterized block in post-positive selection intrathymic maturation of CD4 T cells.
Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis
Authors: Brown Samantha , Higham Thomas , Slon Viviane , Pääbo Svante , Meyer Matthias , Douka Katerina , Brock Fiona , Comeskey Daniel , Procopio Noemi , Shunkov Michael , Derevianko Anatoly , Buckley Michael 
Published: March 2016

AbstractDNA sequencing has revolutionised our understanding of archaic humans during the Middle and Upper Palaeolithic. Unfortunately, while many Palaeolithic sites contain large numbers of bones, the majority of these lack the diagnostic features necessary for traditional morphological identification. As a result the recovery of Pleistocene-age human remains is extremely rare. To circumvent this problem we have applied a method of collagen fingerprinting to more than 2000 fragmented bones from the site of Denisova Cave, Russia, in order to facilitate the discovery of human remains. As a result of our analysis a single hominin bone (Denisova 11) was identified, supported through in-depth peptide sequencing analysis and found to carry mitochondrial DNA of the Neandertal type. Subsequent radiocarbon dating revealed the bone to be >50,000 years old. Here we demonstrate the huge potential collagen fingerprinting has for identifying hominin remains in highly fragmentary archaeological assemblages, improving the resources available for wider studies into human evolution.
Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells
Authors: Pode-Shakked Naomi , Pleniceanu Oren , Gershon Rotem , Shukrun Rachel , Kanter Itamar , Bucris Efrat , Pode-Shakked Ben , Tam Gal , Tam Hadar , Caspi Revital , Pri-Chen Sara , Vax Einav , Katz Guy , Omer Dorit , Harari-Steinberg Orit , Kalisky Tomer , Dekel Benjamin 
Published: March 2016

AbstractWhen assembling a nephron during development a multipotent stem cell pool becomes restricted as differentiation ensues. A faulty differentiation arrest in this process leads to transformation and initiation of a Wilms’ tumor. Mapping these transitions with respective surface markers affords accessibility to specific cell subpopulations. NCAM1 and CD133 have been previously suggested to mark human renal progenitor populations. Herein, using cell sorting, RNA sequencing, in vitro studies with serum-free media and in vivo xenotransplantation we demonstrate a sequential map that links human kidney development and tumorigenesis; In nephrogenesis, NCAM1+CD133− marks SIX2+ multipotent renal stem cells transiting to NCAM1+CD133+ differentiating segment-specific SIX2− epithelial progenitors and NCAM1−CD133+ differentiated nephron cells. In tumorigenesis, NCAM1+CD133− marks SIX2+ blastema that includes the ALDH1+ WT cancer stem/initiating cells, while NCAM1+CD133+ and NCAM1−CD133+ specifying early and late epithelial differentiation, are severely restricted in tumor initiation capacity and tumor self-renewal. Thus, negative selection for CD133 is required for defining NCAM1+ nephron stem cells in normal and malignant nephrogenesis.
A proteomic analysis of mushroom polysaccharide-treated HepG2 cells
Authors: Chai Yangyang , Wang Guibin , Fan Lili , Zhao Min 
Published: March 2016

AbstractThe anti-tumor properties of fungal polysaccharides have gained significant recognition in Asia and tropical America. In this study, the differential expression of proteins in normal HepG2 cells and those treated with polysaccharides that had been isolated from Phellinus linteus (PL), Ganoderma lucidum (GL) and Auricularia auricula (AA) was investigated. Using two-dimensional electrophoresis (2DE), a total of 104 protein spots were determined to be overexpressed in these cells compared with noncancerous regions. A total of 59 differentially expressed proteins were identified through MALDI-TOF-MS. In addition, 400 biological processes (BP), 133 cell components (CC) and 146 molecular functions (MF) were enriched by Gene Ontology (GO) analysis and 78 KEGG pathways were enriched by pathway enrichment. Protein-Protein Interaction (PPI) analysis demonstrated the interaction networks affected by polysaccharides in HepG2 cells. Then, DJ-1 and 14-3-3 were identified as the key proteins in the networks and the expression of the mRNA and proteins were evaluated using Real-time quantitative PCR (qRT-PCR) and Western blotting (WB), respectively. The results were in agreement with the 2DE. These results provided information on significant proteins of hepatocellular carcinoma (HCC) and form an important basis for the future development of valuable medicinal mushroom resources.
Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6
Authors: Nieuwland Jeroen , Stamm Petra , Wen Bo , Randall Ricardo S. , Murray James A. H. , Bassel George W. 
Published: March 2016

AbstractSeeding establishment following seed germination requires activation of the root meristem for primary root growth. We investigated the hormonal and genetic regulation of root meristem activation during Arabidopsis seed germination. In optimal conditions, radicle cell divisions occur only after the completion of germination and require de novo GA synthesis. When the completion of germination is blocked by ABA, radicle elongation and cell divisions occurred in these non-germinating seeds. Conversely under GA-limiting conditions, ABA-insensitive mutants complete germination in the absence of radicle meristem activation and growth. Radicle meristem activation and extension can therefore occur independently of completion of the developmental transition of germination. The cell cycle regulator KRP6 partially represses GA-dependent activation of the cell cycle. Germination of krp6 mutant seeds occurs more rapidly, is slightly insensitive to ABA in dose-response assays, but also hypersensitive to the GA synthesis inhibitor PAC. These conflicting phenotypes suggest the cell cycle uncouples GA and ABA responses in germinating Arabidopsis seeds, and that KRP6 acts downstream of GA to inhibit mitotic cell cycle activation during germination.
Impact of Adsorption on Gas Transport in Nanopores
Authors: Wu Tianhao , Zhang Dongxiao 
Published: March 2016

AbstractGiven the complex nature of the interaction between gas and solid atoms, the development of nanoscale science and technology has engendered a need for further understanding of gas transport behavior through nanopores and more tractable models for large-scale simulations. In the present paper, we utilize molecular dynamic simulations to demonstrate the behavior of gas flow under the influence of adsorption in nano-channels consisting of illite and graphene, respectively. The results indicate that velocity oscillation exists along the cross-section of the nano-channel and the total mass flow could be either enhanced or reduced depending on variations in adsorption under different conditions. The mechanisms can be explained by the extra average perturbation stress arising from density oscillation via the novel perturbation model for micro-scale simulation and approximated via the novel dual-region model for macro-scale simulation, which leads to a more accurate permeability correction model for industrial applications than is currently available.
Suppressive effect of exogenous carbon monoxide on endotoxin-stimulated platelet over-activation via the glycoprotein-mediated PI3K-Akt-GSK3β pathway
Authors: Liu Dadong , Wang Xu , Qin Weiting , Chen Jingjia , Wang Yawei , Zhuang Mingfeng , Sun Bingwei 
Published: March 2016

AbstractPlatelet activation is an important event involved in the pathophysiological processes of the coagulation system. Clinical evidence has shown that platelets undergo distinctive pathological processes during sepsis. Unfortunately, how platelets physiologically respond to inflammation or sepsis is not well understood. In this study, we used a lipopolysaccharide (LPS)-stimulated platelet model to systemically investigate alterations in membrane glycoprotein expression, molecular signaling, morphology and critical functions of platelets. We found that platelet adhesion, aggregation, secretion and spreading on immobilized fibrinogen and the expression of platelet membrane glycoproteins were significantly increased by LPS stimulation and these changes were accompanied by a significant decrease in cGMP levels and an abnormal distribution of platelet α-granules. Exogenous CO reversed these alterations. Profound morphological changes in LPS-stimulated platelets were observed using atomic force microscopy and phase microscopy. Furthermore, the elevated activities of PI3Ks, AKt and GSK-3β were effectively suppressed by exogenous CO, leading to the improvement of platelet function. Together, these results provide evidence that platelet over-activation persists under LPS-stimulation and that exogenous CO plays an important role in suppressing platelet activation via the glycoprotein-mediated PI3K-Akt-GSK3β pathway.
Pitfalls in assessing microvascular endothelial barrier function: impedance-based devices versus the classic macromolecular tracer assay
Authors: Bischoff Iris , Hornburger Michael C. , Mayer Bettina A. , Beyerle Andrea , Wegener Joachim , Fürst Robert 
Published: March 2016

AbstractThe most frequently used parameters to describe the barrier properties of endothelial cells (ECs) in vitro are (i) the macromolecular permeability, indicating the flux of a macromolecular tracer across the endothelium and (ii) electrical impedance of ECs grown on gold-film electrodes reporting on the cell layer’s tightness for ion flow. Due to the experimental differences between these approaches, inconsistent observations have been described. Here, we present the first direct comparison of these assays applied to one single cell type (human microvascular ECs) under the same experimental conditions. The impact of different pharmacological tools (histamine, forskolin, Y-27632, blebbistatin, TRAP) on endothelial barrier function was analyzed by Transwell® tracer assays and two commercial impedance devices (xCELLigence®, ECIS®). The two impedance techniques provided very similar results for all compounds, whereas macromolecular permeability readings were found to be partly inconsistent with impedance. Possible reasons for these discrepancies are discussed. We conclude that the complementary combination of both approaches is highly recommended to overcome the restrictions of each assay. Since the nature of the growth support may contribute to the observed differences, structure-function relationships should be based on cells that are consistently grown on either permeable or impermeable growth supports in all experiments.
Electronic origins of photocatalytic activity in d0 metal organic frameworks
Authors: Nasalevich Maxim A. , Hendon Christopher H. , Santaclara Jara G. , Svane Katrine , van der Linden Bart , Veber Sergey L. , Fedin Matvey V. , Houtepen Arjan J. , van der Veen Monique A. , Kapteijn Freek , Walsh Aron , Gascon Jorge 
Published: March 2016

AbstractMetal-organic frameworks (MOFs) containing d0 metals such as NH2-MIL-125(Ti), NH2-UiO-66(Zr) and NH2-UiO-66(Hf) are among the most studied MOFs for photocatalytic applications. Despite structural similarities, we demonstrate that the electronic properties of these MOFs are markedly different. As revealed by quantum chemistry, EPR measurements and transient absorption spectroscopy, the highest occupied and lowest unoccupied orbitals of NH2-MIL-125(Ti) promote a long lived ligand-to-metal charge transfer upon photoexcitation, making this material suitable for photocatalytic applications. In contrast, in case of UiO materials, the d-orbitals of Zr and Hf, are too low in binding energy and thus cannot overlap with the π* orbital of the ligand, making both frontier orbitals localized at the organic linker. This electronic reconfiguration results in short exciton lifetimes and diminishes photocatalytic performance. These results highlight the importance of orbital contributions at the band edges and delineate future directions in the development of photo-active hybrid solids.
P-Channel InGaN/GaN heterostructure metal-oxide-semiconductor field effect transistor based on polarization-induced two-dimensional hole gas
Authors: Zhang Kexiong , Sumiya Masatomo , Liao Meiyong , Koide Yasuo , Sang Liwen 
Published: March 2016

AbstractThe concept of p-channel InGaN/GaN heterostructure field effect transistor (FET) using a two-dimensional hole gas (2DHG) induced by polarization effect is demonstrated. The existence of 2DHG near the lower interface of InGaN/GaN heterostructure is verified by theoretical simulation and capacitance-voltage profiling. The metal-oxide-semiconductor FET (MOSFET) with Al2O3 gate dielectric shows a drain-source current density of 0.51 mA/mm at the gate voltage of −2 V and drain bias of −15 V, an ON/OFF ratio of two orders of magnitude and effective hole mobility of 10 cm2/Vs at room temperature. The normal operation of MOSFET without freeze-out at 8 K further proves that the p-channel behavior is originated from the polarization-induced 2DHG.
An Exploratory Study on the Pathways of Cr (VI) Reduction in Sulfate-reducing Up-flow Anaerobic Sludge Bed (UASB) Reactor
Authors: Qian Jin , Wei Li , Liu Rulong , Jiang Feng , Hao Xiaodi , Chen Guang-Hao 
Published: March 2016

AbstractElectroplating wastewater contains both Cr (VI) and sulfate. So Cr (VI) removal under sulfate-rich condition is quite complicated. This study mainly investigates the pathways for Cr (VI) removal under biological sulfate-reducing condition in the up-flow anaerobic sludge bed (UASB) reactor. Two potential pathways are found for the removal of Cr (VI). The first one is the sulfidogenesis-induced Cr (VI) reduction pathway (for 90% Cr (VI) removal), in which Cr (VI) is reduced by sulfide generated from biological reduction of sulfate. The second one leads to direct reduction of Cr (VI) which is utilized by bacteria as the electron acceptor (for 10% Cr (VI) removal). Batch test results confirmed that sulfide was oxidized to elemental sulfur instead of sulfate during Cr (VI) reduction. The produced extracellular polymeric substances (EPS) provided protection to the microbes, resulting in effective removal of Cr (VI). Sulfate-reducing bacteria (SRB) genera accounted for 11.1% of the total bacterial community; thus they could be the major organisms mediating the sulfidogenesis-induced reduction of Cr (VI). In addition, chromate-utilizing genera (e.g. Microbacterium) were also detected, which were possibly responsible for the direct reduction of Cr (VI) using organics as the electron donor and Cr (VI) as the electron acceptor.
Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans
Authors: Silberberg Yael , Kupiec Martin , Sharan Roded 
Published: March 2016

AbstractUnderstanding the genetic basis underlying individual responses to drug treatment is a fundamental task with implications to drug development and administration. Pharmacogenomics is the study of the genes that affect drug response. The study of pharmacogenomic associations between a drug and a gene that influences the interindividual drug response, which is only beginning, holds much promise and potential. Although relatively few pharmacogenomic associations between drugs and specific genes were mapped in humans, large systematic screens have been carried out in the yeast Saccharomyces cerevisiae, motivating the constructing of a projection method. We devised a novel approach for the prediction of pharmacogenomic associations in humans using genome-scale chemogenomic data from yeast. We validated our method using both cross-validation and comparison to known drug-gene associations extracted from multiple data sources, attaining high AUC scores. We show that our method outperforms a previous technique, as well as a similar method based on known human associations. Last, we analyze the predictions and demonstrate their biological relevance to understanding drug response.
Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania
Authors: Flegontov Pavel , Butenko Anzhelika , Firsov Sergei , Kraeva Natalya , Eliáš Marek , Field Mark C. , Filatov Dmitry , Flegontova Olga , Gerasimov Evgeny S. , Hlaváčová Jana , Ishemgulova Aygul , Jackson Andrew P. , Kelly Steve , Kostygov Alexei Y. , Logacheva Maria D. , Maslov Dmitri A. , Opperdoes Fred R. , O’Reilly Amanda , Sádlová Jovana , Ševčíková Tereza , Venkatesh Divya , Vlček Čestmír , Volf Petr , Jan Votýpka  , Záhonová Kristína , Yurchenko Vyacheslav , Lukeš Julius 
Published: March 2016

AbstractMany high-quality genomes are available for dixenous (two hosts) trypanosomatid species of the genera Trypanosoma, Leishmania, and Phytomonas, but only fragmentary information is available for monoxenous (single-host) trypanosomatids. In trypanosomatids, monoxeny is ancestral to dixeny, thus it is anticipated that the genome sequences of the key monoxenous parasites will be instrumental for both understanding the origin of parasitism and the evolution of dixeny. Here, we present a high-quality genome for Leptomonas pyrrhocoris, which is closely related to the dixenous genus Leishmania. The L. pyrrhocoris genome (30.4 Mbp in 60 scaffolds) encodes 10,148 genes. Using the L. pyrrhocoris genome, we pinpointed genes gained in Leishmania. Among those genes, 20 genes with unknown function had expression patterns in the Leishmania mexicana life cycle suggesting their involvement in virulence. By combining differential expression data for L. mexicana, L. major and Leptomonas seymouri, we have identified several additional proteins potentially involved in virulence, including SpoU methylase and U3 small nucleolar ribonucleoprotein IMP3. The population genetics of L. pyrrhocoris was also addressed by sequencing thirteen strains of different geographic origin, allowing the identification of 1,318 genes under positive selection. This set of genes was significantly enriched in components of the cytoskeleton and the flagellum.
Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into “Redox mediator-Microbe-Iron oxide” Interaction Process
Authors: Zhu Weihuang , Shi Mengran , Yu Dan , Liu Chongxuan , Huang Tinglin , Wu Fengchang 
Published: March 2016

AbstractThe characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into “redox mediator-iron oxide” interaction in the presence of DIRB. Two pre-incubation reaction systems of the “strain S12- goethite” and the “strain S12-AQS” were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for “Quinone-Iron” interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among “quinone-DIRB- goethite” under biotic/abiotic driven.
Microsurgery-aided in-situ force probing reveals extensibility and viscoelastic properties of individual stress fibers
Authors: Labouesse Céline , Gabella Chiara , Meister Jean-Jacques , Vianay Benoît , Verkhovsky Alexander B. 
Published: March 2016

AbstractActin-myosin filament bundles (stress fibers) are critical for tension generation and cell shape, but their mechanical properties are difficult to access. Here we propose a novel approach to probe individual peripheral stress fibers in living cells through a microsurgically generated opening in the cytoplasm. By applying large deformations with a soft cantilever we were able to fully characterize the mechanical response of the fibers and evaluate their tension, extensibility, elastic and viscous properties.