bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones
Authors: Cardenas Erick , Orellana Luis H. , Konstantinidis Konstantinos T. , Mohn William W. 
Published: February 2018

AbstractForest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profile variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment effects on gene profiles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these effects varied among ecozones. Our results suggest that ecozone-specific nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.
Time-dependent Enhanced Corrosion of Ti6Al4V in the Presence of H2O2 and Albumin
Authors: Zhang Yue , Addison Owen , Yu Fei , Troconis Brendy C. Rincon , Scully John R. , Davenport Alison J. 
Published: February 2018

AbstractThere is increasing concern regarding the biological consequences of metal release from implants. However, the mechanisms underpinning implant surface degradation, especially in the absence of wear, are often poorly understood. Here the synergistic effect of albumin and H2O2 on corrosion of Ti6Al4V in physiological saline is studied with electrochemical methods. It is found that albumin induces a time-dependent dissolution of Ti6Al4V in the presence of H2O2 in physiology saline. Potentiostatic polarisation measurements show that albumin supresses dissolution in the presence of H2O2 at short times (<24 h) but over longer time periods (120 h) it significantly accelerates corrosion, which is attributed to albumin-catalysed dissolution of the corrosion product layer resulting in formation of a thinner oxide film. Dissolution of Ti6Al4V in the presence of albumin and H2O2 in physiological saline is also found to be dependent on potential: the titanium ion release rate is found to be higher (0.57 µg/cm2) at a lower potential (90 mV), where the oxide capacitance and resistance inferred from Electrochemical Impedance Spectroscopy also suggests a less resistant oxide film. The study highlights the importance of using more realistic solutions, and considering behaviour over longer time periods when testing corrosion resistance of metallic biomaterials.
IL-2 Inducible Kinase ITK is Critical for HIV-1 Infection of Jurkat T-cells
Authors: Hain Anika , Krämer Melanie , Linka René M. , Nakhaei-Rad Saeideh , Ahmadian Mohammad Reza , Häussinger Dieter , Borkhardt Arndt , Münk Carsten 
Published: February 2018

AbstractSuccessful replication of Human immunodeficiency virus (HIV)-1 depends on the expression of various cellular host factors, such as the interleukin-2 inducible T-cell kinase (ITK), a member of the protein family of TEC-tyrosine kinases. ITK is selectively expressed in T-cells and coordinates signaling pathways downstream of the T-cell receptor and chemokine receptors, including PLC-1 activation, Ca2+-release, transcription factor mobilization, and actin rearrangements. The exact role of ITK during HIV-1 infection is still unknown. We analyzed the function of ITK during HIV-1 replication and showed that attachment, fusion of virions with the cell membrane and entry into Jurkat T-cells was inhibited when ITK was knocked down. In contrast, reverse transcription and provirus expression were not affected by ITK deficiency. Inhibited ITK expression did not affect the CXCR4 receptor on the cell surface, whereas CD4 and LFA-1 integrin levels were slightly enhanced in ITK knockdown cells and heparan sulfate (HS) expression was completely abolished in ITK depleted T-cells. However, neither HS expression nor other attachment factors could explain the impaired HIV-1 binding to ITK-deficient cells, which suggests that a more complex cellular process is influenced by ITK or that not yet discovered molecules contribute to restriction of HIV-1 binding and entry.
A multiplex serologic platform for diagnosis of tick-borne diseases
Authors: Tokarz Rafal , Mishra Nischay , Tagliafierro Teresa , Sameroff Stephen , Caciula Adrian , Chauhan Lokendrasingh , Patel Jigar , Sullivan Eric , Gucwa Azad , Fallon Brian , Golightly Marc , Molins Claudia , Schriefer Martin , Marques Adriana , Briese Thomas , Lipkin W. Ian 
Published: February 2018

AbstractTick-borne diseases are the most common vector-borne diseases in the United States, with serology being the primary method of diagnosis. We developed the first multiplex, array-based assay for serodiagnosis of tick-borne diseases called the TBD-Serochip. The TBD-Serochip was designed to discriminate antibody responses to 8 major tick-borne pathogens present in the United States, including Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Borrelia miyamotoi, Ehrlichia chaffeensis, Rickettsia rickettsii, Heartland virus and Powassan virus. Each assay contains approximately 170,000 12-mer linear peptides that tile along the protein sequence of the major antigens from each agent with 11 amino acid overlap. This permits accurate identification of a wide range of specific immunodominant IgG and IgM epitopes that can then be used to enhance diagnostic accuracy and integrate differential diagnosis into a single assay. To test the performance of the TBD-Serochip, we examined sera from patients with confirmed Lyme disease, babesiosis, anaplasmosis, and Powassan virus disease. We identified a wide range of specific discriminatory epitopes that facilitated accurate diagnosis of each disease. We also identified previously undiagnosed infections. Our results indicate that the TBD-Serochip is a promising tool for a differential diagnosis not available with currently employed serologic assays for TBDs.
Diffusion mechanism in the sodium-ion battery material sodium cobaltate
Authors: Willis T. J. , Porter D. G. , Voneshen D. J. , Uthayakumar S. , Demmel F. , Gutmann M. J. , Roger M. , Refson K. , Goff J. P. 
Published: February 2018

AbstractHigh performance batteries based on the movement of Li ions in Li
x
CoO2 have made possible a revolution in mobile electronic technology, from laptops to mobile phones. However, the scarcity of Li and the demand for energy storage for renewables has led to intense interest in Na-ion batteries, including structurally-related Na
x
CoO2. Here we have determined the diffusion mechanism for Na0.8CoO2 using diffuse x-ray scattering, quasi-elastic neutron scattering and ab-initio molecular dynamics simulations, and we find that the sodium ordering provides diffusion pathways and governs the diffusion rate. Above T ~ 290 K the so-called partially disordered stripe superstructure provides channels for quasi-1D diffusion, and melting of the sodium ordering leads to 2D superionic diffusion above T ~ 370 K. We obtain quantitative agreement between our microscopic study of the hopping mechanism and bulk self-diffusion measurements. Our approach can be applied widely to other Na- or Li-ion battery materials.
PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry
Authors: Palmigiano Angela , Santaniello Francesco , Cerutti Aurora , Penkov Dmitry , Purushothaman Divya , Makhija Ekta , Luzi Lucilla , di Fagagna Fabrizio d’Adda , Pelicci Pier Giuseppe , Shivashankar Viveswara , Dellino Gaetano Ivan , Blasi Francesco 
Published: February 2018

AbstractThe synthesis of middle-to-late-replicating DNA can be affected independently of the rest of the genome by down-regulating the tumor suppressor PREP1 (PKNOX1). Indeed, DNA combing shows that PREP1 down-regulation affects DNA replication rate, increases the number of simultaneously firing origins and the asymmetry of DNA replication, leading to DNA damage. Genome-wide analysis of replication timing by Repli-seq shows that, upon PREP1 down-regulation, 25% of the genome is replicated earlier in the S-phase. The targeted DNA sequences correspond to Lamin-Associated Domains (LADs), and include late-replicating (LRRs) and temporal transition regions (TTRs). Notably, the distribution of PREP1 DNA binding sites and of its target genes indicates that DNA replication defects are independent of the overall PREP1 transcriptional activity. Finally, PREP1 down-regulation causes a substantial decrease in Lamin B1 levels. This suggests that DNA is released from the nuclear lamina earlier than in the control cells and is available for replication, thus explaining timing defects and DNA damage.This is the first evidence that the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor. This previously unknown function might significantly contribute to the genomic instability observed in human tumors.
Working Memory And Brain Tissue Microstructure: White Matter Tract Integrity Based On Multi-Shell Diffusion MRI
Authors: Chung Sohae , Fieremans Els , Kucukboyaci Nuri E. , Wang Xiuyuan , Morton Charles J. , Novikov Dmitry S. , Rath Joseph F. , Lui Yvonne W. 
Published: February 2018

AbstractWorking memory is a complex cognitive process at the intersection of sensory processing, learning, and short-term memory and also has a general executive attention component. Impaired working memory is associated with a range of neurological and psychiatric disorders, but very little is known about how working memory relates to underlying white matter (WM) microstructure. In this study, we investigate the association between WM microstructure and performance on working memory tasks in healthy adults (right-handed, native English speakers). We combine compartment specific WM tract integrity (WMTI) metrics derived from multi-shell diffusion MRI as well as diffusion tensor/kurtosis imaging (DTI/DKI) metrics with Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV) subtests tapping auditory working memory. WMTI is a novel tool that helps us describe the microstructural characteristics in both the intra- and extra-axonal environments of WM such as axonal water fraction (AWF), intra-axonal diffusivity, extra-axonal axial and radial diffusivities, allowing a more biophysical interpretation of WM changes. We demonstrate significant positive correlations between AWF and letter-number sequencing (LNS), suggesting that higher AWF with better performance on complex, more demanding auditory working memory tasks goes along with greater axonal volume and greater myelination in specific regions, causing efficient and faster information process.
Toxicity Classification of Oxide Nanomaterials: Effects of Data Gap Filling and PChem Score-based Screening Approaches
Authors: Ha My Kieu , Trinh Tung Xuan , Choi Jang Sik , Maulina Desy , Byun Hyung Gi , Yoon Tae Hyun 
Published: February 2018

AbstractDevelopment of nanotoxicity prediction models is becoming increasingly important in the risk assessment of engineered nanomaterials. However, it has significant obstacles caused by the wide heterogeneities of published literature in terms of data completeness and quality. Here, we performed a meta-analysis of 216 published articles on oxide nanoparticles using 14 attributes of physicochemical, toxicological and quantum-mechanical properties. Particularly, to improve completeness and quality of the extracted dataset, we adapted two preprocessing approaches: data gap-filling and physicochemical property based scoring. Performances of nano-SAR classification models revealed that the dataset with the highest score value resulted in the best predictivity with compromise in its applicability domain. The combination of physicochemical and toxicological attributes was proved to be more relevant to toxicity classification than quantum-mechanical attributes. Overall, by adapting these two preprocessing methods, we demonstrated that meta-analysis of nanotoxicity literatures could provide an effective alternative for the risk assessment of engineered nanomaterials.
Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract
Authors: Yeoman Carl J. , Ishaq Suzanne L. , Bichi Elena , Olivo Sarah K. , Lowe James , Aldridge Brian M. 
Published: February 2018

AbstractThe impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.
Temporal structure in spiking patterns of ganglion cells defines perceptual thresholds in rodents with subretinal prosthesis
Authors: Ho Elton , Lorach Henri , Goetz Georges , Laszlo Florian , Lei Xin , Kamins Theodore , Mariani Jean-Charles , Sher Alexander , Palanker Daniel 
Published: February 2018

AbstractSubretinal prostheses are designed to restore sight in patients blinded by retinal degeneration using electrical stimulation of the inner retinal neurons. To relate retinal output to perception, we studied behavioral thresholds in blind rats with photovoltaic subretinal prostheses stimulated by full-field pulsed illumination at 20 Hz, and measured retinal ganglion cell (RGC) responses to similar stimuli ex-vivo. Behaviorally, rats exhibited startling response to changes in brightness, with an average contrast threshold of 12%, which could not be explained by changes in the average RGC spiking rate. However, RGCs exhibited millisecond-scale variations in spike timing, even when the average rate did not change significantly. At 12% temporal contrast, changes in firing patterns of prosthetic response were as significant as with 2.3% contrast steps in visible light stimulation of healthy retinas. This suggests that millisecond-scale changes in spiking patterns define perceptual thresholds of prosthetic vision. Response to the last pulse in the stimulation burst lasted longer than the steady-state response during the burst. This may be interpreted as an excitatory OFF response to prosthetic stimulation, and can explain behavioral response to decrease in illumination. Contrast enhancement of images prior to delivery to subretinal prosthesis can partially compensate for reduced contrast sensitivity of prosthetic vision.
Human neutrophils can mimic myeloid-derived suppressor cells (PMN-MDSC) and suppress microbead or lectin-induced T cell proliferation through artefactual mechanisms
Authors: Negorev Dmitri , Beier Ulf H. , Zhang Tianyi , Quatromoni Jon G. , Bhojnagarwala Pratik , Albelda Steven M. , Singhal Sunil , Eruslanov Evgeniy , Lohoff Falk W. , Levine Matthew H. , Diamond Joshua M. , Christie Jason D. , Hancock Wayne W. , Akimova Tatiana 
Published: February 2018

AbstractWe report that human conventional CD15+neutrophils can be isolated in the peripheral blood mononuclear cell (PBMC) layer during Ficoll gradient separation, and that they can impair T cell proliferationin vitrowithout concomitant neutrophil activation and killing. This effect was observed in a total of 92 patients with organ transplants, lung cancer or anxiety/depression, and in 18 healthy donors. Although such features are typically associated in the literature with the presence of certain myeloid-derived suppressor cell (PMN-MDSC) populations, we found that commercial centrifuge tubes that contained membranes or gels for PBMC isolation led to up to 70% PBMC contamination by CD15+neutrophils, with subsequent suppressive effects in certain cellular assays. In particular, the suppressive activity of human MDSC should not be evaluated using lectin or microbead stimulation, whereas assays involving soluble or plate-bound antibodies or MLR are unaffected. We conclude that CD15+neutrophil contamination, and associated effects on suppressor assays, can lead to significant artefacts in studies of human PMN-MDSC.
Functional analysis of SLC39A8 mutations and their implications for manganese deficiency and mitochondrial disorders
Authors: Choi Eun-Kyung , Nguyen Trang-Tiffany , Gupta Neil , Iwase Shigeki , Seo Young Ah 
Published: February 2018

AbstractSLC39A8 encodes ZIP8, a divalent metal ion transporter. Mutations in the SLC39A8 gene are associated with congenital disorder of glycosylation type II and Leigh syndrome. Notably, affected patients with both disorders exhibited severe manganese (Mn) deficiency. The cellular function of human SLC39A8 (hSLC39A8) and the mechanisms by which mutations in this protein lead to human diseases are unclear. Herein, we show that hSLC39A8 mediates 54Mn uptake by the cells, and its expression is regulated by Mn. While expression of wild-type hSLC39A8 increased 54Mn uptake activity, disease-associated mutations abrogated the ability of the transporter to mediate Mn uptake into the cells, thereby providing a causal link to severe Mn deficiency. All mutants failed to localize on the cell surface and were retained within the endoplasmic reticulum. Interestingly, expression of hSLC39A8 mutants of both CDG type II and Leigh syndrome reduced mitochondrial 54Mn levels and activity of Mn-dependent mitochondrial superoxide dismutase MnSOD, and in turn increased oxidative stress. The expression of wild-type hSLC39A8, but not the disease-associated mutants, promoted mitochondrial functions. Moreover, loss of function analyses further corroborate hSLC39A8’s critical role in mediating Mn uptake and mitochondrial function. Our results provide a potential pathogenic mechanism of diseases that are associated with hSLC39A8 mutations.
High fidelity heralded single-photon source using cavity quantum electrodynamics
Authors: Zhang Xin , Xu Chang , Ren Zhongzhou 
Published: February 2018

AbstractDemands for single-photon sources are ubiquitous in quantum information processing as well as in quantum metrology. In many protocols for producing single photons, a cavity-emitter configuration is used. In such cavity quantum electrodynamical systems, the cavity can enforce a well-defined output mode for the photon and enhance its collection efficiency, while the emitter is indispensable for single photon emission. Here we show the two cavity-one two-level emitter configuration can be used to produce exclusively photon pairs, with each photon in a separate mode. Conditioning on detecting a photon in one of the modes, one heralds with high fidelity a single photon in the other mode. Counterintuitively, upon decreasing the coupling of the emitter to one of the modes, the heralding fidelity can further increase.
Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Authors: Krishnakumar Raga , Sinha Anupama , Bird Sara W. , Jayamohan Harikrishnan , Edwards Harrison S. , Schoeniger Joseph S. , Patel Kamlesh D. , Branda Steven S. , Bartsch Michael S. 
Published: February 2018

AbstractEmerging sequencing technologies are allowing us to characterize environmental, clinical and laboratory samples with increasing speed and detail, including real-time analysis and interpretation of data. One example of this is being able to rapidly and accurately detect a wide range of pathogenic organisms, both in the clinic and the field. Genomes can have radically different GC content however, such that accurate sequence analysis can be challenging depending upon the technology used. Here, we have characterized the performance of the Oxford MinION nanopore sequencer for detection and evaluation of organisms with a range of genomic nucleotide bias. We have diagnosed the quality of base-calling across individual reads and discovered that the position within the read affects base-calling and quality scores. Finally, we have evaluated the performance of the current state-of-the-art neural network-based MinION basecaller, characterizing its behavior with respect to systemic errors as well as context- and sequence-specific errors. Overall, we present a detailed characterization the capabilities of the MinION in terms of generating high-accuracy sequence data from genomes with a wide range of nucleotide content. This study provides a framework for designing the appropriate experiments that are the likely to lead to accurate and rapid field-forward diagnostics.
Short-term acclimation in adults does not predict offspring acclimation potential to hypoxia
Authors: Truebano Manuela , Tills Oliver , Collins Michael , Clarke Charlotte , Shipsides Emma , Wheatley Charlotte , Spicer John I. 
Published: February 2018

AbstractThe prevalence of hypoxic areas in coastal waters is predicted to increase and lead to reduced biodiversity. While the adult stages of many estuarine invertebrates can cope with short periods of hypoxia, it remains unclear whether that ability is present if animals are bred and reared under chronic hypoxia. We firstly investigated the effect of moderate, short-term environmental hypoxia (40% air saturation for one week) on metabolic performance in adults of an estuarine amphipod, and the fitness consequences of prolonged exposure. We then reared the offspring of hypoxia-exposed parents under hypoxia, and assessed their oxyregulatory ability under declining oxygen tensions as juveniles and adults. Adults from the parental generation were able to acclimate their metabolism to hypoxia after one week, employing mechanisms typically associated with prolonged exposure. Their progeny, however, did not develop the adult pattern of respiratory regulation when reared under chronic hypoxia, but instead exhibited a poorer oxyregulatory ability than their parents. We conclude that species apparently hypoxia-tolerant when tested in short-term experiments, could be physiologically compromised as adults if they develop under hypoxia. Consequently, we propose that the increased prevalence of hypoxia in coastal regions will have marked effects in some species currently considered hypoxia tolerant.