bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of aerosols containing Legionella generated upon nebulization
Authors: Allegra Séverine , Leclerc Lara , Massard Pierre André , Girardot Françoise , Riffard Serge , Pourchez Jérémie 
Published: September 2016

AbstractLegionella pneumophila is, by far, the species most frequently associated with Legionnaires’ disease (LD). Human infection occurs almost exclusively by aerosol inhalation which places the bacteria in juxtaposition with alveolar macrophages. LD risk management is based on controlling water quality by applying standardized procedures. However, to gain a better understanding of the real risk of exposure, there is a need (i) to investigate under which conditions Legionella may be aerosolized and (ii) to quantify bacterial deposition into the respiratory tract upon nebulization. In this study, we used an original experimental set-up that enables the generation of aerosol particles containing L. pneumophila under various conditions. Using flow cytometry in combination with qPCR and culture, we determined (i) the size of the aerosols and (ii) the concentration of viable Legionella forms that may reach the thoracic region. We determined that the 0.26–2.5 μm aerosol size range represents 7% of initial bacterial suspension. Among the viable forms, 0.7% of initial viable bacterial suspension may reach the pulmonary alveoli. In conclusion, these deposition profiles can be used to standardize the size of inoculum injected in any type of respiratory tract model to obtain new insights into the dose response for LD.
Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)
Authors: Kissling W. Daniel , Blach-Overgaard Anne , Zwaan Roelof E. , Wagner Philipp 
Published: September 2016

AbstractTo what extent deep-time dispersal limitation shapes present-day biodiversity at broad spatial scales remains elusive. Here, we compiled a continental dataset on the distributions of African lizard species in the reptile subfamily Agaminae (a relatively young, Neogene radiation of agamid lizards which ancestors colonized Africa from the Arabian peninsula) and tested to what extent historical colonization and dispersal limitation (i.e. accessibility from areas of geographic origin) can explain present-day species richness relative to current climate, topography, and climate change since the late Miocene (~10 mya), the Pliocene (~3 mya), and the Last Glacial Maximum (LGM, 0.021 mya). Spatial and non-spatial multi-predictor regression models revealed that time-limited dispersal via arid corridors is a key predictor to explain macro-scale patterns of species richness. In addition, current precipitation seasonality, current temperature of the warmest month, paleo-temperature changes since the LGM and late Miocene, and topographic relief emerged as important drivers. These results suggest that deep-time dispersal constraints — in addition to climate and mountain building — strongly shape current species richness of Africa’s arid-adapted taxa. Such historical dispersal limitation might indicate that natural movement rates of species are too slow to respond to rates of ongoing and projected future climate and land use change.
Novel enterobactin analogues as potential therapeutic chelating agents: Synthesis, thermodynamic and antioxidant studies
Authors: Zhang Qingchun , Jin Bo , Shi Zhaotao , Wang Xiaofang , Liu Qiangqiang , Lei Shan , Peng Rufang 
Published: September 2016

AbstractA series of novel hexadentate enterobactin analogues, which contain three catechol chelating moieties attached to different molecular scaffolds with flexible alkyl chain lengths, were prepared. The solution thermodynamic stabilities of the complexes with uranyl, ferric(III) and zinc(II) ions were then investigated. The hexadentate ligands demonstrate effective binding ability to uranyl ion and the average uranyl affinities are two orders of magnitude higher than 2,3-dihydroxy-N1,N4-bis[(1,2-hydroxypyridinone-6-carboxamide)ethyl]terephthalamide [TMA(2Li-1,2-HOPO)2] ligand with similar denticity. The high affinity of hexadentate ligands could be due to the presence of the flexible scaffold, which favors the geometric agreement between the ligand and the uranyl coordination preference. The hexadentate ligands also exhibit higher antiradical efficiency than butylated hydroxyanisole (BHA). These results provide a basis for further studies on the potential applications of hexadentate ligands as therapeutic chelating agents.
Heat production and error probability relation in Landauer reset at effective temperature
Authors: Neri Igor , López-Suárez Miquel 
Published: September 2016

AbstractThe erasure of a classical bit of information is a dissipative process. The minimum heat produced during this operation has been theorized by Rolf Landauer in 1961 to be equal to kBT ln2 and takes the name of Landauer limit, Landauer reset or Landauer principle. Despite its fundamental importance, the Landauer limit remained untested experimentally for more than fifty years until recently when it has been tested using colloidal particles and magnetic dots. Experimental measurements on different devices, like micro-mechanical systems or nano-electronic devices are still missing. Here we show the results obtained in performing the Landauer reset operation in a micro-mechanical system, operated at an effective temperature. The measured heat exchange is in accordance with the theory reaching values close to the expected limit. The data obtained for the heat production is then correlated to the probability of error in accomplishing the reset operation.
Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids
Authors: Quast Robert B. , Ballion Biljana , Stech Marlitt , Sonnabend Andrei , Varga Balázs R. , Wüstenhagen Doreen A. , Kele Péter , Schiller Stefan M. , Kubick Stefan 
Published: September 2016

AbstractCell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized receptors into microsomal membranes and asparagine-linked glycosylation. Using the cricket paralysis virus internal ribosome entry site and a repetitive synthesis approach enrichment of receptors inside the microsomal fractions was facilitated thereby providing analytical amounts of functional protein. Receptor tyrosine kinase activation was demonstrated by monitoring receptor phosphorylation. Furthermore, an orthogonal cell-free translation system that provides the site-directed incorporation of p-azido-L-phenylalanine is characterized and applied to investigate receptor dimerization in the absence of a ligand by photo-affinity cross-linking. Finally, incorporated azides are used to generate stable covalently linked receptor dimers by strain-promoted cycloaddition using a novel linker system.
Benchmarking Measures of Network Influence
Authors: Bramson Aaron , Vandermarliere Benjamin 
Published: September 2016

AbstractIdentifying key agents for the transmission of diseases (ideas, technology, etc.) across social networks has predominantly relied on measures of centrality on a static base network or a temporally flattened graph of agent interactions. Various measures have been proposed as the best trackers of influence, such as degree centrality, betweenness and k-shell, depending on the structure of the connectivity. We consider SIR and SIS propagation dynamics on a temporally-extruded network of observed interactions and measure the conditional marginal spread as the change in the magnitude of the infection given the removal of each agent at each time: its temporal knockout (TKO) score. We argue that this TKO score is an effective benchmark measure for evaluating the accuracy of other, often more practical, measures of influence. We find that none of the network measures applied to the induced flat graphs are accurate predictors of network propagation influence on the systems studied; however, temporal networks and the TKO measure provide the requisite targets for the search for effective predictive measures.
Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection
Authors: Feger Bryan J. , Thompson J. Will , Dubois Laura G. , Kommaddi Reddy P. , Foster Matthew W. , Mishra Rajashree , Shenoy Sudha K. , Shibata Yoichiro , Kidane Yared H. , Moseley M. Arthur , Carnell Lisa S. , Bowles Dawn E. 
Published: September 2016

AbstractOn Earth, biological systems have evolved in response to environmental stressors, interactions dictated by physical forces that include gravity. The absence of gravity is an extreme stressor and the impact of its absence on biological systems is ill-defined. Astronauts who have spent extended time under conditions of minimal gravity (microgravity) experience an array of biological alterations, including perturbations in cardiovascular function. We hypothesized that physiological perturbations in cardiac function in microgravity may be a consequence of alterations in molecular and organellar dynamics within the cellular milieu of cardiomyocytes. We used a combination of mass spectrometry-based approaches to compare the relative abundance and turnover rates of 848 and 196 proteins, respectively, in rat neonatal cardiomyocytes exposed to simulated microgravity or normal gravity. Gene functional enrichment analysis of these data suggested that the protein content and function of the mitochondria, ribosomes and endoplasmic reticulum were differentially modulated in microgravity. We confirmed experimentally that in microgravity protein synthesis was decreased while apoptosis, cell viability and protein degradation were largely unaffected. These data support our conclusion that in microgravity cardiomyocytes attempt to maintain mitochondrial homeostasis at the expense of protein synthesis. The overall response to this stress may culminate in cardiac muscle atrophy.
Stretch Injury of Human Induced Pluripotent Stem Cell Derived Neurons in a 96 Well Format
Authors: Sherman Sydney A. , Phillips Jack K. , Costa J. Tighe , Cho Frances S. , Oungoulian Sevan R. , Finan John D. 
Published: September 2016

AbstractTraumatic brain injury (TBI) is a major cause of mortality and morbidity with limited therapeutic options. Traumatic axonal injury (TAI) is an important component of TBI pathology. It is difficult to reproduce TAI in animal models of closed head injury, but in vitro stretch injury models reproduce clinical TAI pathology. Existing in vitro models employ primary rodent neurons or human cancer cell line cells in low throughput formats. This in vitro neuronal stretch injury model employs human induced pluripotent stem cell-derived neurons (hiPSCNs) in a 96 well format. Silicone membranes were attached to 96 well plate tops to create stretchable, culture substrates. A custom-built device was designed and validated to apply repeatable, biofidelic strains and strain rates to these plates. A high content approach was used to measure injury in a hypothesis-free manner. These measurements are shown to provide a sensitive, dose-dependent, multi-modal description of the response to mechanical insult. hiPSCNs transition from healthy to injured phenotype at approximately 35% Lagrangian strain. Continued development of this model may create novel opportunities for drug discovery and exploration of the role of human genotype in TAI pathology.
Fabrication of potato-like silver molybdate microstructures for photocatalytic degradation of chronic toxicity ciprofloxacin and highly selective electrochemical detection of H2O2
Authors: Kumar J. Vinoth , Karthik R. , Chen Shen-Ming , Muthuraj V. , Karuppiah Chelladurai 
Published: September 2016

AbstractIn the present work, potato-like silver molybdate (Ag2MoO4) microstructures were synthesized through a simple hydrothermal method. The microstructures of Ag2MoO4were characterized by various analytical and spectroscopic techniques such as XRD, FTIR, Raman, SEM, EDX and XPS. Interestingly, the as-prepared Ag2MoO4showed excellent photocatalytic and electrocatalytic activity for the degradation of ciprofloxacin (CIP) and electrochemical detection of hydrogen peroxide (H2O2), respectively. The ultraviolet-visible (UV-Vis) spectroscopy results revealed that the potato-like Ag2MoO4microstructures could offer a high photocatalytic activity towards the degradation of CIP under UV-light illumination, leads to rapid degradation within 40 min with a degradation rate of above 98%. In addition, the cyclic voltammetry (CV) and amperometry studies were realized that the electrochemical performance of Ag2MoO4modified electrode toward H2O2detection. Our H2O2sensor shows a wide linear range and lower detection limit of 0.04–240 μM and 0.03 μM, respectively. The Ag2MoO4modified electrode exhibits a high selectivity towards the detection of H2O2in the presence of different biological interferences. These results suggested that the development of potato-like Ag2MoO4microstructure could be an efficient photocatalyst as well as electrocatalyst in the potential application of environmental, biomedical and pharmaceutical samples.
Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods
Authors: Keisam Santosh , Romi Wahengbam , Ahmed Giasuddin , Jeyaram Kumaraswamy 
Published: September 2016

AbstractCultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9–52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods.
Reproductive toxicity and gender differences induced by cadmium telluride quantum dots in an invertebrate model organism
Authors: Yan Si-Qi , Xing Rui , Zhou Yan-Feng , Li Kai-Le , Su Yuan-Yuan , Qiu Jian-Feng , Zhang Yun-Hu , Zhang Ke-Qin , He Yao , Lu Xiao-Ping , Xu Shi-Qing 
Published: September 2016

AbstractSexual glands are key sites affected by nanotoxicity, but there is no sensitive assay for measuring reproductive toxicity in animals. The aim of this study was to investigate the toxic effects of cadmium telluride quantum dots (CdTe-QDs) on gonads in a model organism, Bombyx mori. After dorsal vein injection of 0.32 nmol of CdTe-QDs per individual, the QDs passed through the outer membranes of gonads via the generation of ROS in the membranes of spermatocysts and ovarioles, as well as internal germ cells, thereby inducing early germ cell death or malformations via complex mechanisms related to apoptosis and autophagy through mitochondrial and lysosomal pathways. Histological observations of the gonads and quantitative analyses of germ cell development showed that the reproductive toxicity was characterized by obvious male sensitivity. Exposure to QDs in the early stage of males had severe adverse effects on the quantity and quality of sperm, which was the main reason for the occurrence of unfertilized eggs. Ala- or Gly-conjugated QDs could reduce the nanotoxicity of CdTe-QDs during germ cell development and fertilization of their offspring. The results demonstrate that males are preferable models for evaluating the reproductive toxicity of QDs in combined in vivo/in vitro investigations.
Value of Measuring Bone Microarchitecture in Fracture Discrimination in Older Women with Recent Hip Fracture: A Case-control Study with HR-pQCT
Authors: Zhu Tracy Y. , Hung Vivian W. Y. , Cheung Wing-Hoi , Cheng Jack C. Y. , Qin Ling , Leung Kwok-Sui 
Published: September 2016

AbstractWe aimed to determine whether loss of volumetric bone mineral density (vBMD) and deterioration of microarchitecture imaged by high-resolution peripheral quantitative computed tomography at the distal radius/tibia provided additional information in fracture discrimination in postmenopausal women with recent hip fracture. This case-control study involved 24 postmenopausal Chinese women with unilateral femoral neck fracture (average [SD] age: 79.6[5.6]) and 24 age-matched women without any history of fracture. Each SD decrease in T-score at femoral neck (FN) was associated with a higher fracture risk (odds ratio: 6.905, p = 0.001). At the distal radius, fracture women had significantly lower total vBMD (−17.5%), fewer (−20.3%) and more unevenly spaced (81.4%) trabeculae and thinner cortices (−14.0%) (all p < 0.05). At the distal tibia, vBMD was on average −4.7% (cortical) to −25.4% (total) lower, trabecular microarchitecture was on average −19.8% (number) to 102% (inhomogeneity) inferior, cortices were thinner (−21.1%) and more porous (18.2%) (all p < 0.05). Adding parameters of vBMD and microarchitecture in multivariate models did not offer additional discriminative capacity of fracture status compared with using T-score at FN. In old postmenopausal women with already excessive loss of bone mass, measuring bone microarchitecture may provide limited added value to improve identification of risk of femoral neck fracture.
Layer-specific femorotibial cartilage T2 relaxation time in knees with and without early knee osteoarthritis: Data from the Osteoarthritis Initiative (OAI)
Authors: Wirth W. , Maschek S. , Roemer F.W. , Eckstein F. 
Published: September 2016

AbstractMagnetic resonance imaging (MRI)-based spin-spin relaxation time (T2) mapping has been shown to be associated with cartilage matrix composition (hydration, collagen content & orientation). To determine the impact of early radiographic knee osteoarthritis (ROA) and ROA risk factors on femorotibial cartilage composition, we studied baseline values and one-year change in superficial and deep cartilage T2 layers in 60 subjects (age 60.6 ± 9.6 y; BMI 27.8 ± 4.8) with definite osteophytes in one knee (earlyROA, n = 32) and with ROA risk factors in the contralateral knee (riskROA, n = 28), and 89 healthy subjects (age 55.0 ± 7.5 y; BMI 24.4 ± 3.1) without signs or risk factors of ROA. Baseline T2 did not differ significantly between earlyROA and riskROA knees in the superficial (48.0 ± 3.5 ms vs. 48.1 ± 3.1 ms) or the deep layer (37.3 ± 2.5 ms vs. 37.3 ± 1.8 ms). However, healthy knees showed significantly lower superficial layer T2 (45.4 ± 2.3 ms) than earlyROA or riskROA knees (p ≤ 0.001) and significantly lower deep layer T2 (35.8 ± 1.8 ms) than riskROA knees (p = 0.006). Significant longitudinal change in T2 (superficial: 0.5 ± 1.4 ms; deep: 0.8 ± 1.3 ms) was only detected in healthy knees. These results do not suggest an association of early ROA (osteophytes) with cartilage composition, as assessed by T2 mapping, whereas cartilage composition was observed to differ between knees with and without ROA risk factors.
Genome-wide association study suggests common variants within RP11-634B7.4 gene influencing severe pre-treatment pain in head and neck cancer patients
Authors: Reyes-Gibby Cielito C. , Wang Jian , Silvas Mary Rose T. , Yu Robert K. , Hanna Ehab Y. , Shete Sanjay 
Published: September 2016

AbstractPain is often one of the first signs of squamous cell carcinoma of the head and neck (HNSCC). Pain at diagnosis is an important prognostic marker for the development of chronic pain and importantly, for the overall survival time. To identify variants influencing severe pre-treatment pain in 1,368 patients newly diagnosed with HNSCC, we conducted a genome-wide association study based on 730,525 tagging SNPs. The patients were all previously untreated for cancer. About 15% of the patients had severe pre-treatment pain, defined as pain score ≥7 (0 = “no pain” and 10 = “worst pain”). We identified 3 common genetic variants in high linkage disequilibrium for severe pre-treatment pain, representing one genomic region at 1q44 (rs3862188, P = 3.45 × 10−8; rs880143, P = 3.45 × 10−8; and rs7526880, P = 4.92 × 10−8), which maps to the RP11-634B7.4 gene, a novel antisense gene to three olfactory receptor genes. Olfactory receptor genes, upstream effectors of the MAPK signaling cascade, might be novel target genes for pain in HNSCC patients. Future experimental validation to explore biological mechanisms will be key to defining the role of the intronic variants and non-coding RNA for pain in patients with HNSCC.
HydDB: A web tool for hydrogenase classification and analysis
Authors: Søndergaard Dan , Pedersen Christian N. S. , Greening Chris 
Published: September 2016

AbstractH2 metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla and are present in all major ecosystems. We developed a classification system and web tool, HydDB, for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe] and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors’ algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/