bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Sarcopenia and Osteoporosis in Male Tuberculosis Survivors: Korea National Health and Nutrition Examination Survey
Authors: Choi Chang-Jin , Choi Whan-Seok , Kim Churl-Min , Lee Sook-Young , Kim Kyung-Soo 
Published: October 2017

AbstractShort-term prospective studies have suggested that pulmonary tuberculosis (TB) preludes permanent loss of lean tissue and fat mass even when TB treatment is effective. The aim of this study was to estimate the risk of sarcopenia and osteoporosis among Korean male TB survivors. Data of the population-based, Korea National Health and Nutrition Examination Survey (KNHANES) (2008–2011) were analyzed, including 3,228 males aged 50 years or older who underwent chest X-ray (CXR) and dual-energy x-ray absorptiometry (DEXA). TB survivors having both medical history and TB scars on CXR had increased risk of sarcopenia (odds ratio [OR] 3.44, 95% confidence interval [CI] 1.79–6.68) and osteoporosis (OR 1.75, 95% CI 1.04–2.95) after adjusting for age, height, smoking, alcohol, physical activity, serum 25-hydroxyvitamin D, parathyroid hormone level, education, and fat mass index. Having TB scars on CXR without medical history of TB was an independent risk factor of sarcopenia (OR 2.05, 95% CI 1.05–4.00), but not a risk factor of osteoporosis. Sarcopenia and low bone mineral density are prevalent in pulmonary TB survivors with TB scars on CXR. Medical history of TB with TB scars on CXR is an independent risk factor for sarcopenia and osteoporosis.
Self-organisation of small-world networks by adaptive rewiring in response to graph diffusion
Authors: Jarman Nicholas , Steur Erik , Trengove Chris , Tyukin Ivan Y. , van Leeuwen Cees 
Published: October 2017

AbstractComplex networks emerging in natural and human-made systems tend to assume small-world structure. Is there a common mechanism underlying their self-organisation? Our computational simulations show that network diffusion (traffic flow or information transfer) steers network evolution towards emergence of complex network structures. The emergence is effectuated through adaptive rewiring: progressive adaptation of structure to use, creating short-cuts where network diffusion is intensive while annihilating underused connections. With adaptive rewiring as the engine of universal small-worldness, overall diffusion rate tunes the systems’ adaptation, biasing local or global connectivity patterns. Whereas the former leads to modularity, the latter provides a preferential attachment regime. As the latter sets in, the resulting small-world structures undergo a critical shift from modular (decentralised) to centralised ones. At the transition point, network structure is hierarchical, balancing modularity and centrality - a characteristic feature found in, for instance, the human brain.
Oxygen isotope anomaly in tropospheric CO2 and implications for CO2 residence time in the atmosphere and gross primary productivity
Authors: Liang Mao-Chang , Mahata Sasadhar , Laskar Amzad H. , Thiemens Mark H. , Newman Sally 
Published: October 2017

AbstractThe abundance variations of near surface atmospheric CO2isotopologues (primarily16O12C16O,16O13C16O,17O12C16O, and18O12C16O) represent an integrated signal from anthropogenic/biogeochemical processes, including fossil fuel burning, biospheric photosynthesis and respiration, hydrospheric isotope exchange with water, and stratospheric photochemistry. Oxygen isotopes, in particular, are affected by the carbon and water cycles. Being a useful tracer that directly probes governing processes in CO2biogeochemical cycles, Δ17O (=ln(1 + δ17O) − 0.516 × ln(1 + δ18O)) provides an alternative constraint on the strengths of the associated cycles involving CO2. Here, we analyze Δ17O data from four places (Taipei, Taiwan; South China Sea; La Jolla, United States; Jerusalem, Israel) in the northern hemisphere (with a total of 455 measurements) and find a rather narrow range (0.326 ± 0.005‰). A conservative estimate places a lower limit of 345 ± 70 PgC year−1on the cycling flux between the terrestrial biosphere and atmosphere and infers a residence time of CO2of 1.9 ± 0.3 years (upper limit) in the atmosphere. A Monte Carlo simulation that takes various plant uptake scenarios into account yields a terrestrial gross primary productivity of 120 ± 30 PgC year−1and soil invasion of 110 ± 30 PgC year−1, providing a quantitative assessment utilizing the oxygen isotope anomaly for quantifying CO2cycling.
Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes
Authors: Zapata Luis , Susak Hana , Drechsel Oliver , Friedländer Marc R. , Estivill Xavier , Ossowski Stephan 
Published: October 2017

AbstractTumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell fraction, population recurrence, and functional impact of somatic mutations as signatures of selection into a Bayesian model for driver prediction. We demonstrate that our model, cDriver, outperforms competing methods when analyzing solid tumors, hematological malignancies, and pan-cancer datasets. Applying cDriver to exome sequencing data of 21 cancer types from 6,870 individuals revealed 98 unreported tumor type-driver gene connections. These novel connections are highly enriched for chromatin-modifying proteins, hinting at a universal role of chromatin regulation in cancer etiology. Although infrequently mutated as single genes, we show that chromatin modifiers are altered in a large fraction of cancer patients. In summary, we demonstrate that integration of evolutionary signatures is key for identifying mutational driver genes, thereby facilitating the discovery of novel therapeutic targets for cancer treatment.
Plasmodium falciparum specific helicase 3 is nucleocytoplasmic protein and unwinds DNA duplex in 3′ to 5′ direction
Authors: Chauhan Manish , Tarique Mohammed , Tuteja Renu 
Published: October 2017

AbstractPlasmodium falciparum is responsible for most dangerous and prevalent form of malaria. The emergence of multi drug resistant parasite hindered the prevention of malaria burden worldwide. Helicases are omnipresent enzymes, which play important role in nucleic acid metabolism and can be used as potential targets for development of novel therapeutics. The genome wide analysis of P. falciparum 3D7 strain revealed some novel parasite specific helicases, which are not present in human host. Here we report the detailed biochemical characterization of P. falciparum parasite specific helicase 3 (PfPSH3). The characteristic ATPase and helicase activities of PfPSH3 reside in its N-terminal region (PfPSH3N) as it contains all the conserved signature motifs whereas the C-terminal does not show any detectable biochemical activity. PfPSH3N also shows DNA helicase activity in the 3′–5′ direction. The immunofluorescence microscopy results show that PSH3 is localized in nucleus as well as in cytoplasm during different stages such as trophozoite and early schizont stages of intraerythrocytic development. This report sets the foundation for further study of parasite specific helicases and will be helpful in understanding the parasite biology.
Adolescent Ethanol Exposure Enhances NMDA Receptor-Mediated Currents in Hippocampal Neurons: Reversal by Gabapentin
Authors: Swartzwelder H. S. , Park Maeng-Hee , Acheson Shawn 
Published: October 2017

AbstractAdolescent intermittent ethanol (AIE) exposure compromises neural function into adulthood. We have reported that astrocyte-secreted thrombospondins, and their target neuronal receptors (α2δ−1) are upregulated in the hippocampus in adulthood after AIE, suggesting aberrant excitatory synaptogenesis and hyperexcitability in memory-related circuits. Gabapentin antagonizes the interaction of thrombospondins (TSPs) with the α2δ−1 receptor, and thus may reverse or ameliorate the effects of AIE on hippocampal function. Adolescent rats were exposed to AIE or vehicle. In adulthood, hippocampal slices were prepared. Half of the slices from each animal were pre-incubated in normal artificial cerebrospinal fluid (aCSF) while half were pre-incubated in aCSF containing gabapentin. Whole-cell voltage clamp recordings were then made from CA1 pyramidal cells in normal aCSF. Evoked, N-methyl-D-aspartate (NMDA) receptor-mediated currents were recorded at baseline, and after application of the GluN2B antagonist, RO25–6981. Current amplitudes were higher in neurons from AIE-exposed animals. However, no amplitude increase was observed in neurons from slices that had been pre-incubation in gabapentin. GluN2B antagonism reduced NMDA receptor-mediated currents more efficaciously in cells from AIE-exposed animals, an effect that was also reversed by pre-incubation in gabapentin. These findings identify a mechanism underlying the enduring effects of AIE, and a clinically-utilized agent that may ameliorate those effects.
Transgenic Nicotiana benthamiana plants expressing a hairpin RNAi construct of a nematode Rs-cps gene exhibit enhanced resistance to Radopholus similis
Authors: Li Yu , Wang Ke , Lu Qisen , Du Juan , Wang Zhenyue , Wang Desen , Sun Bingjian , Li Honglian 
Published: October 2017

AbstractBurrowing nematodes (Radopholus similis) cause severe harm in many agronomic and horticultural crops and are very difficult to manage. Cathepsin S is one of the most important cysteine proteinases and plays key roles in nematodes and many other parasites. To evaluate the effect of in planta RNAi on the control of this nematode, a specific fragment from the protease gene, cathepsin S (Rs-cps), was cloned into the binary vector pFGC5941 in the forward and reverse orientations to construct recombinant plant RNAi vectors. Transgenic Nicotiana benthamiana plants expressing Rs-cps dsRNA were obtained and studied. The transcript abundance of Rs-cps dsRNA appeared to be diverse in the different transgenic lines. Moreover, the bioassay results revealed that Rs-cps transgenic N. benthamiana plants were resistant to R. similis and the transcription level of Rs-cps in R. similis was drastically decreased. In addition, the reproduction and hatching rate of R. similis isolated from the Rs-cps transgenic plants were also significantly reduced. Our results suggest that Rs-cps is essential for the reproduction and pathogenicity of R. similis. This is the first study to employ in planta RNAi approach to target the Rs-cps gene for the control of plant parasitic nematodes.
Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits
Authors: Naziga Emmanuel B. , Wereszczynski Jeff 
Published: October 2017

AbstractPili are elongated structures that protrude from bacteria and increase their virulence. TheStreptococcus pnuenomaepilus island 1 pili are composed of three subunits, RrgA, RrgB, and RrgC, and are assembled by three class C sortase C (SrtC) enzymes: SrtC-1, SrtC-2, and SrtC-3. Pilin subunits are recognized by SrtC proteins through a pentapeptide sorting signal, and while previous studies have sought to characterize the selectivities of SrtC isoforms for these subunits, the molecular mechanisms underlying these interactions remain unclear. Here, we report a series of molecular dynamics simulations of each SrtC enzyme with the sorting signals of RrgA, RrgB, and RrgC to determine the structural and thermodynamic basis of pilin recognition. Results show that, in accordance with previous studies, both SrtC-1 and SrtC-3 are selective for RrgB, while SrtC-2 is selective for RrgA. This specificity is tuned by the sorting signal binding conformation in which the first two residue sidechains complement hydrophobic residues around the active site, while the third residue projects away from the catalytic triad and makes specific interactions based on its charge and reach. Together, these results provided atomic-scale descriptions of the SrtC substrate selectivity mechanisms and extend the emerging model of pilin construction inS. pnuenomae.
Objective-lens-free Fiber-based Position Detection with Nanometer Resolution in a Fiber Optical Trapping System
Authors: Ti Chaoyang , Ho-Thanh Minh-Tri , Wen Qi , Liu Yuxiang 
Published: October 2017

AbstractPosition detection with high accuracy is crucial for force calibration of optical trapping systems. Most existing position detection methods require high-numerical-aperture objective lenses, which are bulky, expensive, and difficult to miniaturize. Here, we report an affordable objective-lens-free, fiber-based position detection scheme with 2 nm spatial resolution and 150 MHz bandwidth. This fiber based detection mechanism enables simultaneous trapping and force measurements in a compact fiber optical tweezers system. In addition, we achieved more reliable signal acquisition with less distortion compared with objective based position detection methods, thanks to the light guiding in optical fibers and small distance between the fiber tips and trapped particle. As a demonstration of the fiber based detection, we used the fiber optical tweezers to apply a force on a cell membrane and simultaneously measure the cellular response.
Methane fluxes from coastal sediments are enhanced by macrofauna
Authors: Bonaglia Stefano , Brüchert Volker , Callac Nolwenn , Vicenzi Alessandra , Chi Fru Ernest , Nascimento Francisco J. A. 
Published: October 2017

AbstractMethane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.
Genetic induction of hypometabolism by ablation of MC4R does not suppress ALS-like phenotypes in the G93A mutant SOD1 mouse model
Authors: Doshi Shachee , Gupta Preetika , Kalb Robert G. 
Published: October 2017

AbstractDysfunction and death of motor neurons leads to progressive paralysis in amyotrophic lateral sclerosis (ALS). Recent studies have reported organism-level metabolic dysfunction as a prominent but poorly understood feature of the disease. ALS patients are hypermetabolic with increased resting energy expenditure, but if and how hypermetabolism contributes to disease pathology is unknown. We asked if decreasing metabolism in the mutant superoxide dismutase 1 (SOD1) mouse model of ALS (G93A SOD1) would alter motor function and survival. To address this, we generated mice with the G93A SOD1 mutation that also lacked the melanocortin-4 receptor (MC4R). MC4R is a critical regulator of energy homeostasis and food intake in the hypothalamus. Loss of MC4R is known to induce hyperphagia and hypometabolism in mice. In the MC4R null background, G93A SOD1 mice become markedly hypometabolic, overweight and less active. Decreased metabolic rate, however, did not reverse any ALS-related disease phenotypes such as motor dysfunction or decreased lifespan. While hypermetabolism remains an intriguing target for intervention in ALS patients and disease models, our data indicate that the melanocortin system is not a good target for manipulation. Investigating other pathways may reveal optimal targets for addressing metabolic dysfunction in ALS.
Unwavering Pathobiology of Volumetric Muscle Loss Injury
Authors: Greising Sarah M. , Rivera Jessica C. , Goldman Stephen M. , Watts Alain , Aguilar Carlos A. , Corona Benjamin T. 
Published: October 2017

AbstractVolumetric muscle loss (VML) resulting from extremity trauma presents chronic and persistent functional deficits which ultimately manifest disability. Acellular biological scaffolds, or decellularized extracellular matrices (ECMs), embody an ideal treatment platform due to their current clinical use for soft tissue repair, off-the-shelf availability, and zero autogenous donor tissue burden. ECMs have been reported to promote functional skeletal muscle tissue remodeling in small and large animal models of VML injury, and this conclusion was reached in a recent clinical trial that enrolled 13 patients. However, numerous other pre-clinical reports have not observed ECM-mediated skeletal muscle regeneration. The current study was designed to reconcile these discrepancies. The capacity of ECMs to orchestrate functional muscle tissue remodeling was interrogated in a porcine VML injury model using unbiased assessments of muscle tissue regeneration and functional recovery. Here, we show that VML injury incites an overwhelming inflammatory and fibrotic response that leads to expansive fibrous tissue deposition and chronic functional deficits, which ECM repair does not augment.
New insights into the degradation mechanism of metal-organic frameworks drug carriers
Authors: Li X. , Lachmanski L. , Safi S. , Sene S. , Serre C. , Grenèche J. M. , Zhang J. , Gref R. 
Published: October 2017

AbstractA versatile method based on Raman microscopy was developed to follow the degradation of iron carboxylate Metal Organic Framework (MOF) nano- or micro-particles in simulated body fluid (phosphate buffer). The analysis of both the morphology and chemical composition of individual particles, including observation at different regions on the same particle, evidenced the formation of a sharp erosion front during particle degradation. Interestingly, this front separated an intact non eroded crystalline core from an amorphous shell made of an inorganic network. According to Mössbauer spectrometry investigations, the shell consists essentially of iron phosphates. Noteworthy, neither drug loading nor surface modification affected the integrity of the tridimensional MOF network. These findings could be of interest in the further development of next generations of MOF drug carriers.
Electrokinetic Analysis of Energy Harvest from Natural Salt Gradients in Nanochannels
Authors: He Yuhui , Huang Zhuo , Chen Bowei , Tsutsui Makusu , Shui Miao Xiang , Taniguchi Masateru 
Published: October 2017

AbstractThe Gibbs free energy released during the mixing of river and sea water has been illustrated as a promising source of clean and renewable energy. Reverse electrodialysis (RED) is one major strategy to gain electrical power from this natural salinity, and recently by utilizing nanochannels a novel mode of this approach has shown improved power density and energy converting efficiency. In this work, we carry out an electrokinetic analysis of the work extracted from RED in the nanochannels. First, we outline the exclusion potential effect induced by the inhomogeneous distribution of extra-counterions along the channel axis. This effect is unique in nanochannel RED and how to optimize it for energy harvesting is the central topic of this work. We then discuss two important indexes of performance, which are the output power density and the energy converting efficiency, and their dependence on the nanochannel parameters such as channel material and geometry. In order to yield maximized output electrical power, we propose a device design by stepwise usage of the saline bias, and the lengths of the nanochannels are optimized to achieve the best trade-off between the input thermal power and the energy converting efficiency.
Retinal Degeneration Protein 3 (RD3) in normal human tissues: Novel insights
Authors: Aravindan Sheeja , Somasundaram Dinesh Babu , Kam Kwok Ling , Subramanian Karthikeyan , Yu Zhongxin , Herman Terence S. , Fung Kar-Ming , Aravindan Natarajan 
Published: October 2017

AbstractThe 195-amino-acid-long human Retinal Degeneration Protein 3 (RD3) is critical in the regulation of guanylate cyclase (GC) signaling and photoreceptor cell survival. Recently, we identified significant loss of RD3 in high-risk neuroblastoma and the influential role of RD3 in tumor progression. However, the functional characterization of RD3 in tumor systems has been hampered by the dearth of information on its localization in normal tissue and by the lack of antibodies suitable for staining FFPE tissue, primarily due to the inaccessibility of the epitopes. In this study, we validated a custom-synthesized RD3 antibody and investigated the expression/localization of RD3 in assorted human tissues. We observed stratified expression of RD3 in different cell types and subcellular location of retina. We demonstrated extensive positive RD3 immunoreactivity in various normal tissues and particularly strong dot-like perinuclear staining in the lining epithelial cells, suggesting that RD3 may play an important role in the normal functioning of epithelial cells. RD3 expression is limited in the CNS. While neuroblastoma is often RD3-positive, the adrenal medulla, where many neuroblastomas originate, is RD3-negative. Meta-analysis of RD3 transcriptional expression across normal tissues confirmed tissue-specific RD3 mRNA levels. Our results revealed the tissue-specific expression/localization profile of RD3 for the first time.
Three-Dimensional Myoarchitecture of the Lower Esophageal Sphincter and Esophageal Hiatus Using Optical Sectioning Microscopy
Authors: Zifan Ali , Kumar Dushyant , Cheng Leo K. , Mittal Ravinder K. 
Published: October 2017

AbstractStudies to date have failed to reveal the anatomical counterpart of the lower esophageal sphincter (LES). We assessed the LES and esophageal hiatus morphology using a block containing the human LES and crural diaphragm, serially sectioned at 50 μm intervals and imaged at 8.2 μm/pixel resolution. A 3D reconstruction of the tissue block was reconstructed in which each of the 652 cross sectional images were also segmented to identify the boundaries of longitudinal (LM) and circular muscle (CM) layers. The CM fascicles on the ventral surface of LES are arranged in a helical/spiral fashion. On the other hand, the CM fascicles from the two sides cross midline on dorsal surface and continue as sling/oblique muscle on the stomach. Some of the LM fascicles of the esophagus leave the esophagus to enter into the crural diaphragm and the remainder terminate into the sling fibers of the stomach. The muscle fascicles of the right crus of diaphragm which form the esophageal hiatus are arranged like a “noose” around the esophagus. We propose that circumferential squeeze of the LES and crural diaphragm is generated by a unique myo-architectural design, each of which forms a “noose” around the esophagus.