bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial distributions and prognosis of bloodstream infections in patients with liver cirrhosis
Authors: Xie Yangxin , Tu Bo , Xu Zhe , Zhang Xin , Bi Jingfeng , Zhao Min , Chen Weiwei , Shi Lei , Zhao Peng , Bao Chunmei , Qin Enqiang , Xu Dongping 
Published: September 2017

AbstractBloodstream infections (BSIs) are a frequently observed complication in liver cirrhosis patients. This study aimed to investigate the microbiological characteristics and outcomes of BSIs in patients with liver cirrhosis. We retrospectively studied 852 patients with liver cirrhosis who developed a BSI. Patient outcome was evaluated using 30-day mortality and assessed using multivariate stepwise logistic regression analysis. Antibiotic sensitivity of the pathogens was tested. Gram-negative bacteria were responsible for 59.6% of BSIs, and Gram-positive bacteria caused 40.4% of the episodes among liver cirrhosis patients. The bacterial distribution significantly differed between hospital-acquired and community-acquired infections, especially in cases caused by Gram-negative pathogens. The results of the drug sensitivity test suggested that amikacin, cefoperazone/sulbactam, and piperacillin/tazobactam highly suppressed Gram-negative infections, while vancomycin and teicoplanin strongly inhibited Gram-positive BSIs. Liver failure, liver cancer, complications, Child-Pugh grade, septic shock, administration of appropriate antibiotics within 24 h, ICU admission, nosocomial infection, and Gram nature of the bacteria were independent risk factors for 30-day mortality (P < 0.05). The choice of initial empirical antibiotics should be based on the type, severity and origin of infection and on the local epidemiological data on antibiotic resistance. Accurate evaluation of risk factors for mortality may improve appropriate therapeutic choice.
The Cacna1h mutation in the GAERS model of absence epilepsy enhances T-type Ca2+ currents by altering calnexin-dependent trafficking of Cav3.2 channels
Authors: Proft Juliane , Rzhepetskyy Yuriy , Lazniewska Joanna , Zhang Fang-Xiong , Cain Stuart M. , Snutch Terrance P. , Zamponi Gerald W. , Weiss Norbert 
Published: September 2017

AbstractLow-voltage-activated T-type calcium channels are essential contributors to the functioning of thalamocortical neurons by supporting burst-firing mode of action potentials. Enhanced T-type calcium conductance has been reported in the Genetic Absence Epilepsy Rat from Strasbourg (GAERS) and proposed to be causally related to the overall development of absence seizure activity. Here, we show that calnexin, an endoplasmic reticulum integral membrane protein, interacts with the III-IV linker region of the Cav3.2 channel to modulate the sorting of the channel to the cell surface. We demonstrate that the GAERS missense mutation located in the Cav3.2 III-IV linker alters the Cav3.2/calnexin interaction, resulting in an increased surface expression of the channel and a concomitant elevation in calcium influx. Our study reveals a novel mechanism that controls the expression of T-type channels, and provides a molecular explanation for the enhancement of T-type calcium conductance in GAERS.
Voice selectivity in the temporal voice area despite matched low-level acoustic cues
Authors: Agus Trevor R. , Paquette Sébastien , Suied Clara , Pressnitzer Daniel , Belin Pascal 
Published: September 2017

AbstractIn human listeners, the temporal voice areas (TVAs) are regions of the superior temporal gyrus and sulcus that respond more to vocal sounds than a range of nonvocal control sounds, including scrambled voices, environmental noises, and animal cries. One interpretation of the TVA’s selectivity is based on low-level acoustic cues: compared to control sounds, vocal sounds may have stronger harmonic content or greater spectrotemporal complexity. Here, we show that the right TVA remains selective to the human voice even when accounting for a variety of acoustical cues. Using fMRI, single vowel stimuli were contrasted with single notes of musical instruments with balanced harmonic-to-noise ratios and pitches. We also used “auditory chimeras”, which preserved subsets of acoustical features of the vocal sounds. The right TVA was preferentially activated only for the natural human voice. In particular, the TVA did not respond more to artificial chimeras preserving the exact spectral profile of voices. Additional acoustic measures, including temporal modulations and spectral complexity, could not account for the increased activation. These observations rule out simple acoustical cues as a basis for voice selectivity in the TVAs.
Late-stage differentiation of embryonic pancreatic β-cells requires Jarid2
Authors: Cervantes Sara , Fontcuberta-PiSunyer Marta , Servitja Joan-Marc , Fernandez-Ruiz Rebeca , García Ainhoa , Sanchez Lidia , Lee Young-Sook , Gomis Ramon , Gasa Rosa 
Published: September 2017

AbstractJarid2 is a component of the Polycomb Repressor complex 2 (PRC2), which is responsible for genome-wide H3K27me3 deposition, in embryonic stem cells. However, Jarid2 has also been shown to exert pleiotropic PRC2-independent actions during embryogenesis. Here, we have investigated the role of Jarid2 during pancreas development. Conditional ablation of Jarid2 in pancreatic progenitors results in reduced endocrine cell area at birth due to impaired endocrine cell differentiation and reduced prenatal proliferation. Inactivation of Jarid2 in endocrine progenitors demonstrates that Jarid2 functions after endocrine specification. Furthermore, genome-wide expression analysis reveals that Jarid2 is required for the complete activation of the insulin-producing β-cell differentiation program. Jarid2-deficient pancreases exhibit impaired deposition of RNAPII-Ser5P, the initiating form of RNAPII, but no changes in H3K27me3, at the promoters of affected endocrine genes. Thus, our study identifies Jarid2 as a fine-tuner of gene expression during late stages of pancreatic endocrine cell development. These findings are relevant for generation of transplantable stem cell-derived β-cells.
Cleavage of 3′-terminal adenosine by archaeal ATP-dependent RNA ligase
Authors: Yoshinari Shigeo , Liu Yancheng , Gollnick Paul , Ho C. Kiong 
Published: September 2017

AbstractMethanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodiester bonds between the 5′-phosphate and 3′-hydroxyl termini of single-stranded RNAs. It can also react with RNA with a 3′-phosphate end to generate a 2′,3′-cyclic phosphate. Here, we show that MthRnl can additionally remove adenosine from the 3′-terminus of the RNA to produce 3′-deadenylated RNA, RNA(3′-rA). This 3′-deadenylation activity is metal-dependent and requires a 2′-hydroxyl at both the terminal adenosine and the penultimate nucleoside. Residues that contact the ATP/AMP in the MthRnl crystal structures are essential for the 3′-deadenylation activity, suggesting that 3′-adenosine may occupy the ATP-binding pocket. The 3′-end of cleaved RNA(3′-rA) consists of 2′,3′-cyclic phosphate which protects RNA(3′-rA) from ligation and further deadenylation. These findings suggest that ATP-dependent RNA ligase may act on a specific set of 3′-adenylated RNAs to regulate their processing and downstream biological events.
Rewiring of neuronal networks during synaptic silencing
Authors: Wrosch Jana Katharina , Einem Vicky von , Breininger Katharina , Dahlmanns Marc , Maier Andreas , Kornhuber Johannes , Groemer Teja Wolfgang 
Published: September 2017

AbstractAnalyzing the connectivity of neuronal networks, based on functional brain imaging data, has yielded new insight into brain circuitry, bringing functional and effective networks into the focus of interest for understanding complex neurological and psychiatric disorders. However, the analysis of network changes, based on the activity of individual neurons, is hindered by the lack of suitable meaningful and reproducible methodologies. Here, we used calcium imaging, statistical spike time analysis and a powerful classification model to reconstruct effective networks of primary rat hippocampal neurons in vitro. This method enables the calculation of network parameters, such as propagation probability, path length, and clustering behavior through the measurement of synaptic activity at the single-cell level, thus providing a fuller understanding of how changes at single synapses translate to an entire population of neurons. We demonstrate that our methodology can detect the known effects of drug-induced neuronal inactivity and can be used to investigate the extensive rewiring processes affecting population-wide connectivity patterns after periods of induced neuronal inactivity.
Electron beam detection of a Nanotube Scanning Force Microscope
Authors: Siria Alessandro , Niguès Antoine 
Published: September 2017

AbstractAtomic Force Microscopy (AFM) allows to probe matter at atomic scale by measuring the perturbation of a nanomechanical oscillator induced by near-field interaction forces. The quest to improve sensitivity and resolution of AFM forced the introduction of a new class of resonators with dimensions at the nanometer scale. In this context, nanotubes are the ultimate mechanical oscillators because of their one dimensional nature, small mass and almost perfect crystallinity. Coupled to the possibility of functionalisation, these properties make them the perfect candidates as ultra sensitive, on-demand force sensors. However their dimensions make the measurement of the mechanical properties a challenging task in particular when working in cavity free geometry at ambient temperature. By using a focused electron beam, we show that the mechanical response of nanotubes can be quantitatively measured while approaching to a surface sample. By coupling electron beam detection of individual nanotubes with a custom AFM we image the surface topography of a sample by continuously measuring the mechanical properties of the nanoresonators. The combination of very small size and mass together with the high resolution of the electron beam detection method offers unprecedented opportunities for the development of a new class of nanotube-based scanning force microscopy.
Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules
Authors: Buslaev Pavel , Gushchin Ivan 
Published: September 2017

AbstractMolecular dynamics simulations are used extensively to study the processes on biological membranes. The simulations can be conducted at different levels of resolution: all atom (AA), where all atomistic details are provided; united atom (UA), where hydrogen atoms are treated inseparably of corresponding heavy atoms; and coarse grained (CG), where atoms are grouped into larger particles. Here, we study the behavior of model bilayers consisting of saturated and unsaturated lipids DOPC, SOPC, OSPC and DSPC in simulations performed using all atom CHARMM36 and coarse grained Martini force fields. Using principal components analysis, we show that the structural and dynamical properties of the lipids are similar, both in AA and CG simulations, although the unsaturated molecules are more dynamic and favor more extended conformations. We find that CG simulations capture 75 to 100% of the major collective motions, overestimate short range ordering, result in more flexible molecules and 5–7 fold faster sampling. We expect that the results reported here will be useful for comprehensive quantitative comparisons of simulations conducted at different resolution levels and for further development and improvement of CG force fields.
Luminophore Configuration and Concentration-Dependent Optoelectronic Characteristics of a Quantum Dot-Embedded DNA Hybrid Thin film
Authors: Arasu Velu , Dugasani Sreekantha Reddy , Kesama Mallikarjuna Reddy , Chung Ho Kyoon , Park Sung Ha 
Published: September 2017

AbstractTo be useful in optoelectronic devices and sensors, a platform comprising stable fluorescence materials is essential. Here we constructed quantum dots (QDs) embedded DNA thin films which aims for stable fluorescence through the stabilization of QDs in the high aspect ratio salmon DNA (SDNA) matrix. Also for maximum luminescence, different concentration and configurations of core- and core/alloy/shell-type QDs were embedded within SDNA. The QD-SDNA thin films were constructed by drop-casting and investigated their optoelectronic properties. The infrared, UV-visible and photoluminescence (PL) spectroscopies confirm the embedment of QDs in the SDNA matrix. Absolute PL quantum yield of the QD-SDNA thin film shows the ~70% boost due to SDNA matrix compared to QDs alone in aqueous phase. The linear increase of PL photon counts from few to order of 5 while increasing [QD] reveals the non-aggregation of QDs within SDNA matrix. These systematic studies on the QD structure, absorbance, and concentration- and thickness-dependent optoelectronic characteristics demonstrate the novel properties of the QD-SDNA thin film. Consequently, the SDNA thin films were suggested to utilize for the generalised optical environments, which has the potential as a matrix for light conversion and harvesting nano-bio material as well as for super resolution bioimaging- and biophotonics-based sensors.
Identification of stiffness-induced signalling mechanisms in cells from patent and fused sutures associated with craniosynostosis
Authors: Barreto Sara , González-Vázquez Arlyng , R. Cameron Andrew , O’Brien Fergal J. , Murray Dylan J. 
Published: September 2017

AbstractCraniosynostosis is a bone developmental disease where premature ossification of the cranial sutures occurs leading to fused sutures. While biomechanical forces have been implicated in craniosynostosis, evidence of the effect of microenvironmental stiffness changes in the osteogenic commitment of cells from the sutures is lacking. Our aim was to identify the differential genetic expression and osteogenic capability between cells from patent and fused sutures of children with craniosynostosis and whether these differences are driven by changes in the stiffness of the microenvironment. Cells from both sutures demonstrated enhanced mineralisation with increasing substrate stiffness showing that stiffness is a stimulus capable of triggering the accelerated osteogenic commitment of the cells from patent to fused stages. The differences in the mechanoresponse of these cells were further investigated with a PCR array showing stiffness-dependent upregulation of genes mediating growth and bone development (TSHZ2, IGF1), involved in the breakdown of extracellular matrix (MMP9), mediating the activation of inflammation (IL1β) and controlling osteogenic differentiation (WIF1, BMP6, NOX1) in cells from fused sutures. In summary, this study indicates that stiffer substrates lead to greater osteogenic commitment and accelerated bone formation, suggesting that stiffening of the extracellular environment may trigger the premature ossification of the sutures.
Broadband acoustic skin cloak based on spiral metasurfaces
Authors: Wang Xu , Mao Dongxing , Li Yong 
Published: September 2017

AbstractA skin cloak based on the acoustic metasurface made of graded spiral units is proposed and numerically investigated. The presented skin cloak is an acoustical layer consisting of 80 subwavelength-sized unit cells, which provide precise local phase modulation and hence resort the disturbed sound filed in such a way to hide the object to acoustic wave. Numerical simulations show that the suggested skin cloak both work well under normal and small-angled incidences. By taking the advantage of the spiral-typed metasurface, the suggested skin cloak is rather thin with thickness in the order around 1/7 of the wavelength of target frequency, moreover, the intrinsic characteristics of modest dispersion ensure the skin cloak provides remarkable acoustic invisibility in a broad frequency ranging from 2500 Hz to 3600 Hz.
Detailed Balance Limit of Efficiency of Broadband-Pumped Lasers
Authors: Nechayev Sergey , Rotschild Carmel 
Published: September 2017

AbstractBroadband light sources are a wide class of pumping schemes for lasers including LEDs, sunlight and flash lamps. Recently, efficient coupling of broadband light to high-quality micro-cavities has been demonstrated for on-chip applications and low-threshold solar-pumped lasers via cascade energy transfer. However, the conversion of incoherent to coherent light comes with an inherent price of reduced efficiency, which has yet to be assessed. In this paper, we derive the detailed balance limit of efficiency of broadband-pumped lasers and discuss how it is affected by the need to maintain a threshold population inversion and thermodynamically dictated minimal Stokes’ shift. We show that lasers’ slope efficiency is analogous to the nominal efficiency of solar cells, limited by thermalisation losses and additional unavoidable Stokes’ shift. The lasers’ power efficiency is analogous to the detailed balance limit of efficiency of solar cells, affected by the cavity mirrors and impedance matching factor, respectively. As an example we analyze the specific case of solar-pumped sensitized Nd3+:YAG-like lasers and define the conditions to reach their thermodynamic limit of efficiency. Our work establishes an upper theoretical limit for the efficiency of broadband-pumped lasers. Our general, yet flexible model also provides a way to incorporate other optical and thermodynamic losses and, hence, to estimate the efficiency of non-ideal broadband-pumped lasers.
Phylogeography of the sand dollar genus Encope: implications regarding the Central American Isthmus and rates of molecular evolution
Authors: Coppard Simon E. , Lessios H. A. 
Published: September 2017

AbstractVicariant events have been widely used to calibrate rates of molecular evolution, the completion of the Central American Isthmus more extensively than any other. Recent studies have claimed that rather than the generally accepted date of ~3 million years ago (Ma), the Isthmus was effectively complete by the middle Miocene, 13 Ma. We present a fossil calibrated phylogeny of the new world sand dollar genus Encope, based on one nuclear and four mitochondrial genes, calibrated with fossils at multiple nodes. Present day distributions of Encope are likely the result of multiple range contractions and extinction events. Most species are now endemic to a single region, but one widely distributed species in each ocean is composed of morphotypes previously described as separate species. The most recent separation between eastern Pacific and Caribbean extant clades occurred at 4.90 Ma, indicating that the Isthmus of Panama allowed genetic exchange until the Pliocene. The rate of evolution of mitochondrial genes in Encope has been ten times slower than in the closely related genera Mellita and Lanthonia. This large difference in rates suggests that splits between eastern Pacific and Caribbean biota, dated on the assumption of a “universal” mitochondrial DNA clock are not valid.
Selective antibody activation through protease-activated pro-antibodies that mask binding sites with inhibitory domains
Authors: Chen I-Ju , Chuang Chih-Hung , Hsieh Yuan-Chin , Lu Yun-Chi , Lin Wen-Wei , Huang Chien-Chiao , Cheng Ta-Chun , Cheng Yi-An , Cheng Kai-Wen , Wang Yeng-Tseng , Chen Fang-Ming , Cheng Tian-Lu , Tzou Shey-Cherng 
Published: September 2017

AbstractSystemic injection of therapeutic antibodies may cause serious adverse effects due to on-target toxicity to the antigens expressed in normal tissues. To improve the targeting selectivity to the region of disease sites, we developed protease-activated pro-antibodies by masking the binding sites of antibodies with inhibitory domains that can be removed by proteases that are highly expressed at the disease sites. The latency-associated peptide (LAP), C2b or CBa of complement factor 2/B were linked, through a substrate peptide of matrix metalloproteinase-2 (MMP-2), to an anti-epidermal growth factor receptor (EGFR) antibody and an anti-tumor necrosis factor-α (TNF-α) antibody. Results showed that all the inhibitory domains could be removed by MMP-2 to restore the binding activities of the antibodies. LAP substantially reduced (53.8%) the binding activity of the anti-EGFR antibody on EGFR-expressing cells, whereas C2b and CBa were ineffective (21% and 9.3% reduction, respectively). Similarly, LAP also blocked 53.9% of the binding activity of the anti-TNF-α antibody. Finally, molecular dynamic simulation showed that the masking efficiency of LAP, C2b and CBa was 33.7%, 10.3% and −5.4%, respectively, over the binding sites of the antibodies. This strategy may aid in designing new protease-activated pro-antibodies that attain high therapeutic potency yet reduced systemic on-target toxicity.
Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors
Authors: Manasa Justen , Varghese Vici , Pond Sergei L. Kosakovsky , Rhee Soo-Yon , Tzou Philip L. , Fessel W. Jeffrey , Jang Karen S. , White Elizabeth , Rögnvaldsson Thorsteinn , Katzenstein David A. , Shafer Robert W. 
Published: September 2017

AbstractSeveral groups have proposed that genotypic determinants in gag and the gp41 cytoplasmic domain (gp41-CD) reduce protease inhibitor (PI) susceptibility without PI-resistance mutations in protease. However, no gag and gp41-CD mutations definitively responsible for reduced PI susceptibility have been identified in individuals with virological failure (VF) while receiving a boosted PI (PI/r)-containing regimen. To identify gag and gp41 mutations under selective PI pressure, we sequenced gag and/or gp41 in 61 individuals with VF on a PI/r (n = 40) or NNRTI (n = 20) containing regimen. We quantified nonsynonymous and synonymous changes in both genes and identified sites exhibiting signal for directional or diversifying selection. We also used published gag and gp41 polymorphism data to highlight mutations displaying a high selection index, defined as changing from a conserved to an uncommon amino acid. Many amino acid mutations developed in gag and in gp41-CD in both the PI- and NNRTI-treated groups. However, in neither gene, were there discernable differences between the two groups in overall numbers of mutations, mutations displaying evidence of diversifying or directional selection, or mutations with a high selection index. If gag and/or gp41 encode PI-resistance mutations, they may not be confined to consistent mutations at a few sites.
Cadmium effects on DNA and protein metabolism in oyster (Crassostrea gigas) revealed by proteomic analyses
Authors: Meng Jie , Wang Wenxiong , Li Li , Yin Qi , Zhang Guofan 
Published: September 2017

AbstractMarine molluscs, including oysters, can concentrate high levels of cadmium (Cd) in their soft tissues, but the molecular mechanisms of Cd toxicity remain speculative. In this study, Pacific oysters (Crassostrea gigas) were exposed to Cd for 9 days and their gills were subjected to proteomic analysis, which were further confirmed with transcriptomic analysis. A total of 4,964 proteins was quantified and 515 differentially expressed proteins were identified in response to Cd exposure. Gene Ontology enrichment analysis revealed that excess Cd affected the DNA and protein metabolism. Specifically, Cd toxicity resulted in the inhibition of DNA glycosylase and gap-filling and ligation enzymes expressions in base excision repair pathway, which may have decreased DNA repair capacity. At the protein level, Cd induced the heat shock protein response, initiation of protein refolding as well as degradation by ubiquitin proteasome pathway, among other effects. Excess Cd also induced antioxidant responses, particularly glutathione metabolism, which play important roles in Cd chelation and anti-oxidation. This study provided the first molecular mechanisms of Cd toxicity on DNA and protein metabolism at protein levels, and identified molecular biomarkers for Cd toxicity in oysters.