bluuebunny/crossref_metadata_2025_split huggingface dataset:
SUSD2 expression in high-grade serous ovarian cancer correlates with increased patient survival and defective mesothelial clearance
Authors: Sheets J N , Iwanicki M , Liu J F , Howitt B E , Hirsch M S , Gubbels J A A , Drapkin R , Egland K A 
Published: October 2016

AbstractThe cause of death among the majority of epithelial ovarian cancer (EOC) patients involves passive dissemination of cancer cells within the peritoneal cavity and subsequent implantation of cancer spheroids into adjacent organs. Thus, it is important to identify the factors that mediate EOC metastasis and implantation, including clearance of the mesothelium. Sushi domain containing 2 (SUSD2) encodes a type I transmembrane protein containing several functional domains inherent to adhesion molecules. Immunohistochemical analysis determined the presence of SUSD2 in several subtypes of EOC, with the strongest staining observed in high-grade serous ovarian carcinomas (HGSOCs). A high-density, clinically annotated HGSOC tissue microarray was stained with an anti-SUSD2 antibody. Patients with tumors that had a low percentage of SUSD2 staining cells had a shorter median survival (31.7 months) compared with patients who had tumors with extensive SUSD2 staining (49.1 months; P-value=0.0083). To investigate the role of SUSD2 in HGSOCs, stable OVCAR3, OVSAHO and KURAMOCHI cell lines were established with knockdown (KD) or non-targeting (NT) of SUSD2. Boyden chamber and wound-healing assays demonstrated that OVCAR3, OVSAHO and KURAMOCHI SUSD2-KD cells migrated at significantly higher rates compared with their SUSD2 NT counterpart cell lines. Quantitative reverse transcription–PCR and western immunoblot analysis indicated an inverse relationship between SUSD2 and well-characterized mesenchymal proteins, including Twist-1, Zeb-1, N-cadherin, STEAP1, AHNAK, Snail-1, COL5A2 and Snail-3 in OVCAR3, OVSAHO and KURAMOCHI cell line models. In addition, OVCAR3 and KURAMOCHI SUSD2-KD spheroids displayed increased mesothelial clearance ability compared with cells that express endogenous levels of SUSD2. These data suggest that SUSD2 has a role in the inhibition of mesothelial clearance, which is required for metastasis. Altogether, our findings indicate that SUSD2 impedes migration, epithelial-to-mesenchymal transitional and mesothelial clearance of HGSOC cells, consistent with prolonged survival of patients with SUSD2-expressing tumors.
A studyforrest extension, retinotopic mapping and localization of higher visual areas
Authors: Sengupta Ayan , Kaule Falko R. , Guntupalli J. Swaroop , Hoffmann Michael B. , Häusler Christian , Stadler Jörg , Hanke Michael 
Published: October 2016

AbstractThe studyforrest (http://studyforrest.org) dataset is likely the largest neuroimaging dataset on natural language and story processing publicly available today. In this article, along with a companion publication, we present an update of this dataset that extends its scope to vision and multi-sensory research. 15 participants of the original cohort volunteered for a series of additional studies: a clinical examination of visual function, a standard retinotopic mapping procedure, and a localization of higher visual areas—such as the fusiform face area. The combination of this update, the previous data releases for the dataset, and the companion publication, which includes neuroimaging and eye tracking data from natural stimulation with a motion picture, form an extremely versatile and comprehensive resource for brain imaging research—with almost six hours of functional neuroimaging data across five different stimulation paradigms for each participant. Furthermore, we describe employed paradigms and present results that document the quality of the data for the purpose of characterising major properties of participants’ visual processing stream.
Peptide-substituted oligonucleotide synthesis and non-toxic, passive cell delivery
Authors: Shang Shiying , Monfregola Luca , Caruthers Marvin H 
Published: October 2016

AbstractChemically modified oligodeoxynucleotides (ODNs) are known to modulate gene expression by interacting with RNA. An efficient approach for synthesizing amino acid- or peptide-substituted triazolylphosphonate analogs (TP ODNs) has been developed to provide improved stability and cell uptake. The chemistry is quite general, as peptides can be introduced throughout the TP ODN at any preselected internucleotide linkage. These synthetic TP ODNs enter cells through endocytosis in the absence of transfection reagents and localize into perinuclear organelles. The entrapped ODNs are released into the cytoplasm by treatment with endosomal-releasing agents and several are then active as microRNA inhibitors.
Superconducting nanowire single-photon detectors with non-periodic dielectric multilayers
Authors: Yamashita Taro , Waki Kentaro , Miki Shigehito , Kirkwood Robert A. , Hadfield Robert H. , Terai Hirotaka 
Published: October 2016

AbstractWe present superconducting nanowire single-photon detectors (SSPDs) on non-periodic dielectric multilayers, which enable us to design a variety of wavelength dependences of optical absorptance by optimizing the dielectric multilayer. By adopting a robust simulation to optimize the dielectric multilayer, we designed three types of SSPDs with target wavelengths of 500 nm, 800 nm, and telecom range respectively. We fabricated SSPDs based on the optimized designs for 500 and 800 nm, and evaluated the system detection efficiency at various wavelengths. The results obtained confirm that the designed SSPDs with non-periodic dielectric multilayers worked well. This versatile device structure can be effective for multidisciplinary applications in fields such as the life sciences and remote sensing that require high efficiency over a precise spectral range and strong signal rejection at other wavelengths.
Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics
Authors: Riley Blake T. , Ilyichova Olga , Costa Mauricio G. S. , Porebski Benjamin T. , de Veer Simon J. , Swedberg Joakim E. , Kass Itamar , Harris Jonathan M. , Hoke David E. , Buckle Ashley M. 
Published: October 2016

AbstractThe kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.
Energy Transfer Sensitization of Luminescent Gold Nanoclusters: More than Just the Classical Förster Mechanism
Authors: Oh Eunkeu , Huston Alan L. , Shabaev Andrew , Efros Alexander , Currie Marc , Susumu Kimihiro , Bussmann Konrad , Goswami Ramasis , Fatemi Fredrik K. , Medintz Igor L. 
Published: October 2016

AbstractLuminescent gold nanocrystals (AuNCs) are a recently-developed material with potential optic, electronic and biological applications. They also demonstrate energy transfer (ET) acceptor/sensitization properties which have been ascribed to Förster resonance energy transfer (FRET) and, to a lesser extent, nanosurface energy transfer (NSET). Here, we investigate AuNC acceptor interactions with three structurally/functionally-distinct donor classes including organic dyes, metal chelates and semiconductor quantum dots (QDs). Donor quenching was observed for every donor-acceptor pair although AuNC sensitization was only observed from metal-chelates and QDs. FRET theory dramatically underestimated the observed energy transfer while NSET-based damping models provided better fits but could not reproduce the experimental data. We consider additional factors including AuNC magnetic dipoles, density of excited-states, dephasing time, and enhanced intersystem crossing that can also influence ET. Cumulatively, data suggests that AuNC sensitization is not by classical FRET or NSET and we provide a simplified distance-independent ET model to fit such experimental data.
Emodin ameliorates bleomycin-induced pulmonary fibrosis in rats by suppressing epithelial-mesenchymal transition and fibroblast activation
Authors: Guan Ruijuan , Wang Xia , Zhao Xiaomei , Song Nana , Zhu Jimin , Wang Jijiang , Wang Jin , Xia Chunmei , Chen Yonghua , Zhu Danian , Shen Linlin 
Published: October 2016

AbstractAberrant activation of TGF-β1 is frequently encountered and promotes epithelial-mesenchymal transition (EMT) and fibroblast activation in pulmonary fibrosis. The present study investigated whether emodin mediates its effect via suppressing TGF-β1-induced EMT and fibroblast activation in bleomycin (BLM)-induced pulmonary fibrosis in rats. Here, we found that emodin induced apoptosis and inhibited cellular proliferation, migration and differentiation in TGF-β1-stimulated human embryonic lung fibroblasts (HELFs). Emodin suppressed TGF-β1-induced EMT in a dose- and time-dependent manner in alveolar epithelial A549 cells. Emodin also inhibited TGF-β1-induced Smad2, Smad3 and Erk1/2 activation, suggesting that Smad2/3 and Erk1/2 inactivation mediated the emodin-induced effects on TGF-β1-induced EMT. Additionally, we provided in vivo evidence suggesting that emodin apparently alleviated BLM-induced pulmonary fibrosis and improved pulmonary function by inhibiting TGF-β1 signaling and subsequently repressing EMT, fibroblast activation and extracellular matrix (ECM) deposition. Taken together, our data suggest that emodin mediates its effects mainly via inhibition of EMT and fibroblast activation and thus has a potential for the treatment of pulmonary fibrosis.
Use of next generation sequence to investigate potential novel macrolide resistance mechanisms in a population of Moraxella catarrhalis isolates
Authors: Liu Ya-Li , Li Dong-Fang , Xu He-Ping , Xiao Meng , Cheng Jing-Wei , Zhang Li , Xu Zhi-Peng , Chen Xin-Xin , Zhang Ge , Kudinha Timothy , Kong Fanrong , Gong Yan-Ping , Wang Xin-Ying , Zhang Yin-Xin , Wu Hong-Long , Xu Ying-Chun 
Published: October 2016

AbstractAlthough previous studies have confirmed that 23S rRNA gene mutation could be responsible for most of macrolide resistance in M. catarrhalis, a recent study suggested otherwise. Next generation sequence based comparative genomics has revolutionized the mining of potential novel drug resistant mechanisms. In this study, two pairs of resistant and susceptible M. catarrhalis isolates with different multilocus sequence types, were investigated for potential differential genes or informative single nucleotide polymorphisms (SNPs). The identified genes and SNPs were evaluated in 188 clinical isolates. From initially 12 selected differential genes and 12 informative SNPs, 10 differential genes (mboIA, mcbC, mcbI, mboIB, MCR_1794, MCR_1795, lgt2B/C, dpnI, mcbB, and mcbA) and 6 SNPs (C619T of rumA, T140C of rplF, G643A of MCR_0020, T270G of MCR_1465, C1348A of copB, and G238A of rrmA) were identified as possibly linked to macrolide resistance in M. catarrhalis. Most of the identified differential genes and SNPs are related to methylation of ribosomal RNA (rRNA) or DNA, especially MCR_0020 and rrmA. Further studies are needed to determine the function and/or evolution process, of the identified genes or SNPs, to establish whether some novel or combined mechanisms are truly involved in M. catarrhalis macrolide resistance mechanism.
REAC technology modifies pathological neuroinflammation and motor behaviour in an Alzheimer’s disease mouse model
Authors: Lorenzini Luca , Giuliani Alessandro , Sivilia Sandra , Baldassarro Vito Antonio , Fernandez Mercedes , Margotti Matteo Lotti , Giardino Luciana , Fontani Vania , Rinaldi Salvatore , Calzà Laura 
Published: October 2016

AbstractThe search for new therapeutic approaches to Alzheimer disease (AD) is a major goal in medicine and society, also due to the impressive economic and social costs of this disease. In this scenario, biotechnologies play an important role. Here, it is demonstrated that the Radio Electric Asymmetric Conveyer (REAC), an innovative technology platform for neuro- and bio-modulation, used according to the neuro-regenerative protocol (RGN-N), significantly increases astroglial reaction around the amyloid plaques in an AD mouse model, as evaluated by GFAP-immunoreactivity, and reduces microglia-associated neuroinflammation markers, as evaluated by Iba1-immunoreactivity and mRNA expression level of inflammatory cytokines TREM. IL1beta, iNOS and MRC1 were not affected neither by the genotype or by REAC RGN-N treatment. Also observed was an increase in locomotion in treated animals. The study was performed in 24-month-old male Tg2576 mice and age-matching wild-type animals, tested for Y-maze, contextual fear conditioning and locomotion immediately after the end of a specific REAC treatment administered for 15 hours/day for 15 days. These results demonstrated that REAC RGN-N treatment modifies pathological neuroinflammation, and mitigates part of the complex motor behaviour alterations observed in very old Tg2576 mice.
The temporal frequency tuning of continuous flash suppression reveals peak suppression at very low frequencies
Authors: Han Shui’er , Lunghi Claudia , Alais David 
Published: October 2016

AbstractContinuous flash suppression (CFS) is a psychophysical technique where a rapidly changing Mondrian pattern viewed by one eye suppresses the target in the other eye for several seconds. Despite the widespread use of CFS to study unconscious visual processes, the temporal tuning of CFS suppression is currently unknown. In the present study we used spatiotemporally filtered dynamic noise as masking stimuli to probe the temporal characteristics of CFS. Surprisingly, we find that suppression in CFS peaks very prominently at approximately 1 Hz, well below the rates typically used in CFS studies (10 Hz or more). As well as a strong bias to low temporal frequencies, CFS suppression is greater for high spatial frequencies and increases with increasing masker contrast, indicating involvement of parvocellular/ventral mechanisms in the suppression process. These results are reminiscent of binocular rivalry, and unifies two phenomenon previously thought to require different explanations.
Bacterial mimetics of endocrine secretory granules as immobilized in vivo depots for functional protein drugs
Authors: Céspedes María Virtudes , Fernández Yolanda , Unzueta Ugutz , Mendoza Rosa , Seras-Franzoso Joaquin , Sánchez-Chardi Alejando , Álamo Patricia , Toledo-Rubio Verónica , Ferrer-Miralles Neus , Vázquez Esther , Schwartz Simó , Abasolo Ibane , Corchero José Luis , Mangues Ramon , Villaverde Antonio 
Published: October 2016

AbstractIn the human endocrine system many protein hormones including urotensin, glucagon, obestatin, bombesin and secretin, among others, are supplied from amyloidal secretory granules. These granules form part of the so called functional amyloids, which within the whole aggregome appear to be more abundant than formerly believed. Bacterial inclusion bodies (IBs) are non-toxic, nanostructured functional amyloids whose biological fabrication can be tailored to render materials with defined biophysical properties. Since under physiological conditions they steadily release their building block protein in a soluble and functional form, IBs are considered as mimetics of endocrine secretory granules. We have explored here if the in vivo implantation of functional IBs in a given tissue would represent a stable local source of functional protein. Upon intratumoral injection of bacterial IBs formed by a potent protein ligand of CXCR4 we have observed high stability and prevalence of the material in absence of toxicity, accompanied by apoptosis of CXCR4+ cells and tumor ablation. Then, the local immobilization of bacterial amyloids formed by therapeutic proteins in tumors or other tissues might represent a promising strategy for a sustained local delivery of protein drugs by mimicking the functional amyloidal architecture of the mammals’ endocrine system.
Multilocus sequence analysis reveals high genetic diversity in clinical isolates of Burkholderia cepacia complex from India
Authors: Gautam Vikas , Patil Prashant P. , Kumar Sunil , Midha Samriti , Kaur Mandeep , Kaur Satinder , Singh Meenu , Mali Swapna , Shastri Jayanthi , Arora Anita , Ray Pallab , Patil Prabhu B. 
Published: October 2016

AbstractBurkholderia cepacia complex (Bcc) is a complex group of bacteria causing opportunistic infections in immunocompromised and cystic fibrosis (CF) patients. Herein, we report multilocus sequence typing and analysis of the 57 clinical isolates of Bcc collected over the period of seven years (2005–2012) from several hospitals across India. A total of 21 sequence types (ST) including two STs from cystic fibrosis patient’s isolates and twelve novel STs were identified in the population reflecting the extent of genetic diversity. Multilocus sequence analysis revealed two lineages in population, a major lineage belonging to B. cenocepacia and a minor lineage belonging to B. cepacia. Split-decomposition analysis suggests absence of interspecies recombination and intraspecies recombination contributed in generating genotypic diversity amongst isolates. Further linkage disequilibrium analysis indicates that recombination takes place at a low frequency, which is not sufficient to break down the clonal relationship. This knowledge of the genetic structure of Bcc population from a rapidly developing country will be invaluable in the epidemiology, surveillance and understanding global diversity of this group of a pathogen.
Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics
Authors: Pärnänen Katariina , Karkman Antti , Tamminen Manu , Lyra Christina , Hultman Jenni , Paulin Lars , Virta Marko 
Published: October 2016

AbstractAntibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.
Coupling of carbon and silicon geochemical cycles in rivers and lakes
Authors: Wang Baoli , Liu Cong-Qiang , Maberly Stephen C. , Wang Fushun , Hartmann Jens 
Published: October 2016

AbstractCarbon (C) and silicon (Si) biogeochemical cycles are important factors in the regulation of atmospheric CO2 concentrations and hence climate change. Theoretically, these elements are linked by chemical weathering and organism stoichiometry, but this coupling has not been investigated in freshwaters. Here we compiled data from global rivers and lakes in the United States of America and the United Kingdom, in order to characterize the stoichiometry between the biogeochemical cycles of C and Si. In rivers this coupling is confirmed by a significant relationship between HCO3−/Na+ and DSi/Na+, and DSi:HCO3− ratio can reflect the mineral source of chemical weathering. In lakes, however, these characteristic ratios of chemical weathering are altered by algal activity. The lacustrine Si:C atomic ratio is negative feedback regulation by phytoplankton, which may result in this ratio in algal assemblages similar to that in water column. And this regulation suggests lacustrine photosynthetic C fixation in this equilibrium state is quantitative and depends on the DSi concentration. These findings provide new insights into the role of freshwaters in global C and Si biogeochemical cycles.
Microchip-based ultrafast serodiagnostic assay for tuberculosis
Authors: Mani Vigneshwaran , Paleja Bhairav , Larbi Karima , Kumar Pavanish , Tay Jo Ann , Siew Jie Yee , Inci Fatih , Wang ShuQi , Chee Cynthia , Wang Yee Tang , Demirci Utkan , De Libero Gennaro , Singhal Amit 
Published: October 2016

AbstractAccess to point-of-care (POC), rapid, inexpensive, sensitive, and instrument-free tests for the diagnosis of tuberculosis (TB) remains a major challenge. Here, we report a simple and low-cost microchip-based TB ELISA (MTBE) platform for the detection of anti-mycobacterial IgG in plasma samples in less than 15 minutes. The MTBE employs a flow-less, magnet-actuated, bead-based ELISA for simultaneous detection of IgG responses against multiple mycobacterial antigens. Anti-trehalose 6,6′-dimycolate (TDM) IgG responses were the strongest predictor for differentiating active tuberculosis (ATB) from healthy controls (HC) and latent tuberculosis infections (LTBI). The TDM-based MTBE demonstrated superior sensitivity compared to sputum microscopy (72% vs. 56%) with 80% and 63% positivity among smear-positive and smear-negative confirmed ATB samples, respectively. Receiver operating characteristic analysis indicated good accuracy for differentiating ATB from HC (AUC = 0.77). Thus, TDM-based MTBE can be potentially used as a screening device for rapid diagnosis of active TB at the POC.
Adverse Cardiovascular Outcomes associated with Coronary Artery Bypass Surgery and Percutaneous Coronary Intervention with Everolimus Eluting Stents: A Meta-Analysis
Authors: Bundhun Pravesh Kumar , Pursun Manish , Teeluck Abhishek Rishikesh , Bhurtu Akash , Soogund Mohammad Zafooruddin Sani , Huang Wei-Qiang 
Published: October 2016

AbstractThis study aimed to compare the mid-term adverse cardiovascular outcomes associated with Coronary Artery Bypass Surgery (CABG) and Percutaneous Coronary Intervention (PCI) with Everolimus Eluting Stents (EES). Electronic databases were searched for studies comparing the mid-term (>1 year) adverse cardiovascular outcomes between CABG and PCI with EES. Odd Ratios (OR) with 95% Confidence Intervals (CIs) were calculated and the pooled analyses were performed with RevMan 5.3 software. A total number of 5207 patients were involved in this analysis. No significant difference was observed in mortality between CABG and EES with OR: 0.90, 95% CI: 0.73–1.10; P = 0.30. Moreover, CABG was associated with a high stroke rate, with OR: 0.73, 95% CI: 0.45–1.17; P = 0.19, without any statistical significant. CABG was associated with significantly lower Major Adverse Cardiac Events and Myocardial Infarction with OR: 1.46, 95% CI: 1.05–2.04; P = 0.03 and OR: 1.46, 95% CI: 1.01–2.12; P = 0.05 respectively whereas PCI was associated with a significantly higher repeated revascularization with OR: 2.21; 95% CI: 1.76–2.77; P = 0.00001. In conclusion, significant differences were noted in several subgroups analyzing the mid-term cardiovascular outcomes between CABG and EES.