bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fibroblasts profiling in scarring trachoma identifies IL-6 as a functional component of a fibroblast-macrophage pro-fibrotic and pro-inflammatory feedback loop
Authors: Kechagia Jenny Z. , Ezra Daniel G. , Burton Matthew J. , Bailly Maryse 
Published: June 2016

AbstractTrachoma is a conjunctiva scarring disease, which is the leading infectious cause of blindness worldwide. Yet, the molecular mechanisms underlying progressive fibrosis in trachoma are unknown. To investigate the contribution of local resident fibroblasts to disease progression, we isolated conjunctival fibroblasts from patients with scarring trachoma and matching control individuals and compared their gene expression profiles and functional properties in vitro. We show that scarring trachoma fibroblasts substantially differ from control counterparts, displaying pro-fibrotic and pro-inflammatory features matched by an altered gene expression profile. This pro-inflammatory signature was exemplified by increased IL-6 expression and secretion and a stronger response to macrophage-mediated stimulation of contraction. We further demonstrate that scarring trachoma fibroblasts can promote Akt phosphorylation in macrophages in an IL-6 –dependent manner. Overall this work has uncovered a distinctive molecular fingerprint for scarring trachoma fibroblasts and identified IL-6- as a potential contributor to the chronic conjunctival fibrosis, mediating reciprocal pro-fibrotic/pro-inflammatory interactions between macrophages and fibroblasts.
Detection of orbital angular momentum using a photonic integrated circuit
Authors: Rui Guanghao , Gu Bing , Cui Yiping , Zhan Qiwen 
Published: June 2016

AbstractOrbital angular momentum (OAM) state of photons offer an attractive additional degree of freedom that has found a variety of applications. Measurement of OAM state, which is a critical task of these applications, demands photonic integrated devices for improved fidelity, miniaturization, and reconfiguration. Here we report the design of a silicon-integrated OAM receiver that is capable of detecting distinct and variable OAM states. Furthermore, the reconfiguration capability of the detector is achieved by applying voltage to the GeSe film to form gratings with alternate states. The resonant wavelength for arbitrary OAM state is demonstrated to be tunable in a quasi-linear manner through adjusting the duty cycle of the gratings. This work provides a viable approach for the realization of a compact integrated OAM detection device with enhanced functionality that may find important applications in optical communications and information processing with OAM states.
Ultramicroscopy as a novel tool to unravel the tropism of AAV gene therapy vectors in the brain
Authors: Alves Sandro , Bode Julia , Bemelmans Alexis-Pierre , von Kalle Christof , Cartier Nathalie , Tews Björn 
Published: June 2016

AbstractRecombinant adeno-associated viral (AAV) vectors have advanced to the vanguard of gene therapy. Numerous naturally occurring serotypes have been used to target cells in various tissues. There is a strong need for fast and dynamic methods which efficiently unravel viral tropism in whole organs. Ultramicroscopy (UM) is a novel fluorescence microscopy technique that images optically cleared undissected specimens, achieving good resolutions at high penetration depths while being non-destructive. UM was applied to obtain high-resolution 3D analysis of AAV transduction in adult mouse brains, especially in the hippocampus, a region of interest for Alzheimer’s disease therapy. We separately or simultaneously compared transduction efficacies for commonly used serotypes (AAV9 and AAVrh10) using fluorescent reporter expression. We provide a detailed comparative and quantitative analysis of the transduction profiles. UM allowed a rapid analysis of marker fluorescence expression in neurons with intact projections deep inside the brain, in defined anatomical structures. Major hippocampal neuronal transduction was observed with both vectors, with slightly better efficacy for AAV9 in UM. Glial response and synaptic marker expression did not change post transduction.We propose UM as a novel valuable complementary tool to efficiently and simultaneously unravel tropism of different viruses in a single non-dissected adult rodent brain.
Cosmological flux noise and measured noise power spectra in SQUIDs
Authors: Beck Christian 
Published: June 2016

AbstractThe understanding of the origin of 1/f magnetic flux noise commonly observed in superconducting devices such as SQUIDs and qubits is still a major unsolved puzzle. Here we discuss the possibility that a significant part of the observed low-frequency flux noise measured in these devices is ultimately seeded by cosmological fluctuations. We consider a theory where a primordial flux noise field left over in unchanged form from an early inflationary or quantum gravity epoch of the universe intrinsically influences the phase difference in SQUIDs and qubits. The perturbation seeds generated by this field can explain in a quantitatively correct way the form and amplitude of measured low-frequency flux noise spectra in SQUID devices if one takes as a source of fluctuations the primordial power spectrum of curvature fluctuations as measured by the Planck collaboration. Our theoretical predictions are in excellent agreement with recent low-frequency flux noise measurements of various experimental groups. Magnetic flux noise, so far mainly considered as a nuisance for electronic devices, may thus contain valuable information about fluctuation spectra in the very early universe.
The use of green tea polyphenols for treating residual albuminuria in diabetic nephropathy: A double-blind randomised clinical trial
Authors: Borges Cynthia M. , Papadimitriou Alexandros , Duarte Diego A. , Lopes de Faria Jacqueline M. , Lopes de Faria José B. 
Published: June 2016

AbstractPrior research has shown that in experimental diabetes mellitus, green tea reduces albuminuria by decreasing podocyte apoptosis through activation of the WNT pathway. We investigated the effect of green tea polyphenols (GTP) on residual albuminuria of diabetic subjects with nephropathy. We conducted a randomised, double-blind study in 42 diabetic subjects with a urinary albumin-creatinine ratio (UACR) >30 mg/g, despite administration of the maximum recommended dose of renin-angiotensin (RAS) inhibition. Patients were randomly assigned to two equal groups to receive either GTP (containing 800 mg of epigallocatechin gallate, 17 with type 2 diabetes and 4 with type 1 diabetes) or placebo (21 with type 2 diabetes) for 12 weeks. Treatment with GTP reduced UACR by 41%, while the placebo group saw a 2% increase in UACR (p = 0.019). Podocyte apoptosis (p = 0.001) and in vitro albumin permeability (p < 0.001) were higher in immortalized human podocytes exposed to plasma from diabetic subjects compared to podocytes treated with plasma from normal individuals. In conclusion, GTP administration reduces albuminuria in diabetic patients receiving the maximum recommended dose of RAS. Reduction in podocyte apoptosis by activation of the WNT pathway may have contributed to this effect.
A quantitative metabolomics study of high sodium response in Clostridium acetobutylicum ATCC 824 acetone-butanol-ethanol (ABE) fermentation
Authors: Zhao Xinhe , Condruz Stefan , Chen Jingkui , Jolicoeur Mario 
Published: June 2016

AbstractHemicellulose hydrolysates, sugar-rich feedstocks used in biobutanol refinery, are normally obtained by adding sodium hydroxide in the hydrolyze process. However, the resulting high sodium concentration in the hydrolysate inhibits ABE (acetone-butanol-ethanol) fermentation, and thus limits the use of these low-cost feedstocks. We have thus studied the effect of high sodium on the metabolic behavior of Clostridium acetobutyricum ATCC 824, with xylose as the carbon source. At a threshold sodium concentration of 200 mM, a decrease of the maximum cell dry weight (−19.50 ± 0.85%) and of ABE yield (−35.14 ± 3.50% acetone, −33.37 ± 0.74% butanol, −22.95 ± 1.81% ethanol) were observed compared to control culture. However, solvents specific productivities were not affected by supplementing sodium. The main effects of high sodium on cell metabolism were observed in acidogenesis, during which we observed the accumulation of ATP and NADH, and the inhibition of the pentose phosphate (PPP) and the glycolytic pathways with up to 80.73 ± 1.47% and 68.84 ± 3.42% decrease of the associated metabolic intermediates, respectively. However, the NADP+-to-NADPH ratio was constant for the whole culture duration, a phenomenon explaining the robustness of solvents specific productivities. Therefore, high sodium, which inhibited biomass growth through coordinated metabolic effects, interestingly triggered cell robustness on solvents specific productivity.
Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome
Authors: Miyazato Paola , Katsuya Hiroo , Fukuda Asami , Uchiyama Yoshikazu , Matsuo Misaki , Tokunaga Michiyo , Hino Shinjiro , Nakao Mitsuyoshi , Satou Yorifumi 
Published: June 2016

AbstractThe recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive.
Isolation and characterization of a bacteriophage phiEap-2 infecting multidrug resistant Enterobacter aerogenes
Authors: Li Erna , Wei Xiao , Ma Yanyan , Yin Zhe , Li Huan , Lin Weishi , Wang Xuesong , Li Chao , Shen Zhiqiang , Zhao Ruixiang , Yang Huiying , Jiang Aimin , Yang Wenhui , Yuan Jing , Zhao Xiangna 
Published: June 2016

AbstractEnterobacter aerogenes (Enterobacteriaceae) is an important opportunistic pathogen that causes hospital-acquired pneumonia, bacteremia, and urinary tract infections. Recently, multidrug-resistant E. aerogenes have been a public health problem. To develop an effective antimicrobial agent, bacteriophage phiEap-2 was isolated from sewage and its genome was sequenced because of its ability to lyse the multidrug-resistant clinical E. aerogenes strain 3-SP. Morphological observations suggested that the phage belongs to the Siphoviridae family. Comparative genome analysis revealed that phage phiEap-2 is related to the Salmonella phage FSL SP-031 (KC139518). All of the structural gene products (except capsid protein) encoded by phiEap-2 had orthologous gene products in FSL SP-031 and Serratia phage Eta (KC460990). Here, we report the complete genome sequence of phiEap-2 and major findings from the genomic analysis. Knowledge of this phage might be helpful for developing therapeutic strategies against E. aerogenes.
Honeybee economics: optimisation of foraging in a variable world
Authors: Stabentheiner Anton , Kovac Helmut 
Published: June 2016

AbstractIn honeybees fast and efficient exploitation of nectar and pollen sources is achieved by persistent endothermy throughout the foraging cycle, which means extremely high energy costs. The need for food promotes maximisation of the intake rate and the high costs call for energetic optimisation. Experiments on how honeybees resolve this conflict have to consider that foraging takes place in a variable environment concerning microclimate and food quality and availability. Here we report, in simultaneous measurements of energy costs, gains and intake rate and efficiency, how honeybee foragers manage this challenge in their highly variable environment. If possible, during unlimited sucrose flow, they follow an ‘investment-guided’ (‘time is honey’) economic strategy promising increased returns. They maximise net intake rate by investing both own heat production and solar heat to increase body temperature to a level which guarantees a high suction velocity. They switch to an ‘economizing’ (‘save the honey’) optimisation of energetic efficiency if the intake rate is restricted by the food source when an increased body temperature would not guarantee a high intake rate. With this flexible and graded change between economic strategies honeybees can do both maximise colony intake rate and optimise foraging efficiency in reaction to environmental variation.
The hexagonal shape of the honeycomb cells depends on the construction behavior of bees
Authors: Nazzi Francesco 
Published: June 2016

AbstractThe hexagonal shape of the honey bee cells has attracted the attention of humans for centuries. It is now accepted that bees build cylindrical cells that later transform into hexagonal prisms through a process that it is still debated. The early explanations involving the geometers’ skills of bees have been abandoned in favor of new hypotheses involving the action of physical forces, but recent data suggest that mechanical shaping by bees plays a role. However, the observed geometry can arise only if isodiametric cells are previously arranged in a way that each one is surrounded by six other similar cells; here I suggest that this is a consequence of the building program adopted by bees and propose a possible behavioral rule ultimately accounting for the hexagonal shape of bee cells.
Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis
Authors: Martins Polyana Kelly , Mafra Valéria , de Souza Wagner Rodrigo , Ribeiro Ana Paula , Vinecky Felipe , Basso Marcos Fernando , da Cunha Bárbara Andrade Dias Brito , Kobayashi Adilson Kenji , Molinari Hugo Bruno Correa 
Published: June 2016

AbstractReal-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but reliable results depend on the use of stable reference genes for proper normalization. This study proposed to test the expression stability of 13 candidate reference genes in Setaria viridis, a monocot species recently proposed as a new C4 model plant. Gene expression stability of these genes was assayed across different tissues and developmental stages of Setaria and under drought or aluminum stress. In general, our results showed Protein Kinase, RNA Binding Protein and SDH as the most stable genes. Moreover, pairwise analysis showed that two reference genes were sufficient to normalize the gene expression data under each condition. By contrast, GAPDH and ACT were the least stably expressed genes tested. Validation of suitable reference genes was carried out to profile the expression of P5CS and GolS during abiotic stress. In addition, normalization of gene expression of SuSy, involved in sugar metabolism, was assayed in the developmental dataset. This study provides a list of reliable reference genes for transcript normalization in S. viridis in different tissues and stages of development and under abiotic stresses, which will facilitate genetic studies in this monocot model plant.
Rare coding TTN variants are associated with electrocardiographic QT interval in the general population
Authors: Kapoor Ashish , Bakshy Kiranmayee , Xu Linda , Nandakumar Priyanka , Lee Dongwon , Boerwinkle Eric , Grove Megan L. , Arking Dan E. , Chakravarti Aravinda 
Published: June 2016

AbstractWe have shown previously that noncoding variants mapping around a specific set of 170 genes encoding cardiomyocyte intercalated disc (ID) proteins are more enriched for associations with QT interval than observed for genome-wide comparisons. At a false discovery rate (FDR) of 5%, we had identified 28 such ID protein-encoding genes. Here, we assessed whether coding variants at these 28 genes affect QT interval in the general population as well. We used exome sequencing in 4,469 European American (EA) and 1,880 African American (AA) ancestry individuals from the population-based ARIC (Atherosclerosis Risk In Communities) Study cohort to focus on rare (allele frequency <1%) potentially deleterious (nonsynonymous, stop-gain, splice) variants (n = 2,398 for EA; n = 1,693 for AA) and tested their effects on standardized QT interval residuals. We identified 27 nonsynonymous variants associated with QT interval (FDR 5%), 22 of which were in TTN. Taken together with the mapping of a QT interval GWAS locus near TTN, our observation of rare deleterious coding variants in TTN associated with QT interval show that TTN plays a role in regulation of cardiac electrical conductance and coupling and is a risk factor for cardiac arrhythmias and sudden cardiac death.
Alpinetin attenuates inflammatory responses by suppressing TLR4 and NLRP3 signaling pathways in DSS-induced acute colitis
Authors: He Xuexiu , Wei Zhengkai , Wang Jingjing , Kou Jinhua , Liu Weijian , Fu Yunhe , Yang Zhengtao 
Published: June 2016

AbstractAlpinetin, a composition of Alpinia katsumadai Hayata, has been reported to have a number of biological properties, such as antibacterial, antitumor and other important therapeutic activities. However, the effect of alpinetin on inflammatory bowel disease (IBD) has not yet been reported. The purpose of this study was to investigate the anti-inflammatory effect and mechanism of alpinetin on dextran sulfate sodium (DSS)-induced colitis in mice. In vivo, DSS-induced mice colitis model was established by giving mice drinking water containing 5% (w/v) DSS for 7 days. Alpinetin (25, 50 and 100 mg/kg) were administered once a day by intraperitoneal injection 3 days before DSS treatment. In vitro, phorbol myristate acetate (PMA)-differentiated monocytic THP-1 macrophages were treated with alpinetin and stimulated by lipopolysaccharide (LPS). The results showed that alpinetin significantly attenuated diarrhea, colonic shortening, histological injury, myeloperoxidase (MPO) activity and the expressions of tumor necrosis factor (TNF-α) and interleukin (IL-1β) production in mice. In vitro, alpinetin markedly inhibited LPS-induced TNF-α and IL-1β production, as well as Toll-like receptor 4 (TLR4) mediated nuclear transcription factor-kappaB (NF-κB) and NOD-like receptor protein 3 (NLRP3) inflammasome activation. In conclusion, this study demonstrated that alpinetin had protective effects on DSS-induced colitis and may be a promising therapeutic reagent for colitis treatment.
Identification of long non-coding RNAs involved in neuronal development and intellectual disability
Authors: D’haene Eva , Jacobs Eva Z. , Volders Pieter-Jan , De Meyer Tim , Menten Björn , Vergult Sarah 
Published: June 2016

AbstractRecently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
Cervical Spine Clearance in Pediatric Trauma Centers: The Need for Standardization and an Evidence-based Protocol
Authors: Pannu Gurpal S. , Shah Mitesh P. , Herman Marty J. 
Published: June 2016

Background:
Cervical spine clearance in the pediatric trauma patient represents a particularly challenging task. Unfortunately, standardized clearance protocols for pediatric cervical clearance are poorly reported in the literature and imaging recommendations demonstrate considerable variability. With the use of a web-based survey, this study aims to define the methods utilized by pediatric trauma centers throughout North America. Specific attention was given to the identification of personnel responsible for cervical spine care, diagnostic imaging modalities used, and the presence or absence of a written pediatric cervical spine clearance protocol.

Methods:
A 10-question electronic survey was given to members of the newly formed Pediatric Cervical Spine Study Group, all of whom are active POSNA members. The survey was submitted via the online service SurveyMonkey (https://www.surveymonkey.com/r/7NVVQZR). The survey assessed the respondent’s institution demographics, such as trauma level and services primarily responsible for consultation and operative management of cervical spine injuries. In addition, respondents were asked to identify the protocols and primary imaging modality used for cervical spine clearance. Finally, respondents were asked if their institution had a documented cervical spine clearance protocol.

Results:
Of the 25 separate institutions evaluated, 21 were designated as level 1 trauma centers. Considerable variation was reported with regards to the primary service responsible for cervical spine clearance. General Surgery/Trauma (44%) is most commonly the primary service, followed by a rotating schedule (33%), Neurosugery (11%), and Orthopaedic Surgery (8%). Spine consults tend to be seen most commonly by a rotating schedule of Orthopaedic Surgery and Neurosurgery. The majority of responding institutions utilize computed tomographic imaging (46%) as the primary imaging modality, whereas 42% of hospitals used x-ray primarily. The remaining institutions reported using a combination of x-ray and computed tomographic imaging. Only 46% of institutions utilize a written, standardized pediatric cervical spine clearance protocol.

Conclusions:
This study demonstrates a striking variability in the use of personnel, imaging modalities and, most importantly, standardized protocol in the evaluation of the pediatric trauma patient with a potential cervical spine injury. Cervical spine clearance protocols have been shown to decrease the incidence of missed injuries, minimize excessive radiation exposure, decrease the time to collar removal, and lower overall associated costs. It is our opinion that development of a task force or multicenter research protocol that incorporates existing evidence-based literature is the next best step in improving the care of children with cervical spine injuries.

Level of Evidence:
Level 4—economic and decision analyses.