bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enrichment of Viral Nucleic Acids by Solution Hybrid Selection with Genus Specific Oligonucleotides
Authors: Deviatkin Andrei A. , Lukashev Alexander N. , Markelov Mikhail M. , Gmyl Larisa V. , Shipulin German A. 
Published: August 2017

AbstractDespite recent advances, our knowledge of potential and rare human pathogens is far from exhaustive. Current molecular diagnostic tools mainly rely on the specific amplification of marker sequences and may overlook infections caused by unknown and rare pathogens. Using high-throughput sequencing (HTS) can solve this problem; but, due to the extremely low fraction of pathogen genetic material in clinical samples, its application is only cost-effective in special, rather than routine, cases. In this study, we present a method for the semi-specific enrichment of viral conservative sequences in a HTS library by hybridization in solution with genus-specific degenerate biotinylated oligonucleotides. Nucleic acids of the test viruses (yellow fever virus and Japanese encephalitis virus) were enriched by solution hybrid selection using pan-flavivirus oligonucleotides. Moreover, enterovirus (family: Picornaviridae, genus: Enterovirus) sequences were successfully enriched using foot-and-mouth disease virus (family: Picornaviridae, genus: Aphthovirus) oligonucleotide. The enrichment factor relative to the background nucleic acid was about 1,000-fold. As hybridization has less stringent oligonucleotide match requirements than PCR, few oligonucleotides are sufficient to cover the potential sequence variation in the whole genus and may even enrich nucleic acids of viruses of other related genera. Efficient enrichment of viral sequences makes its use in diagnostics cost-efficient.
Species composition and richness of aphid parasitoid wasps in cotton fields in northern China
Authors: Yang Fan , Wu Yue-Kun , Xu Lei , Wang Qian , Yao Zhi-Wen , Žikić Vladimir , Tomanović Željko , Ferrer-Suay Mar , Selfa Jesús , Pujade-Villar Juli , Lu Yan-Hui , Guo Yu-Yuan 
Published: August 2017

AbstractThe cotton aphid, Aphis gossypii (Hemiptera: Aphididae), is a serious pest of cotton across the globe, particularly in the cotton agroecosystems of northern China. Parasitic wasps are deemed to be important natural enemies of A. gossypii, but limited information exists about their species composition, richness and seasonal dynamics in northern China. In this study, we combine sampling over a broad geographical area with intensive field trials over the course of three cropping seasons to describe parasitoid-hyperparasitoid communities in cotton crops. We delineate a speciose complex of primary parasitoids and hyperparasitoids associated with A. gossypii. Over 90% of the primary parasitoids were Binodoxys communis. Syrphophagus sp. and Pachyneuron aphidis made up most of the hyperparasitoids. Parasitism rates changed in a similar way following the fluctuation of the aphid population. Early in the growing period, there were more hyperparasitoids, while later, the primary parasitoids provided control of A. gossypii. The first systematic report of this cotton aphid parasitoid complex and their population dynamics in association with their hosts presented a comprehensive assessment of cotton parasitoid species and provided important information for the establishment and promotion of their biological control of cotton aphids.
The role of Nasoalveolar molding: A 3D Prospective analysis
Authors: Chou Pang-Yun , Hallac Rami R. , Ajiwe Tochi , Xie Xian-Jin , Liao Yu-Fang , Kane Alex A. , Park Yong Jong 
Published: August 2017

AbstractNasoalveolar molding (NAM) is commonly employed to reduce the alveolar segments into proper alignment and to improve nasal symmetry in patients with cleft lip and palate. This study examines the periodical progression of NAM treatment over time. 20 patients with complete unilateral cleft lip and palate were prospectively recruited. A 2 stage NAM treatment protocol was applied. Stage 1 involved adjustment of the alveolar segments (mean age 15.6 days), while Stage 2 added nasal stents and started average 43 days after stage 1. 3D images (n = 241) were obtained prior to NAM initiation and weekly until the end of treatment. The cleft lip area, bilateral nostril areas, and the nostril height and width were measured. Treatment was assessed in the Cleft (C) side and the Non-cleft (N). There was significant difference in the C/N ratio of the nostril area, width, and height at pre-treatment (0.9 ± 0.3, 4.1 ± 1.1, and 0.5 ± 0.2), at the end of stage 1 (1.1 ± 0.3, 2.2 ± 0.6, and 0.8 ± 0.2), and at the end of stage 2 treatment (1.8 ± 0.3, 1.8 ± 0.4, and 1.2 ± 0.1); p < 0.05. Comparative 3D analysis with dense sampling offers a precise methodology for showing effects of NAM treatment. The morphological changes achieved with NAM therapy occur in early treatment phase.
Raman spectroscopy uncovers biochemical tissue-related features of extracellular vesicles from mesenchymal stromal cells
Authors: Gualerzi Alice , Niada Stefania , Giannasi Chiara , Picciolini Silvia , Morasso Carlo , Vanna Renzo , Rossella Valeria , Masserini Massimo , Bedoni Marzia , Ciceri Fabio , Bernardo Maria Ester , Brini Anna Teresa , Gramatica Furio 
Published: August 2017

AbstractExtracellular vesicles (EVs) from mesenchymal stromal cells (MSC) are emerging as valuable therapeutic agents for tissue regeneration and immunomodulation, but their clinical applications have so far been limited by the technical restraints of current isolation and characterisation procedures. This study shows for the first time the successful application of Raman spectroscopy as label-free, sensitive and reproducible means of carrying out the routine bulk characterisation of MSC-derived vesicles before their use in vitro or in vivo, thus promoting the translation of EV research to clinical practice. The Raman spectra of the EVs of bone marrow and adipose tissue-derived MSCs were compared with human dermal fibroblast EVs in order to demonstrate the ability of the method to distinguish the vesicles of the three cytotypes automatically with an accuracy of 93.7%. Our data attribute a Raman fingerprint to EVs from undifferentiated and differentiated cells of diverse tissue origin, and provide insights into the biochemical characteristics of EVs from different sources and into the differential contribution of sphingomyelin, gangliosides and phosphatidilcholine to the Raman spectra themselves.
Non-invasive three-dimension control of light between turbid layers using a surface quasi-point light source for precorrection
Authors: Qiao Mu , Liu Honglin , Pang Guanghui , Han Shensheng 
Published: August 2017

AbstractManipulating light non-invasively through inhomogeneous media is an attractive goal in many disciplines. Wavefront shaping and optical phase conjugation can focus light to a point. Transmission matrix method can control light on multiple output modes simultaneously. Here we report a non-invasive approach which enables three-dimension (3D) light control between two turbid layers. A digital optical phase conjugation mirror measured and conjugated the diffused wavefront, which originated from a quasi-point source on the front turbid layer and passed through the back turbid layer. And then, because of memory effect, the phase-conjugated wavefront could be used as a carrier wave to transport a pre-calculated wavefront through the back turbid layer. The pre-calculated wavefront could project a desired 3D light field inside the sample, which, in our experiments, consisted of two 220-grid ground glass plates spaced by a 20 mm distance. The controllable range of light, according to the memory effect, was calculated to be 80 mrad in solid angle and 16 mm on z-axis. Due to the 3D light control ability, our approach may find applications in photodynamic therapy and optogenetics. Besides, our approach can also be combined with ghost imaging or compressed sensing to achieve 3D imaging between turbid layers.
An enhanced C. elegans based platform for toxicity assessment
Authors: Xiong Huajiang , Pears Catherine , Woollard Alison 
Published: August 2017

AbstractThere is a well-defined regulatory framework governing the approval of chemicals for use as pharmaceuticals or release into the environment. Toxicity assessment is thus a major hurdle in the compound discovery pipeline, currently involving large scale animal testing. The search for alternative testing platforms is therefore an important priority. We have developed a convenient, low cost assay utilising the nematode Caenorhabditis elegans, to rapidly assess both acute toxicity and developmental and reproductive toxicity (DART). However the worm is protected by a robust cuticle that forms a barrier to chemical uptake. We assessed mutants with altered cuticle properties to identify sensitized strains optimized for toxicity assays. Evaluating the trade-off between increased permeability and reduced fitness identifies bus-5(br19) as the most suitable strain for chemical exposure. We demonstrate the applicability of this assay for a range of chemicals with differing properties, including a modified exposure protocol for volatile or less soluble compounds. This work enhances the effectiveness of C. elegans for convenient toxicity assessment, which could contribute to a reduction in the use of vertebrates particularly at the crucial early stages of product development. Strains identified in this work will also enhance the sensitivity of C. elegans based drug discovery platforms.
A Dynamic Metabolic Flux Analysis of Myeloid-Derived Suppressor Cells Confirms Immunosuppression-Related Metabolic Plasticity
Authors: Goffaux Guillaume , Hammami Iness , Jolicoeur Mario 
Published: August 2017

AbstractRecent years have witnessed an increasing interest at understanding the role of myeloid-derived suppressor cells (MDSCs) in cancer-induced immunosuppression, with efforts to inhibit their maturation and/or their activity. We have thus modelled MDSCs central carbon metabolism and bioenergetics dynamic, calibrating the model using experimental data on in vitro matured mice bone marrow cells into MDSCs. The model was then used to probe the cells metabolic state and dynamics, performing a dynamic metabolic flux analysis (dMFA) study. Indeed, MDSCs maturation correlates with a high glycolytic flux contributing to up to 95% of the global ATP turnover rate, while most of the glucose-derived carbon enters the TCA cycle. Model simulations also reveal that pentose phosphate pathway and oxidative phosphorylation activities were kept at minimal levels to ensure NADPH production and anabolic precursors synthesis. Surprisingly, MDSCs immunosuppressive activity, i.e. L-arginine uptake, metabolism and endogenous synthesis, only consumes sparse quantities of energy-rich nucleotides (ATP and NADPH). Therefore, model simulations suggest that MDSCs exhibit a heterogeous metabolic profile similar to tumour cells. This behavior is probably an indirect immunosuppressive mechanism where MDSCs reduce the availability of carbon sources in the tumour periphery microenvironment, which could explain the dysfuntion and death of immune effector cells.
Temporal Stability and Composition of the Ocular Surface Microbiome
Authors: Ozkan Jerome , Nielsen Shaun , Diez-Vives Cristina , Coroneo Minas , Thomas Torsten , Willcox Mark 
Published: August 2017

AbstractTo determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.
In vivo Confocal Microscopy of Posner-Schlossman Syndrome: Comparison with herpes simplex keratitis, HLA-B27 anterior uveitis and acute attack of primary angle closure
Authors: Hong Ying , Wang Miao , Wu Lingling 
Published: August 2017

AbstractTo investigate in vivo confocal microscopy (IVCM) findings in patients with Posner-Schlossman Syndrome (PSS), we compared the IVCM findings from the eyes of patients with: PSS (44 eyes); herpes simplex keratitis (HSK) (45 eyes); HLA-B27 anterior uveitis (B27AU) (45 eyes); and with acute attack of primary angle closure (aPAC) (43 eyes). The central Langerhans cells (LCs) grade at the level of corneal basal epithelial cells of the PSS group (2.33 ± 0.55) was similar to that of the HSK group (2.63 ± 0.67) (χ2 = −1.435, P = 0.174) but was significantly higher than those of the B27AU group (1.80 ± 0.79) (χ2 = 2.311, P = 0.023) and the aPAC group (1.75 ± 0.46) (χ2 = 2.701, P = 0.022). The keratocyte activation grade of the PSS group (1.55 ± 0.76) was similar to that of the HSK group (1.65 ± 0.81) (χ2 = 1.104, P = 0.675) but was significantly higher than those of the B27AU group (1.00 ± 0.71) (χ2 = 2.364, P = 0.025) and aPAC group (1.75 ± 0.46) (χ2 = 2.532, P = 0.027). The LCs and keratocyte activation grades observed by IVCM in patients with PSS were higher than those in patients with B27AU and with aPAC, but they were similar to those in patients with HSK. This implies that PSS might be related to viral infection.
Numerical simulation of seasonality in the distribution and fate of pyrene in multimedia aquatic environments with Markov chains
Authors: Sun Caiyun , Xu Liang , Sun Dazhi , Chen Libo , Zou Jiying , Zhang Zhenxing 
Published: August 2017

AbstractThis case study investigated the distribution and fate of organic pollutants in aquatic environments based on laboratory experiments and modeling. Pyrene (Pyr) is a hydrocarbon pollutant with adverse effects on aquatic ecosystems and human health, and was thus selected for this case study. The movement of Pyr was primarily influenced by its sorption from water onto sediment, and its desorption from sediment into water. Its elimination was mainly via biodegradation by microorganisms in sediment and by volatilization from water into air. The transport and elimination rates for Pyr were considerably influenced by temperature and moisture. Results of modeling with Markov chains revealed that the elimination of Pyr from water/sediment systems was the most rapid under wet conditions. Under average conditions, a Pyr concentration of 100 μg/L of in water in such a system declined to a negligible level over 250 h. Under wet conditions, this decrease occurred over 120 h. Finally, under dry conditions, it took 550 h to achieve the same degree of elimination.
Risk factors for postoperative surgical site infections in patients with Crohn’s disease receiving definitive bowel resection
Authors: Liu Song , Miao Ji , Wang Gefei , Wang Meng , Wu Xiuwen , Guo Kun , Feng Min , Guan Wenxian , Ren Jianan 
Published: August 2017

AbstractSurgical site infection presents as a significant problem that limits the potential benefits of surgical interventions. This study is to investigate risk factors for postoperative SSI in patients with Crohn’s disease receiving definitive bowel resection. A case-control study including 49 patients with SSI and 105 patients without SSI was performed. Demographics, clinical characteristics, laboratory information, medical and surgical data were compared between groups. Significant elements were subsequently brought into logistic regression analysis for further identification. Patients with SSI exhibited higher tobacco usage rate (p = 0.03), lower preoperative hemoglobin (p = 0.02) and pre-albumin level (p = 0.02). Bowel penetration instead of stricture was more frequent in patients with SSI (p = 0.04). Longer duration of operation (p = 0.03) and higher intraoperative lactate level (p = 0.02) were observed in patients with SSI. Logistic analysis identified that preoperative pre-albumin (95% CI: 0.2~0.7; OR = 0.5; p = 0.03), duration of operation (95% CI: 2.3~9.5; OR = 3.8; p = 0.03) and intraoperative lactate level (95% CI: 1.7~7.2; OR = 3.4; p = 0.04) were associated with postoperative surgical site outcome. Our data has identified that lower preoperative pre-albumin, longer duration of operation and higher intraoperative lactate level are risk factors for SSI in patients with Crohn’s disease receiving definitive bowel resection.
Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses
Authors: Mancabelli Leonardo , Milani Christian , Lugli Gabriele Andrea , Turroni Francesca , Mangifesta Marta , Viappiani Alice , Ticinesi Andrea , Nouvenne Antonio , Meschi Tiziana , van Sinderen Douwe , Ventura Marco 
Published: August 2017

AbstractFunctional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS). Notably, the gut microbiota of FC individuals was shown to be depleted of members belonging to Bacteroides, Roseburia and Coprococcus 3. Furthermore, the metabolic capabilities of the gut microbiomes of five FC and five HS individuals were evaluated through shotgun metagenomics using a MiSeq platform, indicating that HS are enriched in pathways involved in carbohydrate, fatty acid and lipid metabolism as compared to FC. In contrast, the microbiomes corresponding to FC were shown to exhibit high abundance of genes involved in hydrogen production, methanogenesis and glycerol degradation. The identified differences in bacterial composition and metabolic capabilities may play an important role in development of FC symptoms.
Temperature and pressure limits of guanosine monophosphate self-assemblies
Authors: Gao Mimi , Harish Balasubramanian , Berghaus Melanie , Seymen Rana , Arns Loana , McCallum Scott A. , Royer Catherine A. , Winter Roland 
Published: August 2017

AbstractGuanosine monophosphate, among the nucleotides, has the unique property to self-associate and form nanoscale cylinders consisting of hydrogen-bonded G-quartet disks, which are stacked on top of one another. Such self-assemblies describe not only the basic structural motif of G-quadruplexes formed by, e.g., telomeric DNA sequences, but are also interesting targets for supramolecular chemistry and nanotechnology. The G-quartet stacks serve as an excellent model to understand the fundamentals of their molecular self-association and to unveil their application spectrum. However, the thermodynamic stability of such self-assemblies over an extended temperature and pressure range is largely unexplored. Here, we report a combined FTIR and NMR study on the temperature and pressure stability of G-quartet stacks formed by disodium guanosine 5′-monophosphate (Na25′-GMP). We found that under abyssal conditions, where temperatures as low as 5 °C and pressures up to 1 kbar are reached, the self-association of Na25′-GMP is most favoured. Beyond those conditions, the G-quartet stacks dissociate laterally into monomer stacks without significantly changing the longitudinal dimension. Among the tested alkali cations, K+ is the most efficient one to elevate the temperature as well as the pressure limits of GMP self-assembly.
Comprehensive in situ co-detection of aneuploid circulating endothelial and tumor cells
Authors: Lin Peter Ping , Gires Olivier , Wang Daisy Dandan , Li Linda , Wang Hongxia 
Published: August 2017

AbstractConventional circulating tumor cell (CTC) detection strategies rely on cell surface marker EpCAM and intracellular cytokeratins (CKs) for isolation and identification, respectively. Application of such methods is considerably limited by inherent heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs. Here, we report a novel strategy, integrating antigen-independent subtraction enrichment and immunostaining-FISH (SE-iFISH), to detect a variety of aneuploid circulating rare cells (CRCs), including CTCs and circulating tumor endothelial cells (CECs). Enriched CRCs, maintained at high viability and suitable for primary tumor cell culture, are comprehensively characterized by in situ co-examination of chromosome aneuploidy by FISH and immunostaining of multiple biomarkers displayed in diverse fluorescence channels. We described and quantified for the first time the existence of individual aneuploid CD31+ CECs and co-existence of “fusion clusters” of endothelial-epithelial aneuploid tumor cells among enriched non-hematopoietic CRCs. Hence, SE-iFISH is feasible for efficient co-detection and in situ phenotypic and karyotypic characterization as well as quantification of various CRCs, allowing for their classification into diverse subtypes upon biomarker expression and chromosome ploidy. Enhanced SE-iFISH technology, assisted by the Metafer-iFISH automated CRC imaging system, provides a platform for the analysis of potential contributions of each subtype of CRCs to distinct clinical outcome.
Probe-based confocal laser endomicroscopy for in vivo evaluation of the tumor vasculature in gastric and rectal carcinomas
Authors: Spessotto Paola , Fornasarig Mara , Pivetta Eliana , Maiero Stefania , Magris Raffaella , Mongiat Maurizio , Canzonieri Vincenzo , De Paoli Paolo , De Paoli Antonino , Buonadonna Angela , Serraino Diego , Panato Chiara , Belluco Claudio , Cannizzaro Renato 
Published: August 2017

AbstractProbe-based Confocal Laser Endomicroscopy (pCLE) is a powerful imaging technique that allows to perform gastrointestinal endomicroscopy at subcellular resolution. The aim of this study was to assess the use of pCLE to evaluate tumor angiogenesis in rectal and gastric cancers. A total of 35 consecutive patients with gastric and 91 with rectal carcinomas underwent endoscopy and pCLE during the same examination. Vascular assessment was based on vessel shape and size, vessel permeability and blood flow, and allowed the creation of an angiogenic score ranging from 0, for normal vasculature, to 4, for aberrant vasculature. A significant difference for the presence of vessels with large diameter and defective blood flow was found between rectal and gastric cancers. Overall, rectal cancers displayed a higher angiogenic score compared to gastric cancers. Conventional therapy induced a striking reduction in the angiogenic score only in rectal cancer patients. Taken together, our findings suggest that the pCLE technology is suitable for the evaluation of the tumor microvasculature abnormalities. Therefore, the real-time assessment of the vasculature status may represent a promising approach to predict the efficacy of the treatments and improve the clinical management of patients with gastric or rectal carcinomas.