bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses to Quadrivalent Influenza Vaccine Reveal Distinct Circulating CD4+CXCR5+ T Cell Subsets in Men Living with HIV
Authors: Cole Megan E. , Saeed Zainab , Shaw A. Torm , Guo Yanping , Höschler Katja , Winston Alan , Cooke Graham S. , Fidler Sarah , Taylor Graham P. , Pollock Katrina M. 
Published: October 2019

AbstractT cell help for B cells may be perturbed in people living with HIV (PLWH), even when HIV is suppressed, as evidenced by reports of suboptimal responses to influenza vaccination. We investigated cTFH responses to the 2017–18 inactivated quadrivalent influenza vaccine (QIV) in men living with antiretroviral therapy (ART)-suppressed HIV infection who were treated in the early or chronic phase of infection, and control subjects. Here we show that seroprotective antibody responses in serum and oral fluid correlated with cTFH activation and were equivalent in all three groups, irrespective of when ART was started. These responses were attenuated in those reporting immunisation with influenza vaccine in the preceding three years, independent of HIV infection. Measurement of influenza-specific IgG in oral fluid was closely correlated with haemagglutination inhibition titre. T-SNE and two-dimensional analysis revealed a subset of CD4+CXCR3+CXCR5+ cTFH activated at one week after vaccination. This was distinguishable from cTFH not activated by vaccination, and a rare, effector memory CD4+CXCR5hiCD32hi T cell subset. The data support the use of QIV for immunisation of PLWH, reveal distinct circulating CD4+CXCR5+ T cell subsets and demonstrate oral fluid sampling for influenza-specific IgG is an alternative to phlebotomy.
Diamond Etching Beyond 10 μm with Near-Zero Micromasking
Authors: Hicks Marie-Laure , Pakpour-Tabrizi Alexander C. , Jackman Richard B. 
Published: October 2019

AbstractTo exploit the exceptional properties of diamond, new high quality fabrication techniques are needed to produce high performing devices. Etching and patterning diamond to depths beyond one micron has proven challenging due to the hardness and chemical resistance of diamond. A new cyclic Ar/O2 - Ar/Cl2 ICP RIE process has been developed to address micromasking issues from the aluminium mask by optimising the proportion of O2 in the plasma and introducing a preferential “cleaning” step. High quality smooth features up to, but not limited to, 10.6 μm were produced with an average etched surface roughness of 0.47 nm at a diamond etch rate of 45 nm/min and 16.9:1 selectivity.
Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
Authors: Alexaki Aikaterini , Hettiarachchi Gaya K. , Athey John C. , Katneni Upendra K. , Simhadri Vijaya , Hamasaki-Katagiri Nobuko , Nanavaty Puja , Lin Brian , Takeda Kazuyo , Freedberg Darón , Monroe Dougald , McGill Joseph R. , Peters Robert , Kames Jacob M. , Holcomb David D. , Hunt Ryan C. , Sauna Zuben E. , Gelinas Amy , Janjic Nebojsa , DiCuccio Michael , Bar Haim , Komar Anton A. , Kimchi-Sarfaty Chava 
Published: October 2019

AbstractSynonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.
An algorithm-based meta-analysis of genome- and proteome-wide data identifies a combination of potential plasma biomarkers for colorectal cancer
Authors: Gawel Danuta R. , Lee Eun Jung , Li Xinxiu , Lilja Sandra , Matussek Andreas , Schäfer Samuel , Olsen Renate Slind , Stenmarker Margaretha , Zhang Huan , Benson Mikael 
Published: October 2019

AbstractScreening programs for colorectal cancer (CRC) often rely on detection of blood in stools, which is unspecific and leads to a large number of colonoscopies of healthy subjects. Painstaking research has led to the identification of a large number of different types of biomarkers, few of which are in general clinical use. Here, we searched for highly accurate combinations of biomarkers by meta-analyses of genome- and proteome-wide data from CRC tumors. We focused on secreted proteins identified by the Human Protein Atlas and used our recently described algorithms to find optimal combinations of proteins. We identified nine proteins, three of which had been previously identified as potential biomarkers for CRC, namely CEACAM5, LCN2 and TRIM28. The remaining proteins were PLOD1, MAD1L1, P4HA1, GNS, C12orf10 and P3H1. We analyzed these proteins in plasma from 80 patients with newly diagnosed CRC and 80 healthy controls. A combination of four of these proteins, TRIM28, PLOD1, CEACAM5 and P4HA1, separated a training set consisting of 90% patients and 90% of the controls with high accuracy, which was verified in a test set consisting of the remaining 10%. Further studies are warranted to test our algorithms and proteins for early CRC diagnosis.
Compartmentalized evolution of Bovine Viral Diarrhoea Virus type 2 in an immunotolerant persistently infected cow
Authors: Colitti Barbara , Nogarol Chiara , Giacobini Mario , Capucchio Maria Teresa , Biasato Ilaria , Rosati Sergio , Bertolotti Luigi 
Published: October 2019

AbstractBovine viral diarrhea virus (BVDV) is one of the most important pathogens of cattle worldwide. BVDV-1 is widely distributed in Italy, while BVDV-2 has been detected occasionally. BVDV can be classified in two biotypes, cytopathic (CP) or noncytopathic (NCP). The characteristic of the virus is linked with the infection of a pregnant dam with a NCP strain: due to viral establishment before maturation of the fetal immune system the calf remains persistently infected (PI) and immunotolerant to the infecting BVDV strain. Thanks to their immunotolerance, PI animals represent a unique model to study the viral distribution and compartmentalization in absence of immunoresponse in vivo. In the present study, NGS sequencing was used to characterize the BVDV2 viral strain infecting a PI calf and to describe the viral quasispecies in tissues. Even if the consensus sequences obtained by all the samples were highly similar, quasispecies was described evaluating the presence and the frequency of variants among all the sequencing reads in each tissue. The results suggest a high heterogeneity of the infecting viral strain suggesting viral compartmentalization. The quasispecies analysis highlights the complex dynamics of viral population structure and can increase the knowledge about viral evolution in BVDV-2 persistently infected animals.
Periodicity of cerebral flow velocity during sleep and its association with white-matter hyperintensity volume
Authors: Lee Woo-Jin , Jung Keun-Hwa , Park Hyun-Min , Sohn Chul-Ho , Lee Soon-Tae , Park Kyung-Il , Chu Kon , Jung Ki-Young , Kim Manho , Lee Sang Kun , Roh Jae-Kyu 
Published: October 2019

AbstractImpaired sleep-related activation of the cerebral waste-clearance system might be related with the brain aging process. We hypothesized that cerebral blood-flow pattern changes during sleep might reflect the activation of the cerebral waste-clearance system and investigated its association with the cerebral white-matter hyperintensity (WMH) volume. Fifty healthy volunteers were prospectively recruited. In addition to the baseline transcranial Doppler parameters, the mean flow velocity (MFV) of the middle cerebral artery was monitored during waking and short-term non-REM sleep. Spectral density analysis was performed to analyze the periodic MFV variation patterns. For the aged subgroup (>50 years, n = 25), the WMH volumes in the total, subcortical, and periventricular regions were measured. The MFV periodic pattern during sleep was substantially augmented over that in the waking status. Spectral density analysis of MFV showed a noticeable peak in the very-low–frequency (VLF) band during sleep status (sleep/waking ratio 2.87 ± 2.71, P < 0.001). In linear regression analysis in the aged subgroup, the sleep/waking ratio of the VLF peak was inversely associated with total (P = 0.013) and subcortical (P = 0.020) WMH volumes. Sleep-related amplification of the cerebral flow-velocity periodicity might reflect the activation of cerebral waste clearance system during sleep, and be related to the pathogenesis of cerebral WMH.
Composites of Platinum-Iridium Alloy Nanoparticles and Graphene
Oxide for the Dimethyl Amine Borane (DMAB) dehydrogenation at ambient conditions: An
Experimental and Density Functional Theory Study
Authors: Sen Betül , Aygun Ayşenur , Şavk Aysun , Çalımlı Mehmet Harbi , Fellah Mehmet Ferdi , Sen Fatih 
Published: October 2019

AbstractIn this paper, we present the synthesis, characterization, catalytic and
computational studies of Composites of Platinum-Iridium Alloy Nanoparticles and
Graphene Oxide (PtIr@GO) for dimethylamine borane (DMAB) dehydrogenation. The
prepared PtIr@GO nanocatalysts were synthesized using an ethanol super-hydride
method, and the characterization procedures for PtIr@GO alloy nanoparticles were
carried out by various advanced spectroscopic methods like X-ray Diffraction (XRD),
X-ray photoelectron spectroscopy (XPS), Transmission Electron Microscopy(TEM) and
high-resolution transmission electron microscopy (HRTEM). Additionally, catalytic
activity, reusability, substrate concentration, and catalyst concentration
experiments were performed for DMAB dehydrogenation catalyzed by PtIr@GO alloy
nanomaterials. According to the results obtained in this study, PtIr@GO NPs catalyst
was found to be active and reusable for the DMAB even at ambient conditions.
Besides, DFT-B3LYP calculations have been utilized on PtIr@GO cluster to reveal the
prepared catalyst activity. The calculated findings based on DFT was found to be a
good agreement with experimental results.
Exploring possible associations of the intestine bacterial microbiome with the pre-weaned weight gaining performance of piglets in intensive pig production
Authors: Ding Xinghua , Lan Wensheng , Liu Gang , Ni Hengjia , Gu Ji-Dong 
Published: October 2019

AbstractThe pre-weaned weight gain is an important performance trait of pigs in intensive pig production. The bacterial microbiome inside the host is vital to host health and growth performance. The purpose of this study was to explore the possible associations of the intestinal microbiome with the pre-weaned weight gain in intensive pig production. In this study, several anatomical sites (jejunum, ileum, cecum, and colon) were examined for bacterial microbiome structure using 16S rRNA V4-V5 region sequencing with Illumina Miseq. The results showed that the microbial richness (estimated by Chao1 index) in jejunum was positively correlated with the pre-weaned weight gain. This study also revealed that the Firmicutes and Bacteroidetes in colon were the weight gaining-related phyla; while the Selenomonas and Moraxella in ileum and the Lactobacillus in both cecum and colon were the weight gaining-related genera for the pre-weaned piglets in intensive pig prodution. Several intra-microbial interactions within commensal microbiome correlated with the pre-weaned weight gain were excavated, as well. Overall, this study provides an expanded view of the commensal bacterial community inside four anatomical intestinal sites of the commercial piglets and the associations of the intestinal microbiome with the pre-weaned weight gaining performance in intensive pig production.
Development of a multiplex and sensitive lateral flow immunoassay for the diagnosis of periprosthetic joint infection
Authors: Tsai Tsung-Ting , Huang Tse-Hao , Ho Natalie Yi-Ju , Chen Yu-Pei , Chen Chung-An , Chen Chien-Fu 
Published: October 2019

AbstractThe diagnosis of periprosthetic joint infection (PJI) remains a challenge. However, recent studies showed that synovial fluid biomarkers have demonstrated greater diagnostic accuracy than the currently used PJI diagnostic tests. In many diagnostic tests, combining several biomarkers into panels is critical for improving diagnostic efficiency, enhancing the diagnostic precision for specific diseases, and reducing cost. In this study, we prove that combining alpha-defensin and C-reactive protein (CRP) as biomarkers possesses the potential to provide accurate PJI diagnosis. To further verify the result, we developed a multi-target lateral flow immunoassay strip (msLFIA) with staking pad design to obtain on-site rapid response for clinical diagnosis of PJI. A total of 10 synovial fluid samples were tested using the msLFIA, and the results showed that the combined measurements of synovial fluid alpha-defensin and CRP levels were consistent with those obtained from a commercial enzyme-linked immunosorbent assay kit. In addition, we developed a multi-target lateral flow immunoassay strip (msLFIA) with staking pad design to obtain on-site rapid response for clinical diagnosis of PJI, which the multi-target design is used to increase specificity and the stacking pad design is to enhance detection sensitivity. As a result, the turnaround time of the highly sensitive test can be limited from several hours to 20 min. We expect that the developed msLFIA possesses the potential for routine monitoring of PJI as a convenient, low-cost, rapid and easy to use detection device for PJI.
Epididymal and ejaculated sperm differ on their response to the cryopreservation and capacitation processes in mouflon (Ovis musimon)
Authors: Martínez-Fresneda Lucía , Castaño Cristina , Bóveda Paula , Tesfaye Dawit , Schellander Karl , Santiago-Moreno Julián , García-Vázquez Francisco A. 
Published: October 2019

AbstractSpermatozoa must undergo the process of capacitation to fertilize the egg which involves a cell destabilizing process. Capacitation-like changes such as protein tyrosine phosphorylation (PTP) are associated with cryopreservation. The aim of this study was to compare the cryoresistance and capacitation response of epididymal and ejaculated sperm of European mouflon (Ovis musimon). Post-thaw sperm parameters were analysed from epididymal and ejaculated samples cryopreserved by slow-freezing or ultrarapid-freezing for comparison. Sperm capacitation status was assessed by the semiquantification of PTP levels, cell localization of PTP and kinematic clustering. Epididymal sperm had higher cryoresistance than ejaculated sperm in both freezing techniques, and slow-freezing rendered better results than ultrarapid-freezing in both sperm samples. Ejaculated sperm had higher PTP levels than epididymal sperm and, additionally, ejaculated sperm showed higher phosphorylation in capacitating (CA) than in non-capacitating (NCA) conditions while there was no effect of medium in epididymal sperm. There was a higher tail PTP in CA than in NCA conditions in both types of sperm. Kinematic analysis revealed that the cluster associated with hyperactivated movement increased in ejaculated sperm incubated in CA whereas no effect of medium was observed in epididymal sperm clusters. In conclusion, epididymal sperm showed better freezability and lower capacitation status compared to ejaculated sperm.
LC-MS based metabolomic profiling for renal cell carcinoma histologic subtypes
Authors: Jing Lun , Guigonis Jean-Marie , Borchiellini Delphine , Durand Matthieu , Pourcher Thierry , Ambrosetti Damien 
Published: October 2019

AbstractRenal cell carcinomas (RCC) are classified according to their histological features. Accurate classification of RCC and comprehensive understanding of their metabolic dysregulation are of critical importance. Here we investigate the use of metabolomic analyses to classify the main RCC subtypes and to describe the metabolic variation for each subtype. To this end, we performed metabolomic profiling of 65 RCC frozen samples (40 clear cell, 14 papillary and 11 chromophobe) using liquid chromatography-mass spectrometry. OPLS-DA multivariate analysis based on metabolomic data showed clear discrimination of all three main subtypes of RCC (R2 = 75.0%, Q2 = 59.7%). The prognostic performance was evaluated using an independent cohort and showed an AUROC of 0.924, 0.991 and 1 for clear cell, papillary and chromophobe RCC, respectively. Further pathway analysis using the 21 top metabolites showed significant differences in amino acid and fatty acid metabolism between three RCC subtypes. In conclusion, this study shows that metabolomic profiling could serve as a tool that is complementary to histology for RCC subtype classification. An overview of metabolic dysregulation in RCC subtypes was established giving new insights into the understanding of their clinical behaviour and for the development of targeted therapeutic strategies.
TGF-β1-induced HSP47 regulates extracellular matrix accumulation via Smad2/3 signaling pathways in nasal fibroblasts
Authors: Kim Hae-Ji , Park Joo-Hoo , Shin Jae-Min , Yang Hyun-Woo , Lee Heung-Man , Park Il-Ho 
Published: October 2019

AbstractHSP47 is required for the production of collagen and serves an important role in tissue remodeling, a pathophysiologic mechanism of chronic rhinosinusitis (CRS). We investigated the relationship between HSP47 expression and tissue remodeling in CRS. We also determined the underlying molecular mechanisms of TGF-β1-induced HSP47 and extracellular matrix (ECM) production in nasal fibroblasts. HSP47, α-SMA, fibronectin, and collagen type I expression levels were measured using real-time PCR, western blotting, and immunofluorescence staining. Fibroblast migration was analyzed using scratch and transwell migration assays. Contractile activity was measured with a collagen gel contraction assay. HSP47 is increased in patients with CRS without nasal polyps. TGF-β1 induced HSP47 expression in nasal fibroblasts. Myofibroblast differentiation and ECM production, which are induced by TGF-β1, were inhibited by siHSP47. We also confirmed that the Smad2/3 signaling pathway is involved in TGF-β1-induced HSP47 expression in nasal fibroblasts. In a functional assay, TGF-β1-enhanced migration and contraction ability were inhibited by HSP47 knockout. Glucocorticoid reversed the stimulatory effects of TGF-β1 on HSP47 expression and ECM production in nasal fibroblasts and ex vivo organ cultures. HSP47 expression is involved in TGF-β1-induced myofibroblast differentiation and ECM production through the Smad2/3 signaling pathway, which might contribute to tissue remodeling in chronic rhinosinusitis.
Association study of AGO1 and AGO2 genes polymorphisms with recurrent pregnancy loss
Authors: Kim Young Ran , Ryu Chang Soo , Kim Jung Oh , An Hui Jeong , Cho Sung Hwan , Ahn Eun Hee , Kim Ji Hyang , Lee Woo Sik , Kim Nam Keun 
Published: October 2019

AbstractAn Argonaute (AGO) protein within the RNA-induced silencing complex binds a microRNA, permitting the target mRNA to be silenced. We hypothesized that variations in AGO genes had the possibility including affected the miRNA function and associated with recurrent pregnancy loss (RPL) susceptibility. Especially, we were chosen the AGO1 (rs595961, rs636832) and AGO2 (rs2292779, rs4961280) polymorphisms because of those polymorphisms have already reported in other diseases excluding the RPL. Here, we conducted a case-control study (385 RPL patients and 246 controls) to evaluate the association of four polymorphisms with RPL. We found that the AGO1 rs595961 AA genotype, recessive model (P = 0.039; P = 0.043, respectively), the AGO1 rs636832 GG genotype, and recessive model (P = 0.037; P = 0.016, respectively) were associated with RPL in women who had had four or more consecutive pregnancy losses. The patients with the AGO1 rs636832 GG genotypes had greater platelet counts (P = 0.023), while the patients with the AGO2 rs4961280 CA genotypes had less homocysteine (P = 0.027). Based on these results, we propose that genetic variations with respect to the AGO1 and AGO2 genotypes are associated with risk for RPL, and might serve as useful biomarkers for the prognosis of RPL.
Trimethylamine-N-Oxide (TMAO) Predicts Cardiovascular Mortality in Peripheral Artery Disease
Authors: Roncal Carmen , Martínez-Aguilar Esther , Orbe Josune , Ravassa Susana , Fernandez-Montero Alejandro , Saenz-Pipaon Goren , Ugarte Ana , Estella-Hermoso de Mendoza Ander , Rodriguez Jose A. , Fernández-Alonso Sebastián , Fernández-Alonso Leopoldo , Oyarzabal Julen , Paramo Jose A. 
Published: October 2019

AbstractPeripheral artery disease (PAD) is a major cause of acute and chronic illness, with extremely poor prognosis that remains underdiagnosed and undertreated. Trimethylamine-N-Oxide (TMAO), a gut derived metabolite, has been associated with atherosclerotic burden. We determined plasma levels of TMAO by mass spectrometry and evaluated their association with PAD severity and prognosis. 262 symptomatic PAD patients (mean age 70 years, 87% men) categorized in intermittent claudication (IC, n = 147) and critical limb ischemia (CLI, n = 115) were followed-up for a mean average of 4 years (min 1-max 102 months). TMAO levels were increased in CLI compared to IC (P < 0.001). Receiver operating characteristic (ROC) curves for severity (CLI) rendered a cutoff of 2.26 µmol/L for TMAO (62% sensitivity, 76% specificity). Patients with TMAO > 2.26 µmol/L exhibited higher risk of cardiovascular death (sub-hazard ratios ≥2, P < 0.05) that remained significant after adjustment for confounding factors. TMAO levels were associated to disease severity and CV-mortality in our cohort, suggesting an improvement of PAD prognosis with the measurement of TMAO. Overall, our results indicate that the intestinal bacterial function, together with the activity of key hepatic enzymes for TMA oxidation (FMO3) and renal function, should be considered when designing therapeutic strategies to control gut-derived metabolites in vascular patients.