bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells
Authors: Rubelt Florian , Bolen Christopher R. , McGuire Helen M. , Heiden Jason A. Vander , Gadala-Maria Daniel , Levin Mikhail , M. Euskirchen Ghia , Mamedov Murad R. , Swan Gary E. , Dekker Cornelia L. , Cowell Lindsay G. , Kleinstein Steven H. , Davis Mark M. 
Published: March 2016

AbstractThe adaptive immune system’s capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T and CD8+ T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level.
Rapid expulsion of microswimmers by a vortical flow
Authors: Sokolov Andrey , Aranson Igor S. 
Published: March 2016

AbstractInteractions of microswimmers with their fluid environment are exceptionally complex. Macroscopic shear flow alters swimming trajectories in a highly nontrivial way and results in dramatic reduction of viscosity and heterogeneous bacterial distributions. Here we report on experimental and theoretical studies of rapid expulsion of microswimmers, such as motile bacteria, by a vortical flow created by a rotating microparticle. We observe a formation of a macroscopic depletion area in a high-shear region, in the vicinity of a microparticle. The rapid migration of bacteria from the shear-rich area is caused by a vortical structure of the flow rather than intrinsic random fluctuations of bacteria orientations, in stark contrast to planar shear flow. Our mathematical model reveals that expulsion is a combined effect of motility and alignment by a vortical flow. Our findings offer a novel approach for manipulation of motile microorganisms and shed light on bacteria–flow interactions.
Immunogenicity of a Trivalent Recombinant Vaccine Against Clostridium perfringens Alpha, Beta, and Epsilon Toxins in Farm Ruminants
Authors: Moreira Gustavo Marçal Schmidt Garcia , Salvarani Felipe Masiero , da Cunha Carlos Eduardo Pouey , Mendonça Marcelo , Moreira Ângela Nunes , Gonçalves Luciana Aramuni , Pires Prhiscylla Sadanã , Lobato Francisco Carlos Faria , Conceição Fabricio Rochedo 
Published: March 2016

AbstractClostridium perfringens is an anaerobic bacterium that produces several toxins. Of these, the alpha, beta, and epsilon toxins are responsible for causing the most severe C. perfringens-related diseases in farm animals. The best way to control these diseases is through vaccination. However, commercially available vaccines are based on inactivated toxins and have many production drawbacks, which can be overcome through the use of recombinant antigens. In this study, we produced recombinant alpha, beta, and epsilon toxins in Escherichia coli to formulate a trivalent vaccine. Its effectiveness was evaluated through a potency test in rabbits, in which the vaccine generated 9.6, 24.4, and 25.0 IU/mL of neutralizing antibodies against the respective toxins. Following this, cattle, sheep, and goats received the same formulation, generating, respectively, 5.19 ± 0.48, 4.34 ± 0.43, and 4.70 ± 0.58 IU/mL against alpha toxin, 13.71 ± 1.17 IU/mL (for all three species) against beta toxin, and 12.74 ± 1.70, 7.66 ± 1.69, and 8.91 ± 2.14 IU/mL against epsilon toxin. These levels were above the minimum recommended by international protocols. As such, our vaccine was effective in generating protective antibodies and, thus, may represent an interesting alternative for the prevention of C. perfringens-related intoxications in farm animals.
New Findings in eNOS gene and Thalidomide Embryopathy Suggest pre-transcriptional effect variants as susceptibility factors
Authors: Kowalski Thayne Woycinck , Fraga Lucas Rosa , Tovo-Rodrigues Luciana , Sanseverino Maria Teresa Vieira , Hutz Mara Helena , Schuler-Faccini Lavínia , Vianna Fernanda Sales Luiz 
Published: March 2016

AbstractAntiangiogenic properties of thalidomide have created an interest in the use of the drug in treatment of cancer. However, thalidomide is responsible for thalidomide embryopathy (TE). A lack of knowledge regarding the mechanisms of thalidomide teratogenesis acts as a barrier in the aim to synthesize a safer analogue of thalidomide. Recently, our group detected a higher frequency of alleles that impair the pro-angiogenic mechanisms of endothelial nitric oxide synthase (eNOS), coded by the NOS3 gene. In this study we evaluated variable number tandem repeats (VNTR) functional polymorphism in intron 4 of NOS3 in individuals with TE (38) and Brazilians without congenital anomalies (136). Haplotypes were estimated for this VNTR with previously analyzed polymorphisms, rs2070744 (−786C > T) and rs1799983 (894T > G), in promoter region and exon 7, respectively. Haplotypic distribution was different between the groups (p = 0.007). Alleles −786C (rs2070744) and 4b (VNTR), associated with decreased NOS3 expression, presented in higher frequency in TE individuals (p = 0.018; OR = 2.57; IC = 1.2–5.8). This association was not identified with polymorphism 894T > G (p = 0.079), which influences eNOS enzymatic activity. These results suggest variants in NOS3, with pre-transcriptional effects as susceptibility factors, influencing the risk TE development. This finding generates insight for a new approach to research that pursues a safer analogue.
Suppression of spin-exciton state in hole overdoped iron-based superconductors
Authors: Lee C. H. , Kihou K. , Park J. T. , Horigane K. , Fujita K. , Waßer F. , Qureshi N. , Sidis Y. , Akimitsu J. , Braden M. 
Published: March 2016

AbstractThe mechanism of Cooper pair formation in iron-based superconductors remains a controversial topic. The main question is whether spin or orbital fluctuations are responsible for the pairing mechanism. To solve this problem, a crucial clue can be obtained by examining the remarkable enhancement of magnetic neutron scattering signals appearing in a superconducting phase. The enhancement is called spin resonance for a spin fluctuation model, in which their energy is restricted below twice the superconducting gap value (2Δs), whereas larger energies are possible in other models such as an orbital fluctuation model. Here we report the doping dependence of low-energy magnetic excitation spectra in Ba1−xKxFe2As2 for 0.5 < x < 0.84 studied by inelastic neutron scattering. We find that the behavior of the spin resonance dramatically changes from optimum to overdoped regions. Strong resonance peaks are observed clearly below 2Δs in the optimum doping region, while they are absent in the overdoped region. Instead, there is a transfer of spectral weight from energies below 2Δs to higher energies, peaking at values of 3Δs for x = 0.84. These results suggest a reduced impact of magnetism on Cooper pair formation in the overdoped region.
The Efficacy and Safety of Knotless Barbed Sutures in the Surgical Field: A Systematic Review and Meta-analysis of Randomized Controlled Trials
Authors: Lin Yifei , Lai Sike , Huang Jin , Du Liang 
Published: March 2016

AbstractThe knotless barbed suture is an innovative type of suture that can accelerate the placement of sutures and eliminate knot tying. However, the outcomes of previous studies are still confounding. This study reviewed the application of different types of barbed sutures in different surgeries. We searched PubMed, EMBASE, CENTRAL and ClinicalTrials.gov to identify randomized controlled trials (RCTs) addressing the application of barbed sutures up to Feb. 2015. Two reviewers independently screened the literature and assessed the risk of bias of included studies. Then meta-analysis was performed using RevMan 5.3 software. Sensitivity analysis and subgroup analysis was performed. Seventeen RCTs (low to moderate risk of bias) involving 1992 patients were included. Compared with conventional sutures, the barbed suture could reduce suture time (SMD=−0.95, 95%CI −1.43 to −0.46, P = 0.0001) and the operative time (SMD=−0.28, 95%CI −0.46 to −0.10, P = 0.003), not significantly increase the estimated blood loss (SMD=−0.09, 95%CI −0.52 to 0.35, P = 0.70), but could lead to more postoperative complications (OR = 1.43, 95%CI 1.05 to 1.96, P = 0.03), These results varied in subgroups. Thus, barbed sutures are effective in reducing the suture and operative time, but the safety evidences are still not sufficient. It need be evaluated based on special surgeries and suture types before put into clinical practice.
Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images
Authors: Gross Polina , Honnorat Nicolas , Varol Erdem , Wallner Markus , Trappanese Danielle M. , Sharp Thomas E. , Starosta Timothy , Duran Jason M. , Koller Sarah , Davatzikos Christos , Houser Steven R. 
Published: March 2016

AbstractDetermination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias.
Chronic unpredictive mild stress leads to altered hepatic metabolic profile and gene expression
Authors: Jia Hong-mei , Li Qi , Zhou Chao , Yu Meng , Yang Yong , Zhang Hong-wu , Ding Gang , Shang Hai , Zou Zhong-mei 
Published: March 2016

AbstractDepression is a complex disease characterized by a series of pathological changes. Research on depression is mainly focused on the changes in brain, but not on liver. Therefore, we initially explored the metabolic profiles of hepatic extracts from rats treated with chronic unpredictive mild stress (CUMS) by UPLC-Q-TOF/MS. Using multivariate statistical analysis, a total of 26 altered metabolites distinguishing CUMS-induced depression from normal control were identified. Using two-stage receiver operating characteristic (ROC) analysis, 18 metabolites were recognized as potential biomarkers related to CUMS-induced depression via 12 metabolic pathways. Subsequently, we detected the mRNA expressions levels of apoptosis-associated genes such as Bax and Bcl-2 and four key enzymes including Pla2g15, Pnpla6, Baat and Gad1 involved in phospholipid and primary bile acid biosynthesis in liver tissues of CUMS rats by real-time qRT-PCR assay. The expression levels of Bax, Bcl-2, Pla2g15, Pnpla6 and Gad1 mRNA were 1.43,1.68, 1.74, 1.67 and 1.42-fold higher and those of Baat, Bax/Bcl-2 ratio mRNA were 0.83, 0.85-fold lower in CUMS rats compared with normal control. Results of liver-targeted metabonomics and mRNA expression demonstrated that CUMS-induced depression leads to variations in hepatic metabolic profile and gene expression and ultimately results in liver injury.
Ca2+ monitoring in Plasmodium falciparum using the yellow cameleon-Nano biosensor
Authors: Pandey Kishor , Ferreira Pedro E. , Ishikawa Takeshi , Nagai Takeharu , Kaneko Osamu , Yahata Kazuhide 
Published: March 2016

AbstractCalcium (Ca2+)-mediated signaling is a conserved mechanism in eukaryotes, including the human malaria parasite, Plasmodium falciparum. Due to its small size (<10 μm) measurement of intracellular Ca2+ in Plasmodium is technically challenging and thus Ca2+ regulation in this human pathogen is not well understood. Here we analyze Ca2+ homeostasis via a new approach using transgenic P. falciparum expressing the Ca2+ sensor yellow cameleon (YC)-Nano. We found that cytosolic Ca2+ concentration is maintained at low levels only during the intraerythrocytic trophozoite stage (30 nM) and is increased in the other blood stages (>300 nM). We determined that the mammalian SERCA inhibitor thapsigargin and antimalarial dihydroartemisinin did not perturb SERCA activity. The change of the cytosolic Ca2+ level in P. falciparum was additionally detectable by flow cytometry. Thus, we propose that the developed YC-Nano-based system is useful to study Ca2+ signaling in P. falciparum and is applicable for drug screening.
Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature
Authors: Reyes-Gutiérrez Paul E. , Kapal Tomáš , Klepetářová Blanka , Šaman David , Pohl Radek , Zawada Zbigniew , Kužmová Erika , Hájek Miroslav , Teplý Filip 
Published: March 2016

AbstractTwo molecules of mistaken identity are addressed. Uncovering these assignment errors led us to formulate more general guidelines about additional misassignments in cases of published bis-imines derived from 1,2-phenylenediamine and hydroxybenzaldehydes having no substituent in ortho-positions. The main purpose of this article is to highlight this repetitive assignment error in the literature and thus increase the likelihood of correct assignments in future papers.
Modelling of the frictional behaviour of the snake skin covered by anisotropic surface nanostructures
Authors: Filippov Alexander E. , Gorb Stanislav N. 
Published: March 2016

AbstractPrevious experimental data clearly revealed anisotropic friction on the ventral scale surface of snakes. However, it is known that frictional properties of the ventral surface of the snake skin range in a very broad range and the degree of anisotropy ranges as well to a quite strong extent. This might be due to the variety of species studied, diversity of approaches used for the friction characterization, and/or due to the variety of substrates used as a counterpart in the experiments. In order to understand the interactions between the nanostructure arrays of the ventral surface of the snake skin, this study was undertaken, which is aimed at numerical modeling of frictional properties of the structurally anisotropic surfaces in contact with various size of asperities. The model shows that frictional anisotropy appears on the snake skin only on the substrates with a characteristic range of roughness, which is less or comparable with dimensions of the skin microstructure. In other words, scale of the skin relief should reflect an adaptation to the particular range of surfaces asperities of the substrate.
TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene
Authors: Liao Jun-Ming , Cao Bo , Deng Jun , Zhou Xiang , Strong Michael , Zeng Shelya , Xiong Jianping , Flemington Erik , Lu Hua 
Published: March 2016

AbstractTumor suppressor p53 transcriptionally regulates hundreds of genes involved in various cellular functions. However, the detailed mechanisms underlying the selection of p53 targets in response to different stresses are still elusive. Here, we identify TFIIS.h, a transcription elongation factor, as a new transcriptional target of p53, and also show that it can enhance the efficiency of transcription elongation of apoptosis-associated bax gene, but not cell cycle-associated p21 (CDKN1A) gene. TFIIS.h is revealed as a p53 target through microarray analysis of RNAs extracted from cells treated with or without inauhzin (INZ), a p53 activator, and further confirmed by RT-q-PCR, western blot, luciferase reporter, and ChIP assays. Interestingly, knocking down TFIIS.h impairs, but overexpressing TFIIS.h promotes, induction of bax, but not other p53 targets including p21, by p53 activation. In addition, overexpression of TFIIS.h induces cell death in a bax- dependent fashion. These findings reveal a mechanism by which p53 utilizes TFIIS.h to selectively promote the transcriptional elongation of the bax gene, upsurging cell death in response to severe DNA damage.
Tilt aftereffect following adaptation to translational Glass patterns
Authors: Pavan Andrea , Hocketstaller Johanna , Contillo Adriano , Greenlee Mark W. 
Published: March 2016

AbstractGlass patterns (GPs) consist of randomly distributed dot pairs (dipoles) whose orientations are determined by specific geometric transforms. We assessed whether adaptation to stationary oriented translational GPs suppresses the activity of orientation selective detectors producing a tilt aftereffect (TAE). The results showed that adaptation to GPs produces a TAE similar to that reported in previous studies, though reduced in amplitude. This suggests the involvement of orientation selective mechanisms. We also measured the interocular transfer (IOT) of the GP-induced TAE and found an almost complete IOT, indicating the involvement of orientation selective and binocularly driven units. In additional experiments, we assessed the role of attention in TAE from GPs. The results showed that distraction during adaptation similarly modulates the TAE after adapting to both GPs and gratings. Moreover, in the case of GPs, distraction is likely to interfere with the adaptation process rather than with the spatial summation of local dipoles. We conclude that TAE from GPs possibly relies on visual processing levels in which the global orientation of GPs has been encoded by neurons that are mostly binocularly driven, orientation selective and whose adaptation-related neural activity is strongly modulated by attention.
Quantification of ethanol in plasma by electrochemical detection with an unmodified screen printed carbon electrode
Authors: Tian Gang , Zhang Xiao-Qing , Zhu Ming-Song , Zhang Zhong , Shi Zheng-Hu , Ding Min 
Published: March 2016

AbstractSimple, rapid and accurate detection of ethanol concentration in blood is very crucial in the diagnosis and management of potential acute ethanol intoxication patients. A novel electrochemical detection method was developed for the quantification of ethanol in human plasma with disposable unmodified screen-printed carbon electrode (SPCE) without sample preparation procedure. Ethanol was detected indirectly by the reaction product of ethanol dehydrogenase (ADH) and cofactor nicotinamide adenine dinucleotide (NAD+). Method validation indicated good quantitation precisions with intra-day and inter-day relative standard deviations of ≤9.4% and 8.0%, respectively. Ethanol concentration in plasma is linear ranging from 0.10 to 3.20 mg/mL, and the detection limit is 40.0 μg/mL (S/N > 3). The method shows satisfactory correlation with the reference method of headspace gas chromatography in twenty human plasma samples (correlation coefficient 0.9311). The proposed method could be applied to diagnose acute ethanol toxicity or ethanol-related death.
Salusin-β induces foam cell formation and monocyte adhesion in human vascular smooth muscle cells via miR155/NOX2/NFκB pathway
Authors: Sun Hai-Jian , Zhao Ming-Xia , Liu Tong-Yan , Ren Xing-Sheng , Chen Qi , Li Yue-Hua , Kang Yu-Ming , Zhu Guo-Qing 
Published: March 2016

AbstractVascular smooth muscle cells (VSMCs) are indispensible components in foam cell formation. Salusin-β is a stimulator in the progression of atherosclerosis. Here, we showed that salusin-β increased foam cell formation evidenced by accumulation of lipid droplets and intracellular cholesterol content and promoted monocyte adhesion in human VSMCs. Salusin-β increased the expressions and activity of acyl coenzyme A:cholesterol acyltransferase-1 (ACAT-1) and vascular cell adhesion molecule-1 (VCAM-1) in VSMCs. Silencing of ACAT-1 abolished the salusin-β-induced lipid accumulation and silencing of VCAM-1 prevented the salusin-β-induced monocyte adhesion in VSMCs. Salusin-β caused p65-NFκB nuclear translocation and increased p65 occupancy at the ACAT-1 and VCAM-1 promoter. Inhibition of NFκB with Bay 11-7082 prevented the salusin-β-induced ACAT-1 and VCAM-1 upregulation, foam cell formation and monocyte adhesion in VSMCs. Scavenging ROS, inhibiting NADPH oxidase or knockdown of NOX2 abolished the effects of salusin-β on ACAT-1 and VCAM-1 expressions, p65-NFκB nuclear translocation, lipid accumulation and monocyte adhesion in VSMCs. Salusin-β increased miR155 expression and knockdown of miR155 prevented the effects of salusin-β on ACAT-1 and VCAM-1 expressions, p65-NFκB nuclear translocation, lipid accumulation, monocyte adhesion and ROS production in VSMCs. These results indicate that salusin-β induces foam formation and monocyte adhesion via miR155/NOX2/NFκB-mediated ACAT-1 and VCAM-1 expressions in VSMCs.
Effects of Berries Consumption on Cardiovascular Risk Factors: A Meta-analysis with Trial Sequential Analysis of Randomized Controlled Trials
Authors: Huang Haohai , Chen Guangzhao , Liao Dan , Zhu Yongkun , Xue Xiaoyan 
Published: March 2016

AbstractThe effects of berries consumption on cardiovascular disease (CVD) risk factors have not been systematically examined. Here, we aimed to conduct a meta-analysis with trial sequential analysis to estimate the effect of berries consumption on CVD risk factors. PubMed, Embase and CENTRAL were searched for randomized controlled trials (RCTs) that regarding the effects of berries consumption in either healthy participants or patients with CVD. Twenty-two eligible RCTs representing 1,251 subjects were enrolled. The pooled result showed that berries consumption significantly lowered the low density lipoprotein (LDL)-cholesterol [weighted mean difference (WMD), −0.21 mmol/L; 95% confidence interval (CI), −0.34 to −0.07; P = 0.003], systolic blood pressure (SBP) (WMD, −2.72 mmHg; 95% CI, −5.32 to −0.12; P = 0.04), fasting glucose (WMD, −0.10 mmol/L; 95% CI, −0.17 to −0.03; P = 0.004), body mass index (BMI) (WMD, −0.36 kg/m2; 95% CI, −0.54 to −0.18, P < 0.00001), Hemoglobin A1c (HbA1c) (WMD, −0.20%; 95% CI, −0.39 to −0.01; P = 0.04) and tumor necrosis factor-α (TNF-α) (WMD, −0.99 ρg/mL; 95% CI, −1.96 to −0.02; P = 0.04). However, no significant changes were seen in other markers. The current evidence suggests that berries consumption might be utilized as a possible new effective and safe supplementary option to better prevent and control CVD in humans.