Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the depletion of high-abundance proteins in blood plasma/serum on the proteome of these media in growing farm animals

The aim of the study was to use hexapeptide combinatorial libraries to evaluate the influence of high-abundance protein depletion on low-abundance protein enrichment, protein concentration, and 2D gel quality in plasma and serum proteomes of growing piglets and calves. Depleted and nondepleted samples of plasma/serum were resolved using 2D electrophoresis (2DE). Bioinformatic analysis of the 2D gels showed an increased number of detected spots on each gel after depletion of excess high-abundance proteins in calf plasma (+26.46%) and in piglet serum (+49.40%). Relative expression of selected low-abundance protein spots in the blood plasma/serum samples was higher after high-abundance protein depletion. Both media showed decreased expressions of high-abundance protein spot clusters on 2D gels after treatment. The results of this study confirm both the high efficiency of high-abundance protein depletion and the increase in concentrations of low-abundance proteins on 2D gels after treatment. The method of depletion is reproducible and it may be used as an alternative to immunodepletion for preparing blood plasma/serum samples from young, growing animals for 2DE. Increased content of the low-abundance proteins on the 2D gels enables complete analysis of plasma/serum proteome and thereby allows for the discovery of novel biomarkers that might be useful in veterinary medicine.
CDK5 phosphorylates eNOS at Ser‐113 and regulates NO production

Phosphorylation of endothelial nitric oxide synthase (eNOS) is key mechanism in response to various forms of cellular stimulation. Through protein nitration by peroxynitrite, eNOS is believed to be responsible for the major abnormalities in several important neurodegenerative diseases including Alzheimer's (AD) and Parkinson's diseases (PD). Recent studies provide important in vivo evidence that hyperactivation of Cdk5 by p25 plays an essential role in the cell death of neurons in experimental models of AD and PD. This study focuses on the functional regulation of eNOS by Cdk5/p35 complex in a phosphorylation dependent manner. Our results showed that Cdk5 can phosphorylate eNOS both in vitro and in vivo. In vitro kinase assay together with the bioinformatic analysis and site direct mutagenesis revealed that Ser‐113 is the major phosphorylation site for Cdk5. Most interestingly, the nitrite production was significantly reduced in eNOS and Cdk5/p35 co‐transfected SH‐SY5Y cells when compared with co‐transfection of Cdk5/p35 and S113A. Together, our data suggest that Cdk5 can phosphorylate eNOS at the Ser‐113 site and down‐regulate eNOS‐derived NO levels. J. Cell. Biochem. 110: 112–117, 2010. © 2010 Wiley‐Liss, Inc.
The Fragile X Family of Disorders: A Model for Autism and Targeted Treatments

CGG-repeat expansion mutations of the fragile X mental retardation 1 (FMR1) gene are the leading known cause of autism and autism spectrum disorders (ASD). Full mutation expansions (>200 CGG repeats) of the gene are gen- erally silenced, resulting in absence of the FMR1 protein and fragile X syndrome. By contrast, smaller expansions in the premutation range (55-200 CGG repeats) result in excess gene activity and RNA toxicity, which is responsible for the neurodegenerative disorder, fragile X-associated tremor/ataxia syndrome (FXTAS), and likely additional cases of devel- opmental delay and autism. Thus, the FMR1 gene is causative of a common (autism) phenotype via two entirely different pathogenic mechanisms, RNA toxicity and gene silencing. The study of this gene and its pathogenic mechanisms there- fore represents a paradigm for understanding gene-brain relationships and the means by which diverse genetic mecha- nisms can give rise to a common behavioral phenotype.
Children's Passive: A View from the By-Phrase

This article argues that children's difficulty with passive constructions is related to properties of the by-phrase. Specifically, we argue that children are in full control of all aspects of the passive construction except for the ability to transmit the external -role of the predicate to the by-phrase; we thus reject Borer and Wexler's (1987) claim regarding the maturation of A-chains. Our conclusion is dictated by the results of an experiment we conducted, and supported by data already present in the literature.
Nintedanib treatment delays prostate dorsolateral lobe cancer progression in the TRAMP model: contribution to the epithelial‐stromal interaction balance

Prostate cancer (PCa) progression mechanism has been linked to epithelial proliferation, tumor invasion ability, and growth factors. Nintedanib (BIBF 1120) has been reported as being FGF and VEGF pathway inhibitors, exhibiting antitumor activity. Thus, the objective herein was to characterize the early Nintedanib treatment effects on the structure and molecules involved in the basal membrane, the extracellular matrix (ECM) maintenance, in addition to the angiogenesis and mitogenic processes at different grades of prostatic tumor development in TRAMP mice. Therefore, 45 male TRAMP mice were divided into control groups: 8‐week‐old mice (TC8), 12‐week‐old mice (TC12), and 16‐week‐old mice (TC16); and treated groups with 10 mg/kg/day Nintedanib dose for 4 weeks. The treated groups were euthanized at 12 (TN12) and 16 (TN16) weeks of age. Samples from the dorsolateral lobe were collected and processed for light microscopy, immunohistochemistry, Western blotting, and microvessel density analysis. The results showed that early Nintedanib treatment led to an increase of healthy epithelium frequency and a reduction of LGPIN and a maximum vascularization density in the TN12 group. Also, treatment led to a well‐differentiated adenocarcinoma decrease and an α and β dystroglycan and also laminin 1 increase in the TN16 group. IGFR1 decreased in the TN16 group. To conclude, early Nintedanib treatment led to a reduction in cancer severity, interfering in both ECM compounds and angiogenesis process to then contribute to a balance, not only in the prostatic epithelium and stroma, but also in the epithelial‐stromal interaction during PCa progression.
Early prosthetic valve endocarditis due to Acinetobacter baumannii: A case report and brief review of the literature

Acinetobacter is a highly resistant microorganism, commonly isolated in intensive and post-operative care units. Although rarely reported, it may constitute 1 of the several causes of early prosthetic valve endocarditis. A diffuse, red maculopapular rash may be encountered in patients with Acinetobacter endocarditis. Here we present a case of early prosthetic valve endocarditis due to Acinetobacter baumannii and accompanied by a cutaneous eruption.
Chinese Consumer Quality Perception and Preference of Traditional Sustainable Rice Produced by the Integrated Rice–Fish System

Historically, humans have created many sustainable practices, and among the most famous and successful sustainable practice is the rice–fish system in China. While previous studies have investigated eco-labeling food from various angles, consumer perception and preference of food produced from traditional sustainable practices (traditional sustainable food) remain unexplored. Taking the historical rice–fish system as an example, we examined consumers’ perception and willingness to pay (WTP) for rice produced by a rice–fish system, by using data from 1422 consumers from China. Our paper shows that most Chinese consumers do understand the meaning of the rice–fish system and perceive the traditional sustainable system as environmentally friendly and producing high-quality food. The premium that consumers are willing to pay for rice from a rice–fish system is about 41%. Consumers who perceive the linkage between sustainable production and food quality and safety have a significantly higher WTP for traditional sustainable rice (p-value = 0.000). Interestingly, the perception of environment risk does not directly cause more traditional sustainable food consumption, but those who self-proclaimed as environmentalists are willing to pay a premium for traditional sustainable rice. Females, people with high family income, and people with children are more willing to pay for traditional sustainable rice. Understanding consumer perception and preference of traditional sustainable food provides critical information for Chinese policymakers to develop a cheap and efficient way to keep traditional sustainable practices and promote sustainable food consumption.
Perinatal and Infant Mortality and Low Birth Weight among Residents near Cokeworks in Great Britain

Abstract With growing evidence of the adverse health effects of air pollution—especially fine particulates—investigators must concentrate on the fetus, neonate, and infant as potentially vulnerable groups. Cokeworks are a major source of smoke and sulfur dioxide. In the current study, the authors investigated whether populations residing near cokeworks had a higher risk of adverse perinatal and infant outcomes. Zones of 7.5-km radius around 22 cokeworks in Great Britain were studied, within which the authors assumed that exposure declined from highest levels within 2 km to background levels. Routinely recorded birth and death data for Great Britain during the period 1981–1992 were analyzed. Each individual record had a postcode that referred to a small geographical area of typically 15–17 addresses. The authors calculated expected numbers on the basis of regional rates, stratified by year, sex, and a small-area socioeconomic deprivation score. For all cokeworks combined, the observed/expected ratio (95% confidence intervals within parentheses) within 2 km of cokeworks was 1.00 (0.95, 1.06) for low-birth-weight (i.e., < 2,500 g) infants; 0.94 (0.78, 1.12) for still births; 0.95 (0.83, 1.09) for infant mortality; 0.86 (0.72, 1.03) for neonatal mortality; 1.10 (0.90, 1.33) for postneonatal mortality; 0.79 (0.30, 1.46) for respiratory postneonatal mortality; and 1.07 (0.77, 1.43) for postneonatal Sudden Infant Death Syndrome. Respiratory postneonatal mortality was low throughout the entire 0–7.5-km study area (observed/expected = 0.74 [0.61, 0.88]). There was no statistically significant decline in risk with distance from cokeworks for any of the outcomes studied. The authors concluded that there was no evidence of an increased risk of low birth weight, stillbirths, and/or neonatal mortality near cokeworks, and there was no strong evidence for any association between residence near cokeworks and postneonatal mortality. One must remember, however, the limited statistical power of the study to detect small risks.
Acute myocardial infarction in Canada: improvement with time.

A patient hospitalized with acute myocardial infarction (AMI) in the year 2000 has a markedly improved chance of survival than would have been possible 10 or even 5 years ago. A study by Louise Pilote and colleagues[1][1] in this issue (page 31) is important because it documents this improvement on
Molecular screening of the CFTR gene in men with anomalies of the vas deferens: identification of three novel mutations.

Many studies have shown that congenital absence of the vas deferens (CAVD) is a genital cystic fibrosis transmembrane conductance regulator (CFTR)-mediated phenotype, with a broad spectrum of abnormalities causing male infertility. The genotype of these patients includes mutations in the CFTR gene, e.g. DeltaDeltaF508, R117H and the T5 allele; all of which are commonly found in CAVD. In this study we have screened the entirety of CFTR gene in 47 males with anomalies of the vas deferens: 37 cases of congenital bilateral absence of the vas deferens, three cases of congenital unilateral absence of the vas deferens and seven cases of obstructive azoospermia with hypoplastic vas deferens. Among the 94 chromosomes studied, 65 mutations, of which three are novel (2789+2insA, L1227S, 4428insGA), were identified. The majority of patients (63.8%) had two detectable CFTR gene mutations. Furthermore, high frequencies of the DeltaDeltaF508 mutation (44.7%), the T5 allele (36.2%) and R117H mutation (19.1%) were observed.
Ancient DNA analysis of human populations.

The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.
Association between genetic polymorphisms of antioxidant enzyme genes and susceptibility to hepatocellular carcinoma : a meta-analysis

This study was to analysis the correlation between genetic polymorphisms in antioxidant enzyme genes and the susceptibility factors to hepatocellular carcinoma (HCC) using meta analysis. Electronic searches were conducted in Pubmed, Embase and Cochrane library. Retrieval keywords included antioxidant enzyme, superoxide dismutases, catalase, glutathione peroxidase, and hepatocellular carcinoma. Retrieval strategy was: ((antioxidant enzyme) OR (superoxide dismutases) OR catalase OR (glutathione peroxidase)) AND (hepatocellular carcinoma) OR HCC) AND polymorphism (OR gene OR based OR Allele * OR Genotyp * OR susceptibility). Selection criteria, data extraction and quality evaluation, and statistical analysis of articles were performed. For MnSOD, there were 2351 cases, including 1048 patients and 1303 control. For CAT, there were 2166 cases, including 987 patients and 1179 control. For GPX1, there were 1437 cases, including 614 patients and 823 control. The recessive model (Ala/Ala vs. Val/Val/Val + Ala) of MnSOD was associated with the risk of HCC (OR = 1.49, [95% CI: 1.04, 2.15]) (P = 0.03). MnSOD (allele model [Ala vs. Val], codominant model [Ala/Ala vs. Val/Val], codominant model [Val/Ala vs. Val/Val], and dominant model [Ala/Ala + Val/Ala vs. Val/Val]), CAT (262 C > T) (allele model [T vs. C], codominant model [TT vs. CC], codominant model [CT vs. CC], dominant model [TT + CT vs. CC], and recessive model [TT vs. CT + CT]), and GPX1 (Pro198Leu) (allele model [Leu vs. Pro], codominant model [Leu/Leu vs. Pro/Pro], codominant model [Leu/ Pro vs. Pro/Pro], dominant model [Leu/Leu + Leu/Pro vs. Pro/Pro] and recessive model [Leu/Leu vs. Pro/Pro + Leu/Pro]) were no significant correlation with the incidence of HCC (P > 0.05). The implicit model (Ala/Ala vs. Val/ Val/Val + Ala) of MnSOD was significantly correlated with the incidence of HCC. However, CAT (262 C > T) and GPX1 (Pro198Leu) were no significant correlation with the incidence of HCC.
Understanding the Economic Potential of Service-Oriented Architecture

Service-oriented architecture (SOA) is one of the most discussed topics in the information systems (IS) discipline. While most computer scientists agree that the service-oriented paradigm has clear benefits in terms of technical quality attributes, it has been difficult to justify SOA economically. The few studies that have investigated the strategic and economic aspects of SOA are mostly exploratory and lack a more comprehensive framework for understanding the sources of its economic potential. Based on IS and SOA literature, our work goes further in suggesting the SOA economic potential model, which describes the causal relationships between the SOA's style characteristics and value it can provide on the business side. Using this model, we investigate 164 SOA cases published between 2003 and 2008 to explore the economic rationale for adopting SOA. Our findings suggest that SOA's business benefits are currently mainly driven by operational and information technology infrastructural improvements. However, enterprises also realize strategic benefits from SOA; for example, by electronically integrating with their business partners by means of SOA. We use the results of our study to derive propositions and suggest a research model for future studies on SOA's economic potential.
Evaluation of the hematoma consequences, neurobehavioral profiles, and histopathology in a rat model of pontine hemorrhage.

OBJECT Primary pontine hemorrhage (PPH) represents approximately 7% of all intracerebral hemorrhages (ICHs) and is a clinical condition of which little is known. The aim of this study was to characterize the early brain injury, neurobehavioral outcome, and long-term histopathology in a novel preclinical rat model of PPH. METHODS The authors stereotactically infused collagenase (Type VII) into the ventral pontine tegmentum of the rats, in accordance with the most commonly affected clinical region. Measures of cerebrovascular permeability (brain water content, hemoglobin assay, Evans blue, collagen Type IV, ZO-1, and MMP-2 and MMP-9) and neurological deficit were quantified at 24 hours postinfusion (Experiment 1). Functional outcome was measured over a 30-day period using a vertebrobasilar scale (the modified Voetsch score), open field, wire suspension, beam balance, and inclined-plane tests (Experiment 2). Neurocognitive ability was determined at Week 3 using the rotarod (motor learning), T-maze (working memory), and water maze (spatial learning and memory) (Experiment 3), followed by histopathological analysis 1 week later (Experiment 4). RESULTS Stereotactic collagenase infusion caused dose-dependent elevations in hematoma volume, brain edema, neurological deficit, and blood-brain barrier rupture, while physiological variables remained stable. Functional outcomes mostly normalized by Week 3, whereas neurocognitive deficits paralleled the cystic cavitary lesion at 30 days. Obstructive hydrocephalus did not develop despite a clinically relevant 30-day mortality rate (approximately 54%). CONCLUSIONS These results suggest that the model can mimic several translational aspects of pontine hemorrhage in humans and can be used in the evaluation of potential preclinical therapeutic interventions.
Transcriptome Changes at the Initiation of Elongation in the Bovine Conceptus1

The majority of embryonic loss in cattle occurs before maternal recognition of pregnancy, at around Day 16 postconception. The origin of the embryo can have a significant impact on the dynamics of embryo mortality. The aim of this study was to examine the temporal changes in transcriptional profile as the embryo develops from a spherical blastocyst on Day 7 to an ovoid conceptus at the initiation of elongation on Day 13 and to highlight differences in these temporal gene expression dynamics between in vivo- and in vitro-derived blastocysts that may be associated with embryonic survival/mortality using the bovine Affymetrix microarray. All embryos were produced either in vitro by in vitro fertilization or in vivo by superovulation. A proportion of Day 7 blastocysts were snap frozen, and the remainder were transferred (n = 10 per recipient) to synchronized heifers, recovered on Day 13, and snap frozen individually. Three pools of Day 7 blastocysts (n = 25 per pool) and Day 13 conceptuses (n = 5 per pool) were used for microarray analysis. In Day 7 blastocysts, 50 genes were found to be differentially expressed (P < 0.05), of which 19 were up-regulated and 31 down-regulated in the in vivo compared to in vitro embryos. In Day 13 conceptuses, 288 genes were found to be differentially expressed (P < 0.05), of which 133 were up-regulated and 155 down-regulated in the in vivo compared to in vitro embryos. The comparison between Day 7 and Day 13 embryos revealed significant temporal changes in transcript profile with 1806 and 909 transcripts differentially expressed in the in vitro- and in vivo-derived embryos, respectively. Across the three array comparisons between Day 7 and Day 13 embryos, 444 genes were consistently exclusively present in the in vivo embryos, whereas 1341 were exclusively present in the in vitro embryos. Regardless of the origin of the embryo, 465 differentially expressed genes between Day 7 and 13 were common to both in vivo- and in vitro-derived embryos; these genes are likely critical for the transition between the blastocyst (Day 7) and ovoid conceptus (Day 13) stages of embryo development. In order to validate the microarray findings, differences in the expression of six genes (CYP51A1, FADS1, TDGF1, HABP2, APOA2, and SLC12A2) were confirmed by quantitative real-time PCR on in vivo- and in vitro-derived embryos on Day 7 and Day 13 using independent samples from those used for the microarray. Subsequent mapping of these differentially expressed genes into relevant functional groups and pathways identified important pathways involved in conceptus elongation in cattle. In conclusion, this analysis has identified genes and pathways crucial for the transition from a spherical blastocyst to an ovoid conceptus as well as those uniquely associated with a greater likelihood of embryonic survival (those unique to in vivo embryos) or loss (those unique to in vitro embryos).