Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of cpn60-Based Real-Time Quantitative PCR Assays for the Detection of 14 Campylobacter Species and Application to Screening of Canine Fecal Samples

ABSTRACT Campylobacter species are important organisms in both human and animal health. The identification of Campylobacter currently requires the growth of organisms from complex samples and biochemical identification. In many cases, the condition of the sample being tested and/or the fastidious nature of many Campylobacter species has limited the detection of campylobacters in a laboratory setting. To address this, we have designed a set of real-time quantitative PCR (qPCR) assays to detect and quantify 14 Campylobacter species, C. coli, C. concisus, C. curvus, C. fetus, C. gracilis, C. helveticus, C. hyointestinalis, C. jejuni, C. lari, C. mucosalis, C. rectus, C. showae, C. sputorum, and C. upsaliensis, directly from DNA extracted from feces. By use of a region of the cpn60 (also known as hsp60 or groEL) gene, which encodes the universally conserved 60-kDa chaperonin, species-specific assays were designed and validated. These assays were then employed to determine the prevalence of Campylobacter species in fecal samples from dogs. Fecal samples were found to contain detectable and quantifiable levels of C. fetus, C. gracilis, C. helveticus, C. jejuni, C. showae, and C. upsaliensis, with the majority of samples containing multiple Campylobacter species. This study represents the first report of C. fetus, C. gracilis, C. mucosalis, and C. showae detection in dogs and implicates dogs as a reservoir for these species. The qPCR assays described offer investigators a new tool to study many Campylobacter species in a culture-independent manner.
β-Amyloid burden in the temporal neocortex is related to hippocampal atrophy in elderly subjects without dementia

Objective: To investigate whether global and regional β-amyloid (Aβ) burden as measured with 11C Pittsburgh compound B (PIB) PET is associated with hippocampal atrophy characterized using MRI in healthy controls and patients with amnestic mild cognitive impairment (aMCI) or Alzheimer disease (AD). Methods: Ninety-two elderly healthy controls, 32 subjects with aMCI, and 35 patients with AD were imaged using 11C-PIB PET and MRI. Hippocampal volume was measured and PIB standardized uptake value ratio was extracted after partial volume correction within 41 regions of interest. Global, regional, and voxel-based correlations between PIB and hippocampal volume were computed for each group. Results: In healthy control participants with elevated neocortex PIB retention, significant correlation was found between PIB retention in the inferior temporal region and hippocampal volume using both region-based and voxel-based approaches. No correlation was found in any other group. Conclusions: The strong correlation between hippocampal atrophy and β-amyloid (Aβ) burden in the Pittsburgh compound B–positive healthy control group suggests that Aβ deposition in the inferior temporal neocortex is related to hippocampal synaptic and neuronal degeneration.
Fusing Similarity-Based Sequence and Dead Reckoning for Indoor Positioning Without Training

The traditional fingerprinting-based positioning approach usually requires a laborious training phase to collect the measurements in an environment, which is a challenge for applications involving large buildings. In this paper, we propose a novel approach to fuse similarity-based sequence and dead reckoning to track the positions of users in wireless indoor environments. The reference fingerprinting map is constructed without the need for training and is based upon the geometrical relationships of the transmitters, whose positions are known and can be obtained offline. The fingerprint used for online positioning is represented by a ranked sequence of transmitters based on the measured received signal strength (RSS), which is referred to as RSS sequence in this paper. The similarities between this sequence and the reference fingerprints are computed and embedded into a particle filter to locate a user. The displacement estimation from inertial measurement unit is then integrated into the particle filter to track a mobile user. Moreover, the proposed approach can be easily extended to include other sources of sensors. In this paper, frequency modulation radio signal measurements are used as the example to fuse with Wi-Fi measurements to achieve a better tracking accuracy. Extensive experiments are also conducted to evaluate the proposed approach.
Short-term and long-term risk of tuberculosis associated with CD4 cell recovery during antiretroviral therapy in South Africa

Objective:To determine the short-term and long-term risks of tuberculosis (TB) associated with CD4 cell recovery during antiretroviral therapy (ART). Design:Observational community-based ART cohort in South Africa. Methods:TB incidence was determined among patients (n = 1480) receiving ART for up to 4.5 years in a South African community-based service. Updated CD4 cell counts were measured 4-monthly. Person-time accrued within a range of CD4 cell count strata (CD4 cell strata) was calculated and used to derive CD4 cell-stratified TB rates. Factors associated with incident TB were identified using Poisson regression models. Results:Two hundred and three cases of TB were diagnosed during 2785 person-years of observation (overall incidence, 7.3 cases/100 person-years). During person-time accrued within CD4 cell strata 0–100, 101–200, 201–300, 301–400, 401–500 and more than 500 cells/μl unadjusted TB incidence rates were 16.8, 9.3, 5.5, 4.6, 4.2 and 1.5 cases/100 person-years, respectively (P < 0.001). During early ART (first 4 months), adjusted TB rates among those with CD4 cell counts 0–200 cells/μl were 1.7-fold higher than during long-term ART (P = 0.026). Updated CD4 cell counts were the only patient characteristic independently associated with long-term TB risk. Conclusion:Updated CD4 cell counts were the dominant predictor of TB risk during ART in this low-resource setting. Among those with baseline CD4 cell counts less than 200 cells/μl, the excess adjusted risk of TB during early ART was consistent with ‘unmasking’ of disease missed at baseline screening. TB incidence rates at CD4 cell counts of 200–500 cells/μl remained high and adjunctive interventions are required. TB prevention would be improved by ART policies that minimized the time patients spend with CD4 cell counts below a threshold of 500 cells/μl.
A critical role for TNF receptor-associated factor 1 and Bim down-regulation in CD8 memory T cell survival

The mechanisms that allow the maintenance of immunological memory remain incompletely defined. Here we report that tumor necrosis factor receptor (TNFR)-associated factor (TRAF) 1, a protein recruited in response to several costimulatory TNFR family members, is required for maximal CD8 T cell responses to influenza virus in mice. Decreased recovery of CD8 T cells in vivo occurred under conditions where cell division was unimpaired. In vitro, TRAF1-deficient, antigen-activated T cells accumulated higher levels of the proapoptotic BH3-only family member Bim, particularly the most toxic isoform, BimS. In the presence of excess IL-15, memory phenotype T cells with similar surface phenotype and comparable levels of Bcl-2 family members could be generated from WT or TRAF1-deficient T cell receptor transgenic OT-I T cells. However, when the memory CD8 T cells were allowed to compete for survival signals in the absence of antigen in vivo, the TRAF1-deficient T cells showed decreased recovery compared with TRAF1-sufficient T cells. This defect in T cell recovery in vivo was alleviated by introduction of siRNA to down-modulate Bim in TRAF1-deficient memory T cells. These studies identify the TRAF1 signaling axis and Bim down-regulation as critical for CD8 memory T cell survival in vivo.
Damaged DNA-binding Protein DDB Stimulates the Excision of Cyclobutane Pyrimidine Dimers in Vitro in Concert with XPA and Replication Protein A*

Human cells contain a protein that binds to UV-irradiated DNA with high affinity. This protein, damaged DNA-binding protein (DDB), is a heterodimer of two polypeptides, p127 and p48. Recent in vivo studies suggested that DDB is involved in global genome repair of cyclobutane pyrimidine dimers (CPDs), but the mechanism remains unclear. Here, we show that in vitro DDB directly stimulates the excision of CPDs but not (6–4)photoproducts. The excision activity of cell-free extracts from Chinese hamster AA8 cell line that lacks DDB activity was increased 3–4-fold by recombinant DDB heterodimer but not p127 subunit alone. Moreover, the addition of XPA or XPA + replication protein A (RPA), which themselves enhanced excision, also enhanced the excision in the presence of DDB. DDB was found to elevate the binding of XPA to damaged DNA and to make a complex with damaged DNA and XPA or XPA + RPA as judged by both electrophoretic mobility shift assays and DNase I protection assays. These results suggest that DDB assists in the recognition of CPDs by core NER factors, possibly through the efficient recruitment of XPA or XPA·RPA, and thus stimulates the excision reaction of CPDs.
MARCKS silencing differentially affects human vascular smooth muscle and endothelial cell phenotypes to inhibit neointimal hyperplasia in saphenous vein

Intimal hyperplasia (IH) limits the patency of all cardiovascular vein bypass grafts. We previously found the myristoylated alanine‐rich C kinase substrate (MARCKS), a key protein kinase C (PKC) substrate, to be up‐regulated in canine models of IH. Here, we further characterize the role of MARCKS in IH and examine the phenotypic consequences of MARCKS silencing by small interfering RNA (siRNA) transfection in human vascular smooth muscle cells (VSMCs) and endothelial cells (ECs) in vitro and use a rapid 10‐min nonviral siRNA transfection technique to determine the effects of MARCKS silencing in human saphenous vein cultured ex vivo. We demonstrate MARCKS silencing attenuates VSMC migration and arrests VSMC proliferation in part through the up‐regulation of the cyclin‐dependent kinase inhibitor p27kip1. Conversely, MARCKS silencing had little or no effect on EC migration or proliferation. These phenotypic changes culminated in reduced neointimal formation in cultured human saphenous vein. These data identify MARCKS as a pathogenic contributor to IH and indicate therapeutic MARCKS silencing could selectively suppress the “atherogenic,” proliferative phenotype of VSMCs without collateral harm to the endothelium. This approach could be readily translated to the clinic to silence MARCKS in vein bypass grafts prior to implantation. — Monahan, T. S. , Andersen, N. D. , Martin, M. C, Malek, J. Y. , Shrikhande, G. V. , Pradhan, L. , Ferran, C, LoGerfo, F. W. MARCKS silencing differentially affects human vascular smooth muscle and endothelial cell phenotypes to inhibit neointimal hyperplasia in saphenous vein. FASEB J. 23, 557–564 (2009)
Multiple ways of silencing E‐cadherin gene expression in lobular carcinoma of the breast

The cell‐cell adhesion receptor gene E‐cadherin (CDH1) is expressed by epithelial cells, in which it mediates adhesion and morphogenesis. Invasive lobular carcinoma (ILC) characteristically infiltrates diffusely as single cells; by immunohistochemistry, many of these tumours lack E‐cadherin expression. In the present study we investigated various ways in which loss of function of the E‐cadherin gene could occur in ILCs, namely, promoter methylation, mutation and allelic loss. We analysed 22 ILCs and found 12 (55%) E‐cadherin‐negative samples by immunohistochemical analysis. Methylation‐specific polymerase chain reaction (PCR) showed that 17/22 (77%) of these tumours had methylation of the CDH1 promoter, including 11/12 (91%) of the E‐cadherin‐negative tumours. All 16 exons of E‐cadherin (including intron‐exon boundaries) were amplified from chromosomal DNA and screened for mutations by conformation‐sensitive gel electrophoresis (CSGE). Bands with altered mobility were analysed by direct sequencing. We identified five frameshift mutations, which resulted in downstream stop codons and one splice site mutation in six different tumours (29%). Loss of heterozygosity (LOH) was assessed using microsatellite markers, and 9/18 (50%) informative tumours showed LOH. We conclude that most ILCs show genetic or epigenetic changes affecting the E‐cadherin gene and that many of these tumours lack E‐cadherin expression. In all cases in which there was loss of expression, this was consistent with biallelic inactivation of CDH1 by promoter methylation, mutation or allelic loss in any combination. © 2001 Wiley‐Liss, Inc.
The nucleoid‐associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle–biofilms in the phytopathogenic bacterium Dickeya dadantii

Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface‐associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle–biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase‐regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid‐associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co‐ordinate basic metabolism, virulence and modifications of lifestyle.
Analysis of White Adipose Tissue Gene Expression Reveals CREB1 Pathway Altered in Huntington's Disease.

BACKGROUND In addition to classical neurological symptoms, Huntington's disease (HD) is complicated by peripheral pathology and both the mutant gene and the protein are found in cells and tissues throughout the body. Despite the adipose tissue gene expression alterations described in HD mouse models, adipose tissue and its gene expression signature have not been previously explored in human HD. OBJECTIVE We investigated gene expression signatures in subcutaneous adipose tissue obtained from control subjects, premanifest HD gene carriers and manifest HD subjects with the aim to identify gene expression changes and signalling pathway alterations in adipose tissue relevant to HD. METHODS Gene expression was assessed using Affymetrix GeneChip® Human Gene 1.0 ST Array. Target genes were technically validated using real-time quantitative PCR and the expression signature was validated in an independent subject cohort. RESULTS In subcutaneous adipose tissue, more than 500 genes were significantly different in premanifest HD subjects as compared to healthy controls. Pathway analysis suggests that the differentially expressed genes found here in HD adipose tissue are involved in fatty acid metabolism pathways, angiotensin signalling pathways and immune pathways. Transcription factor analysis highlights CREB1. Using RT-qPCR, we found that MAL2, AGTR2, COBL and the transcription factor CREB1 were significantly upregulated, with CREB1 and AGT also being significantly upregulated in a separate cohort. CONCLUSIONS Distinct gene expression profiles can be seen in HD subcutaneous adipose tissue, with CREB1 highlighted as a key transcription factor.
Review of select transplant subpopulations at high risk of failure from standard immunosuppressive therapy

Despite improvements in short‐term graft and patient survival rates for solid organ transplants, certain subgroups of transplant recipients experience poorer clinical outcome compared to the general population. Groups including pediatrics, African‐Americans, diabetics, cystic fibrosis patients, and pregnant women require special considerations when designing immunosuppressive regimens that optimize transplant outcomes. Problems specific to pediatric transplant recipients include altered pharmacokinetics of immunosuppressive drugs, such as cyclosporine (CsA) and tacrolimus (poor absorption, increased metabolism, rapid clearance), the need to restore growth post‐transplantation, and a high incidence of drug‐related adverse effects. African‐Americans have decreased drug absorption and bioavailability, high immunologic responsiveness, and a high incidence of post‐transplant diabetes mellitus. Diabetics and cystic fibrosis patients exhibit poor absorption of immunosuppressive agents, which may lead to underimmunosuppression and subsequent graft rejection. Pregnant women undergo physiologic changes that can alter the pharmacokinetics of immunosuppressives, thus requiring careful clinical management to minimize the risks of either under‐ or overimmunosuppression to mother and child. To achieve an optimal post‐transplant outcome in these high‐risk patients, the problems specific to each group must be addressed, and immunosuppressive therapy individualized accordingly. Drug formulation greatly impacts upon pharmacokinetics and the resultant level of immunosuppression. Thus, a formulation with improved absorption (e.g., CsA for microemulsion), higher bioavailability, and less pharmacokinetic variability may facilitate patient management and lead to more favorable outcomes, especially in groups demonstrating low and variable bioavailability. Other strategies aimed at improving transplant outcome include the use of higher immunosuppressive doses, different combinations of immunosuppressive agents, more frequent monitoring, and management of concurrent disease states.
Mitotic recombination as evidence of alternative pathogenesis of gastrointestinal stromal tumours in neurofibromatosis type 1

Background: Neurofibromatosis type 1 (NF1) is a neurocutaneous disorder resulting in the growth of a variety of tumours, and is inherited in an autosomal dominant pattern. Gastrointestinal stromal tumours (GISTs) are mesenchymal tumours that commonly harbour oncogenic mutations in KIT or PDGFRA and are thought to arise from the interstitial cells of Cajal (ICC; the pacemaker cells of the gut). Aim: To characterise two patients with NF1 and GISTs. Methods: Two patients were genotyped for germline mutations in NF1. GISTs from both patients were genotyped for somatic mutations in KIT and PDGFRA. Loss of heterozygosity (LOH) of NF1 in one GIST was assessed by genotyping seven microsatellite markers spanning 2.39 Mb of the NF1 locus in the tumour and in genomic DNA. The known germline mutation in NF1 was confirmed in GIST DNA by sequencing. The copy number of the mutated NF1 allele was determined by multiplex ligand-dependent probe amplification. Results: GISTs from both patients were of wild type for mutations in KIT and PDGFRA. In the GIST with adequate DNA, all seven markers were informative and showed LOH at the NF1 locus; sequencing of NF1 from that GIST showed no wild-type sequence, suggesting that it was lost in the tumour. Multiplex ligand-dependent probe amplification analysis showed that two copies of all NF1 exons were present. Conclusions: This is the first evidence of mitotic recombination resulting in a reduction to homozygosity of a germline NF1 mutation in an NF1-associated GIST. We hypothesise that the LOH of NF1 and lack of KIT and PDGFRA mutations are evidence of an alternative pathogenesis in NF1-associated GISTs.
Deliberate Self-poisoning and Self-injury in Adolescents

In Oxford during the late 1970s and early 1980s a decline in rates of deliberate self-poisoning and self-injury in older female teenagers was followed by a steady increase between 1986 and 1989. Rates for male adolescents and young female adolescents remained relatively stable throughout 1976–89. Applying the Oxford rates to England and Wales suggests a total of 18 000–19 000 hospital-referred cases per year. While self-poisoning with minor tranquillisers and sedatives has declined, there has been a marked increase in paracetamol self-poisoning, such that by 1988–89 it was involved in 48.3% of overdoses. Relationship difficulties were the most frequent problems faced by these adolescents, especially the females, with unemployment and alcohol and drug problems also being common, especially in males, but psychiatric disorders relatively rare. Substantial proportions of the adolescents, especially the males, were not living with either relatives or friends, and had a history of violence or a criminal record. The annual rate of repetition of attempts, which was 8.9% overall, was higher in adolescents not admitted to the general hospital, and in females not referred to the hospital psychiatric service. Adolescent attempted suicide clearly continues to be a major health problem for which both effective preventive and therapeutic strategies are badly needed.
Incomplete double aortic arch with atresia of the distal left arch: distinctive imaging appearance.

OBJECTIVE We present 10 patients with double aortic arch with atresia of the distal left arch segment, a form of incomplete double aortic arch, and describe the distinct MRI and CT findings for this potentially symptomatic vascular ring. CONCLUSION Knowledge of the distinctive imaging appearance of this congenital arch anomaly can direct the radiologist to the correct preoperative diagnosis.
Executive dysfunctions and depression in Behçet’s disease without explicit neurological involvement

Abstract This study aims to assess the executive functions and depression status in patients with Behçet’s disease without explicit neurological involvement and to evaluate cognitive functions in this group of patients independent of accompanying depression. In the present study, 30 patients with Behçet’s disease in the non‐active phase of their illness and 30 healthy volunteers were included. In the evaluation of depression levels, Beck Depression Inventory was employed. The executive functions of the patients were evaluated by Wisconsin Card Sorting Test (WCST) and Stroop Test (ST). Beck Depression Inventory scores measured in the Behçet’s disease group, in which no clinically serious depression was observed, were higher than the control group. Then, it was observed that the scores of neuropsychological tests of the Behçet’s disease group were found to be significantly lower, especially in WCST, while significant relations were revealed between Beck Depression Inventory scores and WCST, ST scores. The authors’ findings suggest that there may be factors other than depression causing executive impairment in patients with Behçet’s disease without explicit neurological symptoms. Executive dysfunctions may occur in association with mild depressive states due to chronic disease stress or silent and/or future neurological involvement of Behçet’s disease, especially in the frontal lobes.