Miracle-dz/UniFAR-FTUs huggingface dataset:
Fitness costs of various mobile genetic elements in Enterococcus faecium and Enterococcus faecalis

Objectives To determine the fitness effects of various mobile genetic elements (MGEs) in Enterococcus faecium and Enterococcus faecalis when newly acquired. We also tested the hypothesis that the biological cost of vancomycin resistance plasmids could be mitigated during continuous growth in the laboratory. Methods Different MGEs, including two conjugative transposons (CTns) of the Tn916 family (18 and 33 kb), a pathogenicity island (PAI) of 200 kb and vancomycin-resistance (vanA) plasmids (80–200 kb) of various origins and classes, were transferred into common ancestral E. faecium and E. faecalis strains by conjugation assays and experimentally evolved (vanA plasmids only). Transconjugants were characterized by PFGE, S1 nuclease assays and Southern blotting hybridization analyses. Single specific primer PCR was performed to determine the target sites for the insertion of the CTns. The fitness costs of various MGEs in E. faecium and E. faecalis were estimated in head-to-head competition experiments, and evolved populations were generated in serial transfer assays. Results The biological cost of a newly acquired PAI and two CTns were both host- and insertion-locus-dependent. Newly acquired vanA plasmids may severely reduce host fitness (25%–27%), but these costs were rapidly mitigated after only 400 generations of continuous growth in the absence of antibiotic selection. Conclusions Newly acquired MGEs may impose an immediate biological cost in E. faecium. However, as demonstrated for vanA plasmids, the initial costs of MGE carriage may be mitigated during growth and beneficial plasmid–host association can rapidly emerge.
Plasma Septin9 versus Fecal Immunochemical Testing for Colorectal Cancer Screening: A Prospective Multicenter Study

Background Screening improves outcomes related to colorectal cancer (CRC); however, suboptimal participation for available screening tests limits the full benefits of screening. Non-invasive screening using a blood based assay may potentially help reach the unscreened population. Objective To compare the performance of a new Septin9 DNA methylation based blood test with a fecal immunochemical test (FIT) for CRC screening. Design: In this trial, fecal and blood samples were obtained from enrolled patients. To compare test sensitivity for CRC, patients with screening identified colorectal cancer (n = 102) were enrolled and provided samples prior to surgery. To compare test specificity patients were enrolled prospectively (n = 199) and provided samples prior to bowel preparation for screening colonoscopy. Measurements Plasma and fecal samples were analyzed using the Epi proColon and OC Fit-Check tests respectively. Results For all samples, sensitivity for CRC detection was 73.3% (95% CI 63.9–80.9%) and 68.0% (95% CI 58.2–76.5%) for Septin9 and FIT, respectively. Specificity of the Epi proColon test was 81.5% (95% CI 75.5–86.3%) compared with 97.4% (95% CI 94.1–98.9%) for FIT. For paired samples, the sensitivity of the Epi proColon test (72.2% –95% CI 62.5–80.1%) was shown to be statistically non-inferior to FIT (68.0%–95% CI 58.2–76.5%). When test results for Epi proColon and FIT were combined, CRC detection was 88.7% at a specificity of 78.8%. Conclusions At a sensitivity of 72%, the Epi proColon test is non- inferior to FIT for CRC detection, although at a lower specificity. With negative predictive values of 99.8%, both methods are identical in confirming the absence of CRC. Trial Registration ClinicalTrials.gov NCT01580540
Breast Cancer-Specific Mortality Pattern and Its Changing Feature According to Estrogen Receptor Status in Two Time Periods

Purpose To determine whether and how the patterns of breast cancer-specific mortality (BCSM) changed along with time periods. Methods We used the Surveillance, Epidemiology and End Results registry to identify 228209 female patients diagnosed with invasive breast cancer between 1990 and 2000 (cohort 1 [C1], 112981) and between 2001 and 2005 (cohort 2 [C2], 115228). BCSM was compared in two cohorts using Cox proportional hazard regression models. We analysed the relative hazard ratios (HRs) and absolute BCSM rates by flexible parametric survival modelling. Results The patterns of BCSM were similar between the two cohorts, with the peak of mortality presenting in the first 2–3 years after diagnosis, and mortality rate significantly decreased in C2 in all cases. In C2, the annual BCSM rate of all cases was 9.64 (per 1000 persons per year) in year 10 with a peak rate of 23.34 in year 2. In ER-negative and high-risk patients, marked survival improvements were achieved mostly in the first 5 years, while in ER-positive and low-risk patients, survival improvements were less but constant up to 10 years. Conclusion There has been a significant improvement of BCSM with substantially decreased mortality within 5 years. The current pattern of BCSM and its changing feature differs according to ER status. Our findings have some clinical implications both for treatment decisions and adjuvant treatment trial design.
Joubert Syndrome: Imaging Features and Illustration of a Case

Summary Background Joubert Syndrome (JS) is a rare autosomal recessive disorder characterised clinically by neonatal breathing dysregulation, developmental delay, intellectual disability, hypotonia, ataxia, nystagmus. Case Report We present another case of this uncommon syndrome in a 12 years old patient presenting with classical complaints of developmental delay, intellectual impairment, weakness in both lower limbs, ataxia and abnormal facies and diagnosed on Computed Tomography. Conclusions Joubert Syndrome should be ruled out in all patients presenting with hypotonia, ataxia, nystagmus, breathing abnormalities and developmental delay. Its neuroimaging hallmarks include molar tooth sign and batwing shaped fourth ventricle. As JS is associated with multiorgan involvement, these patients should enter a diagnostic protocol to assess systemic abnormalities. Extreme caution should be taken while administering drugs in these patients as they are prone to respiratory depression.
Targeting CD44 as a novel therapeutic approach for treating pancreatic cancer recurrence

Pancreatic ductal adenocarcinoma (PDAC) is an extraordinarily lethal disease, which, despite a more or less efficient chemotherapeutic treatment, systematically displays a rapid and uncontrolled progression towards a fatal recurrence. Determining which cells give rise to such tumor recurrence is thus crucial before an improved therapeutics outcome can be envisaged for patients with PDAC. In this regard, we recently reported that following a standard chemotherapy for PDAC, a heterogeneous subpopulation of CD44+ cells proliferates and is responsible for tumor recurrence, as shown by almost all recurrent tumor cells becoming CD44+. We designed a strategy to eliminate these cells based on a weekly administration of an anti-CD44 monoclonal antibody to human PDAC-derived xenografts in mice. We demonstrate that xenografts, which were unresponsive to gemcitabine treatment, are however sensitive to this strategy. In conclusion, CD44 represents an efficient therapeutic target in patients with recurrent PDAC.
Distribution of choline acetyltransferase (ChAT) immunoreactivity in the central nervous system of a chondrostean, the siberian sturgeon (Acipenser baeri)

All studies to date of cholinergic systems of bony fishes have been done in teleosts. To gain further insight into the evolution of the cholinergic systems of bony fishes, we have studied the brain of a chondrostean fish, the Siberian sturgeon (Acipenser baeri, Brandt), by using an antibody against choline acetyltransferase (ChAT). This study showed the presence of ChAT‐immunoreactive (ChAT‐ir) neurons in the preoptic region (parvocellular and magnocellular preoptic nuclei and suprachiasmatic nucleus), the periventricular and tuberal hypothalamus, the saccus vasculosus, the dorsal thalamus, and the habenula. The mesencephalic tegmentum contained ChAT‐ir cells in the torus semicircularis and torus lateralis. The isthmus contained several cholinergic populations: the nucleus isthmi, the lateral nucleus of the valvula, the secondary visceral nucleus, and the dorsal tegmental nucleus. The motor neurons of the cranial nerves and the spinal motor column were strongly immunoreactive. The medial (sensory) trigeminal nucleus also contained a ChAT‐ir neuronal population. The distribution of ChAT‐ir neurons in the sturgeon brain showed some notable differences with that observed in teleosts, such as the absence of cholinergic cells in the telencephalon and the optic tectum. Several brain regions were richly innervated by ChAT‐ir fibers, particularly the telencephalon , optic tectum, thalamus, posterior tubercle, and interpeduncular nucleus. The hypothalamo‐hypophyseal tract, the tract of the saccus vasculosus, the fasciculus retroflexus, and an isthmo‐mesencephalo‐thalamic tract were the most conspicuous cholinergic bundles. Comparative analysis of these results suggests that teleosts have conserved most traits of the cholinergic system of the sturgeon, having acquired new cholinergic populations during evolution. J. Comp. Neurol. 426:602–621, 2000. © 2000 Wiley‐Liss, Inc.
Prospective evaluation of the clinical value of planar bone scans, SPECT, and (18)F-labeled NaF PET in newly diagnosed lung cancer.

UNLABELLED Previous studies have shown that vertebral bone metastases (BM) not seen on planar bone scintigraphy (BS) might be present on (18)F-fluoride PET scans or at MRI. Therefore, we evaluated the effect of SPECT or (18)F-labeled NaF PET ((18)F PET) imaging on the management of patients with newly diagnosed lung cancer. METHODS Fifty-three patients with small cell lung cancer or locally advanced non-small cell lung cancer were prospectively examined with planar BS, SPECT of the vertebral column, and (18)F PET. MRI and all available imaging methods, as well as the clinical course, were used as reference methods. BS with and without SPECT and (18)F PET were compared using a 5-point scale for receiver operating characteristic (ROC) curve analysis. RESULTS Twelve patients had BM. BS produced 6 false-negatives, SPECT produced 1 false-negative, and (18)F PET produced no false-negatives. The area under the ROC curve was 0.779 for BS, 0.944 for SPECT, and 0.993 for (18)F PET. The areas under the ROC curve of (18)F PET and BS complemented by SPECT were not significantly different, and both tomographic methods were significantly more accurate than planar BS. As a result of SPECT or (18)F PET imaging, clinical management was changed in 5 patients (9%) or 6 patients (11%), respectively. CONCLUSION As indicated by the area under the ROC curve analysis, (18)F PET is the most accurate whole-body imaging modality for screening for BM. Routinely performed SPECT imaging is practicable, is cost-effective, and improves the accuracy of BS.
Unspeciated organic emissions from combustion sources and their influence on the secondary organic aerosol budget in the United States

Significance Secondary organic aerosol (SOA) formed from the atmospheric oxidation of gaseous combustion emissions is an important component of global fine-particle pollution, which influences the Earth’s energy budget and affects human health. However, existing models underpredict the amount of SOA measured in laboratory experiments and in the atmosphere. We analyze smog chamber and emissions data to demonstrate that unspeciated organics in combustion emissions are a major class of SOA precursors. We develop source-specific parameterizations for these emissions using surrogate chemical compounds. We find that unspeciated organics dominate SOA mass formed from combustion emissions in the United States; therefore, unspeciated organics must be included in models to simulate ambient fine particulate matter concentrations. Secondary organic aerosol (SOA) formed from the atmospheric oxidation of nonmethane organic gases (NMOG) is a major contributor to atmospheric aerosol mass. Emissions and smog chamber experiments were performed to investigate SOA formation from gasoline vehicles, diesel vehicles, and biomass burning. About 10–20% of NMOG emissions from these major combustion sources are not routinely speciated and therefore are currently misclassified in emission inventories and chemical transport models. The smog chamber data demonstrate that this misclassification biases model predictions of SOA production low because the unspeciated NMOG produce more SOA per unit mass than the speciated NMOG. We present new source-specific SOA yield parameterizations for these unspeciated emissions. These parameterizations and associated source profiles are designed for implementation in chemical transport models. Box model calculations using these new parameterizations predict that NMOG emissions from the top six combustion sources form 0.7 Tg y−1 of first-generation SOA in the United States, almost 90% of which is from biomass burning and gasoline vehicles. About 85% of this SOA comes from unspeciated NMOG, demonstrating that chemical transport models need improved treatment of combustion emissions to accurately predict ambient SOA concentrations.
Face it or hide it: parental socialization of reappraisal and response suppression

Mastery of cognitive emotion regulation strategies is an important developmental task. This paper focuses on two strategies that occur from preschool age onwards (Stegge and Meerum Terwogt, 2007): reappraisal and response suppression. Parental socialization of these strategies was investigated in a sample of N = 219 parents and their children. Informed by the tripartite model of family impact on children's emotion regulation, direct relations of emotion socialization components (modeling and reactions to the child's negative emotions) and indirect relations of parental emotion-related beliefs (such as parental emotion regulation self-efficacy) were examined. Data on emotion socialization components and parental beliefs on emotion regulation were collected via self-report. Data on children's emotion regulation strategies were collected via parent report. Findings showed direct effects of parental modeling and parenting practices on children's emotion regulation strategies, with distinct socialization paths for reappraisal and response suppression. An indirect effect of parental emotion regulation self-efficacy on children's reappraisal was found. These associations were not moderated by parent sex. Findings highlight the importance of both socialization components and parental emotion-related beliefs for the socialization of cognitive emotion regulation strategies and suggest a domain-specific approach to the socialization of emotion regulation strategies.
Effect of individual finger skin temperature on vibrotactile perception threshold

ObjectivesIn healthy people, the vibrotactile perception threshold (VPT) at fingertips depends on a given measurement method and on individual characteristics such as age, gender and finger skin temperature. The aim of the study was to compare the VPT values in 2 groups of healthy subjects with different finger skin temperature.Materials and MethodsThe study group comprised 56 males and 76 females, who formed pairs matched with respect to age, gender and body mass index (BMI) but differing in terms of finger skin temperature at pre-launch testing. The finger skin temperature of less than 29°C indicated the subjects with “cold hands” and that of more than 29°C, the subjects with “warm hands”. The measuring system made use of P8 pallesthesiometer (EMSON-MAT, Poland) and the measurement procedure was in compliance with the ISO 13091-1:2001 standard. VPT measurements were performed for the index, middle and ring fingers of both hands at the frequencies of 4 Hz, 25 Hz, 31.5 Hz, 63 Hz, 125 Hz and 250 Hz.ResultsThe findings of the study revealed that the mean VPTs among the subjects with “cold hands” were significantly higher than the corresponding values among the subjects with “warm hands”. ConclusionsThe type of individual peripheral thermoregulation should be considered when assessing the VPT and determining its reference values.
Effect of high dose vitamin C on Epstein-Barr viral infection

Background Many natural compounds were tested for the ability to suppress viral replication. The present manuscript details an analysis of high dose vitamin C therapy on patients with EBV infection. Material/Methods The data were obtained from the patient history database at the Riordan Clinic. Among people in our database who were treated with intravenous vitamin C (7.5 g to 50 g infusions) between 1997 and 2006, 178 patients showed elevated levels of EBV EA IgG (range 25 to 211 AU) and 40 showed elevated levels of EBV VCA IgM (range 25 to 140 AU). Most of these patients had a diagnosis of chronic fatigue syndrome, with the rest being diagnosed as having mononucleosis, fatigue, or EBV infection. Results Our data provide evidence that high dose intravenous vitamin C therapy has a positive effect on disease duration and reduction of viral antibody levels. Plasma levels of ascorbic acid and vitamin D were correlated with levels of antibodies to EBV. We found an inverse correlation between EBV VCA IgM and vitamin C in plasma in patients with mononucleosis and CFS meaning that patients with high levels of vitamin C tended to have lower levels of antigens in the acute state of disease. In addition, a relation was found between vitamin D levels and EBV EA IgG with lower levels of EBV early antigen IgG for higher levels of vitamin D. Conclusions The clinical study of ascorbic acid and EBV infection showed the reduction in EBV EA IgG and EBV VCA IgM antibody levels over time during IVC therapy that is consistent with observations from the literature that millimolar levels of ascorbate hinder viral infection and replication in vitro.
In vivo depletion of natural killer cell activity leads to enhanced multiplication of Mycobacterium avium complex in mice

Earlier investigations have shown that murine natural killer (NK) cells inhibit the growth of fungal and bacterial pathogens in vivo and in vitro. In order to define the role of NK cells in Mycobacterium avium complex infection, in vivo depletion of NK cells by using anti-NK1.1 monoclonal antibody and conventional anti-asialo-GM1 antibody has been attempted. Repeated injection of 200 micrograms of anti-NK1.1 or 50 micrograms of anti-asialo-GM1 antibody effectively depleted NK activity in the spleens of C57BL/6 mice. The growth kinetics of M. avium complex over a period of 4 weeks showed that the colony counts in the spleens of the antibody-treated group were significantly (P less than 0.01) higher than those of the control group and compared well with those of the genetically NK cell-deficient C57BL/6 bg/bg mutant. The alternate strategy of in vivo stimulation of NK activity by poly(I:C) administration did not show a similar reduction in CFU in the spleen compared with the untreated control. The in vivo antibody depletion of NK activity provides direct evidence on the role of NK cells in the control of intracellular mycobacterial pathogens such as M. avium complex.
Prevalence of human papilloma virus in marginal periodontium and its association with periodontitis: A cross sectional study

Context: Bacterial pathogens in dental plaque are necessary for the development of periodontitis but this etiology alone does not explain all its clinicopathologic features. Researchers have proven the role of certain viruses like herpes virus in periodontal disease which implies that other viral agents like human papilloma virus may also be involved. Aims: This cross-sectional study was conducted to determine the proportion of patients with human papilloma virus (HPV-16) in marginal periodontium by analyzing DNA from the gingival tissue sample and to understand its association with periodontitis. Settings and Design: 102 systemically healthy patients between the age group of 15 and 70 years reporting to the Department of Periodontology who required surgical intervention (flap surgery for patients with periodontitis and crown lengthening for healthy patients) with internal bevel gingivectomy were selected. Materials and Methods: After scaling and root planning, gingival tissue was collected during the respective surgical procedure. DNA was isolated and amplified using specific primers for HPV-16 by polymerase chain reaction (PCR). The amplified products were checked by agarose gel electrophoresis. Results: No HPV DNA was detected in the 102 samples analyzed. Conclusion: Marginal periodontium does not contain HPV in this study population and hence there was no association between HPV and periodontitis.
Integrated process for defect-free copper plating and chemical-mechanical polishing of through-silicon vias for 3D interconnects

The fabrication of through-silicon vias (TSVs) is a major component in the development of three-dimensional (3D) integration technology and advanced 3D packaging approaches. The large diameter and length of TSVs, as compared to traditional interconnects, create some unique process challenges. Via plating and chemical-mechanical polishing (CMP) processes used in standard copper interconnect technology are generally not suitable for TSV fabrication. Therefore, efforts are being made to develop such processes specifically for TSV technology. This paper will describe the development of a void-free Cu electroplating process for TSV filling, along with CMP processing to remove the overburden layer and expose the Cu-filled vias for subsequent metallization. The focus of the paper will be the integration of the TSV plating and CMP processes, with discussion regarding observed integration challenges and their solutions. First, a Cu electroplating process was developed for defect-free, bottom-up filling of silicon vias from 20–200µm in diameter and 150–375µm deep, with aspect ratios from 1:1 to 8:1. Next, CMP tests were conducted using Cu-filled silicon vias of 50µm diameter and 150µm depth, designed for use in a MEMS wafer-level packaging application. These tests indicated that plating nonuniformity and Cu mound defects over filled vias caused significant CMP process issues. The plating process was then modified to eliminate these problems in the Cu films, resulting in improved CMP uniformity and reduced polishing time.
Inter-Industry Wage Differentials and the Bargaining Regime in a Corporatist Country : Belgium

The current understanding of the structure of wages and more particularly inter-industry wage differentials in Belgium is very limited. Moreover, the results as to the influence of the bargaining regimes on inter-industry wage disparities and on wage levels in the countries of continental Europe are fragmentary. Therefore, in this paper we address both issues for the Belgian private sector using the 1995 Structure of Earnings Survey. It is a very rich employer-employee matched database which has never been used in the past. Our results emphasise the existence of inter-industry wage differentials between workers with identical observed individual characteristics and working conditions. They derive partly from the features of the employers in each sector (firm size and wage bargaining regime). Moreover, in an international perspective, they support the existence of a decreasing relation between the dispersion of the inter-industry wage differentials and the degree of corporatism of the OECD countries. Next, they emphasise the existence of a sectoral effect on the workers’ wages in the Belgian private sector, irrespective of the bargaining regime considered. However, they do support the hypothesis that the bargaining regimes that coexist in Belgium have an impact upon the structure of wages. Indeed, we note that the dispersion of inter-interindustry wage differentials is lower where wages are the subject of collective (re)negotiation within the individual establishment. Moreover, all other things being equal, workers covered by a company collective agreement earn 5.1% more than their opposite numbers whose wages are not collectively (re)negotiated within the company.