Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposon Tn5 encodes streptomycin resistance in nonenteric bacteria

Strains of Caulobacter crescentus, Pseudomonas putida, Acinetobacter calcoaceticus, Rhizobium meliloti, and Rhodopseudomonas sphaeroides carrying the kanamycin resistance-encoding transposon Tn5 were 15 to 500 times more resistant to streptomycin than transposon-free strains. The streptomycin resistance determinant, which is separable from the kanamycin resistance determinant of Tn5, was not expressed in Escherichia coli or Klebsiella aerogenes.
Intracranial Meningioma: A Comparative Pathologic Study of 28 Dogs

Intracranial meningiomas were identified in 28 dogs based on histologic examination of tissue. The average age of the dogs was 11 years, and 83% (20/24) were 10 years old or older. German shepherd and mixed breed were most common (31% each, 8/26). Grossly, meningiomas were oval, dome-shaped and flattened masses adherent to the dura and compressing the brain. Forty-eight percent (15/26) of the tumors affected the dorsal surface of the brain, and two thirds of these were located in the anterior half. Histologically, tumor types were transitional (13), meningiotheliomatous (11), angioblastic (three), and fibroblastic (one). There was direct invasion of the brain in 27% (6/22) although we observed neurologic signs and pathologic changes in 88% (23/26) and 90% (18/20) of the dogs, respectively. Intracranial menigioma can be compared and contrasted with this tumor in man and cats.
Does pituitary suppression affect live birth rate in women with congenital hypogonadotrophic hypogonadism undergoing intra-cytoplasmic sperm injection? A multicenter cohort study

Abstract In this retrospective multicenter cohort study, women with congenital hypogonadotrophic hypogonadism (CHH) (n = 57) who underwent intra-cytoplasmic sperm injection in-between 2010–2014 were compared to age-matched controls with tubal factor infertility (n = 114) to assess ovarian stimulation cycle and pregnancy outcomes. Live birth rates (LBRs) per started cycle were 31.6 and 24.6% in CHH and controls groups, respectively (p = 0.36). Comparable success rates were also confirmed with the logistic regression analysis (OR: 1.44, 95% CI: 0.78–2.67, p = 0.24). Of the 57 women with CHH, 19 were stimulated with the gonadotropin-releasing hormone (GnRH) antagonist protocol, 13 with the long-GnRH-agonist protocol. Pituitary suppression (PS) was not employed in the remaining 25 cases. Compared to women with PS, women without PS had significantly higher embryo implantation rates (21.6 versus 52.6%, p = 0.03). Although there was a trend favoring no PS, LBRs (25.0 versus 40.0%, p = 0.26) per cycle were short of statistical significance. LBRs per cycle (57.1 versus 31.2%, p = 0.11) and miscarriage rates (11.1 versus 16.7%, p = 0.75) were similar between CHH women who were given estrogen + progesterone and progesterone alone to support the luteal phase. In conclusion, the optimal stimulation protocol appears to be exogenous gonadotropin stimulation alone, without PS, and progesterone-only luteal phase support in CHH patients.
Coronary calcium in systemic lupus erythematosus is associated with traditional cardiovascular risk factors, but not with disease activity.

OBJECTIVE Cardiovascular disease is a major cause of morbidity and mortality in systemic lupus erythematosus (SLE). The frequency of both subclinical and clinically evident atherosclerosis is greatly increased over healthy controls. We assessed cardiovascular risk factors present in patients with SLE at the baseline visit in a statin intervention trial and their correlation with coronary calcium. METHODS Coronary calcium was measured by helical computed tomography (continuous volumetric data acquisition in a single breath-hold) in 200 patients with SLE enrolled in the Lupus Atherosclerosis Prevention Study. RESULTS Patients had a mean age of 44.3 +/- 11.4 years and were 92% women, 61% Caucasian, 34% African American, 2% Asian, and 2% Hispanic. Coronary calcium was found in 43%. In univariate analysis, coronary calcification was associated with age (p = 0.0001), hypertension (p = 0.0008), body mass index (BMI; p = 0.03), erythrocyte sedimentation rate (ESR; p = 0.03), anti-dsDNA (p = 0.067), and lipoprotein(a) (p = 0.03). Homocysteine (p = 0.050), high-sensitivity C-reactive protein (hsCRP; p = 0.053), and LDL (p = 0.048) had a stronger association when considered as quantitative predictors. In a multiple logistic regression model, only age (p </= 0.0001) and body mass index (p = 0.0014) remained independent predictors. No measure of SLE activity was associated with coronary calcium. We also examined variables independently predictive of a coronary calcium score > 100. Based on a multiple logistic regression model, only age (p = 0.0017) and diabetes mellitus (p = 0.019) remained significant independent predictors of coronary calcium > 100. CONCLUSION Inflammation, measured as ESR or hsCRP, is associated with coronary calcium only in univariate analyses. Age, BMI, and diabetes mellitus are more important associates of coronary calcium in SLE than inflammatory markers and SLE clinical activity.
Diagnosis of herpes simplex virus infection in a clinical setting by a direct antigen detection enzyme immunoassay kit

A commercial 4-h direct herpes simplex virus (HSV) antigen detection enzyme immunoassay (EIA) kit (Du Pont Herpchek) was evaluated by using 273 clinical specimens obtained in a hospital-based infectious disease practice. The EIA was compared with a standard culture method in which WI38 cells were inoculated within 20 min of sample collection. Cultures were observed for 2 weeks, and positive findings were confirmed by fluorescein-labeled monoclonal antibody (FA) staining. The values for the overall HSV detection rate were 40.7% by the standard culture method and 41.4% by EIA. In eight cases, the EIA was positive, while the culture method was negative; however, clinical data and confirmatory blocking EIA suggested that a true HSV infection was present. For six FA-confirmed, culture-positive samples, the direct EIA was negative; however, an EIA performed on the supernatants of these cultures was positive, suggesting that the failure of the EIA to detect these samples was not due to lack of strain specificity of the test. After confirmatory tests of standard culture and EIA discrepant results, the overall sensitivity of the test was 95.0% (113 of 119) and the specificity was 100% (154 of 154).
Truth-telling in cancer: Examining the cultural incompatibility argument in Turkey

This article aims to examine critically the ‘cultural incompatibility’ argument, which asserts that disclosure of cancer-related information to patients is incompatible with Turkey’s cultural context. For this purpose, a brief overview of the approach to truth-telling in Turkey will first be provided, followed by the claims of two different Turkish authors on the issue and a critical analysis of their approach. It will be contended that this argument has actually been formulated with paternalistic concerns and it may be playing an important role in shaping the approach of Turkish health care professionals to the issue. The article will then examine, in the light of study findings and case reports from Turkey, the concept of patient autonomy as it applies to truth-telling issues. It will be concluded that truth-telling can be compatible with Turkey’s cultural context, provided that health care professionals place more emphasis on good communication with their patients.
Multiobjective Particle Swarm Approach for the Design of a Brushless DC Wheel Motor

The roots of swarm intelligence are deeply embedded in the biological study of self-organized behaviors in social insects. Particle swarm optimization (PSO) is one of the modern metaheuristics of swarm intelligence, which can be effectively used to solve nonlinear and non-continuous optimization problems. The basic principle of PSO algorithm is formed on the assumption that potential solutions (particles) will be flown through hyperspace with acceleration towards more optimum solutions. Each particle adjusts its flying according to the flying experiences of both itself and its companions using equations of position and velocity. During the process, the coordinates in hyperspace associated with its previous best fitness solution and the overall best value attained so far by other particles within the group are kept track and recorded in the memory. In recent years, PSO approaches have been successfully implemented to different problem domains with multiple objectives. In this paper, a multiobjective PSO approach, based on concepts of Pareto optimality, dominance, archiving external with elite particles and truncated Cauchy distribution, is proposed and applied in the design with the constraints presence of a brushless DC (Direct Current) wheel motor. Promising results in terms of convergence and spacing performance metrics indicate that the proposed multiobjective PSO scheme is capable of producing good solutions.
Response of Coccinellid Larvae to Conspecific and Heterospecific Larval Tracks: A Mechanism that Reduces Cannibalism and Intraguild Predation

ABSTRACT Cannibalism, where one species feeds on individuals of its own species, and intraguild predation (IGP), where a predator feeds on other predatory species, can both pose significant threats to natural enemies and interfere with their biological control of pests. Behavioral mechanisms to avoid these threats, however, could help maintain superior pest control. Here, we ask whether larvae of Coccinella septempunctata (Coleoptera: Coccinellidae) and Harmonia axyridis (Coleoptera: Coccinellidae) respond to larval tracks deposited by the other and whether this behavioral response reduces the threat of cannibalism and IGP. In petri dish experiments, we show that both H. axyridis and C. septempunctata avoid foraging in areas with conspecific larval tracks. Using a method of preventing larvae from depositing tracks, we then demonstrate that the frequency of cannibalism is greater for both species when larvae are prevented from depositing tracks compared with when the tracks are deposited. For multi-species interactions we show in petri dish experiments that C. septempunctata avoids H. axyridis larval tracks but H. axyridis does not avoid C. septempunctata larval tracks, demonstrating an asymmetry in response to larval tracks that parallels the asymmetry in aggressiveness between these species as intraguild predators. On single plants, we show that the presence of H. axyridis larval tracks reduces the risk of IGP by H. axyridis on C. septempunctata. Our study suggests that larval tracks can be used in more ways than previously described, in this case by changing coccinellid larval behavior in a way that reduces cannibalism and IGP.
Effectiveness of Low-Temperature Domestic Laundry on the Decontamination of Healthcare Workers' Uniforms

Objective. Most professionals in the healthcare environment wear uniforms. For the purpose of this study, we concentrated on nurses' uniforms. In the United Kingdom, many nurses are expected to launder their uniforms at home by using a domestic washing machine that frequently has low-temperature wash cycles. We have investigated whether the use of low-temperature wash cycles results in a microbiologically acceptable product to wear on the wards. Methods. We have assessed the bioburden on uniforms before and after laundry and the effectiveness of low-temperature wash cycles and ironing on removal of methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii. We did not assess the role of tumble drying. Results. We demonstrate contamination of uniforms by gram-negative bacteria after wash, the removal of MRSA at low-temperature wash cycles in the presence of detergent, and the eradication of gram-negative bacteria after ironing. Conclusions. Our conclusions are that laundry in a domestic situation at 60°C (140°F) for 10 minutes is sufficient to decontaminate hospital uniforms and reduces the bacterial load by more than 7-log reduction, that items left in the pockets are decontaminated to the same extent, that the addition of either a biological detergent or a nonbiological detergent is beneficial in removing MRSA from experimentally contaminated swatches, and that uniforms become recontaminated with low numbers of principally gram-negative bacteria after laundry but that these are effectively removed by ironing.
Selection of Drug-Resistant Feline Immunodeficiency Virus (FIV) Encoding FIV/HIV Chimeric Protease in the Presence of HIV-Specific Protease Inhibitors

ABSTRACT An infectious chimeric feline immunodeficiency virus (FIV)/HIV strain carrying six HIV-like protease (PR) mutations (I37V/N55M/V59I/I98S/Q99V/P100N) was subjected to selection in culture against the PR inhibitor lopinavir (LPV), darunavir (DRV), or TL-3. LPV selection resulted in the sequential emergence of V99A (strain S-1X), I59V (strain S-2X), and I108V (strain S-3X) mutations, followed by V37I (strain S-4X). Mutant PRs were analyzed in vitro, and an isogenic virus producing each mutant PR was analyzed in culture for LPV sensitivity, yielding results consistent with the original selection. The 50% inhibitory concentrations (IC50s) for S-1X, S-2X, S-3X, and S-4X were 95, 643, 627, and 1,543 nM, respectively. The primary resistance mutations, V9982A, I5950V, and V3732I, are consistent with the resistance pattern developed by HIV-1 under similar selection conditions. While resistance to LPV emerged readily, similar PR mutations causing resistance to either DRV or TL-3 failed to emerge after passage for more than a year. However, a G37D mutation in the nucleocapsid (NC) was observed in both selections and an isogenic G37D mutant replicated in the presence of 100 nM DRV or TL-3, whereas parental chimeric FIV could not. An additional mutation, L92V, near the PR active site in the folded structure recently emerged during TL-3 selection. The L92V mutant PR exhibited an IC50 of 50 nM, compared to 35 nM for 6s-98S PR, and processed the NC-p2 junction more efficiently, consistent with increased viral fitness. These findings emphasize the role of mutations outside the active site of PR in increasing viral resistance to active-site inhibitors and suggest additional targets for inhibitor development.
Vitamin D and methicillin-resistant Staphylococcus aureus nasal carriage

Abstract Studies have found that vitamin D plays an important role in mediating immune function via a number of pathways, including enhancing the release of antimicrobial peptides in the skin. Given these findings, we hypothesize that low serum vitamin D levels may increase the risk of nasal carriage of methicillin-resistant Staphylococcus aureus (MRSA). A secondary data analysis of the National Health and Nutrition Examination Survey 2001–2004 was performed to investigate the association between serum vitamin D levels and MRSA nasal carriage for the non-institutionalized population of the USA. An estimated 2.7 million persons (1.2% of the population) are MRSA nasal carriers. An estimated 63.3 million persons (28.4% of the population) are vitamin D deficient (serum vitamin D <20 ng/ml). In an adjusted logistic regression analysis controlling for age, race, gender, poverty income ratio, current health status, hospitalization in the past 12 months, and antibiotic use in the past month, individuals with vitamin D deficiency had a statistically significant increased risk of MRSA carriage of 2.04 (95% CI 1.09–3.84). Vitamin D deficiency is associated with an increased risk of MRSA nasal carriage. Further trials may be warranted to determine whether vitamin D supplementation decreases the risk of MRSA colonization.
Under-reporting of conflicts of interest among trialists: a cross-sectional study

Objectives To determine the prevalence of conflicts of interest (COIs) among Danish physicians who are authors of clinical drug trial reports and determine the extent of undisclosed COIs in trial publications. Design Cross-sectional study. Setting The 100 most recent drug trial reports with at least one Danish non-industry employed physician author published in a journal adhering to the International Committee of Medical Journal Editors' (ICMJE) manuscript guidelines. For each article, two observers independently extracted trial characteristics and the authors' COIs. Disclosed COIs were compared to what was registered on the Danish Health and Medicines Authority's public disclosure list. Participants Trial authors who are Danish physicians. Main outcome measures Number of disclosed and undisclosed COIs. Results One observer screened 928 articles and two observers assessed 120 articles for eligibility. The 100 included trials were published from February 2011 to May 2013 and included 318 Danish non-industry employed authors. Eighty-six of the 318 authors (27%) reported one or more COIs in the journal article. We found undisclosed COIs for 40 of 318 authors (13%) related to the trial sponsor or manufacturer of trial drugs. Seventy-nine of 318 authors (25%) had undisclosed COIs related to competing companies manufacturing drugs for the same indication and 136 (43%) had undisclosed COIs with any drug manufacturer. Conclusions Almost half of all authors had undisclosed COIs in clinical trials reported in journals adhering to the International Committee of Medical Journal Editors’ manuscript guidelines. Self-declared COIs cannot be trusted, but public registries may assist editors in ensuring that more COIs are being reported.
Comparing Prompt Emission from X‐ray Flashes and Gamma‐ray Bursts

The final year of the BeppoSAX mission provided a much needed clue as to the nature of X‐ray flashes. The detection of afterglow counterparts and their underlying hosts provides strong evidence that X‐ray flashes and gamma‐ray bursts originate from similar sources in cosmologically distant galaxies. These observations support findings that the prompt emission characteristics of X‐ray flashes are similar to those of traditional gamma‐ray bursts. Using wide‐band observations from BeppoSAX and BATSE, we present the latest results in our on‐going effort to quantify the similarities and differences in prompt emission characteristics.
Adaptation of a trap door technique for the recovery of ovarian cortical biopsies from Cebus apella (capuchin monkey)

Summary There is a paucity of efficient cryopreservation protocols for primordial follicles enclosed in the ovarian tissue from non-human primates (NHP), in special New World primates. Our objective was to establish an optimal procedure for the recovery of ovarian biopsies from capuchin monkeys. To this end, we adapted a trap door biopsy method. Follicular density and quality of the biopsies were evaluated and ultrasound analysis was performed before and continuously after surgery to assess ovarian structure. Ovarian tissue biopsies recovered by the trap door technique allowed the successful harvesting of primordial follicles from capuchin monkeys, and no complication was recorded. The female cycle was not affected by surgery and no adherence was found thereafter. In conclusion, the adaptation of a trap door biopsy method is a safe procedure and allows recovery of healthy primordial follicles.
Graph Matching using Commute Time Spanning Trees

This paper exploits the properties of the commute time for the purposes of graph matching. Our starting point is the random walk on the graph, which is determined by the heat-kernel of the graph and can be computed from the spectrum of the graph Laplacian. We characterise the random walk using the commute time between nodes, and show how this quantity may be computed from the Laplacian spectrum using the discrete Green's function. We use the commute-time to locate the minimum spanning tree of the graph. The spanning trees located using commute time prove to be stable to structural variations. We match the graphs by applying a tree-matching method to the spanning trees. We experiment with the method on synthetic and real-world image data, where it proves to be effective
Retrocollis: Classification, Clinical Phenotype, Treatment Outcomes and Risk Factors

Retrocollis (RC) is a form of cervical dystonia (CD) that produces patterned, repetitive muscle contractions that result in neck extension. We performed a review of consecutive CD patients seen in our Division over a 15-year period. Out of 399 CD patients, 59 (14.8%) had features of RC. Pain was very frequently reported among patients (∼80%). RC was frequently associated with neuroleptic exposure (20.3%) and a history of head/neck trauma (23.7%). Of patients injected with botulinum toxin type A, 24.5% reported excellent, 32.1% moderate, 16.9% mild and 24.5% no response to injections. Oral antidystonic medications had limited contribution to symptom relief.
Growth Factors, Cytokines, Cell Cycle Molecules ERK, p38, and Smad Signaling Pathways Differentially Regulate Transforming Growth Factor- 1 Autoinduction in Proximal Tubular Epithelial Cells

Transforming growth factor (TGF)1 is a mediator of the final common pathway of fibrosis associated with progressive renal disease, a process in which proximal tubular cells (PTCs) are known to play an important part. The aim of the current study was to examine the mechanism of PTC TGF1 autoinduction. The addition of TGF1 led to increased amounts of TGF1 mRNA and increased de novo protein synthesis. The addition of TGF1 led to increased phosphorylation of R-Smads and activation of extracellular signal-regulated kinase mitogen-activated protein (MAP) kinase and p38 MAP kinase pathways. Use of a dominant-negative Smad3 (Smad3 DN) expression vector, Smad3 small interfering RNA, and inhibition of extracellular signal-regulated kinase and p38 MAP kinase pathways with the chemical inhibitors PD98059 or SB203580 suggested that activation of these signaling pathways occurred independently. Smad3 DN expression, Smad3 small interfering RNA, or the addition of PD98059 inhibited TGF1-dependent stimulation of TGF1 mRNA. Furthermore, Smad3 blockade specifically inhibited activation of the transcription factor AP-1 by TGF1, whereas PD98059 prevented TGF1-dependent nuclear factorB activation. In contrast inhibition of p38 MAP kinase inhibited de novo TGF1 protein synthesis but did not influence TGF1 mRNA expression or activation of either transcription factor. In summary, in PTCs, TGF1 autoinduction requires the coordinated action of independently regulated Smad and non-Smad pathways. Furthermore these pathways regulate distinct transcriptional and translational components of TGF1 synthesis. (Am J Pathol 2006, 169:1282–1293; DOI: 10.2353/ajpath.2006.050921)