Miracle-dz/UniFAR-FTUs huggingface dataset:
Amplification of residual DNA sequences in sterile bronchoscopes leading to false-positive PCR results

PCR has been used successfully for the direct detection of Mycobacterium tuberculosis in uncultured patient samples. Its potential is hindered by the risk of false-positive results as a result of either amplicon carryover of cross-contamination between patient samples. In the present study, we investigated whether residual amplifiable human or M. tuberculosis DNA could remain in sterile bronchoscopes and potentially be a cause of false-positive PCR results in subsequent patient samples. Sterilized bronchoscopes were flushed with sterile saline, and the collected eluate was submitted for PCR amplification of IS6110 sequences and exon 8 of the human p53 gene. Of a total of 55 washes of sterile bronchoscopes from two institutions, 2 (3.6%) contained amplifiable M. tuberculosis DNA and 11 (20%) contained residual human DNA. These findings indicate that residual DNA can remain in sterilized bronchoscopes and can be a source of false-positive PCR results.
Identification of the lipooligosaccharide biosynthetic gene cluster from Mycobacterium marinum

Lipooligosaccharides (LOSs) are antigenic glycolipids that are present in some species of Mycobacterium including the Canetti strain of M. tuberculosis. The core LOS structures from several mycobacterial organisms have been established, but the biosynthetic pathways of LOSs remain unknown. In this study, we describe two transposon insertion mutants of M. marinum that exhibit altered colony morphology. Cell wall analysis reveals that the MRS1271 mutant is defective in the synthesis of LOS‐II, whereas the MRS1178 mutant accumulates an intermediate between LOS‐I and ‐II. The genetic lesions were localized to two genes, MM2309 and MM2332. MM2309 encodes a UDP‐glucose dehydrogenase that is involved in the synthesis of d‐xylose. MM2332 is predicted to encode a decarboxylase. These two genes and a previously identified losA gene are localized in a gene cluster likely to be involved in the biosynthesis of LOSs. Our results also show that LOSs play an important role in sliding motility, biofilm formation, and infection of host macrophages. Taken together, our studies have identified, for the first time, a LOS biosynthetic locus. This is an important step in assessing the differential distribution of LOSs among Mycobacterium species and understanding the role of LOSs in mycobacterial virulence.
[Effects of mesenteric lymph duct ligation on apoptosis of renal tubule epithelial cells in rats after two-hits].

OBJECTIVE To explore the effect of mesenteric lymph duct ligation in preventing apoptosis of renal tubule epithelial cells in rats by two-hits including hemorrhage and lipopolysaccharide (LPS) challenge. METHODS Forty-five Wistar rats were randomly divided into three groups: the ligation group, the non-ligation group and sham operation group. The two-hits model was established by withdrawing the blood via the right side carotid artery of rats and intragastric administration 4 mg/kg LPS 6 hours after hemorrhage, and mesenteric lymph flow was blocked by ligating mesenteric lymph duct in ligation group. Twenty-four hours after operation, kidney was harvested for pathological examination, and the apoptosis cells rate of renal tubule epithelial cells were determined by method of terminal-deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL), the expression of apoptosis-correlating gene bcl-2 and bax protein were determined by streptavidin-biotin complex (SABC) immunohistochemical method. RESULTS After two-hits, the apoptosis rate and expression of bax protein of renal tubule epithelial cells in non-ligation group were significantly increased, and expression of bcl-2 protein was significantly lower as compared with those of sham operation group (all P<0.01). But the apoptosis rate and expression of bax protein of renal tubule epithelial cells in ligation group were significantly lower, and expression of bcl-2 protein was significantly increased as compared with non-ligation group (all P<0.01). CONCLUSION The results demonstrate that the ligation of mesenteric lymph duct could ameliorate the apoptosis of renal tubule epithelial cells in rats as produced by hemorrhage and LPS, and its mechanism might relate to the reduction of the down regulation of gene expression of bax protein and enhancement of the expression of bcl-2 protein after ligation of mesenteric lymph duct.
Musculoskeletal Manifestations of Russell-Silver Syndrome

The musculoskeletal manifestations of Russell-Silver syndrome were studied in 25 patients. The most common manifestations were short stature (25 patients), limb-length discrepancy (23 patients), clinodactyly (19 patients) metacarpal bone and phalangeal abnormalities (13 patients), scoliosis (9 patients), foot syndactylism (5 patients), and developmental dysplasia of the hips (3 patients). Five patients underwent lower extremity limb-lengthening procedures for discrepancies greater than 3 cm and three patients had successful pelvic and/or femoral osteotomies for hip dysplasia. All 18 patients studied had retardation of bone age, which peaked at age 7 years.
Genetic and environmental effects on serum cholesterol of dairy cattle of various ages.

Serum cholesterol of dairy cattle, particularly when measured on animals of the same approximate age, is a heritable trait. Heritabilities were . 50 for first lactation cows and . 19 for heifers from 2 to 22 mo of age. Serum cholesterol increases with increasing age. Serum cholesterol was 192.8 mg/100 ml in cows and 121.4 mg/100 ml in heifers. Serum cholesterol was relatively low at the onset of lactation, increased at mid-lactation, and leveled off or decreased in late lactation. Month of calving, year of sampling, and ration did not influence serum cholesterol of first lactation cows. However, variation in both month and year of sampling was significant for heifers.
Modeling the Late Steps in HIV-1 Retroviral Integrase-catalyzed DNA Integration*

Model oligodeoxyribonucleotide substrates representing viral DNA integration intermediates with a gap and a two-nucleotide 5′ overhang were used to examine late steps in human immunodeficiency virus, type 1 (HIV-1) retroviral integrase (IN)-catalyzed DNA integration in vitro. HIV-1 or avian myeloblastosis virus reverse transcriptase (RT) were capable of quantitatively filling in the gap to create a nicked substrate but did not remove the 5′ overhang. HIV-1 IN also failed to remove the 5′ overhang with the gapped substrate. However, with a nicked substrate formed by RT, HIV-1 IN removed the overhang and covalently closed the nick in a disintegration-like reaction. The efficiency of this closure reaction was very low. Such closure was not stimulated by the addition of HMG-(I/Y), suggesting that this protein only acts during the early processing and joining reactions. Addition of Flap endonuclease-1, a nuclease known to remove 5′ overhangs, abolished the closure reaction catalyzed by IN. A series of base pair inversions, introduced into the HIV-1 U5 long terminal repeat sequence adjacent to and/or including the conserved CA dinucleotide, produced no or only a small decrease in the HIV-1 IN-dependent strand closure reaction. These same mutations caused a significant decrease in the efficiency of concerted DNA integration by a modified donor DNA in vitro, suggesting that recognition of the ends of the long terminal repeat sequence is required only in the early steps of DNA integration. Finally, a combination of HIV-1 RT, Flap endonuclease-1, and DNA ligase is capable of quantitatively forming covalently closed DNA with these model substrates. These results support the hypothesis that cellular enzyme(s) may catalyze the late steps of retroviral DNA integration.
Docetaxel plus oxaliplatin with or without fluorouracil or capecitabine in metastatic or locally recurrent gastric cancer: a randomized phase II study.

BACKGROUND Docetaxel/cisplatin/infusional 5-fluorouracil (5-FU; DCF) is a standard chemotherapy regimen for patients with advanced gastric cancer (GC). This phase II study evaluated docetaxel/oxaliplatin (TE), docetaxel/oxaliplatin/5-FU (TEF), and docetaxel/oxaliplatin/capecitabine (TEX) in patients with advanced GC. PATIENTS AND METHODS Patients with metastatic or locally recurrent gastric adenocarcinoma (including carcinoma of the gastro-oesophageal junction) were randomly assigned (1 : 1 : 1) to TE, TEF, or TEX. Each regimen was tested at two doses before full evaluation at optimized dose levels. The primary end point was progression-free survival (PFS). Overall survival (OS), tumour response, and safety were also assessed. A therapeutic index (median PFS relative to the incidence of febrile neutropenia) was calculated for each regimen and compared with DCF (historical data). RESULTS Overall, 248 patients were randomly assigned to receive optimized dose treatment. Median PFS was longer with TEF (7.66 [95% confidence interval (CI): 6.97-9.40] months) versus TE (4.50 [3.68-5.32] months) and TEX (5.55 [4.30-6.37] months). Median OS was 14.59 (95% CI: 11.70-21.78) months for TEF versus 8.97 (7.79-10.87) months for TE and 11.30 (8.08-14.03) months for TEX. The rate of tumour response (complete or partial) was 46.6% (95% CI 35.9-57.5) for TEF versus 23.1% (14.3-34.0) for TE and 25.6% (16.6-36.4) for TEX. The frequency and type of adverse events (AEs) were similar across the three arms. Common grade 3/4 AEs were fatigue (21%), sensory neuropathy (14%), and diarrhoea (13%). Febrile neutropenia was reported in 2% (TEF), 14% (TE), and 9% (TEX) of patients. The therapeutic index was improved with TEF versus TEX, TE, or DCF. CONCLUSION These results suggest that TEF is worthy of evaluation as an arm in a phase III trial or as a backbone regimen for new targeted agents in advanced GC. CLINICALTRIALS.GOV: Identifier Trial registration number: NCT00382720.
Testing Forbearance Experimentally: Duopolistic Competition of Conglomerate Firms

Like Feinberg and Sherman (1985) and Phillips and Mason (1992), we test experimentally whether conglomerate firms, i.e. firms competing on multiple, structurally unrelated markets, effectively limit competition through forbearance. Unlike these authors, our more general analysis assumes differentiated rather than homogeneous products and distinguishes strategic substitutes as well as complements to test their forbearance hypothesis. We vary the duration of the interaction to disentangle effects of forbearance and repetition. Surprisingly, rather than limiting competition, conglomerate firms foster it. In line with our expectations, we find more cooperation with strategic complements than with strategic substitutes and also more cooperation with long term than with short term interaction.
Role models, ethnic identity, and health-risk behaviors in urban adolescents.

BACKGROUND The assumption that role models or mentors constructively influence adolescent psychological functioning has prompted societal investment in mentoring programs. However, there has been little empirical evaluation of the relationship between role model or mentor characteristics and health behaviors. OBJECTIVES To describe role model selection in urban adolescents and examine the relationships between role model characteristics, psychosocial functioning, and health-risk behaviors. DESIGN Cross-sectional survey. PARTICIPANTS A population-based, multiethnic sample of Los Angeles County adolescents aged 12 to 17 years was generated from a 3-stage, area-probability sampling frame. Of 877 adolescents identified, 749 are included in this analysis. METHODS In-person, in-home interviews were conducted. MAIN OUTCOME MEASURES Substance use, academic performance, and self-perception (measures of ethnic identify and self-esteem). Ethnic identity was measured by an adaptation of a scale developed by Phinney (J Adolesc Res. 1992;7:156-176) to assess commonalities across ethnic groups. RESULTS Fifty-six percent of adolescents identified a role model. Higher levels of ethnic identity were associated with moving from identifying no role model to identifying a figure primarily available through the media to identifying a known individual, familial or nonfamilial (P<.001). Having a role model, particularly an individual known to the adolescent, was also associated with higher self-esteem (P<.001) and higher grades (P<.05). For white males without custodial fathers, having a role model was associated with decreased substance use (P<.05). CONCLUSION Role model selection is associated with protective psychosocial characteristics.
Cross‐inhibitory interactions between GABAA and P2X channels in myenteric neurones

Inhibitory interactions between GABAA[induced by γ‐aminobutyric acid (GABA)] and P2X [activated by adenosine 5′‐triphosphate (ATP)] receptors of myenteric neurones from the guinea pig small intestine were characterized using whole‐cell recordings. Currents induced by GABA (IGABA) or ATP (IATP) were inhibited by picrotoxin or pyridoxalphosphate‐6‐azophenyl‐2′,4′‐disulphonic acid, respectively. Currents induced by GABA + ATP (IGABA+ATP) were only as large as the current induced by the most effective transmitter, revealing current occlusion. This occlusion requires maximal activation of at least one of these receptors. Sequential applications of neurotransmitters, and kinetic and pharmacological properties of IGABA+ATP indicate that they are carried through both GABAA and P2X channels. ATP did not affect IGABA in neurones: (i) in which P2X channels were not present; (ii) after inhibiting P2X channels with Ca2+ (iii) in the presence of pyridoxalphosphate‐6‐azophenyl‐2′,4′‐disulphonic acid, a P2X receptor antagonist; (iv) after P2X receptor desensitization or (v) at IATP reversal potential. Similarly, GABA did not affect P2X‐mediated currents in neurones: (i) in which GABAA channels were not present; (ii) in the presence of picrotoxin, a GABAA channel blocker; (iii) after GABAA receptor desensitization or (iv) at the IGABA reversal potential. Current occlusion occurred as fast as current activation and it was still present in the absence of Ca2+, at 11 °C, after adding to the pipette solution a cocktail of protein kinase inhibitors (staurosporine + genistein + K‐252a), after substituting the GTP in the pipette with GDP‐β‐S and after treating the cells with N‐ethylmaleimide. Taken together, all of these results are consistent with a model of cross‐inhibition between GABAA and P2X.
Indicators based on registers and administrative data for breast cancer: routine evaluation of oncologic care pathway can be implemented.

RATIONALE, AIMS AND OBJECTIVES Assuring the best standards of care - in a sustainable way - in chronic diseases as breast cancer is nowadays an important challenge for any health system. The aim of this study was to present the methodology used to define a set of quality indicators, computable from administrative data for the pathway of care of breast cancer, and its application at a population level. METHOD The cohort of 2007-2009 incident cases of breast cancer was identified through a network of six cancer registers in Northern Italy. Cases of sarcoma and lymphoma, patients with multiple primary cancers and those metastatic at diagnosis were excluded; 9614 women were retained for the analysis. For each indicator, the sub-cohort of women eligible for the diagnostic/therapeutic procedures was identified and calculations were performed through record linkage between the cohort and sources of health information. Data on potential available confounders or prognostic factors were also collected. RESULTS For a few indicators, such as cyto-histological assessment before surgery (62%) and intensive follow-up (79%), deviation from recommendations was evident. Younger patients (≤50 years) more frequently needed a short term re-intervention, while older patients less frequently underwent reconstructive surgery and received palliative care. Several indicators had a great variability across hospitals. In some cases, this heterogeneity appeared to be related to the hospital size, with high-volume hospitals being more compliant to guidelines. CONCLUSION It is possible to evaluate the quality of cancer care delivered in clinical practice in recent years, in order to implement interventions aimed to improve adherence to international standards of care.
Multi-Focus Image Fusion using Self-Similarity and Depth Information in Nonsubsampled Shearlet Transform Domain

Combined with the shared similarity among multiple source images and depth of field in a camera, a new image fusion algorithm based on nonsubsampled shearlet transform (NSST) domain is proposed. First, NSST is utilized for decomposition of the source images, the low frequency coefficients is fused by weight votes in the structure-driven regions by using shared similarity and depth of field (SSSID), and then apply larger summodified-Laplacian (SML) with depth of field to the high frequency coefficients, finally the fusion image is gained after we do the inverse NSST to the fused coefficients. The algorithm can not only preserve the information of the source images well, but also suppress pixel distortion due to nonlinear operations in transform domain. Experimental results demonstrate that the proposed method outperforms the state-of-the-art transform domain fusion methods on image quality and objective fusion criteria.
Age-Related Macular Degeneration and Coronary Artery Disease in a VA Population

Objectives Age-related macular degeneration (AMD) is the leading cause of blindness in the United States. Although AMD shares multiple risk factors with coronary artery disease (CAD), the association between AMD and CAD has not been established. The objective of our study was to demonstrate an association between the diagnosis of AMD and CAD and/or major cardiovascular risk factors. Methods We performed a retrospective chart review of >13,000 patients at the Lexington Veterans Affairs Medical Center. Patients diagnosed as having AMD served as cases, and patients diagnosed with cataract and no AMD served as controls. We examined the prevalence of CAD and associated risk factors in both groups using univariate analysis followed by multivariate analyses to examine the association between AMD and CAD after adjusting for known common risk factors. Results We identified 3950 patients with AMD and 9166 controls. Patients with AMD were on average 6 years older than controls (P < 0.001) and had a significantly higher prevalence of CAD (39% vs 34%) and hypertension (88% vs 83%) but lower incidence of diabetes mellitus and smoking. Estimated odds ratio relating CAD to AMD was 1.22 (95% confidence interval 1.13–1.32; P < 0.001). The association between CAD and AMD remained significant in multivariate analyses in older individuals (76 years and older). When we conducted a secondary analysis and matched the AMD and non-AMD groups based on age, the association between CAD and AMD remained significant (39.4% in the AMD group vs 36.6% in the non-AMD group; P = 0.011). Conclusions These findings support the existence of an association between CAD and AMD, particularly in older adult patients in the predominantly male Veterans Affairs population. Such an association between AMD and systemic vascular disease justifies the potential coscreening for these conditions.
Touch screen-based motor bearing fault diagnosis

A combined method with wavelet packet and BP neural network based on touch screen for motor bearing fault diagnosis is presented. Firstly, this method uses the time-frequency technology of wavelet packet for the feature extraction of motor vibration signals. Secondly, BP neural network is designed based on energy feature vector, and the algorithm is realized with MATLAB software. Finally, diagnostic results are displayed on the touch screen, which is based on three typical running states of motor rotor system. Simulation studies show that the proposed algorithm is reliable, and efficient.
Intra- and Interinstitutional Evaluation of an Etest for Vancomycin Minimum Inhibitory Concentration Measurement in Staphylococcus aureus Blood Isolates.

TO THE EDITOR—We read with great interest the study by Cervera and colleagues on the clinical outcome of patients with left-sided endocarditis due to methicillinsusceptible Staphylococcus aureus (MSSA) [1]. They showed a 3-fold higher mortality in patients infected by MSSA isolates with vancomycin minimum inhibitory concentrations (MICs) in the upper end of the susceptible range (≥1.5 μg/mL) as measured by Etest [1]. As pointed out by Kaasch and colleagues in their comment to the above-referenced work [2], the reproducibility of Etest results and interobserver variance of the assay were not investigated. Given the narrow MIC margin for isolate categorization as high susceptible (≤1 μg/mL) vs low susceptible (≥1.5 μg/mL), knowledge of the precision and reproducibility of vancomycin MICs measured by Etest seems of paramount relevance. Our study aimed to address this issue. A total of 100 consecutive cryopreserved (−70°C) S. aureus isolates (MSSA, n = 65; methicillin-resistant S. aureus [MRSA], n = 35) isolated from blood cultures between 2012 and 2015 at the Hospital Clínico Universitario (HCU) were evaluated. Primary subcultures were made on 2 sheep blood agar plates (BD [Beckton Dickinson, Sparks, Maryland]), 1 of which was shipped to the Consorcio Hospital General (HGU) for parallel testing. The Etest was performed simultaneously at both institutions using a 0.5 McFarland standard inoculum (0.98 × 10 and 1.3 × 10 colony-forming units/mL) streaked on Mueller-Hinton agar (BD), followed by the application of vancomycin Etest strips (bioMérieux,Marcy l’Étoile, France). The MIC measurements were made using the same lots of media and Etest strips. The plates were read visually by 2 of the authors (blinded to eachother) at each center after 24 hours of incubation at 35°C in ambient air. Twenty randomly chosen isolates were tested in quintuplicate at HCU for the assessment of within-run precision. The S. aureus American Type Culture Collection 25923 quality-control strain was run in parallel. Minor and major discrepancies were defined when MIC values were within the same or within a distinct susceptibility category (low vs high), respectively. All S. aureus strains evaluated in this study were susceptible to vancomycin.
Absence of differentiation-related expression of keratin 10 in early stages of vulvar squamous carcinoma.

Using specific monoclonal antibodies (DE-K10 and DE-SCK respectively), the expression of some differentiation-related epidermal keratins was studied in 38 human vulvar squamous carcinomas. In the epidermis, expression of keratin 10 (K10) strictly paralleled the extent of differentiation; it was absent in the basal layer, appeared in the first suprabasal layers and increased in concentration towards the granular layer. However, K10 was rarely detected (1 case out of 12) in early stages of vulvar squamous carcinomas (tumours less than 2 cm, clinical stage I) regardless of the tumour grade. In larger and more advanced tumours (greater than 2 cm, clinical stages II and III), K10 was detected in 21 out of 26 cases. Its expression appeared to be related to maturation of malignant keratinocytes, being preferentially detected in more-differentiated parts. Occasionally however, cells that did not show histological signs of keratinisation were also K10-positive. Modified stratum corneum keratins (recognized specifically by monoclonal antibody DE-SCK) were detected in the most keratinized areas (horn pearls and their close vicinity) of some K10-positive tumours, i.e., in a pattern close to their normal expression in terminally differentiated epidermal cells. These data suggest differences in the regulation of K10 expression during the differentiation processes in the normal keratinising squamous epithelium and in squamous carcinomas. While the normal pattern of vulvar epithelial differentiation is accompanied by an increasing expression of K10, malignant keratinocytes, also when these are histologically moderately or well differentiated, cease expressing this keratin in the early stages of tumour development.