Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunocytochemical analysis of prostate stem cell antigen as adjunct marker for detection of urothelial transitional cell carcinoma in voided urine specimens.

PURPOSE Prostate stem cell antigen (PSCA), a homologue of the Ly-6/Thy-1 family of cell surface antigens, has been shown to be increased in a majority of human transitional cell carcinomas. We tested the possibility of using PSCA as an adjunct marker for urine cytology. MATERIALS AND METHODS Immunocytochemical analysis was performed on 44 archived voided urine samples obtained from 3 groups of patients based on initial voided urine cytological results and subsequent followup biopsy findings. Group 1 (14 of 44 patients) had positive findings on cytology and histology, group 2 (16 of 44) had negative cytology but positive histology, and group 3 (14 of 44) had negative findings on cytology and histology. Cytological slides prepared from 10 fresh voided urine samples were also analyzed. Papanicoloau stained archived urine slides were de-stained and re-stained immunocytochemically with a monoclonal antibody against PSCA. Immunofluorescence followed by laser scanning cytometer analysis was also performed on archived slides from 2 representative cases. RESULTS Sensitivity and specificity were 46.7% and 100% for cytology alone, respectively, and 80% and 85.7% for PSCA alone, respectively. PSCA immunostaining was positive in 92.8% group 1, 68.8% group 2 and only 14.3% group 3 samples. The difference in positive PSCA findings in groups 2 and 3 were statistically significant at p <0.01 by chi-square test. Whereas some superficial umbrella cells showed slight staining by immunocytochemistry, it was feasible to distinguish the expression levels between tumor and normal superficial umbrella cells quantitatively using immunofluorescence coupled with laser scan cytometry analysis. CONCLUSIONS Immunocytochemical analysis of PSCA on archived voided urine samples may provide a simple and quantitative adjunct marker for cytological diagnosis of urothelial carcinoma.
Image registration using mutual information with correlation for medical image

Image registration is the process of overlaying images (two or more) of the same scene taken at different times, from different viewpoints, and/or by different sensors. Image registration geometrically aligns two images (the reference and test images). In this paper, we discuss about the problematic issue that arises during the feature matching stage in the mutual information based medical image registration. The matched results shows that by changing (can be decreasing or increasing depending on the image) the windows size of the image more matched points can be obtained. The higher degree of registration is obtained, by using correlation with mutual information. Procedure to measure the angle of rotation between two images, using mutual information is provided in this paper.
Asthma and posttraumatic stress symptoms 5 to 6 years following exposure to the World Trade Center terrorist attack.

CONTEXT The World Trade Center Health Registry provides a unique opportunity to examine long-term health effects of a large-scale disaster. OBJECTIVE To examine risk factors for new asthma diagnoses and event-related posttraumatic stress (PTS) symptoms among exposed adults 5 to 6 years following exposure to the September 11, 2001, World Trade Center (WTC) terrorist attack. DESIGN, SETTING, AND PARTICIPANTS Longitudinal cohort study with wave 1 (W1) enrollment of 71,437 adults in 2003-2004, including rescue/recovery worker, lower Manhattan resident, lower Manhattan office worker, and passersby eligibility groups; 46,322 adults (68%) completed the wave 2 (W2) survey in 2006-2007. MAIN OUTCOME MEASURES Self-reported diagnosed asthma following September 11; event-related current PTS symptoms indicative of probable posttraumatic stress disorder (PTSD), assessed using the PTSD Checklist (cutoff score > or = 44). RESULTS Of W2 participants with no stated asthma history, 10.2% (95% confidence interval [CI], 9.9%-10.5%) reported new asthma diagnoses postevent. Intense dust cloud exposure on September 11 was a major contributor to new asthma diagnoses for all eligibility groups: for example, 19.1% vs 9.6% in those without exposure among rescue/recovery workers (adjusted odds ratio, 1.5 [95% CI, 1.4-1.7]). Asthma risk was highest among rescue/recovery workers on the WTC pile on September 11 (20.5% [95% CI, 19.0%-22.0%]). Persistent risks included working longer at the WTC site, not evacuating homes, and experiencing a heavy layer of dust in home or office. Of participants with no PTSD history, 23.8% (95% CI, 23.4%-24.2%) reported PTS symptoms at either W1 (14.3%) or W2 (19.1%). Nearly 10% (9.6% [95% CI, 9.3%-9.8%]) had PTS symptoms at both surveys, 4.7% (95% CI, 4.5%-4.9%) had PTS symptoms at W1 only, and 9.5% (95% CI, 9.3%-9.8%) had PTS symptoms at W2 only. At W2, passersby had the highest rate of PTS symptoms (23.2% [95% CI, 21.4%-25.0%]). Event-related loss of spouse or job was associated with PTS symptoms at W2. CONCLUSION Acute and prolonged exposures were both associated with a large burden of asthma and PTS symptoms 5 to 6 years after the September 11 WTC attack.
Could We Predict the Result of a Continuous Integration Build? An Empirical Study

Software build integrates modules developed and maintained by different developers in parallel, tests the result of integration, and serves as a crucial step in cooperatiive software development. Predicting the result of build has drawn the interest of academia and industry. In spite of many previous researches, the generalizability of build failure prediction over a wide range of open-source projects remains unclear.In this paper, we used 9 classifiers to construct prediction models and investigated the performance of both cross-validation and on-line predictions on 126 open-source projects available on TravisTorrent with nearly 300,000 build records. We found that for most projects, (a) the prediction performance in cross-validation scenario is pretty well (especial under AUC); (b) when it comes to on-line scenario, the prediction performance falls to a fairly low level.
Shading and litter mediate the effects of soil fertility on the performance of an understorey herb.

BACKGROUND AND AIMS Soil fertility and topographic microclimate are common determinants of plant species distributions. However, biotic conditions also vary along these abiotic gradients, and may mediate their effects on plants. In this study, we investigated whether soils and topographic microclimate acted directly on the performance of a focal understorey plant, or indirectly via changing biotic conditions. METHODS We examined direct and indirect relationships between abiotic variables (soil fertility and topographic microclimate) and biotic factors (overstorey and understorey cover, litter depth and mycorrhizal colonization) and the occurrence, density and flowering of a common understorey herb, Trientalis latifolia, in the Klamath-Siskiyou Mountains, Oregon, USA. RESULTS We found that the positive effects of soil fertility on Trientalis occurrence were mediated by greater overstorey shading and deeper litter. However, we did not find any effects of topographic microclimate on Trientalis distribution that were mediated by the biotic variables we measured. The predictive success of Trientalis species distribution models with soils and topographic microclimate increased by 12 % with the addition of the biotic variables. CONCLUSIONS Our results reinforce the idea that species distributions are the outcome of interrelated abiotic gradients and biotic interactions, and suggest that biotic conditions, such as overstorey density, should be included in species distribution models if data are available.
Incidence of left atrial thrombus prior to atrial fibrillation ablation: is pre-procedural transoesophageal echocardiography mandatory?

AIMS The exact role of transoesphageal echo (TOE) prior to atrial fibrillation (AF) ablation remains unclear. This study examines the incidence and predictors of left atrial (LA) thrombus in patients undergoing AF ablation. METHODS AND RESULTS Patients were treated with warfarin for at least 4 weeks prior to ablation. This was substituted with therapeutic dalteparin 3 days before the procedure. All patients underwent TOE to exclude LA thrombus. Six clinical risk factors for thrombus were defined, known to be risk factors for stroke in AF: age>75, diabetes, hypertension, valve disease, prior stroke, or transient ischaemic attack and cardiomyopathy. A total of 635 procedures were performed. The incidence of thrombus was 12/635 (1.9%) despite therapeutic anti-coagulation. Patients with thrombus had larger LA diameter, mean 50.6+/-6.2 mm vs. 44.2+/-7.6 (P=0.006). In univariate analysis, persistent AF [odds ratio (OR)=10.4 with 95% CI 1.8-19.1], hypertension [OR=11.7 with 95% CI 2.5-54.1], age>75 (OR=4.5 with 95% CI 1.2-17.2), and cardiomyopathy (OR 5.9 with 95% CI 1.8-19.1) were significantly associated with thrombus. In multivariate analysis, hypertension (OR=14.2 with 95% CI 2.6-77.5), age>75 (OR=8.1, 95% CI 1.5-44.9), and cardiomyopathy (OR=10.5 with 95% CI 2.6-77.5) were independently associated with thrombus. There was no thrombus in patients without clinical risk factors. CONCLUSION In patients presenting for AF ablation, LA thrombus is only seen in those with clinical risk factors. TOE is indicated in this group but may be unnecessary in patients without clinical risk factors.
Full spectrum of psychiatric outcomes among offspring with parental history of mental disorder.

CONTEXT While concordant parent/offspring risks for specific mental disorders are well established, knowledge of the broader range of psychiatric outcomes among offspring with parental history of mental disorder is lacking. OBJECTIVE To examine the full range of mental health outcomes among offspring of parents with serious and other mental disorders compared with those whose parents had no such history. DESIGN Population-based cohort study. Offspring were followed up from their 14th birthday for the development of mental disorders based on both outpatient and inpatient hospital data. SETTING Danish population. PARTICIPANTS All offspring born in Denmark between 1980 and 1994 (N = 865 078) with follow-up to December 2008. MAIN OUTCOME MEASURES Incidence rates, incidence rate ratios, and cumulative incidences for offspring psychiatric outcomes. RESULTS Parental serious mental disorder (SMD) (nonaffective or affective psychosis) was found to be positively associated with virtually all offspring psychiatric outcomes, including those not hitherto regarded as clinically related. Offspring of parents without SMD but with a history of "other mental disorder" were also found to be at increased risk of developing a range of mental disorders. The strongest associations were found where both parents had a history of mental disorder (eg, offspring of 2 parents with SMD were 13 times more likely to develop schizophrenia). Elevated risks were not confined to concordant parent/offspring disorders (eg, offspring of 2 parents with SMD were 8 times more likely to develop substance misuse disorders). CONCLUSIONS The impact of parental history of mental disorder was not confined to elevated offspring risk of concordant disorders but rather offspring are at increased risk of a wide range of mental disorders, particularly those with 2 affected parents. Our results imply an important role for etiological factors giving rise to broad, as well as specific, familial vulnerabilities. These findings also have potential implications for diagnostic classification.
Synergistic action of fibroblast growth factor‐2 and transforming growth factor‐beta1 enhances bioprinted human neocartilage formation

Bioprinting as a promising but unexplored approach for cartilage tissue engineering has the advantages of high throughput, digital control, and highly accurate placement of cells and biomaterial scaffold to the targeted 3D locations with simultaneous polymerization. This study tested feasibility of using bioprinting for cartilage engineering and examined the influence of cell density, growth, and differentiation factors. Human articular chondrocytes were printed at various densities, stimulated transiently with growth factors and subsequently with chondrogenic factors. Samples were cultured for up to 4 weeks to evaluate cell proliferation and viability, mechanical properties, mass swelling ratio, water content, gene expression, ECM production, DNA content, and histology. Bioprinted samples treated with FGF‐2/TGF‐β1 had the best chondrogenic properties among all groups apparently due to synergistic stimulation of cell proliferation and chondrogenic phenotype. ECM production per chondrocyte in low cell density was much higher than that in high cell seeding density. This finding was also verified by mechanical testing and histology. In conclusion, cell seeding density that is feasible for bioprinting also appears optimal for human neocartilage formation when combined with appropriate growth and differentiation factors. Biotechnol. Bioeng. 2012;109: 2357–2368. © 2012 Wiley Periodicals, Inc.
Design of a robust and ultra-low-voltage pulse-triggered flip-flop in 28nm UTBB-FDSOI technology

So far, pulse-triggered flip-flops (pulsed-FFs) are mainly used in high-performance digital circuits, thanks to their small data-to-output delay. However, they suffer from a poor robustness to local variations occurring at ultra-low-voltage (ULV). Thanks to an innovative pulse generator, the operability of an energy-efficient pulsed-FF was validated at ultra-low operating supply voltage. Measurements of delays and correct functionality are performed in 28nm FDSOI technology. Then, the effect of back bias voltage, a key point in FDSOI technology, is studied and it is shown that our pulsed-FF reaches a minimum operating supply voltage of 170mV.
Does mindfulness improve outcomes in patients with chronic pain? Systematic review and meta-analysis.

BACKGROUND Chronic pain and its associated distress and disability are common reasons for seeking medical help. Patients with chronic pain use primary healthcare services five times more than the rest of the population. Mindfulness has become an increasingly popular self-management technique. AIM To assess the effectiveness of mindfulness-based interventions for patients with chronic pain. DESIGN AND SETTING Systematic review and meta-analysis including randomised controlled trials of mindfulness-based interventions for chronic pain. There was no restriction to study site or setting. METHOD The databases MEDLINE(®), Embase, AMED, CINAHL, PsycINFO, and Index to Theses were searched. Titles, abstracts, and full texts were screened iteratively against inclusion criteria of: randomised controlled trials of mindfulness-based intervention; patients with non-malignant chronic pain; and economic, clinical, or humanistic outcome reported. Included studies were assessed with the Yates Quality Rating Scale. Meta-analysis was conducted. RESULTS Eleven studies were included. Chronic pain conditions included: fibromyalgia, rheumatoid arthritis, chronic musculoskeletal pain, failed back surgery syndrome, and mixed aetiology. Papers were of mixed methodological quality. Main outcomes reported were pain intensity, depression, physical functioning, quality of life, pain acceptance, and mindfulness. Economic outcomes were rarely reported. Meta-analysis effect sizes for clinical outcomes ranged from 0.12 (95% confidence interval [CI] = -0.05 to 0.30) (depression) to 1.32 (95% CI = -1.19 to 3.82) (sleep quality), and for humanistic outcomes 0.03 (95% CI = -0.66 to 0.72) (mindfulness) to 1.58 (95% CI = -0.57 to 3.74) (pain acceptance). Studies with active, compared with inactive, control groups showed smaller effects. CONCLUSION There is limited evidence for effectiveness of mindfulness-based interventions for patients with chronic pain. Better-quality studies are required.
Phase II clinical trial of peptide cocktail therapy for patients with advanced pancreatic cancer: VENUS‐PC study

We previously conducted a phase I clinical trial combining the HLA‐A*2402‐restricted KIF20A‐derived peptide vaccine with gemcitabine for advanced pancreatic cancer (PC) and confirmed its safety and immunogenicity in cancer patients. In this study, we conducted a multicenter, single‐armed, phase II trial using two antiangiogenic cancer vaccines targeting VEGFR1 and VEGFR2 in addition to the KIF20A peptide. We attempted to evaluate the clinical benefit of the cancer vaccination in combination with gemcitabine. Chemotherapy naïve PC patients were enrolled to evaluate primarily the 1‐year survival rate, and secondarily overall survival (OS), progression free survival (PFS), response rate (RR), disease control rate (DCR) and the peptide‐specific immune responses. All enrolled patients received therapy without the HLA‐A information, and the HLA genotypes were used for classification of the patients. Between June 2012 and May 2013, a total of 68 patients were enrolled. No severe systemic adverse effects of Grade 3 or higher related to these three peptides were observed. The 1‐year survival rates between the HLA‐A*2402‐matched and ‐unmatched groups were not significantly different. In the HLA‐A*2402 matched group, patients showing peptide‐specific CTL induction for KIF20A or VEGFR1 showed a better prognosis compared to those without such induction (P = 0.023, P = 0.009, respectively). In the HLA‐A*2402‐matched group, the patients who showed a strong injection site reaction had a better survival rate (P = 0.017) compared to those with a weak or no injection site reaction. This phase II study demonstrated that this therapeutic peptide cocktail might be effective in patients who demonstrate peptide‐specific immune reactions although predictive biomarkers are needed for patient selection in its further clinical application.
HLA‐DRB1* alleles and temporomandibular joint erosion in patients with various rheumatic diseases

Objective: To investigate the association between HLA antigens and temporomandibular joint (TMJ) erosion, salivary composition, and focal sialadenitis in patients with rheumatic diseases. Methods: Eighty‐four patients, 24 with rheumatoid arthritis (RA), 19 with mixed connective tissue disease (MCTD), 19 with ankylosing spondylitis (AS), and 22 with spondyloarthropathy (SPA) were studied. Each patient underwent clinical examination of the masticatory system, unstimulated and stimulated saliva collection, and minor salivary gland biopsy. Radiographs (OPTG) of the TMJ were obtained, and HLA allele (A, B, C and DRB1*) analysis was performed. Erosion in OPTG was scored from 0 (no erosion) to 4 (condyles totally eroded). In the analysis, scores 0–2 were grouped as normal or mild changes, and scores 3–4 as distinct erosions. One hundred healthy blood donors served as controls for HLA typing. Results: Distinct erosion of the TMJ in OPTG was observed in 22 (27%) patients. It affected four (17%) of the 24 patients with RA, three (17%) of the 18 with MCTD, seven (37%) of the 19 patients with AS and eight (38%) of the 21 with SPA non‐significant (NS). The mean erosion scores were 1.7 for RA, 1.3 for MCTD, 2.5 for SPA, and 1.6 for AS patients [probability (p)=0.04]. The frequency of HLA‐B27 antigen was higher in the AS and SPA patients, and that of HLA‐DRB1*04 allele higher in RA patients than in control subjects. In the whole patient population, HLA‐DRB1*01 allele was significantly associated with erosions 16/36 (44%) versus 6/46 (13%) (p=0.0014). In the SPA group, patients with HLA‐DRB1*01 allele had a significantly higher occurrence of distinct erosions than patients without this allele [8/10 (80%) versus 0/11 (0%) (p=0.0002)], whereas DRB1*06 was protective [0/8 (0%) versus 8/13 (62%) (p=0.018)]. HLA‐DRB1*04 was associated with increased salivary IgG in the RA patients. Conclusion: HLA antigens are significantly associated with the development of destructive lesions in the TMJ, as well as composition of saliva in patients with various rheumatic diseases.
BBC: A DSL for designing cloud-based heterogeneous bigdata pipelines

Several frameworks are available for processing and analyzing the bigdata. But there is limited support available in integrating such heterogeneous bigdata programs to create a bigdata pipeline. In this paper, we introduce BBC, a Domain Specific Language (DSL) designed to create a bigdata pipeline from the heterogeneous programs. The paper focuses on Spark jobs but using a similar approach the DSL can be extended for other frameworks. We have successfully used BBC DSL to design the The Home Depot (THD) search evaluation pipeline that is instrumental in deploying every search feature to the THD website.
Spirometric function in non-smoking workers exposed to aluminum.

BACKGROUND Exposure to aluminum (Al) causes the onset of respiratory disorders. This study is aimed at providing further information on how occupational exposure to Al affects the respiratory apparatus in healthy non-smokers, with particular attention to respiratory function. METHODS A group of 50 male shipyard workers who were exposed to Al underwent medical examination, standard chest X-rays and spirometry in accordance with the C.E. C.A. protocol. The data were compared with those of a homogeneous group of controls, all with blood aluminum (AlB) levels below 7.5 ng/ml. Statistical analysis was performed on the following spirometric parameters: vital capacity (VC), forced vital capacity (FVC), maximum forced expiratory volume in 1 s (FEV1), and mean forced expiratory flow during mid-half of FVC (FEF(25-75%)). Environmental Al levels were also measured at the various workstations. RESULTS Fifty male workers with an average age 31.82 +/- 5.05 years, occupational exposure of 11.81 +/- 3.71 years, presented with average AlB levels of 32.64 +/- 8.69 ng/ml. Environmental monitoring displayed Al levels higher than TLV TWA for all the workstations studied. None of the sample displayed significant pathological conditions. Statistical comparison of the spirometric parameters showed a decrease in the examined values in exposed workers. This decrease was found to be directly proportional to the AlB level. CONCLUSION The authors conclude that Al affects respiratory function and that limit values should be reassessed.
Prevalence and antimicrobial resistance among Gram-negative pathogens in Saudi Arabia

Abstract Antimicrobial resistance among Gram-negative bacteria is a worldwide problem, including in the Kingdom of Saudi Arabia, with major concerns regarding Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae. Although over half of the isolates of P. aeruginosa remain susceptible to carbapenems, quinolones, and aminoglycosides in most reports from Saudi Arabia, resistance is on increase, with a worrying high prevalence of multidrug resistance. Ceftazidime, ciprofloxacin, and aminoglycosides remain active against A. baumannii isolates in some studies from the Kingdom, but recent data suggest increased resistance. Carbapenems are now the treatment of choice for Acinetobacter infections but their activity too is being eroded. Among Enterobacteriaceae, Escherichia coli, Klebsiella pneumoniae, and Enterobacter spp. are the most clinically relevant species. Rates of extended-spectrum beta-lactamase (ESBL) production by these species vary among studies but are generally high in Saudi Arabia, with many ESBL-producing isolates multiresistant to other agents, except carbapenems and nitrofurantoin. A similar pattern is seen for Klebsiella, although with more resistance to quinolones, aminoglycosides, and to nitrofurantoin than in E. coli. Enterobacter is commonly resistant to penicillins, monobactams, and cephalosporins but mostly susceptible to carbapenems. Carbapenemases are beginning to emerge in Enterobacteriaceae.