Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Tissue mRNA and Serum Antigen Levels of Members of the Urokinase-Type Plasminogen Activator System with Clinical and Prognostic Parameters in Prostate Cancer

The objective was to determine the mRNA expression and protein levels of uPA system components in tissue specimens and serum samples, respectively, from prostate cancer (PCa) patients and to assess their association with clinicopathological parameters and overall survival (OS). The mRNA expression levels of uPA, its receptor (uPAR), and its inhibitor type 1 (PAI-1) were analyzed in corresponding malignant and adjacent nonmalignant tissue specimens from 132 PCa patients by quantitative PCR. Preoperative serum samples from 81 PCa patients were analyzed for antigen levels of uPA system members by ELISA. RNA levels of uPA system components displayed significant correlations with each other in the tumor tissues. A significantly decreased uPA mRNA expression in PCa compared to the corresponding nonmalignant tissue was detected. High uPA mRNA level was significantly associated with a high Gleason score. Elevated concentration of soluble uPAR (suPAR) in serum was significantly associated with a poor OS of PCa patients (P = 0.022). PCa patients with high suPAR levels have a significantly higher risk of death (multivariate Cox's regression analysis; HR = 7.12, P = 0.027). The association of high suPAR levels with poor survival of PCa patients suggests a prognostic impact of suPAR levels in serum of cancer patients.
Mutations in the external loops of BK virus VP1 and urine viral load in renal transplant recipients

Polyomavirus‐associated nephropathy (PVAN) is a major complication that occurs after renal transplantation and is induced by reactivation of the human polyomavirus BK (BKV). The structure of the viral capsid protein 1 (VP1) is characterized by the presence of external loops, BC, DE, EF, GH, and HI, which are involved in receptor binding. The pathogenesis of PVAN is not well understood, but viral risk factors are thought to play a crucial role in the onset of this pathology. In an attempt to better understand PVAN pathogenesis, the BKV‐VP1 coding region was amplified, cloned, and sequenced from the urine of kidney transplant recipients who did, and did not, develop the pathology. Urine viral loads were determined by using real time quantitative PCR (Q‐PCR). Amino acid substitutions were detected in 6/8 patients, and 6/7 controls. The BC and EF loop regions were most frequently affected by mutations, while no mutations were found within the GH and HI loops of both patients and controls. Some mutations, that were exclusively detected in the urine of PVAN patients, overlapped with previously reported mutations, although a correlation between changes in amino acids and the development of PVAN was not found. Urine viral loads were higher than that of the proposed cut‐off loads for identification of patients that are at a high risk of developing PVAN (107 copies/ml), both in the PVAN and control groups, thus confirming that urine viral load is not a useful predictive marker for the development of PVAN. J. Cell. Physiol. 222:195–199, 2010. © 2009 Wiley‐Liss, Inc.
UvA-DARE ( Digital Academic Repository ) Kernel codebooks for scene categorization

This paper introduces a method for scene categorization by modeling ambiguity in the popular codebook approach. The codebook approach describes an image as a bag of discrete visual codewords, where the frequency distributions of these words are used for image categorization. There are two drawbacks to the traditional codebook model: codeword uncertainty and codeword plausibility. Both of these drawbacks stem from the hard assignment of visual features to a single codeword. We show that allowing a degree of ambiguity in assigning codewords improves categorization performance for three state-of-the-art datasets.
Facts and fallacies of software engineering

There's a problem with those facts—and, as you might imagine, those fallacies. Many of these fundamentally important facts are learned by a software engineer, but over the short lifespan of the software field, all too many of them have been forgotten. While reading Facts and Fallacies of Software Engineering, you may experience moments of "Oh, yes, I had forgotten that," alongside some "Is that really true? " thoughts.
Heart Disease Prediction System using Data Mining Techniques and Intelligent Fuzzy Approach: A Review

The Healthcare trade usually clinical diagnosis is ended typically by doctor’s knowledge and practice. Computer Aided Decision Support System plays a major task in medical field. Data mining provides the methodology and technology to alter these mounds of data into useful information for decision making. By using data mining techniques it takes less time for the prediction of the disease with more accuracy. Among the increasing research on heart disease predicting system, it has happened to significant to categories the research outcomes and gives readers with an outline of the existing heart disease prediction techniques in each category. Data mining tools can answer trade questions that conventionally in use much time overriding to decide. In this paper we study different papers in which one or more algorithms of data mining used for the prediction of heart disease. As of the study it is observed that Fuzzy Intelligent Techniques increase the accuracy of the heart disease prediction system. The generally used techniques for Heart Disease Prediction and their complexities are summarized in this paper.
How Long Will It Take to Fix This Bug?

Predicting the time and effort for a software problem has long been a difficult task. We present an approach that automatically predicts the fixing effort, i.e., the person-hours spent on fixing an issue. Our technique leverages existing issue tracking systems: given a new issue report, we use the Lucene framework to search for similar, earlier reports and use their average time as a prediction. Our approach thus allows for early effort estimation, helping in assigning issues and scheduling stable releases. We evaluated our approach using effort data from the JBoss project. Given a sufficient number of issues reports, our automatic predictions are close to the actual effort; for issues that are bugs, we are off by only one hour, beating naive predictions by a factor of four.
Application of NMR-based metabonomics suggests a relationship between betaine absorption and elevated creatine plasma concentrations in catheterised sows

The objective of the present explorative study was to determine the absorption dynamics when feeding diets varying in types and levels of dietary fibre in a catheterised animal model. A total of six sows were fed a diet low in fibre (LF), a diet high in soluble fibre and a diet high in insoluble fibre in a repeated 3 × 3 cross-over design. Plasma samples were collected from the mesenteric artery and the portal vein to determine different absorption phases by 1H NMR spectroscopy-based metabonomics. Time profiles were determined for plasma levels of specific metabolites and for the absorption of these metabolites from the small intestine. The LF diet resulted in a higher betaine concentration in the blood than the two high-fibre diets (P = 0·008). This leads to higher plasma concentrations of methionine (P = 0·0028) and creatine (P = 0·020) of endogenous origin. In conclusion, the use of NMR spectroscopy for measuring nutrient uptake in the present study elucidated the relationship between betaine uptake and elevated creatine plasma concentrations.
A vision-based computed torque control for parallel kinematic machines

In this paper, a novel approach for parallel kinematic machine control relying on a fast exteroceptive measure is implemented and validated on the Orthoglide robot. This approach begins with rewriting the robot models as a function of the only end-effector pose. It is shown that such an operation reduces the model complexity. Then, this approach uses a classical Cartesian space computed torque control with a fast exteroceptive measure, reducing the control schemes complexity. Simulation results are given to show the expected performance improvements and experiments prove the practical feasibility of the approach.
Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles

Behavioral isolation is thought to arise early in speciation due to differential sexual and/or natural selection favoring different preferences and traits in different lineages. Alternatively, behavioral isolation can arise due to reinforcement favoring traits and preferences that prevent maladaptive hybridization. In darters, female preference for male coloration has been hypothesized to drive speciation, because behavioral isolation evolves before F1 inviability. However, as with many long-lived organisms, the fitness of second generation hybrids has not been assessed because raising animals to adulthood in the lab is challenging. Recently, reinforcement of male preferences has been implicated in darters because male preference for conspecific females is high in sympatry but absent in allopatry in multiple species pairs. The hypothesis that reinforcement accounts for behavioral isolation in sympatry assumes that hybridization and postzygotic isolation are present. Here, we used genomic and morphological data to demonstrate that hybridization is ongoing between orangethroat and rainbow darters and used hybrids collected from nature to measure postzygotic barriers across two hybrid generations. We observed sex ratio distortion in adult F1s and a dramatic reduction in backcross survival. Our findings indicate that selection to avoid hybridization promotes the evolution of male-driven behavioral isolation via reinforcement in this system.
Circadian Clock Genes of Goldfish, Carassius auratus: cDNA Cloning and Rhythmic Expression of Period and Cryptochrome Transcripts in Retina, Liver, and Gut

Clock genes are known to be the molecular core of biological clocks of vertebrates. They are expressed not only in those tissues considered central pacemakers, but also in peripheral tissues. In the present study, partial cDNAs for 6 of the principal clock genes (Period 1-3 and Cryptochrome 1-3) were cloned from a teleost fish, the goldfish (Carassius auratus ). These genes showed high homology (approximately 90%) with the respective cDNAs of zebrafish (Danio rerio), the only other teleost from which clock genes have been cloned. The daily expression pattern of each gene in retina, gut, and liver of goldfish was investigated using quantitative RT-PCR and cosinor analysis. All clock genes analyzed in the retina showed circadian rhythmicity; however, only Per 2-3 and Cry 2-3 were rhythmic in goldfish liver and gut. The amplitude and phase of the expression in liver and gut were different from those found in goldfish retina. Such differences suggest that other cues, such as feeding time, may contribute to the entrainment of oscillators in goldfish liver and gut. Our results support the use of goldfish as a teleost model to investigate the location and functioning of the circadian oscillators.
Approximation of dynamical time-variant systems by continuous-time recurrent neural networks

This paper studies the approximation ability of continuous-time recurrent neural networks to dynamical time-variant systems. It proves that any finite time trajectory of a given dynamical time-variant system can be approximated by the internal state of a continuous-time recurrent neural network. Given several special forms of dynamical time-variant systems or trajectories, this paper shows that they can all be approximately realized by the internal state of a simple recurrent neural network.
Dopamine modulates the off pathway in light‐adapted mouse retina

DL‐2‐Amino‐4‐phosphonobutyric acid (APB) is often used as a tool to block On pathways in studies of interactions between On and Off pathways in retinas. APB is an agonist of mGluR6 receptors and hyperpolarizes the On cone bipolar cells and rod bipolar cells. How APB affects Off responses of retinal ganglion cells (RGCs) in mouse retinas under dark and light adaptation is not clear. The light‐evoked excitatory postsynaptic currents (light‐evoked EPSCs) from Off and On–Off RGCs cells were recorded using whole‐cell patch‐clamp recording to assess how APB affects Off responses (light‐evoked Off EPSCs) of RGCs in dark‐ and light‐adapted mouse retinas. We found that APB differentially affected Off responses of RGCs in dark‐ and light‐adapted mouse retinas. Under dark adaptation, while the APB‐sensitive Off responses were blocked, APB increased the remaining Off responses (mainly from the secondary rod Off pathways) via removal of inhibition from On pathways to Off pathways. Under light adaptation, APB decreased Off responses. Glycinergic and GABAergic antagonists did not prevent the APB‐induced reduction of Off responses of RGCs; however, a dopaminergic type 1 receptor (D1) blocker (SCH 23390) and a hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channel blocker (ZD 7288) prevented the APB‐induced reduction of Off responses of RGCs under light adaptation. The results indicated afunctional circuit: On cone bipolar cells to Off cone bipolar cells via D1 receptors and HCN channels. © 2012 Wiley Periodicals, Inc.
Investigating the impact of the English health inequalities strategy: time trend analysis

Objective To investigate whether the English health inequalities strategy was associated with a decline in geographical health inequalities, compared with trends before and after the strategy. Design Time trend analysis. Setting Two groups of lower tier local authorities in England. The most deprived, bottom fifth and the rest of England. Intervention The English health inequalities strategy—a cross government strategy implemented between 1997 and 2010 to reduce health inequalities in England. Trends in geographical health inequalities were assessed before (1983-2003), during (2004-12), and after (2013-15) the strategy using segmented linear regression. Main outcome measure Geographical health inequalities measured as the relative and absolute differences in male and female life expectancy at birth between the most deprived local authorities in England and the rest of the country. Results Before the strategy the gap in male and female life expectancy between the most deprived local authorities in England and the rest of the country increased at a rate of 0.57 months each year (95% confidence interval 0.40 to 0.74 months) and 0.30 months each year (0.12 to 0.48 months). During the strategy period this trend reversed and the gap in life expectancy for men reduced by 0.91 months each year (0.54 to 1.27 months) and for women by 0.50 months each year (0.15 to 0.86 months). Since the end of the strategy period the inequality gap has increased again at a rate of 0.68 months each year (−0.20 to 1.56 months) for men and 0.31 months each year (−0.26 to 0.88) for women. By 2012 the gap in male life expectancy was 1.2 years smaller (95% confidence interval 0.8 to 1.5 years smaller) and the gap in female life expectancy was 0.6 years smaller (0.3 to 1.0 years smaller) than it would have been if the trends in inequalities before the strategy had continued. Conclusion The English health inequalities strategy was associated with a decline in geographical inequalities in life expectancy, reversing a previously increasing trend. Since the strategy ended, inequalities have started to increase again. The strategy may have reduced geographical health inequalities in life expectancy, and future approaches should learn from this experience. The concerns are that current policies are reversing the achievements of the strategy.
Similarities and differences between the effects of epidermal growth factor and Rous sarcoma virus

We have derived a line of A431 human tumor cells infected with Rous sarcoma virus (RSV). The infected cells contain the RSV-transforming protein, pp60src, which has characteristic tyrosine specific protein kinase activity. As in other RSV-transformed cells, a 36,000-dalton protein is phosphorylated in RSV-infected A431 cells. Addition of epidermal growth factor (EGF) to the cells induces further phosphorylation of this protein. In contrast, this phosphoprotein is not detected in uninfected A431 cells, except when treated with EGF. Increased phosphorylation of the EGF receptor protein and of an 81,000- dalton cellular protein is dependent upon addition of EGF to the culture fluids, in both control and RSV-infected A431 cells. The results are discussed with reference to the similarities and differences between the tyrosine-specific protein kinases induced by RSV and activated by EGF.
INSTALLATION AND EARLY PERFORMANCE OF A FIELD TEST SECTION OF ASPHALT RUBBER CONCRETE. INTERIM REPORT

Asphalt rubber, which is produced by reacting asphalt cement and crumb rubber, is claimed to increase fatigue life and reduce rutting of asphalt concrete; however, the service life must be increased significantly to offset the additional cost of adding the rubber. In order to assess the performance of asphalt rubber mixtures and how effectively they can be used in construction, test sections of asphalt concrete surface courses using either asphalt rubber binder or the conventional binder were installed on a heavily traveled highway in Northern Virginia. Special equipment was required to blend the asphalt cement and crumb rubber; however, the production of the mixture and construction of the test sections were accomplished with minimal problems. Various laboratory tests including Marshall, gyratory shear, creep, resilient modulus, indirect tensile strength, and stripping were used to evaluate the mixtures in the laboratory. The results indicated that the asphalt rubber mixtures were more susceptible to permanent deformation than the same mixtures without rubber; however, the conventional temperature at which the mixtures were compacted and tested with the gyratory shear machine may not have presented a true estimate of performance because pavement deformation occurs at lower temperatures. Friction numbers of one section of asphalt rubber mixture were significantly lower at a 95% confidence level than friction numbers of the other asphalt rubber section, possibly the result of the pavement surface being filled by soil from a nearby construction project. However, there was no difference at a 95% confidence level between the average friction values of the control and asphalt rubber sections. Surveys of pavement performance, measurements of rut depth, and friction tests will be conducted periodically, and a final report will be published June 30, 1994.
The expiratory capnogram: a measure of ventilation-perfusion inequalities.

Current methods of estimating ventilationperfusion imbalance using radioactive gases (Dollery and Hugh-Jones, 1963), although giving regional localization, require exceptional technical resources, as does the single breath technique of West, Fowler, Hugh-Jones, and O'Donnell (1957). These methods also suffer the disadvantage that the respiratory manceuvres involved, such as breath-holding, may of themselves alter the ventilation-perfusion ratios (Briscoe, 1962). The method of Riley, Cournand, and Donald (1951) gives a measure of overall 'wasted' ventilation and perfusion (physiological dead-space and shunt, respectively) and avoids this latter disadvantage but requires arterial blood gas analysis. The non-uniformity of expired carbon dioxide in emphysema has been known for many years (Roelsen, 1939). This scatter of expired carbon dioxide concentration (expiratory capnogram) is attributable to imbalance between alveolar ventilation and pulmonary capillary perfusion, different areas of lung having different carbon dioxide levels at end-inspiration and emptying asynchronously during expiration (Marshall, Bates, and Christie, 1952; Comroe, Forster, DuBois, Briscoe, and Carlsen, 1962). It has been suggested that the expiratory capnogram could be of value in the diagnosis of emphysema (Dornhorst, Semple, and Young, 1953) and of ventilation-perfusion imbalance in general (Comroe et al., 1962). Kelsey, Oldham, and Horvath (1962), analysing the expiratory capnogram qualitatively, found that it was indeed of use in the diagnosis of chronic non-specific lung disease and could relate abnormal curves to certain conventional lung function test abnormalities. It was decided, in view of the need for a relatively simple test of overall ventilationperfusion imbalance, to investigate the expiratory capnogram further.
Prognostic value of programmed death‐ligand 1 expression in patients with stage III colorectal cancer

The programmed death‐1/programmed death‐ligand 1 (PD‐L1) pathway is a negative feedback pathway that suppresses the activity of T cells. Previous studies reported that high PD‐L1 expression on tumor cells (TC) was associated with poor survival in patients with colorectal cancer; however, the prognostic evaluation of these studies was limited because they included patients at various disease stages. The purpose of the present study was to evaluate the relationship between PD‐L1 status in the immune microenvironment and the clinicopathological features of stage III colorectal cancer. Two hundred and thirty‐five patients were included in the analysis. PD‐L1 expression on TC and tumor‐infiltrating mononuclear cells (TIMC) was evaluated by immunohistochemistry. The median follow‐up of thisi study was 52.9 months. A total of 8.1% of stage III colorectal cancer showed high PD‐L1 expression on TC and 15.3% showed high PD‐L1 expression on TIMC. Patients with high PD‐L1 expression on TC had significantly shorter disease‐free survival (DFS) than patients with low expression (hazard ratio [HR] 2.36; 95% confidence interval [CI], 1.21–4.62; P = 0.012). In addition, patients with high PD‐L1 expression on TIMC were associated with longer DFS than patients with low expression (HR 0.40; 95% CI, 0.16–0.98; P = 0.046). These findings suggest that PD‐L1 expression status may be a new predictor of recurrence for stage III colorectal cancer patients and highlight the necessity of evaluating PD‐L1 expression on TC and TIMC separately in the tumor microenvironment.
Toxicities of Immunosuppressive Treatment of Autoimmune Neurologic Diseases

In parallel to our better understanding of the role of the immune system in neurologic diseases, there has been an increased availability in therapeutic options for autoimmune neurologic diseases such as multiple sclerosis, myasthenia gravis, polyneuropathies, central nervous system vasculitides and neurosarcoidosis. In many cases, the purported benefits of this class of therapy are anecdotal and not the result of good controlled clinical trials. Nonetheless, their potential efficacy is better known than their adverse event profile. A rationale therapeutic decision by the clinician will depend on a comprehensive understanding of the ratio between efficacy and toxicity. In this review, we outline the most commonly used immune suppressive medications in neurologic disease: cytotoxic chemotherapy, nucleoside analogues, calcineurin inhibitors, monoclonal antibodies and miscellaneous immune suppressants. A discussion of their mechanisms of action and related toxicity is highlighted, with the goal that the reader will be able to recognize the most commonly associated toxicities and identify strategies to prevent and manage problems that are expected to arise with their use.