Miracle-dz/UniFAR-FTUs huggingface dataset:
The canadian multicenter double‐blind randomized controlled trial of ursodeoxycholic acid in primary biliary cirrhosis

Ursodeoxycholic acid, a dihydroxyl bile acid normally present in human beings in minimal amounts, becomes incorporated into the bile salt pool when taken orally. In cholestasis, bile acids are retained in the liver and are hepatotoxic. Ursodeoxycholic acid is the least‐known hepatotoxic bile acid, has choleretic properties and is reported to benefit patients with chronic cholestasis. In a nationwide Canadian controlled trial, 222 patients with primary biliary cirrhosis were treated with ursodeoxycholic acid (14 mg/kg/body wt/day) or placebo for 24 mo. Only patients with a diagnosis confirmed by liver biopsy and serum positive for antimitochondrial antibodies were enrolled; 88% were symptomatic on entry. The primary outcome measure was percent change in total serum bilirubin from baseline to final follow‐up. Treated patients (111) and controls (111) were comparable with regard to age, gender, biochemical parameters and liver histological condition. Although treatment was not associated with any improvement in symptoms, ursodeoxycholic acid therapy caused the bilirubin to fall significantly within the first 3 mo of therapy (p<0.001). Significant falls in serum alkaline phosphatase, aminotransferases, cholesterol and IgM levels were also noted in the treated group. Improvement in some histological features was observed but there was no difference between the groups in the number of patients who reached the endpoints of death or liver transplantation. Ursodeoxycholic acid, given to patients with primary biliary cirrhosis, leads to an improvement in serum markers of cholestasis. A larger sample size is needed to determine whether ursodeoxycholic acid therapy has a beneficial effect on the survival of patients with primary biliary cirrhosis. (HEPATOLOGY 1994;19:1149–1156.)
Automating Functional Testing of Components from UML Specifications

A method of functional testing for software components according to model-based testing techniques is proposed. Test cases are generated from UML diagrams and OCL constraints that comprise a component interface and realization specification. The method uses a reduced set of UML artifacts that constitute the main requirements for its application along with a component development process, making use of development artifacts. Also, the set of generated test artifacts are packed together with the provided components to reduce the overall testing effort when clients assemble applications. A tool has been developed to automate the method with test cases generated as Java test components. Test execution and result analysis is also supported. For each component, the tool generates a test component that can be easily upgraded and configured for testing the services provided by a component throughout its life cycle.
Fast non-blind deconvolution based on 2D point spread function database for real-time ultrasound imaging

In the ultrasound medical imaging system, blurring which occurs after passing through ultrasound scanner system, represents Point Spread Function (PSF) that describes the response of the ultrasound imaging system to a point source distribution. So, de-blurring can be achieved by de-convolving the images with an estimated of PSF. However, it is hard to attain an accurate estimation of PSF due to the unknown properties of the tissues of the human body through the ultrasound signal propagates. In addition to, the complexity is very high in order to estimate point spread function and de-convolve the ultrasound image with estimated PSF for real-time implementation of ultrasound imaging. Therefore, conventional methods of ultrasound image restoration are based on a simple 1D PSF estimation [8] that axial direction only by restoring the performance improvement is not in the direction of Lateral. And, in case of 2D PSF estimation, PSF estimation and restoration of the high complexity is not being widely used. In this paper, we proposed new method for selection of the 2D PSF (estimated PSF of the average speed sound and depth) simultaneously with performing fast non-blind 2D de-convolution in the ultrasound imaging system. Our algorithm works on the beam-formed uncompressed radio-frequency data, with pre-measured and estimated 2D PSFs database from actual probe used. In the 2d PSF database, there are pre-measured and estimated 2D PSFs that classified the each different depth (about 5 different depths) and speed of sound (about 1450 or 1540m/s). Using a minimum variance and simple Weiner filter method, we present a novel way to select the optimal 2D PSF in pre-measured and estimated 2D PSFs database that acquired from the actual transducer being used. For de-convolution part with the chosen PSF, we focused on the low complexity issue. So, we are using the Weiner Filter and fast de-convolution technique using hyper-Laplacian priors [11], [12] which is several orders of magnitude faster than existing techniques that use hyper-Laplacian priors. Then, in order to prevent discontinuities between the differently restored each depth image regions, we use the piecewise linear interpolation on overlapping regions. We have tested our algorithm with vera-sonic system and commercial ultrasound scanner (Philips C4-2), in known speed of sound phantoms and unknown speeds in vivo scans. We have applied a non-blind de-convolution with 2D PSFs database for ultrasound imaging system. Using the real PSF from actual transducer being used, our algorithm produces a better restoration of ultrasound image than de-convolution by simulated PSF, and has low complexity for real-time ultrasound imaging. This method is robust and easy to implement. This method may be a realistic candidate for real-time implementation.
Forage breeding and management to increase the beneficial fatty acid content of ruminant products

The declining consumption of ruminant products has been partly associated with their high proportion (but not necessarily content) of saturated fatty acids. Recent studies have focused on the less prominent fact that they are also important sources of beneficial fatty acids, including n-3 fatty acids and conjugated linoleic acids. α-Linolenic acid (18: 3n-3) is of particular interest because it also contributes to improved flavour of beef and lamb. Many recent studies showed large effects of special concentrates on levels of fatty acids in milk and meat. However, the ‘rumen protection’ treatments, needed to ensure a worthwhile level of fatty acid in products, are expensive. Herbage lipids are the cheapest and safest source of these fatty acids and so breeding to increase delivery of fatty acids from plants into ruminant products is an important long-term strategy. Plant lipids usually contain high levels of polyunsaturated fatty acids, particularly 18: 2n-6 and 18:3n-3 which are the precursors of beneficial fatty acids. Whilst some plants are particularly rich in individual fatty acids (e.g. 18:3n-3 in linseed), there are also useful levels in grass and clover (Trifolium Spp.). Levels of fatty acids in forages in relation to species and varieties are considered, as well as management and conservation methods. Relationships between levels of fatty acids and existing traits and genetic markers are identified. The effects of forage treatments on the fatty acid content of ruminant products are reviewed. The higher levels of polyunsaturated fatty acids in milk from cows fed clover silages show that the level of fatty acids in herbage is not the only factor affecting levels of fatty acids in ruminant products. Further effort is needed to characterise susceptibility of unsaturated fatty acids to oxidative loss during field wilting and biohydrogenation losses in the rumen, and the relative importance of plant and microbial processes in these losses. The pathways of lipolysis and lipid oxidation are reviewed and other plant factors which offer potential to breed for reduced losses are considered.
Bendamustine Mitoxantrone and Rituximab (BMR): A New Effective Regimen for Refractory or Relapsed Indolent Lymphomas

Bendamustine (B) and mitoxantrone (M) have been shown to be potent cytotoxic drugs for the treatment of relapsed or refractory indolent lymphomas. The anti-CD20 monoclonal antibody rituximab (R) has produced an overall response rate (ORR) of 50% as a single agent in relapsed or refractory indolent lymphomas. We posed the question whether a combination of the above agents (BMR) could improve these results. This study was an open label, single center pilot study for patients with relapsed or refractory, CD20-positive (indolent) lymphoma or chronic lymphocytic leukaemia. The therapy consisted of bendamustine (80 mg/m 2, day 1-3), mitoxantrone (10 mg/m 2, day 1), rituximab (375 mg/m 2, week 2-5). BM was repeated on day 36 or when the haematological parameters had recovered. The maximum therapy consisted of one BMR-cycle, followed by five BM courses. Treatment was stopped when the disease responded with PR/CR. During March 1999 and December 2000, 20 patients received the BMR-regimen (four secondary high grade lymphoma, 12 indolent lymphoma, four B-CLL). The median age of the patients was 67 years (range 36-82) and their performance status ranged from 0 to 3. Median number of previous treatment regimens was two (1-6). Of the lymphoma patients, 14 had stage IV disease, 1 stage III and 1 stage II. B-CLL patients were all Rai stage IV (Binet C). Overall response rate was 95% (19/20) with seven patients achieving a CR(35%) and 12 patients achieving a PR (60%). Median time to progression is 7 months (1-21) with a median observation time of 7 months (1-21). Response is still durable in 15/20 patients (75%) (1+ to 21+ months after therapy). Symptomatic, reversible grade three or four haematotoxicity occurred in 4/20 patients (20%). Non-symptomatic grade three or four haematotoxicity was seen in 9/20 patients (45%). No major non-haematological toxicity was observed. In conclusion, BMR is a well tolerated, very effective outpatient regimen of treatment for relapsed and refractory indolent lymphoid malignancies.
A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline

In the Drosophila germline, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Whereas small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise mainly from the antisense strand. rasiRNA production appears not to require Dicer-1, which makes microRNAs (miRNAs), or Dicer-2, which makes siRNAs, and rasiRNAs lack the 2′,3′ hydroxy termini characteristic of animal siRNA and miRNA. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. Our data suggest that rasiRNAs protect the fly germline through a silencing mechanism distinct from both the miRNA and RNA interference pathways.
A Heuristic Scheduling Algorithm for Distributed Systems with Workflow Constraints

Distributed systems become one of the most important computing platform because they can efficiently handle large amount of data with a high computing workload. However, the job scheduling in the distributed systems is not a trivial issue. It can be even more complex when dealing with workflow-based composite jobs, i.e., each job has multiple tasks with dependencies between them. As the job scheduling problem has been proven to be an NP-hard, we propose a trail-based algorithm; Large Trail First (LTF), which is an effective heuristic approach for scheduling problem in the distributed systems when workflows exist. In this paper, "trail" of each task is the number of remaining tasks in each workflow. Thus, the idea of the algorithm is that, for each workflow job, the task with the largest size of the trail will be executed earliest. The experimental results show that the proposed approach is more effective and efficient than the other three approaches including a well- known 2-approximation algorithm.
Influence of Ambulatory Inhaled Treatment with Different Devices on the Duration of Acute Asthma Findings in Children

Background. Efficacy of bronchodilator treatment in children with asthma depends on the proper use of inhalation devices. The aim of this study was to compare the efficacy of inhaled bronchodilator treatment with a spacer and a nebulizer in children with acute asthma findings. Methods. Fifty-eight children with acute asthma findings who received ambulatory inhaled bronchodilator treatment with a nebulizer and 39 with a spacer were enrolled in the study. Duration of asthma, inhaled steroid treatment and the number of exacerbations during the previous year were recorded. Duration of current acute symptoms, exacerbation severity score and duration of respiratory findings after initiation of treatment were also recorded. Results. Children in both groups were similar in age (76.5 ± 30.3 months using a nebulizer vs 83.1 ± 25.1 in spacer group, p = 0.26). Duration after diagnosis of asthma, initiation of inhaled steroid treatment and exacerbation symptoms were similar between groups (p = 0.15, 0.76 and 0.93, respectively). Exacerbation severity score in the nebulizer group was not significantly different from the spacer group (2.6 ± 0.7 vs 2.8 ± 0.7 respectively, p = 0.19). Number of exacerbations in the previous year was not different (2.0 ± 1.2 in the nebulizer group vs 1.6 ± 0.9 in the spacer group, p = 0.08). Duration of acute asthma findings after initiation of inhaled bronchodilator treatment was similar between the two groups (6.5 ± 2.9 vs 7.2 ± 4.6 p = 0.34). Conclusion. Nebulizers and spacers have similar influence on the duration of acute asthma findings in children when used in ambulatory home bronchodilator treatment.
Curing gonococci of beta-lactamase production with ethidium, acridius orange or acriflavine.

In 12 B-lactamase producing strains of N gonorrhoeae tested, the coding for enzyme production was sensitive, to varying degrees, to one or more of the three agents ethidium bromide, acridine orange, or acriflavine. The substances tested were able to eliminate the plasmid responsible for B-lactamase production but the time required varied. The Far East type of gonococci (plasmid 4.4 Md) were cured in under a week whereas the Liverpool/Ghana type (plasmid 3.2 Md) required more than 7 days treatment. (JPMA35 171, 1985).
REGRESSION ANALYSIS OF NATURAL SELECTION: STATISTICAL INFERENCE AND BIOLOGICAL INTERPRETATION

Recent theoretical work in quantitative genetics has fueled interest in measuring natural selection in the wild. We discuss statistical and biological issues that may arise in applications of Lande and Arnold's (1983) multiple‐regression approach to measuring selection. We review assumptions involved in estimation and hypothesis testing in regression problems, and we note difficulties that frequently arise as a result of violation of these assumptions. In particular, multicollinearity (extreme intercorrelation of characters) and extrinsic, unmeasured factors affecting fitness may seriously complicate inference regarding selection. Further, violation of the assumption that residuals are normally distributed vitiates tests of significance. For this situation, we suggest applications of recently developed jackknife tests of significance. While fitness regression permits direct assessment of selection in a form suitable for predicting selection response, we suggest that the aim of inferring causal relationships about the effects of phenotypic characters on fitness is greatly facilitated by manipulative experiments. Finally, we discuss alternative definitions of stabilizing and disruptive selection.
Advances in the Diagnosis of Sepsis

Inevitably, sepsis has still remained one of the major challenges at the Intensive Care Units (ICUs) (1). About 30 million cases per year are estimated worldwide and this tendency is continuously increasing (2). Although sepsis is known for a long time, its pathomechanism is not completely understood due to the various triggering factors and also to the altered response of the individuals with different underlying diseases.
The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

Saccharomyces cerevisiae, a well-established model for species as diverse as humans and pathogenic fungi, is more recently a model for population and quantitative genetics. S. cerevisiae is found in multiple environments—one of which is the human body—as an opportunistic pathogen. To aid in the understanding of the S. cerevisiae population and quantitative genetics, as well as its emergence as an opportunistic pathogen, we sequenced, de novo assembled, and extensively manually edited and annotated the genomes of 93 S. cerevisiae strains from multiple geographic and environmental origins, including many clinical origin strains. These 93 S. cerevisiae strains, the genomes of which are near-reference quality, together with seven previously sequenced strains, constitute a novel genetic resource, the “100-genomes” strains. Our sequencing coverage, high-quality assemblies, and annotation provide unprecedented opportunities for detailed interrogation of complex genomic loci, examples of which we demonstrate. We found most phenotypic variation to be quantitative and identified population, genotype, and phenotype associations. Importantly, we identified clinical origin associations. For example, we found that an introgressed PDR5 was present exclusively in clinical origin mosaic group strains; that the mosaic group was significantly enriched for clinical origin strains; and that clinical origin strains were much more copper resistant, suggesting that copper resistance contributes to fitness in the human host. The 100-genomes strains are a novel, multipurpose resource to advance the study of S. cerevisiae population genetics, quantitative genetics, and the emergence of an opportunistic pathogen.
Characterization of PINK1 processing, stability, and subcellular localization

Mutations found in PTEN‐induced putative kinase 1 (PINK1), a putative mitochondrial serine/threonine kinase of unknown function, have been linked to autosomal recessive Parkinson’s disease. It is suggested that mutations can cause a loss of PINK1 kinase activity and eventually lead to mitochondrial dysfunction. In this report, we examined the subcellular localization of PINK1 and the dynamic kinetics of PINK1 processing and degradation. We also identified cytosolic chaperone heat‐shock protein 90 (Hsp90) as an interacting protein of PINK1 by PINK1 co‐immunoprecipitation. Immunofluorescence of PINK1 protein and mitochondrial isolation show that the precursor form of PINK1 translocates to the mitochondria and is processed into two cleaved forms of PINK1, which in turn localize more to the cytosolic than mitochondrial fraction. The cleavage does not occur and the uncleaved precursor stays associated with the mitochondria when the mitochondrial membrane potential is disrupted. Metabolic labeling analyses show that the PINK1 processing is rapid and the levels of cleaved forms are tightly regulated. Furthermore, cleaved forms of PINK1 are stabilized by Hsp90 interaction as the loss of Hsp90 activity decreases PINK1 level after mitochondrial processing. Lastly, we also find that cleaved forms of PINK1 are degraded by the proteasome, which is uncommon for mitochondrial proteins. Our findings support a dual subcellular localization, implying that PINK1 can reside in the mitochondria and the cytosol. This raises intriguing functional roles that bridge these two cellular compartments.
Accounting for Intimate Partner Violence

Intimate partner violence (IPV) is a serious social issue which affects the medium- and long-term health outcomes of many individuals worldwide. The cost of IPV on the physical and psychological well-being of individuals, in addition to its wider economic costs in responding to abused persons, is significant. Presently, there is a lack of understanding about the nature of female-initiated IPV and how men account for their experiences of it. This study examined male victims’ life stories of their IPV experiences from their intimate partners. Using the biographical narrative interpretive method, three cases were analyzed from a social constructionist perspective to examine what narrative strategies men used to account for their experiences of being abused by their female partners. Three dominant narrative strategies were used by respondents: the fatherhood narrative, the good husband narrative, and the abuse narrative. The abuse narrative had a unique narrative form, which reflected respondents’ disassociation between their identities as men and also as abused persons. Dominant conflicting discourses of masculinity and intimate partner abuse disadvantaged men in identifying IPV and secondly in responding appropriately. This study found that men prefer to use dominant discursive identities as legitimate means from which to disclose IPV experiences. The findings from this study illustrate that broad questioning by professionals regarding fatherhood may be most helpful in promoting disclosures of IPV if this is suspected.
B-type natriuretic peptide. Guided vs. conventional care in outpatients with chronic heart failure: a retrospective study.

AIM It is not known whether therapy assisted by determinations of serum B-type natriuretic peptide (BNP) may improve the outcome for outpatients with chronic heart failure (CHF). METHODS A retrospective case-control study was carried out, enrolling patients with acutely decompensated heart failure (ADHF) who were followed up for a mean period of four months. The patients who had died or had new episodes of ADHF were studied as the cases. For each case, one living patient who was free from ADHF-related re-hospitalisations was recruited as control. Cases and controls were also matched for some variables to minimise possible confounding. The possible role of BNP-guided therapy as a predictor of decreased risk of deaths or new hospitalisations related to heart failure was explored. RESULTS Twenty-eight cases and 44 controls were enrolled. A fall in BNP on the fifth day after admission was found to be a predictor of a decreased risk of the composite endpoint "death or new hospitalisation, heart failure-related" (hazard ratio=0.1508; 95% CI: 0.049 to 0.463; P=0.001). On the other hand, low glomerular filtration rate at admission (<60 mL/min/1.73 m2) was associated with increased risk of the abovementioned endpoint (hazard ratio=7.1785; 95% CI: 1.574 to 32.725; P=0.0113). On the contrary, BNP-guided therapy was associated with a similar risk of death and/or CHF-related hospitalisation, compared to the conventional clinical approach. CONCLUSION A fall in BNP ≥60% from baseline on the fifth day after admission was found to be associated with a favorable clinical outcome in outpatients with CHF after four months of follow-up, irrespective whether this finding had been detected in patients treated according to the BNP-guided therapy or in patients treated with conventional clinical criteria. However, among the outpatients with previous ADHF, a substantial improvement in cardiovascular event rates could not be demonstrated in those treated with BNP-guided therapy compared with those undergoing usual, symptom-guided treatment.