Miracle-dz/UniFAR-FTUs huggingface dataset:
Facilitating program parallelisation : a profiling-based approach

The advance of multi-core architectures signals the end of universal speed-up of software over time. To continue exploiting hardware developments, effort must be invested in producing software that can be split up to run on multiple cores or processors. Many solutions have been proposed to address this issue, ranging from explicit to implicit parallelism, but consensus has yet to be reached on the best way to tackle such a problem. In this thesis we propose a profiling-based interactive approach to program parallelisation. Profilers gather dependence information on a program, which is then used to automatically parallelise the program at source-level. The programmer can then examine the resulting parallel program, and using critical path information from the profiler, identify and refactor parallelism bottlenecks to enable further parallelism. We argue that this is an efficient and effective method of parallelising general sequential programs. Our first contribution is a comprehensive analysis of limits of parallelism in several benchmark programs, performed by constructing Dynamic Dependence Graphs (DDGs) from execution traces. We show that average available parallelism is often high, but realising it would require various changes in compilation, language or computation models. As an example, we show how using a spaghetti stack structure can lead to a doubling of potential parallelism. The rest of our thesis demonstrates how some of this potential parallelism can be realised under the popular fork-join parallelism model used by Cilk, TBB, OpenMP and others. We present a tool-chain with two main components: Embla 2, which uses DDGs from profiled dependences to estimate the amount of task-level parallelism in programs; and Woolifier, a source-to-source transformer that uses Embla 2's output to parallelise the programs. Using several case studies, we demonstrate how this tool-chain greatly facilitates program parallelisation by performing an automatic best-effort parallelisation and presenting critical paths in a concise graphical form so that the programmer can quickly locate parallelism bottlenecks, which when refactored can lead to even greater potential parallelism and significant actual speed-ups (up to around 25 on a 32-effective-core machine). Acknowledgements First of all I would like to thank my supervisor, Alan Mycroft, for his invaluable advice and support in all matters. Without his guidance and encouragement I would never have been able to complete this thesis. I would also like to thank Matthew Parkinson, my second supervisor, for his support and guidance. In addition, I am profoundly indebted to Karl-Filip Faxén and Sverker Janson from SICS …
Influence of fasting and transit on ruminal and blood metabolites in beef steers.

Nine ruminally cannulated steers (average weight 477 kg) were randomly assigned to serve as controls (C) or to be fasted (F) or fasted and transported (FT). C steers were allowed free access to alfalfa hay, water and plain salt during the experiment; F steers were deprived of feed and water for 32 hr, and FT steers were deprived of feed and water and transported for 32 hr in a gooseneck trailer. After 32 hr, F and FT steers were allowed access to alfalfa hay, salt and water. Rumen samples were withdrawn via cannula at 0, 18, 32, 36, 46, 56, 80 and 104 hr after the start of the experiment. Jugular blood was sampled at the same times, except for 36 and 46 hours. Rumen pH of F and FT steers increased (P less than .05) during the 32 hr fasting/transit period over that of C steers and then decreased (P less than .05) on refeeding. Total VFA concentrations were lower in F steers (39.5 mmoles/liter) at 32 hr than in FT steers (202.2 mmoles/liter). Total counts of rumen bacteria and protozoa were lower (P less than .05) in F and FT steers than in C steers at all times except 0 and 104 hr, and recovery of microbial numbers was slower in FT and in F steers. VFA data suggest rumen motility may be impaired in FT steers compared with that in F steers. Blood glucose was higher (P less than .05) at 18 an 32 hr in FT than in F steers. Serum glutamic oxaloacetic transaminase was higher (P less than .05) at 18 hr (104.7 IU/liter) in FT steers than in steers in the other two groups (average 84.3 IU/liter). Serum Fe tended to be lower at 18 and 32 hr in FT steers than in F and C steers, and serum triglycerides were lower (P less than .05) in FT steers at 32 and 56 hr than in C. Most other blood constituents were not greatly affected by treatment. These data suggest that the physiological response of fasting alone differs considerably from that of fasting and transit stress, because transit appears to impose influences on rumen fermentation and blood chemistry beyond those imposed by fasting.
Biofeedback therapy in fecal incontinence and constipation

Abstract We examine the collected evidence for efficacy of biofeedback therapy (BFT) in incontinence and constipation by means of meta‐analysis of randomized controlled trials. PubMed search was performed to identify treatment trials that match quality criteria (adequate control groups, randomization). They were entered into meta‐analyses using fixed effect models and computing odds ratio (OR) and 95% confidence interval (CI) of treatment effects. For constipation, eight BFT trials were identified. In four trials, electromyographic (EMG) BFT was compared to non‐BFT treatments (laxatives, placebo, sham training and botox injection), while in the remaining four studies EMG BFT was compared to other BFT (balloon pressure, verbal feedback) modes. Meta‐analyses revealed superiority of BFT to non‐BFT (OR: 3.657; 95% CI: 2.127–6.290, P < 0.001) but equal efficacy of EMG BFT to other BF applications (OR: 1.436; CI: 0.692–3.089; P = 0.319). For fecal incontinence, a total of 11 trials were identified, of which six compared BFT to other treatment options (sensory training, pelvic floor exercise and electrical stimulation) and five compared one BFT option to other modalities of BFT. BFT was equal effective than non‐BFT therapy (OR: 1.189, CI: 0.689–2.051, P = 0.535). No difference was found when various modes BFT were compared (OR: 1.278, CI: 0.736–2.220, P = 0.384). Included trials showed a substantial lack of quality and harmonization, e.g. variable endpoints and missing psychological assessment across studies. BFT for pelvic floor dyssynergia shows substantial specific therapeutic effect while BFT for incontinence is still lacking evidence for efficacy. However, in both conditions the mode of BFT seems to play a minor role.
CIRCADIAN TYPOLOGY AND TEMPERAMENT AND CHARACTER PERSONALITY DIMENSIONS

The purpose of the present study is to explore the relationships between circadian typology and Cloninger’s model of the seven dimensions of personality, taking into account the possible sex interactions. This model considers four temperament dimensions (viz., HA, harm avoidance; NS, novelty seeking; RD, reward dependence; and PS, persistence) and three character dimensions (viz., SD, self-directedness; C, cooperativeness; and ST, self-transcendence). A sample of 862 university students (500 women), between 18 and 30 (21.94 ± 2.64) yrs of age completed the short versions of the Temperament and Character Inventory (TCI-56) and the reduced Morningness-Eveningness Questionnaire (rMEQ). Women showed higher values for HA, RD, and C, while men showed higher values for NS. Evening-type subjects had higher NS but lower HA, PS, and SD scores. Moreover, circadian typology modulated the sex differences in HA and NS, and only evening-type men showed a lower HA score and higher NS score. Circadian typology is related to Cloninger’s model of Temperament and Character personality dimensions. Future studies should further examine possible implications, regarding both the vulnerability of developing psychopathological disorders and the prognosis of response to different treatments. (Author correspondence: aadan@ub.edu)
Predominance of a Versatile-Peroxidase-Encoding Gene, mnp4, as Demonstrated by Gene Replacement via a Gene Targeting System for Pleurotus ostreatus

ABSTRACT Pleurotus ostreatus (the oyster mushroom) and other white rot filamentous basidiomycetes are key players in the global carbon cycle. P. ostreatus is also a commercially important edible fungus with medicinal properties and is important for biotechnological and environmental applications. Efficient gene targeting via homologous recombination (HR) is a fundamental tool for facilitating comprehensive gene function studies. Since the natural HR frequency in Pleurotus transformations is low (2.3%), transformed DNA is predominantly integrated ectopically. To overcome this limitation, a general gene targeting system was developed by producing a P. ostreatus PC9 homokaryon Δku80 strain, using carboxin resistance complemented by the development of a protocol for hygromycin B resistance protoplast-based DNA transformation and homokaryon isolation. The Δku80 strain exhibited exclusive (100%) HR in the integration of transforming DNA, providing a high efficiency of gene targeting. Furthermore, the Δku80 strains produced showed a phenotype similar to that of the wild-type PC9 strain, with similar growth fitness, ligninolytic functionality, and capability of mating with the incompatible strain PC15 to produce a dikaryon which retained its resistance to the corresponding selection and was capable of producing typical fruiting bodies. The applicability of this system is demonstrated by inactivation of the versatile peroxidase (VP) encoded by mnp4. This enzyme is part of the ligninolytic system of P. ostreatus, being one of the nine members of the manganese-peroxidase (MnP) gene family, and is the predominantly expressed VP in Mn2+-deficient media. mnp4 inactivation provided a direct proof that mnp4 encodes a key VP responsible for the Mn2+-dependent and Mn2+-independent peroxidase activity under Mn2+-deficient culture conditions.
Turning Microscopy in the Medical Curriculum Digital: Experiences from The Faculty of Health and Medical Sciences at University of Copenhagen

Familiarity with the structure and composition of normal tissue and an understanding of the changes that occur during disease is pivotal to the study of the human body. For decades, microscope slides have been central to teaching pathology in medical courses and related subjects at the University of Copenhagen. Students had to learn how to use a microscope and envisage three-dimensional processes that occur in the body from two-dimensional glass slides. Here, we describe how a PathXL virtual microscopy system for teaching pathology and histology at the Faculty has recently been implemented, from an administrative, an economic, and a teaching perspective. This fully automatic digital microscopy system has been received positively by both teachers and students, and a decision was made to convert all courses involving microscopy to the virtual microscopy format. As a result, conventional analog microscopy will be phased out from the fall of 2016.
Survival in elderly men in relation to midlife and current BMI.

BACKGROUND the relationship between BMI and mortality is U-shaped in the elderly but may be modified by midlife BMI and change in weight. OBJECTIVE to elucidate mortality prediction by BMI trajectory in older men. SUBJECTS the Oslo cohort of men born in 1923-32 were screened for BMI and cardiovascular risk in 1972-73. Survivors were rescreened at ages of 68-77 years, and all-cause mortality was followed from 2000 to 2011. METHODS we calculated Cox regression proportional hazards for 11-year mortality rates in relation to BMI change among 5,240 men with no reported disease in 1972-73 and complete data. Models were adjusted for demographics, medications and disease. Men with BMI < 25 kg/m(2) in midlife (1972-73) and in 2000 were the reference group. RESULTS men whose BMI changed from <25 kg/m(2) in midlife to 25-29.9 kg/m(2) in 2000 carried the lowest mortality risk (hazard ratio [HR] 0.84; 95% confidence interval [CI] 0.75-0.94). Men with BMI ≥ 30 kg/m(2) in midlife were at highest risk (HR 1.79; 95% CI 1.12-2.88 if reclassified to 25-29.9 kg/m(2) in 2000 and HR 1.39; 95% CI 1.05-1.85 if BMI remained ≥30 kg/m(2) in 2000). Men with BMI 25-29.9 kg/m(2) in midlife that reclassified to <25 kg/m(2) in 2000 had increased risk. Findings were similar when percentage change in BMI was the outcome. CONCLUSION survival in older men with normal weight at midlife was associated with BMI gain after midlife while midlife obesity increased risk regardless of subsequent change.
Securing the Anterior Chamber in Penetrating Keratoplasty: An Innovative Surgical Technique

Purpose: Conventional penetrating keratoplasty (PK) is an open-sky procedure, carrying a worrisome risk of expulsive suprachoroidal hemorrhage and vitreous prolapse in high-risk cases. The authors propose an innovative surgical technique that secures the intraoperative anterior chamber and should reduce the risk of vitreous complications. Methods: In the new stabilized procedure, a deep anterior corneal lamella is excised. A small puncture is made in each quadrant along the groove of the stromal bed, and the anterior chamber is maintained by viscoelastic injection. The viscoelastic-coated graft is sutured near the 4 puncture sites. After sequential cutting of the stromal bed and suturing of the graft, the residual stromal bed is excised and drawn out before the last suture is placed. Fifteen PK patients have undergone this procedure without complications. Results: Satisfactory vision recovery was achieved in all 15 of the stabilized PK eyes, and the mean postoperative endothelial cell loss was comparable to studies performed for open PK. Conclusions: The authors believe that the reduced risks and limited endothelial cell loss verify the significance and practicability of the stabilized PK. This innovative new technique adds security for keratoplasty candidates who are at high risk for vitreous prolapse or suprachoroidal hemorrhage.
A cough conundrum in a patient with a previous history of BCG immunotherapy for bladder cancer

We describe a non-smoker who presented with a persistent cough, weight loss and general malaise, and had a medical history of bladder carcinoma that had been successfully treated with intravesical BCG immunotherapy. Radiology revealed hilar lymphadenopathy, a predominantly mid-zone and lower-zone lung parenchymal nodular pattern with a perilymphatic distribution, a few thickened interlobular septae, and small pleural effusions bilaterally. The T-SPOT.TB blood test was negative. Video-assisted thoracoscopic surgery showed multiple pleural nodules, the histopathology of which showed multiple well-defined non-caseating granulomata. The patient was started on antituberculosis medication for presumed BCGosis—a systemic complication of previous BCG immunotherapy—and the patient showed an excellent clinical and radiological response. This case further adds to previous reports and reinforces the recommendation that all patients should be made fully aware of the potential systemic and delayed complications of BCG immunotherapy when they are consented for treatment.
Energy flow vector of the electromagnetic field

Poynting's choice for the energy flow vector of the electromagnetic field has certain unattractive physical features. In order to eliminate such features Hines proposed an alternative choice. Here we show that Hines's choice does not lead to Larmor's result for the rate of radiation by an accelerated non-relativistic charge.
Conspicuous Consumption, Human Capital, and Poverty

Poor families around the world spend a large fraction of their income on consumption of goods that appear to be useless in alleviating poverty, while saving at very low rates and neglecting investment in health and education. Such consumption patterns seem to be related to the persistence of poverty. We offer an explanation for this observation, based on a trade-off between conspicuous consumption and human capital as signals for unobserved income, under the assumption that individuals care about their status. Despite homothetic preferences, this trade-off gives rise to a convex saving function, which can help explain the persistence of poverty.
Tumor suppressor dual‐specificity phosphatase 6 (DUSP6) impairs cell invasion and epithelial‐mesenchymal transition (EMT)‐associated phenotype

Suppressive effects of DUSP6 in tumorigenesis and EMT‐associated properties were observed. Dual‐specificity phosphatase (DUSP6) is a MAP kinase phosphatase (MKP) negatively regulating the activity of ERK, one of the major molecular switches in the MAPK signaling cascade propagating the signaling responses during malignancies. The impact of DUSP6 in EMT and its contribution to tumor dissemination has not yet been characterized. Due to differences in tumor microenvironments affecting cell signaling during cancer progression, DUSP6 may play varying roles in tumor development. We sought to examine the potential role of DUSP6‐mediated tumorigenesis and EMT‐associated properties in two aerodigestive tract cancers, namely, esophageal squamous cell carcinoma (ESCC) and nasopharyngeal carcinoma (NPC). Significant loss of DUSP6 was observed in 100% of 11 ESCC cell lines and 71% of seven NPC cell lines. DUSP6 expression was down‐regulated in 40% of 30 ESCC tumor tissues and 75% of 20 NPC tumor tissues compared to their respective normal counterparts. Suppressive effects of DUSP6 in tumor formation and cancer cell mobility are seen in in vivo tumorigenicity assay and in vitro colony formation, three‐dimensional Matrigel culture, cell migration and invasion chamber tests. Notably, overexpression of DUSP6 impairs EMT‐associated properties. Furthermore, tissue microarray analysis reveals a clinical association of DUSP6 expression with better patient survival. Taken together, our study provides a novel insight into understanding the functional impact of DUSP6 in tumorigenesis and metastasis of ESCC and NPC.
Determination of chemical composition and genotoxic effects of essential oil obtained from Nepeta nuda on Zea mays seedlings

We aimed to determine the genotoxic potential of essential oil (EO) obtained from Nepeta nuda. The chemical content of EO was measured via gas chromatography/mass spectrometry. The most abundant contents were 4aα,7β,7aα-nepetalactone (18.10%), germacrene (15.68%) and elemol (14.38%). For genotoxic effects of EO, Zea mays’ seeds were exposed to four different concentrations of this oil. Inhibition of root and stem growth were observed with an increase in EO concentrations. Randomly amplified polymorphic DNA (RAPD) method was used to determine the genotoxic effects of EO. Some changes occurred in RAPD profiles of germinated EO-treated seeds. Even though total soluble protein quantity vary, the data observed from the protein profiles of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that there was a little differentiation between band profiles of treated samples and control group. We concluded that the basis of interactions between plants, like allelopathy, may be related with genotoxic effects of EO.
Dynamic slicing of distributed object-oriented programs

Program slicing is a decomposition technique that deals with extracting those statements relevant to a particular computation. The authors propose a novel algorithm for computing dynamic slice of distributed object-oriented programs. The proposed algorithm incorporates graph colouring strategy to compute slice. But to achieve the goal efficiently, the authors have contradicted some key constraints of the traditional graph colouring technique. The state restriction of the slicing criterion is also considered along with dependence analysis while computing slice. The advantage of the proposed algorithm is that it is efficient and faster than the existing algorithms.
Effect of acute ovariectomy on mating in the cyclic rat.

drops from a maximum at pro-oestrus to a minimum on the morning of oestrus (Schwartz & Bartosik, 1962; Schwartz, 1964), by which time ovulation and vaginal cornification have occurred. A great deal of evidence suggests that these changes are due to a cyclic increase in ovarian secretion (see Schwartz, 1964). In a recent investigation of the timing of this ovarian secretion it was demonstrated that ovariectomy at 16.00 hours on the day before pro-oestrus, but not at 10.00 hours on the morning of pro-oestrus, blocked vaginal cornification; however, it was necessary to perform the ovariectomy at 10.00 hours on the day before pro-oestrus in order to block the uterine weight change and the lh discharge (Schwartz, 1964). The present study investigated the time at which ovariectomy would block the mating response. Virgin female rats, running 4or 5-day cycles and kept under previously described conditions (Schwartz & Bartosik, 1962; Schwartz, 1964), were ovariectomized or sham-ovariectomized between 10.00 and 11.00 hours on the morning of pro-oestrus, or between 16.00 and 17\m=. \00hours the previous afternoon (the last day of di-oestrus). Each female was paired with a male after 16.00 hours on the afternoon ofpro-oestrus. The followingmorning (oestrus) the bottom of the cage was inspected for vaginal plugs, and the vaginal smear was examined for cornified cells and sperm. All but four of the sham-operated rats were laparotomized on this day in order to check for uterine swelling; all shams were then followed at least for 8 days and inspected for implantation sites, or were permitted to go to term. The ovariectomized rats were followed for at least 7 days to make sure that vaginal cornification did not recur and then were autopsied; uterine weight was measured as an additional criterion of completeness of ovariectomy. The data are presented in Table 1. Of the sham controls, fewer than 100% showed vaginal cornification at oestrus, in contrast to unmated sham-operated or untreated controls (Schwartz & Bartosik, 1962; Schwartz, 1964). Since all five of the non-cornified sham controls became pregnant and/or had ovulated at oestrus, it is apparent that they were in the proper stage of the cycle. Of the two sham-operated rats in
Prescribed Performance Fault-Tolerant Control of Uncertain Nonlinear Systems With Unknown Control Directions

A low-complexity state feedback fault-tolerant control scheme guaranteeing prescribed tracking performance is proposed for a family of uncertain nonlinear systems with unknown control directions. Contrary to the current state-of-the-art, novel error transformation functions and new update laws related to performance functions are introduced to the control design such that no compensators or approximation structures are needed, in spite of actuation faults, component faults, and unknown nonlinearities. The proposed method is verified via a simulation on an inverted pendulum.
ONYX-015 , an E 1 B Gene-Defective Adenovirus , Induces Cell Death in Human Anaplastic Thyroid Carcinoma Cell Lines

Being one of the most lethal human neoplasms and refractory to such conventional treatment as chemoand radiotherapy, anaplastic thyroid carcinoma is a prime target for innovative therapy. p53 gene inactivation is a constant feature of this neoplasia. Therefore, we evaluated a therapeutic approach based on an E1B 55-kDa gene-defective adenovirus (ONYX015) that replicates only in cells with impaired p53 function and leads to cell death. Here we report that the ONYX-015 virus induces cell death in three human thyroid anaplastic carcinoma cell lines (ARO, FRO, and KAT-4). In addition, we found that the growth of xenograft tumors induced in athymic mice by the injection of ARO cells was drastically reduced by ONYX-015 treatment. The ONYX-015 virus worked synergistically with two antineoplastic drugs (doxorubicin and paclitaxel) in inducing ARO and KAT-4 cell death. These results suggest that ONYX-015 may be a valid tool in the treatment of the human thyroid anaplastic carcinoma. (J Clin Endocrinol Metab 87: 2525–2531, 2002)