Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis and transformation of legacy code

Hardware evolves faster than software. While a hardware system might need replacement every one to five years, the average lifespan of a software system is a decade, with some instances living up to several decades. Inevitably, code outlives the platform it was developed for and may become legacy: development of the software stops, but maintenance has to continue to keep up with the evolving ecosystem. No new features are added, but the software is still used to fulfil its original purpose. Even in the cases where it is still functional (which discourages its replacement), legacy code is inefficient, costly to maintain, and a risk to security. This thesis proposes methods to leverage the expertise put in the development of legacy code and to extend its useful lifespan, rather than to throw it away. A novel methodology is proposed, for automatically exploiting platform specific optimisations when retargeting a program to another platform. The key idea is to leverage the optimisation information embedded in vector processing intrinsic functions. The performance of the resulting code is shown to be close to the performance of manually retargeted programs, however with the human labour removed. Building on top of that, the question of discovering optimisation information when there are no hints in the form of intrinsics or annotations is investigated. This thesis postulates that such information can potentially be extracted from profiling the data flow during executions of the program. A context-aware data dependence profiling system is described, detailing previously overlooked aspects in related research. The system is shown to be essential in surpassing the information that can be inferred statically, in particular about loop iterators. Loop iterators are the controlling part of a loop. This thesis describes and evaluates a system for extracting the loop iterators in a program. It is found to significantly outperform previously known techniques and further increases the amount of information about the structure of a program that is available to a compiler. Combining this system with data dependence profiling improves its results even more. Loop iterator recognition enables other code modernising techniques, like source code rejuvenation and commutativity analysis. The former increases the use of idiomatic code and as a result increases the maintainability of the program. The latter can potentially drive parallelisation and thus dramatically improve runtime performance.
Diaphorina citri Kuway., a vector of the greening disease of Citrus in India.

McClean and Oberholzer (1965a) described the greening disease of citrus from South Africa and produced evidence to show that it is caused by a transmissible virus. A similar disease affecting sweet-orange (mosambi) was observed by the senior author in Andhra Pradesh in 1960 and was transmitted by grafting to greenhouse raised healthy seedlings of sweet-orange [Citrus sinensis (L.) Osbeck], Rangpur lime (limao cravo; C. limonia Osbeck), Indian acid-lime [kagzi nimbu; C. aurantifolia (Christm.) Swingle], and grapefruit (C. paradisi Maef.) cultivar ' Marsh Seedless' at Poona (Capoor, 1966). The identity of the disease and its similarity to the greening disease of South Africa was confirmed in 1966 (Fraser and Singh, 1966; Fraser et al., 1966). Schneider (1966) observed a necrosis of sieve tubes in leaves and in fruits of sweet-orange affected by the greening virus. Large amounts of phloem formed in the leaf veins as a result of the necrosis and caused the veins to be enlarged. The studies reported in the present paper deal with the transmISSIOn of the greening virus by the adults of Diaphorina citri Kuway. , the species of psyllid commonly found on citrus in the country. The insect transmission tests were conducted during June-November 1966, when the population of citrus psylla is usually high on citrus trees in the central and southern India. Diaphorina citri is yet another species of psyllid responsible for the spread of the greening virus (Capoor et al., 1966), since the South African greening virus is spread by a psylla, Trioza (Spanioza) erytreae del Guercio (McClean and Oberholzer, 1965b).
Avaliação econômica do glaucoma primário de ângulo aberto

Objective: To evaluate the cost-utility relation of the initial treatment with laser or primary open-angle glaucoma medications (PLA) in Brazil, considering on the one hand the total costs and on the other side the impact on patients’ quality of life. Methods: The study was performed based on a Markov model, where a theoretical cohort of early-stage GPAA carriers was generated. The parameters used in the model were obtained in the literature and included: direct medical costs (consultations, examinations, treatment); direct non-medical costs (accommodation, transportation, meals, companions); indirect costs (related to incapacity for work); utility values (quality of life measured in QALY - quality-adjusted life year); and probability of transition between stages of health. Three treatment strategies were tested in the model: (1) without treatment; (2) initial treatment with eye drops; (3) initial treatment with laser trabeculoplasty. The measure of outcome was the incremental cost-utility ratio (RCUI). The robustness of the model was tested through sensitivity analysis. Results: The strategies (2) and (3) of the initial treatment of POAG generated gains in quality of life in relation to (1) in Brazil. Initiating the laser treatment generated an average gain of 1 QALY, whereas with medication it gave a gain of 2 QALYs on average. Among the three strategies tested, strategy (2) was cost-effective and was dominant over the other strategies, since it was at the same time the cheapest and the most effective strategy. Conclusion: Both laser trabeculoplasty and medications as primary treatments of early-stage POAG have generated significant gains in quality of life. The strategy of starting treatment with medications was cost-effective, whereas laser trabeculoplasty strategy was not cost-effective, when non-medical costs (direct and indirect) are included.
A Computational Model for Child Inferences of Word Meanings via Syntactic Categories for Different Ages and Languages

Children exploit their morphosyntactic knowledge in order to infer the meanings of words. A recent behavioral study has reported developmental changes in word learning from three to five years of age, with respect to a child’s native language. To understand the computational basis of this phenomenon, we propose a model based on a hidden Markov model (HMM). The HMM acquires syntactic categories of given words as its hidden states, which are associated with observed features. Then, the model infers the syntactic category of a new word, which facilitates the selection of an appropriate visual feature. We hypothesize that using this model with different numbers of categories can replicate the manner in which children of different ages learn words. We perform simulation experiments in three native language environments (English, Japanese, and Chinese), which demonstrate that the model produces similar performances as the children in each environment. Allowing a larger number of categories means that the model can acquire a sufficient number of obvious categories, which results in the successful inference of visual features for novel words. In addition, cross-linguistic differences originating from the acquisition of language-specific syntactic categories are identified, i.e., the syntactic categories learned from English and Chinese corpora are relatively reliant on word orders, whereas the Japanese-trained model exploits morphological cues to infer the syntactic categories.
Antibiotics for COPD exacerbations: does drug or duration matter? A primary care database analysis

Introduction Antibiotics are routinely given to people with chronic obstructive pulmonary disease (COPD) presenting with lower respiratory tract infection (LRTI) symptoms in primary care. Population prescribing habits and their consequences have not been well-described. Methods We conducted a retrospective analysis of antibiotic prescriptions for non-pneumonic exacerbations of COPD from 2010 to 2015 using the UK primary care Optimum Patient Care Research Database. As a proxy of initial treatment failure, second antibiotic prescriptions for LRTI or all indications within 14 days were the primary and secondary outcomes, respectively. We derived a model for repeat courses using univariable and multivariable logistic regression analysis. Results A total of 8.4% of the 9042 incident events received further antibiotics for LRTI, 15.5% further courses for any indication. Amoxicillin and doxycycline were the most common index and second-line drugs, respectively (58.7% and 28.7%), mostly given for 7 days. Index drugs other than amoxicillin, cardiovascular disease, pneumococcal vaccination and more primary care consultations were statistically significantly associated with repeat prescriptions for LRTI (p<0.05). The ORs and 95% CIs were: OR 1.28, 95% CI 1.10 to 1.49; OR 1.37, 95% CI 1.13 to 1.66; OR 1.33, 95% CI 1.14 to 1.55 and OR 1.05, 95% CI 1.02 to 1.07, respectively. Index duration, inhaled steroid use and exacerbation frequency were not statistically significant. The derived model had an area under the curve of 0.61, 95% CI 0.59 to 0.63. Discussion The prescription of multiple antibiotic courses for COPD exacerbations was relatively common—one in twelve patients receiving antibiotics for LRTI had a further course within 2 weeks. The findings support the current preference for amoxicillin as index drug within the limitations of this observational study. Further clinical trials to determine best practice in this common clinical situation appear required.
The Prevalence of Overweight and Obesity and Its Association Factors among MalaysÃ¢Â€Â™ Adolescents: Findings from Seafood Consumption Survey in Peninsular Malaysia

Introduction: Overweight and obesity in Malaysia has been increasing for the past decades. The present study is to determine the prevalence of overweight and obesity among Malay adolescents involved in the “Seafood consumption survey in Peninsular Malaysia, 2008-2009”. The relationship between obesity, socio-demographic and family-related characteristics were investigated. It also compared food patterns that are commonly consumed between obese and nonobese adolescents. Methods: A population-based cross-sectional study was carried out to determine the prevalence of overweight and obesity among Malay school children aged 10-17 years in Peninsular Malaysia and to determine its’ association with some demographic factors and food intake. A stratified two-stage cluster sampling design with proportional allocation was used. Data were collected through faceto-face interviews using pre-design validated questionnaires between February 2008 and May 2009. Weight and height were measured by the interviewers using SECA weighing machine and food intake was estimated with a 3-day dietary diary forms. The adolescent was classified as normal, overweight and obese in accordance with the age and gender-specific body mass index WHO reference 2007 for children 5-19 years old. Statistical analysis was carried out using SPSS version 16. Results: The prevalence of overweight and obesity among subjects (n=484) was 12.4% and 11.6%, respectively. Male students were prone to obesity (14.5%) compared to females (9%). The results in the bivariate analysis showed that having an obese mother (OR=1.92; CI: 1.018-3.622; p=0.044), obese father (OR=2.69; CI: 1.055-6.883; p=0.038), and either one of the parents is obese, were significantly associated with obesity among adolescents (OR=2.178; CI: 1.184-4.004; p=0.012). Having obesity in another family member also increases the risk to 3.77 times for the adolescent to be obese (OR=3.768; CI: 1.703-8.336; p=0.001). Following the adjusted analysis using Multiple Logistic Regression (MLR), adolescents having an obese father (OR=5.599; CI: 1.086-28.884; p=0.04) and staying in the north region (OR=2.056; CI: 1.024-4.127; p=0.043) remained significant risk factors for adolescent obesity. Higher socioeconomic status with a household income of more than RM 3,000 increases the odds by two times (OR=2.240; CI: 1.0054.994; p=0.049), of having an obese adolescent in the house. Obese adolescent consumed significantly (p=0.041) more food (1149 g) compared to non-obese (1036 g) and their consumption were higher during daytime (p=0.053; 1242 g), specifically during lunch (p=0.011; 791 g) and breakfast (p=0.061; 458 g). The most frequent food consumed by the obese adolescent was seafood, vegetables and fruits and they preferred flavoured/malt drinks with sugar and milk. Conclusions: In this study, obese adolescents showed a strong association with household income, a region of residence and obesity in other family members and they consumed more food during the day-time.
Prevalence and distribution of cardiovascular diseases between Tamil Nadu, India and the United States- A comparative study

The burden of cardiovascular diseases (CVD) is increasing all over the world, thus becoming the prime cause of mortality. India is becoming a major part in the global burden of CVD with a 34% rise in prevalence in recent years while the United States (US) has seen a comparative decline of 41% in CVD cases. As India is progressing in westernization towards the US in terms of lifestyle and food habits, comparing the prevalence of CVD helps in assessing the disease progression in future years. Objective: This study systematically reviews the pattern of the prevalence and distribution of cardiovascular diseases in Tamil Nadu, aiming to compare India with United States. Materials and methods: The prevalence and disability-adjusted life years(DALYs) of CVD particularly Ischaemic heart disease, coronary heart disease and stroke burden data were reviewed from different sources including global burden of diseases report 2017, Centre for chronic disease control, Indian Council of Medical Research, American Heart Association, PubMed- Cardiovascular diseases in India and other relevant literatures. The reviewed data were used to compare the prevalence of CVD in Tamil Nadu, India and US. Results: Overall cardiovascular diseases in India has doubled from 1990 to 2016 in comparison to US, contributing 52% death, due to CVD. Crude prevalence of CVD in India has increased from 5%-13% between the age of 20-70yrs. US has seen a marginal decline in prevalence with 23% death, though difference in population size is considered. Globally, India contributes above the average standardised CVD death rate. Further, studies suggest that if this rate continues, the rise in death due to CVD could reach 101 million in India by 2030. Conclusion: The results of this comparative study indicates that prevalence of CVD is increasing rapidly across India including Tamil Nadu. US is showing a declining trend in CVD prevalence due to implementation of population level strategies.
The Effect of Childhood Trauma on Impulsivity in Patients with Bipolar Disorder

Objective: In this present study, we aimed to examine the association between impulsivity and childhood traumas in patients with bipolar disorder. Methods: Sixty-four bipolar disorder patients in remission and seventy volunteers were enrolled in this case-control study. Childhood Trauma Questionnaire (CTQ-28), and Barratt Impulsivity Scale (BIS-11) were administered to all participants. The data were analyzed by Mann-Whitney U, Student T-test, and the chi-square test using the SPSS program. Results: A significant difference was not found between the groups regarding age, gender, and marital status. There was statistically significant positive correlations between total BIS score and scores of CTQ total (r=0.345, p<0.001), physical neglect (r=0.223, p=0.012), emotional abuse (r=0.370, p<0.001), and emotional neglect (r=0.227, p=0.010). There was a statistically significant difference in total BIS-11 (p=0.001), motor impulsiveness (p=0.028), CTQ emotional neglect (p=0.009), and total CTQ (p=0.038) scores in the bipolar disorder group compared to the control group. Conclusions: It can be said that impulsivity is associated with childhood traumas in bipolar disorder. Also, bipolar disorder patients have impulsive features, even in remission periods.
Behavioural abnormalities and novel pharmaceutical intervention in acute and developmental rat models of psychiatric illness

ii ACKNOWLEDGEMENTS . iv DEDICATION . v TABLE OF CONTENTS . vi LIST OF TABLES . xi LIST OF FIGURES . xii LIST OF ABBREVIATIONS . xiv CHAPTER 1: INTRODUCTION . 1 1.1 OUTLINE OF THE THESIS . 1 1.2 RELEVANT PHARMACOLOGY . 2 1.2.1 The dopamine hypothesis . 2 1.2. 2 The glutamate hypothesis . 3 1.2. 2.1 MK-801 and other NMDA receptor antagonists . 5 1.2. 3 Management of psychiatric illness . 8 1.2. 3.1 Conventional antipsychotics . 8 1.2. 3.2 Govadine . 9 1.3 INFLAMMATION IN PREGNANCY AND OFFSPRING PSYCHIATRIC OUTCOMES . 10 1.3.1 Early epidemiological evidence . 10 1.3.2 Clinical prospective birth cohort studies . 11 1.3. 3 The cytokine hypothesis . 12 1.4 ANIMAL MODELS . 14 1.4. 1 Modelling psychiatric illness . 14
An atypical presentation of frontotemporal dementia.

Frontotemporal dementia (FTD) is a group of neurodegenerative conditions affecting the frontal and temporal lobes (1). FTD is the fourth overall most prevalent dementia subtype accounting for <5% of cases, rising to approximately 10% in the ‘early onset’ (under 65) cohort (2).
Cerebral Venous Thrombosis and Acute Pulmonary Embolism following Varicella Infection

Varicella infection is caused by varicella-zoster virus (VZV) and commonly presents as a self-limiting skin manifestation in children. VZV also causes cerebral arterial vasculopathy and antibody-mediated hypercoagulable states leading to thrombotic complications in children, although there are very few such reports in adults. Postulated causal factors include vasculitis, direct endothelial damage, or acquired protein S deficiency secondary to molecular mimicry. These induced autoantibodies to protein S could lead to acquired protein S deficiency and produce a hypercoagulable state causing venous sinus thrombosis. Here we report the case of a 26-year-old man who presented with cortical venous sinus thrombosis and acute pulmonary embolism following varicella infection. Both conditions responded to anticoagulation treatment. LEARNING POINTS Varicella infection caused by varicella-zoster virus (VZV) can rarely present with thrombotic complications after a period of latency. Postulated causal factors include vasculitis, direct endothelial damage, and acquired protein S deficiency secondary to molecular mimicry. The prognosis of post-varicella thrombosis is good, but a prothrombotic screen after recovery to diagnose hereditary prothrombotic states is advisable.
Complete Clinical Response in Locally Advanced Metastatic de novo Breast Cancer after Front-Line Treatment with Ribociclib/Letrozole within the RIBANNA Study.

Introduction Ribociclib is an orally bioavailable cyclin-dependent kinase 4/6 inhibitor. In combination with aromatase inhibitor letrozole, it has approval for treatment of hormone receptor positive (HR+) and human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer. First-line therapy with ribociclib + letrozole significantly improves progression-free survival compared to placebo + letrozole in patients with HR+/HER2- advanced breast cancer. In patients with de novo advanced or metastatic breast cancer, ribociclib was able to provide substantial clinical benefit according to data from the MONALEESA-2 study. Case Presentation Here, we report the complete clinical response in a postmenopausal patient with de novo, locally advanced, pulmonary metastatic breast cancer treated with ribociclib + letrozole. Our patient presented an ulcerated breast-consuming tumor with multiple pulmonary metastases. HR+/HER2- breast cancer was confirmed by tumor biopsy. Ki67 expression was 90%. After three months of initial treatment, the tumor-associated ulcerations disappeared, and no measurable pulmonary disease was detectable on CT scan. Treatment was well tolerated, and after dosage reduction due to neutropenia, no further side effects have been documented. At present, complete clinical response remains after 15 months of ongoing treatment. Conclusion This case report documents an exceptional tumor response of a fast growing, locally advanced, pulmonary metastatic HR+/HER2- de novo breast cancer treated by ribociclib/letrozole combination therapy. Treatment success was long lasting with few side effects. The patient was very satisfied with the treatment and had no specific restrictions in her daily life.
Incidental Renal Disorders Found at Necropsies of Violent Death Victims

Background: The burden of CKD in our environment remains high while biopsy uptake is low, making for high level of uncertainty in the morphologic characterization of renal disorders. Aim: To evaluate kidney necropsy tissues of violent death victims, asymptomatic of renal disorders, with a view to detecting lesions of clinical interest and determining the morphologic features of such lesions. Also to review the literature for silent conditions that advances the course of CKD. Materials and Methods: Prospective cohort study carried out on kidney necropsy tissues of violent death victims who in their antemortem states were asymptomatic of renal disorders. Subjects were firearm and road traffic accident victims irrespective of gender and age brought to UPTH morgue in January 2017, whose close relatives consented. Information confirming that decedents were asymptomatic of a renal disorder was obtained from deceased’s close relatives. Necropsy tissues were processed using standard operating procedures for histopathology of renal biopsies, and slides were read by the authors using light microscopy only. Results: Forty-three tissues were collected-41 males and 2 females. Mean and peak ages were 29.3 (4.9) and 21-30 years with 25/43 (58.1%). Twenty cases (46.5%) showed glomerular pathologies composed of 18.6% FSGS and 27.9% MPGN. Twenty three cases (53.5%) were devoid of histologic evidence of glomerular injury. All cases showed evidence of variable degrees of acute tubular injury with ten cases (23.3%) showing PAS positive casts. Four cases (two each from FSGS and MPGN) displayed chronic interstitial nephritis with mild fibrosis. There was thickening of the arteriolar tunica media in 12 bodies (27.9%). Conclusion: Prevalence of asymptomatic CKD is very high among the youths of our locality. Glomerular lesions constitute common pathogenetic bases unlike tubulointerstitial and vascular lesions which were uncommon. Enunciating measures that targeted the youths aimed at reducing rate of smoking and abuse of common analgesics like paracetamol as well as measures that will improve the overall socioeconomic status and encourage routine medical examinations may reverse the upward trend of asymptomatic CKD among our youths.
Autoantikörperdiagnostik bei rheumatischen Erkrankungen

ZUSAMMENFASSUNG Die Labordiagnostik in der Rheumatologie ist neben den Routinelaboruntersuchungen mit Bestimmung der Entzündungsparameter, sowie hämatologischen und klinisch-chemischen Untersuchungen insbesondere durch den Nachweis spezifischer Autoantikörper definiert. Hierfür steht eine Vielzahl an Antikörpertests zur Verfügung: Für die rheumatoide Arthritis ergänzen Antikörper gegen cyclische citrullinierte Peptide zusätzlich zum Rheumafaktor die Diagnostik; der Nachweis von Antinukleäre Antikörpern (ANA) und die darauffolgenden antigenspezifischen Immunoassays werden für Kollagenosen, die Bestimmung der Anti-Neutrophile Cytoplasmatischen Antikörper (ANCA) zur Sub-Spezifizierung von Kleingefäßvaskulitiden genutzt. Im vorliegenden Beitrag soll eine Übersicht über die Antikörperdiagnostik in der Rheumatologie gegeben werden.