Miracle-dz/UniFAR-FTUs huggingface dataset:
Early field experience with the Software Reconnaissance technique for program comprehension

Paper reprinted from ICSM '96. Software Reconnaissance is a dynamic analysis technique to help programmers locate code that they need to understand, fix, or enhance in an unfamiliar system. The technique was originally motivated by comments by industrial maintainers about the need for better ways of locating software features in large systems. It was then prototyped in a university setting and an initial tool called RECON was developed. This paper describes four case studies applying Reconnaissance to three different industrial programs of moderate site. Reconnaissance seems to be effective in finding "places to start looking" for maintainers of unfamiliar code. It can also be used to recover a traceability relation between program features and program code that may help identify design patterns. The case studies are the initial phase of an ongoing technology transfer project of the Software Engineering Research Center, to make Software Reconnaissance into a usable industrial technique.
Development of an ASAS-endorsed disease activity score (ASDAS) in patients with ankylosing spondylitis

Objectives: To develop a new index for disease activity in ankylosing spondylitis (ASDAS) that is truthful, discriminative and feasible, and includes domains/items that are considered relevant by patients and doctors. Methods: Eleven candidate variables covering six domains of disease activity, selected by ASAS experts in a Delphi exercise, were tested in a three-step approach, similar to the methodology used for the disease activity score in rheumatoid arthritis. Data on 708 patients included in ISSAS (International Study on Starting tumour necrosis factor blocking agents in Ankylosing Spondylitis) were used. Cross validation was carried out in the OASIS cohort (Outcome in Ankylosing Spondylitis International Study). Results: Principal component analysis disclosed three factors with eigenvalues >0.75: patient assessments, peripheral joint assessments and acute phase reactants. Discriminant function analysis resulted in a correct classification in ∼72% of the cases (prior probability ∼50%). Regression analysis resulted in an index with five variables (total back pain, patient global assessment, duration of morning stiffness, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR)). Three additional candidate indices were designed using similar methodology while omitting either ESR or CRP or patient global assessment. All four scores correlated with the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI; r = 0.67–0.80), patient (0.58–0.75) and physician’s global assessment (0.41–0.48) of disease activity. All four candidate ASDAS indices performed better than BASDAI or single-item variables in discriminating between high and low disease activity state, according to doctors as well as patients in the OASIS cohort. Conclusion: The first steps in the development of a new assessment tool of disease activity in AS derived four candidate indices with good face and construct validity, and high discriminant capacity.
Wrapping legacy COBOL programs behind an XML-interface

This paper describes the tools and techniques for encapsulating host COBOL programs with an XML interface. The legacy programs are divided into three classes - online programs, batch programs and subprograms. For each program type, a different wrapping technique and a different tool is employed. Online programs are transformed into data-driven subprograms which process an XML document. Batch programs are adapted to read and write XML documents. Subprograms are left unchanged, but their parameters are set from an XML document. By using XML to implement corporate portals, it has proven possible to reuse existing host programs within new intranet/Internet systems, thus reducing system development costs and development time by more than 60%.
Verifying provisions for post-transaction user input error correction through static program analysis

Software testing is a time-consuming and error-prone process. Automated software verification is an important key to improve software testing. This paper presents a novel approach for the automated approximate verification of provisions of transactions for correcting effects that result from executing database transactions with wrong user inputs. The provision is essential in any database application. The approach verifies the provision through analyzing the source codes of transactions in a database application. It is based on some patterns that in all likelihood exist between the control flow graph of a transaction and the control flow graphs of transactions for correcting some post-transaction user input errors of the former transaction. We have validated the patterns statistically.
An Empirical Study of Refactoring in the Context of FanIn and FanOut Coupling

The aim of refactoring is to reduce software complexity and hence simplify the maintenance process. In this paper, we explore the impact of refactorings on "FanIn" and "FanOut" coupling metrics through extraction of refactoring data from multiple releases of five Java open-source systems, We first considered how a single refactoring modified these metric values, what happened when refactorings had been applied to a single class in unison and finally, what influence a set of refactorings had on the shape of Fan In and Fan Out distributions. Results indicated that, on average, refactored classes tended to have larger FanIn and Fan Out values when compared with non-refactored classes. Where evidence of multiple (different) refactorings applied to the same class was found, the net effect (in terms of FanIn and Fan Out coupling values) was negligible.
Stealthy Profiling and Debugging of Malware Trampolining from User to Kernel Space

A reverse engineer trying to understand protected malware binaries is faced with avoiding detection by antidebugging protections. Advanced protection systems may even load specialized drivers that can re-flash firmware and change the privileges of running applications, significantly increasing the penalty of detection. Hades is a Windows kernel driver designed to aid reverse engineering endeavors. It avoids detection by employing intelligent instrumentation via instruction rerouting in both user and kernel space. This technique allows a reverse engineer to easily debug and profile binaries without fear of invoking protection penalties.
High-resolution MRI for assessment of middle meningeal artery involvement in giant cell arteritis

Giant cell arteritis (GCA) typically involves the superficial cranial arteries, the aorta and its branches. It has been discussed to which extent the vasculitic changes of the cranial arteries continue into the intracranial region. Autopsy findings have indicated that the characteristic signs of arteritic inflammation of GCA end after crossing the dural border.1 In a recent review of several published cases it was concluded that intracranial/intradural involvement in GCA is rare and represents a small subset of GCA that is non-responsive to corticosteroids and has a fatal course.2 Contrast-enhanced, high-resolution MRI allows non-invasive assessment of mural inflammation in the extracranial, superficial arteries in giant cell arteritis.3 Here, we report MRI findings suggestive of intracranial vasculitic involvement in patients with GCA. High-resolution MRI of …
Menopause, postmenopausal hormone use and risk of incident gout

Objective To prospectively study the relation between menopause, postmenopausal hormone use and risk of gout, since female sex hormones have been postulated to decrease gout risk among women. Methods In the Nurses' Health Study, the association between menopause, age at menopause, postmenopausal hormone use and risk of self-reported physician-diagnosed incident gout among 92 535 women without gout at baseline was examined. Multivariate proportional hazards regression analysis was used to adjust for other risk factors for gout such as age, body mass index, diuretic use, hypertension, alcohol intake and dietary factors. Results During 16 years of follow-up (1 240 231 person-years), 1703 incident gout cases were recorded. The incidence rate of gout increased from 0.6 per 1000 person-years in women <45 years of age to 2.5 in women ≥75 years of age (p for trend <0.001). Compared with premenopausal women, postmenopausal women had a higher risk of incident gout (multivariate-adjusted relative risk (RR)=1.26; 95% confidence interval (CI) 1.03 to 1.55). Among women with a natural menopause, women with age at menopause <45 years had a RR of 1.62 (95% CI 1.12 to 2.33) of gout compared with women with age at menopause 50–54 years. Postmenopausal hormone users had a reduced risk of gout (RR=0.82; 95% CI 0.70 to 0.96). Conclusion These prospective findings indicate that menopause increases the risk of gout, whereas postmenopausal hormone therapy modestly reduces gout risk.
Statin use in rheumatoid arthritis in relation to actual cardiovascular risk: evidence for substantial undertreatment of lipid-associated cardiovascular risk?

Background Cardiovascular disease (CVD) is partially attributed to traditional cardiovascular risk factors, which can be identified and managed based on risk stratification algorithms (Framingham Risk Score, National Cholesterol Education Program, Systematic Cardiovascular Risk Evaluation and Reynolds Risk Score). We aimed to (a) identify the proportion of at risk patients with rheumatoid arthritis (RA) requiring statin therapy identified by conventional risk calculators, and (b) assess whether patients at risk were receiving statins. Methods Patients at high CVD risk (excluding patients with established CVD or diabetes) were identified from a cohort of 400 well characterised patients with RA, by applying risk calculators with or without a ×1.5 multiplier in specific patient subgroups. Actual statin use versus numbers eligible for statins was also calculated. Results The percentage of patients identified as being at risk ranged significantly depending on the method, from 1.6% (for 20% threshold global CVD risk) to 15.5% (for CVD and cerebrovascular morbidity and mortality) to 21.8% (for 10% global CVD risk) and 25.9% (for 5% CVD mortality), with the majority of them (58.1% to 94.8%) not receiving statins. The application of a 1.5 multiplier identified 17% to 78% more at risk patients. Conclusions Depending on the risk stratification method, 2% to 26% of patients with RA without CVD have sufficiently high risk to require statin therapy, yet most of them remain untreated. To address this issue, we would recommend annual systematic screening using the nationally applicable risk calculator, combined with regular audit of whether treatment targets have been achieved.
Intranasal administration of recombinant human cartilage glycoprotein-39 as a treatment for rheumatoid arthritis: a phase II, multicentre, double-blind, randomised, placebo-controlled, parallel-group, dose-finding trial

Background Autoantigen-specific immunotherapy by mucosal tolerance induction via the intranasal route is an attractive therapeutic option for the treatment of autoimmune diseases, including rheumatoid arthritis (RA). Human cartilage glycoprotein-39 (HC gp-39) has been identified as a potential key autoantigen in RA. Based on animal studies, intranasal administration of the autoantigen is hypothesised to induce immunological tolerance in patients with RA and to ameliorate disease activity. In a phase I/IIA clinical trial in patients with RA, intranasal application of HC gp-39 was safe and well tolerated. Objective To investigate the efficacy of intranasally administered fully human, recombinant HC gp-39 (Org 39141) by a large clinical study. Methods In a 13-week multicentre, double-blind, randomised, placebo-controlled, parallel-group, dose-finding, proof-of-concept trial, patients with RA (disease-modifying antirheumatic drug (DMARD) naive or after washout of DMARD treatment) were randomised to receive either intranasal applications of placebo or HC gp-39 in doses of 30, 150, 300 or 600 µg, once a week. The primary efficacy variable was the 28 joint count Disease Activity Score (DAS28). Results During the treatment period the DAS28 decreased similarly for all treatment groups—including placebo—indicating lack of efficacy of intranasal HC gp-39 treatment in the current setting. Safety variables were similar for all study groups. Conclusion It was concluded that with the treatment protocol used (dose levels and frequency of dosing), intranasal treatment with Org 39141 was safe but did not result in more clinical improvement than in placebo-treated patients.
Discovery and provision of content in mobile networks with infrastructure support

We consider content discovery and provision in wireless networks with infrastructure, where mobile nodes store, advertise and consume contents while Broker entities running on infrastructure devices let demand and offer meet. We refer to this paradigm as match-making, and study its performance in terms of query success probability, i.e., the probability that a content query is successful. To ensure high success probability, we design a credit-based scheme that entices rational users to provide their contents (thus discouraging free-riding behavior), and that guarantees them a fair treatment. Furthermore, through a feedback and banning mechanism, we effectively counter malicious users whose sole objective is to disrupt the system. The performance of our match-making scheme is shown through ns-3 simulations.
Mitochondrial DNA haplogroups modulate the serum levels of biomarkers in patients with osteoarthritis

Objective To analyse the influence of mitochondrial DNA (mtDNA) haplogroups on serum levels of molecular biomarkers in patients with osteoarthritis (OA). Methods Serum levels of molecular biomarkers of cartilage metabolism (collagen type II markers: C-terminal neoepitope generated by the collagenase-mediated cleavage of collagen type II triple helix (C2C), collagen type II (Coll2-1, and its nitrated form, Coll2-1NO2), procollagen type II (CPII)), synovial metabolism (hyaluronic acid (HA)) and cartilage and synovial turnover (cartilage glycoprotein 39 (YKL-40)) were analysed in 73 patients with OA and 77 healthy controls using ELISAs. All participants had been previously genotyped for the mtDNA haplogroups J, U and H. Non-parametric and multivariate analysis were performed to test the effects of the clinical variables, including gender, age, smoking status, diagnosis, mtDNA haplogroups and radiological Kellgren and Lawrence (K/L) grade on the serum levels of the molecular markers. Results Non-parametric analysis found increased serum levels of HA in patients with OA, while the values for C2C and the C2C/CPII ratio were significantly higher in the healthy controls. A multiple regression analysis showed a relationship between the mtDNA haplogroups and serum levels of the typical collagen type II markers. Carriers of the mtDNA haplogroup H had higher levels while carriers of the mtDNA haplogroup J showed lower levels. Statistically significant interactions between mtDNA haplogroups and diagnosis and between mtDNA haplogroups and radiological K/L grade in the serum levels of molecular markers were also found. Conclusion A new role for mtDNA haplogroups emerges from this work. The results suggest that the mtDNA haplogroups interact significantly with the serum levels of OA-related molecular markers, suggesting the possibility of their use as a complementary assay with these molecular markers.
Bridging psychophysics and cognitive engineering in visual perception

For the prospective design of human machine interfaces in an engineering process, core principles of human performance need to be formulated into a computational theory. This paper presents the results of experiments, demonstrating that even such a core task of visual perception as the detection of symmetry can be decomposed into single well defined information processing steps. To detect symmetry the visual system needs to compare lengths and distances. In classical signal detection theory this process is described on an abstract level as the comparison of two stimuli with different intensity. The proposed theory in this paper emphasizes the spatial nature of the task and describes it as a process of several attention shifts during which inter-object relations are represented as noisy values with a specific variance. By Bayesian inference the visual system is able to guide attention to locations matching a given inter-object relation encoded in a previous step. To test the theory we performed experiments measuring latencies in symmetry perception in an attention guided paradigm. The prediction of the theory and the results from the experiments are compared. The proposed theory facilitates the modeling of information processing in visual perception in a rule based framework, and therefore is suitable to analyze graphical displays in a cognitive engineering approach.
Serum HMGB1 levels are increased in active Wegener's granulomatosis and differentiate between active forms of ANCA-associated vasculitis

High mobility group box 1 (HMGB1) is a non-histone nuclear protein released during cell necrosis and late apoptosis. It contributes to the activation of monocytes/macrophages and induces the secretion of proinflammatory cytokines.1,–,4 HMGB1 serum concentrations are increased in conditions associated with severe tissue damage such as haemorrhagic shock.5 The hypothesis behind this study was that HMGB1 may be released from damaged tissue in antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and serum levels may correlate with disease activity. Furthermore, with respect to the known sources of HMGB1, high levels were expected in particular in Wegener's granulomatosis (WG) which is characterised by granulomatous inflammation. Serum samples were obtained from 46 patients with WG, 44 with …
IL-33 induces neutrophil migration in rheumatoid arthritis and is a target of anti-TNF therapy

Objectives Interleukin 33 (IL-33) is a new member of the IL-1 family of cytokines which signals via its receptor, ST2 (IL-33R), and has an important role in Th2 and mast cell responses. This study shows that IL-33 orchestrates neutrophil migration in arthritis. Methods and results Methylated bovine serum albumin (mBSA) challenge in the knee joint of mBSA-immunised mice induced local neutrophil migration accompanied by increased IL-33R and IL-33 mRNA expression. Cell migration was inhibited by systemic and local treatments with soluble (s)IL-33R, an IL-33 decoy receptor, and was not evident in IL-33R-deficient mice. IL-33 injection also induced IL-33R-dependent neutrophil migration. Antigen- and IL-33-induced neutrophil migration in the joint was dependent on CXCL1, CCL3, tumour necrosis factor α (TNFα) and IL-1β synthesis. Synovial tissue, macrophages and activated neutrophils expressed IL-33R. IL-33 induces neutrophil migration by activating macrophages to produce chemokines and cytokines and by directly acting on neutrophils. Importantly, neutrophils from patients with rheumatoid arthritis successfully treated with anti-TNFα antibody (infliximab) expressed significantly lower levels of IL-33R than patients treated with methotrexate alone. Only neutrophils from patients treated with methotrexate alone or from normal donors stimulated with TNFα responded to IL-33 in chemotaxis. Conclusions These results suggest that suppression of IL-33R expression in neutrophils, preventing IL-33-induced neutrophil migration, may be an important mechanism of anti-TNFα therapy of inflammation.
Lack of understanding in fibromyalgia and rheumatoid arthritis: the Illness Invalidation Inventory (3*I)

Background Patients with rheumatic diseases may face ‘discounting’ (denying and patronising) or ‘lack of understanding’ because of having symptoms without external clinical signs, but instruments to assess such invalidation experiences are lacking. Objectives To develop and evaluate the Illness Invalidation Inventory (3*I), to compare invalidation experiences of two groups of patients who differ in visual signs and laboratory findings—rheumatoid arthritis (RA) and fibromyalgia—and to examine the association of invalidation with health status. Methods A questionnaire (eight items with respect to five sources: spouse, family, medical professionals, work environment and social services) was constructed. It was completed by 142 patients with RA and 167 patients with fibromyalgia. Results Principal axis factoring with oblimin rotation yielded two factors with high internal consistency (α>0.70): ‘discounting’ (five items) and ‘lack of understanding’ (three items). Patients with fibromyalgia experienced significantly more discounting and lack of understanding from their family, medical professionals, colleagues and social services than did patients with RA. Both patient groups experienced more invalidation from social services, colleagues and family than from medical professionals and spouses. More discounting and lack of understanding correlated with poorer mental well-being and social functioning in both patient groups. Discounting correlated with more physical disability and pain in patients with RA. Conclusions The 3*I is a brief, reliable instrument for assessing patients' perceptions of invalidation from different sources, which differ between patient groups and are associated with health status. Future validation research should clarify the clinical impact of invalidation on treatment adherence and outcome.
The prevalence and 1-year outcome of cluster B personality disorders in primary care

Most of the literature on cluster B personality disorder has been derived from studies of psychiatric patients. In particular, little is known about the prevalence and outcome of these disorders in primary care. In this study 303 consecutive attenders to four general practices in south-east England were rated for the presence of a cluster B personality disorder using a standardized assessment. Detailed interviews were conducted with the subgroup of participants that were identified as having cluster B personality disorders. There were 13 of them, corresponding to a prevalence of 4% (95% CI: 2.3-7.2). The whole cohort was followed up at 1 year and the cluster B participants were more likely to be suffering from persistent symptoms of common mental disorder and to report having experienced a threatening life event. The detailed interviews revealed that the cluster B participants were a heterogeneous group of people with high levels of psychosocial problems. In this sample of primary care patients cluster B personality disorders were uncommon. The study highlights the high level of psychiatric morbidity and multiple psychosocial problems faced by people with cluster B personality disorders.
ASAS recommendations for collecting, analysing and reporting NSAID intake in clinical trials/epidemiological studies in axial spondyloarthritis

The amount of NSAID intake could be considered as a clinically relevant outcome measure in ankylosing spondylitis. The information should include at least the following: (1) the type of NSAID; (2) the dose; (3) the number of days taking NSAID during the period of interest. The objectives of this initiative were to propose both an NSAID equivalent score and a way of collecting and analysing this information in longitudinal clinical studies/trials. For the NSAID equivalent scoring system, the recommendations are (1) to refer to a scale in which 0 = no intake, 100 = 150 mg diclofenac, 1000 mg naproxen, 200 mg aceclofenac, 400 mg celecoxib, 600 mg etodolac, 90 mg etoricoxib, 200 mg flurbiprofen, 2400 mg ibuprofen, 150 mg indometacin, 200 mg ketoprofen, 15 mg meloxicam, 400 mg phenylbutazone, 20 mg piroxicam, 20 mg tenoxicam; (2) to present the results as mean daily intake by considering the number of days on which NSAID has been taken during a period of interest. This initiative should facilitate the conduct and analysis of clinical studies/trials.