TA-RE: An Exchange Language for Mining Software Repositories

Software repositories have been getting a lot of attention from researchers in recent years. In order to analyze software repositories, it is necessary to first extract raw data from the version control and problem tracking systems. This poses two challenges: (1) extraction requires a non-trivial effort, and (2) the results depend on the heuristics used during extraction. These challenges burden researchers that are new to the community and make it difficult to benchmark software repository mining since it is almost impossible to reproduce experiments done by another team. In this paper we present the TA-RE corpus. TA-RE collects extracted data from software repositories in order to build a collection of projects that will simplify extraction process. Additionally the collection can be used for benchmarking. As the first step we propose an exchange language capable of making sharing and reusing data as simple as possible.

Frequent atrial premature beats predict paroxysmal atrial fibrillation in stroke patients: an opportunity for a new diagnostic strategy

BACKGROUND AND PURPOSE: For patients having suffered ischemic stroke, the current diagnostic strategies often fail to detect atrial fibrillation as a potential cause of embolic events. The aim of the study was to identify paroxysmal atrial fibrillation in stroke patients. We hypothesized that patients with frequent atrial premature beats (APBs) recorded in 24-hour ECG will show more often atrial fibrillation when followed by repeated long-term ECG recordings than patients without or infrequent APBs. METHODS: 127 patients with acute ischemic stroke and without known AF were enrolled in a prospective study to detect paroxysmal AF. Patients were stratified according to the number of APBs recorded in a 24-hour ECG (> or =70 APBs versus <70 APBs). Subsequently, they all underwent serial 7-day event-recorder monitoring at 0, 3, and 6 months. RESULTS: Serial extended ECG monitoring identified AF in 26% of patients with frequent APBs but only in 6.5% when APBs were infrequent (P=0.0021). A multivariate analysis showed that the presence of frequent APBs in the initial 24-hour ECG was the only independent predictor of paroxysmal AF during follow-up (odds ratio 6.6, 95% confidence intervals 1.6 to 28.2, P=0.01). CONCLUSIONS: In patients with acute ischemic stroke, frequent APBs (> or = 70/24 hours) are a marker for individuals who are at greater risk to develop or have paroxysmal AF. For such patients, we propose a diagnostic workup with repeated prolonged ECG monitoring to diagnose paroxysmal AF.

Somatic CEBPA mutations are a frequent second event in families with germline CEBPA mutations and familial acute myeloid leukemia

PURPOSE: The transcription factor CCAAT/enhancer binding protein-alpha (CEBPA) is crucial for normal myeloid differentiation. Mutations in the CEBPA gene are found in subsets of patients with acute myeloid leukemia (AML). Recently, three families were reported in whom several family members had germline CEBPA mutations and subsequently developed AML. Whereas familial AML is considered a rare event, the frequency of CEBPA germline mutations in AML is not known. PATIENTS AND METHODS: In this study, we screened 187 consecutive AML patients for CEBPA mutations at diagnosis. We detected 18 patients (9.6%) with CEBPA mutations. We then analyzed remission samples and constitutive DNA from these patients. RESULTS: We found that two (11.1%) of 18 AML patients with CEBPA mutations carried a germline N-terminal frameshift CEBPA mutation. Interestingly, additional members in the families of both of these patients have been affected by AML, and the germline CEBPA mutations were also observed in these patients. Additional somatic mutations in AML patients with germline CEBPA mutations in the two families comprised in-frame C-terminal CEBPA mutations in two patients, two nonsilent CEBPA point mutations in one patient, and monosomy 7 in one patient. CONCLUSION: This study shows, for the first time to our knowledge, that germline CEBPA mutations are frequently observed among AML patients with CEBPA mutations. Including the families with germline CEBPA mutations reported previously, additional somatic CEBPA mutations represent a frequent second event in AML with germline CEBPA mutations. Our data strongly indicate that germline CEBPA mutations predispose to AML and that additional somatic CEBPA mutations contribute to the development of the disease.

Left renal vein entrapment: a frequent feature in children with postural proteinuria

In most Asian subjects with postural proteinuria, ultrasonic imaging and Doppler flow scanning disclose entrapment of the left renal vein in the fork between the aorta and the superior mesenteric artery. Little information is available on the possible occurrence of left venal rein entrapment in European subjects with postural proteinuria. Renal ultrasound with Doppler flow imaging was therefore performed on 24 Italian or Swiss patients with postural proteinuria (14 girls and ten boys, aged between 5.2 years and 16 years). Signs of aorto-mesenteric left renal vein entrapment were noted in 18 of the 24 subjects. In conclusion, aorto-mesenteric left renal vein entrapment is common also among European subjects with postural proteinuria.

Frequent sensitization to Candida albicans and profilins in adult eosinophilic esophagitis

BACKGROUND: Eosinophilic esophagitis (EoE) is often associated with atopic airway and skin diseases. More than 80% of EoE patients are sensitized to aero- and/or food allergens. Immunoglobulin (Ig)E-mediated immune responses to microbes have been reported to be deleterious in connection with atopic diseases. AIM: The aim of this study was to obtain a comprehensive overview about the sensitization spectrum of adult EoE patients. METHODS: IgE in sera of 35 patients with active EoE were analyzed for reactivity to Candida albicans, as well as to a panel of recombinant and purified natural allergen components, using a microarray. RESULTS: IgE sensitization to Candida albicans was found in 43% of EoE patients. More than 80% of EoE patients were sensitized to aeroallergens and 22% to food-specific allergen components, whereas 69% of the patients exhibited specific IgE to cross-reactive allergens. Among the latter, profilins were identified as most frequent IgE cross-reactive allergen components. Interestingly, dysphagia, the main symptom of adult EoE patients following rice and/or bread ingestion, was associated with sensitization to cross-reactive allergens such as profilins, pathogenesis-related (PR) 10 and lipid transfer proteins (LTP). Intolerance toward meat rarely correlated with sensitization to animal food allergens. CONCLUSION: Candida albicans and cross-reactive plant allergen components, in particular profilins, were identified as frequent sensitizers in adult EoE patients. Specific elimination therapies are suggested to reveal their actual roles in the pathogenesis of EoE.

Frequent ventricular tachycardias: antiarrhythmic drug treatment or catheter ablation?

Antiarrhythmic drugs are used in at least 50% of patients who received an implantable cardioverter defibrillator (ICD). The potential indications for antiarrhythmic drug treatments in patients with an ICD are generally the following: reduction of the number of ventricular tachycardias (VTs) or episodes of ventricular fibrillation and therefore reduction of the number of ICD therapies, most importantly, the number of disabling ICD shocks. Accordingly, the quality of life should be improved and the battery life of the ICD extended. Moreover, antiarrhythmic drugs have the potential to increase the tachycardia cycle length to allow termination of VTs by antitachycardia pacing and reduction of the number of syncopes. In addition, supraventricular arrhythmias can be prevented or their rate controlled. Recently published or reported trials have shown the efficacy of amiodarone, sotalol and azimilide to significantly reduce the number of appropriate and inappropriate ICD shocks in patients with structural heart disease. However, the use of antiarrhythmic drugs may also have adverse effects: an increase in the defibrillation threshold, an excessive increase in the VT cycle length leading to detection failure. In this situation and when antiarrhythmic drugs are ineffective or have to be stopped because of serious side effects, catheter ablation of both monomorphic stable and pleomorphic and/or unstable VTs using modern electroanatomic mapping systems should be considered. The choice of antiarrhythmic drug treatment and the need for catheter ablation in ICD patients with frequent VTs should be individually tailored to specific clinical and electrophysiological features including the frequency, the rate, and the clinical presentation of the ventricular arrhythmia. Although VT mapping and ablation is becoming increasingly practical and efficacious, ablation of VT is mostly done as an adjunctive therapy in patients with structural heart disease and ICD experiencing multiple shocks, because the recurrence and especially the occurrence of "new" VTs after primarily successful ablation with time and disease progression have precluded a widespread use of catheter ablation as primary treatment.

Frequent floods in the European Alps coincide with cooler periods of the past 2500 years

Severe floods triggered by intense precipitation are among the most destructive natural hazards in Alpine environments, frequently causing large financial and societal damage. Potential enhanced flood occurrence due to global climate change would thus increase threat to settlements, infrastructure, and human lives in the affected regions. Yet, projections of intense precipitation exhibit major uncertainties and robust reconstructions of Alpine floods are limited to the instrumental and historical period. Here we present a 2500-year long flood reconstruction for the European Alps, based on dated sedimentary flood deposits from ten lakes in Switzerland. We show that periods with high flood frequency coincide with cool summer temperatures. This wet-cold synchronism suggests enhanced flood occurrence to be triggered by latitudinal shifts of Atlantic and Mediterranean storm tracks. This paleoclimatic perspective reveals natural analogues for varying climate conditions, and thus can contribute to a better understanding and improved projections of weather extremes under climate change.

Varicella zoster virus reactivation after autologous SCT is a frequent event and associated with favorable outcome in myeloma patients.

The occurrence of varicella zoster virus (VZV) reactivation is increased after allogeneic transplantation, whereas limited data are available for herpes zoster (HZ) after autologous SCT (ASCT). We determined the incidence and the prognostic significance of HZ and its correlation with VZV serology in 191 consecutive myeloma patients undergoing high-dose melphalan chemotherapy with ASCT. We found that VZV reactivation occurred in 57 (30%) patients, in 8.5% during induction and in 21.5% after ASCT peaking at 8 months after ASCT. Disease burden due to HZ was assessed as high or rather high in 70% of the patients. By immune fluorescence and Serion Elisa VZV IgG assessment, 90.8% of all patients had specific anti-VZV antibodies at ASCT. Lower specific antibody titers at transplantation were observed in patients with HZ after ASCT than in those without reactivation (P=0.009). Finally, OS was better in myeloma patients with HZ after ASCT compared with patients without HZ (P=0.007). Our data indicate that VZV reactivation after ASCT is a frequent event carrying a significant disease burden and it is associated with improved survival. Low levels of specific VZV antibodies at ASCT suggest increased vulnerability for VZV reactivation.Bone Marrow Transplantation advance online publication, 19 January 2015; doi:10.1038/bmt.2014.290.

Mining free-text medical records for companion animal enteric syndrome surveillance.

Large amounts of animal health care data are present in veterinary electronic medical records (EMR) and they present an opportunity for companion animal disease surveillance. Veterinary patient records are largely in free-text without clinical coding or fixed vocabulary. Text-mining, a computer and information technology application, is needed to identify cases of interest and to add structure to the otherwise unstructured data. In this study EMR's were extracted from veterinary management programs of 12 participating veterinary practices and stored in a data warehouse. Using commercially available text-mining software (WordStat™), we developed a categorization dictionary that could be used to automatically classify and extract enteric syndrome cases from the warehoused electronic medical records. The diagnostic accuracy of the text-miner for retrieving cases of enteric syndrome was measured against human reviewers who independently categorized a random sample of 2500 cases as enteric syndrome positive or negative. Compared to the reviewers, the text-miner retrieved cases with enteric signs with a sensitivity of 87.6% (95%CI, 80.4-92.9%) and a specificity of 99.3% (95%CI, 98.9-99.6%). Automatic and accurate detection of enteric syndrome cases provides an opportunity for community surveillance of enteric pathogens in companion animals.

Post-mortem whole body computed tomography of opioid (heroin and methadone) fatalities: frequent findings and comparison to autopsy

OBJECTIVE To investigate frequent findings in cases of fatal opioid intoxication in whole-body post-mortem computed tomography (PMCT). METHODS PMCT of 55 cases in which heroin and/or methadone had been found responsible for death were retrospectively evaluated (study group), and were compared with PMCT images of an age- and sex-matched control group. Imaging results were compared with conventional autopsy. RESULTS The most common findings in the study group were: pulmonary oedema (95 %), aspiration (66 %), distended urinary bladder (42 %), cerebral oedema (49 %), pulmonary emphysema (38 %) and fatty liver disease (36 %). These PMCT findings occurred significantly more often in the study group than in the control group (p < 0.05). The combination of lung oedema, brain oedema and distended urinary bladder was seen in 26 % of the cases in the study group but never in the control group (0 %). This triad, as indicator of opioid-related deaths, had a specificity of 100 %, as confirmed by autopsy and toxicological analysis. CONCLUSIONS Frequent findings in cases of fatal opioid intoxication were demonstrated. The triad of brain oedema, lung oedema and a distended urinary bladder on PMCT was highly specific for drug-associated cases of death. KEY POINTS Frequent findings in cases of fatal opioid intoxication were investigated. Lung oedema, brain oedema and full urinary bladder represent a highly specific constellation. This combination of findings in post-mortem CT should raise suspicion of intoxication.

Mining the Ecosystem to Improve Type Inference For Dynamically Typed Languages

Dynamically typed languages lack information about the types of variables in the source code. Developers care about this information as it supports program comprehension. Ba- sic type inference techniques are helpful, but may yield many false positives or negatives. We propose to mine information from the software ecosys- tem on how frequently given types are inferred unambigu- ously to improve the quality of type inference for a single system. This paper presents an approach to augment existing type inference techniques by supplementing the informa- tion available in the source code of a project with data from other projects written in the same language. For all available projects, we track how often messages are sent to instance variables throughout the source code. Predictions for the type of a variable are made based on the messages sent to it. The evaluation of a proof-of-concept prototype shows that this approach works well for types that are sufficiently popular, like those from the standard librarie, and tends to create false positives for unpopular or domain specific types. The false positives are, in most cases, fairly easily identifiable. Also, the evaluation data shows a substantial increase in the number of correctly inferred types when compared to the non-augmented type inference.