Miracle-dz/UniFAR-FTUs huggingface dataset:
ExpressAPR: Efficient Patch Validation for Java Automated Program Repair Systems

Automated program repair (APR) approaches suffer from long patch validation time, which limits their practical application and receives relatively low attention. The patch validation process repeatedly executes tests to filter patches, and has been recognized as the dual of mutation analysis. We systematically investigate existing mutation testing techniques and recognize five families of acceleration techniques that are suitable for patch validation, two of which are never adapted to a general-purpose patch validator. We implement and demonstrate ExpressAPR, the first framework that combines five families of acceleration techniques for patch validation as the complete set. In our evaluation on 30 random Defects4J bugs and four APR systems, ExpressAPR accelerates patch validation for two order-of-magnitudes over plain validation or one order-of-magnitude over the state-of-the-art approach, benefiting APR researchers and users with a much shorter patch validation time. Demo video available at https://youtu.be/7AB-4VvBuuM Tool repo (source code + Docker image + evaluation dataset) available at https://github.com/ExpressAPR/ExpressAPR
Diffusion-Weighted MR Imaging in Biopsy-Proven Creutzfeldt-Jakob Disease

Objective To compare conventional and diffusion-weighted MR imaging in terms of their depiction of the abnormalities occurring in Creutzfeldt-Jakob disease. Materials and Methods We retrospectively analyzed the findings of conventional (T2-weighted and fluid-attenuated inversion recovery) and diffusion-weighted MR imaging in four patients with biopsy-proven Creutzfeldt-Jakob disease. The signal intensity of the lesion was classified by visual assessment as markedly high, slightly high, or isointense, relative to normal brain parenchyma. Results Both conventional and diffusion-weighted MR images demonstrated bilateral high signal intensity in the basal ganglia in all four patients. Cortical lesions were observed on diffusion-weighted MR images in all four, and on fluid-attenuated inversion recovery MR images in one, but in no patient on T2-weighted images. Conventional MR images showed slightly high signal intensity in all lesions, while diffusion-weighted images showed markedly high signal intensity in most. Conclusion Diffusion-weighted MR imaging is more sensitive than its conventional counterpart in the depiction of Creutzfeldt-Jakob disease, and permits better detection of the lesion in both the cerebral cortices and basal ganglia.
Early drug use of dapagliﬂozin prescribed by general practitioners and diabetologists in Germany

Objectives: Dapagliﬂozin is an inhibitor of the human sodium-glucose co-transporter 2 (SGLT2) that has been shown to improve glycaemic control in patients with type 2 diabetes mellitus (T2DM). This study aimed to evaluate the characteristics and treatment patterns of dapagliﬂozin users in comparison to users of other anti-diabetic (AD) treatments in Germany. Methods: Data from patients with T2DM initiating at least one prescription for dapagliﬂozin or other AD therapy between November 2012 and April 2014 were collected from the IMS German Disease Analyzer database. Results: The use of dapagliﬂozin combination therapy ( n = 1034; 74%) was more common than monotherapy ( n = 371; 26%). In comparison with other AD therapy users, a higher percentage of dapagliﬂozin users were 6 64 years of age (62.3% vs. 36.4%), and a higher proportion were male (59.1% vs. 53.6%). The average duration of diabetes was comparable between dapagliﬂozin patients and other AD therapy users (5.7 years vs. 5.5 years), however higher levels of HbA1c were found in dapagliﬂozin users (8.2% (66 mmol/mol) vs. 7.5% (58 mmol/mol). For the vast majority (71.5% of 10 mg dapagliﬂozin users and 88.9% of 5 mg users), dapagliﬂozin was prescribed in combination with other AD therapy. Conclusions: Patients starting on dapagliﬂozin differed in several demographic and health-related respects to patients starting another AD therapy during the same period. Dapagli-ﬂozin was predominantly used as a component of combination therapy, adding on to existing therapy. After initiation, switching to other AD treatments or adding to therapy was comparatively rare during the ﬁrst year. (cid:1) 2016 The Authors. Published by Elsevier Ireland Ltd. Thisisanopenaccessarticleunderthe CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Understanding the Complexity of Inflammatory Bowel Disease from a Multi-Omics

The pathogenesis of inflammatory bowel disease (IBD) is determined by multiple genetic variants and by gut microbiota. The role of interactions between these two factors has emerged recently. In this chapter, we focus on the crosstalk of gut microbiota and IBD genetic risk factors and give a review on the current progress and perspective of this research field
Gene expression studies in different genotypes of an ectomycorrhizal fungus require a 1 high number of reliable reference genes . 2 3

Gene expression studies in different genotypes of an ectomycorrhizal fungus require a 1 high number of reliable reference genes. 2 3 Joske Ruytinx*, Tony Remans and Jan V. Colpaert 4 5 Hasselt University, Centre for Environmental Sciences, Environmental Biology, Agoralaan 6 building D, 3590 Diepenbeek, Belgium 7 8 *for correspondence: 9 joske.ruytinx@uhasselt.be; phone: +32 11 268377; fax: +32 11 268301 10 11 Running title: Gene expression normalization in mycorrhiza 12
Potential Effects of Climate Change and Variability on the Surface Water Resources of the Upper Midwest

Simulated effects of potential climate change on the surface-water resources in the Upper Midwest are compared to the region's historical variability in climate and streamflow, and implications of both climate change and variability on water supply are discussed. Hydrologic models developed for watersheds in Illinois were used to evaluate the response in simulated streamflow to various climate scenarios. The climate scenarios used in the hydrologic simulation are based on outputs from global climate models, and represent a range of potential future climatic conditions. The driest climate scenarios result in a considerable reduction in the simulated flows. The wetter and more moderate climate scenarios generally cause relatively small amounts of change in simulated streamflow amounts, with most estimated streamflow frequency values falling within 15 percent of the simulated record using the 1950–2000 historical climate data. For 5 of the 6 climate scenarios examined in this study, the potential change in average flow is less than 25%. In contrast, there has been considerable historical variability in climatic and hydrologic conditions in the Upper Midwest since the mid-1800s, with variability in the 30-year average precipitation of 10–15 percent and associated changes in average streamflow in excess of 40 percent. Midwestern precipitation and streamflow, in particular, have increased substantially over the last 30 years. It is not known whether the 1971–2000 increase in precipitation and streamflow is a regional manifestation of climate change, or is instead part of the natural variability in the climate. But for now, the recent increasing trends in precipitation may give more credence to the GCM predictions that suggest moderate increases in future precipitation and streamflows.
Something old, something new: Na+/K+/ATPase as a mechanism of intrarenal B cells viability in lupus nephritis

Lupus nephritis ( LN ) remains one of the most severe manifestations of systemic lupus erythematosus ( SLE ) [ 1 ]. Available treatments have demonstrated a limited response rate [ 2 ]. Impor-tantly, irreversible kidney damage can be seen in biopsies from patients with LN despite receiving standard immunosuppressive treatment [ 3 ]. B cells are a cornerstone in the pathogenesis of LN. Their role does not end with autoantibodies production—B cells also act as antigen-presenting cells, promote differentiation and activation of T cells, and secrete cytokines that promote the maturation of naïve B cells into memory or plasma cells, among others [ 2 ]. In 2011, Chang et al . showed clonal expansion of B cells in LN kidney biopsies and T cell:B cell aggregates that correlate with immune complexes deposition [ 4 ]. Despite the important role of B cells in LN, the LUNAR ( Lupus Nephritis Assessment with Rituximab ) and BELONG ( A Study to Evaluate Ocrelizumab in Patients With Nephritis Due to Systemic Lupus Erythematosus
University of Birmingham Gene expression profiling in bladder cancer identifies potential therapeutic targets

Despite advances in management, bladder cancer remains a major cause of cancer related complications. Characterisation of gene expression patterns in bladder cancer allows the identification of pathways involved in its pathogenesis, and may stimulate the development of novel therapies targeting these pathways. Between 2004 and 2005, cystoscopic bladder biopsies were obtained from 19 patients and 11 controls. These were subjected to whole transcript-based microarray analysis. Unsupervised hierarchical clustering was used to identify samples with similar expression profiles. Hypergeometric analysis was used to identify canonical pathways and curated networks having statistically significant enrichment of differentially expressed genes. Osteopontin (OPN) expression was validated by immunohistochemistry. Hierarchical clustering defined signatures, which differentiated between cancer and healthy tissue, muscle-invasive or non-muscle invasive cancer and healthy tissue, grade 1 and grade 3. Pathways associated with cell cycle and proliferation were markedly upregulated in muscle-invasive and grade 3 cancers. Genes associated with the classical complement pathway were downregulated in non-muscle invasive cancer. Osteopontin was markedly over-expressed in invasive cancer compared to healthy tissue. The present study contributes to a growing body of work on gene expression signatures in bladder cancer. The data support an important role for osteopontin in bladder cancer, and identify several pathways worthy of further investigation.
Walking Rehabilitation Using Hybrid Assistive Limb (HAL) and Computer-Controlled Long-Leg Orthosis (C-Brace) for an Individual with Chronic Incomplete Spinal Cord Injury: A Case Report

1. Abstract Many individuals with spinal cord injury (SCI) hope to restore walking function irrespective of their impairment. We present a case with chronic incomplete cervical SCI who could regain community ambulation by gait training with hybrid assistive limb (HAL), followed by fitting and training of microprocessor-con - trolled knee ankle foot
Explorer Compiling language models from a linguistically motivated unification grammar

Systems now exist which are able to compile uni cation grammars into language models that can be included in a speech recognizer, but it is so far unclear whether non-trivial linguistically principled grammars can be used for this purpose. We describe a series of experiments which investigate the question empirically, by incrementally constructing a grammar and discovering what problems emerge when successively larger versions are compiled into nite state graph representations and used as language models for a medium-vocabulary recognition task.
International Journal of Health Geographics Accounting for Regional Background and Population Size in the Detection of Spatial Clusters and Outliers Using Geostatistical Filtering and Spatial Neutral Models: the Case of Lung Cancer in Long Island, New York

Background: Complete Spatial Randomness (CSR) is the null hypothesis employed by many statistical tests for spatial pattern, such as local cluster or boundary analysis. CSR is however not a relevant null hypothesis for highly complex and organized systems such as those encountered in the environmental and health sciences in which underlying spatial pattern is present. This paper presents a geostatistical approach to filter the noise caused by spatially varying population size and to generate spatially correlated neutral models that account for regional background obtained by geostatistical smoothing of observed mortality rates. These neutral models were used in conjunction with the local Moran statistics to identify spatial clusters and outliers in the geographical distribution of male and female lung cancer in Nassau, Queens, and Suffolk counties, New York, USA.
Financial Education, Financial Competence, and Consumer Welfare

Employers routinely attempt to address deficiencies in financial decision making among their employees by deploying educational interventions that are brief and laden with motivational rhetoric. The object of the rhetorical elements is to compensate for brevity by making the material engaging, memorable, and actionable. Prior studies of these interventions evaluate their benefits using criteria that suffer from serious conceptual and practical limitations. In contrast, our research employs a novel method for assessing the quality of decision making that respects each consumer’s underlying tastes and focuses instead on mistakes arising from misconceptions about opportunities. We deploy this method to evaluate a pair of educational interventions targeting two critical topics in personal finance: compound interest and portfolio allocation. Both interventions appear to be effective based on conventional outcome measures; they significantly increase performance on financial literacy tests and, in the case of compound interest, change behavior in a direction that appears to counteract a known bias. Nevertheless, upon applying our methods, we discover that neither intervention improves the quality of financial decision making. In both cases, some consumers benefit while others are harmed; overall, the effect on the average quality of decision making is neutral. We resolve the apparent tension between these findings by studying one of the interventions in greater depth to determine whether its effects are attributable to the substantive elements of instruction or to its motivational and rhetorical components. We find that substance accounts for the improvement in performance on literacy tests, while rhetoric accounts for the changes in financial choices. Thus, our analysis shows that motivational rhetoric can have the unintended effect of distracting from substance and promoting an indiscriminate one-size-fits-all response. Conventional methods for evaluating these programs—unlike our methods— fail to detect these deficiencies.
Automated Digitization and Summarization of Analog Archives

This thesis aimed to create a tool that could assist climate researchers in their fieldwork. Through dialog with researchers at Stockholms University a need and interest for automated digitization and summarization of their handwritten notes could be identified. Climate research may require work conducted out in the field and during fieldwork, many researchers prefer to take handwritten notes which can generate large physical archives. A downside with only physical archives is that the data and knowledge stored here become less available and create a threshold for researchers to use the data since manually digitizing handwritten texts can be very time-consuming. At the end of the thesis, a software program was created which could automatically digitize and summarize handwritten texts to save time for researchers. The tool consists of (1) Google Cloud Vision API used to digitize a photo of handwritten text by using a convolutional neural network (CNN) and (2) the transformer-based algorithm GPT-3 used to summarize the digitized text. The GPT-3 algorithm provided two different engines, Davinci and Curie. The performance of the algorithms was evaluated with a data set consisting of handwritten texts provided by Stockholms University. The results indicated that the performance of Google Cloud Vision API was highly correlated to the quality of the image and the way of handwriting. With a unique handwriting follows a poor classification of letters since the algorithm performed badly on shapes that were unfamiliar. A survey was used to evaluate the performance of GPT-3. The survey got 73 responses where the subjects would grade five summaries conducted by a human and the GPT-3 engines Davinci and Curie respectively from the same text. The results from the survey indicated that the performance of the engine Davinci was comparable to the performance of a human while Curie was not a preferable option. Teknisk-naturvetenskapliga fakulteten, Uppsala
Journal Pre-proof Short video game play improves executive function in the oldest old living in residential care

Action video game play as a form of cognitive training shows promise, but has not been widely tested with participants exclusively over age 80 years. Age-related decline in executive function produces widely varying levels of ability to function independently. This study aimed to examine the change in executive functioning after a 3-week action video game intervention in healthy adults aged 80-97 years living in residential care. Participants were randomly assigned to either an experimental or care-as-usual control group: experimental participants played Star Wars Battlefront © , a commercially available video game, for six supervised sessions of 30 minutes each. Participants completed neuropsychological and quality of life assessments pre-training, post-training, and one month later. The experimental group showed significant improvement in the visual attention and task switching domains, in both post-test and follow-up sessions. Working memory also improved in the experimental group; however, after one month of no game play, memory performance regressed toward baseline levels. Results support the incorporation of video game play as a leisure option for older adults, which may also play a role in enhancing cognitive health. The findings extend previous research conducted below age 80 years to the oldest-old, an age group in which longitudinal follow up data is limited.
A Traﬃc Simulation Model with Interactive Drivers and High-ﬁdelity Car Dynamics

: We integrate a set of game-theoretic driver decision-making models with the high-ﬁdelity car driving simulator The Open Racing Car Simulator (TORCS). The game-theoretic driver models simulate the interactive decision making processes of the drivers and TORCS simulates vehicle dynamics in multi-vehicle highway traﬃc scenarios. We use the integrated simulator to collect human driving data and then use these data to validate and re-calibrate our driver and traﬃc models. Such an integrated simulator can be used in the development, veriﬁcation and validation of automated driving functions.
Electronics reliability of future power fusion machines: numerical investigations at silicon level

The interactions of high energy neutrons produced in D-D and D-T nuclear fusion reactions with natural silicon have been investigated through direct calculation using nuclear cross section libraries, MCNP6 and Geant4 numerical simulations. We provide a detailed analysis of all interactions per type of reacting silicon isotope and an exhaustive classification of all neutron-induced secondary products. Implications for reliability of the electronics in future power fusion machines are discussed on the basis of these first evaluations
HIF-1α Overexpression Using a Protein Transduction Domain to Increase the Osteogenic Potential of SHED

Background: Hypoxia-Inducible Factor 1 (HIF-1) alpha (HIF-1α) is known to be expressed in hypoxia and affects stemness and bone differentiation. Protein Transduction Domains (PTDs) safely and effectively deliver proteins into cells. This study combined HIF-1α delta Oxygen-Dependent Degradation Domain–Transcription Modulation Domain (ntHIF-1α-ΔODD-TMD) with the PTD and then used it to treat Stem cells from Human Exfoliated Deciduous teeth (SHED) to determine its effect on stemness and bone differentiation. Methods: The SHED were treated using PDT-conjugated ntHIF-1α-ΔODD-TMD, and its effects on STRO-1 expression, cytotoxicity, stemness-related gene expression, and osteogenic differentiation were confirmed. These were also transferred to 5-week-old mice in order to confirm the effects in vivo after recellularization of SHED treated using ntHIF-1α-ΔODD-TMD on decellularized tooth specimens. After 9 weeks, they were sacrificed to confirm the expression of genes related to bone differentiation and angiogenesis. Results: ntHIF-1α-ΔODD-TMD increased the expression levels of STRO-1, HIF-1α-related genes, and stemness-related genes in SHED. Osteogenic differentiation was also increased both in vitro and in vivo . Conclusion: These results suggest that ntHIF-1α-ΔODD-TMD maintains or increases the stemness of SHED and also increases the osteogenic potential. SHED have previously been found to have excellent proliferative but low differentiation capacities compared with other cells. However, properly using ntHIF-1α-ΔODD-TMD increases the osteogenic potential of SHED, indicating the potential of using SHED as a useful source for hard-tissue regeneration
Overdrive Is a T-region transer ener which stimulates T nd production in Agrobacterium twmefaciens

SUMMARY: Introduction of a left or right synthetic border repeat together with the overdrive sequence in an octopine Ti-plasmid deletion mutant, lacking the right border, resulted in the complete restoration of the oncogenicity of the mutant strain. However introduction of a border repeat without the overdrive, only restored oncogenicity partially. The overdrive sequence turned out to be able to stimulate the synthetic border mediated T-region transfer, independent of its orientation and position relative to the border repeat. Furthermore the distance between border repeat and overdrive could be enlarged, without a loss of overdrive activity. Here we enlarged the distance between the two sequences up to 6714bp. These results were confirmed by estimating the amount of single stranded T-DNA molecules from induced agrobacteria, containing the various border constructs.
Characterising the Frequency Ripple in Antenna Noise Temperature Using Exponential Analysis

This paper presents a method for characterising the ripple observed in the antenna noise temperature of reflector systems as a function of operating frequency. The ripple, which is superimposed on the dominant power-law shape, must be accurately characterised in order to determine its impact. Traditional methods, such as Fourier transform analysis, typically involve some preprocessing to reduce the effect of the power law, which may inadvertently introduce additional ripple components. To overcome this limitation, it is shown how the Validated EXPonential Analysis (VEXPA) method can be used without the need to remove the trend of the curve. The results demonstrate that VEXPA produces accurate results and is therefore a valuable alternative to traditional methods.