LLukas22/scidocs huggingface dataset:
Who should review my code? A file location-based code-reviewer recommendation approach for Modern Code Review

Software code review is an inspection of a code change by an independent third-party developer in order to identify and fix defects before an integration. Effectively performing code review can improve the overall software quality. In recent years, Modern Code Review (MCR), a lightweight and tool-based code inspection, has been widely adopted in both proprietary and open-source software systems. Finding appropriate code-reviewers in MCR is a necessary step of reviewing a code change. However, little research is known the difficulty of finding code-reviewers in a distributed software development and its impact on reviewing time. In this paper, we investigate the impact of reviews with code-reviewer assignment problem has on reviewing time. We find that reviews with code-reviewer assignment problem take 12 days longer to approve a code change. To help developers find appropriate code-reviewers, we propose RevFinder, a file location-based code-reviewer recommendation approach. We leverage a similarity of previously reviewed file path to recommend an appropriate code-reviewer. The intuition is that files that are located in similar file paths would be managed and reviewed by similar experienced code-reviewers. Through an empirical evaluation on a case study of 42,045 reviews of Android Open Source Project (AOSP), OpenStack, Qt and LibreOffice projects, we find that RevFinder accurately recommended 79% of reviews with a top 10 recommendation. RevFinder also correctly recommended the code-reviewers with a median rank of 4. The overall ranking of RevFinder is 3 times better than that of a baseline approach. We believe that RevFinder could be applied to MCR in order to help developers find appropriate code-reviewers and speed up the overall code review process.
Ten Simple Rules for the Open Development of Scientific Software

Open-source software development has had significant impact, not only on society, but also on scientific research. Papers describing software published as open source are amongst the most widely cited publications (e.g., BLAST [1,2] and Clustal-W [3]), suggesting many scientific studies may not have been possible without some kind of open software to collect observations, analyze data, or present results. It is surprising, therefore, that so few papers are accompanied by open software, given the benefits that this may bring. Publication of the source code you write not only can increase your impact [4], but also is essential if others are to be able to reproduce your results. Reproducibility is a tenet of computational science [5], and critical for pipelines employed in datadriven biological research. Publishing the source for the software you created as well as input data and results allows others to better understand your methodology, and why it produces, or fails to produce, expected results. Public release might not always be possible, perhaps due to intellectual property policies at your or your collaborators’ institutes; and it is important to make sure you know the regulations that apply to you. Open licensing models can be incredibly flexible and do not always prevent commercial software release [5]. Simply releasing the source under an open license, however, is not sufficient if you wish your code to remain useful beyond its publication [6]. The sustainability of software after publication is probably the biggest problem faced by researchers who develop it, and it is here that participating in open development from the outset can make the biggest impact. Grant-based funding is often exhausted shortly after new software is released, and without support, in-house maintenance of the software and the systems it depends on becomes a struggle. As a consequence, the software will cease to work or become unavailable for download fairly quickly [7], which may contravene archival policies stipulated by your journal or funding body. A collaborative and open project allows you to spread the resource and maintenance load to minimize these risks, and significantly contributes to the sustainability of your software. If you have the choice, embracing an open approach to development has tremendous benefits. It allows you to build on the work of other scientists, and enables others to build on your own efforts. To make the development of open scientific software more rewarding and the experience of using software more positive, the following ten rules are intended to serve as a guide for any computational scientist.
Drug Hypersensitivity Reactions: Classification and relationship to T cell activation

The clinical characteristics of drug hypersensitivity reactions are very heterogeneous as drugs can actually elicit all types of immune reactions. The majority of allergic reactions involve either drug-specific IgE or T cells. Their stimulation leads to quite distinct immune responses, which are classified according to Gell and Coombs. Here, an extension of this subclassification, which considers the distinct T-cell functions and immunopathologies, is presented. These subclassifications are clinically useful, as they require different treatment and diagnostic steps. Copyright © 2007 S. Karger AG, Basel
Intravenous administration of Reolysin®, a live replication competent RNA virus is safe in patients with advanced solid tumors

Background Reolysin® is reovirus serotype 3-Dearing strain, a double-stranded replication-competent RNA non-enveloped icosahedral virus. It induces cytopathic and anti-cancer effects in cells with an activated ras pathway due to inhibition of the dsRNA-activated protein kinase. Methods This was a single center dose escalation trial of Reolysin administered intravenously every 4 weeks in doses ranging from 1 × 108 to 3 × 1010 tissue culture infective dose (TCID)50. Serum for neutralizing antibody, and serum, stool, saliva, and urine for viral shedding were collected. Tumor samples were analyzed for activating mutations in the ras and braf oncogenes. Results Eighteen patients received 27 doses of Reolysin in 6 dose cohorts accomplishing a 300 fold dose escalation without a protocol-defined dose limiting toxicity. Drug related grade 2 toxicities included fatigue and fever (1 patient each). All patients developed neutralizing antibody during the course of the study. Viral shedding was observed in 6 patients. One patient with anthracycline and taxane refractory breast cancer experienced a partial response (PR) and her tumor had a ras G12A mutation. Biopsy from her chest wall mass showed evidence of necrosis and viral replication by electron microscopy. Overall clinical benefit (1 PR + 7 stable disease) rate was 45%, and appeared higher in patients with viral shedding (67%) than those without (33%). Conclusion Reolysin administered monthly as a one-hour infusion is safe and well-tolerated even in multiple doses. Reolysin has anti-tumor activity as a single agent warranting further evaluation, including in combination with chemotherapy. Viral shedding may suggest intrapatient replication yielding a benefit and should be studied carefully in future studies.
Greedy, Joint Syntactic-Semantic Parsing with Stack LSTMs

We present a transition-based parser that jointly produces syntactic and semantic dependencies. It learns a representation of the entire algorithm state, using stack long short-term memories. Our greedy inference algorithm has linear time, including feature extraction. On the CoNLL 2008–9 English shared tasks, we obtain the best published parsing performance among models that jointly learn syntax and semantics.
Segmentation of white blood cells and comparison of cell morphology by linear and naïve Bayes classifiers

BACKGROUND
Blood smear microscopic images are routinely investigated by haematologists to diagnose most blood diseases. However, the task is quite tedious and time consuming. An automatic detection and classification of white blood cells within such images can accelerate the process tremendously. In this paper we propose a system to locate white blood cells within microscopic blood smear images, segment them into nucleus and cytoplasm regions, extract suitable features and finally, classify them into five types: basophil, eosinophil, neutrophil, lymphocyte and monocyte.


DATASET
Two sets of blood smear images were used in this study's experiments. Dataset 1, collected from Rangsit University, were normal peripheral blood slides under light microscope with 100× magnification; 555 images with 601 white blood cells were captured by a Nikon DS-Fi2 high-definition color camera and saved in JPG format of size 960 × 1,280 pixels at 15 pixels per 1 μm resolution. In dataset 2, 477 cropped white blood cell images were downloaded from CellaVision.com. They are in JPG format of size 360 × 363 pixels. The resolution is estimated to be 10 pixels per 1 μm.


METHODS
The proposed system comprises a pre-processing step, nucleus segmentation, cell segmentation, feature extraction, feature selection and classification. The main concept of the segmentation algorithm employed uses white blood cell's morphological properties and the calibrated size of a real cell relative to image resolution. The segmentation process combined thresholding, morphological operation and ellipse curve fitting. Consequently, several features were extracted from the segmented nucleus and cytoplasm regions. Prominent features were then chosen by a greedy search algorithm called sequential forward selection. Finally, with a set of selected prominent features, both linear and naïve Bayes classifiers were applied for performance comparison. This system was tested on normal peripheral blood smear slide images from two datasets.


RESULTS
Two sets of comparison were performed: segmentation and classification. The automatically segmented results were compared to the ones obtained manually by a haematologist. It was found that the proposed method is consistent and coherent in both datasets, with dice similarity of 98.9 and 91.6% for average segmented nucleus and cell regions, respectively. Furthermore, the overall correction rate in the classification phase is about 98 and 94% for linear and naïve Bayes models, respectively.


CONCLUSIONS
The proposed system, based on normal white blood cell morphology and its characteristics, was applied to two different datasets. The results of the calibrated segmentation process on both datasets are fast, robust, efficient and coherent. Meanwhile, the classification of normal white blood cells into five types shows high sensitivity in both linear and naïve Bayes models, with slightly better results in the linear classifier.
High bandwidth 0.35μm CMOS transimpedance amplifier

A transimpedance amplifier (TIA) has been designed in a 0.35 μm digital CMOS technology for Gigabit Ethernet. It is based on the structure proposed by Mengxiong Li [1]. This paper presents an amplifier which exploits the regulated cascode (RGC) configuration as the input stage with an integrated optical receiver which consists of an integrated photodetector, thus achieving as large effective input transconductance as that of Si Bipolar or GaAs MESFET. The RGC input configuration isolates the input parasitic capacitance including photodiode capacitance from the bandwidth determination better than common-gate TIA. A series inductive peaking is used for enhancing the bandwidth. The proposed TIA has transimpedance gain of 51.56 dBΩ, and 3-dB bandwidth of 6.57 GHz with two inductor between the RGC and source follower for 0.1 pF photodiode capacitance. The proposed TIA has an input courant noise level of about 21.57 pA/Hz0.5 and it consumes DC power of 16 mW from 3.3 V supply voltage.
Quantitative investigation of palatal bone depth and cortical bone thickness for mini-implant placement in adults.

INTRODUCTION
Cortical bone thickness and overall bone depth are important factors to consider when placing an orthodontic mini-implant. The purpose of this study was to investigate both variables in the palate quantitatively to aid clinicians in planning successful mini-implant placements.


METHODS
Thirty dry skulls were imaged with cone-beam computed tomography technology. Coronal slices were generated on which overall bone depth and cortical bone thickness were measured at 4 levels and 34 palatal placement sites. One-way analysis of variance (ANOVA) was used for data analysis.


RESULTS
Overall bone depth decreased with increasing distance from the midsagittal plane and from the anterior to the posterior palatal regions. Cortical bone thickness decreased from anterior to posterior, but no differences were detectable within measurement levels.


CONCLUSIONS
Bone depth and cortical bone thickness of the palate were most favorable for temporary anchorage device placement at the level of the first and second premolars. This information could aid clinicians in choosing suitable palatal placement sites for orthodontic mini-implants.
Dielectric properties of transformer oils for HVDC applications

The knowledge of the behavior of electric conductivity in mineral oils for possible applications in HVDC converter transformers is of paramount importance for proper design of their insulation system. This study presents the results of measurements of dielectric properties of various transformer oils by means of frequency response technique as well as time domain measurements, including measurements of ion mobility using the reversal polarity method. Influences imposed by varying the measurement voltage level and temperature are investigated. Some important parameters of the investigated oils, e.g. their conductivities, ion mobilities, ionic concentrations and effective ionic radiuses are compared and discussed. The results show that despite of similarities in various physical parameters of insulating mineral oils available on the market, the dielectric behavior and especially ionic conduction vary greatly between different oil types. Changes of these properties with temperature are characterized by different activation energies.
Usability evaluation methods for the web: A systematic mapping study

Context: In recent years, many Usability Evaluation Methods (UEMs) have been employed to evaluate Web applications. However, many of these applications still do not meet most customers’ usability expectations and many companies have folded as a result of not considering Web usability issues. No studies currently exist with regard to either the use of usability evaluation methods for the Web or the benefits they bring. Objective: The objective of this paper is to summarize the current knowledge that is available as regards the Usability Evaluation Methods (UEMs) that have been employed to evaluate Web applications over the last 14 years. Method: A systematic mapping study was performed to assess the UEMs that have been used by researchers to evaluate Web applications and their relation to the Web development process. Systematic mapping studies are useful for categorizing and summarizing the existing information concerning a research question in an unbiased manner. Results: The results show that around 39% of the papers reviewed reported the use of evaluation methods that had been specifically crafted for the Web. The results also show that the type of method most widely used was that of User Testing. The results identify several research gaps, such as the fact that around 90% of the studies applied evaluations during the implementation phase of the Web application development, which is the most costly phase in which to perform changes. A list of the UEMs that were found is also provided in order to guide novice usability practitioners. Conclusions: From an initial set of 2703 papers, a total of 206 research papers were selected for the mapping study. The results obtained allowed us to reach conclusions concerning the state-ofthe-art of UEMs for evaluating Web applications. This allowed us to identify several research gaps, which subsequently provided us with a framework in which new research activities can be more appropriately positioned, and from which useful information for novice usability practitioners can be extracted.
Ambient intelligence: a multimedia perspective

Ambient intelligence opens up a world of unprecedented experiences. The interaction of people with electronic devices will change as context awareness, natural interfaces, and ubiquitous availability of information come to fruition. Ambient intelligence is going to impose major challenges on multimedia research. Distributed multimedia applications and their processing on embedded static and mobile platforms will play a major role in the development of ambient-intelligent environments. The requirements that ambient-intelligent multimedia applications impose on the mechanisms users apply to interact with media call for paradigms substantially different from contemporary interaction concepts. The complexity of media will continually increase in terms of volume and functionality, thus introducing a need for simplicity and ease of use. Therefore, the massively distributed, integrated use of media will require replacing well-known interaction vehicles, such as remote control and menu-driven search and control, with novel more intuitive, and natural concepts. This article reviews the concept of ambient intelligence and elaborates on its relation with multimedia. (The "Advances in media processing" sidebar gives insight into the developments that have set the stage for this new step forward.) The emphasis is on qualitative aspects, highlighting those elements that play a role in realizing ambient intelligence. Multimedia processing techniques and applications are key to realizing ambient intelligence, and they introduce major challenges to the design and implementation of both media-processing platforms and multimedia applications. Technology will not be the limiting factor in realizing ambient intelligence. The ingredients to let the computers disappear are already available, but the true success of the paradigm will depend on the ability to develop concepts that allow natural interaction with digital environments. We must build these digital environments with the invisible technology of the forthcoming century. The role of intelligent algorithms in this respect is apparent because it is the key enabling factor for realizing natural interaction.
Self-management education and regular practitioner review for adults with asthma.

BACKGROUND
A key component of many asthma management guidelines is the recommendation for patient education and regular medical review. A number of controlled trials have been conducted to measure the effectiveness of asthma education programmes. These programmes improve patient knowledge, but their impact on health outcomes is less well established. This review was conducted to examine the strength of evidence supporting Step 6 of the Australian Asthma Management Plan: "Educate and Review Regularly"; to test whether health outcomes are influenced by education and self-management programmes.


OBJECTIVES
The objective of this review was to assess the effects of asthma self-management programmes, when coupled with regular health practitioner review, on health outcomes in adults with asthma.


SEARCH STRATEGY
We searched the Cochrane Airways Group trials register and reference lists of articles.


SELECTION CRITERIA
Randomised trials of self-management education in adults over 16 years of age with asthma.


DATA COLLECTION AND ANALYSIS
Trial quality was assessed and data were extracted independently by two reviewers. Study authors were contacted for confirmation.


MAIN RESULTS
Twenty-five trials were included. Self-management education was compared with usual care in 22 studies. Self-management education reduced hospitalisations (odds ratio 0.57, 95% confidence interval 0.38 to 0.88); emergency room visits (odds ratio 0.71, 95% confidence interval (0.57 to 0.90); unscheduled visits to the doctor (odds ratio 0.57, 95% confidence interval 0.40 to 0.82); days off work or school (odds ratio 0.55, 95% confidence interval 0.38 to 0. 79); and nocturnal asthma (odds ratio 0.53, 95% confidence interval 0.39 to 0.72). Measures of lung function were little changed. Self-management programmes that involved a written action plan showed a greater reduction in hospitalisation than those that did not (odds ratio 0.35, 95% confidence interval 0.18 to 0.68). People who managed their asthma by self-adjustment of their medications using an individualised written plan had better lung function than those whose medications were adjusted by a doctor.


REVIEWER'S CONCLUSIONS
Training in asthma self-management which involves self-monitoring by either peak expiratory flow or symptoms, coupled with regular medical review and a written action plan appears to improve health outcomes for adults with asthma. Training programmes which enable people to adjust their medication using a written action plan appear to be more effective than other forms of asthma self-management.
Aerobic endurance exercise improves executive functions in depressed patients.

BACKGROUND
Aerobic endurance exercise has been shown to improve higher cognitive functions such as executive control in healthy subjects. We tested the hypothesis that a 30-minute individually customized endurance exercise program has the potential to enhance executive functions in patients with major depressive disorder.


METHOD
In a randomized within-subject study design, 24 patients with DSM-IV major depressive disorder and 10 healthy control subjects performed 30 minutes of aerobic endurance exercise at 2 different workload levels of 40% and 60% of their predetermined individual 4-mmol/L lactic acid exercise capacity. They were then tested with 4 standardized computerized neuropsychological paradigms measuring executive control functions: the task switch paradigm, flanker task, Stroop task, and GoNogo task. Performance was measured by reaction time. Data were gathered between fall 2000 and spring 2002.


RESULTS
While there were no significant exercise-dependent alterations in reaction time in the control group, for depressive patients we observed a significant decrease in mean reaction time for the congruent Stroop task condition at the 60% energy level (p = .016), for the incongruent Stroop task condition at the 40% energy level (p = .02), and for the GoNogo task at both energy levels (40%, p = .025; 60%, p = .048). The exercise procedures had no significant effect on reaction time in the task switch paradigm or the flanker task.


CONCLUSION
A single 30-minute aerobic endurance exercise program performed by depressed patients has positive effects on executive control processes that appear to be specifically subserved by the anterior cingulate.