nils-herrmann/clean_scirepeval huggingface dataset:
Generic tools, specific languages

Adapting tools to a particular domain is expensive, and the adaptation is often not very deep. To address this challenge, Generic Tools, Specific Languages shifts the focus from building and adapting tools (windows, buttons, algorithms) to building and adapting languages to a domain. The thesis applies the approach to embedded software development: mbeddr is an extensible set of integrated languages for embedded software development built with JetBrains MPS language workbench. The evaluation of mbeddr suggests that it is a productive tool for embedded software development. The evaluation of the development of mbeddr itself suggests that MPS is a suitable platform for Generic Tools, Specific Languages, and that the approach in general is worthwhile. 1.1 O V E RV I E W A N D C O N T R I B U T I O N This section provides an overview of the thesis. It starts out by describing the contribution and the research methodology. It then discusses mbeddr, the primary artifact built during the dissertation and explains its context, embedded software engineering. A discussion of the technologies used for building mbeddr – language engineering, projectional editing and JetBrains MPS – follows. The section concludes with an overview of the results.  Today’s software engineering tools are hard to adapt to specific domains. A major reason is that while platforms such as Eclipse support easy extension of the tool (views, editors, buttons, menus) they do not easily support the extension of the data formats or languages that underlie a tool. The contribution of this thesis is the introduction and evaluation of a new approach to developing domain-specific software engineering tools called Generic Tools, Specific Languages. It shifts the focus from adapting the engineering tool to adapting the underlying languages to solve the problem of tool adaptation. It relies on language workbenches (the generic tool) and recent advances in language engineering, particularly, user-friendly projectional editing. The problem of tool extensibility, the Generic Tools, Specific Languages approach and the way it is evaluated is discussed in Chapter 2. The specific research questions that arise from the approach (domain-specific extensibility, language modularity and projectional editing, tool scalability, implementation efforts and the learning curve) are introduced and motivated in Section 2.6.  As part of the dissertation, the Generic Tools, Specific Languages approach has been applied to embedded software engineering, resulting in a
ECG-gated dual-source CT for detection of left atrial appendage thrombus in patients undergoing catheter ablation for atrial fibrillation

Left atrial ablation is increasingly used to treat patients with symptomatic atrial fibrillation (AF). Prior to ablation, exclusion of left atrial appendage (LAA) thrombus is important. Whether ECG-gated dual-source computed tomography (DSCT) provides a sensitive means of detecting LAA thrombus in patients undergoing percutaneous AF ablation is unknown. Thus, we sought to determine the utility of ECG-gated DSCT in detecting LAA thrombus in patients with AF. A total of 255 patients (age 58 ± 11 years, 78% male, ejection fraction 58 ± 9%) who underwent ECG-gated DSCT and transesophageal echocardiography (TEE) prior to AF ablation between February 2006 and October 2007 were included. CHADS2 score and demographic data were obtained prospectively. Gated DSCT images were independently reviewed by two cardiac imagers blinded to TEE findings. The LAA was either defined as normal (fully opacified) or abnormal (under-filled) by DSCT. An under-filled LAA was identified in 33 patients (12.9%), of whom four had thrombus confirmed by TEE. All patients diagnosed with LAA thrombus using TEE also had an abnormal LAA by gated DSCT. Thus, sensitivity and specificity for gated DSCT were 100% and 88%, respectively. No cases of LAA filling defects were observed in patients <51 years old with a CHADS2 of 0. In patients referred for AF ablation, thrombus is uncommon in the absence of additional risk factors. Gated DSCT provides excellent sensitivity for the detection of thrombus. Thus, in AF patients with a CHADS2 of 0, gated DSCT may provide a useful stand-alone imaging modality.
A Force-Sensing Bipolar Forceps to Quantify Tool–Tissue Interaction Forces in Microsurgery

The ability to exert an appropriate amount of force on brain tissue during surgery is an important component of instrument handling. It allows surgeons to achieve the surgical objective effectively while maintaining a safe level of force in tool-tissue interaction. At the present time, this knowledge, and hence skill, is acquired through experience and is qualitatively conveyed from an expert surgeon to trainees. These forces can be assessed quantitatively by retrofitting surgical tools with sensors, thus providing a mechanism for improved performance and safety of surgery, and enhanced surgical training. This paper presents the development of a force-sensing bipolar forceps, with installation of a sensory system, that is able to measure and record interaction forces between the forceps tips and brain tissue in real time. This research is an extension of a previous research where a bipolar forceps was instrumented to measure dissection and coagulation forces applied in a single direction. Here, a planar forceps with two sets of strain gauges in two orthogonal directions was developed to enable measuring the forces with a higher accuracy. Implementation of two strain gauges allowed compensation of strain values due to deformations of the forceps in other directions (axial stiffening) and provided more accurate forces during microsurgery. An experienced neurosurgeon performed five neurosurgical tasks using the axial setup and repeated the same tasks using the planar device. The experiments were performed on cadaveric brains. Both setups were shown to be capable of measuring real-time interaction forces. Comparing the two setups, under the same experimental condition, indicated that the peak and mean forces quantified by planar forceps were at least 7% and 10% less than those of axial tool, respectively; therefore, utilizing readings of all strain gauges in planar forceps provides more accurate values of both peak and mean forces than axial forceps. Cross-correlation analysis between the two force signals obtained, one from each cadaveric practice, showed a high similarity between the two force signals.
Intensive lipid lowering with atorvastatin in patients with coronary heart disease and chronic kidney disease: the TNT (Treating to New Targets) study.

This subanalysis of the TNT (Treating to New Targets) study investigates the effects of intensive lipid lowering with atorvastatin in patients with coronary heart disease (CHD) with and without pre-existing chronic kidney disease (CKD).



Cardiovascular disease is a major cause of morbidity and mortality in patients with CKD.



A total of 10,001 patients with CHD were randomized to double-blind therapy with atorvastatin 80 mg/day or 10 mg/day. Patients with CKD were identified at baseline on the basis of an estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m(2) using the Modification of Diet in Renal Disease equation. The primary efficacy outcome was time to first major cardiovascular event.



Of 9,656 patients with complete renal data, 3,107 had CKD at baseline and demonstrated greater cardiovascular comorbidity than those with normal eGFR (n = 6,549). After a median follow-up of 5.0 years, 351 patients with CKD (11.3%) experienced a major cardiovascular event, compared with 561 patients with normal eGFR (8.6%) (hazard ratio [HR] = 1.35; 95% confidence interval [CI] 1.18 to 1.54; p < 0.0001). Compared with atorvastatin 10 mg, atorvastatin 80 mg reduced the relative risk of major cardiovascular events by 32% in patients with CKD (HR = 0.68; 95% CI 0.55 to 0.84; p = 0.0003) and 15% in patients with normal eGFR (HR = 0.85; 95% CI 0.72 to 1.00; p = 0.049). Both doses of atorvastatin were well tolerated in patients with CKD.



Aggressive lipid lowering with atorvastatin 80 mg was both safe and effective in reducing the excess of cardiovascular events in a high-risk population with CKD and CHD.
Performance Evaluation of the CPU Scheduler in XEN

Virtual machines with advances in software and architectural support have emerged as the basis for enterprises to allocate resources recently. One main benefit of virtual machine is server consolidation. However, flexible and complex consolidation results in some unpredictable performance problems and introduces new requirements, such as proper configurations for scheduler and reasonable arrangements for services. In this paper, we present a comparative performance evaluation of several different typical application consolidations in different configurations of scheduler parameters (under Credit scheduler) in Xen. We analyze the impact of the configurations of scheduler and mutual impact between VMs which run different types of applications, present proposals for users to adopt an efficient scheduler configuration in applying virtualization, and offer insight into the relationship of performance and scheduler parameters to motivate future innovation in virtualization.
Diagnostic potential of near-infrared Raman spectroscopy in the stomach: differentiating dysplasia from normal tissue

Raman spectroscopy is a molecular vibrational spectroscopic technique that is capable of optically probing the biomolecular changes associated with diseased transformation. The purpose of this study was to explore near-infrared (NIR) Raman spectroscopy for identifying dysplasia from normal gastric mucosa tissue. A rapid-acquisition dispersive-type NIR Raman system was utilised for tissue Raman spectroscopic measurements at 785 nm laser excitation. A total of 76 gastric tissue samples obtained from 44 patients who underwent endoscopy investigation or gastrectomy operation were used in this study. The histopathological examinations showed that 55 tissue specimens were normal and 21 were dysplasia. Both the empirical approach and multivariate statistical techniques, including principal components analysis (PCA), and linear discriminant analysis (LDA), together with the leave-one-sample-out cross-validation method, were employed to develop effective diagnostic algorithms for classification of Raman spectra between normal and dysplastic gastric tissues. High-quality Raman spectra in the range of 800–1800 cm−1 can be acquired from gastric tissue within 5 s. There are specific spectral differences in Raman spectra between normal and dysplasia tissue, particularly in the spectral ranges of 1200–1500 cm−1 and 1600–1800 cm−1, which contained signals related to amide III and amide I of proteins, CH3CH2 twisting of proteins/nucleic acids, and the C=C stretching mode of phospholipids, respectively. The empirical diagnostic algorithm based on the ratio of the Raman peak intensity at 875 cm−1 to the peak intensity at 1450 cm−1 gave the diagnostic sensitivity of 85.7% and specificity of 80.0%, whereas the diagnostic algorithms based on PCA-LDA yielded the diagnostic sensitivity of 95.2% and specificity 90.9% for separating dysplasia from normal gastric tissue. Receiver operating characteristic (ROC) curves further confirmed that the most effective diagnostic algorithm can be derived from the PCA-LDA technique. Therefore, NIR Raman spectroscopy in conjunction with multivariate statistical technique has potential for rapid diagnosis of dysplasia in the stomach based on the optical evaluation of spectral features of biomolecules.
Applying Principles of Robotics to Understand the Biomechanics, Neuromuscular Control and Clinical Rehabilitation of Human Digits

Given the biomechanical complexity of the human hand, it is not surprising that the grasping ability of individuals after treatment for severe paralysis or injury can seldom be restored to the level of the "normal" hand. Improving clinical outcomes will require i) developing experimental paradigms to evaluate hand function objectively, ii) understanding how the nervous system controls the redundant musculature of the digits, and iii) increasing the clinical impact of computer biomechanical models by validating their anatomical assumptions. Recognizing that the human hand is also a mechanical system, the principles of robotics developed Jbr the analysis of manipulators can be applied to each of these three clinical challenges. This paper is an overview of experimental and theoretical work aimed at understanding individual human digits as serial manipulators.
Key Issues in Multichannel Customer Management : Current Knowledge and Future Directions

Multichannel customer management is “the design, deployment, and evaluation of channels to enhance customer value through effective customer acquisition, retention, and development” (Neslin, Scott A., D. Grewal, R. Leghorn, V. Shankar, M. L. Teerling, J. S. Thomas, P. C. Verhoef (2006), Challenges and Opportunities in Multichannel Management. Journal of Service Research 9(2) 95–113). Channels typically include the store, the Web, catalog, sales force, third party agency, call center and the like. In recent years, multichannel marketing has grown tremendously and is anticipated to grow even further. While we have developed a good understanding of certain issues such as the relative value of a multichannel customer over a single channel customer, several research and managerial questions still remain. We offer an overview of these emerging issues, present our future outlook, and suggest important avenues for future research.
A Survey of Domain Ontology Engineering: Methods and Tools

With the advent of the Semantic Web, the field of domain ontology engineering has gained more and more importance. This innovative field may have a big impact on computer-based education and will certainly contribute to its development. This paper presents a survey on domain ontology engineering and especially domain ontology learning. The paper focuses particularly on automatic methods for ontology learning from texts. It summarizes the state of the art in natural language processing techniques and statistical and machine learning techniques for ontology extraction. It also explains how intelligent tutoring systems may benefit from this engineering and talks about the challenges that face the field.
Computer Vision Malaria Diagnostic Systems—Progress and Prospects

Accurate malaria diagnosis is critical to prevent malaria fatalities, curb overuse of antimalarial drugs, and promote appropriate management of other causes of fever. While several diagnostic tests exist, the need for a rapid and highly accurate malaria assay remains. Microscopy and rapid diagnostic tests are the main diagnostic modalities available, yet they can demonstrate poor performance and accuracy. Automated microscopy platforms have the potential to significantly improve and standardize malaria diagnosis. Based on image recognition and machine learning algorithms, these systems maintain the benefits of light microscopy and provide improvements such as quicker scanning time, greater scanning area, and increased consistency brought by automation. While these applications have been in development for over a decade, recently several commercial platforms have emerged. In this review, we discuss the most advanced computer vision malaria diagnostic technologies and investigate several of their features which are central to field use. Additionally, we discuss the technological and policy barriers to implementing these technologies in low-resource settings world-wide.
Behavioral Phenotyping and Pathological Indicators of Parkinson's Disease in C. elegans Models

Parkinson's disease (PD) is a neurodegenerative disorder with symptoms that progressively worsen with age. Pathologically, PD is characterized by the aggregation of α-synuclein in cells of the substantia nigra in the brain and loss of dopaminergic neurons. This pathology is associated with impaired movement and reduced cognitive function. The etiology of PD can be attributed to a combination of environmental and genetic factors. A popular animal model, the nematode roundworm Caenorhabditis elegans, has been frequently used to study the role of genetic and environmental factors in the molecular pathology and behavioral phenotypes associated with PD. The current review summarizes cellular markers and behavioral phenotypes in transgenic and toxin-induced PD models of C. elegans.
Home-based hand rehabilitation with a robotic glove in hemiplegic patients after stroke: a pilot feasibility study.

To evaluate the feasibility and safety of home rehabilitation of the hand using a robotic glove, and, in addition, its effectiveness, in hemiplegic patients after stroke.



In this non-randomized pilot study, 21 hemiplegic stroke patients (Ashworth spasticity index ≤ 3) were prescribed, after in-hospital rehabilitation, a 2-month home-program of intensive hand training using the Gloreha Lite glove that provides computer-controlled passive mobilization of the fingers. Feasibility was measured by: number of patients who completed the home-program, minutes of exercise and number of sessions/patient performed. Safety was assessed by: hand pain with a visual analog scale (VAS), Ashworth spasticity index for finger flexors, opponents of the thumb and wrist flexors, and hand edema (circumference of forearm, wrist and fingers), measured at start (T0) and end (T1) of rehabilitation. Hand motor function (Motricity Index, MI), fine manual dexterity (Nine Hole Peg Test, NHPT) and strength (Grip test) were also measured at T0 and T1.



Patients performed, over a mean period 56 (49-63) days, a total of 1699 (1353-2045) min/patient of exercise with Gloreha Lite, 5.1 (4.3-5.8) days/week. Seventeen patients (81%) completed the full program. The mean VAS score of hand pain, Ashworth spasticity index and hand edema did not change significantly at T1 compared to T0. The MI, NHPT and Grip test improved significantly (p = 0.0020, 0.0156 and 0.0024, respectively) compared to baseline.



Gloreha Lite is feasible and safe for use in home rehabilitation. The efficacy data show a therapeutic effect which need to be confirmed by a randomized controlled study.
Ontology augmentation: combining semantic web and text resources

This work investigates the process of selecting, extracting and reorganizing content from Semantic Web information sources, to produce an ontology meeting the specifications of a particular domain and/or task. The process is combined with traditional text-based ontology learning methods to achieve tolerance to knowledge incompleteness. The paper describes the approach and presents experiments in which an ontology was built for a diet evaluation task. Although the example presented concerns the specific case of building a nutritional ontology, the methods employed are domain independent and transferrable to other use cases.
Inhibitory effect of N-acetylcysteine on invasion and MMP-9 production of T24 human bladder cancer cells.

MMPs play a crucial role in the process of cancer invasion and metastasis.



The influence of NAC on invasion and MMP-9 production of human bladder cancer cell line T24 was investigated using an in vitro invasion assay, gelatin zymography, Western and Northern blot analyses and RT-PCR assays.



TPA increased the number of invading T24 cells through reconstituted basement membrane more than 10-fold compared to basal condition. NAC inhibited TPA-enhanced invasion dose-dependently. TPA increased the MMP-9 production by T24 cells without altering expression of TIMP-1 gene, while NAC suppressed TPA-enhanced production of MMP-9. Neither TPA nor NAC altered TIMP-1 mRNA level in T24 cells. In vitro experiments demonstrated that MMP-9 was directly inhibited by NAC but was not influenced by TPA.



NAC limits invasion of T24 human bladder cancer cells by inhibiting the MMP-9 production in addition to a direct inhibition of MMP-9 activity.
Geometric and Physical Constraints for Head Plane Crowd Density Estimation in Videos

State-of-the-art methods of people counting in crowded scenes rely on deep networks to estimate people density in the image plane. Perspective distortion effects are handled implicitly by either learning scale-invariant features or estimating density in patches of different sizes, neither of which accounts for the fact that scale changes must be consistent over the whole scene. In this paper, we show that feeding an explicit model of the scale changes to the network considerably increases performance. An added benefit is that it lets us reason in terms of number of people per square meter on the ground, allowing us to enforce physicallyinspired temporal consistency constraints that do not have to be learned. This yields an algorithm that outperforms state-of-the-art methods on crowded scenes, especially when perspective effects are strong.
Language mapping with navigated repetitive TMS: Proof of technique and validation

Lesion-based mapping of speech pathways has been possible only during invasive neurosurgical procedures using direct cortical stimulation (DCS). However, navigated transcranial magnetic stimulation (nTMS) may allow for lesion-based interrogation of language pathways noninvasively. Although not lesion-based, magnetoencephalographic imaging (MEGI) is another noninvasive modality for language mapping. In this study, we compare the accuracy of nTMS and MEGI with DCS.



Subjects with lesions around cortical language areas underwent preoperative nTMS and MEGI for language mapping. nTMS maps were generated using a repetitive TMS protocol to deliver trains of stimulations during a picture naming task. MEGI activation maps were derived from adaptive spatial filtering of beta-band power decreases prior to overt speech during picture naming and verb generation tasks. The subjects subsequently underwent awake language mapping via intraoperative DCS. The language maps obtained from each of the 3 modalities were recorded and compared.



nTMS and MEGI were performed on 12 subjects. nTMS yielded 21 positive language disruption sites (11 speech arrest, 5 anomia, and 5 other) while DCS yielded 10 positive sites (2 speech arrest, 5 anomia, and 3 other). MEGI isolated 32 sites of peak activation with language tasks. Positive language sites were most commonly found in the pars opercularis for all three modalities. In 9 instances the positive DCS site corresponded to a positive nTMS site, while in 1 instance it did not. In 4 instances, a positive nTMS site corresponded to a negative DCS site, while 169 instances of negative nTMS and DCS were recorded. The sensitivity of nTMS was therefore 90%, specificity was 98%, the positive predictive value was 69% and the negative predictive value was 99% as compared with intraoperative DCS. MEGI language sites for verb generation and object naming correlated with nTMS sites in 5 subjects, and with DCS sites in 2 subjects.



Maps of language function generated with nTMS correlate well with those generated by DCS. Negative nTMS mapping also correlates with negative DCS mapping. In our study, MEGI lacks the same level of correlation with intraoperative mapping; nevertheless it provides useful adjunct information in some cases. nTMS may offer a lesion-based method for noninvasively interrogating language pathways and be valuable in managing patients with peri-eloquent lesions.