nils-herrmann/clean_scirepeval huggingface dataset:
Conversational Metaphors in Use: Exploring the Contrast between Technical and Everyday Notions of Metaphor

Much computational work has been done on identifying and interpreting the meaning of metaphors, but little work has been done on understanding the motivation behind the use of metaphor. To computationally model discourse and social positioning in metaphor, we need a corpus annotated with metaphors relevant to speaker intentions. This paper reports a corpus study as a first step towards computational work on social and discourse functions of metaphor. We use Amazon Mechanical Turk (MTurk) to annotate data from three web discussion forums covering distinct domains. We then compare these to annotations from our own annotation scheme which distinguish levels of metaphor with the labels: nonliteral, conventionalized, and literal. Our hope is that this work raises questions about what new work needs to be done in order to address the question of how metaphors are used to achieve social goals in interaction.
Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ).

We assess the reliability of isobaric-tags for relative and absolute quantitation (iTRAQ), based on different types of replicate analyses taking into account technical, experimental, and biological variations. In total, 10 iTRAQ experiments were analyzed across three domains of life involving Saccharomyces cerevisiae KAY446, Sulfolobus solfataricus P2, and Synechocystis sp. PCC 6803. The coverage of protein expression of iTRAQ analysis increases as the variation tolerance increases. In brief, a cutoff point at +/-50% variation (+/-0.50) would yield 88% coverage in quantification based on an analysis of biological replicates. Technical replicate analysis produces a higher coverage level of 95% at a lower cutoff point of +/-30% variation. Experimental or iTRAQ variations exhibit similar behavior as biological variations, which suggest that most of the measurable deviations come from biological variations. These findings underline the importance of replicate analysis as a validation tool and benchmarking technique in protein expression analysis.
External Patch Prior Guided Internal Clustering for Image Denoising

Natural image modeling plays a key role in many vision problems such as image denoising. Image priors are widely used to regularize the denoising process, which is an ill-posed inverse problem. One category of denoising methods exploit the priors (e.g., TV, sparsity) learned from external clean images to reconstruct the given noisy image, while another category of methods exploit the internal prior (e.g., self-similarity) to reconstruct the latent image. Though the internal prior based methods have achieved impressive denoising results, the improvement of visual quality will become very difficult with the increase of noise level. In this paper, we propose to exploit image external patch prior and internal self-similarity prior jointly, and develop an external patch prior guided internal clustering algorithm for image denoising. It is known that natural image patches form multiple subspaces. By utilizing Gaussian mixture models (GMMs) learning, image similar patches can be clustered and the subspaces can be learned. The learned GMMs from clean images are then used to guide the clustering of noisy-patches of the input noisy images, followed by a low-rank approximation process to estimate the latent subspace for image recovery. Numerical experiments show that the proposed method outperforms many state-of-the-art denoising algorithms such as BM3D and WNNM.
Redefining Context Windows for Word Embedding Models: An Experimental Study

Distributional semantic models learn vector representations of words through the contexts they occur in. Although the choice of context (which often takes the form of a sliding window) has a direct influence on the resulting embeddings, the exact role of this model component is still not fully understood. This paper presents a systematic analysis of context windows based on a set of four distinct hyperparameters. We train continuous SkipGram models on two English-language corpora for various combinations of these hyper-parameters, and evaluate them on both lexical similarity and analogy tasks. Notable experimental results are the positive impact of cross-sentential contexts and the surprisingly good performance of right-context windows.
Knowledgeable Explanations for Recommender Systems

Recommender Systems (RS) serve online customers in identifying those items from a variety of choices that best match their needs and preferences. In this context explanations summarize the reasons why a specific item is proposed and strongly increase the users' trust in the system's results. In this paper we propose a framework for generating knowledgeable explanations that exploits domain knowledge to transparently argue why a recommended item matches the user's preferences. Furthermore, results of an online experiment on a real-world platform show that users' perception of the usability of a recommender system is positively influenced by knowledgeable explanations and that consequently users' experience in interacting with the system, their intention to use it repeatedly as well as their commitment to recommend it to others are increased.
New Flexible Silicone-Based EEG Dry Sensor Material Compositions Exhibiting Improvements in Lifespan, Conductivity, and Reliability

This study investigates alternative material compositions for flexible silicone-based dry electroencephalography (EEG) electrodes to improve the performance lifespan while maintaining high-fidelity transmission of EEG signals. Electrode materials were fabricated with varying concentrations of silver-coated silica and silver flakes to evaluate their electrical, mechanical, and EEG transmission performance. Scanning electron microscope (SEM) analysis of the initial electrode development identified some weak points in the sensors' construction, including particle pull-out and ablation of the silver coating on the silica filler. The newly-developed sensor materials achieved significant improvement in EEG measurements while maintaining the advantages of previous silicone-based electrodes, including flexibility and non-toxicity. The experimental results indicated that the proposed electrodes maintained suitable performance even after exposure to temperature fluctuations, 85% relative humidity, and enhanced corrosion conditions demonstrating improvements in the environmental stability. Fabricated flat (forehead) and acicular (hairy sites) electrodes composed of the optimum identified formulation exhibited low impedance and reliable EEG measurement; some initial human experiments demonstrate the feasibility of using these silicone-based electrodes for typical lab data collection applications.
Morphological Changes Induced by Bipolar Radiofrequency Ablation in Thyroid Nodules – a Preclinical Ex Vivo Investigation

Recently, radiofrequency ablation (RFA) has been increasingly used for the treatment of thyroid nodules. However, immediate morphological changes associated with bipolar devices are poorly shown.  To present the results of analysis of gross and microscopic alterations in human thyroid tissue induced by RFA delivered through the application of the original patented device.  In total, there were 37 surgically removed thyroid glands in females aged 32-67 at presentation: 16 nodules were follicular adenoma (labelled as 'parenchymal' solid benign nodules) and adenomatous colloid goitre was represented by 21 cases. The thyroid gland was routinely processed and the nodules were sliced into two parts - one was a subject for histological routine processing according to the principles that universally apply in surgical pathology, the other one was used for the RFA procedure.  No significant difference in size reduction between parenchymal and colloid nodules was revealed (p>0.1, t-test) straight after the treatment. In addition, RFA equally effectively induced necrosis in follicular adenoma and adenomatous colloid goitre (p>0.1, analysis of variance test). As expected, tumour size correlated with size reduction (the smaller the size of the nodule, the greater percentage of the nodule volume that was ablated): r=-0.48 (p<0.0001).  The results make it possible to move from ex vivo experiments to clinical practice.
Leveraging RF-channel fluctuation for activity recognition: Active and passive systems, continuous and RSSI-based signal features

We consider the recognition of activities from passive entities by analysing radio-frequency (RF)-channel fluctuation. In particular, we focus on the recognition of activities by active Software-defined-radio (SDR)-based Device-free Activity Recognition (DFAR) systems and investigate the localisation of activities performed, the generalisation of features for alternative environments and the distinction between walking speeds. Furthermore, we conduct case studies for Received Signal Strength (RSS)-based active and continuous signal-based passive systems to exploit the accuracy decrease in these related cases. All systems are compared to an accelerometer-based recognition system.
Survival in Patients with Degenerative Mitral Stenosis: Results from a Large Retrospective Cohort Study.

Severe mitral annular calcification causing degenerative mitral stenosis (DMS) is increasingly encountered in patients undergoing mitral and aortic valve interventions. However, its clinical profile and natural history and the factors affecting survival remain poorly characterized. The goal of this study was to characterize the factors affecting survival in patients with DMS.



An institutional echocardiographic database was searched for patients with DMS, defined as severe mitral annular calcification without commissural fusion and a mean transmitral diastolic gradient of ≥2 mm Hg. This resulted in a cohort of 1,004 patients. Survival was analyzed as a function of clinical, pharmacologic, and echocardiographic variables.



The patient characteristics were as follows: mean age, 73 ± 14 years; 73% women; coronary artery disease in 49%; and diabetes mellitus in 50%. The 1- and 5-year survival rates were 78% and 47%, respectively, and were slightly worse with higher DMS grades (P = .02). Risk factors for higher mortality included greater age (P < .0001), atrial fibrillation (P = .0009), renal insufficiency (P = .004), mitral regurgitation (P < .0001), tricuspid regurgitation (P < .0001), elevated right atrial pressure (P < .0001), concomitant aortic stenosis (P = .02), and low serum albumin level (P < .0001). Adjusted for propensity scores, use of renin-angiotensin system blockers (P = .02) or statins (P = .04) was associated with better survival, and use of digoxin was associated with higher mortality (P = .007).



Prognosis in patients with DMS is poor, being worse in the aged and those with renal insufficiency, atrial fibrillation, and other concomitant valvular lesions. Renin-angiotensin system blockers and statins may confer a survival benefit, and digoxin use may be associated with higher mortality in these patients.
Critical Thinking , Page 1 Critical Thinking : Its Nature , Measurement , and Improvement

Critical thinking comprises the mental processes, strategies, and representations people use to solve problems, make decisions, and learn new concepts. The study of critical thinking combines the educational, philosophical, and psychological traditions of thought. R. Ennis offers a philosophical taxonomy suggesting that critical thinking results from the interaction of a set of dispositions toward critical thinking with a set of abilities for critical thiuking, while R. Sternberg's psychological taxonomy defines the skills involved in critical thiaking to be of three kinds: metacomponents, performance components, and knowledge-acquisition components. JCLoom's taxonomy of education puts knowledge at the lowest level, followed by comprehension, application, analysis, and synthesis, with evaluation at the highest level. Tests for measuring critical thinking also come from the philosophical and psychological areas. The Matson-Glaser Critical Thinking Appraisal, the Cornell Critical Thinking Test, and the New Jersey Test of Reasoning Skills are derived from the philosophical tradition. The Triarchic Test of Intellectual Skills is psychologically derived, but does not try to separate critical thinking from intelligence. Programs for training critical thieking include Copi's 1978 course in logic, Bransterd and Stein's 1984 course called "The Ideal Problem Solver," Sternberg's 1986 "Understanding and Increasing Intelligence,' and Whimbey and Lochhead's 1982 " Solving and Comprehension.' Educators current concern with critical thinking offers students a new chance for developing critical thinking skills, but training must be brought into all aspects of the classroom to be successful.
De Novo 3q22.3q24 Microdeletion in a Patient With Blepharophimosis–Ptosis–Epicanthus Inversus Syndrome, Dandy-Walker Malformation, and Wisconsin Syndrome

Interstitial deletions affecting the long arm of chromosome 3 have been associated with a broad phenotype. This has included the features of blepharophimosis-ptosis-epicanthus inversus syndrome, Dandy-Walker malformation, and the rare Wisconsin syndrome. The authors report a young female patient presenting with features consistent with all 3 of these syndromes. This has occurred in the context of a de novo 3q22.3q24 microdeletion including FOXL2, ZIC1, and ZIC4. This patient provides further evidence for the role of ZIC1 and ZIC4 in Dandy-Walker malformation and is the third reported case of Dandy-Walker malformation to have associated corpus callosum thinning. This patient is also only the seventh to be reported with the rare Wisconsin syndrome phenotype.
Tendoscopic Procedure Associated With Peroneal Tendons

Tendoscopy of the peroneal tendons is a useful tool to diagnose and treat peroneal tendon disorders. It provides a minimally invasive alternative to the already existing open surgical approaches. Tendoscopic approaches are safe when anatomic landmarks are identified and the portals are performed properly. Advantages of endoscopic procedures over open surgical procedures include reduced morbidity and postoperative pain, earlier mobilization, and better cosmetic results. Results of tendoscopic procedures are encouraging when compared with those following open surgery of the peroneal tendons. This article presents safe, reliable, and reproducible peroneal tendoscopy techniques.
A Control-Theoretic Approach for Dynamic Adaptive Video Streaming over HTTP

User-perceived quality-of-experience (QoE) is critical in Internet video applications as it impacts revenues for content providers and delivery systems. Given that there is little support in the network for optimizing such measures, bottlenecks could occur anywhere in the delivery system. Consequently, a robust bitrate adaptation algorithm in client-side players is critical to ensure good user experience. Previous studies have shown key limitations of state-of-art commercial solutions and proposed a range of heuristic fixes. Despite the emergence of several proposals, there is still a distinct lack of consensus on: (1) How best to design this client-side bitrate adaptation logic (e.g., use rate estimates vs. buffer occupancy); (2) How well specific classes of approaches will perform under diverse operating regimes (e.g., high throughput variability); or (3) How do they actually balance different QoE objectives (e.g., startup delay vs. rebuffering). To this end, this paper makes three key technical contributions. First, to bring some rigor to this space, we develop a principled control-theoretic model to reason about a broad spectrum of strategies. Second, we propose a novel model predictive control algorithm that can optimally combine throughput and buffer occupancy information to outperform traditional approaches. Third, we present a practical implementation in a reference video player to validate our approach using realistic trace-driven emulations.
Alcohol based tissue fixation as an alternative for formaldehyde: influence on immunohistochemistry.

Formaldehyde is commonly used in histopathology to fix tissue. Not only are the carcinogenic properties of this solution a hazard to the people in the workplace, it is also a major burden on the environment, and it crosslinks molecular groups that hinder immunohistochemistry.



The influence of two new alcohol based non-crosslinking fixatives on immunohistochemical staining properties was tested on various tissues.



Fresh tissue samples were cut into three equal pieces, which were then fixed in the alcohol based fixatives Boonfix or RCL2, or in neutral buffered formaldehyde (NBF) as control. After fixation, tissue was routinely processed to paraffin sections. Deparaffinised slides were blocked for endogenous peroxidase and subsequently submitted to the usual NBF based immunohistochemical protocols for 85 different common antibodies either not requiring antigen retrieval (AR), or AR in citrate buffer, EDTA or pepsin.



NBF fixed tissues provided significantly better immunostaining results (84% good staining) than RCL2 (66% good) and Boonfix (60%). The lesser performance of RCL2 and Boonfix was especially caused by pepsin AR which caused significant tissue damage. Omission of pepsin AR resulted in better immunostaining for these antibodies for RCL2 fixed tissues which were overall no longer significantly worse than NBF fixed tissue.



Tissues fixed in non-crosslinking alcohol based fixatives can successfully be immunohistochemically stained for most antibodies following the usual NBF based protocols. Omission of pepsin pretreatment seems to be important to retain proper morphology of immunostained tissues preserved in alcohol based fixatives. Therefore, when switching to less toxic and non-carcinogenic alcohol-based fixatives like RCL2, no major changes in the daily routine of immunohistochemistry are anticipated.
Nursing students' learning dynamics and influencing factors in clinical contexts.

Clinical placements are essential for students to develop clinical skills to qualify as nurses. However, various difficulties encountered by nursing students during their clinical education detract from developing clinical competencies. This constructivist grounded theory study aims to explore nursing students' experiences in clinical nursing education, and to identify the factors that influence the clinical education students receive. Twenty-one individual and six group semi-structured interviews were conducted with sixteen fourth year nursing students and four registered nurses. This research identified six factors that influence nursing students' clinical education: interpersonal, socio-cultural, instructional, environmental, emotional and physical factors. The research has developed a dynamic model of learning in clinical contexts, which offers opportunities to understand how students' learning is influenced multifactorially during clinical placements. The understanding and application of the model can improve nursing instructional design, and subsequently, nursing students' learning in clinical contexts.
Energy Efficient Hadamard Neural Networks

Deep learning has made significant improvements at many image processing tasks in recent years, such as image classification, object recognition and object detection. Convolutional neural networks (CNN), which is a popular deep learning architecture designed to process data in multiple array form, show great success to almost all detection & recognition problems and computer vision tasks. However, the number of parameters in a CNN is too high such that the computers require more energy and larger memory size. In order to solve this problem, we propose a novel energy efficient model Binary Weight and Hadamard-transformed Image Network (BWHIN), which is a combination of Binary Weight Network (BWN) and Hadamard-transformed Image Network (HIN). It is observed that energy efficiency is achieved with a slight sacrifice at classification accuracy. Among all energy efficient networks, our novel ensemble model outperforms other energy efficient models.
Stress-induced cortisol responses, sex differences, and false recollections in a DRM paradigm

The current studies investigated whether acute stress potentiates false recollections (so-called "false memories") in a Deese-Roediger-McDermott (DRM) paradigm, and whether sex differences modulate these effects. Participants were assigned to either a stress (trier social stress test) or a control group. Subsequently, they were subjected to DRM word lists and probed for recall and recognition. Results showed no differences between the stress and control group on measures of false recollections (Study 1; N=60). Even though correct recall was impaired by acute stress, there were no differences between high or low cortisol responders and controls on false recall or recognitions rates (Study 2; N=92). These results suggest that cortisol responses do not directly potentiate false recollections. Neither in Study 1 nor in Study 2 did we find any evidence that the effects of cortisol on false recollections are different in men and women, although there was an indication that independent of stress men produced more commission errors.
Post-acquisition image based compensation for thickness variation in microscopy section series

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji.
Skeletal muscle enzymes and fiber composition in male and female track athletes.

Muscle samples were obtained from the gastrocnemius of 17 female and 23 male track athletes, 10 untrained women, and 11 untrained men. Portions of the specimen were analyzed for total phosphorylase, lactic dehydrogenase (LDH), and succinate dehydrogenase (SDH) activities. Sections of the muscle were stained for myosin adenosine triphosphatase, NADH2 tetrazolium reductase, and alpha-glycerophosphate dehydrogenase. Maximal oxygen uptake (VO2max) was measured on a treadmill for 23 of the volunteers (6 female athletes, 11 male athletes, 10 untrained women, and 6 untrained men). These measurements confirm earlier reports which suggest that the athlete's preference for strength, speed, and/or endurance events is in part a matter of genetic endowment. Aside from differences in fiber composition and enzymes among middle-distance runners, the only distinction between the sexes was the larger fiber areas of the male athletes. SDH activity was found to correlate 0.79 with VO2max, while muscle LDH appeared to be a function of muscle fiber composition. While sprint- and endurance-trained athletes are characterized by distinct fiber compositions and enzyme activities, participants in strength events (e.g., shot-put) have relatively low muscle enzyme activities and a variety of fiber compositions.