nils-herrmann/clean_scirepeval huggingface dataset:
Mean value coordinates for closed triangular meshes

Constructing a function that interpolates a set of values defined at vertices of a mesh is a fundamental operation in computer graphics. Such an interpolant has many uses in applications such as shading, parameterization and deformation. For closed polygons, mean value coordinates have been proven to be an excellent method for constructing such an interpolant. In this paper, we generalize mean value coordinates from closed 2D polygons to closed triangular meshes. Given such a mesh P, we show that these coordinates are continuous everywhere and smooth on the interior of P. The coordinates are linear on the triangles of P and can reproduce linear functions on the interior of P. To illustrate their usefulness, we conclude by considering several interesting applications including constructing volumetric textures and surface deformation.
Randomized controlled trial of yttrium-90-labeled ibritumomab tiuxetan radioimmunotherapy versus rituximab immunotherapy for patients with relapsed or refractory low-grade, follicular, or transformed B-cell non-Hodgkin's lymphoma.

Radioimmunotherapy combines biologic and radiolytic mechanisms to target and destroy tumor cells, thus offering a needed therapeutic alternative for refractory non-Hodgkin's lymphoma (NHL) patients. This phase III randomized study compares the novel radioimmunotherapy yttrium-90 ((90)Y) ibritumomab tiuxetan with a control immunotherapy, rituximab, in 143 patients with relapsed or refractory low-grade, follicular, or transformed CD20(+) transformed NHL.



Patients received either a single intravenous (IV) dose of (90)Y ibritumomab tiuxetan 0.4 mCi/kg (n = 73) or rituximab 375 mg/m(2) IV weekly for four doses (n = 70). The radioimmunotherapy group was pretreated with two rituximab doses (250 mg/m(2)) to improve biodistribution and one dose of indium-111 ibritumomab tiuxetan for imaging and dosimetry. The primary end point, overall response rate (ORR), was assessed by an independent, blinded, lymphoma expert panel.



ORR was 80% for the (90)Y ibritumomab tiuxetan group versus 56% for the rituximab group (P =.002). Complete response (CR) rates were 30% and 16% in the (90)Y ibritumomab tiuxetan and rituximab groups, respectively (P =.04). An additional 4% achieved an unconfirmed CR in each group. Kaplan-Meier estimated median duration of response was 14.2 months in the (90)Y ibritumomab tiuxetan group versus 12.1 months in the control group (P =.6), and time to progression was 11.2 versus 10.1 months (P =.173) in all patients. Durable responses of > or = 6 months were 64% versus 47% (P =.030). Reversible myelosuppression was the primary toxicity noted with (90)Y ibritumomab tiuxetan.



Radioimmunotherapy with (90)Y ibritumomab tiuxetan is well tolerated and produces statistically and clinically significant higher ORR and CR compared with rituximab alone.
"Dumbbell-like" crystals in urine sediment.

Presence of crystals in urine sediment is not an infrequent finding, and its observation does not have any especial clinical signification in most situations. Some factors as pH, temperature, and emission time of the urine may play a part in their formation. Nevertheless, in some diseases such as congenital anomalies or severe liver pathology, some types of crystals (cystine, tyrosine, and leucine) are quite rare and its identification is very important. In urinary cytopathology, crystals such as uric acid, calcium oxalate dihydrate, and ammonium magnesium phosphate (struvite) are among those that may be frequently observed in urine sediment. Taking into account its morphology, they are usually named as ‘‘lemons’’ (uric acid), ‘‘envelopes’’ (calcium oxalate dihydrate), and ‘‘coffin linds’’ (struvite). Here, a type of crystal (calcium oxalate monohydrate), not as frequent as those mentioned earlier is showed . The image belongs to a voided urine smear from a patient suffering acute renal failure. Calcium oxalate monohydrate crystals vary in size and, depending on their position, they give a different projection showing the typical ‘‘dumbbell’’ shape or round–oval morphology with a central depression (they are also described as ‘‘hour-glass" or ‘‘sheaf’’). Factors such as excessive consumption of certain aliments rich in oxalates (spinaches, asparagus, tomatoes, etc), a decrease in the urinary pH, and a scant diuresis may contribute to its development. The presence of calcium oxalate crystals (mono or dihydrate) in the urine sediment does not mean necessary the existence of calculi in the urinary tract. In fresh and unstained urine samples, and depending of their size, this type of crystals must be differentiated from erythrocytes, yeast, and parasitic ova, especially Enterobius vermicularis. However, its high refraction index can solve the problem.
Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors

NMDA receptors mediate excitatory synaptic transmission and regulate synaptic plasticity in the central nervous system, but their dysregulation is also implicated in numerous brain disorders. Here, we describe GluN2A-selective negative allosteric modulators (NAMs) that inhibit NMDA receptors by stabilizing the apo state of the GluN1 ligand-binding domain (LBD), which is incapable of triggering channel gating. We describe structural determinants of NAM binding in crystal structures of the GluN1/2A LBD heterodimer, and analyses of NAM-bound LBD structures corresponding to active and inhibited receptor states reveal a molecular switch in the modulatory binding site that mediate the allosteric inhibition. NAM binding causes displacement of a valine in GluN2A and the resulting steric effects can be mitigated by the transition from glycine bound to apo state of the GluN1 LBD. This work provides mechanistic insight to allosteric NMDA receptor inhibition, thereby facilitating the development of novel classes NMDA receptor modulators as therapeutic agents.
Ginseng in the treatment of fatigue in multiple sclerosis: a randomized, placebo-controlled, double-blind pilot study.

Fatigue is one of the common complaints of multiple sclerosis (MS) patients, and its treatment is relatively unclear. Ginseng is one of the herbal medicines possessing antifatigue properties, and its administration in MS for such a purpose has been scarcely evaluated. The purpose of this study was to evaluate the efficacy and safety of ginseng in the treatment of fatigue and the quality of life of MS patients.



Eligible female MS patients were randomized in a double-blind manner, to receive 250-mg ginseng or placebo twice daily over 3 months. Outcome measures included the Modified Fatigue Impact Scale (MFIS) and the Iranian version of the Multiple Sclerosis Quality Of Life Questionnaire (MSQOL-54). The questionnaires were used after randomization, and again at the end of the study.



Of 60 patients who were enrolled in the study, 52 (86%) subjects completed the trial with good drug tolerance. Statistical analysis showed better effects for ginseng than the placebo as regards MFIS (p = 0.046) and MSQOL (p ≤ 0.0001) after 3 months. No serious adverse events were observed during follow-up.



This study indicates that 3-month ginseng treatment can reduce fatigue and has a significant positive effect on quality of life. Ginseng is probably a good candidate for the relief of MS-related fatigue. Further studies are needed to shed light on the efficacy of ginseng in this field.
An updated evolutionary classification of CRISPR–Cas systems

The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
Increased plasma levels of circulating cell-free mitochondrial DNA in suicide attempters: associations with HPA-axis hyperactivity

Preclinical data suggest that chronic stress may cause cellular damage and mitochondrial dysfunction, potentially leading to the release of mitochondrial DNA (mtDNA) into the bloodstream. Major depressive disorder has been associated with an increased amount of mtDNA in leukocytes from saliva samples and blood; however, no previous studies have measured plasma levels of free-circulating mtDNA in a clinical psychiatric sample. In this study, free circulating mtDNA was quantified in plasma samples from 37 suicide attempters, who had undergone a dexamethasone suppression test (DST), and 37 healthy controls. We hypothesized that free circulating mtDNA would be elevated in the suicide attempters and would be associated with hypothalamic-pituitary-adrenal (HPA)-axis hyperactivity. Suicide attempters had significantly higher plasma levels of free-circulating mtDNA compared with healthy controls at different time points (pre- and post-DST; all P-values<2.98E-12, Cohen's d ranging from 2.55 to 4.01). Pre-DST plasma levels of mtDNA were positively correlated with post-DST cortisol levels (rho=0.49, P<0.003). Suicide attempters may have elevated plasma levels of free-circulating mtDNA, which are related to impaired HPA-axis negative feedback. This peripheral index is consistent with an increased cellular or mitochondrial damage. The specific cells and tissues contributing to plasma levels of free-circulating mtDNA are not known, as is the specificity of this finding for suicide attempters. Future studies are needed in order to better understand the relevance of increased free-circulating mtDNA in relation to the pathophysiology underlying suicidal behavior and depression.
Mesh-Based Broadband Home Network Solution: Setup and Experiments

In this paper, we investigate architectural and practical issues related to the setup of a broadband home network solution. Our experience led us to the consideration of a hybrid, wireless and wired, Mesh-Network to enable high data rate service delivery everywhere in the home. We demonstrate the effectiveness of our proposal using a real experimental testbed. This latter consists of a multi-hop mesh network composed of a home gateway and "extenders" supporting several types of physical connectivity including PLC, WiFi, and Ethernet. The solution also includes a layer 2 implementation of the OLSR protocol for path selection. We developed an extension of this protocol for QoS assurance and to enable the proper execution of existing services. We have also implemented a fast WiFi handover algorithm to ensure service continuity in case of user mobility among the extenders inside the home.
Scientific co-authorship networks

The paper addresses the stability of the co-authorship networks in time. The analysis is done on the networks of Slovenian researchers in two time periods (1991-2000 and 2001-2010). Two researchers are linked if they published at least one scientific bibliographic unit in a given time period. As proposed by Kronegger et al. (2011), the global network structures are examined by generalized blockmodeling with the assumed multi-core--semi-periphery--periphery blockmodel type. The term core denotes a group of researchers who published together in a systematic way with each other. The obtained blockmodels are comprehensively analyzed by visualizations and through considering several statistics regarding the global network structure. To measure the stability of the obtained blockmodels, different adjusted modified Rand and Wallace indices are applied. Those enable to distinguish between the splitting and merging of cores when operationalizing the stability of cores. Also, the adjusted modified indices can be used when new researchers occur in the second time period (newcomers) and when some researchers are no longer present in the second time period (departures). The research disciplines are described and clustered according to the values of these indices. Considering the obtained clusters, the sources of instability of the research disciplines are studied (e.g., merging or splitting of cores, newcomers or departures). Furthermore, the differences in the stability of the obtained cores on the level of scientific disciplines are studied by linear regression analysis where some personal characteristics of the researchers (e.g., age, gender), are also considered.
MVTec D2S: Densely Segmented Supermarket Dataset

We introduce the Densely Segmented Supermarket (D2S) dataset, a novel benchmark for instance-aware semantic segmentation in an industrial domain. It contains 21 000 high-resolution images with pixel-wise labels of all object instances. The objects comprise groceries and everyday products from 60 categories. The benchmark is designed such that it resembles the real-world setting of an automatic checkout, inventory, or warehouse system. The training images only contain objects of a single class on a homogeneous background, while the validation and test sets are much more complex and diverse. To further benchmark the robustness of instance segmentation methods, the scenes are acquired with different lightings, rotations, and backgrounds. We ensure that there are no ambiguities in the labels and that every instance is labeled comprehensively. The annotations are pixel-precise and allow using crops of single instances for articial data augmentation. The dataset covers several challenges highly relevant in the field, such as a limited amount of training data and a high diversity in the test and validation sets. The evaluation of state-of-the-art object detection and instance segmentation methods on D2S reveals significant room for improvement.
Clinical limitations of Invisalign.

Adult patients seeking orthodontic treatment are increasingly motivated by esthetic considerations. The majority of these patients reject wearing labial fixed appliances and are looking instead to more esthetic treatment options, including lingual orthodontics and Invisalign appliances. Since Align Technology introduced the Invisalign appliance in 1999 in an extensive public campaign, the appliance has gained tremendous attention from adult patients and dental professionals. The transparency of the Invisalign appliance enhances its esthetic appeal for those adult patients who are averse to wearing conventional labial fixed orthodontic appliances. Although guidelines about the types of malocclusions that this technique can treat exist, few clinical studies have assessed the effectiveness of the appliance. A few recent studies have outlined some of the limitations associated with this technique that clinicians should recognize early before choosing treatment options.
Automatic Recognition of Auslan Finger-spelling using Hidden Markov Models

In recent years, gesture recognition has received much attention from research communities. Computer vision-based gesture recognition has many potential applications in the area of human-computer interaction as well as sign language recognition. Sign languages use a combination of hand shapes, motion and locations as well as facial expressions. Finger-spelling is a manual representation of alphabet letters, which is often used where there is no sign word to correspond to a spoken word. In Australia, a sign language called Auslan is used by the deaf community and and the finger-spelling letters use two handed motion, unlike the well known finger-spelling of American Sign Language (ASL) that uses static shapes. This thesis presents the Auslan Finger-spelling Recognizer (AFR) that is a real-time system capable of recognizing signs that consists of Auslan manual alphabet letters from video sequences. The AFR system has two components: the first is the feature extraction process that extracts a combination of spatial and motion features from the images. Which classifies a sequence of features using Hidden Markov Models (HMMs). Tests using a vocabulary of twenty signed words showed the system could achieve 97% accuracy at the letter level and 88% at the word level using a finite state grammar network and embedded training.
Study of phenol biodegradation using Bacillus amyloliquefaciens strain WJDB-1 immobilized in alginate–chitosan–alginate (ACA) microcapsules by electrochemical method

An aerobic microorganism with an ability to utilize phenol as sole carbon and energy source was isolated from phenol-contaminated wastewater samples. The isolate was identified as Bacillus amyloliquefaciens strain WJDB-1 based on morphological, physiological, and biochemical characteristics, and 16S rDNA sequence analysis. Strain WJDB-1 immobilized in alginate–chitosan–alginate (ACA) microcapsules could degrade 200 mg/l phenol completely within 36 h. The concentration of phenol was determined using differential pulse voltammetry (DPV) at glassy carbon electrode (GCE) with a linear relationship between peak current and phenol concentration ranging from 2.0 to 20.0 mg/l. Cells immobilized in ACA microcapsules were found to be superior to the free suspended ones in terms of improving the tolerance to the environmental loadings. The optimal conditions to prepare microcapsules for achieving higher phenol degradation rate were investigated by changing the concentrations of sodium alginate, calcium chloride, and chitosan. Furthermore, the efficiency of phenol degradation was optimized by adjusting various processing parameters, such as the number of microcapsules, pH value, temperature, and the initial concentration of phenol. This microorganism has the potential for the efficient treatment of organic pollutants in wastewater.
Running head : FAKING THE IAT Faking the IAT : Aided and Unaided Response Control on the Implicit Association Tests

One pragmatic goal of implicit tools like the Implicit Association Tests (IAT) is to rule out self-presentation and controlled responding. Three experiments examined whether the IAT meets this goal, using Turkish and German groups along with positive and negative traits. Experiment 1 was an Internet study. After completing a naïve IAT pretest, participants were instructed to fake on a posttest in three graded conditions that differed in the explicitness of faking instructions. Experiment 2 replicated and extended the approach in the laboratory, including no-pretest condition. Results demonstrate that participants who intended to fake were successful, provided the experience of a pretest. Experiment 3 ruled out an alternative account of faking in terms of pretest experience. Faking was mostly due to slow-down on compatible trials, but a notable speed-up on incompatible trials also occurred. Faking remained inconspicuous, especially with non-blatant instructions; experts failed to identify faked data sets.
2P-DNN : Privacy-Preserving Deep Neural Networks Based on Homomorphic Cryptosystem

Machine Learning as a Service (MLaaS), such as Microsoft Azure, Amazon AWS, offers an effective DNN model to complete the machine learning task for small businesses and individuals who are restricted to the lacking data and computing power. However, here comes an issue that user privacy is exposed to the MLaaS server, since users need to upload their sensitive data to the MLaaS server. In order to preserve their privacy, users can encrypt their data before uploading it. This makes it difficult to run the DNN model because it is not designed for running in ciphertext domain. In this paper, using the Paillier homomorphic cryptosystem we present a new Privacy-Preserving Deep Neural Network model that we called 2P-DNN. This model can fulfill the machine leaning task in ciphertext domain. By using 2P-DNN, MLaaS is able to provide a Privacy-Preserving machine learning service for users. We build our 2P-DNN model based on LeNet-5, and test it with the encrypted MNIST dataset. The classification accuracy is more than 97%, which is close to the accuracy of LeNet-5 running with the MNIST dataset and higher than that of other existing Privacy-Preserving machine learning models.
On Business Process Redesign and Configuration: Leveraging Data Mining Classification & Outliers and Artifact-Centric Process Modeling

In today's e-business, data increasingly capture many behavioral aspects of our daily life, e.g. operational patterns in production lines, human shopping habit, medical treatment, supply-chain management. We formally define the behavior of tasks (of the business process in question) in connection with conceptually described business artifacts that are manipulated by the tasks. We relate this representation to data mining and nonfunctional requirements to better define the context for process redesign (i.e, design-time changes) and process configuration (i.e, run-time changes). Furthermore, we propose algorithms for business-process redesign and configuration based on the above context. Our research is positioned in the field of business process flexibility – a term coined by van der Aalst  in his thorough literature survey on business processes. We validate our framework using real-life data provided by our industrial partners.
Approaches in Language Teaching : Forward , Central , and Backward Design

The development and implementation of language teaching programs can be approached in several different ways, each of which has different implications for curriculum design. Three curriculum approaches are described and compared. Each differs with respect to when issues related to input, process, and outcomes, are addressed. Forward design starts with syllabus planning, moves to methodology, and is followed by assessment of learning outcomes. Resolving issues of syllabus content and sequencing are essential starting points with forward design, which has been the major tradition in language curriculum development. Central design begins with classroom processes and methodology. Issues of syllabus and learning outcomes are not specified in detail in advance and are addressed as the curriculum is implemented. Many of the ‘innovative methods’ of the 1980s and 90s reflect central design. Backward design starts from a specification of learning outcomes and decisions on methodology and syllabus are developed from the learning outcomes. The Common European Framework of Reference is a recent example of backward design. Examples will be given to suggest how the distinction between forward, central and backward design can clarify the nature of issues and trends that have emerged in language teaching in recent years.
An interactive augmented reality imaging system for minimally invasive orthopedic surgery

In orthopedic surgery, it is important for physicians to completely understand the three-dimensional bone structure for several procedures. To achieve this goal, it is required to image the patient several times using C-arm scanner from different positions during the surgery. This procedure is time consuming and increase the x-ray dose given to both patient and physician. In this paper, we propose an augmented reality imaging system for minimally invasive orthopedic surgery. The system is based on mapping the x-ray image to the real object such that the number of x-ray shots during the surgery can be significantly reduced. We consider two imaging scenarios that can fit with different cases. Results obtained through clinical data indicate that the proposed approach has a potential usefulness in real applications.