Miracle-dz/UniFAR-FTUs huggingface dataset:
A survey of data mining and knowledge discovery software tools

Knowledge discovery in databases is a rapidly growing field, whose development is driven by strong research interests as well as urgent practical, social, and economical needs. While the last few years knowledge discovery tools have been used mainly in research environments, sophisticated software products are now rapidly emerging. In this paper, we provide an overview of common knowledge discovery tasks and approaches to solve these tasks. We propose a feature classification scheme that can be used to study knowledge and data mining software. This scheme is based on the software's general characteristics, database connectivity, and data mining characteristics. We then apply our feature classification scheme to investigate 43 software products, which are either research prototypes or commercially available. Finally, we specify features that we consider important for knowledge discovery software to possess in order to accommodate its users effectively, as well as issues that are either not addressed or insufficiently solved yet.
Oxidative stress, mitochondrial damage and neurodegenerative diseases

Oxidative stress and mitochondrial damage have been implicated in the pathogenesis of several neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Oxidative stress is characterized by the overproduction of reactive oxygen species, which can induce mitochondrial DNA mutations, damage the mitochondrial respiratory chain, alter membrane permeability, and influence Ca2+ homeostasis and mitochondrial defense systems. All these changes are implicated in the development of these neurodegenerative diseases, mediating or amplifying neuronal dysfunction and triggering neurodegeneration. This paper summarizes the contribution of oxidative stress and mitochondrial damage to the onset of neurodegenerative eases and discusses strategies to modify mitochondrial dysfunction that may be attractive therapeutic interventions for the treatment of various neurodegenerative diseases.
Tapering of the Cervical Spinal Canal in Patients with Distended or Nondistended Syringes Secondary to Chiari Type I Malformation

BACKGROUND AND PURPOSE: Steeper tapering of the cervical spinal canal as documented in recent studies is thought to have a role in the pathophysiology of Chiari malformation-associated syringomyelia. This study aimed to determine whether taper ratio of the cervical spinal canal differs between patients with distended and nondistended syringes. MATERIALS AND METHODS: Seventy-seven adolescents (10–18 years) were divided into 2 groups: 44 with distended syrinx and 33 with nondistended syrinx. On T2-weighted MR images, anteroposterior diameter of the spinal canal was measured at each cervical level, and a linear trend line was fit by least squares regression to calculate the taper ratio. Taper ratios were compared between the 2 groups and further evaluated with respect to age and sex. RESULTS: In the nondistended group ND, the taper ratios for C1–C7, C1–C4, and C4–C7 averaged −0.73 ± 0.57, −1.61 ± 0.98, and −0.04 ± 0.54, respectively, all of which were significantly steeper than those observed in the distended group (P = .001, .004, and .033, respectively). Regarding the average diameters plotted by cervical level, the narrowest region of the canal was found to occur at C4 in both groups. In addition, no significant differences in taper ratio were noted between males and females, or between older (>14 years) and younger patients (≤14 years). CONCLUSIONS: Taper ratios of the cervical spinal canal were found to be different between patients with distended and nondistended syringes, indicating a reciprocal interaction between the syrinx and the cervical spine anatomy.
A common variant in the adiponectin gene on weight loss and body composition under sibutramine therapy in obesity

: In this study, we aimed to explore whether a common single nucleotide polymorphism (SNP), rs266729 ( - 11,377C . G), in the adiponectin C1Q and collagen domain containing (ADIPOQ) gene could influence weight reduction and fat change under sibutramine therapy in an obese population. There were 131 obese Taiwanese patients, including 44 in the placebo group and 87 in the sibutramine (10 mg daily) group. We assessed the measures of weight loss and body fat reduction at the end of the 12-week treatment period by analysis of covariance (ANCOVA) models using gender, baseline weight, and baseline percent body fat as covariates. By comparing the placebo and sibutramine groups with ANCOVA, our data revealed a strong effect of sibutramine on percent body fat loss (1.9 ± 0.3 vs 4.6 ± 0.5%; P , 0.001) and on weight reduction (2.8 ± 2.0 vs 7.9 ± 1.6 kg; P , 0.001) for subjects with the CC genotype. On the contrary, sibutramine had no significant effect on percent body fat loss or on weight loss in the GG and GC individuals. The results suggest that the SNP rs266729 of the ADIPOQ gene may contribute to weight reduction and fat loss in response to sibutramine therapy in Taiwanese obese patients.
Choosing the number of clusters

The issue of determining ‘the right number of clusters’ is attracting ever growing interest. The paper reviews published work on the issue with respect to mixture of distributions, partition, especially in k‐means clustering, and hierarchical cluster structures. Some perspective directions for further developments are outlined. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 252–260 DOI: 10.1002/widm.15
An approach to acanthosis nigricans

Acanthosis nigricans (AN) is characterized by dark, coarse and thickened skin with a velvety texture, being symmetrically distributed on the neck, the axillae, antecubital and popliteal fossae, and groin folds, histopathologically characterized by papillomatosis and hyperkeratosis of the skin. A high prevalence of AN has been observed recently. Different varieties of AN include benign, obesity associated, syndromic, malignant, acral, unilateral, medication-induced and mixed AN. Diagnosis is largely clinical with histopathology needed only for confirmation. Other investigations needed are fasting lipoprotein profile, fasting glucose, fasting insulin, hemoglobin and alanine aminotransferase for obesity associated AN and radiological investigations (plain radiography, ultrasonography, magnetic resonance imaging/computerized tomography) for malignancy associated AN. The most common treatment modalities include retinoids and metformin.
Clinical significance of incidental findings on staging positron emission tomography for oesophagogastric malignancies.

INTRODUCTION The aim of this retrospective study was to determine the clinical significance of incidental findings detected on positron emission tomography (PET) in patients undergoing staging of oesophagogastric malignancies. METHODS Patients with oesophagogastric malignancies who underwent PET between June 2007 and May 2012 were included in the study. PET was performed according to hospital protocol. All imaging was interpreted by two consultant radiologists in nuclear medicine. Incidental findings that were unrelated to the primary malignancy were recorded and patients were recommended to have further investigations (imaging, endoscopy and biopsy). RESULTS Overall, 333 patients (240 male, 93 female; mean age: 67 years) with upper gastrointestinal malignancies were eligible for inclusion in the study. Eighty-nine of these patients had PET demonstrating one or more incidental findings. Two patients were found to have a second primary malignancy. One patient had a distant metastasis of his primary cancer and six patients had a premalignant lesion. CONCLUSIONS In this study, incidental findings were discovered in 26.7% of patients with known oesophagogastric cancer. A second primary cancer or premalignant lesion was found in 8.4% of patients with incidental findings. Patients with these findings should be investigated to rule out further malignancy. There were a high proportion of false positive results in our study. It is recommended that each patient is considered on an individual basis and assessed with simultaneous PET and computed tomography.
Model Formulation: MachineProse: An Ontological Framework for Scientific Assertions

OBJECTIVE The idea of testing a hypothesis is central to the practice of biomedical research. However, the results of testing a hypothesis are published mainly in the form of prose articles. Encoding the results as scientific assertions that are both human and machine readable would greatly enhance the synergistic growth and dissemination of knowledge. DESIGN We have developed MachineProse (MP), an ontological framework for the concise specification of scientific assertions. MP is based on the idea of an assertion constituting a fundamental unit of knowledge. This is in contrast to current approaches that use discrete concept terms from domain ontologies for annotation and assertions are only inferred heuristically. MEASUREMENTS We use illustrative examples to highlight the advantages of MP over the use of the Medical Subject Headings (MeSH) system and keywords in indexing scientific articles. RESULTS We show how MP makes it possible to carry out semantic annotation of publications that is machine readable and allows for precise search capabilities. In addition, when used by itself, MP serves as a knowledge repository for emerging discoveries. A prototype for proof of concept has been developed that demonstrates the feasibility and novel benefits of MP. As part of the MP framework, we have created an ontology of relationship types with about 100 terms optimized for the representation of scientific assertions. CONCLUSION MachineProse is a novel semantic framework that we believe may be used to summarize research findings, annotate biomedical publications, and support sophisticated searches.
Verification Based Solution for Structured MAB Problems

We consider the problem of finding the best arm in a stochastic Multi-armed Bandit (MAB) game and propose a general framework based on verification that applies to multiple well-motivated generalizations of the classic MAB problem. In these generalizations, additional structure is known in advance, causing the task of verifying the optimality of a candidate to be easier than discovering the best arm. Our results are focused on the scenario where the failure probability δ must be very low; we essentially show that in this high confidence regime, identifying the best arm is as easy as the task of verification. We demonstrate the effectiveness of our framework by applying it, and matching or improving the state-of-the art results in the problems of: Linear bandits, Dueling bandits with the Condorcet assumption, Copeland dueling bandits, Unimodal bandits and Graphical bandits.
ProFORMA: Probabilistic Feature-based On-line Rapid Model Acquisition

3D models have an extensive range of uses in computer vision, but generating these models can be a difficult and time consuming task. Whilst many automated and semi-automated 3D reconstruction techniques exist, current methods have a variety of drawbacks meaning that ultimately many high quality 3D models are still generated using labour intensive methods or completely by hand. Off-line reconstruction methods have the potential to create highly detailed and accurate 3D reconstructions, but this level of detail usually implies high computational cost. This means that the reconstruction pipeline must be split into two phases: an image sequence or video collection phase (fast), and an off-line processing phase (slow), after which the model is obtained. If at this stage the model is found to be flawed, additional images or an entire video sequence must be collected and the lengthy reconstruction phase repeated. It may take several iterations and many hours before obtaining an acceptable model. Our system, ProFORMA, enables textured 3D models to be acquired on-line in just over a minute, with models being reconstructed fast enough to provide feedback for view planning. The user is free to interact with the object which is robustly tracked using a method that makes immediate use of the partial model [2]. The reconstruction environment is not constrained to a studio and enables models of textured objects to be acquired using a single camera and commodity hardware. Rapid reconstruction is enabled by a novel recursive probabilistic tetrahedron carving algorithm, which uses visibility of point features to rapidly generate a surface model. Parts of an object not yet seen by the system are indicated to the user who can then manipulate the object in order to provide new views. Our on-line reconstruction system uses a fixed-position video camera and allows the user to manipulate the object to be modelled using their hand. This enables the object to be orientated so that all parts of the object (including the base) can be viewed and modelled. No assumptions about the object are made and no prior information is known about the object, although the object must be sufficiently textured.
Joint power allocation, base station assignment and beamformer design for an uplink SIMO heterogeneous network

Consider the max-min problem for an uplink SIMO heterogeneous network, where the base stations (BS) are coordinated dynamically for joint reception under some backhaul overhead constraints. We formulate this problem in the perspective of joint power allocation, BS assignment and beamformer design, and develop an efficient algorithm based on alternating optimization. In particular, we transfer the joint BS assignment and beamformer design subproblem into a group LASSO problem by applying the alternating direction method of multipliers (ADMM). Consequently, the problem is solved in a partially distributed manner and in each iteration a simple closed-form solution is derived. Numerical simulations demonstrate the effectiveness and efficiency of the proposed algorithm.
Antiviral Activity of Shiga Toxin 1: Suppression of Bovine Leukemia Virus-Related Spontaneous Lymphocyte Proliferation

ABSTRACT Human infections with Shiga toxin (Stx)-producing Escherichia coli (STEC) cause hemorrhagic colitis. The Stxs belong to a large family of ribosome-inactivating proteins (RIPs) that are found in a variety of higher plants and some bacteria. Many RIPs have potent antiviral activity for the plants that synthesize them. STEC strains, both virulent and nonvirulent to humans, are frequently isolated from healthy cattle. Interestingly, despite intensive investigations, it is not known why cattle carry STEC. We tested the hypothesis that Stx has antiviral properties for bovine viruses by assessing the impact of Stx type 1 (Stx1) on bovine peripheral blood mononuclear cells (PBMC) from cows infected with bovine leukemia virus (BLV). PBMC from BLV-positive animals invariably displayed spontaneous lymphocyte proliferation (SLP) in vitro. Stx1 or the toxin A subunit (Stx1A) strongly inhibited SLP. Toxin only weakly reduced the pokeweed mitogen- or interleukin-2-induced proliferation of PBMC from normal (BLV-negative) cows and had no effect on concanavalin A-induced proliferation. The toxin activity in PBMC from BLV-positive cattle was selective for viral SLP and did not abrogate cell response to pokeweed mitogen- or interleukin-2-induced proliferation. Antibody to virus or Stx1A was most effective at inhibiting SLP if administered at the start of cell culture, indicating that both reagents likely interfere with BLV-dependent initiation of SLP. Stx1A inhibited expression of BLV p24 protein by PBMC. A well-defined mutant Stx1A (E167D) that has decreased catalytic activity was not effective at inhibiting SLP, suggesting the inhibition of protein synthesis is likely the mechanism of toxin antiviral activity. Our data suggest that Stx has potent antiviral activity and may serve an important role in BLV-infected cattle by inhibiting BLV replication and thus slowing the progression of infection to its malignant end stage.
Study on total phenolics compound, total flavonoids, total monomeric anthocyanins, vitamin E and gamma-oryzanol in pigmented Thai rice

Glass-ionomer cement is a result of combining of fluoroaluminosilicate glass as powder and the polyalkenoic acid as liquid which set by acid-base reaction. Advantages of glass-ionomer cement which are different from other types of direct restorative materials; providing good adhesion to both enamel and dentin by chemical bond, fluoride release and uptake abilities, good biological compatibility and the coefficient of thermal expansion similar to dentin. Glass-ionomer cement can be classified into different types according to modification of acid or type of reinforcement materials. Meanwhile, glass-ionomer cement is continuously developed in terms of improved physical properties, biological properties and esthetic consideration. At present, this cement is widely used as a single restorative material or used with other materials such as amalgam or resin composite. กลาสสไอโอโนเมอรซเมนต เปนวสดทเกดจากการผสมระหวางผงแกวฟลออโรอะลมโนซลเกต และสวนเหลวทมกรดพอลอลคโนอกเปนองคประกอบหลก โดยกอตวดวยปฏกรยากรด-ดาง ขอดของกลาสสไอโอโนเมอรซเมนตทแตกตางจากวสดบรณะชนดอน ๆ คอ ใหการยดตดทดทงกบเคลอบฟนและเนอฟนดวยพนธะเคม สามารถปลดปลอยและดดสะสมฟลออไรด มความเขากนทางชวภาพทด และมคาสมประสทธการขยายตวเมอมการเปลยนแปลงอณหภมทใกลเคยงกบเนอฟน กลาสสไอโอโนเมอรซเมนตสามารถแบงไดเปนหลายประเภท ขนอยกบการปรบสถานะของกรด หรอสารดดแปร ขณะเดยวกนกลาสสไอโอโนเมอรซเมนตยงไดรบการพฒนาอยางตอเนอง โดยปรบปรงสมบตทางกายภาพ ชวภาพ และความสวยงามใหดยงขน ปจจบนมการนำกลาสสไอโอโนเมอรซเมนตมาใชอยางแพรหลาย โดยสามารถนำมาใชเปนวสดบรณะฟนเดยว ๆ หรอสามารถนำมาใชรวมกบวสดบรณะอน ๆ เชน อะมลกม หรอ เรซนคอมโพสตได
Transforming a Chunker to a Parser

Ever since the landmark paper Ramshaw and Marcus (1995), machine learning systems have been used successfully for identifying base phrases (chunks), the bottom constituents of a parse tree. We expand a state-of-the-art chunking algorithm to a bottom-up parser by recursively applying the chunker to its own output. After testing different training configurations we obtain a reasonable parser which is tested against a standard data set. Its performance falls behind that of current state-of-the-art parsers. We give some suggestions for modifications of the parser which may lead to future performance improvements.
Multiply Attenuated, Self-Inactivating Lentiviral Vectors Efficiently Deliver and Express Genes for Extended Periods of Time in Adult Rat Cardiomyocytes In Vivo

Background—Among retroviral vectors, lentiviral vectors are unique in that they transduce genes into both dividing and nondividing cells. However, their ability to provide sustained myocardial transgene expression has not been evaluated. Methods and Results—Multiply attenuated, self-inactivating lentivectors based on human immunodeficiency virus-1 contained the enhanced green fluorescent protein (EGFP) gene under the transcriptional control of either the cytomegalovirus (CMV) immediate-early enhancer/promoter, the elongation factor-1&agr; (EF-1&agr;) promoter, or the phosphoglycerate-kinase (PGK) promoter. Lentivectors transduced adult rat cardiomyocytes in a dose-dependent manner (transduction rates, >90%; multiplicity of infection, ≈5). The CMV promoter achieved higher EGFP expression levels than the EF-1&agr; and PGK promoters. Insertion of the central polypurine tract pol sequence improved gene transfer efficiency by ≈2-fold. In vivo gene transfer kinetics was studied by measuring the copy number of integrated lentivirus DNA and EGFP concentrations in cardiac extracts by real-time polymerase chain reaction and ELISA, respectively. With CMV promoter-containing lentivectors, vector DNA peaked at day 3, declined by ≈4-fold at day 14, but then remained stable up to week 10. Similarly, EGFP expression peaked at day 7, decreased by ≈7-fold at day 14, but was essentially stable thereafter. In contrast, vector DNA and EGFP expression declined rapidly with EF-1&agr; promoter–containing lentivectors. Peak EGFP expression with titer-matched adenovectors was ≈35% higher than with CMV lentivectors but was lost rapidly over time. Conclusions—Lentivectors efficiently transduce and express genes for extended periods of time in cardiomyocytes in vivo. Lentivectors provide a useful tool for studying myocardial biology and a potential system for gene heart therapy.
International Journal of Behavioral Nutrition and Physical Activity Test-retest Reliability of Ipaq Environmental-module in an African Population

Background: There is overwhelming evidence of the benefits of physical activity and the physical environment is increasingly recognized as a promising determinant of physical activity participation. The influence of the environment on physical activity has not been evaluated among black Africans and no specific measure exists for assessing environmental factors related to physical activity in an African environment. The IPAQ E-module was designed to assess environmental factors for physical activity participation and was considered to be relevant to all countries regardless of the stage of economic development. The objective of this study was to assess the test-retest reliability of IPAQ E-module in an African population.
Rethinking the Area Approach: Immigrants and the Labor Market in California, 1960-2005

I show that a CES production-function-based approach with skill differentiation and integrated national labor markets has predictions for the employment effect of immigrants at the local level. The model predicts that if I look at the employment (rather than wage) response by skill to immigration in a state, I can estimate the substitutability-complementarity between natives and immigrants. This allows me to infer, other things constant, how immigrants stimulate or depress the demand for native labor. I also use a novel instrument based on demographic characteristics of total Central American migrants or of the Mexican Population to predict immigration by skill level within California. Looking at immigration to California between 1960 and 2005 my estimates support the assumption of a nationally integrated labor market by skill and they support the hypothesis that natives and immigrants in the same education-experience group are not perfectly substitutable. This, in turn, explains the counter-intuitive fact that there is a zero correlation between immigration and wage and employment outcomes of natives.
Automatic removal of EEG artifacts using ICA and Lifting Wavelet Transform

EEG artifacts significantly affect the accuracy of feature extraction and data classification of Brain-computer interface (BCI) systems. The EEG artifacts derived from ocular and muscular activities are inevitable and unpredictable due to subject's physical conditions. Consequently, the removal of these artifacts is a crucial function for BCI applications to make the system more robust. One of the most prominent techniques employed to remove the EEG artifacts is Independent Component Analysis (ICA). This technique separates EEG signals into Independent Components (ICs) and then discriminates EEG artifacts from neurally generated brain signals. However, the source separation of ICA algorithm is imperfect. Frequently, the IC identified to be an artifact includes brain wave activities useful for data classification. The proposed method will elaborate on the IC with Lifting Wavelet Transform (LWT) to extract the useful neural signals from the artifact component. Experimental results prove the performance and accuracy of the proposed removal algorithm of light and strong eye-blink artifacts. This removal technique implemented in NECTEC's Neurofeedback System for Attention Training was tested in pre-trial sessions with 10 healthy subjects and 5 MCI patients at Chulalongkorn Hospital, Bangkok.