Miracle-dz/UniFAR-FTUs huggingface dataset:
Sputum Smear Concentration May Misidentify Acid-Fast Bacilli As Mycobacterium Tuberculosis in HIV-Infected Patients

Background:Tuberculosis (TB) diagnosis in most resource-limited settings still depends on smear microscopy for identification of acid-fast bacilli (AFB). However, recently developed molecular diagnostics that test for the presence of Mycobacterium tuberculosis (Mtb) DNA have been shown to be superior for confirmation of TB diagnosis. Methods:At regular clinical visits over a 12-month period, we collected sputa from HIV-infected patients presenting with signs or symptoms of TB at 2 Nigerian clinics. Sputa were stained for AFB and tested using the Genotype MTBDRplus to confirm the presence of Mtb. Other species were identified using 16S rRNA sequence. Results:In 56% (233/415) of AFB-positive patients, Mtb was confirmed. The patients on antiretroviral therapy were less likely than those not on antiretroviral therapy to be infected with Mtb [odds ratio (OR) = 0.25, P = 0.003]. In a multivariate logistic regression model using clinical features and diagnostic results, abnormal respiratory findings on auscultation (OR = 3.28, P = 0.03) and a direct sputum smear grade >3/100 (OR = 6.4, 4.6, P < 0.02) were significant predictors of Mtb infection. Concentrated sputum smear was predictive of Mtb infection only at the highest grades (2+, 3+). Interestingly, among 65 samples that could not be confirmed for Mtb, 32 (49%) were found to contain other, possibly novel, actinomycetes, including atypical Mycobacteria, Rhodococcus spp, Nocardia spp, and Corynebacterium spp. Conclusions:We conclude that concentrated sputum smears may misidentify other bacteria as Mtb in HIV-infected patients. The use of molecular diagnostics could reduce unnecessary or inappropriate treatment and improve identification of pathogens in resource-limited settings with high HIV burden.
Mechanisms of motor dysfunction after transient MCA occlusion: persistent transmission failure in cortical synapses is a major determinant.

BACKGROUND AND PURPOSE Failure of prompt motor recovery after spontaneous recirculation or thrombolytic therapy may be due to an unsatisfactory restoration of synaptic activity within cortex and/or blockade of electrical impulses at the severely ischemic subcortical region. METHODS Afferent, efferent, and synaptic activities were focally examined within the rat sensorimotor cortex by recording the somatosensory-evoked potential (SEP) and motor area response evoked by stimulation of premotor afferents (PmEP) intracortically and the motor-evoked potential (MEP) generated by stimulation of the forelimb area from the brain stem. The effect of ischemia on electrical activity in the cortex and on axonal conduction in the subcortical region was studied differentially by proximal or distal occlusion of the MCA. RESULTS MEP consisted of direct and indirect waves generated by direct activation of pyramidal axons and indirect excitation of pyramidal neurons via cortical synapses, respectively. MEP, PmEP, and SEP disappeared on proximal occlusion. Following reperfusion after 1 to 3 hours of ischemia, the direct wave of MEP readily recovered but the indirect wave showed no improvement, suggesting a restored axonal conduction but impaired cortical synaptic transmission. The synaptic defect, which also caused a poor recovery in PmEP and SEP and on electrocorticogram, was persistent and detected 24 hours after 1 hour of proximal occlusion. CONCLUSIONS Our data suggest that motor dysfunction is caused by loss of cortical excitability and blockade of motor action potentials at the subcortical level during ischemia. After brief transient ischemia, axonal conduction readily recovers; however, a persistent transmission failure at cortical synapses leads to motor dysfunction.
From Holonomy of the Ising Model Form Factors to n-Fold Integrals and the Theory of Elliptic Curves

We recall the form factors f (j) N,N corresponding to the -extension C(N,N; ) of the two-point diagonal correlation function of the Ising model on the square lattice and their associated linear differential equations which exhibit both a "Russian-doll" nesting, and a decomposition of the linear differential operators as a direct sum of operators (equivalent to symmetric powers of the differential operator of the complete elliptic integral E). The scaling limit of these differential operators breaks the direct sum structure but not the "Russian doll" structure, the "scaled" linear differential operators being no longer Fuchsian. We then introduce some multiple integrals of the Ising class expected to have the same singularities as the singularities of the n-particle contributions (n) to the susceptibility of the square lattice Ising model. We find the Fuchsian linear differential equations satisfied by these multiple integrals for n = 1,2,3,4 and, only modulo a prime, for n = 5 and 6, thus providing a large set of (possible) new singularities of the (n) . We get the location of these singularities by solving the Landau conditions. We discuss the mathematical, as well as physical, interpretation of these new singularities. Among the singularities found, we underline the fact that the quadratic polynomial condition 1 + 3w + 4w 2 = 0, that occurs in the linear differential equation of (3) , actually corresponds to the occurrence of complex multiplication for elliptic curves. The interpretation of complex multiplication for elliptic curves as complex fixed points of generators of the exact renormalization group is sketched. The other singularities occurring in our multiple integrals are not related to complex multiplication situations, suggesting a geometric interpretation in terms of more general (motivic) mathematical structures beyond the theory of elliptic curves. The scaling limit of the (lattice off-critical) structures as a confluent limit of regular singularities is discussed in the conclusion.
Measuring Magnetic Characteristics of Synchronous Machines by Applying Position Estimation Techniques

The torque produced by synchronous machines is a function of stator current and flux linkage. Due to magnetic saturation, the relation between both is nonlinear. In other words, the inductances of a motor are operating point dependent. In many applications, however, magnetic saturation is neglected in order to simplify the model of the motor. If, on the other hand, a precise model is needed (e.g., for efficiency improvements), it is useful to measure the flux linkage depending on the current (or vice versa). This paper proposes a method that applies position estimation algorithms from anisotropy-based sensorless control schemes to measure the relation between flux linkage and stator current. The method works for different types of synchronous machines. Measurement results of an interior permanent magnet (PM) and a surface PM motor are presented and compared with results obtained with a conventional electromotive force-based measurement method.
Incorporating Knowledge Resources to Enhance Medical Information Extraction

This paper describes a method to extract medical information from texts. The method targets to extract complaints and diagnoses from electronic health record texts. Complaints and diagnoses are fundamental information and can be used for more complex medical tasks. The method utilizes several medical knowledge resources to enhance the performance of extraction. With an evaluation using NTCIR10 MedNLP data, our method marked 86.53 in F1 score with a cross validation. The score is comparable to top scoring teams in NTCIR-10 MedNLP task. The approach taken to incorporate knowledge resources has a high generality. It is not restricted to the resources presented in this paper and can be applied to various other resources.
Image and Collateral Text in Support of Auto-Annotation and Sentiment Analysis

We present a brief overview of the way in which image analysis, coupled with associated collateral text, is being used for auto-annotation and sentiment analysis. In particular, we describe our approach to auto-annotation using the graph-theoretic dominant set clustering algorithm and the annotation of images with sentiment scores from SentiWordNet. Preliminary results are given for both, and our planned work aims to explore synergies between the two approaches.
Retinal vascular tree morphology: a semi-automatic quantification

A semi-automatic method to measure and quantify geometrical and topological properties of continuous vascular trees in clinical fundus images is described. Measurements are made from binary images obtained with a previously described segmentation process. The skeletons of the segmented trees are produced by thinning, ff branch and crossing points are identified and segments of the trees are labeled and stored as a chain code. The operator selects a tree to be measured and decides if it is an arterial or venous tree. An automatic process then measures the lengths, areas and angles of the individual segments of the tree. Geometrical data and the connectivity information between branches from continuous retinal vessel trees are tabulated. A number of geometrical properties and topological indexes are derived. Vessel diameters and branching angles are validated against manual measurements and several derived geometrical and topological properties are extracted from red-free fundus images of ten normotensive and ten age- and sex-matched hypertensive subjects and compared with previously reported results.
Corrosion of iron from heritage buildings: Proposal for degradation indexes based on rust layer composition and electrochemical reactivity

In the present work, the authors tried to establish degradation indices for heritage ferrous artefacts, especially those used in ancient buildings and submitted to indoor atmospheric corrosion. The authors focused on the site of the Amiens Cathedral in the north of France. Samples coming from this reference site were carefully characterised in order to identify the different phases constituting the corrosion scale. The scale consists in a matrix of iron oxyhydroxide goethite embedded with several ferrihydrite marblings. Other phases such as lepidocrocite and akaganeite are scarcely present in the external part of the corrosion scale. Moreover, electrochemical measurements on both references and ancient samples enable to define the reduction reactive phases. From the nature of these phases and their localisation, two degradation indices were defined to evaluate rust reactivity. Finally, a curve that links these two factors is proposed as a first step towards a corrosion diagnosis.
Joint hypermobility syndrome: A common clinical disorder associated with migraine in women

Preliminary studies suggested that headache disorders are more common in patients with joint hypermobility syndrome (JHS). The objectives of this study were to determine if the prevalence, frequency, and disability of migraine differ between female patients with JHS and a control population. Twenty-eight patients with JHS and 232 controls participated in the case-cohort study. Participants underwent a structured verbal interview and were assigned a diagnosis of migraine based on criteria of the International Classification of Headache Disorders, 2nd Edition. The primary outcome measures were the prevalence, frequency, and headache-related disability of migraine. Logistic regression was used for the prevalence analysis and Poisson regression for the frequency and disability analyses. Results indicated that the prevalence of migraine was 75% in JHS patients and 43% in controls. The adjusted odds ratio for the prevalence of migraine was 3.19 (95% CI 1.24, 8.21] in JHS patients. The rate ratios for migraine frequency and headache-related disability were 1.67 (95% CI 1.01, 2.76) and 2.99 (95% CI 1.66, 5.38), respectively, for JHS patients. Our study suggests that JHS is a clinical disorder strongly associated with an increased prevalence, frequency, and disability of migraine in females.
A Perceptual-Statistics Shading Model

The process of surface perception is complex and based on several influencing factors, e.g., shading, silhouettes, occluding contours, and top down cognition. The accuracy of surface perception can be measured and the influencing factors can be modified in order to decrease the error in perception. This paper presents a novel concept of how a perceptual evaluation of a visualization technique can contribute to its redesign with the aim of improving the match between the distal and the proximal stimulus. During analysis of data from previous perceptual studies, we observed that the slant of 3D surfaces visualized on 2D screens is systematically underestimated. The visible trends in the error allowed us to create a statistical model of the perceived surface slant. Based on this statistical model we obtained from user experiments, we derived a new shading model that uses adjusted surface normals and aims to reduce the error in slant perception. The result is a shape-enhancement of visualization which is driven by an experimentally-founded statistical model. To assess the efficiency of the statistical shading model, we repeated the evaluation experiment and confirmed that the error in perception was decreased. Results of both user experiments are publicly-available datasets.
GradientShop: A gradient-domain optimization framework for image and video filtering

We present an optimization framework for exploring gradient-domain solutions for image and video processing. The proposed framework unifies many of the key ideas in the gradient-domain literature under a single optimization formulation. Our hope is that this generalized framework will allow the reader to quickly gain a general understanding of the field and contribute new ideas of their own. We propose a novel metric for measuring local gradient saliency that identifies salient gradients that give rise to long, coherent edges, even when the individual gradients are faint. We present a general weighting scheme for gradient constraints that improves the visual appearance of results. We also provide a solution for applying gradient-domain filters to videos and video streams in a coherent manner. Finally, we demonstrate the utility of our formulation in creating effective yet simple to implement solutions for various image-processing tasks. To exercise our formulation we have created a new saliency-based sharpen filter and a pseudo image-relighting application. We also revisit and improve upon previously defined filters such as nonphotorealistic rendering, image deblocking, and sparse data interpolation over images (e.g., colorization using optimization).
Choosing a Clustering: An A Posteriori Method for Social Networks

Abstract Selecting an appropriate method of clustering for network data a priori can be a frustrating and confusing process. To address the problem we build on an a posteriori approach developed by Grimmer and King (2011) that compares hundreds of possible clustering methods at once through concise and intuitive visualization. We adapt this general method to the context of social networks, extend it with additional visualization features designed to enhance interpretability, and describe its principled use, outlining steps for selecting a class of methods to compare, interpreting visual output, and making a final selection. The interactive method, implemented in R, is demonstrated using Zachary’s karate club, a canonical dataset from the network literature.
Cellular events and intracellular survival of Campylobacter jejuni during infection of HEp-2 cells

Invasion and intracellular survival of Campylobacter jejuni in HEp-2 cells were analyzed by transmission electron microscopy and by viable counts after killing of extracellular bacteria by gentamicin. During the first 30 min after challenge, no bacteria were seen in association with the host cell. After 1 h, campylobacters apparently attached to the cell membrane, with areas of close appositions. In these areas, an intracellular network of actin-like filaments was seen beneath the plasma membrane. Other bacteria were included into endocytic vacuoles. After 3 h, an intense lysosomal response was observed in the host cells, as determined by the presence of myelinic forms and acid phosphatase activity. After 9 h, bacteria still contained in vacuoles showed signs of degradation with a change from spiral to coccal forms. Morphological evidence of phagosome-lysosome fusion was also seen, and these observations by transmission electron microscopy correlated well with a decrease in bacteria viability 9 h after challenge, as determined from separate kinetics studies. Inhibitors of phagocytosis were observed to reduce markedly the entry of C. jejuni into the cells at concentrations which apparently did not affect bacterial viability. These results suggest that the campylobacters were successively attached to the HEp-2 cell membrane, internalized by a phagocytic-like mechanism, and digested after phagosome-lysosome fusion.
Bringing Culture and Human Frailty to Rational Actors: A Critique of Classical Law and Economics

This essay advances two theses: that the law and economics movement has been losing its upward trajectory within law schools, and that its practitioners should increasingly look to psychology and sociology in order to enrich the explanatory power and normative punch of economic analysis. The argument that law and economics lacks richness is hardly new. One of the wisest variations on the theme was Arthur Leff's sidesplitting 1974 review of Richard Posner's Economic Analysis of Law. ' Leff asserted the aridity of the rational-actor model of human behavior that economists employ. The economists' model, in its purest form, is based on elegantly simple propositions about both cognitive capacities and motivations. The model assumes that a person can perfectly process available information about alternative courses of action, and can rank possible outcomes in order of expected utility. The model also assumes that an actor will choose the course of action that will maximize his personal expected utility, which may, of course, reflect a concern for the welfare of others. 2 Leff asserted, as others had long before him, that the assumption of rationality exaggerates actual human cognitive capacities, and that, because a person's received utility is unobservable, the assumption of rational utility-maximization is strictly nonfalsifiable. A richer model for positive analysis, argued Leff, would look to psychology to develop a more realistic view of cognitive processes, and also look to sociology to obtain a more accurate picture of social influences on human behavior. 3
Use of Multiplex PCR To Detect Classical and Newly Described Pyrogenic Toxin Genes in Staphylococcal Isolates

ABSTRACT Staphylococcus aureus may contain one or more genes that encode a variety of immunomodulatory pyrogenic toxins (PTs), including the staphylococcal enterotoxins and toxic shock syndrome toxin (TSST). The PTs interact with several cellular targets to produce disease, such as food poisoning and toxic shock syndrome. At present, nine serologically distinct enterotoxins and one immunoreactive form of TSST have been identified and characterized. As isolates of S. aureus are further assessed, it is anticipated that this number will increase. To facilitate screening, a multiplex PCR was designed to simultaneously determine which of these 10 currently known PT genes an individualS. aureus isolate possesses. We show here, using S. aureus isolates with characterized PT phenotypes, that this novel PCR technique reliably detects each of the known PTs in a single reaction.
An Density-based Energy-efficient Routing Algorithm in Wireless Sensor Networks Using Game Theory

Clustering is an efficient technique that is widely adopted in wireless sensor networks. It divides network into clusters and let cluster heads be responsible for forwarding aggregated data to the sink. With energy efficiency in account, the conflict between an individual node and the entire network remains to be solved. In this paper, we propose a Density-based Energy-efficient Game-theoretic Routing Algorithm (DEGRA). As a clustering algorithm, DEGRA adopts game theory and set a utility function based on the nodes’ density, residual energy and average energy consumption of its neighboring nodes. Cluster heads are iteratively selected. We also design the intra-cluster and multi-hop inter-cluster routing algorithms. Simulation results show that cluster heads are evenly distributed and our proposed routing algorithm do consume much less energy than algorithms such as LEACH and DEER. The network lifetime is also largely prolonged.
Learning manipulation actions from a few demonstrations

To efficiently plan complex manipulation tasks, robots need to reason on a high level. Symbolic planning, however, requires knowledge about the preconditions and effects of the individual actions. In this work, we present a practical approach to learn manipulation skills, including preconditions and effects, based on teacher demonstrations. We believe that requiring only a small number of demonstrations is essential for robots operating in the real world. Therefore, our main focus and contribution is the ability to infer the preconditions and effects of actions based on a small number of demonstrations. Our system furthermore expresses the acquired manipulation actions as planning operators and is therefore able to use symbolic planners to solve new tasks. We implemented our approach on a PR2 robot and present real world manipulation experiments that illustrate that our system allows non-experts to transfer knowledge to robots.
Comment Target Extraction Based on Conditional Random Field & Domain Ontology

Comment target extraction is the first task for sentiment analysis. Conditional random fields (CRF) method has achieved good performance on the Named Entity Recognition. In this paper, CRF model is used for comment target extraction in Chinese in combination with domain ontology of products with word and part of speech as features. Domain ontology of products is considered as a semantic feature, such as the name of the product, the component of the product (model appearance, function etc), synonyms or upper and lower relationships, which are used to extract implicit comment target. Experiments on the third task corpus of COAE2008 showed remarkable performance of the proposed approach. Combination of ontology and CRF method increased the precision and recall of comment target extraction, achieved 86.56% and 77.23% on cell phone data, 83.16% and 73.97% on notebook data.
User Navigation Behavior Mining Using Multiple Data Domain Description

User Navigation Behavior Mining (UNBM) mainly studies the problems of extracting the interesting user access patterns from user access sequences (UAS), which are usually used for user access prediction and web page recommendation. Through analyzing the real world web data, we find most of user access sequences carrying hybrid features of different patterns, rather than a single one.