Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive Value of Clinical Diagnostic Codes for the CDC Case Definition of Pelvic Inflammatory Disease (PID): Implications for Surveillance

Background Reporting of pelvic inflammatory disease (PID) from private providers could be incomplete because of time and staff constraints, lack of knowledge of reporting requirements and of case definitions. Reporting burden can be alleviated with the use of administrative data. Goal The goal of this study was to determine the validity of clinical diagnostic codes assigned in electronic medical records (EMR) for identifying PID and their use in enhancing surveillance. Study Design A random sample of 296 records with a PID International Classification of Diseases, 9th Revision (ICD-9), code (614.9) were reviewed to assess for the presence of the Centers for Disease Control and Prevention (CDC) criteria for the case definition of PID. We used the records meeting the CDC clinical case definition criteria as the reference standard to determine the sensitivity, specificity, and predictive values of various data elements. Results Used alone, the positive predictive value (PPV) of ICD-9 code 614.9 for a CDC case definition of PID was 18.1%. The PPV increased to 100% and 56% when the ICD-9 code visit was associated with a positive test for Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT), respectively. Conclusion In this multispecialty group practice, a positive test for GC and CT coupled with ICD-9 code 614.9 could be used to enhance reporting of cases of PID.
B‐Cell Immunity in the Context of T‐Cell Tolerance after Combined Kidney and Bone Marrow Transplantation in Humans

Five patients with end‐stage kidney disease received combined kidney and bone marrow transplants from HLA haploidentical donors following nonmyeloablative conditioning to induce renal allograft tolerance. Immunosuppressive therapy was successfully discontinued in four patients with subsequent follow‐up of 3 to more than 6 years. This allograft acceptance was accompanied by specific T‐cell unresponsiveness to donor antigens. However, two of these four patients showed evidence of de novo antibodies reactive to donor antigens between 1 and 2 years posttransplant. These humoral responses were characterized by the presence of donor HLA‐specific antibodies in the serum with or without the deposition of the complement molecule C4d in the graft. Immunofluorescence staining, ELISA assays and antibody profiling using protein microarrays demonstrated the co‐development of auto‐ and alloantibodies in these two patients. These responses were preceded by elevated serum BAFF levels and coincided with B‐cell reconstitution as revealed by a high frequency of transitional B cells in the periphery. To date, these B cell responses have not been associated with evidence of humoral rejection and their clinical significance is still unclear. Overall, our findings showed the development of B‐cell allo‐ and autoimmunity in patients with T‐cell tolerance to the donor graft.
Voice Activated Interactive Ambient Information Display

—Normally the primary purpose of an information display is to convey information. If it can be aesthetically interesting, that is an added bonus. Recent research experiments with reversing this imperative. An information display, which is ﬁrst - aesthetically pleasing and second - is able to display information, is designed and implemented. The display presents an e-mail title in a visual form as a collage of images - each image corresponding to one or more words. It next ﬁlters the collage through aesthetic properties speciﬁed by an artist, such as colors, texture, and shape. This ﬁlter renders the original collage as a pleasing art. We propose an extension of this work by: adding a voice activation module; displaying information of user’s request (versus displaying e-mail titles only); and presenting the display in a form of a decorative digital painting hanging on the wall. The advantages of this approach are: being ambient - in a sense of: entering person’s attention when needed, and largely disappearing into the environment when not needed; and being interactive - as in providing information per user’s interest through speech recognition. This produces new interactive, ambient system for aesthetic information display on user’s demand.
Embedded Gene Selection for Imbalanced Microarray Data Analysis

Most of microarray data sets are imbalanced, i.e. the number of positive examples is much less than that of negative, which will hurt performance of classifiers when it is used for tumor classification. Though it is critical, few previous works paid attention to this problem. Here we propose embedded gene selection with two algorithms i.e. EGSEE (Embedded Gene Selection for EasyEnsemble) and EGSIEE (Embedded Gene Selection for Individuals of EasyEnsemble) to treat this problem and improve generalization performance of the EasyEnsemble classifier. Experimental results on several microarray data sets show that compared with the previous two filter feature selection methods, EGSEE and EGSIEE obtain better performance.
Midfoot and Forefoot Injuries

Abstract Sports injuries of the midfoot and forefoot encompass a spectrum of osseous and soft tissue trauma. Magnetic resonance imaging serves as a primary or important supplementary diagnostic modality in evaluation of various injuries, most important of which include Lisfranc complex injury, stress fractures, and injury to the first metatarsophalangeal joint, aka “turf toe. ” Current technical advances in magnetic resonance and improved knowledge of regional anatomy enable thorough evaluation of the complex anatomic structures of the foot and facilitate accurate diagnosis in the setting of trauma.
Shadow Analysis Technique for Extraction of Building Height using High Resolution Satellite Single Image and Accuracy Assessment

Abstract. These High resolution satellite data with metadata information is used to extract the height of the building using shadow. Proposed approach divides into two phases 1) rooftop and shadow extraction and 2) height estimation. Firstly the rooftop and shadow region were extracted by manual/ automatic methods using Example – Based and Rule – Based approaches. After feature extraction next step is estimating height of the building by taking rooftop in association with shadow using Ratio Method and by using the relation between sun-satellite geometry. The performance analysis shows the total mean error of height is 0.67 m from ratio method, 1.51 m from Example – Based Approach and 0.96 m from Rule – Based Approach. Analysis concluded that Ratio Method i.e. manual method is best for height estimation but it is time consuming so the automatic Rule Based approach is best for height estimation in comparison to Example Based Approach because it require more knowledge and selection of more training samples as well as slows the processing rate of the method.
Prevalence and Correlates of Suspected Nonalcoholic Fatty Liver Disease in Chinese Children

Nonalcoholic fatty liver disease (NAFLD) has become a serious public health problem worldwide; however, the availability of information on the prevalence of NAFLD in the general pediatric population is still limited. The primary aim of this study was to reveal the prevalence and correlates of suspected NAFLD in Chinese children at the national level. Data from the China Health and Nutrition Surveys (CHNS) was used. Weight, height, waist circumference (WC), blood pressure (BP) were measured for children aged 7–18 years. Blood samples were collected and analyzed. Children were classified as having suspected NAFLD if common causes of liver disease were excluded, and serum alanine aminotransferase (ALT) values were above the established thresholds (>22.1 IU/L for girls and >25.8 IU/L for boys). A percentage of 9.03% (75 out of 831) of Chinese children was found to have suspected NAFLD. Overweight and obesity according to BMI percentiles, abdominal obesity, hyperuricemia (uric acid (UA) > 327 μmol/L), and elevated total cholesterol (TC) were all detected as the correlates of childhood suspected NAFLD when adjusting for other factors. Our study revealed the prevalence of suspected NAFLD in general Chinese children at the national level for the first time. Our findings indicate that suspected NAFLD in children is associated with increasing childhood morbidities, further studies are needed to better understand the prevalence of childhood NAFLD and its correlates, and large-scale programs should be launched to screen NAFLD in the pediatric population in China.
Finite deformation energy release rate computations in a steady rolling tire

The recent well publicized failures of the Firestone ATX/AT tires has brought to light the poor state of research into the basic physical causes of such failures and the poor state of research into analytic methods suitable for analyzing such failures. The essence of problems of this nature lies in the finite deformation fatigue fracture of elastomers at large strains. The definition of failure criteria is further complicated by the issue of material aging. The computational problem is rather demanding due to the truly 3-D nature of the tire system under load. Finding the failure forces (the singular energy momentum tractions) is made challenging by the spinning reference state normally utilized in computational tire analysis. A true analysis of such problems demands that one address all of these issues; this paper focuses on one aspect of this problem – viz., the formulation of suitable analytic expressions for the computation of the crack tip driving forces in spinning tires.
Nonlinear viscoelastic predictions of uniaxial‐extensional viscosities of entangled polymers

A simplified version of a convective-constraint-release model by Mead, Larson, and Doi1) is used here for predicting steady-state viscoelastic properties of linear polydisperse polymers in uniaxial extensional flow. The model predictions are compared with linear dynamic viscosities and steady-state uniaxial extensional viscosities of polystyrenes for which GPC measurements of the molecular weight distribution were reported2). By using parameter values obtained from data for monodisperse polystyrenes, the predictions for the polydisperse samples are made without adjustable parameters. For well-entangled samples, good agreement is obtained for both linear viscoelastic and extension-thinning regimes. For a weakly-entangled sample3), a transition from extension thinning to extension thickening as the extension rate increases appears to be correctly predicted by the model. The effects of constraint release are pronounced in the stretch ratio and viscosity contribution from each component to the overall viscosity.
Data Visualization with Simultaneous Feature Selection

Data visualization algorithms and feature selection techniques are both widely used in bioinformatics but as distinct analytical approaches. Until now there has been no method of measuring feature saliency while training a data visualization model. We derive a generative topographic mapping (GTM) based data visualization approach which estimates feature saliency simultaneously with the training of the visualization model. The approach not only provides a better projection by modeling irrelevant features with a separate noise model but also gives feature saliency values which help the user to assess the significance of each feature. We compare the quality of projection obtained using the new approach with the projections from traditional GTM and self-organizing maps (SOM) algorithms. The results obtained on a synthetic and a real-life chemoinformatics dataset demonstrate that the proposed approach successfully identifies feature significance and provides coherent (compact) projections
Current Understanding of Molecular Pathology and Treatment of Cardiomyopathy in Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD) is a genetic muscle disorder caused by mutations in the Dmd gene resulting in the loss of the protein dystrophin. Patients do not only experience skeletal muscle degeneration, but also develop severe cardiomyopathy by their second decade, one of the main causes of death. The absence of dystrophin in the heart renders cardiomyocytes more sensitive to stretch-induced damage. Moreover, it pathologically alters intracellular calcium (Ca2+) concentration, neuronal nitric oxide synthase (nNOS) localization and mitochondrial function and leads to inflammation and necrosis, all contributing to the development of cardiomyopathy. Current therapies only treat symptoms and therefore the need for targeting the genetic defect is immense. Several preclinical therapies are undergoing development, including utrophin up-regulation, stop codon read-through therapy, viral gene therapy, cell-based therapy and exon skipping. Some of these therapies are undergoing clinical trials, but these have predominantly focused on skeletal muscle correction. However, improving skeletal muscle function without addressing cardiac aspects of the disease may aggravate cardiomyopathy and therefore it is essential that preclinical and clinical focus include improving heart function. This review consolidates what is known regarding molecular pathology of the DMD heart, specifically focusing on intracellular Ca2+, nNOS and mitochondrial dysregulation. It briefly discusses the current treatment options and then elaborates on the preclinical therapeutic approaches currently under development to restore dystrophin thereby improving pathology, with a focus on the heart.
IslandPath: aiding detection of genomic islands in prokaryotes

UNLABELLED Genomic islands (clusters of genes of potential horizontal origin in a prokaryotic genome) are frequently associated with a particular adaptation of a microbe that is of medical, agricultural or environmental importance, such as antibiotic resistance, pathogen virulence, or metal resistance. While many sequence features associated with such islands have been adopted separately in applications for analysis of genomic islands, including pathogenicity islands, there is no single application that integrates multiple features for island detection. IslandPath is a network service which incorporates multiple DNA signals and genome annotation features into a graphical display of a bacterial or archaeal genome, to aid the detection of genomic islands. AVAILABILITY This application is available at http://www.pathogenomics. sfu.ca/islandpath and the source code is freely available, under GNU public licence, from the authors. SUPPLEMENTARY INFORMATION An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics. sfu.ca/islandpath/current/islandhelp.html
Simple extensions of combinatorial structures

An interval in a combinatorial structure R is a set I of points which are related to every point in R\I in the same way. A structure is simple if it has no proper intervals. Every combinatorial structure can be expressed as an inflation of a simple structure by structures of smaller sizes — this is called the substitution (or modular) decomposition. In this paper we prove several results of the following type: An arbitrary structure S of size n belonging to a class C can be embedded into a simple structure from C by adding at most f(n) elements. We prove such results when C is the class of all tournaments, graphs, permutations, posets, digraphs, oriented graphs and general relational structures containing a relation of arity greater than 2. The function f(n) in these cases is 2, ⌈log 2 ( n + 1)⌉, ⌈( n + 1)/2⌉, ⌈( n + 1)/2⌉, ⌈log 4 ( n + 1)⌉, ⌈log 3 ( n + 1)⌉ and 1, respectively. In each case these bounds are best possible.
Modelling the influence of human behaviour on the spread of infectious diseases: a review

Human behaviour plays an important role in the spread of infectious diseases, and understanding the influence of behaviour on the spread of diseases can be key to improving control efforts. While behavioural responses to the spread of a disease have often been reported anecdotally, there has been relatively little systematic investigation into how behavioural changes can affect disease dynamics. Mathematical models for the spread of infectious diseases are an important tool for investigating and quantifying such effects, not least because the spread of a disease among humans is not amenable to direct experimental study. Here, we review recent efforts to incorporate human behaviour into disease models, and propose that such models can be broadly classified according to the type and source of information which individuals are assumed to base their behaviour on, and according to the assumed effects of such behaviour. We highlight recent advances as well as gaps in our understanding of the interplay between infectious disease dynamics and human behaviour, and suggest what kind of data taking efforts would be helpful in filling these gaps.
A Menagerie of Tracks at Maryland: HARD, Enterprise, QA, and Genomics, Oh My!

This year, the University of Maryland participated in four separate tracks: HARD, enterprise, question answering, and genomics. Our HARD experiments involved a trained intermediary who searched for documents on behalf of the user, created clarification forms manually, and exploited user responses accordingly. The aim was to better understand the nature of single-iteration clarification dialogs and to develop an “ontology of clarifications” that can be leveraged to guide system development. For the enterprise track, we submitted ocial runs to the Known Item Search and the Discussion Search tasks. Document transformation to normalize dates and version numbers was found to be helpful, but suppression of text quoted from earlier messages and expansion of the indexed terms for a message based on subject line threading proved to not be. For the QA track, we submitted a manual run of “other” questions in an eort to quantify human performance on the task. Our genomics track participation was in collaboration with the National Library of Medicine, and is primarily reported in NLM’s overview paper.
Evaluating VR Driving Simulation from a Player Experience Perspective

The majority of HCI research in the field of automotive interfaces and driver-vehicle interaction is conducted utilizing driving simulators. High-fidelity simulators are expensive; in consequence, many researchers use consumer gaming hardware and flat screens as an alternative. In recent years VR devices have become affordable and are applied already in some driving studies. It has not been shown whether driving simulations can use VR to increase immersion in low-cost setups. We conducted a pilot study with 20 participants using a racing game as simulation software. The results of this pilot study indicate that using a VR headset can potentially dissociate participants to a higher degree from the real world compared to the use of flat screens. However, participants felt a higher discomfort using the VR HMD. Despite expectations, today's VR technology does not appear to be a generally better choice than flat screens for driving simulator studies.
The Research of Shock Wave Attenuation Test of UHMWPE-PUF Composite by PVDF Piezoelectric Sensor

In the paper, The PVDF piezoelectric sensor was customized and the structure and test circuit of PVDF piezoelectric sensor is introduced. The polyurethane(PUF) reinforced by ultra high molecular weigh polyethylene (UHMWPE) material(UHMWPE-PUF composites) was synthesized. The pressure in UHMWPE-PUF composites under explosion load was measured and shock wave attenuation waveform is gained and the data is analyzed. The studies showed that PVDF piezoelectric firm sensor is suitable to shock wave measurement in material and UHMWPE- PUF composites can improve maximally shock wave attenuation properties of the material and have good applied outlook in the realm of anti-explosion.
An ad hoc mobility model founded on social network theory

Almost all work on mobile ad hoc networks relies on simulations, which, in turn, rely on realistic movement models for their credibility. Since there is a total absence of realistic data in the public domain, synthetic models for movement pattern generation must be used and the most widely used models are currently very simplistic, the focus being ease of implementation rather than soundness of foundation. Whilst it would be preferable to have models that better reflect the movement of real users, it is currently impossible to validate any movement model against real data. However, it is lazy to conclude from this that all models are equally likely to be invalid so any will do.We note that movement is strongly affected by the needs of humans to socialise in one form or another. Fortunately, humans are known to associate in particular ways that can be mathematically modelled, and that are likely to bias their movement patterns. Thus, we propose a new mobility model that is founded on social network theory, because this has empirically been shown to be useful as a means of describing human relationships. In particular, the model allows collections of hosts to be grouped together in a way that is based on social relationships among the individuals. This grouping is only then mapped to a topographical space, with topography biased by the strength of social tie.We discuss the implementation of this mobility model and we evaluate emergent properties of the generated networks. In particular, we show that grouping mechanism strongly influences the probability distribution of the average degree (i.e., the average number of neighbours of a host) in the simulated network.
A Series of Supramolecular Complexes for Solar Energy Conversion via Water Reduction to Produce Hydrogen: An Excited State Kinetic Analysis of Ru(II),Rh(III),Ru(II) Photoinitiated Electron Collectors

Mixed-metal supramolecular complexes have been designed that photochemically absorb solar light, undergo photoinitiated electron collection and reduce water to produce hydrogen fuel using low energy visible light. This manuscript describes these systems with an analysis of the photophysics of a series of six supramolecular complexes, [{(TL)2Ru(dpp)}2RhX2](PF6)5 with TL = bpy, phen or Ph2phen with X = Cl or Br. The process of light conversion to a fuel requires a system to perform a number of complicated steps including the absorption of light, the generation of charge separation on a molecular level, the reduction by one and then two electrons and the interaction with the water substrate to produce hydrogen. The manuscript explores the rate of intramolecular electron transfer, rate of quenching of the supramolecules by the DMA electron donor, rate of reduction of the complex by DMA from the 3MLCT excited state, as well as overall rate of reduction of the complex via visible light excitation. Probing a series of complexes in detail exploring the variation of rates of important reactions as a function of sub-unit modification provides insight into the role of each process in the overall efficiency of water reduction to produce hydrogen. The kinetic analysis shows that the complexes display different rates of excited state reactions that vary with TL and halide. The role of the MLCT excited state is elucidated by this kinetic study which shows that the 3MLCT state and not the 3MMCT is likely that key contributor to the photoreduction of these complexes. The kinetic analysis of the excited state dynamics and reactions of the complexes are important as this class of supramolecules behaves as photoinitiated electron collectors and photocatalysts for the reduction of water to hydrogen.
Rheological characterization of slips

Differences in the rheological properties of suspensions based on particle concentration and deflocculation state were observed using steady and oscillatory test methods. The stress-controlled rheometer provided a complete rheological characterization of the test suspensions. Information on floc strength, structure and time dependency for these systems was obtained. A correlation was observed between steady and dynamic testing in measuring apparent yield in the samples.