Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating morbidity rates from electronic medical records in general practice. Evaluation of a grouping system.

OBJECTIVES In this study, we evaluated the internal validity of EPICON, an application for grouping ICPC-coded diagnoses from electronic medical records into episodes of care. These episodes are used to estimate morbidity rates in general practice. METHODS Morbidity rates based on EPICON were compared to a gold standard; i.e. the rates from the second Dutch National Survey of General Practice. We calculated the deviation from the gold standard for 677 prevalence and 681 incidence rates, based on the full dataset. Additionally, we examined the effect of case-based reasoning within EPICON using a comparison to a simple, not case-based method (EPI-0). Finally, we used a split sample procedure to evaluate the performance of EPICON. RESULTS Morbidity rates that are based on EPICON deviate only slightly from the gold standard and show no systematic bias. The effect of case-based reasoning within EPICON is evident. The addition of case-based reasoning to the grouping system reduced both systematic and random error. Although the morbidity rates that are based on the split sample procedure show no systematic bias, they do deviate more from the gold standard than morbidity rates for the full dataset. CONCLUSIONS Results from this study indicate that the internal validity of EPICON is adequate. Assuming that the standard is gold, EPICON provides valid outcomes for this study population. EPICON seems useful for registries in general practice for the purpose of estimating morbidity rates.
Assessment of Blood–Brain Barrier Disruption in Stroke

The disease burden of acute ischemic stroke (AIS) is rising in the United States and Canada. It is estimated that in the United States 795 000 people have a stroke each year, which amounts to $34 billion in medical expenses and lost productivity.1 Recent trials have shown the potential benefit of procedural thrombectomy in the management of AIS.2 However, despite substantial research expenditures over the past 2 decades, there have been no new pharmacological agents for the initial treatment of AIS since the approval of recombinant tissue-type plasminogen activator in 1996.3 Recently, the role of the blood–brain barrier (BBB) in the pathogenesis of AIS has emerged as a focus for new therapeutic strategies. After the onset of AIS, the BBB is rapidly disrupted and this disruption persists for days through the acute and early subacute phases of AIS. The disruption of the BBB can be quantified as an increase in the permeability of the BBB (Figure 1). 4 In the setting of AIS, disruption of the BBB is thought to be a precursor to serious clinical consequences such as hemorrhagic transformation (HT),5–7 which refers to the development of a hemorrhage within the ischemic brain tissue. Current research is attempting to elucidate the mechanisms of BBB disruption after AIS and develop therapeutic strategies to mitigate the clinical consequences of BBB disruption. Figure 1. An illustration of the evolution of blood–brain barrier (BBB) disruption after stroke. The extent of BBB disruption is depicted qualitatively and is based on data gathered at our center. The period during which there is greatest disruption of the BBB coincides with the maximum risk of hemorrhagic transformation. Recombinant tissue-type plasminogen activator (r-tPA) can exacerbate BBB disruption. Given these developments, a greater number of preclinical and clinical studies are incorporating assessment of BBB …
On the validity of classifying chemicals for persistence, bioaccumulation, toxicity, and potential for long‐range transport

It is argued that chemical substances can be meaningfully ranked or classified according to their persistence (P), bioaccumulation (B), toxicity (T), and potential for long‐range transport (LRT) only if these attributes can be shown to be intensive, as distinct from extensive, properties of the substance, i.e., they are independent of quantity of substance. It is shown that P, B, and LRT can be considered intensive or quasi‐intensive properties, but toxicity is more problematic. To obtain an intensive metric of toxicity requires selection of one of several possible extensive quantities that define exposure or dose. Ranking of a group of chemicals by toxicity is shown to be very dependent on which quantity is selected. It is suggested that toxicity metrics, such as lethal concentration to 50% of the population (LC50), lethal dose to 50% of the population (LD50), and threshold limit value (TLV) suffer the severe disadvantage of being dependent on the efficiency of delivery of the substance to the site(s) of toxic action in the organism. The use of measured or calculated internal dose is a preferable measure of toxicity since it reduces ambiguities inherent in the other metrics. Also, the primary concern is not the quasi‐intensive property of toxicity; rather, it is the risk of toxic effects, an extensive quantity. To adequately assess the risk of toxic effects, both the toxic hazard and the degree of exposure must be characterized. Since exposure cannot be estimated without knowledge of the emission rate of chemicals to the environment, a compelling case can be made that screening to identify priority P, B, T, and LRT substances should be expanded to include quantity released to the environment as an additional factor.
A comparative study of palmprint feature extraction methods for contact-less biometrics under different environmental conditions

Interest on palmprint biometrics has experimented a strong growth in the last decades due to its useful characteristics as uniqueness, permanence, reliability, user-friendliness, acceptability, non-intrusiveness, and low cost of the acquisition devices, which make it attractive for civil and commercial applications. Accordingly, a wide research has been developed in this field. Nevertheless, there is a lack of evaluation of the results under a common framework which permits to obtain a fair comparison between different methods. In this work an evaluation methodology based on the definitions suggested by the ISO/IDE 19795 norm is provided and applied to evaluate different palmprint feature extraction methods and matching approaches in terms of accuracy and computation time, offering a basis against which to compare future research. Given the growing trend towards touch-less biometrics promoted by the increase in the use of mobile devices, the evaluation has been carried out using two different contact-less hand databases. First database was recorded under totally controlled environmental conditions and providing the user some feedback about the recorded images during the acquisition process, while second database introduces lighting variations as well as no-pose restrictions during the capture.
Semi-supervised Object Detector Learning from Minimal Labels

While traditional machine learning approaches to classification involve a substantial training phase with significant number of training examples, in a semi-supervised setting, the focus is on learning the trends in the data from a limited training set and simultaneously using the trends learned to label unlabeled data. This report focuses on a particular semi-supervised learning technique called Graph-based Regularized Least Squares (LapRLS) that can learn from both labeled and unlabeled data to build a robust object detector capable of learning purely from a single training example and a reasonably large set of unlabeled examples. The algorithm employs multiple feature descriptors such as GIST and Pyramid Histogram of Oriented Gradients (PHOG) for learning these trends. Performance comparisons against traditional supervised learning algorithms demonstrate that LapRLS outperforms the supervised classifiers on several datasets especially when the number of training examples are minimal. As a particular application, the LapRLS performs considerably well on Caltech-101, an object recognition dataset.
Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Mesoamerican population: Evidence for IRF6 and variants at 8q24 and 10q25.

INTRODUCTION Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common of all birth defects. NSCL/P has a multifactorial etiology that includes both genetic and environmental factors. The IRF6 gene and three further susceptibility loci at 8q24, 10q25, and 17q22, which were identified by a recent genome-wide association scan (GWAS), are confirmed genetic risk factors for NSCL/P in patients of European descent. METHODS A case-control association study was performed to investigate whether these four risk loci contribute to NSCL/P in a Mesoamerican population using four single nucleotide polymorphisms to represent IRF6 and the three novel susceptibility loci. A total of 149 NSCL/P patients and 303 controls of Mayan origin were included. RESULTS Single marker analysis revealed a significant association between NSCL/P and risk variants in IRF6 and the 8q24 and 10q25 loci. In contrast to previous findings, the association at the 8q24 locus was driven solely by homozygote carriers of the risk allele. This suggests that this locus might act in a recessive manner in the Mayan population. No evidence for association was found at the 17q22 locus. This may have been attributable to the limited power of the sample. CONCLUSION These results suggest that IRF6 and the 10q25 and 8q24 loci confer a risk for the development of NSCL/P in persons of Mayan origin.
Correlation of volumetric magnetization transfer imaging with clinical data in MS

We examined the relations between quantitative volumetric estimates of cerebral lesion load based on magnetization transfer imaging (MTI), clinical data, and measures of neuropsychological function in 44 patients with clinically diagnosed MS. In this population we assessed the correlation between several volumetric MTI measures, measures of neurologic function (Kurtzke Expanded Disability Status Scale and Ambulation Index), and disease duration using Spearman's correlation coefficient. Patients were classified on the basis of neuropsychological test performance as severely impaired, moderately impaired, and normal. We assessed differences between these groups with respect to MTI results using the Kruskal-Wallis test. MTI measures corrected for brain volume were found to correlate with disease duration (p < 0.01) and showed suggestive correlations with measures of neurologic impairment (p < 0.05). Individual neuropsychological tests correlated with MTI measures corrected and not corrected for brain volume (p < 0.001). An MTI measure not corrected for brain volume differed (p < 0.05) between severely impaired, moderately impaired, and normal patients. These preliminary results suggest that volumetric MTI analysis provides new measures that reflect more accurately the global lesion load in the brain of MS patients, and they may serve as a method to study the natural course of the disease and as an outcome measure to evaluate the effect of drugs.
Random Forest-Based Evaluation of Raman Spectroscopy for Dengue Fever Analysis

This work presents the evaluation of Raman spectroscopy using random forest (RF) for the analysis of dengue fever in the infected human sera. A total of 100 dengue suspected blood samples, collected from Holy Family Hospital, Rawalpindi, Pakistan, have been used in this study. Out of these samples, 45 were dengue-positive based on immunoglobulin M (IgM) capture enzyme-linked immunosorbent assay (ELISA) tests. For highlighting the spectral differences between normal and infected samples, an effective machine learning system is developed that automatically learns the pattern of the shift in spectrum for the dengue compared to normal cases and thus is able to predict the unknown class based on the known example. In this connection, dimensionality reduction has been performed with the principal component analysis (PCA), while RF is used for automatic classification of dengue samples. For the determination of diagnostic capabilities of Raman spectroscopy based on RF, sensitivity, specificity, and accuracy have been calculated in comparison to normally performed IgM capture ELISA. According to the experiment, accuracy of 91%, sensitivity of 91%, and specificity of 91% were achieved for the proposed RF-based model.
Early lethality and neuronal proteinopathy in mice expressing cytoplasm-targeted FUS that lacks the RNA recognition motif

Mutations to the RNA binding protein, fused in sarcoma (FUS) occur in ∼5% of familial ALS and FUS-positive cytoplasmic inclusions are commonly observed in these patients. Altered RNA metabolism is increasingly implicated in ALS, yet it is not understood how the specificity with which FUS interacts with RNA in the cytoplasm can affect its aggregation in vivo. To further understand this, we expressed, in mice, a form of FUS (FUS ΔRRMcyt) that lacked the RNA recognition motif (RRM), thought to impart specificity to FUS-RNA interactions, and carried an ALS-associated point mutation, R522G, retaining the protein in the cytoplasm. Here we report the phenotype and results of histological assessment of the brain of transgenic mice expressing this isoform of FUS. Results demonstrated that neuronal expression of FUS ΔRRMcyt caused early lethality often preceded by severe tremor. Large FUS-positive cytoplasmic inclusions were found in many brain neurons; however, neither neuronal loss nor neuroinflammatory response was observed. In conclusion, the extensive FUS proteinopathy and severe phenotype of these mice suggests that affecting the interactions of FUS with RNA in vivo may augment its aggregation in the neuronal cytoplasm and the severity of disease processes.
Detection of Chlamydia trachomatis by the Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) in Urine Specimens from Men and Women and Endocervical Specimens from Women

ABSTRACT Molecular biology-based amplification methods are significantly more sensitive than other methods for the detection of Chlamydia trachomatis. The performance characteristics of the new Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) with endocervical and urine specimens were compared to those of culture for patients attending two Baltimore City sexually transmitted disease clinics and a clinic for adolescents. AMP CT uses transcription-mediated amplification (TMA) and hybridization protection assay procedures to qualitatively detect C. trachomatis by targeting a 23S rRNA. Discrepant results between culture-negative and AMP CT-positive specimens were resolved by direct fluorescent-antibody staining of sedimented culture transport medium for elementary bodies and by TMA with 16S rRNA as a target. Following discrepant analysis, for 480 female urine specimens AMP CT had a sensitivity of 93.8% and a specificity of 100%. For 464 male urine specimens, the resolved sensitivity and specificity of AMP CT were 95.6 and 98.7%, respectively. For the 479 endocervical swab specimens the sensitivity of AMP CT was 100% and the specificity was 99.5%. Resolved culture sensitivities of AMP CT for female and male swab specimens were 52.3 and 58.9%, respectively. These results demonstrate that AMP CT is highly sensitive for the detection of C. trachomatis in endocervical specimens and in urine specimens from men and women.
Using Unscented Transform in Interference Studies [EM Programmer's Notebook]

When a new telecommunication system is deployed, an interference analysis is usually necessary. This is frequently achieved using the Monte Carlo (MC) method, which simulates the same problem (with different inputs) tens or hundreds of thousands of times to get the final result. In recent years, the unscented transform (UT) has been used as an alternative to the MC method in several engineering problems. This article shows how to analyze the interference between telecommunications systems using the UT. We illustrate this approach using the interference caused by an long-term evolution (LTE)-advanced small cell in the receiver of a television receive-only (TVRO) system. Results show that simulating with only 192 events using the UT produces similar results to simulations with 10,000, or even 100,000, events using the MC method.
Outcome in people with open spina bifida at age 35: prospective community based cohort study

The introduction of the cerebrospinal fluid shunt led to a fourfold increase in survival of babies with open spina bifida in the United Kingdom.1 In 1963 a prospective independent review was set up to record the results and implications of the new treatment.2 3 Such data are crucial to the dilemmas associated with termination of affected pregnancies or treatment at birth.4 We investigated survival, disability, health, and lifestyles in a complete cohort of adults with spina bifida. Between 1963 and 1971, 117 babies had their backs closed at Addenbrooke's Hospital, Cambridge, without any attempt at selection. Before closure of the back each baby had a full neurological examination. When necessary, hydrocephalus was controlled by the insertion of a ventriculoatrial shunt. In spring 2002 we reviewed the cohort by …
Frequent attendance at religious services and mortality over 28 years.

OBJECTIVES This study analyzed the long-term association between religious attendance and mortality to determine whether the association is explained by improvements in health practices and social connections for frequent attenders. METHODS The association between frequent attendance and mortality over 28 years for 5286 Alameda Country Study respondents was examined. Logistic regression models analyzed associations between attendance and subsequent improvements in health practices and social connections. RESULTS Frequent attenders had lower mortality rates than infrequent attenders (relative hazard [RH] = 0.64;95% confidence interval [CI] = 0.53,0.77). Results were stronger for females. Health adjustments had little impact, but adjustments for social connections and health practices reduced the relationship (RH = 0.77; 95% CI = 0.64, 0.93). During follow-up, frequent attenders were more likely to stop smoking, increase exercising, increase social contacts, and stay married. CONCLUSIONS Lower mortality rates for frequent religious attenders are partly explained by improved health practices, increased social contacts, and more stable marriages occurring in conjunction with attendance. The mechanisms by which these changes occur have broad intervention implications.
Reachability Analysis in Verification via Supercompilation

We present an approach to verification of parameterized systems, which is based on program transformation technique known as supercompilation. In this approach the statements about safety properties of a system to be verified are translated into the statements about properties of the program that simulates and tests the system. Supercompilation is used then to establish the required properties of the program. In this paper we show that reachability analysis performed by supercompilation can be seen as the proof of a correctness condition by induction. We formulate suitable induction principles and proof strategies and illustrate their use by examples of verification of parameterized protocols.
Posterior maximization and averaging for Bayesian working model choice in the continual reassessment method

The continual reassessment method (CRM) is a method for estimating the maximum tolerated dose in a dose‐finding study. Traditionally, use is made of a single working model or ‘skeleton’ idealizing an underlying true dose–toxicity relationship. This working model is chosen either by discussion with investigators or published data, before the beginning of the trial or simply on the basis of operating characteristics. To overcome the arbitrariness of the choice of such a single working model, Yin and Yuan (biJ. Am. Statist. Assoc. 2009; 104:954–968) propose a model averaging over a set of working models. Here, instead of averaging, we investigate some alternative Bayesian model criteria that maximize the posterior distribution. We propose three adaptive model‐selecting CRMs using the Bayesian model selection criteria, in which we specify in advance a collection of candidate working models for the dose–toxicity relationship, especially initial guesses of toxicity probabilities, and adaptively select the only one working model among the candidates updated by using the original CRM for each working model, based on the posterior model probability, the posterior predictive loss or the deviance information criteria, during the course of the trial. These approaches were compared via a simulation study with the model averaging approach. Copyright © 2011 John Wiley & Sons, Ltd.
Studying of Classifying Junk Messages Based on The Data Mining

—Traditional SMS filters are basically text-based filtering. However, the filtering mechanisms have limitations: first, the keyword can easily be replaced by other symbols, which increase the difficulty of filtering; second, is garbage in the ongoing renovation of keywords, filtering mechanism of the high demands of intelligent learning, which is difficult to achieve. Send acts based on the analysis of the filter will be able to solve the above problems. Filters in the design of messages added to the idea of data mining, through classification analysis of the sent messages, thus can be extracted to identify the rules of spam text messages and can send messages to the new classification behavior.
Identification and differentiation of Mycobacterium avium and M. intracellulare by PCR

Known DNA sequences coding for the 16S rRNAs of 14 slowly growing Mycobacterium species were analyzed. Three sets of primers were synthesized: MAV and MIN, for M. avium and M. intracellulare, respectively, and MYCOB, for the slowly growing mycobacteria. Whole-cell DNAs of 14 reference species were extracted and amplified by PCR with the MYCOB, MAV, and MIN primers. The MYCOB primer amplified a 0.9-kb segment from the DNAs of all 14 species. The MAV and MIN primers each amplified one highly specific 1.3-kb segment from the homologous DNA, respectively. DNAs from each of 10 clinical isolates of M. avium and M. intracellulare identified by conventional methods were amplified with the MYCOB as well as the MAV and MIN primers; 9 of 10 isolates of each species were identified with their respective primers. One isolate of M. intracellulare was subsequently found to have been mislabeled. One isolate designated M. avium reacted only with the MYCOB primer. The hypervariable region of this strain was shown by DNA sequence analysis to be distinct from all known 16S rRNA sequences of Mycobacterium spp. Our data indicate that the currently identified M. avium-M. intracellulare complex includes strains genetically diverse from M. avium and M. intracellulare.