Miracle-dz/UniFAR-FTUs huggingface dataset:
Gender Differences among Patients with a Single Depressive Episode

Background: Studies on gender differences in depression have usually included a mixture of patients with first-episode, chronic and recurrent depression. Consequently, the results might be confounded by the history of depression among participants. The present study evaluated gender differences in sociodemographic, clinical and treatment variables among patients suffering exclusively from single-episode depression. Method: Systematic recruitment of 301 participants via the Danish Psychiatric Central Research Register and assessment by means of questionnaires and interviews regarding psychiatric diagnoses, personality traits and disorders, stressful life events, family history, and treatment response. Results: Female patients showed a higher level of neuroticism and more residual anxiety symptoms after treatment of the depression. There were no gender differences in severity of depression, psychiatric co-morbidity (including personality disorders), stressful life events prior to onset, family loading of psychiatric disorders, or treatment outcome. Conclusion: The results provide evidence for a higher level of anxiety and neuroticism among females with a recent onset of depression, whereas other clinical characteristics of first-episode depression were equivalent between male and female patients. Only patients with contact to a psychiatric hospital were included; thus, the results cannot be generalized to patients in primary care.
Long Interspersed Nuclear Element 1 Hypomethylation Is a Marker of Poor Prognosis in Stage IA Non–Small Cell Lung Cancer

Purpose: Global hypomethylation and the hypermethylation of gene promoter regions are common events in tumor DNA. The aim of this study was to evaluate the prognostic significance of both global hypomethylation and gene promoter hypermethylation in DNA from non–small cell lung cancer (NSCLC). Experimental Design: Genomic DNA was obtained from the tumor tissue of 379 NSCLC patients who underwent surgery. Methylation levels were measured by real-time PCR following bisulfite modification of DNA and were correlated with clinicopathologic parameters and patient prognosis. Methylation of long interspersed nuclear element 1 (LINE-1) was used as a surrogate marker for global methylation. Hypermethylation of the APC, CDH13, and RASSF1 promoter regions was also evaluated. Results: Tumor tissue showed significantly higher CDH13 and RASSF1 methylation levels compared with normal lung tissue, but lower LINE-1 methylation levels. APC, RASSF1, and LINE-1 methylation levels were significant prognostic factors in univariate analysis of an initial cohort of 234 cases. APC and LINE-1 methylation remained significant prognostic factors in multivariate analysis that included age, gender, smoking history, histologic type, and pathologic stage. LINE-1 methylation showed marginally significant prognostic value in stage IA and IB disease. Expansion of the study cohort to 364 cases revealed that LINE-1 methylation had significant prognostic value for stage IA NSCLC patients in multivariate analysis. Conclusions: LINE-1 hypomethylation was an independent marker of poor prognosis in stage IA NSCLC. Validation of this finding in additional tumor cohorts could have clinical relevance for the management of early-stage NSCLC. Clin Cancer Res; 16(8); 2418–26. ©2010 AACR.
A Comparison Study on Multidomain EEG Features for Sleep Stage Classification

Feature extraction from physiological signals of EEG (electroencephalogram) is an essential part for sleep staging. In this study, multidomain feature extraction was investigated based on time domain analysis, nonlinear analysis, and frequency domain analysis. Unlike the traditional feature calculation in time domain, a sequence merging method was developed as a preprocessing procedure. The objective is to eliminate the clutter waveform and highlight the characteristic waveform for further analysis. The numbers of the characteristic activities were extracted as the features from time domain. The contributions of features from different domains to the sleep stages were compared. The effectiveness was further analyzed by automatic sleep stage classification and compared with the visual inspection. The overnight clinical sleep EEG recordings of 3 patients after the treatment of Continuous Positive Airway Pressure (CPAP) were tested. The obtained results showed that the developed method can highlight the characteristic activity which is useful for both automatic sleep staging and visual inspection. Furthermore, it can be a training tool for better understanding the appearance of characteristic waveforms from raw sleep EEG which is mixed and complex in time domain.
Extracting Template for Knowledge-based Question-Answering Using Conditional Random Fields

In this paper, we present an information extraction system that extracts template elements for a question-answering (QA) system in the domain of encyclopedia. We use Conditional Random Fields to extract templates from the texts of an encyclopedia. Using the proposed approach, we could achieve a 74.89% precision and a 55.77% F1 in the template extraction. In the question classification, we could archive an 83.6% precision and a 65.4% recall. Finally, in the Knowledge-based QA (including template extraction procedure), we could archive an 81.3% precision and a 33.3% recall. The result demonstrated that our approach is feasible and effective for template extraction for QA.
Characterization of a Monomeric Escherichia coli Alkaline Phosphatase Formed upon a Single Amino Acid Substitution*

Alkaline phosphatase (AP) from Escherichia coli as well as APs from many other organisms exist in a dimeric quaternary structure. Each monomer contains an active site located 32 Å away from the active site in the second subunit. Indirect evidence has previously suggested that the monomeric form of AP is inactive. Molecular modeling studies indicated that destabilization of the dimeric interface should occur if Thr-59, located near the 2-fold axis of symmetry, were replaced by a sterically large and charged residue such as arginine. The T59R enzyme was constructed and characterized by sucrose-density gradient sedimentation, size-exclusion chromatography, and circular dichroism (CD) and compared with the previously constructed T59A enzyme. The T59A enzyme was found to exist as a dimer, whereas the T59R enzyme was found to exist as a monomer. The T59A, T59R, and wild-type APs exhibited almost identical secondary structures as judged by CD. The T59R monomeric AP has a melting temperature (Tm) of 43 °C, whereas the wild-type AP dimer has a Tm of 97 °C. The catalytic activity of the T59R enzyme was reduced by 104-fold, whereas the T59A enzyme exhibited an activity similar to that of the wild-type enzyme. The T59A and wild-type enzymes contained similar levels of zinc and magnesium, whereas the T59R enzyme has almost undetectable amounts of tightly bound metals. These results suggest that a significant conformational change occurs upon dimerization, which enhances thermal stability, metal binding, and catalysis.
A Programming Language for Web Service Development

There is now widespread acceptance of Web services and service-oriented architectures. But despite the agreement on key Web services standards there remain many challenges. Programming environments based on WSDL support go some way to facilitating Web service development. However Web services fundamentally rely on XML and Schema, not on contemporary programming language type systems such as those of Java or . NET. Moreover, Web services are based on a messaging paradigm and hence bring forward the traditional problems of messaging systems including concurrency control and message correlation. It is easy to write simple synchronous Web services using traditional programming languages; however more realistic scenarios are surprisingly difficult to implement. To alleviate these issues we propose a programming language which directly supports Web service development. The language leverages XQuery for native XML processing, supports implicit message correlation and has high level join calculus-style concurrency control. We illustrate the features of the language through a motivating example.
Bmc Medical Genetics Genome-wide Association of Sleep and Circadian Phenotypes

Background: Numerous studies suggest genetic influences on sleepiness and circadian rhythms. The Sleep Heart Health Study collected questionnaire data on sleep habits and sleepiness from 2848 Framingham Heart Study Offspring Cohort participants. More than 700 participants were genotyped using the Affymetrix 100K SNP GeneChip, providing a unique opportunity to assess genetic linkage and association of these traits.
Chronotype differences in circadian rhythms of temperature, melatonin, and sleepiness as measured in a modified constant routine protocol

Evening chronotypes typically have sleep patterns timed 2–3 hours later than morning chronotypes. Ambulatory studies have suggested that differences in the timing of underlying circadian rhythms as a cause of the sleep period differences. However, differences in endogenous circadian rhythms are best explored in laboratory protocols such as the constant routine. We used a 27-hour modified constant routine to measure the endogenous core temperature and melatonin circadian rhythms as well as subjective and objective sleepiness from hourly 15-minute sleep opportunities. Ten (8f) morning type individuals were compared with 12 (8f) evening types. All were young, healthy, good sleepers. The typical sleep onset, arising times, circadian phase markers for temperature and melatonin and objective sleepiness were all 2–3 hours later for the evening types than morning types. However, consistent with past studies the differences for the subjective sleepiness rhythms were much greater (5–9 hours). Therefore, the present study supports the important role of subjective alertness/sleepiness in determining the sleep period differences between morning and evening types and the possible vulnerability of evening types to delayed sleep phase disorder.
Context-Aware Video Object Proposals

Recent advances in object proposals have been achieved obvious performance to speed up sliding window based object detection or recognition. However, the spatial-temporal object proposal of multi-objects in video is still a challenging problem. Applying the existing image methods frame by frame will result in three defects. First, no guarantee to keep the consistent proposal results, i.e., it is hard to avoid omitting objects even in consecutive or similar sequences. Second, the latent information contained in time dimension would not be made best use of to improve the detection rate. Third, due to the motion blur caused by motion flow, the efficiency of object proposals relying on contour or edge features would be definitely degraded. In this paper, we propose an efficient method for video object proposals. By introducing image method into context-aware framework, we get the improved detection rate compared to the frame by frame usage, while keeping a controllable computing efficiency. Firstly, the bounding boxes produced by image proposals are used as the input. Then the candidate windows are scored with contextual information by generating motion-based mapping boxes. To evaluate the multi-object proposal results, we build a specific dataset. Experiments show that the proposed method can improve the detection rate of the original image method, and especially achieve better performance when proposing a small set of bounding boxes.
Wada memory testing and hippocampal volume measurements in the evaluation for temporal lobectomy

We examined the relationship of Wada memory performance and MRI hippocampal volume measurements to laterality of ultimate seizure localization in 20 patients with complex partial seizures who later underwent temporal lobectomy. Discriminant function analysis employing both Wada memory test asymmetries and hippocampal volume asymmetries correctly classified 100% of the patients into left and right temporal lobe groups. Wada memory asymmetries alone correctly classified 90% of the sample (80% of the sample when the discriminant function included all patients except the one being classified), and hippocampal volume asymmetries alone correctly classified 90% of the patients. A significant correlation was present between Wada memory asymmetries and hippocampal volume asymmetries (r = 0.78), indicating that structural evidence of reduced hippocampal volume has a functional correlate reflected by Wada memory performance. These data suggest that the combination of functional and structural measures is of value in the preoperative evaluation for epilepsy surgery.
Stress wave propagation in adhesively bonded functionally graded cylinders: an improved model

Abstract This study presents an improved mathematical model to analyse the stress wave propagation in adhesively bonded functionally graded (FG) circular cylinders (butt joint) under an axial impulsive load. The volume fractions of the material constituents in the upper and lower cylinders were functionally tailored through the thickness of each cylinder using a power-law. The effective material properties of both cylinders, which are made of aluminum (Al) and silicon carbide (SiC), at any point were predicted by using the Mori–Tanaka homogenization scheme. In this improved model, the governing equations of the wave propagation include the spatial derivatives of local mechanical properties and were discretized by means of the finite difference method. The influence of these spatial derivatives and the compositional gradient exponent on the displacement and stress distributions of the joint was investigated. The material composition variations of both cylinders affected the displacement and stress fields whereas the compositional gradient exponent had a minor effect. The stress concentrations were alleviated in time, the displacement and stress distributions/variations around/along the upper and lower cylinder-adhesive interfaces were significantly affected by the adhesive layer. The spatial derivatives also affected the temporal histories of the displacement and stress components evaluated at the selected critical points of the upper cylinder, adhesive layer and lower cylinder. The consideration of the spatial local material derivatives provided a more accurate mathematical model of wave propagations through the graded layered structures.
Cortactin Recruitment by Enterohemorrhagic Escherichia coli O157:H7 during Infection In Vitro and Ex Vivo

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important human pathogen that colonizes the gut mucosa via attaching and effacing (A/E) lesions; A/E lesion formation in vivo and ex vivo is dependent on the type III secretion system (T3SS) effector Tir. Infection of cultured cells by EHEC leads to induction of localized actin polymerization, which is dependent on Tir and a second T3SS effector protein, TccP, also known as EspFU. Recently, cortactin was shown to bind both the N terminus of Tir and TccP via its SH3 domain and to play a role in EHEC-triggered actin polymerization in vitro. In this study, we investigated the recruitment of cortactin to the site of EHEC adhesion during infection of in vitro-cultured cells and mucosal surfaces ex vivo (using human terminal ileal in vitro organ cultures [IVOC]). We have shown that cortactin is recruited to the site of EHEC adhesion in vitro downstream of TccP and N-WASP. Deletion of the entire N terminus of Tir or replacing the N-terminal polyproline region with alanines did not abrogate actin polymerization or cortactin recruitment. In contrast, recruitment of cortactin to the site of EHEC adhesion in IVOC is TccP independent. These results imply that cortactin is recruited to the site of EHEC adhesion in vitro and ex vivo by different mechanisms and suggest that cortactin might have a role during EHEC infection of mucosal surfaces.
Diagnosis of intestinal and disseminated microsporidial infections in patients with HIV by a new rapid fluorescence technique.

AIMS--To assess the value of a new rapid fluorescence method for the diagnosis of microsporidiosis in HIV seropositive patients. METHODS--Microsporidian spores in stools were demonstrated by using the fluorochrome stain Uvitex 2B. The new technique was evaluated in three groups of HIV seropositive patients with diarrhoea. Group 1: 19 patients with biopsy confirmed E bieneusi infection (186 stool samples); group 2: 143 consecutive patients from whom faeces were submitted for routine investigation of diarrhoea (318 samples); group 3: 16 patients with small intestinal biopsy specimens negative for microsporidia (55 samples). The new method was used to monitor spore shedding during experimental treatment with paromomycin and albendazole in four patients. RESULTS--Brightly fluorescent spores were detected in all stool samples of patients in group 1. In group 2 16 (11%) patients had spores in their stool samples. E bieneusi was found in 11 patients; in the other five another genus of microsporidia, Encephalitozoon, was recognised. Encephalitozoon spores were also found in the urine of three of these patients and in the maxillary sinus aspirate of two of them, suggesting disseminated infection. The results were confirmed by electron microscopic examination. In group 3 negative biopsy specimens were confirmed by negative stool samples in all cases. Treatment with albendazole and paromomycin did not affect the spore shedding in three patients with E bieneusi infection. By contrast, in a patient with Encephalitozoon sp infection albendazole treatment resulted in clinical improvement together with complete cessation of spore excretion in the stool. CONCLUSION--The Uvitex 2B fluorescence method combines speed, sensitivity, and specificity for the diagnosis and treatment evaluation of intestinal and disseminated microsporidiosis.
Distributed Energy Efficient Clustering (DEEF) in Heterogeneous Wireless Sensor Networks

In this paper, the distributed energy efficient clustering (DEEF) in heterogeneous wireless sensor networks is presented. Distributed Energy-Efficient clustering are algorithms designed for homogenous WSN under consideration so these protocols do not work efficiently under heterogeneous scenarios because these algorithms are unable to treat nodes differently in terms of their energy. Here, we evaluate the performance of DEEC clustering algorithms on the basis of stability period, network life time and throughput for different level of heterogeneous wireless sensor networks. DEEC perform well under three level heterogeneous WSNs containing high energy level difference between normal, advanced and super nodes in terms of stability period.
Coefficients of the Inflated Eulerian Polynomial

It follows from work of Chung and Graham that for a certain family of polynomials $P_{n}(x)$ derived from the descent statistic on permutations, the sequence of nonzero coefficients of $P_{n-1}(x)$ coincides with that of the polynomial $P_{n}(x)/(1+x+x^{2}+\cdots+x^{n})$. We observed computationally that the inflated $\mathbf{s}$-Eulerian polynomials, $Q_{n}^{(\mathbf{s})}(x)$, of which $P_{n}(x)$ is a special case, also have this property for many sequences $\mathbf{s}$. In this work we show that $Q_{n}^{(\mathbf{s})}(x)/\left(1+x+\cdots+x^{s_{n}-1}\right)$ is a polynomial for all positive integer sequences $\mathbf{s}$ and characterize those sequences $\mathbf{s}$ for which the sequence of nonzero coefficients of the $Q_{n-1}^{(\mathbf{s})}(x)$ coincides with that of the polynomial $Q_{n}^{(\mathbf{s})}(x)/\left(1+x+\cdots+x^{s_{n}-1}\right)$. In particular, we show that all nondecreasing sequences satisfy this condition.
BteA Secreted from the Bordetella bronchiseptica Type III Secetion System Induces Necrosis through an Actin Cytoskeleton Signaling Pathway and Inhibits Phagocytosis by Macrophages

BteA is one of the effectors secreted from the Bordetella bronchiseptica type III secretion system. It has been reported that BteA induces necrosis in mammalian cells; however, the roles of BteA during the infection process are largely unknown. In order to investigate the BteA functions, morphological changes of the cells infected with the wild-type B. bronchiseptica were examined by time-lapse microscopy. L2 cells, a rat lung epithelial cell line, spread at 1.6 hours after B. bronchiseptica infection. Membrane ruffles were observed at peripheral parts of infected cells during the cell spreading. BteA-dependent cytotoxicity and cell detachment were inhibited by addition of cytochalasin D, an actin polymerization inhibitor. Domain analyses of BteA suggested that two separate amino acid regions, 200–312 and 400–658, were required for the necrosis induction. In order to examine the intra/intermolecular interactions of BteA, the amino- and the carboxyl-terminal moieties were purified as recombinant proteins from Escherichia coli. The amino-terminal moiety of BteA appeared to interact with the carboxyl-terminal moiety in the pull-down assay in vitro. When we measured the amounts of bacteria phagocytosed by J774A.1, a macrophage-like cell line, the phagocytosed amounts of B. bronchiseptica strains that deliver BteA into the host cell cytoplasm were significantly lower than those of strains that lost the ability to translocate BteA into the host cell cytoplasm. These results suggest that B. bronchiseptica induce necrosis by exploiting the actin polymerization signaling pathway and inhibit macrophage phagocytosis.
Balanced parallel FP-Growth with MapReduce

Frequent itemset mining (FIM) plays an essential role in mining associations, correlations and many other important data mining tasks. Unfortunately, as the volume of dataset gets larger day by day, most of the FIM algorithms in literature become ineffective due to either too huge resource requirement or too much communication cost. In this paper, we propose a balanced parallel FP-Growth algorithm BPFP, based on the PFP algorithm [1], which parallelizes FP-Growth in the MapReduce approach. BPFP adds into PFP load balance feature, which improves parallelization and thereby improves performance. Through empirical study, BPFP outperformed the PFP which uses some simple grouping strategy.
Development of a micro-optofluidic sensor for in-line electrolyte monitoring : towards individualized dialysis treatment

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