Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) P-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that contribute to colorectal carcinogenesis.
From in the wild to in vivo: Video Analysis of Mobile Device Use

The explosion of mobile applications and services presents challenges for evaluation and user study. One successful approach has been to deploy instrumented applications, logging their use over long periods of time. We present an expansion of this by remotely recording video and audio of use, while also capturing device and app context. In vivo combines five data collection techniques -- screen recording, ambient audio recording, wearable cameras, data logging and distributed remote uploads. This data provides a range of insights and we discuss examples from previous work which reveal interaction design issues where interface confusions or task mismatches occur. We see how apps are integrated into ongoing activity and environment (such as how maps are used in situ), and how recorded conversations around and about apps may be used for evaluation purposes. We conclude by arguing that this combinative method helps us to move from considering app use in isolation, to studying app use in interaction.
A pipeline for RNA-seq data processing and quality assessment

Summary: We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive. Availability: The R package is available at www.ebi.ac.uk/tools/rcloud with online documentation at www.ebi.ac.uk/Tools/rwiki/, also available as supplementary material. Contact: angela.goncalves@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
From Glushkov WFAs to K-Expressions

We take an active interest in the problem of conversion of a Weighted Finite Automaton (WFA) into a \mathbb{K}-expression. The known algorithms give an exponential size expression in the number of states of the given automaton. We study the McNaughton-Yamada algorithm in the case of multiplicities and then we show that the resulting \mathbb{K}-expression is in the Star Normal Form (SNF) defined by Bruggemann-Klein [3]. The Glushkov algorithm computes an (n + 1)-state automaton from an expression having n occurrences of letters even in the multiplicity case [5]. We reverse this procedure and get a linear size \mathbb{K}-expression from a Glushkov WFA. A characterization of Glushkov WFAs which are not in SNF is given. This characterization allows us to emphasize a normal form for \mathbb{K}-expressions. As for SNF in the boolean case, we show that every \mathbb{K}-expression has an equivalent one in normal form having the same Glushkov WFA. We end with an algorithm giving a small normal form \mathbb{K}-expression from a Glushkov WFA.
Sarcopenia is a prognostic factor in living donor liver transplantation

The aims of this study were to investigate sarcopenia as a novel predictor of mortality and sepsis after living donor liver transplantation (LDLT) and to evaluate the effects of early enteral nutrition on patients with sarcopenia. Two hundred four patients undergoing preoperative computed tomography within the month before LDLT were retrospectively evaluated. The lengths of the major and minor axes of the psoas muscle were simply measured at the caudal end of the third lumbar vertebra, and the area of the psoas muscle was calculated. A psoas muscle area lower than the 5th percentile for healthy donors of each sex was defined as sarcopenia. Ninety‐six of the 204 patients (47.1%), including 58.3% (60/103) of the male patients and 35.6% (36/101) of the female patients, were diagnosed with sarcopenia. Sarcopenia was independently and significantly associated with overall survival: there was an approximately 2‐fold higher risk of death for patients with sarcopenia versus patients without sarcopenia (hazard ratio = 2.06, P = 0.047). Sarcopenia was an independent predictor of postoperative sepsis (hazard ratio = 5.31, P = 0.009). Other independent predictors were a younger recipient age (P < 0.001) and a higher body mass index (P = 0.02). Early enteral nutrition within the first 48 hours after LDLT was performed for 24.2% in 2003‐2007 and for 100% in 2008‐2011, and the incidence of postoperative sepsis for patients with sarcopenia (n = 96) was 28.2% (11/39) in 2003‐2007 and 10.5% (6/57) in 2008‐2011 (P = 0.03). In conclusion, sarcopenia is an independent predictor of mortality and sepsis after LDLT. The incidence of postoperative sepsis was reduced even in patients with sarcopenia after the routine application of early enteral nutrition. Liver Transpl 20:401–407, 2014. © 2013 AASLD.
X-band substrate integrated waveguide power combiner/divider

In this study an X-band SIRW power divider/combiner structure was designed using a cheap dual layer PCB. The designed structure was then simulated and optimized design was fabricated. The critical analysis of the simulated and the measured results was performed. The final results were very close to the expected results with -3.17 dB output and -32 dB return loss.
Effect of plasma shielding on laser ablation rate of pure metals at reduced pressure

The ablation rate expressed as the amount of removed material per laser shot was calculated for pure metal samples under different experimental conditions: laser fluence (1.3‐16.7 J cm 2 ), buffer gas (air, He and Ar) and gas pressure (10 3 ‐10 5 mbar). Fluence values covered the range between the plasma threshold (~1‐2 J cm 2 for most elements) and 16.7 J cm 2 . The 581 nm output of an excimer-pumped dye laser was used. Results pointed out a strong dependence of ablation rate on experimental parameters. At high fluence, the ablated material efficiently attenuates the incoming laser radiation (plasma shielding) and reduces the ablation rate. The extent of this shielding effect depend also on the experimental variables (buffer gas, pressure) and sample nature. These studies are useful to determine the amount of ablated material as a function of experimental parameters, to understand the extension of the shielding process and to establish the conditions under which it may be avoided. Copyright ” 1999 John Wiley & Sons, Ltd.
Computer-generated watercolor

A watercolor model based on an ordered set of translucent glazes, which are created independently usinig a shallow water fluid simulation. A Kubelka-Munk compositing model is used for simulating the optical effect of the superimposed glazes. The computer generated watercolor model is used as part of an interactive watercolor paint system, or as a method for automatic image “watercolorization. ”
A 3D Sketch-Based Modeling Design System with Paper-and-Pencil Interface

In this study, a 3D curve sketching system that imitates paper-and-pencil design styling for industrial and architectural designers is presented, which allow directly freeform 3D curve modeling. The system coherently integrates three kinds of curve creation methods: single-view with multi-stroke, two-view epipolar and projection surface, to transitions imperceptible from paper-and-pencil based 2D stroke to freeform 3D curve. Other assistant features of this system include an axis widget for projection surface selection, simplified 3D view navigation, and auto gestures semantic recognition. The system aims to apply the fluent and comfortable modeling environment for rapid idea realization in conceptual design process. An evaluation is performed by an unprofessional designer, and it is powerful and convenient of this sketch-based modeling system in expressing the design intent within a real design process.
PADRE: Modulated Backscattering-Based PAssive Data REtrieval in Wireless Sensor Networks

The most difficult challenge for the design of wireless sensor networks (WSN) is to maintain long network lifetimes since the sensor nodes are severely energy-constrained. Traditional WSN assumes employment of conventional RF transmitters which consume most of the stored power on the sensor node. In this regard, modulated backscattering (MB) emerges as a promising communication technique alternative, in which the sensor nodes reflect the incident signal of an RF source and modulate their data on the reflected signal. With the use of MB, the power consumption of the nodes reduce drastically since it replaces the most power consuming component of a typical sensor node, i.e., the RF transmitter. In addition, the nodes acquire relatively long-range communication ability through MB. Furthermore, the incident RF power can be converted into DC power in order to drive the sensing and processing circuitries. This, in turn, leads to the design of battery-free wireless passive sensor networks (WPSN), which stands as a radically distinct solution approach for the energy problems of WSN. The objective of this paper is to revisit the main design challenge of WSN from entirely different perspective. To this end, the fundamental principles of WPSN are first introduced. In addition, in order to realize the potential benefits of WPSN, a new clustering-based energy-efficient communication protocol, i.e., PADRE (PAssive Data REtrieval), is presented for WPSN operating via MB technique. Simulations show that PADRE protocol achieves high performance in terms communication reliability and network lifetime.
Influence of Race and Sex on Thrombogenicity in a Large Cohort of Coronary Artery Disease Patients

Background It is uncertain whether sex and race affect thrombogenicity in patients with coronary artery disease. We evaluated the effects of sex and race on thrombogenicity in patients with coronary artery disease treated with aspirin. Methods and Results Patients on aspirin therapy for 1 week or longer with known or suspected coronary artery disease undergoing nonurgent cardiac catheterization (n=1172), of whom 924 were on aspirin and clopidogrel therapy, were studied. The primary end point was thrombin‐induced platelet‐fibrin clot strength (MAKH) measured by thrombelastography. Secondary end points included coagulation index, a measure of overall coagulation; G, another measure of clot strength; and maximal platelet aggregation. Women had greater MAKH, G, and coagulation index than men, both with and without clopidogrel therapy (with clopidogrel: 68.3±6 versus 65.8±6 mm, P<0.0001; 11.4±3 versus 9.5±4 dyne/cm2, P<0.0001; and 0.12±3 versus −0.7±3, P=0.003, respectively). Platelet aggregation (induced by ADP, thrombin receptor activating peptide, or collagen) did not differ between sexes. Black patients had greater MAKH and G than white patients (with clopidogrel: 67.8±7 versus 66.4±6 mm, P=0.005; 11±4 versus 10±3 dyne/cm2, P=0.02, respectively). Black women had the highest MAKH levels. By multivariate analysis, sex, race, diabetes, platelet count, and hemoglobin level were independently associated with MAKH. Sex, but not race, was also associated with the frequency of MAKH ≥72 mm (a threshold related to ischemic event occurrence in patients undergoing coronary intervention). Conclusions Sex and race independently influence platelet‐fibrin clot strength. Black women appear to have the highest thrombogenicity profile, potentially conferring a high‐risk phenotype for thrombotic event occurrence.
Apoptosis and Oxidative Stress in the Aging Brain

DNA is a primary site of damage during oxidative stress in the brain. DNA fragmentation occurs within minutes of induction of oxidative stress. This DNA fragmentation probably results from the attack of free radicals on DNA and from the activation of endonucleases. Oxidative stress was induced by intracerebroventricular injection of t-butylhydroperoxide. This results in a very rapid flux of t-butylhydroperoxide, which is cleared from the brain within minutes. This flux of t-butylhydroperoxide results in the formation of hydroxyl radical in the brain and probably in the nuclei of brain cells. Necrosis results from extensive DNA fragmentation caused by massive oxidative stress. Cresyl violet stained brain sections demonstrated necrosis in many brain regions. In addition, previous electron microscopy studies showed degradation of cellular nuclei caused by tBuOOH toxicity. Low doses of t-butylhydroperoxide can induce apoptosis, which is a delayed form of cell death. Apoptosis was found in brains stained to visualize apoptotic DNA fragments. Experiments performed in mice aged 2, 8 or 24 months will be discussed. We have also found that apoptosis and DNA fragmentation can be prevented by pretreating mice with the vitamin micotinamide. Nicotinamide is a precursor for NAD. DNA repair requires high levels of NAD in the nucleus for the activity of poly(ADP-ribose) polymerase. Oxidative stress in the brain produces both necrosis and apoptosis, probably as the result of DNA fragmentation. Senescence is associated with an increase in the production of DNA fragments during brain oxidative stress, which probably leads to more necrosis and apoptosis than in younger mice.
Variation and molecular evolution of HmbR, the Neisseria meningitidis haemoglobin receptor

Meningococcal disease caused by serogroup B Neisseria meningitidis remains an important health problem in many parts of the world, and there are currently no comprehensive vaccines. Poor immunogenicity, combined with immunological identity to human sialic acids, have hindered the development of a serogroup B conjugate vaccine, resulting in the development of alternative vaccine candidates, including many outer-membrane protein (OMP)-based formulations. However, the design of protein-based meningococcal vaccines is complicated by the high level of genetic and antigenic diversity of the meningococcus. Knowledge of the extent and structuring of this diversity can have implications for the use of particular proteins as potential vaccine candidates. With this in mind, the diversity of the meningococcal OMP HmbR was investigated among N. meningitidis isolates representative of major hyper-invasive lineages. In common with other meningococcal antigens, the genetic diversity of hmbR resulted from a combination of intraspecies horizontal genetic exchange and de novo mutation. Furthermore, genealogical analysis showed an association of hmbR genes with clonal complexes and the occurrence of two hmbR families, A and B. Three variable regions (VR1–VR3), located in loops 2, 3 and 4, were observed with clonal complex structuring of VR types. A minority of codons (3.9 %), located within putative surface-exposed loop regions of a 2D model, were under diversifying selection, indicating regions of the protein likely to be subject to immune attack.
Can ‘partial’ PTSD explain differences in diagnosis of PTSD by questionnaire self-report and interview after head injury?

Objective: Can the concept of ‘partial’ PTSD explain the disparity between the relatively high incidence of PTSD found using self-report questionnaires and the relatively low incidence using structured interview? It was hypothesized that self-report of greater PTSD symptom severity is associated with increased heart rate and movement when responding to questions about the traumatic event, if ‘partial’ PTSD is an explanation. Research design: A within participants single group design. Methods: Twenty-one adults with head injury underwent self-report (Post-traumatic Stress Disorder Scale) and interview (Clinical Assessment of PTSD) assessments of PTSD, the Traumatic Memory Interview, self-report of mood (Hospital Anxiety and Depression Scale) and cognitive assessment (Wechsler Test of Adult Reading, Auditory Verbal Learning Test, Hayling Test, Digit Symbol Test), during which heart rate and motor activity were recorded. Results: Self-report of greater PTSD symptom severity was not associated with increases in heart rate or movement during questions about the traumatic event. In fact, heart rate decreased from baseline in those with higher self-report scores for PTSD, consistent with curiosity about the traumatic event and not ‘partial’ PTSD. Conclusion: These preliminary findings agree with an emerging theme suggesting that, although PTSD can occur after head injury, it is easily over-diagnosed.
Compressed sensing-based frequency selection for classification of ground penetrating radar signals

In this paper we present an automatic classification system for ground penetrating radar (GPR) signals. The system extracts the magnitude spectra at resonant frequencies and classifies them using support vector machines. To locate the resonant frequencies, we propose an approach based on compressed sensing and orthogonal matching pursuit. The performance of the system is evaluated by classifying GPR traces from different ballast fouling conditions. The experimental results show that the proposed approach, compared to the approach of using frequencies at local maxima, represents the GPR signal more efficiently using a small number of coefficients, and obtains higher classification accuracy.
WDR36 variants in East Indian primary open-angle glaucoma patients

Purpose Glaucoma is a heterogeneous group of optic neuropathies with a complex genetic basis. To date, only the following four genes have been identified: viz. myocilin (MYOC), optineurin (OPTN), WD repeat domain 36 (WDR36), and neurotrophin 4 (NTF4). However, there are conflicting reports regarding the involvement of WDR36 in the pathogenesis of primary open-angle glaucoma (POAG). In the Asian population, mutations in WDR36 appear to play a minor role in POAG pathogenesis but polymorphic variants have been found to be associated with POAG, especially in patients with high tension glaucoma (HTG). The purpose of this study is to determine the role of WDR36 in East Indian POAG patients. To date, no other studies have yet examined this role. Methods Ten single nucleotide polymorphisms (SNPs; rs1971050, rs1993465, rs13153937, rs10038177, rs11241095, rs10043631, rs10038058, rs10491424, rs17553936, and rs13186912) spanning almost the entire WDR36 gene were selected and their association with eastern Indian POAG patients was evaluated. Our study pool consisted of 323 POAG patients. Of these 116 were patients who had HTG with intraocular perssure (IOP) >21mmHg and 207 were found to be non-HTG patients (presenting IOP<21mmHg). The study also included 303 participants as controls. The polymorphisms were genotyped in both the patients and the controls using the PCR-RFLP method. Moreover, the SNP that showed significant association was validated by DNA sequencing. The haplotypes were obtained using Haploview 4.1 software. The allele and haplotype frequencies were compared between the patient group and the control group using Pearson’s χ2 test. Results First, we genotyped the selected SNPs in the 323 POAG patients and 119 of the participants in the control group, in which only rs10038177 (c.710+30C>T) was found to be strongly associated with the HTG cases (OR=2.186; 95% CI=1.458–3.277; p=1.4×10−4). To increase the significance of the study, the SNP was genotyped in an additional 184 of the participants in the control group and it was observed that the SNP retained the association (OR=1.216; 95% CI=1.064–2.306; p=0.002). However, no haplotype was found to have any sustainable association with POAG. Based on the LD pattern and location of rs10038177, exon 5 of WDR36 was sequenced but no suspected disease-causing variant was detected. Conclusions Our study suggests a possible association between WDR36 SNP in a cohort of eastern Indian POAG patients who also have high intraocular pressure (IOP). This study needs to be further validated in a larger patient cohort.
Treatment outcomes of patients with HIV and tuberculosis.

RATIONALE The optimal length of tuberculosis treatment in patients coinfected with HIV is unknown. OBJECTIVES To evaluate treatment outcomes for HIV-infected patients stratified by duration of rifamycin-based tuberculosis therapy. METHODS We retrospectively reviewed data on all patients with tuberculosis reported to the San Francisco Tuberculosis Control Program from 1990 through 2001. Patients were followed for up to 12 months after treatment completion. MEASUREMENTS AND MAIN RESULTS Of 700 patients, 264 (38%) were HIV infected, 315 (45%) were not infected, and 121 (17%) were not tested. Mean duration of treatment was extended to 10.2 months for HIV-infected patients versus 8.4 months for uninfected/unknown patients (p < 0.001). Seventeen percent of the HIV-infected and 37% of the HIV uninfected/unknown patients received 6 months of rifamycin-based therapy. The relapse rate among HIV-infected was 9.3 per 100 person-years versus 1.0 in HIV-uninfected/unknown patients (p < 0.001). HIV-infected individuals who received a standard 6-month rifamycin-based regimen were more likely to relapse than those treated longer (adjusted hazard ratio, 4.33; p = 0.02). HIV-infected individuals who received intermittent therapy were also more likely to relapse than those treated on daily basis (adjusted hazard ratio, 4.12; p = 0.04). The use of highly active antiretroviral therapy was associated with more rapid conversion of smears and cultures and with improved survival. CONCLUSIONS HIV-infected patients who received a 6-month rifamycin-based course of tuberculosis treatment or who received intermittent therapy had a higher relapse rate than HIV-infected subjects who received longer therapy or daily therapy, respectively. Standard 6-month therapy may be insufficient to prevent relapse in patients with HIV.