Miracle-dz/UniFAR-FTUs huggingface dataset:
IFGFA: Identification of featured genes from genomic data using factor analysis.

In this study, a software tool (IFGFA) for identification of featured genes from gene expression data based on latent factor analysis was developed. Despite the availability of computational methods and statistical models appropriate for analyzing special genomic data, IFGFA provides a platform for predicting colon cancer-related genes and can be applied to other cancer types. The computational framework behind IFGFA is based on the well-established Bayesian factor and regression model and prior knowledge about the gene from OMIM. We validated the predicted genes by analyzing somatic mutations in patients. An interface was developed to enable users to run the computational framework efficiently through visual programming. IFGFA is executable in a Windows system and does not require other dependent software packages. This program can be freely downloaded at http://www.fupage. org/downloads/ifgfa.zip.
All At-Risk Patients Are Not Created Equal: Analysis of Braden Pressure Ulcer Risk Scores to Identify Specific Risks

PURPOSE: To improve identification of risk factors for pressure ulcer development and enhance targeted interventions and prevention strategies. SUBJECTS AND SETTING: The records of 12,566 adult patients hospitalized in intensive or progressive care units within Mayo Clinic were analyzed. Inclusion criteria were Braden Scale of 18 or less during the hospitalization; exclusion criteria were preexisting pressure ulcer or length of stay less than 24 hours. METHODS: This study is a retrospective cohort analysis of electronic medical record data from January 1, 2007, to December 31, 2007. Only iatrogenic stage 2 to 4 pressure ulcers were considered as incident events. Demographic and clinical data were extracted from the medical record, including total Braden Scale score and Braden subscale scores at hospital admission, length of stay, admission to the intensive care unit at the time of hospitalization, and presence of acute respiratory failure, acute renal failure, or diabetes. Time to event was calculated based on time from admission to pressure ulcer occurrence or to hospital discharge. RESULTS: Four hundred sixteen (3.3%) of patients developed a pressure ulcer during their hospitalizations. The Braden Scale score total by itself was found to be highly predictive of pressure ulcer development (P ⩽ .0001, C = 0.71), as were all individual subscores. The friction/shear subscale had the greatest predictive power among Braden Scale scores (subscores and total score) (C = 0.83). The multivariate model after selection included 5 Braden Scale subscales, surgery, and acute respiratory failure (C = 0.91). CONCLUSIONS: The total Braden Scale score is predictive of pressure ulcer development but does not assist the clinician to develop an individualized targeted prevention plan. In contrast, the use of subscale scores can enhance prevention programs and resource utilization by focusing care on the risk factors specific to the individual patient.
The UAB Proteomics Database

SUMMARY The University of Alabama at Birmingham (UAB) Proteomics Database (UPD) (http://www.uab.edu/proteinmenu) was created to provide a repository for the storage and linkage of two-dimensional (2D) gel images and the associated information obtained through mass spectrometry analysis of the proteins excised from the 2D gels in a manner similar to the SWISS-2DPAGE database and the Stanford Microarray Database. This was accomplished through the development of a web interface, a relational database, image maps and hyperlinks stored in the database. In addition to the internally generated data, UPD provides links to the National Center for Biotechnology Information via accession number hyperlinks. UPD currently contains information on 44 individual proteins derived from four experiments conducted by four UAB faculty members. Images of the gels from which each of these proteins was isolated are accessed by hyperlinks embedded in the database. AVAILABILITY The UAB Proteomics Database can be accessed at http://www.uab. edu/proteinmenu.
Single Center Experience With Robotic Kidney Transplantation for Recipients With BMI of 40 kg/m2 Or Greater: A Comparison With the UNOS Registry

Background Obesity represents a barrier to kidney transplantation, but the increasing prevalence among renal failure patients has forced some centers to carefully consider such candidates. Morbidly obese patients may be at increased risk of delayed graft function, higher postoperative complications, and inferior graft outcomes. Nevertheless, mortality on the waiting list remains significantly higher than after transplant. We have applied minimally invasive surgery to perform kidney transplant in individuals with body mass index (BMI) of 40 kg/m2 or greater. We compared our results to the national United Network of Organ Sharing database. Methods The United Network of Organ Sharing registry was reviewed for adult living donor kidney transplant recipients with BMI of 40 kg/m2 or greater performed from September 2009 to December 2014. We compared transplants performed with robotic technique (RKT) versus patients performed with open surgery at all US centers including our own (open kidney transplant). Subgroup analysis in patients with BMI of 45 kg/m2 or greater was conducted. We compared outcomes including patient and graft survival, renal function, and technical complications. Results Robotic kidney transplantation group had a significantly higher mean BMI overall. The 1-year patient and graft survival rates were similar between groups. Renal function was also similar at 6, 12, and 36 months. Thrombosis caused 1.3% of the graft losses in open kidney transplant and 0% in the RKT group. Interestingly, 52.8% of the overall experience in patients with BMI of 45 kg/m2 or greater was performed with the robotic technique. Conclusions Robotic surgery offers similar patient and graft survivals with comparable renal function to open technique. Robotic kidney transplantation permits transplantation in extreme BMI categories without additional technical complications. Further studies are required to establish the role of RKT for obese candidates but preliminary data are encouraging.
Effect of Atropa belladonna L. on skin wound healing: Biomechanical and histological study in rats and in vitro study in keratinocytes, 3T3 fibroblasts, and human umbilical vein endothelial cells

The effect of Atropa belladonna L. (AB) aqueous extract on skin wound healing was studied in male Sprague–Dawley rats subjected to two parallel full‐thickness skin incisions on the back. Specimens for histological evaluation were collected on days 2 and 5 whereas for biomechanical testing, they were collected on day 5. In the in vitro study, a different concentration of AB extract was used to test the differentiation of keratinocytes using a panel of selected antibodies, proliferation, and cell survival of 3T3 fibroblasts and human umbilical vein endothelial cells using the MTT‐assay. Results of the in vivo experiments showed in AB‐treated wounds a shortened process of inflammation and accelerated collagen formation, as well as significantly increased wound stiffness as compared with control tissues. The in vitro examination showed that control keratinocytes were cytokeratin 19 free, while samples exposed to the highest AB extract concentration expressed CK19. Moreover, all concentrations were stimulatory to human umbilical vein endothelial cell proliferation. In addition, only the AB extract at the lowest tested concentration increased fibroblast growth, but higher concentrations decreased cell survival. In conclusion, our results indicate that the AB water extract positively affects early phases of skin wound healing in rats. However, the in vitro results on the inverse relation between the concentration of the AB extract and its effects on cell proliferation may be important for future research.
Comparative Analysis of Expression Profiles of Panicle Development among Tolerant and Sensitive Rice in Response to Drought Stress

Water deficit caused a serious threat to crops, especially panicle development at reproductive growth phase. We investigated grain yield components and gene expression profiles of panicle among tolerant and sensitive rice in response to drought stress. Panicle morphologies exhibited that secondary branches per panicle were more severely affected as compared to primary branches per panicle. Moreover, grain weight per panicle showed significant decrease for both tolerant and sensitive varieties except for MILT1444. Expression profile analysis revealed that 783 differentially expressed genes (DEGs) were identified to be drought-induced from young panicles in 2 cm length. Hierarchical clustering indicated that 76.8% of DEGs were up-regulated for all six rice varieties, and the percentage of down-regulated genes was higher in sensitive group than tolerant group. Biological process category revealed that the shared Gene Ontology (GO) terms were involved in response to abiotic stimulus and stress, whereas the specific GO terms in tolerant group were identified as regulation of biological quality, homeostatic process, cell growth, anatomical structure morphogenesis and development, and the unique terms in sensitive varieties were identified as lipid metabolic process and secondary metabolic process. Furthermore, the gene-based association analysis narrowed down list of DEGs, and four genes common to all six varieties were selected as candidate for breeders. Together, we found several shared and distinct biological processes between tolerant and sensitive varieties, and candidate stress-responsive genes. These findings provided insight into functional mechanisms regulating drought stress response in panicle development and may also help to crop tolerant improvement.
A Stereo Vision Framework for 3-D Underwater Mosaicking

Research on automatic mosaic creation for underwater applications has been investigated in the last fifteen years. The reconstruction of complex 3-D structures is useful in several underwater applications; in particular, 3-D mosaicking constitutes an important tool for seabed exploration, improving visualization and navigation in the underwater medium. Moreover, underwater measurement systems have been used extensively in marine research to estimate the size of interesting objects such as organisms and structures. In addition, visual sensing can be an enabling technology for Autonomous Underwater Vehicles (AUVs), which have the critical requirement to maintain an ongoing representation of its relative position with respect to an environmental representation. In these contexts, a better perception of the underwater environment can be achieved by using image processing algorithms for a suitable representation of the seabed. In optic sensing field and underwater environment, shape acquisition concerns with sensing activity including Shape from Stereopsis, Shape from Photometric Stereo, Shape from Motion and Active Stereo. Main aspects about Shape from Stereopsis will be presented focusing the attention on synchronism in the acquisition at hardware/soft ware levels. The usage of triggered expensive equipments in synchronized stereo sequence acquisitions could present some technical limitations, such as low frame rate and poor images resolution, demoting the quality of the 3-D mosaic. For the previous reasons, an ad-hoc algorithmic solution will be detailed to limit asynchronism problems due to time gap (delay) in stereo frames acquisition, when low-cost non-professional (non-triggered) hardware is used. To achieve a metric reconstruction, the presented framework requires a calibration phase whereas a new stereo frame-selection scheme based on the Epipolar Gap Evaluation (EGE) will be discussed to overcome asynchronisms. Normally, dense depth maps obtained by evaluating dense disparity maps allow the construction of high quality 3-D mosaics. A detailed discussion about methodologies for dense stereo matching will be addressed to handle the ill-posed stereo correspondence problem. A jo ined use of local (respectively global) matching methods and imaging enhancement algorithms will be considered to identify an appropriate amount of right correspondences in severe underwater conditions (backscattering, brightness constancy violation condition). The chapter treats an important aspect of the 3-D mosaic reconstruction as the registration by ego-motion and camera pose estimation. Classical solutions (i.e. Iterative Closest Point algorithm) and new trend in the Open Access Database www.i-techonline.com
On Semi-Automated Web Taxonomy Construction

The subject of this paper is the semi-automatic constructio n of taxonomies over the Web. We address the problem of discovering high-quality resources that belong in a partic ular node of a taxonomy. We show that minimal additional effort is required to provide relevance feedback in a hyperl inked environment, resulting in significant and consistent improvement in quality. Furthermore, this feedback is espe cially valuable for topics for which it is more difficult to find high-quality pages. Enroute, we describe novel algorit hms for hyperlink relevance feedback.
An Urban School District's Parent Involvement: A Study of Teachers' and Administrators' Beliefs and Practices.

This quantitative study examines the practices and beliefs of administra tors and teachers regarding parent involvement in an urban school district following the first year of the implementation of an action plan based on six national standards for parent involvement (National PTA, 1997). The theoreti cal framework is based upon Bandura’s social cognitive theory of self-efficacy. Administrators and teachers from an urban school district were surveyed. The instrument used for this study was adapted from “The Parent Involvement Inventory” published by the Illinois State Board of Education (1994). A twotailed t-test was conducted and findings indicate some statistically significant differences between many beliefs and practices. The results of this study show a mismatch between teachers’ and administrators’ beliefs and practices about parent involvement. Although teachers and administrators have strong beliefs about parent involvement and its importance in strengthening student achievement, what they practice in their schools and classrooms is not congruent with these beliefs.
An Improved Hybrid Re-Encryption Scheme for Mobile Cloud Computing Environment

Cloud computing is a technology or distributed network where user can move their data and any application software on it. But there is some issues in cloud computing, the main one is security because every user store their useful data on the network so they want their data should be protected from any unauthorized access, any changes that is not done on user’s behalf. There are different encryption and re-encryption techniques used for security purpose like FDE and FHE. In this paper, we have used the symmetric key agreement algorithm named Diffie Hellman, for improving cloud manager based scheme. OTP(One Time Password) is created which provides more security. The paper focuses to improve the cloud manager based scheme so that the security and integrity can be enhanced.
Complete Genomic Sequence of Dengue Virus Serotype 4 Isolated from Plasma Collected from a Haitian Child in 2014

ABSTRACT While data are limited, there is increasing evidence that infections by dengue viruses are endemic in Haiti. In 2014, an outbreak caused by dengue virus 4 (DENV-4) followed a chikungunya fever outbreak. We present here the complete genome sequence of one isolate grouped within the genotype II South America and Caribbean DENV-4 clades.
Serum Endotoxins and Flagellin and Risk of Colorectal Cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC) Cohort

Background: Chronic inflammation and oxidative stress are thought to be involved in colorectal cancer development. These processes may contribute to leakage of bacterial products, such as lipopolysaccharide (LPS) and flagellin, across the gut barrier. The objective of this study, nested within a prospective cohort, was to examine associations between circulating LPS and flagellin serum antibody levels and colorectal cancer risk. Methods: A total of 1,065 incident colorectal cancer cases (colon, n = 667; rectal, n = 398) were matched (1:1) to control subjects. Serum flagellin- and LPS-specific IgA and IgG levels were quantitated by ELISA. Multivariable conditional logistic regression models were used to calculate ORs and 95% confidence intervals (CI), adjusting for multiple relevant confouding factors. Results: Overall, elevated anti-LPS and anti-flagellin biomarker levels were not associated with colorectal cancer risk. After testing potential interactions by various factors relevant for colorectal cancer risk and anti-LPS and anti-flagellin, sex was identified as a statistically significant interaction factor (Pinteraction < 0.05 for all the biomarkers). Analyses stratified by sex showed a statistically significant positive colorectal cancer risk association for men (fully-adjusted OR for highest vs. lowest quartile for total anti-LPS + flagellin, 1.66; 95% CI, 1.10–2.51; Ptrend, 0.049), whereas a borderline statistically significant inverse association was observed for women (fully-adjusted OR, 0.70; 95% CI, 0.47–1.02; Ptrend, 0.18). Conclusion: In this prospective study on European populations, we found bacterial exposure levels to be positively associated to colorectal cancer risk among men, whereas in women, a possible inverse association may exist. Impact: Further studies are warranted to better clarify these preliminary observations. Cancer Epidemiol Biomarkers Prev; 25(2); 291–301. ©2016 AACR.
Lods, wrods, and mods: The interpretation of lod scores calculated under different models

In this paper we examine the relationships among classical lod scores, “wrod” scores (lod scores calculated under the wrong genetic model), and “mod” scores (lod scores maximized over genetic model parameters). We compare the behavior of these scores when the state of nature is linkage to their behavior when the state of nature is no linkage. We describe sufficient conditions for mod scores to be valid and discuss their use to determine the correct genetic model. We show that lod scores represent a likelihood‐ratio test for independence. We explain the “ascertainment‐assumption‐free” aspect of using mod scores to determine mode of inheritance and we set this aspect into a well‐established statistical framework. Finally, we summarize practical guidelines for the use of mod scores.
The Influence of Culture on Parenting Practices of East Asian Families and Emotional Intelligence of Older Adolescents

Academic success among East Asian students is well known and almost stereotypical. Yet the attention to emotional well-being continues to be minimal. The discrepancy between academic success and social/emotional difficulties appears to be a problem among East Asian adolescents. This qualitative grounded theory study examines how the cultural influences in parenting practices of East Asian parents impact the different aspects of emotional intelligence in older adolescents. Twenty older adolescents (ages 16—19) and their mothers, from Chinese and Korean heritage, living in the Southern Bay area in California participated in the study. The main form of data collection was through formal, in-depth and open-ended interviews and administration of standardized emotional intelligence questionnaires. The findings suggest that East Asian beliefs in hierarchy in family order, ‘saving face’, hard work/education, respect for elders and sibling relations have an impact on parent/child interaction. In addition, acculturation and globalization contributed to the change in cultural norms. The repeating themes related to parenting practices were correlated with very low, low, medium and high emotional intelligence levels. Distinct attitudinal and perceptual differences between adolescents with very low and high EQ were found.
Determination of Solar Energy for the Bioclimatic Design of Housing in the City of Juliaca Peru

Solar energy is an inexhaustible source, clean and does not pollute the environment being a resource that can be used. The objective of this research work is to determine solar energy for the bioclimatic design of houses in the city of Juliaca for two systems: solar photovoltaic for the generation of electric power and solar thermal for water heating. In the development of this project the daily measurement for three months of the solar irradiation was made with a solar measuring instrument MAC-SOLAR Solarimeter SLM018c-2, where the Peak Sun Hours (HSP) were determined with the methodology of negative asymmetric distribution of 6.632 kwh/m2/day and an average irradiation value of 1110.04 w/m2 in the city of Juliaca, with an optimum time interval from 9:00 am to 3:00 pm irradiation during the day, which has allowed modeling the behavior of solar energy for the design of a photovoltaic and thermal solar system; In addition, an experimental radiant floor module has been built in a bioclimatic room, which by recirculation of hot water through the floor reaches an average temperature of 20.93oC from 6:00 am to 9:00 pm, being within the zone of comfort of the Givoni Psychometric Diagram and the Peruvian Technical Standard (NTP).
Assessing the Effect of Inconsistent Assessors on Summarization Evaluation

We investigate the consistency of human assessors involved in summarization evaluation to understand its effect on system ranking and automatic evaluation techniques. Using Text Analysis Conference data, we measure annotator consistency based on human scoring of summaries for Responsiveness, Readability, and Pyramid scoring. We identify inconsistencies in the data and measure to what extent these inconsistencies affect the ranking of automatic summarization systems. Finally, we examine the stability of automatic metrics (ROUGE and CLASSY) with respect to the inconsistent assessments.
Multivariate time-to-event models for studies of recurrent childhood diseases.

BACKGROUND Standard Poisson regression analyses of infectious disease incidence may not be optimal when covariates change over time. When a longitudinal study is of sufficient duration so that multiple disease episodes per person may occur, within-subject correlation may be present and require special statistical consideration. Seasonality of disease incidence is a common feature of field studies of respiratory and diarrhoeal diseases in children. Accurate analysis may require keeping the children aligned with respect to the same baseline hazard function. These data features often are ignored in the analysis of such studies. METHODS Methods for accounting for multiple events are discussed. We propose the use of a counting process model to retain the alignment with respect to season. This model is supplemented by a simple bootstrap procedure to account for the within-child correlation. RESULTS The bootstrap technique is illustrated with data from a randomized trial of the effects of vitamin A supplementation on childhood morbidity. Standard errors for the main effect of vitamin A are larger using the bootstrap, indicating the presence of positive correlation. CONCLUSIONS Time-to-event models can be useful in the analysis of studies of childhood morbidity, especially for situations with seasonality, waning of effect, or multiple events. The bootstrap provides an appropriate, straightforward method for handling within-child correlation in such settings.