Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined genome-wide scan for prostate cancer susceptibility genes.

BACKGROUND Prostate cancer represents a substantial public health burden worldwide. It is the second leading cause of cancer death among men in the United States. A family history of the disease is among the most well-established risk factors for prostate cancer. Efforts to localize prostate cancer susceptibility alleles by using genetic linkage analysis methods have been hindered by genetic heterogeneity, incomplete penetrance, disease phenocopies, and the lack of DNA samples from parents of individuals with late-onset prostate cancer. METHODS We performed a combined genome-wide linkage analysis among 426 families from four existing hereditary prostate cancer (HPC) study populations to systematically search for prostate cancer susceptibility genes. To decrease the degree of locus heterogeneity, we analyzed subsets of families with similar clinical and demographic characteristics. Nonparametric multipoint linkage was the primary method of analysis. Results are presented as allele-sharing logarithm of the odds (LOD) scores, and all reported P values are two-sided. RESULTS The strongest evidence for prostate cancer linkage was found at chromosome region 17q22 (nonparametric multipoint Kong and Cox allele-sharing LOD score = 3.16 at marker D17S787; P =.00007). Stratified analyses revealed several additional chromosomal regions that are likely to segregate prostate cancer susceptibility genes among specific subsets of HPC families, including 15q11 among families with late-onset disease (allele-sharing LOD = 5.57 at marker D15S128; P<.00001) and 4q35 among families with four or more affected family members (allele-sharing LOD = 3.10 at marker D4S1615; P =.00008). CONCLUSION Fine mapping studies to facilitate identification of prostate cancer susceptibility genes in these linked regions are warranted.
Burden of Cancers Related to Smoking among the Indonesian Population: Premature Mortality Costs and Years of Potential Life Lost.

BACKGROUND As smoking is the leading preventable cause of multiple diseases and premature cancer deaths, estimating the burden of cancer attributable to smoking has become the standard in documenting the adverse impact of smoking. In Indonesia, there is a dearth of studies assessing the economic costs of cancers related to smoking. This study aimed to estimate indirect mortality costs of premature cancer deaths and years of potential life lost (YPLL) attributable to smoking among the Indonesian population. MATERIALS AND METHODS A prevalence based method was employed. Using national data, we estimated smoking-attributable cancer mortality in 2013. Premature mortality costs and YPLL were estimated by calculating number of cancer deaths, life expectancy, annual income, and workforce participation rate. A human capital approach was used to calculate the present value of lifetime earnings (PVLE). A discount rate of 3% was applied. RESULTS The study estimated that smoking attributable cancer mortality was 74,440 (30.6% of total cancer deaths), comprised of 95% deaths in men and 5% in women. Cancers attributed to smoking were responsible for 1,207,845 YPLL. Cancer mortality costs caused by smoking accounted for USD 1,309 million in 2013. Among all cancers, lung cancer is the leading cause of death and economic burden. CONCLUSIONS Cancers related to smoking pose an enormous economic burden in Indonesia. Therefore, tobacco control efforts need to be prioritized in order to prevent more losses to the nation. The data of this study are important for advocating national tobacco control policy.
Effect of 3D nitrogen, dry mass per area and local irradiance on canopy photosynthesis within leaves of contrasted heterogeneous maize crops.

BACKGROUND AND AIMS Nitrogen partitioning within stands has been described fairly comprehensively, especially for C(3) plants in dense stands where the horizontal heterogeneity of foliage distribution is relatively small. Nitrogen has been shown to be distributed vertically and in parallel to light, maximizing carbon assimilation and stand productivity. Conversely, row crops such as maize (C(4) plants) are characterized by strong horizontal heterogeneity of foliage distribution, and a three-dimensional (3D) approach is required to investigate the combined effect of spatial distribution of nitrogen and light on canopy photosynthesis. MODEL The 3D geometry of maize canopies was modelled with varying densities and at different developmental stages using plant digitizing under field conditions. For lamina parts, photosynthesis was measured and nitrogen content per unit area (N(a)) was described from analysis of nitrogen content per unit mass (N(m)) and dry mass per unit area (M(a)). Hyperbolic relationships between photosynthesis at irradiance saturation (P(max)) and N(a) were established as well as a linear relationship between dark respiration (R(d)) and N(a), whereas quantum efficiency (alpha) was found to be independent of N(a). KEY RESULTS AND CONCLUSIONS N(m), M(a) and N(a) were shown to change over time vertically (i.e. between laminae), which has been largely reported previously, and horizontally (i.e. within laminae), which has scarcely been described previously. Even if M(a) played a major role in N(a), a strong relationship between N(a) and M(a) could not be demonstrated, whereas several previous studies have found that N(a) was essentially related to M(a) rather than N(m). From simulations of radiative exchange using a 3D volume-based approach and lamina photosynthesis using a hyperbola, it was shown that real patterns of N(a) partitioning could increase daily crop photosynthesis by up to 8 % compared with uniform patterns of N(a), especially for the earliest stages of stand development.
A simplified deterministic channel model for user mobility investigations in 5G networks

High frequency bands are considered for the fifth generation (5G) mobile networks to handle the continuous increase in the demand for cellular data traffic. However, the propagation conditions in high frequency bands are more challenging than in low frequency bands, making the radio link more susceptible to obstruction. These new radio aspects impose new challenges on the design of user mobility procedures which shall be tested by means of simulations. Current statistical propagation models lack the accuracy in capturing spatial correlation, channel degradation when the user is obstructed and frequency correlation among different layers. On the other hand, deterministic channel models are too complex and inappropriate for mobility investigations since they require a high computational time. This paper proposes a simplified deterministic channel model which captures the propagation aspects that are relevant for mobility investigations. In addition, a model for signal measurement is proposed considering the impact of analog beamforming which is a key component in 5G networks. Simulations are performed to show the characteristics of the channel and received signal. The results corroborate that the signal degradation due to obstruction is faster for higher carrier frequency and user velocity, and slower for higher diffraction angle.
Satisfying Common Criteria Security Evaluation Testing Requirements : Two Case Studies Using a High-Assurance Operating System

In this paper, we describe results of two case studies designed to satisfy the testing requirements mandated by higher levels of the Common Criteria for security evaluations. These requirements include 1) Demonstrable independence of individual test cases 2) Demonstrable coverage of both user level specifications and implementation code. The case studies are based on a highly secure smart card operating system. In the first case study, we used automated specification based test generation, together with fault injection, to demonstrate that self-contained test cases are independent and do not lead to fault masking. The goal of the second case study was to demonstrate adequate code coverage, while retaining the ability to generate expected outputs based on specifications. To that end, we first established mappings between the specification and implementation code elements. Test cases were then generated from the user level specification to identify the executed code elements and we attempted to use static analysis to map the unexecuted code elements to the corresponding elements in the user level specification. In this second case study, we found that, given a sufficiently expressive user level specification, and a test generation system that is able to effectively use such a specification, the resulting tests will cover the vast majority of the code branches that are able to be covered. Therefore, the benefit of a feedback-directed system will be limited. We further provide evidence that the static analysis required to generate feedback in these cases tends to be difficult, involving inferring the semantics of the internal implementation of data structures. In particular, we observed that the internal states at the implementation level in a high security application pose significant challenges to this mapping process.
HIV-1 adaptation to NK cell-mediated immune pressure

The observation, by Alter et al., of the enrichment of NK cell “escape” variants in individuals carrying certain Killer-cell Immunoglobulin-like Receptor (KIR) genes is compelling evidence that natural killer (NK) cells exert selection pressure on HIV-1. Alter et al hypothesise that variant peptide, in complex with HLA class I molecules binds KIR receptors and either increases NK cell inhibition or decreases NK cell activation compared to wild type peptide thus leading to virus escape from the NK cell response. According to this hypothesis, in order for NK cells to select for an escape variant, an individual must carry both the KIR and an HLA ligand that binds the variant peptide. In this study we estimate the proportion of the population that is capable of selecting for escape variants and use both epidemiological modelling and a model-free approach to investigate whether this proportion explains the observed variant enrichment. We found that the fraction of individuals within whom the variant would have a selective advantage was low and was unable to explain the high degree of enrichment observed. We conclude that whilst Alter et al’s data is consistent with selection pressure, the mechanism that they postulate is unlikely. The importance of this work is two-fold. Firstly, it forces a re-evaluation of some of the clearest evidence that NK cells exert a protective effect in HIV-1 infection. Secondly, it implies that there is a significant aspect of immunology that is not understood: it is possible that KIRs bind much more widely than was previously appreciated; that a gene in linkage with the KIR genes is responsible for considerable peptide-dependent selection or that variant peptides are indirectly impacting KIR ligation.
Modeling cyber attacks on a critical infrastructure scenario

Critical infrastructures, such as electrical grids, are monitored and controlled by SCADA (Supervisory Control And Data Acquisition) systems. Cyber attacks against SCADA might put CI and in turn industrial production, environment integrity and human safety at risk. Here, with reference to an actual case study, constituted by an electrical grid, its SCADA system and a corporate network, we discuss how cyber threats, vulnerabilities and attacks might degrade the functionalities of SCADA and corporate network and, in turn, lead to outages of the electrical grid. We represent SCADA and corporate network under malware propagation, Denial of Service and Man In The Middle attacks, and predict their consequent functionalities. Particularly, we use Netlogo to identify possible malware propagation in relation to SCADA & corporate security policies adopted from the utility and NS2 simulator to compute the consequences of such cyber attacks on SCADA and in turn on electrical grid functionalities.
Injection Laryngoplasty for Type 1 Laryngeal Cleft in Children

Objective. To review the 2-year, single-institution experience with injection laryngoplasty for diagnosis and treatment of type 1 laryngeal clefts (LC-1). Study Design. Case series with chart review. Setting. Tertiary care academic children’s hospital. Subjects and Methods. Patients at our institution who underwent injection laryngoplasty for LC-1 from January 2008 to December 2009. Outcome measures included patient demographics, surgical and anesthetic technique, effect on swallowing, and complications. Preoperative and postoperative swallowing evaluations were compared, and quality and duration of effects were calculated. Results. Sixteen children, 9 male and 7 female, underwent injection laryngoplasty for LC-1. Mean gestational age was 36.4 weeks (SD, 4.0 weeks; range, 27-41 weeks). Six patients had a major congenital anomaly (37.5%). Mean age at injection was 11.8 months (SD, 8.9 months; range, 2.9-33.5 months). Nine patients (56%) demonstrated complete resolution of penetration and aspiration on postoperative modified barium swallow (MBS), 4 patients (25%) had some improvement, and 3 patients (19%) showed no change. There were no complications. Mean duration of symptom improvement was 3.3 months (SD, 3.0 months; range, 0-11 months). Five patients went on to have definitive surgical LC-1 repair. Conclusion. Injection laryngoplasty was found to have favorable results in this group of patients with LC-1. Most patients experienced complete resolution of aspiration on MBS, and no patients experienced complications. These findings support the further study of injection laryngoplasty for LC-1 as both a diagnostic and therapeutic technique. Longer follow-up intervals are necessary to elucidate the predictive value with regard to success of formal cleft repair.
Laboratory, Reading Center, and Coordinating Center Data Management Methods in the Jackson Heart Study

Background:Cardiovascular disease (CVD) is the leading cause of death in the United States. In comparison to whites, African-Americans have a higher risk of dying from CVD and have a worse risk factor profile. The Jackson Heart Study (JHS) is designed to investigate the origin and natural history of CVD in African-Americans. Methods:Reading centers for electrocardiograms, echocardiograms, carotid ultrasonograms, pulmonary function tests, and ambulatory blood pressure monitoring provide training for data accrual, quality assurance assessments, and specialized measurements for research objectives. Laboratories adhering to well-established quality assurance programs provide blood and urine analyses, as well as storage of specimens for future assays. A new Coordinating Center was created to perform functions analogous to those of coordinating centers for multisite studies, including protocol development, data management, statistical analyses, and operational support for the study. An established coordinating center serves as a resource to the JHS Coordinating Center, providing assistance in preparing procedure manuals and data collection forms. This group also designed and developed the JHS data management system. Results:This network of specialized research organizations is implementing state- of-the-science methodologies to assess prevalence, progression, and incidence of CVD and subclinical atherosclerosis, and to evaluate a myriad of risk factors. From November 2000 through March 2004, JHS collected 4000 data fields on each of more than 5300 African-American participants. Conclusions:This article describes the roles of specialized research agencies contributing to JHS, and the methodologies being utilized to accumulate study data. A diverse collection of scientific disciplines is required to collect the information needed to meet the objectives of the JHS.
Characterization and horizontal transfer of class 1 integrons in Escherichia coli isolates from cooked meat products.

INTRODUCTION Escherichia coli is a commensal bacterium in humans, animals, and the environment that is one of the microorganisms commonly resistant to antimicrobials. Cooked meat products, which are popular in China, are easily contaminated by E. coli during processing and storage. METHODOLOGY In this study, a total of 75 E. coli isolates from cooked meat products in Henan province, China, were assayed for the presence of and horizontal transfer of class 1 integrons. RESULTS Class 1 integrons were detected in 11 (14.7%) of these isolates, and contained four groups of resistance gene cassettes, including dfrA17-aadA5, dfrA1-aadA1, dfrA12-orfF-aadA2, and an uncommon array of aacA4-catB8-aadA1. The transfer frequency of selected integron-positve donors ranged from 10(-6) to 10(-4) transconjugants per recipient cell, and the integron-containing DNA from the donors could be transferred to E. coli J53Azr with the transformation frequency of 10(-7) to 10(-5). CONCLUSIONS Class 1 integrons could be transferred to recipient E. coli J53 by conjugation and natural transformation. These findings suggest the role of commensal E. coli isolates from cooked meats as an important reservoir for integrons and the possible transfer of antimicrobial resistance genes to humans via the food chain.
Comparative bioinformatic analysis of the conserved domains, amino acid residues, and binding grooves of tumor necrosis factor.

AIM Comparative structural bioinformatic analysis of the conserved domains and amino acid residues, binding grooves of the tumor necrosis factor (TNF)α and β in order to elucidate structurebased inhibitor development was conducted. METHODS We carried out the bioinformatics study of TNF proteins at the Department of Bio-informatics (Galgotias University, India) between June and December 2012. TNFα and TNF-β functional protein sequences in FASTA format were obtained from the NCBI database for analysis. The online tool ClustalW from the European Bioinformatic Institute was used for multiple sequence alignment to record similarities. The Jmol server was used for 3D visualization of alpha helix, beta sheet and loops of TNF proteins. The PyMOL molecular visualization system was used to generate surface cavity and to identify binding grooves of TNF proteins. RESULTS This study showed highly conserved amino acids residues such as LYS11, PRO12, ALA14, HIS15, VAL50, PRO51, GLY54, LEU55, TYR56, LEU57, TYR59, SER60, GLN61, GLY122, VAL123, PHE124, PHE152, and GLY153 are consequent amino acids in TNF-β while residues such as ALA31, HIS32, SER77, GLN78, PHE166, and GLY167 are consequent amino acids in TNF-β. Surface cavity and binding grooves showed TNF-β with larger surface cavities than TNF-α with higher chances for drug development since small drug-like molecules can bind easily into the groove. CONCLUSION The results illustrate the structure of TNF proteins and the novel findings may guide future research on TNF and in the process of assisting the optimization of the pharmacological properties involving the two crucial proteins.
Severity assessment of circular orifice synthetic jet based on sound pressure level

Severity Assessment from the viewpoint of noise exposure is the preliminary stage for application of noise reduction technique to solve noise problems. In this paper, the severity assessment of circular orifice synthetic jet is presented based on sound pressure level. Synthetic jet generates substantial noise when operated in air as surrounding fluid. The effect of orifice diameter, orifice height and excitation voltage on sound pressure level of circular orifice synthetic jet is experimentally documented here. The excitation frequency to the synthetic jet actuator for the present study is 100 – 700 Hz. This parametric study is valuable from viewpoint of selection of synthetic jet configuration without violating Environmental Protection Agency standard and for obtaining maximum jet velocity and minimum sound pressure level.
A simple model-driven approach to energy disaggregation

Energy disaggregation is to discover the energy consumption of individual appliances from their aggregated energy values. To solve the problem, most existing approaches rely on either appliances' signatures or their state transition patterns, both hard to obtain in practice. Aiming at developing a simple, universal model that works without depending on sophisticated machine learning techniques or auxiliary equipments, we make use of easily accessible knowledge of appliances and the sparsity of the switching events to design a Sparse Switching Event Recovering (SSER) method. By minimizing the total variation (TV) of the (sparse) event matrix, SSER can effectively recover the individual energy consumption values from the aggregated ones. To speed up the process, a Parallel Local Optimization Algorithm (PLOA) is proposed to solve the problem in active epochs of appliance activities in parallel. Using real-world trace data, we compare the performance of our method with that of the state-of-the-art solutions, including the popular Least Square Estimation (LSE) methods and a recently-developed machine learning method using iterative Hidden Markov Model (HMM). The results show that our approach has an overall better performance in both detection accuracy and overhead.
Prototype of a vision-based gaze-driven man-machine interface

This paper describes preliminary work on a non-intrusive gaze-driven interface for man-machine interaction based on vision techniques. The current computer screen location pointed at by the user is evaluated using a linear model of image-to-screen mapping, which can be easily auto-calibrated at run-time on the basis of the current relative position of camera and user and camera settings. A simple active deformable model of the eye is defined, which is used both to track user's movements and estimate the current position of the user's pupil in the image in a decoupled fashion. Experiments show that the proposed approach is fast and accurate enough for the design of low-cost man-machine interfaces, with applications ranging from the assistance to the disabled people to multimedia systems.
A Modular Shared L2 Memory Design for 3-D Integration

Large required size, and tolerance to latency and variations in memory access time make L2 memory a suitable option for 3-D integration. In this paper, we present a synthesizable 3-D-stackable L2 memory IP component, which can be attached to a cluster-based multicore platform through its network-on-chip interfaces offering high-bandwidth memory access with low average latency. Our design implements a scalable 3-D-nonuniform memory access (NUMA) architecture based on low latency logarithmic interconnects, which allows stacking of multiple identical memory dies (MDs), supports multiple outstanding transactions, and achieves high clock frequencies due to its highly pipelined nature. We implemented our design with STMicroelectronics CMOS-28-nm low-power technology and obtained a clock frequency of 500 MHz (limited by the access time of the memory arrays, whereas its logic components can operate up to 1 GHz), up to eight stacked dies (4 MB) with a memory density loss of 9%. Benchmark simulation results demonstrate that the addition of 3-D-NUMA to a multicluster system can lead to an average performance boost of 34%. Furthermore, experiments and estimations confirm that 3-D-NUMA is energy and power efficient (38% power reduction due to an architectural clock gating scheme), temperature friendly (over 40°C temperature reduction), and has unique features suitable for low-cost manufacturing (2.3× cost reduction due to identical MD layouts). Finally, 22% yield improvement is achievable in 3-D-NUMA compared with its 2-D counterparts, using the state of the art through-silicon-via technologies.