Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuroprofile: a web-based service for personalized neuroprediction from anatomical brain scans

Recent findings from cognitive neuroscience indicate that individual differences in various cognitive traits such as personality and intelligence are reflected in macroscopic brain structure that can be quantified with magnetic resonance imaging (MRI) techniques. While the initial aim of such research was to identify brain regions where structural variation correlated with cognitive functions, the flurry of correlational findings suggest that MRI scans of the human brain can be used to make predictions about individuals. We have confirmed this idea by constructing highly accurate prediction models for a multitude of cognitive traits using a machine learning technique called elastic net. We are currently implementing those prediction models on a web-based service called Neuroprofile where anyone can upload their brain scan to view the predicted cognitive traits. This service will be provided to make the contents of MRI-based brain health check-ups much richer and more informative.
Complete Scanpaths Analysis Toolbox

This paper presents a complete open software environment for control, data processing and assessment of visual experiments. Visual experiments are widely used in research on human perception physiology and the results are applicable to various visual information-based man-machine interfacing, human-emulated automatic visual systems or scanpath-based learning of perceptual habits. The toolbox is designed for Matlab platform and supports infra-red reflection-based eyetracker in calibration and scanpath analysis modes. Toolbox procedures are organized in three layers: the lower one, communicating with the eyetracker output file, the middle detecting scanpath events on a physiological background and the one upper consisting of experiment schedule scripts, statistics and summaries. Several examples of visual experiments carried out with use of the presented toolbox complete the paper
Scavenger Decapping Activity Facilitates 5′ to 3′ mRNA Decay

ABSTRACT mRNA degradation occurs through distinct pathways, one primarily from the 5′ end of the mRNA and the second from the 3′ end. Decay from the 3′ end generates the m7GpppN cap dinucleotide, which is subsequently hydrolyzed to m7Gp and ppN in Saccharomyces cerevisiae by a scavenger decapping activity termed Dcs1p. Although Dcs1p functions in the last step of mRNA turnover, we demonstrate that its activity modulates earlier steps of mRNA decay. Disruption of the DCS1 gene manifests a threefold increase of the TIF51A mRNA half-life. Interestingly, the hydrolytic activity of Dcs1p was essential for the altered mRNA turnover, as Dcs1p, but not a catalytically inactive Dcs1p mutant, complemented the increased mRNA stability. Mechanistic analysis revealed that 5′ to 3′ exoribonucleolytic activity was impeded in the dcs1Δ strain, resulting in the accumulation of uncapped mRNA. These data define a new role for the Dcs1p scavenger decapping enzyme and demonstrate a novel mechanism whereby the final step in the 3′ mRNA decay pathway can influence 5′ to 3′ exoribonucleolytic activity.
Discussion of paper by Mira and Baddeley

This very impressive paper brings together an enormous number of ideas from seemingly disconnected flelds. There are frequentist ideas associated with estimating equations for general stochastic processes, and approaches to optimality associated with the names of Godambe and Heyde; connections with the method of maximum likelihood and the method of moments, also pseudo-likelihood, general Bayes estimators and a new concept called the pseudo-posterior; connections with admissibility theory; connections with ideas of ordering Markov chains in terms of their rates of convergence in difierent metrics; and there is even a passing reference to the Stein (or Stein-Chen) method of probability approximation, which is usually regarded as a means of obtaining explicit upper bounds in rate-of-convergence problems. With so many ideas interacting, it is di‐cult to identify any one speciflc theme to concentrate on for a discussion. In my discussion, I would like to give my own perspective on what is going on. I hope that by so doing, I can persuade other to read the paper and form their own perspective of what are the most important themes.
Searching in the Dark: Phenotyping Diabetic Retinopathy in a De-Identified Electronic Medical Record Sample of African Americans

A hurdle to EMR-based studies is the characterization and extraction of complex phenotypes not readily defined by single diagnostic/procedural codes. Here we developed an algorithm utilizing data mining techniques to identify a diabetic retinopathy (DR) cohort of type-2 diabetic African Americans from the Vanderbilt University de-identified EMR system. The algorithm incorporates a combination of diagnostic codes, current procedural terminology billing codes, medications, and text matching to identify DR when gold-standard digital photography results were unavailable. DR cases were identified with a positive predictive value of 75.3% and an accuracy of 84.8%. Controls were classified with a negative predictive value of 1.0% as could be assessed. Limited studies of DR have been performed in African Americans who are at an elevated risk of DR. Identification of EMR-based African American cohorts may help stimulate new biomedical studies that could elucidate differences in risk for the development of DR and other complex diseases.
Evaluation of benign vs malignant hepatic lesions with positron emission tomography.

BACKGROUND In most malignant cells, the relatively low level of glucose-6-phosphatase leads to accumulation and trapping of [18F]fluorodeoxyglucose (FDG) intracellularly, allowing the visualization of increased uptake compared with normal cells. OBJECTIVES To assess the value of FDG positron emission tomography (PET) to differentiate benign from malignant hepatic lesions and to determine in which types of hepatic tumors PET can help evaluate stage, monitor response to therapy, and detect recurrence. DESIGN Prospective blinded-comparison clinical cohort study. SETTING Tertiary care university hospital and clinic. PATIENTS One hundred ten consecutive referred patients with hepatic lesions 1 cm or larger on screening computed tomographic (CT) images who were seen for evaluation and potential resection underwent PET imaging. There were 60 men and 50 women with a mean (+/-SD) age of 59 +/- 14 years. Follow-up was 100%. INTERVENTIONS A PET scan using static imaging was performed on all patients. The PET scan imaging and biopsy, surgery, or both were performed, providing pathological samples within 2 months of PET imaging. All PET images were correlated with CT scan to localize the lesion. However, PET investigators were unaware of any previous interpretation of the CT scan. MAIN OUTCOME MEASURES Visual interpretation, lesion-to-normal liver background (L/B) ratio of radioactivity, and standard uptake value (SUV) were correlated with pathological diagnosis. RESULTS All (100%) liver metastases from adenocarcinoma and sarcoma primaries in 66 patients and all cholangiocarcinomas in 8 patients had increased uptake values, L/B ratios greater than 2, and an SUV greater than 3.5. Hepatocellular carcinoma had increased FDG uptake in 16 of 23 patients and poor uptake in 7 patients. All benign hepatic lesions (n = 23), including adenoma and fibronodular hyperplasia, had poor uptake, an L/B ratio of less than 2, and an SUV less than 3.5, except for 1 of 3 abscesses that had definite uptake. CONCLUSIONS The PET technique using FDG static imaging was useful to differentiate malignant from benign lesions in the liver. Limitations include false-positive results in a minority of abscesses and false-negative results in a minority of hepatocellular carcinoma. The PET technique was useful in tumor staging and detection of recurrence, as well as monitoring response to therapy for all adenocarcinomas and sarcomas and most hepatocellular carcinomas. Therefore, pretherapy PET imaging is recommended to help assess new hepatic lesions.
MECHANICS OF SINGLE MOLECULES Lecture Outline

The contents of this lecture outline are solely for educational purposes. 2 Mechanics of single molecules CONTENTS Page Introduction 4 Why study single molecules? 4 Principles and techniques of single-molecule manipulation 5 A. Optical tweezer 5 B. Atomic force microscopy 6 C. Force measurement and stiffness calibration 6 D. Attachment of molecules 9 E. Experimental layout and data analysis 9 Mechanics of nucleic acid molecules and nucleoprotein complexes 12 A. Elasticity of DNA molecules 12 B. Chromatin 13 C. Chromosomes 14 C. Elasticity and structure of single RNA molecules 15 Mechanics of motor proteins 16 A. Types of motor proteins? 16 B. Common structural and mechanical aspects of motor proteins 16 C. Manipulation of single motor proteins 18 Mechanics of single protein molecules 19 A. Prototype protein: the giant muscle protein titin 19 B. Force response of the titin molecule 19 C. Stretching titin with the AFM 21 Mechanics of inter-molecular interactions 23 References and Suggested reading 25 3 Mechanics of single molecules
Functional and Structural Characterization Reveals Novel FBXW7 Biology

This thesis aims to examine aspects of FBXW7 biology, a protein that is frequently mutated in a variety of cancers. The first part of this thesis describes the characterization of FBXW7 isoform and mutant substrate profiles using a proximity-dependent biotinylation assay. Isoform-specific substrates were validated, revealing the involvement of FBXW7 in the regulation of several protein complexes. Characterization of FBXW7 mutants also revealed siteand residue-specific consequences on the binding of substrates and, surprisingly, possible neo-substrates. In the second part of this thesis, we utilize high-throughput peptide binding assays and statistical modelling to discover novel features of the FBXW7-binding phosphodegron. In contrast to the canonical motif, a possible preference of FBXW7 for arginine residues at the +4 position was discovered. I then attempted to validate this feature in vivo and in vitro on a novel substrate discovered through BioID.
Estimating Real Human Trajectories through Mobile Phone Data

Nowadays, the huge worldwide mobile-phone penetration is increasingly turning the mobile network into a gigantic ubiquitous sensing platform, enabling large-scale analysis and applications. In recent years, mobile data-based research reaches important conclusions about various aspects of human mobility patterns and trajectories. But how accurately do these conclusions reflect the reality? In order to evaluate the difference between the reality and the approximation methods, we study in this paper the error between real human trajectory and the one obtained through mobile phone data using different interpolation methods (linear, cubic, nearest and spline interpolations) while taking into account some mobility parameters. From extensive evaluations based on real cellular network activity data of the Boston metropolitan area, we show that the linear interpolation offers the best estimation for sedentary people and the cubic one for commuters. Moreover, the nearest interpolation appears as the best one for “ordinary people” doing regular stops and standard displacements. Another important experimental finding described in this paper is that trajectory estimation methods show different error regimes whether used within or outside the “territory” of the user defined by the radius of gyration.
Performance Analysis of TCP NewReno over a Cellular Last-Mile: Buffer and Channel Losses

TCP NewReno is one of the most widely deployed TCP versions in today's Internet. However, a full understanding of the complex inter-dependencies between the losses due to wireless channel errors and those due to buffer overflows, and their (joint) impact on TCP NewReno's congestion control algorithm in wireless and wired-cum-wireless networks is still lacking. In this paper, we develop a comprehensive analytical model for, and study the performance of, TCP NewReno with a cellular last-mile access, taking into account both types of losses. We assume a frame-level Markovian loss model, and build a model that features the system's basic controllable parameters (such as the number of retransmissions and the buffer size), so as to study how they (jointly) affect the TCP-level throughput. We model certain finer aspects, e.g., correlations in wireless and buffer losses and their cross-correlation. We provide a summary of numerical results highlighting several non-trivial findings. In particular, we demonstrate that there exist optimal (i.e., TCP throughput maximizing) pairs of the number of retransmissions and the buffer size.
Optimizing PARSEC for Knights Landing

PARSEC is a massively parallel Density-Functional-Theory (DFT) code. Within the modernization effort towards the new Intel Knights Landing platform, we adapted the main computational kernel, represented as high-order finite-difference stencils, to use hybrid MPI and OpenMP* runtimes. We also employed MPI-3 non-blocking neighborhood collectives for the halo exchange. We present performance data on the Knights Landing platform including MPI traces portraying our exploration of communication-computation overlap in a hybrid MPI and OpenMP application, and the fine-tuning of the interplay between the load-balancing - static at the MPI level and dynamic in OpenMP.
Optimal Coding of Generalized-Gaussian-Distributed Frequency Spectra for Low-Delay Audio Coder With Powered All-Pole Spectrum Estimation

We present an optimal coding scheme that parameterizes the maximum-likelihood estimate of variance for frequency spectra belonging to the generalized Gaussian distribution, the distribution covering the Laplacian and the Gaussian. By slightly modifying the all-pole model of the conventional linear prediction (LP), we can estimate the variance with the same method as in LP, which has low computational costs. Experimental results show that incorporating the coding scheme in a state-of-the-art wide-band audio coder enhances its objective and subjective quality in a low-bit-rate and low-delay situation by increasing the compression efficiency. Thus, this coding scheme will be useful in applications like mobile communications, which requires highly efficient compression.
Use of Prestudy Heparin Did Not Influence the Efficacy and Safety of Rivaroxaban in Patients Treated for Symptomatic Venous Thromboem‐bolism in the EINSTEIN DVT and EINSTEIN PE Studies

Abstract Objectives In the EINSTEIN DVT and EINSTEIN PE studies, the majority of patients received heparins to bridge the period during venous thromboembolism (VTE) diagnosis confirmation and the start of the study. In contrast to vitamin K antagonists (VKAs), rivaroxaban may not require initial heparin treatment. Methods To evaluate the effect of prestudy heparin on the efficacy and safety of rivaroxaban relative to enoxaparin/VKA, the 3‐month incidence of recurrent VTE, and the 14‐day incidence of major and nonmajor clinically relevant bleeding were compared in patients who did and did not receive prestudy heparin. Results Of the 8,281 patients randomized, 6,937 (83.8%) received prestudy heparin (mean ± SD duration = rivaroxaban: 1.04 [± 0.74] days; enoxaparin 1.03 [± 0.42] days), and 1,344 (16.2%) did not. In patients who did not receive prestudy heparin, the incidences of recurrent VTE were similar in rivaroxaban (15 of 649, 2.3%) and enoxaparin/VKA (13 of 695, 1.9%) patients (adjusted hazard ratio [HR] = 1.11; 95% confidence interval [CI] = 0.52 to 2.37). The incidences of recurrent VTE were also similar in rivaroxaban (54 of 3,501, 1.5%) and enoxaparin/VKA (69 of 3,436, 2.0%) patients who did receive prestudy heparin (adjusted HR = 0.74; 95% CI = 0.52 to 1.06; pinteraction = 0.32). The incidences of major or nonmajor clinically relevant bleeding with rivaroxaban were not significantly different from those with enoxaparin/VKA, either with (105 of 3,485, 3.0% vs. 104 of 3,428, 3.0%; adjusted HR = 0.98; 95% CI = 0.75 to 1.29) or without (24 of 645, 3.7% vs. 30 of 688, 4.4%; adjusted HR = 0.81; 95% CI = 0.46 to 1.40; pinteraction = 0.68) prestudy heparin. Conclusions Although the majority of patients in the EINSTEIN studies received prestudy heparin, there were no notable differences in treatment effect of rivaroxaban versus enoxaparin/VKA in those who did and did not receive it.
CMOS Current Mode Logic Gates for High-Speed Applications

This paper presents results of a design that uses CMOS current mode logic that can be used to implement the high precision, speed critical elements of the mixed-signal systems. The design is based upon the 0.25-µm CMOS TSMC process. The propagation delays of the new current mode logic are compared to those of equivalent gates implemented in conventional CMOS logic. The results show a propagation delay improvement of more than 200% using the current mode logic. The application of the proposed current mode building blocks is illustrated in a typical mixed-signal circuit, the phase detector for a high-speed phase locked loop with good speed improvement over conventional CMOS logic.
A Global Assessment of the SRTM Performance

The NASA/NGA Shuttle Radar Topography Mission (SRTM) collected interferometric radar data which has been used by the Jet Propulsion Laboratory to generate a near-global topography data product for latitudes smaller than 60°. One of the primary goals of the mission was to produce a data set that was globally consistent and with quantified errors. To achieve this goal, an extensive global ground campaign was conducted by NGA and NASA to collect ground truth that would allow for the global validation of this unique data set. This paper documents the results of this SRTM validation effort using this global data set. The table shown below summarizes our results (all quantities represent 90 percent errors in meters).
Linear Least Squares CFO Estimation and Kalman Filtering Based I/Q Imbalance Compensation in MIMO SC-FDE Systems

This paper investigates carrier frequency offset (CFO) estimation and inphase/quadrature (I/Q) imbalance compensation in time-varying frequency-selective channels. We first propose a linear least squares (LLS) CFO estimation approach which has a lower complexity and a higher accuracy than the previous nonlinear CFO estimation methods. We then propose a Kalman filtering based I/Q imbalance compensation approach in the presence of CFO, which demonstrates a good ability to track the channel time variations with a fast convergence speed, by nulling the cyclic prefix (CP) and including the CFO in the state vector of the equivalent channel model. The proposed Kalman filtering based I/Q imbalance compensation approach with associated equalization tracks the time variation with a fast convergence speed. Simulation results show that the proposed compensation approach for CFO and I/Q imbalance provides a bit error rate (BER) performance close to the ideal case with perfect channel state information (CSI), no CFO and no I/Q imbalance.
Improving Lifetime of Cell-Edge Smart Sensing Devices by Incentive Architecture Based on Dynamic Charging

In smart cities, a large number of smart sensing devices face the problem of limited portable battery capacity, which limits the working lifetime of smart sensing devices. However, wireless energy harvesting is an effective means to prolong their lifetime as soon as they are rechargeable. Most existing methods (e.g., mobile charging vehicles and dedicated power-beacons) are vulnerable to the smart sensing devices in complex terrain and difficult to care for all the charged objects. Moreover, they have high hardware maintaining cost. Therefore, we present a novel incentive architecture based on the dynamic charging to improve the lifetime of the cell-edge smart sensing devices. It leverages smart terminals carried by users as chargers to first provide wireless energy to a set of cell-edge smart sensing devices and then collect data from these sensing devices. Also, the smart terminals collecting data will act as forwarders, which will help the sensing devices transmit data to the data center through the base stations. The challenge is how to incentivize a smart terminal to act as both a charger and a forwarder. We propose the non-cooperative game for a set of smart terminals to address this issue, which can make these smart terminals get a satisfactory return and let the corresponding smart sensing devices improve their working lifetime. We conduct extensive simulations and demonstrate the effectiveness of our incentive architecture with the numerical results.
Combining Object-oriented Systems and Software Configuration Management

The objective of this paper is to analyze combinations of software configuration management (SCM) and object-oriented (OO) systems that synergistically increase the effectiveness of both systems. After reviewing the two areas, the central concepts of each are shown to be analogous to one another. The paper then diverges to look at existing literature by considering reification of variants and attempts at producing SCM object models. It is then proposed that SCMs could better serve in OO environments by working at a higher-level than the file model. Finally, a holistic approach to software is proposed that fully integrates the design and implementation aspects of OO techniques and the management aspect of SCMs.
Status of HER 2 Amplification , Polysomy 17 and Histopathological Features of 425 Pakistani Breast Cancer Patients

Breast cancer is one of the most common cancers occurring among women throughout the world, and is the leading cause of death from cancer. Globally, it averages more than 1.1 million new cases, where developed countries face 55% of the burden; the incidence is rapidly catching up in the developing world as well (Parkin et al., 2005). In Pakistan like other Asian countries, breast cancer among females is frequently reported at an advanced stage, which is most likely due to lack of awareness and early screening programs (Ahmad, 1991; Naeem et al., 2008). Being a heterogeneous disease, breast cancer is characterized by multiple subtypes as revealed by differential gene expression profiles. Its diverse nature points towards the involvement of multiple prognostic and predictive tumor markers (Turaga et al., 2010). Epidermal growth receptor 2, commonly known as HER2 is a crucial breast cancer oncogene, which is located on the long arm of chromosome 17 and encodes a 185-KDa cell surface receptor with tyrosine kinase activity (Akiyama et al., 1986; Slamon et al., 1989). Although, early studies have
Head Pose Estimation System Based on Particle Filtering with Adaptive Diffusion Control

In this paper, we propose a new tracking system based on a stochastic filtering framework for reliably estimating the 3D pose of a user’s head in real-time. Our system estimates the pose of a user’s head in each image frame whose 3D model is automatically obtained at an initialization step. In particular, our estimation method is designed to control the difusion factor of a motion model adaptively. This technique contributes significantly to improving the following performance simultaneously: the robust tracking against abrupt head motion and the accurate pose estimation when the user is staring at a point in a scene. The performance of our proposed method has been successfully demonstrated via experiments.
In the Virtual Extension

To ensure the timely publication of articles, Communications created the Virtual Extension (VE) to expand the page limitations of the print edition by bringing readers the same high-quality articles in an online-only format. VE articles undergo the same rigorous review process as those in the print edition and are accepted for publication on merit. The following synopses are from articles now available in their entirety to ACM members via the Digital Library.