Miracle-dz/UniFAR-FTUs huggingface dataset:
Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes

Telomeres are terminal repetitive DNA sequences on chromosomes, and are considered to comprise almost exclusively hexameric TTAGGG repeats. We have evaluated telomere sequence content in human cells using whole-genome sequencing followed by telomere read extraction in a panel of mortal cell strains and immortal cell lines. We identified a wide range of telomere variant repeats in human cells, and found evidence that variant repeats are generated by mechanistically distinct processes during telomerase- and ALT-mediated telomere lengthening. Telomerase-mediated telomere extension resulted in biased repeat synthesis of variant repeats that differed from the canonical sequence at positions 1 and 3, but not at positions 2, 4, 5 or 6. This indicates that telomerase is most likely an error-prone reverse transcriptase that misincorporates nucleotides at specific positions on the telomerase RNA template. In contrast, cell lines that use the ALT pathway contained a large range of variant repeats that varied greatly between lines. This is consistent with variant repeats spreading from proximal telomeric regions throughout telomeres in a stochastic manner by recombination-mediated templating of DNA synthesis. The presence of unexpectedly large numbers of variant repeats in cells utilizing either telomere maintenance mechanism suggests a conserved role for variant sequences at human telomeres.
Improving Energy Efficiency Via Multi-Rate Diversity in 802 . 11 Wireless Networks

Energy efficiency is one of the most important concerns in wireless networks because wireless clients usually have limited battery power. The aim of this work is to reduce energy consumption by exploiting multi-rate diversity in 802.11 wireless networks. An important observation is that “probabilistic rate combination” in transmission can significantly reduce power consumption. We formulate the energy efficient probabilistic rate combination as a non-convex optimization problem. A noncooperative rate adaption scheme is presented to reduce power consumption without information exchange. Each node selects rate combination and computes its transmission probability based on the weighted average interface queue length. Due to the wellknown “rate anomaly” problem, selfish nodes may choose to transmit at a lower rate free-ride from the other nodes. To mitigate this problem, we propose a joint consecutive packet transmission and contention window adaptation mechanism. We prove the stability of our proposed algorithm, and to the best of our knowledge, this is the first control theoretic analysis in 802.11 on “multi-rate” wireless networks. Simulation results show that the proposal can significantly save battery power, even up to 600% times compared with standard 802.11a/h protocol.
A Retargetable Static Binary Translator for the ARM Architecture

Machines designed with new but incompatible Instruction Set Architecture (ISA) may lack proper applications. Binary translation can address this incompatibility by migrating applications from one legacy ISA to a new one, although binary translation has problems such as code discovery for variable-length ISA and code location issues for handling indirect branches. Dynamic Binary Translation (DBT) has been widely adopted for migrating applications since it avoids those problems. Static Binary Translation (SBT) is a less general solution and has not been actively researched. However, SBT performs more aggressive optimizations, which could yield more compact code and better code quality. Applications translated by SBT can consume less memory, processor cycles, and power than DBT and can be started more quickly. These advantages are even more critical for embedded systems than for general systems. In this article, we designed and implemented a new SBT tool, called LLBT, which translates ARM instructions into LLVM IRs and then retargets the LLVM IRs to various ISAs, including ×86, ×86--64, ARM, and MIPS. LLBT leverages two important functionalities from LLVM: comprehensive optimizations and retargetability. More importantly, LLBT solves the code discovery problem for ARM/Thumb binaries without resorting to interpretation. LLBT also effectively reduced the size of the address mapping table, making SBT a viable solution for embedded systems. Our experiments based on the EEMBC benchmark suite show that the LLBT-generated code can run more than 6× and 2.3× faster on average than emulation with QEMU and HQEMU, respectively.
A survey paper on Biometric based Face detection techniques

As continual research is being conducted in the area of Biometrics, one of the most practical applications under strong development is in the construction of a face detection system. a comprehensive description of biometric recognition based on the most popular human biometric traits is provided. The term Biometrics is becoming highly important in computer security world. The human physical characteristics like fingerprints, face, hand geometry, voice and iris are known as biometrics. We present a comprehensive and critical survey of face detection algorithms. Face detection is a necessary first-step in face recognition systems, with the purpose of localizing and extracting the face region from the background. It also has several applications in areas such as content-based image retrieval, video coding, video conferencing, crowd surveillance, and intelligent human–computer interfaces. However, it was not until recently that the face detection problem received considerable attention among researchers. The human face is a dynamic object and has a high degree of variability in its appearance, which makes face detection a difficult problem in computer vision. A great emphasis was placed on the face characteristics, particularly on the state of the art of the component-based face detection. While the problem of recognizing faces under gross variations remains largely unsolved, a demonstration system as proof of concept that such systems are now becoming practical have been developed. A system capable of reliable detection, with reduced constraints in regards to the facial position and expression of the face and the illumination variation and background of the image has been implemented. In this paper, an attempt is made to compare existing face detection algorithms which are widely used and subject of interest.
Risk Factors for Meniscectomy After Meniscal Repair

Background: Previous research suggests that a substantial percentage of meniscal repairs fail, resulting in a subsequent meniscectomy. Risk factors for failure have been investigated using small cohorts, providing ambiguous results. Purpose: To measure the frequency of and elucidate risk factors for subsequent meniscectomies after meniscal repair using a large study population from multiple surgical centers. Study Design: Case-control study; Level of evidence, 3. Methods: A total of 9529 patients who underwent 9609 outpatient meniscal repairs between 2003 and 2010 were identified from a statewide database of all ambulatory surgery in New York. Patients who subsequently underwent a meniscectomy were then identified. A Cox regression analysis was used to calculate the hazard ratio and 95% confidence intervals. The model included patient age, sex, comorbidities, concomitant arthroscopic procedures, laterality of the meniscus, and surgeon’s yearly meniscal repair volume. Results: The overall frequency of subsequent meniscectomies was 8.9%. Patients were at a decreased risk for subsequent meniscectomies if they underwent a concomitant anterior cruciate ligament (ACL) reconstruction (P < .001). Patients undergoing isolated meniscal repairs (without concomitant ACL reconstruction) were at a decreased risk if they were older (P < .001), had a lateral meniscal injury (P = .002), or were operated on by a surgeon with a higher annual meniscal repair volume (>24 cases/year; P < .001). Conclusion: A meniscectomy after meniscal repair is performed infrequently, supporting the notion that repairing a meniscus is a safe and effective procedure in the long term. The risk for undergoing subsequent meniscectomies is decreased in patients undergoing a concomitant ACL reconstruction, in cases of isolated meniscal repairs for patients of older age, and in patients undergoing meniscal repair by surgeons with a high case volume.
ADVANCES IN EARTH RADIATION BUDGET OBSERVATIONS FROM CERES TERRA

The goal of the Clouds and the Earth's Radiant Energy System (CERES) project is to provide a long-term record of radiation budget at the top-of-atmosphere (TOA), within the atmosphere, and at the surface with consistent cloud and aerosol properties at climate accuracy [1]. CERES consists of an integrated instrument-algorithm-validation science team that provides development of higher-level products (Levels 1-3) and investigations. It involves a high level of data fusion, merging inputs from 25 unique input data sources to produce 18 CERES data products. Over 90% of the CERES data product volume involves two or more instruments. At the heart of the CERES project are the CERES instruments. Thus far, five CERES instruments (PFM, FM1-FM4) have flown on three different spacecraft: TRMM, EOS-Terra and EOS-Aqua. CERES FM5 is scheduled for launch on the NPP spacecraft, and FM6 will fly on NPOESS C1. Each CERES instrument is a scanning broadband radiometer that measures filtered radiances in the SW (wavelengths between 0.3-5 m), total (TOT) (wavelengths between 0.3-200 m) and WN (wavelengths between 8-12 m) regions. On Terra, CERES has a spatial resolution of approximately 20 km (equivalent diameter). the filtered radiances to unfiltered reflected solar, unfiltered emitted terrestrial LW and WN radiances [2]. These are then used to determine SW, LW and WN TOA radiative fluxes by applying Angular Disitrbution Models (ADMs) [3] constructed from two years of CERES Terra biaxial scan data using MODIS cloud property retrievals for scene identification [4]. MODIS cloud and aerosol retrievals, meteorological data from the Global Modeling and Assimilation Office—Goddard Earth Observing System Model, and aerosol assimilation data from the Model of Atmospheric Transport and Chemistry (MATCH) are used as input to a modified version of the [5] radiative transfer code to provide computed SW, LW and net radiative fluxes at several levels within the atmosphere and at the surface. Surface radiative fluxes are also estimated using simpler parameterizations [6]. In order to account for diurnal variations in clouds and radiation, the CERES and MODIS observations on Terra are combined with data from five geostationary instruments to produce 1°1° gridded TOA, within-atmosphere and surface radiative fluxes at 3-hourly, daily, and monthly time scales. Considerable effort is spent on verifying the consistency of the many instruments and inputs to ensure that the CERES data product reflect real changes in the climate system as opposed to artificial changes associated with the input data.
Achieving Geometric Consistency for Mixed Reality using Reconstructed 3 D Models

Abstract – Recent years, MR (Mixed Reality) systems have been used for virtual reconstruction of cultural heritage assets. In outdoor environment, it’s difficult to achive the geometric consistency because of illumination changes and a lot of obstacles (occlusions). If the portions of the buildings still remain, it is advantageous to use 3d models obtained from the remained objects to solve these issues. Therefore, we propose a robust method to achieve geometric consistency between real and virtul objects under various illumination conditions by using 3D geometric models. The experimental results in which the proposed method is applied to reconstruct the Roman cultural heritage site show the effectiveness of our method.
Algorithms and concepts for an onboard train localization system for safety-relevant services

This paper describes a system that enables a railway vehicle to determine its position in a track network accurately. The system does not rely on trackside hardware like balises or axle counters but is based solely on onboard sensors. It is composed out of drift-free velocity estimates of an eddy current sensor, a GNSS sensor, and a geodetic and topological track map. The paper develops an algorithm based on a probabilistic modeling that fuses the data of those sensors and determines position estimates robustly. We describe how we can treat ambiguities and stochastic uncertainty adequately and we introduce the concept of virtual balises that replace in software what is implemented by trackside balises in present train protection systems. The technique of onboard train localization is one important contribution to future train protection systems that are based on onboard sensors rather than trackside infrastructure and that are more flexible and less expensive than today's systems without loss of safety.
Changes in the Metabolome in Response to Low-Dose Exposure to Environmental Chemicals Used in Personal Care Products during Different Windows of Susceptibility

The consequences of ubiquitous exposure to environmental chemicals remain poorly defined. Non-targeted metabolomic profiling is an emerging method to identify biomarkers of the physiological response to such exposures. We investigated the effect of three commonly used ingredients in personal care products, diethyl phthalate (DEP), methylparaben (MPB) and triclosan (TCS), on the blood metabolome of female Sprague-Dawley rats. Animals were treated with low levels of these chemicals comparable to human exposures during prepubertal and pubertal windows as well as chronically from birth to adulthood. Non-targeted metabolomic profiling revealed that most of the variation in the metabolites was associated with developmental stage. The low-dose exposure to DEP, MPB and TCS had a relatively small, but detectable impact on the metabolome. Multiple metabolites that were affected by chemical exposure belonged to the same biochemical pathways including phenol sulfonation and metabolism of pyruvate, lyso-plasmalogens, unsaturated fatty acids and serotonin. Changes in phenol sulfonation and pyruvate metabolism were most pronounced in rats exposed to DEP during the prepubertal period. Our metabolomics analysis demonstrates that human level exposure to personal care product ingredients has detectable effects on the rat metabolome. We highlight specific pathways such as sulfonation that warrant further study.
High-precision shortest distance estimation for large-scale social networks

Over the past decades, many large-scale social network systems, such as Facebook and Twitter, have been deployed in different countries. How to efficiently analyze the topological characteristics of large-scale social networks has been a challenging problem in the research community. One of the critical topological characteristics is the shortest distance between two nodes in a network. The existing shortest distance algorithms, such as Breadth First Search (BFS), work well with small networks. For a network with billions of nodes, calculating the pairwise shortest distances with these algorithms requires an overlong period of time. In this paper, we present a high-precision ShOrtest Distance Approximation (SODA) scheme, which utilizes a small set of pre-calculated distances to estimate the shortest distance between each pair of nodes in large-scale social networks. Compared with the existing shortest distance estimation schemes for social networks, SODA leads to high estimation accuracy since it utilizes a novel optimization method, Robust Discrete Matrix Decomposition (RDMD), to eliminate the impact of significant errors/outliers and generate the coordinates of the nodes in a network simultaneously. In addition, SODA differentiates the asymmetric distances in directed graphs. Consequently, SODA works well with both directed and undirected social networks. Finally, SODA only involves convex optimization. Therefore, SODA is highly competitive in terms of computation complexity. Our experimental results indicate that SODA outperforms the state-of-the-art shortest distance estimation schemes in terms of estimation accuracy and running time.
The new frontier in muscular dystrophy research: booster genes

More than 30 different forms of muscular dystrophy (MD) have been molecularly characterized and can be diagnosed, but progress toward treatment has been slow. Gene replacement therapy has met with great difficulty because of the large size of the defective genes and because of difficulties in delivering a gene to all muscle groups. Cell replacement therapy has also been difficult to realize. Will it even be possible to design specific therapy protocols for all MDs? Or is a more realistic goal to treat some of the secondary manifestations that are common to several forms of MD, such as membrane instability, necrosis, and inflammation, and to promote regeneration? As reviewed here, enhanced expression of a range of proteins provides a boost for degenerating dystrophic muscle in mouse models. Expression of a mini‐agrin promotes basement membrane formation instead of laminin α2; integrin α7, GalNac transferase, and ADAM12 promote cell adhesion and muscle stability in the absence of dystrophin; calpastatin prevents muscle necrosis; and nitric oxide synthase prevents inflammation. ADAM12, IGF‐I, and myostatin blockade promote regeneration and reduce fibrosis. One can envision numerous other candidate booster genes which encode proteins that promote survival and/or regeneration of the compromised muscle or proteins that affect post‐translational modifications of critical proteins. Finally, fibrosis, which is the curse of many human diseases, may also be attacked. Once the mechanisms of the boosters are better understood, drugs may be developed to provide the boost to muscle. Some of the experiences in models of muscular dystrophy may inspire new approaches in other genetic degenerative diseases as well. —Engvall, E. , Wewer, U. M. The new frontier in muscular dystrophy research: booster genes. FASEB J. 17, 1579–1584 (2003)
AlGaN/GaN HEMTs on Silicon Carbide Substrates for Microwave Power Operation

Results from technology and microwave characterization of large periphery AlGaN/GaN power HEMTs on insulating SiC substrates are presented. The influence of processing steps on device performance is discussed. DC characteristics reveal current densities above 1.2 A/mm and extrinsic transconductances of 275 mS/mm. A power density of 5.2 W/mm @ 2 GHz is obtained for devices up to 2 mm gate width. The maximum power level achieved on-wafer is 13.8 W @ 2 GHz for 4 mm wide devices. A hybrid amplifier using packaged 4 mm devices delivers 15.1 W.
Capacity Augmentation Bound of Federated Scheduling for Parallel DAG Tasks

We present a novel federated scheduling approach for parallel real-time tasks under a general directed acyclic graph (DAG) model. We provide a capacity augmentation bound of 2 for hard real-time scheduling; here we use the worst-case execution time and critical-path length of tasks to determine schedulability. This is the best known capacity augmentation bound for parallel tasks. By constructing example task sets, we further show that the lower bound on capacity augmentation of federated scheduling is also 2 for any m > 2. Hence, the gap is closed and bound 2 is a strict bound for federated scheduling. The federated scheduling algorithm is also a schedulability test that often admits task sets with utilization much greater than 50%m. Type of Report: Other Department of Computer Science & Engineering Washington University in St. Louis Campus Box 1045 St. Louis, MO 63130 ph: (314) 935-6160 Capacity Augmentation Bound of Federated Scheduling for Parallel DAG Tasks Jing Li, Abusayeed Saifullah, Kunal Agrawal, Christopher Gill, and Chenyang Lu Department of Computer Science and Engineering Washington University in St. Louis {li.jing, saifullah}@go.wustl. edu, {kunal, cdgill, lu}@cse.wustl. edu
Tracking granules on the Sun's surface and reconstructing velocity fields - II. Error analysis

Context: The determination of horizontal velocity fields at the solar surface is crucial to understanding the dynamics and magnetism of the convection zone of the sun. These measurements can be done by tracking granules. Aims: Tracking granules from ground-based observations, however, suffers from the Earth's atmospheric turbulence, which induces image distortion. The focus of this paper is to evaluate the influence of this noise on the maps of velocity fields. Methods: We use the coherent structure tracking algorithm developed recently and apply it to two independent series of images that contain the same solar signal. Results: We first show that a k-? filtering of the times series of images is highly recommended as a pre-processing to decrease the noise, while, in contrast, using destretching should be avoided. We also demonstrate that the lifetime of granules has a strong influence on the error bars of velocities and that a threshold on the lifetime should be imposed to minimize errors. Finally, although solar flow patterns are easily recognizable and image quality is very good, it turns out that a time sampling of two images every 21 s is not frequent enough, since image distortion still pollutes velocity fields at a 30% level on the 2500 km scale, i.e. the scale on which granules start to behave like passive scalars. Conclusions: The coherent structure tracking algorithm is a useful tool for noise control on the measurement of surface horizontal solar velocity fields when at least two independent series are available.
Sandwiched: Exploring role and identity of middle managers in the genuine middle

This article explores middle managers in the professions from their position in the sandwiched middle. Based upon interviews with senior academics in management roles and their subordinates in UK business schools, we investigate this experienced middle through a metaphor that informs one particular subject position: to be an umbrella carrier. This position entails protecting subordinates from what is seen as unnecessary and/or damaging initiatives and information from top management above, in order to allow for good professional work to take place below. This form of countermanagement, which aims to weaken hierarchical pressure rather than enforce or uphold it, is informed by a stronger identification with the profession and subordinates below than with the leader role or the superiors above, and aids the middle managers in their identity work.
Modeling of airway in 4D lung CT images

Lung cancer is a disease that consists of uncontrolled cell growth in tissues of the lungs. There are a number of different treatment options available for lung cancer. Radiation therapy is a process in which high energy radiation is applied to kill cancer cells and shrink tumors. A treatment plan of patient is developed before radiation therapy in which the clinician spent a lot of time on manually marking the airways on the CT scan images so that airways can be protected while doing the radiotherapy. Work in this paper is a step towards automating the airway segmentation.
An Interactive Freight-Pooling Service for Efficient Last-Mile Delivery

The existing practices of the urban section of freight transport chain result in traffic congestion, air pollution and resources being wasted. We focus on the final stage of freight distribution and propose an interactive freight-pooling service, in an effort to reduce the undesirable effects and the cost of freight transport in urban areas. Our service empowers city and state authorities to orchestrate the distribution network through interactive interfaces. We break the problem into three distinct phases that collectively helps us set constraints related to the quality of service and find inexpensive routes. In this regard, our proposed freight-pooling approach becomes an attractive option for efficient distribution, that guarantees cost minimization without sacrificing the level of quality.