Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical target and dose and dose-rate responses for the induction of chromosomal instability by ionizing radiation.

To investigate the critical target, dose response and dose-rate response for the induction of chromosomal instability by ionizing radiation, bromodeoxyuridine (BrdU)-substituted and unsubstituted GM10115 cells were exposed to a range of doses (0.1-10 Gy) and different dose rates (0.092-17.45 Gy min(-1)). The status of chromosomal stability was determined by fluorescence in situ hybridization approximately 20 generations after irradiation in clonal populations derived from single progenitor cells surviving acute exposure. Overall, nearly 700 individual clones representing over 140,000 metaphases were analyzed. In cells unsubstituted with BrdU, a dose response was found, where the probability of observing delayed chromosomal instability in any given clone was 3% per gray of X rays. For cells substituted with 25-66% BrdU, however, a dose response was observed only at low doses (<1.0 Gy); at higher doses (>1.0 Gy), the incidence of chromosomal instability leveled off. There was an increase in the frequency and complexity of chromosomal instability per unit dose compared to cells unsubstituted with BrdU. The frequency of chromosomal instability appeared to saturate around approximately 30%, an effect which occurred at much lower doses in the presence of BrdU. Changing the gamma-ray dose rate by a factor of 190 (0.092 to 17.45 Gy min(-1)) produced no significant differences in the frequency of chromosomal instability. The enhancement of chromosomal instability promoted by the presence of the BrdU argues that DNA comprises at least one of the critical targets important for the induction of this end point of genomic instability.
File System Workload Analysis For Large Scientific Computing Applications

Parallel scientific applications require high-performanc e I/O support from underlying file systems. A comprehensive understanding of the expected workload is t herefore essential for the design of high-performance parallel file systems. We re-examine the w orkload characteristics in parallel computing environments in the light of recent technology ad vances and new applications.
Discovering Shared Interests Among People Using Graph Analysis

An important problem faced by users of large networks is how to discover resources of interest, such as data or people. In this paper we focus on locating people with particular interests or expertise. The usual approach is to build interest group lists from explicitly registered data. However, doing so assumes one knows what lists should be built, and who should be included in each list. We present an alternative approach, which can support a more fine grained and dynamically adaptive notion of shared interests. Our approach deduces interests from the history of electronic mail communication, using a set of heuristic graph algorithms. We demonstrate the algorithms by applying them to data collected from 15 sites for two months. Using these algorithms we were able to deduce shared interest lists for people far beyond the data collection sites. The algorithms we present are powerful, and if abused can threaten privacy. We propose guidelines that we believe should underly the ethical use of these algorithms. We discuss several possible applications that we believe do not threaten privacy, including discovering resources other than people, such as file system data. CR
Proteome Modulation in H9c2 Cardiac Cells by microRNAs miR-378 and miR-378*

MicroRNAs are a novel class of powerful endogenous regulators of gene expression. MiR-378 and miR-378* are localized in the first intron of the Ppargc1b gene that codes the transcriptional co-activator PGC-1β. The latter regulates energy expenditure as well as mitochondrial biogenesis. The miR-378:miR-378* hairpin is highly expressed in cardiac cells. To better assess their role in cardiomyocytes, we identified miR-378 and miR-378* targets via a proteomic screen. We established H9c2 cellular models of overexpression of miR-378 and miR-378* and identified a total of 86 down-regulated proteins in the presence of either one of these miRs. Functional annotation clustering showed that miR-378 and miR-378* regulate related pathways in cardiomyocytes, including energy metabolism, notably glycolysis, cytoskeleton, notably actin filaments and muscle contraction. Using bioinformatics algorithms we found that 20 proteins were predicted as direct targets of the miRs. We validated eight of these targets by quantitative RT-PCR and luciferase reporter assay. We found that miR-378 targets lactate dehydrogenase A and impacts on cell proliferation and survival whereas miR-378* targets cytoskeleton proteins actin and vimentin. Proteins involved in endoplasmic reticulum stress response such as chaperone and/or calcium buffering proteins GRP78, PPIA (cyclophilin A), calumenin, and GMMPA involved in glycosylation are repressed by these miRs. Our results show that the miR-378/378* hairpin establishes a connection among energy metabolism, cytoskeleton remodeling, and endoplasmic reticulum function through post-transcriptional regulation of key proteins involved in theses pathways.
Measures for Term and Sentence Relevances: an Evaluation for German

Terms, term relevances, and sentence relevances are concepts that figure in many NLP applications, such as Text Summarization. These concepts are implemented in various ways, though. In this paper, we want to shed light on the impact that different implementations can have on the overall performance of the systems. In particular, we examine the interplay between term definitions and sentence-scoring functions. For this, we define a gold standard that ranks sentences according to their significance and evaluate a range of relevant parameters with respect to the gold standard.
Injury of Bacteria by Sanitizers

Injury of test cultures was quantitated by differences in colony counts obtained with a complete medium and those obtained on conventional selective media. Staphylococcus aureus, Streptococcus faecalis, and several strains of Escherichia coli were injured when exposed to the quaternary ammonium compound methylalkyltrimethyl ammonium chloride. Representative hypochlorite sanitizers also caused injury of E. coli ML30. Sanitizer concentration appeared to be the main factor in the cause of death and injury, a higher concentration being needed to cause death. Increases in temperature did not result in substantial increases in injury; however, the lethal effect was greater at higher temperatures. Varying the cell concentration from 107 to 109 cells per ml did not change the fraction of cell population killed or injured. The inability or failure of common selective media to detect injured bacteria in food could have serious public health consequences.
ATP: a reliable transport protocol for ad hoc networks

Existing works have approached the problem of reliable transport in ad hoc networks by proposing mechanisms to improve TCP's performance over such networks, In this paper, we show through detailed arguments and simulations that several of the design elements in TCP are fundamentally inappropriate for the unique characteristics of ad hoc networks. Given that ad hoc networks are typically stand-alone, we approach the problem of reliable transport from the perspective that it is justifiable to develop an entirely new transport protocol that is not a variant of TCP. Toward this end, we present a new reliable transport layer protocol for ad hoc networks called ATP (ad hoc transport protocol). We show through ns2-based simulations that ATP outperforms default TCP as well as TCP-ELFN and ATCP.
Simultaneous Visual Data Completion and Denoising Based on Tensor Rank and Total Variation Minimization and Its Primal-Dual Splitting Algorithm

Tensor completion has attracted attention because of its promising ability and generality. However, there are few studies on noisy scenarios which directly solve an optimization problem consisting of a noise inequality constraint. In this paper, we propose a new tensor completion and denoising model including tensor total variation and tensor nuclear norm minimization with a range of values and noise inequalities. Furthermore, we developed its solution algorithm based on a primal-dual splitting method, which is computationally efficient as compared to tensor decomposition based non-convex optimization. Lastly, extensive experiments demonstrated the advantages of the proposed method for visual data retrieval such as for color images, movies, and 3D-volumetric data.
Characterization of the Viscoelastic Fracture of Solvated Semi-Interpenetrating Polymer Network Silicone Hydrogels

The unique compressive, optical, and biocompatible properties of silicone hydrogels allow them to be used in a wide variety of applications in the biomedical field. However, the relatively weak mechanical behavior, as well as the highly deformable nature of these elastomeric materials, presents a myriad of challenges when attempting to understand their constitutive and fracture properties in order to improve hydrogel manufacturing and performance in applications. In this thesis, a series of experimental techniques were developed or adapted from common engineering approaches in order to investigate the effects of rate and temperature on the viscoelastic constitutive and fracture behavior of two solvated semi-interpenetrating polymer network silicone hydrogel systems. Viscoelastic characterization of these material systems was performed by implementing a series of uniaxial tension and dynamic mechanical analysis shear tests in order to generate relevant master curves and corresponding thermal shift factors of such properties as shear relaxation modulus, dynamic moduli, and the loss factor. Concurrently, the cohesive fracture properties were studied by utilizing a “semi-infinite” strip geometry under constrained tension in which thin pre-cracked sheets of these cured hydrogels were exposed to several different loading conditions. Fracture tests were performed over a relevant range of temperatures and crosshead rates to determine and generate a master curve of the subcritical strain energy release rate. Experimental methods utilizing high-speed camera images and digital image correlation to monitor viscoelastic strain recovery in the wake of a propagating crack were explored. The results from this thesis may prove useful in an investigation of the interfacial fracture of these hydrogel systems on several different polymer substrates associated with an industrial manufacturing problem.
Theophylline exhibits anti-cancer activity via suppressing SRSF3 in cervical and breast cancer cell lines

Caffeine, theophylline, and theobromine are the most well-known members of methylxanthines. Caffeine-induced serine/arginine-rich splicing factor 2, SRSF2, and SRSF3 are required for the alternative splicing of a subset of cancer-associated genes. However, it remains to be investigated whether and how theophylline and theobromine as well as caffeine exert their antitumor effects through mediating the alternative splicing process. Here, we reveal that theophylline down-regulated SRSF3 expression and switched p53 from alpha into a beta isoform as caffeine did in HeLa and MCF-7 cells via the reverse-transcriptase polymerase chain reaction and Western blot analysis. Further functional studies show that theophylline induced cellular apoptosis, senescence, and decreased colony formation. Interestingly, theophylline had a suppressive effect on cellular proliferation, whereas caffeine enhanced cellular proliferation rates via the 5-bromo-2-deoxyuridine analysis. Theophylline and caffeine had no effect on MCF-10A cells, which is a normal breast cell line. Our results provide an insight that theophylline as well as caffeine could be repurposed as antitumor leading compounds via the downregulation of splicing factor SRSF3 and its target genes.
A lion lentivirus related to feline immunodeficiency virus: epidemiologic and phylogenetic aspects

Feline immunodeficiency virus (FIV) is a novel lentivirus that is genetically homologous and functionally analogous to the human AIDS viruses, human immunodeficiency virus types 1 and 2. FIV causes immunosuppression in domestic cats by destroying the CD4 T-lymphocyte subsets in infected hosts. A serological survey of over 400 free-ranging African and Asian lions (Panthera leo) for antibodies to FIV revealed endemic lentivirus prevalence with an incidence of seropositivity as high as 90%. A lion lentivirus (FIV-Ple) was isolated by infection of lion lymphocytes in vitro. Seroconversion was documented in two Serengeti lions, and discordance of mother-cub serological status argues against maternal transmission (in favor of horizontal spread) as a major route of infection among lions. A phylogenetic analysis of cloned FIV-Ple pol gene sequences from 27 lions from four African populations (from the Serengeti reserve, Ngorongoro Crater, Lake Manyara, and Kruger Park) revealed remarkably high intra- and interindividual genetic diversity at the sequence level. Three FIV-Ple phylogenetic clusters or clades were resolved with phenetic, parsimony, and likelihood analytical procedures. The three clades, which occurred not only together in the same population but throughout Africa, were as divergent from each other as were homologous pol sequences of lentivirus isolated from distinct feline species, i.e., puma and domestic cat. The FIV-Ple clades, however, were more closely related to each other than to other feline lentiviruses (monophyletic for lion species), suggesting that the ancestors of FIV-Ple evolved in allopatric (geographically isolated) lion populations that converged recently. To date, there is no clear evidence of FIV-Ple-associated pathology, raising the possibility of a historic genetic accommodation of the lion lentivirus and its host leading to a coevolved host-parasite symbiosis (or commensalism) in the population similar to that hypothesized for endemic simian immunodeficiency virus without pathology in free-ranging African monkey species.
Cytotoxicity of diesel engine exhaust among the Chinese occupational population: a complement of cytokinesis-block micronucleus cytome

Abstract Diesel engine exhaust (DEE), a ubiquitous environmental pollutant, has been associated with adverse health effects. Revelation of cellular and molecular changes is critical for understanding environmental exposure-related diseases. Although the molecular-level effects of DEE exposure have been investigated, whether it is associated with aberrant changes at cellular level is largely unknown at the population level. In the present study, we measured urinary concentrations of 6 mono-hydroxylated PAHs (OH-PAHs) and cytotoxicity-related endpoints including apoptosis and necrosis frequencies, and nuclear division cytotoxicity index (NDCI) in peripheral blood lymphocytes (PBLs) of 79 DEE-exposed workers and 59 non-DEE-exposed workers. We found that DEE-exposed workers had significantly higher necrosis frequency and lower NDCI than did non-DEE-exposed workers (both p < 0.001). In all study subjects and nonsmoking workers, urinary summed OH-PAHs was associated with increased necrosis frequency and reduced NDCI. In nonsmoking workers, an interquartile range increase in urinary summed OH-PAHs was associated with 105.03% increase in necrosis frequency and 8.70% decrease in NDCI. Taking advantage of the previous measure of micronucleus frequency, we observed that micronucleus frequency was positively correlated with apoptosis and necrosis frequencies (r = 0.277, p = 0.047 and r = 0.452, p = 0.001, respectively) and negatively correlated with NDCI (r = −0.477, p < 0.001). In conclusion, our results suggested that DEE exposure was associated with increased necrosis frequency and further with reduced NDCI in PBLs, providing evidence of DEE exposure-induced cytotoxicity in humans.
Development and characterization of a gelatin‐based coating with unique sealing properties

The experimental results on the development of thin (∼ 1.5 μm) gelatin-based coatings and the investigation on their sealing attribute when applied onto oriented polypropylene (OPP) are reported. The sealing performance, expressed as the strain energy required to separate the sealed joints, was studied as a function of three different influencing factors. pH of the hydrogel solution was varied between 5 and 11. The highest seal strength values were obtained for pH values beyond the isoelectric point (IEP) of the gelatin molecule. The effect of the plasticizer (glycerol) was studied by changing its concentration from 2.5 wt % to 7.5 wt % to the total weight of the hydrogel solution. Glycerol concentration = 7.5 wt % was found to be the best for achieving adequate strain energy values. The influence of a hydrophobic component on the capability of the coating to act as a sealant has also been assessed. The hydrophobic component had a positive effect only up to a certain level (1 wt %, weight percent), whereas beyond this value, it affected the seal strength attribute. According to the best setting conditions, seal strength values for the OPP biocoated films of ∼ 61 N × mm were attained, with a corresponding maximum force required to break the joints of 2.4 N. These results are discussed by taking into consideration the modality of seals opening. Interestingly, the heat-seal (temperature: 90°C; dwell time: 1 s; pressure: 4 bar) failed in both peeling and tearing mode failure, as confirmed by microscopy, spectrophotometric, and particle size analyzes. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2010
An Efficient Tree Structure for Delay Sensitive Data Gathering in Wireless Sensor Networks

It is important to design an energy efficient data gathering tree structure for wireless sensor networks. As for the energy efficiency, network's overall energy consumption and per-node fairness have been studied. Note that the minimum degree spanning tree (MDST) is optimal in the sense of per-node fairness. We believe that the per-node fairness is of practical interest and that the delay bound associated with it must be investigated. Unfortunately, no such efforts have been made so far. In this paper, we propose a tree structure, called the DB- MDST, which modifies MDST to reduce the height and extend its degree. With the DB-MDST, the near optimal delay bound (i.e., comparable to the one obtained using the shortest path tree) can be achieved at the cost of as much energy as consumed by the MDST while it cannot be achieved with the MDST. Simulation results support the claim stated.
Risk Factors for Ocular Chlamydia after Three Mass Azithromycin Distributions

Background An important component of the World Health Organization's comprehensive trachoma elimination strategy is the provision of repeated annual mass azithromycin distributions, which are directed at reducing the burden of ocular chlamydia. Knowledge of characteristics associated with infection after mass antibiotic treatments could allow trachoma programs to focus resources to those most likely to be infected with ocular chlamydia. Methodology/Principal Findings We monitored 12 communities in rural Ethiopia that had received 3 annual mass azithromycin treatments as part of a cluster-randomized trial for trachoma. One year after the third treatment, a random sample of children from each village received conjunctival examination for follicular trachomatous inflammation (TF) and intense trachomatous inflammation (TI), conjunctival swabbing for chlamydial RNA and DNA, and a household survey. The primary outcome for this study was RNA evidence of ocular chlamydia, which we detected in 41 of 573 swabbed children (7.2%, 95%CI 2.7–17.8). In multivariate mixed effects logistic regression models, ocular chlamydial RNA was significantly associated with ocular discharge (OR 2.82, 95%CI 1.07–7.42), missing the most recent mass azithromycin treatment (OR 2.49, 95%CI 1.02–6.05), having a sibling with ocular chlamydia (OR 4.44, 95%CI 1.60–12.29), and above-median community population (OR 7.81, 95%CI 1.56–39.09). Ocular chlamydial infection was also independently associated with TF (OR 3.42, 95%CI 1.56–7.49) and TI (OR 5.39, 95%CI 2.43–11.98). Conclusions/Significance In areas with highly prevalent trachoma treated with multiple rounds of mass azithromycin, trachoma programs could consider continuing mass azithromycin treatments in households that have missed prior mass antibiotic treatments, in households with clinically active trachoma, and in larger communities.
A model of grain boundary diffusion in polycrystals with evolving microstructure

Abstract We consider grain boundary diffusion in a polycrystal in which normal grain growth occurs simultaneously with diffusion. We assume that any point within the diffusion zone is swept a number of times by migrating grain boundaries, and develop a model which operates with the average concentrations of the diffusant in the planes parallel to diffusion front. We derive analytical expressions describing the diffusion profiles both for constant source and instantaneous source boundary conditions. Finally, we suggest a practical method for extracting the grain boundary diffusion coefficient from experimentally measured diffusion profiles. This method relies on microstructure characterization and requires the grain growth constant and grain growth exponent to be determined in the independent set of experiments.
Routing path optimization in optical burst switched networks

It is usually assumed that optical burst switched (OBS) networks employ shortest path routing along with next- hop burst forwarding. Shortest path routing minimizes delay and optimizes the utilization of resources, however, it often causes certain links to become congested while others remain underutilized. In a buffer-less OBS network in which burst drop probability is the primary metric of interest, the existence of a few highly congested links may lead to unacceptable performance for the entire network. In this paper, we take a traffic engineering approach to path selection in OBS networks with the objective of balancing the traffic across the network links in order to reduce congestion and improve overall performance. We present an approximate integer linear optimization problem, as well as a simple integer relaxation heuristic to solve the problem efficiently for large networks. Numerical results demonstrate that our approach is effective in reducing the network-wide burst drop probability, in many cases significantly, over shortest path routing.