Miracle-dz/UniFAR-FTUs huggingface dataset:
Micro- and Nanoscale Topographies on Silk Regulate Gene Expression of Human Corneal Epithelial Cells

Purpose Corneal basement membrane has topographical features that provide biophysical cues to direct cell adherence, migration, and proliferation. In this study, we hypothesize that varying topographic pitch created on silk films can alter epithelial cell morphology, adhesion, and the genetic expression involved in cytoskeletal dynamics-related pathways. Methods Silicon wafers with parallel ridge widths of 2000, 1000, and 800 nm were produced and used to pattern silk films via soft lithography. Human corneal epithelial cells were cultured onto silk. After 72 hours of incubation, images were taken to study cell morphology and alignment. Cytoskeletal structures were studied by immunofluorescent staining. RNA was collected from cultured cells to perform RNA-Seq transcriptome analysis using the Illumina Hiseq 2500 sequencing system. Differentially expressed genes were identified using DNAstar Qseq then verified using quantitative real-time PCR. These genes were used to perform pathway analyses using Ingenuity Pathways Analysis. Results Primary human corneal epithelial cell alignment to the surface pattern was the greatest on 1000-nm features. Fluorescent microscopy of f-actin staining showed cell cytoskeleton alignment either in parallel (2000 nm) or perpendicular (1000 and 800 nm) to the long feature axis. Z-stack projection of vinculin staining indicated increased focal adhesion formation localized on the cellular basal surface. RNA-seq analysis revealed differentially expressed genes involved in actin organization, integrin signaling, and focal adhesion kinase signaling (−log (P)>5). Conclusions Patterned silk film substrates may serve as a scaffold and provide biophysical cues to corneal epithelial cells that change their gene expression, alter cellular adherence, morphology, and may offer a promising customizable material for use in ocular surface repair.
Disease Patterns in the CWD Eradication Zone Final Report

Project Summary: This project investigated the infection patterns of chronic wasting disease (CWD) in the Disease Eradication Zone (DEZ) in south-central Wisconsin. Infection patterns related to age and sex, vulnerability of infected animals to harvest, and factors related to transmission of CWD among adult females were determined in this study. Findings in the research project are summarized as follows. Chronic wasting disease (CWD) is a fatal disease of white-tailed deer (Odocoileus virginianus) caused by transmissible protease resistant prions. Since the discovery of CWD in southern Wisconsin in 2001, more than 20,000 deer have been removed from a >2,500 km 2 disease eradication zone surrounding the three initial cases. Nearly all deer removed were tested for CWD infection and sex, age, and harvest location were recorded. Our analysis used data from a 310 km 2 core study area where disease prevalence was higher than surrounding areas. We found no difference in harvest rates between CWD infected and non-infected deer. Our results show that the probability of infection increased with age and that adult males were more likely to be infected than adult females. Six fawns tested positive for CWD, five fawns from the core study area, including the youngest (5 months) free-ranging cervid to test positive. The increase in male prevalence with age is nearly twice the increase found in females. We concluded that CWD is not randomly distributed among deer and that differential transmission among sex and age classes is likely driving the observed patterns in disease prevalence. We discuss alternative hypotheses for CWD transmission and spread and, in addition, discuss several possible non-linear relationships between prevalence and age. Understanding CWD transmission in free-ranging cervid populations will be essential to the development of strategies to manage this disease in areas where CWD is found as well as for surveillance strategies in areas where CWD threatens to spread. We evaluated the hypothesis of socially facilitated transmission of chronic wasting disease (CWD) among adult female white-tailed deer using spatial location and genetic relatedness for 1,387 female deer, as well as the spatial location of 1,321 adult male deer harvested during 2002-2004 CWD control efforts in Wisconsin, USA. There was little correlation between genetic relatedness and geographic distance among all pairs of adult females separated by up to 10 km. At small distances (<0.8 km), CWD positive deer were more related than random individuals in the population, indicating a weak association between relatedness …
Association of Examination Rates with Children’s National Caries Indices in Finland

The objective was to assess the effect of examination rates on national caries indices of 5, 12 and 17-year-old children/adolescents in Finland. The data were gathered from patient records of the Public Dental Service (PDS) units (n=205, 73%) and from a national register. The data included PDS-specific total numbers of examined children/adolescents and means of decayed (d/D) teeth, dmft/DMFT-values and proportions of caries-free. For analytical purposes, the PDS-specific mean values weighted by the PDS population were calculated to imply the traditionally calculated figures. New PDS-specific examination-rate-adjusted mean values were calculated by using the predicted outcome values at 100% examination rates. The results showed that low examination rates were associated with slightly poorer oral health. The examination-rate-adjusted mean d/D- values indicated better oral health than the traditional indices. The adjustment slightly worsened oral health in proportions of caries-free, and had almost no effect on dmft/DMFT-value. Overall, the influence was modest. The high proportions of healthy children that are examined (against recommendation) and the relatively small number of those having extensive disease (frequently examined as recommended) probably mask the influence of examination rates on the indices in Finland. We conclude that in international comparisons, traditionally calculated indices seem to be sufficiently valid.
Approximation of geometry based stochastic channel models

A geometry-based stochastic channel model discussed in this paper was developed in IST-WINNER I, WINNER II, and WINNER+ projects. The model is based on the same principles as, e.g., 3GPP SCM and ITU-R IMT-Advanced channel models, and the results are applicable to them as well. The complexity of the channel model has been under discussion within ITU-R working groups as well as in industry planning to perform system level simulations. The complexity reduction (approximation, simplification) is one key task to improve the model usability. However, the complexity reduction should be made without reducing the model accuracy and generality too much. When application of the model is known, more approximation can often be done. Therefore, this paper studies first application independent and then application dependent approximation. Approximation of an accurate model is always possible, and the methods are known, but doing vice versa is impossible without additional information. This paper proposes a number of approximation steps, and shows the impact of some steps on the outage capacity and semi-analytical BER. The results show that only very little approximation can be done when application is unknown, but much more approximation is possible for narrowband single-input single-output (SISO) systems.
Feedback generation for performance problems in introductory programming assignments

Providing feedback on programming assignments manually is a tedious, error prone, and time-consuming task. In this paper, we motivate and address the problem of generating feedback on performance aspects in introductory programming assignments. We studied a large number of functionally correct student solutions to introductory programming assignments and observed: (1) There are different algorithmic strategies, with varying levels of efficiency, for solving a given problem. These different strategies merit different feedback. (2) The same algorithmic strategy can be implemented in countless different ways, which are not relevant for reporting feedback on the student program. We propose a light-weight programming language extension that allows a teacher to define an algorithmic strategy by specifying certain key values that should occur during the execution of an implementation. We describe a dynamic analysis based approach to test whether a student's program matches a teacher's specification. Our experimental results illustrate the effectiveness of both our specification language and our dynamic analysis. On one of our benchmarks consisting of 2316 functionally correct implementations to 3 programming problems, we identified 16 strategies that we were able to describe using our specification language (in 95 minutes after inspecting 66, i.e., around 3%, implementations). Our dynamic analysis correctly matched each implementation with its corresponding specification, thereby automatically producing the intended feedback.
Contraceptive switching after method-related discontinuation: levels and differentials.

The purpose of this study is to add to the knowledge of contraceptive-use dynamics by documenting probabilities of method switching in a large number of countries using the most recent DHS calendar data. In addition it examines disparities or inequalities in switching among different groups within countries and specifically compares the switching behavior between better- and less-educated women between wealthy urban couples and poor rural couples and between women who are motivated by spacing and by family-size limitation.
Improvement of State Feedback Controller Design for Networked Control Systems

A new method is proposed to improve the state feedback controller design for networked control systems (NCSs) taking both network-induced time delay and packet dropout into account in this paper. An appropriate Lyapunov functional is introduced to establish the improved sufficient stabilizability conditions for NCSs with memoryless state feedback controller by considering an additional useful term when estimating the upper bound of the derivative of Lyapunov functional and introducing new free weight matrices. Based on this less conservative existence condition, a networked controller design method is derived, which is equivalent to the solvability of a set of linear matrix inequalities. Numerical example is given to demonstrate the effectiveness and benefits of the proposed method.
An efficient, nonenzymatic method for isolation and culture of murine aortic endothelial cells and their response to inflammatory stimuli

SummaryGiven the utility of murine models and the physiological and pathological significance of the aortic endothelium, we developed a simplified, nonenzymatic method for isolation and culture of murine aortic endothelial cells (MAECs). Aortic explants were initially cultured on fibronectin-coated plastic. Murine aortic endothelial cells migrated from the explants and proliferated. This expansion allowed for cultures to be established from the aortas of one or three mice. Murine aortic endothelial cells were then purified from expanded cultures by fluorescence-activated cell sorting for the uptake of 1,1′-dioctadecyl-3,3,3′,3′ tetramethyl-indocarbocyanine perchlorate-labeled acetylated low-density lipoprotein. The majority of the cells in expanded cultures were as positive as human umbilical vein endothelial cells labeled in the same way. The most positive half of the labeled MAEC population was placed back in culture, and the cells formed “cobblestone” monolayers at confluence. Smooth muscle α-actin, which was present in aortic tissue and to a lesser extent in explant cultures before sorting, was not detected in selected MAECs. Western blotting and immunostaining also demonstrated the presence of the endothelial markers, platelet endothelial cell adhesion molecule-1, factor VIII-related antigen, and Bandeiraea simplicifolia lectin 1 binding. Murine aortic endothelial cells retained expected inflammatory functions: vascular cell adhesion molecule-1 protein was induced by bacterial endotoxin, and NO production was synergistically induced by the combination of endotoxin and interferon-γ. Our simple, efficient method will facilitate investigations of aortic endothelial cell function in vitro using murine models.
Utility of Bilirubins and Bile Acids as Endogenous Biomarkers for the Inhibition of Hepatic Transporters

It is useful to identify endogenous substrates for the evaluation of drug-drug interactions via transporters. In this study, we investigated the utility of bilirubins, substrates of OATPs and MRP2, and bile acids and substrates of NTCP and BSEP, as biomarkers for the inhibition of transporters. In rats administered 20 and 80 mg/kg rifampicin, the plasma levels of bilirubin glucuronides were elevated, gradually decreased, and almost returned to the baseline level at 24 hours after administration without an elevation of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). This result indicates the transient inhibition of rOatps and/or rMrp2. Although the correlation between free plasma concentrations and IC50 values of rOatps depended on the substrates used in the in vitro studies, the inhibition of rOatps by rifampicin was confirmed in the in vivo study using valsartan as a substrate of rOatps. In rats administered 10 and 30 mg/kg cyclosporin A, the plasma levels of bile acids were elevated and persisted for up to 24 hours after administration without an elevation of ALT and AST. This result indicates the continuous inhibition of rNtcp and/or rBsep, although there were differences between the free plasma or liver concentrations and IC50 values of rNtcp or rBsep, respectively. This study suggests that the monitoring of bilirubins and bile acids in plasma is useful in evaluating the inhibitory potential of their corresponding transporters.
Sphingosine-1-phosphate Inhibits Motility of Human Breast Cancer Cells Independently of Cell Surface Receptors 1

Exogenous sphingosine-1-phosphate (SPP) inhibits chemotactic motility of several transformed cell lines. We have found that SPP at high micromolar concentrations decreased chemotaxis of estrogen-independent (MDA-MB-231 and BT 549) and estrogen-dependent (MCF-7 and ZR75-1) human breast cancer cells. Because SPP has been implicated as a lipid-signaling molecule with novel dual intraand intercellular actions, it was of interest to determine whether the effect of SPP on chemotactic motility of human breast cancer cells is mediated intracellularly or through the recently identified endothelial differentiation gene (EDG) family of G protein-coupled SPP receptors. There was no detectable specific binding of [P]SPP to MDA-MB-231 or MCF-7 cells; however, reverse transcription-PCR analysis revealed that both MDA-MB-231 and MCF-7 cells expressed moderate levels of EDG-3, neither expressed EDG-1, and EDG-5 mRNA was expressed in MCF-7 but not in MDAMB-231 cells. In contrast to SPP, sphinganine-1-phosphate, which binds to and signals through SPP receptors EDG-1, EDG-3, and EDG-5, had no effect on chemotactic motility of MDA-MB-231 or MCF-7 cells. To further discriminate between intracellular and receptor-mediated actions of SPP, we used caged SPP, a photolyzable derivative of SPP that elevates intracellular levels of SPP after illumination. Caged SPP inhibited chemotactic motility of MDA-MB-231 cells only upon UV irradiation. In addition, in MCF-7 cells, overexpression of sphingosine kinase, the enzyme that produces SPP, inhibited chemotactic motility compared with vector-transfected cells and markedly increased cellular SPP levels in the absence of detectable secretion. Our results suggest that the inhibitory effect of SPP on chemotactic motility of human breast cancer cells is likely mediated through intracellular actions of SPP rather than through cell surface receptors.
Simple Analytical Formulation of the TCP Send Rate in Optical Burst-Switched Networks

This paper presents an analytical model to calculate the send rate of TCP sources as a function of the main design parameters of optical burst-switched (OBS) networks. The novelty of the work is the possibility to deal with generic source speed that was previously evaluated only by simulation. The pretty good accuracy of the model is proved by comparisons with simulation results. The practical significance of the model is shown by an application example where burst loss is consequence of contention in OBS core nodes.
Structure extraction from various kinds of decorated characters using multi-scale images

Decorated characters are widely used in various documents. Practical optical character reader is required to deal with not only common fonts but also complex designed fonts. However, since appearances of decorated characters are complicated, most general character recognition systems cannot give good performances on decorated characters. In this paper, an algorithm that can extract character's essential structure from a decorated character is proposed. This algorithm is applied in preprocessing of character recognition. The proposed algorithm consists of three parts: global structure extraction, interpolation of structure, and smoothing. By using multi-scale images, topographical features such as ridges and ravines are detected for structure extraction. Ridges are used for extracting global structure, and ravines are used for interpolation. Experimental results show clear character structures are extracted from very complex decorated characters.
Extending the effectiveness of 3D-stacked DRAM caches with an adaptive multi-queue policy

3D-integration is a promising technology to help combat the ¿memory wall¿ in future multi-core processors. Past work has considered using 3D-stacked DRAM as a large last-level cache (LLC). While significant performance benefits can be gained with such an approach, there remain additional opportunities beyond the simple integration of commodity DRAM chips. In this work, we leverage the hardware organization typical of DRAM architectures to propose new cache management policies that would otherwise not be practical for standard SRAM-based caches. We propose a cache where each set is organized as multiple logical FIFO or queue structures that simultaneously provide performance isolation between threads as well as reduce the number of entries occupied by dead lines. Our results show that beyond the simplistic approach of stacking DRAM as cache, such tightly-integrated 3D architectures enable new opportunities for optimizing and improving system performance.
A 6.2-GFlops Floating-Point Multiply-Accumulator With Conditional Normalization

A pipelined single-precision floating-point multiply-accumulator (FPMAC) featuring a single-cycle accumulate loop using base 32 and internal carry-save arithmetic with delayed addition is described. A combination of algorithmic, logic, and circuit techniques enables multiply-accumulate operations at speeds exceeding 3 GHz with single-cycle throughput. The optimizations allow removal of the costly normalization step from the critical accumulate loop. This logic is conditionally powered down using dynamic sleep transistors on long accumulate operations, saving active and leakage power. In addition, an improved leading-zero anticipator (LZA) and overflow prediction logic applicable to carry-save format is presented. In a 90-nm seven-metal dual-VT CMOS process, the 2 mm2 custom design contains 230K transistors. The fully functional first silicon achieves 6.2 GFlops of performance while dissipating 1.2 W at 3.1 GHz, 1.3-V supply
Scheduling to Minimize Total Completion Time of Jobs in a Printing Firm.

The problem of scheduling a set of jobs on a single machine in order to minimize the total completion time of all jobs with release dates was considered. The case of a printing firm that is involved in the production of scientific publications such as monographs and workshop proceedings was studied. Real life data were collected from the firm using a standard work order format. Existing solution methods (AEO and BESTA) for this problem were selected from the literature and then applied to the data collected alongside the company’s policy of first-come first-serve (FC). Experimental results on the performance of the solution methods were presented. Based on substantial reduction in production cost of 41.12% the AEO solution method was recommended to the firm as an alternative to the firm’s current policy. The recommended solution method (AEO) is also easy to implement.
Diagnosing Natural Language Answers to Support Adaptive Tutoring

Understanding answers to open-ended explanation questions is important in intelligent tutoring systems. Existing systems use natural language techniques in essay analysis, but revert to scripted interaction with short-answer questions during remediation, making adapting dialogue to individual students difficult. We describe a corpus study that shows that there is a relationship between the types of faulty answers and the remediation strategies that tutors use; that human tutors respond differently to different kinds of correct answers; and that re-stating correct answers is associated with improved learning. We describe a design for a diagnoser based on this study that supports remediation in open-ended questions and provides an analysis of natural language answers that enables adaptive generation of tutorial feedback for both correct and faulty answers.
On the diversity gain region of the Z-interference channels

In this work, we analyze the diversity gain region (DGR) of the single-antenna Rayleigh fading Z-Interference channel (ZIC). More specifically, we characterize the achievable DGR of the fixed-power split Han-Kobayashi (HK) approach under these assumptions. Our characterization comes in a closed form and demonstrates that the HK scheme with only a common message is a singular case, which achieves the best DGR among all HK schemes for certain multiplexing gains. Finally, we show that generalized time sharing, with variable rate and power assignments for the common and private messages, does not improve the achievable DGR.
Reproducibility of neuroimaging analyses across operating systems

Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception. We find that these packages use mathematical functions based on single-precision floating-point arithmetic whose implementations in operating systems continue to evolve. While these differences have little or no impact on simple analysis pipelines such as brain extraction and cortical tissue classification, their accumulation creates important differences in longer pipelines such as subcortical tissue classification, fMRI analysis, and cortical thickness extraction. With FSL, most Dice coefficients between subcortical classifications obtained on different operating systems remain above 0.9, but values as low as 0.59 are observed. Independent component analyses (ICA) of fMRI data differ between operating systems in one third of the tested subjects, due to differences in motion correction. With Freesurfer and CIVET, in some brain regions we find an effect of build or operating system on cortical thickness. A first step to correct these reproducibility issues would be to use more precise representations of floating-point numbers in the critical sections of the pipelines. The numerical stability of pipelines should also be reviewed.