Miracle-dz/UniFAR-FTUs huggingface dataset:
A Connection Between Score Matching and Denoising Autoencoders

Denoising autoencoders have been previously shown to be competitive alternatives to restricted Boltzmann machines for unsupervised pretraining of each layer of a deep architecture. We show that a simple denoising autoencoder training criterion is equivalent to matching the score (with respect to the data) of a specific energy-based model to that of a nonparametric Parzen density estimator of the data. This yields several useful insights. It defines a proper probabilistic model for the denoising autoencoder technique, which makes it in principle possible to sample from them or rank examples by their energy. It suggests a different way to apply score matching that is related to learning to denoise and does not require computing second derivatives. It justifies the use of tied weights between the encoder and decoder and suggests ways to extend the success of denoising autoencoders to a larger family of energy-based models.
A New Histogram Modification Based Reversible Data Hiding Algorithm Considering the Human Visual System

In this letter, we propose an improved histogram modification based reversible data hiding technique. In the proposed algorithm, unlike the conventional reversible techniques, a data embedding level is adaptively adjusted for each pixel with a consideration of the human visual system (HVS) characteristics. To this end, an edge and the just noticeable difference (JND) values are estimated for every pixel, and the estimated values are used to determine the embedding level. This pixel level adjustment can effectively reduce the distortion caused by data embedding. The experimental results and performance comparison with other reversible data hiding algorithms are presented to demonstrate the validity of the proposed algorithm.
β-Catenin and its relation to VEGF and cyclin D1 expression in pT3 rectosigmoid cancers.

BACKGROUND/AIMS β-Catenin is a critical component of the Wnt signaling pathway that regulates cell proliferation and differentiation. Wnt signaling leads to the stabilization of cytosolic β-catenin and to translocation to the nucleus, where it binds with T-cell factor and promotes the transcription and changes in target gene expression, including vascular endothelial growth factor and cyclin D1. The aim of this study was to assess the expression of cyclin D1 and vascular endothelial growth factor and to correlate them with β-catenin expression and some clinicopathologic parameters. METHODS In this study, we analyzed paraffin-embedded specimens from 42 patients with pT3 rectosigmoid cancer for β-catenin, vascular endothelial growth factor and cyclin D1 expression using immunohistochemistry. RESULTS Thirty-six (85.7%) and 24 (57.1%) tumors expressed vascular endothelial growth factor and cyclin D1, respectively. Nuclear expression of β-catenin was detected in only 26.1% of tumors. It was revealed that cytoplasmic β-catenin expression was significantly related to vascular endothelial growth factor expression (p=0.011). No association was found between nuclear or cytoplasmic β-catenin and cyclin D1 expression. No significant association was seen between β-catenin, vascular endothelial growth factor or cyclin D1 expression and some investigated clinicopathologic features. CONCLUSIONS Our results may contribute to knowledge regarding the functional interaction between β-catenin and vascular endothelial growth factor. We suggest that the overexpression of cyclin D1 in rectosigmoid cancers may be more complicated than purely upregulation by β-catenin. Further larger studies on Wnt/β-catenin and target gene activity and protein expression are necessary to better understand and define their roles in the pathogenesis of colorectal carcinoma.
Control of Residual Thermal Stresses in Shape Deposition Manufacturing

Layer-level thermal and mechanical modeling of the microcasting stage of ShaPe Deposition Manufacturing is presented. Thermo-mechanical models of carbon steel deposited onto a carbon steel substrate are described. Mechanics modeling addresses the issue of residual stress build-up. The effects of substrate heating and bending constraint on the build-up of residual stresses are shown. Results show that thermal cycling from newly applied droplets drastically changes the stress state in the top of the substrate. Originally unstressed regions go through an inelastic compression-tension stress cycle. Residual stresses reach values that may cause yielding in carbon steel. Moderate heating of the substrate above room temperature prior to droplet deposition reduces stresses significantly. Bending constraint during part manufacture allows partial relaxation of stresses as the constraint is removed.
SAMHD1-Deficient CD14+ Cells from Individuals with Aicardi-Goutières Syndrome Are Highly Susceptible to HIV-1 Infection

Myeloid blood cells are largely resistant to infection with human immunodeficiency virus type 1 (HIV-1). Recently, it was reported that Vpx from HIV-2/SIVsm facilitates infection of these cells by counteracting the host restriction factor SAMHD1. Here, we independently confirmed that Vpx interacts with SAMHD1 and targets it for ubiquitin-mediated degradation. We found that Vpx-mediated SAMHD1 degradation rendered primary monocytes highly susceptible to HIV-1 infection; Vpx with a T17A mutation, defective for SAMHD1 binding and degradation, did not show this activity. Several single nucleotide polymorphisms in the SAMHD1 gene have been associated with Aicardi-Goutières syndrome (AGS), a very rare and severe autoimmune disease. Primary peripheral blood mononuclear cells (PBMC) from AGS patients homozygous for a nonsense mutation in SAMHD1 (R164X) lacked endogenous SAMHD1 expression and support HIV-1 replication in the absence of exogenous activation. Our results indicate that within PBMC from AGS patients, CD14+ cells were the subpopulation susceptible to HIV-1 infection, whereas cells from healthy donors did not support infection. The monocytic lineage of the infected SAMHD1 -/- cells, in conjunction with mostly undetectable levels of cytokines, chemokines and type I interferon measured prior to infection, indicate that aberrant cellular activation is not the cause for the observed phenotype. Taken together, we propose that SAMHD1 protects primary CD14+ monocytes from HIV-1 infection confirming SAMHD1 as a potent lentiviral restriction factor.
Overexpression of an Acidic Endo-β-1,3-1,4-glucanase in Transgenic Maize Seed for Direct Utilization in Animal Feed

Background Incorporation of exogenous glucanase into animal feed is common practice to remove glucan, one of the anti-nutritional factors, for efficient nutrition absorption. The acidic endo-β-1,3-1,4-glucanase (Bgl7A) from Bispora sp. MEY-1 has excellent properties and represents a potential enzyme supplement to animal feed. Methodology/Principal Findings Here we successfully developed a transgenic maize producing a high level of Bgl7AM (codon modified Bgl7A) by constructing a recombinant vector driven by the embryo-specific promoter ZM-leg1A. Southern and Western blot analysis indicated the stable integration and specific expression of the transgene in maize seeds over four generations. The β-glucanase activity of the transgenic maize seeds reached up to 779,800 U/kg, about 236-fold higher than that of non-transgenic maize. The β-glucanase derived from the transgenic maize seeds had an optimal pH of 4.0 and was stable at pH 1.0–8.0, which is in agreement with the normal environment of digestive tract. Conclusion/Significance Our study offers a transgenic maize line that could be directly used in animal feed without any glucanase production, purification and supplementation, consequently simplifying the feed enzyme processing procedure.
Compressive Strength of Mineral Trioxide Aggregate with and without Disodium Hydrogen Phosphate at Different Mixing Ratios

Introduction: Mineral Trioxide Aggregate (MTA) is a substance with favorable physical-mechanical properties. Disodium hydrogen phosphate (DHP) is sometimes added to MTA to reduce its setting time. Therefore, this study was conducted to evaluate the effect of various ratios of liquid to powder of white MTA (WMTA) and addition of DHP on its compressive strength. Methods and Materials: One hundred and twenty samples were prepared with a two-piece stainless steel mold with a height of 6 mm and a diameter of 4 mm in order to evaluate the compressive strength where WMTA was used in 60 samples and DHP in white MTA composition (DHPWMTA) was used in other 60 samples. The compressive strength of WMTA and DHPWMTA was measured in various ratios of liquid to powder including 50, 60 and 70% and at 24 h and 21 days (n=10). Univariate Analysis of Variance test with SPSS 16 software were used to determine the difference between groups. The level of significance was set at 0.05. Results: The maximum and minimum compressive strength of WMTA groups were 63.25±1.96 (50% ratio and 21 days) and 37.79±1.28 (70% ratio and 24 h), respectively. The maximum and minimum compressive strength of DHPWMTA groups were 63.96±1.40 (60% ratio and 21 days) and 37.37±1.62 (70% ratio and 24 h), respectively. The effect of each of factors (type of material, powder to liquid ratio and time) alone were significant on the compressive strength (P<0.05). However, the interactive effect of three factors (type of material, powder to liquid ratio and time) were not statistically significant on compressive strength (P>0.05). Conclusion: Adding 2.5 wt% of DHP to white MTA increased samples compressive strength. Compressive strength in liquid to powder ratios of 50 and 60% compare to 70% and at 21 days compared to 24 h was high.
Serum γ-glutamyl Transferase Levels, Insulin Resistance and Liver Fibrosis in Patients with Chronic Liver Diseases

Background and Aims Serum levels of γ-glutamyl-transpeptidase(γ-GT) were associated with liver disease severity and metabolic alterations, which in turn are able to affect hepatic damage. In patients with nonalcoholic fatty liver disease (NAFLD), genotype 1 chronic hepatitis C (G1CHC) and chronic hepatitis B (CHB), we assessed the link between liver fibrosis and γ-GT serum levels, and we evaluated if normal or high γ-GT serum levels affect the association between insulin resistance (IR) and severity of liver fibrosis. Methods 843 consecutive patients with chronic liver disease (CLD)(193 NAFLD, 481 G1CHC, 169 CHB) were evaluated by liver biopsy (Kleiner and Scheuer scores) and clinical and metabolic measurements. IR was diagnosed if HOMA>3. A serum γ-GT concentration of >36 IU/L in females and >61 IU/L in males was considered the threshold value for identifying high levels of γ-GT. Results By multivariate logistic regression analysis, abnormal γ-GT serum levels were independently linked to severe liver fibrosis in patients with NAFLD (OR2.711,CI1.120–6.564,p = 0.02), G1CHC (OR3.461,CI2.138–5.603,p<0.001) and CHB (OR2.778,CI1.042–7.414,p = 0.04), together with IR and liver necroinflammation, and with a negative predictive value>80%. Interestingly, among patients with high or normal γ-GT values, even if IR prevalence was significantly higher in patients with severe fibrosis compared to those without, IR remained significantly associated with severe fibrosis in patients with abnormal γ-GT values only (OR4.150,CI1.079–15.970,p = 0.03 for NAFLD; OR2.250,CI1.211–4.181,p = 0.01 for G1CHC; OR3.096,CI2.050–34.220,p = 0.01 for CHB). Conclusions In patients with CLD, IR is independently linked to liver fibrosis only in patients with abnormal γ-GT values, without differences according to liver disease etiology, and suggesting a role of γ-GT as a marker of metabolic-induced liver damage. These data could be useful for the clinical and pharmacologic management of patients with CLD.
Automatic Tuberculosis Screening Using Chest Radiographs

Tuberculosis is a major health threat in many regions of the world. Opportunistic infections in immunocompromised HIV/AIDS patients and multi-drug-resistant bacterial strains have exacerbated the problem, while diagnosing tuberculosis still remains a challenge. When left undiagnosed and thus untreated, mortality rates of patients with tuberculosis are high. Standard diagnostics still rely on methods developed in the last century. They are slow and often unreliable. In an effort to reduce the burden of the disease, this paper presents our automated approach for detecting tuberculosis in conventional posteroanterior chest radiographs. We first extract the lung region using a graph cut segmentation method. For this lung region, we compute a set of texture and shape features, which enable the X-rays to be classified as normal or abnormal using a binary classifier. We measure the performance of our system on two datasets: a set collected by the tuberculosis control program of our local county's health department in the United States, and a set collected by Shenzhen Hospital, China. The proposed computer-aided diagnostic system for TB screening, which is ready for field deployment, achieves a performance that approaches the performance of human experts. We achieve an area under the ROC curve (AUC) of 87% (78.3% accuracy) for the first set, and an AUC of 90% (84% accuracy) for the second set. For the first set, we compare our system performance with the performance of radiologists. When trying not to miss any positive cases, radiologists achieve an accuracy of about 82% on this set, and their false positive rate is about half of our system's rate.
Comparative Analysis of SET Domain Proteins in Maize and Arabidopsis Reveals Multiple Duplications Preceding the Divergence of Monocots and Dicots1[w]

Histone proteins play a central role in chromatin packaging, and modification of histones is associated with chromatin accessibility. SET domain [Su(var)3-9, Enhancer-of-zeste, Trithorax] proteins are one class of proteins that have been implicated in regulating gene expression through histone methylation. The relationships of 22 SET domain proteins from maize (Zea mays) and 32 SET domain proteins from Arabidopsis were evaluated by phylogenetic analysis and domain organization. Our analysis reveals five classes of SET domain proteins in plants that can be further divided into 19 orthology groups. In some cases, such as the Enhancer of zeste-like and trithorax-like proteins, plants and animals contain homologous proteins with a similar organization of domains outside of the SET domain. However, a majority of plant SET domain proteins do not have an animal homolog with similar domain organization, suggesting that plants have unique mechanisms to establish and maintain chromatin states. Although the domains present in plant and animal SET domain proteins often differ, the domains found in the plant proteins have been generally implicated in protein-protein interactions, indicating that most SET domain proteins operate in complexes. Combined analysis of the maize and Arabidopsis SET domain proteins reveals that duplication of SET domain proteins in plants is extensive and has occurred via multiple mechanisms that preceded the divergence of monocots and dicots.
Human activity recognition in pervasive single resident smart homes: State of art

The increasing number of elderly persons, in addition to the lack of infrastructures designed to manage them brings an awareness of the importance of maintaining them at home by developing assistive technologies. Recent research on the latter focused on Human Activity Recognition (HAR). HAR aims to recognize the sequence of actions by a specific resident at home using sensor readings. In eldercare applications, HAR allows for a continuous evaluation of older people physical and cognitive capabilities by monitoring the completion of their Activities of Daily Living (ADLs). After the recognition step, assistive technologies may intervene to provide them with the necessary support to live independently at home. Most of the work in single resident HAR has been done in computer vision. Because, HAR is generally performed in a private setting (i.e. smart homes), the camera based solution would not be suitable due to human privacy concerns. Recently, many researchers are interested in the use of pervasive sensors to recognize single resident ADLs. This paper reviews recent approaches applied for HAR in pervasive single resident smart homes. It presents the latest developments and highlights the open issues in this field.
Cost-Effectiveness of Routine Screening for Critical Congenital Heart Disease in US Newborns

OBJECTIVES: Clinical evidence indicates newborn critical congenital heart disease (CCHD) screening through pulse oximetry is lifesaving. In 2011, CCHD was added to the US Recommended Uniform Screening Panel for newborns. Several states have implemented or are considering screening mandates. This study aimed to estimate the cost-effectiveness of routine screening among US newborns unsuspected of having CCHD. METHODS: We developed a cohort model with a time horizon of infancy to estimate the inpatient medical costs and health benefits of CCHD screening. Model inputs were derived from new estimates of hospital screening costs and inpatient care for infants with late-detected CCHD, defined as no diagnosis at the birth hospital. We estimated the number of newborns with CCHD detected at birth hospitals and life-years saved with routine screening compared with no screening. RESULTS: Screening was estimated to incur an additional cost of $6.28 per newborn, with incremental costs of $20 862 per newborn with CCHD detected at birth hospitals and $40 385 per life-year gained (2011 US dollars). We estimated 1189 more newborns with CCHD would be identified at birth hospitals and 20 infant deaths averted annually with screening. Another 1975 false-positive results not associated with CCHD were estimated to occur, although these results had a minimal impact on total estimated costs. CONCLUSIONS: This study provides the first US cost-effectiveness analysis of CCHD screening in the United States could be reasonably cost-effective. We anticipate data from states that have recently approved or initiated CCHD screening will become available over the next few years to refine these projections.
The Value of Vocational Rehabilitation in Substance User Treatment: A Cost-Effectiveness Framework

Vocational rehabilitation (VR) programs within addiction treatment traditionally consider employment as the desired outcome. This singular focus ignores other benefits, such as reduced substance use. A framework for evaluating the cost-effectiveness of VR within addiction treatment is presented and illustrated with data from the Alcohol and Drug Services Study (ADSS, 1996–1999). VR was associated with a 2.5% increase in probability of abstinence at an $883 increase in cost per admission. Thus, the estimated cost-effectiveness of VR in promoting abstinence is $35,000 per additional abstinent client ($883/0.025), indicating that VR is a cost-effective contributor to other goals of addiction treatment.
Perceptual Issues in Haptic Digital Watermarking

The growing interest in haptic applications suggests that haptic digital media will soon become widely available, and the need will arise to protect digital haptic data from misuse. In this article, we present our study and findings on psychophysical experiments regarding human abilities to perceive a digital watermark, or hidden signal, through a haptic interface.
Does the Performance of LDPC Codes Depend on the Channel?

In this letter, we discuss the performance of low-density parity-check (LDPC) codes on memoryless channels. Using a recently proposed analysis technique based on extrinsic information transfer (EXIT) charts, we present an interpretation of the known fact that the bit-error rate (BER) performance of an ensemble of LDPC codes shows little dependence on the specific memoryless channel. This result has been partially observed in the literature for symmetric channels and is here extended to asymmetric channels. We conjecture and demonstrate that the performance of an ensemble of LDPC codes depends primarily and solely on the mutual information (MI) between the input and the output of the channel. As a validation of this conjecture, we compare the performance of a few LDPC codes with various rates for five representative memoryless (both symmetric and asymmetric) channels, obtaining results in excellent agreement with the EXIT chart-based prediction
A Comparison of Physiologic and Physical Discomfort Responses Between Exercise Modalities

Turner, MJ, Williams, AB, Williford, AL, and Cordova, ML. A comparison of physiologic and physical discomfort responses between exercise modalities. J Strength Cond Res 24(3): 796-803, 2010-To determine differences in physiologic responses and perceived discomfort during maximal and submaximal exercise with 2 common exercise modalities, the elliptical cross-trainer (ECT) and the arc trainer (ARC) were used, which undergoes an excursion of motion using an arc pathway. Eighteen subjects (10 male and 8 female; age = 24.7 ± 2.6 yr, height = 172.2 ± 10.3 cm, mass = 69.8 ± 14.9 kg, %fat = 22.5 ± 8.1%; mean ± SD) performed maximal exercise protocols on a treadmill (TML), the ECT, and ARC. Subjects also performed 3 10-minute submaximal exercise bouts on the ECT and ARC at 55%, 65%, and 75% of TML maximal oxygen uptake (&OV0312;O2max) in which heart rate (HR), &OV0312;O2, ventilation, respiratory exchange ratio, and hip, knee, and low-back discomfort were monitored. All testing on the ECT and ARC were performed in a counterbalanced order. The &OV0312;O2max was greater during TML exercise compared with ECT (p = 0.007) but similar to the ARC. Both ECT and ARC elicited lower maximal HR values compared with maximal TML exercise (p = 0.0001). No difference was observed between ECT and ARC for &OV0312;O2 during the submaximal exercise bouts (p > 0.05). However, HR was greater during submaximal ECT exercise (p < 0.0001). Perception of discomfort was not different between ECT and ARC for knees (p > 0.05) and lower back (p > 0.05) but different for the hips (p = 0.02). Similar &OV0312;O2max values were observed with ARC and TML modalities. Greater perceptions of discomfort were observed with ECT compared with ARC at similar submaximal exercise intensities, suggesting individuals with, or at risk for, lower-extremity joint pathology may benefit from exercise with modalities other than the ECT.
Complex bifurcation from real paths

A new bifurcation phenomenon, called complex bifurcation, is studied. The basic idea is simply that real solution paths of real analytic problems frequently have complex paths bifurcating from them. It is shown that this phenomenon occurs at fold points, at pitchfork bifurcation points, and at isola centers. It is also shown that perturbed bifurcations can yield two disjoint real solution branches that are connected by complex paths bifurcating from the perturbed solution paths. This may be useful in finding new real solutions. A discussion of how existing codes for computing real solution paths may be trivially modified to compute complex paths is included, and examples of numerically computed complex solution paths for a nonlinear two point boundary value problem, and a problem from fluid mechanics are given.
Methods to Perform High Velocity LTE Experiments at Low Velocities

LTE is designed to support user velocities of up to 500 km/h where experiments are expensive, time-consuming and dangerous. Fortunately, such experiments can be emulated at lower velocities by time-stretching the transmit signals. This method preserves the spatial properties of the mobile radio channel but performs a spectral compression. In this paper, we propose a new set of methods that preserve the spectral properties by inserting additional subcarriers. Next, we compare the method of time-stretching to the new set of methods by applying them to LTE downlink signals. We evaluate the properties and the main drawbacks of the proposed methods by simulations using standard-compliant LTE signals. Finally, we highlight practical aspects to be considered when implementing the proposed high speed emulation techniques.