Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequency-directed run-length (FDR) codes with application to system-on-a-chip test data compression

We showed recently that Golomb codes can be used for efficiently compressing system-on-a-chip test data. We now present a new class of variable-to-variable-length compression codes that are designed using the distributions of the runs of 0s in typical test sequences. We refer to these as frequency-directed run-length (FDR) codes. We present experimental results for the ISCAS 89 benchmark circuits to show that FDR codes outperform Golomb codes for test data compression. We also present a decompression architecture for FDR codes, and an analytical characterization of the amount of compression that can be expected using these codes. Analytical results show that FDR codes are robust, i.e. they are insensitive to variations in the input data stream.
Ex-Post Equilibrium and VCG Mechanisms

Consider an abstract social choice setting with incomplete information, where the number of alternatives is large. Albeit natural, implementing VCG mechanisms is infeasible due to the prohibitive communication constraints. However, if players restrict attention to a subset of the alternatives, feasibility may be recovered. This article characterizes the class of subsets that induce an ex-post equilibrium in the original game. It turns out that a crucial condition for such subsets to exist is the availability of a type-independent optimal social alternative for each player. We further analyze the welfare implications of these restrictions. This work follows that of Holzman et al. [2004] and Holzman and Monderer [2004] where similar analysis is done for combinatorial auctions.
Description of a computer code to simulate the satellite signal in the solar spectrum : the 5S code

Abstract A computer code (acronym 5S) has been developed that allows estimation of the solar radiation backscattered by the Earth-surface-atmosphere system, as it is observed by a satellite sensor. Given the Lambertian ground reflectance, the apparent reflectance of the observed pixel is estimated by taking into account the effects of gaseous absorption, scattering by molecules and aerosols and, to some extent, inhomogeneity in the ground reflectance. The input parameters (observation geometry, atmosphere model, ground reflectance and spectral band) can be either selected from some proposed standard conditions (e.g. spectral bands of a satellite sensor) or user-defined. Besides the pixel apparent reflectance, the code provides the gaseous transmittance, the irradiance at the surface and the different contributions to the satellite signal according to the origin of the measured radiance. Some complementary results are also available; among others, benchmark calculations permit assessment of the code accuracy.
Disturbance observer and feedforward design for a high-speed direct-drive positioning table

Design and implementation of a discrete-time tracking controller for a precision positioning table actuated by direct-drive motors is considered. The table has acceleration capabilities in excess of 5 G, positioning accuracy at the micron level, and is used in applications such as semiconductor packaging. The controller proposed uses a disturbance observer and proportional derivative (PD) compensation in the feedback path and a zero phase error tracking controller and zero phase low-pass filter in the feedforward path. The existing disturbance observer design techniques are extended to account for time delay in the plant. Practical difficulties with excessive feedforward gains are examined and a low-order filter design method is proposed. Experimental results for quantized low-order position reference trajectories, which are commonly used in industrial systems, demonstrate the effectiveness of the approach.
Seaweed Dietetic Food for the Functional Gastrointestinal Complaint Treatment

Despite the common nature of dyspeptic complaints, the treatment is still a problem. There is very little research done on the impact of dietary nutrition on the general health of the patients with dyspeptic complaints and overall nutritional safety. Study Objective: To evaluate the clinical effectiveness of the brown seaweed dietary product “Vitamarine” for the treatment of dyspepsia, as well as product safety. Material and Methods: An open, uncontrolled pilot study with questionnaires before and after the vitamarine course with the patient’s self-perception reports. Data were processed with multivariate analysis. Results: The study included 46 patients with 45 valid end result questionnaires for data processing. After 8 to 10 days use of vitamarine, 33 (76.8%) patients noted symptom disappearance or significant improvement, no improvement of symptoms or their increase was noted by 10 patients (23.2%). Complaints about weakness, fatigue and rapid tiredness significantly decreased or disappeared entirely (p = 0.04), including months long epi-gastric pain (p = 0.02) and constipation (p = 0.01). Conclusions: 1) Use of the dietetic food product “Vitamarine” with a dose of 50 - 60 g per day in two cases out of three improve the general well-being of the patients: months long dyspeptic abdominal pain and constipation disappear or significantly decrease. 2) In the first 8 - 10 days of the vitamarine course clinical effectiveness already can be noted. 3) Use of vitamarine is safe, including patients with a history of allergies to medications, elderly and patients with concomitant diseases.
In vitro effects of hydrogen peroxide combined with different activators for the in-office bleaching technique on enamel

Abstract Objective. The aim of this study was to evaluate the alteration of human enamel bleached with high concentrations of hydrogen peroxide associated with different activators. Materials and methods. Fifty enamel/dentin blocks (4 × 4 mm) were obtained from human third molars and randomized divided according to the bleaching procedure (n = 10): G1 = 35% hydrogen peroxide (HP – Whiteness HP Maxx); G2 = HP + Halogen lamp (HL); G3 = HP + 7% sodium bicarbonate (SB); G4 = HP + 20% sodium hydroxide (SH); and G5 = 38% hydrogen peroxide (OXB – Opalescence Xtra Boost). The bleaching treatments were performed in three sessions with a 7-day interval between them. The enamel content, before (baseline) and after bleaching, was determined using an FT-Raman spectrometer and was based on the concentration of phosphate, carbonate, and organic matrix. Statistical analysis was performed using two-way ANOVA for repeated measures and Tukey’s test. Results. The results showed no significant differences between time of analysis (p = 0.5175) for most treatments and peak areas analyzed; and among bleaching treatments (p = 0.4184). The comparisons during and after bleaching revealed a significant difference in the HP group for the peak areas of carbonate and organic matrix, and for the organic matrix in OXB and HP+SH groups. Tukey’s analysis determined that the difference, peak areas, and the interaction among treatment, time and peak was statistically significant (p < 0.05). Conclusion. The association of activators with hydrogen peroxide was effective in the alteration of enamel, mainly with regards to the organic matrix.
Molecular Pathways Molecular Pathways : The Metabolic Regulator Estrogen-Related Receptor a as a Therapeutic Target in Cancer

The estrogen-related receptor a (ERRa) is an orphan member of the nuclear receptor superfamily of transcription factors whose activity is regulated by the expression level and/or activity of its obligate coregulators, peroxisome proliferator-activated receptor g coactivator-1 a and b (PGC-1a or PGC-1b). Under normal physiologic conditions, and in responding to different environmental stimuli, the ERRa/ PGC-1 complex is involved in regulatingmetabolic homeostasis under conditions of high energy demand in brown adipocytes, proliferating T cells, and muscle. Interestingly, increased expression and activity of the ERRa/PGC-1 axis has also been shown to correlate with unfavorable clinical outcomes in both breast and ovarian tumors. The observation that ERRa activity ismanifest in all breast tumor subtypes with particularly high activity being evident in ERa-negative, HER2-positive, and triple-negative breast cancers has raised significant interest in targeting this receptor for the treatment of those breast cancers for which therapeutic options are limited. Clin Cancer Res; 18(22); 6089–95. 2012 AACR.
Polycomb Group Gene rae28 Is Required for Sustaining Activity of Hematopoietic Stem Cells

The rae28 gene (rae28), also designated as mph1, is a mammalian ortholog of the Drosophila polyhomeotic gene, a member of Polycomb group genes (PcG). rae28 constitutes PcG complex 1 for maintaining transcriptional states which have been once initiated, presumably through modulation of the chromatin structure. Hematopoietic activity was impaired in the fetal liver of rae28-deficient animals (rae28 −/−), as demonstrated by progressive reduction of hematopoietic progenitors of multilineages and poor expansion of colony forming units in spleen (CFU-S12) during embryonic development. An in vitro long-term culture-initiating cell assay suggested a reduction in hematopoietic stem cells (HSCs), which was confirmed in vivo by reconstitution experiments in lethally irradiated congenic recipient mice. The competitive repopulating units (CRUs) reflect HSCs supporting multilineage blood-cell production. CRUs were generated, whereas the number of CRUs was reduced by a factor of 20 in the rae28 − / − fetal liver. We also performed serial transplantation experiments to semiquantitatively measure self-renewal activity of CRUs in vivo. Self-renewal activity of CRUs was 15-fold decreased in rae28 − / −. Thus the compromised HSCs were presumed to reduce hematopoietic activity in the rae28 − / − fetal liver. This is the first report to suggest that rae28 has a crucial role in sustaining the activity of HSCs to maintain hematopoiesis.
Trigger phosphodiesterases as a novel class of c-di-GMP effector proteins

The bacterial second messenger c-di-GMP controls bacterial biofilm formation, motility, cell cycle progression, development and virulence. It is synthesized by diguanylate cyclases (with GGDEF domains), degraded by specific phosphodiesterases (PDEs, with EAL of HD-GYP domains) and sensed by a wide variety of c-di-GMP-binding effectors that control diverse targets. c-di-GMP-binding effectors can be riboswitches as well as proteins with highly diverse structures and functions. The latter include ‘degenerate’ GGDEF/EAL domain proteins that are enzymatically inactive but still able to bind c-di-GMP. Surprisingly, two enzymatically active ‘trigger PDEs’, the Escherichia coli proteins PdeR and PdeL, have recently been added to this list of c-di-GMP-sensing effectors. Mechanistically, trigger PDEs are multifunctional. They directly and specifically interact with a macromolecular target (e.g. with a transcription factor or directly with a promoter region), whose activity they control by their binding and degradation of c-di-GMP—their PDE activity thus represents the c-di-GMP sensor or effector function. In this process, c-di-GMP serves as a regulatory ligand, but in contrast to classical allosteric control, this ligand is also degraded. The resulting kinetics and circuitry of control are ideally suited for trigger PDEs to serve as key components in regulatory switches. This article is part of the themed issue ‘The new bacteriology’.
Systematic Analysis of a Xenograft Mice Model for KSHV+ Primary Effusion Lymphoma (PEL)

Kaposi's sarcoma-associated herpesvirus is the causative agent of primary effusion lymphoma (PEL), which arises preferentially in the setting of infection with human immunodeficiency virus (HIV). Even with standard cytotoxic chemotherapy, PEL continues to cause high mortality rates, requiring the development of novel therapeutic strategies. PEL xenograft models employing immunodeficient mice have been used to study the in vivo effects of a variety of therapeutic approaches. However, it remains unclear whether these xenograft models entirely reflect clinical presentations of KSHV+ PEL, especially given the recent description of extracavitary solid tumor variants arising in patients. In addition, effusion and solid tumor cells propagated in vivo exhibit unique biology, differing from one another or from their parental cell lines propagated through in vitro culture. Therefore, we used a KSHV+ PEL/BCBL-1 xenograft model involving non-obese diabetic/severe-combined immunodeficient (NOD/SCID) mice, and compared characteristics of effusion and solid tumors with their parent cell culture-derived counterparts. Our results indicate that although this xenograft model can be used for study of effusion and solid lymphoma observed in patients, tumor cells in vivo display unique features to those passed in vitro, including viral lytic gene expression profile, rate of solid tumor development, the host proteins and the complex of tumor microenvironment. These items should be carefully considered when the xenograft model is used for testing novel therapeutic strategies against KSHV-related lymphoma.
Association between Parkinson's disease and the HLA‐DRB1 locus

Two genome‐wide association studies (GWASs) recently highlighted the HLA‐DRA and HLA‐DRB5 genes as associated with Parkinson disease (PD). However, because HLA‐DRA displays a low level of polymorphisms and HLA‐DRB5 is only present in approximately 20% of the population, these findings are difficult to interpret. Our aims were: (1) to replicate and investigate in greater detail the association between PD and the HLA‐DR region; (2) to identify PD‐associated HLA alleles; and (3) to perform a meta‐analysis of our top finding. As part of 2 French population‐based case–control studies of PD including highly ethnically homogeneous participants, we investigated the association between PD and 51 Single‐nucleotide polymorphisms (SNPs) in the HLA‐DR region. HLA‐DRB1 alleles were imputed using the HLA*IMP software. HLA typing was performed in a subsample of the participants. We performed a meta‐analysis of our top finding based on 4 GWAS data sets. Among 499 cases and 1123 controls, after correction for multiple testing, we found an association with rs660895 (OR/minor allele, 0.70; 95% CI, 0.57–0.87) within the HLA‐DRB1 gene, which encodes the most polymorphic HLA‐DR chain (DRβ). A meta‐analysis (7996 cases, 36455 controls) confirmed this association (OR, 0.86; 95% CI, 0.82–0.91; P < .0001). SNP‐based imputation of HLA alleles showed an inverse association between PD and the HLA‐DRB1*04 allele. We replicated an association between PD and the HLA‐DR region and provided further insight into the loci and alleles involved. The highly polymorphic HLA‐DRB1 locus contains rs660895, which represents a more legitimate candidate than previous ones. Our finding is in agreement with the hypothesis of an immune component in PD pathophysiology. © 2012 Movement Disorder Society
Studies on Sediment of Kharaland (Saline) Ponds of Ratnagiri with Reference to Prawn Culture

The coastal saline ponds have great potential for prawn culture. In order to understand the sediment characteristics of coastal saline ponds, the study was conducted in six Kharland ponds at Ratnagiri during September 1999 to August 2001. The pond soil is composed of sand (40.15-70.15%), silt (18.27-49.7%) and clay (6.39-20.43%). pH varied from 2.33 to 8.38, specific conductivity from 0.39 to 16.74 mS, total dissolved solids from 0.19 to 8.37%, available nitrogen from 1.12 to 26.6 mg/100 g soil and organic carbon from 0.0 to 2.85%. From this study, it is concluded that the sediment characteristics of these Kharaland ponds are suitable for the culture of prawns, Macrobrachium rosenbergii and Penaeus monodon separately or along with cultivable species of fishes.
Polyamine measurements in the uterine cervix

Cervical cancer remains a significant health problem. New strategies based on the molecular aspects of cervical carcinogenesis are needed. Chemoprevention represents a novel strategy for cervical cancer prevention. Our group plans phase I and II trials using α‐difluoromethylornithine, a suicide inhibitor of ornithine decarboxylase and potent antiproliferative chemopreventive agent. We conducted a study to identify which polyamines in tissue could best serve as surrogate endpoint biomarkers for future trials. Thirty patients with biopsy‐proven cervical intraepithelial neoplasia grade 3 underwent colposcopically directed biopsies of normal and abnormal areas of the uterine cervix for analysis of polyamine synthesis biomarkers. Statistically significant differences were found in the ornithine decarboxylase value and the spermidine:spermine ratio between normal and abnormal areas of the cervix. In general, the ranges in measurements varied widely. Differences in polyamine synthesis biomarkers between colposcopically normal and abnormal areas can be demonstrated. However, studies using polyamine synthesis biomarkers in the cervix would require large numbers of patients to achieve significance. J. Cell. Biochem. Suppls. 28/29:125–132. Published 1998 Wiley‐Liss, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.
A comprehensive review of pesticides and the immune dysregulation: mechanisms, evidence and consequences

Abstract Nowadays, in many communities, there is a growing concern about possible adverse effects of pesticides on human health. Reports indicate that during environmental or occupational exposure, pesticides can exert some intense adverse effects on human health through transient or permanent alteration of the immune system. There is evidence on the relation between pesticide-induced immune alteration and prevalence of diseases associated with alterations of the immune response. In the present study, direct immunotoxicity, endocrine disruption and antigenicity have been introduced as the main mechanisms working with pesticides-induced immune dysregulation. Moreover, the evidence on the relationship between pesticide exposure, dysregulation of the immune system and predisposition to different types of psychiatric disorders, cancers, allergies, autoimmune and infectious diseases are criticized.
Regularized metric adaptation for unconstrained face verification

In this work, we propose a metric adaptation method for set-based face verification and evaluate it on the newly released IARPA Janus Benchmark A (IJB-A) dataset and its extended version, the Janus Challenging Set 2 (CS2). A template-specific metric is trained to adaptively learn the discriminative information in test templates and the negative training set, which contains subjects that are mutually exclusive to subjects in test templates. The proposed regularized joint Bayesian metric learning framework not only alleviates the over-fitting problem but also provides a way to efficiently reduce the model size. We also analyze the selection of the compact and representative negative set to speed up the training time and to reduce storage space. Experiments on the IJB-A and CS2 datasets yield promising results.
Targeted Estimation of Nuisance Parameters to Obtain Valid Statistical Inference

Abstract In order to obtain concrete results, we focus on estimation of the treatment specific mean, controlling for all measured baseline covariates, based on observing independent and identically distributed copies of a random variable consisting of baseline covariates, a subsequently assigned binary treatment, and a final outcome. The statistical model only assumes possible restrictions on the conditional distribution of treatment, given the covariates, the so-called propensity score. Estimators of the treatment specific mean involve estimation of the propensity score and/or estimation of the conditional mean of the outcome, given the treatment and covariates. In order to make these estimators asymptotically unbiased at any data distribution in the statistical model, it is essential to use data-adaptive estimators of these nuisance parameters such as ensemble learning, and specifically super-learning. Because such estimators involve optimal trade-off of bias and variance w.r. t. the infinite dimensional nuisance parameter itself, they result in a sub-optimal bias/variance trade-off for the resulting real-valued estimator of the estimand. We demonstrate that additional targeting of the estimators of these nuisance parameters guarantees that this bias for the estimand is second order and thereby allows us to prove theorems that establish asymptotic linearity of the estimator of the treatment specific mean under regularity conditions. These insights result in novel targeted minimum loss-based estimators (TMLEs) that use ensemble learning with additional targeted bias reduction to construct estimators of the nuisance parameters. In particular, we construct collaborative TMLEs (C-TMLEs) with known influence curve allowing for statistical inference, even though these C-TMLEs involve variable selection for the propensity score based on a criterion that measures how effective the resulting fit of the propensity score is in removing bias for the estimand. As a particular special case, we also demonstrate the required targeting of the propensity score for the inverse probability of treatment weighted estimator using super-learning to fit the propensity score.
Phytoextraction Potential of Poplar (Populus alba L. var. pyramidalis Bunge) from Calcareous Agricultural Soils Contaminated by Cadmium

To investigate the phytoextraction potential of Populus alba L. var. pyramidalis Bunge for cadmium (Cd) contaminated calcareous soils, a concentration gradient experiment and a field sampling experiment (involving poplars of different ages) were conducted. The translocation factors for all experiments and treatments were greater than 1. The bioconcentration factor decreased from 2.37 to 0.25 with increasing soil Cd concentration in the concentration gradient experiment and generally decreased with stand age under field conditions. The Cd concentrations in P. pyramidalis organs decreased in the order of leaves > stems > roots. The shoot biomass production in the concentration gradient experiment was not significantly reduced with soil Cd concentrations up to or slightly over 50 mg kg–1. The results show that the phytoextraction efficiency of P. pyramidalis depends on both the soil Cd concentration and the tree age. Populus pyramidalis is most suitable for remediation of slightly Cd contaminated calcareous soils through the combined harvest of stems and leaves under actual field conditions.