Miracle-dz/UniFAR-FTUs huggingface dataset:
GRO‐TDC with gate‐switch‐based delay cell halving resolution limit

In this paper, we propose a time‐to‐digital converter (TDC) with first‐order noise‐shaping. The proposed gated ring oscillator (GRO)‐TDC overcomes the limitation associated with GRO's intrinsic resolution by adopting two GROs, whose delay difference is equal to half the delay of a delay cell. The GRO is composed of 17 stages of a newly proposed delay cell, which utilizes a gate‐switched configuration to solve the charge redistribution problem. The proposed GRO‐TDC is designed using a 65‐nm process technology, with an area of 0.015 mm2 and a supply voltage of 1 V. The sampling rate and the effective resolution of the proposed GRO‐TDC are 50 MS/s and 1.22 ps, respectively. Finally, the proposed GRO‐TDC consumes a power of 9.08 and 2.41 mW in the calibration and conversion modes, respectively. Copyright © 2017 John Wiley & Sons, Ltd.
Frequency and bases of abnormal performance by healthy adults on neuropsychological testing

The frequency and determinants of abnormal test performance by normal individuals are critically important to clinical inference. Here we compare two approaches to predicting rates of abnormal test performance among healthy individuals with the rates actually shown by 327 neurologically normal adults aged 18–92 years. We counted how many participants produced abnormal scores, defined by three different cutoffs with test batteries of varied length, and the number of abnormal scores they produced. Observed rates generally were closer to predictions based on a series of Monte Carlo simulations than on the binomial model. They increased with the number of tests administered, decreased as more stringent cutoffs were used to identify abnormality, varied with the degree of correlation among test scores, and depended on individual differences in age, education, race, sex, and estimated premorbid IQ. Adjusting scores for demographic variables and premorbid IQ did not reduce rates of abnormal performance. However, it eliminated the contribution of these variables to rates of abnormal test performance. These findings raise fundamental questions about the nature and interpretation of abnormal test performance by normal, healthy adults. (JINS, 2008, 14, 436–445.)
LPP3, LPA and self-generated chemotactic gradients in biomedical science

ABSTRACT Chemotaxis is a major driver of cancer spread, but in most cases we do not know where gradients of attractant come from. In the case of melanoma, chemotaxis to LPA is an important driver of metastasis, and the gradients are made by the tumour cells themselves, by locally breaking down ambient LPA. We have now made a general assay for self-generated chemotaxis, and used it to show that the enzyme LPP3 is responsible for breaking down LPA and thus creating the gradients. Further analysis shows LPP3 is important in several invasion assays, in particular 3D ones in which cells spread outwards through matrix. The new assays will illuminate where physiological self-generated gradients occur; we believe they will be common throughout biology and pathology.
Improvement of Mechanical Ductile Properties of Poly(3-hydroxybutyrate) by Using Vegetable Oil Derivatives

Poly(3-hydroxybutyrate), P3HB is a thermoplastic polyester synthesized from bacterial fermentation with potential uses in packaging due to its biodegradability. Nevertheless, P3HB is a fragile material and its processing temperature window is very narrow which restricts its use. This study explores the potential of vegetable oil-derived plasticizers, i.e., maleinized linseed oil (MLO) and an epoxidized fatty acid ester (EFAE) in the 5–20 phr range as environmentally friendly solutions for P3HB industrial formulations with improved toughness. The results show that optimum balance between ductile properties is achieved with low plasticizer content (5 phr) for both plasticizer types. Elongation at break and the impact resistance are increased by 28 and 71% respectively after addition of 5 phr MLO. With regard to EFAE, the elongation at break is improved by 40% and the impact resistance is increased to twice the value of P3HB. Another effect that both plasticizers provide is the thermal stabilization with a delay in the onset degradation temperature.
The non-coding 3′ UTR of CD44 induces metastasis by regulating extracellular matrix functions

The importance of non-coding RNA transcripts in regulating microRNA (miRNA) functions, especially the 3′-untranslated region (3′ UTR), has been revealed in recent years. Genes encoding the extracellular matrix normally produce large mRNA transcripts including the 3′ UTR. How these large transcripts affect miRNA functions and how miRNAs modulate extracellular matrix protein expression are largely unknown. Here, we demonstrate that the overexpression of the CD44 3′ UTR results in enhanced cell motility, invasion and cell adhesion in human breast carcinoma cell line MDA-MB-231. Furthermore, we found that expression of the CD44 3′ UTR enhances metastasis in vivo. We hypothesize that increased expression of the CD44 3′ UTR affects miRNA binding and modulates synthesis of the extracellular matrix. Computational analysis indicated that miRNAs that interact with the CD44 3′ UTR also have binding sites in other matrix-encoding mRNA 3′ UTRs, including collagen type 1α1 (Col1α1) repressed by miR-328 and fibronectin type 1 (FN1) repressed by miR-512-3p, miR-491 and miR-671. Protein analysis demonstrated that expression of CD44, Col1α1 and FN1 were synergistically upregulated in vitro and in vivo upon transfection of the CD44 3′ UTR. The non-coding 3′ UTR of CD44 interacts with multiple miRNAs that target extracellular matrix properties and thus can be used to antagonize miRNA activities.
A new method for rapid determination of sperm concentration in turkey semen.

The routine determination of sperm concentration not only provides a measure of semen quality but also supplies a means of delivering precise sperm numbers in modern artificial insemination (AI) programs. Methods for estimating sperm numbers in laboratory settings (e.g., hemacytometer) are not practical for use in breeding facilities. A microprocessor-controlled semen analyzer (Densimeter, Model 534-B-Mod1, Animal Reproductive Systems) is commercially available for evaluating stallion semen. We calibrated and modified the semen analyzer to determine sperm concentration in turkey semen and to provide information on the required dilution for a constant AI dose. To calibrate the semen analyzer for turkeys, six samples of pooled semen (10 toms per sample) were collected by abdominal massage. A dilution curve of undiluted and 1:0.5, 1:1, 1:1.5, 1:2, 1:3, 1:5, and 1:10 diluted semen was established using Beltsville Poultry Semen Extender. Sperm concentration in diluted samples was determined by hemacytometer counts. The hemacytometer counts were used to develop an equation for estimating sperm concentration from the semen analyzer's absorbance readings and the equation programmed into the instrument. The newly developed program on the semen analyzer was subsequently validated by comparing instrument values for sperm concentrations with concurrent hemacytometer counts, which compared well to concentrations determined by a previously calibrated photoelectric colorimeter (Klett). Correlation coefficients between the semen analyzer and hemacytometer counts and the Klett and hemacytometer counts were r = 0.996 and r = 0.992, respectively (P < 0.001). The semen analyzer method was accurate and precise and could be beneficial to commercial turkey AI programs because it is easy to use, requires limited technological skills, and provides results for determining sperm concentration and AI dose in approximately 1 min.
Simulated annealing for improving software quality prediction

In this paper, we propose an approach for the combination and adaptation of software quality predictive models. Quality models are decomposed into sets of expertise. The approach can be seen as a search for a valuable set of expertise that when combined form a model with an optimal predictive accuracy. Since, in general, there will be several experts available and each expert will provide his expertise, the problem can be reformulated as an optimization and search problem in a large space of solutions.We present how the general problem of combining quality experts, modeled as Bayesian classifiers, can be tackled via a simulated annealing algorithm customization. The general approach was applied to build an expert predicting object-oriented software stability, a facet of software quality. Our findings demonstrate that, on available data, composed expert predictive accuracy outperforms the best available expert and it compares favorably with the expert build via a customized genetic algorithm.
Supervised Lazy Random Walk Classifier

Incorporating the k-nearest neighbor information and lazy random walks on graph, this paper presents a supervised classifier, namely supervised lazy random walk (SLRW) classifier. First, a partially labeled graph is built over the input data, where the edge weight represents the locally scaled pair wise similarity based on the k-nearest neighbors. And then the SLRW classifier is trained with lazy random walk technique so as to predict the labels of test data. This study brings random walk technology into classification problem without unlabeled training data and enriches its application into supervised learning area. Tests conducted over the real data sets demonstrate the effective robustness of our model to noise and comparisons to other classifiers indicate its excellent classification performance.
Repetitive Model of Mild Traumatic Brain Injury Produces Cortical Abnormalities Detectable by Magnetic Resonance Diffusion Imaging, Histopathology, and Behavior

Abstract Noninvasive detection of mild traumatic brain injury (mTBI) is important for evaluating acute through chronic effects of head injuries, particularly after repetitive impacts. To better detect abnormalities from mTBI, we performed longitudinal studies (baseline, 3, 6, and 42 days) using magnetic resonance diffusion tensor imaging (DTI) and diffusion kurtosis imaging (DKI) in adult mice after repetitive mTBI (r-mTBI; daily × 5) or sham procedure. This r-mTBI produced righting reflex delay and was first characterized in the corpus callosum to demonstrate low levels of axon damage, astrogliosis, and microglial activation, without microhemorrhages. High-resolution DTI-DKI was then combined with post-imaging pathological validation along with behavioral assessments targeted for the impact regions. In the corpus callosum, only DTI fractional anisotropy at 42 days showed significant change post-injury. Conversely, cortical regions under the impact site (M1–M2, anterior cingulate) had reduced axial diffusivity (AD) at all time points with a corresponding increase in axial kurtosis (Ka) at 6 days. Post-imaging neuropathology showed microglial activation in both the corpus callosum and cortex at 42 days after r-mTBI. Increased cortical microglial activation correlated with decreased cortical AD after r-mTBI (r = −0.853; n = 5). Using Thy1-YFP-16 mice to fluorescently label neuronal cell bodies and processes revealed low levels of axon damage in the cortex after r-mTBI. Finally, r-mTBI produced social deficits consistent with the function of this anterior cingulate region of cortex. Overall, vulnerability of cortical regions is demonstrated after mild repetitive injury, with underlying differences of DTI and DKI, microglial activation, and behavioral deficits.
A Statistical Method for Reassociating Human Tali and Calcanei from a Commingled Context

In a commingled context, assessing that a talus and a calcaneus correspond to the same individual could become a primary step for accurately sorting human remains. For this purpose, the lengths and widths of the trochlea, posterior calcaneal articular surface, and posterior talar articular surface were measured in 197 individuals (105 males, 92 females) from the Athens Collection. A total of 12 highly accurate equations for reassociating tali and calcanei were developed, using simple and multiple linear regression analysis and they were found to be suitable for sorting commingled human remains. Bilateral asymmetry and sex did not have an effect on the accuracy of the method.
Anomalous Extratemporal Facial Nerve in Oculoauriculovertebral Spectrum

Facial nerve dysfunction is common in oculoauriculovertebral spectrum (OAVS). However, the course of the nerve has rarely been described. A 23-year-old woman with OAVS underwent excision of microtic ear remnants in preparation for an osseointegrated prosthesis and suffered iatrogenic transection of the facial nerve—the pes anserinus was within the subcutaneous tissue 15 mm posterior and 15 mm cephalad to the external acoustic meatus. The patient underwent primary nerve repair and regained nearly complete preoperative function. When considering reconstruction for OAVS patients, clinicians should have a high index of suspicion for anomalous facial nerve anatomy.
EXIT chart analysis for turbo LDS-OFDM receivers

In this paper, the mutual information transfer characteristics of turbo Multiuser Detector (MUD) for a novel air interface scheme, called Low Density Signature Orthogonal Frequency Division Multiplexing (LDS-OFDM) are investigated using Extrinsic Information Transfer (EXIT) charts. LDS-OFDM uses Low Density Signature structure for spreading the data symbols in frequency domain. This technique benefits from frequency diversity besides its ability of supporting parallel data streams more than the number of subcarriers (overloaded condition). The turbo MUD couples the data symbols' detector of LDS scheme with users' FEC (Forward Error Correction) decoders through the message passing principle. The effect of overloading on LDS scheme's performance is evaluated using EXIT chart. The results show that at Eb/N0 as low as 0.3, LDS-OFDM can support loads up to 300%.
LABORATORY ASSESSMENT OF CEMENTITIOUS COATINGS AS A BARRIER TO RADON GAS ENTRY

This paper assesses the effectiveness of cementitious coatings as barriers to radon gas entry. Twelve commercially available brushed-on coatings were evaluated for air permeability and radon diffusion as cast samples to determine their individual radon gas transport properties. The sealant materials were also applied to standard ingredient (1:2:4 cement-to-sand-to-pea gravel) concrete samples. Water to cement ratios were varied to change the radiological transport properties of the concrete. The radon gas transport properties of the concrete samples were evaluated before and after the sealant application utilizing three innovative test systems: a porosity, a permeability and a diffusion apparatus. Laboratory experiments also measured the thickness of the cementitious coating as well as evaluated the relative adherence of the sealants to a concrete substrate. Details of these innovative experimental setups and procedures are discussed. The experimentation has identified two cementitious coatings that can be employed as superior radon gas barriers: Polysulfide (with a diffusion coefficient of D = 5.91 x 10"' cmVs and an average radon diffusion coefficient percent reduction of 98.4%) and Epoxy-no filler (with a diffusion coefficient of D = 5.05 x lo'* cmvs and an average radon diffusion coefficient percent reduction of 97.7%). The results of this study have shown that the application of cementitious coatings can be utilized an effective alternative tool in radon-resistant residential construction technology.
Auxin Response Factors (ARFs) are potential mediators of auxin action in tomato response to biotic and abiotic stress (Solanum lycopersicum)

Survival biomass production and crop yield are heavily constrained by a wide range of environmental stresses. Several phytohormones among which abscisic acid (ABA), ethylene and salicylic acid (SA) are known to mediate plant responses to these stresses. By contrast, the role of the plant hormone auxin in stress responses remains so far poorly studied. Auxin controls many aspects of plant growth and development, and Auxin Response Factors play a key role in the transcriptional activation or repression of auxin-responsive genes through direct binding to their promoters. As a mean to gain more insight on auxin involvement in a set of biotic and abiotic stress responses in tomato, the present study uncovers the expression pattern of SlARF genes in tomato plants subjected to biotic and abiotic stresses. In silico mining of the RNAseq data available through the public TomExpress web platform, identified several SlARFs as responsive to various pathogen infections induced by bacteria and viruses. Accordingly, sequence analysis revealed that 5’ regulatory regions of these SlARFs are enriched in biotic and abiotic stress-responsive cis-elements. Moreover, quantitative qPCR expression analysis revealed that many SlARFs were differentially expressed in tomato leaves and roots under salt, drought and flooding stress conditions. Further pointing to the putative role of SlARFs in stress responses, quantitative qPCR expression studies identified some miRNA precursors as potentially involved in the regulation of their SlARF target genes in roots exposed to salt and drought stresses. These data suggest an active regulation of SlARFs at the post-transcriptional level under stress conditions. Based on the substantial change in the transcript accumulation of several SlARF genes, the data presented in this work strongly support the involvement of auxin in stress responses thus enabling to identify a set of candidate SlARFs as potential mediators of biotic and abiotic stress responses.
Effect of varying period of early nutrient restriction on growth compensation and carcass characteristics of male broilers.

An experiment was conducted to determine growth and carcass characteristics of male broilers subjected to varying periods of early nutrient restriction. Nutrient restriction was achieved by feeding a starter diet in which the major ingredients were replaced with 50% oat hulls. Five treatments involved feeding this diluted diet for 6 d, either continuous or split into shorter periods in different ways, all starting at 6 d of age. On completion of the 6 d of nutrient restriction, all birds received undiluted starter diet, followed by grower and finisher diets to trial termination at 49 d. All birds fed the diluted diet exhibited reduced nutrient intake. Complete growth compensation by all birds that previously received the diluted diet was attained by 35 d, due largely to their superior (P < .05) feed efficiencies relative to the control birds during realimentation. Varying the period of nutrient restriction did not affect growth compensation. Birds that received the diluted diet for 6 continuous d tended to be leaner at 42 d compared with those that consumed the diluted diet for shorter periods. This latter effect may relate to variable ME intake. There was no statistical difference in other carcass characteristics measured at both 42 and 49 d of age.
Cytotoxicological Response to Engineered Nanomaterials: A Pathway-Driven Process

Cytotoxicological Response to Engineered Nanomaterials: A Pathway-Driven Process. (May 2012) Amelia Antonia Romoser, B.S., Texas A&M University Co-Chairs of Advisory Committee: Dr. Christie M. Sayes Dr. Michael F. Criscitiello Nanoparticles, while included in a growing number of consumer products, may pose risks to human health due to heavy metal leaching and/or the production of reactive oxygen species following exposures. Subcellular mechanisms of action triggered as a result of exposure to various nanoparticles are still largely unexplored. In this work, an effort to elucidate such toxicological parameters was accomplished by evaluating oxidative stress generation, changes in gene and protein expression, and cell cycle status after low-dose exposures to a variety of metal and carbon-based nanomaterials in primary human dermal cells. Additionally, mitigation of nanoparticle toxicity via microencapsulation was investigated to assess the feasibility of utilizing nanomaterials in dermally implantable biosensor applications. Cellular immune and inflammatory processes were measured via qPCR and immunoblotting, which revealed gene and protein expression modulation along the NFκB pathway after a variety of nanoparticle exposures. The role of immunoregulatory transcription factor NF-κB was examined in an oxidative stress context in cells exposed to a panel of nanoparticles, whereby glutathione conversion and modulation of oxidative
Partition-Merge: Distributed Inference and Modularity Optimization

This paper presents a novel meta-algorithm, Partition-Merge (PM), which takes existing centralized algorithms for graph computation and makes them distributed and faster. In a nutshell, PM divides the graph into small subgraphs using our novel randomized partitioning scheme, runs the centralized algorithm on each partition separately, and then <italic>stitches</italic> the resulting solutions to produce a global solution. We demonstrate the efficiency of the PM algorithm on two popular problems: computation of Maximum A Posteriori (MAP) assignment in an arbitrary pairwise Markov Random Field (MRF) and modularity optimization for community detection. We show that the resulting distributed algorithms for these problems become fast, which run in time linear in the number of nodes in the graph. Furthermore, PM leads to performance comparable – or even better – to that of the centralized algorithms as long as the graph has polynomial growth property. More precisely, if the centralized algorithm is a <inline-formula> <tex-math notation="LaTeX">$\mathcal {C}-$ </tex-math></inline-formula>factor approximation with constant <inline-formula> <tex-math notation="LaTeX">$\mathcal {C}\ge 1$ </tex-math></inline-formula>, the resulting distributed algorithm is a <inline-formula> <tex-math notation="LaTeX">$(\mathcal {C}+\delta)$ </tex-math></inline-formula>-factor approximation for any small <inline-formula> <tex-math notation="LaTeX">$\delta >0$ </tex-math></inline-formula>; and even if the centralized algorithm is a non-constant (e.g., logarithmic) factor approximation, then the resulting distributed algorithm becomes a constant factor approximation. For general graphs, we compute explicit bounds on the loss of performance of the resulting distributed algorithm with respect to the centralized algorithm. To show the efficiency of our algorithm, we conducted extensive experiments both on real-world networks and on synthetic networks. The experiments demonstrate that the PM algorithm provides a good trade-off between accuracy and running time.