Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-amyloid aggregation activity of novel carotenoids: implications for Alzheimer’s drug discovery

Alzheimer’s disease (AD) is the leading cause of dementia, affecting approximately 33.5 million people worldwide. Aging is the main risk factor associated with AD. Drug discovery based on nutraceutical molecules for prevention and treatment of AD is a growing topic. In this sense, carotenoids are phytochemicals present mainly in fruits and vegetables with reported benefits for human health. In this research, the anti-amyloidogenic activity of three carotenoids, cryptocapsin, cryptocapsin-5,6-epoxide, and zeaxanthin, was assessed. Cryptocapsin showed the highest bioactivity, while cryptocapsin-5,6-epoxide and zeaxanthin exhibited similar activity on anti-aggregation assays. Molecular modeling analysis revealed that the evaluated carotenoids might follow two mechanisms for inhibiting Aβ aggregation: by preventing the formation of the fibril and through disruption of the Aβ aggregates. Our studies provided evidence that cryptocapsin, cryptocapsin-5,6-epoxide, and zeaxanthin have anti-amyloidogenic potential and could be used for prevention and treatment of AD.
A STATISTICAL APPROACH TO SEMI-SUPERVISED SPEECH ENHANCEMENT WITH LOW-ORDER NON-NEGATIVE MATRIX FACTORIZATION Shoaib Mohammed

Compared to generic source separation, NMF for speech enhancement is relatively underexplored. When applied to the latter problem, NMF is bereft of performance consistency (across runs and data samples), esp. with small-sized dictionaries. This limitation raises the need for higher-order representations, leading to increased computational costs. In this paper, we propose a statistical-estimation technique that attempts to bridge this gap. Our approach combines multiple low-order NMF decompositions of noisy speech to increase the overall enhancement performance. We show PESQ improvements of up to 0.24 beyond what is achievable by a single NMF parametrization and, at iso-performance levels, major reductions in computational cost.
High Incidence and Levels of Ochratoxin A in Wines Sourced from the United States

Ochratoxin A (OTA) is one of the most prevalent mycotoxin contaminants of food crops. Among the agricultural products consequently contaminated by OTA is wine. In the present study, a sample of wines sourced from the United States was assessed for OTA. Wines were primarily analyzed by high-performance liquid chromatography with fluorescence detection (HPLC-FD) coupled to a liquid-liquid extraction (LLE) technique which was developed and validated as a simplified sample preparation approach. More than 85% of the wines evaluated were found to contain OTA, at levels above the limit-of-detection (LOD = 0.1 µg L−1), and 76% were above the limit-of-quantitation (LOQ = 0.3 µg L−1) for the LLE/HPLC-FD method. More than two-thirds of the wines above the LOQ were found to exceed 1 µg L−1. Complementary analysis by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) confirmed OTA in 74% of the OTA-positive wines (i.e., >LOQ by HPLC-FD). Overall, both the occurrence and measured levels of OTA were generally high, specifically relative to previous assessments of OTA in wine, and two of the wines were above the only current (European Union) regulatory limit of two parts-per-billion (ppb, ~2 µg L−1). Possible trends with respect to geographical region and/or growing climate are noted. As the first assessment of U.S. wines in more than a decade, the overall high occurrence and levels of OTA in wine, and possible geographic and climatic trends, point to a need for regular surveillance of wines, as well as investigation of the relevant contributors to OTA occurrence toward mitigating contamination and exposure risks.
Robust controller design for the cloud-based robotic visual servo system with time-delay uncertainty

The control performance of the cloud-based robotic visual servo system is always limited by the varying time delay for the data transmission and image processing. The varying image processing delay produced by the varying number of the extracted features for pose estimation and the data transmission delay are modeled as a stochastic process. The cloud-based robotic visual servo system is modeled as a discrete-time linear uncertain system, and the uncertain system matrix reflects the variation nature of the time varying delay. In the present paper, our primary work is presenting the robust control method to deal with the stabilization problem for the considered system. Then the sufficient asymptotic stabilization conditions and the feedback controller are derived. An experiment is conducted to validate the proposed approach.
Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure

Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource. Cis-eQTLs, also known as allele-specific expression (ASE) polymorphisms, are generally single-nucleotide polymorphisms in the promoter regions of genes that affect expression of the gene, such as by inhibiting the binding of transcription factors. Trans-eQTLs are genes that regulate mRNA levels for many genes, and are generally thought to be SNPs in trans-acting transcription or translation factors. In this study, we focused our attention on alternative splicing events that are affected by lead exposure. Splicing QTLs (sQTLs), which can be caused by SNPs that alter splicing or alternative splicing (AS), such as by changing the sequence-specific binding affinity of splicing factors to the pre-mRNA. We applied two methods in search for sQTLs by using RNA-seq data from control and lead-exposed w1118 Drosophila heads. First, we used the fraction of reads in a gene that falls in each exon as the phenotype. Second, we directly compared the transcript counts among the various splicing isoforms as the phenotype. Among the 1,236 potential Pb-responsive sQTLs (p < 0.0001, FDR < 0.39), mostly cis-sQTLs, one of the most distinct genes is Dscam1 (Down Syndrome Cell Adhesion Molecule), which has over 30,000 potential alternative splicing isoforms. We have also identified a candidate Pb-responsive trans-sQTL hotspot that appears to regulate 129 genes that are enriched in the “cation channel” gene ontology category, suggesting a model in which alternative splicing of these channels might lead to an increase in the elimination of Pb2+ from the neurons encoding these channels. To our knowledge, this is the first paper that uses sQTL analyses to understand the neurotoxicology of an environmental toxin in any organism, and the first reported discovery of a candidate trans-sQTL hotspot.
Validate the Correctness of Object Oriented Program with Regression Testing

Regression testing is used to validate the correctness of upgrades version of any program or software. The newly introduced features in the system under test are compared with the existing versions which determine the proper implementation of regression testing. The verification is done in a way that the modification made in the SUT does not interfere with the existing features, in this paper two program with new version of each are being put to regression testing with old and new test cases to check the satisfiability of regression testing. Software developers often face the challenge of projecting the difference in behaviour of one version of a program unit as compared to the upgraded on of the same program unit, for such situations, the developers need to generated test cases between the existing and upgraded version, if any exist.
Cognitive Deficits in Korean Women Treated With Chemotherapy for Breast Cancer

Background: Cognitive deficits have been reported as detrimental side effects in chemotherapy-treated breast cancer patients and survivors. Korean women treated for breast cancer may experience unrecognized cognitive deficits related to their treatment. However, no research has examined cognitive test performance in chemotherapy-treated Korean breast cancer survivors. Objective: The objectives of this study were 2-fold: (1) to examine differences in occurrence and severity of cognitive deficits in Korean women treated with adjuvant chemotherapy for breast cancer as compared with a control group of women without breast cancer and (2) to examine the relationship of selected demographic and cultural factors with cognitive test performance. Methods: Sixty-four Korean women, 32 women treated for localized breast cancer and 32 healthy controls, were enrolled. Breast cancer participants were assessed with established cognitive measures within 4 months after chemotherapy, and healthy controls, within 6 months after negative screening mammography. Results: The breast cancer group showed a significantly higher occurrence and greater severity of cognitive deficits than controls did. Importantly, older age, less education, greater collectivist tendency, and greater childrearing burden were reliably associated with poorer attention and working memory test performance. Conclusions: Cognitive deficits were found in chemotherapy-treated Korean women with moderate to large effect sizes compared with controls. Cultural characteristics contributed to worse cognitive performance. Implications for Practice: Healthcare providers should recognize that Korean women may be highly vulnerable to cognitive deficits. Cultural factors also need to be considered when assessing cognitive function and designing therapeutic interventions to counteract negative cognitive outcomes.
Daily Step Count Predicts Acute Exacerbations in a US Cohort with COPD

Background COPD is characterized by variability in exercise capacity and physical activity (PA), and acute exacerbations (AEs). Little is known about the relationship between daily step count, a direct measure of PA, and the risk of AEs, including hospitalizations. Methods In an observational cohort study of 169 persons with COPD, we directly assessed PA with the StepWatch Activity Monitor, an ankle-worn accelerometer that measures daily step count. We also assessed exercise capacity with the 6-minute walk test (6MWT) and patient-reported PA with the St. George's Respiratory Questionnaire Activity Score (SGRQ-AS). AEs and COPD-related hospitalizations were assessed and validated prospectively over a median of 16 months. Results Mean daily step count was 5804±3141 steps. Over 209 person-years of observation, there were 263 AEs (incidence rate 1.3±1.6 per person-year) and 116 COPD-related hospitalizations (incidence rate 0.56±1.09 per person-year). Adjusting for FEV1 % predicted and prednisone use for AE in previous year, for each 1000 fewer steps per day walked at baseline, there was an increased rate of AEs (rate ratio 1.07; 95%CI = 1.003–1.15) and COPD-related hospitalizations (rate ratio 1.24; 95%CI = 1.08–1.42). There was a significant linear trend of decreasing daily step count by quartiles and increasing rate ratios for AEs (P = 0.008) and COPD-related hospitalizations (P = 0.003). Each 30-meter decrease in 6MWT distance was associated with an increased rate ratio of 1.07 (95%CI = 1.01–1.14) for AEs and 1.18 (95%CI = 1.07–1.30) for COPD-related hospitalizations. Worsening of SGRQ-AS by 4 points was associated with an increased rate ratio of 1.05 (95%CI = 1.01–1.09) for AEs and 1.10 (95%CI = 1.02–1.17) for COPD-related hospitalizations. Conclusions Lower daily step count, lower 6MWT distance, and worse SGRQ-AS predict future AEs and COPD–related hospitalizations, independent of pulmonary function and previous AE history. These results support the importance of assessing PA in patients with COPD, and provide the rationale to promote PA as part of exacerbation-prevention strategies.
Rich Media e-Compendiums: A New Tool for Enhanced Learning in Higher Education

Electronically supported learning has increasingly been introduced and accepted into the academic community over recent decades, and a variety of new digital learning tools have been developed to serve students both for distance education and on-campus blended learning. To serve our distance education nursing students, we recently developed unique rich media ecompendiums, based on a combination of PDF and Flash technologies, as a substitute for oncampus lectures. Our e-compendiums are also available for our on-campus students as a supplement to their other learning tools (e.g., lectures, textbooks and podcasts). The aim of this study was to explore students’ perceptions of the e-compendiums as a learning tool compared with the other e-learning tools and more traditional tools used in a first-semester course. The study had a descriptive quantitative design and the data were collected by means of a questionnaire developed for this study. We found that a clear majority of the students scored the e-compendiums as a better learning tool than lectures, multiple-choice questions, podcasts and textbooks. Our results indicate that rich media e-compendiums were perceived as better learning tools than both traditional learning tools and other electronically supported learning tools.
Nicotine Inhibits Clostridium difficile Toxin A-Induced Colitis but Not Ileitis in Rats

Nicotine is protective in ulcerative colitis but not Crohn's disease of the small intestine, but little is known about the effects of nicotine on Clostridium difficile toxin A-induced enteritis. Isolated ileal or colonic segments in anesthetized rats were pretreated with nicotine bitartrate or other pharmacological agents before intraluminal injection of toxin A. After 3 hours, the treated segments were removed and inflammation was assessed. Nicotine biphasically inhibited toxin A colitis but not ileitis. Pretreatment with the nicotinic receptor antagonist, hexamethonium, blocked the effects of nicotine. Pretreating the colonic segments with hexamethonium before toxin A administration resulted in more inflammation than seen with toxin A alone, suggesting that a tonic nicotinic anti-inflammatory condition exists in the colon. Nicotine also inhibited toxin A-induced increased colonic concentrations of the TRPV1 (transient receptor potential vanilloid subtype 1) agonist, leukotriene B4 (LTB4), and release of the proinflammatory neuropeptide, substance P. Pretreatment with nicotine did not protect against direct TRPV1-mediated colitis caused by intraluminal capsaicin. Nicotinic cholinergic receptors tonically protect the colon against inflammation and nicotine inhibits toxin A colitis but not toxin A ileitis in rats in part by inhibition of toxin A-induced activation of TRPV1 by endogenous TRPV1 agonists such as LTB4.
Family-Based Analysis of Serotonin Transporter Gene Polymorphisms in Migraine With and Without Aura

Genetic epidemiological twin studies have demonstrated a significant heritability for migraine, with >60% of liability to migraine either with or without aura coming from additive genetic factors. Because of the essential role of serotonin in the pathophysiology and treatment of migraine, genes of the serotonin system are candidates for involvement in migraine. Consequently, we examined two functional VNTR polymorphisms in the serotonin transporter gene, the 5-HTTLPR and the intron 2 VNTR, in a sample of 212 family trios each with a proband with childhood migraine, 153 with migraine without aura (MoA) and 59 with migraine with aura (MA). For the first time, we used transmission disequilibrium test analysis with the program TDTPHASE to examine the transmission of these two markers and their haplotypes to offspring affected by migraine. We found no significant transmission distortion of any marker, with the common L allele of the 5-HTTLPR transmitted 170 times and not transmitted 178 times, and the S allele 130 vs. 122 times. Likewise, the common 12 allele of the intron 2 VNTR was transmitted 201 times and not transmitted 188 times, and the 10 allele 107 vs. 120 times. The markers were not associated with MoA and MA and none of the haplotypes was associated with overall migraine, MoA or MA. The 5-HTTLPR and the intron 2 VNTRs do not play a major role in susceptibility to migraine.
Diagnosis of hold time defects

In modern technologies, process variations can be quite substantial, often causing design timing failures. It is essential that those errors be correctly and quickly diagnosed. In this work, we analyze failures caused by the hold-time-violations. We investigate the feasibility of using circuit-timing information to guide the hold-time-fault diagnosis. We propose a novel and efficient diagnostic approach based on timing window propagation. For each identified candidate, our method locates the source of the hold-time violation and determines the most probable defect size. Experimental results indicate that the new method diagnoses hold-time related defects with very good resolution.
Emotional Intelligence as a Predictor of Career Longevity Among Special Education Teachers in the Houston County, Georgia, School System

In an effort to provide for a better understanding of the factors that exert influence on the career decisions of special educators, the present study sought to examine the influence of emotional intelligence and various demographic factors on the career longevity of special educators. One hundred twenty nine special education teachers in the Houston Count, Georgia School System completed a two-part survey consisting of the General Emotional Intelligence Scale and a researcher-created demographic questionnaire. The following overarching research question was answered through this studyWhat is the role of emotional intelligence in the career decisions of special education teachers? In addition, the following research sub-questions were answeredTo what extent does emotional intelligence depend on the career longevity of special education teachers? ; To what extent does the mean emotional intelligence of special education teachers vary by school level factors? ; To what extent does the mean emotional intelligence of special education
A Bayesian Analysis of Extrasolar Planet Data for HD 73526

A new Bayesian tool for nonlinear model fitting has been developed that employs a parallel tempering Markov chain Monte Carlo algorithm with a novel statistical control system. The algorithm has been used to reanalyze precision radial velocity data for HD 73526. For a single-planet model, three possible orbits were found with periods of 127.88, 190.4, and 376.2 days. The 128 day orbit, with an eccentricity of 0.56 ± 0.03, has a maximum value of prior × likelihood that is 16 times larger than for the next highest solution at 376 days. However, the 376 day orbit, with an eccentricity of 0.10, is formally more probable because for this sparse data set there is a much larger volume of parameter space with a significant probability density in the vicinity of the 376 day peak. The previously reported orbit (Tinney et al. 2003) of 190.5 ± 3.0 days corresponds to our least probable orbit. The analysis highlights the need for measurements around phase 0.5 for the 376 day period.
Bioengineering the Liver: Scale-Up and Cool Chain Delivery of the Liver Cell Biomass for Clinical Targeting in a Bioartificial Liver Support System

Abstract Acute liver failure has a high mortality unless patients receive a liver transplant; however, there are insufficient donor organs to meet the clinical need. The liver may rapidly recover from acute injury by hepatic cell regeneration given time. A bioartificial liver machine can provide temporary liver support to enable such regeneration to occur. We developed a bioartificial liver machine using human-derived liver cells encapsulated in alginate, cultured in a fluidized bed bioreactor to a level of function suitable for clinical use (performance competence). HepG2 cells were encapsulated in alginate using a JetCutter to produce ∼500 μm spherical beads containing cells at ∼1.75 million cells/mL beads. Within the beads, encapsulated cells proliferated to form compact cell spheroids (AELS) with good cell-to-cell contact and cell function, that were analyzed functionally and by gene expression at mRNA and protein levels. We established a methodology to enable a ∼34-fold increase in cell density within the AELS over 11–13 days, maintaining cell viability. Optimized nutrient and oxygen provision were numerically modeled and tested experimentally, achieving a cell density at harvest of >45 million cells/mL beads; >5×1010 cells were produced in 1100 mL of beads. This process is scalable to human size ([0.7–1]×1011). A short-term storage protocol at ambient temperature was established, enabling transport from laboratory to bedside over 48 h, appropriate for clinical translation of a manufactured bioartificial liver machine.
Attenuation of transcriptional bursting in mRNA transport

Because of the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising from a bursting input is reshaped by a transport reaction which is either linear or of the Michaelis–Menten type. A slow transport rate smoothes out fluctuations at the output end and minimizes the impact of bursting on the downstream cellular activities. In the context of gene expression in eukaryotic cells, our results indicate that transcriptional bursting can be substantially attenuated by the transport of mRNA from nucleus to cytoplasm. Saturation of the transport mediators or nuclear pores contributes further to the noise reduction. We suggest that the mRNA transport should be taken into account in the interpretation of relevant experimental data on transcriptional bursting.
Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals

A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6‐31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154–1166, 2001