Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Renal Function and Other Health Outcomes in Vegetarians versus Omnivores in Taiwan

Renal disease is one of the top 10 leading causes of death, and the incidence of end-stage renal disease in Taiwan is the highest in the world. Many dietitians consider the diet of plant origin consumed by vegans to be ‘lighter’ and ‘more healthful’ than the diet of both plant and animal origin consumed by omnivores. Dietary protein has significant effects on renal functions. The study explored the effects of both the diets on renal functions. The study subjects included 102 Buddhist nun vegetarians and an equal number of matched control group (omnivores). A cross-sectional study was performed to investigate the effects of the diet of plant origin and the diet of both plant and animal origin on renal functions. There was no difference in the renal functions between the two groups. However, systolic blood pressure, blood urea nitrogen, serum sodium, glucose, cholesterol levels, and urinary specific gravity were lower in the vegetarian group. Although these results were compatible with general concepts regarding diet of plant origin, after adjusting for age, the duration of intake of this diet had no effect on the renal functions. Based on the findings, it is concluded that the renal functions, in terms of the estimated glomerular filtration rate, were not different between the vegetarians and the omnivores.
Characterization of the Bradyrhizobium japonicum CycY Protein, a Membrane-anchored Periplasmic Thioredoxin That May Play a Role as a Reductant in the Biogenesis of c-Type Cytochromes*

A new member of membrane-anchored periplasmic thioredoxin-like proteins was identified in Bradyrhizobium japonicum It is the product of cycY, the last gene in a cluster of cytochrome c biogenesis genes. Mutational analysis revealed that cycY is essential for the biosynthesis of all c-type cytochromes in this bacterium. The CycY protein was shown to be exported to the periplasm by its N-terminal signal sequence-like domain. Results from Western blot analyses of membrane and soluble fractions indicated that the CycY protein remains bound to the membrane. A soluble version of the protein devoid of its N-terminal membrane anchor (CycY*) was expressed in Escherichia coli and purified to homogeneity from the periplasmic fraction. The protein showed redox reactivity and properties similar to other thioredoxins such as fluorescence quenching in the oxidized form. Its equilibrium constant with glutathione was determined to be 168 mM, from which a standard redox potential of −0.217 V was calculated, suggesting that CycY might act as a reductant in the otherwise oxidative environment of the periplasm. This is in agreement with our hypothesis that CycY is required, directly or indirectly, for the reduction of the heme-binding site cysteines in the CXXCH motif of c-type apocytochromes before heme attachment occurs.
Inhibitory effect of okadaic acid derivatives on protein phosphatases. A study on structure-affinity relationship.

The effect of structural modifications of okadaic acid (OA), a polyether C38 fatty acid, was studied on its inhibitory activity toward type 1 and type 2A protein phosphatases (PP1 and PP2A) by using OA derivatives obtained either by isolation from natural sources or by chemical processes. The dissociation constant (Ki) for the interaction of OA with PP2A was estimated to be 30 (26-33) nM [median (95% confidence limits)]. The OA derivatives used and their affinity for PP2A, expressed as Ki (in brackets) were as follows: 35-methyl-OA (DTX1) [19 (12-25) pM], OA-9,10-episulphide (acanthifolicin) [47 (25-60) pM], 7-deoxy-OA [69 (31-138) pM], 14,15-dihydro-OA [315 (275-360) pM], 2-deoxy-OA [899 (763-1044) pM], 7-O-palmitoyl-OA [greater than 100 nM], 7-O-palmitoyl-DTX1 [greater than 100 nM], methyl okadate [much greater than 100 nM], 2-oxo-decarboxy-OA [much greater than 100 nM] and the C-15-C-38 fragment of OA [much greater than 100 nM]. The sequence of the affinity of these derivatives for PP1 was essentially the same as that observed with PP2A, although the absolute values of Ki were very different for the enzymes. The inhibitory effect of OA on PP2A was reversed by applying a murine monoclonal antibody against OA, which recognizes modifications of the 7-hydroxyl group of the OA molecule. It has been shown by n.m. r. spectroscopy and X-ray analysis that one end (C-1-C-24) of the OA molecule assumes a circular conformation. The present results suggest the importance of the conformation for the inhibitory action of OA on the protein phosphatases. The ratios of the Ki values for PP1 to that for PP2A, which were within the range 10(3)-10(4), tended to be smaller for the derivatives with lower affinity, indicating that the structural changes in OA impaired the affinity for PP2A more strongly than that for PP1.
High thyroid volume in children with excess dietary iodine intakes

We read with concern the article by Tangpricha et al (1) on tanning and vitamin D status in a recent issue of the Journal. They concluded, on the basis of their study, that “tanning beds may also provide some medical benefit. ” Our concern is based on several factors. First, Tangpricha et al recruited a convenience sample via an online bulletin board and newspaper advertisement. Hence, their study population was likely not representative of the general population. As a consequence, their results could be biased by the selfselected nature of their study participants. Furthermore, their comparison of vitamin D concentrations in tanners and nontanners may have been biased by their failure to account for differences in ethnic group, multivitamin consumption, or sunlight exposure between the 2 groups—factors that may have led to spuriously low vitamin D concentrations in nontanners relative to tanners. Second, patrons of commercial tanning parlors are unable to distinguish whether the lamps to which they are exposed emit pure ultraviolet (UV) A radiation (ie, wavelengths between 320 and 400 nm), which will not result in the photosynthesis of vitamin D in human skin, or emit a mixture of UV B (ie, wavelengths between 280 and 320 nm) and UVA radiation, which will result in the photosynthesis of vitamin D in human skin, nor can they tell how much UVB radiation is emitted by these lamps. Third, the investigators imply that artificial tanning lamps may be useful for improving vitamin D status, but they downplay their carcinogenicity. Artificial tanning has been linked to multiple types of skin cancers. Oral vitamin supplements are a safer, much less expensive, and more convenient method for improving vitamin D status. Fourth, the authors of the article acknowledge having received support from the UV Foundation for their work, and the senior author is a consultant for this foundation. However, the authors failed to note the close connection between the UV Foundation and the commercial tanning industry. Were the readers aware of this close connection, they might infer that the implicit endorsement of tanning parlors in this article is related to the authors’ financial connections with the commercial tanning industry.
FOHM: a fundamental open hypertext model for investigating interoperability between hypertext domains

The Open Hypermedia Systems community has been largely concerned with interoperability between hypertext systems which share the same paradigm. It has evolved a component based framework for this purpose, in which specific but incompatible middleware components are designed for each hypertext domain, such as navigational hypertext, spatial hypertext or taxonomic hypertext. This paper investigates the common features of these domains and introduces FOHM, a Fundamental Open Hypertext Model, which defines a common data model and set of related operations that are applicable for all three domains. Using this layer the paper explores the possible semantics of linking between different hypertext domains, and shows that each can introduce features which benefit the other domains.
Towards A Serum-Free Medium: Growth Receptors And Signaling Pathways That Regulate Multipotency In Human Mesenchymal Stem Cells

Human mesenchymal stem cells (MSCs) are capable of being used in human therapeutic procedures such as tissue repair and gene therapy due to their multipotency. However, the expansion of MSCs is limited by the restricted use of fetal bovine serum (FBS) as the nutritional supplement. Hence, contamination by pathogens from the xenogenic component can be eliminated if a serum-free media were used. In this paper, we identified the human growth receptors (HGRs) and corresponding signaling pathways expressed in undifferentiated proliferative MSCs by analyzing available microarray data. The microarray datasets were generated by Affymetrix GeneChips and Illumina BeadArrays. The MSC samples used were cultured in both fetal bovine serum (FBS) and autologous serum (AS) at passage one. Results from the different platforms indicated 94 similarly expressed human growth receptors. Affymetrix was also able to detect 129.19% more HGRs than Illumina. We also discovered that HGR expressions across different types of serum were similar, indicating that type of serum had little impact on proliferation mechanisms in early passages. Next, Ingenuity Pathway Analysis identified 11 signaling pathways that were expressed in all four MSC cultures. In particular, the Notch Signaling Pathway and Transforming Growth Factor - Beta Signaling Pathway were consistently expressed in all MSC cultures. These 11 signaling pathways and 94 HGRs are important in understanding the maintenance of MSC undifferentiated proliferative state, and the corresponding growth factors are possibly required minimally in developing a serum-free medium for MSC expansion.
Vehicular pollution dispersion modelling along roads using CALINE4 model - a review

The present paper presents a review of vehicular pollution dispersion models with particular focus on CALINE4 model. The CALINE4 model is one of the most extensively used model for prediction of vehicular pollution along highways/roads. The CALINE4 model is easy handing and less input data requirement makes it useful for screening purposes. The paper also briefly discusses about the performance evaluation, sensitivity analysis of CALINE4 model along with uncertainty due to limitations in terms of input data provided in CALINE4 model's output.
Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits

Prediction of genetic merit using dense SNP genotypes can be used for estimation of breeding values for selection of livestock, crops, and forage species; for prediction of disease risk; and for forensics. The accuracy of these genomic predictions depends in part on the genetic architecture of the trait, in particular number of loci affecting the trait and distribution of their effects. Here we investigate the difference among three traits in distribution of effects and the consequences for the accuracy of genomic predictions. Proportion of black coat colour in Holstein cattle was used as one model complex trait. Three loci, KIT, MITF, and a locus on chromosome 8, together explain 24% of the variation of proportion of black. However, a surprisingly large number of loci of small effect are necessary to capture the remaining variation. A second trait, fat concentration in milk, had one locus of large effect and a host of loci with very small effects. Both these distributions of effects were in contrast to that for a third trait, an index of scores for a number of aspects of cow confirmation (“overall type”), which had only loci of small effect. The differences in distribution of effects among the three traits were quantified by estimating the distribution of variance explained by chromosome segments containing 50 SNPs. This approach was taken to account for the imperfect linkage disequilibrium between the SNPs and the QTL affecting the traits. We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage) than for a trait with no loci of large effect (overall type), provided the method of analysis takes advantage of the distribution of loci effects.
Frodo: Take off the Ring! Practical, Quantum-Secure Key Exchange from LWE

Lattice-based cryptography offers some of the most attractive primitives believed to be resistant to quantum computers. Following increasing interest from both companies and government agencies in building quantum computers, a number of works have proposed instantiations of practical post-quantum key exchange protocols based on hard problems in ideal lattices, mainly based on the Ring Learning With Errors (R-LWE) problem. While ideal lattices facilitate major efficiency and storage benefits over their non-ideal counterparts, the additional ring structure that enables these advantages also raises concerns about the assumed difficulty of the underlying problems. Thus, a question of significant interest to cryptographers, and especially to those currently placing bets on primitives that will withstand quantum adversaries, is how much of an advantage the additional ring structure actually gives in practice. Despite conventional wisdom that generic lattices might be too slow and unwieldy, we demonstrate that LWE-based key exchange is quite practical: our constant time implementation requires around 1.3ms computation time for each party; compared to the recent NewHope R-LWE scheme, communication sizes increase by a factor of 4.7x, but remain under 12 KiB in each direction. Our protocol is competitive when used for serving web pages over TLS; when partnered with ECDSA signatures, latencies increase by less than a factor of 1.6x, and (even under heavy load) server throughput only decreases by factors of 1.5x and 1.2x when serving typical 1 KiB and 100 KiB pages, respectively. To achieve these practical results, our protocol takes advantage of several innovations. These include techniques to optimize communication bandwidth, dynamic generation of public parameters (which also offers additional security against backdoors), carefully chosen error distributions, and tight security parameters.
Accommodation or deterrence in the face of commercial piracy: the impact of intellectual property rights protection

In this paper, we study when the original product developer makes costly investment to deter a commercial pirate in a given regime of intellectual property rights (IPR) protection. We find that when the consumers' tastes are sufficiently diverse and the IPR protection is weak, it is profitable for the original producer to accommodate the pirate. In all other cases, it is profitable to deter. In the comparative statics analysis, we find a non-monotonic relationship between the optimal level of deterrence and the degree of IPR protection in the economy. We also find interesting relationships between the rate of piracy and other parameters like the strength of IPR protection, consumers' tastes, and quality of the pirated product. We find that from the commercial pirate's point of view, the most profitable way to survive in the market is to produce a pirated product of moderate quality. Copyright 2012 Oxford University Press 2011 All rights reserved, Oxford University Press.
Congestion pricing and user adaptation

The problem of sharing bandwidth in a communication network has been the focus of much research aimed at guaranteeing an appropriate quality of service to users. This is particularly challenging in an environment with a great diversity of users and applications, which makes it difficult, if not impossible, to tightly constrain user attributes and requirements. This motivates shifting the burden of rate allocation from the network to the end-systems. We propose a decentralized scheme for user adaptation and study its dynamics. The proposed scheme uses congestion prices as a mechanism for providing both feedback and incentives to end-systems.
Murine Endogenous Retrovirus MuERV-L Is the Progenitor of the “Orphan” Epsilon Viruslike Particles of the Early Mouse Embryo

ABSTRACT Viruslike particles which displayed a peculiar wheellike appearance that distinguished them from A-, B- or C-type particles had previously been described in the early mouse embryo. The maximum expression of these so-called epsilon particles was observed in two-cell-stage embryos, followed by their rapid decline at later stages of development and no particles detected at the zygote one-cell stage. Here, we show that these particles are in fact produced by a newly discovered murine endogenous retrovirus (ERV) belonging to the widespread family of mammalian ERV-L elements and named MuERV-L. Using antibodies that we raised against the Gag protein of these elements, Western blot analysis and in toto immunofluorescence studies of the embryos at various stages disclosed the same developmental expression profile as that observed for epsilon particles. Using expression vectors for cloned, full-length, entirely coding MuERV-L copies and cell transfection, direct identification of the epsilon particles was finally achieved by high-resolution electron microscopy.
Low-rank matrix completion using alternating minimization

Alternating minimization represents a widely applicable and empirically successful approach for finding low-rank matrices that best fit the given data. For example, for the problem of low-rank matrix completion, this method is believed to be one of the most accurate and efficient, and formed a major component of the winning entry in the Netflix Challenge [17]. In the alternating minimization approach, the low-rank target matrix is written in a bi-linear form, i.e. X = UV†; the algorithm then alternates between finding the best U and the best V. Typically, each alternating step in isolation is convex and tractable. However the overall problem becomes non-convex and is prone to local minima. In fact, there has been almost no theoretical understanding of when this approach yields a good result. In this paper we present one of the first theoretical analyses of the performance of alternating minimization for matrix completion, and the related problem of matrix sensing. For both these problems, celebrated recent results have shown that they become well-posed and tractable once certain (now standard) conditions are imposed on the problem. We show that alternating minimization also succeeds under similar conditions. Moreover, compared to existing results, our paper shows that alternating minimization guarantees faster (in particular, geometric) convergence to the true matrix, while allowing a significantly simpler analysis.
The Bromodomain BET Inhibitor JQ1 Suppresses Tumor Angiogenesis in Models of Childhood Sarcoma

The bromodomain and extra-terminal domain inhibitor JQ1 has marked antitumor activity against several hematologic malignancies as well as solid tumor models. Here, we investigated its activity in vitro and in vivo against models of childhood rhabdomyosarcoma and Ewing sarcoma. In vitro, JQ1 (but not the inactive enantiomer JQ1R) inhibited cell proliferation and increased G1 fraction of cells, although there was no correlation between cell line sensitivity and suppression of c-MYC or MYCN. In vivo, xenografts showed significant inhibition of growth during the period of treatment, and rapid regrowth after treatment was stopped, activity typical of antiangiogenic agents. Furthermore, xenografts derived from cell lines intrinsically resistant or sensitive to JQ1 in vitro had similar sensitivity in vivo as xenografts. Further investigation showed that JQ1 reduced tumor vascularization. This was secondary to both drug-induced downregulation of tumor-derived growth factors and direct effects of JQ1 on vascular elements. JQ1 suppressed VEGF-stimulated vascularization of Matrigel plugs in mice, and in vitro suppressed differentiation, proliferation, and invasion of human umbilical cord vascular endothelial cells (HUVEC). In HUVECs, JQ1 partially suppressed c-MYC levels, but dramatically reduced AP-1 levels and activity through suppression of the AP-1–associated protein FOSL1. Our data suggest that the antitumor activity of JQ1 in these sarcoma models is largely a consequence of its antiangiogenic activity. Mol Cancer Ther; 15(5); 1018–28. ©2016 AACR.
Implant-based oral rehabilitation of a variant model of type I dentinal dysplasia: A rare case report

Dentin dysplasia is an exceptionally rare, autosomal-dominant, hereditary condition, primarily characterized by defective dentin formation affecting both the deciduous and permanent dentitions. The etiology remains imprecise to date, in spite of the numerous hypotheses put forward and the constant updates on this condition. This case report of type I dentin dysplasia exhibits radiographic findings that are unique and diverse from the classical findings of various subtypes of this disease reported to date. This article also depicts the implant-based oral rehabilitation of the young patient diagnosed with this variant model of dentin dysplasia type I. Early diagnosis and implementation of this preventive and curative therapy is vital for avoiding premature exfoliation of deciduous and permanent dentition and the associated residual ridge resorption, thereby overcoming functional and esthetic deficits and ensuring protection of the remaining dentition from further harm.
Automated Classification of L/R Hand Movement EEG Signals using Advanced Feature Extraction and Machine Learning

In this paper, we propose an automated computer platform for the purpose of classifying Electroencephalography (EEG) signals associated with left and right hand movements using a hybrid system that uses advanced feature extraction techniques and machine learning algorithms. It is known that EEG represents the brain activity by the electrical voltage fluctuations along the scalp, and Brain-Computer Interface (BCI) is a device that enables the use of the brain's neural activity to communicate with others or to control machines, artificial limbs, or robots without direct physical movements. In our research work, we aspired to find the best feature extraction method that enables the differentiation between left and right executed fist movements through various classification algorithms. The EEG dataset used in this research was created and contributed to PhysioNet by the developers of the BCI2000 instrumentation system. Data was preprocessed using the EEGLAB MATLAB toolbox and artifacts removal was done using AAR. Data was epoched on the basis of Event-Related (De) Synchronization (ERD/ERS) and movement-related cortical potentials (MRCP) features. Mu/beta rhythms were isolated for the ERD/ERS analysis and delta rhythms were isolated for the MRCP analysis. The Independent Component Analysis (ICA) spatial filter was applied on related channels for noise reduction and isolation of both artifactually and neutrally generated EEG sources. The final feature vector included the ERD, ERS, and MRCP features in addition to the mean, power and energy of the activations of the resulting Independent Components (ICs) of the epoched feature datasets. The datasets were inputted into two machine- learning algorithms: Neural Networks (NNs) and Support Vector Machines (SVMs). Intensive experiments were carried out and optimum classification performances of 89.8 and 97.1 were obtained using NN and SVM, respectively. This research shows that this method of feature extraction holds some promise for the classification of various pairs of motor movements, which can be used in a BCI context to mentally control a computer or machine. Keywords—EEG; BCI; ICA; MRCP; ERD/ERS; machine learning; NN; SVM