Miracle-dz/UniFAR-FTUs huggingface dataset:
Garcinia kola Extract Potentiates a Pro-inflammatory Response While Not Affecting Type 1 Diabetes Incidence in an Experimental Mouse Model

Type 1 diabetes (T1D) is a non-preventable autoimmune disease where autoreactive T cells orchestrate the destruction of insulin-producing pancreatic beta cells. Individuals with T1D are committed to a life-long dependency on insulin, which it and T1D associated care is expensive, and in many regions around the world is unattainable. Thus, there is an imperative to find an accessible and efficient alternative. The seeds of Garcinia kola are commonly used for cultural and medicinal purposes in West Africa. Previous studies have shown that Garcinia kola seed extract (GKE) has hypoglycemic and anti-inflammatory effects which suit is as a candidate for preventing disease development. It was hypothesized that treatment with GKE would prevent T1D development through its anti-inflammatory action in an experimental mouse model. Male seven-week-old C57BL/6J mice were treated with aqueous or ethanol GKE (100 mg/kg) in their drinking water for five weeks and were chemically induced with T1D at eight weeks of age. Biweekly body weight and glycemia measurements were performed from nine to 13 weeks of age. Mice were euthanized at days 11 and 30 after the initial STZ injection to evaluate GKE’s effects on T cells. Treatment with GKE had no effect on glycemia, diabetes incidence or prevalence. However, the immunomodulatory activity of GKE displayed a shift to a proinflammatory response, suggesting potential therapeutic benefits for other diseases. This study did not confirm the anti-diabetic potential of GKE, however, it did highlight the need for more consistent research on herbal compounds.
The role of ERK and Smad2 signal pathways in the alternatively activated macrophages induced by TGF-β1 and high-ambient glucose

Abstract Macrophages can be alternatively activated by TGF-β1 and high-ambient glucose, in which the role of Smad2 and the crosstalk between ERK and Smad2 pathways are not fully understood. The activation of ERK and Smad2 pathways and the expression of arginase-1 were detected by Western blot. The role of Smad2 and the relationship between ERK and Smad2 pathways were investigated by using biochemical inhibitors. The protein of arginase-1 was significantly overexpressed in RAW264.7 cells stimulated by TGF-β1 and high-ambient glucose, which can be partially blocked by not only U0126 (ERK inhibitor) but also SB431542 (Smad2 inhibitor). Furthermore, simply inhibiting one pathway had no effect on the other pathway. In conclusion, both ERK and Smad2 signal pathways are involved in the activation of macrophages induced by TGF-β1 and high-ambient glucose, while there is no crosstalk shown in the process.
Improving Text Segmentation by Combining Endogenous and Exogenous Methods

Topic segmentation was addressed by a large amount of work from which it is not easy to draw conclusions, especially about the need for knowledge. In this article, we propose to combine in the same framework two methods for improving the results of a topic segmenter based on lexical reiteration. The first one is endogenous and exploits the distributional similarity of words in a document for discovering its topics. These topics are then used to facilitate the detection of topical similarity between discourse units. The second approach achieves the same goal by relying on external resources. Two resources are tested: a network of lexical co-occurrences built from a large corpus and a set of word senses induced from this network. An evaluation of the two approaches and their combination is performed in a reference framework and shows the interest of this combination both for French and English.
Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

The genomes of many vertebrates show a characteristic variation in GC content. To explain its origin and evolution, mainly three mechanisms have been proposed: selection for GC content, mutation bias, and GC-biased gene conversion. At present, the mechanism of GC-biased gene conversion, i.e., short-scale, unidirectional exchanges between homologous chromosomes in the neighborhood of recombination-initiating double-strand breaks in favor for GC nucleotides, is the most widely accepted hypothesis. We here suggest that DNA methylation also plays an important role in the evolution of GC content in vertebrate genomes. To test this hypothesis, we investigated one mammalian (human) and one avian (chicken) genome. We used bisulfite sequencing to generate a whole-genome methylation map of chicken sperm and made use of a publicly available whole-genome methylation map of human sperm. Inclusion of these methylation maps into a model of GC content evolution provided significant support for the impact of DNA methylation on the local equilibrium GC content. Moreover, two different estimates of equilibrium GC content, one that neglects and one that incorporates the impact of DNA methylation and the concomitant CpG hypermutability, give estimates that differ by approximately 15% in both genomes, arguing for a strong impact of DNA methylation on the evolution of GC content. Thus, our results put forward that previous estimates of equilibrium GC content, which neglect the hypermutability of CpG dinucleotides, need to be reevaluated.
Reduced 5-Methylcytosine Level as a Potential Progression Predictor in Patients with T1 or Non-Invasive Urothelial Carcinoma

This study aims to elucidate the level of DNA methylation in urothelial carcinomas (UCs) using 5-methylcytosine (5-MeC) immunohistochemistry (IHC). We examined the relationship among 5-MeC levels, DNA (cytosine-5)-methyltransferase 1 (DNMT1) immunostaining levels, and clinicopathologic features. Tissue samples included 23 normal urothelia and 150 urothelial neoplasia, which comprised 40 non-invasive and 110 invasive UCs. The levels of 5-MeC and DNMT1 were assessed based on their immunoreactivities and then divided into low and high levels. In addition, we collected information on clinical variables, pathologic features, and recurrent status from patient questionnaires and medical records. Chi-square test and multivariate logistic regression model were used for analyses. Results showed that 5-MeC levels were positively associated with DNMT1 levels in UC (p = 0.0288). Both 5-MeC and DNMT1 were low in approximately 50% (76/150) of UC. The percentage of low 5-MeC levels was higher in invasive UC (65/110; 59%) than in normal urothelia (2/23; 13%) and non-invasive UC (18/40; 45%). Clinical factors were independently associated with low 5-MeC levels after adjusting for age and sex, including cancer stages II–IV, presence of UC in situ, and marked inflammation. Low 5-MeC levels in stage I invasive UC were not significantly different from those of non-invasive tumors (p = 0.8478). Low DNMT1 levels were only associated with UC with squamous differentiation (p = 0.0365). Neither 5-MeC nor DNMT1 levels were associated with UC recurrence. In conclusion, a low 5-MeC level could predict the progression of UC invasion into muscle.
Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112T and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112T has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B12). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with 13C3-glycerol demonstrated that L. reuteri JCM 1112T could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112T to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri.
An arbitration on cache replacements based on frequency — Recency product values

Evolving an efficient cache replacement policy has been a challenge since the last few decades. LRU (Least Recently Used) and LFU (Least Frequently Used) cache replacement techniques and a variety of their combinations were the most sought after. This paper proposes a new combination of the LRU and LFU in such a style that the time and complexity to replace moves below the current benchmarks. Here, a frequency-recency product value is computed which dictates the cache replacement arbitration. It out performs the existing methods by a significant reduction in computational overhead.
Analysis of Gonadotropin Releasing Hormone (GnRH), Leutinizing Hormone (LHb) and Follicle Stimulating Hormone (FSHb) Genes in Indian Spiny Loach (Lepidocephalus thermalis)

India recites more than 10% of global fish biodiversity and it also ranks second in the world in total fish production. The capture fisheries were considered as the major contributor of marine sector whereas in inland fisheries, aquaculture constitutes nearly 77% of total production. India has a rich natural heritage and nurtures a unique biodiversity placing it among the 12 most biodiverse countries. Out of 31,100 extant fish species 2438 are known from Indian SubContinent (Froese and Pauly, 2009). The index of biodiversity utilized for aquaculture in India was of the order of 0.13 (~85% from Indian major carps; ~ 5% air-breathing fishes; ~10% rest all species together). Hence, more species need to be brought into culture practice, for the sustainability of aquaculture (Ayyappan et International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 04 (2019) Journal homepage: http://www.ijcmas. com
Amino acid composition of the whole body, flesh and exoskeleton of female common West African fresh water crab Sudananautes africanus africanus

The amino acid composition of the whole body (edible parts), flesh and exoskeleton of the female common West African fresh water crab Sudananautes africanus africanus was determined on a dry weight basis. The total essential amino acids ranged from 349.8 mg/g to 387.3 mg/g crude protein or from 48.5% to 49.8% of the total amino acid. Both the total amino acid and the total essential amino acid showed no significant differences among the samples at P<0.05. The amino acid score showed that lysine ranged from 0.9 to 1.2, making it a good food fortifier. The predicted protein efficiency ratio was 2.6–3.4, showing that the quality of protein was high. The carbohydrate content was high (57.5–59.1 g/100 g) but the protein was lower (15.7–18.6 g/100 g). The low level of the crude fibre in the flesh will make it good to serve as a food complement.
Therapeutic use of new pharmaceutical preparations containing antitumoral drugs bound to hyaluronic acid in the treatment of neoplasias

The present invention describes the new use in the oncologic field of bioconjugates as differentiating agents obtained by the conjugation between hyaluronic acid (HA) and a chemotherapeutic product (identified hereafter with the trade-name ONCOFID TM ) among which, in particular, Irinotecan, Doxorubicin, Paclitaxel, Cis-platinum and 5-Fluorouracyl (5-FU) for treating primary tumors and metastasis. In particular, the biological behaviour is described in terms of action mechanism, efficacy and tolerability of pharmaceutical preparations of derivative of ONCOFID TM soluble in water. More specifically, the invention relates to the surprising biological and pharmacological effect demonstrated by formulations based on ONCOFID-S (HA-SN38 conjugates) and ONCOFID-D (HA-Doxorubicin conjugates) in promoting the differentiation of tumoral cells towards a untransformed phenotype, compared with the reference drug Irinotecan (or CPT11 whose active form is represented by SN38) and Doxorubicin.
Evaluation of carcinogenic potential of the herbicide glyphosate, drawing on tumor incidence data from fourteen chronic/carcinogenicity rodent studies

Abstract Glyphosate, an herbicidal derivative of the amino acid glycine, was introduced to agriculture in the 1970s. Glyphosate targets and blocks a plant metabolic pathway not found in animals, the shikimate pathway, required for the synthesis of aromatic amino acids in plants. After almost forty years of commercial use, and multiple regulatory approvals including toxicology evaluations, literature reviews, and numerous human health risk assessments, the clear and consistent conclusions are that glyphosate is of low toxicological concern, and no concerns exist with respect to glyphosate use and cancer in humans. This manuscript discusses the basis for these conclusions. Most toxicological studies informing regulatory evaluations are of commercial interest and are proprietary in nature. Given the widespread attention to this molecule, the authors gained access to carcinogenicity data submitted to regulatory agencies and present overviews of each study, followed by a weight of evidence evaluation of tumor incidence data. Fourteen carcinogenicity studies (nine rat and five mouse) are evaluated for their individual reliability, and select neoplasms are identified for further evaluation across the data base. The original tumor incidence data from study reports are presented in the online data supplement. There was no evidence of a carcinogenic effect related to glyphosate treatment. The lack of a plausible mechanism, along with published epidemiology studies, which fail to demonstrate clear, statistically significant, unbiased and non-confounded associations between glyphosate and cancer of any single etiology, and a compelling weight of evidence, support the conclusion that glyphosate does not present concern with respect to carcinogenic potential in humans.
Highly Efficient Forward and Backward Propagation of Convolutional Neural Networks for Pixelwise Classification

We present highly efficient algorithms for performing forward and backward propagation of Convolutional Neural Network (CNN) for pixelwise classification on images. For pixelwise classification tasks, such as image segmentation and object detection, surrounding image patches are fed into CNN for predicting the classes of centered pixels via forward propagation and for updating CNN parameters via backward propagation. However, forward and backward propagation was originally designed for whole-image classification. Directly applying it to pixelwise classification in a patch-by-patch scanning manner is extremely inefficient, because surrounding patches of pixels have large overlaps, which lead to a lot of redundant computation. The proposed algorithms eliminate all the redundant computation in convolution and pooling on images by introducing novel d-regularly sparse kernels. It generates exactly the same results as those by patch-by-patch scanning. Convolution and pooling operations with such kernels are able to continuously access memory and can run efficiently on GPUs. A fraction of patches of interest can be chosen from each training image for backward propagation by applying a mask to the error map at the last CNN layer. Its computation complexity is constant with respect to the number of patches sampled from the image. Experiments have shown that our proposed algorithms speed up commonly used patch-by-patch scanning over 1500 times in both forward and backward propagation. The speedup increases with the sizes of images and patches.
A score to estimate the likelihood of detecting advanced colorectal neoplasia at colonoscopy

Objective This study aimed to develop and validate a model to estimate the likelihood of detecting advanced colorectal neoplasia in Caucasian patients. Design We performed a cross-sectional analysis of database records for 40-year-old to 66-year-old patients who entered a national primary colonoscopy-based screening programme for colorectal cancer in 73 centres in Poland in the year 2007. We used multivariate logistic regression to investigate the associations between clinical variables and the presence of advanced neoplasia in a randomly selected test set, and confirmed the associations in a validation set. We used model coefficients to develop a risk score for detection of advanced colorectal neoplasia. Results Advanced colorectal neoplasia was detected in 2544 of the 35 918 included participants (7.1%). In the test set, a logistic-regression model showed that independent risk factors for advanced colorectal neoplasia were: age, sex, family history of colorectal cancer, cigarette smoking (p<0.001 for these four factors), and Body Mass Index (p=0.033). In the validation set, the model was well calibrated (ratio of expected to observed risk of advanced neoplasia: 1.00 (95% CI 0.95 to 1.06)) and had moderate discriminatory power (c-statistic 0.62). We developed a score that estimated the likelihood of detecting advanced neoplasia in the validation set, from 1.32% for patients scoring 0, to 19.12% for patients scoring 7–8. Conclusions Developed and internally validated score consisting of simple clinical factors successfully estimates the likelihood of detecting advanced colorectal neoplasia in asymptomatic Caucasian patients. Once externally validated, it may be useful for counselling or designing primary prevention studies.
A Cognitive Agent Model for Simulation-Based Mindreading and Empathic Understanding

This paper focuses on modelling capabilities to interpret another person’s mind, with a special focus on emotions. First a cognitive agent model to generate emotional responses and feelings is introduced. This model involves the generation and sensing of body states in response to certain stimuli. For the case these stimuli concern another person’s body state, it is shown how this model can be used to model emotion reading, following the Simulation Theory approach to mindreading. Furthermore, by taking (internal) mental states instead of stimuli as a source for emotional responses, it is shown how to model the way in which a person associates feelings to mental states. Moreover, again following the Simulation Theory, it is shown how another person can obtain empathic understanding of person by simulating the way in which feelings are associated to mental states. This cognitive agent model describes how the empathic agent deals with another agent’s mental states and the associated feelings, thus not only understanding the other agent’s mental state but at the same time feeling the accompanying emotion of the other agent.
Spectral Affine‐Kernel Embeddings

In this paper, we propose a controllable embedding method for high‐ and low‐dimensional geometry processing through sparse matrix eigenanalysis. Our approach is equally suitable to perform non‐linear dimensionality reduction on big data, or to offer non‐linear shape editing of 3D meshes and pointsets. At the core of our approach is the construction of a multi‐Laplacian quadratic form that is assembled from local operators whose kernels only contain locally‐affine functions. Minimizing this quadratic form provides an embedding that best preserves all relative coordinates of points within their local neighborhoods. We demonstrate the improvements that our approach brings over existing nonlinear dimensionality reduction methods on a number of datasets, and formulate the first eigen‐based as‐rigid‐as‐possible shape deformation technique by applying our affine‐kernel embedding approach to 3D data augmented with user‐imposed constraints on select vertices.
Hepatic De Novo Lipogenesis in Obese Youth Is Modulated by a Common Variant in the GCKR Gene.

OBJECTIVE This study's aim was to evaluate whether the GCKR rs1260326 variant increases hepatic de novo lipogenesis (DNL). SETTING AND DESIGN To test this hypothesis, 14 adolescents, seven homozygous for the common allele (CC) and seven homozygous for the risk allele (TT), underwent measurement of hepatic DNL during the fasting state and after consumption of a carbohydrate (CHO) drink (75 g glucose and 25 g fructose). DNL was assessed through incorporation of deuterium in the palmitate contained in the very low-density lipoprotein. RESULTS Subjects with TT demonstrated higher fasting fractional DNL (P = .036) and a lower increase in fractional DNL after the CHO challenge (P = .016). With regard to absolute lipogenesis, TT subjects had both higher fasting rates (P = .015) and 44% greater area under the curve of absolute lipogenesis during the study (P = .016), compared to CC subjects. Furthermore, subjects carrying the TT genotype showed higher basal rates of glucose oxidation (P = .0028) and a lower ability than CC subjects to increase the rates of glucose oxidation after the CHO load (P = .054). CONCLUSIONS This study reports for the first time rates of DNL in obese adolescents and suggests that the GCKR rs1260326 gene variant, which is associated with greater glycolysis, increases hepatic DNL. These data highlight the role of glycolytic carbon flux in liver lipid synthesis and hypertriglyceridemia in these youngsters.
SIGSBEE_2A Synthetic Subsalt Dataset - Image Quality as Function of Migration Algorithm and Velocity Model Error

Consistent high quality subsalt imaging in the Gulf of Mexico is to this point still an eluding goal. The SMAART JV calculated an acoustic FD dataset modeled after the Sigsbee escarpment to increase the understanding of the imaging failure in this environment. I used this dataset to investigate a) the relationship between imaging algorithms and subsalt image quality and b) the sensitivity to errors in the velocity model. The results indicate that the way to significantly increased subsalt image quality is through increased accuracy in the determination of the salt shape combined with wavefield imaging. I propose a new technique to establish the salt shape using the velocity model independent multifocusing stack.