Miracle-dz/UniFAR-FTUs huggingface dataset:
A mixed finite volume element method for accurate computation of fluid velocities in porous media

A key ingredient in the simulation of flow in porous media is the accurate determination of the velocities that drive the flow. Large-scale irregularities of the geology, such as faults, fractures, and layers, suggest the use of irregular grids in the simulation. In this study, the approach to this problem was to apply the finite volume element methodology, developed by McCormick, in conjunction with mixed methods, developed by Raviart and Thomas. The resulting mixed finite volume element discretization scheme developed here can be applied in a clear and straightforward way to irregular grids and is appealing because of its local conservation properties and its direct and accurate representation of physical intercell flux terms. Several multilevel algorithms are developed that provide efficient methods for solving the set of equations that this discretization produces. This thesis includes numerical results from a variety of test problems, from Poisson's equation to problems with anisotropic, discontinuous, and tensor diffusion coefficients. These results show that this approach has the potential to generate accurate approximate fluid velocities and that the multilevel methods can provide fast solvers.
Study on Preparation of Vitamin A-Curcumin Liposome and Its Cytotoxicity

OBJECTIVE To prepare Hepatic stellate cell targeting Vitamin A-curcumin liposome and to investigate its cytotoxicity in vitro.METHODS Reverse phase evaporation was used to prepare VA-curcumin liposome and the entrapment efficiency and the VA binding rate was determined.Entrapment efficiency,VA binging rate and peroxide value were determined to evaluate the stability of liposome at 4 and 25 ℃ for 30 d.MTT assay was used to investigate the cytotoxicity and targeting ability of the liposome in rat hepatic stellate cells HSC-T6 with high expression of retinol binding protein and human esophageal cancer cells A-549 without expression of retinol binding protein.RESULTS The average entrapment efficiency for curcumin was 89.32%,and binding rate for VA was 61.34%. The liposome stored at 4 ℃ was stable.The results of MTT assay showed that IC50 of curcumin,curcumin liposome,and VA-curcumin liposome in HSC-T6 cell were 31.53,14.95 and 8.28 μg·mL-1,respectively.Curcumin liposome and VA-curcumin liposome had same cytotoxic effects in A-549 cell.CONCLUSION The optimized conditions were obtained with high entrapment efficiency and good stability.VA-curcumin liposome could specifically target HSC and promote therapeutic effect of curcumin.
Participation de l’équipe du LIMICS à DEFT 2020 (Participation of team LIMICS in the DEFT 2020 challenge )

Nous présentons dans cet article les méthodes conçues et les résultats obtenus lors de notre participation à la tâche 3 de la campagne d’évaluation DEFT 2020, consistant en la reconnaissance d’entités nommées du domaine médical. Nous proposons deux modèles différents permettant de prendre en compte les entités imbriquées, qui représentent une des difficultés du jeu de données proposées, et présentons les résultats obtenus. Notre meilleur run obtient la meilleure performance parmi les participants, sur l’une des deux sous-tâches du défi.
CARACTERÍSTICAS IN VITRO E FERTILIDADE DO SÊMEN CAPRINO ARMAZENADO A 5°C POR 24 HORAS UTILIZANDO DUAS CONCENTRAÇÕES DE GEMA DE OVO NO DILUENTE

The objective of this study was to evaluate by in vitro tests and in vivo fertility, two concentrations of egg yolk (T1 = 20% or T2 = 2.5%) in egg yolk-citrate semen extender for storing goat semen at 5°C for 24 hours. Ninety semen collections were performed in four goats. The semen was split and diluted in two different semen extenders and stored in refrigerator at 5°C for 24 hours, until the semen evaluation and insemination procedures. The average values for cooled semen, respectively, for T1 and T2 were motility, 68.5 ± 15.4 and 78.0 ± 5.5 (p < 0.05); vigor, 2.5 ± 0.6 and 3.2 ± 0.3 (p < 0.05), supravital test, 59.4 ± 17.2 and 71.1 ± 10.5 (p < 0.05) and hypoosmotic test, 42.2 ± 15.7 and 56.2 ± 11.5 (p < 0.05). The fertility rate was greater (p < 0.05) in T1 (31.3%) than in T2 (66.7%) and the prolificacy did not differ (p < 0.05) between T1 (1.3 ± 0.5) and T2 (1.4 ± 0.5). In conclusion, the egg yolk-citrate extender with a low concentration (2.5%) of egg yolk was more effective in preserving the viability and fertility of goat semen stored at 5°C for 24 hours. KEYWORDS : artificial insemination; extender; goat; semen; spermatozoa.
A Universal Error Correction Method for Memristive Stateful Logic Devices for Practical Near‐Memory Computing

Memristive stateful logic allows complete in‐memory computing and is considered to be a next‐generation computing technology for low power edge applications. Since the first stateful IMP gate was proposed in 2010, few studies have yet addressed the operating reliability issues that should be resolved before the technology is practically realized. Herein, a feasible near‐memory error correction method for a typical bipolar‐type memristor stateful logic system is proposed. An error correction principles using a HfO2‐based crossbar array device is explained, and two types of error correction methods checking if the number of FALSE data is zero and if the number of TRUE data is odd are proposed. Although the error correction modules require additional circuits and processing time, the resulting computing efficiency is comparable with conventional stateful logic techniques. Its application with a one‐bit full adder is demonstrated and its feasibility for practical stateful logic devices is validated.
Modeling Previous Trial Effect in Human Manipulation through Iterative Learning Control

In the execution of repetitive tasks, humans can capitalize on experience to improve their motor performance. Prominent examples of this ability can be recognized in our capacity of grasping and manipulating in uncertain conditions. With the aim of providing a mathematical description for such behavior, experiments are considered where participants are required to lift an object with an unexpected mass distribution. By repeating multiple times the same lifting action, participants can learn the correct motor command for task accomplishment. Three models are proposed that combine reactive terms and a learned anticipatory action to explain experimental data. The models feature intratrial and intertrial memory, and the effect of slowly and fast adaptive sensory receptors. The architectures’ effectiveness in explaining experimental data is compared with a general‐purpose state of the art model. The proposed algorithms conspicuously outperform the state of the art in all the considered validation routines. Global and within‐trial human behavior is predicted with 88% of accuracy in nominal conditions. When the object's center of mass is moved, the accuracy is maintained up to 83%. Finally, convergence properties of proposed algorithms are analytically discussed, and their stability and robustness against measurement noise are evaluated in simulation.
Lipopolysaccharide-induced activation of haematopoietic stem cells in vivo

Haematopoietic stem cells (HSCs) are the best-characterised adult stem cells and ensure life-long maintenance of the blood system. Under homeostatic conditions most of the HSCs are found in a quiescent state, but can be activated in response to stress (Wilson et al., 2008). Infection is a major source of natural stress to the haematopoietic system, leading to exhaustion of large amounts of immune cells during the defence against invading pathogens. Reestablishment of homeostasis following infection depends on the replacement of immune cells by haematopoietic progenitors. Interestingly, recent studies have indicated that HSCs themselves can be activated in response to infection (Essers et al., 2009; Sato et al., 2009; Baldridge et al., 2010; Takizawa et al., 2011). However, whether HSCs are able to directly sense the infectious state remains unclear. In this work, we have investigated the in vivo short-term response of HSCs to lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria. Low dose administration of LPS to mice induces a rapid TLR4 dependent proliferation of even the most dormant HSCs, without impairing their long-term repopulating potential. This activation is accompanied by upregulation of stem cell antigen 1 (Sca-1) and dependent on the expression of Sca-1 on HSCs. Both in vitro and in vivo data demonstrate that activation of HSCs via LPS is not a direct effect of LPS on HSCs. Instead, LPS treatment stimulates myeloid cells in the BM, most probably inflammatory monocytes, to produce inflammatory cytokines, which in turn induce the activation of HSCs. Furthermore, our results suggest that the activation of HSCs is mediated by initial cell-cell-interaction of these myeloid cells with HSCs. Using genetic mouse models we show that the activation of HSCs is regulated by combined IFNa, IFNg and TNFa signalling. Moreover, TNFa alone induces a Sca-1 dependent activation of HSCs in vivo, making these cells susceptible to chemotherapy. In addition to IFN and TNFa signalling also IL-1b signalling is necessary to mediate the LPS-induced activation of HSCs. Interestingly, IL-1b itself leads to increased proliferation of HSCs, most likely through direct activation of IL-1 signalling in these cells. Thus, our work provides novel cellular and genetic insights into the identity of LPS induced cytokine production, leading to HSC activation. Thus, providing a way to rapidly induce the production of mature immune cells upon infection, leading to a fast restoration of homeostasis upon bacterial infections. Furthermore, our work provides new insights into the role of the pro-inflammatory cytokines TNFa and IL-1b in the regulation of HSC function.
A furin/MMP-14 proteolytic cascade generates Vasculostatin-40 from extracellular BAI1: Implications for angiogenesis and tumorigenesis

A furin/MMP-14 proteolytic cascade generates Vasculostatin-40 from extracellular BAI1: Implications for angiogenesis and tumorigenesis By Sarah M. Cork, B.S. Vascular integrity or function is compromised in many neurological diseases, underscoring the importance of elucidating fundamental mechanisms of brain angioregulation. Notably, the exuberant vascular proliferation of glioblastoma multiforme (GBM), the most common brain malignancy in adults, significantly contributes to its rapid, aggressive growth and dismal prognosis. Improved understanding of brain-specific angiogenesis may thus prove a source of therapeutic potential for GBM, and the seventransmembrane receptor Brain angiogenesis inhibitor 1 (BAI1) presents a promising target for such investigation. A potent anti-tumor agent in in vivo models, we show that expression of BAI1 is reduced in human gliomas in proportion to tumor severity, and higher levels of BAI1 are significantly associated with prolonged survival in astrocytoma but not GBM patients. While the forces driving BAI1 loss in gliomas are incompletely understood, BAI1 mRNA expression is inversely correlated with levels of pathological GBM vasculature, implicating an anti-angiogenic mechanism. Previous work has shown that the anti-tumor effect of BAI1 derives from the proteolysis and secretion of its large extracellular domain, named Vasculostatin-120 (Vstat120), a potent angiogenesis inhibitor. Here we show that extracellular BAI1 is proteolytically cleaved to generate an abundant 40-kilodalton product named Vasculostatin-40 (Vstat40), and identify the site of processing. We demonstrate that cleavage of Vstat40 from BAI1 depends on a two-step process of activation. In the final step of the cascade, Vstat40 is directly processed from extracellular BAI1 by matrix metalloproteinase 14 (MMP-14), and this proteolytic event is greatly facilitated by the upstream activity of proprotein convertases, particularly furin. Vstat40 is observed to inhibit endothelial cell migration and cord formation in a CD36-dependent manner, and interferes with vascularization in vivo. While expression of Vstat40 in an LN229-derived inducible orthotopic xenograft mouse model does not significantly increase subject survival, tumors expressing Vstat40 show significantly inhibited vascularization as well as altered tumor cell morphology and reduced levels of apoptosis markers. Taken together, these findings represent an important advance in our understanding of BAI1 as both a therapeutic molecule and a receptor with diverse roles in neurobiology.
Nuclear exclusion of TET1 is associated with loss of 5-hydroxymethylcytosine in IDH1 wildtype gliomas

IDH1 mutations are associated with a CpG island methylator phenotype in glioblastomas. Cells harboring IDH1 mutations produce 2-hydroxyglutarate inhibiting TET enzymes involved in the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Glioma tissues and cell lines were investigated by RT-PCR, immunohistochemistry and pyrosequencing for the expression of TET enzymes, 5hmC content and IDH1 status respectively. 61% of gliomas revealed no immunoreactivity for 5-hmC and no correlation was observed between IDH1 mutations and loss of 5hmC. The subcellular localization of TET1 showed remarkable differences. IDH1 mutations were significantly correlated with nuclear accumulation of TET1. 70% of 5-hmC negative gliomas showed either exclusive or dominant cytoplasmic expression of TET1 suggesting that its nuclear exclusion may influence the 5hmC content of cells.
Identification and characterization of multiple Spidroin 1 genes encoding major ampullate silk proteins in Nephila clavipes

Spider dragline silk is primarily composed of proteins called major ampullate spidroins (MaSps) that consist of a large repeat array flanked by nonrepetitive N‐ and C‐terminal domains. Until recently, there has been little evidence for more than one gene encoding each of the two major spidroin silk proteins, MaSp1 and MaSp2. Here, we report the deduced N‐terminal domain sequences for two distinct MaSp1 genes from Nephila clavipes (MaSp1A and MaSp1B) and for MaSp2. All three MaSp genes are co‐expressed in the major ampullate gland. A search of the GenBank database also revealed two distinct MaSp1 C‐terminal domain sequences. Sequencing confirmed that both MaSp1 genes are present in all seven Nephila clavipes spiders examined. The presence of nucleotide polymorphisms in these genes confirmed that MaSp1A and MaSp1B are distinct genetic loci and not merely alleles of the same gene. We experimentally determined the transcription start sites for all three MaSp genes and established preliminary pairing between the two MaSp1 N‐ and C‐terminal domains. Phylogenetic analysis of these new sequences and other published MaSp N‐ and C‐terminal domain sequences illustrated that duplications of MaSp genes may be widespread among spider species.
Optimization of Fermentation Conditions of Microbial Enzymatic Synthesis of L-cysteine

Pseudomonas sp.TS1138 was used as the test strain to produce L-cysteine,and microbial enzymatic synthesis of L-cysteine was studied.In the medium optimization,it was found that glucose and urea were the best carbon and nitrogen source for enzyme production,respectively.Effect of DL-ATC on enzyme production was carried out,and the experimental result showed that a initial concentration of 5 g/L DL-ATC was found to be optimal for enzyme production.Effect of inoculum size,initial pH and liquid volume on enzyme production were investigated.The results indicated that the optimum inoculum size was 10%,and the optimum initial pH was 8.0,and the optimum liquid volume was 40 mL culture medium in a 500 mL shaking flask.
Plumage coloration, differential attraction of vectors and haematozoa infections in birds

1. Haematozoa (blood parasites) infect the majority of passerine bird species, yet there is considerable variation among species in the prevalence of infections. The ecological and evolutionary causes and consequences of this variation are not well understood. 2. Tests of Hamilton & Zuk's hypothesis on parasites and sexual selection using haematozoa and 'plumage brightness' have produced mixed results. Debates about how to interpret these results and construct further tests have considered properties of the parasites and hosts, yet have virtually ignored the vectors of the parasites. 3. Many of the Diptera that transmit haematozoa show similar patterns of differential attraction to particular colours. Thus, variation among avian species in prevalence of haematozoa may result from some plumage colours attracting more parasite vectors. 4. Using a comparative analysis that controlled for potentially confounding effects of phylogeny and variables already demonstrated to be correlated with plumage and parasite variation, we tested this vector-attraction hypothesis, but did not find the predicted positive relationship between plumage colours that attract vectors and haematozoa infections. 5. Further analysis of the parasite data, however, revealed a problem for species-wide explanations of haematozoa parasitism. Relative haematozoa prevalence in the same species sampled at different locations was not strongly correlated. This result suggests that any species-wide explanations for variation in haematozoa parasites are, at best, extremely difficult to test, and, at worst, untenable.
Recombinant expression and immuno-screening for vaccine candidates in Plasmodium falciparum

Plasmodium faiciparum is the major cause of human malaria morbidity and mortality. Despite considerable research efforts, no effective vaccine against P.falciparum malaria is yet available. There is thus urgent need for basic pre-clinical and clinical research on vaccine development. To obtain antigens in suitable state for initiating vaccine prototype development it will be necessary to scale up production, in optimal expression systems, of recombinant proteins that are correctly folded and which induce appropriate antibody responses. In the intra-erythrocytic parasite, only mature forms can adhere to the host endothelial surfaces and thus sequester in different organs. This sequestration appears to be mediated by parasite-encoded molecules exported to the erythrocyte surface. The best understood, and probably the most important of these molecules is the P. falciparum erythrocyte membrane protein-i PfEMP-l. Although PfEMP-1 is highly polymorphic it nevertheless has structurally conserved features and these are considered possible vaccine targets. Antibodies directed to these molecules could protect patients from the clinical symptoms by blocking cytoadhesion. Humans make antibody responses to these molecules and particularly agglutinating antibody responses to PfEMP1 have been shown to correlate with the development of acquired immunity in endemic areas. The main aim of this study was to develop a fast and efficient way of expressing P. faiciparum antigenic epitopes as conformationally conserved antigenic structures whose expression can be readily 'scaled-up' for clinical testing. The E. coil and P. pastoris systems were used, both singly and as linked production systems using 'shuttle vectors' that can be dually expressed in both microorganisms. Initially a proof-of-principle experiment to express the CIDR1 domain of PfEMP1 has been conducted. It was expressed and purified in good quantity and used to immunize rabbits. Polyclonal antibodies from rabbit were then assessed with immunoblotting, ELISA studies and immuno-fluorescence. The sequenced 3D7 P. falciparum genome was then exploited to construct degenerate primers for several domains of PfEMP1 (namely DBLa, P and ny). These primers were used to amplify targets from FCR3CSA parasites. PCR products were then ligated into the dual expression vector
Microbial Sterility of the Intestinal Content of the Immature Honey Bee, Apis mellifera,,

White (1921) stated that the intestinal content of freshly emerged honey bees, Apis mellifera L. , was microbially sterile. However, he gave no data to support this conclusion. Kluge (1963) attributed this sterility to the antibiotic properties of larval food. Moreover, when she liberated young bees from their cells shortly before emergence and placed them in a sterile environment, they were microbially sterile for the remainder of their lives. Haisig and Kamburov (1966) found yeasts and molds in a small percentage of larvae which were at least 3 days old. However, Lotmar (1946) stated that prior to emergence the entire intestinal tract of bees was sterile, but her observations were based solely on histological examination of the alimentary tract.
MOLECULAR PHYLOGENY OF CALCAREOUS SPONGES USING 18S RRNA AND 28S RRNA SEQUENCES

In a recently published work, the phylogeny of Calcispongia was investigated using 18S rRNA data and morphological characters, supporting the monophyly of Calcispongia and their subdivision into Calcaronea and Calcinea, and proposing parsimony-based evolutionary scenarios for a few morphological characters. In a search for a better understanding of body plan evolution in Calcispongia, especially regarding symmetries and the organization of the aquiferous system, the present study analyzes a new dataset of 28S rRNA sequences, alone and in combination with the 18S rRNA data. Independent analyses of the two datasets provide corroboration of the monophyly of Calcispongia, Calcinea and Calcaronea, and of several clades within Calcaronea. The combined analyses of 18S and 28S rRNA provide a better resolution of the phylogeny which leads us to refine hypotheses of morphological character evolution. The asconoid aquiferous system would be primitive for the Calcispongia, with independent acquisitions of the syconoid and leuconoid types within Calcinea and Calcaronea. There is confirmation of the primitive nature of axial symmetry in Calcispongia, with two independent inferred losses, within Calcinea and Calcaronea.
Isolation and partial characterization of a low molecular weight antimicrobial protein from coconut (Cocos nucifera L.) milk.

A low molecular weight protein from coconut (Cocos nucifera L.) milk was extracted using phosphate buffer solution pH 7.6, ammonium sulfate precipitation, and dialysis. The insoluble fraction had higher protein concentration (22.39 μg/mL) than the soluble fraction (9.95 μg/ mL) and the electrophoretic profile on SDS-PAGE also showed that the low molecular weight proteins were concentrated in the insoluble fraction. The fraction containing the low molecular weight proteins were purified using DEAE-Cellulose ion-exchange chromatography followed by gel filtration chromatography using Sephadex G-75. The isolated protein has an estimated molecular weight of 19kDa using the electrophoretic mobility on SDS-PAGE and on the elution parameter by gel filtration chromatography. The low molecular weight protein showed antimicrobial properties against food spoilage yeasts, Debaryomyces hansenii and Candida albicans.