Miracle-dz/UniFAR-FTUs huggingface dataset:
Différenciation géographique et structure génétique des populations de Solea vulgaris

Des echantillons de solea vulgaris preleves sur une periode de 5 ans en mer egee, mediterranee ouest, golfe de gascogne et manche ont ete analyses a 26 locus enzymatiques et 3 locus proteiques. La diversite globale de l'espece est importante (h#0=0,118) et sa composante inter-regionale est faible (5% de la diversite globale). La faible diversite de l'echantillon de mer egee suggere son passage par un goulot d'etranglement. Une structure geographique a ete mise en evidence par des analyses factorielles des correspondances (afc) bien que l'etude des distances genetiques et des fst revele une tres faible differenciation, ce qui suggere un flux genique important entre regions. En effet, seul l'echantillon de la mer egee se differencie de facon marquee. Des deficits en heterozygotes ont ete observes beaucoup plus frequemment chez les juveniles que chez les adultes et il existe une differenciation a certains locus entre differentes cohortes d'une meme localite. De plus, l'evolution des cohortes o#+ pendant leur sejour estival en nurserie parait non aleatoire. Ces resultats sont difficiles a expliquer sans faire appel (au moins en partie) a des phenomenes de selection
Cytologic evaluation of primary and secondary myelodysplastic syndromes in the dog.

Myelodysplastic syndromes are a heterogeneous group of acquired primary and secondary alterations of hematopoietic stem cells that result in cytopenias in blood and cytologic features of dysplasia in blood and/or bone marrow. To better understand the cytologic features that would permit differentiation of primary and secondary forms of myelodysplasia, we reviewed 267 consecutive bone marrow reports from dogs. These reports indicated that 34 dogs (12.7%) had dysgranulopoiesis, dyserythropoiesis, and/or dysthrombopoiesis in >10% of granulopoietic cells, erythroid cells, and/or megakaryocytes, respectively. Thirteen dogs had primary myelodysplastic syndromes, and 21 had secondary myelodysplastic syndromes. Of the 13 dogs with primary myelodysplasia, 4 were subclassified as myelodysplastic syndrome with refractory anemia (MDS-RA), and 9 were subclassified as myelodysplastic syndrome with excess blasts (MDS-EB). Secondary conditions associated with dysplasia in the bone marrow included malignant lymphoma (n = 5), myelofibrosis (n = 3), immune-mediated thrombocytopenia (n = 4), immune-mediated hemolytic anemia (n = 5), multiple myeloma with melphalan administration (n = 1), pyometra with estrogen administration (n = 1), polycythemia vera (n = 1), and thrombopathia (n = 1). MDS-RA was characterized by <5% myeloblasts in bone marrow, normal granulocyte maturation ratio, increased erythroid maturation ratio, and dysplastic changes in >15% of erythroid cells. MSD-EB was characterized by >/=5% myeloblasts in bone marrow, high granulocyte maturation and erythroid maturation ratios, >/=32% dysplastic granulocytes, and the presence of small atypical immature myeloid cells. Secondary myelodysplastic syndromes were characterized by <5% myeloblasts in bone marrow, variable granulocyte maturation and erythroid maturation ratios, and variable dysplastic features. These results indicate that morphology alone cannot be used to distinguish primary and secondary myelodysplastic syndromes in dogs.
Antidiabetic potential of Citrus sinensis and Punica granatum peel extracts in alloxan treated male mice

An investigation on the effects of four different concentrations of peel extract from Citrus sinensis (CS) or Punica granatum (PG) in male mice revealed the maximum glucose lowering and antiperoxidative activities at 25 mg/kg of CS and 200 mg/kg of PG. In a separate experiment their potential was evaluated with respect to the regulation of alloxan induced diabetes mellitus. While a single dose of alloxan (120 mg/kg) increased the serum levels of glucose and α‐amylase activity, rate of water consumption and lipid peroxidation (LPO) in hepatic, cardiac and renal tissues with a parallel decrease in serum insulin level, administration of 25 mg/kg of CS or 200 mg/kg of PG was found to normalize all the adverse changes induced by alloxan, revealing the antidiabetic and anti peroxidative potential of test fruit peel extracts. Subsequent phytochemical analysis indicated that the high content of total polyphenols in the test peels might be related to the antidiabetic and antiperoxidative effects of the test peels.
BioSM: Metabolomics Tool for Identifying Endogenous Mammalian Biochemical Structures in Chemical Structure Space

The structural identification of unknown biochemical compounds in complex biofluids continues to be a major challenge in metabolomics research. Using LC/MS, there are currently two major options for solving this problem: searching small biochemical databases, which often do not contain the unknown of interest or searching large chemical databases which include large numbers of nonbiochemical compounds. Searching larger chemical databases (larger chemical space) increases the odds of identifying an unknown biochemical compound, but only if nonbiochemical structures can be eliminated from consideration. In this paper we present BioSM; a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSM identifies endogenous mammalian biochemical structures with high accuracy. In a leave-one-out cross validation experiment, BioSM correctly predicted 95% of 1388 Kyoto Encyclopedia of Genes and Genomes (KEGG) compounds as endogenous mammalian biochemicals using 1565 scaffolds. Analysis of two additional biological data sets containing 2330 human metabolites (HMDB) and 2416 plant secondary metabolites (KEGG) resulted in biochemical annotations of 89% and 72% of the compounds, respectively. When a data set of 3895 drugs (DrugBank and USAN) was tested, 48% of these structures were predicted to be biochemical. However, when a set of synthetic chemical compounds (Chembridge and Chemsynthesis databases) were examined, only 29% of the 458,207 structures were predicted to be biochemical. Moreover, BioSM predicted that 34% of 883,199 randomly selected compounds from PubChem were biochemical. We then expanded the scaffold list to 3927 biochemical compounds and reevaluated the above data sets to determine whether scaffold number influenced model performance. Although there were significant improvements in model sensitivity and specificity using the larger scaffold list, the data set comparison results were very similar. These results suggest that additional biochemical scaffolds will not further improve our representation of biochemical structure space and that the model is reasonably robust. BioSM provides a qualitative (yes/no) and quantitative (ranking) method for endogenous mammalian biochemical annotation of chemical space and, thus, will be useful in the identification of unknown biochemical structures in metabolomics. BioSM is freely available at http://metabolomics.pharm. uconn.edu.
Bioinformatical analysis of gene expression signatures of different glioma subtypes

The aim of the present study was to identify the common molecular mechanisms of multiple glioma subtypes, including astrocytoma, glioblastoma and oligodendroglioma, in addition to the specific mechanisms of different types. The gene expression profile set GSE4290 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) from three types of glioma, relative to non-tumor tissue, were calculated by the t-test method with a linear regression model. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs was performed. GeneVenn online analysis software was used for the comparison of the DEGs between subtypes. A total of 795 DEGs, including 619 up and 176 downregulated DEGs were screened from the astrocytoma expression profiles; these were enriched in the KEGG pathways of ‘neuroactive ligand-receptor interaction’ (upregulated) and ‘Wnt signaling pathway’ (downregulated). Protein-protein interaction networks for astrocytoma, glioblastoma and oligodendroglioma were constructed with 1,617, 7,027 and 1,172 pairs, respectively. A total of 595 common DEGs were obtained between the three subtypes, which were enriched in pathways associated with neural signaling. Glioblastoma is a subtype of astrocytoma; there were 195 DEGs common between these subtypes that were not also associated with oligodendroglioma. DEGs unique to astrocytoma, glioblastoma and oligodendroglioma were associated with the development of the nervous system, the cell cycle and cell matrix components, respectively. The screened DEG p53 gene is likely to be critical for glioma development, including via the Wnt and p53 signaling pathways. Brain-derived neurotrophic factor and cyclin-dependent kinase 1 genes were also likely to be important in the mechanism of glioma development, and were associated with the cell cycle and p53 signaling pathways. Immune system-associated and cell matrix component pathways may be unique signaling pathways associated with astrocytoma and oligodendroglioma, respectively.
Stimulation of the subthalamic nucleus compared with the globus pallidus internus in patients with Parkinson disease.

OBJECT The authors compared the effects of deep brain stimulation (DBS) in the globus pallidus internus (GPi) with those in the subthalamic nucleus (STN) in patients with Parkinson disease (PD) in whom electrodes had been bilaterally implanted in both targets. METHODS Eight of 14 patients with advanced PD in whom electrodes had been implanted bilaterally in both the GPi and STN for DBS were selected on the basis of optimal DBS effects and were studied 2 months postsurgery in off- and on-stimulus conditions and after at least 1 month of pharmacological withdrawal. Subcutaneous administration of an apomorphine test dose (0.04 mg/kg) was also performed in both conditions. Compared with the off status, the results showed less reduction in the Unified PD Rating Scale Section III scores during DBS in the GPi (43.1%) than during DBS of the STN (54.5%) or DBS of both the STN and GPi (57.1%). The difference between the effects of DBS in the GPi compared with that in the STN or simultaneous DBS was statistically significant (p < 0.01). In contrast, no statistical difference was found between DBS in the STN and simultaneous DBS in the STN and GPi (p < 0.9). The improvement induced by adding apomorphine administration to DBS was similar in all three stimulus modalities. The abnormal involuntary movements (AIMs) induced by apomorphine were almost abolished by DBS of the GPi, but were not affected by stimulation of the STN. The simultaneous stimulation of STN and GPi produced both antiparkinsonian and anti-AIM effects. CONCLUSIONS The improvement of parkinsonian symptoms during stimulation of the GPi, STN, and both nuclei simultaneously may indicate a similar DBS mechanism for both nuclei in inducing antiparkinsonian effects, although STN is more effective. The antidyskinetic effects produced only by DBS of the GPi, with or without STN, may indicate different mechanisms for the antidyskinetic and antiparkinsonian activity related to DBS of the GPi or an additional mechanism in the GPi. These findings indicate that implantation of double electrodes for DBS should not be proposed as a routine procedure, but could be considered as a possible subsequent choice if electrode implantation for DBS of the STN does not control AIMs.
Investigation of a Capillary-Based Surface Plasmon Resonance Sensor for Biosensing

We report a capillary-based surface plasmon resonance sensor that integrates sample collection, injection, and measurement. The sensor reported here can be fabricated at low cost and possesses a small and robust package. The hollow structure of the capillary not only can be used as a fluid channel but also allows light to travel along a spiral and straight line, which is very helpful for reducing the length of the sensing region. The operation wavelength of the sensor can be tuned with a harmless high-index dielectric layer, which makes it possible to generate a reference signal to correct the effect of changes in the bulk refractive index or temperature. Our experiments show that the sensor can operate at room temperature and is capable of performing label-free detection and real-time monitoring through a single sensing device. Furthermore, similar to needles and insertable probes, the sensor could also potentially be used for minimally invasive medical diagnostics and monitoring. As a biosensor, it will be a practical and specific detection device that can be widely used, such as in biological and life sciences research, and rapid diagnostics.
SERINC5 protein inhibits HIV-1 fusion pore formation by promoting functional inactivation of envelope glycoproteins

The host proteins, SERINC3 and SERINC5, have been recently shown to incorporate into HIV-1 particles and compromise their ability to fuse with target cells, an effect that is antagonized by the viral Nef protein. Envelope (Env) glycoproteins from different HIV-1 isolates exhibit a broad range of sensitivity to SERINC-mediated restriction, and the mechanism by which SERINCs interfere with HIV-1 fusion remains unclear. Here, we show that incorporation of SERINC5 into virions in the absence of Nef inhibits the formation of small fusion pores between viruses and cells. Strikingly, we found that SERINC5 promotes spontaneous functional inactivation of sensitive but not resistant Env glycoproteins. Although SERINC5-Env interaction was not detected by co-immunoprecipitation, incorporation of this protein enhanced the exposure of the conserved gp41 domains and sensitized the virus to neutralizing antibodies and gp41-derived inhibitory peptides. These results imply that SERINC5 restricts HIV-1 fusion at a step prior to small pore formation by selectively inactivating sensitive Env glycoproteins, likely through altering their conformation. The increased HIV-1 sensitivity to anti-gp41 antibodies and peptides suggests that SER5 also delays refolding of the remaining fusion-competent Env trimers.
Security in the Industrial Internet of Things - The C-SEC Approach

A revolutionary development in machine-to-machine communications, the “Internet of Things” (IoT) is often characterized as an evolution of Supervisory Control and Data Acquisition (SCADA) networks. SCADA networks have been used for machine-to-machine communication and controlling automated processes since before the widespread use of the Internet. The adoption of open internet protocols within these systems has created unforeseen security vulnerabilities. In this paper we detail the Cyber-SCADA Evaluation Capability (C-SEC), a US Department of Defense research effort aimed at securing SCADA networks. We also demonstrate how the C-SEC framework could enhance the security posture of the emerging IoT paradigm.
Randomized, double-blind, controlled trial of early endoscopic ultrasound-guided celiac plexus neurolysis to prevent pain progression in patients with newly diagnosed, painful, inoperable pancreatic cancer.

PURPOSE Celiac plexus neurolysis (CPN) is currently used as salvage therapy for morphine-resistant pancreatic cancer pain. Endoscopic ultrasound-guided CPN (EUS-CPN) can be performed early, at the time of EUS. We hypothesized that early EUS-CPN would reduce pain and morphine consumption, increase quality of life (QOL), and prolong survival. PATIENTS AND METHODS Patients were eligible if referred for EUS for suspected pancreatic cancer with related pain. If EUS and EUS-guided fine-needle aspiration cytology confirmed inoperable adenocarcinoma, patients were randomly assigned to early EUS-CPN or conventional pain management. Pain scores (7-point Likert scale), morphine equivalent consumption, and QOL scores (Digestive Disease Questionnaire-15) were assessed at 1 and 3 months. RESULTS Five hundred eighty eligible patients were seen between April 2006 and December 2008. Ninety-six patients were randomly assigned (48 patients per study arm). Pain relief was greater in the EUS-CPN group at 1 month and significantly greater at 3 months (difference in mean percent change in pain score = -28.9 [95% CI, -67.0 to 2.8], P = .09, and -60.7 [95% CI, -86.6 to -25.5], P = .01, respectively). Morphine consumption was similar in both groups at 1 month (difference in mean change in morphine consumption = -1.0 [95% CI, -47.7 to 49.2], P = .99), but tended toward lower consumption at 3 months in the neurolysis group (difference in mean change in morphine consumption = -49.5 [95% CI, -127.5 to 7.0], P = .10). There was no effect on QOL or survival. CONCLUSION Early EUS-CPN reduces pain and may moderate morphine consumption in patients with painful, inoperable pancreatic adenocarcinoma. EUS-CPN can be considered in all such patients at the time of diagnostic and staging EUS.
Legal issues in GNSS applications: Past, today and tomorrow

Essential developments on computer systems and space technologies have given rise to GNSS (Global Navigation Satellite Systems) enter into our daily lives. The positional and navigational advantages provided by GNSS have caused it to be perceived as a basic requirement from the application point of view particularly in developed countries. On the other hand, the applications of GNSS have generally proceeded without taking into consideration legal issues up to now. And this lack of legal issues may cause serious problems for GNSS applications in near future. Because, US GPS (Global Positioning System) has been used as the only global positioning system as open service to all users and thus all the rules were determined and dictated by USA until now. But later on other countries such as Russia, EU, China etc. began to establish their own satellite systems in order to get rid of US GPS dependency only. As a result, currently, there are mainly three global (i.e. GPS, GLONASS and GALILEO) and three regional (QZSS, Beidou/Compass, IRNSS/GAGAN) GNSS service providers in use and thus it seems that legal issues are going to be more important when all these satellite systems become fully operational in space in 2020.
von Willebrand factor in juvenile dermatomyositis.

OBJECTIVE To evaluate whether plasma von Willebrand factor (vWF) levels are a useful indicator of disease activity in juvenile dermatomyositis (DM). METHODS Serum vWF levels were prospectively measured in 15 patients with juvenile DM and were compared to serum muscle enzyme levels, muscle strength, and presence of extramuscular manifestations. RESULTS 6/15 active disease periods were accompanied by an increase in vWF; 9 were not. Elevated vWF levels did not relate to the presence of active skin disease or calcinosis. vWF was not consistently related to muscle strength, CPK, or aldolase in the study group. Two patients had elevations of vWF in association with viral infections while their DM was quiescent. CONCLUSION An elevated vWF level is often indicative of a disease exacerbation in DM, and thus may be helpful in managing difficult cases. However, it is not consistently elevated in, nor specific for active disease in DM. It therefore cannot be recommended as a routine test in patients with DM. When used, results should be interpreted with caution.
Quantification of the spatial distribution of rectally applied surrogates for microbicide and semen in colon with SPECT and magnetic resonance imaging.

AIMS We sought to describe quantitatively the distribution of rectally administered gels and seminal fluid surrogates using novel concentration-distance parameters that could be repeated over time. These methods are needed to develop rationally rectal microbicides to target and prevent HIV infection. METHODS Eight subjects were dosed rectally with radiolabelled and gadolinium-labelled gels to simulate microbicide gel and seminal fluid. Rectal doses were given with and without simulated receptive anal intercourse. Twenty-four hour distribution was assessed with indirect single photon emission computed tomography (SPECT)/computed tomography (CT) and magnetic resonance imaging (MRI), and direct assessment via sigmoidoscopic brushes. Concentration-distance curves were generated using an algorithm for fitting SPECT data in three dimensions. Three novel concentration-distance parameters were defined to describe quantitatively the distribution of radiolabels: maximal distance (D(max) ), distance at maximal concentration (D(Cmax) ) and mean residence distance (D(ave) ). RESULTS The SPECT/CT distribution of microbicide and semen surrogates was similar. Between 1 h and 24 h post dose, the surrogates migrated retrograde in all three parameters (relative to coccygeal level; geometric mean [95% confidence interval]): maximal distance (D(max) ), 10 cm (8.6-12) to 18 cm (13-26), distance at maximal concentration (D(Cmax) ), 3.8 cm (2.7-5.3) to 4.2 cm (2.8-6.3) and mean residence distance (D(ave) ), 4.3 cm (3.5-5.1) to 7.6 cm (5.3-11). Sigmoidoscopy and MRI correlated only roughly with SPECT/CT. CONCLUSIONS Rectal microbicide surrogates migrated retrograde during the 24 h following dosing. Spatial kinetic parameters estimated using three dimensional curve fitting of distribution data should prove useful for evaluating rectal formulations of drugs for HIV prevention and other indications.
The Prokaryotic Origin of the Pathways for Synthesis and Post-Synthetic Modification of Deoxyribonucleic Acid

A previous study showed that in mammals the pathways leading to synthesis and post-synthetic modification of DNA employ methionine as common donor of atoms: the carbon coming from the methyl group of this amino acid is needed for replication; its entire methyl group is needed to build m5C on semiconservatively newly replicating chains. This work showed that the two pathways originate in bacteria where an enzymatic system forms, on DNA, m6A in addition to m5C. The formation rate of m6A gradually decreased during the bacterial CGC, while that of m5C reached an optimum in its middle. This shift suggested that the dcm and dam methyltransferase activities, as well as the activities of the methyltransferase moieties of the RM enzymes, are uncoupled.
Secure & efficient delegation of system of linear equation to a malicious cloud server

Cloud computing offers an economical solution to the computationally weak clients. It enables the client to execute large computations beyond their computation capacity by outsourcing their computation load to the massive cloud servers. However, outsourcing of data and the computation to a third-party cloud server bring many security and privacy concern. In this paper, we are addressing the problem of system of linear equation (LE), which is a basic engineering and scientific problem that has application in various areas. We are employing efficient linear transformation technique using the concepts of linear algebra. The proposed algorithm transform the dataset to some other form to hide the original dataset. The algorithm provides a non-interactive proof of solution therefore, the algorithm executes with an optimal one round of communication. The proposed algorithm also employs an efficient result verification method to perceive deceitful server behavior with an optimal probability, thus preserving the data integrity. The result verification method is very efficient and run with modest overhead. The proposal has been verified through theoretical and experimental analysis to demonstrate the practical usability of the proposed algorithm.
Identification of pathogenic yeast species by polymerase chain reaction amplification of the RPS0 gene intron fragment

Aims: This work focuses on the development of a method for the identification of pathogenic yeast. With this aim, we target the nucleotide sequence of the RPS0 gene of pathogenic yeast species with specific PCR primers. PCR analysis was performed with both the genomic DNA, whole cells of clinical isolates of Candida species and clinical samples.