Miracle-dz/UniFAR-FTUs huggingface dataset:
Purification and Characterization of Exo-β-d-Glucosaminidase from a Cellulolytic Fungus,Trichoderma reesei PC-3-7

ABSTRACT Chitosan-degrading activities induced by glucosamine (GlcN) orN-acetylglucosamine (GlcNAc) were found in a culture filtrate of Trichoderma reesei PC-3-7. One of the chitosan-degrading enzymes was purified to homogeneity by precipitation with ammonium sulfate followed by anion-exchange and hydrophobic-interaction chromatographies. The enzyme was monomeric, and its molecular mass was 93 kDa. The optimum pH and temperature of the enzyme were 4.0 and 50°C, respectively. The activity was stable in the pH range 6.0 to 9.0 and at a temperature below 50°C. Reaction product analysis from the viscosimetric assay and thin-layer chromatography and 1H nuclear magnetic resonance spectroscopy clearly indicated that the enzyme was an exo-type chitosanase, exo-β-d-glucosaminidase, that releases GlcN from the nonreducing end of the chitosan chain. 1H nuclear magnetic resonance spectroscopy also showed that the exo-β-d-glucosaminidase produced a β-form of GlcN, demonstrating that the enzyme is a retaining glycanase. Time-dependent liberation of the reducing sugar from partially acetylated chitosan with exo-β-d-glucosaminidase and the partially purified exo-β-d-N-acetylglucosaminidase from T. reesei PC-3-7 suggested that the exo-β-d-glucosaminidase cleaves the glycosidic link of either GlcN-β(1→4)-GlcN or GlcN-β(1→4)-GlcNAc.
Reproductive toxicity of butylated triphenyl phosphate and tricresyl phosphate fluids in F344 rats.

The effects of tricresyl phosphate (TCP) and butylated triphenyl phosphate (BTP)-based hydraulic fluid on reproduction were studied in F344 rats using a modification of the National Toxicology Program's Continuous Breeding Protocol. Groups of breeding pairs received single daily oral doses of an equal volume of either 0, 0.6, 1.0 g BTP/kg or 0.4 TCP/kg in sesame oil or 1.7 g neat BTP/kg for up to 135 days. A naive control group allowed to breed, but not dosed or handled daily, demonstrated that daily dosing and handling of the rats had no effect on reproduction. The fertility index and number of litters born were significantly decreased in rats exposed to 1.0 and 1.7 g BTP/kg and 0.4 g TCP/kg. The number of pups per litter was significantly decreased in the TCP group. A crossover mating experiment using 0.4 g TCP/kg/day and 1.0 g BTP/kg/day groups, each mated with vehicle controls, demonstrated that TCP caused 100% infertility in male rats but did not affect reproduction in females. BTP caused a significant decline in reproduction in female rats characterized by low mating and fertility indices, decreased number of litters, and abnormal estrous cycles. Fertility was decreased in the BTP-dosed male rats. Both sexes of rats in the crossover experiment with TCP and BTP had significant decreases in terminal body weights and increases in adrenal gland and liver weights. Only TCP-dosed male rats had significantly decreased testicular and epididymal weights. (ABSTRACT TRUNCATED AT 250 WORDS)
Maturity-Onset Diabetes of the Young Due to a Mutation in the Hepatocyte Nuclear Factor-4α Binding Site in the Promoter of the Hepatocyte Nuclear Factor-1α Gene

Recent studies have shown that mutations in the transcription factor hepatocyte nuclear factor (HNF)-1α are the cause of one form of maturity-onset diabetes of the young (MODY3). These studies have identified mutations in the mRNA and protein coding regions of this gene that result in the synthesis of an abnormal mRNA or protein. Here, we report an Italian family in which an A→C substitution at nucleotide -58 of the promoter region of the HNF-1α gene cosegregates with MODY. This mutation is located in a highly conserved region of the promoter and disrupts the binding site for the transcription factor HNF-4α, mutations in the gene encoding HNF-4α being another cause of MODY (MODY1). This result demonstrates that decreased levels of HNF-1α per se can cause MODY. Moreover, it indicates that both the promoter and coding regions of the HNF-1α gene should be screened for mutations in subjects thought to have MODY because of mutations in this gene.
Virtual Resectoscope Interface for a Surgery Simulation Training System of the Prostate

In this work is presented the current state of the development of a virtual resectocope interface for a surgery simulation system for training Transurethral Resection of the Prostate (TURP). The interface consists of two parts, the (cid:2)rst part is a mechatronics device that emulates a real resectosope and allows to perform the most important movements of the surgical tool during a TURP. The second part is a software interface that consist on a collision detection mechanism that allows to calculate in real-time the interactions between the mechatronic device and the deformable tissue model of the prostate, in order to simulate tissue resection and deformation. The current prototype has (cid:2)ve degrees of freedom, which are enough to have a realistic simulation of the surgery movements. The results show that the interface is suitable for a real-time surgery simulation training system of the prostate without force feedback.
SEED DISPERSAL AND THE HOLOCENE MIGRATION OF WOODLAND HERBS

The distribution of many woodland herbs extends 1000-2000 km in a north- south direction, yet the majority of these species grow clonally, have little recruitment by seed, and possess no obvious mechanism for long-distance seed dispersal. Although aware that woodland herbs disperse poorly, ecologists have tacitly assumed that, given long periods of time, even small dispersal distances would allow woodland herbs to colonize the vast geographic region they now occupy. We examined this assumption for the understory herb Asarum canadense. To estimate long-term rates of spread by seed, we calibrated seed- dispersal diffusion models with life history data and with data on seed carries by ants. We supplemented our field observations and modeling results forA. canadensewith a literature survey on the dispersal capabilities of other plant species. Ants transported A. canadense seeds up to 35 m, the largest distance ants are known to move the seeds of any woodland herb. Empirically calibrated diffusion models indicated that over the last 16 000 yr A. canadense should only have traveled 10-11 km from its glacial refugia. In actuality, A. canadense moved hundreds of kilometers during this time. Models that examined the tail of A. canadense's seed-dispersal curve indicated that oc- casional dispersal events had to have a high frequency ($0.001 on a per seed basis) and a large magnitude (dispersal distance .1 km) for A. canadense to have traveled over 200 km in 16 000 yr. The literature survey showed that most woodland herbs and many other forest, desert, coastal, and open-habitat plant species have limited seed-dispersal capabil- ities, similar to those in A. canadense. We conclude that woodland herbs, as well as many other plants, disperse so slowly that there is no documented mechanism by which most of these species could have reached their present geographical range since the last glacial maximum. This suggests that occasional events leading to long-distance dispersal dominate the Holocene colonization of northern temperate forest by woodland herbs, and this, in turn, has implications for issues ranging from the importance of genetic analyses to the structure of metapopulation models.
The role of the influenza virus RNA polymerase in host shut-off

Viruses induce an antiviral host response by activating the expression of antiviral host genes. However, viruses have evolved a wide range of strategies to counteract antiviral host responses. One of the strategies used by many viruses is the general inhibition of host gene expression, also referred to as a host shut-off mechanism. Here we discuss our recent findings that influenza virus infection results in the inhibition and degradation of host RNA polymerase II (Pol II) and that the viral RNA polymerase plays a critical role in this process. In particular, we found that Pol II is ubiquitylated in influenza virus infected cells and ubiquitylation can be induced by the expression of the RNA polymerase. Moreover, the expression of an antiviral host gene could be inhibited by the over-expression of the RNA polymerase. Both ubiquitylation and the inhibition of the host gene were dependent on the ability of the RNA polymerase to bind to Pol II. Further studies will be required to understand the interplay between the host and viral transcriptional machineries and to elucidate the exact molecular mechanisms that lead to the inhibition and degradation of Pol II as a result of viral RNA polymerase binding. These findings extend our understanding of how influenza virus counteracts antiviral host responses and underpin studies into the mechanisms by which the RNA polymerase determines virulence.
Solitary excitations in discrete two-dimensional nonlinear Schrodinger models with dispersive dipole-dipole interactions

The dynamics of discrete two-dimensional nonlinear Schrodinger models with long-range dispersive inter- actions is investigated. In particular, we focus on the cases where the dispersion arises from a dipole-dipole interaction, assuming the dipole moments at each lattice site to be aligned either in the lattice plane ~anisotropic case! or perpendicular to the lattice plane ~isotropic case! We investigate the nature of the linear dispersion relation for these two cases, and derive a criterion for the modulational instability of a plane wave with respect to long-wavelength perturbations. Furthermore, we study the on-site localized stationary states of the system numerically and analytically using a variational approach. In general, the narrow, intrinsically localized states are found to be stable, while broad, ''continuumlike'' excitations are unstable and may either collapse into intrinsically localized modes or disperse when a small perturbation is applied. @S0163-1829~98! 02318-2#
Silver impregnation of whole retinas.

Although much has been learned about the basic structure of the retina through the use of histoanalytic methods such as silver impregnation (Golgi, 1 Cajal 2 ) or methylene blue (Dogiel 3 ), a great deal of work has yet to be done in order to clarify the connections and physiology of its elements. This has been confirmed by recent studies that demonstrate the occurrence of several types of glia (Wolter 4 ) and of exogenous fibers in the retina (Ventura and Mathieu 5 ). Most of the histologic investigations on intraretinal connections have been performed on sectioned specimens, which frequently do not give a clear idea of the extent of these cellular relations. Methylene blue staining of whole-mount retinas has produced good results in the hands of some authors but is unsuitable for studying the fine terminations of cellular processes. This is also true for the Golgi method, 6 which, owing to the
Fibre-based functional meat products

Epidemiological studies have demonstrated a relationship between a diet containing an excess of energy-dense food rich in fats and sugar and the emergence of a range of chronic diseases, including colon cancer, obesity, cardiovascular diseases and several other disorders [12, 49, 9, 77, 13, 14]. As the presence of fibre in food produces a diminution in their caloric content, thus, an increase in the level of dietary fibre in the daily diet has been recommended [32, 47, 13). Studies have proven that dietary fibres have the potential to reduce blood low density lipoprotein cholesterol [18], risk of diabetes mellitus type 2 [94], coronary heart disease [7], blood pressure [87], obesity [56] and colorectal cancer [79]. Fibre is suitable for addition to meat products and has previously been used in cooked meat products to increase the cooking yield due to its water-binding and fat-binding properties and to improve texture [23, 13, 15]. Fibre from various types of sources like vegetables, legumes, cereal byproducts, fruit, etc. have been studied alone or combined with other ingredients for formulations of reduced-fat-high-fibre meat products, largely ground and restructured products [28, 57] and meat emulsions [22, 21, 40, 53, 55, 15]. This paper reviews and discusses some of the findings published in recent years regarding fibre-based functional meat products.
Three-Dimensional Pareto-Optimal Design of Inductive Superconducting Fault Current Limiters

The inductive-type superconducting fault current limiters (LSFCLs) mainly consist of a primary copper coil, a secondary complete or partial superconductor cylinder, and a closed or open magnetic iron core. Satisfactory performance of such device significantly depends on optimal selection of its employed materials and construction dimensions, as well as its electrical, thermal, and magnetic parameters. Therefore, it is very important to identify a comprehensive model describing the LSFCL behavior in a power system prior to its fabrication. When a fault occurs, the dynamic model should essentially characterize the overall phenomena to compare the simulation results by varying LSFCL parameters to maximize the merits of a fault current limiter while minimizing its drawbacks during the normal state. The principle object of this paper is to achieve a feasible and full penetrative approach in 3-D alignments, i.e., a Pareto-optimal design of LSFCLs by means of multicriteria decision-making techniques after defining the LSFCL model in a power system CAD/electromagnetic transients including dc environment.
A deep learning approach to fingerprinting indoor localization solutions

Fingerprinting Localization Solutions (FPSs) enjoy huge popularity due to their good performance and minimal environment information requirement. Considered as a data-driven approach, many modern data analytics can be used to improve its performance. In this paper, we propose tow learning algorithms, namely a deep learning architecture for regression and Support Vector Machine (SVM) for classification, to output the estimated location directly from the measured fingerprints. The design issues of the proposed neural network is discussed including the training algorithm, regularization and hyperparameter selection. It is discussed how data augmentation methods can be utilized to extend the measurements. The deep learning approach can be used to save the data collection time significantly using a pre-trained model. Moreover the run-time complexity is significantly reduced. The numerical analysis show that in some case, only 10 percent of original training database is enough to get acceptable performance on a pre-trained model.
Circularization of Tn916 is required for expression of the transposon‐encoded transfer functions: characterization of long tetracycline‐inducible transcripts reading through the attachment site

A detailed transcriptional analysis of the conjugative transposon Tn916 was carried out, which revealed that transcription of the transfer functions requires excision of the element and dramatically increases in the presence of tetracycline. The key components of this regulatory system are two contiguous transposon‐borne genes, orf7 and orf8, located downstream from and having the same polarity of transcription as the tetracycline resistance determinant tetM. The gene orf7 encodes a 140‐amino‐acid (aa) protein exhibiting limited homology with σF of Bacillus subtilis, whereas orf8 encodes a 76‐aa peptide that does not share any sequence homology with any cognate proteins. In the presence of tetracycline, an attenuation mechanism enables the transcription of orf7 and orf8 from the tetM promoter. The resulting increased synthesis of ORF7 and ORF8 activates the promoter Porf7 located upstream from orf7, which then directs the expression of the transfer functions in the transposon circular intermediate through long transcripts encompassing the attachment site. The apparently non‐regulated promoter Pxis located upstream of the excisionase encoding gene xis could also participate in the expression of the tra genes. We also demonstrate that Tn916 carries another regulated promoter, Porf9, which directs transcription of a single gene, orf9, located downstream from and transcribed counterclockwise to tetM. This gene encodes a 117‐aa putative transcriptional repressor, but the exact role of this protein in the mobility of Tn916, as well as the regulation of its expression, remains to be elucidated. Our results constitute the molecular basis for the observation that tetracycline increased the transfer frequency of this type of element.
Toward a Better Understanding of Information Technology Organization: A Comparative Case Study

The role of information technology (IT) has changed from being merely a tool for processing transactions to a weapon that can affect an organization's competitive position. Because of this change, previous organizational structures for IT groups ma no longer be adequate. Organizational theorists have shown that the appropriate structure is influenced by the organization's external environment and strategy. The study contributes toward a better understanding of IT organization by exploring the relationship between the organizational structure of IT groups and the effectiveness of IT support in two companies with similar IT environments. Specifically, the study uses: (1) qualitative analysis to examine IT organizational structure in two very similar companies; (2) quantitative analysis to determine which company has more effective IT support; and (3) an expert panel to identify those difference sin IT organizational structure that appear to facilitate effective IT support. Several propositions from these findings are presented and discussed.
Ethanol metabolism alters major histocompatibility complex class I–restricted antigen presentation in liver cells

The proteasome is a major enzyme that cleaves proteins for antigen presentation. Cleaved peptides traffic to the cell surface, where they are presented in the context of major histocompatibility complex (MHC) class I. Recognition of these complexes by cytotoxic T lymphocytes is crucial for elimination of cells bearing “nonself” proteins. Our previous studies revealed that ethanol suppresses proteasome function in ethanol‐metabolizing liver cells. We hypothesized that proteasome suppression reduces the hydrolysis of antigenic peptides, thereby decreasing the presentation of the peptide MHC class I complexes on the cell surface. To test this we used the mouse hepatocyte cell line (CYP2E1/ADH‐transfected HepB5 cells) or primary mouse hepatocytes, both derived from livers of C57Bl/6 mice, which present the ovalbumin peptide, SIINFEKL, complexed with H2Kb. To induce H2Kb expression, HepB5 cells were treated with interferon gamma (IFNγ) and then exposed to ethanol. In these cells, ethanol metabolism decreased not only proteasome activity, but also hydrolysis of the C‐extended peptide, SIINFEKL‐TE, and the presentation of SIINFEKL‐H2Kb complexes measured after the delivery of SIINFEKL‐TE to cytoplasm. The suppressive effects of ethanol were, in part, attributed to ethanol‐elicited impairment of IFNγ signaling. However, in primary hepatocytes, even in the absence of IFNγ, we observed a similar decline in proteasome activity and antigen presentation after ethanol exposure. Conclusion: Proteasome function is directly suppressed by ethanol metabolism and indirectly by preventing the activating effects of IFNγ. Ethanol‐elicited reduction in proteasome activity contributes to the suppression of SIINFEKL‐H2Kb presentation on the surface of liver cells. (HEPATOLOGY 2009.)
Apprentissage de sphères maximales d’exclusion avec garanties théoriques

Dans ce papier, nous proposons une methode d'apprentissage automatique avec garanties theoriques pour generer des spheres maximales d'exclusion sur des donnees binaires presentant un fort desequilibre. Notre objectif est d'apprendre un ensemble de spheres locales, centrees sur les exemples de la classe minoritaire, qui excluent les exemples de la classe majoritaire. Notre contribution est double : 1) le probleme est aborde comme un probleme d'apprentissage de metrique et 2) nous demontrons des resultats de stabilite uniforme sur le rayon et la metrique apprise par notre algorithme. Nos experiences sur des jeux de donnees reelles montrent l'interet de notre approche.
Constraints on polyploid evolution: a test of the minority cytotype exclusion principle

Polyploid evolution is often considered a mechanism of instant speciation; yet the establishment of rare tetraploids within diploid populations may be constrained by a frequency–dependent mating disadvantage (minority cytotype exclusion principle). I tested this hypothesis using experimental populations of Chamerion angustifolium (Onagraceae) that contained different proportions of tetraploids and diploids. Fitness, measured as total seed production over the entire flowering season, was calculated from a census of flower number and estimates of ovule number per flower and proportion of seed set per fruit. The fitness of tetraploids relative to diploids was frequency dependent, increasing from 0.4, when tetraploids were rare, to 0.7 when at 50% and 1.15 when they were in the majority (67%). This pattern exists because of a negative relationship between tetraploid frequency and seed set per fruit in diploids. Seed set in tetraploids was independent of cytotype frequency. The frequency–independent effect in tetraploids reflects higher assortative mating, partly because of non–random patterns of bee visitation. Bees visited a disproportionately high number of diploid inflorescences; however, the proportion of successive flights between tetraploids increased above random expectations as the frequency of tetraploids decreased. These results provide the first experimental test of frequency–dependent fitness in diploid–polyploid mixtures and suggest an important role for more gradual, population processes governing the evolution of polyploidy in natural populations.
Comparative in vitro Activity of Three Fluoroquinolones against Clinical Isolates by E Test

The in vitro susceptibility of levofloxacin, ciprofloxacin and moxifloxacin against several gram-positive and gram-negative clinical isolates was tested by E test. We found that the MIC50 and MIC90 values against all members of the Enterobacteriaceae family except Serratia were <0.5 mg/l for ciprofloxacin and levofloxacin (MIC range 0.006–32 mg/l) based on the in vitro susceptibility data. The susceptibility rates for ciprofloxacin and levofloxacin were more than 85% for Escherichia coli, Citrobacter, Enterobacter cloacae, Enterobacter aerogenes and Klebsiella pneumoniae, although Serratia and Acinetobacter exhibited more or less similar susceptibility rates (about 80%). Pseudomonas aeruginosa demonstrated significant resistance to fluoroquinolones (MIC90 >32 mg/l) and decreased bactericidal rates (<65%) to levofloxacin and ciprofloxacin. Respiratory pathogens such as Streptococcus pneumoniae and Haemophilus influenzae were highly susceptible (100%) to levofloxacin and moxifloxacin. The ineffectiveness of fluoroquinolones for treating coagulase-positive Staphylococcus aureus was demonstrated by poor in vitro susceptibility rates with levofloxacin (52%) and moxifloxacin (57%). Coagulase-negative staphylococci demonstrated significantly decreased bactericidal rates to levofloxacin (21%), while the in vitro susceptibility to moxifloxacin was higher (66%) than that to levofloxacin. We propose that the beneficial effect of inclusion of any of these three fluoroquinolones in treating Enterococcus infections is marginal, as demonstrated by significantly reduced susceptibility rates (<32%). These data demonstrate the utility of fluoroquinoles to treat several gram-negative bacterial infections (with the exception of Acinetobacter and P. aeruginosa), as well as S. pneumoniae and H. influenzae.