Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial susceptibility testing of Mycobacterium tuberculosis (EUCAST document E.DEF 8.1)--report of the Subcommittee on Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis of the European Committee for Antimicrobial Susceptibility Testing (EUCAST) of the European Society of Clin

This review describes the methods available for drug susceptibility testing of Mycobacterium tuberculosis. The methods have been developed over several decades and are restricted to specialised centres in most European countries, as they are technically demanding, require appropriate isolation facilities and can be difficult to interpret. The absolute concentration, resistance ratio and proportion methods can all give accurate results, provided that they are carefully quality-controlled and standardised. Automated rapid culture and molecular methods have been evaluated at large reference centres and in multicentre collaborations, and perform well for testing susceptibility to most first- and second-line anti-tuberculosis drugs. Accuracy is more important than rapid testing, and this is most reliably achieved if drug susceptibility tests are done in a small number of well-equipped, experienced laboratories that participate and perform well in an international drug susceptibility testing quality assessment scheme. The WHO Supranational Laboratory Quality Control Network offers a global scheme that assesses the ability of participating laboratories to identify isoniazid, rifampicin, ethambutol and streptomycin resistance. Second-line drug resistance testing is currently being standardised, and such testing should only be performed at the national reference laboratories in western and central European countries because of the relatively small number of cases and the concomitant difficulty of maintaining testing proficiency in multiple centres performing small numbers of tests. There is a need to expand international external quality assessment to include second-line drug susceptibility testing.
Cel9D, an Atypical 1,4-β-d-Glucan Glucohydrolase from Fibrobacter succinogenes: Characteristics, Catalytic Residues, and Synergistic Interactions with Other Cellulases

ABSTRACT The increasing demands of renewable energy have led to the critical emphasis on novel enzymes to enhance cellulose biodegradation for biomass conversion. To identify new cellulases in the ruminal bacterium Fibrobacter succinogenes, a cell extract of cellulose-grown cells was separated by ion-exchange chromatography and cellulases were located by zymogram analysis and identified by peptide mass fingerprinting. An atypical family 9 glycoside hydrolase (GH9), Cel9D, with less than 20% identity to typical GH9 cellulases, was identified. Purified recombinant Cel9D enhanced the production of reducing sugar from acid swollen cellulose (ASC) and Avicel by 1.5- to 4-fold when mixed separately with each of four other glucanases, although it had low activity on these substrates. Cel9D degraded ASC and cellodextrins with a degree of polymerization higher than 2 to glucose with no apparent endoglucanase activity, and its activity was restricted to β-1→4-linked glucose residues. It catalyzed the hydrolysis of cellulose by an inverting mode of reaction, releasing glucose from the nonreducing end. Unlike many GH9 cellulases, calcium ions were not required for its function. Cel9D had increased k cat /K m values for cello-oligosaccharides with higher degrees of polymerization. The k cat /K m value for cellohexaose was 2,300 times higher than that on cellobiose. This result indicates that Cel9D is a 1,4-β-d-glucan glucohydrolase (EC 3.2.1.74) in the GH9 family. Site-directed mutagenesis of Cel9D identified Asp166 and Glu612 as the candidate catalytic residues, while Ser168, which is not present in typical GH9 cellulases, has a crucial structural role. This enzyme has an important role in crystalline cellulose digestion by releasing glucose from accessible cello-oligosaccharides.
The RFX Protein RfxA Is an Essential Regulator of Growth and Morphogenesis in Penicillium marneffei

ABSTRACT Fungi are small eukaryotes capable of undergoing multiple complex developmental programs. The opportunistic human pathogen Penicillium marneffei is a dimorphic fungus, displaying vegetative (proliferative) multicellular hyphal growth at 25°C and unicellular yeast growth at 37°C. P. marneffei also undergoes asexual development into differentiated multicellular conidiophores bearing uninucleate spores. These morphogenetic processes require regulated changes in cell polarity establishment, cell cycle dynamics, and nuclear migration. The RFX (regulatory factor X) proteins are a family of transcriptional regulators in eukaryotes. We sought to determine how the sole P. marneffei RFX protein, RfxA, contributes to the regulation of morphogenesis. Attempts to generate a haploid rfxA deletion strain were unsuccessful, but we did isolate an rfxA+/rfxAΔ heterozygous diploid strain. The role of RfxA was assessed using conditional overexpression, RNA interference (RNAi), and the production of dominant interfering alleles. Reduced RfxA function resulted in defective mitoses during growth at 25°C and 37°C. This was also observed for the heterozygous diploid strain during growth at 37°C. In contrast, overexpression of rfxA caused growth arrest during conidial germination. The data show that rfxA must be precisely regulated for appropriate nuclear division and to maintain genome integrity. Perturbations in rfxA expression also caused defects in cellular proliferation and differentiation. The data suggest a role for RfxA in linking cellular division with morphogenesis, particularly during conidiation and yeast growth, where the uninucleate state of these cell types necessitates coupling of nuclear and cellular division tighter than that observed during multinucleate hyphal growth.
Analysis of Mycobacterium Species for the Presence of a Macrolide Toxin, Mycolactone

ABSTRACT Mycobacterium ulcerans is an environmental organism which is responsible for the disease Buruli ulcer, a necrotizing skin disease emerging in west Africa. M. ulcerans produces the polyketide-derived macrolide mycolactone, which is required for the immunosuppression and tissue damage which characterizes Buruli ulcer. We have extracted lipids from the cell envelope and culture filtrate from 52 isolates of Mycobacterium species, analyzed them with thin-layer chromatography, and tested them in a murine fibroblast cell line (L929) cytotoxicity assay to investigate whether these mycobacterial species produce mycolactone. For these studies chloroform-methanol (2:1, vol/vol) extracts were prepared from representative fast- and slow-growing mycobacterial species. Isolates tested included 16 uncharacterized, slow-growing, environmental mycobacterial species isolated from areas in which M. ulcerans infection is endemic. Although several strains of mycobacteria studied produced cytopathic lipids, none of these produced a phenotype on cultured cells consistent with that produced by mycolactone. Two mycobacterial species, M. scrofulaceum and M. kansasii, and eight of the environmental mycobacterial isolates contained cell-associated lipids cytopathic to fibroblasts at concentrations of 33 to 1,000 μg/ml. In contrast, mycolactone produces cytotoxicity at less than 2 ng/ml. Analysis of 16S rRNA sequences from the eight environmental isolates suggests that these are novel mycobacterial species. Results from these studies suggest that, although production of cytopathic lipids is relatively common among mycobacterial species, the production of mycolactone as a cell-associated or secreted molecule appears so far to be restricted to M. ulcerans.
Herpes Simplex Virus Type 1 Latency-Associated Transcript Gene Promotes Neuronal Survival

ABSTRACT A complex interaction has evolved between the host's peripheral nervous system (PNS) and herpes simplex virus type 1 (HSV-1). Sensory neurons are permissive for viral replication, yet the virus can also enter a latent state in these cells. The interplay of viral and neuronal signals that regulate the switch between the viral lytic and latent states is not understood. The latency-associated transcript (LAT) regulates the establishment of the latent state and is required for >65% of the latent infections established by HSV-1 (R. L. Thompson and N. M. Sawtell, J. Virol. 71:5432–5440, 1997). To further investigate how LAT functions, a 1.9-kb deletion that includes the entire LAT promoter and 827 bp of the 5′ end of the primary LAT mRNA was introduced into strain 17syn+. The wild-type parent, three independently derived deletion mutants, and two independently derived genomically rescued variants of the mutants were analyzed in a mouse ocular model. The number of latent sites established in trigeminal ganglion (TG) neurons was determined using a single-cell quantitative PCR assay for the viral genome on purified TG neurons. It was found that the LAT null mutants established ∼75% fewer latent infections than the number established by the parental strain or rescued variant. The reduced establishment phenotype of LAT null mutants was due at least in part to a dramatic increase in the loss of TG neurons in animals infected with the LAT mutants. Over half of the neurons in the TG were destroyed following infection with the LAT mutants, and this was significantly more than were lost following infection with wild type. This is the first demonstration that the HSV LAT locus prevents the destruction of sensory neurons. The death of these neurons did not appear to be the result of increased apoptosis as measured by a terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling assay. Animals latently infected with the LAT null mutants reactivated less frequently in vivo and this was consistent with the reduction in the number of neurons in which latency was established. Thus, one function of the LAT gene is to protect sensory neurons and enhance the establishment of latency in the PNS.
VEGF levels in diagnosis of vasculitic neuropathy.

BACKGROUND Vascular endothelial growth factor (VEGF) is secreted from endothelial cells and pericytes in response to hypoxia. It induces angiogenesis and microvascular hyperpermeability. We observe serum VEGF concentrations in some patients with vasculitic neuropathy. METHODS Plasma VEGF was measured using GenWay's human VEGF ELISA Kit, which is based on standard sandwich enzyme-linked immune-sorbent assay technology. Human VEGF specific-specific monoclonal antibodies are precoated onto 96-well plates. The human specific detection polyclonal antibodies are biotinylated. The test samples and biotinylated detection antibodies were added to the wells subsequently and then followed by washing with PBS or TBS buffer. Avidin-Biotin-Peroxidase Complex was added and unbound conjugates were washed away with PBS or TBS buffer. HRP substrate TMB was used to visualize HRP enzymatic reaction. The VEGF levels were measured in 5 patients with vasculitic neuropathy and 8 healthy controls. RESULTS Plasma VEGF was higher in subjects with vasculitic neuropathy as compared to controls. In the control group, we obtained VEGF levels from 9.8 pg/mL up to 15 pg/mL with an average of 11.6 pg/mL for males and 8.9 pg/mL up to 14.5 pg/mL with average of 11.2 pg/mL for females. In female patients with vasculitic neuropathy the plasma VEGF levels were between 79.9 pg/mL and 111.2 pg/mL, with an average of 92.375 pg/mL. We had one case with vasculitic neuropathy in men, in which the plasma VEGF level was 102.9 pg/mL. CONCLUSIONS The results from our study indicate that plasma VEGF levels are significantly associated with vasculitic neuropathy and may be used to predict this disease.
Prévisions d'ensemble à l'échelle saisonnière : mise en place d'une dynamique stochastique

La prevision d'ensemble a l'echelle saisonniere avec des modeles de circulation generale a connu un essor certain au cours des vingt dernieres annees avec la croissance exponentielle des capacites de calcul, l'amelioration de la resolution des modeles, et l'introduction progressive dans ceux-ci des differentes composantes (ocean, atmosphere, surfaces continentales et glace de mer) regissant l'evolution du climat a cette echelle. Malgre ces efforts, prevoir la temperature et les precipitations de la saison a venir reste delicat, non seulement sur les latitudes temperees mais aussi sur des regions sujettes a des aleas climatiques forts comme l'Afrique de l'ouest pendant la saison de mousson. L'une des cles d'une bonne prevision est la prise en compte des incertitudes liees a la formulation des modeles (resolution, parametrisations, approximations et erreurs). Une methode eprouvee est l'approche multi-modele consistant a regrouper les membres de plusieurs modeles couples en un seul ensemble de grande taille. Cette approche a ete mise en œuvre notamment dans le cadre du projet europeen ENSEMBLES, et nous montrons qu'elle permet generalement d'ameliorer les retro-previsions saisonnieres des precipitations sur plusieurs regions d'Afrique par rapport aux modeles pris individuellement. On se propose dans le cadre de cette these d'etudier une autre piste de prise en compte des incertitudes du modele couple CNRM-CM5, consistant a ajouter des perturbations stochastiques de la dynamique du modele d'atmosphere ARPEGE-Climat. Cette methode, baptisee “dynamique stochastique”, consiste a introduire des perturbations additives de temperature, humidite specifique et vorticite corrigeant des estimations d'erreur de tendance initiale du modele. Dans cette these, deux methodes d'estimation des erreurs de tendance initiale ont ete etudiees, basees sur la methode de nudging (guidage) du modele vers des donnees de reference. Elles donnent des resultats contrastes en termes de scores des retro-previsions selon les regions etudiees. Si on estime les corrections d'erreur de tendance initiale par une methode de nudging itere du modele couple vers les reanalyses ERA-Interim, on ameliore significativement les scores sur l'hemisphere Nord en hiver en perturbant les previsions saisonnieres en tirant aleatoirement parmi ces corrections. Cette amelioration est accompagnee d'une nette reduction des biais de la hauteur de geopotentiel a 500 hPa. Une retro-prevision en utilisant des perturbations dites“optimales” correspondant aux corrections d'erreurs de tendance initiale du mois en cours de prevision montre l'existence d'une information a l'echelle mensuelle qui pourrait permettre de considerablement ameliorer les previsions. La derniere partie de cette these explore l'idee d'un conditionnement des perturbations en fonction de l'etat du modele en cours de prevision, afin de se rapprocher si possible des ameliorations obtenues avec ces perturbations optimales
Association of tumor necrosis factor-alpha and interleukin-1 gene polymorphisms with silicosis.

Silicosis, an interstitial lung disease prevalent among miners, sand blasters, and quarry workers, is manifested as a chronic inflammatory response leading to severe pulmonary fibrotic changes. Proinflammatory cytokines, such as TNFalpha and IL-1, produced in the lung by type II epithelial cells and alveolar macrophages, have been strongly implicated in the formation of these lesions. Recently, a number of single nucleotide polymorphisms (SNPs), which quantitatively affect mRNA synthesis, have been identified in the TNFalpha promoter and IL-1 gene cluster and their frequency is associated with certain chronic inflammatory diseases. To assess the role of these SNPs in silicosis, we examined their frequency in 325 ex-miners with moderate and severe silicosis and 164 miners with no lung disease. The odds ratio of disease for carriers of the minor variant, TNFalpha (-238), was markedly higher for severe silicosis (4.0) and significantly lower for moderate silicosis (0.52). Regardless of disease severity, the odds ratios of disease for carriers of the IL-1RA (+2018) or TNFalpha (-308) variants were elevated. There were no significant consistent differences in the distribution of the IL-1alpha (+4845) or IL-1beta (+3953) variants with respect to disease status. In addition, several significant gene-gene and gene-gene-environment interactions were observed. Different associations between moderate cases and controls versus severe cases and controls were also observed in a number of these multigene comparisons. These studies suggest that gene-environment interactions involving cytokine polymorphisms play a significant role in silicosis by modifying the extent of and susceptibility to disease.
A Communist Takeover in the Dream Factory — Appropriation of Popular Genres by the East German Film Industry

Abstract During the 1960s the East German state-controlled film studio DEFA drastically increased their production of popular genre films. This development was propelled by the competition from an unrelenting flow of western radio- and television signals transgressing the Berlin Wall. These East German genre films took their iconographical cues from the commercial genres of Western Europe and Hollywood, but filled the forms with appropriate socialist content. In this article I investigate this appropriation of internationally established film genres in the GDR as a point of convergence between the transsystemic discourse of popular culture and the strong isolationist efforts of the GDR state. Through empirically informed close analysis of the musical Heißer Sommer and the western Spur des Falken, I aim to show how these very awkward negotiations between isolation and integration led to a reinvention of the genres in question, and how this process can be traced in the films' narratives.
Hardware implementation for permutation function of multiplication-hardened sponge BlaMka

In the information security field, varions algorithms are applied to provide users with a variety of security services. Although many of the algorithms are implemented in software, there is a rapidly growing demand for hardware implementations. The BlaMka algorithm is a cryptographic sponge algorithm, used in password hashing schemes (PHS) such as Lyra2 and Argon2, which are algorithms that generate a pseudo-random sequence of bits from a particular secret value. BlaMka was proposed as a modification of Blake2b algorithm by including multiplications in some stages of its implementation, specifically in its permutation function, aiming to reduce its performance in hardware platforms. As far as we are concerned, there is no hardware implementation for the BlaMka algorithm. Thus, this work presents a hardware implementation for the permutation function of BlaMka, which is the structure that contains multiplications, with some different architectures to address the trade-off between latency, area and power, besides verifying the impact of the inclusion of multiplications in its performance compared with a hardware implementation for the permutation function of Blake2b. All the circuits presented herein were described using VHDL language and synthesized for ASICs using the tools and the 90nm cell library provided by Synopsys. Combinational and sequential circuits were synthesized covering a range of possible choices taking into account the throughput, and the costs for area and power. The results for throughput ranged from 0.907 Gbps to 2.426 Gbps, area utilization ranged from 14.13 kGE to 52.82 kGE, and power consumption ranged from 0.384 mW to 98.462 mW. The results were compared to an implementation of the permutation function of Blake2b, verifying that the performance decrease is quite marked when multiplications are included in the permutation function.
The natural history of adolescent alcohol use disorders.

AIM To examine clinically relevant research on the development, course and outcomes of adolescence alcohol use disorders (AUDs). METHODS Observational studies with adolescent samples were selected for inclusion based on systematic assessment of AUDs and clinical relevance. The literature was searched using Medline and Psychinfo. Articles on childhood predictors, characteristics, course, complications and adult outcomes of adolescent AUDs were reviewed. RESULTS The developmental trajectory toward adolescent AUDs begins with the emergence of childhood mental disorders. These problems are transmitted from parent to child in a developmentally specific fashion, reflect psychological dysregulation dimensions and predict adolescent AUDs. While most DSM-IV AUD diagnostic criterion items are valid for adolescents, tolerance and impaired control items are problematic, and some adolescents with significant alcohol problems are not identified by this diagnostic system. Understanding the psychosocial and biomedical complications that accompany AUDs requires attention to factors other than alcohol involvement itself, including childhood maltreatment and comorbid psychopathology. While some adolescents with AUDs manifest chronic alcohol dependence in adulthood, a substantial proportion overcome alcohol problems and transition to abstinence or normative drinking. CONCLUSIONS Developmentally specific phenotypic characteristics define the natural history of adolescent AUDs, inform clinical assessment and provide the developmental context for treatment research. While alcohol consumption may be the primary treatment focus, other important consequences, comorbidities and complications need to be addressed for successful developmental outcomes to result.
Expression of P16 protein and Bcl-2 protein in malignant eyelid tumors.

OBJECTIVE To investigate the relationship between P16 gene (the tumor suppressor gene) and the bcl-2 gene (the apoptosis inhibitor gene) and the incidence and development of malignant eyelid tumors. METHODS The streptavidin-biotin-peroxidase complex immunohistochemistry method was used to study the expression of P16 gene and the bcl-2 gene in 96 cases of malignant eyelid tumors. RESULTS Among the 96 cases, there were 40 basal cell carcinomas (BCCs), 33 squamous carcinomas and 23 sebaceous carcinoma, with P16 protein positive (nuclear staining) rates 70%, 54.6% and 56.5%, respectively. The P16 positive rate was negatively correlated with the degree of tumor histological differentiation, and the rate difference between the high differentiated carcinomas was significant (P < 0.05). Positive Bcl-2 protein expression was detected in the cytoplasm. All 40 BCC cases were Bcl-2 positive, and nearly all of the tumor cells showed positive cytoplasmic expression, while in the 33 squamous cell carcinoma cases only one showed positive focal reaction, and the staining in the other 32 cases was relatively faint. None of the 23 sebaceous carcinomas expressed Bcl-2. CONCLUSIONS The expression of the P16 protein was related to the occurrence and degree of differentiation of malignant eyelid tumors. The overexpression of the Bcl-2 protein suggests that suppression of apoptosis might play a role in the tumorigenesis of BCC.
Quality evaluation of government websites

This article describes a study on the quality evaluation of governmental websites of 20 countries with the highest level of competitiveness. The accessibility assessment was carried out to verify compliance with the Web Content Accessibility Guidelines 2.0 (WCAG 2.0) published by the World Wide Web Consortium (W3C). The main goal of this study is to determine whether people with disabilities are able to access and use government websites. In addition, we considered the Website Accessibility Conformance Evaluation Methodology (WCAG-EM) to determine how easily a website can be accessed according to WCAG 2.0. The WCAG-EM provides guidance on how to use the methodology and considerations for specific situations. From the results, we conclude that the majority of the websites do not achieve an acceptable level of compliance. The websites of governmental institutions with the highest level of competitiveness do not show a greater level of web accessibility. Several non-compliance errors were found on the websites; by performing this evaluation, we have identified that there are major barriers for a large number of users. Therefore, there is significant work pending to make the websites examples of best practice in e-government sites.