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  1. Book ; Online: C-AllOut

    Silva, Guilherme D. F. / Akoglu, Leman / Cordeiro, Robson L. F.

    Catching & Calling Outliers by Type

    2021  

    Abstract: ... within a context, e.g., a particularly short basketball player; and (c) collective outliers are isolated micro ... This paper presents C-AllOut: a novel and effective outlier detector that annotates outliers by type. It is ... needed. We show that C-AllOut achieves on par or significantly better performance than state-of-the-art ...

    Abstract Given an unlabeled dataset, wherein we have access only to pairwise similarities (or distances), how can we effectively (1) detect outliers, and (2) annotate/tag the outliers by type? Outlier detection has a large literature, yet we find a key gap in the field: to our knowledge, no existing work addresses the outlier annotation problem. Outliers are broadly classified into 3 types, representing distinct patterns that could be valuable to analysts: (a) global outliers are severe yet isolate cases that do not repeat, e.g., a data collection error; (b) local outliers diverge from their peers within a context, e.g., a particularly short basketball player; and (c) collective outliers are isolated micro-clusters that may indicate coalition or repetitions, e.g., frauds that exploit the same loophole. This paper presents C-AllOut: a novel and effective outlier detector that annotates outliers by type. It is parameter-free and scalable, besides working only with pairwise similarities (or distances) when it is needed. We show that C-AllOut achieves on par or significantly better performance than state-of-the-art detectors when spotting outliers regardless of their type. It is also highly effective in annotating outliers of particular types, a task that none of the baselines can perform.

    Comment: 9+4 pages, 3 figures, 11 tables
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
    Subject code 006
    Publishing date 2021-10-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: An Efficient Floating-Point Bit-Blasting API for Verifying C Programs

    Gadelha, Mikhail R. / Cordeiro, Lucas C. / Nicole, Denis A.

    2020  

    Abstract: ... of-the-shelf SMT solvers during the verification of several C programs. The new floating-point API is part ... of the SMT backend in ESBMC, a state-of-the-art bounded model checker for C and C++. For the evaluation ...

    Abstract We describe a new SMT bit-blasting API for floating-points and evaluate it using different out-of-the-shelf SMT solvers during the verification of several C programs. The new floating-point API is part of the SMT backend in ESBMC, a state-of-the-art bounded model checker for C and C++. For the evaluation, we compared our floating-point API against the native floating-point APIs in Z3 and MathSAT. We show that Boolector, when using floating-point API, outperforms the solvers with native support for floating-points, correctly verifying more programs in less time. Experimental results also show that our floating-point API implemented in ESBMC is on par with other state-of-the-art software verifiers. Furthermore, when verifying programs with floating-point arithmetic, our new floating-point API produced no wrong answers.

    Comment: 20 pages
    Keywords Computer Science - Logic in Computer Science ; Computer Science - Software Engineering
    Publishing date 2020-04-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Safety of Etanercept in the treatment of rheumatic disease patients with Hepatitis C virus infection.

    Teixeira, Lídia / Fonseca, Cristina / Sousa, Sandra / Vinagre, Filipe / Cordeiro, Ana / Gonçalves, Pedro / Santos, Maria José / Canas da Silva, José

    Acta reumatologica portuguesa

    2018  Volume 43, Issue 2, Page(s) 159–160

    Abstract: Hepatitis C virus (HCV) infection is a major public health problem. Because Tumour Necrosis Factor ... with a TNFi, etanercept (ETN), for a period ranging from 4 months to 4 years without hepatitis C treatment and ...

    Title translation Safety of Etanercept in the treatment of rheumatic disease patients with Hepatitis C virus infection.
    Abstract Hepatitis C virus (HCV) infection is a major public health problem. Because Tumour Necrosis Factor (TNF) seems to have an important role in immune response to HCV infection, suppression by TNFi (TNF inhibitors) may pose a potential worsening of chronic HCV infection. We report our experience with 3 cases of patients with chronic HCV infection and advanced liver disease, with different Rheumatic diseases, treated with a TNFi, etanercept (ETN), for a period ranging from 4 months to 4 years without hepatitis C treatment and, in two of them, concomitant therapy with direct-acting antiviral agents (DAA) and afterwards. Although increasing number of clinical reports support the short-term safety and efficacy of TNFi in patients with HCV, some uncertainties remain regarding long-term. These cases suggests that the risk of HCV reactivation related to TNFi remains low even without concomitant antiviral therapy. Nevertheless, a strict collaboration between rheumatologists and gastroenterologists/hepatologists. Our results also showed a good tolerance and efficacy when used concomitantly the new direct-acting antivirals drugs with ETN.
    MeSH term(s) Antirheumatic Agents/adverse effects ; Antirheumatic Agents/therapeutic use ; Etanercept/adverse effects ; Etanercept/therapeutic use ; Female ; Hepatitis C, Chronic/complications ; Humans ; Male ; Middle Aged ; Rheumatic Diseases/complications ; Rheumatic Diseases/drug therapy
    Chemical Substances Antirheumatic Agents ; Etanercept (OP401G7OJC)
    Language English
    Publishing date 2018-09-27
    Publishing country Portugal
    Document type Case Reports ; Journal Article
    ZDB-ID 442031-7
    ISSN 0303-464X
    ISSN 0303-464X
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Structural Insights into the Intrinsically Disordered GPCR C-Terminal Region, Major Actor in Arrestin-GPCR Interaction.

    Guillien, Myriam / Mouhand, Assia / Fournet, Aurélie / Gontier, Amandine / Martí Navia, Aleix / Cordeiro, Tiago N / Allemand, Frédéric / Thureau, Aurélien / Banères, Jean-Louis / Bernadó, Pau / Sibille, Nathalie

    Biomolecules

    2022  Volume 12, Issue 5

    Abstract: ... to the structural impact of GPCR C-terminal disordered regions. Here, we used an integrated biophysical strategy ... to describe the basal conformations of the C-terminal domains of three class A GPCRs, the vasopressin V2 ... structure conformational preferences in the C-terminal regions of GPCRs could be a central feature ...

    Abstract Arrestin-dependent pathways are a central component of G protein-coupled receptor (GPCRs) signaling. However, the molecular processes regulating arrestin binding are to be further illuminated, in particular with regard to the structural impact of GPCR C-terminal disordered regions. Here, we used an integrated biophysical strategy to describe the basal conformations of the C-terminal domains of three class A GPCRs, the vasopressin V2 receptor (V2R), the growth hormone secretagogue or ghrelin receptor type 1a (GHSR) and the β2-adernergic receptor (β2AR). By doing so, we revealed the presence of transient secondary structures in these regions that are potentially involved in the interaction with arrestin. These secondary structure elements differ from those described in the literature in interaction with arrestin. This suggests a mechanism where the secondary structure conformational preferences in the C-terminal regions of GPCRs could be a central feature for optimizing arrestins recognition.
    MeSH term(s) Arrestin/metabolism ; Arrestins/metabolism ; Protein Structure, Secondary ; Receptors, G-Protein-Coupled/metabolism
    Chemical Substances Arrestin ; Arrestins ; Receptors, G-Protein-Coupled
    Language English
    Publishing date 2022-04-21
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom12050617
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Guanosine Prevents against Glutamatergic Excitotoxicity in C. elegans.

    da Silveira, Tássia Limana / Machado, Marina Lopes / Arantes, Leticia Priscilla / Zamberlan, Daniele Coradini / Cordeiro, Larissa Marafiga / Obetine, Fabiane Bicca Baptista / da Silva, Aline Franzen / Tassi, Cintia Letícia / Soares, Felix Alexandre Antunes

    Neuroscience

    2019  Volume 414, Page(s) 265–272

    Abstract: ... in mammals. However, GUO action in Caenorhabditis elegans, as well as on C. elegans glutamatergic ... that C. elegans strains are useful models to study new compounds that could be used in glutamate ...

    Abstract Glutamatergic neurotransmission is present in most mammalian excitatory synapses and plays a key role in central nervous system homeostasis. When over-activated, it can induce excitotoxicity, which is present in several neuropathologies. The nucleoside guanosine (GUO) is a guanine-based purine known to have neuroprotective effects by modulating glutamatergic system during glutamate excitotoxicity in mammals. However, GUO action in Caenorhabditis elegans, as well as on C. elegans glutamatergic excitotoxicity model, is not known. The GUO effects on behavioral parameters in Wild Type (WT) and knockouts worms for glutamate transporters (GLT-3, GLT-1), glutamate vesicular transporter (EAT-4), and NMDA and non-NMDA receptors were used to evaluate the GUO modulatory effects. The GUO tested concentrations did not alter the animals' development, but GUO reduced pharyngeal pumps in WT animals in a dose-dependent manner. The same effect was observed in pharyngeal pumps, when the animals were treated with 4 mM of GUO in glr-1, nmr-1 and eat-4, but not in glt-3 and glt-3;glt-1 knockouts. The double mutant glt-3; glt-1 for GluTs had decreased body bends and an increased number of reversions. This effect was reverted after treatment with GUO. Furthermore, GUO did not alter the sensory response in worms with altered glutamatergic signaling. Thus, GUO seems to modulate the worm's glutamatergic system in situations of exacerbated glutamatergic signaling, which are represented by knockout strains to glutamate transporters. However, in WT animals, GUO appears to reinforce glutamatergic signaling in specific neurons. Our findings indicate that C. elegans strains are useful models to study new compounds that could be used in glutamate-associated neurodegenerative diseases.
    MeSH term(s) Animals ; Animals, Genetically Modified ; Behavior, Animal/drug effects ; Caenorhabditis elegans ; Caenorhabditis elegans Proteins/genetics ; Dose-Response Relationship, Drug ; Excitatory Amino Acid Transporter 2/genetics ; Glucose Transporter Type 3/genetics ; Glutamic Acid/metabolism ; Guanosine/pharmacology ; Neurons/drug effects ; Neuroprotective Agents/pharmacology ; Receptors, AMPA/genetics ; Synapses/drug effects ; Synaptic Transmission/drug effects
    Chemical Substances Caenorhabditis elegans Proteins ; Excitatory Amino Acid Transporter 2 ; Glucose Transporter Type 3 ; Neuroprotective Agents ; Receptors, AMPA ; glr-1 protein, C elegans ; Guanosine (12133JR80S) ; Glutamic Acid (3KX376GY7L)
    Language English
    Publishing date 2019-07-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 196739-3
    ISSN 1873-7544 ; 0306-4522
    ISSN (online) 1873-7544
    ISSN 0306-4522
    DOI 10.1016/j.neuroscience.2019.07.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A time series analysis of detection and mortality of hepatitis C in Brazil, 2008-2018.

    de Brito, Rodrigo José Videres Cordeiro / da Silva, Leonardo Feitosa / Santos, Márcio Bezerra / de Moura, Patrícia Muniz Mendes Freire / de Souza, Carlos Dornels Freire / do Carmo, Rodrigo Feliciano

    BMC infectious diseases

    2022  Volume 22, Issue 1, Page(s) 81

    Abstract: ... hepatitis C virus (HCV) infection by 2030. In Brazil, efforts have been undertaken to achieve this goal; there are ... the time trend of the incidence and mortality of hepatitis C in Brazil during the period from 2008 to 2018 ... of hepatitis C reported between 2008 and 2018, in all regions of Brazil, were included. The indicators were ...

    Abstract Background: The 69th World Health Assembly approved the Global Health Sector Strategy to eliminate hepatitis C virus (HCV) infection by 2030. In Brazil, efforts have been undertaken to achieve this goal; there are, however, great challenges. It is important to understand the disease profile in different regions of the country in order to design strategies to fight the disease nationwide. The objective of this study was to analyse the time trend of the incidence and mortality of hepatitis C in Brazil during the period from 2008 to 2018 according to sociodemographic and clinical characteristics.
    Methods: All newly diagnosed cases of hepatitis C reported between 2008 and 2018, in all regions of Brazil, were included. The indicators were obtained from the databases of the Brazilian Ministry of Health. For the time series analysis, a joinpoint regression model was used.
    Results: Between 2008 and 2018, 136,759 newly diagnosed cases of hepatitis C were reported considering anti-HCV and HCV RNA positivity, and 271,624 newly diagnosed cases were reported considering one or another positive test. The majority of the records were concentrated in the Southeast (61%) and South (26.2%) Regions. The joinpoint regression model indicated an increasing trend in the detection rate of hepatitis C in Brazil, but there was a decreasing trend in the mortality rate during the period analysed.
    Conclusions: Differences were observed in the time trend of hepatitis C and in the sociodemographic and clinical characteristics in different regions of Brazil. These data can provide support to design strategies for the elimination of hepatitis C in Brazil, according to regional particularities.
    MeSH term(s) Brazil/epidemiology ; Hepacivirus/genetics ; Hepatitis C/diagnosis ; Hepatitis C/epidemiology ; Humans ; Incidence ; Time Factors
    Language English
    Publishing date 2022-01-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-022-07063-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: Finding Software Vulnerabilities in Open-Source C Projects via Bounded Model Checking

    de Sousa, Janislley Oliveira / de Farias, Bruno Carvalho / da Silva, Thales Araujo / Filho, Eddie Batista de Lima / Cordeiro, Lucas C.

    2023  

    Abstract: ... popular open-source C projects, where we have found real software vulnerabilities that their developers ...

    Abstract Computer-based systems have solved several domain problems, including industrial, military, education, and wearable. Nevertheless, such arrangements need high-quality software to guarantee security and safety as both are mandatory for modern software products. We advocate that bounded model-checking techniques can efficiently detect vulnerabilities in general software systems. However, such an approach struggles to scale up and verify extensive code bases. Consequently, we have developed and evaluated a methodology to verify large software systems using a state-of-the-art bounded model checker. In particular, we pre-process input source-code files and guide the respective model checker to explore them systematically. Moreover, the proposed scheme includes a function-wise prioritization strategy, which readily provides results for code entities according to a scale of importance. Experimental results using a real implementation of the proposed methodology show that it can efficiently verify large software systems. Besides, it presented low peak memory allocation when executed. We have evaluated our approach by verifying twelve popular open-source C projects, where we have found real software vulnerabilities that their developers confirmed.

    Comment: 27 pages, submitted to STTT journal
    Keywords Computer Science - Cryptography and Security ; Computer Science - Software Engineering
    Subject code 005
    Publishing date 2023-11-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans

    Kevin I Manage / Alicia K Rogers / Dylan C Wallis / Celja J Uebel / Dorian C Anderson / Dieu An H Nguyen / Katerina Arca / Kristen C Brown / Ricardo J Cordeiro Rodrigues / Bruno FM de Albuquerque / René F Ketting / Taiowa A Montgomery / Carolyn Marie Phillips

    eLife, Vol

    2020  Volume 9

    Abstract: piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA- ... ...

    Abstract piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex.
    Keywords piRNAs ; siRNAs ; germline ; RNA silencing ; germ granules ; nuage ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Liver expression of IL-22, IL-22R1 and IL-22BP in patients with chronic hepatitis C with different fibrosis stages.

    de Brito, Rodrigo José Videres Cordeiro / do Carmo, Rodrigo Feliciano / Silva, Bruna Manuella Souza / Costa, Ana Clara Santos / Rocha, Sura Wanessa Santos / Vasconcelos, Luydson Richardson Silva / Pereira, Leila Maria Moreira Beltrão / de Moura, Patrícia Muniz Mendes Freire

    Cytokine

    2021  Volume 150, Page(s) 155784

    Abstract: ... with chronic hepatitis C.: Methods and results: The number of IL-22-producing cells was significantly higher ... in the mechanisms of liver fibrosis in patients with chronic hepatitis C. ...

    Abstract Aims: Liver fibrosis is the result of an exacerbated wound-healing response associated with chronic liver injury. Interleukin-22 (IL-22) plays a key role in liver disease, through either a protective or an adverse role, depending on the context. The relationship between IL-22 and its receptors IL-22R1 and IL-22BP (soluble inhibitor) in liver fibrosis is unknown. In this study, we assessed the presence and quantity of IL-22, IL-22R1, and IL-22BP-producing cells in liver tissues of patients with chronic hepatitis C.
    Methods and results: The number of IL-22-producing cells was significantly higher in stages F1, F2, and F3 when compared to F0 or F4 (p < 0.05). The immunostaining of IL-22R1 decreased as liver fibrosis increased from F1 to F4. On the other hand, the concentration of IL-22BP-producing cells was higher in patients with cirrhosis (F4). Furthermore, the IL-22BP:IL-22 ratio was highest in patients with cirrhosis.
    Conclusions: Our results suggest that IL-22, IL-22R1 and IL-22BP may be involved in the mechanisms of liver fibrosis in patients with chronic hepatitis C.
    MeSH term(s) Hepatitis C, Chronic/complications ; Humans ; Interleukins ; Liver ; Liver Cirrhosis/complications ; Receptors, Interleukin ; Interleukin-22
    Chemical Substances Interleukins ; Receptors, Interleukin ; interleukin-22 receptor
    Language English
    Publishing date 2021-12-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1018055-2
    ISSN 1096-0023 ; 1043-4666
    ISSN (online) 1096-0023
    ISSN 1043-4666
    DOI 10.1016/j.cyto.2021.155784
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Trabeculectomy with mitomycin C alone or coupled with intracamerular bevacizumab? A 2-year comparative study.

    José, Patrícia / Teixeira, Filipa Jorge / Barão, Rafael / Sousa, David Cordeiro / Marques, Raquel Esteves / Barata, Andre Diogo De Oliveira / Marques-Neves, Carlos / Alves, Marta / Papoila, Ana Luísa / Stalmans, Ingeborg / Silva, José Pedro / Abegão Pinto, Luis

    The British journal of ophthalmology

    2021  Volume 106, Issue 10, Page(s) 1399–1405

    Abstract: Purpose: To compare outcomes of primary trabeculectomy using either mitomycin C (MMC) alone versus ...

    Abstract Purpose: To compare outcomes of primary trabeculectomy using either mitomycin C (MMC) alone versus MMC augmented with intracamerular bevacizumab in patients with open-angle glaucoma.
    Methods: Retrospective, cohort, two-centre, comparative study. Patients' data were screened between October 2015 and March 2019, with inclusion requiring a minimum follow-up of 24 months. Primary outcome was intraocular pressure (IOP) lowering at 24 months, with surgical success defined with different maximum IOP targets (≤18, ≤16 and ≤14 mm Hg) and at least 30% reduction and higher than 5 mm Hg. Absolute success was achieved if no IOP-lowering medication was needed and a qualified success if otherwise. Safety outcomes were analysed.
    Results: A total of 110 eyes underwent trabeculectomy with MMC, 51 of these combined with intracamerular bevacizumab. Both strategies were effective in terms of IOP lowering (baseline vs 2 years postoperatively: 24.4 (8.0) mm Hg vs 12.1 (5.3) mm Hg in the MMC group; 25.1 (8.7) vs 10.8 (3.8) mm Hg in the MMC+bevacizumab group; p<0.001 in both comparisons). The MMC+bevacizumab group had a significant difference towards higher efficacy on absolute success rates at all targets (IOP≤14 or ≤16 or ≤18 mm Hg; p=0.010, p=0.039 and p=0.007, respectively). The large majority (93%) of the MMC+bevacizumab group was drop-free at 24 months, and 41% had IOP below 10 mm Hg. Complication rates were low and similar between groups, with no systemic adverse events.
    Conclusions: Intracamerular bevacizumab in MMC-augmented primary trabeculectomy increases the chances of obtaining low IOP outcomes. This strategy may be useful when planning for surgeries aiming at target pressures in the low teens.
    Trial registration number: ISRCTN93098069.
    MeSH term(s) Adolescent ; Angiogenesis Inhibitors/therapeutic use ; Bevacizumab/therapeutic use ; Follow-Up Studies ; Glaucoma, Open-Angle/drug therapy ; Glaucoma, Open-Angle/surgery ; Humans ; Intraocular Pressure ; Mitomycin/therapeutic use ; Retrospective Studies ; Trabeculectomy ; Treatment Outcome ; Vascular Endothelial Growth Factor A
    Chemical Substances Angiogenesis Inhibitors ; Vascular Endothelial Growth Factor A ; Bevacizumab (2S9ZZM9Q9V) ; Mitomycin (50SG953SK6)
    Language English
    Publishing date 2021-04-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 80078-8
    ISSN 1468-2079 ; 0007-1161
    ISSN (online) 1468-2079
    ISSN 0007-1161
    DOI 10.1136/bjophthalmol-2021-319039
    Database MEDical Literature Analysis and Retrieval System OnLINE

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