A Parallel Algorithm for Large-Scale Multiple Sequence Alignment

Multiple sequence alignment is a central topic of extensive research in computational biology. Basically, two or more protein sequences are compared to evaluate their similarity and to identify conserved regions. This work reports a methodology for parallel processing of a multiple sequence alignment algorithm (ClustalW) in an environment of networked computers. A detailed description of the modules that compose the distributed system is provided, giving special attention to the way a dynamic programming algorithm is run in multilevel parallelism. Extensive experiments were done to evaluate performance and scalability of the reported method. Results suggest that the proposed method is very promising for large-scale multiple protein sequence alignment

Fractal Subsystem Symmetries, 't Hooft Anomalies, and UV/IR Mixing

In this work, we study unconventional anisotropic topologically ordered phases in 3d that manifest type-II fractonic physics along sub-manifolds. While they behave as usual topological order along a preferred spatial direction, their physics along perpendicular planes is dictated by the presence of fractal subsystem symmetries, completely restricting the mobility of anyonic excitations and their bound states. We consider an explicit lattice model realization of such phases and proceed to study their properties under periodic boundary conditions and, later, in the presence of boundaries. We find that for specific lattice sizes, the system possesses line and fractal membrane symmetries that are mutually anomalous, resulting in a non-trivially gapped ground state space. This amounts to the spontaneous breaking of the fractal symmetries, implying a sub-extensive ground state degeneracy. For the remaining system sizes the fractal symmetries are explicitly broken by the periodic boundary conditions, which is intrinsically related to the uniqueness of the ground state. Despite of that, the system is still topologically ordered since locally created quasi-particles have nontrivial mutual statistics and, in the presence of boundaries, it still presents anomalous edge modes. The intricate symmetry interplay dictated by the lattice size is a wild manifestation of ultraviolet/infrared (UV/IR) mixing.Comment: 7+7 pages, 5+5 figure

Promotion of mental health literacy and mental well-being in a Portuguese unemployed population sample : effectiveness assessment of a capacity building community-based intersectoral intervention

Copyright © 2017 Published by Elsevier Masson SASIntroduction: Economic crises have consequences on labor market, with impacts on mental health (MH) and psychological well-being (PWB). We describe the effectiveness of an intervention among unemployed, performed within EEA Grants Healthy Employment project.Objectives Evaluate the effectiveness of an intervention for MH literacy, PWB and resilience among unemployed. Aims MH and PWB promotion, common mental disorders prevention and inequalities reduction linked to unemployment.Methods A five modules intervention (life-work balance; impact of unemployment on PWB and MH; stigma; depression and anxiety; health promotion) distributed by 20 hours was developed based on literature reviews and a Delphi panel. It was delivered to unemployees from two public employment centers (PECs).Inclusion criteria: 18–65 years old; registration in PEC for less than a year; minimum of nine years of formal education. Control groups from the same PECs received the care-as-usual. Measures of psychological WB, MH self-reported symptoms, life satisfaction,resilience and mental health literacy were collected through an online survey before and one week after intervention.Results Overall, 87 unemployed participated,48% allocated to the intervention group (IG); 56% women (21–64 years old), average education was 15 years. Mixed measures ANOVA showed that the interaction between time and group was significant for PWB and MH literacy measures. The IG showed better self-reported PWB and improved MH literacy after intervention, compared to controls. No significant interactions were found for MH symptoms, life satisfaction and resilience.Conclusions This study shows the contribution of short-term community-based interventions in increasing MH literacy and PWB among unemployed.info:eu-repo/semantics/publishedVersio

Estudo de Caso do Uso de Linguagens de Script em Jogos

Este artigo introduz o conceito de linguagens de script,apresentando características das linguagens mais usadas. Também apresenta um exemplo de uma aplicação que integra a linguagem de script Ruby e C++, usando um interpretador Ruby embarcado para uso em jogo

Use of threshold electrolyte concentration analysis to determine salinity and sodicity limit of irrigation water

This research studied threshold electrolyte concentration (TEC) of irrigation water and its effect on the infiltration rate of two contrasting soils from Pernambuco state, Brazil. The experiment was conducted in the Soil Chemistry and Salinity Laboratory of Federal Rural University of Pernambuco. Each soil was packed in five Buchner funnels, where one funnel from each soil was submitted to treatment with solution of electrical conductivity (EC) of 0.5, 1.0, 2.0, 4.0 or 8.0 dS m-1. For each funnel containing soil, an increasing ratio of NaCl to CaCl2 was applied in a treatment solution to achieve 10 increasing values of sodium adsorption ratio (SAR) from 0 to 100. These solutions were applied through a Mariotte bottle, with a constant hydraulic head of ~2 cm (pressure potential). After a liter of solution had drained, in the flux was collected for a known time interval, until steady state was reached. Darcy's equation was used to calculate saturated hydraulic conductivity (Ksat) and a mathematical model used to calculate the TEC as a 20% reduction in Ksat. By increasing SAR similar behavior was noted between the two soils, whereby Ksat decreased, although the relative decrease in Ksat was greater for SAR of 100 in the soil with higher clay content

Immune Activation Caused By Vascular Oxidation Promotes Fibrosis And Hypertension

Vascular oxidative injury accompanies many common conditions associated with hypertension. In the present study, we employed mouse models with excessive vascular production of ROS (tg(sm/p22phox) mice, which overexpress the NADPH oxidase subunit p22(phox) smooth muscle, and mice with vascular-specific deletion of extracellular SOD) and have shown that these animals develop vascular collagen deposition, aortic stiffening, renal dysfunction, and hypertension with age. T cells from tg(5m/p22phox) mice produced high levels of IL-17A and IFN-gamma. Crossing tg(sm/p22phox) mice with lymphocyte-deficient Rag1(-/-) mice eliminated vascular inflammation, aortic stiffening, renal dysfunction, and hypertension; however, adoptive transfer of T cells restored these processes. Isoketal-protein adducts, which are immunogenic, were increased in aortas, DCs, and macrophages of tg(sm/P22Phox) mice. Autologous pulsing with tg(sm/p22phox) aortic homogenates promoted DCs of tg(sm/p22phox) mice to stimulate T cell proliferation and production of IFN-gamma, IL-17A, and TNF-alpha. Treatment with the superoxide scavenger tempol or the isoketal scavenger 2-hydroxybenzylamine (2-HOBA) normalized blood pressure; prevented vascular inflammation, aortic stiffening, and hypertension; and prevented DC and T cell activation. Moreover, in human aortas, the aortic content of isoketal adducts correlated with fibrosis and inflammation severity. Together, these results define a pathway linking vascular oxidant stress to immune activation and aortic stiffening and provide insight into the systemic inflammation encountered in common vascular diseases.12615067NIH [DK059637, DK020593]NIH R01 [HL105294, HL039006, HL108701]VITA [HHSN268201400010C]American Heart Association predoctoral fellowship [13PRE14480008]NIH K08 [1K08HL121671]Vanderbilt Physician Scientist Development AwardNIH F32 [1F32HL124972-01][P01 HL58000

L-asparaginase production review: bioprocess design and biochemical characteristics

In the past decades, production of biopharmaceuticals has gained high interest due to its high sensitivity, specificity and lower risk of negative effects to patients. Biopharmaceuticals are mostly therapeutic recombinant proteins produced through biotechnological processes. In this context, L-Asparaginase (L-Asparagine amidohydrolase, L-ASNase (E.C. 3.5.1.1)) is a therapeutic enzyme that has been abundantly studied by researchers due to its antineoplastic properties. As a biopharmaceutical, L-ASNase has been used in the treatment of acute lymphoblastic leukemia (ALL), acute myeloblastic leukemia (AML) and other lymphoid malignancies, in combination with other drugs. Besides its application as a biopharmaceutical, this enzyme is widely used in food processing industries as an acrylamide mitigation agent and as a biosensor for the detection of L-Asparagine in physiological fluids at nano-levels. The great demand for L-ASNase is supplied by recombinant enzymes from Escherichia coli and Erwinia chrysanthemi. However, production processes are associated to low yields and proteins associated to immunogenicity problems, which leads to the search for a better enzyme source. Considering the L-ASNase pharmacological and food importance, this review provides an overview of the current biotechnological developments in L-ASNase production and biochemical characterization aiming to improve the knowledge about its production.publishe

HPLC-DAD analysis, antinociceptive and anti-inflammatory properties of the ethanolic extract of Hyptis umbrosa in mice

Hyptis umbrosa (syn. Mesosphaerum sidifolium) (Lamiaceae Family) has been used to treat several conditions such as gastrointestinal disorders, skin infections, nasal congestion, fever and cramps. The objective of this study was to evaluate the chemical composition, analgesic and anti-inflammatory profiles of ethanol extract from leaves of Hyptis umbrosa (EEB). HPLC-DAD was used to determine the fingerprint chromatogram of the extract. Male Swiss mice were orally pretreated with EEB (100, 200 or 400 mg/kg; 60 min before initiating algesic stimulation) and antinociceptive activity was assessed using the acetic acid-induced writhing model, formalin test and hyperalgesia induced by glutamate or capsaicin. Also, peritonitis was induced by the intrathoracic injection of carrageenan to quantify the total number of leukocytes. The presence of phenolic compounds in the extract was confirmed using HPLC-DAD. The treatment with EEB, at all doses, produced a significant analgesic effect against acetic acid-induced antinociceptive activity. In the formalin test, only the 400-mg/kg-dose of EEB had a significant effect in the first phase. However, all doses tested were able to reverse nociception in the second phase. The effect of all doses of EEB also showed a significant antinociceptive effect in the glutamate and capsaicin tests and inhibited the carrageenan-induced leukocyte migration to the peritoneal cavity. The present study suggests that the EEB possesses peripheral analgesic action and showed potential in reducing the spreading of the inflammatory processes. Also, it seems to be related with vanilloid and glutamate receptors

Stress and psychological health: testing the mediating role of cognitive appraisal

This study tested the mediating role of primary (e.g., threat and challenge perceptions) and secondary (e.g., coping potential and control perception) cognitive appraisal in the relationship between occupational stress and psychological health. This mediation was tested using a cross-sectional study based on self-reported measures. The total sample consisted of 2,302 nurses, 1,895 females (82.3%) and 407 males (17.7%), who completed an evaluation protocol with measures of occupational stress, cognitive appraisal, and psychological health. To test the mediating role of cognitive appraisal in the relationship between cognitive appraisal and psychological health, we used Structural Equation Modeling (SEM). The results confirmed that primary and secondary cognitive appraisals partially mediated the relationship between occupational stress and psychological health; however, the direct effects of stress on psychological health cannot be ignored. The findings indicated that cognitive appraisal is an important underlying mechanism in explaining adaptation at work.This study was conducted at Psychology Research Centre (UID/PSI/01662/2013), University of MInho, and supported by the Portuguese Foundation for Science and Technology and the Portuguese Ministry of Science, Technology and Higher Education through national funds and co-financed by FEDER through COMPETE2020 under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007653)

The Porto European Cancer Research Summit 2021

Key stakeholders from the cancer research continuum met in May 2021 at the European Cancer Research Summit in Porto to discuss priorities and specific action points required for the successful implementation of the European Cancer Mission and Europe's Beating Cancer Plan (EBCP). Speakers presented a unified view about the need to establish high-quality, networked infrastructures to decrease cancer incidence, increase the cure rate, improve patient's survival and quality of life, and deal with research and care inequalities across the European Union (EU). These infrastructures, featuring Comprehensive Cancer Centres (CCCs) as key components, will integrate care, prevention and research across the entire cancer continuum to support the development of personalized/precision cancer medicine in Europe. The three pillars of the recommended European infrastructures – namely translational research, clinical/prevention trials and outcomes research – were pondered at length. Speakers addressing the future needs of translational research focused on the prospects of multiomics assisted preclinical research, progress in Molecular and Digital Pathology, immunotherapy, liquid biopsy and science data. The clinical/prevention trial session presented the requirements for next-generation, multicentric trials entailing unified strategies for patient stratification, imaging, and biospecimen acquisition and storage. The third session highlighted the need for establishing outcomes research infrastructures to cover primary prevention, early detection, clinical effectiveness of innovations, health-related quality-of-life assessment, survivorship research and health economics. An important outcome of the Summit was the presentation of the Porto Declaration, which called for a collective and committed action throughout Europe to develop the cancer research infrastructures indispensable for fostering innovation and decreasing inequalities within and between member states. Moreover, the Summit guidelines will assist decision making in the context of a unique EU-wide cancer initiative that, if expertly implemented, will decrease the cancer death toll and improve the quality of life of those confronted with cancer, and this is carried out at an affordable cost.Where authors are identified as personnel of the International Agency for Research on Cancer/World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer/World Health Organization. JT reports personal financial interest in form of scientific consultancy role for Array Biopharma, AstraZeneca, Avvinity, Bayer, Boehringer Ingelheim, Chugai, DaiichiSankyo, F. Hoffmann‐La Roche Ltd, Genentech Inc, HalioDX SAS, Hutchison MediPharma International, Ikena Oncology, IQVIA, Lilly, Menarini, Merck Serono, Merus, MSD, Mirati, Neophore, Novartis, Orion Biotechnology, Peptomyc, Pfizer, Pierre Fabre, Samsung Bioepis, Sanofi, Seattle Genetics, Servier, Taiho, Tessa Therapeutics and TheraMyc. And also educational collaboration with Imedex, Medscape Education, MJH Life Sciences, PeerView Institute for Medical Education and Physicians Education Resource (PER). JT also declares institutional financial interest in form of financial support for clinical trials or contracted research for Amgen Inc, Array Biopharma Inc, AstraZeneca Pharmaceuticals LP, BeiGene, Boehringer Ingelheim, Bristol Myers Squibb, Celgene, Debiopharm International SA, F. Hoffmann‐La Roche Ltd, Genentech Inc, HalioDX SAS, Hutchison MediPharma International, Janssen‐Cilag SA, MedImmune, Menarini, Merck Health KGAA, Merck Sharp & Dohme, Merus NV, Mirati, Novartis Farmacéutica SA, Pfizer, Pharma Mar, Sanofi Aventis Recherche & Développement, Servier, Taiho Pharma USA Inc, Spanish Association Against Cancer Scientific Foundation and Cancer Research UK. MB has received funding for his research projects and for educational grants to the University of Dresden by Bayer AG (2016‐2018), Merck KGaA (2014‐open) and Medipan GmbH (2014‐2018). He is on the supervisory board of HI‐STEM GmbH (Heidelberg) for the German Cancer Research Center (DKFZ, Heidelberg) and also member of the supervisory body of the Charité University Hospital, Berlin. As former chair of OncoRay (Dresden) and present CEO and Scientific Chair of the German Cancer Research Center (DKFZ, Heidelberg), he has been or is responsible for collaborations with a multitude of companies and institutions, worldwide. In this capacity, he has discussed potential projects and signed contracts for research funding and/or collaborations with industry and academia for his institute(s) and staff, including but not limited to pharmaceutical companies such as Bayer, Boehringer Ingelheim, Bosch, Roche and other companies such as Siemens, IBA, Varian, Elekta, Bruker, etc. In this role, he was/is also responsible for the commercial technology transfer activities of his institute(s), including the creation of start‐ups and licensing. This includes the DKFZ‐PSMA617 related patent portfolio [WO2015055318 (A1), ANTIGEN (PSMA)] and similar IP portfolios. MB confirms that, to the best of his knowledge, none of the above funding sources were involved in the preparation of this paper. BB has received research funding from 4D Pharma, Abbvie, Amgen, Aptitude Health, AstraZeneca, BeiGene, Blueprint Medicines, BMS, Boehringer Ingelheim, Celgene, Cergentis, Cristal Therapeutics, Daiichi‐Sankyo, Eli Lilly, GSK, Inivata, Janssen, Onxeo, OSE immunotherapeutics, Pfizer, Roche‐Genentech, Sanofi, Takeda, Tolero Pharmaceuticals. FC declares consultancy role for: Amgen, Astellas/Medivation, AstraZeneca, Celgene, Daiichi‐Sankyo, Eisai, GE Oncology, Genentech, GlaxoSmithKline, Macrogenics, Medscape, Merck‐Sharp, Merus BV, Mylan, Mundipharma, Novartis, Pfizer, Pierre‐Fabre, prIME Oncology, Roche, Sanofi, Samsung Bioepis, Seagen, Teva. SF is a consulting or advisory board member at Bayer, Illumina, Roche; has received honoraria from Amgen, Eli Lilly, PharmaMar, Roche; has received research funding from AstraZeneca, Pfizer, PharmaMar, Roche; has received sponsorship of travel or accommodation expenses by Amgen, Eli Lilly, Illumina, PharmaMar, Roche. SG owns AstraZeneca stock and is a full‐time employee of AstraZeneca. PN has had an advisory role at Bayer, MSD Oncology, has received honoraria from Bayer, Novartis and MSD Oncology, and has had travel expenses paid by Novartis. JO has been an advisory board member at Roche, Novartis, Bayer, Merck, Eisai, Astrazeneca, Pierre Fabre Medicament and Bristol‐Myers Squibb. He has also received research funding by IPO Porto, Astrazeneca, Fundação para a Ciencia e a Tecnologia (FCT) and Liga Portuguesa Contra o Cancro (LPCC). AR is an employee of European Federation of Pharmaceutical Industries and Associations, Brussels, MSD International Business GmbH, Kriens, Switzerland[CvG1], and Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ USA, who may own stock and/or hold stock options in the Company.RS serves as principal investigator of the ASCO TAPUR study. ASCO receives research grants from the following companies in support of the study: Astra‐Zeneca, Bayer, Boehringer‐Ingelheim, Bristol Myers Squibb, Genentech, Lilly, Merck, Pfizer, Seattle Genetics. Dr. Schilsky serves as a member of the managing board of Clariifi and as a consultant to Bryologyx, Cellworks Group, EQRx, and Scandion Oncology. The Netherlands Cancer Institute receives research support via EV from Roche, Astrazeneca, Eisai, Novartis, GSK, Clovis, BMS, MSD, Pfizer, Amgen, Bayer, Lilly, Janssen and Seagen. LZ is founder of everImmune, member of the board of directors of Transgene, member of the scientific advisory board of Transgene, EpiVax, Lytix Biopharma. LZ has also had research contracts with: Merus, Roche, Tusk, Kaleido, GSK, BMS, Incyte, Pileje, Innovate Pharma, and Transgene and has received honoraria by Transgene. All other authors have no conflicts of interest to declare. Regarding the design of innovative and adaptive clinical trials, two examples were illustrated: the first European multimodular, two‐part academic CCE‐endorsed Basket of Baskets (BoB) study, and the recently launched CCE Building Data Rich Clinical Trials (DART) Consortium, which is supported by EU’s Horizon 2020 research and innovation programme (Box 13 ). We are grateful for the support by Carolina Espina, International Agency for Research on Cancer; Christina von Gertten, European Academy of Cancer Sciences; Ana Augusta Silva, Portuguese Oncology Institute of Porto; and Teresa Tavares, Ministry of Science, Technology and Higher Education, Portugal for their excellent cooperation. Carmen Jeronimo, Portuguese Oncology Institute of Porto, collaborated in the presentation of Porto Comprehensive Cancer Center by Raquel Seruca