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The number of alignments between two DNA sequences

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International Journal of Biomathematics 2016年第4期9卷 75-80页

作者： Helena andrade Juan J. nieto Angela Torres Departamento de Andlisis Matemdtico Facultad de Matemdticas Universidad de Santiago de Compostela Spain Department of Mathematics Faculty of ScienceKing Abdulaziz University Jeddah 21589 Saudi Arabia Departamento de Psiquiatrla Radiologla y Salud Publica Facultad de Medicina Universidad de Santiago de Compostela Spain

We consider two DNA sequences and compare both sequences. One of the crucial issues in bioinformatics is to measure the similarity of two DNA sequences. To this purpose one has to consider different alignments between both sequences. The number of alignments grows very rapidly with the length of the sequences. In this paper we give exact, explicit and computable formulas for the number of different possible alignments and for some classes of reduced alignments. We provide a new insight into the theory of DNA sequence alignment.

关键词： DNA sequence alignment difference equation.

King's College criteria and the Clichy-Villejuif criteria require adjustments for assessing acute liver failure due to yellow fever

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World Journal of Transplantation 2025年第1期15卷 124-134页

作者： Bruno da Silva Athanasio Antonio Marcio de Faria andrade Vivian Vasconcelos Costa Juliano Felix Castro Silverio Leonardo Macedo Garcia Mauro Martins Teixeira Daniele da Gloria Souza Paula Vieira Teixeira Vidigal Cristiano Xavier Lima Department of Surgery Federal University of Minas GeraisBelo Horizonte 30130-100Minas GeraisBrazil Liver Transplantation Unit Felicio Rocho HospitalBelo Horizonte 30110-934Minas GeraisBrazil Department of Morphology Federal University of Minas GeraisBelo Horizonte 31270-901Minas GeraisBrazil Department of Biochemistry and Immunology Federal University of Minas GeraisBelo Horizonte 31270-901Minas GeraisBrazil Department of Pathology Federal University of Minas GeraisBelo Horizonte 30130-100Minas GeraisBrazil

BACKGROUND Acute liver failure(ALF)is a severe condition characterized by rapid deterioration of liver function in individuals without preexisting liver *** transplantation(LT)is the most impactful *** fever(YF)is an infectious disease that primarily affects the liver and has a high mortality ***,LT can be a viable option for treating rare cases with extensive liver ***,the criteria for assessing the severity of ALF and determining the indications for transplantation have not been specifically validated for cases caused by *** To present necessary adjustments to established scoring systems for ALF secondary to *** This was an observational,retrospective,single-center *** consecutive patients with confirmed ALF due to YF were monitored in the intensive care unit by a specialized liver transplant team during a three-month epidemic outbreak in *** hospitalization,general supportive therapeutic measures were implemented,and the patients were regularly assessed using the King's College criteria and the Clichy-Villejuif criteria to determine the severity of liver *** is considered a viable measure for patients with signs of end-stage liver *** Eight of 14(57%)patients developed severe neurological alterations within the first 96 hours after hospital *** patients underwent emergency LT,and despite a moderate viral infection of the graft after transplantation,the 5-year survival rate was 50%.Although the King's College criteria and the Clichy-Villejuif criteria are the main scoring systems for ALF,they are insufficient for predicting the risk of mortality in this context,primarily because of low serum bilirubin levels in the final stage of the disease and significant disparities between coagulation abnormalities and patient *** To ensure good applicability in cases of YF-induced ALF,the authors suggest adaptations to the King's College and Clichy-Vill

关键词： Yellow fever Acute liver failure Liver transplantation King's College criteria Clichy-Villejuif criteria

Effects of submergence in water on seed germination and vigor of the Copaifera lucens(Fabaceae) seedlings

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Journal of Forestry Research 2014年第4期25卷 903-908页

作者： Daniela Baldez Vidal Isis Leite andrade Eusinia Louzada Pereira andrade Marcelo Schramm Mielke Department of Agricultural and Environmental Sciences State University of Santa Cruz BR 415 km 16 Ilhéus 45662-300 Bahia Brazil Department of Biological Sciences State University of Santa Cruz BR 415 km 16 Ilhéus 45662-300 Bahia Brazil

We analyzed the tolerance of Copaifera lucens seeds to sub- mersion in water to assess the use of this species for direct seeding in riparian forest restoration programs. Seeds were submerged in water for 2, 4, 8, 16 and 32 days or not submerged （control = 0 days of submer- gence）. For the control and at the end of each period of submersion, germination and seedling vigor tests were carried out. For germination tests, seeds were sown in plastic pots containing sand and kept in labora- tory conditions. The percentage of seed germination, the germination rate and the average germination time were analyzed. For seedlings, total biomass, leaf area, leaf mass per area and leaf area ratio were analyzed. Submersion time drastically affected the dissolved oxygen content and seed germination. Between 4 and 8 days of submersion there was a de- crease from 83.8% to 15.6% in the germination percentage. No seed germination occurred after 16 days of submersion. Although there was a significant decrease in the percentage of seed germination between 4 and 8 days of submersion, seedling vigor was not affected. Seeds of this species were partially tolerant to submersion in water, suggesting that C. lucens is a promising species for direct seeding in riparian forest restora- tion projects.

关键词： Copaiba Brazilian Atlantic Forest forest restoration germi-nation vigor

Impact of Cascade Disconnection of Distributed Energy Resources on Bulk Power System Stability:Modeling and Mitigation Requirements

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Journal of Modern Power Systems and Clean Energy 2023年第2期11卷 412-420页

作者： Fabricio andrade Mourinho Tatiana Mariano Lessa Assis Electrical Engineering Department of the Federal University of Rio de Janeiro(COPPE/UFRJ) Rio de JaneiroRJBrazil

This work presents a new approach to establishing the minimum requirements for anti-islanding protection of distributed energy resources(DERs)with focus on bulk power system *** proposed approach aims to avoid cascade disconnection of DERs during major disturbances in the transmission network and to compromise as little as possible the detection of real islanding *** proposed approach concentrates on the rate-of-change of frequency(RoCoF)protection function and it is based on the assessment of dynamic security regions with the incorporation of a new and straightforward approach to represent the disconnection of DERs when analyzing the bulk power system ***,the impact of disconnection of DERs on the Brazilian Interconnected Power System(BIPS)stability is analyzed,highlighting the importance of modeling such disconnection in electromechanical stability studies,even considering low penetration levels of ***,the proposed approach is applied to the BIPS,evidencing its benefits when specifying the minimum requirements of anti-islanding protection,without overestimating them.

关键词： Anti-islanding protection bulk power system stability distributed energy resource(DER) dynamic security region(DSR)

Machine learning applied to road safety modeling:A systematic literature review

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Journal of Traffic and Transportation Engineering(English Edition) 2020年第6期7卷 775-790页

作者： Philippe Barbosa Silva Michelle andrade Sara Ferreira Department of Civil Engineering Goiano Federal Institute-Rio Verde CampusRio Verde 75901-970Brazil Department of Civil and Environmental Engineering University of BrasiliaBrasilia 70910-900Brazil Research Centre for Territory Transports and EnvironmentUniversity of PortoPorto 4200-465Portugal

Road safety modeling is a valuable strategy for promoting safe mobility,enabling the development of crash prediction models(CPM)and the investigation of factors contributing to crash *** modeling has traditionally used statistical techniques despite acknowledging the limitations of this kind of approach(specific assumptions and prior definition of the link functions),which provides an opportunity to explore alternatives such as the use of machine learning(ML)*** study reviews papers that used ML techniques for the development of CPM.A systematic literature review protocol was conducted,that resulted in the analysis of papers and their *** types of models were identified:crash frequency,crash classification by severity,and crash frequency and *** first is a regression problem,the second,a classificatory one and the third can be approached either as a combination of the preceding two or as a regression model for the expected number of crashes by severity *** main groups of techniques used for these purposes are nearest neighbor classification,decision trees,evolutionary algorithms,support-vector machine,and artificial neural *** last one is used in many kinds of approaches given the ability to deal with both regression and classification problems,and also multivariate response *** paper also presents the main performance metrics used to evaluate the models and compares the results,showing the clear superiority of the ML-based models over the statistical *** addition,it identifies the main explanatory variables used in the models,which shows the predominance of road-environmental aspects as the most important factors contributing to crash *** review fulfilled its objective,identifying the various approaches and the main research characteristics,limitations,and opportunities,and also highlighting the potential of the usage of ML in crash analyses.

关键词： Transportation engineering Road safety modeling Crash prediction Crash injury severity Machine learning Systematic literature review

Lineament analysis as a seismic precursor:The El Mayor Cucapah earthquake of April 4,2010(MW7.2),Baja California,Mexico

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Geodesy and Geodynamics 2023年第2期14卷 121-129页

作者： Rosendo Romero-andrade Manuel E.Trejo-Soto Karan Nayak Daniel Hernández-andrade Naccieli Bojorquez-Pacheco Faculty of Earth and Space Sciences Autonomous University of Sinaloa80013Culiacan RosalesSinaloaMexico

An earthquake called the MW7.2“El Mayor Cucapah”earthquake on April 4,2010 has been analyzed for seismic *** changes in the lineament system concerning its pattern and time intervals were analyzed during the earthquake preparation period and occurrence using the automated lineament detection *** Landsat 5 TM images were processed using LESSA and ADALGEO software obtaining similar *** statistical analysis revealed the stress accumulation due to plate interaction during earthquake *** study shows that the number of extracted lineaments changes rapidly about 23 months before the earthquake,and the systems return to the initial stage after 23 *** lineaments coincide with the extension of the San Andreas Fault as NW direction is the dominant ***,it can be concluded that the featural changes within the Rose diagram corresponding to the different strokes direction along with oriented elongation lines as disclosed in the present study using satellite images could be identified as a mid-term and/or short-term precursors of the ***,even though the dynamism of the El Mayor Cucapah earthquake is found in the extracted lineaments,it is possible to isolate more significant earthquakes even if new ones appear near the ***,using two algorithms for lineament detection allows for the tectonics to corroborate the obtained lineaments and dynamism.

关键词： Lineament analysis Earthquake Landsat images Seismic precursor

Anti-predator behavior along elevational and latitudinal gradients in dark-eyed juncos

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Current Zoology 2020年第3期66卷 239-245页

作者： Madelin andrade Daniel T.BLUMSTEIN Department of Ecology and Evolutionary Biology University of California621 Young Drive SouthLos AngelesCA 90095-1606USA

Flight-initiation distance(FID),the distance between an individual and experimenter when it begins to flee,can be used to quantify *** other factors,prior studies have shown that latitude explains significant variation in avian FID:at lower latitudes,individuals and species have longer FIDs than those living at higher *** prior studies have focused on the effect of elevation on *** the similar patterns of seasonality,climate,and potentially predator density,that covary between latitude and elevation,birds at higher elevations might tolerate closer *** asked whether elevation or latitude would explain more variation in the FID of a common passerine bird species,dark-eyed juncos(Junco hyemalis).Juncos live in a variety of habitats along both latitudinal and elevational *** found that statistical models containing elevation as a variable explained more of the variation in FID than did models containing *** also found,unexpectedly,that birds at higher elevation fled at greater *** more predators were sighted per hour at higher elevations than at lower elevations,the frequency of predator sightings did not explain a significant amount of variation in *** result questions whether predator density is the main driver of risk perception along elevational ***,because elevation explains more variation in FID than latitude in at least one species,these findings have direct implications on how human impacts on birds are ***,those designing set-back zones to reduce human impact on birds may consider modifying them based on both latitude and elevation.

关键词： antipredator behavior FID latitude elevation dark-eyed junco Junco hyemalis

Kainate receptors in the CA2 region of the hippocampus

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Neural Regeneration Research 2023年第2期18卷 320-321页

作者： Yuniesky andrade-Talavera Antonio Rodríguez-Moreno Laboratorio de Neurociencia Celulary Plasticidad Departamento de FisiologíaAnatomía y Biología CelularUniversidad Pablo de OlavideSevillaSpain

The hippocampus is involved in important brain functions such as learning and memory,spatial navigation,fear processing,and social behavior(Dudek et al,2016).The most prominent areas of the hippocampus are typically denoted as the dentate gyrus and the three areas of the cornu ammonis(CA1,CA2,and CA3).Discovered by Lorente de Nó(1934),the CA2 region of the hippocampus is a relatively small area interposed between CA3 and CA1 that forms the nexus linking the input of the entorhinal cortex to the output of CA1(Chevaleyre and Siegelbaum,2010).

关键词： CA2 cortex linking

Multigrid Solution of a Lavrentiev-Regularized State-Constrained Parabolic Control Problem

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Numerical Mathematics(Theory,Methods and Applications) 2012年第1期5卷 1-18页

作者： Alfio Borzì Sergio González andrade Institut für Mathematik Universität WürzburgCampus Hubland NordEmil-Fischer-Str.3097074 WürzburgGermany Research Group on Optimization Departamento de MatemáticaEscuela Politécnica NacionalLadrón de Guevara E11-253QuitoEcuador

A mesh-independent,robust,and accurate multigrid scheme to solve a linear state-constrained parabolic optimal control problem is *** first consider a Lavrentiev regularization of the state-constrained optimization ***,a multigrid scheme is designed for the numerical solution of the regularized optimality *** to this scheme is the construction of an iterative pointwise smoother which can be formulated as a local semismooth Newton *** of numerical experiments and theoretical twogrid local Fourier analysis estimates demonstrate that the proposed scheme is able to solve parabolic state-constrained optimality systems with textbook multigrid efficiency.

关键词： Multigrid methods Lavrentiev regularization semismooth Newton methods parabolic partial differential equations optimal control theory