bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelagem de Aliciamento de Menores em Mensagens Instantâneas de Texto
Authors: Santin Priscilla L. L. , Freitas Cinthia O. A. , Paraíso Emerson C. , Santin Altair O.
Published: August 2022

As abordagens existentes na literatura não são modeladas para detecção do aliciamento sexual de menores, mas apenas fazem a descoberta do estágio de aliciamento numa comunicação entre o agressor e sua vítima. Além disto, mostram baixa eficiência em função do emprego de um perfil único para a descoberta dos estágios. Este artigo considera a descoberta dos estágios de aliciamento com o perfil do agressor e da vítima separadamente. Esta abordagem, baseada em avaliação estocástica (i.e. HMM), visa a modelagem individual de cada perfil para aumentar a eficiência da detecção. Os experimentos mostram taxas de acerto promissoras com resultados próximos a 91%.
Arquitetura de um sistema integrado de defesa cibernética para detecção de botnets
Authors: Silva Sérgio dos Santos Cardoso , Salles Ronaldo Moreira
Published: August 2022

Este trabalho tem por objetivo apresentar uma proposta de arquitetura para um sistema de defesa cibernética capaz de detecar bots e bloquear a comunicação entre os bots e as botnets. Também é proposto um algoritmo de detecção de bots baseado em grafos de relacionamento. Foram realizados experimentos por meio da análise de registros de consultas DNS com o objetivo de encontrar máquinas suspeitas de serem zumbis. Resultados preliminares mostram que os mecanismos empregados permitem filtrar os registros de DNS e identificar máquinas suspeitas de pertencerem a uma botnet.
Panorama Brasileiro do Ensino e Aprendizagem de Programação de Computadores na Educação Básica
Authors: Ribeiro Natália Gallo , Martins Lavínia de Oliveira , Berssanette João Henrique
Published: August 2022

Este estudo apresenta um panorama brasileiro do ensino e aprendizagem de programação de computadores na Educação Básica, por meio do desenvolvimento de um estudo de Mapeamento Sistemático da Literatura (MSL). A partir da execução do protocolo MSL, pode-se recuperar, inicialmente, 445 estudos, que foram submetidos ao processo de seleção, com base em critérios estipulados pelo protocolo MSL desenvolvido, restando, ao final desse processo, 81 estudos selecionados. Em seguida, os estudos selecionados foram analisados com vistas a se responder às questões de pesquisa propostas. Por meio dessa análise, foi possível perceber que a abordagem mais utilizada é o uso ou o desenvolvimento de ferramentas para o apoio ao processo de ensino e aprendizagem. Além disso, verificou-se que a maior contribuição relatada nos estudos é o aumento do interesse e da motivação dos estudantes, bem como a principal dificuldade relatada tem relação com falhas na infraestrutura disponibilizada para o processo de ensino e aprendizado.
Development of the Software Engineering Education Virtual Classroom Prototype: An Experience Report
Authors: Fernandes Filipe , Castro Diego , Rodrigues Claudia , Werner Cláudia
Published: August 2022

COVID-19 pandemic forced educational institutions to reinvent themselves by using digital information and communication technologies to support the continuity of distance learning. Google Meet and Zoom were one of the tools adopted as solution. However, the learning process presented challenges, mainly related to the lack of engagement and growing demotivation of students. Immersive Learning (iL) is a research topic that has the potential to improve learning outcomes. Through immersive environments, students have access to new ways of viewing and interacting, providing more engagement in learning. Therefore, the objective of this work is to present the development of a Virtual Classroom prototype, a virtual environment to support Software Engineering Education (SEE). An initial evaluation with a specialist was carried out and it was found that the usability of the environment is satisfactory, but aspects of performance must be improved. As future work, apart from adjusting the indicated points for improvement, a user experience evaluation with 3 to 5 extended reality specialists and another evaluation with students in order to verify the influence of the Virtual Classrooms on learning outcomes will be carried out.
What did I get Wrong? Supporting the Feedback Process in Computer Science Education
Authors: Falcão Taciana Pontual , Arêdes Verenna , Wagner Samuel Souza , Uchoa João Pedro Cavalcanti , Luisi Victoria , Mello Rafael Ferreira
Published: August 2022

In learning processes, feedback given to students by instructors is essential to guide students and help them improve from their mistakes. However, in higher education, instructors feel unable to give quality and timely feedback due to work overload and lack of time. As online classes became common due to the Covid 19 pandemic, and with increasing numbers of students per class, giving feedback beyond grades became even less realistic. We interviewed Computer Science instructors and students to investigate the specific difficulties and barriers related to giving and receiving feedback. We present the findings derived from qualitative analysis of the interviews and propose Tutoria, a platform designed to support a better feedback experience for all.
Programa de Educação Tutorial: Uma Análise Retrospectiva das Ações Realizadas para Auxiliar na Formação Pessoal e Profissional dos Alunos do Curso de Sistemas de Informação
Authors: Pinheiro Francisco Victor da S. , Lima Ronier da S. , Ferreira Ana Kely L. , Lima Francisco Victor S. de , Tavares Wladimir Araújo
Published: August 2022

Este trabalho tem como objetivo, apresentar um relato sobre as ações do Programa de Educação Tutorial do curso de Sistemas de Informação (PET-SI) da Universidade Federal do Ceará - Campus de Quixadá, elencando seus resultados e as perspectivas futuras sobre tais ações. Na Seção 2, são destacadas tais ações, que são voltadas para o público acadêmico e social. Além disso, as ações realizadas pelo PET-SI buscam englobar os eixos de ensino, pesquisa e extensão, como a atividade de Letramento Digital, objetivando levar o ensino de informática básica aos professores do município de Quixadá e a atividade de Seminários Internos, que incentiva os bolsistas discentes à pesquisa.
Teaching Qualitative Research Methodology at Undergraduate Courses in Computing: An Evidence-Based Proposal
Authors: Mello Rafael de , Mello Fernanda de
Published: August 2022

The teaching of scientific methodology is a mandatory component for the Brazilian undergraduate courses in Computing. However, this component typically does not address qualitative research despite its increasing dissemination and relevance in Computer Science research. In this paper, we introduce the proposal of a qualitative research methodology course tailored to undergraduate courses in Computing. Among others, the didactic proposal of the course includes resources for stimulating students to think qualitatively, the linked teaching of data collection techniques, the discussion and analysis of real studies, and the conduction of group dynamics. We applied the course of qualitative research methodology as an elective course in the context of the Bachelor's Degree in Computer Science offered by Cefet/RJ, Brazil. Despite the challenges posed by exceptional remote learning, we achieved good levels of retention and approval. Through an opinion survey, we found a considerably positive perception about the learning experience and the didactic resources applied.
Uma abordagem para a Interdisciplinaridade no Curso Técnico Integrado em Informática
Authors: Castro Bianca P. , Lattari Lucas G. , Moura Marcela Z. de , Lima Sérgio M. B.
Published: August 2022

Este trabalho trata de um relato de experiência, cujo objetivo foi elaborar abordagem interdisciplinar em um Curso Técnico Integrado em Informática, por meio de atividades integradoras. Várias ações integradas foram executadas no âmbito das disciplinas ministradas pelos autores: Montagem e Manutenção de Computadores, Algoritmos e Inglês. Dentre essas atividades, destacaram-se: sincronização de conteúdos, avaliações integradas e projetos integradores. Os resultados obtidos sugerem a preferência dos estudantes em serem protagonistas do processo ensino-aprendizagem, por meio de atividades integradoras e a necessidade de conscientizar a gestão escolar, docentes e discentes sobre a cultura da autonomia necessária aos discentes para o conhecer global.
Quando a Teoria é Aplicada: Um Relato de Experiência da Aplicação de Metodologias de Desenvolvimento de Sistemas Computacionais dentro do PETComp-UFMA
Authors: Dovera Italo , Bessa Matheus , Nascimento Brenno , Silva Felipe , Gomes Rafaela , Braz Junior Geraldo , Nogueira Adriana , Rivero Luis
Published: August 2022

Na computação, existe um avanço rápido e constante de novas ferramentas de desenvolvimento de software, o que leva os profissionais da área ao aprimoramento também constante de seus conhecimentos sobre essas novas ferramentas. Porém, essa rápida evolução dificulta a escolha de uma metodologia eficiente aos times de desenvolvimento. Nesse contexto, este artigo visa relatar a experiência de desenvolver sistemas, além de apresentar ferramentas e metodologias que auxiliem grupos iniciantes em tal processo. A equipe do Programa de Educação Tutorial em Computação (PETComp) da Universidade Federal do Maranhão definiu um processo de treinamento e desenvolvimento, com funções divididas entre equipes de desenvolvimento e design. Ao todo, uma equipe de discentes com pouca experiência em desenvolvimento realizou atividades como: prototipação, reuniões de validação e aprendizagem de ferramentas. Como resultado, obteve-se a criação de sites para eventos, sites para o curso de graduação e aplicativos móveis.
Panorama Comparativo da Atuação Acadêmica e Profissional de Egressas e Egressos de um Curso de Bacharelado em Ciência da Computação
Authors: Ferreira Mércia , Barbosa Alice , Braga Reinaldo , Saraiva Daniel , Oliveira Carina
Published: August 2022

A área de tecnologia vem promovendo diversas oportunidades de emprego. Apesar disso, existe uma baixa representatividade de mulheres na área, o que coloca em dúvida se ações efetivas estão sendo realizadas para alterar essa realidade. Nesse contexto, este trabalho apresenta um panorama comparativo de egressas e egressos de um curso de Bacharelado em Ciência da Computação, a partir das seguintes temáticas: desempenho acadêmico, formação extracurricular, atuação profissional, faixa salarial e mobilidade. A ferramenta Tableau é utilizada para realização das análises. A pesquisa aponta que, apesar da baixa quantidade de egressas do curso, elas possuem atuações positivas nas temáticas analisadas. Discussões sobre possíveis razões para tal cenário são apresentadas como uma das contribuições do trabalho.
Computational Thinking Game Design Based on the Bebras Challenge: A Controlled Experiment
Authors: Laisa Jéssica , Henrique Eduardo
Published: August 2022

The use of games is a promising approach to engage students and to teach computational few educational games are related to this topic. One reason for that is the difficult to create CT Game Designs. In this context, this work has the objective of verifying if interesting computational thinking games can be created from the analysis of Bebras Challenge tasks, an international initiative that presents a set of attractive and well-elaborated tasks to exercise and evaluate computational thinking (CT) abilities. A controlled experiment was performed and the achieved results indicate that Bebras tasks are a good source of inspiration for designing CT games. Hence, their use can support the creation of new CT games, ensuring a balanced level of educational and entertainment aspects.
Currículo Base para o Ensino de Pensamento Computacional para Pessoas com Deficiência Intelectual e Múltipla: um relato de experiência com usuários da APAE de Serra Talhada-PE
Authors: Santos Romário Elias da Silva , Lopes Júlio César da Costa , Silva Rildo de Cássio Estácio da , Souza Ellen Polliana Ramos , Silva Paulo Mello da , Felix Zildomar Carlos
Published: August 2022

Este artigo traz um relato de experiência do ensino de informática básica e robótica para Pessoas com Deficiência Intelectual e Múltipla atendidas pela Associação de Pais e Amigos dos Excepcionais do município de Serra Talhada-PE. O objetivo deste trabalho é apresentar um currículo base de informática e robótica, assim como sua aplicação nas oficinas que são realizadas semanalmente no laboratório de informática da associação. O currículo se mostrou adequado para PcD, aprimorando suas habilidades e promovendo a inclusão sociodigital.
Análise de Sobrevivência: um estudo de caso em um Curso de Sistemas de Informação
Authors: Souza Joubert Alexandrino de , Komati Karin Satie , Andrade Jefferson Oliveira
Published: August 2022

A evasão do ensino superior é um problema grave que tem sido investigado há décadas e causa grandes danos aos indivíduos, instituições de ensino e à sociedade como um todo. Este artigo apresenta um estudo de caso sobre a aplicação da técnica de análise de sobrevivência combinada com a construção de modelos preditivos na identificação dos elementos determinantes da evasão em um curso de graduação em Sistemas de Informação de uma instituição pública de ensino superior no Brasil. Métodos de mineração de dados educacionais e modelagem probabilística foram aplicados aos dados dos alunos para modelar a conclusão esperada dos alunos do curso, semestre a semestre. Os resultados da análise de sobrevivência indicam que o maior risco de evasão está nos semestres iniciais do curso, enquanto a identificação das características determinantes da evasão deixa claro que as disciplinas dos dois primeiros semestres retêm cerca de 50% da população estudantil.
MOOC Internet e Informação: entrelaçando ensino, pesquisa e extensão em prol do combate à desinformação em rede
Authors: Santos Débora Abdalla , Santos Juliana Maria Oliveira dos , Oliveira Emilly Tifanny Santos Conceição de
Published: August 2022

O aumento do volume de informações compartilhadas colocou em evidência um problema recorrente no Brasil, as fake news. Nesse cenário, a Universidade Pública deve engendrar esforços para mitigar os efeitos da propagação de notícias falsas de qualquer natureza, informando e formando cidadãos críticos e conscientes. Com esse propósito nasceu o projeto "MOOC Internet e Informação". O objetivo deste artigo é compartilhar a experiência realizada na articulação de atividades de extensão universitária com o ensino na área de computação e pesquisa em ambientes educacionais digitais de aprendizagem como forma de intensificar e apoiar o movimento de combate à desinformação.
A new species of Paranecepsia (Euphorbiaceae-Acalyphoideae) from Madagascar and its relationships among the ‘alchorneoids clade’
Authors: Barberá Patricia , Lachenaud Olivier , Riina Ricarda
Published: August 2022

The formerly monotypic genus Paranecepsia Radcl.-Sm. is expanded with the description and illustration of a second species, Paranecepsia andrafiabensis Barberá & O.Lachenaud sp. nov. Molecular phylogenetic analyses of plastid rbcL and trnL-F data confirm a sister relationship between the new species and P. alchorneifolia Radcl.-Sm., as members of the alchorneoids clade. Paranecepsia andrafiabensis sp. nov. is notable for expanding the character states for the genus (now including both 2- and 3-locular ovary species) and broadening the geographic range of the genus from continental Africa to Madagascar. The new species adds to the diverse karst limestone endemics of northwestern Madagascar, where it has a very restricted distribution at the base of the western wall of the Ankarana tsingy. An amended generic description of Paranecepsia and a key to the species are also presented. Paranecepsia andrafiabensis sp. nov. is provisionally assessed as VU D1 based on the IUCN Red List criteria.
Is protest action in South Africa bringing positive change or is it threatening our human right to security?
Authors: Carmichael T R
Published: August 2022

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A mixed-methods study on evaluating an updated, francophone version of ETAT+ training in Madagascar
Authors: Galatsch M , Lang H-J , Noa C , Raveloharimino H , Robinson A , Rabesandratana N , Magera L I , Weigel R , Köcher-Andrianarimanana D
Published: August 2022

Background. Madagascar needs major efforts to achieve the UN Sustainable Development Goals, despite the considerable reduction of child mortality during past years. In this context, implementation of emergency triage assessment and treatment (ETAT) plays an important role. In recent years, ETAT training activities rarely took place in Madagascar. To strengthen ETAT in Madagascar, a pilot training course was conducted in December 2019 at the University Hospital Mahajanga.

Objective. This study aims to evaluate if the ETAT+ pilot training content matches clinical needs in Madagascar and whether participants achieved their learning objectives.Methods. In this cross-sectional mixed-methods study, a 41-item questionnaire was used at the end of the ETAT+ training to evaluate their learning experience from the 12 participants (paediatricians, physicians, nurses and midwives). Six weeks after the training, guided interviews were conducted among five participants to describe how training content could be transferred into clinical practice in five health facilities.

Results. Results suggest that this pilot project designed to contribute to the re-establishment of ETAT in Madagascar meets participants’ needs and is adapted to clinical realities in terms of transmitted knowledge, skills and competencies. However, results also show that considerable multi- disciplinary efforts are needed to advance ETAT+ implementation in Madagascar.Conclusions. Implementation processes of ETAT training programmes need re-evaluation to assure their validity to contribute to quality of care improvements efficiently. Further operational research is required to evaluate sustainable, innovative implementation strategies adapted to contexts in Madagascar.
Iatrogenic blood loss in critical care: A prospective observational study conducted at Universitas Academic Hospital in the Free State Province, South Africa
Authors: Adams J C , Barrett C , Spruyt M
Published: August 2022

Background. Prevention of iatrogenic blood loss is an essential component of patient blood management (PBM) in intensive care units (ICUs). The amount of iatrogenic blood loss from diagnostic phlebotomy in the ICUs at Universitas Academic Hospital, Free State Province, South Africa, is unknown.Objective. To quantify diagnostic phlebotomy volumes, and volumes submitted in excess for diagnostic testing in the ICU.

Methods. We conducted a prospective descriptive observational study on adults who were admitted to ICUs at a single centre over a period of 14 days. The weight of each filled phlebotomy tube was calculated using the specific gravity of blood and averages of empty phlebotomy tubes, establishing the total volume.Results. Data from 59 participants with a median length of stay at the ICU of 3 days were analysed. The median phlebotomy volume was 7.0 mL day and 13.6 mL/ICU admission. The volume of blood required for analysis daily and ICU admission was 0.7 mL and 2.2 mL, respectively. The median phlebotomy volume in excess of the amount required for analysis daily and ICU admission was 5.05 mL and 12.11 mL, respectively.

Conclusion. While the median excess daily phlebotomy volume in this present study may seem insignificant and underestimating the true excess of phlebotomy volume, interventions to reduce phlebotomy volumes and development of a PBM guideline for appropriate phlebotomy volumes and preventing wastage of patients’ blood in the ICU is required.
THE ROLES AND POLICIES FOR THE USE OF TELEMEDICINE IN HANDLING COVID-19 SELF-ISOLATION: LITERATURE REVIEW
Authors: Yonathan Rafika Stany , Nadjib Mardiati
Published: August 2022

The current COVID-19 pandemic has had various impacts on the world. The unpredictable spike in cases led to an explosion in patient numbers. The problem of limited treatment facilities forces patients to self-isolate at home. Along with technological advances, various facilities have also been created, one of which is telemedicine. This study aims to look at the role of telemedicine as a strategy for handling COVID-19 self-isolated patients in various countries. This study was conducted descriptively with a literature review. The search was carried out on articles published in Indonesian and English through Google Scholar, Pubmed, and Science Direct searches with the keywords COVID-19, home isolation, self-isolation, telemedicine, and telehealth. The search results obtained that the handling of COVID-19 patients in self-isolation with telemedicine is a solution to the need for monitoring patient health, where hospitals have difficulty being able to serve all patients who need hospitalization. It can be concluded that COVID-19 is a newly emerging disease, clinical symptoms and emergencies of each patient can certainly be different and difficult to predict. Telemedicine as a remote health service can be a means to facilitate clinical monitoring of patients during self-isolation. The implementation of telemedicine ensures the continuity of health services quite effectively and efficiently, the way telemedicine works helps protect patients and health workers from exposure to infection and reduces the burden on hospitals, so it is quite appropriate to be used as a strategy in handling if there is a spike in COVID-19 cases in the future or application to other similar circumstances.
Crystal growth and electronic transport property of ternary Pd-based tellurides
Authors: Qiu Hang-Qiang , Xie Xiao-Meng , Liu Yi , Li Yu-Ke , Xu Xiao-Feng , Jiao Wen-He ,   School of Science, Zhejiang University of Science and Technology, Hangzhou 310023, China,   Key Laboratory of Quantum Precision Measurement of Zhejiang Province, School of Science, Zhejiang University of Technology, Hangzhou 310023, China,   School of Physics, Hangzhou Normal University, Hangzhou 311121, China
Published: August 2022

Ternary transition-metal chalcogenides are a series of compounds that possess both low-dimensional structures and correlated electrons, and display rich electronic ground states, depending on their different compositions. Among the chalcogen (S, Se, Te), Te has lower electronegativity and heavier atomic mass than S and Se. Thus, transition-metal tellurides take on distinct crystal structures, electronic structures and physical properties. In recent years, we have successively discovered novel superconductors Ta4Pd3Te16 and Ta3Pd3Te14, topological Dirac semimetals TaTMTe5 (TM = Pd, Pt, Ni),etc., further expanding the investigations of physical properties of the family of tellurides and laying a foundation for exploring their potential applications . The basis of further investigating and exploring the potential applications is the obtaining of the high-quality crystals with large dimensions. In this work, we first introduce the whole procedures of the single-crystal growth in growing the four ternary Pd-based tellurides (Ta4Pd3Te16, Ta3Pd3Te14, TaPdTe5, and Ta2Pd3Te5) by employing the self-flux method and chemical vapor transport method, and then give the chemical reaction equations in chemical vapor transport. The superconducting transition width of the Ta4Pd3Te16 crystal and Ta3Pd3Te14 crystal are as small as 0.57 K and 0.13 K, respectively, and by fitting the temperature-dependent resistivity of the topological insulator Ta2Pd3Te5, the band gap is derived to be 23.37 meV. Finally, we comparatively analyse the crystal-growth processes of the four ternary Pd-based tellurides by employing the flux method, which can provide the inspiration and reference for growing the crystals of other transition-metal tellurides by employing the similar methods.
Method of compensating for time measurement error of photomultiplier tube
Authors: Wang Chong , Dang Wen-Bin , Zhu Bing-Li , Yang Kai , Yang Jia-Hao , Han Jiang-Hao ,   School of Electronic Engineering, Xi’an University of Posts & Telecommunications, Xi’an 710121, China,   Key Laboratory of Ultra-Rapid Diagnostic Technology, Xi’an Institute of Optoelectronic Precision Machinery, Chinese Academy of Sciences, Xi’an 710119, China,   Chinese Academy of Sciences University, Beijing 100049, China
Published: August 2022

In order to improve the temporal resolution of photomultiplier tubes, our research group has conducted the in-depth research on photomultiplier tubes based on microchannel plates that are widely used at present. The time resolution of photomultiplier tube based on microchannel plate is limited by the transit time of photoelectric signal in each part, including the transit time of photoelectric signal in the transmission process of photocathode to microchannel plate, the transit time of photoelectric signal in microchannel plate time, the transit time of the photoelectric signal from the microchannel plate to the detector anode, and the transit time of the photoelectric signal on the anode to the electrode port. The transit time of the whole process has a certain degree of influence on the time information measurement of the optoelectronic signal. In this study, various parameters affecting the time resolution of the photomultiplier tube are analyzed, and it is found that the different positions of the photoelectron signal on the anode will bring errors to the measurement of the arrival time of the signal at the anode, and the photoelectric signal is transmitted to the electrode port at the affected point of the anode The spent time will cause the signal measurement time to lag behind the real time, which indirectly affects the time resolution of the system. Therefore, a specific study is carried out on the time measurement error of the signal on the anode, and it is determined that the difference of the photoelectron signal on the anode position is an important factor causing the signal time measurement error, and a simple and effective method of compensating for error is proposed. In the research process, the delay line anode is used, and the positional resolution principle of the photoelectric signal is used to obtain the position information of the photoelectron signal on the anode, and the position information is converted into the time information transmitted from the position to the electrode port. The theoretical value of the transit time on the anode is offset, eliminating unnecessary time in the time-of-arrival measurement of the photoelectron signal. The time measurement error of the optoelectronic signal is compensated for by this time information. The experimental results show that the error compensation method can effectively improve the time measurement accuracy of optoelectronic signals, and provide solutions and theoretical basis for improving the time resolution of photomultiplier tubes based on microchannel plates.
The VINE complex is an endosomal VPS9-domain GEF and SNX-BAR coat
Authors: Shortill Shawn P , Frier Mia S , Wongsangaroonsri Ponthakorn , Davey Michael , Conibear Elizabeth
Published: August 2022

Membrane trafficking pathways perform important roles in establishing and maintaining the endosomal network. Retrograde protein sorting from the endosome is promoted by conserved SNX-BAR-containing coat complexes including retromer which enrich cargo at tubular microdomains and generate transport carriers. In metazoans, retromer cooperates with VARP, a conserved VPS9-domain GEF, to direct an endosomal recycling pathway. The function of the yeast VARP homolog Vrl1 has been overlooked due to an inactivating mutation found in commonly studied strains. Here, we demonstrate that Vrl1 has features of a SNX-BAR coat protein and forms an obligate complex with Vin1, the paralog of the retromer SNX-BAR protein Vps5. Unique features in the Vin1 N-terminus allow Vrl1 to distinguish it from Vps5, thereby forming a complex that we have named VINE. The VINE complex occupies endosomal tubules and redistributes a conserved mannose 6-phosphate receptor-like protein from endosomes. We also find that membrane recruitment by Vin1 is essential for Vrl1 GEF activity, suggesting that VINE is a multifunctional coat complex that regulates trafficking and signaling events at the endosome.
Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature
Authors: Ogran Ariel , Havkin-Solomon Tal , Becker-Herman Shirly , David Keren , Shachar Idit , Dikstein Rivka
Published: August 2022

The transformation of normal to malignant cells is accompanied by substantial changes in gene expression programs through diverse mechanisms. Here, we examined the changes in the landscape of transcription start sites and alternative promoter (AP) usage and their impact on the translatome in TCL1-driven chronic lymphocytic leukemia (CLL). Our findings revealed a marked elevation of APs in CLL B cells from Eµ-Tcl1 transgenic mice, which are particularly enriched with intra-genic promoters that generate N-terminally truncated or modified proteins. Intra-genic promoter activation is mediated by (1) loss of function of ‘closed chromatin’ epigenetic regulators due to the generation of inactive N-terminally modified isoforms or reduced expression; (2) upregulation of transcription factors, including c-Myc, targeting the intra-genic promoters and their associated enhancers. Exogenous expression of Tcl1 in MEFs is sufficient to induce intra-genic promoters of epigenetic regulators and promote c-Myc expression. We further found a dramatic translation downregulation of transcripts bearing CNY cap-proximal trinucleotides, reminiscent of cells undergoing metabolic stress. These findings uncovered the role of Tcl1 oncogenic function in altering promoter usage and mRNA translation in leukemogenesis.
Multistep loading of a DNA sliding clamp onto DNA by replication factor C
Authors: Schrecker Marina , Castaneda Juan C , Devbhandari Sujan , Kumar Charanya , Remus Dirk , Hite Richard K
Published: August 2022

The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3’ end (3’ ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3’ ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA.
How failure to falsify in high-volume science contributes to the replication crisis
Authors: Rajtmajer Sarah M , Errington Timothy M , Hillary Frank G
Published: August 2022

The number of scientific papers published every year continues to increase, but scientific knowledge is not progressing at the same rate. Here we argue that a greater emphasis on falsification – the direct testing of strong hypotheses – would lead to faster progress by allowing well-specified hypotheses to be eliminated. We describe an example from neuroscience where there has been little work to directly test two prominent but incompatible hypotheses related to traumatic brain injury. Based on this example, we discuss how building strong hypotheses and then setting out to falsify them can bring greater precision to the clinical neurosciences, and argue that this approach could be beneficial to all areas of science.
A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag
Authors: Yim Willa Wen-You , Yamamoto Hayashi , Mizushima Noboru
Published: August 2022

Monitoring autophagic flux is necessary for most autophagy studies. The autophagic flux assays currently available for mammalian cells are generally complicated and do not yield highly quantitative results. Yeast autophagic flux is routinely monitored with the green fluorescence protein (GFP)-based processing assay, whereby the amount of GFP proteolytically released from GFP-containing reporters (e.g. GFP-Atg8), detected by immunoblotting, reflects autophagic flux. However, this simple and effective assay is typically inapplicable to mammalian cells because GFP is efficiently degraded in lysosomes while the more proteolytically resistant red fluorescent protein (RFP) accumulates in lysosomes under basal conditions. Here, we report a HaloTag (Halo)-based reporter processing assay to monitor mammalian autophagic flux. We found that Halo is sensitive to lysosomal proteolysis but becomes resistant upon ligand binding. When delivered into lysosomes by autophagy, pulse-labeled Halo-based reporters (e.g. Halo-LC3 and Halo-GFP) are proteolytically processed to generate Haloligand when delivered into lysosomes by autophagy. Hence, the amount of free Haloligand detected by immunoblotting or in-gel fluorescence imaging reflects autophagic flux. We demonstrate the applications of this assay by monitoring the autophagy pathways, macroautophagy, selective autophagy, and even bulk nonselective autophagy. With the Halo-based processing assay, mammalian autophagic flux and lysosome-mediated degradation can be monitored easily and precisely.
Nine best practices for research software registries and repositories
Authors: Garijo Daniel , Ménager Hervé , Hwang Lorraine , Trisovic Ana , Hucka Michael , Morrell Thomas , Allen Alice ,   Task Force on Best Practices for Software Registries,   SciCodes Consortium
Published: August 2022

Scientific software registries and repositories improve software findability and research transparency, provide information for software citations, and foster preservation of computational methods in a wide range of disciplines. Registries and repositories play a critical role by supporting research reproducibility and replicability, but developing them takes effort and few guidelines are available to help prospective creators of these resources. To address this need, the FORCE11 Software Citation Implementation Working Group convened a Task Force to distill the experiences of the managers of existing resources in setting expectations for all stakeholders. In this article, we describe the resultant best practices which include defining the scope, policies, and rules that govern individual registries and repositories, along with the background, examples, and collaborative work that went into their development. We believe that establishing specific policies such as those presented here will help other scientific software registries and repositories better serve their users and their disciplines.
Effects of sliding window variation in the performance of acceleration-based human activity recognition using deep learning models
Authors: Jaén-Vargas Milagros , Reyes Leiva Karla Miriam , Fernandes Francisco , Barroso Gonçalves Sérgio , Tavares Silva Miguel , Lopes Daniel Simões , Serrano Olmedo José Javier
Published: August 2022

Deep learning (DL) models are very useful for human activity recognition (HAR); these methods present better accuracy for HAR when compared to traditional, among other advantages. DL learns from unlabeled data and extracts features from raw data, as for the case of time-series acceleration. Sliding windows is a feature extraction technique. When used for preprocessing time-series data, it provides an improvement in accuracy, latency, and cost of processing. The time and cost of preprocessing can be beneficial especially if the window size is small, but how small can this window be to keep good accuracy? The objective of this research was to analyze the performance of four DL models: a simple deep neural network (DNN); a convolutional neural network (CNN); a long short-term memory network (LSTM); and a hybrid model (CNN-LSTM), when variating the sliding window size using fixed overlapped windows to identify an optimal window size for HAR. We compare the effects in two acceleration sources’: wearable inertial measurement unit sensors (IMU) and motion caption systems (MOCAP). Moreover, short sliding windows of sizes 5, 10, 15, 20, and 25 frames to long ones of sizes 50, 75, 100, and 200 frames were compared. The models were fed using raw acceleration data acquired in experimental conditions for three activities: walking, sit-to-stand, and squatting. Results show that the most optimal window is from 20–25 frames (0.20–0.25s) for both sources, providing an accuracy of 99,07% and F1-score of 87,08% in the (CNN-LSTM) using the wearable sensors data, and accuracy of 98,8% and F1-score of 82,80% using MOCAP data; similar accurate results were obtained with the LSTM model. There is almost no difference in accuracy in larger frames (100, 200). However, smaller windows present a decrease in the F1-score. In regard to inference time, data with a sliding window of 20 frames can be preprocessed around 4x (LSTM) and 2x (CNN-LSTM) times faster than data using 100 frames.
Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts
Authors: Hui Min , Wang Aiyang , Cheng Jiao , Sha Zhongli
Published: August 2022

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.
Development of a COVID-19 risk assessment model for participants at outdoor music festivals: evaluation of the validity and control measure effectiveness based on two actual events in Japan and Spain
Authors: Murakami Michio , Fujita Tsukasa , Li Pinqi , Imoto Seiya , Yasutaka Tetsuo
Published: August 2022

We developed an environmental exposure model to estimate the coronavirus disease 2019 (COVID-19) risk among participants at outdoor music festivals and validated the model using two real events—one in Japan (Event 1) and one in Spain (Event 2). Furthermore, we considered a hypothetical situation in which Event 1 was held but enhanced measures were implemented to evaluate the extent to which the risk could be reduced by additional infection control measures, such as negative antigen tests on the day of the event, wearing of masks, disinfection of environmental surfaces, and vaccination. Among 7,392 participants, the total number of already- and newly-infected individuals who participated in Event 1 according to the new model was 47.0 (95% uncertainty interval: 12.5–185.5), which is in good agreement with the reported value (45). The risk of infection at Event 2 (1.98 × 10−2; 95% uncertainty interval: 0.55 × 10−2–6.39 × 10−2), calculated by the model in this study, was also similar to the estimated value in the previous epidemiological study (1.25 × 10−2). These results for the two events in different countries highlighted the validity of the model. Among the additional control measures in the hypothetical Event 1, vaccination, mask-wearing, and disinfection of surfaces were determined to be effective. Based on the combination of all measures, a 94% risk reduction could be achieved. In addition to setting a benchmark for an acceptable number of newly-infected individuals at the time of an event, the application of this model will enable us to determine whether it is necessary to implement additional measures, limit the number of participants, or refrain from holding an event.
Imaginar otro mundo es posible: la producción del futuro en los tiempos del Antropoceno
Authors: Aguirre Orellana Gonzalo
Published: August 2022

Este ensayo explora el estudio del futuro, en relación a las transformaciones contemporáneas del medioambiente y sus representaciones. En lo cotidiano, el encuentro con imágenes que reflejan las crisis ambientales por las que pasa el planeta es algo común. Desde una sociología que toma al futuro como objeto de investigación, las imágenes que anticipan otros estados del mundo tienen poderosas consecuencias en el presente. Las ciencias sociales son centrales para analizar, debatir y alcanzar los futuros así anticipados. Sin embargo, la alta circulación de imágenes sobre el futuro climático, junto con las limitadas posibilidades de actuar significativamente en el presente, producen una sensación de impotencia reflexiva. El Antropoceno, nombre propuesto para designar la actual época geológica, problematiza nuestra forma de concebir el mundo, planteando preguntas sobre la forma en que lo humano y lo no humano enredan sus dominios. Por un lado, el Antropoceno anticipa condiciones climáticas mucho más duras en los tiempos que vienen. Por el otro, invita a buscar formas de producir nuevos y mejores futuros, donde existan mundos habitables. Todos los esfuerzos por alcanzar este fin son igualmente necesarios. Distintos dispositivos de anticipación, como el modelamiento del clima, la ficción y las mitologías, juegan un rol fundamental en la tarea de producirmundos en el futuro.
Reflexiones epistémicas acerca del estudio de la subjetividad en movimientos populares
Authors: Palumbo María Mercedes
Published: August 2022

El objetivo de este artículo es socializar una serie de reflexiones epistémicas acerca del estudio de los movimientos populares, particularmente en su abordaje desde el enfoque de la construcción de subjetividades. Estas reflexiones tienen su origen en un trabajo de investigación doctoral llevado adelante en vinculación con movimientos populares del Área Metropolitana de Buenos Aires, Argentina. Desde una perspectiva inscripta en las epistemologías críticas, se considera clave retomar la categoría de colocación, estructurante del pensamiento epistémico de Hugo Zemelman, en la búsqueda por tematizar el posicionamiento subjetivo de los/as investigadores en su presente histórico tanto como las mediaciones que operan en la relación de éstos/as con la realidad. Con base en una reelaboración de la categoría zemelmaniana, planteamos dos dimensiones de la colocación: el colocarse-entre y el colocarse-con. La primera dimensión da cuenta del carácter dinámico y complejo de la realidad social y sus influencias en la aproximación al objeto, las elecciones categoriales y las decisiones metodológicas tomadas por los/as investigadores. La segunda recupera la condición intersubjetiva que atraviesa el quehacer investigativo y sus implicancias en la subjetividad de los/as investigadores donde se entraman política, ética y epistemología. Las conclusiones advierten acerca de la centralidad de realizar ejercicios reflexivos sobre la práctica investigativa, partiendo de experiencias concretas, como aporte al necesario debate en torno a los procesos de construcción de conocimiento en el campo de las Ciencias Sociales.
Políticas de permisos parentales en Chile y Suiza desde una mirada institucional y de género
Authors: Vera Rojas Daniel
Published: August 2022

Los permisos parentales son instrumentos de política pública para la conciliación trabajo y vida familiar, brindando apoyo en tiempo y dinero a padres y madres con hijos/as recién nacidos. Estos permisos les permiten hacer una pausa en su actividad laboral remunerada con el fin de que puedan dedicarse a su cuidado. Específicamente, este estudio compara las políticas de permisos parentales de Chile y Suiza desde una perspectiva institucional y de género, analizando similitudes y diferencias en las dimensiones de generosidad, equidad de género y complementariedad entre cuidados y trabajo remunerado, y sus implicancias en políticas trabajo y familia. Usando un método comparativo internacional, los resultados muestran que en Chile conviven un arreglo de género tradicional y de doble proveedor y una política de permisos parentales que limita la equidad de género entre padres. En Suiza conviven un arreglo de género tradicional modificado y de doble proveedor, y una política de permiso parental que promueve moderadamente la corresponsabilidad de género.
Posiciones discursivas sobre la ciudadanía: tensiones entre la hegemonía adultista y la participación protagónica en centros educativos de Chile
Authors: Lay-Lisboa Siu , Yáñez-Yáñez Susan , Mercado Guerra Javier , Véliz-García Oscar
Published: August 2022

Se presenta un estudio cualitativo que tiene por objetivo describir las posiciones discursivas de estudiantes, docentes y familias respecto de la ciudadanía. Se realizaron 16 grupos de conversación a 107 participantes de centros educativos de dos ciudades chilenas. Tras un análisis estructural, los hallazgos dan cuenta de una estructura discursiva compuesta por diez posiciones discursivas. Encontramos dos grandes agrupaciones, la hegemónica (ciudadanía escolarizada, patriótica, burguesa, tutelada, infantilizadora, des-politizante y sexista) y la contra-hegemónica (contra-ciudadanía, cuerpo-parlante y protagónica). Estas posiciones se organizan en una estructura relacional que dispone y propone formas de comprender las distintas prácticas ciudadanas. Se concluye que el concepto hegemónico de ciudadanía regula las relaciones sociales para la formación de futuros ciudadanos y ciudadanas que logren convivir, integrar y reproducir una sociedad desigual. Asimismo, los espacios de enunciación de las disidencias o resistencias entregan pistas sobre las posibles grietas del modelo de ciudadanía que se impone en las escuelas.