Searching and Navigating UniProt Databases.

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt website receives about 800,000 unique visitors per month and is the primary means to access UniProt. It provides 10 searchable datasets and four main tools. The key UniProt datasets are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), the UniProt Archive (UniParc), and protein sets for completely sequenced genomes (Proteomes). Other supporting datasets include information about proteins that is present in UniProtKB protein entries, such as literature citations, taxonomy, and subcellular locations, among others. This article focuses on how to use UniProt datasets. The first basic protocol describes navigation and searching mechanisms for the UniProt datasets, and two additional protocols build on the first protocol to describe advanced search and query building. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Searching UniProt datasets Basic Protocol 2: Advanced search and query building Basis Protocol 3: Adding parameters using advanced search.

Twitter as research data Tools, costs, skill sets, and lessons learned.

Scholars increasingly use Twitter data to study the life sciences and politics. However, Twitter data collection tools often pose challenges for scholars who are unfamiliar with their operation. Equally important, although many tools indicate that they offer representative samples of the full Twitter archive, little is known about whether the samples are indeed representative of the targeted population of tweets. This article evaluates such tools in terms of costs, training, and data quality as a means to introduce Twitter data as a research tool. Further, using an analysis of COVID-19 and moral foundations theory as an example, we compared the distributions of moral discussions from two commonly used tools for accessing Twitter data (Twitter's standard APIs and third-party access) to the ground truth, the Twitter full archive. Our results highlight the importance of assessing the comparability of data sources to improve confidence in findings based on Twitter data. We also review the major new features of Twitter's API version 2.

Evaluating the influence of environmental variables on the length-weight relationship and prediction modelling in flathead grey mullet, Mugil cephalus Linnaeus, 1758.

Fish stocks that are grown under diverse environmental conditions have different biometric relationships and growth patterns. The biometric length-weight relationship (LWR) is an essential fishery assessment tool, as fish growth is continuous and depends on genetic and environmental factors. The present study attempts to understand the LWR of the flathead grey mullet, Mugil cephalus Linnaeus, 1758, from different locations. The study area encompassed its distribution in the wild across freshwater location (one), coastal habitats (eight locations), and estuaries (six locations) in India to determine the relationship between various environmental parameters. Specimens (n = 476) of M. cephalus were collected from commercial catches and the length and weight of individual specimens were recorded. Monthly data from the study locations were extracted for nine environmental variables from the datasets downloaded from the Physical Oceanography Distributed Active Archive Center (PO.DAAC) and the Copernicus Marine Environment Monitoring Service (CMEMS) over 16 years (2002 to 2017) on the Geographical Information System platform. The parameters of the LWR, intercept 'a' and slope or regression coefficient 'b', varied from 0.005321 to 0.22182 and 2.235 to 3.173, respectively. The condition factor ranged from 0.92 to 1.41. The partial least squares (PLS) score scatter plot matrix indicated differences in the environmental variables between the locations. PLS analysis of the regression coefficient and environment parameters revealed that certain environment variables viz., sea surface temperature, salinity, dissolved oxygen, nitrate, and phosphate, played a positive role. However, chlorophyll, pH, silicate, and iron played a negative role in influencing weight growth across various locations. The results revealed that the M. cephalus specimens from three locations, Mandapam, Karwar, and Ratnagiri, possessed significantly higher fitness to their environment than those from the other six locations. The PLS model can be used to predict weight growth under the various environmental conditions of different ecosystems. The three identified locations are useful sites for the mariculture of this species considering their growth performance, the environmental variables, and their interactions. The results of this study will improve the management and conservation of exploited stocks in regions affected by climate change. Our results will also aid in making environment clearance decisions for coastal development projects and will improve the efficiency of mariculture systems.

Fingerprints, barcode sequences and quasi-phylogenies-Tools for analysing polyphonic music.

A data flow is presented for visualising the evolution of elementary structures of polyphonic music from early Baroque to late Romantic, using quasi-phylogenies based on fingerprint diagrams and barcode sequence data of 2-tuples of consecutive vertical pitch class sets (pcs). The present methodological study, which sees itself as a proof of concept for a data-driven approach, uses examples of music from the Baroque, the Viennese School and the Romantic era to show that such quasi-phylogenies can be generated from multi-track MIDI (v. 1) files that largely correspond to the eras and the chronology of compositions and composers. The method presented is considered to have the potential to support the analysis of a wide range of musicological questions. In the context of collaborative work on quasi-phylogenies of polyphonic music, a public data archive could be established that provides multi-track MIDI files with contextual data.

On the artistic production of the alienated: history of theories and practices of Brazilian alienism, 1852-1902. / Da produção artística dos alienados: histórias de teorias e práticas do alienismo brasileiro, 1852-1902.

The article deals with the presence of artistic manifestations of inmates of the Hospício de Pedro II, the first psychiatric institution in Latin America (1852-1902). The methodological framework chosen focused on the historicisation of the framing processes of mental illness, in order to demonstrate its consequences for the notion of the subject and the art he produces and in the process of circulation of this knowledge in Brazil. Derrida's concept of archive fever was used to analyse the reasons why such manifestations and the therapies used based on them were ignored by local narratives about the artistic manifestations of individuals in asylums.

O artigo trata da presença de manifestações artísticas de internos do Hospício de Pedro II, primeira instituição psiquiátrica da América Latina (1852-1902). O referencial metodológico escolhido centrou-se na historicização dos processos de enquadramento das doenças mentais, com vistas a demonstrar suas consequências para a noção de sujeito e da arte que ele produz e no processo de circulação desses saberes no Brasil. O conceito de mal de arquivo, de Derrida, foi utilizado para analisar os motivos pelos quais tais manifestações e as terapêuticas utilizadas a partir delas foram ignoradas pelas narrativas locais acerca das manifestações artísticas de indivíduos internados em asilos.

The degree course in psychology in Rome in the history of Italian psychology.

Italian academic psychology found its first location in the Anthropological Museum of the Faculty of Natural Sciences at the University of Rome, where in 1890 a Laboratory of Experimental Psychology was established. In 1905, the first three Chairs of Experimental Psychology at the Universities of Turin, Rome, and Naples were created. These were followed in the subsequent years by others, until 1930, in other academic institutions. After many years and a long period of crisis linked to the fascist regime, only after the World War II (WWII), with the rebirth of the country, did psychology gradually rebuild its status as a scientific discipline. Within this framework of the renewal of society and university studies, in 1971, two degree courses were instituted in Rome and Padua. Based on research in central and local academic archives and on an analysis of the secondary literature, the gestation phase of the 4-year degree course in Psychology, the progressive establishment of the Psychology Departments, and the 5-year reform of the courses up to the birth of the first Faculty of Psychology at an Italian university are reconstructed. The aim of this article is to propose a well-founded discontinuist historiographical reading of the process of sedimentation of psychological experimentation that, after being born in the Faculty of Sciences and later transferring to the Faculty of Medicine and Surgery, also led to important developments in the Faculty of Education, with the recognition of an autonomous academic space of scientific discipline with a degree course, departments and finally the Faculty of Psychology. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Research in the Time of COVID: Virtual Fellowships at the Linda Hall Library.

When COVID-19 prevented scholars from traveling to libraries, archives, and museums, staff at those institutions devised creative strategies for providing remote access to their holdings. This article examines one such initiative launched by the Linda Hall Library of Science, Engineering, and Technology in Kansas City, Missouri. The Library's prioritization of print over archival materials, experience fulfilling document delivery requests, and investments in digitization infrastructure facilitated the transition to a completely virtual fellowship program during the 2021-22 academic year. Although virtual fellowships could not replicate every aspect of in-person residencies, they nonetheless supplied scholars with much-needed funding, research materials, and membership in a scholarly community. Based on the program's initial success, the Library plans to continue offering virtual fellowships to scholars otherwise unable to conduct research on site.

Value Exploration and Application of Digital Archive Information Resources under the Information Ecological Environment.

A significant amount of electronic documents have been produced as a result of the quick advancements in computer and network technology as well as the ongoing promotion of e-government, and the amount of material available in digital archives has significantly expanded. It is challenging for traditional archives focused on entity management to fulfil modern demands. It is essential to gradually encourage the creation of digital archives in order to meet the utilization needs of archival information resources in the information age. Many issues that are not favourable to the development and utilization of information resources of digital archives have gradually emerged in the course of the development and utilization of information resources of digital archives. These issues are influenced by a number of factors, including service concept and personnel information literacy. The related attributes of information resources are sorted and processed using the ID3 algorithm in this study. Decision-making attributes of management techniques are identified, and the data mining Apriori algorithm is used to address the issue of increasing the retrieval speed of users of digital archives. When the new software system is finished, archive resources can be developed and used in a complete and practical way, increasing the utilization efficiency of archive information resources by 37.32 percent. As a result, it is possible to fully exploit the information resources of the digital archives, further appreciate their value, and ensure their long-term growth.

Locura en el archivo: metodologías para el estudio de las disciplinas psi

No dia 09 de setembro de 2021 ocorreu o lançamento do livro Locura en el archivo: fuentes y metodologías para el estudio de las disicplinas psi, editado pela Universidad Nacional Autonoma de Mexico. Na ocasião do lançamento, o Encontro às Quintas, promovido pela Casa de Oswaldo Cruz, recebeu as pesquisadoras Teresa Ordorika (Universidade Nacional Autônoma do México), Alejandra Golcman (Universidade Nacional de Tucumán, Argentina) e Cristina Sacristán (Instituto Mora, México) para falarem sobre fontes e metodologias no estudo das disciplinas psi.

The Politics of Sources Meets the Practices of the Librarian: An Interview with Esther Chen.

[I] want to single out one phenomenon that could be called the 'politics of sources'. It points to the extent to which the histories that both scientists and historians can write are artifacts of the available sources. The Rockefeller Foundation not only opened its archives very early on for historical work but also invested a lot in making the archives readily available for historical exploration. During the 1980s, many young historians took advantage of this opportunity. Thus, in a relatively early phase of the professional historiography of molecular biology, one could have gained the impression that the development of the new biology as a whole was a bio-politically directed enterprise of the Rockefeller Foundation sustained by the vision that social processes could ultimately be controlled by biological processes.

New Meanings in the Archive: Privacy, Technological Change and the Status of Sources.

This essay reflects on how technological changes in biomedicine can affect what archival sources are available for historical research. Historians and anthropologists have examined the ways in which old biomedical samples can be made to serve novel scientific purposes, such as when decades-old frozen tissue specimens are analyzed using new genomic techniques. Those uses are also affected by shifting ethical regimes, which affect who can do what with old samples, or whether anything can be done with them at all. Archival collections are subject to similar dynamics, as institutional change and shifts in ethical guidelines and privacy laws affect which sources can be accessed and which are closed. I witnessed just such a change during my research into human genetics using archives in the Wellcome Collection. A few years into my project, those archives had their privacy conditions reassessed, and I saw how some sources previously seen as neutral were now understood to contain personal sensitive information. This paper describes the conditions of this shift-including the effects of technological change, new ethical considerations, and changing laws around privacy. I reflect on how these affected my understanding of the history of human genetics, and how I and others might narrate it.

[Images of chemistry kits: male dominance in representations of science]. / As imagens dos conjuntos científicos de química: dominância masculina nas representações sobre a ciência.

This article shows how images relating to chemistry sets express the predominance of the male gender in toys that simulate technical, gestural, and laboratory-related aspects of science, creating patterns of conduct towards the professional vocation of being a scientist. Priority is given to documents produced by the companies Gilbert (1920) and Chemcraft (1922) that are kept in the archives of the Chemical Heritage Foundation in the USA. What Joan Scott calls the social organization of sexual difference is discussed and the illustrations are analyzed, demonstrating a predominance of male figures showing how to "be a child," playing at being a scientist.

O artigo apresenta o modo como as imagens relativas aos conjuntos de química expressam as representações sobre a predominância do gênero masculino nas brincadeiras que simulam aspectos técnicos, gestuais, de laboratório, criando padrões de conduta que direcionam para a vocação profissional: o ser cientista. Foram privilegiadas as documentações produzidas pelas empresas Gilbert (1920) e Chemcraft (1922), presentes no acervo da Chemical Heritage Foundation (EUA). Discute-se o que Joan Scott chama de organização social da diferença sexual, enquanto são analisadas as ilustrações que privilegiam a dominância do gênero masculino, nas formas de "ser criança", brincando de cientista.

[Materialities and transnational scientific culture of objects: the 12th International Congress of Zoology, Lisbon, 1935]. / Materialidades e cultura científica transnacional dos objetos: o 12º Congresso Internacional de Zoologia, Lisboa, 1935.

The material memory of the 12th International Congress of Zoology, held in Lisbon in 1935 includes insignias - the starfish - and caricatures of zoologists. Through an investigation of the archives at the University of Lisbon's National Museum of Natural History and Science, we intend to investigate the material landscape as conceived by the zoologist Artur Ricardo Jorge by drawing epistemologically on the potentialities of the biography of scientific objects. This research note reveals a scientific discourse translated into materialities circulated in public spaces in the globalized Europe of the 1930s, with references from scientific power, in the context of Portugal's Estado Novo regime, enshrined in its 1933 constitution.

O 12º Congresso Internacional de Zoologia realizou-se em Lisboa, em 1935. Da sua memória concreta constam insígnias ­ estrela-do-mar ­ e caricaturas de zoólogos. A partir de investigação no Arquivo do Museu Nacional de História Natural e da Ciência/Universidade de Lisboa, pretendemos interrogar a cenografia material, pensada pelo zoólogo Artur Ricardo Jorge pela aproximação epistémica às potencialidades da biografia de objetos científicos. Esta nota de pesquisa pretende deixar a marca de um discurso científico traduzido em materialidades de circulação em espaço público, na Europa globalizante dos anos 1930, com referências de poder científico, no contexto do Estado Novo português, inaugurado, constitucionalmente, em 1933.

Medical record archives in the era of digitalisation.

No abstract available.