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Minha intenção, no presente artigo, é a de fornecer certos elementos permitindo-nos compreender como a ciência moderna ( a que se constituiu a partir do século XVII ) já nasceu como instituição marcadamente "patriarcal" e ”machista“.

Conta a História do Brasil que Pedro Álvares Cabral desembarcou em Porto Seguro, lugar de calmaria, de tranquilidade e de segurança. Lugar onde as caravelas portuguesas abrigaram-se, ficaram protegidas contra as intempéries do tempo e as borrascas do mar. Verdadeira ou não essa estória, gostaria de utilizar a metáfora do ’'Porto Seguro” para postular a instauração de uma pedagogia da incerteza, da insegurança e da provisoriedade, incapaz de parâmetros dogmáticos e absolutos ou de verdades definitivas.

*O presente trabalho foi encomendado no ano de 2014, por ocasião de conferência ministrada pelo Prof.Hilton Japiassú na UFT. Após a conferência, a então gestão da Universidade Federal do Tocantins instituiu o Prêmio Hilton Japiassú de Excelência em Pesquisa, através de sua Pró-Reitoria de Pesquisa e Pós-graduação. Em homenagem ao referido professor, a comissão editorial de Desafios decidiu manter o texto original, tal como foi enviado em sua primeira versão. O Prof.Hilton Japiassu faleceu, no Rio de Janeiro, no ano de 2015.

*O presente trabalho foi encomendado no ano de 2014, por ocasião de conferência ministrada pelo Prof.Hilton Japiassú na UFT. Após a conferência, a então gestão da Universidade Federal do Tocantins instituiu o Prêmio Hilton Japiassú de Excelência em Pesquisa, através de sua Pró-Reitoria de Pesquisa e Pós-graduação. Em homenagem ao referido professor, a comissão editorial de Desafios decidiu manter o texto original, tal como foi enviado em sua primeira versão. O Prof.Hilton Japiassu faleceu, no Rio de Janeiro, no ano de 2015.

Abstract Background There is recent interest in the role of carotid bifurcation anatomy, geometry and hemodynamic factors in the pathogenesis of carotid artery atherosclerosis. Certain anatomical and geometric configurations at the carotid bifurcation have been linked to disturbed flow. It has been proposed that vascular dimensions are selected to minimize energy required to maintain blood flow, and that this occurs when an exponent of 3 relates the radii of parent and daughter arteries. We evaluate whether the dimensions of bifurcation of the extracranial carotid artery follow this principle of minimum work. Methods This study involved subjects who had computed tomographic angiography (CTA) at our institution between 2006 and 2007. Radii of the common, internal and external carotid arteries were determined. The exponent was determined for individual bifurcations using numerical methods and for the sample using nonlinear regression. Results Mean age for 45 participants was 56.9 ± 16.5 years with 26 males. Prevalence of vascular risk factors was: hypertension-48%, smoking-23%, diabetes-16.7%, hyperlipidemia-51%, ischemic heart disease-18.7%. The value of the exponent ranged from 1.3 to 1.6, depending on estimation methodology. Conclusions The principle of minimum work (defined by an exponent of 3) may not apply at the carotid bifurcation. Additional factors may play a role in the relationship between the radii of the parent and daughter vessels.

A significação aparente da ciência encontra-se nas intenções subjetivas dos próprios cientistas, cuja preocupação fundamental seria a busca do conhecimento,e nas intenções dos que elaboram a política científica, tendo em vista o aumento da produção de bens como decorrência da produção de conhecimentos.O cientista, no mundo atual, saiu da ficção neutralista e com ele a ciência. Por isso estamos diante de dois mitos da ciência: o mito da ciência-que-conduz-necessariamente-ao-progresso e o da ciência-pura-e-imaculada. Segundo o primeiro a ciência se expõe a ser julgada pelo valor social de seus resultados e de acordo com o segundo a ciência é seu próprio fim,não tendo que prestar contas a nenhuma instância exterior. Se há crise na ciência é porque os cientistas se interrogam sobre a significação e função reais, na sociedade, de seus trabalhos (H.B.) Abstract One can find the apparent meaning of science in the subjective intentions of the scientists themselves, in which the fundamental preocupation would be the search of knowledge, and in the intentions of those who are responsible for science policy, having in mind the growth of the produce of wealth as a resultof the produce of knowledge.Nowadays the neutrality was left out by the scientist and so was science. That's why we're facing the twomyths of science: the science that leads to progressand the pure and immaculate one. According to the first one science exposes itself to be judged by the social value of its results, whereas to the secondone science is not affected by any exterior instance. Whether there's a crisis in science it is because the scientists ask themselves about the real meaning and function of their works in society.(M.P.)

The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative research project aimed at identifying all the functional elements in the human and mouse genomes. Data generated by the ENCODE consortium are freely accessible at the ENCODE portal (https://www.encodeproject.org/), which is developed and maintained by the ENCODE Data Coordinating Center (DCC). Since the initial portal release in 2013, the ENCODE DCC has updated the portal to make ENCODE data more findable, accessible, interoperable and reusable. Here, we report on recent updates, including new ENCODE data and assays, ENCODE uniform data processing pipelines, new visualization tools, a dataset cart feature, unrestricted public access to ENCODE data on the cloud (Amazon Web Services open data registry, https://registry.opendata.aws/encode-project/) and more comprehensive tutorials and documentation., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Brevibacillus laterosporus is often present in beehives, including presence in hives infected with the causative agent of American Foulbrood (AFB), Paenibacillus larvae . In this work, 12 B. laterosporus bacteriophages induced bactericidal products in their host. Results demonstrate that P. larvae is susceptible to antimicrobials induced from field isolates of the bystander, B. laterosporus . Bystander antimicrobial activity was specific against the pathogen and not other bacterial species, indicating that the production was likely due to natural competition between the two bacteria. Three B. laterosporus phages were combined in a cocktail to treat AFB. Healthy hives treated with B. laterosporus phages experienced no difference in brood generation compared to control hives over 8 weeks. Phage presence in bee larvae after treatment rose to 60.8 ± 3.6% and dropped to 0 ± 0.8% after 72 h. In infected hives the recovery rate was 75% when treated, however AFB spores were not susceptible to the antimicrobials as evidenced by recurrence of AFB. We posit that the effectiveness of this treatment is due to the production of the bactericidal products of B. laterosporus when infected with phages resulting in bystander-killing of P. larvae . Bystander phage therapy may provide a new avenue for antibacterial production and treatment of disease.

We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course at Brigham Young University. The phages were isolated primarily from bee debris and lysogens.

We present here the complete genomes of eight phages that infect Paenibacillus larvae , the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA., (Copyright © 2018 Walker et al.)

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Database Url: https://www.encodeproject.org/.

Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages., (Copyright © 2017 Esplin et al.)

Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.

Some cyanobacteria are capable of differentiating a variety of cell types in response to environmental factors. For instance, in low nitrogen conditions, some cyanobacteria form heterocysts, which are specialized for N2 fixation. Many heterocyst-forming cyanobacteria have DNA elements interrupting key N2 fixation genes, elements that are excised during heterocyst differentiation. While the mechanism for the excision of the element has been well-studied, many questions remain regarding the introduction of the elements into the cyanobacterial lineage and whether they have been retained ever since or have been lost and reintroduced. To examine the evolutionary relationships and possible function of DNA sequences that interrupt genes of heterocyst-forming cyanobacteria, we identified and compared 101 interruption element sequences within genes from 38 heterocyst-forming cyanobacterial genomes. The interruption element lengths ranged from about 1 kb (the minimum able to encode the recombinase responsible for element excision), up to nearly 1 Mb. The recombinase gene sequences served as genetic markers that were common across the interruption elements and were used to track element evolution. Elements were found that interrupted 22 different orthologs, only five of which had been previously observed to be interrupted by an element. Most of the newly identified interrupted orthologs encode proteins that have been shown to have heterocyst-specific activity. However, the presence of interruption elements within genes with no known role in N2 fixation, as well as in three non-heterocyst-forming cyanobacteria, indicates that the processes that trigger the excision of elements may not be limited to heterocyst development or that the elements move randomly within genomes. This comprehensive analysis provides the framework to study the history and behavior of these unique sequences, and offers new insight regarding the frequency and persistence of interruption elements in heterocyst-forming cyanobacteria.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL: www.encodeproject.org., (© The Author(s) 2016. Published by Oxford University Press.)

Brevibacillus laterosporus has been isolated from many different environments, including beehives, and produces compounds that are toxic to many organisms. Five B. laterosporus phages have been isolated previously. Here, we announce five additional phages that infect this bacterium, including the first B. laterosporus siphoviruses to be discovered., (Copyright © 2015 Merrill et al.)

Biological N2 fixation is an important nitrogen source for surface ocean microbial communities. However, nearly all information on the diversity and gene expression of organisms responsible for oceanic N2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. Using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from the Amazon River plume, an area characterized by salinity and nutrient gradients. Diazotroph genome and transcript sequences were most abundant in the transitional waters compared with lower salinity or oceanic water masses. We were able to distinguish two genetically divergent phylotypes within the Hemiaulus-associated Richelia sequences, which were the most abundant diazotroph sequences in the data set. Photosystem (PS)-II transcripts in Richelia populations were much less abundant than those in Trichodesmium, and transcripts from several Richelia PS-II genes were absent, indicating a prominent role for cyclic electron transport in Richelia. In addition, there were several abundant regulatory transcripts, including one that targets a gene involved in PS-I cyclic electron transport in Richelia. High sequence coverage of the Richelia transcripts, as well as those from Trichodesmium populations, allowed us to identify expressed regions of the genomes that had been overlooked by genome annotations. High-coverage genomic and transcription analysis enabled the characterization of distinct phylotypes within diazotrophic populations, revealed a distinction in a core process between dominant populations and provided evidence for a prominent role for noncoding RNAs in microbial communities.

Diatoms with symbiotic N₂-fixing cyanobacteria are often abundant in the oligotrophic open ocean gyres. The most abundant cyanobacterial symbionts form heterocysts (specialized cells for N₂ fixation) and provide nitrogen (N) to their hosts, but their morphology, cellular locations and abundances differ depending on the host. Here we show that the location of the symbiont and its dependency on the host are linked to the evolution of the symbiont genome. The genome of Richelia (found inside the siliceous frustule of Hemiaulus) is reduced and lacks ammonium transporters, nitrate/nitrite reductases and glutamine:2-oxoglutarate aminotransferase. In contrast, the genome of the closely related Calothrix (found outside the frustule of Chaetoceros) is more similar to those of free-living heterocyst-forming cyanobacteria. The genome of Richelia is an example of metabolic streamlining that has implications for the evolution of N₂-fixing symbiosis and potentially for manipulating plant-cyanobacterial interactions.

The maturation of emergency medicine (EM) as a specialty has coincided with dramatic increases in emergency department (ED) visit rates, both in the United States and around the world. ED crowding has become a public health problem where periodic supply and demand mismatches in ED and hospital resources cause long waiting times and delays in critical treatments. ED crowding has been associated with several negative clinical outcomes, including higher complication rates and mortality. This article describes emergency care systems and the extent of crowding across 15 countries outside of the United States: Australia, Canada, Denmark, Finland, France, Germany, Hong Kong, India, Iran, Italy, The Netherlands, Saudi Arabia, Catalonia (Spain), Sweden, and the United Kingdom. The authors are local emergency care leaders with knowledge of emergency care in their particular countries. Where available, data are provided about visit patterns in each country; however, for many of these countries, no national data are available on ED visits rates or crowding. For most of the countries included, there is both objective evidence of increases in ED visit rates and ED crowding and also subjective assessments of trends toward higher crowding in the ED. ED crowding appears to be worsening in many countries despite the presence of universal health coverage. Scandinavian countries with robust systems to manage acute care outside the ED do not report crowding is a major problem. The main cause for crowding identified by many authors is the boarding of admitted patients, similar to the United States. Many hospitals in these countries have implemented operational interventions to mitigate crowding in the ED, and some countries have imposed strict limits on ED length of stay (LOS), while others have no clear plan to mitigate crowding. An understanding of the causes and potential solutions implemented in these countries can provide a lens into how to mitigate ED crowding in the United States through health policy interventions and hospital operational changes., (© 2011 by the Society for Academic Emergency Medicine.)

Objectives: The primary study aim was to examine the variations in crowding when an emergency department (ED) initiates ambulance diversion., Methods: This retrospective, multicenter study included nine geographically disparate EDs. Daily ED operational variables were collected during a 12-month period (January 2009 to December 2009), including total number of ED visits, mean overall length of stay (LOS), number of ED beds, and hours on ambulance diversion. The primary outcome variable was the "ED workload rate," a surrogate marker for daily ED crowding. It was calculated as the total number of daily ED visits multiplied by the overall mean LOS (in hours) and divided by the number of ED beds available for acute treatment in a given day. The primary predictor variables were ambulance diversion, as a dichotomous variable of whether or not an ED went on diversion at least once during a 24-hour period, diversion hour quintiles, and sites., Results: The annual ED census ranged from 43,000 to 101,000 patients. The percentage of days that an ED went on diversion at least once varied from 4.9% to 86.6%. On days with ambulance diversion, the mean ED workload rate varied from 17.1 to 62.1 patient LOS hours per ED bed among sites. The magnitude of variation in ED workload rate was similar on days without ambulance diversion. Differences in ED workload rate varied among sites, ranging from 1.0 to 6.0 patient LOS hours per ED bed. ED workload rate was higher on average on diversion days compared to nondiversion days. The mean difference between diversion and nondiversion was statistically significant for the majority of sites., Conclusions: There was marked variation in ED workload rates and whether or not ambulance diversion occurred during a 24-hour period. This variability in initiating ambulance diversion suggests different or inconsistently applied decision-making criteria for initiating diversion., (© 2011 by the Society for Academic Emergency Medicine.)

The decision to admit a patient to the hospital after an emergency department (ED) visit is expensive, frequently not evidence-based, and variable. Outpatient critical pathways are a promising approach to reduce hospital admission after emergency care. Critical pathways exist to risk stratify patients for potentially serious diagnoses (e.g., acute myocardial infarction [AMI]) or evaluate response to therapy (e.g., community-acquired pneumonia) within a short time period (i.e., less than 36 hours), to determine if further hospital-based acute care is needed. Yet, such pathways are variably used while many patients are admitted for conditions for which they could be treated as outpatients. In this article, the authors propose a model of post-ED critical pathways, describe their role in emergency care, list common diagnoses that are amenable to critical pathways in the outpatient setting, and propose a research agenda to address barriers and solutions to increase the use of outpatient critical pathways. If emergency providers are to routinely conduct rapid evaluations in outpatient or observation settings, they must have several conditions at their disposal: 1) evidence-based tools to accurately risk stratify patients for protocolized care, 2) systems of care that reliably facilitate workup in the outpatient setting, and 3) a medical environment conducive to noninpatient pathways, with aligned risks and incentives among patients, providers, and payers. Increased use of critical pathways after emergency care is a potential way to improve the value of emergency care., (© 2011 by the Society for Academic Emergency Medicine.)

In 2006, the Institute of Medicine (IOM) advanced the concept of "coordinated, regionalized, and accountable emergency care systems" to address significant problems with the delivery of emergency medical care in the United States. Achieving this vision requires the thoughtful implementation of well-aligned, system-level structures and processes that enhance access to emergency care and improve patient outcomes at a sustainable cost. Currently, the delivery of emergency medical care is supported by numerous administrative systems, including economic; reimbursement; legal and regulatory structures; licensure, credentialing, and accreditation processes; medicolegal systems; and quality reporting mechanisms. In addition, many regionalized systems may not optimize patient outcomes because of current administrative barriers that make it difficult for providers to deliver the best care. However, certain administrative barriers may also threaten the sustainability of integration efforts or prevent them altogether. This article identifies significant administrative challenges to integrating networks of emergency care in four specific areas: reimbursement, medical-legal, quality reporting mechanisms, and regulatory aspects. The authors propose a research agenda for indentifying optimal approaches that support consistent access to quality emergency care with improved outcomes for patients, at a sustainable cost. Researching administrative challenges will involve careful examination of the numerous natural experiments in the recent past and will be crucial to understand the impact as we embark on a new era of health reform., (2010 by the Society for Academic Emergency Medicine.)

Objectives: This study sought to determine if emergency department (ED) crowding was associated with longer ED length of stay (LOS) and time to ordering medications (nebulizers and steroids) in patients treated and discharged with acute asthma and to study how delays in ordering may affect the relationship between ED crowding and ED LOS., Methods: A retrospective cohort study was performed in adult ED patients aged 18 years and older with a primary International Classification of Diseases, 9th Revision (ICD-9), diagnosis of asthma who were treated and discharged from two EDs from January 1, 2007, to January 1, 2009. Four validated measures of ED crowding (ED occupancy, waiting patients, admitted patients, and patient-hours) were assigned at the time of triage. The associations between the level of ED crowding and overall LOS and time to treatment orders were tested by analyzing trends across crowding quartiles, testing differences between the highest and lowest quartiles using Hodges-Lehmann distances, and using relative risk (RR) regression for multivariable analysis., Results: A total of 1,716 patients were discharged with asthma over the study period (932 at the academic site and 734 at the community site). LOS was longer at the academic site than the community site for asthma patients by 90 minutes (95% confidence interval [CI] = 79 to 101 minutes). All four measures of ED crowding were associated with longer LOS and time to treatment order at both sites (p < 0.001). At the highest level of ED occupancy, patients spent 75 minutes (95% CI = 58 to 93 minutes) longer in the ED compared to the lowest quartile of ED occupancy. In addition, comparing the highest and lowest quartiles of ED occupancy, time to nebulizer order was 6 minutes longer (95% CI = 1 to 13 minutes), and time to steroid order was 16 minutes longer (95% CI = 0 to 38 minutes). In the multivariable analysis, the association between ED crowding and LOS remained significant. Delays in nebulizer and steroid orders explained some, but not all, of the relationship between ED crowding and ED LOS., Conclusions: Emergency department crowding is associated with longer ED LOS (by more than 1 hour) in patients who ultimately get discharged with asthma flares. Some but not all of longer LOS during crowded times is explained by delays in ordering asthma medications.

Emergency department (ED) crowding has been identified as a major public health problem in the United States by the Institute of Medicine. ED crowding not only is associated with poorer patient outcomes, but it also contributes to lost demand for ED services when patients leave without being seen and hospitals must go on ambulance diversion. However, somewhat paradoxically, ED crowding may financially benefit hospitals. This is because ED crowding allows hospitals to maximize occupancy with well-insured, elective patients while patients wait in the ED. In this article, the authors propose a more holistic model of hospital flow and revenue that contradicts this notion and offer suggestions for improvements in ED and hospital management that may not only reduce crowding and improve quality, but also increase hospital revenues. Also proposed is that increased efficiency and quality in U.S. hospitals will require changes in systematic microeconomic and macroeconomic incentives that drive the delivery of health services in the United States. Finally, the authors address several questions to propose mutually beneficial solutions to ED crowding that include the realignment of hospital incentives, changing culture to promote flow, and several ED-based strategies to improve ED efficiency.