ResearchPad - History https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[The house sparrow in the service of basic and applied biology]]> https://www.researchpad.co/product?articleinfo=N574686f2-22b6-4aa0-aadf-a211a5623182

From the northernmost tip of Scandinavia to the southernmost corner of Patagonia, and across six continents, house sparrows (Passer domesticus) inhabit most human-modified habitats of the globe. With over 7,000 articles published, the species has become a workhorse for not only the study of self-urbanized wildlife, but also for understanding life history and body size evolution, sexual selection and many other biological phenomena. Traditionally, house sparrows were studied for their adaptations to local biotic and climatic conditions, but more recently, the species has come to serve as a focus for studies seeking to reveal the genomic, epigenetic and physiological underpinnings of success among invasive vertebrate species. Here, we review the natural history of house sparrows, highlight what the study of these birds has meant to bioscience generally, and describe the many resources available for future work on this species.

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<![CDATA[Claire Fraser, RN, MD, OMG: history of medicine in the Outlander novels and series]]> https://www.researchpad.co/product?articleinfo=N119debbf-57b9-4db2-883c-9c34840da79c

This article discusses how Claire Randall, RN, MD, the fictional protagonist of Diana Gabaldon’s widely popular Outlander series, uses her knowledge of twentieth century medicine in her adventures in eighteenth century Scotland, France, and America.

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<![CDATA[Modeling the Relationship of Groundwater Salinity to Neonatal and Infant Mortality From the Bangladesh Demographic Health Survey 2000 to 2014]]> https://www.researchpad.co/product?articleinfo=N282f9af1-03b6-46af-ab8d-637967f089d1

Abstract

We evaluated the relationship of drinking water salinity to neonatal and infant mortality using Bangladesh Demographic Health Surveys of 2000, 2004, 2007, 2011, and 2014. Point data of groundwater electrical conductivity (EC)— a measure of salinity—were collated from the Bangladesh Water Development Board and digitizing salinity contour map. Data for groundwater dissolved elements (sodium, calcium, magnesium, and potassium) data came from a national hydrochemistry survey in Bangladesh. Point EC and dissolved minerals data were then interpolated over entire Bangladesh and extracted to each cluster location, the primary sampling unit of Bangladesh Demographic Health Surveys. We used restricted cubic splines and survey design‐specific logistic regression models to determine the relationship of water salinity to neonatal and infant mortality. A U‐shaped association between drinking water salinity and neonatal and infant mortality was found, suggesting higher mortality when salinity was very low and high. Compared to mildly saline (EC ≥0.7 and < 2 mS/cm) water drinkers, freshwater (EC < 0.7 mS/cm) drinkers had 1.37 (95% CI: 1.01, 1.84) times higher neonatal mortality and 1.43 (95% CI: 1.08, 1.89) times higher infant mortality. Compared to mildly saline water drinkers, severe‐saline (EC ≥10 mS/cm) water drinkers had 1.77 (95% CI: 1.17, 2.68) times higher neonatal mortality and 1.93 (95% CI: 1.35, 2.76) times higher infant mortality. We found that mild‐salinity water had a high concentration of calcium and magnesium, whereas severe‐salinity water had a high concentration of sodium. Freshwater had the least concentrations of salubrious calcium and magnesium.

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<![CDATA[Alexander von Humboldt’s contribution to the biomedical sciences and scientific illustration. In honor of his 250th anniversary]]> https://www.researchpad.co/product?articleinfo=N14e7e037-0be4-4ad8-98d3-ea62c136a6b1

Alexander von Humboldt (1769–1859) is one of the most prominent Germans. His multidisciplinary activity set standards to science at the beginning of modern era. His personality is celebrated worldwide. The Alexander von Humboldt Foundation in Bonn is still preserving his memory and endorsing research in all the fields. This paper is a historical sketch presenting his contributions to the development of medical sciences and also to the progress of scientific illustrations. We also introduce personalities of the Cluj-Napoca medical school who were fellows of the Alexander von Humboldt Foundation.

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<![CDATA[The Most Influential Scientists in the Development of Medical Informatics (25): Rolf Hansen (1931-1993)]]> https://www.researchpad.co/product?articleinfo=Naa2e17e0-76dc-4489-bdca-8eb1343c8141 ]]> <![CDATA[IVF: The women who helped make it happen]]> https://www.researchpad.co/product?articleinfo=5c686359d5eed0c4840236c6

In this paper I pay tribute to four named women and 280 unidentified women patients for their essential roles in supporting Bob Edwards and Patrick Steptoe during the pioneering early days of IVF. The four named women are Jean Purdy, Muriel Harris, Lillian Lincoln Howell and Ruth Fowler.

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<![CDATA[Consolidated mathematical growth model of the primary tumor and secondary distant metastases of breast cancer (CoMPaS)]]> https://www.researchpad.co/product?articleinfo=5b4a287f463d7e4513b897f8

The goal of this research is to improve the accuracy of predicting the breast cancer (BC) process using the original mathematical model referred to as CoMPaS. The CoMPaS is the original mathematical model and the corresponding software built by modelling the natural history of the primary tumor (PT) and secondary distant metastases (MTS), it reflects the relations between the PT and MTS. The CoMPaS is based on an exponential growth model and consists of a system of determinate nonlinear and linear equations and corresponds to the TNM classification. It allows us to calculate the different growth periods of PT and MTS: 1) a non-visible period for PT, 2) a non-visible period for MTS, and 3) a visible period for MTS. The CoMPaS has been validated using 10-year and 15-year survival clinical data considering tumor stage and PT diameter. The following are calculated by CoMPaS: 1) the number of doublings for the non-visible and visible growth periods of MTS and 2) the tumor volume doubling time (days) for the non-visible and visible growth periods of MTS. The diameters of the PT and secondary distant MTS increased simultaneously. In other words, the non-visible growth period of the secondary distant MTS shrinks, leading to a decrease of the survival of patients with breast cancer. The CoMPaS correctly describes the growth of the PT for patients at the T1aN0M0, T1bN0M0, T1cN0M0, T2N0M0 and T3N0M0 stages, who does not have MTS in the lymph nodes (N0). Additionally, the CoMPaS helps to consider the appearance and evolution period of secondary distant MTS (M1). The CoMPaS correctly describes the growth period of PT corresponding to BC classification (parameter T), the growth period of secondary distant MTS and the 10-15-year survival of BC patients considering the BC stage (parameter M).

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<![CDATA[Inequity in out-of-pocket payments for hospitalisation in India: Evidence from the National Sample Surveys, 1995–2014]]> https://www.researchpad.co/product?articleinfo=5b58a831463d7e4da2d63a52

Objective

We report inequity in out-of-pocket payments (OOPP) for hospitalisation in India between 1995 and 2014 contrasting older population (60 years or more) with a population under 60 years (younger population).

Methods

We used data from nationwide healthcare surveys conducted in India by the National Sample Survey Organisation in 1995–96, 2004 and 2014 with the sample sizes ranging from 333,104 to 629,888. We used generalised linear and fractional response models to study the determinants of OOPP and their burden (share of OOPP in household consumption expenditure) at a constant price. The relationship between predicted OOPP and its burden with monthly per capita consumption expenditure (MPCE) quintiles and selected socioeconomic characteristics were used to examine vertical and horizontal inequities in OOPP.

Results

The older population had higher OOPP for hospitalisation at all time points (range: 1.15–1.48 times) and a greater increase between 1995–96 and 2014 than the younger population (2.43 vs 1.88 times). Between 1995–96 and 2014, the increase in predicted mean OOPP for hospitalisation was higher for the poorest than the richest (3.38 vs 1.85 times) older population. The increase in predicted mean OOPP was higher for the poorest (2.32 vs 1.46 times) and poor (2.87 vs 1.05 times) older population between 1995–96 and 2004 than in the latter decade. In 2014, across all MPCE quintiles, the burden of OOPP was higher for the less developed states, females, private hospitals, and non-communicable disease and injuries, more so for the older than the younger population. In 2014, the predicted absolute OOPP for hospitalisation was positively associated with MPCE quintiles; however, the burden of OOPP was negatively associated with MPCE quintiles indicating a regressive system of healthcare financing.

Conclusion

High OOPP for hospitalisation and greater inequity among older population calls for better risk pooling and prepayment mechanisms in India.

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<![CDATA[]]> https://www.researchpad.co/product?articleinfo=5b4cf31e463d7e123c5b854b ]]> <![CDATA[The rediscovery of Palmyra and its dissemination in Philosophical Transactions]]> https://www.researchpad.co/product?articleinfo=5bce087340307c536040dfab <![CDATA[Explaining the visible and the invisible: Public knowledge of genetics, ancestry, physical appearance and race in Colombia]]> https://www.researchpad.co/product?articleinfo=5bc6a5d040307c4e0b192334

Using data from focus groups conducted in Colombia, we explore how educated lay audiences faced with scenarios about ancestry and genetics draw on widespread and dominant notions of nation, race and belonging in Colombia to ascribe ancestry to collectivities and to themselves as individuals. People from a life sciences background tend to deploy idioms of race and genetics more readily than people from a humanities and race-critical background. When they considered individuals, people tempered or domesticated the more mechanistic explanations about racialized physical appearance, ancestry and genetics that were apparent at the collective level. Ideas of the latency and manifestation of invisible traits were an aspect of this domestication. People ceded ultimate authority to genetic science, but deployed it to work alongside what they already knew. Notions of genetic essentialism co-exist with the strategic use of genetic ancestry in ways that both fix and unfix race. Our data indicate the importance of attending to the different epistemological stances through which people define authoritative knowledge and to the importance of distinguishing the scale of resolution at which the question of diversity is being posed.

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<![CDATA[País de gordos/país de muertos: Obesity, death and nation in biomedical and forensic genetics in Mexico]]> https://www.researchpad.co/product?articleinfo=5bc6a5ce40307c4e0b192333

This article provides a comparison between genomic medicine and forensic genetics in Mexico, in light of recent depictions of the nation as a ‘país de gordos’ (country of the fat) and a ‘país de muertos’ (country of the dead). We examine the continuities and ruptures in the public image of genetics in these two areas of attention, health and security, focusing especially on how the relevant publics of genetic science are assembled in each case. Publics of biomedical and forensic genetics are assembled through processes of recruitment and interpellation, in ways that modulate current theorizations of co-production. The comparison also provides a vista onto discussions regarding the involvement of genetics in regimes of governance and citizenship and about the relationship between the state and biopower in a context of perceived health crisis and war-like violence.

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<![CDATA[Colombian forensic genetics as a form of public science: The role of race, nation and common sense in the stabilization of DNA populations]]> https://www.researchpad.co/product?articleinfo=5bc6a5c140307c4e0b19232f

This article examines the role that vernacular notions of racialized-regional difference play in the constitution and stabilization of DNA populations in Colombian forensic science, in what we frame as a process of public science. In public science, the imaginations of the scientific world and common-sense public knowledge are integral to the production and circulation of science itself. We explore the origins and circulation of a scientific object – ‘La Tabla’, published in Paredes et al. and used in genetic forensic identification procedures – among genetic research institutes, forensic genetics laboratories and courtrooms in Bogotá. We unveil the double life of this central object of forensic genetics. On the one hand, La Tabla enjoys an indisputable public place in the processing of forensic genetic evidence in Colombia (paternity cases, identification of bodies, etc.). On the other hand, the relations it establishes between ‘race’, geography and genetics are questioned among population geneticists in Colombia. Although forensic technicians are aware of the disputes among population geneticists, they use and endorse the relations established between genetics, ‘race’ and geography because these fit with common-sense notions of visible bodily difference and the regionalization of race in the Colombian nation.

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<![CDATA[Genetics against race: Science, politics and affirmative action in Brazil]]> https://www.researchpad.co/product?articleinfo=5bc6a5be40307c4e0b19232e

This article analyses interrelations between genetic ancestry research, political conflict and social identity. It focuses on the debate on race-based affirmative action policies, which have been implemented in Brazil since the turn of the century. Genetic evidence of high levels of admixture in the Brazilian population has become a key element of arguments that question the validity of the category of race for the development of public policies. In response, members of Brazil’s black movement have dismissed the relevance of genetics by arguing, first, that in Brazil race functions as a social – rather than a biological – category, and, second, that racial classification and discrimination in this country are based on appearance, rather than on genotype. This article highlights the importance of power relations and political interests in shaping public engagements with genetic research and their social consequences.

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<![CDATA[Building the genomic nation: ‘Homo Brasilis’ and the ‘Genoma Mexicano’ in comparative cultural perspective]]> https://www.researchpad.co/product?articleinfo=5bc6a5c440307c4e0b192330

This article explores the relationship between genetic research, nationalism and the construction of collective social identities in Latin America. It makes a comparative analysis of two research projects – the ‘Genoma Mexicano’ and the ‘Homo Brasilis’ – both of which sought to establish national and genetic profiles. Both have reproduced and strengthened the idea of their respective nations of focus, incorporating biological elements into debates on social identities. Also, both have placed the unifying figure of the mestizo/mestiço at the heart of national identity constructions, and in so doing have displaced alternative identity categories, such as those based on race. However, having been developed in different national contexts, these projects have had distinct scientific and social trajectories: in Mexico, the genomic mestizo is mobilized mainly in relation to health, while in Brazil the key arena is that of race. We show the importance of the nation as a frame for mobilizing genetic data in public policy debates, and demonstrate how race comes in and out of focus in different Latin American national contexts of genomic research, while never completely disappearing.

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<![CDATA[Genomic research, publics and experts in Latin America: Nation, race and body]]> https://www.researchpad.co/product?articleinfo=5bc6a5cb40307c4e0b192332

The articles in this issue highlight contributions that studies of Latin America can make to wider debates about the effects of genomic science on public ideas about race and nation. We argue that current ideas about the power of genomics to transfigure and transform existing ways of thinking about human diversity are often overstated. If a range of social contexts are examined, the effects are uneven. Our data show that genomic knowledge can unsettle and reinforce ideas of nation and race; it can be both banal and highly politicized. In this introduction, we outline concepts of genetic knowledge in society; theories of genetics, nation and race; approaches to public understandings of science; and the Latin American contexts of transnational ideas of nation and race.

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<![CDATA[Generalization through similarity: motif discourse in the discovery and elaboration of zinc finger proteins]]> https://www.researchpad.co/product?articleinfo=5b7d92c4463d7e1bdfb00269

Background

Biological organisms and their components are better conceived within categories based on similarity rather than on identity. Biologists routinely operate with similarity-based concepts such as "model organism" and "motif." There has been little exploration of the characteristics of the similarity-based categories that exist in biology. This study uses the case of the discovery and classification of zinc finger proteins to explore how biological categories based in similarity are represented.

Results

The existence of a category of "zinc finger proteins" was based in 1) a lumpy gradient of similarity, 2) a link between function and structure, 3) establishment of a range of appearance across systems and organisms, and 4) an evolutionary locus as a historically based common-ground.

Conclusion

More systematic application of the idea of similarity-based categorization might eliminate the assumption that biological characteristics can only contribute to narrow categorization of humans. It also raises possibilities for refining data-driven exploration efforts.

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<![CDATA[Corpus Refactoring: a Feasibility Study]]> https://www.researchpad.co/product?articleinfo=5b7d1d2b463d7e3b62b87738

Background

Most biomedical corpora have not been used outside of the lab that created them, despite the fact that the availability of the gold-standard evaluation data that they provide is one of the rate-limiting factors for the progress of biomedical text mining. Data suggest that one major factor affecting the use of a corpus outside of its home laboratory is the format in which it is distributed. This paper tests the hypothesis that corpus refactoring – changing the format of a corpus without altering its semantics – is a feasible goal, namely that it can be accomplished with a semi-automatable process and in a time-effcient way. We used simple text processing methods and limited human validation to convert the Protein Design Group corpus into two new formats: WordFreak and embedded XML. We tracked the total time expended and the success rates of the automated steps.

Results

The refactored corpus is available for download at the BioNLP SourceForge website http://bionlp.sourceforge.net. The total time expended was just over three person-weeks, consisting of about 102 hours of programming time (much of which is one-time development cost) and 20 hours of manual validation of automatic outputs. Additionally, the steps required to refactor any corpus are presented.

Conclusion

We conclude that refactoring of publicly available corpora is a technically and economically feasible method for increasing the usage of data already available for evaluating biomedical language processing systems.

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<![CDATA[Nano-Bio-Genesis: tracing the rise of nanotechnology and nanobiotechnology as 'big science']]> https://www.researchpad.co/product?articleinfo=5b7ce83d463d7e27ec65a7ca

Nanotechnology research has lately been of intense interest because of its perceived potential for many diverse fields of science. Nanotechnology's tools have found application in diverse fields, from biology to device physics. By the 1990s, there was a concerted effort in the United States to develop a national initiative to promote such research. The success of this effort led to a significant influx of resources and interest in nanotechnology and nanobiotechnology and to the establishment of centralized research programs and facilities. Further government initiatives (at federal, state, and local levels) have firmly cemented these disciplines as 'big science,' with efforts increasingly concentrated at select laboratories and centers. In many respects, these trends mirror certain changes in academic science over the past twenty years, with a greater emphasis on applied science and research that can be more directly utilized for commercial applications.

We also compare the National Nanotechnology Initiative and its successors to the Human Genome Project, another large-scale, government funded initiative. These precedents made acceptance of shifts in nanotechnology easier for researchers to accept, as they followed trends already established within most fields of science. Finally, these trends are examined in the design of technologies for detection and treatment of cancer, through the Alliance for Nanotechnology in Cancer initiative of the National Cancer Institute. Federal funding of these nanotechnology initiatives has allowed for expansion into diverse fields and the impetus for expanding the scope of research of several fields, especially biomedicine, though the ultimate utility and impact of all these efforts remains to be seen.

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<![CDATA[Applied information retrieval and multidisciplinary research: new mechanistic hypotheses in Complex Regional Pain Syndrome]]> https://www.researchpad.co/product?articleinfo=5b7c6909463d7e17f029b044

Background

Collaborative efforts of physicians and basic scientists are often necessary in the investigation of complex disorders. Difficulties can arise, however, when large amounts of information need to reviewed. Advanced information retrieval can be beneficial in combining and reviewing data obtained from the various scientific fields. In this paper, a team of investigators with varying backgrounds has applied advanced information retrieval methods, in the form of text mining and entity relationship tools, to review the current literature, with the intention to generate new insights into the molecular mechanisms underlying a complex disorder. As an example of such a disorder the Complex Regional Pain Syndrome (CRPS) was chosen. CRPS is a painful and debilitating syndrome with a complex etiology that is still unraveled for a considerable part, resulting in suboptimal diagnosis and treatment.

Results

A text mining based approach combined with a simple network analysis identified Nuclear Factor kappa B (NFκB) as a possible central mediator in both the initiation and progression of CRPS.

Conclusion

The result shows the added value of a multidisciplinary approach combined with information retrieval in hypothesis discovery in biomedical research. The new hypothesis, which was derived in silico, provides a framework for further mechanistic studies into the underlying molecular mechanisms of CRPS and requires evaluation in clinical and epidemiological studies.

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