Search results for: catalog

Authors: Lesley Northrop, Justin DeGrazia, Jessica Greenwood

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ASPIRA Labs now offers an en-suit and ready-to-implement technology transfer solution to enable labs and hospitals that lack the resources to build it themselves to offer in-house genetic testing. This unique platform employs a patented Molecular Inversion Probe (MIP) technology that combines the specificity of a hybrid capture protocol with the ease of an amplicon-based protocol and utilizes an advanced bioinformatics analysis pipeline based on machine learning. To demonstrate its efficacy, two independent genetic tests were validated on this technology transfer platform: expanded carrier screening (ECS) and hereditary cancer testing (HC). The analytical performance of ECS and HC was validated separately in a blinded manner for calling three different types of variants: SNVs, short indels (typically, <50 bp), and large indels/CNVs defined as multi-exonic del/dup events. The reference set was constructed using samples from Coriell Institute, an external clinical genetic testing laboratory, Maine Molecular Quality Controls Inc. (MMQCI), SeraCare and GIAB Consortium. Overall, the analytical performance showed a sensitivity and specificity of >99.4% for both ECS and HC in detecting SNVs. For indels, both tests reported specificity of 100%, and ECS demonstrated a sensitivity of 100%, whereas HC exhibited a sensitivity of 96.5%. The bioinformatics pipeline also correctly called all reference CNV events resulting in a sensitivity of 100% for both tests. No additional calls were made in the HC panel, leading to a perfect performance (specificity and F-measure of 100%). In the carrier panel, however, three additional positive calls were made outside the reference set. Two of these calls were confirmed using an orthogonal method and were re-classified as true positives leaving only one false positive. The pipeline also correctly identified all challenging carrier statuses, such as positive cases for spinal muscular atrophy and alpha-thalassemia, resulting in 100% sensitivity. After confirmation of additional positive calls via long-range PCR and MLPA, specificity for such cases was estimated at 99%. These performance metrics demonstrate that this tech-transfer solution can be confidently internalized by clinical labs and hospitals to offer mainstream ECS and HC as part of their test catalog, substantially increasing access to quality germline genetic testing for labs of all sizes and resources levels.

Keywords: clinical genetics, genetic testing, molecular genetics, technology transfer

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Authors: Juan Manuel Brito-Diaz

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The emergence of urban environmentalism in Spain is related to the processes of economic transformation and growing urbanization that occurred during the end of the Franco regime and the democratic transition. This paper analyzes the urban environmental mobilizations and their impacts as relevant democratizing agents in the processes of political change in cities. It’s an under-researched topic and studies on environmental movements in Spain have paid little attention to it. This research takes as its starting point the close link between democratization and environmentalism, since it considers that environmental conflicts are largely a consequence of democratic problems, and that the impacts of environmental movements are directly linked to the democratization. The study argues that the environmental movements that emerged in Spain at the end of the dictatorship and the democratic transition are an important part of the broad and complex associative fabric that promoted the democratization process. The research focuses on investigating the environmental protest in Las Palmas de Gran Canaria—the most important city in the Canary Islands—between 1970 and 1983, concurrently with the last local governments of the dictatorship and the first democratic city councils. As it is a case study, it opens up the possibility to ask multiple specific questions and assess each of the responses obtained. Although several research methodologies have been applied, such as the analysis of historical archives documentation or oral history interviews, mainly a very widespread methodology in the sociology of social movements, although very little used by social historians, has been used: the Protest Event Analysis (PEA). This methodology, which consists of generating a catalog of protest events by coding data around previously established variables, has allowed me to map, analyze and interpret the occurrence of protests over time and space, and associated factors, through content analysis. For data collection, news from local newspapers have provided a large enough sample to analyze the properties of social protest -frequency, size, demands, forms, organizers, etc.—and relate them to another type of information related to political structures and mobilization repertoires, encouraging the establishment of connections between the protest and the political impacts of urban movements. Finally, the study argues that the environmental movements of this period were essential to the construction of the new democratic city in Spain, not only because they established the issues of sustainability and urban environmental justice on the public agenda, but also because they proposed that conflicts derived from such matters should ultimately be resolved through public deliberation and citizen participation.

Keywords: democratization, environmental movements, political impacts, social movements

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Authors: Kailash Chandra, Devanshu Gupta

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The Himalayan Mountains of India fall under two biogeographic zones Trans Himalaya (TH) and Himalaya and seven biotic provinces (TH-Ladakh Mountains, TH-Tibetan Plateau, TH-Sikkim, North-West Himalaya, West Himalaya, Central Himalaya, and East Himalaya). Because of the extreme environment and altitudinal variations, unique physiography, varied ecological conditions, and different vegetations, the Himalaya exhibit a rich assemblage of life, both flora, and fauna, further subjected to the impacts of climate change. To the authors’ best knowledge, there is no comprehensive account except for sporadic faunal investigations, to assess or interpret the insect diversity and their biogeographic distribution in Indian Himalaya (IH), one of the biodiversity hotspots. Therefore, in this paper, a compelling review of the extensive knowledge of insect diversity of IH is presented for the first time to the best of our knowledge. The inventory of the known insect species of IH was compiled from the exploration cum faunal-study data ready with the zoological survey of India, Kolkata as well as from the information published in the scientific literature till date. The species were listed with their valid names with their distribution in seven biotic provinces of IH. The insect fauna of IH represents about 38% of the identified insect diversity of India. The interpretation of data provided significant information in detecting possible gap areas in the taxonomic representation of different insect orders. Archaeognatha, Zygentoma, Ephemeroptera, Phasmida, Embioptera, Psocoptera, Phthiraptera, Strepsiptera, Megaloptera, Raphidioptera, Siphonaptera, and Mecoptera need revisions, and it is required to collect more samples from remote areas of the region. Scope for finding new taxa even in the most diverse orders, Coleoptera, Lepidoptera, Hymenoptera, Diptera, and Hemiptera cannot be overlooked. Exploration of cold deserts of Trans Himalaya and East Himalaya (Arunachal Pradesh) may result in a good number of new species from these regions. The most notable data was that many of the species recorded from Himalaya are still known from their type localities only, so there is an urgency to revisit and resurvey those collection localities for the evaluation of the status of those species. It is also required to assess and monitor the impact of climate change on the diversity of insects inhabiting in the fragile Himalayan ecosystem. DNA barcoding especially pests and biological control agents to solve the problems of identification in species complexes is also the need of the hour. In a nutshell, it can be concluded that the inventory of insects of this region is extensive but is far from final as every year hundreds of new species are described.

Keywords: catalog, climate change, diversity, DNA barcoding

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Authors: Olena Kavats, Dmitry Khramov, Kateryna Sergieieva, Vladimir Vasyliev, Iurii Kavats

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Geoinformation technologies of space agromonitoring are a means of operative decision making support in the tasks of managing the agricultural sector of the economy. Existing technologies use satellite images in the optical range of electromagnetic spectrum. Time series of optical images often contain gaps due to the presence of clouds and haze. A geoinformation technology is created. It allows to fill gaps in time series of optical images (Sentinel-2, Landsat-8, PROBA-V, MODIS) with radar survey data (Sentinel-1) and use information about agrometeorological conditions of the growing season for individual monitoring years. The technology allows to perform crop classification and mapping for spring-summer (winter and spring crops) and autumn-winter (winter crops) periods of vegetation, monitoring the dynamics of crop state seasonal changes, crop yield forecasting. Crop classification is based on supervised classification algorithms, takes into account the peculiarities of crop growth at different vegetation stages (dates of sowing, emergence, active vegetation, and harvesting) and agriculture land state characteristics (row spacing, seedling density, etc.). A catalog of samples of the main agricultural crops (Ukraine) is created and crop spectral signatures are calculated with the preliminary removal of row spacing, cloud cover, and cloud shadows in order to construct time series of crop growth characteristics. The obtained data is used in grain crop growth tracking and in timely detection of growth trends deviations from reference samples of a given crop for a selected date. Statistical models of crop yield forecast are created in the forms of linear and nonlinear interconnections between crop yield indicators and crop state characteristics (temperature, precipitation, vegetation indices, etc.). Predicted values of grain crop yield are evaluated with an accuracy up to 95%. The developed technology was used for agricultural areas monitoring in a number of Great Britain and Ukraine regions using EOS Crop Monitoring Platform (https://crop-monitoring.eos.com). The obtained results allow to conclude that joint use of Sentinel-1 and Sentinel-2 images improve separation of winter crops (rapeseed, wheat, barley) in the early stages of vegetation (October-December). It allows to separate successfully the soybean, corn, and sunflower sowing areas that are quite similar in their spectral characteristics.

Keywords: geoinformation technology, crop classification, crop yield prediction, agricultural monitoring, EOS Crop Monitoring Platform

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Authors: Caroline Lavratti, Pedro Dal Lago, Gustavo Reinaldo, Gilson Dorneles, Andreia Bard, Laira Fuhr, Daniela Pochmann, Alessandra Peres, Luciane Wagner, Viviane Elsner

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Approximately 1% of the world's population is affected by schizophrenia (SZ), a chronic and debilitating neurodevelopmental disorder. Among possible factors, reduced levels of Brain-derived neurotrophic factor (BDNF) has been recognized in physiopathogenesis and course of SZ. In this context, peripheral BDNF levels have been used as a biomarker in several clinical studies, since this neurotrophin is able to cross the blood-brain barrier in a bi-directional manner and seems to present a strong correlation with the central nervous system fluid levels. The patients with SZ usually adopts a sedentary lifestyle, which has been partly associated with the increase in obesity incidence rates, metabolic syndrome, type 2 diabetes and coronary heart disease. On the other hand, exercise, a non-invasive and low cost intervention, has been considered an important additional therapeutic option for this population, promoting benefits to physical and mental health. To our knowledge, few studies have been pointed out that the positive effects of exercise in SZ patients are mediated, at least in part, to enhanced levels of BDNF after training. However, these studies are focused on evaluating the effect of single bouts of exercise of chronic interventions, data concerning the short- and long-term exercise outcomes on BDNF are scarce. Therefore, this study aimed to evaluate the effect of a concurrent exercise protocol (CEP) on plasma BDNF levels of SZ patients in different time-points. Material and Methods: This study was approved by the Research Ethics Committee of the Centro Universitário Metodista do IPA (no 1.243.680/2015). The participants (n=15) were subbmited to the CEP during 90 days, 3 times a week for 60 minutes each session. In order to evaluate the short and long-term effects of exercise, blood samples were collected pre, 30, 60 and 90 days after the intervention began. Plasma BDNF levels were determined with the ELISA method, from Sigma-Aldrich commercial kit (catalog number RAB0026) according to manufacturer's instructions. Results: A remarkable increase on plasma BDNF levels at 90 days after training compared to baseline (p=0.006) and 30 days (p=0.007) values were observed. Conclusion: Our data are in agreement with several studies that show significant enhancement on BDNF levels in response to different exercise protocols in SZ individuals. We might suggest that BDNF upregulation after training in SZ patients acts in a dose-dependent manner, being more pronounced in response to chronic exposure. Acknowledgments: This work was supported by Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/Brazil.

Keywords: exercise, BDNF, schizophrenia, time-points

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Authors: Ayesha Anjum, Arbaz Basha

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Active Galactic Nuclei (AGN) are the actively accreting centers of the galaxies that host supermassive black holes. AGN emits radiation in all wavelengths and also shows variability across all the wavelength bands. The analysis of flux variability tells us about the morphology of the site of emission radiation. Some of the major classifications of AGN are (a) Blazars, with featureless spectra. They are subclassified as BLLacertae objects, Flat Spectrum Radio Quasars (FSRQs), and others; (b) Seyferts with prominent emission line features are classified into Broad Line, Narrow Line Seyferts of Type 1 and Type 2 (c) quasars, and other types. Sloan Digital Sky Survey (SDSS) is an optical telescope based in Mexico that has observed and classified billions of objects based on automated photometric and spectroscopic methods. A sample of blazars is obtained from the third Fermi catalog. For variability analysis, we searched for light curves for these objects in Wide-Field Infrared Survey Explorer (WISE) and Near Earth Orbit WISE (NEOWISE) in two bands: W1 (3.4 microns) and W2 (4.6 microns), reducing the final sample to 256 objects. These objects are also classified into 155 BLLacs, 99 FSRQs, and 2 Narrow Line Seyferts, namely, PMNJ0948+0022 and PKS1502+036. Mid-infrared variability studies of these objects would be a contribution to the literature. With this as motivation, the present work is focused on studying a final sample of 256 objects in general and the Seyferts in particular. Owing to the fact that the classification is automated, SDSS has miclassified these objects into quasars, galaxies, and stars. Reasons for the misclassification are explained in this work. The variability analysis of these objects is done using the method of flux amplitude variability and excess variance. The sample consists of observations in both W1 and W2 bands. PMN J0948+0022 is observed between MJD from 57154.79 to 58810.57. PKS 1502+036 is observed between MJD from 57232.42 to 58517.11, which amounts to a period of over six years. The data is divided into different epochs spanning not more than 1.2 days. In all the epochs, the sources are found to be variable in both W1 and W2 bands. This confirms that the object is variable in mid-infrared wavebands in both long and short timescales. Also, the sources are observed for color variability. Objects either show a bluer when brighter trend (BWB) or a redder when brighter trend (RWB). The possible claim for the object to be BWB (present objects) is that the longer wavelength radiation emitted by the source can be suppressed by the high-energy radiation from the central source. Another result is that the smallest radius of the emission source is one day since the epoch span used in this work is one day. The mass of the black holes at the centers of these sources is found to be less than or equal to 108 solar masses, respectively.

Keywords: active galaxies, variability, Seyfert galaxies, SDSS, WISE

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Authors: Helen Bartsch, Markus Feldmann

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The dimensioning of steel structures subject to fatigue loads, such as wind turbines, bridges, masts and towers, crane runways and weirs or components in crane construction, is often dominated by fatigue verification. The fatigue details defined by the welded connections, such as butt or cruciform joints, longitudinal welds, welded-on or welded-in stiffeners, etc., are decisive. In Europe, the verification is usually carried out according to EN 1993-1-9 on a nominal stress basis. The basis is the detailed catalog, which specifies the fatigue strength of the various weld and construction details according to fatigue classes. Until now, a relation between fatigue classes and weld imperfection sizes is not included. Quality levels for imperfections in fusion-welded joints in steel, nickel, titanium and their alloys are regulated in EN ISO 5817, which, however, doesn’t contain direct correlations to fatigue resistances. The question arises whether some imperfections might be tolerable to a certain extent since they may be present in the test data used for detail classifications dating back decades ago. Although current standardization requires proof of satisfying limits of imperfection sizes, it would also be possible to tolerate welds with certain irregularities if these can be reliably quantified by non-destructive testing. Fabricators would be prepared to undertake carefully and sustained weld inspection in view of the significant economic consequences of such unfavorable fatigue classes. This paper presents investigations on the fatigue behavior of common welded details containing imperfections. In contrast to the common nominal stress concept, local fatigue concepts were used to consider the true stress increase, i.e., local stresses at the weld toe and root. The actual shape of a weld comprising imperfections, e.g., gaps or undercuts, can be incorporated into the fatigue evaluation, usually on a numerical basis. With the help of the effective notch stress concept, the fatigue resistance of detailed local weld shapes is assessed. Validated numerical models serve to investigate notch factors of fatigue details with different geometries. By utilizing parametrized ABAQUS routines, detailed numerical studies have been performed. Depending on the shape and size of different weld irregularities, fatigue classes can be defined. As well load-carrying welded details, such as the cruciform joint, as non-load carrying welded details, e.g., welded-on or welded-in stiffeners, are regarded. The investigated imperfections include, among others, undercuts, excessive convexity, incorrect weld toe, excessive asymmetry and insufficient or excessive throat thickness. Comparisons of the impact of different imperfections on the different types of fatigue details are made. Moreover, the influence of a combination of crucial weld imperfections on the fatigue resistance is analyzed. With regard to the trend of increasing efficiency in steel construction, the overall aim of the investigations is to include a more economical differentiation of fatigue details with regard to tolerance sizes. In the long term, the harmonization of design standards, execution standards and regulations of weld imperfections is intended.

Keywords: effective notch stress, fatigue, fatigue design, weld imperfections

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Authors: Fernanda Piculo, Giovana Vesentini, Gabriela Marini, Debora Cristina Damasceno, Angelica Mercia Pascon Barbosa, Marilza Vieira Cunha Rudge

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Introduction: Women with previous gestational diabetes mellitus (GDM) were significantly more likely to have urinary incontinence (UI) and pelvic floor muscle dysfunction compared to non-diabetic women two years after a cesarean section. Additional results demonstrated that induced diabetes causes detrimental effects on pregnant rat urethral muscle. These results indicate the need for exploration of the mechanistic role of a recovery factor in female UI. Chemokine ligand 7 (CCL7) was significantly over expressed in rat serum, urethral and vaginal tissues immediately following induction of stress UI in a rat model simulating birth trauma. CCL7 over expression has shown potency for stimulating targeted stem cell migration and provide a translational link (clinical measurement) which further provide opportunities for treatment. The aim of this study was to investigate the CCL7 levels profile in diabetic pregnant women with urinary incontinence during pregnancy over the first year postpartum. Methods: This study was conducted in the Perinatal Diabetes Research Center of the Botucatu Medical School/UNESP, and was approved by the Research Ethics Committee of the Institution (CAAE: 20639813.0.0000.5411). The diagnosis of GDM was established between 24th and 28th gestational weeks, by the 75 g-OGTT test according to ADA’s criteria. Urinary incontinence was defined according to the International Continence Society and the CCL7 levels was measured by ELISA (R&D Systems, Catalog Number DCC700). Two hundred twelve women were classified into four study groups: normoglycemic continent (NC), normoglycemic incontinent (NI), diabetic continent (DC) and diabetic incontinent (DI). They were evaluated at six-time-points: 12-18, 24-28 and 34-38 gestational weeks, 24-48 hours, 6 weeks and 6-12 months postpartum. Results: At 12-18 weeks, it was possible to consider only two groups, continent and incontinent, because at this early gestational period has not yet been the diagnosis of GDM. The group with GDM and UI (DI group) showed lower levels of CCL7 in all time points during pregnancy and postpartum, compared to normoglycemic groups (NC and NI), indicating that these women have not recovered from child birth induced UI during the 6-12 months postpartum compared to their controls, and that the progression of UI and/or lack of recovery throughout the first postpartum year can be related with lower levels of CCL7. Instead, serum CCL7 was significantly increased in the NC group. Taken together, these findings of overexpression of CCL7 in the NC group and decreased levels in the DI group, could confirm that diabetes delays the recovery from child birth induced UI, and that CCL7 could potentially be used as a serum marker of injury. Conclusion: This study demonstrates lower levels of CCL7 in the DI group during pregnancy and postpartum and suggests that the progression of UI in diabetic women and/or lack of recovery throughout the first postpartum year can be related with low levels of CCL7. This provides a translational potential where CCL7 measurement could be used as a surrogate for injury after delivery. Successful controlled CCL7 mediated stem cell homing to the lower urinary tract could one day introduce the potential for non-operative treatment or prevention of stress urinary incontinence.

Keywords: CCL7, gestational diabetes, pregnancy, urinary incontinence

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