| 1. |
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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Hudson, Lawrence N, et al.
(author)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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In: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Journal article (peer-reviewed)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 3. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 4. |
- Sartelli, Massimo, et al.
(author)
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Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
- 2023
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In: WORLD JOURNAL OF EMERGENCY SURGERY. - 1749-7922. ; 18:1
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Research review (peer-reviewed)abstract
- Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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| 5. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
- Migueles, Jairo H., et al.
(author)
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Comparability of accelerometer signal aggregation metrics across placements and dominant wrist cut points for the assessment of physical activity in adults
- 2019
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In: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
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Journal article (peer-reviewed)abstract
- Large epidemiological studies that use accelerometers for physical behavior and sleep assessment differ in the location of the accelerometer attachment and the signal aggregation metric chosen. This study aimed to assess the comparability of acceleration metrics between commonly-used body-attachment locations for 24 hours, waking and sleeping hours, and to test comparability of PA cut points between dominant and non-dominant wrist. Forty-five young adults (23 women, 18-41 years) were included and GT3X + accelerometers (ActiGraph, Pensacola, FL, USA) were placed on their right hip, dominant, and non-dominant wrist for 7 days. We derived Euclidean Norm Minus One g (ENMO), Low-pass filtered ENMO (LFENMO), Mean Amplitude Deviation (MAD) and ActiGraph activity counts over 5-second epochs from the raw accelerations. Metric values were compared using a correlation analysis, and by plotting the differences by time of the day. Cut points for the dominant wrist were derived using Lins concordance correlation coefficient optimization in a grid of possible thresholds, using the nondominant wrist estimates as reference. They were cross-validated in a separate sample (N = 36, 10 women, 22-30 years). Shared variances between pairs of acceleration metrics varied across sites and metric pairs (range in r(2) : 0.19-0.97, all p amp;lt; 0.01), suggesting that some sites and metrics are associated, and others are not. We observed higher metric values in dominant vs. non-dominant wrist, thus, we developed cut points for dominant wrist based on ENMO to classify sedentary time (amp;lt;50 mg), light PA (50-110 mg), moderate PA (110-440 mg) and vigorous PA (amp;gt;= 440 mg). Our findings suggest differences between dominant and non-dominant wrist, and we proposed new cut points to attenuate these differences. ENMO and LFENMO were the most similar metrics, and they showed good comparability with MAD. However, counts were not comparable with ENMO, LFENMO and MAD.
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| 7. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 8. |
- Broitman, Esteban, et al.
(author)
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Microstructural, nanomechanical, and microtribological properties of Pb thin films prepared by pulsed laser deposition and thermal evaporation techniques
- 2016
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In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 34:2, s. 021505-
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Journal article (peer-reviewed)abstract
- In this work, the authors compare the morphological, structural, nanomechanical, and microtribological properties of Pb films deposited by thermal evaporation (TE) and pulsed laser deposition (PLD) techniques onto Si (111) substrates. Films were investigated by scanning electron microscopy, surface probe microscopy, and x-ray diffraction in theta-2 theta geometry to determine their morphology, root-mean-square (RMS) roughness, and microstructure, respectively. TE films showed a percolated morphology with densely packed fibrous grains while PLD films had a granular morphology with a columnar and tightly packed structure in accordance with the zone growth model of Thornton. Moreover, PLD films presented a more polycrystalline structure with respect to TE films, with RMS roughness of 14 and 10 nm, respectively. Hardness and elastic modulus vary from 2.1 to 0.8 GPa and from 14 to 10 GPa for PLD and TE films, respectively. A reciprocal friction test has shown that PLD films have lower friction coefficient and wear rate than TE films. Our study has demonstrated for first time that, at the microscale, Pb films do not show the same simple lubricious properties measured at the macroscale. (C) 2015 American Vacuum Society.
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| 9. |
- Calatrava-Nicolás, Francisco M., et al.
(author)
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Robotic-Based Well-Being Monitoring and Coaching System for the Elderly in Their Daily Activities
- 2021
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In: Sensors. - : MDPI. - 1424-8220. ; 21:20
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Journal article (peer-reviewed)abstract
- The increasingly ageing population and the tendency to live alone have led science and engineering researchers to search for health care solutions. In the COVID 19 pandemic, the elderly have been seriously affected in addition to suffering from isolation and its associated and psychological consequences. This paper provides an overview of the RobWell (Robotic-based Well-Being Monitoring and Coaching System for the Elderly in their Daily Activities) system. It is a system focused on the field of artificial intelligence for mood prediction and coaching. This paper presents a general overview of the initially proposed system as well as the preliminary results related to the home automation subsystem, autonomous robot navigation and mood estimation through machine learning prior to the final system integration, which will be discussed in future works. The main goal is to improve their mental well-being during their daily household activities. The system is composed of ambient intelligence with intelligent sensors, actuators and a robotic platform that interacts with the user. A test smart home system was set up in which the sensors, actuators and robotic platform were integrated and tested. For artificial intelligence applied to mood prediction, we used machine learning to classify several physiological signals into different moods. In robotics, it was concluded that the ROS autonomous navigation stack and its autodocking algorithm were not reliable enough for this task, while the robot's autonomy was sufficient. Semantic navigation, artificial intelligence and computer vision alternatives are being sought.
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| 10. |
- Diliegros-Godines, C. J., et al.
(author)
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Mechanical and tribological properties of CdO + SnO2 thin films prepared by sol–gel
- 2015
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In: Journal of Sol-Gel Science and Technology. - : Springer. - 0928-0707 .- 1573-4846. ; 74:1, s. 114-120
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Journal article (peer-reviewed)abstract
- We report the mechanical and tribological properties of transparent conductive oxide CdO + SnO2 coatings. The films were deposited on glass substrates by the sol–gel technique using, as precursor solution, a mixture of CdO and SnO2 solutions obtained at room temperature. Depending on the Sn atomic concentration percentage values the X-ray diffraction patterns show three types of films constituted of (1) CdO + Cd2SnO4, (2) Cd2SnO4 and (3) Cd2SnO4 + CdSnO3 crystals. Reciprocal microfriction tests revealed that films with Cd2SnO4 phase have friction values in the range 0.48–0.51 and a low wear rate of ~5 × 10−5 mm3 N−1 m−1. Nanoindentation tests have shown an increment of the elastic modulus from 50 GPa for CdO + Cd2SnO4 films to 90 GPa for Cd2SnO4 films, while the hardest coating was the one constituted by Cd2SnO4 crystals with H = 5.7 GPa, comparable to the hardness and elastic modulus reported for ITO films.
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| 11. |
- Plaza-Florido, Abel, et al.
(author)
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Cardiorespiratory fitness in children with overweight/obesity : Insights into the molecular mechanisms
- 2021
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In: Scandinavian Journal of Medicine and Science in Sports. - : Wiley. - 0905-7188 .- 1600-0838. ; 31:11, s. 2083-2091
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Journal article (peer-reviewed)abstract
- Objectives High cardiorespiratory fitness (CRF) levels reduce the risk of developing cardiovascular disease (CVD) during adulthood. However, little is known about the molecular mechanisms underlying the health benefits of high CRF levels at the early stage of life. This study aimed to analyze the whole-blood transcriptome profile of fit children with overweight/obesity (OW/OB) compared to unfit children with OW/OB. Design 27 children with OW/OB (10.14 +/- 1.3 years, 59% boys) from the ActiveBrains project were evaluated. VO(2)peak was assessed using a gas analyzer, and participants were categorized into fit or unfit according to the CVD risk-related cut-points. Whole-blood transcriptome profile (RNA sequencing) was analyzed. Differential gene expression analysis was performed using the limma R/Bioconductor software package (analyses adjusted by sex and maturational status), and pathways enrichment analysis was performed with DAVID. In addition, in silico validation data mining was performed using the PHENOPEDIA database. Results 256 genes were differentially expressed in fit children with OW/OB compared to unfit children with OW/OB after adjusting by sex and maturational status (FDR < 0.05). Enriched pathway analysis identified gene pathways related to inflammation (eg, dopaminergic and GABAergic synapse pathways). Interestingly, in silico validation data mining detected a set of the differentially expressed genes to be related to CVD, metabolic syndrome, hypertension, inflammation, and asthma. Conclusion The distinct pattern of whole-blood gene expression in fit children with OW/OB reveals genes and gene pathways that might play a role in reducing CVD risk factors later in life.
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| 12. |
- Altmae, Signe, et al.
(author)
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Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transfer
- 2016
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In: Reproductive BioMedicine Online. - : Elsevier BV. - 1472-6483 .- 1472-6491. ; 32:6, s. 597-613
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Journal article (peer-reviewed)abstract
- Little consensus has been reached on the best protocol for endometrial preparation for frozen embryo transfer (FET). It is not known how, and to what extent, hormone supplementation in artificial cycles influences endometrial preparation for embryo implantation at a molecular level, especially in patients who have experienced recurrent implantation failure. Transcriptome analysis of 15 endometrial biopsy samples at the time of embryo implantation was used to compare two different endometrial preparation protocols, natural versus artificial cycles, for FET in women who have experienced recurrent implantation failure compared with fertile women. IPA and DAVID were used for functional analyses of differentially expressed genes. The TRANSFAC database was used to identify oestrogen and progesterone response elements upstream of differentially expressed genes. Cluster analysis demonstrated that natural cycles are associated with a better endometrial receptivity transcriptome than artificial cycles. Artificial cycles seemed to have a stronger negative effect on expression of genes and pathways crucial for endometrial receptivity, including ESR2, FSHR, LEP, and several interleukins and matrix metalloproteinases. Significant overrepresentation of oestrogen response elements among the genes with deteriorated expression in artificial cycles (P < 0.001) was found; progesterone response elements predominated in genes with amended expression with artificial cycles (P = 0.0052).
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| 13. |
- Altmäe, Signe, et al.
(author)
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Guidelines for the design, analysis and interpretation of 'omics' data : focus on human endometrium
- 2013
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In: Human Reproduction Update. - : Oxford University Press (OUP). - 1355-4786 .- 1460-2369. ; 20:1, s. 12-28
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Research review (peer-reviewed)abstract
- BACKGROUND 'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data.METHODS Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013.RESULTS The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies.CONCLUSION A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.
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| 14. |
- Altmäe, Signe, 1978-, et al.
(author)
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MicroRNAs miR-30b, miR-30d, and miR-494 Regulate Human Endometrial Receptivity
- 2013
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In: Reproductive Sciences. - : Springer Science and Business Media LLC. - 1933-7191 .- 1933-7205. ; 20:3, s. 308-317
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Journal article (peer-reviewed)abstract
- MicroRNAs (miRNAs) act as important epigenetic posttranscriptional regulators of gene expression. We aimed to gain more understanding of the complex gene expression regulation of endometrial receptivity by analyzing miRNA signatures of fertile human endometria. We set up to analyze miRNA signatures of receptive (LH + 7, n = 4) versus prereceptive (LH + 2, n = 5) endometrium from healthy fertile women. We found hsa-miR-30b and hsa-miR-30d to be significantly upregulated, and hsa-miR-494 and hsa-miR-923 to be downregulated in receptive endometrium. Three algorithms (miRanda, PicTar, and TargetScan) were used for target gene prediction. Functional analyses of the targets using Ingenuity Pathways Analysis and The Database for Annotation, Visualization and Integrated Discovery indicated roles in transcription, cell proliferation and apoptosis, and significant involvement in several relevant pathways, such as axon guidance, Wnt/β-catenin, ERK/MAPK, transforming growth factor β (TGF-β), p53 and leukocyte extravasation. Comparison of predicted miRNA target genes and our previous messenger RNA microarray data resulted in a list of 12 genes, including CAST, CFTR, FGFR2, and LIF that could serve as a panel of genes important for endometrial receptivity. In conclusion, we suggest that a subset of miRNAs and their target genes may play important roles in endometrial receptivity.
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| 15. |
- Dayton, Kyle, et al.
(author)
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Deep magma storage during the 2021 La Palma eruption
- 2023
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 9:6
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Journal article (peer-reviewed)abstract
- The 2021 La Palma eruption provided an unpreceded opportunity to test the relationship between earthquake hypocenters and the location of magma reservoirs. We performed density measurements on CO2-rich fluid in-clusions (FIs) hosted in olivine crystals that are highly sensitive to pressure via calibrated Raman spectroscopy. This technique can revolutionize our knowledge of magma storage and transport during an ongoing eruption, given that it can produce precise magma storage depth constraints in near real time with minimal sample prep-aration. Our FIs have CO2 recorded densities from 0.73 to 0.98 g/cm3, translating into depths of 15 to 27 km, which falls within the reported deep seismic zone recording the main melt storage reservoir.
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| 16. |
- Debortoli, Guilherme, et al.
(author)
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Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data
- 2020
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Journal article (peer-reviewed)abstract
- The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.
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| 17. |
- Leynaert, Benedicte, et al.
(author)
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Gender differences in prevalence, diagnosis and incidence of allergic and non-allergic asthma : a population-based cohort
- 2012
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In: Thorax. - : BMJ. - 0040-6376 .- 1468-3296. ; 67:7, s. 625-631
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Journal article (peer-reviewed)abstract
- Background Although women with severe non-allergic asthma may represent a substantial proportion of adults with asthma in clinical practice, gender differences in the incidence of allergic and non-allergic asthma have been little investigated in the general population. Methods Gender differences in asthma prevalence, reported diagnosis and incidence were investigated in 9091 men and women randomly selected from the general population and followed up after 8-10 years as part of the European Community Respiratory Health Survey. The protocol included assessment of bronchial responsiveness, IgE specific to four common allergens and skin tests to nine allergens. Results Asthma was 20% more frequent in women than in men over the age of 35 years. Possible under-diagnosis of asthma appeared to be particularly frequent among non-atopic individuals, but was as frequent in women as in men. The follow-up of subjects without asthma at baseline showed a higher incidence of asthma in women than in men (HR 1.94; 95% CI 1.40 to 2.68), which was not explained by differences in smoking, obesity or lung function. More than 60% of women and 30% of men with new-onset asthma were non-atopic. The incidence of non-allergic asthma was higher in women than in men throughout all the reproductive years (HR 3.51; 95% CI 2.21 to 5.58), whereas no gender difference was observed for the incidence of allergic asthma. Conclusions This study shows that female sex is an independent risk factor for non-allergic asthma, and stresses the need for more careful assessment of possible non-allergic asthma in clinical practice, in men and women.
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