29 results on '"Abdullah, Syafiq"'
Search Results
2. Genomic analyses inform on migration events during the peopling of Eurasia
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Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait
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Human Genome ,Biotechnology ,Genetics ,Generic health relevance ,Africa ,Animals ,Asia ,Datasets as Topic ,Estonia ,Europe ,Fossils ,Gene Flow ,Genetics ,Population ,Genome ,Human ,Genomics ,Heterozygote ,History ,Ancient ,Human Migration ,Humans ,Native Hawaiian or Other Pacific Islander ,Neanderthals ,New Guinea ,Population Dynamics ,Racial Groups ,General Science & Technology - Abstract
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
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- 2016
3. A recent bottleneck of Y chromosome diversity coincides with a global change in culture
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Karmin, Monika, Saag, Lauri, Vicente, Mário, Sayres, Melissa A Wilson, Järve, Mari, Talas, Ulvi Gerst, Rootsi, Siiri, Ilumäe, Anne-Mai, Mägi, Reedik, Mitt, Mario, Pagani, Luca, Puurand, Tarmo, Faltyskova, Zuzana, Clemente, Florian, Cardona, Alexia, Metspalu, Ene, Sahakyan, Hovhannes, Yunusbayev, Bayazit, Hudjashov, Georgi, DeGiorgio, Michael, Loogväli, Eva-Liis, Eichstaedt, Christina, Eelmets, Mikk, Chaubey, Gyaneshwer, Tambets, Kristiina, Litvinov, Sergei, Mormina, Maru, Xue, Yali, Ayub, Qasim, Zoraqi, Grigor, Korneliussen, Thorfinn Sand, Akhatova, Farida, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Ricaut, François-Xavier, Kusuma, Pradiptajati, Razafindrazaka, Harilanto, Pierron, Denis, Cox, Murray P, Sultana, Gazi Nurun Nahar, Willerslev, Rane, Muller, Craig, Westaway, Michael, Lambert, David, Skaro, Vedrana, Kovačevic´, Lejla, Turdikulova, Shahlo, Dalimova, Dilbar, Khusainova, Rita, Trofimova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Lichman, Daria V, Isakova, Jainagul, Pocheshkhova, Elvira, Sabitov, Zhaxylyk, Barashkov, Nikolay A, Nymadawa, Pagbajabyn, Mihailov, Evelin, Seng, Joseph Wee Tien, Evseeva, Irina, Migliano, Andrea Bamberg, Abdullah, Syafiq, Andriadze, George, Primorac, Dragan, Atramentova, Lubov, Utevska, Olga, Yepiskoposyan, Levon, Marjanovic´, Damir, Kushniarevich, Alena, Behar, Doron M, Gilissen, Christian, Vissers, Lisenka, Veltman, Joris A, Balanovska, Elena, Derenko, Miroslava, Malyarchuk, Boris, Metspalu, Andres, Fedorova, Sardana, Eriksson, Anders, Manica, Andrea, Mendez, Fernando L, Karafet, Tatiana M, Veeramah, Krishna R, Bradman, Neil, Hammer, Michael F, Osipova, Ludmila P, Balanovsky, Oleg, Khusnutdinova, Elza K, Johnsen, Knut, Remm, Maido, Thomas, Mark G, Tyler-Smith, Chris, Underhill, Peter A, Willerslev, Eske, Nielsen, Rasmus, Metspalu, Mait, Villems, Richard, and Kivisild, Toomas
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Biological Sciences ,Genetics ,Human Genome ,Base Sequence ,Chromosomes ,Human ,Y ,DNA ,Mitochondrial ,Evolution ,Molecular ,Genetic Variation ,Genetics ,Population ,Haplotypes ,Humans ,Male ,Models ,Genetic ,Phylogeny ,Racial Groups ,Sequence Analysis ,DNA ,Medical and Health Sciences ,Bioinformatics - Abstract
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
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- 2015
4. Autonomous industrial tank floor inspection robot.
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Wun Chen Lee, Abdullah Syafiq Abdul Salam, Mohd Faisal Ibrahim, Ashrani Aizzuddin Abd. Rahni, and Abdullah Zawawi Mohamed
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- 2015
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5. Iron-fortified klutuk banana (Musa balbisiana Colla) flour supplementation prevented growth failure by suppressing FGF21 in malnourished rats
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Abdullah Syafiq Edyanto, Emy Huriyati, Ainun Nisa, Bira Arumndari Nurrahma, and Arta Farmawati
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Nutrition and Dietetics ,Food Science - Abstract
Purpose Malnutrition during childhood precedes growth failure and affects the child’s well-being later in life. This study aims to investigate the potency of iron-fortified klutuk banana (Musa balbisiana Colla) flour on growth parameters and fibroblast growth factor 21 (FGF21) expression in malnourished rat model. Design/methodology/approach Rats were allocated into normal control (NC), untreated malnutrition (MC), malnutrition + iron-fortified klutuk banana flour (IBF) and malnutrition + Indonesian Government-issued biscuit (GB). Malnutrition was induced by an isoenergetic low-protein diet for five weeks. The IBF and GB groups were supplemented with IBF 1.2 g/200 gBW and GB 1.2 g/200 gBW, respectively, via gavage daily for three weeks. The body weight and length, the levels of plasma and liver FGF21 and red blood cell indices were analyzed. Findings After three weeks of supplementation, the IBF group showed higher body weight (245 ± 13.6 g vs 201.8 ± 16.3 g; p = 0.0004) and length (20.9 ± 0.5 cm vs 19.8 ± 0.5 cm; p = 0.021) compared with the untreated group. The plasma FGF21 level decreased in the IBF group (p = 0.034). The IBF group altered mean corpuscular volume and mean corpuscular hemoglobin, suggesting the IBF might attenuate malnutrition-induced anemia. Overall, the IBF prevented growth failure in malnourished condition. This might be mediated by the suppression of FGF21 expression, along with the prevention of malnutrition and anemia. Originality/value This study provides preliminary information about the potential use of rarely consumed banana, klutuk banana, as a supplement to treat malnutrition. This study might help the developing countries to eliminate the widespread malnutrition in economically challenged communities.
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- 2023
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6. Adolescents with Internet Gaming Disorder are more likely to have Lower Score of Cognitive Function: A Cross-sectional Study among Junior High School Students in Yogyakarta, Indonesia
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Indarwati Setyaningsih, Abdullah Syafiq Edyanto, Agus Budi Bowo Leksono, Paryono Muhrodji, and Amelia Nur Vidyanti
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medicine.medical_specialty ,Multivariate analysis ,Recall ,business.industry ,Cross-sectional study ,Public health ,Addiction ,media_common.quotation_subject ,education ,Cognition ,General Medicine ,language.human_language ,Indonesian ,language ,Medicine ,business ,Association (psychology) ,Clinical psychology ,media_common - Abstract
BACKGROUND: Internet Gaming Disorder (IGD) has emerged as a rapidly rising public health problem mostly affecting children and adolescent worldwide, as a result of massive growth of technology and internet usage in recent years. Adolescents are the most vulnerable age group to problematic internet gaming use due to lack of cognitive control. AIM: This study aims to investigate the association between IGD and cognitive function among junior high school- students in Indonesia. METHODS: The subjects of this cross-sectional study were students at two randomly selected junior high schools in Yogyakarta, Indonesia. The Game Addiction Scale-7 Indonesian version and the Modified Mini Mental State Examination for Children-Indonesian version were used to assess IGD and cognitive function, respectively. Multivariate analysis with linear regression was used to determine the relationship between IGD and cognitive function. RESULTS: There were 142 subjects with a mean age of 14 years. Students with IGD significantly had lower score of cognitive function, particularly for domains of attention (p = 0.000), recall memory (p = 0.000), and language (p = 0.002), compared with the counterpart group. Furthermore, multivariate analysis showed that students with IGD were more likely to have lower cognitive function score by 1.40 points than those without IGD (B = –1.40, 95% CI -2.51–-0.29, R2 = 0.469). CONCLUSIONS: IGD was negatively associated with cognitive function. Junior high school students with IGD in Indonesia had lower score of cognitive function compared with students without IGD, particularly in the domains of attention, recall memory, and language. Clinicians, teachers, and parents should be more aware of the detrimental effect of IGD. Further study with larger sample size, diverse subjects, and wider age range is still needed.
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- 2021
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7. Arithmetic and Variables Operation in Hypertext Preprocessor (PHP)
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Ahmad, Danial Kafi, Ahmad, Mariam Farida, Ahmad, Abdullah Syafiq, Mohd Nazmi Ahmad, and Khaleed, Faiz
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- 2022
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8. KLASIFIKASI DIABETIC RETINOPATHY BERBASIS PENGOLAHAN CITRA FUNDUS DAN DEEP LEARNING
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Abdullah, Syafiq Hilmi, primary, Magdalena, Rita, additional, and Fu'adah, R Yunendah Nur, additional
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- 2022
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9. HUMAN GENOMICS: Global diversity, population stratification, and selection of human copy-number variation
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Sudmant, Peter H., Mallick, Swapan, Nelson, Bradley J., Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P., Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B., Posukh, Olga L., Sahakyan, Hovhannes, Watkins, Scott W., Yepiskoposyan, Levon, Abdullah, Syafiq M., Bravi, Claudio M., Capelli, Cristian, Hervig, Tor, Wee, Joseph T. S., Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R., Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B., Ayodo, George, Beall, Cynthia M., Di Rienzo, Anna, Hammer, Michael F., Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A., Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E.
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- 2015
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10. Adolescents with Internet Gaming Disorder are more likely to have Lower Score of Cognitive Function: A Cross-sectional Study among Junior High School Students in Yogyakarta, Indonesia
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Setyaningsih, Indarwati, primary, Leksono, Agus Budi Bowo, additional, Muhrodji, Paryono, additional, Edyanto, Abdullah Syafiq, additional, and Vidyanti, Amelia Nur, additional
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- 2021
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11. Modeling Covid-19 Pandemic Responses in Malaysia for the First 145 Days Duration (Jan. 25 – June 17, 2020)
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Danial Kafi Ahmad, Ahmad Selamat, Mohd Nazmi Ahmad, and Abdullah Syafiq Ahmad
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Background At 145 days from Jan. 25, the Covid-19 recovery rate was 92.5% of the total cumulative cases of 8,515 with 1.4% fatalities were recorded in Malaysia. On top of the provided medical services and facilities, the recoveries could be mainly resulted from the Movement Control Order (MCO) enforcements in six phases for mitigating the pandemic nationwide. To understand the Covid-19 pandemic trend and dynamic mathematically to the MCO phases, the applicability of the proposed models ( tri-logistic growth model) on covid-19 related responses was studied by using the ‘matured’ 145-day data duration. The study also aimed at, (1) identifying information/parameters obtained through modeling technique that could be used in explaining the pattern of dynamic subjected to MCO enforcements, and (2) forecasting the quantitative information for postdate days beyond the used data duration. Methods Each serial layered-logistic growth of cumulative cases, recoveries, fatalities, and active cases were linked among them via the asymptotic cumulative cases and the nature of the recovery-fatality complementarity. The used data of Jan. 25 – Jun. 17, 2020 were quite ‘matured’ trend as observed in the ‘plateauing’ of cumulative cases. The appropriate R2 was used for model fitness analysis. The innovative SAS program writing of SAS9.4 version was used for the analysis. Conclusion Predicted cumulative cases, recoveries, fatalities, and active cases vs. days were significantly fitted to the observed values (R2 > 99 %), indicating the validity of the tri-logistic growth proposed model. Via the derivative of cumulative cases function, the daily cases or dynamic model was significant (R2=70%) with the fluctuating daily cases moved around the predicted curve. The authority has been classified the pandemic as of two waves (Jan. 25 – Feb. 26, 2020, and Feb. 27, 2020 onwards), and these were regrouped as wave 1 (primary wave) in this study. Within this one wave, the study shows that covid-19 in Malaysia has three cycles: cycle 1(1o cycle) [Jan. 25 – Apr.27], cycle 2 [Apr. 28 – May 14] and cycle 3 [May 15 and onwards] with the aggressiveness order of wave 1 > wave 3 > wave 2 (wave 3 had mainly caused by local foreigners). The observed cumulative cases were slightly higher than the predicted (by 0.07% -0.49%) during Jun 13 – 17 suggesting small room of resources still available for covid-19 infection, thus, maintaining the current MCO is crucial. Beyond Jun.17, the forecasts of cumulative cases, recoveries, fatalities, and active cases at June 30 would be 8500, 8168, 128, and 202 cases, respectively, with daily cases of 1 case day-1 . If no any further odd-extraordinary wave occurrence, the country would probably be enjoying a non-significant covid or ‘covid-free’ pandemic by the July end or mid-August, 2020. The model had validated the correctness and appropriateness of the MCO phases’ enforcements. The active cases model was the resultant of linkages of all models via asymptotic cumulative cases. Based on above resultant and the logistic growth function applicability in various fields, the modeling approach involving serial tri-logistic functions could probably be used in analyzing covid or covid-related epidemic elsewhere and in the future.
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- 2020
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12. Cancer Patients’ Perspectives on Integrating Cancer Care in Primary Care Settings: A Qualitative Inquiry
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Idris, Fazean, primary, Chien, Seit Mei, primary, Ghouse, Hashmet Parveen, primary, Abdullah, Syafiq, primary, and Venkatasalu, Munikumar Ramasamy, primary
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- 2020
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13. Modeling Covid-19 Pandemic Responses in Malaysia for the First 145 Days Duration (Jan. 25 – June 17, 2020)
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Ahmad, Danial Kafi, primary, Selamat, Ahmad, additional, Ahmad, Mohd Nazmi, additional, and Ahmad, Abdullah Syafiq, additional
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- 2020
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14. Genomic insights into the peopling of the Southwest Pacific
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Skoglund, Pontus, Posth, Cosimo, Sirak, Kendra, Spriggs, Matthew, Valentin, Frederique, Bedford, Stuart, Clark, Geoffrey R., Reepmeyer, Christian, Petchey, Fiona, Fernandes, Daniel, Fu, Qiaomei, Harney, Eadaoin, Lipson, Mark, Mallick, Swapan, Novak, Mario, Rohland, Nadin, Stewardson, Kristin, Abdullah, Syafiq, Cox, Murray P., Friedlaender, Franoise R., Friedlaender, Jonathan S., Kivisild, Toomas, Koki, George, Kusuma, Pradiptajati, Merriwether, D. Andrew, Ricaut, Francois-X., Wee, Joseph T. S., Patterson, Nick, Krause, Johannes, Pinhasi, Ron, and Reich, David
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Population genetics -- Research ,Genetic research ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Pontus Skoglund (corresponding author) [1, 2, 3]; Cosimo Posth [4, 5]; Kendra Sirak [6, 7]; Matthew Spriggs [8, 9]; Frederique Valentin [10]; Stuart Bedford [9, 11]; Geoffrey R. Clark [...]
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- 2016
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15. Portable electrocardiography with cloud based features: A review of current technologies
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Rosmina Jaafar and Abdullah Syafiq Abdul Salam
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Rest (physics) ,business.industry ,Computer science ,Server ,Software design ,Usability ,The Internet ,Mobile technology ,Cloud computing ,business ,Mobile device ,Computer hardware - Abstract
With recent trend of mobile devices being affordable and handy, portable electrocardiography (ECG) composed in smart and compact systems for use in out-of-hospital settings are being made commercially available. Mobile ECG devices are important medical innovation which has high potential to transform to homecare. We performed this review to learn on the current availability of portable ECG mobile technologies with respect to their scope, ease of use, data transmission capabilities, diagnostic accuracy and cloud based features. We conducted and Internet searches for "handheld" or "patch" or "portable" electrocardiography devices to enlist current available technologies. We also searched specific mobile ECG devices to obtain additional citations. We classified available devices as a "single limb lead ECG recording devices" and chest-lead "ECG recording devices." Three electrodes ECG devices also defined as the conventional electrocardiography or Holter machine are excluded from this review. A total of 12 devices have been reviewed and identified as "handheld", "patch" and "portable" with four devices fall into each of the categories. Nine of the reviewed ECG devices have electrode attachment in the chest and the rest are handheld devices. All devices are very lightweight as they weight under 150g and easy to bring everywhere. We concluded that the number of available devices that can record and analyze ECG signals is on the rise. ECG devices with cloud based monitoring and analysis system involves various fields such as sensor technology, communication, software design, signal processing and data mining.
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- 2019
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16. Portable electrocardiography with cloud based features: A review of current technologies
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Jaafar, Rosmina, primary and Abdul Salam, Abdullah Syafiq, additional
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- 2019
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17. Survival of primary lung cancer patients in Brunei Darussalam, 1987–2012
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Naing, Lin, primary, Abdullah, Amalina, additional, Abdullah, Syafiq, additional, and Kifli, Nurolaini, additional
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- 2017
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18. Autonomous industrial tank floor inspection robot
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Mohd Faisal Ibrahim, Abdullah Syafiq Abdul Salam, Wun Chen Lee, Ashrani Aizzuddin Abd Rahni, and Abdullah Zawawi Mohamed
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Highly skilled ,Operator (computer programming) ,Computer science ,Storage tank ,Real-time computing ,Robot ,Repetitive task ,Simultaneous localisation and mapping ,Simultaneous localization and mapping ,Robot operating system ,Simulation - Abstract
Many storage tanks used in industry are inspected manually in order to identify leakage and corrosion. This repetitive task can harm the operator as the operator has to expose themselves to danger inside the tank. The environment of the tank can be harmful because it might contain highly hazardous substances. Additionally, the manual inspection process also requires highly skilled operators for precision. This project proposes the use of an autonomous inspection robot to overcome this problem. The proposed robot is based on the TurtleBot with the Microsoft Kinect camera as a distance sensor. The MinnowBoard MAX board is used as the computing platform running the Robot Operating System (ROS) for tank floor mapping and navigation of the robot. The GMapping Simultaneous Localization and Mapping (SLAM) algorithm is used to do perform the mapping process. Evaluation was performed by comparison against physical measurement of the foyer of the Faculty of Engineering and Built Environment (FKAB) at Universiti Kebangsaan Malaysia (UKM). The results show that the GMapping algorithm is able to generate relatively accurate maps even with the low cost platform and will perform even better with more accurate sensors.
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- 2015
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19. Selective sweep on human amylase genes postdates the split with Neanderthals
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Inchley, Charlotte E., primary, Larbey, Cynthia D. A., additional, Shwan, Nzar A. A., additional, Pagani, Luca, additional, Saag, Lauri, additional, Antão, Tiago, additional, Jacobs, Guy, additional, Hudjashov, Georgi, additional, Metspalu, Ene, additional, Mitt, Mario, additional, Eichstaedt, Christina A., additional, Malyarchuk, Boris, additional, Derenko, Miroslava, additional, Wee, Joseph, additional, Abdullah, Syafiq, additional, Ricaut, François-Xavier, additional, Mormina, Maru, additional, Mägi, Reedik, additional, Villems, Richard, additional, Metspalu, Mait, additional, Jones, Martin K., additional, Armour, John A. L., additional, and Kivisild, Toomas, additional
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- 2016
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20. Multi-layered population structure in Island Southeast Asians
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Mörseburg, Alexander, primary, Pagani, Luca, additional, Ricaut, Francois-Xavier, additional, Yngvadottir, Bryndis, additional, Harney, Eadaoin, additional, Castillo, Cristina, additional, Hoogervorst, Tom, additional, Antao, Tiago, additional, Kusuma, Pradiptajati, additional, Brucato, Nicolas, additional, Cardona, Alexia, additional, Pierron, Denis, additional, Letellier, Thierry, additional, Wee, Joseph, additional, Abdullah, Syafiq, additional, Metspalu, Mait, additional, and Kivisild, Toomas, additional
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- 2016
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21. Germline hemizygous deletion of CDKN2A–CDKN2B locus in a patient presenting with Li–Fraumeni syndrome
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Chan, Sock Hoai, primary, Lim, Weng Khong, additional, Michalski, Scott T, additional, Lim, Jing Quan, additional, Ishak, Nur Diana Binte, additional, Met-Domestici, Marie, additional, Young, Cedric Ng Chuan, additional, Vikstrom, Karen, additional, Esplin, Edward D, additional, Fulbright, Jennifer, additional, Ang, Mei Kim, additional, Wee, Joseph, additional, Sittampalam, Kesavan, additional, Farid, Mohamad, additional, Lincoln, Stephen E, additional, Itahana, Koji, additional, Abdullah, Syafiq, additional, Teh, Bin Tean, additional, and Ngeow, Joanne, additional
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- 2016
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22. Autonomous industrial tank floor inspection robot
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Lee, Wun Chen, primary, Salam, Abdullah Syafiq Abdul, additional, Ibrahim, Mohd. Faisal, additional, Rahni, Ashrani A. Abd., additional, and Mohamed, Abdullah Zawawi, additional
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- 2015
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23. Roundtable
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Abdullah, Syafiq Alfonse, primary and Hermitte, Marguerite, additional
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- 1999
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24. Genomic analyses inform on migration events during the peopling of Eurasia
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Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Wilson Sayres, Melissa A, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Skaro, Vedrana, Mulahasanovic, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait
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Estonia ,Gene Flow ,Heterozygote ,New Guinea ,Asia ,Continental Population Groups ,Fossils ,Genome, Human ,Human Migration ,Population Dynamics ,Datasets as Topic ,Genomics ,3. Good health ,Europe ,Oceanic Ancestry Group ,Genetics, Population ,Africa ,Animals ,Humans ,History, Ancient ,Neanderthals - Abstract
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago., Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.).
25. Selective sweep on human amylase genes postdates the split with Neanderthals
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Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Mormina, Maru, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas
- Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
26. Selective sweep on human amylase genes postdates the split with Neanderthals
- Author
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Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas
- Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
- Full Text
- View/download PDF
27. Selective sweep on human amylase genes postdates the split with Neanderthals
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Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas
- Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
- Full Text
- View/download PDF
28. Selective sweep on human amylase genes postdates the split with Neanderthals
- Author
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Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas
- Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
- Full Text
- View/download PDF
29. Selective sweep on human amylase genes postdates the split with Neanderthals
- Author
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Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., Kivisild, Toomas, Inchley, Charlotte E., Larbey, Cynthia D.A., Shwan, Nzar A.A., Pagani, Luca, Saag, Lauri, Antão, Tiago, Jacobs, Guy, Hudjashov, Georgi, Metspalu, Ene, Mitt, Mario, Eichstaedt, Christina A., Malyarchuk, Boris, Derenko, Miroslava, Wee, Joseph, Abdullah, Syafiq, Ricaut, François-Xavier, Mormina, Maru, Mägi, Reedik, Villems, Richard, Metspalu, Mait, Jones, Martin K., Armour, John A.L., and Kivisild, Toomas
- Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
- Full Text
- View/download PDF
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