Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong–Mien People

Hmong–Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Effective On-Chip Communication for Message Passing Programs on Multi-Core Processors

Shared memory is the most popular parallel programming model for multi-core processors, while message passing is generally used for large distributed machines. However, as the number of cores on a chip increases, the relative merits of shared memory versus message passing change, and we argue that message passing becomes a viable, high performing, and parallel programming model. To demonstrate this hypothesis, we compare a shared memory architecture with a new message passing architecture on a suite of applications tuned for each system independently. Perhaps surprisingly, the fundamental behaviors of the applications studied in this work, when optimized for both models, are very similar to each other, and both could execute efficiently on multicore architectures despite many implementations being different from each other. Furthermore, if hardware is tuned to support message passing by supporting bulk message transfer and the elimination of unnecessary coherence overheads, and if effective support is available for global operations, then some applications would perform much better on a message passing architecture. Leveraging our insights, we design a message passing architecture that supports both memory-to-memory and cache-to-cache messaging in hardware. With the new architecture, message passing is able to outperform its shared memory counterparts on many of the applications due to the unique advantages of the message passing hardware as compared to cache coherence. In the best case, message passing achieves up to a 34% increase in speed over its shared memory counterpart, and it achieves an average 10% increase in speed. In the worst case, message passing is slowed down in two applications—CG (conjugate gradient) and FT (Fourier transform)—because it could not perform well on the unique data sharing patterns as its counterpart of shared memory. Overall, our analysis demonstrates the importance of considering message passing as a high performing and hardware-supported programming model on future multicore architectures.

Research data management and sharing awareness, attitude, and behavior of academic researchers

This study assesses the research data management (RDM) awareness, attitude, practices, and behaviors of Pakistan's academic researchers. By using an internationally designed structured questionnaire as a data collection instrument. Quantitative survey research method was opted to meet the research objectives and data was collected from academicians and researchers of four premier universities of Pakistan. The study reveals used and produced data file formats, data acquisition sources, data storage patterns, metadata and tagging practices, data sharing patterns, RDM awareness, attitude, and behavior of the respondents by investigating the self-opinion of respondents on extensive sets of structured questionnaire items. It is a comprehensive assessment of the phenomenon from a developing country's perspective where research data management policies are absent at national and institutional level. The findings have theoretical implications for researchers and practical implications for policymakers, university administrators, university library administrators, and educational trainers.

Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people

Hmong-Mien-speaking (HM) populations, widely distributed in South China, North of Thailand, Laos and Vietnam, have experienced different settlement environments, dietary habits and pathogen exposure. However, their specific biological adaptation also remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations and also identified one new ancestral lineage specifically exited in HM people, which spatially distributed from Sichuan and Guizhou in the North to Thailand in the South and temporally dated to at least 500 years. The sharing patterns of the newly-identified homogeneous ancestry component combined the estimated admixture times via the decay of Linkage Disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward recently, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically-informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese population genomic diversity project (CPGDP), especially in the ethnolinguistic regions.

FrAnTK: A Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets

Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyse their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualisation of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.

A DESCRIPTIVE STUDY ON NUTRITIONAL STATUS ASSESSMENT AND MORBIDITY PATTERN OF ADOLESCENTS (10–16 YEARS) RESIDING IN URBAN SLUMS OF AMRITSAR, PUNJAB

Objectives: To assess the nutritional status and morbidity pattern of adolescents age 10–16 years and to determine the various factors associated with under-nutrition. Methods: A descriptive cross-sectional study was conducted among 1600 households which were selected by systematic random sampling method from 64 slum areas. All adolescents aged 10–16 years were included. Required information was collected on a pretested performa. Height and weight were measured to assess their nutritional status and haemoglobin estimation was done by Sahli’s method. Descriptive statistics (frequencies and proportions) and univariate logistic regression were done to determine various factors associated with under nutrition. Results: Out of 603 study participants, 75% of adolescents were under-weight. About 82.3% had anemia. About 36% suffered from one or more infectious disease in the last 3 months. Going to school, occupation, female sex, and suffering from any infectious disease in the past 3 months were found to be associated with malnutrition. Addiction was reported in 9% of study participants. Conclusions: High prevalence of under-nutrition and anemia in our study reflects inequitable distribution of resources, low purchasing capacity of foods, and unequal food sharing patterns in families making them socially and biologically vulnerable.

Analysing Twitter semantic networks: the case of 2018 Italian elections

Social media play a key role in shaping citizens’ political opinion. According to the Eurobarometer, the percentage of EU citizens employing online social networks on a daily basis has increased from 18% in 2010 to 48% in 2019. The entwinement between social media and the unfolding of political dynamics has motivated the interest of researchers for the analysis of users online behavior—with particular emphasis on group polarization during debates and echo-chambers formation. In this context, semantic aspects have remained largely under-explored. In this paper, we aim at filling this gap by adopting a two-steps approach. First, we identify the discursive communities animating the political debate in the run up of the 2018 Italian Elections as groups of users with a significantly-similar retweeting behavior. Second, we study the mechanisms that shape their internal discussions by monitoring, on a daily basis, the structural evolution of the semantic networks they induce. Above and beyond specifying the semantic peculiarities of the Italian electoral competition, our approach innovates studies of online political discussions in two main ways. On the one hand, it grounds semantic analysis within users’ behaviors by implementing a method, rooted in statistical theory, that guarantees that our inference of socio-semantic structures is not biased by any unsupported assumption about missing information; on the other, it is completely automated as it does not rest upon any manual labelling (either based on the users’ features or on their sharing patterns). These elements make our method applicable to any Twitter discussion regardless of the language or the topic addressed.

Analisis Sistem Keuntungan Pola Bagi Hasil Nelayan Kelong Apung Pulau Pucung Desa Malang Rapat Kabupaten Bintan

The local government of Bintan Regency in this case the Department of Marine and Fisheries has allocated funds in the form of fishing gear facilities and infrastructure including kelong. The efforts of the Bintan district government through the Ministry of Marine Affairs and Fisheries have made efforts to improve the welfare of fishermen in Bintan Regency, but whether these efforts have been directly felt by fishermen on the island of Pucung, Malang Village, Bintan District Meeting. Where the majority of fishermen on the coast of Bintan Regency use the Floating Kelong Fishing Equipment. This study aims to determine the profit sharing pattern between kelong owners "Toke" with floating kelong fishermen on Pucung Island Malang Village Bintan District Meeting.. The research was conducted using primary data obtained directly from fishermen in the form of daily reports. The study was conducted for 4 (four) months from April to July 2018. The number of respondents in the study were 78 people. Pucung Island fishermen apply 3 profit sharing patterns for fishing activities using floating kelong, namely: Salary System, 1: 1 and 2: 1.

Evidence of misuse of nonparametric tests in the presence of heteroscedasticity within obesity research

Background: Classic nonparametric tests (cNPTs), like Kruskal–Wallis or Mann–Whitney U, are sometimes used to detect differences in central tendency (i.e., means or medians). However, when the tests’ assumptions are violated, such as in the presence of unequal variance and other forms of heteroscedasticity, they are no longer valid for testing differences in central tendency. Yet, sometimes researchers erroneously use cNPTs to account for heteroscedasticity. Objective: To document the appropriateness of cNPT use in obesity literature, characterize studies that use cNPTs, and evaluate the citation and public sharing patterns of these articles. Methods: We reviewed obesity studies published in 2017 to determine whether the authors used cNPTs: (1) to correct for heteroscedasticity (invalid); (2) when heteroscedasticity was clearly not present (correct); or (3) when it was unclear whether heteroscedasticity was present (unclear). Open science R packages were used to transparently search literature and extract data on how often papers with errors have been cited in academic literature, read in Mendeley, and disseminated in the media. Results: We identified nine studies that used a cNPT in the presence of heteroscedasticity (some because of the mistaken rationale that the test corrected for heteroscedasticity), 25 articles that did not explicitly state whether heteroscedasticity was present when a cNPT was used, and only four articles that appropriately reported that heteroscedasticity was not present when a cNPT was used. Errors were found in observational and interventional studies, in human and rodent studies, and only when studies were unregistered. Studies with errors have been cited 113 times, read in Mendeley 123 times, and disseminated in the media 41 times, by the public, scientists, science communicators, and doctors. Conclusions: Examples of inappropriate use of cNPTs exist in the obesity literature, and those articles perpetuate the errors via various audiences and dissemination platforms.

Cracking Open the News Feed

In this study, we analyze for the first time newly available engagement data covering millions of web links shared on Facebook to describe how and by which categories of U.S. users different types of news are seen and shared on the platform. We focus on articles from low-credibility news publishers, credible news sources, purveyors of clickbait, and news specifically about politics, which we identify through a combination of curated lists and supervised classifiers. Our results support recent findings that more fake news is shared by older users and conservatives and that both viewing and sharing patterns suggest a preference for ideologically congenial misinformation. We also find that fake news articles related to politics are more popular among older Americans than other types, while the youngest users share relatively more articles with clickbait headlines. Across the platform, however, articles from credible news sources are shared over 5 times more often and viewed over 7 times more often than articles from low-credibility sources. These findings offer important context for researchers studying the spread and consumption of information — including misinformation — on social media.