Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example

Genomic approaches to the study of population demography rely on accurate SNP calling and by-proxy the site frequency spectrum (SFS). Two main questions for the design of such studies remain poorly investigated: do reduced genomic sequencing summary statistics reflect that of whole genome, and how do sequencing strategies and derived summary statistics impact demographic inferences? To address those questions, we applied the ddRAD sequencing approach to 254 individuals and whole genome resequencing approach to 35 mountain goat (Oreamnos americanus) individuals across the species range with a known demographic history. We identified SNPs with 5 different variant callers and used ANGSD to estimate the genotype likelihoods (GLs). We tested combinations of SNP filtering by linkage disequilibrium (LD), minor allele frequency (MAF) and the genomic region. We compared the resulting suite of summary statistics reflective of the SFS and quantified the relationship to demographic inferences by estimating the contemporary effective population size (Ne), isolation-by-distance and population structure, FST, and explicit modelling of the demographic history with δaδi. Filtering had a larger effect than sequencing strategy, with the former strongly influencing summary statistics. Estimates of contemporary Ne and isolation-by-distance patterns were largely robust to the choice of sequencing, pipeline, and filtering. Despite the high variance in summary statistics, whole genome and reduced representation approaches were overall similar in supporting a glacial induced vicariance and low Ne in mountain goats. We discuss why whole genome resequencing data is preferable, and reiterate support the use of GLs, in part because it limits user-determined filters.

Assessing the Viability of the Sarasota Bay Community of Bottlenose Dolphins

Population models, such as those used for Population Viability Analysis (PVA), are valuable for projecting trends, assessing threats, guiding environmental resource management, and planning species conservation measures. However, rarely are the needed data on all aspects of the life history available for cetacean species, because they are long-lived and difficult to study in their aquatic habitats. We present a detailed assessment of population dynamics for the long-term resident Sarasota Bay common bottlenose dolphin (Tursiops truncatus) community. Model parameters were estimated from 27 years of nearly complete monitoring, allowing calculation of age-specific and sex-specific mortality and reproductive rates, uncertainty in parameter values, fluctuation in demographic rates over time, and intrinsic uncertainty in the population trajectory resulting from stochastic processes. Using the Vortex PVA model, we projected mean population growth and quantified causes of variation and uncertainty in growth. The ability of the model to simulate the dynamics of the population was confirmed by comparing model projections to observed census trends from 1993 to 2020. When the simulation treated all losses as deaths and included observed immigration, the model projects a long-term mean annual population growth of 2.1%. Variance in annual growth across years of the simulation (SD = 3.1%) was due more to environmental variation and intrinsic demographic stochasticity than to uncertainty in estimates of mean demographic rates. Population growth was most sensitive to uncertainty and annual variation in reproduction of peak breeding age females and in calf and juvenile mortality, while adult survival varied little over time. We examined potential threats to the population, including increased anthropogenic mortality and impacts of red tides, and tested resilience to catastrophic events. Due to its life history characteristics, the population was projected to be demographically stable at smaller sizes than commonly assumed for Minimum Viable Population of mammals, but it is expected to recover only slowly from any catastrophic events, such as disease outbreaks and spills of oil or other toxins. The analyses indicate that well-studied populations of small cetaceans might typically experience slower growth rates (about 2%) than has been assumed in calculations of Potential Biological Removal used by management agencies to determine limits to incidental take of marine mammals. The loss of an additional one dolphin per year was found to cause significant harm to this population of about 150 to 175 animals. Beyond the significance for the specific population, demographic analyses of the Sarasota Bay dolphins provide a template for examining viability of other populations of small cetaceans.

ECONOMIC SECURITY OF THE REGION IN THE CONTEXT OF ITS POSITIONING

The article summarizes scientific approaches to the economic security of the region in the context of its positioning. The key risks of economic security of the Ukrainian regions have been identified as well as the most important criteria for regions positioning: the gross regional product (GRP) structure, the volume and rates of industrial development, the volume and dynamics of investments; natural resource production and scientific and technical potential; resource efficiency; competitiveness of the region's economy; unemployment rate; the quality of life, the degree of income differentiation, the provision of the population with material benefits and services; energy dependence; integration into the national economy etc. It is noted that the main problem of economic security is to ensure effective management of regional policy, as well as the evaluation of the regions positioning in the context of economic security can be carried out in the main directions: the level of poverty and unemployment in the region; the quality of life of the population; demographic component of the socio-economic security of the region; the ability of the region's economy to sustainably grow; stability of the region's financial system; support of the scientific potential of the region; dependence of the region's economy on imports of the most important types of products; relations of the region with the countries of the European Union. The modern positioning of some security sectors and the consequences of such positioning have been characterized. A system of main indicators has been formed that allows to quantify the level of economic security of the region in the context of its positioning. The methodical approach to evaluating the economic security of a region in the context of its positioning is highlighted. It is noted that despite the goals that are taken into account when positioning the region, the whole process can be structured into the following blocks: organizational and analytical support; methodical and informational support; conceptual software. The article presents the functional components of the mechanism for ensuring the economic security of regions in the context of their positioning. It has been proved that the effective functioning of the mechanism for ensuring the economic security of regions in the context of their positioning requires the effective functioning of all subjects synchronously, which made it possible to formulate a synergistic effect in a formalized form.

Pendampingan Penyajian dan Pengolahan Data Demografi Kesehatan Penduduk Aparat Desa Negeri Hutumuri Kecamatan Leitimur Selatan Kota Ambon

ABSTRAK Negeri Hutumuri merupakan desa terpadat di wilayah Kecamatan Leitimur Selatan Kota Ambon dengan jumlah penduduk mencapai 4.657 jiwa serta kepadatan penduduk sebesar 310 jiwa setiap km2. Keberadaan profil status jumlah penduduk yang lebih besar memungkinkan peluang munculnya berbagai persoalan kependudukan khususnya kesehatan penduduk apabila tidak dikelola dengan baik. Tujuan dari program Pengabdian Kepada Masyarakat ini adalah untuk meningkatkan pengetahuan aparat desa sebagai ujung tombak pembangunan desa terkait penyajian dan pengolahan data demografi kesehatan penduduk. Metode pelaksanaan kegiatannya meliputi pelatihan dan pendampingan tentang analisis statistik data demografi kesehatan penduduk yang meliputi pengukuran dasar data demografi kependudukan desa. Hasil dari pelaksanaan kegiatan ini, dapat menunjang pemahaman, menambah pengetahuan dan pengembangan softskill aparat desa dalam mengelola statistik demografi kesehatan penduduk yang berdampak pada peningkatan kualitas pengelolaan dan penataan data kependudukan yang dapat digunakan untuk pembangunan dan mempermudah pelayanan terhadap masyarakat desa. Kata Kunci: Demografi Kesehatan Penduduk, Penyajian dan Pengolahan Data, Softskill Aparat Desa ABSTRACT Negeri Hutumuri is the most populous village in the South Leitimur Subdistrict, Ambon City, with a population of 4,657 people and a population density of 310 people per km2. The existence of a larger population status profile allows opportunities for various population problems to arise, especially population health if it is not managed properly. The purpose of this Community Service program is to increase the knowledge of village officials as the spearhead of village development related to the presentation and processing of population health demographic data. The method of implementing its activities includes training and assistance on a statistical analysis of population health demographic data which includes basic measurement of village population demographic data. The results of the implementation of this activity can support understanding, increase knowledge and develop soft skills of village officials in managing demographic health statistics of the population which have an impact on improving the quality of management and structuring of population data that can be used for development and facilitating services to village communities. Keywords: Population Health Demographics, Data Presentation, and Processing, Soft Skills for Village Officials.

The Profile of Psoriasis Vulgaris Patients: A Descriptive Study

Background: Psoriasis is a skin disease that occurs due to proliferation and differentiation disturbances of the epidermis. This chronic condition often reduces the human quality of life. There have been studies investigating psoriatic patient profiles and treatments, but few are conducted in Surabaya. Hence, those studies cannot fully represent the population demographic in Surabaya. Purpose: To investigate the prevalence of psoriasis vulgaris and the sociodemographic profile of the patients in Dr Soetomo General Academic Hospital. Methods: This was a Retrospective study psoriasis vulgaris patients in January 2016–December 2018. The data were collected by retrieving Electronic Medical Records (EMR) as secondary data. Result: The psoriasis vulgaris prevalence of outpatients was 0.46% and 4.59% in inpatients. Most study subjects were adults aged 18 and above (98.1%), most of the patients were obese (46.3%), the most common provoking factor was focal tooth infection (33.8%) and stress (28.8%), and none reported family history of psoriasis. Conclusion: Some results are similar to other studies conducted in Surabaya, which were the obesity and Type 2 Diabetes Mellitus (DM) being strong a factor to psoriasis development. However, the result on psoriasis family history was not in line with other studies.

AIDS-Defining Opportunistic Illnesses in Qatar, 2000-2016 : A Cohort Study

Background Human immune deficiency virus (HIV) infection remains a major health problem since discovery of the virus in 1981. Globally, since introduction of antiretroviral therapy, AIDS related death felt by more than 25% between 2005 &2011. Also, HIV related opportunistic infections (OIs) are less common, especially with use of prophylaxis to prevent such infections (3). We aim in this study to assess the incidence of HIV infection and related OIs in Qatar for 17-year period, and assess the spectrum of these infections, risk factors and treatment outcome. Methods retrospective cohort study for all HIV infected patients registered in Qatar from 2000-2016. Incidence of HIV infection and related opportunistic illness was calculated per 100000 population. Demographic and Clinical characteristic were compared between two groups of patients with and without opportunistic illness. Results of 167 cases with HIV infection 54 (32.3%) of them had opportunistic illness. The average incidence rate of HIV infection over 17 years is 0.69 per 100000 population, and the incidence rate for opportunistic illness is 0.27 per 100000 population, figure1. The most common opportunistic illness is pneumocystis jirovecii pneumonia (PCP) 25% of cases, followed by CMV retinitis 7.2%, Tuberculosis 5.4%, Toxoplasmosis 4.2% and less than 2% for Kaposi sarcoma, lymphoma and cryptococcal infection.

Treatment with Non-invasive respiratory support in severe COVID-19: Clinical effectiveness observational study

Introduction: The study aimed to analyse the clinical response and short-term outcomes with the use of high-flow oxygen therapy (HFOT), non-invasive mechanical ventilation (NIMV) with bilevel positive airway pressure, or continuous positive airway pressure (CPAP) in severe COVID-19 patients. Methods: We conducted an observational, prospective, single-center study, approved by Ethics Committee of “Instituto de Investigación Sanitaria Fundación Jiménez Díaz” (EO102-20-HRJC). We included a total of 130 patients ≥18 years-old, with proved SARS-CoV-2 infection and secondary Acute Respiratory Failure (ARF) that required treatment with Non-invasive Respiratory Support (NIRS). We collected data about population demographic characteristics, clinical factors, and evolution during the incoming. A baseline of patients treated with HFO, CPAP and NIMV were compared with one-way ANOVA test, while categorical variables were expressed as numbers and percentages and were compared using the chi-square test or Fisher’s exact test when appropriate. Results: The cohort was distributed as follows: CPAP 54.6% (n = 71), NIMV 30% (n = 39), HFO 15.4% (n = 20). There were no differences between NIRS subgroups regarding age, comorbidity, or functional status. At the beginning of NIRS treatment, PaO2/FiO2 value was 149.3 ± 69.7. After 24 hours, PaO2/FiO2 was significantly higher in the CPAP group (CPAP vs NIMV, p-value = 0.0042; CPAP vs HFO, p-value = 0.000169). The overall ICU admission evaded rate was 69.1% and TF rate was 43.8%, without differences between the three therapies (p-value = 0.281). The mortality rate was 37.2%, without significant differences between subgroups. Conclusions: Our data suggest that CPAP versus treatment with NIMV or HFO improves PaO2/FiO2 rate in severe ARF patients, significantly reducing ICU admission. No differences were observed in mortality or therapeutic failure.

Attitude and Knowledge Relationship with Sexual Behavior at Risk of Sexually Transmitted Infection (STI) in Male Adolescents in Indonesia (IDHS Data Analysis 2017)

Introduction: Indonesia Population Demographic Survey in 2017 recorded that 8% of teenage boys and 2% of teenage girls admitted to having sexual intercourse. This certainly worries all of us who hope today's youth will be a demographic bonus. Sexual behavior is at risk of impacting the issue of Unwanted Pregnancy (KTD), abortion, Sexually Transmitted Infections (STIs), and the ongoing incidence of HIV and AIDS. Objective: to confirm the relationship of attitudes and knowledge with risky sexual behavior in adolescent boys in Indonesia. Methods: This type of research is quantitative analytics using a cross-sectional design and sourced from secondary data of the Indonesian Health Demographic Survey 2017. The population in this study was 13,079 adolescent men aged 15-24, sampling 10,710 with saturated sampling techniques. Bivariate data analysis using the chi-square test (0.05). Results: were obtained by adolescents with a positive attitude of 52.1%, knowledgeable 77.8%, and 13.1% risky sexual behavior. Test results showed there was an attitude relationship with risky sexual behavior with p-value = 0.000 and there was a knowledge relationship with risky sexual behavior with p-value = 0.000. Conclusions: This study are expected to be used as input for the creation of risky sexual behavior prevention programs in adolescents and form the basis for the creation of an educational model related to adolescent reproductive health for parents and educational institutions.

Determinants of Vaccine Acceptance against COVID-19 in China: Perspectives on Knowledge and DrVac-COVID19S Scale

Background: This study determined the knowledge and attitudes regarding COVID-19 and assessed the acceptance of the COVID-19 vaccine among the Chinese population. Methods: An online and offline cross-sectional study was conducted from 1 to 18 June 2021 among the Chinese population. Demographic characteristics, attitudes, knowledge, values, impact, and autonomy regarding the COVID-19 vaccine were collected using questionnaire. The variables in our study were analyzed by Mann-Whitney test and chi-square test. Results: A total of 93.8% participants were willing to be vaccinated, 2.7% refused, and 3.5% hesitated. In regards to knowledge about the COVID-19 vaccine, 94.3% citizens surveyed knew about the spread of droplets and 65% had knowledge about surfaces touched by an infected person. In addition, 93.8% of participants had knowledge of the common symptoms related to COVID-19, such as fever and cough (93.8%), shortness of breath/anorexia/fatigue/nausea/vomiting/diarrhea (80.2%), and panic and chest tightness (69.4%). Most participants had a strong self-prevention awareness, such as washing hands regularly (92.1%) and wearing a facemask (94.1%). Besides, over ninety percent of respondents would report exposure to SARS-CoV-2 (96.6%) and exposure to symptoms possibility related to COVID-19 (92.9%). If necessary, most respondents would agree to isolate at home (93.5%) or an isolation in hospital (96.3%). Knowledge of COVID-19, including transmission, symptoms, protective measures, and vaccines itself, is associated with vaccination attitude. Values, perceived impacts, knowledge, and autonomy, assessed by the scale of DrVac-COVID19S, have also been revealed as important determinants to vaccine acceptance. Conclusions: Almost 93% of Chinese people surveyed in this study showed a willing attitude toward COVID-19 vaccination. Based on the above results, government and social workers can take measures from these perspectives to improve the vaccination attitude, so as to increase vaccine immunization rates.