The impact of the Turkish population variome on the genomic architecture of rare disease traits.

Purpose: The variome of the Turkish (TK) population, a population with a considerable history of admixture and consanguinity, has not been deeply investigated for insights on the genomic architecture of disease.

Methods: We generated and analyzed a database of variants derived from exome sequencing data of 773 TK unrelated, clinically affected individuals with various suspected Mendelian disease traits and 643 unaffected relatives.

Results: Using uniform manifold approximation and projection, we showed that the TK genomes are more similar to those of Europeans and consist of 2 main subpopulations: clusters 1 and 2 ( = 235 and 1181, respectively), which differ in admixture proportion and variome (https://turkishvariomedb.

Clinical and Genetic Analysis of Patients With TK2 Deficiency.

Objectives: Thymidine kinase 2 deficiency (TK2d) is a rare autosomal recessive disorder that stems from a perturbation of the mitochondrial DNA maintenance. Nucleoside treatment has recently shown promise as a disease-modifying therapy. TK2d was initially associated with rapidly progressive fatal myopathy in children featuring mitochondrial DNA depletion.

Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology.

Sepsis is among the most common causes of death in intensive care units. Septic shock is a type of circulatory shock that shows signs and symptoms that are similar to non-septic shock. Despite the impact of shock on patients and the economic burden, knowledge of the pathophysiology of septic shock is scarce.

Pharmacogenetic Sex-Specific Effects of Methotrexate Response in Patients with Rheumatoid Arthritis.

Methotrexate (MTX) is a commonly used drug for the treatment of rheumatoid arthritis (RA), but its effectiveness can vary greatly among patients. Pharmacogenetics, the study of how genetic variations can affect drug response, has the potential to improve the personalized treatment of RA by identifying genetic markers that can predict a patient's response to MTX. However, the field of MTX pharmacogenetics is still in its early stages and there is a lack of consistency among studies.

Frequency, location, and diameter of the anastomosis between the posterior superior alveolar artery and the infraorbital artery in imaging studies: systematic review and meta-analysis.

The anastomosis between the posterior superior alveolar artery (PSAA) and the infraorbital artery (IOA) courses along half of the lateral wall of the maxillary sinus. Risk of injury to the anastomosis between PSAA and IOA during surgical procedures has been reported. The aim of the present study was to carry out a systematic review and meta-analysis to determine the frequency, location, and diameter of the anastomosis between PSAA and IOA in imaging studies (cone-beam computed tomography, spiral cone-beam computed tomography, and computed tomography).

Metabolic Profiling at COVID-19 Onset Shows Disease Severity and Sex-Specific Dysregulation.

Background: metabolic changes through SARS-CoV-2 infection has been reported but not fully comprehended. This metabolic dysregulation affects multiple organs during COVID-19 and its early detection can be used as a prognosis marker of severity. Therefore, we aimed to characterize metabolic and cytokine profile at COVID-19 onset and its relationship with disease severity to identify metabolic profiles predicting disease progression.

Dolutegravir plus rilpivirine: benefits beyond viral suppression: DORIPEX retrospective study.

Switching dual therapy with dolutegravir (DTG) plus rilpivirine (RPV) was assessed in the SWORD-1 and SWORD-2 studies. Real-life data regarding the immunological impact of this approach on CD4+ and CD8+ T lymphocyte counts and the CD4/CD8 ratio are scarce. We evaluated this strategy on the basis of clinical practice data.

Plasma miRNA profile at COVID-19 onset predicts severity status and mortality.

Background: MicroRNAs (miRNAs) have a crucial role in regulating immune response against infectious diseases, showing changes early in disease onset and before the detection of the pathogen. Thus, we aimed to analyze the plasma miRNA profile at COVID-19 onset to identify miRNAs as early prognostic biomarkers of severity and survival.

Methods And Results: Plasma miRNome of 96 COVID-19 patients that developed asymptomatic/mild, moderate and severe disease was sequenced together with a group of healthy controls.

Differences in the hepatitis C virus cascade of care and time to initiation of therapy among vulnerable subpopulations using a mobile unit as point-of-care.

Background And Aims: People who inject drugs (PWID) and other marginalized populations with high hepatitis C virus (HCV) infection rates represent a unique challenge for treatment initiation due to health, administrative and social barriers. We analysed the HCV cascade of care (CoC) in some vulnerable subpopulations in Madrid, Spain, when using a mobile point-of-care (PoC).

Methods: From 2019 to 2021, a mobile unit was used to screen active HCV using a linkage-to-care and two-step PoC-based strategy.

Are Reduced Levels of Coagulation Proteins Upon Admission Linked to COVID-19 Severity and Mortality?

The link between coagulation system disorders and COVID-19 has not yet been fully elucidated. Evaluating the association of non-previously reported coagulation proteins with COVID-19 severity and mortality. Cross-sectional study of 134 COVID-19 patients recruited at admission and classified according to the highest COVID-19 severity reached (asymptomatic/mild, moderate, or severe) and 16 healthy control individuals.

Human inbreeding has decreased in time through the Holocene.

The history of human inbreeding is controversial. In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear. Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.

Crop prices, farm incomes, and food security during the COVID-19 pandemic in India: Phone-based producer survey evidence from Haryana State.

In March 2020, India declared a nationwide lockdown in response to the COVID-19 pandemic. Such restrictions on mobility interrupted the normal functioning of agricultural value chains. For a sample of 1767 tomato and wheat producers in the state of Haryana, we study to what extent the lockdown limited access to inputs, labor, machinery, and markets to produce, harvest, and sell their crops.

Short-term impacts of COVID-19 on food security and nutrition in rural Guatemala: Phone-based farm household survey evidence.

This article examines the short-term effects of the COVID-19 lockdown on food security and nutrition in rural Guatemala. We rely on a comprehensive panel dataset of 1,824 small agricultural households collected over two survey rounds, on November-December 2019 and May-June 2020. We place special emphasis on changes in agricultural and nonagricultural income sources, including remittances, and changes in dietary diversity, including consumption of animal source foods (ASF) and fruits and vegetables (F&V).

Oral ingestion versus endoscopic delivery of endoscopic capsule in patients with previous gastrointestinal surgery (ORENCES study): A Spanish multicentre observational study.

Background: Small Bowel Capsule Endoscopy is the first-choice technique for investigating the majority of small bowel diseases. Its most common complications are related to incomplete examinations and capsule retention. There is no consensus on how patients with previous gastrointestinal surgery should receive the capsule.

Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study.

The analysis of the effects of autozygosity, measured as the change of the mean value of a trait among offspring of genetic relatives, reveals the existence of directional dominance or overdominance. In this study we detect evidence of the effect of autozygosity in 4 out of 13 cardiometabolic disease-associated traits using data from more than 10,000 sub-Saharan African individuals recruited from Ghana, Burkina Faso, Kenya and South Africa. The effect of autozygosity on these phenotypes is found to be sex-related, with inbreeding having a significant decreasing effect in men but a significant increasing effect in women for several traits (body mass index, subcutaneous adipose tissue, low-density lipoproteins and total cholesterol levels).

Assessing the use of cell phones to monitor health and nutrition interventions: Evidence from rural Guatemala.

In-person (face-to-face) data collection methods offer many advantages but can also be time-consuming and expensive, particularly in areas of difficult access. We take advantage of the increasing mobile phone penetration rate in rural areas to evaluate the feasibility of using cell phones to monitor the provision of key health and nutrition interventions linked to the first 1,000 days of life, a critical period of growth and development. We examine response rates to calendarized text messages (SMS) and phone calls sent to 1,542 households over a period of four months.

Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data.

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).

Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot ().

Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi).

Is the "Habsburg jaw" related to inbreeding?

The "Habsburg jaw" has long been associated with inbreeding due to the high prevalence of consanguineous marriages in the Habsburg dynasty. However, it is thought that mandibular prognathism (MP) is under the influence of a dominant major gene. To investigate the relationship between the "Habsburg jaw" and the pedigree-based inbreeding coefficient () as a relative measure of genome homozygosity.

Correction to: Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories.

In the Original article published, the figure number 5: Genomic distribution of ROH is incorrectly published. The correct figure is given below.

Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories.

The study of runs of homozygosity (ROH) can shed light on population demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 worldwide populations. Using high-density SNP coverage, we could accurately identify ROH > 300 kb using PLINK software.

Inbreeding in the last ruling dynasty of Portugal: The house of Braganza.

Objectives: To determine whether: (1) there are high levels of inbreeding in a European royal dynasty that continues until the 20th century, and (2) whether inbreeding is negatively associated with pre-reproductive survival and longevity.

Methods: Genealogical information of all Braganza monarchs (1640-1910) was used to compute the individual's inbreeding coefficient (F) and the coefficient of kinship (θ) of the marriage which were examined in relation to two life-history traits.

Results: Mean F of the monarchs was 0.