Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observed among multiple ethnic groups sampled throughout Ethiopia. Anthropologists have proposed two competing theories to explain the origins of the Ari Blacksmiths as (i) remnants of a population that inhabited Ethiopia prior to the arrival of agriculturists (e.g. Cultivators), or (ii) relatively recently related to the Cultivators but presently marginalized in the community due to their trade. Two recent studies by different groups analysed genome-wide DNA from samples of Ari Blacksmiths and Cultivators and suggested that genetic patterns between the two groups were more consistent with model (i) and subsequent assimilation of the indigenous peoples into the expanding agriculturalist community. We analysed the same samples using approaches designed to attenuate signals of genetic differentiation that are attributable to allelic drift within a population. By doing so, we provide evidence that the genetic differences between Ari Blacksmiths and Cultivators can be entirely explained by bottleneck effects consistent with hypothesis (ii). This finding serves as both a cautionary tale about interpreting results from unsupervised clustering algorithms, and suggests that social constructions are contributing directly to genetic differentiation over a relatively short time period among previously genetically similar groups

Profile and genetic parameters of dairy cattle locomotion score and lameness across lactation

This study investigated the profile of locomotion score and lameness before the first calving and throughout the first (n=237) and second (n=66) lactation of 303 Holstein cows raised on a commercial farm. Weekly heritability estimates of locomotion score and lameness, and their genetic and phenotypic correlations with milk yield, body condition score, BW and reproduction traits were derived. Daughter future locomotion score and lameness predictions from their sires’ breeding values for conformation traits were also calculated. First-lactation cows were monitored weekly from 6 weeks before calving to the end of lactation. Second-lactation cows were monitored weekly throughout lactation. Cows were locomotion scored on a scale from one (sound) to five (severely lame); a score greater than or equal to two defined presence of lameness. Cows’ weekly body condition score and BW was also recorded. These records were matched to corresponding milk yield records, where the latter were 7-day averages on the week of inspection. The total number of repeated records amounted to 12 221. Data were also matched to the farm’s reproduction database, from which five traits were derived. Statistical analyses were based on uni- and bivariate random regression models. The profile analysis showed that locomotion and lameness problems in first lactation were fewer before and immediately after calving, and increased as lactation progressed. The profile of the two traits remained relatively constant across the second lactation. Highest heritability estimates were observed in the weeks before first calving (0.66 for locomotion score and 0.54 for lameness). Statistically significant genetic correlations were found for first lactation weekly locomotion score and lameness with body condition score, ranging from −0.31 to −0.65 and from −0.44 to −0.76, respectively, suggesting that cows genetically pre-disposed for high body condition score have fewer locomotion and lameness issues. Negative (favourable) phenotypic correlations between first lactation weekly locomotion score/lameness and milk yield averaged −0.27 and −0.17, respectively, and were attributed to management factors. Also a phenotypic correlation between lameness and conception rate of −0.19 indicated that lame cows were associated with lower success at conceiving. First-lactation daughter locomotion score and/or lameness predictions from sires’ estimated breeding values for conformation traits revealed a significant linear effect of rear leg side view, rear leg rear view, overall conformation, body condition score and locomotion, and a quadratic effect of foot angle

Identification of evolutionary trajectories shared across human betacoronaviruses

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, whilst the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), whilst a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1 and SARS-CoV-2), we developed a methodological pipeline to classify shared non-synonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection, and draw upon protein structure data to identify potential biological implications. We find 30 candidate mutations, from which four [codon sites 18121 (nsp14/residue 28), 21623 (spike/21), 21635 (spike/25) and 23948 (spike/796); SARS-CoV-2 genome numbering] further display evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity

What Changes Have Occurred in Opioid Prescriptions and the Prescribers of Opioids Before TKA and THA?: A Large National Registry Study

BACKGROUND: Opioid use before TKA or THA is linked to a higher risk of revision surgery and less functional improvement. In Western countries, the frequency of preoperative opioid use has varied, and robust information on temporal changes in opioid prescriptions over time (in the months before surgery as well as annual changes) and among prescribers is necessary to pinpoint opportunities to improve on low-value care patterns, and when they are recognized, to target physician populations for intervention strategies. QUESTIONS/PURPOSES: (1) What proportion of patients undergoing arthroplasties receive an opioid prescription in the year before TKA or THA, and what were the preoperative opioid prescription rates over time between 2013 and 2018? (2) Does the preoperative prescription rate vary between 12 and 10 months and between 3 and 1 months in the year before TKA or THA, and did it change between 2013 and 2018? (3) Which medical professionals were the main prescribers of preoperative opioids 1 year before TKA or THA? METHODS: This was a large-database study drawn from longitudinally maintained national registry sources in the Netherlands. The Dutch Foundation for Pharmaceutical Statistics was linked to the Dutch Arthroplasty Register from 2013 to 2018. TKAs and THAs performed because of osteoarthritis in patients older than 18 years, which were also uniquely linked by age, gender, patient postcode, and low-molecular weight heparin use, were eligible. Between 2013 and 2018, 146,052 TKAs were performed: 96% (139,998) of the TKAs were performed for osteoarthritis in patients older than 18 years; of them, 56% (78,282) were excluded because of our linkage criteria. Some of the linked arthroplasties could not be linked to a community pharmacy, which was necessary to follow patients over time, leaving 28% (40,989) of the initial TKAs as our study population. Between 2013 and 2018, 174,116 THAs were performed: 86% (150,574) were performed for osteoarthritis in patients older than 18 years, one arthroplasty was excluded because of an outlier opioid dose, and a further 57% (85,724 of 150,574) were excluded because of our linkage criteria. Some of the linked arthroplasties could not be linked to a community pharmacy, leaving 28% (42,689 of 150,574) of THAs, which were performed between 2013 and 2018. For both TKA and THA, the mean age before surgery was 68 years, and roughly 60% of the population were women. We calculated the proportion of patients undergoing arthroplasties who had at least one opioid prescription in the year before arthroplasty and compared data from 2013 to 2018. Opioid prescription rates are given as defined daily dosages and morphine milligram equivalents (MMEs) per arthroplasty. Opioid prescriptions were assessed by preoperative quarter and by operation year. Possible changes over time in opioid exposure were investigated using linear regression, adjusted for age and gender, in which the month of operation since January 2013 was used as the determinant and MME as the outcome. This was done for all opioids combined and per opioid type. Possible changes in opioid prescription rates in the year before arthroplasty were assessed by comparing the time period of 1 to 3 months before surgery with the other quarters. Additionally, preoperative prescriptions per operation year were assessed per prescriber category: general practitioners, orthopaedic surgeons, rheumatologists, and others. All analyses were stratified by TKA or THA. RESULTS: The proportion of patients undergoing arthroplasties who had an opioid prescription before TKA increased from 25% (1079 of 4298) in 2013 to 28% (2097 of 7460) in 2018 (difference 3% [95% CI 1.35% to 4.65%]; p < 0.001), and before THA increased from 25% (1111 to 4451) to 30% (2323 to 7625) (difference 5% [95% CI 3.8% to 7.2%]; p < 0.001). The mean preoperative opioid prescription rate increased over time between 2013 and 2018 for both TKA and THA. For TKA, an adjusted monthly increase of 3.96 MME was observed (95% CI 1.8 to 6.1 MME; p < 0.001). For THA, the monthly increase was 3.8 MME (95% CI 1.5 to 6.0; p = 0.001. For both TKA and THA, there was a monthly increase in the preoperative oxycodone rate (3.8 MME [95% CI 2.5 to 5.1]; p < 0.001 and 3.6 [95% CI 2.6 to 4.7]; p < 0.001, respectively). For TKA, but not for THA, there was a monthly decrease in tramadol prescriptions (-0.6 MME [95% CI -1.0 to -0.2]; p = 0.006). Regarding the opioids prescribed in the year before surgery, there was a mean increase of 48 MME (95% CI 39.3 to 56.7 MME; p < 0.001) for TKA between 10 and 12 months and the last 3 months before surgery. For THA, this increase was 121 MME (95% CI 110 to 131 MME; p < 0.001). Regarding possible differences between 2013 and 2018, we only found differences in the period 10 to 12 months before TKA (mean difference 61 MME [95% CI 19.2 to 103.3]; p = 0.004) and the period 7 to 9 months before TKA (mean difference 66 MME [95% CI 22.0 to 110.9]; p = 0.003). For THA, there was an increase in the MMEs prescribed between 2013 and 2018 for all four quarters, with mean differences ranging from 43.9 to 55.4 MME (p < 0.05). The average proportion of preoperative opioid prescriptions prescribed by general practitioners ranged between 82% and 86% (41,037 of 49,855 for TKA and 49,137 of 57,289 for THA), between 4% and 6% (2924 of 49,855 for TKA and 2461 of 57,289 for THA), by orthopaedic surgeons, 1% by rheumatologists (409 of 49,855 for TKA and 370 of 57,289 for THA), and between 9% and 11% by other physicians (5485 of 49,855 for TKA and 5321 of 57,289 for THA). Prescriptions by orthopaedic surgeons increased over time, from 3% to 7% for THA (difference 4% [95% CI 3.6 to 4.9]) and 4% to 10% for TKA (difference 6% [95% CI 5% to 7%]; p < 0.001). CONCLUSION: Between 2013 and 2018, preoperative opioid prescriptions increased in the Netherlands, mainly because of a shift to more oxycodone prescriptions. We also observed an increase in opioid prescriptions in the year before surgery. Although general practitioners were the main prescribers of preoperative oxycodone, prescriptions by orthopaedic surgeons also increased during the study period. Orthopaedic surgeons should address opioid use and its associated negative effects in preoperative consultations. More intradisciplinary collaboration seems important to limit the prescribing of preoperative opioids. Additionally, research is necessary to assess whether opioid cessation before surgery reduces the risk of adverse outcomes. LEVEL OF EVIDENCE: Level III, therapeutic study

Out-of-hospital opioid prescriptions after knee and hip arthroplasty: prescribers and the first prescribed opioid

Background: We determined the first prescribed opioid and the prescribers of opioids after knee and hip arthroplasty (KA/HA) between 2013 and 2018 in the Netherlands. We also evaluated whether the first prescribed opioid dose was associated with the total dispensed dose and long-term opioid use in the first postoperative year. Methods: The Dutch Foundation for Pharmaceutical Statistics was linked to the Dutch Arthroplasty Register. Stratified for KA/HA, the first out-of-hospital opioid within 30 days of operation was quantified as median morphine milligram equivalent (MME). Opioid prescribers were orthopaedic surgeons, general practitioners, rheumatologists, anaesthesiologists, and other physicians. Long-term use was defined as ≥1 opioid prescription for >90 postoperative days. We used linear and logistic regression analyses adjusted for confounders. Results: Seventy percent of 46 106 KAs and 51% of the 42 893 HAs were prescribed ≥1 opioid. Oxycodone increased as first prescribed opioid (from 44% to 85%) whereas tramadol decreased (64–11%), but their dosage remained stable (stronger opioids were preferred by prescribers). An increase in the first prescription of 1% MME resulted in a 0.43%/0.37% increase in total MME (KA/HA, respectively). A 100 MME increase in dose of the first dispensed opioid had a small effect on long-term use (prevalence: 25% KA, 20% HA) (odds ratio=1.02/1.01 for KA/HA, respectively). Orthopaedic surgeons increasingly prescribed the first prescription between 2013 and 2018 (44–69%). General practitioners mostly prescribed consecutive prescriptions (>50%). Conclusion: Oxycodone increased as first out-of-hospital prescription between 2013 and 2018. The dose of the first prescribed opioid was associated with the total dose and a small increased risk of prolonged use. First prescriptions were mostly written by orthopaedic surgeons and consecutive prescriptions by general practitioners

Clinical and self-reported markers of reproductive function in female survivors of childhood Hodgkin lymphoma

Purpose: To evaluate the impact of treatment for Hodgkin lymphoma (HL) on clinical reproductive markers and pregnancy outcomes.Methods: This study was embedded within the DCOG LATER-VEVO study; a Dutch, multicenter, retrospective cohort study between 2004 and 2014. Serum anti-Müllerian hormone (AMH), follicle stimulating hormone (FSH), inhibin B, antral follicle count (AFC), and self-reported (first) pregnancy outcomes were evaluated in female childhood HL survivors and controls.Results: 84 HL survivors and 798 controls were included, aged 29.6 and 32.7 years old at time of assessment. Median age at HL diagnosis was 13.4 years. Cyclophosphamide equivalent dose (CED-score) exceeded 6000 mg/m2 in 56 women and 14 survivors received pelvic irradiation.All clinical markers were significantly deteriorated in survivors (odds-ratio for low AMH (&lt; p10) 10.1 [95% CI 4.9; 20.6]; low AFC (&lt; p10) 4.6 [95% CI 2.1; 9.9]; elevated FSH (&gt; 10 IU/l) 15.3 [95% CI 5.7; 41.1], low Inhibin B (&lt; 20 ng/l) 3.6 [95% CI 1.7; 7.7], p &lt; 0.001). Pregnancy outcomes were comparable between survivors and controls (± 80% live birth, ± 20% miscarriage). However, survivors were significantly younger at first pregnancy (27.0 years vs 29.0 years, P = 0.04). Adjusted odds-ratio for time to pregnancy &gt; 12 months was 2.5 [95% CI 1.1; 5.6] in survivors, p = 0.031. Adverse outcomes were specifically present after treatment with procarbazine and higher CED-score.Conclusion: HL survivors appear to have an impaired ovarian reserve. However, chance to achieve pregnancy seems reassuring at a young age. Additional follow-up studies are needed to assess fertile life span and reproductive potential of HL survivors, in particular for current HL treatments that are hypothesized to be less gonadotoxic.</p

Genomic analysis of 18th-century kazakh individuals and their oral microbiome

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome