Copy number and selection of MHC genes in ruminants are related to habitat, average life span and diet

The ruminants, as the main group of livestock, have been extensively studied in terms of their physiology, endocrinology, biochemistry, genetics, and nutrition. Despite the wide geographic distribution and habitat diversity of animals in this group, their ecology and evolution remain poorly understood. In this study, we analyzed the gene copy number, selection, and ecological and evolutionary processes that have affected the evolution of major histocompatibility complex (MHC) genes across ruminant lineages based on available genomic data. The 51 species analyzed represented all six families of ruminants. Our finding indicated that the architecture of the MHC region is conserved in ruminants, but with variable copy numbers of MHC-I, MHC-IIA, and MHC-IIB genes. No lineage-specific gene duplication was observed in the MHC genes. The phylogenetic generalized least squares regression (PGLS) model revealed association between ecological and biological factors (habitat and lifespan) and gene duplication in DQA and DQB, but not in DRB. The selection pressure of DQA and DQB were related with lifespan, diet, and the ratio of genetic repeat elements. These results suggest that the MHC evolution in ruminants, including copy number and selection, has been influenced by genetic repeat elements, pathogen exposure risk, and intrinsic cost of possessing multiple MHC genes.

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

BACKGROUND

The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown.

RESULTS

Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness.

CONCLUSIONS

Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.

The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size

To concisely describe how genetic variation, at individual loci or across whole genomes, changes over time, and to follow transitory allelic changes, we introduce a quantity related to entropy, that we term pseudoentropy. This quantity emerges in a diffusion analysis of the mean time a mutation segregates in a population. For a neutral locus with an arbitrary number of alleles, the mean time of segregation is generally proportional to the pseudoentropy of initial allele frequencies. After the initial time point, pseudoentropy generally decreases, but other behaviours are possible, depending on the genetic diversity and selective forces present. For a biallelic locus, pseudoentropy and entropy coincide, but they are distinct quantities with more than two alleles. Thus for populations with multiple biallelic loci, the language of entropy suffices. Then entropy, combined across loci, serves as a concise description of genetic variation. We used individual based simulations to explore how this entropy behaves under different evolutionary scenarios. In agreement with predictions, the entropy associated with unlinked neutral loci decreases over time. However, deviations from free recombination and neutrality have clear and informative effects on the entropy's behaviour over time. Analysis of publicly available data of a natural D. melanogaster population, that had been sampled over seven years, using a sliding-window approach, yielded considerable variation in entropy trajectories of different genomic regions. These mostly follow a pattern that suggests a substantial effective population size and a limited effect of positive selection on genome-wide diversity over short time scales.

Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data

Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.

The validity of the selection methods for recruitment to UK core psychiatry training: cohort study

AIMS AND METHOD

Selection into core psychiatry training in the UK uses a computer-delivered Multi-Specialty Recruitment Assessment (MSRA; a situational judgement and clinical problem-solving test) and, previously, a face-to-face Selection Centre. The Selection Centre assessments were suspended during the COVID-19 pandemic. We aimed to evaluate the validity of this selection process using data on 3510 psychiatry applicants. We modelled the ability of the selection scores to predict subsequent performance in the Clinical Assessment of Skills and Competencies (CASC). Sensitivity to demographic characteristics was also estimated.

RESULTS

All selection assessment scores demonstrated positive, statistically significant, independent relationships with CASC performance and were sensitive to demographic factors.

IMPLICATIONS

All selection components showed independent predictive validity. Re-instituting the Selection Centre assessments could be considered, although the costs, potential advantages and disadvantages should be weighed carefully.

Heritable human genome editing: correction, selection and treatment

Heritable human genome editing (HHGE) to correct a nuclear gene sequence that would result in a serious genetic condition in a future child is presented as 'treatment' in various ethics and policy materials, and as morally preferable to the 'selection' practice of preimplantation genetic testing (PGT), which is subject to the disability critique. However, whether HHGE is 'treatment' for a future child, or another form of 'selection', or whether HHGE instead 'treats' prospective parents, are now central questions in the debate regarding its possible legalisation. This article argues that the idea of 'treatment' for a future child is largely a proxy for 'seriousness of purpose', intended to distinguish HHGE to avoid serious genetic conditions from less obviously justifiable uses; that HHGE is best understood, and morally justified, as a form of 'treatment' for prospective parents who strongly desire an unaffected genetically related child and who have no, or poor, options to achieve this; that HHGE would be morally permissible if consistent with that child's welfare; that legalisation is supportable with reference to the right to respect for private and family life under Article 8 of the European Convention on Human Rights; and that HHGE is morally distinguishable from PGT.

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

Responsive deep brain stimulation for the treatment of Tourette syndrome

To report the results of 'responsive' deep brain stimulation (DBS) for Tourette syndrome (TS) in a National Institutes of Health funded experimental cohort. The use of 'brain derived physiology' as a method to trigger DBS devices to deliver trains of electrical stimulation is a proposed approach to address the paroxysmal motor and vocal tic symptoms which appear as part of TS. Ten subjects underwent bilateral staged DBS surgery and each was implanted with bilateral centromedian thalamic (CM) region DBS leads and bilateral M1 region cortical strips. A series of identical experiments and data collections were conducted on three groups of consecutively recruited subjects. Group 1 (n = 2) underwent acute responsive DBS using deep and superficial leads. Group 2 (n = 4) underwent chronic responsive DBS using deep and superficial leads. Group 3 (n = 4) underwent responsive DBS using only the deep leads. The primary outcome measure for each of the 8 subjects with chronic responsive DBS was calculated as the pre-operative baseline Yale Global Tic Severity Scale (YGTSS) motor subscore compared to the 6 month embedded responsive DBS setting. A responder for the study was defined as any subject manifesting a ≥ 30 points improvement on the YGTSS motor subscale. The videotaped Modified Rush Tic Rating Scale (MRVTRS) was a secondary outcome. Outcomes were collected at 6 months across three different device states: no stimulation, conventional open-loop stimulation, and embedded responsive stimulation. The experience programming each of the groups and the methods applied for programming were captured. There were 10 medication refractory TS subjects enrolled in the study (5 male and 5 female) and 4/8 (50%) in the chronic responsive eligible cohort met the primary outcome manifesting a reduction of the YGTSS motor scale of ≥ 30% when on responsive DBS settings. Proof of concept for the use of responsive stimulation was observed in all three groups (acute responsive, cortically triggered and deep DBS leads only). The responsive approach was safe and well tolerated. TS power spectral changes associated with tics occurred consistently in the low frequency 2-10 Hz delta-theta-low alpha oscillation range. The study highlighted the variety of programming strategies which were employed to achieve responsive DBS and those used to overcome stimulation induced artifacts. Proof of concept was also established for a single DBS lead triggering bi-hemispheric delivery of therapeutic stimulation. Responsive DBS was applied to treat TS related motor and vocal tics through the application of three different experimental paradigms. The approach was safe and effective in a subset of individuals. The use of different devices in this study was not aimed at making between device comparisons, but rather, the study was adapted to the current state of the art in technology. Overall, four of the chronic responsive eligible subjects met the primary outcome variable for clinical effectiveness. Cortical physiology was used to trigger responsive DBS when therapy was limited by stimulation induced artifacts.

Development and validation of an objective virtual reality tool for assessing technical aptitude among potential candidates for surgical training

BACKGROUND

Good technical skills are crucial for surgeons. Yet although surgical training programs strive to assess technical aptitude when selecting surgical residents, valid assessments of such aptitude are still lacking. Surgical simulators have been proposed as a potentially effective tool for this purpose. The current study aims to develop a technical aptitude test using a virtual reality surgical simulator, and to validate its use for the selection of surgical residents.

METHODS

The study had three phases. In Phase 1, we developed an initial version of the technical aptitude test using the Lap-X-VR laparoscopic simulator. In Phases 2 and 3 we refined the test and collected empirical data to evaluate four main sources of validity evidence (content, response process, internal structure, and relationships with other variables), and to evaluate the feasibility and acceptability of the test. Specifically, Phase 2 comprised a review of the test by 30 senior surgeons, and in Phase 3 a revised version of the test was administered to 152 interns to determine its psychometric properties.

RESULTS

Both the surgeons and interns rated the test as highly relevant for selecting surgical residents. Analyses of the data obtained from the trial administration of the test supported the appropriateness of the score calculation process and showed good psychometric properties, including reliability (α = 0.83) and task discrimination (mean discrimination = 0.5, SD = 0.1). The correlations between test scores and background variables revealed significant correlations with gender, surgical simulator experience, and video game experience (ps < 0.001). These variables, however, explained together only 10% of the variance in test scores.

CONCLUSIONS

We describe the systematic development of an innovative virtual reality test for assessing technical aptitude in candidates for surgical training, and present evidence for its validity, feasibility and acceptability. Further validation is required to support the application of the test for selection, as well as to discern the impact of gender, surgical simulator experience, and video game experience on the fairness of test results. However, the test appears to be a promising tool that may help training programs assess the suitability of candidates for surgical training.

Urology Residency Applicant Selection: Program Directors' New Criteria

OBJECTIVE

To evaluate the impact of the recent changes to the urology residency application process on the criteria utilized by residency program directors (PDs) for interview invitations and their perspectives concerning these changes.

METHODS

One hundred thirty-seven urology residency PDs were invited to participate in an anonymous survey to explore interview selection criteria and the impact of the increase in preference signals (PS) per applicant.

RESULTS

Fifty-eight PDs (42.8%) completed the survey. The highest-ranked criteria were letters of recommendation (LoR) and successful sub-internship (sub-I) at the PD's institution, without statistically significant differences between these two. Gender, ethnicity and medical school prestige were the lowest rated criteria, without significant differences between these three. Compared to before the increase in the number of PS per applicant, 80.7% of PDs reported that not receiving a PS from an applicant this cycle would more negatively impact the chances of offering an interview to that applicant. Moreover, 12.2% stated they would not interview any applicants who did not send a PS. Finally, 62.1% of PDs believed recent changes worsened the process.

CONCLUSION

Recent changes impacted PDs applicant evaluation, with the highest ranked criteria being LoRs and sub-I. Paradoxically, the increase in the number of PS per applicant has increased their importance as applicants are much less likely to receive interview offers from programs they have not signaled. Lastly, most PDs believe changes have worsened the evaluation process.

Positive cases of bovine genital campylobacteriosis and bovine trichomonosis in the eradication program of La Pampa, Argentina: 2008-2021

Bovine genital campylobacteriosis, caused by the gram-negative bacteria Campylobacter fetus venerealis, and bovine trichomonosis, caused by the parasite protozoan Tritrichomonas foetus, are venereal diseases that occur with long intercalving periods and abortion. The control of both diseases relies on microbiological testing and culling infected bulls. Vaccination and antibiotic treatment may help in controlling campylobacteriosis but are not recommended for trichomonosis control. Several regions of the world have active control programs for trichomonosis, not campylobacteriosis. In Argentina, the state of La Pampa aims to eradicate trichomonosis and campylobacteriosis by imposing annual diagnostic testing of every bull and slaughtering positive animals. Prior studies indicated a declining trend in the prevalence of campylobacteriosis and trichomonosis in La Pampa. It was also proposed that the prevalence of one disease could be estimated from the prevalence of the other. The purpose of this retrospective analysis of data gathered from 2008 to 2021 was to determine the La Pampa program's efficacy. Descriptive statistics were employed to determine the reason behind the correlation between tricomonosis and campylobacteriosis diagnostic results. The outcomes refute the notion that this program of venereal eradication was a success. Furthermore, an excess of false positives in both diagnoses may have contributed to the correlation between the prevalences of campylobactriosis and trichomonosis. The practice of killing animals without verifying positive results hinders the determination of disease prevalence and results in the death of numerous healthy animals.

Genome-wide analysis of cellulose synthase gene superfamily in Tectona grandis L.f

This study aimed to explore Cellulose synthase gene superfamily of teak, and its evolutionary relationship with homologous genes of other woody species. The incidence of evolutionary events like gene duplication and gene loss, influence of the selection pressure, and consequent adaptive functional divergence of the duplicated TgCes gene were assessed alongside it's role in wood coloration. This study identified 39 full-length non-redundant proteins belonging to CesA and Csl gene families. TgCesA and TgCsl proteins with Cellulose synthase domain repeats indicated tandem gene duplication and probable genetic variability, enabling local adaptation. Further, multi-domain protein (MYB-like DNA-binding domain and CesA domain) with maximum introns was also identified indicating gene fusion and formation of complex protein with novel functions. Phylogenetic analysis grouped the genes into seven subfamilies (CesA, CslA, CslC, CslD, CslE, CslG, and CslM) with each undergoing gene duplication and loss along their evolutionary history. Post-species gene duplications and probable neofunctionalization were identified in TgCesA and TgCsl gene families. Each subfamily was found to be under strong purifying selection with a few or no sites under positive selection. Functional divergence analysis further revealed site-specific selective constraints in CesA and Csl genes of the teak Cellulose synthase gene family. Furthermore, protein-protein interaction network analysis identified co-expression of Cellulose synthase gene with flavonoid 3',5'-hydroxylase (F3'5'H, CYP75A), involved in the biosynthesis of xylem anthocyanin compounds, probably responsible for wood coloration. This study thus offers a foundation for future research in wood formation and wood property traits specific to teak and its provenances.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03927-6.

Pricing above value: Selling to a market with selection problems

This paper shows that selection incentives in downstream markets distort upstream prices. It is possible for inputs to be priced above the value that the good has for final consumers. We apply this idea to pharmaceutical companies selling drugs to a health insurance market with selection problems. We specify the conditions under which drugs are sold at prices exceeding treatment value. Another feature of the model is an excessive private incentive to reduce market size, e.g. in the form of personalized medicine.

Enhancing in vitro regeneration via somatic embryogenesis and Fusarium wilt resistance of Egyptian cucumber (Cucumis sativus L.) cultivars

BACKGROUND

Somatic embryogenesis offers a reliable method for cucumber (Cucumis sativus L.) regeneration and genetic enhancement against Fusarium wilt. This study aimed to establish a tailored somatic embryogenesis system for Egyptian cultivars, fostering genetic improvements and Fusarium wilt-resistance lines.

RESULTS

Employing the Optimal Arbitrary Design (OAD) approach, we optimized the induction medium, initiating prolific embryogenic calli (53.3 %) at 1 mg/L 2,4-D. The cotyledonary leaf (CL) was the preferred explant, showing 60 % embryogenic callus development. Bieth Alpha exhibited higher responsiveness, generating ∼ 18 somatic embryos per explant compared to Prince's ∼ 10. Somatic embryogenesis system validation used quantitative RT-PCR, showing Cucumis sativus splicing factor 3B subunit (CUS1) and an embryogenesis marker gene expression exclusively within embryogenic calli and mainly during embryogenesis initiation. Evaluating fungal toxin filtrate concentrations for selecting embryogenic calli, the S2 selection (25 % filtrate, four subculture cycles) was chosen for somatic embryo development. To gauge the ramifications of selection at the genetic stratum, an in-depth analysis was executed. A cluster analysis grounded in ISSR banding patterns revealed a distinct separation between in vivo-cultivated plants of the two cultivars and regenerated plants devoid of pathogen filtrate treatment or those regenerated post-filtrate treatment. This segregation distinctly underscores the discernible genetic impact of the selection process.

CONCLUSIONS

The highest embryogenic capacity (53.3%) was achieved in this study by optimizing the induction stage, which demonstrated the optimal concentrations of BA and 2,4-D for induced proembryonic masses. Moreover, consistent gene expression throughout both stages of embryogenesis suggests that our system unequivocally follows the somatic embryogenesis pathway.

Heritability and genetic correlations of rumination time with milk-yield and milking traits in Holstein-Friesian cows using an automated milking system

Knowledge of the values of genetic parameters is a prerequisite for conducting a breeding program. This is especially important for rumination, which is considered an indicator of cow's health. Exploring the genetic relations between rumination time, milk yield, and milking traits could make it a valuable tool in dairy cattle breeding strategies. The objective of the research was to estimate heritability, repeatability, and genetic and phenotypic correlations of rumination time (RT), as well as traits associated with milk yield and milking of dairy cows of the Polish Holstein-Friesian breed kept in herds equipped with an automatic milking system. The research takes into consideration daily results for milking in the first lactation and second lactation, from 1 486 cows of the breed milked between 2013 and 2015 year. Cows were housed in 24 free-stall barns and fed a Partial Mixed Ration feed. The barns had an automated milking system (Astronaut A4 - Lely Industry). The cows received a varied dose of the concentrate, either in the milking robot or the feeding station, depending on the level of their milk yield. Our research has shown that RT was a low heritable trait (0.140 ± 0.039) and had a medium repeatability (0.572 ± 0.007). We detected a positive genetic correlation between RT and milk yield (0.341); however, a statistically significant negative relationship was identified between RT and urea content (-0.418) in milk. Estimations of genetic correlations suggest that selecting for higher RT may correspond to reduced urea content in milk. Investigating the genetics aspect of RT and the relationship with milk yield and milking traits may turn this into one of the useful criterion selections for dairy cattle breeding strategies, but should be used carefully. Further analyses on larger data sets and different populations are necessary.

Nitrogen use efficiency, growth and physiological parameters in different tomato genotypes under high and low N fertilisation conditions

Identification of novel genotypes with enhanced nitrogen use efficiency (NUE) is a key challenge for a sustainable tomato production. In this respect, the performance of a panel of thirty tomato accessions were evaluated under high (HN; 5 mM N) and low (LN; 0.5 mM N) nitrogen irrigation solutions. For each treatment, when 50% of plants reached the first flower bud stage, plant growth and biomass traits, chlorophyll, flavonol and anthocyanin indexes, nitrogen balance index (NBI), C:N ratio in leaves, stems, and roots, and NUE were evaluated. Significant (p < 0.05) effects were observed for accession, N treatment, and their interaction across all the traits. Under LN, plants showed a delayed development (40 days for HN vs. 65 days for LN) and reduced growth and biomass. On average, LN condition led to 41.8% decrease in nitrogen uptake efficiency (NUpE) but also 189.0% increase in NUtE, resulting in 62.2% overall increase in NUE. A broad range of variation among accessions was observed under both HN and LN conditions. Under LN conditions, chlorophyll index and NBI decreased, while flavonol and anthocyanin indexes increased. Leaf C:N ratio was positively correlated with nitrogen utilisation efficiency (NUtE) in both N treatments. Multi-trait analyses identified top-performing accessions under each condition, allowing to identify one accession among top performers under both conditions. Correlation analysis revealed that high root biomass and leaf C:N ratio are useful markers for selecting high NUE accessions. These findings offer valuable insights for improving tomato NUE under varying nitrogen fertilization conditions and for breeding high-NUE cultivars.

Is Anopheles gambiae (sensu stricto), the principal malaria vector in Africa prone to resistance development against new insecticides? Outcomes from laboratory exposure of An. gambiae (s.s.) to sub-lethal concentrations of chlorfenapyr and clothianidin

Indiscriminate use of pesticides in the public health and agriculture sectors has contributed to the development of resistance in malaria vectors following exposure to sub-lethal concentrations. To preserve the efficacy of vector control tools and prevent resistance from spreading, early resistance detection is urgently needed to inform management strategies. The introduction of new insecticides for controlling malaria vectors such as clothianidin and chlorfenapyr requires research to identify early markers of resistance which could be used in routine surveillance. This study investigated phenotypic resistance of Anopheles gambiae (sensu stricto) Muleba-Kis strain using both WHO bottle and tube assays following chlorfenapyr, clothianidin, and alpha-cypermethrin selection against larvae and adults under laboratory conditions. High mortality rates were recorded for both chlorfenapyr-selected mosquitoes that were consistently maintained for 10 generations (24-h mortality of 92-100% and 72-h mortality of 98-100% for selected larvae; and 24-h mortality of 95-100% and 72-h mortality of 98-100% for selected adults). Selection with clothianidin at larval and adult stages showed a wide range of mortality (18-91%) compared to unselected progeny where mortality was approximately 99%. On the contrary, mosquitoes selected with alpha-cypermethrin from the adult selection maintained low mortality (28% at Generation 2 and 23% at Generation 4) against discrimination concentration compared to unselected progeny where average mortality was 51%. The observed resistance in the clothianidin-selected mosquitoes needs further investigation to determine the underlying resistance mechanism against this insecticide class. Additionally, further investigation is recommended to develop molecular markers for observed clothianidin phenotypic resistance.

Hypobaric hypoxia drives selection of altitude-associated adaptative alleles in the Himalayan population

Genetic variants play a crucial role in shaping the adaptive phenotypes associated with high-altitude populations. Nevertheless, a comprehensive understanding of the specific impacts of different environments associated with increasing altitudes on the natural selection of these genetic variants remains undetermined. Hence, this study aimed to identify genetic markers responsible for high-altitude adaptation with specific reference to different altitudes, majorly focussing on an altitude elevation range of ∼1500 m and a corresponding decrease of ≥5 % in ambient oxygen availability. We conducted a comprehensive genome-wide investigation (n = 192) followed by a validation study (n = 514) in low-altitude and three high-altitude populations (>2400 m) of Nubra village (NU) (3048 m), Sakti village (SKT) (3812 m), and Tso Moriri village (TK) (4522 m). Extensive genetic analysis identified 86 SNPs that showed significant associations with high-altitude adaptation. Frequency mapping of these SNPs revealed 38 adaptive alleles and specific haplotypes that exhibited a strong linear correlation with increasing altitude. Notably, these SNPs spanned crucial genes, such as ADH6 and NAPG along with the vastly studied genes like EGLN1 and EPAS1, involved in oxygen sensing, metabolism, and vascular homeostasis. Correlation analyses between these adaptive alleles and relevant clinical and biochemical markers provided evidence of their functional relevance in physiological adaptation to hypobaric hypoxia. High-altitude population showed a significant increase in plasma 8-isoPGF2α levels as compared to low-altitude population. Similar observation showcased increased blood pressure in NU as compared to TK (P < 0.0001). In silico analyses further confirmed that these alleles regulate gene expression of EGLN1, EPAS1, COQ7, NAPG, ADH6, DUOXA1 etc. This study provides genetic insights into the effects of hypobaric-hypoxia on the clinico-physiological characteristics of natives living in increasing high-altitude regions. Overall, our findings highlight the synergistic relationship between environment and evolutionary processes, showcasing physiological implications of genetic variants in oxygen sensing and metabolic pathway genes in increasing high-altitude environments.

Reframing selection as a learning experience: Insights from a residency selection assessment

PURPOSE

Selection for postgraduate medical training is high-stakes and complex. The learning value of assessments for selection has, thus far, been underexplored, limiting their uptake as potentially meaningful learning experiences. The aim of this study was to explore the learning value residency applicants derive from an intelligence, personality, motivation and competency selection assessment and what factors influence the experienced learning value.

METHODS

In Autumn 2020 and Spring 2021, we conducted individual semi-structured interviews with sixteen applicants for pediatric residency training. Selection outcomes were unknown at the time of the interview. Interviews were transcribed verbatim and thematically analyzed.

RESULTS

Participants reported that the assessment was valuable in fostering self-reflection and self-awareness, embracing self-acceptance, pursuing development goals, assessing professional fit, and harnessing motivational drivers in work. The experienced learning value was influenced by applicants' ability to interpret its results, their focus on the high-stakes selection process and concerns regarding the acceptability and credibility of the selection tool.

CONCLUSIONS

While the selection assessment showed learning potential, its learning value was impeded by a preoccupation with the high-stakes nature of the selection procedure. Intentional integration of the selection assessment in the learning curriculum may play a pivotal role in realizing its learning potential.

Assessing the predictive validity of pre-admission criteria on dental students' academic performance: a cross-sectional study

BACKGROUND

This study examines the multifaceted factors influencing academic performance among dental students in Saudi Arabia, exploring the complex relationships between demographic, educational, and psychological variables and students' Grade Point Averages (GPAs) to enhance global dental education admission strategies.

METHODS

Data on demographics, academic performance indicators (including GPA, high school grades, test scores), accommodation type, parental education, suspension history, and English proficiency were collected through an English-language electronic questionnaire from 900 dental students across multiple institutions in Riyadh. The study employed Pearson's correlation analysis to examine relationships between GPA and various academic and demographic factors. A detailed regression analysis, using a stepwise selection based on Akaike's information criteria (AIC), identified significant GPA predictors and evaluated the average marginal effects of pre-admission variables on GPA, alongside rigorous diagnostic checks to validate the model's robustness.

RESULTS

The study revealed a complex interplay of factors impacting GPA among dental students. High school grades, achievement, and aptitude test scores showed moderate positive correlations with GPA, while negative correlations were observed with age and number of times suspended. Regression analysis highlighted age, marital status, high school grades, and test scores as key predictors, with complex interaction effects demonstrating the layered influences of these factors. For instance, the negative impact of age on GPA was moderated by high school grade and aptitude test score. The analysis also highlighted the significant marginal effects of various pre-admission variables on GPA, such as the negative average impact of age and the positive impact of high school grades.

CONCLUSIONS

This study provides valuable insights into the multifaceted determinants of academic success in dental education. Our findings underscore the significant roles of high school grades, achievement, and aptitude test scores, as well as the nuanced influence of age and marital status on GPA. These results advocate for a holistic approach in evaluating candidates for dental programs and have broader implications for global dental education, emphasizing the need for comprehensive admission strategies.

New evidence on the validity of the selection methods for recruitment to general practice training: a cohort study

BACKGROUND

Selection into UK-based GP training has used the multi-specialty recruitment assessment (MSRA) and a face-to-face selection centre. The MSRA comprises of a situational judgement test (SJT) and clinical problem solving (CPS) test. The selection centre was suspended during the Covid-19 pandemic. Evidence is needed to guide national and international selection policy.

AIM

To evaluate the validity of GP training selection.

DESIGN & SETTING

A retrospective cohort study using data from UK-based national recruitment to GP training, from 2015 to 2021.

METHODS

Data were available for 32,215 GP training applicants. The ability of scores from the specialty selection process to predict subsequent performance in the clinical skills assessment of the Membership of the Royal College of General Practitioners (MRCGP) examination was modelled using path analysis. The effect-sizes for gender, professional family background and world region of qualification were estimated.

RESULTS

All component scores of the selection process demonstrated statistically significant independent relationships with clinical skills assessment performance, thus establishing their predictive validity. All were sensitive to demographic factors. The selection centre scores had the weakest relationship with future clinical skills assessment performance. However, for candidates with MSRA scores below the lowest quartile the relative contribution of the selection centre scores to predicting clinical skills assessment performance was similar to that observed for MSRA components.

CONCLUSION

The MSRA has predictive validity in this context. Re-instituting a selection centre for those with relatively low MSRA scores should be considered. However, the relative costs and potential advantages and disadvantages should be carefully weighed.

[Hypothesis of Genetic Diversity Selection in the Occurrence and Development of Lung Cancer: Molecular Evolution and Clinical Significance]

So far, the monoclonal hypothesis of tumor occurrence and development cannot be justified. The genetic diversity selection hypothesis for the occurrence and development of lung cancer links Mendelian genetics with Darwin's theory of evolution, suggesting that the genetic diversity of tumor cell populations with polyclonal origins-monoclonal selection-subclonal expansion is the result of selection pressure. Normal cells acquire mutations in oncogenic driver genes and have a selective advantage over other cells, becoming tumor initiating cells; In the interaction with the tumor microenvironment (TME), the vast majority of initiating cells are recognized and killed by the human immune system. If immune escape occurs, the incidence of malignant tumors will greatly increase, and subclonal expansion, intratumour heterogeneity, etc. will occur. This article proposed the hypothesis of genetic diversity selection and analyzed its clinical significance.
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Predicting ranger attrition

Elite military programs such as the 75th Ranger Regiment's Ranger Assessment and Selection Program (RASP) see rates of attrition often in excess of 50%, and amplify the need to identify and screen candidates based on their probability of successful matriculation. Models were developed (and cross-validated) to predict attrition from RASP using the physical abilities, cognitive abilities, and personality scores collected during candidate admissions screening. We report both regression weights and standardized odds ratios for optimum models of candidate success over three program timeframes to enable an understanding of the relative importance of each predictor. In spite of physical abilities scores being used to select RASP candidates, they were the strongest predictors of RASP attrition. Personality scores accounted for more variance in predicting candidate success than cognitive ability scores. Personality predictors, especially dimensions related to Openness, were better at predicting week one attrition than attrition in later weeks. The use of a single, aggregated candidate probability score for making admissions decisions is discussed, along with additional practical and scientific implications.

Pharmaceutical demand response to utilization management

Prescription drug insurance increasingly imposes prior authorization (requiring providers to request coverage before claim approval) to manage utilization. Prior authorization has been criticized because of its administrative burden on providers. The primary alternative to managing utilization is imposing out-of-pocket (OOP) payment to incentivize beneficiaries to seek lower-cost care, effectively providing beneficiaries with partial insurance. Would beneficiaries prefer indirectly paying for prior authorization through higher premiums; or would they prefer prior authorization was replaced by higher OOP costs? This tradeoff depends on how much OOP costs could be displaced by prior authorization, which depends on their relative impact on demand. I estimate the effect of prior authorization and OOP costs on pharmaceutical demand in Medicare Part D, addressing endogeneity caused by unobserved drug quality and selection into plans. Despite criticism of prior authorization, I find that Medicare beneficiaries would prefer higher premiums to pay for prior authorization, over higher OOP costs.

Somatic Cell Fusion in Host Defense and Adaptation

Evidence of fusion of somatic cells has been noted in health and in disease for more than a century. The most obvious but uncertain hallmark has been the presence of multiple nuclei in cells. Although multinucleated cells are found in normal and diseased tissues, the benefit or harm of such cells can be difficult to elucidate. Still more difficult however is the identification of mononuclear cells previously formed by fusion of somatic cells with one or more nuclei disposed. The later process can introduce mutations that promote viral diversification, cancer, and tissue senescence. Less obvious the potential benefits of cell fusion. Recent work in cell biology, immunology, and genomic analysis however makes it possible to postulate benefits and potentially arrive at novel therapeutic agents and approaches that replicate or enhance these benefits.

From unequal injuries to unequal learning? Socioeconomic gradients in childhood concussions and the impact on children's academic performance

Previous research identifies stark socioeconomic disparities in child injuries, yet research on the repercussions hereof on other aspects of children's lives remains sparse. This paper tests whether social gradients in minor traumatic brain injuries (mTBIs or concussions) contribute to corresponding inequalities in children's academic performance. Previous research on this topic is mostly based on small samples and confounded by non-random selection into experiencing mTBIs. We improve on prior research by using high quality, large N, administrative registry data. Further, we control for selection into having an mTBI via comparing the test score progression of children having an mTBI with children who experience an mTBI in later years (staggered difference-in-differences). Based on Danish ER/hospital records and national test score data, we find that children from families with lower earnings and less education are more likely to experience an mTBI and that having an mTBI negatively correlates with reading test scores. However, comparing present with future mTBI cases, we show that having an mTBI within a year before a test does not negatively affect children's reading scores. Our findings suggest that negative correlations between mTBIs and academic performance more likely reflect socioeconomic gradients in mTBI incidents rather than a direct causal effect. Further, socioeconomic gradients in mTBI incidents do not significantly contribute to corresponding disparities in academic performance.

Candidate SNPs for meat quality and carcass composition in free-range Iberian pigs

Several genetic markers, previously associated with meat quality traits, have been proposed to be included in Iberian pig breeding programs. However, before being implemented, effects of these candidate SNPs on premium cuts' yield should be evaluated to avoid potential undesirable antagonistic effects. Therefore, the main goals of this study were to evaluate the effects of a set of 26 polymorphisms on premium cuts weights and to corroborate their effects on meat quality in a larger population. Phenotypic data of approximately 1550 Iberian pigs were recorded. The PRKAG3_rs319678464C and PRKAG3_rs1108399077G alleles were associated with an increase of shear force, water losses and color values and a reduction of average daily gain (ADG). The CAST_rs196949783G > A and ADIPOQ_rs3476515794T > G SNPs mainly affected IMF content, with this last SNP being the only one with significant effects on any of the carcass measures, specifically Longissimus thoracis et lumborum (LTL) weight. The ELOVL6_rs3473714672A, FASN_rs331694510A, MTTP_rs335896411C and ACACA_rs340781986C alleles were linked to a higher percentage of oleic acid and monounsaturated FA and a decrease in palmitic, palmitoleic and saturated FA. Besides, suggestive effects were observed between ELOVL6_rs3473714672A > G and ham and shoulder weights, and between MTTP_rs335896411T > C and LTL muscle weight. Finally, the NR6A1_rs326780270T allele was associated with a significant increase in ADG and tended to reduce the ham weight. The SNPs mapped to PRKAG3 (rs319678464G > C), ACACA, FASN and CAST genes could be implemented in breeding programs to improve meat quality traits without undesirable effects on carcass composition. The SNPs mapped to PRKAG3 (rs1108399077G > A) ELOVL6, MTTP and NR6A1 should continue to be tested in a larger number of animals.

Role of paralogs in the sex-bias transcriptional and metabolic regulation of the brain-placental axis in mice

INTRODUCTION

Duplicated genes or paralogs play important roles in the adaptive function of eukaryotic genomes. Animal studies have shown evidence for the functional role of paralogs in pregnancy, but our knowledge about the role of paralogs in the fetoplacental regulation remains limited. In particular, if fetoplacental metabolic regulation is modulated by differential expression of paralogs remains unexamined.

METHODS

In this study, gene expression profiles of day-15 placenta and fetal brain were compared to identify families or groups of paralogous genes expressed in the placenta and brain of male versus female fetuses in mice. A Bayesian modeling was applied to infer directional relationship of transcriptional variation of the paralogs relative to the phylogenetic variation of the genes in each family. Gas chromatography-mass spectrometry (GC-MS) was used to perform untargeted metabolomics analysis of day-15 placenta and fetal brain of both sexes.

RESULTS

We identified paralog groups that were expressed in a sex and/or tissue biased manner between the placenta and fetal brain. Bayesian modeling showed evidence for directional relationship between expression and phylogeny of specific paralogs. These relationships were sex specific. GC-MS analysis identified metabolites that were expressed in a sex-bias manner between the placenta and fetal brain. By performing integrative analysis of the metabolomics and gene expression data, we showed that specific groups of metabolites and paralogous genes were expressed in a coordinated manner between the placenta and fetal brain.

DISCUSSION

The findings of this study collectively suggest that paralogs play an influential role in the regulation of the brain-placental axis in mice.

Flower color polymorphism of a wild Iris on the Qinghai-Tibet plateau

BACKGROUND

Flower color plays a crucial role in attracting pollinators and facilitating environmental adaptation. Investigating the causes of flower color polymorphism and understanding their potential effects on both ecology and genetics can enhance our understanding of flower color polymorphism in wild plant.

RESULTS

In this study, we examined the differences of potential male and female fitness between purple- and yellow- flower individuals in Iris potaninii on the Qinghai-Tibet Plateau, and screened key genes and positively selective genes involved in flower color change. Our results showed that yellow flower exhibited a higher pollen-to-ovule ratio. Yellow flowers were derived from purple flowers due to the loss of anthocyanins, and F3H could be an essential gene affecting flower color variation though expression regulation and sequence polymorphism in this species. Furthermore, our findings suggest that genes positively selected in yellow-flowered I. potaninii might be involved in nucleotide excision repair and plant-pathogen interactions.

CONCLUSIONS

These results suggest that F3H induces the flower color variation of Iris potaninii, and the subsequent ecological and additive positive selection on yellow flowers may further enhance plant adaptations to alpine environments.

Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis

Cancer occurs as a consequence of multiple somatic mutations that lead to uncontrolled cell growth. Mutual exclusivity and co-occurrence of mutations imply-but do not prove-that mutations exert synergistic or antagonistic epistatic effects on oncogenesis. Knowledge of these interactions, and the consequent trajectories of mutation and selection that lead to cancer has been a longstanding goal within the cancer research community. Recent research has revealed mutation rates and scaled selection coefficients for specific recurrent variants across many cancer types. However, there are no current methods to quantify the strength of selection incorporating pairwise and higher-order epistatic effects on selection within the trajectory of likely cancer genotoypes. Therefore, we have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation (flux), dependent on somatic cancer genotype. Coupling this continuous-time Markov chain model with a deconvolution approach provides estimates of underlying mutation rates and selection across the trajectory of oncogenesis. We demonstrate computation of fluxes and selection coefficients in a somatic evolutionary model for the four most frequently variant driver genes (TP53, LRP1B, KRAS and STK11) from 565 cases of lung adenocarcinoma. Our analysis reveals multiple antagonistic epistatic effects that reduce the possible routes of oncogenesis, and inform cancer research regarding viable trajectories of somatic evolution whose progression could be forestalled by precision medicine. Synergistic epistatic effects are also identified, most notably in the somatic genotype TP53 LRP1B for mutations in the KRAS gene, and in somatic genotypes containing KRAS or TP53 mutations for mutations in the STK11 gene. Large positive fluxes of KRAS variants were driven by large selection coefficients, whereas the flux toward LRP1B mutations was substantially aided by a large mutation rate for this gene. The approach enables inference of the most likely routes of site-specific variant evolution and estimation of the strength of selection operating on each step along the route, a key component of what we need to know to develop and implement personalized cancer therapies.

Creating a Diverse Physician Workforce Through Training in Diversity, Bias, and Selection: An Innovative Approach to Preparing Medical Students as Future Academic Leaders

Medical students are the future of academic medicine. They will serve as admissions committee members, deans, and program directors with responsibility for selecting future physicians. At the same time, schools and programs are working to diversify the physician workforce to care for diverse patient populations. At UAB Heersink School of Medicine, we developed an elective course, Holistic Review: Creating a Mission-Driven Physician Workforce, to train learners in bias, diversity, and data-informed decision-making. Students applied lessons to the admissions process by participating in application screening and multiple-mini interview rating. Student reflections demonstrated course applicability for careers in medicine and beyond.

Does Gaia Play Dice? Simple Models of Non-Darwinian Selection

In this article, we introduce some simple models, based on rolling dice, to explore mechanisms proposed to explain planetary habitability. The idea is to study these selection mechanisms in an analytically tractable setting, isolating their consequences from other details which can confound or obscure their effect in more realistic models. We find that the observable of interest, the face value shown on the die, "improves" over time in all models. For two of the more popular ideas, Selection by Survival and Sequential Selection, this is down to sampling effects. A modified version of Sequential Selection, Sequential Selection with Memory, implies a statistical tendency for systems to improve over time. We discuss the implications of this and its relationship to the ideas of the "Inhabitance Paradox" and the "Gaian bottleneck."

Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

BACKGROUND

Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products.

RESULTS

We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe.

CONCLUSIONS

Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

Immune markers in goats selected for reduced gastrointestinal nematode egg count under artificial infection conditions

This study aimed to further investigate the mechanisms responsible for inhibition of gastrointestinal nematode egg production in a line of Scottish Cashmere Goat selected for low faecal egg count. Animals were chosen as the lowest egg producers from a line selected for low egg output (selected group) with a second group from the wider herd based on high faecal egg count as controls. All animals were artificially infected with Teladorsagia circumcincta and Trichostrongylus vitrinus, then treated with anthelmintic and challenge infected prior to euthanasia and post mortem sampling. There was no effect on body weight between groups at any point in the study. Mean faecal egg count was reduced by 68 % in the selected group when compared with the controls. Circulating eosinophil counts were consistently elevated in the selected group, but this was only marginally significant (P = 0.045). Most of the circulating and tissue antibodies (IgG, IgA and IgE) measured were slightly elevated in the selected group but not significantly. Mucosal mast cells, eosinophils and globule leukocyte levels were higher in the abomasal and intestinal tissues in selected animals. Following challenge infection there was no difference in numbers of parasites, however there were more early stage parasite larvae and fewer late stage larvae in the both the abomasum and duodenum of the selected group compared with the unselected group, indicating some inhibition of parasite development. Overall, the study further demonstrated that selection based on low egg count has resulted in a line of goats producing significantly fewer parasites under identical infection with no effect on bodyweight. This appears to be associated with elevation in antibody and effector cells. Some evidence of host inhibition of parasite development was observed in the selected animals.

Selection tools and student diversity in health professions education: a multi-site study

Student diversity in health professions education (HPE) can be affected by selection procedures. Little is known about how different selection tools impact student diversity across programs using different combinations of traditional and broadened selection criteria. The present multi-site study examined the chances in selection of subgroups of applicants to HPE undergraduate programs with distinctive selection procedures, and their performance on corresponding selection tools. Probability of selection of subgroups (based on gender, migration background, prior education, parental education) of applicants (N = 1935) to five selection procedures of corresponding Dutch HPE undergraduate programs was estimated using multilevel logistic regression. Multilevel linear regression was used to analyze performance on four tools: prior-education grade point average (pe-GPA), biomedical knowledge test, curriculum-sampling test, and curriculum vitae (CV). First-generation Western immigrants and applicants with a foreign education background were significantly less likely to be selected than applicants without a migration background and with pre-university education. These effects did not vary across programs. More variability in effects was found between different selection tools. Compared to women, men performed significantly poorer on CVs, while they had higher scores on biomedical knowledge tests. Applicants with a non-Western migration background scored lower on curriculum-sampling tests. First-generation Western immigrants had lower CV-scores. First-generation university applicants had significantly lower pe-GPAs. There was a variety in effects for applicants with different alternative forms of prior education. For curriculum-sampling tests and CVs, effects varied across programs. Our findings highlight the need for continuous evaluation, identifying best practices within existing tools, and applying alternative tools.

Pre-exposure to seawater or chloride salts influences the avoidance-selection behavior of zebrafish larvae in a conductivity gradient

The risk assessment of freshwater salinization is constructed around standard assays and using sodium chloride (NaCl), neglecting that the stressor is most likely a complex mixture of ions and the possibility of prior contact with it, triggering acclimation mechanisms in the freshwater biota. To date, as far as we are aware of, no information has been generated integrating both acclimation and avoidance behavior in the context of salinization, that may allow these risk assessments upgrading. Accordingly, 6-days-old Danio rerio larvae were selected to perform 12-h avoidance assays in a non-confined 6-compartment linear system to simulate conductivity gradients using seawater (SW) and the chloride salts MgCl2, KCl, and CaCl2. Salinity gradients were established from conductivities known to cause 50% egg mortality in a 96-h exposure (LC50,96h,embryo). The triggering of acclimation processes, which could influence organisms' avoidance-selection under the conductivity gradients, was also studied using larvae pre-exposed to lethal levels of each salt or SW. Median avoidance conductivities after a 12-h of exposure (AC50,12h), and the Population Immediate Decline (PID) were computed. All non-pre-exposed larvae were able to detect and flee from conductivities corresponding to the LC50,96h,embryo, selecting compartments with lower conductivities, except for KCl. The AC50,12h and LC50,96h overlapped for MgCl2 and CaCl2, though the former is considered as more sensitive as it was obtained in 12 h of exposure. The AC50,12h for SW was 1.83-fold lower than the LC50,96h, thus, reinforcing the higher sensitivity of the parameter ACx and its adequacy for risk assessment frameworks. The PID, at low conductivities, was solely explained by the avoidance behavior of non-pre-exposed larvae. Larvae pre-exposed to lethal levels of salt or SW were found to select higher conductivities, except for MgCl2. Results indicated that avoidance-selection assays are ecologically relevant and sensitive tools to be used in risk assessment processes. Stressor pre-exposure influenced organisms' avoidance-selection behavior under conductivity gradients, suggesting that under salinization events organisms may acclimate, remaining in altered habitats.

Effects of candidates' demographics and evaluation of the virtual Multiple Mini Interview (vMMI) as a tool for selection into paediatric training in Queensland

INTRODUCTION

The Queensland Basic Paediatric Training Network (QBPTN) is responsible for the selection of candidates into paediatric training in Queensland. The COVID-19 pandemic necessitated interviews to be conducted 'virtually' as virtual Multiple-Mini-Interviews (vMMI). The study aimed to describe the demographic characteristics of candidates applying for selection into paediatric training in Queensland, and to explore their perspectives and experiences with the vMMI selection tool.

METHODOLOGY

The demographic characteristics of candidates and their vMMI outcomes were collected and analysed with a mixed methods approach. The qualitative component was comprised of seven semi-structured interviews with consenting candidates.

RESULTS

Seventy-one shortlisted candidates took part in vMMI and 41 were offered training positions. The demographic characteristics of candidates at various stages of selection were similar. The mean vMMI scores were not statistically different between candidates from the Modified Monash Model 1 (MMM1) location and others [mean (SD): 43.5 (5.1) versus 41.7 (6.7), respectively, p = 0.26]. However, there was a statistically significant difference (p value 0.03) between being offered and not offered a training position for candidates from MMM2 and above. The analysis of the semi-structured interviews suggested that candidate experiences of the vMMI were influenced by the quality of the management of the technology used. Flexibility, convenience, and reduced stress were the main factors that influenced candidates' acceptance of vMMI. Perceptions of the vMMI process focused on the need to build rapport and facilitate communication with the interviewers.

DISCUSSION

vMMI is a viable alternative to face-to-face (FTF) MMI. The vMMI experience can be improved by facilitating enhanced interviewer training, by making provision for adequate candidate preparation and by having contingency plans in place for unexpected technical challenges. Given government priorities in Australia, the impact of candidates' geographical location on the vMMI outcome for candidates from MMM >1 location needs to be further explored.

Examining the continuum of resistance model in two population-based screening studies in Sweden

In studies recruited on a voluntary basis, lack of representativity may impair the ability to generalize findings to the target population. Previous studies, primarily based on surveys, have suggested that generalizability may be improved by exploiting data on individuals who agreed to participate only after receiving one or several reminders, as such individuals may be more similar to non-participants than what early participants are. Assessing this idea in the context of screenings, we compared sociodemographic characteristics and health across early, late, and non-participants in two large population-based screening studies in Sweden: STROKESTOP II (screening for atrial fibrillation; 6,867 participants) and SCREESCO (screening for colorectal cancer; 39,363 participants). We also explored the opportunities to reproduce the distributions of characteristics in the full invited populations, either by assuming that the non-participants were similar to the late participants, or by applying a linear extrapolation model based on both early and late participants. Findings showed that early and late participants exhibited similar characteristics along most dimensions, including civil status, education, income, and health examination results. Both these types of participants in turn differed from the non-participants, with fewer married, lower educational attainments, and lower incomes. Compared to early participants, late participants were more likely to be born outside of Sweden and to have comorbidities, with non-participants similar or even more so. The two empirical models improved representativity in some cases, but not always. Overall, we found mixed support that data on late participation may be useful for improving representativeness of screening studies.

The dynamics of deltamethrin resistance evolution in Aedes albopictus has an impact on fitness and dengue virus type-2 vectorial capacity

BACKGROUND

Worldwide invasion and expansion of Aedes albopictus, an important vector of dengue, chikungunya, and Zika viruses, has become a serious concern in global public health. Chemical insecticides are the primary means currently available to control the mosquito populations. However, long-term and large-scale use of insecticides has selected for resistance in the mosquito that is accompanied by a genetic load that impacts fitness.

RESULTS

A number of laboratory strains representing different resistance mechanisms were isolated and identified from laboratory-derived, deltamethrin-resistant Ae. albopictus recovered in previous work. Resistance levels and fitness costs of the strains were evaluated and compared to characterize the evolution of the resistance genotypes and phenotypes. The heterozygous F1534S mutation (1534F/S) in the voltage gated sodium channel (vgsc) gene product (VGSC), first detected in early stages of resistance evolution, not only confers high-level resistance, but also produces no significant fitness costs, leading to the rapid spread of resistance in the population. This is followed by the increase in frequency of homozygous F1534S (1534S/S) mosquitoes that have significant fitness disadvantages, prompting the emergence of an unlinked I1532T mutation with fewer side effects and a mating advantage better adapted to the selection and reproductive pressures imposed in the experiments. Metabolic resistance with no significant fitness cost and mediating a high-tolerance resistance phenotype may play a dominant role in the subsequent evolution of resistance. The different resistant strains had similar vector competence for dengue virus type-2 (DENV-2). Furthermore, a comparative analysis of vectorial capacity revealed that increased survival due to deltamethrin resistance balanced the negative fitness cost effects and contributed to the risk of dengue virus (DENV) transmission by resistant populations. The progressive evolution of resistance results in mosquitoes with both target-site insensitivity and metabolic resistance with lower fitness costs, which further leads to resistant populations with both high resistance levels and vectorial capacity.

CONCLUSIONS

This study reveals a possible mechanism for the evolution of deltamethrin resistance in Aedes albopictus. These findings will help guide practical strategies for insecticide use, resistance management and the prevention and control of mosquito-borne disease.

The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates

BACKGROUND

The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments.

RESULTS

The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4.

CONCLUSION

The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.

Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis)

The wild boar (Sus scrofa meridionalis) arrived in Sardinia with the first human settlers in the early Neolithic with the potential to hybridize with the domestic pig (S. s. domesticus) throughout its evolution on the island. In this paper, we investigated the possible microevolutionary effects of such introgressive hybridization on the present wild boar population, comparing Sardinian wild specimens with several commercial pig breeds and Sardinian local pigs, along with a putatively unadmixed wild boar population from Central Italy, all genotyped with a medium density SNP chip. We first aimed at identifying hybrids in the population using different approaches, then examined genomic regions enriched for domestic alleles in the hybrid group, and finally we applied two methods to find regions under positive selection to possibly highlight instances of domestic adaptive introgression into a wild population. We found three hybrids within the Sardinian sample (3.1% out of the whole dataset). We reported 11 significant windows under positive selection with a method that looks for overly differentiated loci in the target population, compared with other two populations. We also identified 82 genomic regions with signs of selection in the domestic pig but not in the wild boar, two of which overlapped with genomic regions enriched for domestic alleles in the hybrid pool. Genes in these regions can be linked with reproductive success. Given our results, domestic introgression does not seem to be pervasive in the Sardinian wild boar. Nevertheless, we suggest monitoring the possible spread of advantageous domestic alleles in the coming years.

Creating a context for recipient vessel selection in deep inferior epigastric perforator flap breast reconstruction

BACKGROUND

In autologous tissue breast reconstruction, recipient vessels are important for artery perfusion and venous drainage to ensure free flap survival. There are insufficient clinical outcomes to select efficient recipient vessels in bi-pedicled deep inferior epigastric perforator (DIEP) flap reconstruction.

METHODS

We presented a retrospective observational series of 108 patients regarding the diameter, anastomosis time, and re-anastomosis rate in internal mammary (IM), circumflex scapular (CS), thoracodorsal (TD), thoracoacromial (TA), lateral thoracic (LT), and internal mammary perforator (IMP) vessels of bi-pedicled DIEP flaps for breast reconstruction after mastectomy. The outcomes were the vessel re-anastomosis rate, flap failure rate, vessel anastomosis time, and complications. Data were gleaned from the chi-square test, Fisher's test, and analysis of variance using Scheffe's test as a post hoc analysis. The level of significance was p < 0.05.

RESULTS

There were no significant differences in the diameters of the artery, first vein, and second vein across the recipient vessels (p > 0.05). However, the anastomosis time was longer in IM and TA than in CS, TD, and LT (p < 0.001). Also, there were no significant differences for re-anastomosis, flap necrosis, and fat necrosis among different recipient vessels (p > 0.05).

CONCLUSIONS

Because of the altered mastectomy incisions, this study provides complete anatomical vascular properties and suggests that altering recipient vessel selection for bi-pedicled DIEP flaps can shorten anastomosis time and better conceal scars.

Information encoded in gene-frequency trajectories

In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random genetic drift, is encoded within gene-frequency trajectories. We determine approximate, time-dependent, gene-frequency trajectory statistics, assuming additive selection. We use the probability of fixation to test and illustrate the approximation scheme introduced. For the case where the strength of selection and the effective population size have constant values, we show how a standard diffusion approximation result, for the probability of fixation, systematically emerges when increasing numbers of approximate trajectory statistics are taken into account. We then provide examples of how time-dependent parameters influence gene-frequency statistics.

Haplotype based testing for a better understanding of the selective architecture

BACKGROUND

The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies.

RESULTS

Using simulated data, we show that compared to SNP based test, our approach has higher power, especially when the number of candidate haplotypes is small or moderate. To improve power when the number of haplotypes is large, we investigate methods to combine them with a moderate number of haplotype subsets. Haplotype frequencies can often be recovered with less noise than SNP frequencies, especially under pool sequencing, giving our test an additional advantage. Furthermore, spurious outlier SNPs may lead to false positives, a problem usually not encountered when working with haplotypes. Post hoc tests for the number of selected haplotypes and for differences between their selection coefficients are also provided for a better understanding of the underlying selection dynamics. An application on a real data set further illustrates the performance benefits.

CONCLUSIONS

Due to less multiple testing correction and noise reduction, haplotype based testing is able to outperform SNP based tests in terms of power in most scenarios.

Local ancestry and selection in admixed Sanjiang cattle

The majority of native cattle are taurine × indicine cattle of diverse phenotypes in the central region of China. Sanjiang cattle, a typical breed in the central region, play a central role in human livelihood and have good adaptability, including resistance to dampness, heat, roughage, and disease, and are thus regarded as an important genetic resource. However, the genetic history of the successful breed remains unknown. Here, we sequenced 10 Sanjiang cattle genomes and compared them to the 70 genomes of 5 representative populations worldwide. We characterized the genomic diversity and breed formation process of Sanjiang cattle and found that Sanjiang cattle have a mixed ancestry of indicine (55.6%) and taurine (33.2%) dating to approximately 30 generations ago, which has shaped the genome of Sanjiang cattle. Through ancestral fragment inference, selective sweep and transcriptomic analysis, we identified several genes linked to lipid metabolism, immune regulation, and stress reactions across the mosaic genome of Sanjiang cattle showing an excess of taurine or indicine ancestry. Taurine ancestry might contribute to meat quality, and indicine ancestry is more conducive to adaptation to hot climate conditions, making Sanjiang cattle a valuable genetic resource for the central region of China. Our results will help us understand the evolutionary history and ancestry components of Sanjiang cattle, which will provide a reference for resource conservation and selective breeding of Chinese native cattle.

Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium

Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.

Review: Improving pig survival with a focus on birthweight: a practical breeding perspective

Survival of growing pigs through to slaughter age is not only a key driver of profitability but also has implications for animal welfare. Changing preweaning mortality by over 3% gives a similar change in profit per pig as changing postweaning mortality by 1%. There is significant scope to improve both traits through management and breeding to improve survival. The aim of this literature review was to explore the relationship between litter size and piglet birthweight and the detrimental impact this negative association has had on pig survival, along with genetic strategies that have been implemented in breeding programmes. It is suggested that the primary effect of litter size on mortality was indirect, through the effects of litter size on individual piglet birthweights. The circumstances affecting the litter a piglet was born into were the most important for determining the birthweight of individual piglets, rather than the genetic make-up of the individual piglet itself. Therefore, breeding programmes should include the average piglet birthweight of a litter (i.e., a sow trait) rather than individual piglet birthweight to maintain the weight of piglets at birth. The relative weighting of litter size and average piglet birthweight should be done in a manner that avoids selecting heavy pigs from small litters. Additional genetic strategies to improve survival include survival at the litter level, or survival of individual piglets or enhanced through the use of genomic information. At the litter level, litter size at day 5 and weaning can be considered as sow traits, but the use of these traits depends on the recording environment. At the individual piglet level, pre- and postweaning survival can be recorded as 0/1 traits and analysed directly. Although heritabilities are low for all these traits, genetic improvements can be made. For preweaning survival, the genes of the nurse sow are more important than the genes of the individual piglet. The nurse sow model captures both the lactation and gestation effects, and the information obtained when piglets born from different litters are reared together. However, once a piglet is weaned, its own genes became more important for the expression of postweaning mortality outcomes. Finally, for a successful selection programme, combining the average piglet birthweight at the litter level and mortality data based on individual piglet records (not solely birthweight) might yield the best response in piglet survival.

Mitochondrial phylogeography and molecular evolution of the rhodopsin visual pigment in troglobitic populations of Astyanax mexicanus (De Filippi, 1853)

Cave-adapted animals provide a unique opportunity to study the evolutionary mechanisms underlying phenotypic, metabolic, behavioral, and genetic evolution in response to cave environments. The Mexican tetra ( Astyanax mexicanus) is considered a unique model system as it shows both surface and cave-dwelling morphs. To date, at least 33 different cave populations have been identified, with phylogenetic studies suggesting an origin from at least two independent surface lineages, thereby providing a unique opportunity to study parallel evolution. In the present study, we carried out the most exhaustive phylogeographic study of A. mexicanus to date, including cave and surface localities, using two mitochondrial markers (cytochrome b (cyt b) and cytochrome c oxidase subunit I ( COI)) and nuclear rhodopsin visual pigment ( rho). Additionally, we inferred the molecular evolution of rho within the two contrasting environments (cave and surface) and across three geographic regions (Sierra de El Abra, Sierra de Guatemala, and Micos). In total, 267 individuals were sequenced for the two mitochondrial fragments and 268 individuals were sequenced for the rho visual pigment from 22 cave and 46 surface populations. Phylogeographic results based on the mitochondrial data supported the two-lineage hypothesis, except for the Pachón and Chica caves, whose introgression has been largely documented. The Sierra de El Abra region depicted the largest genetic diversity, followed by the Sierra de Guatemala region. Regarding the phylogeographic patterns of rho, we recovered exclusive haplogroups for the Sierra de El Abra (Haplogroup I) and Sierra de Guatemala regions (Haplogroup IV). Moreover, a 544 bp deletion in the rho gene was observed in the Escondido cave population from Sierra de Guatemala, reducing the protein from seven to three intramembrane domains. This change may produce a loss-of-function (LOF) but requires further investigation. Regarding nonsynonymous ( dN) and synonymous ( dS) substitution rates (omega values ω), our results revealed the prevailing influence of purifying selection upon the rho pigment for both cave and surface populations (ω<1), but relaxation at the El Abra region. Notably, in contrast to the other two regions, we observed an increase in the number of dN mutations for Sierra de El Abra. However, given that a LOF was exclusively identified in the Sierra de Guatemala region, we cannot dismiss the possibility of a pleiotropic effect on the Rho protein.

Do immigrants benefit from selection? Migrant educational selectivity and its association with social networks, skills and health

Recent scholarship suggests that immigrant selectivity - the degree to which immigrants differ from non-migrants in their sending countries - can help us understand their labour market outcomes in the receiving country. The selectivity hypothesis rests on three assumptions: first, that immigrants differ from non-migrants in their observed characteristics, such as education; second, that there is an association between such observed selection and (usually) unobserved characteristics, and third that this association drives positive relationships between observed selection and immigrant outcomes. While there is some evidence for a relationship between the degree of immigrants' selectivity and their children's outcomes, a comprehensive assessment of these assumptions for immigrants' own labour market outcomes remains lacking. We use high-quality, nationally representative data for the UK, with large numbers of immigrants from a wide range of different origins and with a rich set of measures of networks, traits and characteristics, as well as economic outcomes, not typically found in surveys of immigrants. This enables us to conduct a comprehensive assessment of the selectivity hypothesis and its assumptions. We find that immigrants to the UK are on average positively selected on educational attainment. However, counter to theoretical assumptions, educational selection has little association with labour market outcomes: it is not or negatively associated with employment; and it is only associated with pay for those with tertiary qualifications and with occupational position for women. We show that the general lack of economic benefits from selection is consistent with an absence of association between educational selectivity and (typically unobserved) mechanisms assumed to link selection and labour market outcomes: social networks, cognitive and non-cognitive skills, and mental and physical health. We contextualise our findings with heterogeneity analysis by migration regime, sending country characteristics, level of absolute education and location of credential.