Program Directors' Selection Criteria for General Surgery and Internal Medicine Residency Programs: A Cross-Sectional Study.

Background and aims General surgery is a specialty that calls for a variety of abilities such as strong hand-eye coordination, the ability to function well under pressure, and the ability to make quick, informed decisions. On the other hand, internal medicine focuses on diagnosing, treating, and preventing adult non-surgical disorders. The present study aims to investigate the commonly used selection criteria employed by program directors (PDs) for general surgery and internal medicine residency programs. It also identifies how PDs value those criteria in the western and central regions of Saudi Arabia. Methods A retrospective cross-sectional study was conducted using a questionnaire adopted from the literature and modified following expert opinion. It was distributed to PDs in both the central and the western regions of Saudi Arabia. Results In total, 34 PDs completed the questionnaire, of which 32 (94.1%) were men. The mean age of participants was 42.53 ± 5.05 years; 21 (61.8%) PDs were general surgeons, and 47.1% were from the Jeddah region. Conclusion The study showed that the most selected criterion for both specialties was communication skills followed by clinical rotation in the same hospital; leadership skills were also highly considered by PDs.

Water and ion diffusion in partially-water saturated compacted kaolinite: Role played by vapor-phase diffusion in water mobility.

Diffusion is the main transport process of water and solutes in clay-rich porous media owing to their very low permeability, so they are widely used as barriers against contaminant spreading. However, the prediction of contaminant mobility can be very complicated when these media are partially water-saturated. We conducted diffusion experiments for water (HTO and HDO) and ions (22Na+ and 125I-) through partially water saturated compacted kaolinite, a weakly charged clay material, to quantify the distinct diffusive behavior of these species. The osmosis method was used to set kaolinite samples at 67, 86 and 100% saturation. The results showed that desaturation led to a sharp decrease in diffusive rates by factors of 6.5, 18 and 35 for HTO, 125I- and 22Na+, respectively, from 100 to 67% of the degree of saturation. Thus, to interpret water diffusivities, we proposed a model taking into account the diffusion of water in both gas and liquid phases, using diffusion data obtained for ions, considered as inert species. This model was capable of properly predicting water diffusive flux, especially at a low degree of saturation (67% saturation), for which the assumption made for the occurrence of air phase continuity throughout the sample appears to be more relevant than at 86% saturation.

Sexual selection drives the evolution of male wing interference patterns.

The seemingly transparent wings of many insects have recently been found to display unexpected structural coloration. These structural colours (wing interference patterns: WIPs) may be involved in species recognition and mate choice, yet little is known about the evolutionary processes that shape them. Furthermore, to date investigations of WIPs have not fully considered how they are actually perceived by the viewers' colour vision. Here, we use multispectral digital imaging and a model of Drosophila vision to compare WIPs of male and female Drosophila simulans from replicate populations forced to evolve with or without sexual selection for 68 generations. We show that WIPs modelled in Drosophila vision evolve in response to sexual selection and provide evidence that WIPs correlate with male sexual attractiveness. These findings add a new element to the otherwise well-described Drosophila courtship display and confirm that wing colours evolve through sexual selection.

Diffusion of organic anions in clay-rich media: Retardation and effect of anion exclusion.

The transport of emerging organic contaminants through the geosphere is often an environmental issue. The sorption of organic compounds slows their transport in soils and porous rocks and retardation is often assessed by extrapolation of batch experiments. However, transport experiments are preferable to strengthen migration data and modelling. In this context, we evaluated the adsorption of various organic acids by means of through-diffusion experiments in a sedimentary clay-rich rock (Callovo-Oxfordian, East of Paris Basin, France). A low diffusivity of organic anions was quantified with effective diffusion coefficients, De, ranged between 0.5 and 7 10-12 m2 s-1. These values indicated an organic anion exclusion. As for chloride, the porosity accessible to organic anions was lower than that of water: εa(organic anions) < ε(water). The partial exclusion of organic anions from rock porosity was linked to both charge and size effects. A significant retardation was observed for organic anions such as oxalate, citrate or α-isosaccharinate. Yet, retardation measured by diffusion experiments was significantly lower than expected from batch experiments on crushed samples. An empirical correction factor is proposed to account for a possible decrease of retardation with accessible porosity of diffusing solute. This feature has significant implications for the estimation of migration parameters of organic compounds in the environment.

De novo transcriptome assembly facilitates characterisation of fast-evolving gene families, MHC class I in the bank vole (Myodes glareolus).

The major histocompatibility complex (MHC) plays a central role in the adaptive immune response and is the most polymorphic gene family in vertebrates. Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying MHC genes, its potential to facilitate early steps in the characterisation of MHC variation in nonmodel organism has not been fully explored. In this study we evaluated the usefulness of de novo transcriptome assembly in characterisation of MHC sequence diversity. We found that although de novo transcriptome assembly of MHC I genes does not reconstruct sequences of individual alleles, it does allow the identification of conserved regions for PCR primer design. Using the newly designed primers, we characterised MHC I sequences in the bank vole. Phylogenetic analysis of the partial MHC I coding sequence (2-4 exons) of the bank vole revealed a lack of orthology to MHC I of other Cricetidae, consistent with the high gene turnover of this region. The diversity of expressed alleles was characterised using ultra-deep sequencing of the third exon that codes for the peptide-binding region of the MHC molecule. High allelic diversity was demonstrated, with 72 alleles found in 29 individuals. Interindividual variation in the number of expressed loci was found, with the number of alleles per individual ranging from 5 to 14. Strong signatures of positive selection were found for 8 amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.

MHC, parasites and antler development in red deer: no support for the Hamilton & Zuk hypothesis.

The Hamilton-Zuk hypothesis proposes that the genetic benefits of preferences for elaborated secondary sexual traits have their origins in the arms race between hosts and parasites, which maintains genetic variance in parasite resistance. Infection, in turn, can be reflected in the expression of costly sexual ornaments. However, the link between immune genes, infection and the expression of secondary sexual traits has rarely been investigated. Here, we explored whether the presence and identity of functional variants (supertypes) of the highly polymorphic major histocompatibility complex (MHC), which is responsible for the recognition of parasites, predict the load of lung and gut parasites and antler development in the red deer (Cervus elaphus). While we found MHC supertypes to be associated with infection by a number of parasite species, including debilitating lung nematodes, we did not find support for the Hamilton-Zuk hypothesis. On the contrary, we found that lung nematode load was positively associated with antler development. We also found that the supertypes that were associated with resistance to certain parasites at the same time cause susceptibility to others. Such trade-offs may undermine the potential genetic benefits of mate choice for resistant partners.

The locus of sexual selection: moving sexual selection studies into the post-genomics era.

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.

Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure.

Genes of the major histocompatibility complex, which are the most polymorphic of all vertebrate genes, are a pre-eminent system for the study of selective pressures that arise from host-pathogen interactions. Balancing selection capable of maintaining high polymorphism should lead to the homogenization of MHC allele frequencies among populations, but there is some evidence to suggest that diversifying selection also operates on the MHC. However, the pattern of population structure observed at MHC loci is likely to depend on the spatial and/or temporal scale examined. Here, we investigated selection acting on MHC genes at different geographic scales using Venezuelan guppy populations inhabiting four regions. We found a significant correlation between MHC and microsatellite allelic richness across populations, which suggests the role of genetic drift in shaping MHC diversity. However, compared to microsatellites, more MHC variation was explained by differences between populations within larger geographic regions and less by the differences between the regions. Furthermore, among proximate populations, variation in MHC allele frequencies was significantly higher compared to microsatellites, indicating that selection acting on MHC may increase population structure at small spatial scales. However, in populations that have significantly diverged at neutral markers, the population-genetic signature of diversifying selection may be eradicated in the long term by that of balancing selection, which acts to preserve rare alleles and thus maintain a common pool of MHC alleles.

Accuracy of allele frequency estimation using pooled RNA-Seq.

For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele-specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.

Heterozygosity and orange coloration are associated in the guppy (Poecilia reticulata).

The good-genes-as-heterozygosity hypothesis predicts that more elaborate male sexual ornaments are associated with higher levels of heterozygosity. Recent theoretical work suggests that such associations are likely to arise in finite, structured populations. We investigated the correlation between multilocus heterozygosity (MLH), which was estimated using 13 microsatellite loci, and male coloration in a wild population of guppies (Poecilia reticulata), a model species in sexual selection research. We found that MLH was a significant predictor of the relative area of orange spots, a trait that is subject to strong female preference in this species. Neither the relative area of black spots nor the number of black or orange spots was significantly correlated with MLH. We found no statistical support for local effects (i.e. strong effects of heterozygosity at specific markers), which suggests that relative orange spots area reflects genome-wide heterozygosity.

Contrasting patterns of selection acting on MHC class I and class II DRB genes in the Alpine marmot (Marmota marmota).

The major histocompatibility complex (MHC) genes code for proteins that play a critical role in the immune system response. The MHC genes are among the most polymorphic genes in vertebrates, presumably due to balancing selection. The two MHC classes appear to differ in the rate of evolution, but the reasons for this variation are not well understood. Here, we investigate the level of polymorphism and the evolution of sequences that code for the peptide-binding regions of MHC class I and class II DRB genes in the Alpine marmot (Marmota marmota). We found evidence for four expressed MHC class I loci and two expressed MHC class II loci. MHC genes in marmots were characterized by low polymorphism, as one to eight alleles per putative locus were detected in 38 individuals from three French Alps populations. The generally limited degree of polymorphism, which was more pronounced in class I genes, is likely due to bottleneck the populations undergone. Additionally, gene duplication within each class might have compensated for the loss of polymorphism at particular loci. The two gene classes showed different patterns of evolution. The most polymorphic of the putative loci, Mama-DRB1, showed clear evidence of historical positive selection for amino acid replacements. However, no signal of positive selection was evident in the MHC class I genes. These contrasting patterns of sequence evolution may reflect differences in selection pressures acting on class I and class II genes.

Long-term survival of a urodele amphibian despite depleted major histocompatibility complex variation.

Depletion of polymorphism at major histocompatibility complex (MHC) genes has been hypothesized to limit the ability of populations to respond to emerging pathogens, thus putting their survival at risk. As pathogens contribute substantially to the global amphibian decline, assessing patterns of MHC variation is important in devising conservation strategies. Here, we directly compare levels of MHC class II and neutral variation between multiple populations of the great crested newt (Triturus cristatus) from refugial (REF: Romania) and postglacial expansion (PGE: Germany, Poland and UK) areas. REF populations harboured high levels of adaptive variation (24 expressed alleles), exhibiting clear signatures of historical positive selection, which points to the overall importance of MHC class II variation in this species. On the other hand, PGE populations were extremely depauperate (two alleles) but nevertheless have survived for c. 10,000 years, since the postglacial expansion. Variation in putative MHC class II pseudogenes, microsatellites and allozymes also showed a significant southern richness-northern purity pattern. The populations in the postglacial expansion area thus provide the clearest example to date of the long-term survival of populations in which MHC variation, historically under positive selection, has been depleted.

Contrasting patterns of variation in MHC loci in the Alpine newt.

Major histocompatibility complex (MHC) genes are essential in pathogen recognition and triggering an adaptive immune response. Although they are the most polymorphic genes in vertebrates, very little information on MHC variation and patterns of evolution are available for amphibians, a group known to be declining rapidly worldwide. As infectious diseases are invoked in the declines, information on MHC variation should contribute to devising appropriate conservation strategies. In this study, we examined MHC variation in 149 Alpine newts (Mesotriton alpestris) from three allopatric population groups in Poland at the northeastern margin of the distribution of this species. The genetic distinctiveness of the population groups has previously been shown by studies of skin graft rejection, allozymes and microsatellites. Two putative expressed MHC II loci with contrasting levels of variation and clear evidence of gene conversion/recombination between them were detected. The Meal-DAB locus is highly polymorphic (37 alleles), and shows evidence of historical positive selection for amino acid replacements and substantial geographical differentiation in allelic richness. On the contrary, the Meal-DBB locus exhibits low polymorphism (three alleles differing by up to two synonymous substitutions) and a uniform distribution of three alleles among geographical regions. The uniform frequencies of the presumptively neutral Meal-DBB alleles may be explained by linkage to Meal-DAB. We found differences in allelic richness in Meal-DAB between regions, consistent with the hypothesis that genetic drift prevails with increasing distance from glacial refugia. Pseudogene loci appear to have evolved neutrally. The level of DAB variation correlated with variation in microsatellite loci, implying that selection and drift interplayed to produce the pattern of MHC variation observed in marginal populations of the Alpine newt.

Randomized trial comparing cryoablation and external beam radiotherapy for T2C-T3B prostate cancer.

The objective was to evaluate the relative efficacy of cryoablation (CRYO) versus external beam radiation (EBRT) for clinically locally advanced prostate cancer in a randomized clinical trial. Patients with histologically proven, clinically staged as T2C, T3A or T3B disease were randomized with 6 months of perioperative hormone therapy to one of the two procedures. Owing largely to a shift in practice to longer term adjuvant hormonal therapy and higher doses of radiation for T3 disease, only 64 out of the planned 150 patients were accrued. Twenty-one of 33 (64%) in the CRYO group and 14 of 31 (45%) in the EBRT-treated group who had met the ASTRO definition of failure were also classified as treatment failure. The mean biochemical disease-free survival (bDFS) was 41 months for the EBRT group compared to 28 months for the CRYO group. The 4-year bDFS for EBRT and CRYO groups were 47 and 13%, respectively. Disease-specific survival (DSS) and overall survival (OS) for both groups were very similar. Serious complications were uncommon in either group. EBRT patients exhibited gastrointestinal (GI) adverse effects more frequently. Taking into account the relative deficiency in numbers and the original trial design, this prospective randomized trial indicated that the results of CRYO were less favorable compared to those of EBRT, and was suboptimal primary therapy in locally advanced prostate cancer.

MHC-DRB3 variation in a free-living population of the European bison, Bison bonasus.

MHC genes play a crucial role in pathogen recognition and are the most polymorphic genes in vertebrates. Loss of variation in these genes in bottlenecked species is thought to put their survival at risk. We examined variation at the MHC II DRB3 locus in the European bison, Bison bonasus, a species that has undergone an extreme bottleneck: the current population originated from only 12 founders. We also tested for the association of DRB3 genes with the incidence of posthitis, a disease affecting the reproductive organs of bulls and posing a new threat to the survival of the species. We found very limited MHC diversity, with only four alleles segregating in a sample of 172 individuals from a free-ranging Bialowieza population. The alleles were highly divergent and revealed the hallmark of positive selection acting on them in the past, that is, a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen-binding sites, suggesting that selection was driven by pathogens. However, we did not observe departures from Hardy-Weinberg equilibrium, an indicator of strong ongoing selection. Neither have we found a significant association between DRB3 alleles or genotypes and susceptibility to posthitis. Alleles conferring resistance to males may have been lost during the extreme bottleneck the species had undergone.

Assessing the prognostic significance of transrectal ultrasound extracapsular extension in prostate cancer.

AIMS: To determine the prognostic value of transrectal ultrasound (TRUS)-detected extraprostatic disease for prostate cancer in patients receiving radical external-beam radiation therapy (EBRT). MATERIALS AND METHODS: A chart review of 181 patients treated with radical EBRT for prostate cancer was conducted. All patients underwent TRUS assessment by one radiologist. The median radiation dose delivered to the prostate was 66 Gy (range 53-70 Gy) in 33 fractions (range 20-39 fractions). Median follow-up time for all patients was 6.5 years. Sixty-four (35%) out of 181 patients were found to have extracapsular disease on TRUS. Clinical relapse was defined as the first occurrence of either salvage hormonal therapy administration by the treating oncologist or clinical, radiological, and/or pathologic evidence of recurrent or progressive disease. In terms of biochemical failure, two prognostic variable analyses were carried out using both the American Society for Therapeutic Radiology and Oncology (ASTRO) consensus guidelines and the Houston definition of biochemical failure. The primary end point for the prognostic variable analyses was time to first clinical or biochemical failure (CBF). RESULTS: For time to CBF using the ASTRO consensus guidelines for biochemical failure, univariable analysis revealed that the prostate-specific antigen (PSA) (P = 0.018), clinical T stage (P = 0.002), Gleason score (P = 0.021), adjuvant hormonal therapy (P = 0.032) and TRUS T staging (P = 0.0001) were statistically significant prognostic factors. On multivariable analysis, clinical T stage (P = 0.051) was of borderline statistical significance, whereas PSA (P = 0.036), TRUS T stage (P = 0.0002) and adjuvant hormonal therapy (P = 0.015) were found to be independent prognostic factors. For time to CBF using the Houston definition of biochemical failure, univariable analysis revealed that PSA (P = 0.001), Gleason score (P = 0.026) and prostate volume (P = 0.013) were statistically significant prognostic factors. On multivariable analysis, PSA (P = 0.002), Gleason score (P = 0.012), and adjuvant hormonal therapy (P = 0.041) were found to be independent prognostic factors. TRUS T staging was not found to be independently significant. CONCLUSIONS: A clear role for TRUS staging as an independent prognostic factor, in the setting of other more established variables, such as Gleason grade, PSA, and digital rectal examination (DRE) T stage, was not confirmed in this study, population.

Sequence diversity of the MHC DRB gene in the Eurasian beaver (Castor fiber).

Major histocompatibility complex (MHC) genes, coding molecules which play an important role in immune response, are the most polymorphic genes known in vertebrates. However, MHC polymorphism in some species is limited. MHC monomorphism at several MHC class I and II loci was previously reported for two neighbouring northern European populations of the Eurasian beaver (Castor fiber) and reduced selection for polymorphism has been hypothesized. Here, we analysed a partial sequence of the second exon of the MHC II DRB locus from seven relict European and Asian beaver populations. We detected 10 unique alleles among 76 beavers analysed. Only a western Siberian population was polymorphic, with four alleles detected in 10 individuals. Each of the remaining populations was fixed for a different allele. Sequences showed considerable divergence, suggesting the long persistence of allelic lineages. A significant excess of nonsynonymous substitutions was detected at the antigen binding sites, indicating that sequence evolution of beaver DRB was driven by positive selection. Current MHC monomorphism in the majority of populations may be the result of the superimposition of the recent bottleneck on pre-existing genetic structure resulting from population subdivision and differential pathogen pressure.

Effect of inbreeding and heritability of sperm competition success in the bulb mite Rhizoglyphus robini.

Sperm competition is a potent evolutionary force shaping the reproductive biology of most animal species. Here, we estimated the heritability of sperm competition success in the promiscuous bulb mite Rhizoglyphus robini. Sperm competition success was measured with the sterile male technique as the proportion of eggs fertilised by the second of three males mated with a single female. Sperm competition success responded significantly to selection. The heritability estimated from the response to five generations of selection was 0.13. We also estimated the effect of inbreeding on sperm competition success. Males produced by sib-mating (F=0.25) had a significantly lower sperm competition success than outbred males. The estimated coefficient of inbreeding depression was 0.53. Such high inbreeding depression together with moderately low heritability is consistent with the view that sperm competitive ability is under strong directional selection and strongly influences the reproductive success of males.

Testing the status-dependent ESS model: population variation in fighter expression in the mite Sancassania berlesei.

The conditional evolutionarily stable strategy (ESS) with status-dependent tactics is the most commonly invoked ESS for alternative reproductive tactics within the sexes. Support for this model has recently been criticized as apparent rather than real. We address key predictions of the status-dependent ESS in three populations of the male dimorphic mite Sancassania berlesei. In S. berlesei'fighter' males are characterized by a thickened pair of legs used for killing rivals; 'scramblers' are benign. Most males in each population could be manipulated to become fighters by decreasing density, fulfilling the prediction that males make a 'decision'. There was evidence of genetic covariance between sire status and offspring morph, but also a strong effect of sire morph on offspring morph ratio. This was consistent with considerable genetic variation for the status-dependent switch point as a breeding experiment found no support for single-locus inheritance. We also found evidence that switch points evolve independently of distributions of status. This study supports the current status-dependent ESS model.

Cleavage of prothrombin bound in immune complexes results in high thrombin enzymatic activity.

Thrombin plays a pivotal role in blood clotting as well as in the regulation of vascular remodeling and oxidative stress. Recent evidence suggests that auto-antibodies directed against prothrombin, may play an important role in the pathogenesis of atherosclerosis. It is however not clear, if prothrombin bound in an immune complex retains its clotting and regulatory properties or acts solely by increasing vascular inflammation. In order to answer this question, we used a newly developed stain for the detection of thrombin activity of such complexes. Plasma and serum samples were subjected to rocket immunoelectrophoresis in an anti-prothrombin antiserum containing agarose gel. Gel plates, covered with a nitrocellulose membrane were soaked with chromogenic thrombin substrate. The product of thrombin activity was diazotized to red azo dye bound to nitrocellulose. Activity stain revealed barely discernible rockets in plasma, but heavily stained ones in serum. Pre-incubation with trypsin enhanced activity of immunoprecipitates deriving from plasma, but not from serum. Densitometric analysis showed, that the trypsin-enhanced activity in plasma derived immune complexes was twice as high as in serum derived immunoprecipitates. Thrombin active centre is not blocked by anti-prothrombin antiserum allowing to retain thrombin activity. Moreover, prothrombin in immunoprecipitate is readily cleaved by proteolytic enzymes. This cleavage could potentially be enhanced by antibody binding, although these results need to be confirmed using different antibodies.