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PubMed1999

A comparison of CD34+ cell selected and unselected autologous peripheral blood stem cell transplantation for multiple myeloma: a case controlled analysis.

Following ASCT for multiple myeloma, it is unclear whether relapse is due solely to the presence of residual myeloma cells after myeloablation, or whether it is in part attributable to contamination of the stem cell harvest with viable malignant cells. Positive selection of CD34+ cells markedly reduces plasma cell contamination. We performed a case controlled analysis in which 15 patients with myeloma who underwent autologous PBSCT with CD34+cell selection using the Ceprate System (index group), were compared with 15 matched controls. All subjects received an identical preparative regimen. The median times to neutrophils >/=0.5 x 10(9)/l and unsupported platelets >/=50 x 10(9)/l were 14 and 23 days for the CD34+cell selected group and 11 (P = 0.03) and 14 (P = 0.029) for the case controls. Median follow-up of purged patients from autologous PBSCT was 32 months (range 18-43). At 36 months, the probability of PFS was 47 +/- 14% and 46 +/- 14% in the index and control groups (P = 0.44). The 3 year probability of OS was 69 +/- 13% for the CD34+ cell selected arm and 66 +/- 12.4% in unpurged patients (P = 0.91). Median PFS for the cell selected group is 24 months (CI 19.1-36.0), and 29 months for controls (CI 7.1-50.9). Eleven patients undergoing cell selection remain alive, seven of whom are progression free. At the same time-point after unpurged autologous PBSCT, the corresponding figures are 12 patients alive, with seven remaining progression free. Autologous PBSCT with CD34+ cell selection is both feasible and safe, but results in delayed engraftment as compared to case controls. The 3 year probability of PFS and OS in the cell selected arm was similar to that of the unpurged controls. Our findings indicate that autologous PBSCT with CD34+ cell selection appears not to have any favourable effect on disease progression. However, the results of this case controlled analysis should be cautiously interpreted, and the role of CD34+ selection in autologous PBSCT should be further investigated by large randomised trials.

Adult↗
PubMed2001

Combined positive and negative cell selection from allogeneic peripheral blood progenitor cells (PBPC) by use of immunomagnetic methods.

Twenty-four mobilized peripheral blood products from healthy donors for allogeneic transplantation were positively selected for CD34(+) cells and depleted of CD4(+) and CD8(+) cells (+/- selection) by combining clinical grade immunomagnetic methods. A sequential, "two-step" strategy combining positive selection of CD34(+) cells by use of the Isolex 300i (versions 1 and 2) device and T cell depletion (TCD) using the MaxSep device and a simultaneous, "one-step" method of CD34(+)cell selection and TCD using the Isolex 300i (software versions 1 and 2) have been investigated. Using these magnetic bead separation systems, two groups of sequential +/- selection (Isolex 300i version 1/MaxSep and Isolex 300i version 2/MaxSep) and two groups of simultaneous +/- selection (Isolex 300i versions 1 and 2) were analysed. In the sequential +/- selection, logarithms of TCD (CD3(+) cell depletion) obtained by the positive selection step had median values of 3.7 with the version 1 (n = 5) and 4.5 with version 2 software of the Isolex 300i (n = 5) (P = 0.07). Version 2 also gave a higher CD34(+) cell purity and yield than did version 1 (92% vs77%, P < 0.05 and 55% vs 34%, P = 0.3, respectively). Additional TCD obtained in the second step with the MaxSep device for the two groups had a median value of 0.9 log and 7% CD34(+)cell losses. In the simultaneous +/- selection, the Isolex 300i version 2 (n = 10) gave a median TCD of 5.1 log and version 1 (n = 4) of 4 log (P < 0.005). Higher CD34(+)cell purity and yield were also obtained with version 2 than with version 1 (97% and 76%, P < 0.005 and 57% and 39%, P = 0.07, respectively). These data indicate that simultaneous, "one-step" +/- selection in the Isolex 300i version 2 achieves a high TCD with a high CD34(+) cell purity and an acceptable CD34(+) cell yield.

Algorithms↗
PubMed1998

Provision of positive and negative selections in retroviral vectors containing the cytosine deaminase gene.

The E. coli cytosine deaminase (CD) provides a negative selection system for suicide gene therapy as CD transfectants are eliminated following 5-fluorocytosine (5FC) treatment. Here we report a positive selection system for the CD gene using 5-fluorouracil (5FU) and cytosine in selection medium to screen for CD-positive transfectants. It is based on the relief of 5FU toxicity by uracil which is converted from cytosine via CD catalysis, as uracil competes with the toxic 5FU in subsequent pyrimidine metabolism. Hence, a retroviral vector containing the CD gene may provide both positive and negative selections after gene transfer. The CD transfectants selected with the positive selection system showed susceptibility to 5FC in subsequent negative selection in vitro and in vivo. Therefore, this dual selection system is useful not only for combination therapy with transgene and CD gene, but can also act to eliminate selectively transduced cells after the transgene has furnished its effects or upon undesired conditions if 5FC is applied for negative selection in vivo.

Animals↗
PubMed2000

The evolution of the G matrix: selection or drift?

The evolution of quantitative characters can be described by the equation Deltaz=GP-1S where Deltaz is the vector of mean responses, G is the matrix of additive genetic variances and covariances, P is the matrix of phenotypic variances and covariances and S is the vector of selection differentials. This equation can be used to predict changes in trait values or to retrospectively estimate the selection gradient and is thus a central equation of evolutionary quantitative genetics. Genetic variances and covariances will be reduced by stabilizing selection, directional selection and drift, and increased by mutation. Changes in trait values resulting from directional selection that are comparable with differences observed among species are readily obtainable in short geological time spans (<5000 generations) with selection intensities so small that they would have an insignificant effect on the G matrix (of course it is possible that such changes came about by strong selection over a few generations, followed by long periods of stasis; there is insufficient evidence to presently distinguish these two possibilities). On the other hand, observed effective population sizes are sufficiently small that considerable changes in G can be expected from drift alone. The action of drift can be distinguished from selection because the former produces a proportional change in G whereas the latter, in general, will not. A survey of studies examining variation in G suggests that the null hypothesis that most of the variation can be attributed to drift rather than selection cannot be rejected. However, more research on the predicted statistical distribution of G as a result of selection and/or drift is required and further development of statistical tests to distinguish these two forces needs to be made.

Animals↗
PubMed1992

Selection of platelets for refractory patients by HLA matching and prospective crossmatching.

A multi-site clinical study compared platelets chosen for refractory patients by prospective platelet crossmatching using stored donor platelets and HLA-based selection. Seventy-three patients who were refractory to random-donor platelets received two plateletpheresis components, one chosen by HLA-based criteria and the other by crossmatching. Patients were carefully evaluated to exclude nonimmune factors that could adversely affect transfusion results. Each of the five study sites used a crossmatch procedure with which it had experience. Results from this study indicate the following: 1) The overall rate of successful transfusion was similar when an HLA-based method of donor selection that includes all grades of matching and mismatching was compared to a crossmatch-based method of donor selection. 2) HLA-based selection that restricts recipients to grade A and BU matches was superior to a selection method based upon crossmatching alone. Donor selection based on HLA matching (grades A or BU) was also superior to selection based on any degree of HLA mismatching (grades BX, C, or D). 3) Selection of donors based on HLA-cross-reactive groups (defined by in vitro serologic crossreactivity) was no more successful than that based on grade C and D mismatches and was no more successful than selection by crossmatching alone. 4) Lymphocytotoxic and platelet antibodies were not detected in many of the enrolled patients, even though patients demonstrating nonimmune factors were eliminated from the study. It can be concluded that HLA-compatible (grades A and BU) platelets provide optimal support for refractory patients, but that crossmatch-selected platelets are acceptable as an alternative component.

Adult↗
PubMed1993

Species selection on variability.

Most analyses of species selection require emergent, as opposed to aggregate, characters at the species level. This "emergent character" approach tends to focus on the search for adaptations at the species level. Such an approach seems to banish the most potent evolutionary property of populations--variability itself--from arguments about species selection (for variation is an aggregate character). We wish, instead, to extend the legitimate domain of species selection to aggregate characters. This extension of selection theory to the species level will concentrate, instead, on the relation between fitness and the species character, whether aggregate or emergent. Examination of the role of genetic variability in the long-term evolution of clades illustrates the cogency of broadening the definition of species selection to include aggregate characters. We reinterpret, in this light, a classic case presented in support of species selection. As originally presented, the species selection explanation of volutid neogastropod evolution was vulnerable to a counterinterpretation at the organism level. Once this case is recast within a definition of species selection that reflects the essential structure and broad applicability of hierarchical selection models, the organism-level reinterpretation of variability loses its force. We conclude that species selection on variability is a major force of macroevolution.

Journal Article↗
PubMed2000

Lipoprotein lipase-mediated selective uptake from low density lipoprotein requires cell surface proteoglycans and is independent of scavenger receptor class B type 1.

Lipoprotein lipase (LpL) hydrolyzes chylomicron and very low density lipoprotein triglycerides to provide fatty acids to tissues. Aside from its lipolytic activity, LpL promotes lipoprotein uptake by increasing the association of these particles with cell surfaces allowing for the internalization by receptors and proteoglycans. Recent studies also indicate that LpL stimulates selective uptake of lipids from high density lipoprotein (HDL) and very low density lipoprotein. To study whether LpL can mediate selective uptake of lipids from low density lipoprotein (LDL), LpL was incubated with LDL receptor negative fibroblasts, and the uptake of LDL protein, labeled with (125)I, and cholesteryl esters traced with [(3)H]cholesteryl oleoyl ether, was compared. LpL mediated greater uptake of [(3)H]cholesteryl oleoyl ether than (125)I-LDL protein, a result that indicated selective lipid uptake. Lipid enrichment of cells was confirmed by measuring cellular cholesterol mass. LpL-mediated LDL selective uptake was not affected by the LpL inhibitor tetrahydrolipstatin but was nearly abolished by heparin, monoclonal anti-LpL antibodies, or chlorate treatment of cells and was not found using proteoglycan-deficient Chinese hamster ovary cells. Selective uptake from HDL, but not LDL, was 2-3-fold greater in scavenger receptor class B type I overexpressing cells (SR-BI cells) than compared control cells. LpL, however, induced similar increases in selective uptake from LDL and HDL in either control or SR-BI cells, indicative of the SR-BI-independent pathway. This was further supported by ability of LpL to promote selective uptake from LDL in human embryonal kidney 293 cells, cells that do not express SR-BI. In Chinese hamster ovary cell lines that overexpress LpL, we also found that selective uptake from LDL was induced by both endogenous and exogenous LpL. Transgenic mice that overexpress human LpL via a muscle creatine kinase promoter had more LDL selective uptake in muscle than did wild type mice. In summary LpL stimulates selective uptake of cholesteryl esters from LDL via pathways that are distinct from SR-BI. Moreover this process also occurs in vivo in tissues where abundant LpL is present.

Animals↗
PubMed1998

Modulation of thymic selection by expression of an immediate-early gene, early growth response 1 (Egr-1).

The potential involvement of early growth response (Egr)-1, a zinc-finger transcription factor belonging to the immediate-early genes, in positive/negative selection of thymocytes has been implicated by its expression in the population of CD4(+)CD8(+) double positive (DP) cells undergoing selection. To further investigate this possibility, transgenic mice overexpressing Egr-1 in thymocytes were bred with a transgenic mouse line expressing a T cell receptor (TCR) recognizing the H-Y male antigen in the context of H-2(b) class I major histocompatibility complex (MHC) molecules. In Egr-1/TCR H-Y double-transgenic mice, efficient positive selection of H-Y CD8(+) T cells occurred, even in mice on either a nonselecting H-2(d) background or a beta2-microglobulin (beta2m)-deficient background in which the expression of class I MHC heavy chains is extremely low; no positive selection was observed on a Kb-/-Db-/-beta2m-/- background where class I MHC expression is entirely absent. Similarly, when the Egr-1 transgene was introduced into a class II MHC-restricted TCR transgenic mouse line, Egr-1/TCR double-transgenic mice revealed increased numbers of CD4(+) T cells selected by class II MHC, as well as significant numbers of CD8(+) T cells selected by class I MHC (for which the transgenic TCR might have weak affinity). Thus, Egr-1 overexpression allows positive selection of thymocytes via TCR-MHC interactions of unusually low avidity, possibly by lowering the threshold of avidity required for positive selection. Supporting this possibility, increased numbers of alloreactive T cells were positively selected in Egr-1 transgenic mice, resulting in a strikingly enhanced response against allo-MHC. These results suggest that expression of Egr-1 and/or its target gene(s) may directly influence the thresholds required for thymocyte selection.

Animals↗
PubMed2003

Drug selection of mutant methylguanine methyltransferase from different oncoretroviral backbones results in multilineage hematopoietic transgene expression in primary and secondary recipients.

Optimized hematopoietic gene therapy requires vectors with strong expression in the desired target cell population and the ability to select for the expressing transduced cells. In the context of drug resistance selection of repopulating hematopoietic stem cells in the mouse, we examined tissue expression after transduced marrow transplantation of the drug selection gene, G156A mutant O6-methylguanine-DNA methyltransferase (G156A MGMT). To gain more experience with the rigor of the impact of selection on tissue-specific gene expression, we also asked whether there are expression differences between three different onco-retroviral backbones--MPSV, SF, and MFG. MGMT expression was compared after O6-benzylguanine (BG) and 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU) drug selection in vivo. After mice were transplanted with cells transduced with MPSV, MFG, or SF retroviral vectors expressing G156A MGMT and drug treated, nearly complete replacement by transduced progenitors was observed in the marrow. Each backbone supported MGMT expression in all four hematopoietic lineages in vivo indicating that MGMT-mediated selection is indeed robust. Expression in marrow, spleen, and thymus was very similar between the vectors and differences were most likely due to differences in gene copy number per selected cell. In primary and secondary recipients, the highest expression was observed in MFG and this was the vector that transduced at the greatest proviral copy number per cell. These data indicate that strong selection pressure using the MGMT gene to protect primary and secondary repopulating murine stem cells from the toxicity of BCNU. Regardless of the vector backbone used, multiorgan expression was observed without evidence of gene silencing. These data help establish mutant, BG-resistant MGMT as a potent selection gene for stem cell selection in vivo.

Animals↗
PubMed2004

Orientation and direction selectivity of neurons in V1 of alert monkeys: functional relationships and laminar distributions.

We studied orientation selectivity in V1 of alert monkeys and its relationship to other physiological parameters and to anatomical organization. Single neurons were stimulated with drifting bars or with sinusoidal gratings while compensating for eye position. Orientation selectivity based on spike counts was quantified by circular variance and by the bandwidth of the orientation tuning curve. The circular variance distribution was bimodal, suggesting groups with low and with high selectivity. Orientation selectivity was clearly correlated with spontaneous activity, classical receptive field (CRF) size and the strength of surround suppression. Laminar distributions of neuronal properties were distinct. Neurons in the output layers 2/3, 4B and 5 had low spontaneous activity, small CRFs and high orientation selectivity, while the input layers had greater diversity. Direction-selective cells were among the neurons most selective for orientation and most had small CRFs. A narrow band of direction- and orientation-selective cells with small CRFs was located in the middle of layer 4C, indicating appearance of very selective cells at an early stage of cortical processing. We suggest that these results reflect interactions between excitatory and inhibitory mechanisms specific to each sublamina. Regions with less inhibition have higher spontaneous activity, larger CRFs and broader orientation tuning. Where inhibition is stronger, spontaneous activity almost disappears, CRFs shrink, and orientation selectivity is high.

Action Potentials↗
PubMed2002

CD53, a thymocyte selection marker whose induction requires a lower affinity TCR-MHC interaction than CD69, but is up-regulated with slower kinetics.

The molecular mechanisms that govern the survival, maturation and export of thymocytes are the subject of intense study, and candidates for involvement in these processes might be identified by their differential expression during thymocyte selection. One such molecule is the tetraspanin CD53, which is not expressed on most CD4(+)CD8(+) double-positive (DP) cells in the normal mouse. We have examined CD53 expression on DP from several class I- and class II-restricted TCR transgenic (Tg) mice, and have found a strong correlation between CD53 expression and positive selection. CD53 expression in DP was formally demonstrated to be dependent upon MHC recognition as evidenced by studying DP from MHC-deficient mice which totally lack expression of this molecule. This link between selection and CD53 expression was reminiscent of CD69, and indeed the majority of selected DP from normal mice that express CD53 also express CD69. We compared CD53 and CD69 induction in vitro using pre-selected thymocytes from TCR-Tg mice that were stimulated either with mAb against TCR or with antigen-presenting cells (APC) pulsed with peptides. The data shows that with either stimulus, CD69 is induced rapidly on the thymocyte surface with expression detected in as little as 2 h. CD53 induction is slower with maximal expression taking up to 20 h. We also stimulated pre-selected thymocytes from the OT-1 TCR-Tg strain with APC pulsed with peptides of varying affinities for the TCR. Here low-affinity peptides which induce CD69 expression poorly were able to induce significant levels of CD53 expression. These data demonstrate that the induction of CD53 and CD69 upon selection is not identical. Thus a combination of the CD69 and CD53 selection markers may be a powerful tool to isolate thymocytes that have either been very recently selected or have arisen from differing MHC--TCR affinity interactions during selection.

Animals↗
PubMed2005

Selectivity of ertapenem for Pseudomonas aeruginosa mutants cross-resistant to other carbapenems.

OBJECTIVES: Ertapenem and other carbapenems will be used increasingly, as extended-spectrum beta-lactamases become more prevalent even among community-acquired pathogens. There is, however, concern that this use will select for resistances to imipenem and meropenem in nosocomial pathogens, notably Pseudomonas aeruginosa, and we investigated the validity of this concern. METHODS: Single-step selection experiments were performed by plating P. aeruginosa cultures on to agar containing doubling dilutions of ertapenem. MIC patterns, outer membrane protein profiles and the effects of efflux inhibitors were examined for selected mutants. RESULTS: At 2-8 x MIC, ertapenem selected (i) for OprD(-) mutants of P. aeruginosa, with cross-resistance only to carbapenems, (ii) for putative efflux types with broader cross-resistance, and also (iii) for various less familiar phenotypes. Efflux mutants were predominantly, but not exclusively, selected from carbenicillin-hypersusceptible strains and OprD(-) mutants largely from strains with normal levels of carbenicillin susceptibility. Whilst these data indicate potential cross-selectivity, they must be set against the observation that 20% serum raised the ertapenem MICs, and the drug concentrations needed for mutant selection, by over four-fold, reflecting the compound's strong protein binding. Since, following a 1 g intravenous dose the free ertapenem concentration in the serum falls below 4 mg/L--corresponding to the lower of two MIC(50) estimates--within 4 h (17% of the dosage interval) selectivity in vivo should be minimized. CONCLUSIONS: Whilst ertapenem can select for P. aeruginosa mutants with cross-resistance to imipenem and ertapenem in vitro, this selectivity should be minimal under clinical conditions.

Carbapenems↗
PubMed1998

Selection index updating for maximizing rate of annual genetic gain in laying hens.

Four selection strategies aimed at maximizing egg production in laying hens were compared with respect to expected annual genetic gain (GA). The selection strategies were: 1) (S1P) Traditional single-stage selection based on a single-house production system using partial records for both the individual and its ancestors, 2) Single-stage selection based on a single-house production system using full records for both the individual and its ancestors (S1F), 3) Single-stage selection based on a two-house production system using partial records for the individual and full records for its ancestors (S2P), and 4) Multistage selection based on a two-house production system using partial records for the individual and all available ancestral records (M2P). Strategy M2P resulted in the shortest generation interval (0.538 yr) and was the most efficient (deltaGA4 = 3.620 eggs per year), whereas strategy S1F generated the longest generation interval (2 yr) and was the least efficient (deltaGA2 = 1.334 eggs per year). Strategies S1P and S2P resulted in generation intervals of 1 yr, and were intermediate in efficiency (deltaGA1 = 2.232 eggs per year, deltaGA3 = 2.593 eggs per year). It was concluded that a two-house production system utilizing multistage selection was the most effective selection methodology. Further, selection based on M2P is expected to improve persistency of lay, whereas selection on S1P will not.

Animals↗
PubMed1985

The Emory prospective randomized trial: selective versus nonselective shunt to control variceal bleeding. Ten year follow-up.

From 1971 to 1975, 55 patients with variceal bleeding secondary to cirrhosis were entered into a prospective randomized trial comparing distal splenorenal (selective) and H-graft interposition (nonselective) shunt. This 10-year follow-up documents that selective shunt is better (p less than 0.05) in four of the five variables monitored. Control of bleeding: selective shunt prevented variceal bleeding better than interposition shunt due to the higher (0.05 less than p less than 0.1) occlusion rate (30%) of interposition shunt. Selective shunt maintained postoperative portal perfusion better (p less than 0.01) than patent interposition shunt. Seventy-five per cent of selective shunt survivors have portal perfusion at 10 years: no patient with a patent nonselective shunt perfuses the liver. Quantitative liver function was better preserved (p less than 0.01) 10 years after selective shunt than nonselective shunt. Postoperative encephalopathy occurred in fewer (p less than 0.01) selective (27%) than nonselective (75%) shunt patients over the 10 years. Survival: in the randomized population, the improved survival in the selective shunt subgroup did not reach statistical significance. However, improved survival was confirmed in nonalcoholics. Five of eight nonalcoholics operated with selective shunt are alive at 10 years with patent shunts. No nonalcoholic, of seven total, operated with nonselective shunt survived 10 years with a patent shunt. These data show that selective shunt was superior to nonselective shunt. There was less rebleeding and encephalopathy after distal splenorenal shunt; postoperative portal perfusion and hepatic function were maintained.

Clinical Trials as Topic↗
PubMed1992

Selective decontamination of the digestive tract in the intensive care unit: current status and future prospects.

OBJECTIVE: To evaluate the available data on selective decontamination of the digestive tract. This therapy aims to prevent infection in critically ill patients admitted to ICUs. Microbial carriage in the oropharynx, stomach, and gut; infection; mortality rate; and antibiotic resistance are the outcome events that are being reviewed. DATA SOURCES: Published indices, abstract booklets, and conference proceedings up to the end of 1990. STUDY SELECTION: Sixteen controlled trials of selective decontamination were identified. None of these trials was conducted as a randomized, placebo-controlled, double-blind trial. DATA EXTRACTION: Each of the three authors independently conducted a meta-analysis (thorough review) of the data from the 16 studies. DATA SYNTHESIS: Of the 16 trials, 15 show significant reduction of acquired infection among patients who received selective decontamination. Of the 14 studies that consider carriage of disease-causing microorganisms as an outcome event, 13 demonstrate a reduction in carriage of Gram-negative bacilli. Only ten studies consider mortality as an end-point, of which four demonstrate that the administration of selective decontamination is associated with decreased mortality rates in certain subgroups but not in the overall mortality rate. Of 11 studies that provide data about antibiotic resistance during selective decontamination, ten reported no increase in resistant microorganisms. Selective decontamination has been reported to be effective in controlling an outbreak of multi-resistant microorganisms. CONCLUSIONS: There is a general consensus about the efficacy of selective decontamination in diminishing microbial carriage and acquired infection rates, although conclusions about benefits related to mortality rates vary. Differences in mortality rate are found in the selective decontamination studies of patients with curable diseases, including multitrauma and cardiovascular patients. More data on resistance, collected over a longer period of time, are needed. Practical problems of blinding and the major ecological effect of selective decontamination may explain the lack of a randomized, placebo-controlled, double-blind trial.

Anti-Bacterial Agents↗
PubMed2025

A model for background selection in non-equilibrium populations.

In many taxa, levels of genetic diversity are observed to vary along their genome. The framework of background selection models this variation in terms of linkage to constrained sites, and recent applications have been able to explain a large portion of the variation in human genomes. However, these studies have also yielded conflicting results, stemming from two key limitations. First, existing models are inaccurate in a critical region of parameter space (), where the local reduction in diversity is sharpest. Second, they assume a constant population size over time. Here, we develop predictions for diversity under background selection based on the Hill-Robertson system of two-locus statistics, which allows for population size changes. We treat the joint effect of multiple selected loci independently, but we show that interference among them is well captured through local rescaling of mutation, recombination and selection in an iterative procedure that converges quickly. We further accommodate existing background selection theory to non-equilibrium demography, bridging the gap between weak and strong selection. Simulations show that our predictions are accurate across the entire range of selection coefficients. We characterize the temporal dynamics of linked selection under population size changes and demonstrate that patterns of diversity can be misinterpreted by other models. Specifically, biases due to the incorrect assumption of equilibrium carry over to downstream inferences of the distribution of fitness effects and deleterious mutation rate. Jointly modeling demography and linked selection therefore improves our understanding of the genomic landscape of diversity, which will help refine inferences of linked selection in humans and other species.

Journal Article↗
PubMed2025

Accessible, realistic genome simulation with selection using stdpopsim.

Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting selection and to explore theoretical predictions. stdpopsim is a community-maintained simulation library that already provides an extensive catalog of species-specific population genetic models. Here we present a major extension to the stdpopsim framework that enables simulation of various modes of selection, including background selection, selective sweeps, and arbitrary distributions of fitness effects (DFE) acting on annotated subsets of the genome (for instance, exons). This extension maintains stdpopsim's core principles of reproducibility and accessibility while adding support for species-specific genomic annotations and published DFE estimates. We demonstrate the utility of this framework by comparing methods for demographic inference, DFE estimation, and selective sweep detection across several species and scenarios. Our results demonstrate the robustness of demographic inference methods to selection on linked sites, reveal the sensitivity of DFE-inference methods to model assumptions, and show how genomic features, like recombination rate and functional sequence density, influence power to detect selective sweeps. This extension to stdpopsim provides a powerful new resource for the population genetics community to explore the interplay between selection and other evolutionary forces in a reproducible, user-friendly framework.

Journal Article↗
PubMed1993

Selective control of muscle activation with a multipolar nerve cuff electrode.

Acute experiments were performed on adult cats to study selective activation of medial gastrocnemius, soleus, tibialis anterior, and extensor digitorum longus with a cuff electrode. A spiral nerve cuff containing twelve "dot" electrodes was implanted around the sciatic nerve and evoked muscle twitch forces were recorded in six experiments. Spatially isolated "dot" electrodes in four geometries: monopolar, longitudinal tripolar, tripolar with four common anodes, and two parallel tripoles, were combined with transverse field steering current(s) from an anode(s) located 180 degrees around from the cathode(s) to activate different regions of the nerve trunk. To quantify the degree of selectivity, a selectivity index was defined as the ratio of the force in one muscle to the force in all four muscles in response to a particular stimulus. The selectivity index was used to construct recruitment curves for a muscle with the optimal degree of selectivity. Physiological responses were correlated with the anatomical structure of the sciatic nerve by identifying the nerve fascicles innervating the four muscles, and by determining the relative positions of the electrodes and the nerve fascicles. The results indicated that the use of transverse field steering current improved selectivity. We also found that tripoles with individual dot anodes were more selective than tripoles with four common dot anodes. Stimulation with two parallel tripoles was effective in activating selectively fascicles that could not be activated selectively with only a single tripole. The multipolar cuff proved an effective method to control selectively and progressively the force in muscles innervated by fascicles that were well defined at the level of the cuff.

Animals↗