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Evolutionary feedback mediated through population density, illustrated with viruses in chemostats.

A cornerstone of evolutionary ecology is that population density affects adaptation: r and K selection is the obvious example. The reverse is also appreciated: adaptation impacts population density. Yet, empirically demonstrating a direct connection between population density and adaptation is challenging. Here, we address both evolution and ecology of population density in models of viral (bacteriophage) chemostats. Chemostats supply nutrients for host cell growth, and the hosts are prey for viral reproduction. Two different chemostat designs have profoundly different consequences for viral evolution. If host and virus are confined to the same chamber, as in a predator-prey system, viral regulation of hosts feeds back to maintain low viral density (measured as infections per cell). Viral adaptation impacts host density but has a small effect on equilibrium viral density. More interesting are chemostats that supply the viral population with hosts from a virus-free refuge. Here, a type of evolutionary succession operates: adaptation at low viral density leads to higher density, but high density then favors competitive ability. Experiments support these models with both phenotypic and molecular data. Parallels to these designs exist in many natural systems, so these experimental systems may yield insights to the evolution and regulation of natural populations.

Adaptation, Biological↗

Rheology measurement for on-line monitoring of filaments proliferation in activated sludge tanks.

Rheological behaviour of filamentous sludges originated from activated sludge reactors was studied. Filamentous bulking was detected via a hysteresis loop developed from rheograms resulting from increasing-decreasing shear rates. The rheological parameter reduced hysteresis area (rHa), corresponding to the loop area developed by rheograms was used to quantify filamentous bulking. Application to the evolution of several bulkings was carried out and it was shown that filaments proliferation and disappearance were correlated with, respectively, the increasing and decreasing of the value of the parameter rHa. In parallel with rheological measurement, parameters used for the study of sludge quality, such as sludge volume index (SVI) and settling initial flow (F0), were determined for comparison during the evolution of several bulkings. It was shown that rHa was more sensitive to the appearance of filamentous bulking than SVI and F0, therefore it was concluded that detection of filamentous bulking can be shown from rHa.

Biofilms↗

Evolution of tumor subclones and T-cell dynamics underlie variable ibrutinib responses in Waldenström macroglobulinemia.

To elucidate the molecular basis underlying differential responses and resistance to ibrutinib in Waldenström macroglobulinemia (WM), we conducted a prospective phase 2 trial of ibrutinib monotherapy in treatment-naïve patients. A total of 74 sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell multiomics. BM cells were segregated primarily into B-cell/plasma cell and T-cell compartments. Longitudinal clonal tracking of malignant B cells/plasma cells identified 3 distinct evolutionary patterns: evolution (early clone contraction with late clone expansion and increasing genomic complexity), devolution (early clone expansion with late clone contraction and genomic simplification), and no evolution (stable clonal architecture). The evolution pattern was strongly associated with disease progression, whereas devolution correlated with durable clinical response. Transcriptomic profiling of resistant clones enabled development and validation of the Waldenström ibrutinib prediction (WIP) score, which predicted treatment response at baseline. Within the WIP signature, LYN emerged as a key regulator; LYN knockdown or inhibition significantly increased WM cell sensitivity to ibrutinib, suggesting a rational combination strategy. In parallel, GZMB+ CD8+ effector-memory T cells expanded after treatment in patients with progressive disease and coexisted with tumor evolution. These cells exhibited persistently impaired cytotoxic programs (eg, GNLY), a dedifferentiated memory-like state, elevated PDCD1 expression, and reduced T-cell receptor diversity. Together, this study provides, to our knowledge, the first single-cell framework of tumor clonal evolution and T-cell dysfunction under ibrutinib in WM, introduces the WIP score as a predictive biomarker for treatment response, and identifies actionable tumor-intrinsic and immune mechanisms driving resistance. This trial was registered at www.ClinicalTrials.gov as NCT02604511.

Aged↗

Homoplasy and adaptation in the atelid postcranium.

Homoplasy is a ubiquitous phenomenon in phylogenetic investigations, but it is rarely investigated on its own. As a case study in the pattern and basis of homoplasy in primates, the atelid postcranium is discussed here. Characters available from Ford's ([1986] in Erwin J, Swindler DR, eds: Comparative Primate Biology I: Systematics, Evolution, and Anatomy (New York: Alan R. Liss), p 73-135; [1994] in Fleagle JG, Kay RF, eds: Anthropoid Origins (New York: Plenum Press), p 595-674) analyses of New World monkeys are mapped onto alternative phylogenetic trees for the family Atelidae to contrast patterns of character evolution and to develop explanatory hypotheses for differences in the trees. In an unrooted phylogenetic network, pitheciines do not group together because those pitheciines that routinely adopt hind limb suspensory postures (Chiropotes, Cacajao) share traits with atelines. Ford's (1986) work on phylogeny has shown that these traits are homoplastic and also identified potential synapomorphies of a clade comprised of modern pitheciins and atelines. However, following that work, congruence between studies of craniodental and molecular data suggested a still broader definition of atelids (including Callicebus and Cebupithecia), and in this case only one trait may define atelids, and several traits arise in parallel. The homoplastic characters in this phylogeny suggest that the phylogenetic signal in this set of postcranial data is overwhelmed by parallel adaptations to the use of climbing behaviors in all of Ford's atelids and suspensory postures in a more restricted set of taxa. These parallelisms probably indicate a bias of selective pressures in the South American environment, especially given the frequent, independent evolution of suspensory mammals there. This highlights the fact that homoplasy can be a dominant source of similarity in data partitions strongly influenced by a particular behavioral regime, in this case positional behavior.

Adaptation, Physiological↗

[Social institutions and tempering of affects as "contraints" of social change. Norbert Elias' theory on the civilization theory in light of the biologic system theory of evolution].

This study is to be regarded as a contribution to interdisciplinary research and represents an attempt to clarify the question of whether and to what extent concepts that have been developed in the field of theoretical biology and which have a high degree of importance here can also be applied to sociological phenomena. In particular it is intended to examine the question of whether the civilizing process can be adequately treated using the evolutionary concept of "Constraints". This term, which has only recently been introduced into the discussion by PERE ALBERCH as an evolutionary factor, comprises all of the internal factors which influence the further course of the evolution of a system by ruling out certain possibilities, thus showing a limiting effect. Although "Constraints" go beyond the scope of Darwinian teachings about selection by the environment, they are increasingly accepted today as evolution factors by well-known exponents of Darwinian theory (cf. MAYNARD-SMITH 1985). The increase in popularity of "constraints" is also an expression of the rediscovery of a phenomenon which was originally expressed by RUPERT RIEDL and was introduced by him into German literature in the seventies. In the clarification of this question, special reference is made to the "theory of the civilizing process" by NORBERT ELIAS, since here a highly respected scholar has presented an important sociological theory. Moreover, there is such good scientific access to ELIAS because this author exemplifies his theses in historical terms and thus to a certain extent makes his explanations verifiable in scientific terms. In the treatment of this topic, the central terms and theses of ELIAS will be presented from the considerable scope of his work, and then illustrated with the help of several selected historical case studies. Furthermore, reference will be made at the relevant points to parallels and analogies which the works of ELIAS have to other, predominantly system-theoretical concepts of evolution and which cause it to appear compatible to the latter.

Civilization↗

Mitochondrial genome variation and the origin of modern humans.

The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.

Africa↗

Evolution of dietary antioxidants.

Oxygen is vital for most organisms but, paradoxically, damages key biological sites. Oxygenic threat is met by antioxidants that evolved in parallel with our oxygenic atmosphere. Plants employ antioxidants to defend their structures against reactive oxygen species (ROS; oxidants) produced during photosynthesis. The human body is exposed to these same oxidants, and we have also evolved an effective antioxidant system. However, this is not infallible. ROS breach defences, oxidative damage ensues, accumulates with age, and causes a variety of pathological changes. Plant-based, antioxidant-rich foods traditionally formed the major part of the human diet, and plant-based dietary antioxidants are hypothesized to have an important role in maintaining human health. This hypothesis is logical in evolutionary terms, especially when we consider the relatively hypoxic environment in which humans may have evolved. In this paper, the human diet is discussed briefly in terms of its evolutionary development, different strategies of antioxidant defence are outlined, and evolution of dietary antioxidants is discussed from the perspectives of plant need and our current dietary requirements. Finally, possibilities in regard to dietary antioxidants, evolution, and human health are presented, and an evolutionary cost-benefit analysis is presented in relation to why we lost the ability to make ascorbic acid (vitamin C) although we retained an absolute requirement for it.

Animals↗

Red Light-Dependent CO(2) Uptake and Oxygen Evolution in Guard Cell Protoplasts of Vicia faba L.: Evidence for Photosynthetic CO(2) Fixation.

Suspensions of dark-adapted guard cell protoplasts of Vicia faba L. alkalinized their medium in response to irradiation with red light. The alkalinization peaked within about 50 minutes and reached steady state shortly thereafter. Simultaneous measurements of O(2) concentrations and medium pH showed that oxygen evolved in parallel with the red light-induced alkalinization. When the protoplasts were returned to darkness, they acidified their medium and consumed oxygen. Both oxygen evolution and medium alkalinization were inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). In photosynthetically competent preparations, light-dependent medium alkalinization is diagnostic for photosynthetic carbon fixation, indicating that guard cell chloroplasts have that capacity. The striking contrast between the responses of guard cell protoplasts to red light, which induces alkalinization, and that to blue light, which activates proton extrusion, suggests that proton pumping and photosynthesis in guard cells are regulated by light quality.

Journal Article↗

[Triple-blind clinical trial with placebo control to evaluate the efficacy of a heparin of low molecular weight (bemiparin) for treating slow-responding ulcers in diabetic foot in primary care].

OBJECTIVES: To establish the degree of efficacy of bemiparin treatment over 3 months in the improvement of slow-responding ulcers in diabetic foot. Also, to evaluate the safety of bemiparin and quality of life and to compare the evolution of retinopathy and nephropathy against placebo. DESIGN: Stage III clinical trial to evaluate efficacy and safety in a new indication of a medicine already on the market, parallel in two branches, randomised, triple-blind, and controlled with placebo. SETTING: Health care centres in Mallorca, Spain. PARTICIPANTS: 42 patients per branch, over 18, with type-1 or 2 DM of over 3 years evolution, and one or more first or second-degree ulcers on the Wagner scale, distal to the knee, that did not heal in three months of health care. Randomised allocation in blocks of four.Interventions. The experimental drug was bemiparin (heparin of low molecular weight), injected subcutaneously at 3500 IU/day for the first 10 days and 2500 IU/day up to 90 days. As control, physiological serum was injected sub-cutaneously in a similar volume for masking. MAIN MEASUREMENTS: An "effect"was defined as a reduction of at least 50% in its surface area and/or a favourable evolution in status to a degree between the control at the start of treatment and at three months. Other measurements included proteinuria, retinography and quality of life (SF-36). Analysis of efficacy through principle of intention to treat.

Adult↗

The heterogeneous course of schizophrenia.

Findings on the course and outcome of schizophrenia, the limitations of Kraepelin's opinion, and data supporting a continuum hypothesis of endogenous psychoses are presented. The European long-term investigations, the Zürich, Lausanne and Bonn studies are consistent with the view that diagnoses must be made independently of outcome; nearly a quarter show full psychopathological and 56% a social remission. Several factors are relevant to the long-term course and outcome. In the Bonn Study, 43% of subjects showed long-term remission, with only a mild deficit state ('pure defect') consisting of dynamic and cognitive basic symptoms, and 35% revealed characteristic schizophrenic residues. Eighty-seven per cent were living at home permanently at the most recent follow-up; 56% were socially recovered, i.e., fully employed, yet only 38.6% were at their previous occupational level. Twelve course types could be differentiated and were ranked according to social remission rate. The results led to a revision of classical descriptions of an incessant progression of schizophrenia. The outcome is largely independent of the duration of illness; there is no increasing deterioration in the later decades of the disease, often showing a trend toward improvement (the 'second, positive bend'), even 20-40 years after onset. According to Zubin, the results of the European long-term studies and the Vermont Study have revolutionized our knowledge about schizophrenia and emancipated it from the yoke of inevitable chronicity. The findings of the Bonn Study, the first systematic study of prodromes, and of the prospective basic symptom-oriented study on the early diagnosis of schizophrenia led, in parallel with the gradual development of the basic symptom concept, to a new view of the evolution of schizophrenia.

Disease Progression↗

Contemporary psychoanalysis and hypnosis.

The relationship between psychoanalysis and hypnosis is presented in three parts: past, present, and future. First, the parallel developments in psychoanalysis and hypnosis over the past 100 years are summarized. Four major theoretical evolutions in psychoanalysis (drive theory, ego psychology, object relations theory, and self psychology) are described, with their corresponding influences on the practice of psychoanalytically informed hypnosis. Second, four contemporary movements in psychoanalysis are enumerated (postmodernism, spontaneity, pluralism, and integrationism), with commentary on these movements' likely impact on the current and future practice of hypnosis. Finally, the impact of shrinking mental health dollars on the practice of psychoanalysis and psychoanalytically informed treatments is presented. Hypnosis is offered as uniquely positioned, with its history of multitheoretically informed brief interventions, grounded in research and clinical practice, to provide psychoanalysis with a life raft into the next 100 years of practice.

Humans↗

Free radicals in aging: causal complexity and its biomedical implications.

Superoxide generated adventitiously by the mitochondrial respiratory chain can give rise to much more reactive radicals, resulting in random oxidation of all classes of macromolecules. Harman's 1956 suggestion that this process might drive aging has been a leading strand of biogerontological thinking since the discovery of superoxide dismutase. However, it has become apparent that the many downstream consequences of free radical damage can also be caused by processes not involving oxidation. Moreover, free radicals have been put to use by evolution to such an extent that their wholesale elimination would certainly be fatal. This multiplicity of parallel pathways and side-effects illustrates why attempts to postpone aging by "cleaning up" metabolism will surely fail for the foreseeable future: we simply understand metabolism too poorly. This has led me to pursue the alternative, "repair and maintenance" approach that sidesteps our ignorance of metabolism and may be feasible relatively soon.

Aging↗

Self-limited autoimmune disease related to transient donor B cell activation in mice neonatally injected with semi-allogeneic F1 cells.

BALB/c mice injected at birth with 10(8) semi-allogeneic (C57BL/6 x BALB.IgHb)F1 spleen cells develop a lupus-like syndrome in which autoantibodies bear exclusively the donor allotype. We have analyzed the evolution of donor B cell chimerism and the autoimmune manifestations during the first year of life in these mice. Anti-DNA, -histone, and -cardiolipin IgG antibodies as well as circulating immune complexes appeared in the second week of life, reached the highest values around the sixth week, and then progressively dropped to normal values after the sixth month in most mice. The kinetics of the evolution of the autoimmune manifestations, as well as the kinetics of serum donor Ig allotype, were parallel to the kinetics of donor B cell chimerism, which was particularly prominent in the spleens in early weeks of life, and progressively decreased after remission of the autoimmune syndrome. Membrane-proliferative glomerulonephritis, which was followed as the more representative histological abnormality in this model, was particularly evident after 10 weeks of life, but disappeared by the end of the follow-up. Interestingly, when mice with a self-limited disease were re-injected with 10(8) F1 spleen cells i.v., a flare in the serological manifestations was observed. In these re-injected mice a predominance of anti-DNA, IgG1 antibodies bearing exclusively the donor allotype was also observed, as in the early weeks of life.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Patterns in randomly evolving networks: idiotypic networks.

We present a model for the evolution of networks of occupied sites on undirected regular graphs. At every iteration step in a parallel update, I randomly chosen empty sites are occupied and occupied sites having occupied neighbor degree outside of a given interval (t(l),t(u)) are set empty. Depending on the influx I and the values of both lower threshold and upper threshold of the occupied neighbor degree, different kinds of behavior can be observed. In certain regimes stable long-living patterns appear. We distinguish two types of patterns: static patterns arising on graphs with low connectivity and dynamic patterns found on high connectivity graphs. Increasing I patterns become unstable and transitions between almost stable patterns, interrupted by disordered phases, occur. For still larger I the lifetime of occupied sites becomes very small and network structures are dominated by randomness. We develop methods to analyze the nature and dynamics of these network patterns, give a statistical description of defects and fluctuations around them, and elucidate the transitions between different patterns. Results and methods presented can be applied to a variety of problems in different fields and a broad class of graphs. Aiming chiefly at the modeling of functional networks of interacting antibodies and B cells of the immune system (idiotypic networks), we focus on a class of graphs constructed by bit chains. The biological relevance of the patterns and possible operational modes of idiotypic networks are discussed.

Journal Article↗

Vitamin D and the epidemiology of prostate cancer.

Mortality rates from prostate cancer are significantly higher among African Americans than Caucasian Americans and are inversely related to the availability of ultraviolet (UV) radiation. These findings support the hypothesis, originally proposed in 1990, that prostate cancer may be caused by vitamin D deficiency. In 1992, specific receptors for 1,25-dihydroxyvitamin D [1,25(OH)2D] were demonstrated in human prostate cells. We and others have shown that 1,25(OH)2D exerts prodifferentiating, antiproliferative, and antimetastatic effects on these cells. In 1998 we demonstrated that normal prostate cells express 1alpha-hydroxylase and synthesize their own 1,25(OH)2D. Thus, 1,25(OH)2D is an autocrine hormone in the prostate. The consensus emerging from analytic epidemiologic studies is that low levels of UV radiation/vitamin D are indeed associated with an increased risk of prostate cancer in individual men. The evolution of our understanding of the role of vitamin D in the epidemiology of prostate cancer parallels our understanding of the role of vitamin D in the epidemiology of rickets. In both diseases, ecologic observations about UV radiation preceded experimental observations and were subsequently validated by them.

Animals↗

Fitting discrete probability distributions to evolutionary events.

The assumptions underlying the use of the Poisson distribution are essentially that the probability of an event is small but nearly identical for all occurrences and that the occurrence of an event does not alter the probability of recurrence of such events. These assumptions do not seem to be met for evolutionary events since (i) the probability of fixing nucleotide codon substitutions is not equal for all substitutions at a codon, and probably varies for the same substitution in different lineages; (ii) the probability of fixing codon substitutions varies among positions of a cistron; and (iii) the fixation of a nucleotide codon substitution at one position in a cistron modifies, and may even promote, the fixation of a codon substitution elsewhere along the cistron. Natural selection presumably is the causative factor that acts to modify the probability of a nucleotide codon substitution's being fixed in a population. The use of the negative binomial distribution is consistent with the evidence that selective pressure on amino acid or nucleotide codon positions varies both among codon positions of a cistron and at a particular position during evolutionary time. If the number of fixations of nucleotide codon substitutions per position of cistrons encoding cytochromes c are phyletically inferred (phylogeny based on a paleontological record) rather than phenetically inferred (based on paired comparisons of extant species' differences in the absence of a phylogeny) the distribution of these fixation data cannot be described adequately by a single Poisson distribution. The fit of these same data to a negative binomial distribution is very satisfactory. It has been argued that the fit of phenetically inferred fixation data, which do not take account of parallel or reverse fixations, to the Poisson distribution was supportive evidence for the hypothesis that protein evolution results from the fixation of selectively neutral codon substitutions. This argument now appears to be undercut by the evidence that data on nucleotide codon fixation are more probably distributed according to the negative binomial distribution. The fact that fixation data can be described by a particular discrete probability distribution does not of itself provide insight into the mechanisms of the evolutionary process. However, the facts-(i) that the assumptions underlying the use of the negative binomial distribution adequately deal with the varying probability of fixing amino acid or nucleotide codon substitutions at and among the positions of a cistron and (ii) that the negative binomial distribution provides an excellent fit for the phyletically inferred fixation data-suggest that the negative binomial is a very appropriate discrete probability distribution for describing evolutionary events. Amino acids or their nucleotide codon substitutions may be fixed at a position of a cistron as though selectively neutral relative to the codon being replaced, even though the codon position will not be selectively neutral, since many amino acids cannot function there. The negative binomial distribution treats this situation well whereas a single Poisson distribution could only be satisfactory if all codon positions that could vary were selectively neutral.

Amino Acid Sequence↗

Computer-aided sleep staging in clinical environment.

In the present paper we will comment on how we have been implementing computer-aided sleep staging (CAS) in the Department of Psychiatry, Erasmus Hospital (Free University of Brussels). Major features of our CAS include real-time stage estimation, full report and hypnogram available in the morning, and evolution of state variables throughout the night (e.g. electroencephalographic spectral characteristics, eye movement density, myographic activity). Parallel, we report an extensive validation study of this system on 50 subjects divided in two groups of 25 patients with psychiatric diseases, and 25 normal subjects.

Adult↗

Kidney donor profile in Spain: risks factors and characteristics of the organs rejected for transplantation.

During recent years organ donation in Spain has increased by 100%, with important changes seen in the donor profile. Mean age has increased by more than 10 years, being nowadays more than 33% of our donors over 60 years. Ten years ago road traffic trauma was the main cause of death, while now most of our donors die due to stroke and only 21% die in a traffic accident. This changes lead to an increase in the number of kidneys discarded for transplantation every year. Among the 2517 kidneys retrieved during 2001, 567 were discarded, mainly due to different glomerular, interstitial or vascular pathologic damage. The older is the donor the higher is the percentage of kidneys discarded. It has to be underlined that an increased number of livers from donors, whose kidneys could not be used, are being grafted (141 in 2001 over 281 donors from whom no kidney could be grafted and over a total number of 1335 donors). Only 5% of kidneys were discarded due to technical problems. An important number of kidneys were discarded due to malignancy suspicion or diagnosis (12.3%). Organ donation has improved but kidney transplantation did not in parallel, due to the increasing number of kidneys discarded for transplantation in close relation with the evolution of donor's characteristics. Organ donation rate is around 33 donors per million population while efficient organ donation rate is around 30 donors per million. Only from 67% of donors both kidneys can be grafted and from 20% of donors no kidney can be used. These data will not change our policy, at least by the moment, we will continue to evaluate every potential brain death donor with the aim of studying if organs can be used. It is true that in 50% of cases over 70 years no organ can be used after retrieval and microscopic exam, but in the other 50% we can proceed.

Age Factors↗