Analysis of Genetic and Non-Genetic Factors Influencing Timing and Time Perception.
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ABSTRACT:
SUBMITTER: Bartholomew AJ
PROVIDER: S-EPMC4671567 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Time is an important dimension of brain function, but little is yet known about the underlying cognitive principles and neurobiological mechanisms. The field of timing and time perception has witnessed tremendous growth and multidisciplinary interest in the recent years with the advent of modern neuroimaging and neurophysiological approaches. In this article, I used a data mining approach to analyze the timing literature published by a select group of researchers (n = 202) during the period 2000-2015 and highlight important reviews as well as empirical articles that meet the criterion of a minimum of 100 citations. The qualifying articles (n = 150) are listed in a table along with key details such as number of citations, names of authors, year and journal of publication as well as a short summary of the findings of each study. The results of such a data-driven approach to literature review not only serve as a useful resource to any researcher interested in timing, but also provides a means to evaluate key papers that have significantly influenced the field and summarize recent progress and popular research trends in the field. Additionally, such analyses provides food for thought about future scientific directions and raises important questions about improving organizational structures to boost open science and progress in the field. I discuss exciting avenues for future research that have the potential to significantly advance our understanding of the neurobiology of timing, and propose the establishment of a new society, the Timing Research Forum, to promote open science and collaborative work within the highly diverse and multidisciplinary community of researchers in the field of timing and time perception.
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Project description:While large datasets of HIV-1 sequences are increasingly being generated, many studies rely on a single gene or fragment of the genome and few comparative studies across genes have been done. We performed genome-based and gene-specific Bayesian phylogenetic analyses to investigate how certain factors impact estimates of the infection dates in an acute HIV-1 infection cohort, RV217. In this cohort, HIV-1 diagnosis corresponded to the first RNA positive test and occurred a median of four days after the last negative test, allowing us to compare timing estimates using BEAST to a narrow window of infection. We analyzed HIV-1 sequences sampled one week, one month and six months after HIV-1 diagnosis in 39 individuals. We found that shared diversity and temporal signal was limited in acute infection, and insufficient to allow timing inferences in the shortest HIV-1 genes, thus dated phylogenies were primarily analyzed for env, gag, pol and near full-length genomes. There was no one best-fitting model across participants and genes, though relaxed molecular clocks (73% of best-fitting models) and the Bayesian skyline (49%) tended to be favored. For infections with single founders, the infection date was estimated to be around one week pre-diagnosis for env (IQR: 3-9 days) and gag (IQR: 5-9 days), whilst the genome placed it at a median of 10 days (IQR: 4-19). Multiply-founded infections proved problematic to date. Our ability to compare timing inferences to precise estimates of HIV-1 infection (within a week) highlights that molecular dating methods can be applied to within-host datasets from early infection. Nonetheless, our results also suggest caution when using uniform clock and population models or short genes with limited information content.
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Project description:The mainstay of acute myeloid leukemia chemotherapy is the nucleoside analog cytarabine (ara-C). Numerous studies suggest that the intracellular concentrations of the ara-C active metabolite, ara-CTP, vary widely among patients and, in turn, are associated with variability in clinical response to acute myeloid leukemia treatment. Thus, genetic variation in key genes in the ara-C metabolic pathway--specifically, deoxycytidine kinase (a rate-limiting activating enzyme), 5 nucleotidase, cytidine deaminase and deoxycytidylate deaminase (all three are inactivating enzymes), human equilibrative nucleoside transporter (ara-C uptake transporter) and ribonucleotide reductase (RRM1 and RRM2--enzymes regulating intracellular deoxycytidine triphosphate pools)--form the molecular basis of the interpatient variability observed in intracellular ara-CTP concentrations and response to ara-C. Understanding genetic variants in the key candidate genes involved in the metabolic activation of ara-C, as well as the pharmacodynamic targets of ara-C, will provide an opportunity to identify patients at an increased risk of adverse reactions or decreased likelihood of response, based upon their genetic profile, which in future could help in dose optimization to reduce drug toxicity without compromising efficacy. The pharmacogenetic studies on ara-C would also be equally applicable to other nucleoside analogs, such as gemcitabine, decitabine, clofarabine and so on, which are metabolized by the same pathway.
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Project description:ObjectivesThe primary objective of this study is to identify the biographic, audiologic, and electrode position factors that influence speech perception performance in adult cochlear implant (CI) recipients implanted with a device from a single manufacturer. The secondary objective is to investigate the independent association of the type of electrode (precurved or straight) with speech perception.DesignIn a cross-sectional study design, speech perception measures and ultrahigh-resolution computed tomography scans were performed in 129 experienced CI recipients with a postlingual onset of hearing loss. Data were collected between December 2016 and January 2018 in the Radboud University Medical Center, Nijmegen, the Netherlands. The participants received either a precurved electrode (N = 85) or a straight electrode (N = 44), all from the same manufacturer. The biographic variables evaluated were age at implantation, level of education, and years of hearing loss. The audiometric factors explored were preoperative and postoperative pure-tone average residual hearing and preoperative speech perception score. The electrode position factors analyzed, as measured from images obtained with the ultrahigh-resolution computed tomography scan, were the scalar location, angular insertion depth of the basal and apical electrode contacts, and the wrapping factor (i.e., electrode-to-modiolus distance), as well as the type of electrode used. These 11 variables were tested for their effect on three speech perception outcomes: consonant-vowel-consonant words in quiet tests at 50 dB SPL (CVC50) and 65 dB SPL (CVC65), and the digits-in-noise test.ResultsA lower age at implantation was correlated with a higher CVC50 phoneme score in the straight electrode group. Other biographic variables did not correlate with speech perception. Furthermore, participants implanted with a precurved electrode and who had poor preoperative hearing thresholds performed better in all speech perception outcomes than the participants implanted with a straight electrode and relatively better preoperative hearing thresholds. After correcting for biographic factors, audiometric variables, and scalar location, we showed that the precurved electrode led to an 11.8 percentage points (95% confidence interval: 1.4-20.4%; p = 0.03) higher perception score for the CVC50 phonemes compared with the straight electrode. Furthermore, contrary to our initial expectations, the preservation of residual hearing with the straight electrode was poor, as the median preoperative and the postoperative residual hearing thresholds for the straight electrode were 88 and 122 dB, respectively.ConclusionsCochlear implantation with a precurved electrode results in a significantly higher speech perception outcome, independent of biographic factors, audiometric factors, and scalar location.
| S-EPMC8221708 | biostudies-literature
Project description:Time is a fundamental dimension of our behavior and enables us to guide our actions and to experience time such as predicting collisions or listening to music. In this study, we investigate the regulation and covariation of motor timing and time perception functions in left- and right-handers who are characterized by distinct brain processing mechanisms for cognitive-motor control. To this purpose, we use a combination of tasks that assess the timed responses during movements and the perception of time intervals. The results showed a positive association across left- and right-handers between movement-driven timing and perceived interval duration when adopting a preferred tempo, suggesting cross-domain coupling between both abilities when an intrinsic timescale is present. Handedness guided motor timing during externally-driven conditions that required cognitive intervention, which specifies the relevance of action expertise for the performance of timed-based motor activities. Overall, our results reveal that individual variation across domain-general and domain-specific levels of organization plays a steering role in how one predicts, perceives and experiences time, which accordingly impacts on cognition and behavior.
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Project description:BackgroundDespite identical genotypes and seemingly uniform environments, stochastic gene expression and other dynamic intracellular processes can produce considerable phenotypic diversity within clonal microbes. One trait that provides a good model to explore the molecular basis of stochastic variation is the timing of host lysis by bacteriophage (phage).ResultsIndividual lysis events of thermally-inducible λ lysogens were observed using a temperature-controlled perfusion chamber mounted on an inverted microscope. Both mean lysis time (MLT) and its associated standard deviation (SD) were estimated. Using the SD as a measure of lysis time stochasticity, we showed that lysogenic cells in controlled environments varied widely in lysis times, and that the level of lysis time stochasticity depended on allelic variation in the holin sequence, late promoter (pR') activity, and host growth rate. In general, the MLT was positively correlated with the SD. Both lower pR' activities and lower host growth rates resulted in larger SDs. Results from premature lysis, induced by adding KCN at different time points after lysogen induction, showed a negative correlation between the timing of KCN addition and lysis time stochasticity.ConclusionsTaken together with results published by others, we conclude that a large fraction of λ lysis time stochasticity is the result of random events following the expression and diffusion of the holin protein. Consequently, factors influencing the timing of reaching critical holin concentrations in the cell membrane, such as holin production rate, strongly influence the mean lysis time and the lysis time stochasticity.
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Project description:ObjectivesDiagnosing biliary atresia (BA) quickly is critical, because earlier treatment correlates with delayed or reduced need for liver transplantation. However, diagnosing BA quickly is also difficult, with infants usually treated after 60 days of life. In this study, we aim to accelerate BA diagnosis and treatment, by better understanding factors influencing the diagnostic timeline.MethodsInfants born between 2007 and 2014 and diagnosed with BA at our institution were included (n = 65). Two periods were examined retrospectively: P1, the time from birth to specialist referral, and P2, the time from specialist referral to treatment. How sociodemographic factors associate with P1 and P2 were analyzed with Kaplan-Meier curves and Cox proportional hazard models. In addition, to better characterize P2, laboratory results and early tissue histology were studied.ResultsP1 associated with race/ethnicity, with shorter times in non-Hispanic white infants compared to non-Hispanic black and Hispanic infants (P = 0.007 and P = 0.004, respectively). P2 associated with referral age, with shorter times in infants referred after 30, 45, or 60 days of life (P < 0.001, P < 0.001, and P = 0.001, respectively). One potential reason for longer P2 in infants referred ≤30 days is that aminotransferase levels were normal or near-normal. However, despite reassuring laboratory values, tissue histology in early cases showed key features of BA.ConclusionsOur findings suggest 2 opportunities to accelerate BA diagnosis and treatment. First, to achieve prompt referrals for all races/ethnicities, universal screening strategies should be considered. Second, to ensure efficient evaluations independent of age, algorithms designed to detect early features of BA can be developed.
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Project description:Despite the potential for efavirenz (EFV) to be an effective alternative antiretroviral agent, its sources of wide inter- and intra-individual pharmacokinetic (PK) variability are not well-characterized in children. We investigated the effects of genetic and non-genetic factors, including demographic, treatment duration, baseline clinical, and biochemical characteristics, on the PKs of EFV through population-PK modeling. Antiretroviral therapy (ART) naïve HIV infected children, 3-16 years (n = 100), were enrolled in Ethiopia and received EFV-based combination ART. EFV concentrations after the first dose and at steady-state collected over a span of 1 year were modeled using population-based methods. A one-compartment model with first-order absorption kinetics described the observed EFV data adequately. The CYP2B6*6 and ABCB1c.4036A>G genotypes were identified as major factors influencing EFV clearance. The typical estimates of oral clearance, volume of distribution, and absorption rate constant for typical 22 kg children with CYP2B6 *1/*1 and ABCB1c.4036G/G genotypes were 4.3 L/h, 124 L, and 0.776/h, respectively. Clearance was reduced by 28% and 72% in CYP2B6*1/*6 and CYP2B6*6/*6 genotypes, respectively. Compared to week 1, clearance was higher from weeks 8 and 12 in CYP2B6*1/*6 and CYP2B6*1/*1 genotypes, respectively. Simulations indicated that EFV 12-h concentrations were comparable across weight bands, but more than 80% of subjects with CYP2B6*6/*6 had EFV concentrations greater than 4 μg/mL. EFV PK variability among children is partly explained by body weight, treatment duration, CYP2B6*6, and ABCB1 rs3842 genotypes. Therefore, in addition to body weight, pediatric dosing of EFV should consider pharmacogenetic variability, duration of therapy, and individual treatment outcomes.
| S-EPMC10272302 | biostudies-literature
Project description:BackgroundPatients at higher than average risk of heritable cancer may process risk information differently than the general population. However, little is known about clinical, demographic, or psychosocial predictors that may impact risk perception in these groups. The objective of this study was to characterize factors associated with perceived risk of developing cancer in groups at high risk for cancer based on genetics or family history.MethodsWe searched Ovid MEDLINE, Ovid Embase, Ovid PsycInfo, and Scopus from inception through April 2009 for English-language, original investigations in humans using core concepts of "risk" and "cancer." We abstracted key information and then further restricted articles dealing with perceived risk of developing cancer due to inherited risk.ResultsOf 1028 titles identified, 53 articles met our criteria. Most (92%) used an observational design and focused on women (70%) with a family history of or contemplating genetic testing for breast cancer. Of the 53 studies, 36 focused on patients who had not had genetic testing for cancer risk, 17 included studies of patients who had undergone genetic testing for cancer risk. Family history of cancer, previous prophylactic tests and treatments, and younger age were associated with cancer risk perception. In addition, beliefs about the preventability and severity of cancer, personality factors such as "monitoring" personality, the ability to process numerical information, as well as distress/worry also were associated with cancer risk perception. Few studies addressed non-breast cancer or risk perception in specific demographic groups (e.g. elderly or minority groups) and few employed theory-driven analytic strategies to decipher interrelationships of factors.ConclusionsSeveral factors influence cancer risk perception in patients at elevated risk for cancer. The science of characterizing and improving risk perception in cancer for high risk groups, although evolving, is still relatively undeveloped in several key topic areas including cancers other than breast and in specific populations. Future rigorous risk perception research using experimental designs and focused on cancers other than breast would advance the field.
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Project description:In formulation development, amorphous solid dispersions (ASD) are considered to improve the bioavailability of poorly water-soluble active pharmaceutical ingredients (APIs). However, the crystallization of APIs often limits long-term stability and thus the shelf life of ASDs. It has already been shown earlier that the long-term stability of ASDs strongly depends on the storage conditions (relative humidity, temperature), the manufacturing methods, and the resulting particle sizes. In this work, ASDs composed of the model APIs Griseofulvin (GRI) or Itraconazole (ITR) and the polymers poly (vinylpyrrolidone-co-vinyl acetate) (PVPVA) or Soluplus® were manufactured via spray drying and hot-melt extrusion. Each API/polymer combination was manufactured using the two manufacturing methods with at least two different API loads and two particle-size distributions. It was a priori known that these ASDs were metastable and would crystallize over time, even in the dry stage. The amount of water absorbed by the ASD from humid air (40 °C/75% relative humidity), the solubility of the API in the ASD at humid conditions, and the resulting glass-transition temperature were predicted using the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) and the Gordon-Taylor approach, respectively. The onset of crystallization was determined via periodic powder X-ray diffraction (PXRD) measurements. It was shown that simple heuristics such as "larger particles always crystallize later than smaller particles" are correct within one manufacturing method but cannot be transferred from one manufacturing method to another. Moreover, amorphous phase separation in the ASDs was shown to also influence their crystallization kinetics. Counterintuitively, phase separation accelerated the crystallization time, which could be explained by the glass-transition temperatures of the evolving phases.
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