Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many ...noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald’s methods became routine. This work dives into the effects of minute vdW radii shifts on RNA tetranucleotide, B-DNA, and Z-DNA model systems described by commonly used Amber force fields. Using multidimensional replica exchange molecular dynamics (M-REMD), the GACC RNA tetranucleotide demonstrated changes in the structural distribution between the NMR minor and anomalous structure populations based on the O2′ vdW radii scanning. However, no significant change in the NMR Major conformation population was observed. There were minimal changes in the B-DNA structure but there were more substantial improvements in Z-DNA structural descriptions, specifically with the Tumuc1 force field. This occurred with both LJbb vdW radii adjustments and incorporation of the CUFIX nonbonded parameter modifications. Though the limited vdW modifications tested did not provide a universal fix to the challenge of simulating the various known nucleic acid structures, they do provide direction and a greater understanding for future force field development efforts.
Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, ...dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields. The reproducibility and accuracy of the force fields are imperative in order to produce biologically relevant data. The Amber nucleic acid force fields have been used widely since the mid-1980s, and improvement of these force fields has been a community effort with several artifacts revealed, corrected, and reevaluated by various research groups. Here, we focus on the Amber force fields for use with double-stranded DNA and present the assessment of two recently developed force field parameter sets (OL21 and Tumuc1). Extensive MD simulations were performed with six test systems and two different water models. We observe the improvement of OL21 and Tumuc1 compared to previous generations of the Amber DNA force. We did not detect any significant improvement in the performance of Tumuc1 compared to OL21 despite the reparameterization of bonded force field terms in the former; however, we did note discrepancies in Tumuc1 when modeling Z-DNA sequences.
The aim was to compare the outcomes of subdural electrode (SDE) implantations versus stereotactic electroencephalography (SEEG), the 2 predominant methods of intracranial electroencephalography ...(iEEG) performed in difficult-to-localize drug-resistant focal epilepsy.
The Surgical Therapies Commission of the International League Against Epilepsy created an international registry of iEEG patients implanted between 2005 and 2019 with ≥1 year of follow-up. We used propensity score matching to control exposure selection bias and generate comparable cohorts. Study endpoints were: (1) likelihood of resection after iEEG; (2) seizure freedom at last follow-up; and (3) complications (composite of postoperative infection, symptomatic intracranial hemorrhage, or permanent neurological deficit).
Ten study sites from 7 countries and 3 continents contributed 2,012 patients, including 1,468 (73%) eligible for analysis (526 SDE and 942 SEEG), of whom 988 (67%) underwent subsequent resection. Propensity score matching improved covariate balance between exposure groups for all analyses. Propensity-matched patients who underwent SDE had higher odds of subsequent resective surgery (odds ratio OR = 1.4, 95% confidence interval CI 1.05, 1.84) and higher odds of complications (OR = 2.24, 95% CI 1.34, 3.74; unadjusted: 9.6% after SDE vs 3.3% after SEEG). Odds of seizure freedom in propensity-matched resected patients were 1.66 times higher (95% CI 1.21, 2.26) for SEEG compared with SDE (unadjusted: 55% seizure free after SEEG-guided resections vs 41% after SDE).
In comparison to SEEG, SDE evaluations are more likely to lead to brain surgery in patients with drug-resistant epilepsy but have more surgical complications and lower probability of seizure freedom. This comparative-effectiveness study provides the highest feasible evidence level to guide decisions on iEEG. ANN NEUROL 2021;90:927-939.
Purpose Factors that determine renal function after partial nephrectomy are not well- defined, including the impact of cold vs warm ischemia, and the relative importance of modifiable and ...nonmodifiable factors. We studied these determinants in a large cohort of patients with a solitary functioning kidney undergoing partial nephrectomy. Materials and Methods From 1980 to 2009, 660 partial nephrectomies were performed at 4 centers for tumor in a solitary functioning kidney under cold (300) or warm (360) ischemia. Data were collected in institutional review board approved registries and followup averaged 4.5 years. Preoperative and postoperative glomerular filtration rates were estimated via the Chronic Kidney Disease-Epidemiology Study equation. Results At 3 months after partial nephrectomy median glomerular filtration rate decreased by equivalent amounts with cold or warm ischemia (21% vs 22%, respectively, p = 0.7), although median cold ischemic times were much longer (45 vs 22 minutes respectively, p <0.001). On multivariable analyses increasing age, larger tumor size, lower preoperative glomerular filtration rate and longer ischemia time were associated with decreased postoperative glomerular filtration rate (p <0.05). When percentage of parenchyma spared was incorporated into the analysis, this factor and preoperative glomerular filtration rate proved to be the primary determinants of ultimate renal function, and duration of ischemia lost statistical significance. Conclusions This nonrandomized, comparative study suggests that within the relatively strict parameters of conventional practice, ie predominantly short ischemic intervals and liberal use of hypothermia, ischemia time was not an independent predictor of ultimate renal function after partial nephrectomy. Long-term renal function after partial nephrectomy is determined primarily by the quantity and quality of renal parenchyma preserved, although type and duration of ischemia remain the most important modifiable factors, and warrant further study.
Electronic health records and quality of diabetes care Cebul, Randall D; Love, Thomas E; Jain, Anil K ...
New England journal of medicine/The New England journal of medicine,
09/2011, Letnik:
365, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Available studies have shown few quality-related advantages of electronic health records (EHRs) over traditional paper records. We compared achievement of and improvement in quality standards for ...diabetes at practices using EHRs with those at practices using paper records. All practices, including many safety-net primary care practices, belonged to a regional quality collaborative and publicly reported performance.
We used generalized estimating equations to calculate the percentage-point difference between EHR-based and paper-based practices with respect to achievement of composite standards for diabetes care (including four component standards) and outcomes (five standards), after adjusting for covariates and accounting for clustering. In addition to insurance type (Medicare, commercial, Medicaid, or uninsured), patient-level covariates included race or ethnic group (white, black, Hispanic, or other), age, sex, estimated household income, and level of education. Analyses were conducted separately for the overall sample and for safety-net practices.
From July 2009 through June 2010, data were reported for 27,207 adults with diabetes seen at 46 practices; safety-net practices accounted for 38% of patients. After adjustment for covariates, achievement of composite standards for diabetes care was 35.1 percentage points higher at EHR sites than at paper-based sites (P<0.001), and achievement of composite standards for outcomes was 15.2 percentage points higher (P=0.005). EHR sites were associated with higher achievement on eight of nine component standards. Such sites were also associated with greater improvement in care (a difference of 10.2 percentage points in annual improvement, P<0.001) and outcomes (a difference of 4.1 percentage points in annual improvement, P=0.02). Across all insurance types, EHR sites were associated with significantly higher achievement of care and outcome standards and greater improvement in diabetes care. Results confined to safety-net practices were similar.
These findings support the premise that federal policies encouraging the meaningful use of EHRs may improve the quality of care across insurance types.
Temperature rise in Lithium-ion batteries (LIBs) due to solid electrolyte interfaces breakdown, uncontrollable exothermic reactions in electrodes and Joule heating can result in the catastrophic ...failures such as thermal runaway, which is calling for reliable real-time electrode temperature monitoring. Here, we present a customized LIB setup developed for early detection of electrode temperature rise during simulated thermal runaway tests incorporating a modern additive manufacturing-supported resistance temperature detector (RTD). An advanced RTD is embedded in a 3D printed polymeric substrate and placed behind the electrode current collector of CR2032 coin cells that can sustain harsh electrochemical operational environments (acidic electrolyte without Redox, short-circuiting, leakage etc.) without participating in electrochemical reactions. The internal RTD measured an average 5.8 °C higher temperature inside the cells than the external RTD with almost 10 times faster detection ability, prohibiting thermal runaway events without interfering in the LIBs' operation. A temperature prediction model is developed to forecast battery surface temperature rise stemming from measured internal and external RTD temperature signatures.
Our primary aim was to evaluate the effects of 2 family-based obesity management interventions compared with a control group on BMI in low-income adolescents with overweight or obesity.
In this ...randomized clinical trial, 360 urban-residing youth and a parent were randomly assigned to 1 of 2 behaviorally distinct family interventions or an education-only control group. Eligible children were entering the sixth grade with a BMI ≥85th percentile. Interventions were 3 years in length; data were collected annually for 3 years. Effects of the interventions on BMI slope (primary outcome) over 3 years and a set of secondary outcomes were assessed.
Participants were primarily African American (77%), had a family income of <25 000 per year, and obese at enrollment (68%). BMI increased over time in all study groups, with group increases ranging from 0.95 to 1.08. In an intent-to-treat analysis, no significant differences were found in adjusted BMI slopes between either of the family-based interventions and the control group (
= .35). No differences were found between the experimental and control groups on secondary outcomes of diet, physical activity, sleep, perceived stress, or cardiometabolic factors. No evidence of effect modification of the study arms by sex, race and/or ethnicity, household income, baseline levels of child and parent obesity, or exposure to a school fitness program were found.
In this low-income, adolescent population, neither of the family-based interventions improved BMI or health-related secondary outcomes. Future interventions should more fully address poverty and other social issues contributing to childhood obesity.
Protein flexible loop regions were once thought to be simple linkers between other more functional secondary structural elements. However, as it becomes clearer that these loop domains are critical ...players in a plethora of biological processes, accurate conformational sampling of 3D loop structures is vital to the advancement of drug design techniques and the overall growth of knowledge surrounding molecular systems. While experimental techniques provide a wealth of structural information, the resolution of flexible loop domains is sometimes low or entirely absent due to their complex and dynamic nature. This highlights an opportunity for de novo structure prediction using in silico methods with molecular dynamics (MDs). This study evaluates some of the AMBER protein force field's (ffs) ability to accurately model dihydrofolate reductase (DHFR) conformations, a protein complex characterized by specific arrangements and interactions of multiple flexible loops whose conformations are determined by the presence or absence of bound ligands and cofactors. Although the AMBER ffs, including ff19SB, studied well model most protein structures with rich secondary structure, results obtained here suggest the inability to significantly sample the expected DHFR loop-loop conformations - of the six distinct protein-ligand systems simulated, a majority lacked consistent stabilization of experimentally derived metrics definitive the three enzyme conformations. Although under-sampling and the chosen ff parameter combinations could be the cause, given past successes with these MD approaches for many protein systems, this suggests a potential misbalance in available ff parameters required to accurately predict the structure of multiple flexible loop regions present in proteins.
Communicated by Ramaswamy H. Sarma
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic ...inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C
perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.
Severe asthma occurs more often in older adult patients. We hypothesized that the greater risk for severe asthma in older individuals is due to aging, and is independent of asthma duration.
This is a ...cross-sectional study of prospectively collected data from adult participants (N=1130; 454 with severe asthma) enrolled from 2002 - 2011 in the Severe Asthma Research Program.
The association between age and the probability of severe asthma, which was performed by applying a Locally Weighted Scatterplot Smoother, revealed an inflection point at age 45 for risk of severe asthma. The probability of severe asthma increased with each year of life until 45 years and thereafter increased at a much slower rate. Asthma duration also increased the probability of severe asthma but had less effect than aging. After adjustment for most comorbidities of aging and for asthma duration using logistic regression, asthmatics older than 45 maintained the greater probability of severe asthma OR: 2.73 (95 CI: 1.96; 3.81). After 45, the age-related risk of severe asthma continued to increase in men, but not in women.
Overall, the impact of age and asthma duration on risk for asthma severity in men and women is greatest over times of 18-45 years of age; age has a greater effect than asthma duration on risk of severe asthma.
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