TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input.

Anthropometric discriminators of type 2 diabetes among White and Black American adults.

Background: The aim of the present study was to determine the best anthropometric discriminators of type 2 diabetes mellitus (T2DM) among White and Black males and females in a large US sample.

Methods: We used Atherosclerosis Risk in Communities study baseline data (1987-89) from 15 242 participants (1827 with T2DM) aged 45-65 years. Anthropometric measures included a body shape index (ABSI), body adiposity index (BAI), body mass index, waist circumference (WC), waist:  height ratio (WHtR), and waist:  hip ratio (WHR).

Initial Response to Program, Program Participation, and Weight Reduction Among 375 MOVE! Participants, Augusta, Georgia, 2008-2010.

Introduction: Obesity management guidelines specify initial goals for participation and weight reduction for the first 6 months of a weight-reduction intervention, but guidelines do not specify when to assess early response and make adjustments. We aimed to determine whether very early or early weight reduction in the weight-reduction program MOVE! predicted later participation or achievement of weight-reduction goals.

Methods: Using clinical data from 375 MOVE! participants enrolled from July 2008 through May 2010, we examined program participation and weight reduction.

Associations between hematopoietic growth factors and risks of venous thromboembolism, stroke, ischemic heart disease and myelodysplastic syndrome: findings from a large population-based cohort of women with breast cancer.

Purpose: To determine the risk of venous thromboembolism (VTE), stroke, ischemic heart disease, and myelodysplastic syndrome (MDS) in association with the receipt of colony-stimulating factors (CSFs) and/or erythropoiesis-stimulating agents (ESAs) in women with breast cancer.

Methods: We studied 77,233 women with breast cancer aged ≥65 in 1992-2009 from the Surveillance, Epidemiology, and End Results-Medicare linked data with up to 19 years of follow-up.

Results: Incidence of VTE increased from 9 cases in women receiving no chemotherapy and no CSFs/ESAs to 22.

The need for culturally-tailored smartphone applications for weight control.

Background: Approximately 35% of U.S. adults are obese, and this rate is expected to increase by almost 50% by 2030.

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients.

Smartphone Applications for Promoting Healthy Diet and Nutrition: A Literature Review.

Background: Rapid developments in technology have encouraged the use of smartphones in health promotion research and practice. Although many applications (apps) relating to diet and nutrition are available from major smartphone platforms, relatively few have been tested in research studies in order to determine their effectiveness in promoting health.

Methods: In this article, we summarize data on the use of smartphone applications for promoting healthy diet and nutrition based upon bibliographic searches in PubMed and CINAHL with relevant search terms pertaining to diet, nutrition, and weight loss through August 2015.

Comparative Study of Injury Models for Studying Muscle Regeneration in Mice.

Background: A longstanding goal in regenerative medicine is to reconstitute functional tissues or organs after injury or disease. Attention has focused on the identification and relative contribution of tissue specific stem cells to the regeneration process. Relatively little is known about how the physiological process is regulated by other tissue constituents.

Evaluation of an Algorithm to Predict Menstrual-Cycle Phase at the Time of Injury.

Context: Women are 2 to 8 times more likely to sustain an anterior cruciate ligament (ACL) injury than men, and previous studies indicated an increased risk for injury during the preovulatory phase of the menstrual cycle (MC). However, investigations of risk rely on retrospective classification of MC phase, and no tools for this have been validated.

Objective: To evaluate the accuracy of an algorithm for retrospectively classifying MC phase at the time of a mock injury based on MC history and salivary progesterone (P4) concentration.

Nicotine Directly Induces Endoplasmic Reticulum Stress Response in Rat Placental Trophoblast Giant Cells.

Nicotine exposure during pregnancy leads to placental insufficiency impairing both fetal and neonatal development. Previous studies from our laboratory have demonstrated that in rats, nicotine augmented endoplasmic reticulum (ER) stress in association with placental insufficiency; however, the underlying mechanisms remain elusive. Therefore, we sought to investigate the possible direct effect of nicotine on ER stress in Rcho-1 rat placental trophoblast giant (TG) cells during differentiation.

Discrepancies between bilinguals' performance on the Spanish and English versions of the WAIS Digit Span task: Cross-cultural implications.

This study explored within-subjects differences in the performance of 40 bilingual participants on the English and Spanish versions of the Wechsler Adult Intelligence Scale (WAIS) Digit Span task. To test the linguistic hypothesis that individuals would perform worse in Spanish because of its syllabic demand, we compared the number of syllables correctly recalled by each participant for every correct trial. Our analysis of the correct number of syllables remembered per trial showed that participants performed significantly better (i.

Effect of Catheter Dwell Time on Risk of Central Line-Associated Bloodstream Infection in Infants.

Background And Objective: Central venous catheters in the NICU are associated with significant morbidity and mortality because of the risk of central line-associated bloodstream infections (CLABSIs). The purpose of this study was to determine the effect of catheter dwell time on risk of CLABSI.

Methods: Retrospective cohort study of 13,327 infants with 15,567 catheters (93% peripherally inserted central catheters [PICCs], 7% tunneled catheters) and 256,088 catheter days cared for in 141 NICUs.

Adverse effects of perinatal nicotine exposure on reproductive outcomes.

Nicotine exposure during pregnancy through cigarette smoking, nicotine replacement therapies or e-cigarette use continues to be a widespread public health problem, impacting both fetal and postnatal health. Yet, at this time, there remains limited data regarding the safety and efficacy in using these nicotine products during pregnancy. Notably, reports assessing the effect of nicotine exposure on postnatal health outcomes in humans, including reproductive health, are severely lacking.

The synthesis of recombinant membrane proteins in yeast for structural studies.

Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets.

The Willow Hill Community Health Assessment: Assessing the Needs of Children in a Former Slave Community.

The overall purpose of this community needs assessment was to explore the perceptions of health and educational needs among youth residing in a rural Georgia community, document existing assets that could be utilized to meet those needs, and to identify socioeconomic barriers and facilitators in health education. A sequential mixed method design was used. Intercept surveys were conducted followed by individual, key informant interviews and a focus group.

Inferior vena cava occlusion causing syncope during upper extremity exertion treated with iliocaval venous revascularization.

Inferior vena cava (IVC) thrombosis is rare, but its incidence is increased in those with IVC filters or inflammatory bowel disease. Once the IVC is thrombosed, venous return is via collateral channels on the torso and retroperitoneum. Limitations in this collateral venous return can result in symptoms, usually in the lower extremities.

Higher Hepatic miR-29 Expression in Undernourished Male Rats During the Postnatal Period Targets the Long-Term Repression of IGF-1.

A nutritional mismatch in postnatal life of low birth weight offspring increases the risk of developing the metabolic syndrome. Moreover, this is associated with decreased hepatic Igf1 expression, leading to impaired growth and metabolism. Previously, we have demonstrated that the timing of nutritional restoration in perinatal life can differentially program hepatic gene expression.

The effect of chronic shoulder pain on maximal force of shoulder abduction.

Unlabelled: The aim of this study was to determine if chronic shoulder pain had an effect on arm abduction strength and recruitment strategies of the serratus anterior, middle deltoid, and upper trapezius.

Method: The maximal isometric force at 30° arm abduction and the electromyographic activity of the serratus anterior, middle deltoid, and upper trapezius were recorded for 14 subjects with unilateral chronic shoulder pain and 11 healthy subjects.

Results: Relative to the group without pain, the group with chronic shoulder pain showed no significant difference in maximal force production during isometric arm abduction.

High-resolution photoelectron spectra of the pyrimidine-type nucleobases.

High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.

Diagnostic Utility of the International HIV Dementia Scale for HIV-Associated Neurocognitive Impairment and Disorder in South Africa.

Studies in sub-Saharan Africa indicate that most HIV seropositive persons have HIV-associated neurocognitive disorder (HAND). HAND diagnosis is facilitated by specific screening. Seventy participants were recruited from an HIV voluntary counseling and testing clinic in Durban, South Africa.

Remodeling of the plasma membrane in preparation for sperm-egg recognition: roles of acrosomal proteins.

The interaction of sperm with the egg's extracellular matrix, the zona pellucida (ZP) is the first step of the union between male and female gametes. The molecular mechanisms of this process have been studied for the past six decades with the results obtained being both interesting and confusing. In this article, we describe our recent work, which attempts to address two lines of questions from previous studies.

Maternal nicotine exposure leads to impaired disulfide bond formation and augmented endoplasmic reticulum stress in the rat placenta.

Maternal nicotine exposure has been associated with many adverse fetal and placental outcomes. Although underlying mechanisms remain elusive, recent studies have identified that augmented endoplasmic reticulum (ER) stress is linked to placental insufficiency. Moreover, ER function depends on proper disulfide bond formation--a partially oxygen-dependent process mediated by protein disulfide isomerase (PDI) and ER oxidoreductases.

Antenatal exposure to the selective serotonin reuptake inhibitor fluoxetine leads to postnatal metabolic and endocrine changes associated with type 2 diabetes in Wistar rats.

Hypothesis: 10-15% of women take antidepressant medications during pregnancy. A recent clinical study reported that the use of selective serotonin reuptake inhibitor antidepressants during pregnancy is linked with an increased risk of postnatal obesity. While obesity is often associated with fatty liver, dyslipidemia and inflammation, to date, the effects of perinatal exposure to SSRIs on these outcomes are unknown.

Multilevel summation method for electrostatic force evaluation.

The multilevel summation method (MSM) offers an efficient algorithm utilizing convolution for evaluating long-range forces arising in molecular dynamics simulations. Shifting the balance of computation and communication, MSM provides key advantages over the ubiquitous particle–mesh Ewald (PME) method, offering better scaling on parallel computers and permitting more modeling flexibility, with support for periodic systems as does PME but also for semiperiodic and nonperiodic systems. The version of MSM available in the simulation program NAMD is described, and its performance and accuracy are compared with the PME method.