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Background: Drains may be placed during robotic retromuscular ventral hernia repair (rVHR) to decrease wound morbidity, but their use is controversial. We aimed to assess the impact of retromuscular drain placement on wound morbidity after robotic rVHR., Methods: Patients with and without drains after robotic rVHR in the Abdominal Core Health Quality Collaborative (ACHQC) registry were compared using a propensity score-matched analysis. Outcomes included surgical site occurrences (SSO), surgical site infections (SSI), and surgical site occurrences requiring procedural interventions (SSOPI) at 30 days., Results: Propensity score matching compared 580 patients with drains to 580 without drains. The groups were well matched with respect to hernia width (drain: 8.0 cm [IQR 6.0; 10.0] vs no drain: 8.0 cm [IQR 5.0; 10.0]; P = 0.399) and transversus abdominis release (drain: 409 (70.5%) vs no drain: 408 (70.3%); P = 0.949). At 30 days, patients with drains had fewer seromas than those without drains (22 (3.8%) vs 88 (15.2%); P < 0.0001). Rates of SSIs and SSOPIs were similar between the two groups at 30 days. Logistic regression analysis showed drain placement lowered the risk of an SSO compared to no drain placement (OR 0.32, CI 0.21-0.47; P < 0.0001). Hospital stay was longer for patients with drains than those without drains (2.0 days [IQR 1.0; 3.0] vs 1.0 day [IQR 1.0; 2.0], respectively; P < .0001)., Conclusion: Drain placement during robotic rVHR is associated with decreased postoperative seroma occurrence., (© 2022. The Author(s), under exclusive licence to Springer-Verlag France SAS, part of Springer Nature.)

Purpose: Seromas can occur after ventral hernia repairs (VHR), but little is known about their relevance to short- and long-term outcomes. We aimed to determine if there is a correlation between seroma occurrence after clean VHR with mesh and patient-reported and clinical outcomes., Methods: Patients with and without seromas in the Abdominal Core Health Quality Collaborative registry were compared using a propensity score-matched analysis. Outcomes included hospital readmissions, postoperative antibiotics use, and procedural interventions. Pain and hernia-related quality of life were assessed at 30 days and 1 year. Composite hernia recurrence rates were compared at 1 year., Results: Propensity score matching compared 218 patients with a seroma to 649 without a seroma. At 30 days, patients with seromas were more likely to be readmitted (27 (12%) vs 28 (4%), respectively; P < 0.001), receive postoperative antibiotics (25 (12%) vs 18 (3%), respectively; P < 0.001), and undergo procedural interventions (41 (19%) vs 23 (4%), respectively; P < 0.001) than patients without seromas. Surgical site occurrences were more common in patients with seromas than those without seromas at 1 year (12 (11%) vs 12 (4%), respectively; P = 0.01).Pain and hernia-related quality of life were similar for both groups at 30 days and 1 year. Composite hernia recurrence rates were similar for both groups at 1 year (37 seroma (17%) vs 115 no seroma (18%); P = 0.80)., Conclusion: Seromas after clean VHR with mesh were associated with short- and long-term morbidity, but they did not significantly impact quality of life or hernia recurrences at 1 year., (© 2022. The Author(s), under exclusive licence to Springer-Verlag France SAS, part of Springer Nature.)

Purpose: Chronic postoperative inguinal pain (CPIP), a complication of inguinal hernia repair, may negatively affect mental health. The rates of psychological disorders in patients with CPIP are unknown. We aimed to describe the prevalence of psychological disorders coinciding with CPIP., Methods: A retrospective chart review was performed of all patients seen at the Cleveland Clinic Center for Abdominal Core Health's inter-disciplinary Chronic Groin Pain Clinic. This clinic is unique in that all patients are evaluated by a surgeon, a sonographer and radiologist, and a behavioral medicine psychologist. Patient psychological history and treatment, Depression Anxiety and Stress Scale (DASS) scores, pain catastrophizing, and trauma or abuse history were captured., Results: From January 2018 to January 2022, 61 patients were evaluated and included in the study. Psychological treatment had been provided to 37 (61%) patients (present: 16 (27%), past: 21 (35%)). The most common psychological disorders represented were depression (N = 13, 22%), anxiety (N = 10, 17%), and post-traumatic stress disorder (N = 5, 8%). DASS scores indicated that 20 (33%) patients were reporting symptoms of depression and 16 (27%) patients were reporting symptoms of anxiety. Of the 40 patients assessed for pain catastrophizing, 28 (70%) reported rumination, 9 (23%) reported magnification, and 23 (58%) reported feelings of helplessness. A childhood history of emotional or physical abuse was reported by 11 (18%) patients., Conclusion: An inter-disciplinary groin pain clinic has revealed that patients with CPIP frequently have pre-existing complex psychosocial issues. A multi-specialty approach to CPIP may improve preoperative assessments and identify patients who may benefit from further psychological evaluation and treatment., (© 2022. The Author(s), under exclusive licence to Springer-Verlag France SAS, part of Springer Nature.)

Introduction: Robotic inguinal hernia repair is growing in popularity among general surgeons despite little high-quality evidence supporting short- or long-term advantages over traditional laparoscopic inguinal hernia repair. The original RIVAL trial showed increased operative time, cost, and surgeon frustration for the robotic approach without advantages over laparoscopy. Here we report the 1- and 2-year outcomes of the trial., Methods: This is a multi-center, patient-blinded, randomized clinical study conducted at six sites from 2016 to 2019, comparing laparoscopic versus robotic transabdominal preperitoneal (TAPP) inguinal hernia repair with follow-up at 1 and 2 years. Outcomes include pain (visual analog scale), neuropathic pain (Leeds assessment of neuropathic symptoms and signs pain scale), wound morbidity, composite hernia recurrence (patient-reported and clinical exam), health-related quality of life (36-item short-form health survey), and physical activity (physical activity assessment tool)., Results: Early trial participation included 102 patients; 83 (81%) completed 1-year follow-up (45 laparoscopic vs. 38 robotic) and 77 (75%) completed 2-year follow-up (43 laparoscopic vs. 34 robotic). At 1 and 2 years, pain was similar for both groups. No patients in either treatment arm experienced neuropathic pain. Health-related quality of life and physical activity were similar for both groups at 1 and 2 years. No long-term wound morbidity was seen for either repair type. At 2 years, there was no difference in hernia recurrence (1 laparoscopic vs. 1 robotic; P = 1.0)., Conclusions: Laparoscopic and robotic inguinal hernia repairs have similar long-term outcomes when performed by surgeons with experience in minimally invasive inguinal hernia repairs., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Parastomal hernias are often repaired with mesh to reduce recurrences, but the presence of an ostomy increases the wound class from clean to clean-contaminated/contaminated and makes the choice of mesh more controversial than in a strictly clean case. We aimed to compare the outcomes of biologic and synthetic mesh for parastomal hernia repair., Study Design: This is a post hoc analysis of parastomal hernia repairs in a randomized trial comparing biologic and synthetic mesh in contaminated ventral hernia repairs. Outcomes included rates of surgical site occurrences requiring procedural intervention (SSOPI), reoperations, stoma/mesh-related adverse events, parastomal hernia recurrence rates (clinical, patient-reported, and radiographic) at 2 years, quality of life (EQ-5D, EQ-5D Visual Analog Scale, and Hernia-Related Quality of Life Survey), and hospital costs up to 30 days., Results: A total of 108 patients underwent parastomal hernia repair (57 biologic [53%] and 51 synthetic [47%]). Demographic and hernia characteristics were similar between the two groups. No significant differences in SSOPI rates or reoperations were observed between mesh types. Four mesh erosions into an ostomy requiring reoperations (2 biologic vs 2 synthetic) occurred. At 2 years, parastomal hernia recurrence rates were similar for biologic and synthetic mesh (17 [29.8%] vs 13 [25.5%], respectively; p = .77). Overall and hernia-related quality of life improved from baseline and were similar between the two groups at 2 years. Median total hospital cost and median mesh cost were higher for biologic compared with synthetic mesh., Conclusion: Biologic and synthetic mesh have similar wound morbidity, reoperations, 2-year hernia recurrence rates, and quality of life in parastomal hernia repairs. Cost should be considered in mesh choice for parastomal hernia repairs., (Copyright © 2022 by the American College of Surgeons. Published by Wolters Kluwer Health, Inc. All rights reserved.)

Introduction: Collecting accurate operative details remains a limitation of surgical research. Surgeon-entered data in clinical registries offers one solution, but natural language processing (NLP) has emerged as a modality for automating manual chart review (MCR). This study aims to compare the accuracy and efficiency of NLP and MCR with a surgeon-entered, prospective registry data in determining the rate of gross bile spillage (GBS) during cholecystectomy., Methods: Bile spillage rates were abstracted from an institutional, surgeon-entered clinical registry from July 2018 to January 2019. These rates were compared to those documented in the electronic medical record (EMR) using NLP and MCR to determine the sensitivity, specificity, and efficiency of each approach., Results: Of the 782 registry entries, 191 cases (24.4%) had surgeon-reported bile spillage. MCR identified bile spillage in 121 cases (15.6%); however, bile spillage information was either missing or ambiguous in 454 cases (58.1%). NLP identified 99 cases (12.7%) of bile spillage. Data abstraction times for the registry, NLP, and MCR were 3 min, 5 min, and 12 h, respectively. When compared to the registry, MCR was 45% sensitive and 94% specific, while NLP was 27.2% sensitive and 92% specific for detecting bile spillage. These differences were significant (X 2  = 19.446, P =  < 0.001)., Conclusion: Operative details, such as GBS, may not be abstracted by NLP or MCR if not clearly documented in the EMR. Clinical registries capture operative details, but they rely on surgeons to input the data., (© 2022. The Society for Surgery of the Alimentary Tract.)

Background: Parastomal hernia, common after stoma creation, negatively impacts patient quality of life. For patients with a permanent stoma, durable parastomal hernia repair remains a challenge, with few high-quality studies for guidance. An alternative to open retromuscular parastomal hernia repair with retromuscular "keyhole" mesh is the recent Sugarbaker modification. We aim to compare these two techniques in a head-to-head prospective study., Methods: This is a registry-based randomized controlled trial designed to investigate whether the retromuscular Sugarbaker technique is superior to the retromuscular keyhole technique for parastomal hernia repair. The primary study endpoint is parastomal hernia recurrence at 2 years. Secondary endpoints include hospital length-of-stay, readmission, wound morbidity, mesh-related complications, re-operation, all 30-day morbidity, and patient-reported outcomes, including hernia-related quality of life, stoma-specific quality of life, pain, and decision regret., Discussion: Based on the post hoc analysis of a recent randomized controlled trial, we hypothesize that the retromuscular Sugarbaker technique will reduce parastomal hernia recurrence by 20% at 2 years compared to the retromuscular keyhole mesh technique. The results of this study may provide evidence-based guidance for surgeons repairing parastomal hernias., Trial Registration: ClinicalTrials.gov NCT03972553. Registered on 3 June 2019., (© 2022. The Author(s).)

Accurately predicting the impacts of climate change on wildlife health requires a deeper understanding of seasonal rhythms in host-pathogen interactions. The amphibian pathogen, Batrachochytrium dendrobatidis (Bd), exhibits seasonality in incidence; however, the role that biological rhythms in host defences play in defining this pattern remains largely unknown. The aim of this study was to examine whether host immune and microbiome defences against Bd correspond with infection risk and seasonal fluctuations in temperature and humidity. Over the course of a year, five populations of Southern leopard frogs (Rana [Lithobates] sphenocephala) in Tennessee, United States, were surveyed for host immunity, microbiome and pathogen dynamics. Frogs were swabbed for pathogen load and skin bacterial diversity and stimulated to release stored antimicrobial peptides (AMPs). Secretions were analysed to estimate total hydrophobic peptide concentrations, presence of known AMPs and effectiveness of Bd growth inhibition in vitro. The diversity and proportion of bacterial reads with a 99% match to sequences of isolates known to inhibit Bd growth in vitro were used as an estimate of predicted anti-Bd function of the skin microbiome. Batrachochytrium dendrobatidis dynamics followed the expected seasonal fluctuations-peaks in cooler months-which coincided with when host mucosal defences were most potent against Bd. Specifically, the concentration and expression of stored AMPs cycled synchronously with Bd dynamics. Although microbiome changes followed more linear trends over time, the proportion of bacteria that can function to inhibit Bd growth was greatest when risk of Bd infection was highest. We interpret the increase in peptide storage in the fall and the shift to a more anti-Bd microbiome over winter as a preparatory response for subsequent infection risk during the colder periods when AMP synthesis and bacterial growth is slow and pathogen pressure from this cool-adapted fungus is high. Given that a decrease in stored AMP concentrations as temperatures warm in spring likely means greater secretion rates, the subsequent decrease in prevalence suggests seasonality of Bd in this host may be in part regulated by annual immune rhythms, and dominated by the effects of temperature., (© 2020 British Ecological Society.)

Wildlife diseases are a major threat for species conservation and there is a growing need to implement disease surveillance programs to protect species of concern. Globally, amphibian populations have suffered considerable losses from disease, particularly from chytrid fungi (Batrachochytrium dendrobatidis [Bd] and Batrachochytrium salamandrivorans [Bsal]) and ranavirus. Hellbenders (Cryptobranchus alleganiensis) are large riverine salamanders historically found throughout several watersheds of the eastern and midwestern US. Populations of both subspecies (Ozark hellbender, Cryptobranchus alleganiensis bishopi; eastern hellbender, Cryptobranchus alleganiensis alleganiensis) have experienced precipitous declines over at least the past five decades, and emerging pathogens are hypothesized to play a role. We surveyed Ozark hellbender populations in Arkansas (AR) and eastern hellbender populations in Middle Tennessee (MTN) and East Tennessee (ETN) for both chytrid fungi and ranavirus from swabs and tail tissue, respectively, from 2011 to 2017. Overall, we detected Bd on hellbenders from nine out of 15 rivers, with total prevalence of 26.7% (54/ 202) that varied regionally (AR: 33%, 28/86; MTN: 11%, 4/36; ETN: 28%, 22/80). Ranavirus prevalence (9.0%, 18/200) was comparatively lower than Bd, with less regional variation in prevalence (AR: 6%, 5/ 85; MTN: 11%, 4/36; ETN: 10%, 8/79). We did not detect Bsal in any hellbender populations. We detected a significant negative correlation between body condition score and probability of ranavirus infection (β=-0.13, SE=0.06, 95% confidence interval: -0.24, -0.02). Evaluation of infection load of positive individuals revealed different trends than prevalence alone for both ranavirus and Bd, with MTN having a significantly greater average ranaviral load than both other regions. We documented a variety of lesions that likely have multiple etiologies on hellbenders located within all geographic regions. Our data represent a multiyear pathogen dataset across several regions of C. alleganiensis, and we emphasize the need for continued pathogen surveillance., (© Wildlife Disease Association 2020.)

Drag sampling and flagging are two of the most effective and widely applied techniques to monitor tick populations. Despite the importance of this sampling strategy, there is a lack of standardized protocols for the construction of an inexpensive tick drag/flag. To this end, we provide a step-by-step protocol that details the construction of a tick drag/flag. We provide evidence of efficacy by comparing results obtained over 3-months at 108 locations within the William B. Bankhead National Forest, Alabama, USA. Overall, our drag/flag sampling approach yielded 1127 larvae, 460 nymphs, and 53 adults for a total of 1640 ticks representing three species. We detected significant patterns in Amblyomma americanum abundance for nymphs and adults with greater counts in June (β = 0.91 ± 0.36, 95% CI 0.55-1.27; β = 2.44 ± 0.63, 95% CI 1.81-3.07, respectively) and July (β = 0.73 ± 0.36, 95% CI 0.37-1.09; β = 1.65 ± 0.66, 95% CI 0.99-2.31, respectively) as compared to August. We also detected a significant difference in tick captures by tick drag/flag fabric type with greater captures when muslin was used as compared to flannel (β = 1.07 ± 0.06, 95% CI 1.01-1.13). Our goal is to provide instructions to assemble a highly effective tick drag/flag using minimal supplies. Evaluation and improvements of sampling techniques is essential to understand impacts of landscape management and larger stressors, such as climate change on tick populations but also for enhancing detection of invasive non-native species.

Born in Norfolk, England, on September 29, 1758, Horatio Nelson was the sixth of eleven children in a working-class family. With the help of his uncle, Maurice Suckling, a captain in the Royal Navy, Nelson began his naval career as a 13-year-old midshipman on the British battleship Raisonnable. His courage and leadership in the battle marked him for promotion, and he rose quickly from midshipman to admiral, serving in the West Indies, East Indies, North America, Europe, and even the Arctic. As his rank ascended, Nelson's consistent strategy was close engagement, an approach that led to success in combat but placed him in direct danger. Thus, Britain's greatest warrior was also her most famous patient: Nelson suffered more injuries and underwent more operations than any other flag officer in Royal Navy history. His career reached a climax off Cape Trafalgar, where he not only led the Royal Navy to victory over the combined French and Spanish fleets but also met his own death.

We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.

Background: The U.S. Navy's casualty-receiving ships provide remote damage control resuscitation platforms to treat injured combatants deployed afloat and ashore. We report a significant mass casualty incident aboard the USS Bataan, and the most warm fresh whole blood (WFWB) transfused at sea for traumatic hemorrhagic shock since the Vietnam War., Methods: Casualty-receiving ships have robust medical capabilities, including a frozen blood bank with packed red blood cells (pRBC) and fresh frozen plasma (FFP). The blood supply can be augmented with WFWB collected from a "walking blood bank.", Results: Following a helicopter crash, six patients were transported by MV-22 Osprey to the USS Bataan. Patient 1 had a pelvic fracture, was managed with a pelvic binder, and received 4 units of pRBC, 2 units of FFP, and 6 units of WFWB. Patient 2, with a comminuted tibia and fibula fracture, underwent lower extremity four-compartment fasciotomy, and received 4 units of WFWB. Patient 3 underwent several procedures, including left anterior thoracotomy, aortic cross-clamping, exploratory laparotomy, small bowel resection, and tracheostomy. He received 8 units of pRBC, 8 units of FFP, and 28 units of WFWB. Patients 4 and 5 had suspected spine injuries and were managed nonoperatively. Patient 6, with open tibia and fibula fractures, underwent lower extremity four-compartment fasciotomy with tibia external fixation and received 1 unit of WFWB. All patients survived aeromedical evacuation to a role 4 medical facility and subsequent transfer to local hospitals., Conclusion: Maritime military mass casualty incidents are challenging, but the U.S. Navy's casualty-receiving ships are ready to perform remote damage control resuscitation at sea. Activation of the ship's walking blood bank to transfuse WFWB is essential for hemostatic resuscitations afloat., Level of Evidence: Study type: case series, level V.

Objective: To compare implantation and ongoing pregnancy rates in freeze-only versus fresh transfer cycles., Design: Retrospective matched cohort study., Setting: Not applicable., Patient(s): Women selected using a matching algorithm for similar distributions of clinical characteristics for a total of 2,910 cycles (1,455 fresh cohort and 1,455 freeze-only cohort)., Intervention(s): None., Main Outcome Measure(s): Implantation and ongoing pregnancy rates., Result(s): Implantation and ongoing pregnancy rates were statistically significantly higher in the freeze-only transfer cohort than in the matched fresh transfer cohort: ongoing pregnancy rate for freeze-only was 52.0% (95% confidence interval [CI], 49.4-54.6) and for fresh was 45.3% (95% CI, 42.7-47.9), odds ratio (OR) 1.31 (95% CI, 1.13-1.51). In a stratified analysis, the odds of ongoing pregnancy after freeze-only transfer were statistically significantly higher for women both above and below age 35 with progesterone concentration >1.0 ng/mL (age ≤35: OR 1.38 [1.11-1.71]; age >35: OR 1.73 [1.34-2.24]). For women with progesterone concentration ≤1.0 ng/mL, no statistically significant difference in freeze-only odds of ongoing pregnancy was observed in either age group. The sensitivity analysis revealed that increasing maternal age alone (regardless of progesterone) trended toward a more beneficial effect of freeze-only cycles. A lower progesterone concentration was associated with statistically significantly higher ongoing pregnancy odds for fresh but not freeze-only cycles., Conclusion(s): Freeze-only transfer protocols are associated with statistically significantly higher ongoing implantation and pregnancy rates compared with fresh transfer cycles. This effect is most pronounced for cycles with progesterone >1.0 ng/mL at trigger and may also be stronger for older patients., (Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.)

Background: The use of prehospital blood transfusion (PBT) in air medical transport has become more widespread. However, the effect of PBT remains unknown. The aim of this study was to examine the impact of PBT on 24-hour and overall in-hospital mortality., Methods: This is a retrospective cohort study of all trauma patients carried by air medical transport from the scene to a Level I trauma center from 2007 to 2013. We excluded patients who died on the helipad or in the emergency department. Primary outcomes measured were 24-hour and overall in-hospital mortality. Multivariable logistic regressions using all available patient data or the propensity score (for receiving PBT)-matched patient data were performed to study the effect of PBT on these outcomes., Results: Of the 5,581 patients included in the study, 231 (4%) received PBT. Multivariable regression analyses did not show evidence of PBT effect on 24-hour in-hospital mortality (odds ratio [OR], 1.22; 95% confidence interval [CI], 0.61-2.44) and on overall in-hospital mortality (OR, 1.20; 95% CI, 0.55-1.79). In addition, using 1:1 propensity score-matched data, the analysis did not show evidence of PBT effect on 24-hour in-hospital mortality (OR, 1.04; 95% CI, 0.54-1.98) and on overall in-hospital mortality (OR, 1.05; 95% CI, 0.56-1.96). Factors associated with increased 24-hour mortality were advanced age, penetrating injury, increased blood transfusion requirement in the first 24 hours, and decreased Glasgow Coma Scale (GCS) score (p < 0.05). These factors were also associated with overall mortality, in addition to increased Injury Severity Score (ISS) (p < 0.05)., Conclusion: This is the largest study to date of trauma patients who received PBT and were transported from the scene by air medical transport. Our results show no effect of PBT on 24-hour and overall in-hospital mortality. Previous studies also suggest no benefit of PBT, which is counterintuitive to damage-control resuscitation. Prospective data on PBT are needed to assess risk, cost, and benefit., Level of Evidence: Therapeutic study, level III.

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.

We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations., (© 2015 The Protein Society.)

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

Thyroid hormone (T3) has been known to regulate the basal metabolic rate for more than a century, but mechanistic understanding is lacking both at the level of the intact organism and in terms of how T3 alters energy expenditure in individual tissues. The current studies investigate the question of which metabolically relevant genes respond acutely as T3 concentrations increase through the physiologic range in liver cells. Because this has been technically unfeasible historically, we developed a modified protocol for extracellular flux analysis using a 96-well Extracellular Flux Analyzer (Seahorse Bioscience). Using a modified extracellular flux protocol and LH86 human hepatoma cells, we established an experimental system where small but significant changes in O2 consumption could be reproducibly quantified as hypothyroid cells were exposed to near-physiologic final concentrations of T3 approximately 2 orders of magnitude lower than most studies (0.04 nM free T3), in only 6-7 hours. Taking advantage of the nondestructive nature of 96-well Extracellular Flux Analyzer measurements, the acute, direct, transcriptional changes that occur were measured in the exact same cells demonstrating increased O2 consumption. An unbiased, genome-wide microarray analysis identified potential candidate genes related to fatty acid oxidation, angiogenesis, nucleotide metabolism, immune signaling, mitochondrial respiration, and cell proliferation. The identified transcriptome is likely enriched in the genes most important for mediating the energetic effects of T3 in hepatoma cells.

Objective: The incidence and prevalence of breast cancer continue to rise. Therapies may contribute to patient weight gain. Obesity, a major predictor of surgical complications, may affect reconstructive outcome. The goal of this study was to quantify weight gain/change after the diagnosis and treatment of breast cancer in women choosing reconstruction after mastectomy., Methods: Retrospective review of patients undergoing mastectomy with reconstruction at a dedicated Cancer Center from 1996 to 2011 was conducted. Patient demographics, body mass index (BMI), and surgical complications were reported. Patients were stratified as normal weight (BMI <25 kg/m(2)) and overweight/obese (BMI >25 kg/m(2)). Body mass index at the time of mastectomy was compared with BMI postreconstruction., Results: A total of 443 patients had mastectomy and reconstruction. Forty-nine percent of patients were classified as normal weight (BMI <25 kg/m(2)) at the time of mastectomy and 51% as overweight/obese (body mass index > 25 kg/m(2)). Mean body mass index at the time of mastectomy was 26.1 kg/m(2) (4.9 SD) and 26.4 kg/m(2) (5.1 SD) at the final follow-up. Median follow-up time was 2.7 years (range <1 to 15 years). There was no statistically significant change in BMI before and after cancer treatment (P > .05). However, overweight/obese patients with complications were more likely to require an unanticipated return to the operating room (P = .0124)., Conclusions: Despite the stress of breast cancer diagnosis, surgical treatment, and reconstruction, we find that patients' weight does not change significantly over time. Overweight and obese patients are not always at higher risk for surgical complications but may have more severe complications when they do occur.

We present a new method for enhanced sampling for constant-pH simulations in explicit water based on a two-dimensional (2D) replica exchange scheme. The new method is a significant extension of our previously developed constant-pH simulation method, which is based on enveloping distribution sampling (EDS) coupled with a one-dimensional (1D) Hamiltonian exchange method (HREM). EDS constructs a hybrid Hamiltonian from multiple discrete end state Hamiltonians that, in this case, represent different protonation states of the system. The ruggedness and heights of the hybrid Hamiltonian's energy barriers can be tuned by the smoothness parameter. Within the context of the 1D EDS-HREM method, exchanges are performed between replicas with different smoothness parameters, allowing frequent protonation-state transitions and sampling of conformations that are favored by the end-state Hamiltonians. In this work, the 1D method is extended to 2D with an additional dimension, external pH. Within the context of the 2D method (2D EDS-HREM), exchanges are performed on a lattice of Hamiltonians with different pH conditions and smoothness parameters. We demonstrate that both the 1D and 2D methods exactly reproduce the thermodynamic properties of the semigrand canonical (SGC) ensemble of a system at a given pH. We have tested our new 2D method on aspartic acid, glutamic acid, lysine, a four residue peptide (sequence KAAE), and snake cardiotoxin. In all cases, the 2D method converges faster and without loss of precision; the only limitation is a loss of flexibility in how CPU time is employed. The results for snake cardiotoxin demonstrate that the 2D method enhances protonation-state transitions, samples a wider conformational space with the same amount of computational resources, and converges significantly faster overall than the original 1D method.

The anomalous behavior in the partial molar volumes of ethanol-water mixtures at low concentrations of ethanol is studied using molecular dynamics simulations. Previous work indicates that the striking minimum in the partial molar volume of ethanol VE as a function of ethanol mole fraction XE is determined mainly by water-water interactions. These results were based on simulations that used one water model for the solute-water interactions but two different water models for the water-water interactions. This is confirmed here by using two more water models for the water-water interactions. Furthermore, the previous work indicates that the initial decrease is caused by association of the hydration shells of the hydrocarbon tails, and the minimum occurs at the concentration where all of the hydration shells are touching each other. Thus, the characteristics of the hydration of the tail that cause the decrease and the features of the water models that reproduce this type of hydration are also examined here. The results show that a single-site multipole water model with a charge distribution that mimics the large quadrupole and the p-orbital type electron density out of the molecular plane has "brittle" hydration with hydrogen bonds that break as the tails touch, which reproduces the deep minimum. However, water models with more typical site representations with partial charges lead to flexible hydration that tends to stay intact, which produces a shallow minimum. Thus, brittle hydration may play an essential role in hydrophobic association in water.

Recent availability of large publicly accessible databases of chemical compounds and their biological activities (PubChem, ChEMBL) has inspired us to develop a web-based tool for structure activity relationship and quantitative structure activity relationship modeling to add to the services provided by CHARMMing (www.charmming.org). This new module implements some of the most recent advances in modern machine learning algorithms-Random Forest, Support Vector Machine, Stochastic Gradient Descent, Gradient Tree Boosting, so forth. A user can import training data from Pubchem Bioassay data collections directly from our interface or upload his or her own SD files which contain structures and activity information to create new models (either categorical or numerical). A user can then track the model generation process and run models on new data to predict activity., (© 2014 Wiley Periodicals, Inc.)

Objective: To determine the clinically recognizable error rate with the use of quantitative polymerase chain reaction (qPCR)-based comprehensive chromosomal screening (CCS)., Design: Retrospective study., Setting: Multiple fertility centers., Patient(s): All patients receiving euploid designated embryos., Intervention(s): Trophectoderm biopsy for CCS., Main Outcome Measure(s): Evaluation of the pregnancy outcomes following the transfer of qPCR-designated euploid embryos. Calculation of the clinically recognizable error rate., Result(s): A total of 3,168 transfers led to 2,354 pregnancies (74.3%). Of 4,794 CCS euploid embryos transferred, 2,976 gestational sacs developed, reflecting a clinical implantation rate of 62.1%. In the cases where a miscarriage occurred and products of conception were available for analysis, ten were ultimately found to be aneuploid. Seven were identified in the products of conception following clinical losses and three in ongoing pregnancies. The clinically recognizable error rate per embryo designated as euploid was 0.21% (95% confidence interval [CI] 0.10-0.37). The clinically recognizable error rate per transfer was 0.32% (95% CI 0.16-0.56). The clinically recognizable error rate per ongoing pregnancy was 0.13% (95% CI 0.03-0.37). Three products of conception from aneuploid losses were available to the molecular laboratory for detailed examination, and all of them demonstrated fetal mosaicism., Conclusion(s): The clinically recognizable error rate with qPCR-based CCS is real but quite low. Although evaluated in only a limited number of specimens, mosaicism appears to play a prominent role in misdiagnoses. Mosaic errors present a genuine limit to the effectiveness of aneuploidy screening, because they are not attributable to technical issues in the embryology or analytic laboratories., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)

A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.

A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.

This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The p K a values estimated with the EDS-HREX method agree well with the experimental p K a values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 p K a units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 p K a units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated p K a values.

Most mutations at position 15 in the N-terminal arm of the regulatory protein AraC leave the protein incapable of responding to arabinose and inducing the proteins required for arabinose catabolism. Mutations at other positions of the arm do not have this behavior. Simple energetic analysis of the interactions between the arm and bound arabinose do not explain the uninducibility of AraC with mutations at position 15. Extensive molecular dynamics (MD) simulations, carried out largely on the Open Science Grid, were done of the wild-type protein with and without bound arabinose and of all possible mutations at position 15, many of which were constructed and measured for this work. Good correlation was found for deviation of arm position during the simulations and inducibility as measured in vivo of the same mutant proteins. Analysis of the MD trajectories revealed that preservation of the shape of the arm is critical to inducibility. To maintain the correct shape of the arm, the strengths of three interactions observed to be strong in simulations of the wild-type AraC protein need to be preserved. These interactions are between arabinose and residue 15, arabinose and residues 8-9, and residue 13 and residue 15. The latter interaction is notable because residues L9, Y13, F15, W95, and Y97 form a hydrophobic cluster which needs to be preserved for retention of the correct shape., (Copyright © 2012 Wiley Periodicals, Inc.)

Temperature replica exchange molecular dynamics (T-REM) has been successfully used to improve the conformational search for model peptides and small proteins. However, for larger and more complicated systems, the use of T-REM is computationally intensive since the complexity of the free energy landscape and number of replicas required increase with system size. Achieving convergence of systems with slow transition kinetics is often difficult. Several methods have been proposed to overcome the size and convergence speed issues of standard T-REM. One of these is the Reservoir Replica Exchange Method (R-REM), in which the conformational search and temperature equilibration are separated by exchanging with a pre-existing reservoir of structures. This approach allows the integration of computationally efficient search algorithms with replica exchange. The Conformational Space Annealing (CSA) method has been shown to be able to determine the global energy minimum of proteins efficiently and has been used in structure prediction successfully. CSA uses a genetic algorithm to generate a diverse set of conformations to determine the minimum energy structure. We combine these methods by using conformations generated by the CSA method to build a reservoir. R-REM is then used to seed the top replica with the structures from the reservoir; fast convergence at every temperature is observed. The efficiency of this method is then demonstrated with model peptides and small proteins, and significant improvement of efficiency is observed while maintaining the overall shape of the free energy landscape.

Dimension reduction is often necessary when attempting to reach longer length and time scales in molecular simulations. It is realized by constraining degrees of freedom or by coarse-graining the system. When evaluating the accuracy of a dimensional reduction, there is a practical challenge: the models yield vectors with different lengths, making a comparison by calculating their dot product impossible. This article investigates mapping procedures for normal mode analysis. We first review a horizontal mapping procedure for the reduced Hessian techniques, which projects out degrees of freedom. We then design a vertical mapping procedure for the "implosion" of the all-atom (AA) Hessian to a coarse-grained scale that is based upon vibrational subsystem analysis. This latter method derives both effective force constants and an effective kinetic tensor. Next, a series of metrics is presented for comparison across different scales, where special attention is given to proper mass-weighting. The dimension-dependent metrics, which require prior mapping for proper evaluation, are frequencies, overlap of normal mode vectors, probability similarity, Hessian similarity, collectivity of modes, and thermal fluctuations. The dimension-independent metrics are shape derivatives, elastic modulus, vibrational free energy differences, heat capacity, and projection on a predefined basis set. The power of these metrics to distinguish between reasonable and unreasonable models is tested on a toy alpha helix system and a globular protein; both are represented at several scales: the AA scale, a Gō-like model, a canonical elastic network model, and a network model with intentionally unphysical force constants., (Published 2012 Wiley Periodicals, Inc.)

One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Background: Tumescence is the injection of local anesthetic and crystalloid into the subcutaneous tissue to establish a bloodless plane for surgical dissection. The aim of our study was to evaluate outcomes after mastectomy with tumescent technique compared to electrocautery dissection., Methods: We conducted a single-institution retrospective evaluation of patients who underwent mastectomy between 2007 and 2011. The tumescent technique was performed by injecting 1% lidocaine with epinephrine mixed in a 10% ratio with lactated Ringer solution into the mastectomy flaps followed by sharp dissection. Significance testing was done to evaluate for outcome differences between the two surgical groups., Results: Among the 134 patients, 64 underwent electrocautery and 70 underwent tumescent-assisted dissection. The overall complication rate was 21.6% (tumescent, 20.0%; electrocautery, 23.4%, P = 0.63). Flap necrosis requiring operative debridement was the most common complication in the tumescent group (n = 6). On multivariate analysis, tumescent technique was not associated with an increased complication rate. Immediate reconstruction was the only factor that increased the risk of complication (odds ratio 12.95, P < 0.001)., Conclusions: The tumescence surgery technique should be utilized with caution in patients undergoing immediate reconstruction, as a trend for higher complication rates was observed in these cases, and flap viability is particularly important in this setting. Future prospective studies are needed to further evaluate blood loss, operative time, postoperative pain, and duration of drainage catheters after tumescent mastectomy technique.

The type 2 iodothyronine selenodeiodinase (D2) is a critical determinant of local thyroid signaling, converting T(4) to the active form T(3) at the cytoplasmic face of the endoplasmic reticulum, thus supplying the nucleus with T(3) without immediately affecting circulating thyroid hormone levels. Although inhibitors of the cholesterol synthesis/isoprenylation pathway, such as hydroxy-methyl-glutaryl-coenzyme A reductase inhibitors (statins) have been to shown to down-regulate selenoproteins via interruption of normal selenocysteine incorporation, little is known about the effect of statins on D2. Here, we report that statins and prenyl transferase inhibitors actually increase D2 activity in cells with endogenous D2 expression. Although we confirmed that lovastatin (LVS) decreases the activity of transiently expressed D2 in HEK-293 cells, the prenyl transferase inhibitors increase activity in this system as well. LVS treatment increases endogenous Dio2 mRNA in MSTO-211H cells but does not alter transiently expressed Dio2 mRNA in HEK-293 cells. The prenyl transferase inhibitors do not increase Dio2 mRNA in either system, indicating that a posttranscriptional mechanism must exist. Cotreatment with LVS or the prenyl transferase inhibitors with the proteasome inhibitor MG-132 did not lead to additive increases in D2 activity, indirectly implicating the ubiquitin-proteasomal system in the mechanism. Finally, C57BL/6J mice treated with LVS or farnesyl transferase inhibitor-277 for 24 h exhibited increased D2 activity in their brown adipose tissue. These data indicate that statins and downstream inhibitors of the isoprenylation pathway may increase thyroid signaling via stimulation of D2 activity.

Memory operations such as encoding and retrieval require the coordinated interplay of cortical regions with distinct functional contributions. The mechanistic nature of these interactions, however, remains unspecified. During the performance of a face memory task during fMRI scanning, we measured the magnitude (a measure of the strength of coupling between areas) and phase (a measure of the relative timing across areas) of coherence between regions of interest and the rest of the brain. The fusiform face area (FFA) showed robust coherence with a distributed network of subregions in the prefrontal cortex (PFC), posterior parietal cortex (PPC), precuneus, and hippocampus across both memory operations. While these findings reveal significant overlap in the cortical networks underlying mnemonic encoding and retrieval, coherence phase analyses revealed context-dependent differences in cortical dynamics. During both encoding and retrieval, PFC and PPC exhibited earlier activity than in the FFA and hippocampus. Also, during retrieval, PFC activity preceded PPC activity. These findings are consistent with prior physiology studies suggesting an early contribution of PFC and PPC in mnemonic control. Together, these findings contribute to the growing literature exploring the spatio-temporal dynamics of basic memory operations.

Background: Breast magnetic resonance imaging (MRI) is increasingly used for breast cancer treatment planning. The aim of this study was to evaluate rates of mastectomy and breast-conserving surgery (BCS) in patients who undergo preoperative MRI., Methods: We retrospectively reviewed charts of patients who underwent surgical treatment of breast cancer at a single center between 2002 and 2009. Exclusion criteria included stage IV disease, previous breast cancer, Hodgkin lymphoma, and positive BRCA status. Univariate and multivariate analysis evaluated differences in patient demographics, surgical management, and tumor characteristics among women who underwent mastectomy compared to BCS., Results: Patients who underwent MRI were more likely to have mastectomy than those without MRI (43 vs. 28%; P = 0.002). Multivariate analysis revealed that younger age, larger tumor size, positive lymph node status, infiltrating lobular carcinoma, and preoperative MRI were independent predictors for mastectomy (P < 0.05). MRI detected occult contralateral breast cancer in 2.7% of patients. Among patients treated with BCS, preoperative MRI was not significantly associated with lower reexcision rates (MRI, 14%; no MRI, 18%; P = 0.34)., Conclusions: Preoperative MRI was associated with higher rates of mastectomy and detection of occult contralateral breast cancer, but was not associated with lower reexcision rates.

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used., (Copyright © 2011 Wiley Periodicals, Inc.)

Elite sports performance fundamentally relies on a complex set of brain functions engaged once visual signals are relayed from the eye. In this review, we overview a series of these neural mechanisms-focusing specifically on the critical role of attention in sculpting the visual processing that takes place leading up to a decision. These brain functions are introduced within the theoretical concept of the 'Perception-Action Cycle.' Vision does not stop at the eye but requires a coordinated set of brain mechanisms called on to convert visual input into rapid decisions about action.

The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme (e.g. QM/MM ONIOM-type), and extends its support to classical force fields, coarse grained modeling (e.g. ENM, GNM, etc.), and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent, but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard MPI communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples; (1) subtractive QM/MM and QM/QM calculations; (2) multi-force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e. coarse grain / all-atom) normal mode analysis. The potential of this new tool is clearly established and in conclusion an interesting mathematical problem is highlighted and future improvements are proposed.

The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.

Different categories of visual objects evoke distinct stimulus-evoked sensory responses in extrastriate visual cortex. Although numerous lines of evidence support a distinct representational neural architecture, the mechanisms underlying the modulation of the category selectivity by top-down influences remains uncertain. In this study, we investigate the causal role of the PFC in the modulation of evoked activity to face and scene stimuli in the extrastriate cortex. We used two experimental approaches to disrupt prefrontal cortical function-repetitive TMS to PFC in healthy participants (Experiment 1) and focal PFC lesions in stroke patients (Experiment 2). After these perturbations to normal PFC function (pre- vs. post-TMS and lesion vs. intact hemisphere), stimulus-evoked activity in extrastriate cortex exhibited less distinct category selectivity to faces and scenes. These two experiments provide convergent evidence highlighting a direct role of PFC in the top-down modulation of bottom-up visual signals.

Objective: To elucidate the physiologic mechanism responsible for the supraphysiologic gonadotropin release from the pituitary induced by gonadotropin-releasing hormone (GnRH) agonist in female rats primed with GnRH antagonist., Design: Controlled experimental intervention., Setting: Government research facility., Animal(s): Forty 8-week-old Sprague-Dawley rats., Intervention(s): Forty oophorectomized rats were randomized into four treatment groups of 10: group A, control vehicles; group B, GnRH agonist (leuprolide acetate; 1.7 microg/kg twice a day) on day 4; group C, GnRH antagonist (Nal-Lys; 3 mg/kg each day) days 1 to 4; or group D, GnRH antagonist (Nal-Lys; 3 mg/kg each day) days 1 to 4 plus GnRH agonist (1.7 microg/kg twice a day) on day 4., Main Outcome Measure(s): Immunohistochemical methods, Northern and in situ hybridization to quantitate pituitary follicle-stimulating hormone beta (FSH-beta), luteinizing hormone beta (LH-beta), and GnRH receptor (GnRH-R) messenger RNA (mRNA), and receptor protein levels in all treatment groups., Result(s): Treatment with GnRH antagonist was associated with increased storage of gonadotropin in the pituitary for FSH-beta and LH-beta, but mRNA levels were unchanged. The GnRH-R mRNA decreased after GnRH-agonist treatment but remained stable in the GnRH-antagonist treatment groups. Levels of GnRH-R were decreased after GnRH-antagonist treatment., Conclusion(s): These data indicate that the in vivo mechanism responsible for the exaggerated release of gonadotropins in rats primed with GnRH antagonist and treated with GnRH agonist was an increase in releasable gonadotropin pools coupled with a reduction in GnRH-R, but receptor function was preserved., (Published by Elsevier Inc.)

Objective: A mutation of B-type RAF kinase (B-RAF) represents the most common genetic alteration in papillary thyroid cancer (PTC), possibly signifying a more aggressive biology. Fine needle aspiration (FNA) represents the most useful initial diagnostic tool of thyroid nodules. Molecular analysis of the mutation status of B-RAF in thyroid nodule FNAs may provide guidance for treatment planning., Study Design: Cross-sectional study., Subjects and Methods: A retrospective chart review was undertaken for clinically relevant data of papillary thyroid cancer (PTC), follicular variant of PTC (FV-PTC), and nonmalignant goiters. After blinded pathologic review, histologic and cytologic samples were analyzed by LightCycler PCR (LCPCR) with allele-specific fluorescent probe melting curve analysis (FMCA) for the V600E mutation of B-RAF., Results: Of the 45 patient samples analyzed, B-RAF mutation was found to be significantly higher in papillary carcinomas when compared to follicular variant of papillary thyroid carcinomas (55.6% vs 14.3%, P = 0.05). Pathologic B-RAF mutational status significantly correlated with cytologic B-RAF mutational status (P < 0.0001), cytologic interpretation (P = 0.012), and histologic diagnosis (P = 0.011)., Conclusions: Determination of B-RAF V600E mutation of thyroid nodule FNAs by LCPCR may be a useful tool to guide treatment planning. These data support investigating the utility of this molecular marker in a prospective manner.

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.

A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation, and dynamics). The infrastructure used to implement the web application is described. Two additional programs have been developed and integrated with CHARMMing: GENRTF, which is employed to define structural features not supported by the standard CHARMM force field, and a job broker, which is used to provide a portable method for using grid and cluster computing with CHARMMing. The use of the program is described with three proteins: 1YJP , 1O1O , and 1UFY . Source code is provided allowing CHARMMing to be downloaded, installed, and used by supercomputing centers and research groups that have a CHARMM license. Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations.

Objective: To determine whether male age influences embryo development and reproductive potential in assisted reproductive technology cycles., Design: Retrospective cohort analysis., Setting: Private IVF center., Patient(s): One thousand twenty-three male partners participating in anonymous oocyte donation cycles., Intervention(s): Infertile couples undergoing 1,023 anonymous oocyte donation cycles., Main Outcome Measure(s): Live birth rate., Result(s): A significant increase in pregnancy loss, decrease in live birth rate, and decrease in blastocyst formation rate were noted in men >50 years of age. There was no significant difference in implantation rate, pregnancy rate, or early embryo development through the cleavage stage (demonstrated by fertilization rate, embryo cleavage rate, percentage of nonfertilized or polyspermic embryos, rate of embryo arrest, or seven or more cell embryo development on day 3). Men < or =45 years of age had significantly more semen volume and more motile sperm than men >45 years of age. There was no significant change in sperm morphology or concentration., Conclusion(s): After controlling for female age with use of the donor oocyte model, male age >50 years significantly affected pregnancy outcomes and blastocyst formation rates. Semen volume and total motility decreased with increasing male age. Initial embryo morphology through the cleavage stage was not affected.