Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations.

Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation─from system preparation to property calculations.

Management of Bulky Inguinal and Pelvic Lymph Nodes.

Penile cancer with bulky inguinal metastasis has a high probability of harboring pathologically involved lymph nodes best managed in a multidisciplinary care setting. Appropriate staging with cross-sectional imaging and fine-needle aspirate cytology of suspicious nodes guide decision-making for the use of platinum-based neoadjuvant chemotherapy followed by inguinal lymph node dissection. Surgical resection plays an important diagnostic, therapeutic, and guiding role in disease management.

Robotic or open superficial inguinal lymph node dissection as staging procedures for clinically node negative high risk penile cancer.

Objective: To evaluate perioperative and oncologic outcomes of a cohort of clinically node negative high-risk penile cancer patients undergoing robotic assisted inguinal lymph node dissection (RAIL) compared to patients undergoing open superficial inguinal lymph node dissection (OSILND).

Patients And Methods: We retrospectively reviewed the clinical characteristics and outcomes of clinically node negative high-risk penile cancer patients undergoing RAIL at MDACC from 2013-2019. We sought to compare this to a contemporary open cohort of clinically node negative patients treated from 1999 to 2019 at MDACC and Moffit Cancer Center (MCC) with an OSILND.

Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics.

Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale.

Long-Term Oncological Outcomes in Patients Diagnosed With Nonmetastatic Plasmacytoid Variant of Bladder Cancer: A 20-Year University of Texas MD Anderson Cancer Center Experience.

Purpose: The treated natural history of nonmetastatic plasmacytoid variant of bladder cancer (PV-BCa) is poorly understood owing to its rarity. We sought to examine the disease recurrence and metastasis patterns in this select group of patients in order to identify opportunities for intervention.

Materials And Methods: We conducted a natural language processing algorithm-augmented retrospective chart review of 56 consecutive patients who were treated with curative intent for nonmetastatic PV-BCa at our institution between 1998 and 2018.

15-year biochemical failure, metastasis, salvage therapy, and cancer-specific and overall survival rates in men treated with robotic radical prostatectomy for PSA-screen detected prostate cancer.

Background: An informed decision regarding a treatment option requires data on its long-term efficacy and side-effect profile. While the side-effects of robotic radical prostatectomy have been well-quantified, the data on its long-term efficacy are lacking. We here provide 15-year oncological outcomes of clinically-localized prostate cancer (CLPCa) patients treated with robot-assisted laparoscopic prostatectomy (RALP).

Multiple coinfections and Guillain Barré syndrome following outdoor travel to the American Northeast.

A 66-year-old immunocompetent man with preceding travel through the Northeastern United States developed Guillain-Barré syndrome. A broad search for infections revealed intraerythrocytic parasites on blood smear and positive polymerase chain reaction for ; elevated IgM/IgG serologies for ; elevated IgM/IgG serologies and qualitative polymerase chain reaction for Epstein-Barr virus; and fecal culture growth of . In this report, we discuss the known or suspected association of these infectious agents with Guillain-Barré syndrome.

Broad chemical transferability in structure-based coarse-graining.

Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher resolution reference, making the CG model chemically specific. Unfortunately, chemical specificity can be at odds with compound-screening strategies, which call for transferable parameterizations.

The Acute Complications After Surgery for Penile Carcinoma and Strategies for Their Management: A Systematic Review of the Literature.

Objectives: To investigate the contemporary rates of 30-day complications after surgery for penile cancer and to discuss the currently used preventative and therapeutic practices aimed at mitigation of these postoperative adverse events.

Data Sources: A systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was performed, and studies reporting on the contemporary rates, nature, or management of acute complications following primary penile surgery or inguinal lymph node dissection for penile cancer were abstracted. Medline (PubMed) and EMBASE libraries were used to retrieve the articles published between January 1984 and December 2021 (n = 170 articles).

Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions.

We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at investigating whether relatively small differences in the tail of the radial distribution functions result in contrasting thermodynamic properties. Our results suggest that the attractive potential favours the nucleation of long-range structures.

PEG-coated patch parenchymal closure technique and initial outcomes during minimally invasive partial nephrectomy.

Introduction: The Hemopatch is a novel polyethylene glycol-coated (PEG-coated) collagen patch that acts as a topical hemostatic agent. It has been applied to a variety of surgical techniques. Here, we present our series and technique using a PEG-coated patch for minimally invasive partial nephrectomy (MIPN).

Preferential interaction of platelets with prostate cancer cells with stem cell markers.

Background: Prostate cancer (PCa) may be initiated by CD133+/CD44+ expressing stem cell-like cells (PCSC), which are also thought to drive metastasis. Platelets also contribute to metastasis via tumor cell-induced platelet aggregation (TCIPA), which in part enhances cancer cell invasion. Moreover, activated platelets secrete stromal derived growth factor-1α (SDF-1α) that can mobilize CSCs via the CXCR4 receptor.

Platelets stimulate programmed death-ligand 1 expression by cancer cells: Inhibition by anti-platelet drugs.

Background: Platelets facilitate hematogenous metastasis in part by promoting cancer cell immunoevasion, although our understanding of platelet function in modulating the adaptive immune system in cancer is limited. A major negative regulator of the adaptive response is the immune checkpoint protein Programmed Death Ligand 1 (PD-L1).

Objectives: As platelets secrete factors that may increase PD-L1 expression, we investigated whether they up-regulate cancer cell PD-L1, thus promoting immunoevasion, and whether common anti-platelet drugs inhibit this process.

Dynamical properties across different coarse-grained models for ionic liquids.

Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The significance of electrostatic interactions in RTILs results in long characteristic length- and timescales, and has motivated the development of a number of coarse-grained (CG) simulation models. In this study, we aim to better understand the connection between certain CG parameterization strategies and the dynamical properties and transferability of the resulting models.

Cognitive impairment related to arterial stiffness in cardiovascular disease patients with severe periodontitis.

Severe periodontal disease (SPD) associated with systemic peripheral inflammation, cognitive impairment (CI) and arterial stiffness (AS) has been recognized. The aim of this study was to investigate whether CI and arterial stiffness (AS) occur in cardiovascular disease (CVD) patients with SPD. A crosssectional case-control study included hospitalized patients with CVD.

Coarse-grained conformational surface hopping: Methodology and transferability.

Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a reduced level. The SH scheme couples distinct conformational basins (states), each described by its own force field (surface), resulting in a significant improvement of the approximation to the many-body potential of mean force [T. Bereau and J.

Active surveillance for low-risk prostate cancer - in pursuit of a standardized protocol.

Introduction: Active surveillance (AS) is a management option recommended by most guidelines for low risk clinically-localized prostate cancer (LR-CLPC). Data shows that AS is being increasingly adopted into clinical practice worldwide. Our aim was to review the up-to date guidelines and observational studies in regards to AS in LR-CLRPC to gain insight into principles of contemporary clinical practice.

The role of the androgen receptor in prostate cancer-induced platelet aggregation and platelet-induced invasion.

Background: Metastatic prostate cancer progresses from a hormone sensitive androgen receptor expressing phenotype to a hormone insensitive androgen receptor-independent subtype with low overall survival. Human platelets contribute to metastasis via tumor cell-induced platelet aggregation, which in part enhances cancer cell invasion. Given the more aggressive nature of hormone insensitive prostate cancer, we hypothesized that androgen receptor-negative prostate cancer cells exhibit higher platelet aggregation potency and invasive response compared to cells with androgen receptor.

Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.

Intrinsically disordered proteins (IDPs) play an important role in an array of biological processes but present a number of fundamental challenges for computational modeling. Recently, simple polymer models have regained popularity for interpreting the experimental characterization of IDPs. Homopolymer theory provides a strong foundation for understanding generic features of phenomena ranging from single-chain conformational dynamics to the properties of entangled polymer melts, but is difficult to extend to the copolymer context.

Are urologic surgeons performing robot-assisted radical prostatectomy at the University of Alberta meeting surgical quality performance benchmarks? The PROCURE-02 quality assurance study.

Introduction: Robot-assisted radical prostatectomy (RARP) is a standard of care primary treatment for men with clinically localized prostate cancer (CLPC). The 2010 Canadian Urological Association (CUA) consensus guideline examining surgical quality performance for radical prostatectomy suggested benchmarks for surgical performance. To date, no study has examined whether Canadian surgeons are achieving these benchmarks.

Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations.

Coarse-grained (CG) models are often parameterized to reproduce one-dimensional structural correlation functions of an atomically detailed model along the degrees of freedom governing each interaction potential. While cross correlations between these degrees of freedom inform the optimal set of interaction parameters, the correlations generated from the higher-resolution simulations are often too complex to act as an accurate proxy for the CG correlations. Instead, the most popular methods determine the interaction parameters iteratively while assuming that individual interactions are uncorrelated.

Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics.

Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations.

Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics.

Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed. Here, we extend the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately sample the conformational ensemble of a classical system in equilibrium.

Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models.

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition.

Fostering Interprofessional Education Through a Multidisciplinary, Community-Based Pandemic Mass Vaccination Exercise.

We expanded health care services to economically disadvantaged individuals in an interprofessional, student-driven vaccination effort that also served as a pandemic planning drill. Health care professional students from colleges in and around Rockford, Illinois participated in implementing a mass vaccination event from 2011 to 2014 that targeted the underserved population. There was a 459% increase in total vaccinations administered to at-risk patients from year 1 to year 4.