A Picture is Worth a Thousand Timesteps: Excess Entropy Scaling for Rapid Estimation of Diffusion Coefficients in Molecular-Dynamics Simulations of Fluids.

In molecular-dynamics simulations of fluids, the Einstein-Helfand (EH) and Green-Kubo (GK) relationships are frequently used to compute a variety of transport coefficients, including diffusion coefficients. These relationships are formally valid in the limit of infinite sampling time: The error in the estimate of a transport coefficient (relative to an infinitely long simulation) asymptotically approaches zero as more dynamics are simulated and recorded. In practice, of course, one can only simulate a finite number of particles for a finite amount of time.

Towards realizing nano-enabled precision delivery in plants.

Nanocarriers (NCs) that can precisely deliver active agents, nutrients and genetic materials into plants will make crop agriculture more resilient to climate change and sustainable. As a research field, nano-agriculture is still developing, with significant scientific and societal barriers to overcome. In this Review, we argue that lessons can be learned from mammalian nanomedicine.

Transperineal Versus Transrectal Magnetic Resonance Imaging-targeted and Systematic Prostate Biopsy to Prevent Infectious Complications: The PREVENT Randomized Trial.

Background And Objective: The transrectal biopsy approach is traditionally used to detect prostate cancer. An alternative transperineal approach is historically performed under general anesthesia, but recent advances enable transperineal biopsy to be performed under local anesthesia. We sought to compare infectious complications of transperineal biopsy without antibiotic prophylaxis versus transrectal biopsy with targeted prophylaxis.

Getting over the hump with KAMEL-LOBE: Kernel-averaging method to eliminate length-of-bin effects in radial distribution functions.

Radial distribution functions (RDFs) are widely used in molecular simulation and beyond. Most approaches to computing RDFs require assembling a histogram over inter-particle separation distances. In turn, these histograms require a specific (and generally arbitrary) choice of discretization for bins.

Protocol of a multicentre randomised controlled trial assessing transperineal prostate biopsy to reduce infectiouscomplications.

Introduction: Approximately one million prostate biopsies are performed annually in the USA, and most are performed using a transrectal approach under local anaesthesia. The risk of postbiopsy infection is increasing due to increasing antibiotic resistance of rectal flora. Single-centre studies suggest that a clean, percutaneous transperineal approach to prostate biopsy may have a lower risk of infection.

TADA: The Topology-Accommodating Direction Assignment Algorithm for Liquid Crystals.

Despite the fact that topological defects are a hallmark of liquid crystalline materials, current computational techniques for identifying topological defects in particle-based simulations of these materials─which rest upon Q-tensor theory─do not leverage topological features of the system. In this work, we describe the topology-accommodating direction assignment (TADA) algorithm, a novel approach for identifying disclination cores in liquid crystalline materials, which is sensitive to topology: this method assigns to each mesogen a unique vector, thereby extending the concept of the liquid crystal director field down to the scale of mesogens. In systems containing disclination cores, TADA identifies line segments along which this assigned vector field is discontinuous, with cores located at the interior termination points of these line segments.

Excess Entropy Scaling in Active-Matter Systems.

Active-matter systems feature discrete particles that can convert stored or ambient free energy into motion. To realize the engineering potential of active matter, there is a strong need for predictive and theoretically grounded techniques for describing transport in these systems. In this work, we perform molecular-dynamics (MD) simulations of a model active-matter system, in which we vary the total fraction of active particles (0.

How to produce confidence intervals instead of confidence tricks: Representative sampling for molecular simulations of fluid self-diffusion under nanoscale confinement.

Ergodicity (or at least the tantalizing promise of it) is a core animating principle of molecular-dynamics (MD) simulations: Put simply, sample for long enough (in time), and you will make representative visits to states of a system all throughout phase space, consistent with the desired statistical ensemble. However, one is not guaranteed a priori that the chosen window of sampling in a production run is sufficiently long to avoid problematically non-ergodic observations; one is also not guaranteed that successive measurements of an observable are statistically independent of each other. In this paper, we investigate several particularly striking and troublesome examples of statistical correlations in MD simulations of nanoconfined fluids, which have profound implications on the quantification of uncertainty for transport phenomena in these systems.

Social distancing slows down steady dynamics in pedestrian flows.

Amidst the ongoing pandemic, social distancing has been broadly adopted as an effective front-line defense strategy for mitigating disease transmission. Viewed through the lens of particle-based simulations of flow, the practice of social distancing corresponds to a (significant) increase in an internal length scale of the flow, namely, the radius within which particles (pedestrians) strongly repel fellow particles. In this study, we report the results of two-dimensional pedestrian dynamics simulations modeling pedestrian counter-flows under confinement, in which individual pedestrians are described as active particles that aim to maintain a target speed while avoiding collisions.

Variation in Magnetic Resonance Imaging-Ultrasound Fusion Targeted Biopsy Outcomes in Asian American Men: A Multicenter Study.

Purpose: Asian American men have distinctly different prostate cancer epidemiology than other men. To our knowledge the role of multiparametric magnetic resonance imaging and targeted biopsy for elevated prostate specific antigen in this population has not been assessed. We sought to define imaging and targeted biopsy outcomes in Asian American men compared to other men.

Layered Fluid Structure and Anomalous Diffusion under Nanoconfinement.

Molecular diffusion under nanoconfinement can differ significantly from diffusion in bulk fluids. Using molecular dynamics simulations and molecular mechanics arguments, we elucidate the effect of layering at the confining boundaries on the self-diffusion of a simple, single-phase, confined fluid. In particular, we show that anomalous diffusion due to layering is controlled by the degree of layering as quantified by the recently proposed Wall number ( Wa), which compares the strength of the wall-fluid interaction to the thermal energy.

Silencing the Snail-Dependent RNA Splice Regulator ESRP1 Drives Malignant Transformation of Human Pulmonary Epithelial Cells.

Epithelial-to-mesenchymal transition (EMT) is organized in cancer cells by a set of key transcription factors, but the significance of this process is still debated, including in non-small cell lung cancer (NSCLC). Here, we report increased expression of the EMT-inducing transcription factor Snail in premalignant pulmonary lesions, relative to histologically normal pulmonary epithelium. In immortalized human pulmonary epithelial cells and isogenic derivatives, we documented Snail-dependent anchorage-independent growth and primary tumor growth and metastatic behavior Snail-mediated transformation relied upon silencing of the tumor-suppressive RNA splicing regulatory protein ESRP1.

Phase I Trial of Intratumoral Injection of Gene-Modified Dendritic Cells in Lung Cancer Elicits Tumor-Specific Immune Responses and CD8 T-cell Infiltration.

A phase I study was conducted to determine safety, clinical efficacy, and antitumor immune responses in patients with advanced non-small cell lung carcinoma (NSCLC) following intratumoral administration of autologous dendritic cells (DC) transduced with an adenoviral (Ad) vector expressing the gene (Ad-CCL21-DC). We evaluated safety and tumor antigen-specific immune responses following vaccination (ClinicalTrials.gov: NCT01574222).

Association of Aromatase With Bladder Cancer Stage and Long-Term Survival: New Insights Into the Hormonal Paradigm in Bladder Cancer.

Background: Hormonal factors may play a role in bladder cancer (BCa). We investigated the expression of aromatase and estrogen receptor (ER)β and its association with pathological variables and survival outcomes.

Patients And Methods: BCa specimens from 40 patients were evaluated.

Combination Treatment with Apricoxib and IL-27 Enhances Inhibition of Epithelial-Mesenchymal Transition in Human Lung Cancer Cells through a STAT1 Dominant Pathway.

Background: The cyclooxygenase 2 (COX-2) pathway has been implicated in the molecular pathogenesis of many malignancies, including lung cancer. Apricoxib, a selective COX-2 inhibitor, has been described to inhibit epithelial-mesenchymal transition (EMT) in human malignancies. The mechanism by which apricoxib may alter the tumor microenvironment by affecting EMT through other important signaling pathways is poorly defined.

Risk stratification of patients undergoing pulmonary metastasectomy for soft tissue and bone sarcomas.

Objectives: Our objective was to identify risk factors associated with survival in patients who underwent pulmonary metastasectomy for soft tissue or bone sarcoma and to create a risk stratification model.

Methods: A retrospective review of the prospectively maintained University of California Los Angeles Sarcoma Database was performed. Clinical, pathologic, and treatment variables were analyzed for overall survival and disease-free survival.

IL-27 inhibits epithelial-mesenchymal transition and angiogenic factor production in a STAT1-dominant pathway in human non-small cell lung cancer.

Background: Interleukin-27 signaling is mediated by the JAK-STAT pathway via activation of STAT1 and STAT3, which have tumor suppressive and oncogenic activities, respectively. Epithelial-mesenchymal transition (EMT) and angiogenesis are key processes in carcinogenesis. Although IL-27 has been shown to have potent anti-tumor activity in various cancer models, the role of IL-27 in EMT and angiogenesis is poorly understood.

CCL21 Chemokine Therapy for Lung Cancer.

Lung cancer remains a challenging health problem with more than 1.1 million deaths worldwide annually. With current therapy, the long term survival for the majority of lung cancer patients remains low, thus new therapeutic strategies are needed.

Laparoendoscopic single site live donor nephrectomy: single institution report of initial 100 cases.

Purpose: Laparoendoscopic single site surgery is a recent advance in minimally invasive urology. We report outcomes from our initial 100 consecutive laparoendoscopic single site live donor nephrectomies done by a single surgeon and provide a matched comparison of conventional laparoscopic live donor nephrectomies done by the same surgeon.

Materials And Methods: From 2009 to 2010 at a tertiary referral center 100 consecutive laparoendoscopic single site live donor nephrectomies were performed by a single surgeon through a periumbilical incision using the GelPoint® system.

Comparison of laparoendoscopic single-site donor nephrectomy and conventional laparoscopic donor nephrectomy: donor and recipient outcomes.

Objective: To present a comparison of perioperative donor outcomes and recipient graft function in a series of patients undergoing laparoendoscopic single-site donor nephrectomy (LESS-DN) versus conventional laparoscopic donor nephrectomy (LDN).

Methods: Data were collected for 50 consecutive LESS-DN patients and a matched cohort of 50 LDN patients. The donor outcomes analyzed included operative time, estimated blood loss, complications, visual analog pain scores, and recovery time.

Hsp90 inhibition increases p53 expression and destabilizes MYCN and MYC in neuroblastoma.

Neuroblastoma is a childhood cancer that exhibits either a favorable or an unfavorable phenotype. MYCN and MYC are oncoproteins that play crucial roles in determining the malignancy of unfavorable neuroblastoma. The Hsp90 superchaperone complex assists in the folding and function of a variety of oncogenic client proteins.

Early oncological outcomes for bladder urothelial carcinoma patients treated with robotic-assisted radical cystectomy.

Objective: • To determine oncological outcomes including early survival rates among unselected bladder urothelial carcinoma (BUC) patients treated with robotic-assisted radical cystectomy (RRC).

Patients And Methods: • Clinicopathologic and survival data were prospectively gathered for 85 consecutive BUC patients treated with RRC. • The decision to undergo a robotic rather than open approach was made without regard to tumor volume or surgical candidacy.

Critical analysis of complications after robotic-assisted radical cystectomy with identification of preoperative and operative risk factors.

Objective: To better characterize short- and long-term complications in patients after robotic-assisted radical cystectomy (RRC) using standardized complications-reporting systems, and to identify preoperative and operative risk factors predicting their occurrence.

Patients And Methods: Data were collected for 79 consecutive patients with bladder cancer undergoing RRC with extracorporeal urinary diversion by one surgeon at our institution. Complications occurring < or =90 days after RRC were graded according to two standardized reporting methods (Memorial Sloan Kettering Cancer Center and Modified Clavien), and additionally stratified by organ system.