Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps.

Capturing rare yet pivotal events poses a significant challenge for molecular simulations. Path sampling provides a unique approach to tackle this issue without altering the potential energy landscape or dynamics, enabling recovery of both thermodynamic and kinetic information. However, despite its exponential acceleration compared to standard molecular dynamics, generating numerous trajectories can still require a long time. By harnessing our recent algorithmic innovations-particularly subtrajectory moves with high acceptance, coupled with asynchronous replica exchange featuring infinite swaps-we establish a highly parallelizable and rapidly converging path sampling protocol, compatible with diverse high-performance computing architectures. We demonstrate our approach on the liquid-vapor phase transition in superheated water, the unfolding of the chignolin protein, and water dissociation. The latter, performed at the ab initio level, achieves comparable statistical accuracy within days, in contrast to a previous study requiring over a year.

PyRETIS 3: Conquering rare and slow events without boundaries.

We present and discuss the advancements made in PyRETIS 3, the third instalment of our Python library for an efficient and user-friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) and its variations. Apart from a general rewiring of the internal code towards a more modular structure, several recently developed sampling strategies have been implemented. These include recently developed Monte Carlo moves to increase path decorrelation and convergence rate, and new ensemble definitions to handle the challenges of long-lived metastable states and transitions with unbounded reactant and product states. Additionally, the post-analysis software PyVisa is now embedded in the main code, allowing fast use of machine-learning algorithms for clustering and visualising collective variables in the simulation data.

Ecological filtering shapes the impacts of agricultural deforestation on biodiversity.

The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability-proxied by drier and more seasonal climates under a greater disturbance regime-and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation.

Protocol for a comparative cross-sectional study on characterisation of auditory impairment in sickle cell disease and sickle cell trait and its impact on health-related quality of life in Nigeria.

INTRODUCTION: Sickle cell disease (SCD) and sickle cell traits (SCT) are genetically inherited red blood cell disorders common among people of African descent. Nigeria has a high prevalence of SCD, with a prevalence of 2.28%-3% and SCT, 25%-30%. Poorly managed SCD and SCT can lead to sensorineural hearing loss and health-related quality of life (HRQoL) issues. This research aims to assess these possible complications of SCD and SCT in Nigeria. METHODS AND ANALYSIS: The study will use a comparative cross-sectional design at study power 80% to investigate the association between SCD/SCT, hearing impairment and HRQoL. Participants will be divided into two groups: a cohort and a control group. Hearing levels will be assessed through audiometric assessments and categorised by type and severity of hearing impairments using WHO classifications. HRQoL will also be assessed using WHO Disability Assessment Schedule 2.0. Statistical analyses will be performed using the SAS V.9.4, with parametric or non-parametric analysis depending on the distribution. Relationship between key variables will be determined via correlational tests, χ2, Fisher's exact test and multivariable logistic regression analyses. ETHICS AND DISSEMINATION: The proposal has been fully reviewed and registered by the University of Cape Town's Faculty of Health Sciences Human Research Ethics Committee (HREC REF 228/2022) and the University of Abuja Teaching Hospital Human Research Ethics Committee (HREC/PR/2020/08/007). Information dissemination will be through conferences, peer-review publication and personal communications. The Strengthening the Reporting of Observational Studies in Epidemiology statement will be followed in writing the manuscript.

The Global Otolaryngology-Head and Neck Surgery Workforce.

Importance: A core component of delivering care of head and neck diseases is an adequate workforce. The World Health Organization report, Multi-Country Assessment of National Capacity to Provide Hearing Care, captured primary workforce estimates from 68 member states in 2012, noting that response rates were a limitation and that updated more comprehensive data are needed. Objective: To establish comprehensive workforce metrics for global otolaryngology-head and neck surgery (OHNS) with updated data from more countries/territories. Design, Setting, and Participants: A cross-sectional electronic survey characterizing the OHNS workforce was disseminated from February 10 to June 22, 2022, to professional society leaders, medical licensing boards, public health officials, and practicing OHNS clinicians. Main Outcome: The OHNS workforce per capita, stratified by income and region. Results: Responses were collected from 121 of 195 countries/territories (62%). Survey responses specifically reported on OHNS workforce from 114 countries/territories representing 84% of the world's population. The global OHNS clinician density was 2.19 (range, 0-61.7) OHNS clinicians per 100 000 population. The OHNS clinician density varied by World Bank income group with higher-income countries associated with a higher density of clinicians. Regionally, Europe had the highest clinician density (5.70 clinicians per 100 000 population) whereas Africa (0.18 clinicians per 100 000 population) and Southeast Asia (1.12 clinicians per 100 000 population) had the lowest. The OHNS clinicians deliver most of the surgical management of ear diseases and hearing care, rhinologic and sinus diseases, laryngeal disorders, and upper aerodigestive mucosal cancer globally. Conclusion and Relevance: This cross-sectional survey study provides a comprehensive assessment of the global OHNS workforce. These results can guide focused investment in training and policy development to address disparities in the availability of OHNS clinicians.

An Exploration of Australian Online Government Portals for Women Experiencing Domestic Violence During the COVID-19 Pandemic.

Domestic violence against women increased during COVID-19 lockdowns. This inaugural study examined the content of Australian government online portals, for women seeking support and help for domestic violence, during the 2021 COVID-19 pandemic. This mixed methods study incorporated four phases: a search; measurement of portal quality standard using DISCERN; enumeration of portal items; and a qualitative exploration of portal text. Australian governments must continue to work alongside domestic violence services as we found some portals were better than others. Continued review, revision, and funding are needed to meet the demands associated with this evolving public health emergency.

Path sampling with memory reduction and replica exchange to reach long permeation timescales.

Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to compute membrane permeability. Next, recent and current developments in three RETIS aspects are discussed: several new Monte Carlo moves in the path-sampling algorithm, memory reduction by reducing pathlengths, and exploitation of parallel computing with CPU-imbalanced replicas. Finally, the memory reduction presenting a new replica exchange implementation, coined REPPTIS, is showcased with a permeant needing to pass a membrane with two permeation channels, either representing an entropic or energetic barrier. The REPPTIS results showed clearly that inclusion of some memory and enhancing ergodic sampling via replica exchange moves are both necessary to obtain correct permeability estimates. In an additional example, ibuprofen permeation through a dipalmitoylphosphatidylcholine membrane was modeled. REPPTIS succeeded in estimating the permeability of this amphiphilic drug molecule with metastable states along the permeation pathway. In conclusion, the presented methodological advances allow for deeper insight into membrane biophysics even if the pathways are slow, as RETIS and REPPTIS push the permeability calculations to longer timescales.

Enhanced path sampling using subtrajectory Monte Carlo moves.

Path sampling allows the study of rare events, such as chemical reactions, nucleation, and protein folding, via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD) trajectories with specific start- and end-conditions. As in configuration MC, its efficiency highly depends on the types of MC moves. Since the last two decades, the central MC move for path sampling has been the so-called shooting move in which a perturbed phase point of the old path is propagated backward and forward in time to generate a new path. Recently, we proposed the subtrajectory moves, stone-skipping (SS) and web-throwing, that are demonstrably more efficient. However, the one-step crossing requirement makes them somewhat more difficult to implement in combination with external MD programs or when the order parameter determination is expensive. In this article, we present strategies to address the issue. The most generic solution is a new member of subtrajectory moves, wire fencing (WF), that is less thrifty than the SS but more versatile. This makes it easier to link path sampling codes with external MD packages and provides a practical solution for cases where the calculation of the order parameter is expensive or not a simple function of geometry. We demonstrate the WF move in a double-well Langevin model, a thin film breaking transition based on classical force fields, and a smaller ruthenium redox reaction at the ab initio level in which the order parameter explicitly depends on the electron density.

Exchanging Replicas with Unequal Cost, Infinitely and Permanently.

We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different types of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble-based criterion in which the other ensembles represent an environment that might or might not participate in the Monte Carlo move. In addition, based on a recent algorithm for computing permanents, we effectively increase the exchange rate to infinite without the steep factorial scaling as a function of the number of replicas. We illustrate the effectiveness of this replica exchange methodology by combining it with a quantitative path sampling method, replica exchange transition interface sampling (RETIS), in which the costs for a Monte Carlo move can vary enormously as paths in a RETIS algorithm do not have the same length and the average path lengths tend to vary considerably for the different path ensembles that run in parallel. This combination, coined ∞RETIS, was tested on three model systems.

The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide.

Using molecular dynamics and path sampling techniques we investigated the effect of pressure and defects in the wurtzite to rock salt transition in cadmium selenide (CdSe). In the pressure range 2-10 GPa, rate constants of transition are in the order of 10-23 to 105 s-1 for the transformation of a relatively small wurtzite crystal consisting of 1024 atoms with periodic boundary conditions. The transition paths predominantly evolve through an intermediate 5-coordinated structure, as reported before, though its typical lifetime within the transition paths is particularly long in the intermediate pressure range (4-6 GPa). The defects were created by removing Cd-Se pairs from an otherwise perfect crystal. The removals were either selected fully randomized or grouped in clusters (cavity creation). We find that the rate of transition due to the defects increases by several orders of magnitude even for a single pair removal. This is caused by a change in the transition mechanism that no longer proceeds via the intermediate 5-coordinated structure, when defects are present. Further, the cavity creation yields a lower rate than the fully randomized removal.

The role of endometrial staining for CD138 as a marker of chronic endometritis in predicting live birth.

PURPOSE: Chronic endometritis (CE) is diagnosed via endometrial biopsy and staining for plasma cells. A threshold plasma cell count that identifies CE and predicts pregnancy outcomes has not been established, and the prevalence of plasma cells in the general infertile population is unknown. The purpose of this study was to determine the prevalence of plasma cells in the general infertile population and whether a threshold exists which predicts live birth. METHODS: Endometrial samples were obtained prospectively from 80 women undergoing IVF, embedded in paraffin, and stained for plasma cells using mouse mono-clonal antibody for CD138. Slides were reviewed at 20× magnification and 10 random images captured. Three reviewers graded each image for plasma cells. Participants underwent single, euploid, and frozen blastocyst transfer. RESULTS: Forty-nine percent of samples had ≥1 plasma cell across 10 HPFs, 11% had ≥5 cells across 10 HPFs, and 4% had ≥10 cells across 10 HPFs. There was no difference in prevalence between those who did and did not achieve live birth. Using thresholds of 1, 5, and 10 plasma cells per 10 HPFs, there were no differences in implantation, clinical pregnancy, clinical pregnancy loss, or live birth rates between patients with and without CE. CONCLUSION: Endometrial plasma cells are present in half the general infertile population and do not predict implantation, clinical pregnancy, clinical pregnancy loss, or live birth rates at low levels.

Genome sequence of an obligate hydrocarbonoclastic bacterium Alcanivorax marinus NMRL4 isolated from oil polluted seawater of the Arabian Sea.

Alcanivorax belongs to the hydrocarbonoclastic group of bacteria that are known for their preferential growth on alkanes and other related compounds. Here we report the genomic features of Alcanivorax marinus strain NMRL4 (=MCC 4632) isolated from oil polluted seawater of the Arabian Sea. Its 4,062,055 bp genome with 66.1% GC content encodes for 3935 coding sequences. The genome annotations of strain NMRL4 revealed the presence of multiple hydrocarbon degradation genes suggestive of its wider hydrocarbon substrate range. The strain encodes for three alkane monooxygenases, two cytochrome P450 and two flavin binding monooxygenases for degradation of short and long-chain alkanes. The genome shows capabilities for scavenging of nutrients, biofilm formation at oil-water interfaces, chemotaxis, motility and habitat specific adaptation. The genomic insights showed that the strain NMRL4 is an ideal candidate for bioremediation of pollutant petroleum hydrocarbons from the marine environment.

Individual-oocyte transcriptomic analysis shows that genotoxic chemotherapy depletes human primordial follicle reserve in vivo by triggering proapoptotic pathways without growth activation.

Gonadotoxic chemotherapeutics, such as cyclophosphamide, can cause early menopause and infertility in women. Earlier histological studies showed ovarian reserve depletion via severe DNA damage and apoptosis, but others suggested activation of PI3K/PTEN/Akt pathway and follicle 'burn-out' as a cause. Using a human ovarian xenograft model, we performed single-cell RNA-sequencing on laser-captured individual primordial follicle oocytes 12 h after a single cyclophosphamide injection to determine the mechanisms of acute follicle loss after gonadotoxic chemotherapy. RNA-sequencing showed 190 differentially expressed genes between the cyclophosphamide- and vehicle-exposed oocytes. Ingenuity Pathway Analysis predicted a significant decrease in the expression of anti-apoptotic pro-Akt PECAM1 (p = 2.13E-09), IKBKE (p = 0.0001), and ANGPT1 (p = 0.003), and reduced activation of PI3K/PTEN/Akt after cyclophosphamide. The qRT-PCR and immunostaining confirmed that in primordial follicle oocytes, cyclophosphamide did not change the expressions of Akt (p = 0.9), rpS6 (p = 0.3), Foxo3a (p = 0.12) and anti-apoptotic Bcl2 (p = 0.17), nor affect their phosphorylation status. There was significantly increased DNA damage by γH2AX (p = 0.0002) and apoptosis by active-caspase-3 (p = 0.0001) staining in the primordial follicles and no change in the growing follicles 12 h after chemotherapy. These data support that the mechanism of acute follicle loss by cyclophosphamide is via apoptosis, rather than growth activation of primordial follicle oocytes in the human ovary.

Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling.

Several simulations strategies have emerged to predict the permeability of solutes across membranes, which is important for many biological or industrial processes such as drug design. The widespread inhomogeneous solubility-diffusion (ISD) model is based on the Smoluchowski equation and describes permeation as purely diffusive. The counting method, which counts membrane transitions in a long molecular dynamics (MD) trajectory, is free of this diffusive assumption, but it lacks sufficient statistics when the permeation involves high free energy barriers. Metadynamics and variations thereof can overcome such barriers, but they generally lack the kinetics information. The milestoning framework has been used to describe permeation as a rare event, but it still relies on the Markovian assumption between the milestones. Replica Exchange Transition Interface Sampling (RETIS) has been shown to be an effective method for sampling rare events while simultaneously describing the kinetics without assumptions. This paper is the first permeation application of RETIS on an all-atom lipid bilayer consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) to compute the entrance, escape and complete transition of molecular oxygen. Conventional MD was performed as a benchmark, and the MD rates from counting were converted to rate constants, giving good agreement with the RETIS values. Moreover, a correction factor was derived to convert the collective order parameter in RETIS, which was aimed to improve efficiency, to a single-particle order parameter. With this work, we showed how the exact kinetics of drug molecules permeation can be assessed with RETIS even if the permeation is truly a rare event or if the permeation is non-Markovian. RETIS will therefore be a valuable tool for future permeation studies.

Predation Pressure in Tea (Camellia sinensis) Plantations in Southeastern China Measured by the Sentinel Prey Method.

Tea (Camellia sinensis) is an important food product with thousands of years of human use. Being a non-washable food, no pesticide residues are allowed, which increases the importance of natural means of plant protection. Predation, a component of natural pest control, is an important contributor to this, but its level and sustainability are not known in most of the areas of tea production. We quantified predation intensity using the artificial sentinel prey method in a tea-growing landscape containing remnants of the original forest vegetation in Fujian Province, China. The most common predators were chewing arthropods (49.8% of predation events) and birds (48.1%). Overall, predation rates at the edges of forest fragments (18.9% d-1) were lower than either in fragment interiors (25.4%d-1) or in the surrounding tea plantations (19.2-24.1%d-1). Arthropod predation was higher inside, and at the edge of, forest fragments than within plantations, and generally decreased with increasing distance from a fragment edge, indicating limited spillover of arthropod predators from the native habitat remnants to the cultivated matrix at the local scale. Bird predation, though, showed a different trend: it was lower on the inside of forest fragments than in the tea planation, and bird attack rates increased at increasing distances (up to 40 m) from the forest fragment edge. We also found a reciprocal relationship between attack rates by birds and arthropods, suggesting intra-guild predation. Measures protecting arthropod natural enemies could increase the combined pest suppression effect, contributing to pesticide-free tea production in China.

A Comparative Study of Compressible and Conductive Vertically Aligned Carbon Nanotube Forest in Different Polymer Matrixes for High-Performance Piezoresistive Force Sensors.

In the present scenario, conducting and lightweight flexible polymer nanocomposites rival metallic and inorganic semiconducting materials as highly sensitive piezoresistive force sensors. Herein, we explore the feasibility of vertically aligned carbon nanotube (VACNT) nanocomposites impregnated in different polymer matrixes, envisioned as highly efficient piezoresistors in sensor applications. Polymer nanocomposites are selectively designed and fabricated using three different polymer matrixes, i.e., polydimethylsiloxane (PDMS), polyurethane (PU), and epoxy resins with ideal reinforcement of VACNTs to enhance the thermal stability, conductivity, compressibility, piezoresistivity, and sensitivity of these nanocomposites. To predict the best piezoresistive force sensor, we evaluated the structural, optical, thermal, electrical, mechanical, and piezoresistive properties of the nanocomposites using field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), Raman spectroscopy, thermogravimetric analysis (TGA), I-V measurements, compressive stress-strain measurements, hysteresis, sensitivity, and force studies. The results demonstrate that the PDMS/VACNT nanocomposite is capable of sustaining large force with almost complete recovery and enhanced sensitivity, thereby fulfilling the desirable need for a highly efficient conductive and flexible force sensor as compared to PU/VACNT and epoxy/VACNT nanocomposites.

PyRETIS 2: An improbability drive for rare events.

The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface-based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open-source Python-based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

ENT Outreach in Africa: Rules of Engagement.

To address inequality of access to ear, nose, and throat (ENT) care, there must be significant and sustained investment in education and training of surgeons, audiologists, speech therapists, clinical officers, anesthetists, and specialized nurses engaged in ENT in sub-Saharan Africa and other developing nations. Outreach by ENT surgeons from developed countries is essential if we are to address the critical lack of access to ENT care in SSA. However, it should be based on mutual respect, shared values, aspirations, a desire to create a durable and sustainable impact, and internationally accepted best practice. In this article, we propose rules of engagement for outreach projects in SSA and other developing countries to optimize their contributions by making them useful, sustainable, productive, and developmental. These proposed rules of engagement are based on our personal experiences and observations-good and bad-of outreach activities in our countries.

Multiscale partial charge estimation on graphene for neutral, doped and charged flakes.

The minimal-basis iterative stockholder (MBIS) and restrained electrostatic potential (RESP) methods were applied to examine the effects of edges and of nitrogen and boron dopants on the atomic partial charges of neutral and charged graphene flakes. The results provided the parameters to fit a second-order atom-condensed Kohn-Sham DFT model (ACKS2), accurately determining the partial charges, the dipole and local electric fields in large graphene flakes with negligible cost. Our approach can lead to improvements of graphene force fields in charged conditions and guide the design of media for catalytic applications.

Diffusion of gas mixtures in the sI hydrate structure.

Replacing methane with carbon dioxide in gas hydrates has been suggested as a way of harvesting methane, while at the same time storing carbon dioxide. Experimental evidence suggests that this process is facilitated if gas mixtures are used instead of pure carbon dioxide. We studied the free energy barriers for diffusion of methane, carbon dioxide, nitrogen, and hydrogen in the sI hydrate structure using molecular simulation techniques. Cage hops between neighboring cages were considered with and without a water vacancy and with a potential inclusion of an additional gas molecule in either the initial or final cage. Our results give little evidence for enhanced methane and carbon dioxide diffusion if nitrogen is present as well. However, the inclusion of hydrogen seems to have a substantial effect as it diffuses rapidly and can easily enter occupied cages, which reduces the barriers of diffusion for the gas molecules that co-occupy a cage with hydrogen.