Stochastic dynamics of model proteins on a directed graph

A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical features are shown to yield an effective estimate of the time scales associated with the folding and with the equilibration processes. This conclusion is drawn by comparing molecular dynamics simulations at constant temperature with the dynamics on the graph, defined by a temperature dependent Markov process. The main advantage of the graph representation is that its dynamics can be naturally renormalized by collecting nodes into "hubs", while redefining their connectivity. We show that both topological and dynamical properties are preserved by the renormalization procedure. Moreover, we obtain clear indications that the heteropolymers exhibit common topological properties, at variance with the homopolymer, whose peculiar graph structure stems from its spatial homogeneity. In order to obtain a clear distinction between a "fast folder" and a "slow folder" in the heteropolymers one has to look at kinetic features of the directed graph. We find that the average time needed to the fast folder for reaching its native configuration is two orders of magnitude smaller than its equilibration time, while for the bad folder these time scales are comparable. Accordingly, we can conclude that the strategy described in this paper can be successfully applied also to more realistic models, by studying their renormalized dynamics on the directed graph, rather than performing lengthy molecular dynamics simulations.Comment: 15 pages, 12 figure

Awareness of the Importance of and Adherence to Patients’ Rights Among Physicians and Nurses in Oman: An analytical cross-sectional study across different levels of healthcare

Objectives: This study aimed to determine the extent to which physicians and nurses in Oman were aware of the importance of and adhere to patients’ rights and whether this differed according to role, nationality, position and institutional healthcare level. Methods: This analytical cross-sectional study was carried out between December 2015 and March 2016 at various governmental healthcare institutions in Oman. A self-administered questionnaire was distributed to 1,385 practitioners at all healthcare levels. Results: A total of 1,213 healthcare practitioners (response rate: 87.58%) completed the survey, of which 685 (56.47%) were nurses and 528 (43.53%) were physicians. Overall, awareness of the importance of patients’ rights was high (91.51%), although adherence to these rights in practice was low (63.81%). The right of the patient to be informed was considered least important and was least adhered to (81.2% and 56.39%). Nationality, role and institutional level were significantly associated with awareness (P = 0.002, 0.024 and 0.034, respectively). Non-Omani staff were significantly more likely than Omani staff to be aware of (odds ratio [OR] = 1.696; P = 0.032) and adhere to (OR = 2.769; P <0.001) patient rights. Furthermore, tertiary care staff were twice as likely as primary care staff to perceive the importance of patient rights (OR = 2.076; P = 0.019). While physicians were more likely than nurses to be aware of the importance of patient rights, this difference was not significant (OR = 1.516; P = 0.126). Conclusion: These findings may help inform measures to enhance awareness of and adherence to patients’ rights in Oman.Keywords: Medical Ethics; Patient Rights; Awareness; Adherence; Physicians; Nurses; Oman

Marine health of the Arabian Gulf: Drivers of pollution and assessment approaches focusing on desalination activities

The Arabian Gulf is one of the most adversely affected marine environments worldwide, which results from combined pollution drivers including climate change, oil and gas activities, and coastal anthropogenic disturbances. Desalination activities are one of the major marine pollution drivers regionally and internationally. Arabian Gulf countries represent a hotspot of desalination activities as they are responsible for nearly 50% of the global desalination capacity. Building desalination plants, up-taking seawater, and discharging untreated brine back into the sea adversely affects the biodiversity of the marine ecosystems. The present review attempted to reveal the potential negative effects of desalination plants on the Gulf's marine environments. We emphasised different conventional and innovative assessment tools used to assess the health of marine environments and evaluate the damage exerted by desalination activity in the Gulf. Finally, we suggested effective management approaches to tackle the issue including the significance of national regulations and regional cooperation

Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity.

Death due to sepsis remains a persistent threat to critically ill patients confined to the intensive care unit and is characterized by colonization with multi-drug-resistant healthcare-associated pathogens. Here we report that sepsis in mice caused by a defined four-member pathogen community isolated from a patient with lethal sepsis is associated with the systemic suppression of key elements of the host transcriptome required for pathogen clearance and decreased butyrate expression. More specifically, these pathogens directly suppress interferon regulatory factor 3. Fecal microbiota transplant (FMT) reverses the course of otherwise lethal sepsis by enhancing pathogen clearance via the restoration of host immunity in an interferon regulatory factor 3-dependent manner. This protective effect is linked to the expansion of butyrate-producing Bacteroidetes. Taken together these results suggest that fecal microbiota transplantation may be a treatment option in sepsis associated with immunosuppression

Seismic microzonation for Muscat region, Sultanate of Oman

Site characterization was carried out for Muscat region using the ambient noise measurements applying the horizontal-to-vertical spectral ratio (HVSR) technique and using active seismic survey utilizing the multichannel analysis of surface waves (MASW) of survey data. Microtremors measurements were carried out at 459 sites using short-period sensors. This extensive survey allowed the fundamental resonance frequency of the soft soil to be mapped and areas prone to site amplification to be identified. The results indicate a progressive decrease in the fundamental resonance frequencies from the southern and eastern parts, where the bedrock outcrops, toward the northern coast where a thickness of sedimentary cover is present. Shear wave velocity (Vs) was evaluated using the 2-D MASW at carefully selected 99 representative sites in Muscat. These 99 sites were investigated with survey lines of 52 m length. 1-D and interpolated 2-D profiles were generated up to a depth range 20–40 m. The vertical Vs soundings were used in the SHAKE91 software in combination with suitable seismic input strong motion records to obtain the soil effect. Most of the study area has amplification values less than 2.0 for all the considered spectral periods. The estimated fundamental frequencies obtained using the H/V spectral ratio method and using SHAKE91 are found to be in a relatively good agreement. Maps of spectral amplification, earthquake characteristics on the ground surface for peak ground and spectral accelerations at 0.1, 0.2, 0.3, 1.0, and 2.0 s, for 475 years return period are produced. The surface ground motion maps show that the hazard level is moderate with expected PGA in the range 0.059–0.145 g for 475 years return period.Oman Ministerial Cabinet (project # 22409017

Managing data for the international, multicentre INTERGROWTH-21st Project

The INTERGROWTH-21st Project data management was structured incorporating both a centralised and decentralised system for the eight study centres, which all used the same database and standardised data collection instruments, manuals and processes. Each centre was responsible for the entry and validation of their country-specific data, which were entered onto a centralised system maintained by the Data Coordinating Unit in Oxford. A comprehensive data management system was designed to handle the very large volumes of data. It contained internal validations to prevent incorrect and inconsistent values being captured, and allowed online data entry by local Data Management Units, as well as real-time management of recruitment and data collection by the Data Coordinating Unit in Oxford. To maintain data integrity, only the Data Coordinating Unit in Oxford had access to all the eight centres’ data, which were continually monitored. All queries identified were raised with the relevant local data manager for verification and correction, if necessary. The system automatically logged an audit trail of all updates to the database with the date and name of the person who made the changes. These rigorous processes ensured that the data collected in the INTERGROWTH-21st Project were of exceptionally high quality

Mapping of aeolian deposits of an industrial site in the arid region using the TIR bands of ASTER and study of physicochemical characters and stabilization of sand erosion

This study describes the spectral emissive character of silicate and carbonate minerals of aeolian deposits and maps the deposits and sand encroachments that occurred in and around the site 5/6 of Qatar Fertilizer Company (QAFCO), Qatar using thermal infrared (TIR) bands of ASTER. The results of studies show that the quartz and unaltered silicates have spectral features between 8.12 and 9.27 µm, and the calcite and dolomite have emissivity minima near 11.4 and 11.2 µm, respectively. The mapping of deposits, dunes, and carbonate formations using the bands, and quartz index (QI), and carbonate index (CI) displayed their occurrence, distribution, and direction of sand movement from NW to SE. The sand encroachment was mapped using high spatial resolution satellite data of WorldView-2. The study of physicochemical characteristics of field samples showed the occurrence of sand grains up to 99.81% and the XRD and geochemical analyses represented the presence of quartz, calcite, dolomite, albite, and halite minerals in the deposits. In addition, the bacterial strains isolated from the samples indicated high urease activity leading to precipitation of carbonate minerals via microbially induced calcite precipitation (MICP) processes, and demonstrated high potential for utilization for sand stabilization of the QAFCO site