Simulation of the sedimentary fill of basins

There are many forward models that simulate sedimentary processes. The significance and utility of any particular model is a matter of need, computer hardware, and programming resources. Some forward-model simulations are one-dimensional; they are used to define third-order sea-level curves to infer the origin of peritidal cyclic carbonates, model the interdependence of sea level, depth-dependent carbonate accumulation, and the flexural response of the earths crust, and handle diagenesis of carbonate in relation to the eustatic record. Other simulations are two-dimensional and may handle clastics alone; they are used to create synthetic seismograms for sediment packages by modeling subsidence, sea level, sediment supply, and erosion, provide sedimentation rates for clastic fluvial systems using sediment compaction and tectonic movement, and simulate transport, deposition, erosion, and compaction of clastic sediments, emphasizing fluid velocity. Other simulations are two-dimensional carbonate shelf models that respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions; still others are two-dimensional mixed clastic and carbonate basin fill models. Both of these last kinds of models respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions. The program SEDPAK models some of the functions described and tests seismic interpretations based on sea-level curves. These curves are input parameters to the program. The program responds to tectonic movement, eustasy, and sedimentation, modeling sedimentary bypass and erosion. It reproduces clastic systems (including lacustrine, alluvial, and coastal plains, marine shelf, basin slope, and basin floor systems, and carbonate systems) and accounts for progradation, development of hardgrounds, downslope aprons, keep-up, catch-up, back-step, and drowned reef systems, and lagoonal and epeiric sea settings. SEDPAK simulates extensional vertical faulting of the basin, sediment compaction, and isostatic response to sediment loading. Sediment geometries can be viewed immediately on a graphics terminal as they are computed. Based on the observed geometric patterns, the user can repeatedly change the parameter and rerun the program until satisfied with the resultant geometry. This simulation is implemented in the C programming language (Kernighan and Ritchie, 1978), uses the X window system for graphical plotting functions (Scheifler and Gettys, 1986), and is operated on a Unix-based workstation, such as DEC 3 100, Sun, and Apollo. The simulation output is illustrated with examples from the Permian basin of West Texas and New Mexico, the Permian of the Sichuan basin, and the Upper Devonian of western Canada

Simulation of the sedimentary fill of basins

There are many forward models that simulate sedimentary processes. The significance and utility of any particular model is a matter of need, computer hardware, and programming resources. Some forward-model simulations are one-dimensional; they are used to define third-order sea-level curves to infer the origin of peritidal cyclic carbonates, model the interdependence of sea level, depth-dependent carbonate accumulation, and the flexural response of the earths crust, and handle diagenesis of carbonate in relation to the eustatic record. Other simulations are two-dimensional and may handle clastics alone; they are used to create synthetic seismograms for sediment packages by modeling subsidence, sea level, sediment supply, and erosion, provide sedimentation rates for clastic fluvial systems using sediment compaction and tectonic movement, and simulate transport, deposition, erosion, and compaction of clastic sediments, emphasizing fluid velocity. Other simulations are two-dimensional carbonate shelf models that respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions; still others are two-dimensional mixed clastic and carbonate basin fill models. Both of these last kinds of models respond to sea-level changes and erosion, allowing redeposition of sediment with user-defined production functions. The program SEDPAK models some of the functions described and tests seismic interpretations based on sea-level curves. These curves are input parameters to the program. The program responds to tectonic movement, eustasy, and sedimentation, modeling sedimentary bypass and erosion. It reproduces clastic systems (including lacustrine, alluvial, and coastal plains, marine shelf, basin slope, and basin floor systems, and carbonate systems) and accounts for progradation, development of hardgrounds, downslope aprons, keep-up, catch-up, back-step, and drowned reef systems, and lagoonal and epeiric sea settings. SEDPAK simulates extensional vertical faulting of the basin, sediment compaction, and isostatic response to sediment loading. Sediment geometries can be viewed immediately on a graphics terminal as they are computed. Based on the observed geometric patterns, the user can repeatedly change the parameter and rerun the program until satisfied with the resultant geometry. This simulation is implemented in the C programming language (Kernighan and Ritchie, 1978), uses the X window system for graphical plotting functions (Scheifler and Gettys, 1986), and is operated on a Unix-based workstation, such as DEC 3 100, Sun, and Apollo. The simulation output is illustrated with examples from the Permian basin of West Texas and New Mexico, the Permian of the Sichuan basin, and the Upper Devonian of western Canada

Piperidinols that show anti-tubercular activity as inhibitors of arylamine N-acetyltransferase: an essential enzyme for mycobacterial survival inside macrophages

Latent M. tuberculosis infection presents one of the major obstacles in the global eradication of tuberculosis (TB). Cholesterol plays a critical role in the persistence of M. tuberculosis within the macrophage during latent infection. Catabolism of cholesterol contributes to the pool of propionyl-CoA, a precursor that is incorporated into cell-wall lipids. Arylamine N-acetyltransferase (NAT) is encoded within a gene cluster that is involved in the cholesterol sterol-ring degradation and is essential for intracellular survival. The ability of the NAT from M. tuberculosis (TBNAT) to utilise propionyl-CoA links it to the cholesterol-catabolism pathway. Deleting the nat gene or inhibiting the NAT enzyme prevents intracellular survival and results in depletion of cell-wall lipids. TBNAT has been investigated as a potential target for TB therapies. From a previous high-throughput screen, 3-benzoyl-4-phenyl-1-methylpiperidinol was identified as a selective inhibitor of prokaryotic NAT that exhibited antimycobacterial activity. The compound resulted in time-dependent irreversible inhibition of the NAT activity when tested against NAT from M. marinum (MMNAT). To further evaluate the antimycobacterial activity and the NAT inhibition of this compound, four piperidinol analogues were tested. All five compounds exert potent antimycobacterial activity against M. tuberculosis with MIC values of 2.3-16.9 µM. Treatment of the MMNAT enzyme with this set of inhibitors resulted in an irreversible time-dependent inhibition of NAT activity. Here we investigate the mechanism of NAT inhibition by studying protein-ligand interactions using mass spectrometry in combination with enzyme analysis and structure determination. We propose a covalent mechanism of NAT inhibition that involves the formation of a reactive intermediate and selective cysteine residue modification. These piperidinols present a unique class of antimycobacterial compounds that have a novel mode of action different from known anti-tubercular drugs

Double trouble at high density::Cross-level test of ressource-related adaptive plasticity and crowding-related fitness.

Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels, we used an individual-based population model that is based on dynamic energy budget theory. Each of the hypotheses, represented by a sub-model, is based on specific assumptions on how the uptake and allocation of energy are altered under conditions of resource shortage or crowding. For cross-level testing of different hypotheses, we explored how well the sub-models fit individual level data and also how well they predict population dynamics under different conditions of resource availability. Only operating resource-related and crowding-related hypotheses together enabled accurate model predictions of D. magna population dynamics and size structure. Whereas this study showed that various mechanisms might play a role in the negative feedback between population density and individual life history, it also indicated that different density levels might instigate the onset of the different mechanisms. This study provides an example of how the integration of dynamic energy budget theory and individual-based modelling can facilitate the exploration of mechanisms behind the regulation of population size. Such understanding is important for assessment, management and the conservation of populations and thereby biodiversity in ecosystems

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Please refer to companion article, “The Giant Oil Field Evaporite Association: A Function of the Wilson Cycle, Climate, Basin Position and Sea Level, ” Search and Discovery Article #40471 (2009).

The world's source rocks include black shale and carbonates, and these large accumulations of organic matter and petroleum have an irregular temporal beat. The higher concentrations of organic matter are tied to sporadic super-plumes, plate configurations, climate, east coast / west coast ocean circulation, monsoons, allochthonous vs. autochthonous carbon, preservation mechanisms, and other phenomena. Most of the world's largest oil fields are restricted to areas along the southern margin of the Tethys, where specific areas are sweet and others not so productive! We argue that though 60 % of the globe's (preserved) oil deposits are associated with super-plume timing; the explanation for its (preserved) oil potential is also controlled by a combination of an enveloping continental rain shadow, lack of clastic input, and organic production fostering concentrations of organic matter in the geological section from the Precambrian through the Phanerozoic, particularly the Mesozoic, This is principally true of the lee shore of Pangea and the resulting Middle Eastern Giant Fields. Here accumulation of organic-rich sediments appears tied to marine transgressions with shelf-margin flooding as one of the major factors controlling accumulations of organic-rich sediment. Evidence for this relationship is recorded in the Cretaceous section of the southern Mediterranean margin and the Eastern Arabian shelf. The Silurian section of northern Gondwanaland records a glacial ice-cap melt

Sequence stratigraphy: methodology and nomenclature

The recurrence of the same types of sequence stratigraphic surface through geologic time defines cycles of change in accommodation or sediment supply, which correspond to sequences in the rock record. These cycles may be symmetrical or asymmetrical, and may or may not include all types of systems tracts that may be expected within a fully developed sequence. Depending on the scale of observation, sequences and their bounding surfaces may be ascribed to different hierarchical orders.Stratal stacking patterns combine to define trends in geometric character that include upstepping, forestepping, backstepping and downstepping, expressing three types of shoreline shift: forced regression (forestepping and downstepping at the shoreline), normal regression (forestepping and upstepping at the shoreline) and transgression (backstepping at the shoreline). Stacking patterns that are independent of shoreline trajectories may also be defined on the basis of changes in depositional style that can be correlated regionally. All stratal stacking patterns reflect the interplay of the same two fundamental variables, namely accommodation (the space available for potential sediment accumulation) and sediment supply. Deposits defined by specific stratal stacking patterns form the basic constituents of any sequence stratigraphic unit, from sequence to systems tract and parasequence. Changes in stratal stacking patterns define the position and timing of key sequence stratigraphic surfaces.Precisely which surfaces are selected as sequence boundaries varies as a function of which surfaces are best expressed within the context of the depositional setting and the preservation of facies relationships and stratal stacking patterns in that succession. The high degree of variability in the expression of sequence stratigraphic units and bounding surfaces in the rock record means ideally that the methodology used to analyze their depositional setting should be flexible from one sequence stratigraphic approach to another. Construction of this framework ensures the success of the method in terms of its objectives to provide a process-based understanding of the stratigraphic architecture. The purpose of this paper is to emphasize a standard but flexible methodology that remains objective