Bell Model Research Articles

A novel model for count data: zero-inflated Probit Bell model with applications

A novel model for count data is proposed in this work. This new model is briefly called the Zero-Inflated Probit Bell (ZIPBell) model. The ZIPBell model can be used to simulate and analyze traditional count data and can be used well in the simulation and analysis of count data with the phenomenon that the frequency for zero occupies a very high percentage. In the scope of this study, we first provide the general formula, functions or related equations for the ZIPBell model. The results of asymptotic inferences for the ZIPBell model are also given in this work. Maximum likelihood estimator (MLE) is used to check its performance of the proposed model. According to the numerical illustrations via several simulation researches and the analysis of a practical data set, it has been seen that the MLE method has offered correct and reliable inferences. Finally, the inferences and conclusions of this study are mentioned.

Comparative analysis of folding and unfolding dynamics and free-energy landscapes in homologous cold shock proteins with variable thermal stabilities

Cold shock proteins from the mesophilic organism (BsCSP), the thermophilic organism (BcCSP), and the hyperthermophilic organism (TmCSP) are homologous proteins with similar native structure but quite different thermal stabilities, which makes them promising candidates for investigating the general and specific aspects the folding and unfolding dynamics of proteins and free-energy landscapes. In this study, we employed magnetic tweezers to explore the force-dependent folding and unfolding rates of BsCSP, BcCSP, and TmCSP at forces from several pN to tens of pN. Our results indicate similar force-dependent folding rates for these three proteins, while the unfolding rate of BsCSP, BcCSP, and TmCSP decreases sequentially, consistent with previous biochemical findings. Comparing with TmCSP, BcCSP shows lower but sufficient stability with folding free energy of 8.0 kBT, and its force-dependent unfolding rates exhibit tremendous nonlinear behavior deviated from Bell's model like TmCSP. BsCSP has very low stability with folding free energy of only 3.9 kBT, and its force-dependent unfolding rates at 3–10 pN exhibit almost linear behavior. Comprehensive free-energy landscapes are constructed, revealing common barriers that governs folding and unfolding dynamics for BcCSP and TmCSP but a wide merged barrier for BsCSP. Our findings provide valuable insights into the folding and unfolding mechanisms of these CSPs, shedding light on the relationship between protein structure, stability, and mechanical properties. Published by the American Physical Society 2024

C-H Bond Oxidation by MnIV-Oxo Complexes: Hydrogen-Atom Tunneling and Multistate Reactivity.

The reactivity of six MnIV-oxo complexes in C-H bond oxidation has been examined using a combination of kinetic experiments and computational methods. Variable-temperature studies of the oxidation of 9,10-dihydroanthracene (DHA) and ethylbenzene by these MnIV-oxo complexes yielded activation parameters suitable for evaluating electronic structure computations. Complementary kinetic experiments of the oxidation of deuterated DHA provided evidence for hydrogen-atom tunneling in C-H bond oxidation for all MnIV-oxo complexes. These results are in accordance with the Bell model, where tunneling occurs near the top of the transition-state barrier. Density functional theory (DFT) and DLPNO-CCSD(T1) computations were performed for three of the six MnIV-oxo complexes to probe a previously predicted multistate reactivity model. The DFT computations predicted a thermal crossing from the 4B1 ground state to a 4E state along the C-H bond oxidation reaction coordinate. DLPNO-CCSD(T1) calculations further confirm that the 4E transition state offers a lower energy barrier, reinforcing the multistate reactivity model for these complexes. We discuss how this multistate model can be reconciled with recent computations that revealed that the kinetics of C-H bond oxidation by this set of MnIV-oxo complexes can be well-predicted on the basis of the thermodynamic driving force for these reactions.

Elevated TRPV2 expression in the facial nerve of rats by cold stimulation: Implications for Bell's palsy

ObjectiveBell's palsy, also referred to as clinical manifestations of unilateral facial nerve palsy, encompasses downward angling of the corners of the mouth, the absence of forehead creases, and unilateral incomplete eyelid closure. The incidence of Bell's palsy has increased progressively in recent years, but the underlying mechanism of its occurrence remains unknown; therefore, it is essential to investigate both the cause and treatment of Bell's palsy. Member 2 of the Subfamily V Transient Receptor Potential Cation Channel is a mechanically and thermally sensitive ion channel that plays a crucial role in neural growth and development. Using a novel modeling technique, we endeavored to develop an animal model of Bell's palsy and determine whether TRPV2 expression is altered throughout the course of a facial nerve injury. Materials and methodsThe rats were categorized into 3 groups, and their facial nerve function was assessed using RT-qPCR, WB, and pathologic testing, respectively, after undergoing unilateral cold air stimulation for 1, 3, and 7 days. TRPV2 expression was identified using these techniques. ResultsIn response to cold stimulation, rats exhibited facial nerve paralysis symptoms, demyelinating lesions in the facial nerve, and increased TRPV2 expression. ConclusionsExtended cold stimulation of the facial nerve in rats may lead to an imbalance in facial nerve homeostasis and increased TRPV2 expression. These findings will contribute to the understanding of the potential mechanism by which cold stimulation affects the facial nerve. Moreover, this finding implies that TRPV2 could possibly function as an additional diagnostic marker or therapeutic target in the context of Bell's palsy.

Assessment of marine fish stocks within India’s ExclusiveEconomic Zone: Status report 2022

India is one of the major fishing nations in the Indian Ocean, with commercial marine fishlandings in the country comprising of nearly 1000 species. A comprehensive and periodicassessment of the stocks is crucial for achieving the goals of sustainable fisheries harvestand management. The ICAR-Central Marine Fisheries Research Institute, Ministry ofAgriculture and Farmers’ Welfare, Govt. of India, is mandated to monitor and assess themarine fisheries resources in the Indian EEZ. In the present study, 135 stocks across 70species were assessed using monthly length-frequency data. The health status of the stockis projected based on a combination of indicators such as relative biomass or spawningstock biomass (B/Bmsy or SSB/SSB0) and relative fishing pressure (F/Fmsy) estimated usinga standard length-based dynamic pool model (i.e., Thompson and Bell Model). Based onthe comparison of estimated values of indicators against the thresholds, the stocks wereclassified as sustainable, overfishing, overfished and rebuilding. The study revealed that91.1% of the assessed fish stocks have a healthy biomass level (sustainable stocks andthose subjected to overfishing), 8.2% of stocks are overfished, whereas 0.7% are in theprocess of rebuilding. Biology-based, Healthy stocks, Length-frequency,Stock assessment, Sustainable, Tropical

For whom the bell (really) tolls: A grounded theory of millennial academic supervisors’ sensemaking of communitarian values as a springboard to enrich their transformational leadership attributes

ABSTRACT The emergence of millennials in strategic positions of academic organizations paved the way for a peculiar execution of leadership practices due to their work ethic and generational stereotypes. Scholars argue that one of the neo-charismatic modalities that they embrace is transformational leadership. By and large, the said leadership paradigm becomes a multifaceted phenomenon if viewed from the specific generational and professional lenses. There is a paucity of studies that discovers its translation on developing countries that imbue a communitarian schema of values. Through a Glaserian grounded theory, the qualitative inquiry purported to provide a model which would uncover the process of sensemaking of communitarian values to enrich the transformational leadership attributes of the millennial academic supervisors. Twenty (20) information-rich cases from various comprehensive universities in the Philippines participated in the inquiry. Interestingly, the study revealed four (4) distinct yet interwoven stages of Build up, Engage in, Lean on, and Live through. The ‘BELL Model of Culturally Sensitive Transformational Leadership Attribute Enrichment among Millennial Academic Supervisors’ can serve as a pragmatic framework that could assist the teacher-leaders hailing from communitarian societies with a scaffolding that resonates with their modern-day sensibilities and celebrates their indigeneity.

Effects of surface chemistry on the mechanochemical decomposition of tricresyl phosphate.

The growth of protective tribofilms from lubricant antiwear additives on rubbing surfaces is initiated by mechanochemically promoted dissociation reactions. These processes are not well understood at the molecular scale for many important additives, such as tricresyl phosphate (TCP). One aspect that needs further clarification is the extent to which the surface properties affect the mechanochemical decomposition. Here, we use nonequilibrium molecular dynamics (NEMD) simulations with a reactive force field (ReaxFF) to study the decomposition of TCP molecules confined and pressurised between sliding ferrous surfaces at a range of temperatures. We compare the decomposition of TCP on native iron, iron carbide, and iron oxide surfaces. We show that the decomposition rate of TCP molecules on all the surfaces increases exponentially with temperature and shear stress, implying that this is a stress-augmented thermally activated (SATA) process. The presence of base oil molecules in the NEMD simulations decreases the shear stress, which in turn reduces the rate constant for TCP decomposition. The decomposition is much faster on iron surfaces than iron carbide, and particularly iron oxide. The activation energy, activation volume, and pre-exponential factor from the Bell model are similar on iron and iron carbide surfaces, but significantly differ for iron oxide surfaces. These findings provide new insights into the mechanochemical decomposition of TCP and have important implications for the design of novel lubricant additives for use in high-temperature and high-pressure environments.

Assessing stock of reef octopus Octopus cyanea in southwest Madagascar using age-based population modelling

The reef octopus Octopus cyanea fishery is the most economically important fishery in southwest Madagascar. The substantial increase of octopus exploitation in the region has raised concerns over the sustainability of this fishery. While a growing number of measures have been implemented to sustainably manage the octopus stock, there is a lack of information on the status of this octopus stock. In this study, we analyse the status of octopus stock in southwest Madagascar by investigating the interannual and seasonal variability in recruitment and fishing mortality using virtual population analysis (VPA) performed on monthly basis from 2020 to 2022. Yield per recruit is also predicted using a Thomson and Bell model. Our results indicate that octopus fishery national closures (December 15 to January 31 each year) result overall in increase of catches and stock biomass, evidencing the positive impacts of the implemented fisheries regulations in the region. Recruitment exhibits high interannual and seasonal variability with a peak observed between October and December. The simulation model suggests that yield per recruit remains almost unchanged from one year to the next and not exceeding the maximum yield per recruit. Overall, this study shows the importance of understanding the status of octopus stock for sustainable octopus fisheries in southwest Madagascar.

Analysis of the Influencing Factors of High-speed Railway Brand Image Based on the Bell Model

Analysis of the Influencing Factors of High-speed Railway Brand Image Based on the Bell Model

Length-based stock assessment for Procambarus clarkii aquaculture management in China: An alarming of ongoing recruitment overfishing

Procambarus clarkii is a commercially significant species both domestically and internationally, and has become the most extensively farmed fishery species in China. However, accurately assessing stocks is often challenging, especially for data-poor fisheries, which undermines effective fishery management. This study aims to identify gaps in the stock status of P. clarkii and provide guidance for effective aquaculture management to promote the sustainability in the P. clarkii aquaculture industry. A total of 2035 crayfish were collected to obtain length-frequency data from March 2016 to February 2017 in the Selection and Reproduction Center of Crayfish, Houhu management area, Qianjiang, China. The seasonally oscillating von Bertalenffy Growth Function (VBGF) was fitted using two optimized ELEFAN approaches (ELEFAN_SA, a simulated annealing algorithm; ELEFAN_GA, a genetic algorithm) to estimate the growth, mortality, and exploitation rates of P. clarkii population. ELEFAN_SA provided a better fit and was subsequently used to derive the following results: an asymptotic total length (Linf) of 130.86 mm, a growth coefficient (K) of 0.63 year−1, initial condition parameter (t0) of −0.32 year−1, expected longecity (tmax) of 4.44 year−1, a total mortality (Z) of 1.96 year−1, a natural mortality (M) of 0.58 year−1, a fishing mortality (F) of 1.38 year−1 and a exploitation rate (E) of 0.70. The Thompson and Bell model estimated the overall stock biomass at approximately 1.92 tons, with the biological reference levels of F0.1 = 0.78 year−1, F0.5 = 0.59 year−1, E0.1 = 0.40, and E0.5 = 0.30. The current F and E (1.38 year−1 and 0.70) exceeded the established thresholds, indicating a high risk of overexploitation of the P. clarkii population. Jones' length-based cohort analysis demonstrated P. clarkii individuals with a total length ranging from 86 mm to 102 mm were more vulnerable to fishing pressure, and that the current fishing selectivity primarily targeted at immature juvenile P. clarkii. The results of GTG-LBSPR model estimated the stock's spawning potential ratio (SPR) at 0.33, which was below the target SPR of 0.4, suggesting a possible ongoing recruitment overfishing. Based on the findings of this study, it strongly advocates for collaborative efforts among researchers, fishery managers, and fish farmers in finding practical and effective measures, such as implementing the size limit for the first capture, that ensure the long-term reproductive capacity and sustainability of P. clarkii populations. Furthermore, it highly encourages moderate fishing pressure on fast-growing and reproductive potential individuals to offset negative impacts of overfishing and promote high SPR and sustainability.

Instability evolution of a shock-accelerated thin heavy fluid layer in cylindrical geometry

Instability evolutions of shock-accelerated thin cylindrical SF $_6$ layers surrounded by air with initial perturbations imposed only at the outer interface (i.e. the ‘Outer’ case) or at the inner interface (i.e. the ‘Inner’ case) are numerically and theoretically investigated. It is found that the instability evolution of a thin cylindrical heavy fluid layer not only involves the effects of Richtmyer–Meshkov instability, Rayleigh–Taylor stability/instability and compressibility coupled with the Bell–Plesset effect, which determine the instability evolution of the single cylindrical interface, but also strongly depends on the waves reverberated inside the layer, thin-shell correction and interface coupling effect. Specifically, the rarefaction wave inside the thin fluid layer accelerates the outer interface inward and induces the decompression effect for both the Outer and Inner cases, and the compression wave inside the fluid layer accelerates the inner interface inward and causes the decompression effect for the Outer case and compression effect for the Inner case. It is noted that the compressible Bell model excluding the compression/decompression effect of waves, thin-shell correction and interface coupling effect deviates significantly from the perturbation growth. To this end, an improved compressible Bell model is proposed, including three new terms to quantify the compression/decompression effect of waves, thin-shell correction and interface coupling effect, respectively. This improved model is verified by numerical results and successfully characterizes various effects that contribute to the perturbation growth of a shock-accelerated thin heavy fluid layer.

Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation.

Steered molecular dynamics (SMD) simulations are used to study molecular dissociation events by applying a harmonic force to the molecules and pulling them at a constant velocity. Instead of constant-velocity pulling, we use a constant force: the constant-force SMD (CF-SMD) simulation. The CF-SMD simulation employs a constant force to reduce the activation barrier of molecular dissociation, thereby enhancing the dissociation event. Here, we present the capability of the CF-SMD simulation to estimate the dissociation time at equilibrium. We performed all-atom CF-SMD simulations for NaCl and protein-ligand systems, producing dissociation time at various forces. We extrapolated these values to the dissociation rate without a constant force using Bell's model or the Dudko-Hummer-Szabo model. We demonstrate that the CF-SMD simulations with the models predicted the dissociation time in equilibrium. A CF-SMD simulation is a powerful tool for estimating the dissociation rate in a direct and computationally efficient manner.

Divergent Richtmyer–Meshkov instability on a heavy gas layer

Experiments on divergent Richtmyer–Meshkov (RM) instability at a heavy gas layer are performed in a specially designed shock tube. A novel soap-film technique is extended to generate gas layers with controllable thicknesses and shapes. An unperturbed gas layer is first examined and its two interfaces are found to move uniformly at the early stage and be decelerated later. A general one-dimensional theory applicable to an arbitrary-thickness layer is established, which gives a good prediction of the layer motion in divergent geometry. Then, six kinds of perturbed SF $_6$ layers with various thicknesses and shapes surrounded by air are examined. At the early stage, the amplitude growths of the inner interface for various-thickness layers collapse quite well and also can be predicted by the Bell model for cylindrical RM instability at a single interface, which indicates a negligible interface coupling effect. Later, a rarefaction wave accelerates the inner interface, causing a dramatic rise in the growth rate. It is found that a thicker gas layer will result in a larger extent that the rarefaction wave can promote the instability growth. A modified Bell model accounting for both Rayleigh–Taylor (RT) instability and interface stretching caused by a rarefaction wave is established, which well reproduces the quick instability growth. At late stages, reverberating waves inside the layer are negligibly weak such that the inner interface growth is dominated by RM instability and RT stability. The major factors driving the outer interface development are a compression wave and interface coupling. A new interface coupling phenomenon existing uniquely in divergent geometry caused by the gradual thinning of the gas layer is observed and also modelled.

Single molecule magnetic tweezers for unfolding dynamics of Acyl-CoA binding protein

There are significant differences in mechanical stability and unfolding dynamics among proteins with different structural compositions. Compared with proteins with β-sheets and subjected to shearing forces, proteins that are composed entirely of α-helices often undergo rapid unfolding under low stretching forces, thus requiring quantitative studies by using experimental tools that can precisely control forces on a pico-Newton scale. Magnetic tweezers with intrinsic force-control capability and great stability for long-time continuous measurement are suitable to measure force-induced conformation transitions of protein subjected to low forces of several pico-Newton. Acyl-CoA binding protein (ACBP) is a model protein used to study the folding/unfolding kinetics of complete α-helices protein. It is composed of 86 amino acid residues, forming a helical bundle of four α-helices. When its N- and C-terminal are stretched, the first and last α-helix are subjected to shear force in parallel. Previous biochemical studies showed that ACBP folding and unfolding in a two-state manner. In this paper, we use magnetic tweezers to stretch ACBP from its N- and C-end and obtain the distribution of the unfolding force at different loading rates ranging from 0.25 pN/s to 4 pN/s. The most probable unfolding forces are all less than 10 pN, which confirms that ACBP is not mechanically stable. At a constant loading rate, the unfolding force distribution and the most probable unfolding force as a function of loading rate have well-defined analytical formulas based on Bell’s model. Therefore, the experimental results of unfolding force can be fitted directly to obtain the important kinetic parameter of unfolding distance which is defined as the difference in extension between the native state and the transition state. Data analysis shows that ACBP has an extraordinarily long unfolding distance of 7.8 nm. Steered molecular dynamics simulations of ACBP stretching gives the transition state with N-terminal α-helix fully unfolded and C-terminal α-helix partially unfolded, which is consistent with the long unfolding distance obtained in the experiment on magnetic tweezers. According to the simulation results, the unfolding of α-helices is less cooperative than that of β-sheet structures. This characteristic makes α-helix proteins sensitive to mechanical forces, rendering them suitable as force sensors in cells. This study shows that single-molecule stretching experiment combined with molecular dynamics simulations is a reliable method to reveal the molecular mechanism of protein conformationtransitions under stretching forces.

Simulating Mesh-size and Selection Pattern Impacts on the Lake Turkana Fisheries Sustainability in Kenya

The study compared impacts of different gear mesh sizes and landing sizes (Lcap) through gillnet and knife-edge selection patterns on Tilapia and Nile perch of Lake Turkana. The results will help contribute to the debate on whether to capture large and protect small fish or vice versa. R simulation employing the 1934 Thompson and Bell's model for data-deficient stocks was used to simulate fish cohorts using secondary input data for the two species. Gillnet selection pattern with recommended mesh size (127 mm) produced an 80% increase in Tilapia YPR while ESS and SPR ratios reduced by 12.5%. and 14.3% respectively when fishing mortality (F) was tripled to 3.0. Nile perch's YPR increased by 90% while ESS and SPR dropped by 70 and 75% each when F increased to 0.8. Tilapia YPR maximized by reducing mesh size to 101.6 mm at F=2, and maintained ESS and SPR at 20% each, while the Nile perch YPR dropped by 20% and 66.7% respectively at F=1.0. Small mesh-sized (<40 mm) gears had no effect on Tilapia’s ESS and SPR but produced the lowest YPR ratios. The 152.4 mm mesh for Nile perch produced a 25% YPR increase and maintained optimal ESS and SPR at F=0.5. Knife-edge selection pattern utilizing 127 mm, 20 cm Lcap and F=1.5, produced 50% YPR, ESS, and SPR for Tilapia, and maintained at F=3.0. Large-sized Nile perch using 152.4 mm gear resulted in about 40% YPR of the stock. Reduction of Lcap using 127 mm gear, produced a 75% increase in YPR. ESS and SPR depicted Nile perch collapse at F>0.65. Mesh size and selection pattern impacts are dependent on F. Small mesh gillnets are not damaging if F is controlled and caution should be taken with them in a knife-edge selection. This study recommends 101.6 mm and 152.4 mm mesh sizes for Tilapia and Nile perch respectively in Lake Turkana

Dhokra craft: socio-economic conditions of artisans, economics and marketing challenges in Kondagaon district of Chhattisgarh state, India

Indian handicrafts have a long and illustrious history. However, the state of the artisans in India has been deplorable. Among all the bell metal crafts, one of the most ancient crafts dating back to the Harrapan civilisation. This study investigates the socio-economic conditions and marketing challenges faced by artisans. Using a sample rate of 30 per cent, data was collected through a field survey involving 100 respondents from a total of 320 artisans. In-depth interviews and focussed group discussions were conducted to gain insights. Based on existing literature, a clear concept of costs and returns is constructed and explored further. Results indicate that artisans are engaged nearly 90 days a year and earn around US $1300. Although there is a strong demand for these products in international and domestic markets, the artisans cannot cope with the production due to higher costs of raw materials and ancient production technologies. Marketing challenges in the form of intermediaries and connectivity to the markets act as significant hurdles. The study proposed a BELL model to integrate the current government programmes and cause a convergence in existing institutions to overcome the issues faced by the artisans.

Shear-driven reactions of organosulfur compounds on ferrous surfaces: A molecular dynamics study

Reactive molecular dynamics simulations were used to investigate reactions between di-tert-butyl disulfide and ferrous surfaces. Tribochemical reactions were characterized with and without a model base oil, n-dodecane, and on either Fe(100) or H-passivated Fe2O3 surfaces. Reaction yield increased with both temperature and pressure for all model systems. The presence of the base oil did not significantly affect the reaction yield or pathway, but the base oil impeded transmission of shear stress to the reactants. Replacing the ideal Fe(100) with H-passivated Fe2O3 surfaces enabled reaction pathways involving oxygen from the surface and decreased the reaction yield. The rate-limiting step of the reactions was analyzed in the context of the Bell model as a step towards better understanding tribochemical reactions.

GEE-based Bell model for longitudinal count outcomes

Longitudinal count models are usually constructed based on Poisson and negative binomial distributions. Recently, a single-parameter discrete Bell distribution has been presented as an alternative to well-known count distributions. In this study, a new marginal model is proposed for longitudinal count responses based on Bell distribution to handle overdispersion and dependency structure. Bell distribution is more practical in that it has fewer parameters than the negative binomial distribution and still handle overdispersion with a single parameter. Focusing on demonstrating that regression diagnostics supplement the Bell marginal model based on GEE to serve as sensitivity analysis. The Bell marginal model is used to analyze the number of accidents caused injuries in Greece during the 5-year time period. The half-normality plots indicate that the Bell marginal model provides better fit than other marginal models for the accident dataset. The common working covariance selection criterias and properties of parameter estimations are investigated for the Bell marginal model in the simulation study. Parameter estimations of the new model based on GEEs are obtained by geeM R package with the user-defined function. Diagnostic measures and simulated envelope algorithm are also provided for the proposed model.

A Note About Model Selection and Hypothesis Test Procedure to Discriminate Poisson and Bell Models

A Note About Model Selection and Hypothesis Test Procedure to Discriminate Poisson and Bell Models

Molecular dynamics simulation of calcium silicate hydrate/tannic acid interfacial interactions at different temperatures: configuration, structure and dynamic

In the paper, the effect of temperature on tannic acid molecular conformation and the interaction between tannic acid and substrate were investigated systematically by molecular dynamics. The tensile force of tannin acid separation from CSH matrix at three temperatures was calculated by SMD simulation, and then the adhesion energy between tannin acid and CSH was calculated by Bell Model. The results showed that high temperature affects the gyration of the single bond in the tannic acid, which leads to the increase of tannic acid molecular chain size and radius of gyration. Tannic acid molecules are more extended and the contact area with the substrate became larger in high temperature, which enhanced interfacial adhesion energy. Further, by analyzing the structure and dynamics of the composite, it comes out that not only the substrate has more sites available for tannic acid but also the interfacial ionic bonding formed is more stable after high temperature. Enhanced interfacial chemical bonds limit the bending motion of tannic acid molecular, which leave them in a well-stretched state, to causes tannic acid to be stably adsorbed on the substrate.