Miracle-dz/UniFAR-FTUs huggingface dataset:
Oceanic vertical mixing: a review and a model with a nonlocal boundary layer parameterization

If model parameterizations of unresolved physics, such as the variety of upper ocean mixing processes, are to hold over the large range of time and space scales of importance to climate, they must be strongly physically based. Observations, theories, and models of oceanic vertical mixing are surveyed. Two distinct regimes are identified: ocean mixing in the boundary layer near the surface under a variety of surface forcing conditions (stabilizing, destabilizing, and wind driven), and mixing in the ocean interior due to internal waves, shear instability, and double diffusion (arising from the different molecular diffusion rates of heat and salt). Mixing schemes commonly applied to the upper ocean are shown not to contain some potentially important boundary layer physics. Therefore a new parameterization of oceanic boundary layer mixing is developed to accommodate some of this physics. It includes a scheme for determining the boundary layer depth h, where the turbulent contribution to the vertical shear of a bulk Richardson number is parameterized. Expressions for diffusivity and nonlocal transport throughout the boundary layer are given. The diffusivity is formulated to agree with similarity theory of turbulence in the surface layer and is subject to the conditions that both it and its vertical gradient match the interior values at h. This nonlocal “K profile parameterization” (KPP) is then verified and compared to alternatives, including its atmospheric counterparts. Its most important feature is shown to be the capability of the boundary layer to penetrate well into a stable thermocline in both convective and wind-driven situations. The diffusivities of the aforementioned three interior mixing processes are modeled as constants, functions of a gradient Richardson number (a measure of the relative importance of stratification to destabilizing shear), and functions of the double-diffusion density ratio, Rρ. Oceanic simulations of convective penetration, wind deepening, and diurnal cycling are used to determine appropriate values for various model parameters as weak functions of vertical resolution. Annual cycle simulations at ocean weather station Papa for 1961 and 1969–1974 are used to test the complete suite of parameterizations. Model and observed temperatures at all depths are shown to agree very well into September, after which systematic advective cooling in the ocean produces expected differences. It is argued that this cooling and a steady salt advection into the model are needed to balance the net annual surface heating and freshwater input. With these advections, good multiyear simulations of temperature and salinity can be achieved. These results and KPP simulations of the diurnal cycle at the Long-Term Upper Ocean Study (LOTUS) site are compared with the results of other models. It is demonstrated that the KPP model exchanges properties between the mixed layer and thermocline in a manner consistent with observations, and at least as well or better than alternatives.
Protein Z modulates the metastasis of lung adenocarcinoma cells

Abstract Protein Z (PZ), a vitamin-K-dependent anticoagulant glycoprotein, is reported to be highly expressed in various malignant tissues and correlated with a poor prognosis in patients with lung cancer. This study aimed to investigate the pathological activity of PZ on lung cancer cell migration, invasion, and metastasis. PZ was assessed by Western blot in three non-small-cell lung cancer cell lines (A549, H1299, and H1975). Meanwhile,western blot was used to detect the expression of EMT pathway-related proteins (Slug, Vimentin, and N-cadherin) in the A549 cells knocked down with siRNA. The cellular proliferation, migration, and invasion were detected by Cell Counting Kit (CCK)-8, wound healing, and Transwell assays in the A549 cells. The results showed that PZ expression was higher in A549, H1299, and H1975 cells, according to Western blot. CCK-8, wound healing, and Transwell assays showed that knockdown of PZ significantly decreased cellular proliferation, migration, and invasion, as well as the protein levels of Slug, Vimentin, and N-cadherin in the A549 cells. In conclusion, the pro-metastasis activity of PZ may modulate the epithelial–mesenchymal transition pathway in lung cancer A549 cells. Graphical abstract Epithelial–mesenchymal transition (EMT)-related proteins (Slug, vimentin, and N-cadherin) are downregulated by Protein Z silencing, which significantly prohibits cellular proliferation and EMT activity (decrease of cellular migration and invasion) in non-small-cell lung cancer cells.
I/O Access Patterns in HPC Applications: A 360-Degree Survey

The high-performance computing I/O stack has been complex due to multiple software layers, the inter-dependencies among these layers, and the different performance tuning options for each layer. In this complex stack, the definition of an “I/O access pattern” has been reappropriated to describe what an application is doing to write or read data from the perspective of different layers of the stack, often comprising a different set of features. It has become common to have to redefine what is meant when discussing a pattern in every new study, as no assumption can be made. This survey aims to propose a baseline taxonomy, harnessing the I/O community’s knowledge over the past 20 years. This definition can serve as a common ground for high-performance computing I/O researchers and developers to apply known I/O tuning strategies and design new strategies for improving I/O performance. We seek to summarize and bring a consensus to the multiple ways to describe a pattern based on common features already used by the community over the years.
Bargraphs in bargraphs

Abstract: Bargraphs are lattice paths in N0 that start at the origin and end upon their first return to the x -axis. Each bargraph is represented by a sequence of column heights π1π2 · · ·πm such that column j contains πj cells. In this paper, we study the number of bargraphs with n cells and m columns according to the distribution for the statistic that records the number of times a given shape lies entirely within a bargraph for various small shapes.
THE EFFECT OF CHAOS THEORY ON THE PREDICTABILITY OF THE ATMOSPHERE

It is known that atmosphere is a dynamical system that constantly changing and moving. It is a very difficult problem to completely determine and explain the change in the atmosphere. But the mathematical models can help us to understand and explain the dynamical processes in the atmosphere. Examination of the movements of the atmosphere is one of the most exciting applications of chaos theory. The main goals of this presentation will be try to discuss the effect of chaos theory on the predictability of the atmosphere. For this purpose, we focus on one of the most specific examples of atmosphere events, is global climate change.
Direct computation of cyclotomic $p$-adic multiple zeta values

Cyclotomic $p$-adic multiple zeta values are $p$-adic periods of the crystalline pro-unipotent fundamental groupoid of $\mathbb{P}^{1} - \{0,\mu_{N},\infty\}$. We generalize their definition by replacing the Frobenius by the iterated Frobenius. We establish jointly a lower bound of the valuation and a recursive formula for cyclotomic $p$-adic multiple zeta values and, more generally, for the values of the iterated Frobenius at the canonical De Rham paths. This will be used as a technical preliminary for the definitions of pro-unipotent harmonic actions in subsequent papers. This paper is the part I-1 of a work called \emph{Cyclotomic $p$-adic multiple zeta values and pro-unipotent harmonic actions}.
The method of Weighted Multi objective Fractional Linear Programming Problem (MOFLPP)

More theories and algorithms in non-linear programming with titles convexity (Convex). When the objective function is fractional function, will not have to have any swelling, but can get other good properties have a role in the development of algorithms decision problem.In this work we focus on the weights method- (one of the classical methods to solve Multi objective convex case problem). Since we have no convex or no concave objective functions, and this condition is essential part on this method implementation, we these valid conditions under method as generator sets efficient and weakly efficient this problem. This raises the need to a detailed study of pseudoconvex idea, cause convex idea, Invex, pseudoinvex idea,…, etc. concepts. Offer a numerical example to show the valid by the conditions previously set generate all weakly efficient set our problem.
The influence of carbon dioxide on cerebral metabolism and oxygen consumption: combining multimodal monitoring with dynamic systems modelling

Hypercapnia increases cerebral blood flow, but the effect on cerebral metabolism in humans remains incompletely understood. Either increased or reduced oxygen consumption has been predicted from Fick models incorporating cerebral oxygen extraction fraction and cerebral blood flow. Hypercapnia also results in oxidation of cytochrome c oxidase, complex IV of the mitochondrial respiratory chain, implicating a change in cellular metabolism. The aim of this study was to combine systems modelling with non-invasive measurements of cerebral tissue oxygenation, cerebral blood flow, and cytochrome c oxidase redox state to evaluate any metabolic effects of hypercapnia. Cerebral tissue oxygen saturation and cytochrome oxidase redox state were measured with broadband near infrared spectroscopy and cerebral blood flow velocity using transcranial Doppler ultrasound. Data collected during 5-minutes hypercapnia in human volunteers were analyzed using a Fick model to determine changes in brain oxygen consumption and a mathematical model of cerebral hemodynamics and metabolism (BrainSignals) to inform on the potential mechanisms of any observed changes. Systemic physiology - blood pressure, arterial oxygen saturations and end-tidal carbon dioxide - served as model inputs. The extent of the hypercapnic oxidation of cytochrome oxidase required modifications of the BrainSignals model; simulations compared two possible modifications that could cause this oxidation - a decrease in metabolic substrate supply or an increase in metabolic demand. Only the decrease in substrate supply was able to explain both the enzyme redox state changes and the Fick calculated drop in brain oxygen consumption. These modelled outputs are consistent with, but do not prove, previous reports of CO2 inhibition of succinate dehydrogenase, complex II of the mitochondrial respiratory chain. These findings suggest that hypercapnia may have physiologically significant effects suppressing oxidative metabolism in humans and perturbing mitochondrial signaling pathways in health and disease.
A parametric finite element model of leg campaniform sensilla in Drosophila to study CS location and arrangement

Campaniform sensilla (CS) are mechanosensors embedded within the cuticle of many insects at key locations such as nearby leg segment joints or halters. CS located at leg segments were found to respond to cuticle bending which can be induced by walking or jumping movements or by the underlying tensile forces of the muscles. For Drosophila it is unclear how CS location and material property variation influence stress levels within and around CS but this information is crucial to understand how flies might use CS input to adjust walking behaviour. Here, we designed a parametric model of the femoral CS field for Drosophila to allow for a systematic testing of the influence of CS location, orientation and material property variation on stress levels. The model consists of 7 changeable parameters per CS and 12 which can be changed for the CS field. Simulations of leg bending are in line with general beam bending theory: At the specific proximal CS field location nearby the trochantero-femoral leg joint, displacements are smaller than distal, while stresses are higher. When changing CS location towards more distal leg parts the situation changes towards more displacement and less stress. Changes in material property values for CS substructures or whole CS fields have a very low influence on stress or displacement magnitudes (regarding curve shape and amplitude) at the CS caps to which the nerve cells attach. Taken together, our simulation results indicate that for CS fields located at proximal leg parts, the displacements induced by other sources such as muscle tensile forces might be more relevant stimuli than the overall leg bending induced by typical locomotion scenarios. Future parametric finite element models should contain experimentally validated information on the anisotropic and viscoelastic properties of materials contained in this sensory system to further our understanding of CS activation patterns.
Macroecological laws in experimental microbial systems

Historically, ecology has benefited by characterizing statistical patterns of biodiversity within and across communities. This approach, known as macroecology, has achieved considerable success in microbial ecology in recent years, having identified universal patterns of diversity and abundance that can be captured by effective models that do not require interactions between community members. Experimentation has simultaneously played a crucial role in the field’s development, as the manipulation of high-replication time-series has revealed novel forces that govern community dynamics. However, there remains a gap between microbial experiments performed in the laboratory and macroecological patterns documented in natural systems. Here, we work to bridge the gap between the experimental manipulation of communities and their macroecological effects. Using high-replication time-series of experimental microbial communities, we demonstrate that macroecological laws observed in nature can be readily recapitulated in a laboratory setting and unified under the Stochastic Logistic Model of growth (SLM). We find that demographic manipulations and their effect on community-level variation can alter empirical patterns in a manner that diverges from our predictions, though the predictive capacity of the SLM can be restored by incorporating explicit experimental details. Finally, we demonstrate the extent that experimental manipulations are capable of altering macroecological patterns under the SLM, establishing a demarcation between macroecological effects we can and cannot observe in a laboratory setting.
Structural coverage of the human interactome

Complex biological processes in cells are embedded in the interactome, representing the complete set of protein-protein interactions. Mapping and analyzing the protein structures are essential to fully comprehending these processes’ molecular details. Therefore, knowing the structural coverage of the interactome is essential to show the current limitations. Structural modeling of protein-protein interactions requires accurate protein structures. In this study, we mapped all experimental structures to the reference human proteome. Later, we found the enrichment in structural coverage when complementary methods such as homology modeling and deep learning (AlphaFold) are included. We then collected the interactions from the literature and databases to form the reference human interactome resulting in 117,897 non-redundant interactions. When we analyzed the structural coverage of the interactome, we found that the number of experimentally determined protein complex structures is scarce, corresponding to 3.95% of all binary interactions. We also analyzed known and modeled structures to potentially construct the structural interactome with a docking method. Our analysis showed that 12.97% of the interactions from HuRI, 73.62%, and 32.94% from the filtered versions of STRING and HIPPIE could potentially be modeled with a high structural coverage or accuracy, respectively. Overall, this paper provides an overview of the current state of structural coverage of the human proteome and interactome. Significance Statement We gathered binary protein-protein interactions from three prominent interactome databases to create a comprehensive human reference interactome. We quantified the structural coverage of the human interactome using already available structural data from four different sources. We further evaluate the percentage of interactions that can be accurately predicted using docking methods.
Changes in dorsomedial striatum activity mediate expression of goal-directed vs. habit-like cue-induced cocaine seeking

A preclinical model of cue exposure therapy, cue extinction, reduces cue-induced cocaine seeking when drug seeking is goal-directed but not habitual. Goal-directed and habitual behaviors differentially rely on the dorsomedial striatum (DMS) and dorsolateral striatum (DLS), but the effects of cue extinction on dorsal striatal responses to cue-induced drug seeking are unknown. We used fiber photometry to examine how dorsal striatal intracellular calcium and extracellular dopamine activity differs between goal-directed and habitual cue-induced cocaine seeking and how it is impacted by cue extinction. Rats trained to self-administer cocaine paired with an audiovisual cue on schedules of reinforcement that promote goal-directed or habitual cocaine seeking had different patterns of dorsal striatal calcium and dopamine responses to cue-reinforced lever presses. Cue extinction reduced calcium and dopamine responses during subsequent drug seeking in the DMS, but not in the DLS. Therefore, cue extinction may reduce goal-directed behavior through its effects on the DMS, whereas habitual behavior and the DLS are unaffected.
A cline within an ecotype of the yellow monkeyflower, Mimulus guttatus

Premise A key goal of evolutionary biologists is to understand how and why genetic variation is partitioned within species. In the yellow monkeyflower, Mimulus guttatus (syn. Erythranthe guttata), coastal perennial populations collectively constitute a single genetically and morphologically differentiated ecotype compared to inland populations of M. guttatus. While the distinctiveness of the coastal ecotype has now been well documented, there is also variation in environmental factors across the range of the coastal ecotype that could drive differentiation among its component populations in a more continuous way. Methods Based on previous observations of a potential cline within this ecotype, we quantified plant height across coastal perennial accessions from 66 total populations in a greenhouse common garden experiment. To evaluate possible environmental factors driving the relationship between trait variation and latitude, we regressed height against multiple climatic factors, including temperature, precipitation, and coastal wind speeds. Results The most significant relationship discovered in our experiment was a negative correlation between plant height and latitude. Plant height correlated negatively with annual precipitation and mean wind speed. Height was positively correlated with mean annual temperature. We hypothesize that one or more of these climatic factors drove the evolution of clinal variation within the coastal ecotype. Conclusion Overall, our study illustrates the complexity of how the distribution of environmental variation can simultaneously drive the evolution of distinct ecotypes as well as continuous clines within those ecotypes. These results are discussed in the context of the classic criticisms of ecotypes being intermediates in the process of speciation.
Learning Neural Representations in Task-Switching Guided by Context Biases

The ability to switch between tasks effectively in response to external stimuli is a hallmark of cognitive control. Our brain can filter and integrate external information to accomplish goal-directed behavior. Task switching occurs rapidly and efficiently, allowing us to perform multiple tasks with ease. Similarly, artificial neural networks can be tailored to exhibit multi-task capabilities and achieve high performance across domains. In terms of explainability, understanding how neural networks make predictions is crucial for their deployment in many real-world scenarios. In this study, we delve into neural representations learned by task-switching networks, which use task-specific bias for multitasking. Task-specific biases, mediated by context inputs, are learned by alternating the tasks the neural network learns during training. By using the MNIST dataset and binary tasks, we find that task-switching networks produce representations that resemble other multitasking paradigms, namely parallel networks in the early stages of processing and sequential networks in the last stages, respectively. We analyze the importance of inserting task contexts in different stages of processing and its role in aligning the task with relevant features. Moreover, we visualize how networks generalize neural representations during task-switching for different tasks. The use of context inputs improves the interpretability of simple neural networks for multitasking, helping to pave the way for the future study of architectures and tasks of higher complexity.
Fixed point theory for generalized'-weak contractions

(1.1)The concept of the weak contraction was defined by Alber and Guerre-Delabriere [1] in 1997. Actually in [1], the authorsdefined such mappings for single-valued maps on Hilbert spaces and proved the existence of fixed points. Rhoades [6]showed that most results of [1] are still true for any Banach space. Also Rhoades [6] proved the following very interestingfixed point theorem which is one of generalizations of the Banach contraction principle because it contains contractions asspecial cases (
On the structure and interpretation of Polish passives

The realization of Polish passives is influenced by the specific properties that a given participle shares with its verbal base. These include: argument structure and aspectual type, the conjugation class and the phonological properties of the stem. This paper offers an account of how these variables are reflected in the exponence and morphophonology of Polish passives. The paper presents an analysis of the distribution of Passive Participle Markers -l- /ɫ/, -t- /t/, -n- /n/ and -on- /ɔn/ in Polish within a syntactic approach to word formation (Jablonska 2004; Caha 2009, Embick & Marantz 2008). I also address the issue of the morphophonological mutations attested in Polish passive participles and postulate that they should not be given a uniform analysis. The alternation between /ɛ/ and /a/ attested in Polish ej- and e-verbs is suppletive in nature, while mutations attested in the thematic marker -ną-~-nie- /nɔ/~/ɲɛ/ and the Passive Participle Marker -on-~-eni- /ɔn/~/ɛɲ/ are triggered by the integration.