Miracle-dz/UniFAR-FTUs huggingface dataset:
Mental Simulation of Action in the Service of Action Perception

We used the quantitative 14C-deoxyglucose method to map the activity pattern throughout the frontal cortex of rhesus monkeys, which either grasped a three-dimensional object or observed the same grasping movements executed by a human. We found that virtually the same frontal cortical networks were recruited for the generation and the perception of action, including the primary motor cortex (MI/F1), premotor cortical areas (F2, F5, and F6), the primary (SI) and supplementary (SSA) somatosensory cortex, medial cortical areas (8m and 9m), and the anterior cingulate. The overlapping networks for action execution and action observation support the notion that mental simulation of action could underlie the perception of others' actions. We suggest that the premotor and the somatotopic MI/F1 activations induced by action observation reflect motor grasp of the observed action, whereas the somatotopic SI and the SSA activations reflect recruitment of learned sensory–motor associations enabling perceptual understanding of the anticipated somatosensory feedback. We also found that the premotor activations were stronger for action observation, in contrast to the primary somatosensory–motor ones, which were stronger for action execution, and that activations induced by observation were bilateral, whereas those induced by execution were contralateral to the moving forelimb. We suggest that these differences in intensity and lateralization of activations between the executive and the perceptual networks help attribute the action to the correct agent, i.e., to the “self” during action execution and to the “other” during action observation. Accordingly, the “sense of agency” could be articulated within the core components of the circuitry supporting action execution/observation.
Antigenic variation in Plasmodium chabaudi: analysis of parent and variant populations by cloning

Summary Nineteen of 22 recrudescent populations of Plasmodium chabaudi AS strain were found to be significantly less sensitive to the protective activity of pools of immune serum, than the parent population from which they were derived. The immune sera were collected from donor mice which had been infected with the parent population and had just reduced the patent primary parasitaemia to subpatent levels. Clones prepared from the parent population (which had previously been cloned) and recrudescent variant populations were tested for their sensitivity to the immune sera. It was found that all the clones from the parent population were sensitive to the immune sera but some were more sensitive than others and that a recrudescent variant population could include both sensitive and insensitive parasites. Two insensitive clones of the recrudescent population were found to be different from each other
Programming evolvable web services

Web services have emerged as a technology for designing and composing distributed applications. Recent research increasingly addressed the need to adapt such systems based on changing requirements and environmental constraints. From the developers point of view, it is already a daunting task to update the description, implementation, or configuration of individual services that are already deployed in the runtime environment. A major undertaking is update and maintenance of large scale service environments. In this work, we introduce a programming model enabling the adaptation and evolution of service-oriented systems in a simple and intuitive way. Most existing work focuses on self-adaptation aspects. We present a user-centric approach and a framework supporting both automatic mechanisms for adaptation and foremost a programming model to reduce the burden of reconfiguration, update, and customization of service-based applications. We implemented the programming model on top of Genesis, a Java-based Web services framework.
Operations modeling and analysis of open pit copper mining using GPS tracking data

Open pit copper mining plants usually comprise two major components, the open pit mining operation and the copper ore enrichment plant. An open pit copper mine is an excavation or graze made into the surface of the ground for the purpose of extracting ore. A series of data obtained by a transportation control system with GPS (Global Positioning System) technology is utilized to perform the simulation. Operations in the mine are based on a mining plan and must be optimized because the transportation costs are expensive. In this paper, procedures are proposed to obtain an optimized number of trucks and to estimate the maximum mining capacity at an open copper pit. Then, the creation of a truck dispatching control table for meeting the maximum mining capacity is demonstrated by performing a simulation.
Doxycycline delivery from PLGA microspheres prepared by a modified solvent removal method

We report on the development of a modified solvent removal method for the encapsulation of hydrophilic drugs within poly(lactic-co-glycolic acid) (PLGA). Using a water/oil/oil double emulsion, hydrophilic doxycycline was encapsulated within PLGA spheres with particle diameters ranging from approximately 600 nm to 19 µm. Encapsulation efficiencies of up to 74% were achieved for theoretical loadings from 1% to 10% (w/w), with biphasic release over 85 days with nearly complete release at the end of this time course. About 1% salt was added to the formulations to examine its effects on doxycycline release; salt modulated release only by increasing the magnitude of initial release without altering kinetics. Fourier transform infrared spectroscopy indicated no characteristic differences between doxycycline-loaded and control spheres. Differential scanning calorimetry and X-ray diffraction suggest that there may be a molecular dispersion of the doxycycline within the spheres and the doxycycline may be in an amorphous state, which could explain the slow, prolonged release of the drug.
Advanced 3D Mapping of Hydrodynamic Parameters for the Analysis of Complex Flow Motions in a Submerged Bedrock Canyon of the Tocantins River, Brazil

Validation and scaling of sophisticated physical and numerical fluvial hydraulic models to real field conditions are limited by temporal and spatial constraints of field measurement technologies. These limitations increase when analyzing hydraulic properties of complex river forms such as submerged bedrock canyons. The analysis of flow under these conditions has demonstrated non-linear behavior, strong secondary circulation and a high level of turbulence. The objective of this paper is to obtain and analyze turbulence and secondary current information for flow analysis, by evaluating the spatial distribution of bed shear stress and eddy viscosity with acoustic Doppler current profiler (ADCP) measurements. The real field-scale case study was the Lourenco Rock Canyon in Tocantins River, Brazil. A total of 10,531 velocity profiles were measured with an ADCP adapted to a moving boat. The data were post-processed by decomposing the velocity data measurements and calculating the standard deviations. Three different methods are compared for bed shear stress: total kinetic energy (TKE), law of the wall and the depth–slope product. The eddy viscosity was estimated with the Boussinesq approach. The initial data processing confirmed turbulence and flow velocity characteristics described in similar literature findings. The results for the bed shear stress for the canyon area were 8 times greater than the outside and for eddy viscosity, 10 times higher. For the surroundings area, the eddy viscosity showed reasonable results with values around the regular 1.0 m2/s used for rivers. It is concluded that turbulent values can be calculated to better represent physical processes with the intention to improve hydrodynamic numerical models calibrations.
Designing Digital Mindfulness: Presence-In and Presence-With versus Presence-Through

The digital health and wellbeing movement has led to development of digital mindfulness applications that aim to help people to become mindful. In this paper we suggest a broad scheme for classifying and ordering apps intended to support mindfulness. This scheme consists of four levels of what we here term digital mindfulness. One crucial aspect of the fourth level is that artifacts at this level allow for what we term as presence-with and presence-in as opposed to presence-through, which occurs at the first three levels. We articulate our four levels along with specific design qualities through concrete examples of existing mindfulness apps and through research through design (RtD) work conducted with design fiction examples. We then use a working design case prototype to further illustrate the possibilities of presence-with and presence-in. We hope our four levels of digital mindfulness framework will be found useful by other researchers in discussing and planning the design of their own mindfulness apps and digital artifacts.
Quantification of Environmental Flow Requirements to Support Ecosystem Services of Oasis Areas: A Case Study in Tarim Basin, Northwest China

Recently, a wide range of quantitative research on the identification of environmental flow requirements (EFRs) has been conducted. However, little focus is given to EFRs to maintain multiple ecosystem services in oasis areas. The present study quantifies the EFRs in oasis areas of Tarim Basin, Xinjiang, Northwest China on the basis of three ecosystem services: (1) maintenance of riverine ecosystem health, (2) assurance of the stability of oasis–desert ecotone and riparian (Tugai) forests, and (3) restoration of oasis–desert ecotone groundwater. The identified consumptive and non-consumptive water requirements are used to quantify and determine the EFRs in Qira oasis by employing the summation and compatibility rules (maximum principle). Results indicate that the annual maximum, medium, and minimum EFRs are 0.752 × 108, 0.619 × 108, and 0.516 × 108 m3, respectively, which account for 58.75%, 48.36%, and 40.29% of the natural river runoff. The months between April and October are identified as the most important periods to maintain the EFRs. Moreover, the water requirement for groundwater restoration of the oasis–desert ecotone accounts for a large proportion, representing 48.27%, 42.32%, and 37.03% of the total EFRs at maximum, medium, and minimum levels, respectively. Therefore, to allocate the integrated EFRs, focus should be placed on the water demand of the desert vegetation’s groundwater restoration, which is crucial for maintaining desert vegetation to prevent sandstorms and soil erosion. This work provides a reference to quantify the EFRs of oasis areas in arid regions.
Micro- and Macro-Level Validation in Agent-Based Simulation: Reproduction of Human-Like Behaviors and Thinking in a Sequential Bargaining Game

This paper addresses both micro- and macro-level validation in agent-based simulation (ABS) to explore validated agents that can reproduce not only human-like behaviors externally but also human-like thinking internally. For this purpose, we employ the sequential bargaining game, which can investigate a change in humans' behaviors and thinking longer than the ultimatum game (i.e., one-time bargaining game), and compare simulation results of Q-learning agents employing any type of the three types of action selections (i.e., the e-greedy, roulette, and Boltzmann distribution selections) in the game. Intensive simulations have revealed the following implications: (1) Q-learning agents with any type of three action selections can reproduce human-like behaviors but not human-like thinking, which means that they are validated from the macro-level viewpoint but not from the micro-level viewpoint; and (2) Q-learning agents employing Boltzmann distribution selection with changing the random parameter can reproduce both human-like behaviors and thinking, which means that they are validated from both micro- and macro-level viewpoints.
Dynamic Switching of Active Promoter and Enhancer Domains Regulates Tet1 and Tet2 Expression during Cell State Transitions between Pluripotency and Differentiation

ABSTRACT The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb “superenhancer” of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.
Analysis of Block Parareal Preconditioners for Parabolic Optimal Control Problems

In this paper, we describe block matrix algorithms for the iterative solution of a large-scale linear-quadratic optimal control problem involving a parabolic partial differential equation over a finite control horizon. We consider an “all at once” discretization of the problem and formulate three iterative algorithms. The first algorithm is based on preconditioning a symmetric positive definite reduced linear system involving only the unknown control variables; however inner-outer iterations are required. The second algorithm modifies the first algorithm to avoid inner-outer iterations by introducing an auxiliary variable. It yields a symmetric indefinite system with a positive definite block preconditioner. The third algorithm is the central focus of this paper. It modifies the preconditioner in the second algorithm by a parallel-in-time preconditioner based on the parareal algorithm. Theoretical results show that the preconditioned algorithms have optimal convergence properties and parallel scalability. Numerical experiments confirm the theoretical results.
Microstructure and Cerebral Blood Flow within White Matter of the Human Brain: A TBSS Analysis

Background White matter (WM) fibers connect different brain regions and are critical for proper brain function. However, little is known about the cerebral blood flow in WM and its relation to WM microstructure. Recent improvements in measuring cerebral blood flow (CBF) by means of arterial spin labeling (ASL) suggest that the signal in white matter may be detected. Its implications for physiology needs to be extensively explored. For this purpose, CBF and its relation to anisotropic diffusion was analyzed across subjects on a voxel-wise basis with tract-based spatial statistics (TBSS) and also across white matter tracts within subjects. Methods Diffusion tensor imaging and ASL were acquired in 43 healthy subjects (mean age = 26.3 years). Results CBF in WM was observed to correlate positively with fractional anisotropy across subjects in parts of the splenium of corpus callosum, the right posterior thalamic radiation (including the optic radiation), the forceps major, the right inferior fronto-occipital fasciculus, the right inferior longitudinal fasciculus and the right superior longitudinal fasciculus. Furthermore, radial diffusivity correlated negatively with CBF across subjects in similar regions. Moreover, CBF and FA correlated positively across white matter tracts within subjects. Conclusion The currently observed findings on a macroscopic level might reflect the metabolic demand of white matter on a microscopic level involving myelination processes or axonal function. However, the exact underlying physiological mechanism of this relationship needs further evaluation.
Evaluating color texture descriptors under large variations of controlled lighting conditions

The recognition of color texture under varying lighting conditions remains an open issue. Several features have been proposed for this purpose, ranging from traditional statistical descriptors to features extracted with neural networks. Still, it is not completely clear under what circumstances a feature performs better than others. In this paper, we report an extensive comparison of old and new texture features, with and without a color normalization step, with a particular focus on how these features are affected by small and large variations in the lighting conditions. The evaluation is performed on a new texture database, which includes 68 samples of raw food acquired under 46 conditions that present single and combined variations of light color, direction, and intensity. The database allows us to systematically investigate the robustness of texture descriptors across large variations of imaging conditions.
Sexual Selection and Genital Evolution in Mammals: A Phylogenetic Analysis of Baculum Length

Studies in invertebrate taxa suggest that postcopulatory sexual selection is an important factor in genital evolution. However, despite wide interspecific variation in genital morphology, evidence for an influence of sexual selection on mammalian genitalia is equivocal. Here I conduct phylogenetically controlled comparative analyses across four mammalian orders to assess how one aspect of this variation—male genital length—scales with (a) male body mass and (b) relative testis mass, the latter providing an index of the intensity of sperm competition. In all four orders, baculum (=os penis) length is found to scale only weakly with male body mass. Both baculum and glans penis length in rodents and baculum length in carnivores are found to vary positively with relative testis mass. In contrast, there is no evidence to support an association between baculum length and relative testis mass in either bats or primates. These results suggest that postcopulatory sexual selection influences genital length in at least some mammals, but significant questions remain both as to why selection on the baculum should differ between mammalian groups and as to the precise mechanistic basis through which males benefit from increased genital length.
N-Terminally Myristoylated Feline Foamy Virus Gag Allows Env-Independent Budding of Sub-Viral Particles

Foamy viruses (FVs) are distinct retroviruses classified as Spumaretrovirinae in contrast to the other retroviruses, the Orthoretrovirinae. As a unique feature of FVs, Gag is not sufficient for sub-viral particle (SVP) release. In primate and feline FVs (PFV and FFV), particle budding completely depends on the cognate FV Env glycoproteins. It was recently shown that an artificially added N-terminal Gag myristoylation signal (myr-signal) overcomes this restriction in PFV inducing an Orthoretrovirus-like budding phenotype. Here we show that engineered, heterologous N-terminal myr-signals also induce budding of the distantly related FFV Gag. The budding efficiency depends on the myr-signal and its location relative to the N-terminus of Gag. When the first nine amino acid residues of FFV Gag were replaced by known myr-signals, the budding efficiency as determined by the detection of extracellular SVPs was low. In contrast, adding myr-signals to the intact N-terminus of FFV Gag resulted in a more efficient SVP release. Importantly, budding of myr-Gag proteins was sensitive towards inhibition of cellular N-myristoyltransferases. As expected, the addition or insertion of myr-signals that allowed Env-independent budding of FFV SVPs also retargeted Gag to plasma membrane-proximal sites and other intracellular membrane compartments. The data confirm that membrane-targeted FV Gag has the capacity of SVP formation.
Zebrafish adult-derived hypothalamic neurospheres generate gonadotropin-releasing hormone (GnRH) neurons

ABSTRACT Gonadotropin-releasing hormone (GnRH) is a hypothalamic decapeptide essential for fertility in vertebrates. Human male patients lacking GnRH and treated with hormone therapy can remain fertile after cessation of treatment suggesting that new GnRH neurons can be generated during adult life. We used zebrafish to investigate the neurogenic potential of the adult hypothalamus. Previously we have characterized the development of GnRH cells in the zebrafish linking genetic pathways to the differentiation of neuromodulatory and endocrine GnRH cells in specific regions of the brain. Here, we developed a new method to obtain neural progenitors from the adult hypothalamus in vitro. Using this system, we show that neurospheres derived from the adult hypothalamus can be maintained in culture and subsequently differentiate glia and neurons. Importantly, the adult derived progenitors differentiate into neurons containing GnRH and the number of cells is increased through exposure to either testosterone or GnRH, hormones used in therapeutic treatment in humans. Finally, we show in vivo that a neurogenic niche in the hypothalamus contains GnRH positive neurons. Thus, we demonstrated for the first time that neurospheres can be derived from the hypothalamus of the adult zebrafish and that these neural progenitors are capable of producing GnRH containing neurons.
Cancer Management and Research Dovepress the Role of Epithelial–mesenchymal Transition Programming in Invasion and Metastasis: a Clinical Perspective

Epithelial–mesenchymal transition (EMT) is involved in normal developmental cellular processes, but it may also be co-opted by a subset of cancer cells, to enable them to invade and form metastases at distant sites. Several gene transcription factors regulate EMT, including Snail1, Snail2, Zeb1, Zeb2, and Twist; ongoing studies continue to identify and elucidate other drivers. Specific micro ribonucleic acids (RNAs) have also been found to regulate EMT, including the microRNA-200 (miR-200) family, which targets Zeb1/Zeb2. Cancer " stem cells " – with the ability to self-renew and to regenerate all the cell types within the tumor – have been found to express EMT markers, further implicating both cancer stem cells and EMT with metastasis. Microenvironmental cues, including transforming growth factor-β, can direct EMT tumor metastasis, such as by regulating miR-200 expression. In human tumors, EMT markers and regulators may be expressed in a subset of tumor cells, such as in cells at the invasive front or tumor–microenvironment interface, though certain subtypes of cancer can show widespread mesenchymal-like features. In terms of therapeutic targeting of EMT in patients, potential areas of exploration could include targeting the cancer stem cell subpopulation, as well as microRNA-based therapeutics that reintroduce miR-200. This review will examine evidence for a role of EMT in invasion and metastasis, with the focus being on studies in lung and breast cancers. We also carry out analyses of publicly-available gene expression profiling datasets in order to show how EMT-associated genes appear coordinately expressed across human tumor specimens.