Miracle-dz/UniFAR-FTUs huggingface dataset:
Activin-Nodal signaling is involved in propagation of mouse embryonic stem cells

Embryonic stem (ES) cells are self-renewing cells that maintain pluripotency to differentiate into all types of cells. Because of their potential to provide a variety of tissues for use in regenerative medicine, there is great interest in the identification of growth factors that govern these unique properties of ES cells. However, the signaling pathways controlling ES cell proliferation remain largely unknown. Since transforming growth factor β (TGFβ) superfamily members have been implicated in the processes of early embryogenesis, we investigated their roles in ES cell self-renewal. Inhibition of activin-Nodal-TGFβ signaling by Smad7 or SB-431542 dramatically decreased ES cell proliferation without decreasing ES pluripotency. By contrast, inhibition of bone morphogenetic protein (BMP) signaling by Smad6 did not exhibit such effects, suggesting that activin-Nodal-TGFβ signaling, but not BMP signaling, is indispensable for ES cell propagation. In serum-free culture, supplementation of recombinant activin or Nodal, but not TGFβ or BMP, significantly enhanced ES cell propagation without affecting pluripotency. We also found that activin-Nodal signaling was constitutively activated in an autocrine fashion in serum-free cultured ES cells, and that inhibition of such endogenous signaling by SB-431542 decreased ES cell propagation in serum-free conditions. These findings suggest that endogenously activated autocrine loops of activin-Nodal signaling promote ES cell self-renewal.
Maximum Likelihood Estimator and Kullback--Leibler Information in Misspecified Markov Chain Models

Suppose we have specified a parametric model for the transition distribution of a Markov chain, but the true transition distribution does not belong to the model. Then the maximum likelihood estimator estimates the parameter which maximizes the Kullback--Leibler information between the true transition distribution and the model. We prove that the maximum likelihood estimator is asymptotically efficient in a nonparametric sense if the true transition distribution is unknown.
Specific Activation of K-RasG12D Allele in the Bladder Urothelium Results in Lung Alveolar and Vascular Defects

K-ras is essential for embryogenesis and its mutations are involved in human developmental syndromes and cancer. To determine the consequences of K-ras activation in urothelium, we used uroplakin-II (UPK II) promoter driven Cre recombinase mice and generated mice with mutated KrasG12D allele in the urothelium (UPK II-Cre;LSL-K-rasG12D). The UPK II-Cre;LSL-K-rasG12D mice died neonatally due to lung morphogenesis defects consisting of simplification with enlargement of terminal air spaces and dysmorphic pulmonary vasculature. A significant alteration in epithelial and vascular basement membranes, together with fragmentation of laminin, points to extracellular matrix degradation as the causative mechanism of alveolar and vascular defects. Our data also suggest that altered protease activity in amniotic fluid might be associated with matrix defects in lung of UPK II-Cre;LSL-K-rasG12. These defects resemble those observed in early stage human neonatal bronchopulmonary dysplasia (BPD), although the relevance of this new mouse model for BPD study needs further investigation.
Functional Domains in Dorsal Striatum of the Nonhuman Primate Are Defined by the Dynamic Behavior of Dopamine

The dorsal striatum comprises a continuum of distinct functional domains, limbic, associative, and sensorimotor. In the primate it exclusively subdivides further into two nuclei, the putamen and caudate. Dopamine (DA) transmission is differentially affected between these nuclei in neurodegenerative diseases such as Parkinson's and by psychostimulants such as cocaine. Because rodent systems can offer only limited insight into DA systems of the human brain, a fuller appreciation of DA transmission and its role in dysfunction requires direct study in primates. DA behavior was explored in the major functional domains of the caudate nucleus and compared with the putamen, using fast-scan cyclic voltammetry in striatal sections from the marmoset (Callithrix jacchus). There was domain-specific variation in extracellular DA transients [i.e., concentration ([DA]o) released by a single stimulus and the rate maximum of DA uptake,Vmax]. Across nuclei, functional rather than anatomical regions were differentiated by these dynamics. The largest, fastest DA transients were at motor-associated loci. Evoked [DA]o at physiological frequencies was differently frequency-sensitive between functional domains but not between anatomical nuclei. In contrast, presynaptic depression was not an index of regional differentiation, recovering with similar kinetics at all loci. Within a given functional domain of dorsal striatum, the dynamics of DA release and uptake are similar for the putamen and the caudate nucleus. Conversely, distinct functional domains are defined by these DA dynamics, in a manner more marked in primates than in rodents. These data from the primate brain highlight differences in DA availability that may be central to DA function and dysfunction in the human.
Cell-Autonomous TrkB Signaling in Presynaptic Retinal Ganglion Cells Mediates Axon Arbor Growth and Synapse Maturation during the Establishment of Retinotectal Synaptic Connectivity

BDNF contributes to the activity-dependent establishment and refinement of visual connectivity. In Xenopus, BDNF applications in the optic tectum influence retinal ganglion cell (RGC) axon branching and promote synapse formation and stabilization. The expression patterns of BDNF and TrkB suggest that BDNF specifically regulates the maturation of RGC axons at the target. It is possible, however, that BDNF modulates retinotectal synaptic connectivity by differentially influencing presynaptic RGC axons and postsynaptic tectal cells. Here, we combined single-cell expression of a dominant-negative TrkB–enhanced green fluorescent protein (GFP) fusion protein with confocal microscopy imaging in live Xenopus tadpoles to differentiate between presynaptic and postsynaptic actions of BDNF. Disruption of TrkB signaling in individual RGCs influenced the branching and synaptic maturation of presynaptic axon arbors. Specifically, GFP–TrkB.T1 overexpression increased the proportion of axons with immature, growth cone-like morphology, decreased axon branch stability, and increased axon arbor degeneration. In addition, GFP–TrkB.T1 overexpression reduced the number of red fluorescent protein–synaptobrevin-labeled presynaptic specializations per axon terminal. In contrast, overexpression of GFP–TrkB.T1 in tectal neurons did not alter synaptic number or the morphology or dynamic behavior of their dendritic arbors. Electron microscopy analysis revealed a significant decrease in the number of mature synaptic profiles and in the number of docked synaptic vesicles at retinotectal synapses made by RGC axons expressing GFP–TrkB.T1. Together, our results demonstrate that presynaptic TrkB signaling in RGCs is a key determinant in the establishment of visual connectivity and indicate that changes in tectal neuron synaptic connectivity are secondary to the BDNF-elicited enhanced stability and growth of presynaptic RGCs.
"Plug and test" - software agents in virtual environments

James, a Java based agent modeling environment for simulation has been developed to support the compositional construction of test beds for multi-agent systems and their execution in distributed environments. The modeling formalism of James imposes only few constraints on the modeling of agents and facilitates a "plug and test" with pieces of agent code which has been demonstrated in earlier work. However, even entire agents can be run in James as they are run in their run-time environment. The integration of agents as a whole is based on model templates which serve as the agents' interface and representative during the simulation run. The effort which is put into defining model templates for selected agent systems obviates the need for the single agent programmer to get acquainted with the underlying modeling and simulation formalism. Instead, the agent programmer can compose the experimental frame and test the programmed agents as they are. The approach is illustrated with agents of the mobile agent system, Mole.
Invasive Intraneural Interfaces: Foreign Body Reaction Issues

Intraneural interfaces are stimulation/registration devices designed to couple the peripheral nervous system (PNS) with the environment. Over the last years, their use has increased in a wide range of applications, such as the control of a new generation of neural-interfaced prostheses. At present, the success of this technology is limited by an electrical impedance increase, due to an inflammatory response called foreign body reaction (FBR), which leads to the formation of a fibrotic tissue around the interface, eventually causing an inefficient transduction of the electrical signal. Based on recent developments in biomaterials and inflammatory/fibrotic pathologies, we explore and select the biological solutions that might be adopted in the neural interfaces FBR context: modifications of the interface surface, such as organic and synthetic coatings; the use of specific drugs or molecular biology tools to target the microenvironment around the interface; the development of bio-engineered-scaffold to reduce immune response and promote interface-tissue integration. By linking what we believe are the major crucial steps of the FBR process with related solutions, we point out the main issues that future research has to focus on: biocompatibility without losing signal conduction properties, good reproducible in vitro/in vivo models, drugs exhaustion and undesired side effects. The underlined pros and cons of proposed solutions show clearly the importance of a better understanding of all the molecular and cellular pathways involved and the need of a multi-target action based on a bio-engineered combination approach.
PHYSICAL CHARACTERISTICS OF BIOMASS AND ITS INFLUENCE IN SELF-COMBUSTION

The necessity to find new sources to produce a cleaner energy, reducing the CO2 emissions, leads to consider biomass as a potential sustainable feedstock to be used instead of coal in power plants. Biomass and coal present significant differences in terms of both chemical composition and physical properties. Biomass usually has an increased thermal sensitivity and a greater ease of ignition. Also, biomass particles commonly have more irregular shapes and larger sizes than pulverized coal, thus it is necessary to establish the parameters of these materials to avoid the self-combustion tendency. In the same way than coal, biomass stored are potentially able to absorb oxygen to produce exothermic oxidation reactions. If the generated heat in these reactions is not properly dispersed, causes a self-heating of the organic matter that can cause breakdown and ignition. In the field of possible self-combustion in the storage and handling of the biomass there are several factors which have influence in biomass thermal susceptibility, i.e. its tendency to oxidation and subsequent ignition of the substance. In this respect, the different biomass analysis to determine their behavior is shown here. This study has been developed using biomass obtained from agriculture, forestry, olive oil waste and aromatic plant waste. Those products have different chemical composition and it could imply different behavior. Samples tested have been prepared by different physical processes to assess the influence of different factors in their self-combustion. All products tested are commercial products available in the market for potential use in gasification plants. Methods employed were based on classical techniques of thermogravimetry, differential scanning calorimetry, analysis of composition and physical analysis as shape factor and particle size distribution. Methodologies used in the thermal analysis are not standard tests, but that are based on a long experience in the application of these techniques to coals and other products. In order to compare results, test widely used in previous research works has been carried out to define the characteristic parameters of the experimental methodology.
Geometrical modeling of H&N cancer tumor

Purpose – Most of the current radiation treatment planning systems use pre‐treatment computed tomography (CT) images to detect the tumor location and then plan the radiation therapy to be delivered during the treatment period. It is assumed that the tumor geometry will not change throughout the treatment course; however, tumor geometry is shown to be changing over time. The purpose of this paper is to present results of an ongoing research in 3‐D modeling and reconstruction of head and neck cancer tumors. The results from this phase of the project will be used in developing a prediction model for tumor deformation during radiation treatment of cancer patients.Design/methodology/approach – By using CT scan data in the 3‐D ASCII format, the tumor's progressive geometric changes during the treatment period are quantified. After constructing slice contours, both triangular and rectangular patch approaches are applied to map and analyze the tumor surface and volume. The changes in tumor location are calculated.
A New Random Graph Model with Self-Optimizing Nodes: Connectivity and Diameter

We introduce a new random graph model. In our model, n, n ≥ 2, vertices choose a subset of potential edges by considering the (estimated) benefits or utilities of the edges. More precisely, each vertex selects k, k ≥ 1, incident edges it wishes to set up, and an undirected edge between two vertices is present in the graph if and only if both of the end vertices choose the edge. First, we examine the scaling law of the smallest k needed for graph connectivity with increasing n and prove that it is Θ(log (n)). Second, we study the diameter of the random graph and demonstrate that, under certain conditions on k, the diameter is close to log (n)/log (log (n)) with high probability. In addition, as a byproduct of our findings, we show that, for all sufficiently large n, if k > β⋆log (n), where β⋆ ≈ 2.4626, there exists a connected Erds–Rnyi random graph that is embedded in our random graph, with high probability.
Vocal biomarkers to discriminate cognitive load in a working memory task

Early, accurate detection of cognitive load can help reduce risk of accidents and injuries, and inform intervention and rehabilitation in recovery. Thus, simple noninvasive biomarkers are desired for determining cognitive load under cognitively complex tasks. In this study, a novel set of vocal biomarkers are introduced for detecting different cognitive load conditions. Our vocal biomarkers use phoneme- and pseudosyllable-based measures, and articulatory and source coordination derived from cross-correlation and temporal coherence of formant and creakiness measures. A ~2-hour protocol was designed to induce cognitive load by stressing auditory working memory. This was done by repeatedly requiring the subject to recall a sentence while holding a number of digits in memory. We demonstrate the power of our speech features to discriminate between high and low load conditions. Using a database consisting of audio from 13 subjects, we apply classification models of cognitive load, showing a ~7% detection equal-error rate from features derived from 40 sentence utterances (~4 minutes of audio). the MIT Committee on the Use of Humans as Experimental Subjects (COUHES). Audio data are collected with a DPA acoustic lapel microphone (with a Roland Octa-Capture audio interface. setup and training, each subject engages in the primary task of verbally recalling with varying levels of cognitive load, as determined by the number of digits being held in working trial of a string
Mixed close-packed cobalt molybdenum nitrides as non-noble metal electrocatalysts for the hydrogen evolution reaction.

A two-step solid-state reaction for preparing cobalt molybdenum nitride with a nanoscale morphology has been used to produce a highly active and stable electrocatalyst for the hydrogen evolution reaction (HER) under acidic conditions that achieves an iR-corrected current density of 10 mA cm(-2) at -0.20 V vs RHE at low catalyst loadings of 0.24 mg/cm(2) in rotating disk experiments under a H2 atmosphere. Neutron powder diffraction and pair distribution function (PDF) studies have been used to overcome the insensitivity of X-ray diffraction data to different transition-metal nitride structural polytypes and show that this cobalt molybdenum nitride crystallizes in space group P63/mmc with lattice parameters of a = 2.85176(2) Å and c = 10.9862(3) Å and a formula of Co0.6Mo1. 4N2. This space group results from the four-layered stacking sequence of a mixed close-packed structure with alternating layers of transition metals in octahedral and trigonal prismatic coordination and is a structure type for which HER activity has not previously been reported. Based on the accurate bond distances obtained from time-of-flight neutron diffraction data, it is determined that the octahedral sites contain a mixture of divalent Co and trivalent Mo, while the trigonal prismatic sites contain Mo in a higher oxidation state. X-ray photoelectron spectroscopy (XPS) studies confirm that at the sample surface nitrogen is present and N-H moieties are abundant.
Anisotropy in Longitudinal Modulus of Polymer Gels Containing Ferrite

The effects of magnetization direction on the longitudinal modulus of magnetic gels, which consist of magnetized barium ferrite and poly(vinyl alcohol), have been investigated using 10 MHz ultrasonic waves. The modulus change due to magnetization depends on both the crosslinking density and magnetization direction. The modulus change increased and decreased when the strain direction was perpendicular and parallel to magnetization, respectively.
Under load. The effect of verbal and motoric cognitive load on gesture production

It has been hypothesized that speech and gesture work together, with people relying more on gesture when speaking is hard, and relying more on speech when gesturing is hard. Indeed, previous work showed that when speaking is hard, gesture production can reduce cognitive load and thereby help the speech process. However, it is yet unknown what happens in speech and gesture production when gesturing is hard. In the current study, participants described complex tangram figures. Difficulty in either speech or gesture production was manipulated by having speakers do a secondary task which placed them under either verbal or motoric cognitive load. Results showed an increase in representational gesture rate when participants were under motoric load, as compared to the baseline condition, but only a weak effect of verbal load, and no difference between the verbal and motoric load conditions. Based on these findings, we conclude that making speaking hard caused a marginal increase in gesture production, and making gesturing hard actually led to more gestures. In sum, we find no evidence to support a two-way trade-off between speech and gestures. To our knowledge, this is the first study assessing the effects of a secondary motoric task on gesture production.
NN-Grams: Unifying Neural Network and n-Gram Language Models for Speech Recognition

We present NN-grams, a novel, hybrid language model integrating n-grams and neural networks (NN) for speech recognition. The model takes as input both word histories as well as n-gram counts. Thus, it combines the memorization capacity and scalability of an n-gram model with the generalization ability of neural networks. We report experiments where the model is trained on 26B words. NN-grams are efficient at run-time since they do not include an output soft-max layer. The model is trained using noise contrastive estimation (NCE), an approach that transforms the estimation problem of neural networks into one of binary classification between data samples and noise samples. We present results with noise samples derived from either an n-gram distribution or from speech recognition lattices. NN-grams outperforms an n-gram model on an Italian speech recognition dictation task.
A Primer on Autonomous Aerial Vehicle Design

There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV), such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM) solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers.
The purification and characterization of ATP synthase complexes from the mitochondria of four fungal species

The ATP synthases have been isolated by affinity chromatography from the mitochondria of the fungal species Yarrowia lipolytica, Pichia pastoris, Pichia angusta and Saccharomyces cerevisiae. The subunit compositions of the purified enzyme complexes depended on the detergent used to solubilize and purify the complex, and the presence or absence of exogenous phospholipids. All four enzymes purified in the presence of n-dodecyl-β-D-maltoside had a complete complement of core subunits involved directly in the synthesis of ATP, but they were deficient to different extents in their supernumerary membrane subunits. In contrast, the enzymes from P. angusta and S. cerevisiae purified in the presence of n-decyl-β-maltose neopentyl glycol and the phospholipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, cardiolipin (diphosphatidylglycerol) and 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] had a complete complement of core subunits and also contained all of the known supernumerary membrane subunits, e, f, g, j, k and ATP8 (or Aap1), plus an additional new membrane component named subunit l, related in sequence to subunit k. The catalytic domain of the enzyme from P. angusta was more resistant to thermal denaturation than the enzyme from S. cerevisiae, but less stable than the catalytic domain of the bovine enzyme, but the stator and the integrity of the transmembrane proton pathway were most stable in the enzyme from P. angusta. The P. angusta enzyme provides a suitable source of enzyme for studying the structure of the membrane domain and properties associated with that sector of the enzyme complex.