Miracle-dz/UniFAR-FTUs huggingface dataset:
Bapx1 regulates patterning in the middle ear: altered regulatory role in the transition from the proximal jaw during vertebrate evolution

The middle ear apparatus is composed of three endochondrial ossicles (the stapes, incus and malleus) and two membranous bones, the tympanic ring and the gonium, which act as structural components to anchor the ossicles to the skull. Except for the stapes, these skeletal elements are unique to mammals and are derived from the first and second branchial arches. We show that, in combination with goosecoid (Gsc), the Bapx1 gene defines the structural components of the murine middle ear. During embryogenesis, Bapx1 is expressed in a discrete domain within the mandibular component of the first branchial arch and later in the primordia of middle ear-associated bones, the gonium and tympanic ring. Consistent with the expression pattern of Bapx1, mouse embryos deficient for Bapx1 lack a gonium and display hypoplasia of the anterior end of the tympanic ring. At E10.5, expression of Bapx1 partially overlaps that of Gsc and although Gsc is required for development of the entire tympanic ring, the role of Bapx1 is restricted to the specification of the gonium and the anterior tympanic ring. Thus, simple overlapping expression of these two genes appears to account for the patterning of the elements that compose the structural components of the middle ear and suggests that they act in concert. In addition, Bapx1 is expressed both within and surrounding the incus and the malleus. Examination of the malleus shows that the width, but not the length, of this ossicle is decreased in the mutant mice. In non-mammalian jawed vertebrates, the bones homologous to the mammalian middle ear ossicles compose the proximal jaw bones that form the jaw articulation (primary jaw joint). In fish, Bapx1 is responsible for the formation of the joint between the quadrate and articular (homologues of the malleus and incus, respectively) enabling an evolutionary comparison of the role of a regulatory gene in the transition of the proximal jawbones to middle ear ossicles. Contrary to expectations, murine Bapx1 does not affect the articulation of the malleus and incus. We show that this change in role of Bapx1 following the transition to the mammalian ossicle configuration is not due to a change in expression pattern but results from an inability to regulate Gdf5 and Gdf6, two genes predicted to be essential in joint formation.
Severely Impaired Learning and Altered Neuronal Morphology in Mice Lacking NMDA Receptors in Medium Spiny Neurons

The striatum is composed predominantly of medium spiny neurons (MSNs) that integrate excitatory, glutamatergic inputs from the cortex and thalamus, and modulatory dopaminergic inputs from the ventral midbrain to influence behavior. Glutamatergic activation of AMPA, NMDA, and metabotropic receptors on MSNs is important for striatal development and function, but the roles of each of these receptor classes remain incompletely understood. Signaling through NMDA-type glutamate receptors (NMDARs) in the striatum has been implicated in various motor and appetitive learning paradigms. In addition, signaling through NMDARs influences neuronal morphology, which could underlie their role in mediating learned behaviors. To study the role of NMDARs on MSNs in learning and in morphological development, we generated mice lacking the essential NR1 subunit, encoded by the Grin1 gene, selectively in MSNs. Although these knockout mice appear normal and display normal 24-hour locomotion, they have severe deficits in motor learning, operant conditioning and active avoidance. In addition, the MSNs from these knockout mice have smaller cell bodies and decreased dendritic length compared to littermate controls. We conclude that NMDAR signaling in MSNs is critical for normal MSN morphology and many forms of learning.
Motion-Sensitive Responses in Visual Area V4 in the Absence of Primary Visual Cortex

Neurons in cortical ventral-stream area V4 are thought to contribute to important aspects of visual processing by integrating information from primary visual cortex (V1). However, how V4 neurons respond to visual stimulation after V1 injury remains unclear: While electrophysiological investigation of V4 neurons during reversible V1 inactivation suggests that virtually all responses are eliminated (Girard et al., 1991), fMRI in humans and monkeys with permanent lesions shows reliable V1-independent activity (Baseler et al., 1999; Goebel et al., 2001; Schmid et al., 2010). To resolve this apparent discrepancy, we longitudinally assessed neuronal functions of macaque area V4 using chronically implanted electrode arrays before and after creating a permanent aspiration lesion in V1. During the month after lesioning, we observed weak yet significant spiking activity in response to stimuli presented to the lesion-affected part of the visual field. These V1-independent responses showed sensitivity for motion and likely reflect the effect of V1-bypassing geniculate input into extrastriate areas.
An Algorithm for Combining Electrical Mobility and Aerodynamic Size Distributions Data when Measuring Ambient Aerosol Special Issue of Aerosol Science and Technology on Findings from the Fine Particulate Matter Supersites Program

Ambient aerosol particles vary in size from a few nanometers to several micrometers. No instrument is currently available to cover such a wide size range, and so a combination of several instruments is usually used. One such combination is that of electrical mobility classifiers and an aerodynamic sizer. Because of the differences in measurement principles between the instruments, difficulties arise in the combination of the measurements into a single size distribution. Here we report a simple algorithm that was developed to combine aerosol size distributions measured with commercially available scanning mobility particle sizers (SMPS; TSI Inc.) and an aerodynamic particle sizer (APS; TSI Inc.). This algorithm was tested during July 2001 in the Pittsburgh Air Quality Study. The aerosol during the study had both urban and regional origin and is characteristic of urban atmosphere in the Northeastern U.S. The integrated volume concentrations from the SMPS–APS showed a good correlation with PM2.5 mass concentration measurements using a TEOM. The relation of the aerosol mass to its volume is an “effective” density, a ratio of the bulk aerosol density to the shape factor. As a result of the comparison with the TEOM the ambient aerosol in the Pittsburgh area was found to have an effective density of 1.5 ± 0.3 g cm−3. Given that the aerosol during the study was found to always contain water, the particles are expected to be spherical and thus the shape factor may be assumed to be 1. This assumption has been supported by a comparison with the MOUDI, using the aerosol density of 1.5 g/cm3. It should be noted that the estimated aerosol density and the shape factor are applicable to this study only and may be different in other locations.
Auscultation et surveillance des pertubations hydromécaniques d'ouvrages souterrains par la mesure et l'analyse de la propagation d'ondes dans les roches

The excavation of a drift creates a disturbed zone, which is called EDZ (Excavation Disturbed or Damaged Zone). The study of the mechanical characteristics of this zone is essential to estimate the stability of such a drift at short, mean or long term. The propagation of ultrasonic waves is used as a mean of analysis in rock mechanics since the 1960s. Initially, it was used to determine the dynamic elastic properties. Then, it was gradually adapted to the study of the other properties of the material such as cracking, porosity, saturation, etc. With the computer tools continuously more powerful, a more elaborated treatment of the signals became possible, which allows characterization of the "EDZ". The Tests carried out in laboratory, allowed us to correlate P-wave and mechanical parameters of the studied media in elastic and plastic phases. Besides, the mechanical modeling of the EDZ around a drift allows understanding the mechanical phenomena on the scale of the work. Finally, the results of an in-site experiment allowed us to locate the EDZ around an underground mine pillar. It contributed to have a better understanding of the mechanical models available and to estimate the pillar stability.
Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

Homologous recombination (HR) is the major pathway for repairing double strand breaks (DSBs) in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC) we used high resolution melting (HRM) analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536) was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432–4.969; p = 0.38) compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion.
On the achievable forwarding capacity of an infinite wireless network

We consider the problem of finding the maximum directed packet flow that can be sustained in an infinite wireless multihop network. This ability of the network to relay traffic is called the forwarding capacity, and the problem appears when the spatial scales corresponding to the end-to-end paths (routing) and the neighboring nodes (forwarding) are strongly separated in a massively dense network. We assume a Boolean interference model. The infinite network is approximated with a finite but large network where the node locations form a spatial Poisson process. We study two constructive approaches to tighten the lower bound for the forwarding capacity by a significant amount. In path scheduling the packets traverse the network using predefined paths that do not interfere with each other, and coordination is thus required only between the nodes of a path. In greedy maximum weight scheduling, the transmissions are scheduled greedily according to queue-length based weights of the links. In addition to a fixed transmission radius, we consider greedy maximum weight scheduling with a transmission radius adjustable up to a given maximum. We are able to produce numerical results that characterize the achievable forwarding capacity under global coordination of the transmissions, providing, e.g., concrete points of reference for practical distributed implementations.
Propagation of viruses on micropatterned host cells.

We have developed a technique to characterize the in vitro propagation of viruses. Microcontact printing was used to generate linear arrays of alkanethiols on gold surfaces, which served as substrates for the patterned culture of baby hamster kidney (BHK-21) cells. Vesicular stomatitis virus (VSV) was added to unpatterned cell reservoirs adjacent to the patterned cells and incubated, setting in motion a continuously advancing viral infection into the patterned cells. At different incubation times, multiple arrays were chemically fixed to stop the viral propagation. Viral propagation distances into the patterned cells were determined by indirect immunofluorescent labeling and visualization of the VSV surface glycoprotein (G). The infection spread at approximately 50 microm/h in the 140-microm lines. Moreover, different temporal stages of the infection process were simultaneously visualized along individual lines. These stages included initiation of infection, based on G protein expression; cell-cell fusion, based on virus-induced clustering of cell nuclei; and cytoskeletal degradation, based on localized release of cells from the surface. This work sets a foundation for parallel, high-throughput characterization of viral and cellular processes.
Smart Camera Networks in Virtual Reality

This paper presents our research towards smart camera networks capable of carrying out advanced surveillance tasks with little or no human supervision. A unique centerpiece of our work is the combination of computer graphics, artificial life, and computer vision simulation technologies to develop such networks and experiment with them. Specifically, we demonstrate a smart camera network comprising static and active simulated video surveillance cameras that provides extensive coverage of a large virtual public space, a train station populated by autonomously self-animating virtual pedestrians. The realistically simulated network of smart cameras performs persistent visual surveillance of individual pedestrians with minimal intervention. Our innovative camera control strategy naturally addresses camera aggregation and handoff, is robust against camera and communication failures, and requires no camera calibration, detailed world model, or central controller.
Data exchange: getting to the core

Data exchange is the problem of taking data structured under a source schema and creating an instance of a target schema that reflects the source data as accurately as possible. Given a source instance, there may be many solutions to the data exchange problem, that is, many target instances that satisfy the constraints of the data exchange problem. In an earlier paper, we identified a special class of solutions that we call universal. A universal solution has homomorphisms into every possible solution, and hence is a "most general possible" solution. Nonetheless, given a source instance, there may be many universal solutions. This naturally raises the question of whether there is a "best" universal solution, and hence a best solution for data exchange. We answer this question by considering the well-known notion of the core of a structure, a notion that was first studied in graph theory, but has also played a role in conjunctive-query processing. The core of a structure is the smallest substructure that is also a homomorphic image of the structure. All universal solutions have the same core (up to isomorphism); we show that this core is also a universal solution, and hence the smallest universal solution. The uniqueness of the core of a universal solution together with its minimality make the core an ideal solution for data exchange. Furthermore, we show that the core is the best among all universal solutions for answering unions of conjunctive queries with inequalities. After this, we investigate the computational complexity of producing the core. Well-known results by Chandra and Merlin imply that, unless P = NP, there is no polynomial-time algorithm that, given a structure as input, returns the core of that structure as output. In contrast, in the context of data exchange, we identify natural and fairly broad conditions under which there are polynomial-time algorithms for computing the core of a universal solution. Finally, we analyze the computational complexity of the following decision problem that underlies the computation of cores: given two graphs G and H, is H the core ofG? Earlier results imply that this problem is both NP-hard and coNP-hard. Here, we pinpoint its exact complexity by establishing that it is a DP-complete problem.
Tree Distance and Some Other Variants of Evalb

Some alternatives to the standard evalb measures for parser evaluation are considered, principally the use of a tree-distance measure, which assigns a score to a linearity and ancestry respecting mapping between trees, in contrast to the evalb measures, which assign a score to a span preserving mapping. Additionally, analysis of the evalb measures suggests some further variants, concerning different normalisations, the portions of a tree compared and whether scores should be micro or macro averaged. The outputs of 6 parsing systems on Section 23 of the Penn Treebank were taken. It is shown that the ranking of the parsing systems varies as the alternative evaluation measures are used. For a fixed parsing system, it is also shown that the ranking of the parses from best to worst will vary according to whether the evalb or tree-distance measure is used. It is argued that the tree-distance measure ameliorates a problem that has been noted concerning over-penalisation of attachment errors.
High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

The ability to reprogram somatic cells into induced pluripotent stem cells (iPSCs) with four transcription factors Oct4, Sox2, Klf4 and cMyc (abbreviated as OSKM)1 has provoked interest to define the molecular characteristics of this process2-7. Despite important progress, the dynamics of epigenetic reprogramming at high resolution in correctly reprogrammed iPSCs and throughout the entire process remain largely undefined. This gap in understanding results from the inefficiency of conventional reprogramming methods coupled with the difficulty of prospectively isolating the rare cells that eventually correctly reprogram into iPSCs. Here we characterize cell fate conversion from fibroblast to iPSC using a highly efficient deterministic murine reprogramming system engineered through optimized inhibition of Gatad2a-Mbd3/NuRD repressive sub-complex. This comprehensive characterization provides single-day resolution of dynamic changes in levels of gene expression, chromatin modifications, TF binding, DNA accessibility and DNA methylation. The integrative analysis identified two transcriptional modules that dominate successful reprogramming. One consists of genes whose transcription is regulated by on/off epigenetic switching of modifications in their promoters (abbreviated as ESPGs), and the second consists of genes with promoters in a constitutively active chromatin state, but a dynamic expression pattern (abbreviated as CAPGs). ESPGs are mainly regulated by OSK, rather than Myc, and are enriched for cell fate determinants and pluripotency factors. CAPGs are predominantly regulated by Myc, and are enriched for cell biosynthetic regulatory functions. We used the ESPG module to study the identity and temporal occurrence of activating and repressing epigenetic switching during reprogramming. Removal of repressive chromatin modifications precedes chromatin opening and binding of RNA polymerase II at enhancers and promoters, and the opposite dynamics occur during repression of enhancers and promoters. Genome wide DNA methylation analysis demonstrated that de novo DNA methylation is not required for highly efficient conducive iPSC reprogramming, and identified a group of super-enhancers targeted by OSK, whose early demethylation marks commitment to a successful reprogramming trajectory also in inefficient conventional reprogramming systems. CAPGs are distinctively regulated by multiple synergystic ways: 1) Myc activity, delivered either endogenously or exogenously, dominates CAPG expression changes and is indispensable for induction of pluripotency in somatic cells; 2) A change in tRNA codon usage which is specific to CAPGs, but not ESPGs, and favors their translation. In summary, our unbiased high-resolution mapping of epigenetic changes on somatic cells that are committed to undergo successful reprogramming reveals interleaved epigenetic and biosynthetic reconfigurations that rapidly commission and propel conducive reprogramming toward naïve pluripotency.
Probabilistic occupancy grid map building for Neobotix MP500 robot

In vehicle and robot navigation low-level tasks such as path planning, obstacle avoidance and autonomous operation are extensively studied nowadays. Most of these task require map building. In this paper a map representation is discussed with the focus for the singular domain of our Neobotix MP500 mobile robot. Among others the state of the art map building techniques will be introduced such as topological map, line map, landmark-based map and of course in more detail the occupancy grid based map. The probabilistic representation of the occupancy grid will be examined as a map building problem for the given mobile robot.
Chord Recognition Using Duration-explicit Hidden Markov Models

We present an audio chord recognition system based on a generalization of the Hidden Markov Model (HMM) in which the duration of chords is explicitly considered - a type of HMM referred to as a hidden semi-Markov model, or duration-explicit HMM (DHMM). We find that such a system recognizes chords at a level consistent with the state-of-the-art systems ‐ 84.23% on Uspop dataset at the major/minor level. The duration distribution is estimated from chord duration histograms on the training data. It is found that the state-of-the-art recognition result can be improved upon by using several duration distributions, which are found automatically by clustering song-level duration histograms. The paper further describes experiments which shed light on the extent to which context information, in the sense of transition matrices, is useful for the audio chord recognition task. We present evidence that the context provides surprisingly little improvement in performance, compared to isolated frame-wise recognition with simple smoothing. We discuss possible reasons for this, such as the inherent entropy of chord sequences in our training database.
Cornea EphA 2 / Ephrin-A 1 Mediate Corneal Epithelial Cell Compartmentalization via ADAM 10 Regulation of EGFR Signaling

Nihal Kaplan, Rosa Ventrella, Han Peng, Sonali Pal-Ghosh, Constadina Arvanitis, Joshua Z. Rappoport, Brian J. Mitchell, Mary Ann Stepp, Robert M. Lavker, and Spiro Getsios Department of Dermatology, Northwestern University, Chicago, Illinois, United States Department of Anatomy and Regenerative Biology, The George Washington University Medical Center, Washington, District of Columbia, United States Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois, United States
Precoding of orthogonal STBC with channel covariance feedback for minimum error probability

This paper develops the linear transformation (or precoding) of orthogonal space-time block codes (STBC) for minimizing probability of decoding error, when the channel covariance matrix is available at the transmitter. We build on recent work that stated the optimization problem without solving for the transformation. Specifically, we provide a closed-form solution for the multi-input single-output (MISO) systems, and a numerical solution for the multi-input multi-output (MIMO) systems. Our results confirm that eigen-beamforming is optimal at low SNR or highly correlated channels, and full diversity is optimal at high SNR or weakly correlated channels.