Miracle-dz/UniFAR-FTUs huggingface dataset:
Tbx20 Interacts With Smads to Confine Tbx2 Expression to the Atrioventricular Canal

Rationale: T-box transcription factors play critical roles in the coordinated formation of the working chambers and the atrioventricular canal (AVC). Tbx2 patterns embryonic myocardial cells to form the AVC and suppresses their differentiation into chamber myocardium. Tbx20-deficient embryos, which fail to form chambers, ectopically express Tbx2 throughout the entire heart tube, providing a potential mechanism for the function of Tbx20 in chamber differentiation. Objective: To identify the mechanism of Tbx2 suppression by Tbx20 and to investigate the involvement of Tbx2 in Tbx20-mediated chamber formation. Methods and Results: We generated Tbx20 and Tbx2 single and double knockout embryos and observed that loss of Tbx2 did not rescue the Tbx20-deficient heart from failure to form chambers. However, Tbx20 is required to suppress Tbx2 in the developing chambers, a prerequisite to localize its strong differentiation-inhibiting activity to the AVC. We identified a bone morphogenetic protein (Bmp)/Smad-dependent Tbx2 enhancer conferring AVC-restricted expression and Tbx20-dependent chamber suppression of Tbx2 in vivo. Unexpectedly, we found in transfection and localization studies in vitro that both Tbx20 and mutant isoforms of Tbx20 unable to bind DNA attenuate Bmp/Smad-dependent activation of Tbx2 by binding Smad1 and Smad5 and sequestering them from Smad4. Conclusions: Our data suggest that Tbx20 directly interferes with Bmp/Smad signaling to suppress Tbx2 expression in the chambers, thereby confining Tbx2 expression to the prospective AVC region.
The Ribosome Can Prevent Aggregation of Partially Folded Protein Intermediates: Studies Using the Escherichia coli Ribosome

Background Molecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone ‘foldases’ that are distinct from chaperone’ holdases’ that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC) located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA) is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains. Results We demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII) and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein. Conclusion The ribosome can behave like a ‘holdase’ chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.
Optimal control methods suitable for biomechanical systems

Optimal control theory plays a key role in the study of biological movement. Further progress requires optimal control methods for realistic biomechanical systems, that have a number of distinguishing characteristics. Here we consider available control methods in light of those characteristics, compare them empirically on a 2-link arm model, and propose appropriate extensions.
Drying of Industrial Ceramic Bricks: An Experimental Investigation in Oven

The purpose of this paper is to present an experimental study of clay brick drying. For the drying experiments, industrial holed bricks were dried in an oven under controlled conditions of velocity, temperature (constant and variable) and relative humidity of air. The continuous drying experiments ended when the mass reached constant weight. Experimental tests were performed under atmospheric pressure. Results of the drying and heating kinetics and volume variations during the process are shown and analyzed. It was verified that the drying process happens in the falling drying rate period, and air temperature has large influence in the drying rate during process. It was verified that the largest temperature, moisture content and stress gradients are located in the vertexes of the brick.
The Pro-Survival Role of Autophagy Depends on Bcl-2 Under Nutrition Stress Conditions

Autophagy can be induced under nutrition stress conditions. Bcl-2 is a pro-survival protein which inhibits apoptosis and autophagy. However, the role of Bcl-2 in autophagy regulation and cell survival under nutrition deprivation has not been fully understood. This study sought to investigate if Bcl-2 upregulation is essential in limiting autophagic activity and prevent cell death under nutrition deprivation conditions. Autophagic activity was monitored by the changes in GFP-LC3 localization and protein levels of Beclin1, LC3-II, cathepsin D and p62 in neuroblastoma SH-SY5Y cells underwent serum deprivation. Manipulation of Bcl-2 function was achieved with siRNAs and small molecular inhibitors. The cell viability and apoptosis were assessed with MTT assay and Annexin V/PI staining. The results showed that serum starvation increased protein levels of LC3-II and Beclin1 but decreased autophagy substrate p62. Autophagy activation induced by serum deprivation and rapamycin was accompanied by an upregulation of Bcl-2 protein levels. When Bcl-2 was knocked down with siRNA or inhibited with HA 14-1 or ABT-737, serum starvation induced profound cell death and enhanced autophagic flux under nutrition deprivation conditions, while knockdown of autophagic gene Beclin1 or autophagy inhibitors (bafilomycin A1 and E64D), rescued cell death. In contrast, overexpression of Bcl-2 inhibited autophagy and blocked cell death in response to serum deprivation. These data suggest that Bcl-2 plays an essential role in limiting autophagy activation and preventing initiation of programmed cell death. Thus Bcl-2 may be an important mechanism for balancing beneficial and detrimental impacts of autophagy on cell survival.
Performance of the RealStar Chikungunya Virus Real-Time Reverse Transcription-PCR Kit

ABSTRACT A novel commercial Chikungunya virus real-time reverse transcription-PCR (RT-PCR) kit was evaluated on a comprehensive panel of original patient samples. The assay was 100% sensitive and specific in comparison to a published real-time RT-PCR. Viral loads from both assays were highly correlated. The kit proved to be suitable for routine use in patient care.
Mobi_System: A personal travel assistance for electrical vehicles in smart cities

In this work it is proposed the design of a mobile system to assist car drivers in a smart city environment oriented to the upcoming reality of Electric Vehicles (EV). Taking into account the new reality of smart cites, EV introduction, Smart Grids (SG), Electrical Markets (EM), with deregulation of electricity production and use, drivers will need more information for decision and mobility purposes. A mobile application to recommend useful related information will help drivers to deal with this new reality, giving guidance towards traffic, batteries charging process, and city mobility infrastructures (e.g. public transportation information, parking places availability and car & bike sharing systems). Since this is an upcoming reality with possible process changes, development must be based on agile process approaches (Web services).
Making Friends in Life and Online: Equivalence, Micro-Correlation and Value in Spatial and Transpatial Social Networks

Social networks are increasingly constructed and maintained by online social networking tools in addition to traditional face-to-face interactions. This paper reports on how the structure of social ties established by online tools relate to those ties established by face-to-face interactions. We explore and map the social ties within a cohort of 2602 users, for whom we study the social ties mediated by both physical co-presence and Facebook. Our results suggest that the spatial social network consisting of face-to-face interactions exhibits similar characteristics to the transpatial social network consisting of Facebook ties. However, we find that individuals’ involvement in each network varies considerably.
DrMAD: Distilling Reverse-Mode Automatic Differentiation for Optimizing Hyperparameters of Deep Neural Networks

The performance of deep neural networks is well-known to be sensitive to the setting of their hyperparameters. Recent advances in reverse-mode automatic differentiation allow for optimizing hyperparameters with gradients. The standard way of computing these gradients involves a forward and backward pass of computations. However, the backward pass usually needs to consume unaffordable memory to store all the intermediate variables to exactly reverse the forward training procedure. In this work we propose a simple but effective method, DrMAD, to distill the knowledge of the forward pass into a shortcut path, through which we approximately reverse the training trajectory. Experiments on several image benchmark datasets show that DrMAD is at least 45 times faster and consumes 100 times less memory compared to state-of-the-art methods for optimizing hyperparameters with minimal compromise to its effectiveness. To the best of our knowledge, DrMAD is the first research attempt to make it practical to automatically tune thousands of hyperparameters of deep neural networks. The code can be downloaded from this https URL
Estimation of the spatial profile of neuromodulation and the temporal latency in motor responses induced by focused ultrasound brain stimulation

This study investigates the spatial profile and the temporal latency of the brain stimulation induced by the transcranial application of pulsed focused ultrasound (FUS). The site of neuromodulation was detected using 2-deoxy-2-[18F]fluoro-D-glucose PET immediately after FUS sonication on the unilateral thalamic area of Sprague–Dawley rats. The latency of the stimulation was estimated by measuring the time taken from the onset of the stimulation of the appropriate brain motor area to the corresponding tail motor response. The brain area showing elevated glucose uptake from the PET image was much smaller (56±10% in diameter, 24±6% in length) than the size of the acoustic focus, which is conventionally defined by the full-width at half-maximum of the acoustic intensity field. The spatial dimension of the FUS-mediated neuromodulatory area was more localized, approximated to be full-width at 90%-maximum of the acoustic intensity field. In addition, the time delay of motor responses elicited by the FUS sonication was 171±63 (SD) ms from the onset of sonication. When compared with latencies of other nonultrasonic neurostimulation techniques, the longer time delay associated with FUS-mediated motor responses is suggestive of the nonelectrical modes of neuromodulation, making it a distinctive brain stimulation method.
Effect of MyBP-C Binding to Actin on Contractility in Heart Muscle

In contrast to skeletal muscle isoforms of myosin binding protein C (MyBP-C), the cardiac isoform has 11 rather than 10 fibronectin or Ig modules (modules are identified as C0 to C10, NH2 to COOH terminus), 3 phosphorylation sites between modules C1 and C2, and 28 additional amino acids rich in proline in C5. Phosphorylation between C1 and C2 increases maximum Ca-activated force (Fmax), alters thick filament structure, and increases the probability of myosin heads on the thick filament binding to actin on the thin filament. Unphosphorylated C1C2 fragment binds to myosin, but phosphorylation inhibits the binding. MyBP-C also binds to actin. Using two types of immunoprecipitation and cosedimentation, we show that fragments of MyBP-C containing C0 bind to actin. In low concentrations C0-containing fragments bind to skinned fibers when the NH2 terminus of endogenous MyBP-C is bound to myosin, but not when MyBP-C is bound to actin. C1C2 fragments bind to skinned fibers when endogenous MyBP-C is bound to actin but not to myosin. Disruption of interactions of endogenous C0 with a high concentration of added C0C2 fragments produces the same effect on contractility as extraction of MyBP-C, namely decrease in Fmax and increase in Ca sensitivity. These results suggest that cardiac contractility can be regulated by shifting the binding of the NH2 terminus of MyBP-C between actin and myosin. This mechanism may have an effect on diastolic filling of the heart.
Two Methods for Target Localization in Multistatic Passive Radar

This paper compares two algorithms for three-dimensional target localization from passive radar measurements. The algorithms use bistatic range measurements from multiple transmitter-receiver pairs to calculate the target position. The algorithms derived are based on the methods known for time-difference-of-arrival (TDOA) systems, namely spherical interpolation (SI) and spherical intersection (SX). Both algorithms rely on closed-form equations. A theoretical accuracy analysis of the algorithms is provided. This analysis is verified with Monte-Carlo simulations and a real-life example is presented.
A neurofunctional model of speech production including aspects of auditory and audio-visual speech perception

A computer-implemented neurofunctional model of speech production is introduced, which is capable of articulating vowels, VC-, and CV-syllables (C = voiced plosives; V = vowels). It will be shown in this paper that this production model is capable of simulating basic effects of auditory and audio-visual speech perception like (i) categorical perception of consonants and vowels and (ii) the McGurk effect. These typical features of speech perception directly result from the topological ordering of stored speech items at a supra-modal neural level, called a phonetic map of this model. This phonetic map is a self-organizing neural map which is trained and structured during early phases of speech acquisition. The neurofunctional model introduced here illustrates the close relationship between speech production and speech perception.
The Information Content of Sudden Insider Silence

We present evidence of investors underreacting to the absence of events in financial markets. Routine-based insiders strategically choose to be silent when they possess private information not yet reflected in stock prices. Consistent with our hypothesis, insider silence following a routine sell (buy) predicts positive (negative) future returns, as well as fundamentals. The return predictability of insider silence is stronger among firms with a poor information environment and facing higher arbitrage costs, and a large fraction of abnormal returns concentrates on future earnings announcements. A long–short strategy that exploits insiders’ strategic silence behavior generates abnormal returns of 6% to 10% annually.
Presence of human papillomavirus type 16 genome in bladder carcinoma in situ of a patient with mild immunodeficiency.

Using blot hybridization, we analyzed 10 bladder tumors (1 transitional cell carcinoma in situ, 1 adenocarcinoma, and 8 papillary tumors) for the presence of human papillomavirus (HPV) DNA. We detected HPV 16 DNA in a transitional cell carcinoma in situ, whereas no HPV DNA was found in the other bladder tumors. The patient, a 40-year-old female, who harbored HPV 16 DNA in the bladder tumor, had mild immunodeficiency and recently suffered from the bladder tumor, common warts on the right hand, Bowen's disease of the vulva, and severe dysplasia of the vaginal wall. From each of these lesions, we detected the DNA of HPV 16 or an unclassified HPV. HPV DNAs existed in nonintegrated form in all lesions examined. To our knowledge, this is the first case in which a bladder tumor was shown to harbor HPV DNA. However, HPV does not seem to be regularly present in bladder tumor, because we could not detect HPV DNA from the most common bladder tumor, i.e., papillary tumor. Our demonstration of HPV 16 DNA in a transitional cell carcinoma in situ of the bladder suggests that HPV may be associated with some of the bladder tumors of this type.
Lensfree Fluorescent On-Chip Imaging of Transgenic Caenorhabditis elegans Over an Ultra-Wide Field-of-View

We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2–8 cm2 with a spatial resolution of ∼10µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2–8 cm2, without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research.
Combining Multiple Knowledge Sources for Discourse Segmentation

We predict discourse segment boundaries from linguistic features of utterances, using a corpus of spoken narratives as data. We present two methods for developing segmentation algorithms from training data: hand tuning and machine learning. When multiple types of features are used, results approach human performance on an independent test set (both methods), and using cross-validation (machine learning).
Sexual arousal in women with provoked vestibulodynia: the application of laser Doppler imaging to sexual pain.

Introduction. Women with provoked vestibulodynia (PVD) report lower sexual arousal than nonaffected women, however, laboratory studies of arousal have reported contradictory results about whether group differences exist in genital and subjective arousal. Aim. To examine genital and subjective sexual arousal in women with and without PVD. Methods. Eligible women with and without PVD (N = 42) attended a laboratory session that included an interview, questionnaire completion, and genital imaging. A direct measure of superficial blood flow-laser Doppler imaging-was used to assess vulvar blood flow levels while participants watched three films, including an erotic film. Participants answered questions about their level of sexual arousal before, during, and after the erotic film. Main Outcome Measures. Average vulvar blood flow levels during the baseline and erotic films, numerical ratings of subjective sexual arousal and anxiety, as well as questionnaire measures of arousal. Results. There was a significant group difference in genital arousal, whereby the PVD group showed a lower genital response to the erotic film, as well as a significant interaction between baseline blood flow and group membership. Separate group regression analyses demonstrated that baseline blood flow explained a substantial amount of the variance in erotic film blood flow in the control group (70%), while only 27% was explained by this variable in the PVD group. There were no differences in subjective sexual arousal or anxiety between the groups. Across questionnaire measures, women with PVD reported lower sexual arousal than the control group. Conclusions. The results suggest that women with PVD show lower genital responsiveness than nonaffected women to sexual stimuli in a laboratory setting and that their genital arousal is likely impacted by a number of biopsychosocial factors. Boyer SC, Pukall CF, and Chamberlain SM. Sexual arousal in women with provoked vestibulodynia: The application of laser Doppler imaging to sexual pain. J Sex Med **;**:**-**.
Cerebrospinal fluid cytokines and matrix metalloproteinases in human immunodeficiency seropositive and seronegative patients of tuberculous meningitis

Background: Some important clinical differences exist between human immunodeficiency virus (HIV)-seropositive and HIV-seronegative patients. Alterations in the cerebrospinal fluid (CSF) cytokines and matrix metalloproteinase have been noted in tuberculous meningitis. In HIV-infected patients, the immunopathogenesis is expected to be different. Materials and Methods: In this study, 64 patients of tuberculous meningitis (28 HIV seropositive and 36 seronegative) were included. The patients were followed up for six months. Cerebrospinal fluid (CSF) samples of tuberculous meningitis patients and 20 controls were subjected to tissue necrosis factor (TNF)-α, interleukin (IL)-1β, interferon (IFN)-γ, IL-10, matrix metalloproteinase (MMP)-2, and MMP-9 estimations. The levels were correlated with the patients’ baseline clinical characteristics, CSF parameters, neuroimaging findings, and the outcome. The outcome was assessed and modified with the Barthel index. Results: The CSF cytokines and MMP levels were significantly elevated in tuberculous meningitis when compared with the controls. There was no significant difference seen between HIV seropositive and seronegative tuberculous meningitis, except for the IL-1β level, which was significantly lower in the HIV-infected patients. The cytokine and MMP levels did not correlate with the baseline clinical characteristics, disease severity, cerebrospinal fluid characteristics, neuroimaging findings, and outcome. Conclusion: In conclusion, HIV infection did not affect a majority of the CSF cytokines and MMP levels in tuberculous meningitis except for IL-1β level. None of the estimated inflammatory parameters correlated with the outcome.
Photoluminescence from AlxIn1−xN layers doped with Tb3+ ions

AlxIn1−xN films (0 ≤ x ≤ 1) have been sputter deposited and annealed, both without and with terbium co-doping, to obtain a series of matrices whose band gap energies span the range from around 2 eV to 6 eV. The terbium green luminescence spectra (excitation wavelength 230 nm, i.e. 5.4 eV) are measured at room temperature as a function of the aluminium content (band gap route) and of the terbium concentration (concentration route). The green luminescence assumes a maximum of the integrated intensity at a band gap energy of 4.1 eV (x = 0.7) which can be argued to result from a resonant energy transfer from the host matrix into the Tb luminescence centres. Furthermore, the dependence of this maximum integrated intensity as a function of the Tb concentration, i.e. of the average distance between the Tb centres, suggests the energy transfer from the host material into the Tb luminescent centres to be due to dipole-dipole interaction via an exciton bound to the centre.