Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterium tuberculosis protein tyrosine phosphatase (PtpA) excludes host vacuolar-H+–ATPase to inhibit phagosome acidification

Mycobacterium tuberculosis (Mtb) pathogenicity depends on its ability to inhibit phagosome acidification and maturation processes after engulfment by macrophages. Here, we show that the secreted Mtb protein tyrosine phosphatase (PtpA) binds to subunit H of the macrophage vacuolar-H+-ATPase (V-ATPase) machinery, a multisubunit protein complex in the phagosome membrane that drives luminal acidification. Furthermore, we show that the macrophage class C vacuolar protein sorting complex, a key regulator of endosomal membrane fusion, associates with V-ATPase in phagosome maturation, suggesting a unique role for V-ATPase in coordinating phagosome–lysosome fusion. PtpA interaction with host V-ATPase is required for the previously reported dephosphorylation of VPS33B and subsequent exclusion of V-ATPase from the phagosome during Mtb infection. These findings show that inhibition of phagosome acidification in the mycobacterial phagosome is directly attributed to PtpA, a key protein needed for Mtb survival and pathogenicity within host macrophages.
Characterization of node disjoint (parallel) path in star graphs

This paper presents an analysis that leads to the complete characterization of the node disjoint (parallel) paths in a star graph. It is shown that by exploiting the cycle structure of permutations (same as the conjugacy class) one can decentralize a routing algorithm for transfer of packets between a pair of nodes in these graphs. <<ETX>>
Immunoregulatory roles of eosinophils: a new look at a familiar cell

Eosinophils are usually considered as end‐stage degranulating effector cells of innate immunity. However, accumulating evidence has revealed additional roles for eosinophils that are immunoregulatory in nature in both the adaptive and innate arms of immunity. Specifically, eosinophils have key immunoregulatory roles as professional antigen‐presenting cells and as modulators of CD4+ T cell, dendritic cell, B cell, mast cell, neutrophil, and basophil functions. This review addresses the emerging immunoregulatory roles of eosinophils with a focus on recent data that support this new paradigm. Recognizing both the effector and immunoregulatory functions of eosinophils will enable a fuller understanding of the roles of eosinophils in allergic airways inflammation and may be pertinent to therapies that target eosinophils both for their acute and ongoing immunomodulatory functions.
Pulsed laser deposition and characterization of (BiFeO3)0.7-(PbTiO3)0.3 thin films

Development of ferroelectric materials and their composites has been a subject of intensive investigation in recent years due to their promise in next generation electronic devices. In this work, we report on the pulsed laser deposition of thin films of bismuth ferrite lead titanate (BiFeO3)x-(PbTiO3)1-x on platinized Si (100) substrates. The growth conditions were optimised by changing a range of growth parameters such as background pressure, growth temperature and laser frequency. The film structure was studied using X-ray diffraction (XRD), and scanning electron microscopy (SEM). We found that films become highly Pb and Bi deficient upon increasing the deposition temperatures up to 600°C. A stoichiometric BFPT 7030 phase was observed at a substrate temperature of 450°C. In addition, it was observed that the phase orientation of films prepared at a substrate temperature of 450°C can be enhanced by post deposition annealing resulting in a dense columnar grain growth of the film.
Fouling Tendency of Ash Resulting From Burning Mixtures of Biofuels

Specified mixtures of peat with bark and peat with straw were burned in a lab-scale entrained flow reactor that simulates conditions in the superheater region of a biomass-fired boiler. Deposits were collected on an air-cooled probe that was inserted into the reactor at the outlet. For both mixtures, the deposition behaviour followed a non-linear pattern, which suggests that physico-chemical interaction between the ashes of the different fuels has taken place. The results indicate that it is possible to burn up to 30 wt-% bark (renewable biofuel and pulp mill waste) and up to 70 wt-% straw (renewable biofuel and agricultural waste) in mixtures with peat without encountering increased deposition rates in the reactor. The deposit composition was compared to the fuel ash composition using chemical fractionation analysis and SEM/EDX. While the composition of deposits obtained from pure fuels resembles the feed composition, a considerable change is observed in deposits obtained from mixtures. K and S compounds are attached to Si spheres and the substrate surface. The deposition rate is significantly lowered when removing K, S, Cl and Na in bark prior to burning by washing and mechanical/thermal dewatering.Copyright © 2005 by ASME
Ubiquitination and Proteasomal Degradation of Endogenous and Exogenous Inositol 1,4,5-Trisphosphate Receptors in αT3-1 Anterior Pituitary Cells*

In αT3-1 mouse anterior pituitary gonadotropes, chronic activation of gonadotropin-releasing hormone (GnRH) receptors causes inositol 1,4,5-trisphosphate (InsP3) receptor down-regulation (Willars, G. B., Royall, J. E., Nahorski, S. R., El-Gehani, F., Everest, H. and McArdle, C. A. (2001)J. Biol. Chem. 276, 3123–3129). In the current study, we sought to define the mechanism behind this adaptive response. We show that GnRH induces a rapid and dramatic increase in InsP3 receptor polyubiquitination and that proteasome inhibitors block InsP3 receptor down-regulation and cause the accumulation of polyubiquitinated receptors. Thus, the ubiquitin/proteasome pathway is active in αT3-1 cells, and GnRH regulates the levels of InsP3 receptors via this mechanism. Given these findings and further characterization of this system, we also examined the possibility that αT3-1 cells could be used to examine the ubiquitination of exogenous InsP3 receptors introduced by cDNA transfection. This was found to be the case, since exogenous wild-type InsP3 receptors, but not binding-defective mutant receptors, were polyubiquitinated in a GnRH-dependent manner, and agents that inhibited the polyubiquitination of endogenous receptors also inhibited the polyubiquitination of exogenous receptors. Further, we used this system to determine whether phosphorylation was involved in triggering InsP3 receptor polyubiquitination. This was not the case, since mutation of serine residues 1588 and 1755 (the predominant phosphorylation sites in the type I receptor) did not inhibit polyubiquitination. In total, these data show that the ubiquitin/proteasome pathway is active in anterior pituitary cells, that this pathway targets both endogenous and exogenous InsP3 receptors in GnRH-stimulated αT3-1 cells, and that, in contrast to the situation for many other substrates, phosphorylation does not trigger InsP3 receptor polyubiquitination.
National Center for Genome Analysis support leverages XSEDE to support life science research

The National Center for Genome Analysis Support (NCGAS) is a response to the concern that NSF-funded life scientists were underutilizing the national cyberinfrastructure, because there has been little effort to tailor these resources to the life scientist communities needs. NCGAS is a multi-institutional service center that provides computational resources, specialized systems support to both the end-user and systems administrators, curated sets of applications, and most importantly scientific consultations for domain scientists unfamiliar with next generation DNA sequence data analysis. NCGAS is a partnership between Indiana University Pervasive Technology Institute, Texas Advanced Computing Center, San Diego Supercomputing Center, and the Pittsburgh Supercomputing Center. NCGAS provides hardened bioinformatic applications and user support on all aspects of a user's data analysis, including data management, systems usage, bioinformatics, and biostatistics related issues.
Intonation Conversion from Neutral to Expressive Speech

Intonation is one of the most important factors of speech expressivity. This paper presents a conversion method for the F0 contours. The F0 segments are represented with discrete cosine transform (DCT) coefficients at the syllable level. Multi-level dynamic features are added to model the temporal correlation between syllables and to constrain the F0 contour at the phrase level. Gaussian mixture models (GMM) are used to map the prosodic features between neutral and expressive speech, and the converted F0 contour is generated under the dynamic features constraints. Experimental evaluation using a database of acted emotional speech shows the effectiveness of the proposed F0 model and conversion method.
First Insights into the Phylogenetic Diversity of Mycobacterium tuberculosis in Nepal

Background Tuberculosis (TB) is a major public health problem in Nepal. Strain variation in Mycobacterium tuberculosis may influence the outcome of TB infection and disease. To date, the phylogenetic diversity of M. tuberculosis in Nepal is unknown. Methods and Findings We analyzed 261 M. tuberculosis isolates recovered from pulmonary TB patients recruited between August 2009 and August 2010 in Nepal. M. tuberculosis lineages were determined by single nucleotide polymorphisms (SNP) typing and spoligotyping. Drug resistance was determined by sequencing the hot spot regions of the relevant target genes. Overall, 164 (62.8%) TB patients were new, and 97 (37.2%) were previously treated. Any drug resistance was detected in 50 (19.2%) isolates, and 16 (6.1%) were multidrug-resistant. The most frequent M. tuberculosis lineage was Lineage 3 (CAS/Delhi) with 106 isolates (40.6%), followed by Lineage 2 (East-Asian lineage, includes Beijing genotype) with 84 isolates (32.2%), Lineage 4 (Euro-American lineage) with 41 (15.7%) isolates, and Lineage 1 (Indo-Oceanic lineage) with 30 isolates (11.5%). Based on spoligotyping, we found 45 different spoligotyping patterns that were previously described. The Beijing (83 isolates, 31.8%) and CAS spoligotype (52, 19.9%) were the dominant spoligotypes. A total of 36 (13.8%) isolates could not be assigned to any known spoligotyping pattern. Lineage 2 was associated with female sex (adjusted odds ratio [aOR] 2.58, 95% confidence interval [95% CI] 1.42–4.67, p = 0.002), and any drug resistance (aOR 2.79; 95% CI 1.43–5.45; p = 0.002). We found no evidence for an association of Lineage 2 with age or BCG vaccination status. Conclusions We found a large genetic diversity of M. tuberculosis in Nepal with representation of all four major lineages. Lineages 3 and 2 were dominating. Lineage 2 was associated with clinical characteristics. This study fills an important gap on the map of the M. tuberculosis genetic diversity in the Asian region.
Structural and Functional Changes of the Human Macula during Acute Exposure to High Altitude

Background This study aimed to quantify structural and functional changes at the macula during acute exposure to high altitude and to assess their structure/function relationship. This work is related to the Tuebingen High Altitude Ophthalmology (THAO) study. Methodology/Principal Findings Spectral domain optical coherence tomography and microperimetry were used to quantify changes of central retinal structure and function in 14 healthy subjects during acute exposure to high altitude (4559 m). High-resolution volume scans and fundus-controlled microperimetry of the posterior pole were performed in addition to best-corrected visual acuity (BCVA) measurements and assessment of acute mountain sickness. Analysis of measurements at altitude vs. baseline revealed increased total retinal thickness (TRT) in all four outer ETDRS grid subfields during acute altitude exposure (TRTouter = 2.80±1.00 μm; mean change±95%CI). This change was inverted towards the inner four subfields (TRTinner = −1.89±0.97 μm) with significant reduction of TRT in the fovea (TRTfoveal = −6.62±0.90 μm) at altitude. BCVA revealed no significant difference compared to baseline (0.06±0.08 logMAR). Microperimetry showed stable mean sensitivity in all but the foveal subfield (MSfoveal = −1.12±0.68 dB). At baseline recordings before and >2 weeks after high altitude exposure, all subjects showed equal levels with no sign of persisting structural or functional sequels. Conclusions/Significance During acute exposure to high altitude central retinal thickness is subject to minor, yet statistically significant changes. These alterations describe a function of eccentricity with an increase in regions with relatively higher retinal nerve fiber content and vascular arcades. However, these changes did not correlate with measures of central retinal function or acute mountain sickness. For the first time a quantitative approach has been used to assess these changes during acute, non-acclimatized high altitude exposure.
Towards objective and reproducible study of patient-doctor interaction: Automatic text analysis based VR-CoDES annotation of consultation transcripts

While increasingly appreciated for its importance, the interaction between health care professionals (HCP) and patients is notoriously difficult to study, with both methodological and practical challenges. The former has been addressed by the so-called Verona coding definitions of emotional sequences (VR-CoDES) - a system for identifying and coding patient emotions and the corresponding HCP responses - shown to be reliable and informative in a number of independent studies in different health care delivery contexts. In the preset work we focus on the practical challenge of the scalability of this coding system, namely on making it easily usable more widely and on applying it on larger patient cohorts. In particular, VR-CoDES is inherently complex and training is required to ensure consistent annotation of audio recordings or textual transcripts of consultations. Following up on our previous pilot investigation, in the the present paper we describe the first automatic, computer based algorithm capable of providing coarse level coding of textual transcripts. We investigate different representations of patient utterances and classification methodologies, and label each utterance as either containing an explicit expression of emotional distress (a ‘concern’), an implicit one (a ‘cue’), or neither. Using a data corpus comprising 200 consultations between radiotherapists and adult female breast cancer patients we demonstrate excellent labelling performance.
Probing/Manipulating the Interfacial Atomic Bonding between High k Dielectrics and InGaAs for Ultimate CMOS

Abstract : The MOS technology using high-k dielectrics on high carrier mobility semiconductors of InGaAs leading to a faster speed at lower power is now at the International Technology Roadmap for Semiconductors (ITRS). Great efforts have been dedicated to understand the high k/InGaAs interface. This project involves an examination of interfacial electronic structure of in-situ HfO2 on In0.53Ga0. 47As\(001)-4x2 probed by synchrotron radiation photoemission. The dielectric film was prepared by atomic layer deposition (ALD) with the precursors as tetrakis[ethylmethylamino] Hafnium (TEMAHf) and water. Samples were kept under ultra-high-vacuum (UHV) throughout from MBE/ALD preparation to data-acquisition photoemission chambers in the synchrotronradiation facility. The high-resolution work with a short inelastic mean-free path allowed for the first time identification of atom-toatom interaction at this interface. This work has elucidated the mechanism and nature of the bonding between the Hf atom in TEMAHf and In/As atoms of the reconstructed In0.53Ga0. 47As(001)-4x2 surface. The TEMAHf precursor is either intact, or loses one ethylmethylamino ligand to become tri-EMAHf. The initial purge of the TEMAHf precursors effectively passivates all the edge As atoms in the top row. As a result, no oxygen bonding was found at either surface As or In atoms. The subsequent water purge reacts with tri-EMAHf to facilitate the growth of hafnium oxides there. The interface obtained by ALD in the present study found no evidence of oxygen bonding to any atom in the trough. The unpassivated surface In atoms may contribute to the frequency dispersion in the accumulation region of n-In0.53Ga0. 47As MOSCAP.
Mandibular Trauma Age Determination Prevalence of Dental Anomalies in Down Syndrome Patients Locating Unerupted Teeth Stylohyoid Ligament Calcification

The most common manifestations of atherosclerosis are coronary artery disease, peripheral vascular disease and cerebrovascular accidents stroke.1 In the USA, 731,000 suffer a stroke each year with 165,000 not surviving.2 There are approximately 4 million stroke survivors. Lifelong disabilities such as loss of mobility, aphasia, and depression often afflict survivors.3 Estimated healthcare costs related to acute and chronic management of strokes are $40 billion annually. Atheroma-related formations of thrombi and emboli in the carotid artery is the most frequent cause of stroke.4 Early detection of carotid atherosclerosis has the potential to save lives and reduce medical expenditures. Since 1981, Friedlander and his colleagues have actively promoted panoramic radiology as an aid in detecting patients at risk of stroke.5 Calcified atherosclerotic lesions at the carotid bifurcation can be seen in the lower corners of the panoramic radiograph adjacent to the cervical spine and hyoid bone (Fig. 1-3). Such atheroma may appear as a nodular radiopaque mass or as double radio-opaque vertical lines within the neck. These calcifications are found at the level of the lower margin of the third and the entirety of the fourth cervical vertebra, about 1.5 to 2.5 cm Panoramic radiology and the detection of carotid atherosclerosis
A Localization Algorithm for Mobile Wireless Sensor Networks

Localization is very important for wireless sensor networks. Many applications require the location information. In this paper, we propose a range based Monte Carlo localization algorithm, which builds upon the Monte Carlo localization algorithm. We improve the localization accuracy and efficiency by introducing the RSSI (received signal strength indication) ranging technique, which is a low power, low cost and low complexity ranging method. The ranging error of RSSI is always very large and always varying with the change of the real environment. Although the low accuracy and high uncertainty of the range measurements would appear to make the localization more difficult, our approach exploits it to improve the accuracy and efficiency of localization. Simulation results show that its performance is better than some other localization algorithms.
Learning to Focus Attention on Discriminative Regions for Object Detection

A major task of visual attention is to focus processing on regions of interest to enable rapid and robust object search. Instead of integrating generic feature extraction into object specific interpretation we strictly pursue a top-down approach. Early features are tuned to selectively respond to task related visual features, i.e., locally discriminative information that is useful in object recognition. In this work we determine discriminative regions from the information content in the local appearance patterns. A rapid mapping from appearances to discriminative regions is estimated using decision trees. The focus of attention on discriminative patterns enables then efficient detection of a searched object, but also the definition of sparse object representations to respond only to task relevant information. In the experiments, the performance in object recognition from single imagettes dramatically increased considering only discriminative patterns. Evaluation of complete image analysis under various degrees of partial occlusion and image noise resulted in highly robust recognition even in the presence of severe occlusion and noise effects. Finally, preliminary results on attentive object detection in cluttered environments demonstrated successful indexing to relevant locations.
Capsular Serotyping of Streptococcus pneumoniae Using the Quellung Reaction

There are over 90 different capsular serotypes of Streptococcus pneumoniae (the pneumococcus). As well as being a tool for understanding pneumococcal epidemiology, capsular serotyping can provide useful information for vaccine efficacy and impact studies. The Quellung reaction is the gold standard method for pneumococcal capsular serotyping. The method involves testing a pneumococcal cell suspension with pooled and specific antisera directed against the capsular polysaccharide. The antigen-antibody reactions are observed microscopically. The protocol has three main steps: 1) preparation of a bacterial cell suspension, 2) mixing of cells and antisera on a glass slide, and 3) reading the Quellung reaction using a microscope. The Quellung reaction is reasonably simple to perform and can be applied wherever a suitable microscope and antisera are available.
Robust Angle-Sensorless Control of a PMSM Bearingless Pump

In the semiconductor industry, where bearingless pump systems are employed as the state-of-the-art technology, the trend goes toward higher fluid temperatures (150degC and more) in order to further increase process efficiency. This fact translates into the requirement of a high-temperature bearingless pump system and/or the elimination of thermal-critical components such as Hall sensors. This paper introduces a new method for a hall-sensorless control of a permanent-magnet synchronous machine bearingless pump in its operating range from 0 to 8000 r/min and from zero load to full load. The sensorless operation is performed by the following three novel control functionalities: a controlled startup routine, enabling a sure levitation and zero-angle setting; an open-loop angle estimation based on stator voltage and stator current measurement and known machine parameters; and an angle synchronization establishing a robust operation of the pump in the whole operating range even for a large machine parameter drift. In particular, considering the temperature degrading of the permanent-magnet flux density, the novel robust control concept is of great benefit for bearingless pump systems employed in high-temperature applications.
Visual and Adaptive Constraint Programming in Music

We propose an environment for musical constraint solving, adapted to contemporary composition, in the visual programming language OpenMusic. We describe the use of two algorithms, a complete one and an incomplete one. The latter is a local search algorithm, called adaptive search. Adaptive search refines the concept of cost function by taking into account the weight of each variable. We show that an incomplete algorithm is well adapted for musical problems. The first experimental results on real musical problems are satisfying, including in terms of computation