Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-classical B Cell Memory of Allergic IgE Responses

The long-term effectiveness of antibody responses relies on the development of humoral immune memory. Humoral immunity is maintained by long-lived plasma cells that secrete antigen-specific antibodies, and memory B cells that rapidly respond to antigen re-exposure by generating new plasma cells and memory B cells. Developing effective immunological memory is essential for protection against pathogens, and is the basis of successful vaccinations. IgE responses have evolved for protection against helminth parasites infections and against toxins, but IgE is also a potent mediator of allergic diseases. There has been a dramatic increase in the incidence of allergic diseases in recent decades and this has provided the impetus to study the nature of IgE antibody responses. As will be discussed in depth in this review, the IgE memory response has unique features that distinguish it from classical B cell memory.
Genome-Wide Identification of Host Genes Required for Toxicity of Bacterial Cytolethal Distending Toxin in a Yeast Model

Background Aggregatibacter actinomycetemcomitans, a periodontal pathogen, secretes a cytolethal distending toxin (AaCDT) that causes host cell cycle arrest and cell death. Although CDT could be an important virulence factor, it is unclear how it enters the nucleus to exert its cytotoxicity. Objective To investigate the mechanisms of AaCDT by genome-wide screening for host mutations that confer resistance to the catalytic subunit, AaCdtB, in a Saccharomyces cerevisiae model. Methods We transformed the yeast haploid deletion library, a collection of yeast mutants with single gene deletions of virtually all non-essential ORFs in the genome, with plasmids carrying galactose-inducible AaCdtB. Yeast mutants that showed resistance to AaCdtB were selected and rescreened by a spotting assay. AaCdtB expression was confirmed by western blot analysis; any mutants that showed no or weak expression of AaCdtB were omitted from the analysis. The lists of genes whose mutations confer resistance to AaCdtB were analyzed for Gene Ontology (GO) term enrichments. Localization of AaCdtB-EGFP was examined using fluorescent microscopy. Nuclear localization relative to EGFP control was calculated and compared to wild-type. Results Out of approximately 5,000 deletion mutants, we isolated 243 mutants that are resistant to AaCdtB. GO analyses indicated that genes associated with organic anion transport are significantly enriched (16 genes). Furthermore, several genes associated with the nucleus and endoplasmic reticulum (ER) were identified. Localization studies of AaCdtB, in mutants with the deletion of genes associated with the GO term organic anion transport, showed lower nuclear localization than wild-type. The results suggest that these genes may be required for AaCdtB translocation into the nucleus and its cytotoxicity. Conclusion The genome-wide screen in the yeast deletion library allowed us to identify a large number of host genes required for AaCdtB cytotoxicity. Further investigation could lead to more insights into the mechanisms of CdtB intoxication.
The global surgery blood drought: frontline provider data on barriers and solutions in Bihar, India

ABSTRACT Background: Limited access to safe, timely banked blood is a critical barrier to providing basic surgical care in resource-limited settings globally. Contextual, locally driven data are required to elucidate country needs, develop effective interventions, and guide policy decisions. Objective: We employ qualitative methodology to describe barriers faced and solutions proposed by front-line obstetric providers in Bihar – a poor, populous Indian state where maternal mortality exceeds the national average. We aim to make locally driven recommendations for ongoing policy work in India to strengthen the country’s blood transfusion system. Methods: From February to May 2016, two researchers conducted semi-structured interviews with 19 obstetric providers across Bihar. Snowball sampling was employed until thematic saturation was reached. Following immersion into de-identified texts and dual codebook development, a primary analyst completed topical coding, and a secondary analyst confirmed reproducibility. Results: Providers report that pervasive banked blood shortages force hospitals to require replacement donation, but patients’ families often cannot or will not donate. Providers wait one to six hours for blood, depending on availability of staff and supplies, blood bank proximity, and the ability of the patient being treated to navigate the system. Providers feel forced to refer their patients, often to distant, poorly equipped centers. Providers identify donor education, improved infrastructure, and improved local coordination as focus areas for intervention. Conclusions: A multi-stakeholder approach that aims to increase blood donation through community education, mitigate limited infrastructure through short-term workarounds, and improve local-level coordination through state support and policy change is required in Bihar. This study generates data to guide policy and future research aimed at generating affordable, contextually appropriate interventions to the blood drought.
Bayesian mmWave Channel Estimation via Exploiting Joint Sparse and Low-Rank Structures

We consider the problem of channel estimation for millimeter wave (mmWave) systems, where both the base station and the mobile station employ a single radio frequency (RF) chain to reduce the hardware cost and power consumption. Recent real-world channel measurements reveal that the mmWave channels incur a certain amount of spread over the angular domains due to the scattering clusters. The angular spreads give rise to a joint sparse and low-rank channel matrix in the angular domain. To utilize this joint sparse and low-rank structure, we address the channel estimation problem within a Bayesian framework. Specifically, we adopt a matrix factorization formulation and translate the problem of channel estimation into one of searching for two-factor matrices. To encourage a joint sparse and low-rank solution, independent sparsity-promoting priors are placed on entries of the two-factor matrices, which aims to promote sparse factor matrices with only a few non-zero columns. Based on the proposed prior model, we develop a variational Bayesian inference method for the mmWave channel estimation. The simulation results show that our proposed method presents a considerable performance improvement over the state-of-the-art compressed sensing-based channel estimation methods.
A Hybrid Adaptive Control Strategy for Industrial Robotic Joints

This paper presents a hybrid adaptive approximation-based control (HAAC) strategy for a class of uncertain robotic joints’ system. The proposed control structure consists of a robust sliding mode controller and an adaptive approximation-based controller. The robust sliding mode controller is designed by using the super-twisting algorithm, which is a particularly effective method to decrease the chattering caused by the traditional sliding mode control (SMC) and compensate the disturbances. Another improvement of the robust sliding mode controller is that the robust control parameters only subject to the upper bound of the derivative of the external disturbances, rather than choosing a relatively large value. Moreover, the designed adaptive approximation-based controller has the following two distinctive features: 1) the control parameters are designed to be adjusted in real time and 2) the prior knowledge of actual robotic model is not required to be known. These features contribute to compensating the uncertainties. The stability of the closed-loop system is proved by using the Lyapunov theory, and the simulation results demonstrate the effectiveness of the proposed control method. Finally, the proposed HAAC could apply in the experiments of industrial robotic joints’ system.
A guide to hyaluronan and related enzymes in breast cancer: biological significance and diagnostic value

Hyaluronan (HA) is a unique nonsulfated glycosaminoglycan that contributes to breast cancer cells growth and functional properties, including cell migration, invasion, adhesion, as well as tumor‐associated angiogenesis in different stages of breast cancer progression and especially metastasis. Latest data show that the levels of HA and/or low molecular mass HA in blood serum and plasma of breast cancer patients may be a useful biomarker for breast cancer prognosis, differential diagnosis, and patients' treatment monitoring. Therefore, the qualitative and quantitative determination of HA in biological samples is an emerging area of research. This review gathers, categorizes, and sums up all the currently used methodologies to analyze HA and HA‐related enzymes. The advantages, disadvantages, limitations in use, and the information they provide, are critically considered and discussed. Moreover, emphasis is given to the significance of HA determination in breast cancer, as well as of its related enzymes, for diagnosis and prognosis of this type of cancer.
Pointing Novel Objects in Image Captioning

Image captioning has received significant attention with remarkable improvements in recent advances. Nevertheless, images in the wild encapsulate rich knowledge and cannot be sufficiently described with models built on image-caption pairs containing only in-domain objects. In this paper, we propose to address the problem by augmenting standard deep captioning architectures with object learners. Specifically, we present Long Short-Term Memory with Pointing (LSTM-P) --- a new architecture that facilitates vocabulary expansion and produces novel objects via pointing mechanism. Technically, object learners are initially pre-trained on available object recognition data. Pointing in LSTM-P then balances the probability between generating a word through LSTM and copying a word from the recognized objects at each time step in decoder stage. Furthermore, our captioning encourages global coverage of objects in the sentence. Extensive experiments are conducted on both held-out COCO image captioning and ImageNet datasets for describing novel objects, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, we obtain an average of 60.9% in F1 score on held-out COCO dataset.
Three‐dimensional attenuation model of Sierra Negra Volcano, Galápagos Archipelago

The shallow magma system beneath Sierra Negra was imaged using attenuation tomographic methods. The t∗ spectral decay method for P wave phases was used to highlight regions of high Qp−1 which suggest the presence of magma melt. High‐ Qp−1 anomalies ranging from 0.005 to 0.04 are concentrated below the caldera from 0.5 to 10.5 km depths. Attenuation is sensitive to temperature and fluid presence; thus, this high attenuation is interpreted as possible zones of magma accumulation. An imaged shallow body is consistent with geodetic studies on caldera deformation that modeled a magma sill or flattopped diapir of unknown thickness at ∼1 km depth below sea level.
Proceedings of Meetings on Acoustics

Superharmonic imaging (SHI) targets a combination of the 3rd to 5th harmonics. It was proven to have certain advantages in comparison with the established imaging standards in medical utrasound. SHI enhances the spatial resolution and improves the quality of echographic images, mainly by eliminating reverberation artifacts at the chest wall. However, SHI suffers from ripple artifacts, originating from the spectral gaps in between harmonics, and degrading the temporal resolution. To solve this a chirp-based SHI protocol was employed and its characteristics investigated, i.e. point spread function (PSF). The protocol was implemented for an interleaved phased array probe (44+44 elements tuned at 1.0+3.7MHz), connected to a fully programmable ultrasound system. A linear chirp (center frequency 1MHz; bandwidth 40%) was used for excitation. To obtain the PSF, the RF traces were recorded at focus along the lateral axis and convolved with the decoding signal. This was computed using KZK simulations. A PSF comparison between a superharmonic chirp and the 3rd-harmonic of a 2.5-cycle Gaussian apodized sinus burst at 1MHz showed a decrease in axial pulse length of 46% at -6dB and 32% at the -20dB level in favor of SHI. Chirp based SHI is virtually free of ripple artifacts and therefore feasible.
Proceedings of Meetings on Acoustics

Graded porous materials are of growing interest because of their ability to improve the impedance matching between air and material itself. Theoretical models have been developed to predict the acoustical properties of these media. Traditionally, graded materials have been manufactured by stacking a discrete number of homogeneous porous layers with different pore microstructure. More recently a novel foaming process for the manufacturing of porous materials with continuous pore stratification has been developed. This paper reports on the application of the numerical procedure proposed by De Ryck to invert the parameters of the pore size distribution from the impedance tube measurements for materials with continuously stratified pore microstructure. Specifically, this reconstruction procedure has been successfully applied to retrieve the flow resistivity and tortuosity profiles of graded porous materials manufactured with the method proposed by Mahasaranon et al. In this work the porosity and standard deviation in pore size are assumed constant and measured using methods which are applied routinely for homogenous materials characterisation. The numerical method is based on the wave splitting together with the transmission Green's functions approach, yielding an analytical expression of the objective function in the Least-square sense.
Proceedings of Meetings on Acoustics

There are many means to generate a virtual sound source, or sources in the region of interest. For example, WFS (Wave Field Synthesis) or HOA (Higher Order Ambisonics) are good examples. These methods normally assume that loudspeakers are spatially distributed in the space. The region of interest where the desired sound is generated can have arbitrary shape; enclosed by surrounding loudspeakers or partially enclosed. Therefore, the performance of the method would be affected by the boundary conditions as well as the wave length of desired wave field. In other words, how the waves are distributed in the selected space. In recent work [J. -W. Choi, and Y. -H. Kim, IEEE Trans. Speech Audio Process. , vol. 20, no. 7, pp. 1976-1989, Sept. 2012], a new approach was proposed to generate virtual sources in the space that is enclosed by an array of loudspeakers, which have been believed to be problematic with well-known methods. It is proved to be mathematically exact solution. However, "exact solution" does not necessarily mean that it is better than the others. In this paper, performances of these three methods are compared. Theoretical and experimental comparisons have been attempted and observed in this paper.
Proceedings of Meetings on Acoustics

Conversation is one of the most important channels for human beings. To help communications, speech recognition technologies have been developed. Above all, in a conversation, not only contents of utterances but also intonations and tones include important information regarding a speaker's intention. To study the sphere of human speech, microphones are typically used to record voices. However, since microphones have to be set around a space, their existences affect a physical behavior of the sound field. To challenge this problem, we have suggested a recording method using a high-speed camera. By using a high-speed camera for recording sound vibrations, it can record two or more points within the range of the camera at the same time and can record from a distance, without interfering with the sound fields. In this study, we extract voice information using high-speed videos which capture both a face and a cervical part of the subject. This method allows recording skin vibrations which contain voices with individuality and extrapolating sound waves by using an image processing method. The result of the experiment shows that a high-speed camera is capable of recording voice information.
Proceedings of Meetings on Acoustics

The detection and recognition of communication signals in natural soundscapes is a difficult task that animals and birds in particular excel at. We have used a neuroethological approach to quantify the recognition performance for propagated communication signals in the zebra finch, specifically regarding the information about individual identity. The propagated signals were analyzed using a regularized discriminant function analyses on a complete spectrographic representation of the signals. We found 1) a reduction in the informative frequency range a long distances yielding a frequency band sweet-spot, 2) that call duration and pitch are important parameters at short distances and 3) that frequency modulation gains are important parameters at longer distances. Operant conditioning experiments showed that female songbirds were able to discriminate male calls at up to 128m but not at 256m. Finally, neurophysiological recordings showed a similar pattern in that high neural discrimination for calls was observed at 16 m and that this information degraded as a function of distance. We are currently analyzing the tuning properties of neurons that showed the most invariant responses to propagated sounds and hypothesized that these will be tuned to the parameters that we found were the most informative in the discriminant function analysis.
Proceedings of Meetings on Acoustics

The near-surface sound levels propagated at distance from a known source show a large variability on the long term. This variability is essentially caused by the weather-dependence of the refractive characteristics: wind and temperature stratifications, turbulence. An approach to document this variability is to simulate the sound propagation under these varying characteristics at the selected site. This study uses a numerical model which physically describes the sound propagation including in presence of turbulence. The model is based on the parabolic equation, it ingests standard atmospheric parameters as input. The predicted sound levels for an example 40Hz-frequency sound propagating at a 1.5kmrange are shown to combine the impacts of stratification and turbulence. The results are used to form the sound level climatology at several sites over the globe, based on existing climatological data. The obtained statistics are modulated by the dominant wind regimes, the seasonal and diurnal cycles. The sensitivity of these results to turbulence assessment is discussed.
Proceedings of Meetings on Acoustics

Over the last decade there has been significant interest in the design and production of acoustic metamaterials with physical qualities not seen in naturally occurring media. Progress in this area has been stimulated by the desire to create materials that exhibit novel behaviour such as negative refraction due to negative material parameters, and band gaps in the frequency response of the material. An acoustic metamaterial is presented that consists of an acoustically transparent mesh with an array of split hollow spheres. Split hollow spheres are analogous to the split ring resonators found in many electromagnetic metamaterials and act as Helmholtz resonators providing a resonant band gap at low frequencies where achieving a Bragg gap would be impractical, and providing a dispersive effective bulk modulus that can become negative. Since an eventual goal of the work is to produce such materials on a micro-scale, the metamaterial is designed for, and produced using, 3D printing techniques (additive layer manufacturing). Results are presented for material comparing theory and experiment, and methods for increasing the bandwidth of the behaviour in question are proposed, including a mixed resonator solution.
Brazilian Journal of Chemical Engineering PREPARATION AND APPLICATION OF CHITOSAN NANOPARTICLES AND NANOFIBERS

Encapsulation and immobilization technology is important for the food processing and bioengineering industries. Chitosan is a natural polysaccharide prepared by the N-deacetylation of chitin. It has been widely used in food and bioengineering industries, including the encapsulation of active food ingredients, in enzyme immobilization, and as a carrier for controlled drug delivery, due to its significant biological and chemical properties such as biodegradability, biocompatibility, bioactivity, and polycationicity. In this work, chitosan nanoparticles and nanofibers used to encapsulate bioactive substances and immobilize enzymes were reviewed. Preparation of chitosan nanoparticles and nanofibers, including the work achieved in our group on chitosan nanoparticles for enzyme immobilization, were also introduced. Some problems encountered with nano-structured chitosan carriers for bioactive substance encapsulation and enzyme immobilization were discussed, together with the future prospects of such systems.
Brazilian Journal of Chemical Engineering METHANOGENIC POTENTIAL AND MICROBIAL COMMUNITY OF ANAEROBIC BATCH REACTORS AT DIFFERENT METHYLAMINE / SULFATE RATIOS

Methylamine and sulfate are compounds commonly found in wastewaters. This study aimed to determine the methanogenic potential of anaerobic reactors containing these compounds and to correlate it with their microbial communities. Batch experiments were performed at different methylamine/sulfate ratios of 0.71, 1.26 and 2.18 (with respect to mass concentration). Control and experimental runs were inoculated with fragmented granular sludge. The maximum specific methane formation rates were approximately 2.3 mmol CH4 L g TVS day for all conditions containing methylamine, regardless of sulfate addition. At the end of the experiment, total ammonium-N and methane formation were proportional to the initial concentrations of methylamine. In the presence of methylamine and sulfate, Firmicutes (46%), Deferribacteres (13%) and Proteobacteria (12%) were the predominant phyla of the Bacteria domain, while Spirochaetes (40%), Deferribacteres (17%) and Bacteroidetes (16%) predominated in the presence of methylamine only. There was no competition for methylamine between sulfate-reducing bacteria and methanogenic archaea.
Politics of identification in the use of lingua francas in student mobility to Finland and France

This chapter examines the mobility of students to Finland and France. I am interested in the perceptions of the use of lingua francas in these contexts. The students have to speak languages of which they are not always “native speakers” and finding a common ground often results in using a lingua franca. In the chapter, English and French are the main lingua francas used by the students. Even though the cases of Finland and France are different in relation to the number of speakers of their languages (6 million people live in Finland compared to 70 million in France), the results show that similar attitudes and opinions seem to be shared by students who have spent time in these countries.