Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronic intranasal administration of mould spores or extracts to unsensitized mice leads to lung allergic inflammation, hyper‐reactivity and remodelling

Allergic asthma is a serious multifaceted disease characterized by eosinophil‐rich airway inflammation, airway hyperreactivity and airway wall modifications known as remodelling. We previously demonstrated that the spores of two allergenic moulds, Alternaria alternata and Cladosporium herbarum, were potent inducers of immunoglobulin E (IgE) production. Moreover, mice sensitized by two intraperitoneal injections before intranasal challenge with A. alternata or C. herbarum spores developed an allergic lung inflammation and hyperreactivity. Here we report on the effect of chronic intranasal administration of C. herbarum spores or A. alternata extracts to unsensitized BALB/c mice. Our results demonstrate that this chronic treatment led to an increase of total serum IgE and the appearance of specific IgE and IgG1. Total cell number in bronchoalveolar lavage fluid from treated mice was highly increased compared to phosphate‐buffered‐saline‐treated mice because of the accumulation of macrophages, neutrophils, lymphocytes and eosinophils. Airway hyperreactivity appeared after 3 weeks (extract) and 7 weeks (spores) and was maintained during the whole treatment. Increased interleukin‐13 mRNA expression in the lungs and T helper type 2 cytokines (interleukin‐4, ‐5, ‐6 and ‐13) and transforming growth factor‐β secretion in bronchoalveolar lavage fluid were also observed. Lung hydroxyproline and fibronectin contents indicated increased fibrosis in mice treated with mould allergen. These observations were confirmed by histological analysis demonstrating airway wall remodelling and strong mucus production. These observations show that this model, using chronic intranasal administration of relevant particulate allergens, is an interesting tool for the study of mechanisms leading to allergic pulmonary diseases and lung remodelling.
3D Architectural Modeling: Coarse-to-fine model fitting on point cloud

We present a coarse-to-fine model fitting approach that automatically generates a detailed CAD like model from a point cloud. We first developed a library of detailed parametric models for each of the architectural elements. The parameter estimate of these models is obtained using an efficient 3D shape fitting and peak finding approach that operates on the planar and 1D projections of the point clouds The approach performs coarse-to-fine veals intrinsic details resulting in efficient and accurate parameter estimation significantly increases the amount of details in the recovered 3D model.
The Conjunctiva-Associated Lymphoid Tissue in Chronic Ocular Surface Diseases

Abstract Ocular surface diseases (OSDs) represent a widely investigated field of research given their growing incidence and the negative impact on quality of life. During OSDs, cytokines generated by damaged epithelia trigger and deregulate the lymphoid cells composing the eye-associated lymphoid tissues, inducing an immune-mediated chronic inflammation that amplifies and propagates the disease during time. The conjunctiva-associated lymphoid tissue (CALT), given its particular position that permits immune cells covering the cornea, might play a crucial role in the development of OSDs. Despite the recognized inflammatory role of mucosa-associated lymphoid tissues in other stations taking contact with the external environment (gut or bronchus), CALT did not gain the deserved consideration. In the last years, the diffusion of the in vivo confocal microscopy (IVCM) stimulated the interest to CALT, especially in dry eye, ocular allergy, and glaucoma. Though the initial stimuli were different, IVCM documented similar changes, represented by increased lymphoid cells within the diffuse layer, follicles and interfollicular spaces. These findings, which need to be validated by immunohistology, support the CALT stimulation during OSDs. However, while an involvement of the CALT in OSDs is hypothesizable, the exact role of this structure in their pathogenesis remains unclear and warrants further investigations.
Long-Wave Approximation to the 3-D Capillary-Gravity Waves

This is a follow-up paper to [M. Ming, P. Zhang, and Z. Zhang, Arch. Ration. Mech. Anal. , 204 (2012), pp. 387--444], where we proved that in the regime of weakly transverse long waves, given long-wave initial data, the nondimensionalized water-wave system in an infinite strip under the influence of gravity and surface tension on the upper free interface has a unique solution on $[0,{T}/\varepsilon]$ for some $\varepsilon$ independent of constant $T. $ The purpose of this paper is to show that on the same time interval, these solutions can be accurately approximated by sums of solutions of two decoupled Kadomtsev--Petviashvili (KP) equations for the strong and weak surface tension case, when the Bond number is positive and away from $\frac13. $ In the case when the Bond number $\alpha=\frac13,$ the coefficients of the third-order dispersion terms in $(KP)^\pm$ equations vanish and the resulting equations become ill-posed. To capture the dispersive nature of the water-wave problem for this parameter regime, w.
Neonatologists are using much less dexamethasone

Two historical cohorts (1993–1994 and 2001) of preterm infants ventilated for respiratory distress syndrome were compared. Dexamethasone administration fell from 22% to 6%. Chronic lung disease in survivors rose slightly from 13% to 17%, and mortality fell from 21% to 15% (other causes). The effect of restriction of dexamethasone use on chronic lung disease and mortality remains to be seen.
Motion-compensation using variable-size block-matching with binary partition trees

A new approach to variable size block matching is proposed, based on the binary partitioning of blocks. If a particular block does not allow for accurate motion compensation, then it is split into two using the horizontal or vertical line that achieves the maximum reduction in motion compensation error. This method causes partitioning to occur along motion boundaries, thus substantially reducing blocking artifacts. In addition, small blocks are placed in regions of complex motion, while large blocks cover regions of uniform motion. The proposed technique provides significant gains in picture quality of 1.5 to 3.0 dB, when compared to fixed size block matching at the same total rate.
Larval vision contributes to gregarious settlement in barnacles: adult red fluorescence as a possible visual signal

Gregarious settlement, an essential behavior for many barnacle species that can only reproduce by mating with a nearby barnacle, has long been thought to rely on larval ability to recognize chemical signals from conspecifics during settlement. However, the cyprid, the settlement stage larva in barnacles, has one pair of compound eyes that appear only at the late nauplius VI and cyprid stages, but the function(s) of these eyes remains unknown. Here we show that cyprids of the intertidal barnacle Balanus (=Amphibalanus) amphitrite can locate adult barnacles even in the absence of chemical cues, and prefer to settle around them probably via larval sense of vision. We also show that the cyprids can discriminate color and preferred to settle on red surfaces. Moreover, we found that shells of adult B. amphitrite emit red auto-fluorescence and the adult extracts with the fluorescence as a visual signal attracted cyprid larvae to settle around it. We propose that the perception of specific visual signals can be involved in behavior of zooplankton including marine invertebrate larvae, and that barnacle auto-fluorescence may be a specific signal involved in gregarious larval settlement.
Improving Correlation with Human Judgments by Embedding Second Order Vectors with Semantic Similarity

Vector space methods that measure semantic similarity and relatedness often rely on distributional information such as co--occurrence frequencies or statistical measures of association to weight the importance of particular co-occurrences. In this paper we extend these methods by embedding a measure of semantic similarity based on a human curated taxonomy into a second--order vector representation. This results in a measure of semantic relatedness that combines both the contextual information available in a corpus--based vector space representation with the semantic knowledge found in a biomedical ontology. Our results show that embedding semantic semantic similarity into a second order co--occurrence matrix improves correlation with human judgments for both similarity and relatedness.
Quantitative Evaluation of Commercially Available Test Kit for Ciguatera in Fish

Reliability of the commercially available Cigua-Check(R) test kits to identify ciguateric fish was evaluated by assessing the uniformity of conclusions by multiple readers examining identical sticks. One hundred and eighty-eight samples of two types of reef fish were tested for ciguatera using Cigua-Check(R) test strips. Paired subsamples of all specimens were also analyzed via the more rigorous N2a neuroblastoma mouse bioassay that is specific for aberration of Na+-channel activity that is presumptive for ciguatera fish poisoning. In a double blind trial, four individuals visually examined identical Cigua-Check(R) strips to conclude whether the samples were positive or negative for ciguatera. Of the 121 samples that were shown to be positively ciguatoxic via bioassay, the four strip readers were in agreement in concluding positive ciguateric status in 9.9% of the samples; these four readers concluded these positive samples were negative for ciguatera in 26.2% of these bioassay-positive samples. Of the 67 samples that were shown in N2a bioassay to be negatively ciguatoxic, the four readers were in agreement in concluding a negative ciguateric status in 26.9% of the samples; these four strip readers concluded these same samples were positive for ciguatera in 14.9% of these negative samples. The low levels of uniform conclusions among readers examining identical test strips, and the low frequency of agreement with the correct ciguateric status as shown by separate N2a neuroblastoma analyses indicate severe short-comings in the reliability of these test kits to accurately reflect the ciguateric status of samples. The level of uncertainty associated with Cigua-Check(R) test kits indicate a continuing need for improvement of a simple, rapid, and reliable means to identify ciguateric fish.
Simple Scoring System and Artificial Neural Network for Knee Osteoarthritis Risk Prediction: A Cross-Sectional Study

Background Knee osteoarthritis (OA) is the most common joint disease of adults worldwide. Since the treatments for advanced radiographic knee OA are limited, clinicians face a significant challenge of identifying patients who are at high risk of OA in a timely and appropriate way. Therefore, we developed a simple self-assessment scoring system and an improved artificial neural network (ANN) model for knee OA. Methods The Fifth Korea National Health and Nutrition Examination Surveys (KNHANES V-1) data were used to develop a scoring system and ANN for radiographic knee OA. A logistic regression analysis was used to determine the predictors of the scoring system. The ANN was constructed using 1777 participants and validated internally on 888 participants in the KNHANES V-1. The predictors of the scoring system were selected as the inputs of the ANN. External validation was performed using 4731 participants in the Osteoarthritis Initiative (OAI). Area under the curve (AUC) of the receiver operating characteristic was calculated to compare the prediction models. Results The scoring system and ANN were built using the independent predictors including sex, age, body mass index, educational status, hypertension, moderate physical activity, and knee pain. In the internal validation, both scoring system and ANN predicted radiographic knee OA (AUC 0.73 versus 0.81, p<0.001) and symptomatic knee OA (AUC 0.88 versus 0.94, p<0.001) with good discriminative ability. In the external validation, both scoring system and ANN showed lower discriminative ability in predicting radiographic knee OA (AUC 0.62 versus 0.67, p<0.001) and symptomatic knee OA (AUC 0.70 versus 0.76, p<0.001). Conclusions The self-assessment scoring system may be useful for identifying the adults at high risk for knee OA. The performance of the scoring system is improved significantly by the ANN. We provided an ANN calculator to simply predict the knee OA risk.
Large Scale Population Assessment of Physical Activity Using Wrist Worn Accelerometers: The UK Biobank Study

Background Physical activity has not been objectively measured in prospective cohorts with sufficiently large numbers to reliably detect associations with multiple health outcomes. Technological advances now make this possible. We describe the methods used to collect and analyse accelerometer measured physical activity in over 100,000 participants of the UK Biobank study, and report variation by age, sex, day, time of day, and season. Methods Participants were approached by email to wear a wrist-worn accelerometer for seven days that was posted to them. Physical activity information was extracted from 100Hz raw triaxial acceleration data after calibration, removal of gravity and sensor noise, and identification of wear / non-wear episodes. We report age- and sex-specific wear-time compliance and accelerometer measured physical activity, overall and by hour-of-day, week-weekend day and season. Results 103,712 datasets were received (44.8% response), with a median wear-time of 6.9 days (IQR:6.5–7.0). 96,600 participants (93.3%) provided valid data for physical activity analyses. Vector magnitude, a proxy for overall physical activity, was 7.5% (2.35mg) lower per decade of age (Cohen’s d = 0.9). Women had a higher vector magnitude than men, apart from those aged 45-54yrs. There were major differences in vector magnitude by time of day (d = 0.66). Vector magnitude differences between week and weekend days (d = 0.12 for men, d = 0.09 for women) and between seasons (d = 0.27 for men, d = 0.15 for women) were small. Conclusions It is feasible to collect and analyse objective physical activity data in large studies. The summary measure of overall physical activity is lower in older participants and age-related differences in activity are most prominent in the afternoon and evening. This work lays the foundation for studies of physical activity and its health consequences. Our summary variables are part of the UK Biobank dataset and can be used by researchers as exposures, confounding factors or outcome variables in future analyses.
Protein ^ protein interactionandquaternary structure

Protein–protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein–protein complexes, oligomeric proteins, viral capsids and protein–nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.
An inexact-Newton method for short-range microwave imaging within the second-order Born approximation

A new approach to noninvasive inspection of dielectric targets at microwave frequencies is proposed. Cylindrical dielectric objects are reconstructed under the second-order Born approximation. A multi-illumination configuration is considered. The continuous model is discretized by the moment method and an efficient inexact-Newton method is applied. The dielectric profile is iteratively reconstructed starting from the measured scattered data, which are related to the unknown target through the inverse scattering equations written in a variational setting. Several numerical results are reported, which are aimed at assessing the capabilities of the approach in dealing with the nonlinear ill-posed inverse problem associated to the short-range microwave imaging. Single, multilayer, and separate cylinders are reconstructed in noiseless and noisy environments.
Three-dimensional solution structure of mu-conotoxin GIIIB, a specific blocker of skeletal muscle sodium channels.

The three-dimensional solution structure of mu-conotoxin GIIIB, a 22-residue polypeptide from the venom of the piscivorous cone snail Conus geographus, has been determined using 2D 1H NMR spectroscopy. GIIIB binds with high affinity and selectivity to skeletal muscle sodium channels and is a valuable tool for characterizing both the structure and function of these channels. Structural restraints consisting of 289 interproton distances inferred from NOEs and 9 backbone and 5 side chain dihedral angle restraints from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. In addition to the 1H NMR derived information, the 13C resonances of GIIIB were assigned at natural abundance, and hydroxyproline C beta and C gamma chemical shifts were used to distinguish between the cis and trans peptide bond conformations. The final set of 20 structures had mean pairwise rms differences over the whole molecule of 1.22 A for the backbone atoms and 2.48 A for all heavy atoms. For the well-defined region encompassing residues 3-21, the corresponding values were 0.74 and 2.54 A, respectively. GIIIB adopts a compact structure consisting of a distorted 310-helix, a small beta-hairpin, a cis-hydroxyproline, and several turns. The molecule is stabilized by three disulfide bonds, two of which connect the helix and the beta-sheet, forming a structural core with similarities to the CS alpha beta motif [Cornet, B. , Bonmatin, J.-M. , Hetru, C. , Hoffmann, J. A. , Ptak, M. , & Vovelle, F. (1995) Structure 3, 435-448]. This motif is common to several families of small proteins including scorpion toxins and insect defensins. Other structural features of GIIIB include the presence of eight arginine and lysine side chains that project into the solvent in a radial orientation relative to the core of the molecule. These cationic side chains form potential sites of interaction with anionic sites on sodium channels. The global fold is similar to that reported for mu-conotoxin GIIIA, and the structure of GIIIB determined in this study provides the basis for further understanding of the structure-activity relationships of the mu-conotoxins and for their binding to skeletal muscle sodium channels.
miR-375 Targets 3′-Phosphoinositide–Dependent Protein Kinase-1 and Regulates Glucose-Induced Biological Responses in Pancreatic β-Cells

OBJECTIVE—MicroRNAs are short, noncoding RNAs that regulate gene expression. We hypothesized that the phosphatidylinositol 3-kinase (PI 3-kinase) cascade known to be important in β-cell physiology could be regulated by microRNAs. Here, we focused on the pancreas-specific miR-375 as a potential regulator of its predicted target 3′-phosphoinositide–dependent protein kinase-1 (PDK1), and we analyzed its implication in the response of insulin-producing cells to elevation of glucose levels. RESEARCH DESIGN AND METHODS—We used insulinoma-1E cells to analyze the effects of miR-375 on PDK1 protein level and downstream signaling using Western blotting, glucose-induced insulin gene expression using quantitative RT-PCR, and DNA synthesis by measuring thymidine incorporation. Moreover, we analyzed the effect of glucose on miR-375 expression in both INS-1E cells and primary rat islets. Finally, miR-375 expression in isolated islets was analyzed in diabetic Goto-Kakizaki (GK) rats. RESULTS—We found that miR-375 directly targets PDK1 and reduces its protein level, resulting in decreased glucose-stimulatory action on insulin gene expression and DNA synthesis. Furthermore, glucose leads to a decrease in miR-375 precursor level and a concomitant increase in PDK1 protein. Importantly, regulation of miR-375 expression by glucose occurs in primary rat islets as well. Finally, miR-375 expression was found to be decreased in fed diabetic GK rat islets. CONCLUSIONS—Our findings provide evidence for a role of a pancreatic-specific microRNA, miR-375, in the regulation of PDK1, a key molecule in PI 3-kinase signaling in pancreatic β-cells. The effects of glucose on miR-375 are compatible with the idea that miR-375 is involved in glucose regulation of insulin gene expression and β-cell growth.
BOLD fMRI signal characteristics of S1- and S2-SSFP at 7 Tesla

Object: To compare the BOLD fMRI signal characteristics at in the cortex and on the pial surface for a non-balanced steady-state free precession sequence (nb-SSFP) at 7 T. Materials and Methods: A multi-echo nb-SSFP sequence was used for high resolution fMRI at 7 T. Two S1 (S+) echoes at different echo times were acquired together with an S2 (S−) echo. The primary visual cortex (V1) was examined using a reversing checkerboard paradigm at an isotropic resolution of 0.75 mm, with 35 volumes acquired and a total scan time of 27 min. Results: Significant activation was observed in all subjects for all three acquired echoes. For the S1 signal at the longer TE, the activation induced signal change was about 4% in the cortex and 10% at the cortical surface, while for S2 the corresponding values were 3 and 5%. Conclusion: For both S1 and S2 data, the BOLD signal peaks at the pial surface. The large pial surface signal change in S2 may be caused by dynamic averaging around post-capillary vessels embedded within CSF. This is made possible by the long diffusion times of the pathways contributing to the S2 signal and the relatively high diffusion coefficient of CSF. The results indicate that S2-SSFP might not be a suited alternative to spin-echo for high-resolution fMRI at 7 T.