Miracle-dz/UniFAR-FTUs huggingface dataset:
Human peripheral blood B‐cell compartments: A crossroad in B‐cell traffic

A relatively high number of different subsets of B‐cells are generated through the differentiation of early B‐cell precursors into mature B‐lymphocytes in the bone marrow (BM) and antigen‐triggered maturation of germinal center B‐cells into memory B‐lymphocytes and plasmablasts in lymphoid tissues. These B‐cell subpopulations, which are produced in the BM and lymphoid tissues, recirculate through peripheral blood (PB), into different tissues including mucosa and the BM, where long‐living plasma cells produce antibodies. These circulating PB B‐cells can be classified according to their maturation stage into i) immature/transitional, ii) naïve, and iii) memory B‐lymphocytes, and iv) plasmablasts/plasma cells. Additionally, unique subsets of memory B‐lymphocytes and plasmablasts/plasma cells can be identified based on their differential expression of unique Ig‐heavy chain isotypes (e.g.: IgM, IgD, IgG, IgA). In the present paper, we review recent data reported in the literature about the distribution, immunophenotypic and functional characteristics of these cell subpopulations, as well as their distribution in PB according to age and seasonal changes. Additional information is also provided in this regard based on the study of a population‐based cohort of 600 healthy adults aged from 20 to 80 years, recruited in the Salamanca area in western Spain. Detailed knowledge of the distribution and traffic of B‐cell subsets through PB mirrors the immune status of an individual subject and it may also contribute to a better understanding of B‐cell disorders related to B‐cell biology and homeostasis, such as monoclonal B‐cell lymphocytosis (MBL). © 2010 International Clinical Cytometry Society
Dielectric relaxation and polarization response in relaxor ferroelectric P(VDF-TrFE) copolymer

Dielectric responses are characterized for high-energy electron irradiated P(VDF-TrFE) 65/35 mol% copolymer system, which exhibits many features resembling to be relaxor ferroelectric behavior observed in inorganic systems. In this paper we explore the relation between the relaxor ferroelectric behavior observed in irradiated copolymer system with fundamental polarization relaxation processes. The dielectric behavior of copolymer is investigated over a broad frequency (0.01Hz-10MHz) and temperature (-40 /spl deg/C - 80 /spl deg/C) range to cover the change in polarization dynamics of the copolymer system. In contrast to the inorganic relaxor ferroelectric system where the freezing of polar units occurs at a very high frequency region, the relaxor ferroelectric copolymer system clearly shows the freezing process in the measurable frequency range. The results of analysis suggest that the observed V-F freezing process is due to the increased coupling among the local polar chain segment motions in the crystalline region, frustrated by the randomness due to the irradiation which prevents the formation of macroscopic polarization. It is confirmed that the V-F freezing does not show any correlation with glass transition, which appeared due to the amorphous nature of the copolymer system.
Disability and Intellectual Function in Multiple Sclerosis Patients

Forty-eight multiple sclerosis patients were rated on the Kurtzke Disability Status Examination and tested on the Wechsler Adult Intelligence Scale. Their disability status scores, ranging from 1 to 9, with a mean of 3.98, correlated significantly only with duration of illness (r = .33, significant at the .05 level). Severity of disability was not significantly correlated with age of patient, age at onset of multiple sclerosis symptoms, Verbal IQ, Performance IQ, or Full Scale IQ. Wechsler Adult Intelligence Scale mean subtest scores ranged from average to bright normal. Scores on Performance subtests with a large motor component were lower than on Verbal subtests measuring verbal overlearned information, abstract reasoning, and vocabulary.
Interactive rendering of large volume data sets

We present a new algorithm for rendering very large volume data sets at interactive frame rates on standard PC hardware. The algorithm accepts scalar data sampled on a regular grid as input. The input data is converted into a compressed hierarchical wavelet representation in a preprocessing step. During rendering, the wavelet representation is decompressed on-the-fly and rendered using hardware texture mapping. The level of detail used for rendering is adapted to the local frequency spectrum of the data and its position relative to the viewer. Using a prototype implementation of the algorithm we were able to perform an interactive walkthrough of large data sets such as the visible human on a single off-the-shelf PC.
Example-Based Object Detection in Images by Components

We present a general example-based framework for detecting objects in static images by components. The technique is demonstrated by developing a system that locates people in cluttered scenes. The system is structured with four distinct example-based detectors that are trained to separately find the four components of the human body: the head, legs, left arm, and right arm. After ensuring that these components are present in the proper geometric configuration, a second example-based classifier combines the results of the component detectors to classify a pattern as either a "person" or a "nonperson. " We call this type of hierarchical architecture, in which learning occurs at multiple stages, an adaptive combination of classifiers (ACC). We present results that show that this system performs significantly better than a similar full-body person detector. This suggests that the improvement in performance is due to the component-based approach and the ACC data classification architecture. The algorithm is also more robust than the full-body person detection method in that it is capable of locating partially occluded views of people and people whose body parts have little contrast with the background.
Cloning and characterization of a gene encoding an outer membrane protein required for siderophore-mediated uptake of Fe3+ in Pseudomonas putida WCS358

In iron-limited environments plant-growth-stimulating Pseudomonas putida WCS358 produces a yellow-green fluorescent siderophore called pseudobactin 358. Ferric pseudobactin 358 is efficiently taken up by cells of WCS358 but not by cells of another rhizophere-colonizing strain, Pseudomonas fluorescens WCS374. A gene bank containing partial Sau3A DNA fragments from WCS358 was constructed in a derivative of the broad-host-range cosmid pLAFR1. By mobilization of this gene bank to strain WCS374 a cosmid clone, pMR, which made WCS374 competent for the utilization of pseudobactin 358 was identified. By subcloning of the 29.4-kilobase (kb) insert of pMR the essential genetic information was localized on a BglII fragment of 5.3 kb. Tn5 mutagenesis limited the responsible gene to a region of approximately 2.5 kb within this fragment. Since the gene encodes an outer membrane protein with a predicted molecular mass of 90,000 daltons, it probably functions as the receptor for ferric pseudobactin 358. The gene is flanked by pseudobactin 358 biosynthesis genes on both sides and is on a separate transcriptional unit. WCS374 cells carrying pMR derivatives with Tn5 insertions in the putative receptor gene did not produce the 90,000-dalton protein anymore and were unable to take up Fe3+ via pseudobactin 358. In WCS358 cells as well as in WCS374 cells the gene is expressed only under iron-limited conditions.
Splenic salvage after intraoperative splenic injury during colectomy.

OBJECTIVE To determine the optimal surgical management of splenic injury encountered during colectomy. DESIGN Retrospective review from 1992 to 2007. SETTING Mayo Clinic in Rochester, Minnesota, a tertiary care center. PATIENTS A cohort of patients who sustained splenic injury during colectomy from 1992 to 2007. MAIN OUTCOME MEASURES Overall 30-day major morbidity and mortality and overall 5-year survival. RESULTS Of 13,897 colectomies, we identified 59 splenic injuries (0.42%). Of these, 33 (56%) were in men; there was a median age of 68 years (range, 30-93 years) and a median body mass index of 25.5 (range, 15-54). Thirty-seven injuries (63%) occurred during elective surgery, 6 (10%) occurred without splenic flexure mobilization, and 5 (8.4%) occurred during minimally invasive surgery. Injury was successfully managed by primary repair in 10 (17%), splenorrhaphy in 4 (7%), and splenectomy in 45 cases (76%). Four injuries (7%) were unrecognized and resulted in reoperation and splenectomy. Multiple attempts at splenic salvage were performed in 30 (51%); of these, 21 (70%) required splenectomy. More than 2 attempts at salvage was associated with splenectomy (P = .03). The 30-day major morbidity and mortality rates were 34% and 17%, respectively. Sepsis was the most common complication, with no confirmed episodes of postsplenectomy sepsis. Median survival after splenic injury was 7.25 years. There was no significant association between the surgical management of splenic injuries and short- or long-term outcomes. CONCLUSIONS Splenic injury is an infrequent but morbid complication. Splenic salvage is frequently unsuccessful; our data suggest that surgeons should not be reluctant to perform splenectomy when initial repair attempts fail.
Atlas-Free Cervical Spinal Cord Segmentation on Midsagittal T2-Weighted Magnetic Resonance Images

An automatic atlas-free method for segmenting the cervical spinal cord on midsagittal T2-weighted magnetic resonance images (MRI) is presented. Pertinent anatomical knowledge is transformed into constraints employed at different stages of the algorithm. After picking up the midsagittal image, the spinal cord is detected using expectation maximization and dynamic programming (DP). Using DP, the anterior and posterior edges of the spinal canal and the vertebral column are detected. The vertebral bodies and the intervertebral disks are then segmented using region growing. Then, the anterior and posterior edges of the spinal cord are detected using median filtering followed by DP. We applied this method to 79 noncontrast MRI studies over a 3-month period. The spinal cords were detected in all cases, and the vertebral bodies were successfully labeled in 67 (85%) of them. Our algorithm had very good performance. Compared to manual segmentation results, the Jaccard indices ranged from 0.937 to 1, with a mean of 0.980 ± 0.014. The Hausdorff distances between the automatically detected and manually delineated anterior and posterior spinal cord edges were both 1.0 ± 0.5 mm. Used alone or in combination, our method lays a foundation for computer-aided diagnosis of spinal diseases, particularly cervical spondylotic myelopathy.
Portable, scalable, per-core power estimation for intelligent resource management

Performance, power, and temperature are now all first-order design constraints. Balancing power efficiency, thermal constraints, and performance requires some means to convey data about real-time power consumption and temperature to intelligent resource managers. Resource managers can use this information to meet performance goals, maintain power budgets, and obey thermal constraints. Unfortunately, obtaining the required machine introspection is challenging. Most current chips provide no support for per-core power monitoring, and when support exists, it is not exposed to software. We present a methodology for deriving per-core power models using sampled performance counter values and temperature sensor readings. We develop application-independent models for four different (four- to eight-core) platforms, validate their accuracy, and show how they can be used to guide scheduling decisions in power-aware resource managers. Model overhead is negligible, and estimations exhibit 1.1%–5.2% per-suite median error on the NAS, SPEC OMP, and SPEC 2006 benchmarks (and 1.2%–4.4% overall).
Revisiting detection thresholds for redirected walking: combining translation and curvature gains

Redirected walking enables the exploration of large virtual environments while requiring only a finite amount of physical space. Unfortunately, in living room sized tracked areas the effectiveness of common redirection algorithms such as Steer-to-Center is very limited. A potential solution is to increase redirection effectiveness by applying two types of perceptual manipulations (curvature and translation gains) simultaneously. This paper investigates how such combination may affect detection thresholds for curvature gain. To this end we analyze the estimation methodology and discuss selection process for a suitable estimation method. We then compare curvature detection thresholds obtained under different levels of translation gain using two different estimation methods: method of constant stimuli and Green's maximum likelihood procedure. The data from both experiments shows no evidence that curvature gain detection thresholds were affected by the presence of translation gain (with test levels spanning previously estimated interval of undetectable translation gain levels). This suggests that in practice currently used levels of translation and curvature gains can be safely applied simultaneously. Furthermore, we present some evidence that curvature detection thresholds may be lower that previously reported. Our estimates indicate that users can be redirected on a circular arc with radius of either 11.6m or 6.4m depending on the estimation method vs. the previously reported value of 22m. These results highlight that the detection threshold estimates vary significantly with the estimation method and suggest the need for further studies to define efficient and reliable estimation methodology.
Exploration into Single Image Super-Resolution via Self Similarity by Sparse Representation

A novel method for single image super resolution without any training samples is presented in the paper. By sparse representation, the method attempts to recover at each pixel its best possible resolution increase based on the self similarity of the image patches across different scale and rotation transforms. The experiments indicate that the proposed method can produce robust and competitive results.
Rheology of latex films bonded to wood: influence of cross-linking

Abstract Parallel-plate rheological analysis was conducted on two types of cross-linking poly(vinyl acetate) latex films: dry freestanding films, and dry films bonded directly to wood (composites). For each sample type, three levels of cross-linking were used: (1) little or no cross-linking of unaltered latex; (2) substantial cross-linking through AlCl3 catalysis of N-methylolacrylamide co-monomer; and (3) greater cross-linking from a phenol-formaldehyde resol additive, in addition to AlCl3 catalysis. Simple thermal scans revealed a strong wood/adhesive interaction; wood increased the base polymer T g by ∼5°C in all adhesives. Relative to the simple thermal scans, time-temperature master curves provided more insight and information about the wood/adhesive interaction. Storage modulus and tan δ master curves both indicated that wood retarded adhesive cross-linking. Using time-temperature superposition, a segmental coupling analysis demonstrated that wood actually narrowed the breadth of the glass transition, or reduced segmental coupling. Cross-linking influenced segmental coupling, but in a fashion that was dependent on the presence or absence of wood. Wood-induced reductions in cross-linking and in segmental coupling were attributed to the diffusion of water-soluble reactive compounds away from the adhesive layer and into the bulk wood. Time/temperature equivalence provides a sensitive means to detect interactions between wood and viscoelastic adhesives.
Long‐term retention of pristine multi‐walled carbon nanotubes in rat lungs after intratracheal instillation

As a result of the growing potential industrial and medical applications of multi‐walled carbon nanotubes (MWCNTs), people working in or residing near facilities that manufacture them may be exposed to airborne MWCNTs in the future. Because of concerns regarding their toxicity, quantitative data on the long‐term clearance of pristine MWCNTs from the lungs are required. We administered pristine MWCNTs well dispersed in 0.5 mg ml−1 Triton‐X solution to rats at doses of 0.20 or 0.55 mg via intratracheal instillation and investigated clearance over a 12‐month observation period. The pristine MWCNTs pulmonary burden was determined 1, 3, 7, 28, 91, 175 and 364 days after instillation using a method involving combustive oxidation and infrared analysis, combined with acid digestion and heat pretreatment. As 0.15‐ and 0.38‐mg MWCNTs were detected 1 day after administration of 0.20 and 0.55 mg MWCNTs, respectively, approximately 30% of administrated MWCNTs may have been cleared by bronchial ciliary motion within 24 h of administration. After that, the pulmonary MWCNT burden did not decrease significantly over time for up to 364 days after instillation, suggesting that MWCNTs were not readily cleared from the lung. Transmission electron microscopy (TEM) showed that alveolar macrophages internalized the MWCNTs and retained in the lung for at least 364 days after instillation. MWCNTs were not detected in the liver or brain within the 364‐day study period (<0.04 mg per liver, < 0.006 mg per brain). Copyright © 2015 The Authors Journal of Applied Toxicology Published by John Wiley & Sons Ltd.
Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing

To better understand and characterize chromosomal structural variation during breast cancer progression, we enumerated chromosomal rearrangements for 11 patients by performing low-coverage whole-genome sequencing of 11 primary breast tumors and their 13 matched distant metastases. The tumor genomes harbored a median of 85 (range 18-404) rearrangements per tumor, with a median of 82 (26-310) in primaries compared to 87 (18-404) in distant metastases. Concordance between paired tumors from the same patient was high with a median of 89% of rearrangements shared (range 61-100%), whereas little overlap was found when comparing all possible pairings of tumors from different patients (median 3%). The tumors exhibited diverse genomic patterns of rearrangements: some carried events distributed throughout the genome while others had events mostly within densely clustered chromothripsis-like foci at a few chromosomal locations. Irrespectively, the patterns were highly conserved between the primary tumor and metastases from the same patient. Rearrangements occurred more frequently in genic areas than expected by chance and among the genes affected there was significant enrichment for cancer-associated genes including disruption of TP53, RB1, PTEN, and ESR1, likely contributing to tumor development. Our findings are most consistent with chromosomal rearrangements being early events in breast cancer progression that remain stable during the development from primary tumor to distant metastasis.
A comparison of preconditioners for incompressible Navier–Stokes solvers

We consider solution methods for large systems of linear equations that arise from the finite element discretization of the incompressible Navier–Stokes equations. These systems are of the so‐called saddle point type, which means that there is a large block of zeros on the main diagonal. To solve these types of systems efficiently, several block preconditioners have been published. These types of preconditioners require adaptation of standard finite element packages. The alternative is to apply a standard ILU preconditioner in combination with a suitable renumbering of unknowns. We introduce a reordering technique for the degrees of freedom that makes the application of ILU relatively fast. We compare the performance of this technique with some block preconditioners. The performance appears to depend on grid size, Reynolds number and quality of the mesh. For medium‐sized problems, which are of practical interest, we show that the reordering technique is competitive with the block preconditioners. Its simple implementation makes it worthwhile to implement it in the standard finite element method software. Copyright © 2007 John Wiley & Sons, Ltd.
Tightness: A novel heuristic and a clustering mechanism to improve the interpretation of association rules

In this paper we present a clustering-based approach to mitigate the ‘rule immensity’ and the resulting ‘understandability’ problem in association rule (AR) mining. Clustering ‘similar’ rules facilitates exploration of connections among rules and the discovery of underlying structures. We first introduce the notion of ‘tightness’ of an AR. It reveals the strength of binding between various items present in an AR. We elaborate on its usefulness in the retail market-basket context and develop a distance-function on the basis of ‘tightness. ’ Usage of this distance function is exemplified by clustering a small artificial set of ARs with the help of average-linkage method. Clusters thus obtained are compared with those obtained by running a standard method (from recent data mining literature) on the same data set.
Lysophosphatidylinositol Causes Neurite Retraction via GPR55, G13 and RhoA in PC12 Cells

GPR55 was recently identified as a putative receptor for certain cannabinoids, and lysophosphatidylinositol (LPI). Recently, the role of cannabinoids as GPR55 agonists has been disputed by a number of reports, in part, because studies investigating GPR55 often utilized overexpression systems, such as the GPR55-overexpressing HEK293 cells, which make it difficult to deduce the physiological role of endogenous GPR55. In the present study, we found that PC12 cells, a neural model cell line, express endogenous GPR55, and by using these cells, we were able to examine the role of endogenous GPR55. Although GPR55 mRNA and protein were expressed in PC12 cells, neither CB1 nor CB2 mRNA was expressed in these cells. GPR55 was predominantly localized on the plasma membrane in undifferentiated PC12 cells. However, GPR55 was also localized in the growth cones or the ruffled border in differentiated PC12 cells, suggesting a potential role for GPR55 in the regulation of neurite elongation. LPI increased intracellular Ca2+ concentration and RhoA activity, and induced ERK1/2 phosphorylation, whereas endogenous and synthetic cannabinoids did not, thereby suggesting that cannabinoids are not GPR55 agonists. LPI also caused neurite retraction in a time-dependent manner accompanied by the loss of neurofilament light chain and redistribution of actin in PC12 cells differentiated by NGF. This LPI-induced neurite retraction was found to be Gq-independent and G13-dependent. Furthermore, inactivation of RhoA function via C3 toxin and GPR55 siRNA knockdown prevented LPI-induced neurite retraction. These results suggest that LPI, and not cannabinoids, causes neurite retraction in differentiated PC12 cells via a GPR55, G13 and RhoA signaling pathway.
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches

Time-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed.