Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct imaging of magnetic field gradients by group spin‐echoselection

A new image processing method for single‐echo gradient echo imaging is presented which extracts local phase gradient information by k‐space filtering instead of by phased reconstruction and spatial differentiation. It is shown that localphase gradient directions and semiquantitative local phase gradient magnitudes can be directly measured, even in regions where phased image reconstruction suffers from multiple phase foldovers due to strong phase modulations. The directional information thus obtained can be used as a reference to identify and correct phase modulation foldovers i phase maps which may be computed from the same raw data. The method is applied here to measure static magnetic field gradients and illustrates fundamental k‐space signal properties of gradient echo imaging. Based on this concept, image artifacts caused by conventional strong k‐space filtering in gradient echo imaging are discussed.
Microorganism penetration in dentinal tubules of instrumented and retreated root canal walls. In vitro SEM study

Objectives This in vitro study aimed to investigate the ability of Candida albicans (C. albicans) and Enterococcus faecalis (E. faecalis) to penetrate dentinal tubules of instrumented and retreated root canal surface of split human teeth. Materials and Methods Sixty intact extracted human single-rooted teeth were divided into 4 groups, negative control, positive control without canal instrumentation, instrumented, and retreated. Root canals in the instrumented group were enlarged with endodontic instruments, while root canals in the retreated group were enlarged, filled, and then removed the canal filling materials. The teeth were split longitudinally after canal preparation in 3 groups except the negative control group. The teeth were inoculated with both microorganisms separately and in combination. Teeth specimens were examined by scanning electron microscopy (SEM), and the depth of penetration into the dentinal tubules was assessed using the SMILE view software (JEOL Ltd). Results Penetration of C. albicans and E. faecalis into the dentinal tubules was observed in all 3 groups, although penetration was partially restricted by dentin debris of tubules in the instrumented group and remnants of canal filling materials in the retreated group. In all 3 groups, E. faecalis penetrated deeper into the dentinal tubules by way of cell division than C. albicans which built colonies and penetrated by means of hyphae. Conclusions Microorganisms can easily penetrate dentinal tubules of root canals with different appearance based on the microorganism size and status of dentinal tubules.
Improving Data Quality with an Accumulated Reputation Model in Participatory Sensing Systems

The ubiquity of mobile devices brings forth a sensing paradigm, participatory sensing, to collect and interpret sensory information from the environment. Participants join in multifarious sensing tasks and share their data. The sensing result can be obtained in light of shared data. It is not uncommon that some corrupted data is provided by participants, which makes sensing result unreliable accordingly. To address this nontrivial issue, we proposed the accumulated reputation model (ARM) to improve the accuracy of the sensing result. In ARM, participants' reputation will be computed and accumulated based on their sensing data. The sensing data from reputable participants make higher contributions to the sensing result. ARM performs well on calculating accurate sensing results, even in extreme scenarios, where there are many inexperienced or malicious participants.
CENet: A Cabinet Environmental Sensing Network

For data center cooling and intelligent substation systems, real time cabinet environmental monitoring is a strong requirement. Monitoring data, such as temperature, humidity, and noise, is important for operators to manage the facilities in cabinets. We here propose a sensing network, called CENet, which is energy efficient and reliable for cabinet environmental monitoring. CENet achieves above 93% reliable data yield and sends fewer beacons compared to periodic beaconing. It does so through a data-aided routing protocol. In addition, based on B-MAC, we propose a scheduling scheme to increase the lifetime of the network by reducing unnecessary message snooping and channel listening, thus it is more energy efficient than B-MAC. The performance of CENet is evaluated by simulations and experiments.
Complex Pattern of Membrane Type 1 Matrix Metalloproteinase Shedding

Membrane type 1 matrix metalloproteinase (MT1-MMP) is a type I transmembrane MMP shown to play a critical role in normal development and in malignant processes. Emerging evidence indicates that MT1-MMP is regulated by a process of ectodomain shedding. Active MT1-MMP undergoes autocatalytic processing on the cell surface, leading to the formation of an inactive 44-kDa fragment and release of the entire catalytic domain. Analysis of the released MT1-MMP forms in various cell types revealed a complex pattern of shedding involving two major fragments of 50 and 18 kDa and two minor species of 56 and 31–35 kDa. Protease inhibitor studies and a catalytically inactive MT1-MMP mutant revealed both autocatalytic (18 kDa) and non-autocatalytic (56, 50, and 31–35 kDa) shedding mechanisms. Purification and sequencing of the 18-kDa fragment indicated that it extends from Tyr112 to Ala255. Structural and sequencing data indicate that shedding of the 18-kDa fragment is initiated at the Gly284-Gly285 site, followed by cleavage between the conserved Ala255 and Ile256residues near the conserved methionine turn, a structural feature of the catalytic domain of all MMPs. Consistently, a recombinant 18-kDa fragment had no catalytic activity and did not bind TIMP-2. Thus, autocatalytic shedding evolved as a specific mechanism to terminate MT1-MMP activity on the cell surface by disrupting enzyme integrity at a vital structural site. In contrast, functional data suggest that the non-autocatalytic shedding generates soluble active MT1-MMP species capable of binding TIMP-2. These studies suggest that ectodomain shedding regulates the pericellular and extracellular activities of MT1-MMP through a delicate balance of active and inactive enzyme-soluble fragments.
Some converse limit theorems for exchangeable bootstraps

The bootstrap Glivenko-Cantelli and bootstrap Donsker theorems of Gine and Zinn (1990) contain both necessary and sufficient conditions for the asymptotic validity of Efron’s nonparametric bootstrap. In the more general case of exchangeably weighted bootstraps, Praestgaard and Wellner (1993) and Van der Vaart and Wellner (1996) give analogues of the sufficiency half of the Theorems of Gine and Zinn (1990), but did not address the corresponding necessity parts of the theorems. Here we establish a new lower bound for exchangeably weighted processes and show that the necessity half of the a.s. bootstrap Glivenko-Cantelli theorem holds for exchangeably weighted bootstraps. We also make some progress toward the conjectured necessity parts of the bootstrap Donsker theorems with exchangeable weights.
Opportunistic Use of Vision to Push Back the Path-Planning Horizon

Mobile robots need maps or other forms of geometric information about the environment to navigate. The mobility sensors (LADAR, stereo, etc.) on these robotic vehicles can however populate these maps only up to a distance of a few tens of meters. A navigation system has no knowledge about the world beyond this sensing horizon. As a result, path planners that rely only on this knowledge are unable to anticipate obstacles sufficiently early and have no choice but to resort to an inefficient local obstacle avoidance behavior. However, recent developments in the computer vision community allows us to collect geometric information about the environment far beyond this sensing horizon. The coarse 3D geometric estimation that can be recovered is derived from an appearance-based model. That uses a multiple-hypothesis framework to robustly estimate scene structure from a single image and estimating confidences for each geometric label. This 3D geometric estimation is used with a previously presented navigation strategy that reasons about sensor constraints and plans for measurements while navigating towards the goal. The validity of the sensing method and navigation strategy is supported by results from simulations as well as field experiments with a real robotic platform. These results also show that significant reduction in path length can be achieved by using this framework
Cleaning to achieve sterility

NASA planetary protection regulations state that a surface may be considered "sterile" if a microbial burden of less than 300 aerobic bacterial spores per square meter can be further treated to achieve a 10 4 fold reduction in viable endospores (spores). The results of previous studies have suggested that surfaces might be cleaned to a level that is essentially sterile. Here, we report the results of a comparative analysis of the efficacy/ability of three different cleaning approaches to remove bacterial spores from a series of surrogate spacecraft surfaces. In order to accomplish the most realistic and reproducible spore deposition, an aerosol chamber capable of nebulizing innocuous Bacillus atrophaeus (ATCC, 9372 [formerly B. subtilis var niger]) spores was developed and used. This enabled the relatively uniform inoculation of spores as individual entities at a concentration in excess of 105 spores per 2.2 cm2 surrogate surface coupon. Coupons prepared in this fashion were subsequently delivered to three cleaning facilities: vendor A for cleaning via standard aerospace precision cleaning protocols, vendor B for cleaning via ultra-pure water, and vendor C for cleaning via liquid boundary layer disruption. Variations in the chemistry of the cleaning solutions were also explored. Preliminary results suggest that "sterility," as defined by NASA, may indeed be achieved by various cleaning procedures, despite the fact that none of these methods were originally designed, nor are they currently conducted, with such a goal in mind
The proteins of green leaves. IV. A high molecular weight protein comprising a large part of the cytoplasmic proteins.

Previous work has shown that the soluble cytoplasmic proteins comprise about 30 per cent of the total protein contained in spinach and tobacco leaves (1, 2). Thus, on a dry weight basis, the cytoplasmic proteins constitute in the neighborhood of 10 per cent of the total dry matter of the leaf, including cellulose. In an attempt to resolve the soluble proteins present in leaf cytoplasm, resort was made to electrophoretic analysis. The results indicated that most of the cytoplasmic proteins migrated as a single boundary under the conditions studied. Although the shapes of the scanning patterns were sufficiently asymmetrical to suggest some heterogeneity among the cytoplasmic proteins, nevertheless the impression was gained from electrophoresis and other experiments that a substantial portion of the soluble cytoplasmic proteins consisted of a single protein component with respect to mobility. Ultracentrifugal analysis, however, achieved better resolution of this mixture, and examination by this method of the cytoplasmic proteins extracted from several species of plant leaves reveals clearly the presence of a high molecular weight component comprising from 23 to 50 per cent of the total cytoplasmic proteins in each of the cytoplasms investigated. Moreover, the behavior of this component during ultracentrifugation suggests a high degree of homogeneity, with respect to molecular weight. It therefore appears that an appreciable part of the total dry weight of the leaf can be considered as consisting of a single kind of protein, which, in accord with our previous usage, we shall call Fraction I protein. A preliminary report of this work has been presented (3).
Differences and similarities in the trajectories of self-esteem and positive and negative affect in persons with chronic illness: an explorative longitudinal study

Background Chronic illness is a risk factor for low self-esteem, and the research literature needs to include more studies of self-esteem and its development in chronic illness groups using longitudinal and comparative designs. The aim of this study was to explore the trajectories of self-esteem and of positive and negative affect in persons with morbid obesity and in persons with chronic obstructive pulmonary disease (COPD). Methods Patient education course attendants in Norway having morbid obesity (n=139) or COPD (n=97) participated in the study. Data concerning self-esteem, positive and negative affect, and sociodemographic background were collected at the start and at the end of the patient education, with subsequent follow-ups at 3, 6, and 12 months. Data were analyzed using linear mixed models for repeated measures. Results Taking all measurements into account, our data revealed a statistically significant increase in self-esteem for participants with morbid obesity but not for those with COPD. There were no significant differences in levels of negative and positive affect between the two groups, and the time-trajectories were also similar. However, participants in both groups achieved lower levels of negative affect for all the successive measurement points. Conclusion An increase in self-esteem during the first year after the patient education course was observed for persons with morbid obesity, but not for persons with COPD. Initial higher levels of self-esteem in the participants with COPD may indicate that they are less troubled with low self-esteem than people with morbid obesity are. The pattern of reduced negative affect for both groups during follow-up is promising.
Task representations, strategy variability, and base-rate neglect

The authors present a new model called RCCL (pronounced "ReCyCLe"; Represent the task, Construct a set of action strategies consistent with the task representation, Choose from among those strategies according to their success rates, and Learn new success rates for the strategies based on experience). The model explains the different ways in which people combine base-rate and case-specific cues to produce choice. It also makes additional predictions regarding variability in people's choices over time. Experiment 1 tested 58 college-age students in a problem-solving task and showed that task representations can be influenced by feedback from the environment, producing changes in base rate and cue sensitivity. Experiment 2 tested 80 college-age students in a delayed match-to-sample task and showed that variations in the format of a task can lead to different representations, which in turn produce much different base-rate and cue sensitivities. Moreover, both experiments showed systematic variability in choice over time in ways predicted by the model.
Systematic parameter estimation in data-rich environments for cell signalling dynamics

Motivation: Computational models of biological signalling networks, based on ordinary differential equations (ODEs), have generated many insights into cellular dynamics, but the model-building process typically requires estimating rate parameters based on experimentally observed concentrations. New proteomic methods can measure concentrations for all molecular species in a pathway; this creates a new opportunity to decompose the optimization of rate parameters. Results: In contrast with conventional parameter estimation methods that minimize the disagreement between simulated and observed concentrations, the SPEDRE method fits spline curves through observed concentration points, estimates derivatives and then matches the derivatives to the production and consumption of each species. This reformulation of the problem permits an extreme decomposition of the high-dimensional optimization into a product of low-dimensional factors, each factor enforcing the equality of one ODE at one time slice. Coarsely discretized solutions to the factors can be computed systematically. Then the discrete solutions are combined using loopy belief propagation, and refined using local optimization. SPEDRE has unique asymptotic behaviour with runtime polynomial in the number of molecules and timepoints, but exponential in the degree of the biochemical network. SPEDRE performance is comparatively evaluated on a novel model of Akt activation dynamics including redox-mediated inactivation of PTEN (phosphatase and tensin homologue). Availability and implementation: Web service, software and supplementary information are available at www.LtkLab. org/SPEDRE Supplementary information: Supplementary data are available at Bioinformatics online. Contact: LisaTK@nus.edu. sg
Hypoxic-Preconditioned Bone Marrow Stem Cell Medium Significantly Improves Outcome After Retinal Ischemia in Rats

Purpose We have previously demonstrated the protective effect of bone marrow stem cell (BMSC)-conditioned medium in retinal ischemic injury. We hypothesized here that hypoxic preconditioning of stem cells significantly enhances the neuroprotective effect of the conditioned medium and thereby augments the protective effect in ischemic retina. Methods Rats were subjected to retinal ischemia by increasing intraocular pressure to 130 to 135 mm Hg for 55 minutes. Hypoxic-preconditioned, hypoxic unconditioned, or normoxic medium was injected into the vitreous 24 hours after ischemia ended. Recovery was assessed 7 days after injections by comparing electroretinography measurements, histologic examination, and apoptosis (TUNEL, terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling assay). To compare proteins secreted into the medium in the groups and the effect of hypoxic exposure, we used rat cytokine arrays. Results Eyes injected with hypoxic BMSC–conditioned medium 24 hours after ischemia demonstrated significantly enhanced return of retinal function, decreased retinal ganglion cell layer loss, and attenuated apoptosis compared to those administered normoxic or hypoxic unconditioned medium. Hypoxic-preconditioned medium had 21 significantly increased protein levels compared to normoxic medium. Conclusions The medium from hypoxic-preconditioned BMSCs robustly restored retinal function and prevented cell loss after ischemia when injected 24 hours after ischemia. The protective effect was even more pronounced than in our previous studies of normoxic conditioned medium. Prosurvival signals triggered by the secretome may play a role in this neuroprotective effect.
lvgA, a Novel Legionella pneumophila Virulence Factor

ABSTRACT Several novel Legionella pneumophila virulence genes were previously discovered by use of signature-tagged mutagenesis (P. H. Edelstein, M. A. Edelstein, F. Higa, and S. Falkow, Proc. Natl. Acad. Sci. 96:8190-8195, 1999). One of these mutants appeared to be defective in multiplication in guinea pig lungs and spleens, yet it multiplies normally in guinea pig alveolar macrophages. Here we report further characterization of the mutated gene and its protein and the virulence role of the gene. The complete sequence of the gene, now called lvgA, is 627 bp long, and its protein product is approximately 27 kDa in size. lvgA was present in all 50 strains of L. pneumophila tested. No significant nucleic acid or protein homology was found in the GenBank database for the gene, nor were any distinctive motifs discovered in a search of other databases. The expression of both DotA and IcmX in the lvgA mutant was normal. Subcellular fractionation studies localized LvgA to the outer membrane fraction, and protease digestion studies suggested that at least some of the protein is surface expressed. No change in bacterial lipopolysaccharide composition or reactivity to serogroup-specific antisera was detected in the mutant. Growth competition studies with alveolar macrophages showed that the mutant was outcompeted by its parent 3-fold in 24 h and 24-fold in 48 h, in contrast to what was observed with the null phenotype in parallel testing with alveolar macrophages or with the A549 alveolar epithelial cell line. This macrophage defect of the mutant bacterium was due to slower growth, as the mutant invaded alveolar macrophages normally. Electron microscopy showed that the mutant bacterium resided in a ribosome-studded phagosome in alveolar macrophages, with no distinction from its parent. The lvgA mutant was outcompeted by its parent about sixfold in guinea pig lungs and spleens; prolonged observation of infected animals showed no late-onset virulence of the mutant. Transcomplementation of the mutant restored the parental phenotype in guinea pigs. The lvgA mutant was twofold more susceptible to killing by human β-defensin 2 but not to killing by other cationic peptides, serum complement, or polymorphonuclear neutrophils. lvgA is a novel virulence gene that is responsible for pleiotropic functions involving both extracellular and intracellular bacterial resistance mechanisms.
Lesions in the splenium of the corpus callosum: Clinical and radiological implications

Background: Brain MRI may unexpectedly display abnormalities in splenium of the corpus callosum (SCC). However, the clinical implications of this lesion are unclear and are not always consistent with ischemic infarctions. We performed this study to clarify the clinical and radiological implications in patients with SCC lesions. Methods: We retrospectively reviewed consecutive patients with MRIreported SCC changes between 2009 and 2012. We analyzed clinical and radiological findings, etiologies, cognitive impairment, and clinical outcomes. Results: We found 30 patients (16 females; mean 50.5 years) who had SCC lesions on MRI. Confusion was the most common clinical finding in 50% of cases. Cerebral infarction was the most common etiology (50%). The most consistent SCC changes on MRI were low signal in T1WI, high signal on T2WI and FLAIR, and high signal on DWI. We classified SCC lesions into in situ SCC lesions (SCC only) and multiple (SCC plus) lesions for patients with multiple lesions. The clinical symptoms of SCC only lesions were relatively mild. Cognitive functions were evaluated by Mini Mental State Examination (MMSE) and clinical dementia rating (CDR) scale at the time of discharge and patients with SCC only lesions showed less impaired cognition compared with those with SCC plus lesions. Clinical outcomes were evaluated by the modified Rankin scale at 1 month and patients with SCC only lesions revealed good clinical outcomes compared with those with SCC plus lesions. Conclusions: MRI-reported SCC lesions may have heterogeneous etiologies and present with various symptoms. The clinical course and outcome are relatively good, particularly in small isolated and oval shaped SCC lesions.