Miracle-dz/UniFAR-FTUs huggingface dataset:
Clostridium perfringens Enterotoxin Utilizes Two Structurally Related Membrane Proteins as Functional Receptors in Vivo *

Human and mouse cDNAs showing homology to theClostridium perfringens enterotoxin (CPE) receptor gene (CPE-R) from Vero cells (DDBJ/EMBL/GenBankTMaccession no. D88492) (Katahira, J., Inoue, N., Horiguchi, Y., Matsuda, M., and Sugimoto, N. (1997) J. Cell Biol. 136, 1239–1247) were cloned. They were classified into two groups, the Vero cell CPE receptor homologues and rat androgen withdrawal apoptosis protein (RVP1; accession no. M74067) homologues, based on the similarities of primary amino acid sequences. L929 cells that were originally insensitive to CPE became sensitive to CPE on their transfection with cDNAs encoding either the CPE receptor or RVP1 homologues, indicating that these gene products are not only structurally similar but also functionally active as receptors for CPE. By binding assay, the human RVP1 homologue showed differences in affinity and capacity of binding from those of the human CPE receptor. Northern blot analysis showed that mouse homologues of the CPE receptor and RVP1 are expressed abundantly in mouse small intestine. The expression ofCPE-R mRNA in the small intestine was restricted to cryptic enterocytes, indicating that the CPE receptor is expressed in intestinal epithelial cells. These results are consistent with reports that CPE binds to the small intestinal cells via two different kinds of receptors. High levels of expression of CPE-R and/orRVP1 mRNA were also detected in other organs, including the lungs, liver, and kidneys, but only low levels were expressed in heart and skeletal muscles. These results indicate that CPE uses structurally related cellular proteins as functional receptors in vivo and that organs that have not so far been recognized as CPE-sensitive have the potential to be targets of CPE.
Vitrification of toxic wastes: a brief review

Abstract Whilst the vitrification of waste materials is a well established technology, hitherto it has not been economically viable on any substantial scale when applied to non-radioactive wastes. However new UK and European legislation may affect this situation. The present paper briefly reviews published work pertaining to waste vitrification in terms of legislation, waste compositions, energy, emissions and economic assessments. The focus is on vitrification of ashes arising from the incineration of municipal solid waste (MSW) and sewage sludge in terms of their composition, glass melting and reuse potential. The conclusion is that the high compositional variability of these and other wastes tends to preclude their use in many applications. However, the use of modern sorting and separation technology coupled with better control of waste treatment procedures may help to improve the range of potential uses for these wastes.
Development of MMSE Macro-Diversity Receiver with Delay Difference Correction Technique

We have been developing a minimum mean square error macro-diversity (MMSE-MD) reception system using distributed remote antennas and radio-on-fiber (RoF) links for use in live broadcasts of road races. For the system to be feasible, we have to consider the propagation delay differences among diversity branches due to RoF links and radio propagation. This paper describes a hardware implementation of an MMSE-MD receiver embodying our delay difference correction (DDC) technique and indoor and outdoor performance evaluations. Our prototype receiver perfectly corrected the propagation delay difference among diversity branches in less than 11 symbols duration in a time-varying multipath fading environment, and it was capable of the MD reception without outage on an actual road race course.
Labeled Random Finite Sets With Moment Approximation

The probability hypothesis density (PHD) filter was proposed as a practical approximation of the multitarget Bayes filter. The cardinalized PHD (CPHD) filter improves on the PHD filter by propagating cardinality distribution. However, both the PHD and CPHD filters have limitations in dealing with missed detections, extracting target state in their particle implementations, and maintaining track continuity. In this paper, based on the labeled random finite set theory, <inline-formula><tex-math notation="LaTeX">$\tau$</tex-math></inline-formula>-labeled PHD and CPHD ( <inline-formula><tex-math notation="LaTeX">$\tau$</tex-math></inline-formula>-LPHD/LCPHD) filtering approaches, in which the PHD components are separated and uniquely identified by a tag <inline-formula><tex-math notation="LaTeX"> $\tau$</tex-math></inline-formula>, are proposed. Based on the information from the <inline-formula> <tex-math notation="LaTeX">$\tau$</tex-math></inline-formula>-LPHD/LCPHD filtering processes, new <inline-formula> <tex-math notation="LaTeX">$\delta$</tex-math></inline-formula>-generalized labeled PHD and CPHD filtering approaches are proposed to address the issues in the <inline-formula><tex-math notation="LaTeX">$\tau$</tex-math></inline-formula> -LPHD/LCPHD filters, which are similar to the issues in the standard PHD/CPHD filters. The two proposed methods interact with each other and inherit the advantages of the <inline-formula><tex-math notation="LaTeX">$\delta$ </tex-math></inline-formula>-generalized labeled multi-Bernoulli filter, with substantial savings in computation resources.
Impact of Antibiotic-Resistant Pathogens Colonizing the Respiratory Secretions of Patients in an Extended-Care Area of the Emergency Department

Abstract Objective: To determine the incidence of acquired infection, and the incidence, risk factors, and molecular typing of multidrug-resistant bacterial organisms (MROs) colonizing respiratory secretions or the oropharynx of patients in an extended-care area of the emergency department (ED) in a tertiary-care university hospital. Methods: A case-control study was conducted regarding risk factors for colonization with MROs in ED patients from July 1996 to August 1998. The most prevalent MRO strains were determined using plasmid and genomic analysis with PFGE. Results: MROs colonized 59 (25.4%) of 232 ED patients and 173 controls. The mean ED length of stay for the 59 cases was 13.9 days versus 9.8 days for the 173 controls. The mean length of stay prior to the first isolation of MROs was 9.9 days. MRO species included Acinetobacter baumannii, Staphylococcus aureus, and Pseudomonas aeruginosa. The rate of hospital-acquired infection was 32.7 per 1,000 ED patient-days. The case fatality rate was significantly higher for cases. Univariate analysis identified mechanical ventilation, nebulization, nasogastric intubation, urinary catheterization, antibiotic therapy, and number of antibiotics as risk factors for MRO colonization. Multivariate regression analysis found that mechanical ventilation and nasogastric intubation independently predicted MRO colonization. Endemic clones were identified by PFGE in ED patients and were also found in patients in other parts of the hospital. Conclusions: Prolonged stay in the ED posed a risk for colonization with MROs and for contracting nosocomial infections, both of which were associated with increased mortality. Patients colonized with antibiotic-resistant A. baumannii may serve as a reservoir for spread in this hospital.
On Minimizing Delay for MHWN Based on Multi-Hop Activity Estimation

In this paper, we present a method for minimizing multi-hop transmission delay by optimally setting data rate along selected paths in Multi-hop Wireless Network (MHWN) based on multi-hop activity aware delay analysis. We develop an analytic model that enables us to obtain closed form expressions for delay in terms of multi-hop activity variables. A measuring deviation algorithm is used to derive the number of saturated nodes over a given set of topology. Numerical results and simulations are presented for different network topologies and compared with traditional studies.
Broadband excitation pulses for high‐field solid‐state nuclear magnetic resonance spectroscopy

In nuclear magnetic resonance spectroscopy, experimental limits due to the radiofrequency transmitter and/or coil means that conventional radiofrequency pulses (“hard pulses”) are sometimes not sufficiently powerful to excite magnetization uniformly over a desired range of frequencies. Effects due to nonuniform excitation are most frequently encountered at high magnetic fields for nuclei with a large range of chemical shifts. Using optimal control theory, we have designed broadband excitation pulses that are suitable for solid‐state samples under magic‐angle‐spinning conditions. These pulses are easy to implement, robust to spinning frequency variations, and radiofrequency inhomogeneities, and only four times as long as a corresponding hard pulse. The utility of these pulses for uniformly exciting 13C nuclei is demonstrated on a 900 MHz (21.1 T) spectrometer. Copyright © 2012 John Wiley & Sons, Ltd.
Innovation Network and Performance of Technology Clusters: Evidence from Communication Equipment Manufacturing

This paper focuses on the performance of technology clusters over the period 1998-2005 in Communication equipment industry within USA. We explore the relationship between the cluster network properties and the cluster performance at the cluster level. Our analysis shows that the average network distance has a negative impact on the cluster performance. We also find that the cluster coefficient has positive influence on the cluster performance. This finding is consistent with a view that knowledge spillover plays important role in the economic performance of technology clusters.
Quantification of external limiting membrane disruption caused by diabetic macular edema from SD-OCT.

PURPOSE Disruption of external limiting membrane (ELM) integrity on spectral-domain optical coherence tomography (SD-OCT) is associated with lower visual acuity outcomes in patients suffering from diabetic macular edema (DME). However, no automated methods to detect ELM and/or determine its integrity from SD-OCT exist. METHODS Sixteen subjects diagnosed with clinically significant DME (CSME) were included and underwent macula-centered SD-OCT (512 × 19 × 496 voxels). Sixteen subjects without retinal thickening and normal acuity were also scanned (200 × 200 × 1024 voxels). Automated quantification of ELM disruption was achieved as follows. First, 11 surfaces were automatically segmented using our standard 3-D graph-search approach, and the subvolume between surface 6 and 11 containing the ELM region was flattened based on the segmented retinal pigment epithelium (RPE) layer. A second, edge-based graph-search surface-detection method segmented the ELM region in close proximity "above" the RPE, and each ELM A-scan was classified as disrupted or nondisrupted based on six texture features in the vicinity of the ELM surface. The vessel silhouettes were considered in the disruption classification process to avoid false detections of ELM disruption. RESULTS In subjects with CSME, large areas of disrupted ELM were present. In normal subjects, ELM was largely intact. The mean and 95% confidence interval (CI) of the detected disruption area volume for normal and CSME subjects were mean(normal) = 0.00087 mm(3) and CI(normal) = (0.00074, 0.00100), and mean(CSME) = 0.00461 mm(3) and CI(CSME) = (0.00347, 0.00576) mm(3), respectively. CONCLUSIONS In this preliminary study, we were able to show that automated quantification of ELM disruption is feasible and can differentiate continuous ELM in normal subjects from disrupted ELM in subjects with CSME. We have started determining the relationships of quantitative ELM disruption markers to visual outcome in patients undergoing treatment for CSME.
MATHEMATICAL MODEL COUPLING PHASE TRANSFORMATIONS AND TEMPERATURE EVOLUTIONS IN STEELS

A mathematical model for calculating phase transformations in steels during rapid heating and cooling is presented. It is based on a rule of additivity. The isothermal kinetics are modelled by Johnson-Mehl-Avrami law. The model describes the kinetics of austenitization during heating, the state of austenite at the end of heating (carbon content, grain size), the kinetics of transformations during cooling, the final microstructure and hardness. The model is worked out firstly on dilatometric specimens without thermal gradients in order to validate the modelling and the input data. Then the application of the model to massive cylinders heated up and cooled down with high thermal gradients is presented.
Effective Triphone Mapping for Acoustic Modeling in Speech Recognition

This paper presents effective triphone mapping for acoustic models training in automatic speech recognition, which allows the synthesis of unseen triphones. The description of this data-driven model clustering, including experiments performed using 350 hours of a Slovak audio database of mixed read and spontaneous speech, are presented. The proposed technique is compared with treebased state tying, and it is shown that for bigger acoustic models, at a size of 4000 states and more, a triphone mapped HMM system achieves better performance than a tree-based state tying system. The main gain in performance is due to latent application of triphone mapping on monophones with multiple Gaussian pdfs, so the cloned triphones are initialized better than with single Gaussians monophones. Absolute decrease of word error rate was 0.46% (5.73% relatively) for models with 7500 states, and decreased to 0.4% (5.17% relatively) gain at 11500 states.
Kolmogorov's structure functions with an application to the foundations of model selection

Kolmogorov (1974) proposed a non-probabilistic approach to statistics, an individual combinatorial relation between the data and its model. We vindicate, for the first time, the rightness of the original "structure function", proposed by Kolmogorov: minimizing the data-to-model code length (finding the ML estimator or MDL estimator), in a class of contemplated models of prescribed maximal (Kolmogorov) complexity, always results in a model of best fit (expressed as minimal randomness deficiency). We show that both the structure function and the minimum randomness deficiency function can assume all shapes over their full domain (improving an old result of L.A. Levin and both an old and a recent one of VV Vyugin). We determine the (un)computability properties of the various functions and "algorithmic sufficient statistic. ".
Neuropilin-1/GIPC1 Signaling Regulates α5β1 Integrin Traffic and Function in Endothelial Cells

Neuropilin 1 (Nrp1) is a coreceptor for vascular endothelial growth factor A165 (VEGF-A165, VEGF-A164 in mice) and semaphorin 3A (SEMA3A). Nevertheless, Nrp1 null embryos display vascular defects that differ from those of mice lacking either VEGF-A164 or Sema3A proteins. Furthermore, it has been recently reported that Nrp1 is required for endothelial cell (EC) response to both VEGF-A165 and VEGF-A121 isoforms, the latter being incapable of binding Nrp1 on the EC surface. Taken together, these data suggest that the vascular phenotype caused by the loss of Nrp1 could be due to a VEGF-A164/SEMA3A-independent function of Nrp1 in ECs, such as adhesion to the extracellular matrix. By using RNA interference and rescue with wild-type and mutant constructs, we show here that Nrp1 through its cytoplasmic SEA motif and independently of VEGF-A165 and SEMA3A specifically promotes α5β1-integrin-mediated EC adhesion to fibronectin that is crucial for vascular development. We provide evidence that Nrp1, while not directly mediating cell spreading on fibronectin, interacts with α5β1 at adhesion sites. Binding of the homomultimeric endocytic adaptor GAIP interacting protein C terminus, member 1 (GIPC1), to the SEA motif of Nrp1 selectively stimulates the internalization of active α5β1 in Rab5-positive early endosomes. Accordingly, GIPC1, which also interacts with α5β1, and the associated motor myosin VI (Myo6) support active α5β1 endocytosis and EC adhesion to fibronectin. In conclusion, we propose that Nrp1, in addition to and independently of its role as coreceptor for VEGF-A165 and SEMA3A, stimulates through its cytoplasmic domain the spreading of ECs on fibronectin by increasing the Rab5/GIPC1/Myo6-dependent internalization of active α5β1. Nrp1 modulation of α5β1 integrin function can play a causal role in the generation of angiogenesis defects observed in Nrp1 null mice.
Diff Graphs for a fast Incremental Pointer Analysis

A wide range of optimizations and program analyses, including bug finding by means of escape or race analyses, need accurate pointer information. Since accuracy takes time, there is a need for a fast incremental pointer analysis that re-uses prior results and only re-analyzes program changes and their effects instead of the whole program. We present such an incremental pointer analysis that employs novel diff graphs to represent how a method accesses and/or modifies memory. Regardless of the number of call sites, we only need to analyze a method once; the resulting diff-graph is then used at every call site. If a method changes, we re-generate its diff-graph, and (unless its diff-graph stays the same) its callers' diff graphs, and so on. Our algorithm is flow sensitive and context insensitive, does not leak information between call sites, can perform strong updates (even for method calls), and is fast (14 000 LOC with 25 000 bytecode instructions in 3 minutes). When used incrementally for each of the commits of an open-source software repository our incremental approach derives more precise pointer information than established (full) analyses like Spark -- albeit in about the same time.
Image segmentation by a new weighted student's t-mixture model

In this study, the authors introduce a new weighted Student's t -mixture model (WSMM) for image segmentation. Gaussian distribution and Student's t -distribution are the two commonly used probabilities in the finite mixture model (FMM). The Student's t -mixture model has come to be regarded as an alternative to Gaussian mixture models, as it is heavily tailed and more robust for outliers. Moreover, the pixels are considered independent of each other in the FMM. Although some existing methods incorporate the spatial relationship between neighbouring pixels, they do not consider the relationship between spatial information and clustering information, thus those reported methods remain sensitive to noise. The advantages of the authors method are as follows: first, the authors introduce WSMM to incorporate the local spatial information, pixel intensity value and clustering information in an image. Second, the authors model is simple, easy to implement and has a good balance between noise insensitiveness and image detail preservation. Third, they adopt the gradient method and expectation maximisation algorithm, which allow for simultaneous estimation of optimal parameters. Finally, the most useful statistical tool for image segmentation, the well-known hidden Markov random field model, is a special case of their model. Thus, their method is general enough for model-based techniques construction. Experimental results on synthetic and real images demonstrate the improved robustness and effectiveness of their approach.
Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity

Abnormal alteration of bone morphogenetic protein (BMP) signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2) tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5) or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2), as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189) will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.
Extracting Word Sets with Non-Taxonomical Relation

At least two kinds of relations exist among related words: taxonomical relations and thematic relations. Both relations identify related words useful to language understanding and generation, information retrieval, and so on. However, although words with taxonomical relations are easy to identify from linguistic resources such as dictionaries and thesauri, words with thematic relations are difficult to identify because they are rarely maintained in linguistic resources. In this paper, we sought to extract thematically (non-taxonomically) related word sets among words in documents by employing case-marking particles derived from syntactic analysis. We then verified the usefulness of word sets with non-taxonomical relation that seems to be a thematic relation for information retrieval.
OCEAN: 2 1/2D Interactive Visual Data Mining of Text Documents

OCEAN is a tool for a posteriori visual data mining that uses the output of a text miner to help users better explore a document space. Clustered documents are transformed into a hierarchical 3D representation analog to reconfigurable disk trees. An intermediary document representation allows for interface customization and offers a generic approach to 3D structuring of text miner outputs. An interactive exploration is offered that avoids tree manipulation and provides local 2 frac12D view of the disks. A user evaluation is reported that outlines the benefit of controlled document hierarchy traversal and 2 frac12D document layout