Miracle-dz/UniFAR-FTUs huggingface dataset:
Runx1 Activities in Superficial Zone Chondrocytes, Osteoarthritic Chondrocyte Clones and Response to Mechanical Loading

Runx1, the hematopoietic lineage determining transcription factor, is present in perichondrium and chondrocytes. Here we addressed Runx1 functions, by examining expression in cartilage during mouse and human osteoarthritis (OA) progression and in response to mechanical loading. Spared and diseased compartments in knees of OA patients and in mice with surgical destabilization of the medial meniscus were examined for changes in expression of Runx1 mRNA (Q‐PCR) and protein (immunoblot, immunohistochemistry). Runx1 levels were quantified in response to static mechanical compression of bovine articular cartilage. Runx1 function was assessed by cell proliferation (Ki67, PCNA) and cell type phenotypic markers. Runx1 is enriched in superficial zone (SZ) chondrocytes of normal bovine, mouse, and human tissues. Increasing loading conditions in bovine cartilage revealed a positive correlation with a significant elevation of Runx1. Runx1 becomes highly expressed at the periphery of mouse OA lesions and in human OA chondrocyte ‘clones’ where Runx1 co‐localizes with Vcam1, the mesenchymal stem cell (MSC) marker and lubricin (Prg4), a cartilage chondroprotective protein. These OA induced cells represent a proliferative cell population, Runx1 depletion in MPCs decreases cell growth, supporting Runx1 contribution to cell expansion. The highest Runx1 levels in SZC of normal cartilage suggest a function that supports the unique phenotype of articular chondrocytes, reflected by upregulation under conditions of compression. We propose Runx1 co‐expression with Vcam1 and lubricin in murine cell clusters and human ‘clones’ of OA cartilage, participate in a cooperative mechanism for a compensatory anabolic function. J. Cell. Physiol. 230: 440–448, 2015. © 2014 Wiley Periodicals, Inc.
Towards Creative Environments: Conclusions from Creative Space

In recent papers and a book [1], [2], we have investigated diverse types of knowledge creation processes based on the concept of Creative Space (a metamodel of knowledge creation processes). This paper comments first on recent changes of understanding the problem of knowledge and technology creation, then recalls the concepts of Creative Space and diverse spirals and models of processes of knowledge creation discerned in this space, including the Triple Helix of normal knowledge creation. This is followed by comments on a new understanding of the role of systems science in the new era of knowledge civilization. Based on these results, we present a review of the needs and possibilities of constructing diverse types of dedicated Creative Environments (information technology systems for supporting creativity) for knowledge and, in particular, technology creation.
OSGi Enablement in UIMA Framework

Migration of existing software systems to OSGi is gaining momentum with wide acceptance of the OSGi technology as a standard way of managing software life-cycle through a service-oriented component-based approach. Although the technical merits of the OSGi approach are broadly recognized, the migration of existing systems may require significant efforts, such as modularizing the system code and embracing service based design. An alternative approach is adapting existing software for component based OSGi environment by putting a thin layer between the OSGi Service Platform and existing software systems. Adaptation, as opposed to migration, eliminates the necessity of modularizing or redesigning existing systems, which is particularly important when the existing software platform and associated programming model is mature and has already penetrated into the market place. As a case study of such an adaptation approach, this report demonstrates an OSGi adaptation of a popular open source Java platform built by IBM Research for integration of software analytics, processing unstructured information. The major challenge is providing analytic and application developers with all the benefits of the component based OSGi platform without entailing substantial modifications of existing framework code base and/or programming model. This report presents a comprehensive solution for integrating analytics and other resources in OSGi environment. The results of this report are applicable not only to a particular framework, but also to a wider class of Java frameworks.
Improving prioritization of software weaknesses using security models with AVUS

Testing tools for application security have become an integral part of secure development life-cycles. Despite their ability to spot important software weaknesses, the high number of findings require rigorous prioritization. Most testing tools provide generic ratings to support prioritization. Unfortunately, ratings from established tools lack context information especially with regard to the security requirements of respective components or source code. Thus experts often spend a great deal of time re-assessing the prioritization provided by these tools. This paper introduces our lightweight tool AVUS that adjusts context-free ratings of software weaknesses according to a user-defined security model. We also present a first evaluation applying AVUS to a well-known open source project and the findings of a popular, commercially available application security testing tool.
[Applications of RHD zygosity test through polymerase chain reaction for prediction of fetus Rh D-positive phenotype].

OBJECTIVE To explore a molecular method for the determination of RHD zygosity. METHODS Two pairs of primers were designed specific for downstream rhesus box and hybrid rhesus box according to the sequences in GenBank. Together with a pair of internal control primer, a dual-tube polymerase chain reaction (PCR) method was established for determination of the RHD zygosity. Thirty RhD-positive, D-negative and weak D phenotype samples were evaluated by taking a recent restriction fragment length polymorphism (RFLP) method as reference. RESULTS The results of the dual-tube PCR and RFLP are identical in 29 samples, which are also in concordance with the Rh phenotype, respectively. In one weak D sample, however, both methods tested as RHD(-)/RHD(-), which showed that there was one RHD(-) haplotype in this individual, but a false negative result in testing downstream rhesus box. CONCLUSIONS The dual-tube PCR is a less-labored method for RHD zygosity detection. It can be used clinically in prenatal test to determine RHD zygosity of pregnant women's partner for prediction of fetus RhD phenotype.
A Novel Intrusion Tolerant System Using Live Migration

SUMMARY This letter proposes a novel intrusion tolerant system consisting of several virtual machines (VMs) that refresh the target system periodically and by live migration , which monitors the many features of the VMs to identify and replace exhausted VMs. The proposed scheme provides adequate performance and dependability against denial of service (DoS) attacks. To show its e ﬃ ciency and security, we conduct experiments on the CSIM20 simulator, which showed 22% improvement in a normal situation and approximately 77.83% improvement in heavy tra ﬃ c in terms of the response time compared to that reported in the literature. We measure and compare the response time. The result show that the proposed scheme has shorter response time and maintains than other systems and supports services during the heavy tra ﬃ c.
Turbo detection of symbol-based non-binary LDPC-coded space-time signals using sphere packing modulation

A recently proposed space-time signal construc- tionmethodthatcombinesorthogonal designwith spherepack- ing, referred to here as (STBC-SP), has shown useful perfor- mance improvements over Alamouti's conventional orthogo- nal design. As a further advance, non-binary LDPC codes have been capable of attaining substantial performance im- provements over their binary counterparts. In this paper, we demonstrate that the performance of STBC-SP systems can be further improved by concatenating sphere packing aided mod- ulation with non-binary LDPC codes and performing symbol- based turbo detection. We present simulation results for the proposed scheme communicating over a correlated Rayleigh fading channel. At a BER of 10 −6 , the proposed symbol- based turbo-detected STBC-SP scheme was capable of achiev- ing a coding gain of approximately 26.6dB over the identical- throughput1bit/symboluncodedSTBC-SPbenchmarker sche- me. The proposed scheme also achieved a coding gain of ap- proximately 3dB at a BER of 10 −6 over a recently proposed bit-based turbo-detected STBC-SP benchmarker scheme.
Training feedforward networks with the Marquardt algorithm

The Marquardt algorithm for nonlinear least squares is presented and is incorporated into the backpropagation algorithm for training feedforward neural networks. The algorithm is tested on several function approximation problems, and is compared with a conjugate gradient algorithm and a variable learning rate algorithm. It is found that the Marquardt algorithm is much more efficient than either of the other techniques when the network contains no more than a few hundred weights.
Expression Profile and Cellular Localization of Maize Rpd3-Type Histone Deacetylases during Plant Development1

We analyzed the expression profile and cellular localization of the maize (Zea mays) Rpd3-type histone deacetylases genes ZmRpd3/101, ZmRpd3/102, and ZmRpd3/108 (indicated as ZmHDA101, ZmHDA102, and ZmHDA108 in the Plant Chromatin Database). This study shows that maize Rpd3 transcripts are present in all the organs and cellular domains analyzed, but we found that their amounts change during development, accumulating in the inner region of the endosperm, in vascular zones of the nucellus, in the tapetum, and in the tetrads. A similar expression profile and nucleus-cytoplasmic localization was observed for ZmRpd3 proteins. Glutathione S-transferase pull-down assays show that ZmRpd3 proteins can interact with the maize retinoblastoma-related (ZmRBR1) protein, an important regulator of cell cycle progression, and with the maize retinoblastoma-associated protein (ZmRbAp1). However, the three ZmRpd3 proteins do not mutually compete in the binding. These results suggest a general role of ZmRpd3 genes in the plant cell cycle and development. These observations also provide indications on possible mechanisms regulating their transcription and protein accumulation. Similarities in the gene expression profiles and protein interactions may indicate that functional redundancy among members of the ZmRpd3 gene family exists. However, a degree of functional divergence is also supported by our findings.
A RAPD‐PCR method for large‐scale typing of Bacillus cereus

A robust RAPD-PCR procedure for large-scale typing of Bacillus cereus was developed. It is based on a simple DNA preparation, involving only freezing and boiling of cells in water with active carbon. By using a computerized system for data collection and processing, an efficient system for handling RAPD patterns for large-scale investigations was achieved. The procedure was highly discriminatory for Bacillus cereus strains and was found to give reproducible classification of RAPD fingerprints for five reference strains.
Robust sliding-mode position/force set-point control of underactuated constrained manipulator

In this paper, a robust position/force set-point control strategy based on a sliding-mode is designed for constrained underactuated manipulator. At first, the reduced underactuated position/force dynamic model is obtained by considering a coordination transformation. Then, a controller based on a sliding-mode is designed to drive the closed-loop system states to reach the adopted sliding model surface. Considering the parametric uncertainties of the manipulator, a robust control strategy is applied to bound compensation. Furthermore, we can obtain a global asymptotic stability result for the positions error in the Lyapunov sense and the error of constraint force is bounded with a controllable bound. Finally, the simulation results of a three-DOF manipulator system illustrate the validity and the feasibility of the proposed method in this paper.
Expression of T lymphocyte chemoattractants and activation markers in vernal keratoconjunctivitis

Background/aims: T lymphocytes are present in increased numbers in the conjunctiva of patients with vernal keratoconjunctivitis (VKC) and their activation has a central role in the pathogenesis of the chronic allergic inflammatory reactions seen in VKC. The aims of this study were to examine the expression of three recently described potent T lymphocyte chemoattractants, PARC (pulmonary and activation regulated chemokine), macrophage derived chemokine (MDC), and I-309, the MDC receptor CCR4, and T lymphocyte activation markers, CD25, CD26, CD62L, CD71, and CD30, and to correlate them with the counts of CD3+ T lymphocytes in the conjunctiva of patients with VKC. Method: Conjunctival biopsy specimens from 11 patients with active VKC, and eight control subjects were studied by immunohistochemical techniques using a panel of monoclonal and polyclonal antibodies directed against PARC, MDC, I-309, CCR4, CD25, CD26, CD62L, CD71, and CD30. The numbers of positively stained cells were counted. The phenotype of inflammatory cells expressing chemokines was examined by double immunohistochemistry. Results: In the normal conjunctiva, vascular endothelial cells in the upper substantia propria showed weak immunoreactivity for CD26. There was no immunoreactivity for the other antibodies. VKC specimens showed inflammatory cells expressing PARC, MDC, and I-309. The numbers of PARC+ inflammatory cells were higher than the numbers of MDC+ and I-309+ inflammatory cells and the mean values of the three groups differed significantly (17.0 (SD 10.1); 9.5 (9.9), and 4.3 (7.9), respectively, p = 0.0117, ANOVA). The numbers of PARC+ inflammatory cells had the strongest correlation with the numbers of CD3+ T lymphocytes. Few CCR4+ inflammatory cells were observed in only three specimens. Double immunohistochemistry revealed that all inflammatory cells expressing chemokines were CD68+ monocytes/macrophages. The numbers of CD25+ T lymphocytes were higher than the numbers of CD26+, CD62L+, CD71+, and CD30+ T lymphocytes and the mean values of the five groups differed significantly (46.2 (27.9), 30.7 (16.0), 20.1 (8.6), 7.8 (7.7), and 6.5 (4.0), respectively, p <0.001, ANOVA). The numbers of CD25+ T lymphocytes had the strongest correlation with the numbers of CD3+ T lymphocytes. Conclusion: These results suggest a potential role for PARC, MDC, and I-309 in attracting T lymphocytes into conjunctiva in VKC. T lymphocytes in VKC are activated and express several activation markers which might contribute to the pathogenesis of VKC.
Using the Virtual World to Improve Quality of Life in the Real World

Mental health professionals are increasingly integrating advances in technology to improve the health of those in their care (American Psychological Association, 2000). The authors describe the immersive properties of virtual reality and its importance for clinical purposes and then review the literature describing current clinical applications of virtual reality (VR) and research documenting its efficacy. Virtual reality has been used in the treatment of specific phobias, posttraumatic stress disorder, eating disorders, and pain management.
The MerR-Like Regulator BrlR Confers Biofilm Tolerance by Activating Multidrug Efflux Pumps in Pseudomonas aeruginosa Biofilms

ABSTRACT A defining characteristic of biofilms is antibiotic tolerance that can be up to 1,000-fold greater than that of planktonic cells. In Pseudomonas aeruginosa, biofilm tolerance to antimicrobial agents requires the biofilm-specific MerR-type transcriptional regulator BrlR. However, the mechanism by which BrlR mediates biofilm tolerance has not been elucidated. Genome-wide transcriptional profiling indicated that brlR was required for maximal expression of genes associated with antibiotic resistance, in particular those encoding the multidrug efflux pumps MexAB-OprM and MexEF-OprN. Chromatin immunoprecipitation (ChIP) analysis revealed a direct regulation of these genes by BrlR, with DNA binding assays confirming BrlR binding to the promoter regions of the mexAB-oprM and mexEF-oprN operons. Quantitative reverse transcriptase PCR (qRT-PCR) analysis further indicated BrlR to be an activator of mexAB-oprM and mexEF-oprN gene expression. Moreover, immunoblot analysis confirmed increased MexA abundance in cells overexpressing brlR. Inactivation of both efflux pumps rendered biofilms significantly more susceptible to five different classes of antibiotics by affecting MIC but not the recalcitrance of biofilms to killing by bactericidal agents. Overexpression of either efflux pump in a ΔbrlR strain partly restored tolerance of ΔbrlR biofilms to antibiotics. Expression of brlR in mutant biofilms lacking both efflux pumps partly restored antimicrobial tolerance of biofilms to wild-type levels. Our results indicate that BrlR acts as an activator of multidrug efflux pumps to confer tolerance to P. aeruginosa biofilms and to resist the action of antimicrobial agents.
Maturation of the Regulation of GLUT4 Activity by p38 MAPK during L6 Cell Myogenesis*

Insulin stimulates glucose uptake in skeletal muscle cells and fat cells by promoting the rapid translocation of GLUT4 glucose transporters to the plasma membrane. Recent work from our laboratory supports the concept that insulin also stimulates the intrinsic activity of GLUT4 through a signaling pathway that includes p38 MAPK. Here we show that regulation of GLUT4 activity by insulin develops during maturation of skeletal muscle cells into myotubes in concert with the ability of insulin to stimulate p38 MAPK. In L6 myotubes expressing GLUT4 that carries an exofacial myc-epitope (L6-GLUT4myc), insulin-stimulated GLUT4myc translocation equals in magnitude the glucose uptake response. Inhibition of p38 MAPK with SB203580 reduces insulin-stimulated glucose uptake without affecting GLUT4myc translocation. In contrast, in myoblasts, the magnitude of insulin-stimulated glucose uptake is significantly lower than that of GLUT4myc translocation and is insensitive to SB203580. Activation of p38 MAPK by insulin is considerably higher in myotubes than in myoblasts, as is the activation of upstream kinases MKK3/MKK6. In contrast, the activation of all three Akt isoforms and GLUT4 translocation are similar in myoblasts and myotubes. Furthermore, GLUT4myc translocation and phosphorylation of regulatory sites on Akt in L6-GLUT4myc myotubes are equally sensitive to insulin, whereas glucose uptake and phosphorylation of regulatory sites on p38 MAPK show lower sensitivity to the hormone. These observations draw additional parallels between Akt and GLUT4 translocation and between p38 MAPK and GLUT4 activation. Regulation of GLUT4 activity by insulin develops upon muscle cell differentiation and correlates with p38 MAPK activation by insulin.
Caregivers' descriptions of sleep changes and depressive symptoms.

PURPOSE/OBJECTIVES To describe caregiver sleep and depression using caregiver narratives. To compare qualitative descriptions with quantitative scores. DESIGN Descriptive, one-time, open-ended interview followed by structured sleep and depression questions. SETTING Interview conducted in person or via telephone at caregiver's preference. SAMPLE 47 caregivers of patients with advanced stage cancer. Caregivers had a mean age of 54 years, and most were female (81%), Caucasian (82%), and spouses (61%). They provided care for a mean of 24 months. Patients' diagnoses were lung cancer (36%), colorectal cancer (13%), or recurrences (51%). METHODS Two cancer care sites in southern California provided participants. After consent, the researcher conducted interviews. The Pittsburgh Sleep Quality Index (PSQI) and Center for Epidemiological Studies-Depression (CES-D) instruments were administered following interviews. MAIN RESEARCH VARIABLES Sleep pattern changes and depression levels over time as defined by caregivers. FINDINGS Caregivers described severe fluctuations in sleep patterns over time and how these changes affected caregiver depressive symptoms. PSQI and CES-D scores matched narrative comments. CONCLUSIONS Caregivers' narratives suggest they suffer progressive sleep deprivation that affects their emotions and ability to continue as caregivers. IMPLICATIONS FOR NURSING Nurses must recognize the severe sleep problems experienced by caregivers and respond with interventions to increase sleep quality and decrease depression.
A vector multiprocessor for real-time multi-user detection in spread-spectrum communication

Multi-user detection in spread-spectrum communications involves repeatedly solving a system of equations to decouple multiple-access interference among users communicating with a basestation. This paper proposes a vector multiprocessor to provide the necessary computing performance. Two vector processors with parallel vector pipelines that are optimized for vector multiply-add operations achieve sustained gigaflop-level performance with a 100 MHz internal clock. Performance analysis of vector assembly-language code on eight vector units indicates that matrix-vector multiplication for a 32/spl times/32 problem can be performed in less than 2 /spl mu/s, and that matrix inversion can be performed in less than 200 /spl mu/s.
Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers.

A method is presented to estimate the biometric parameters of a quantitative trait locus linked to a genetic marker when both loci are segregating in the F-2 generation of a cross between two inbred lines. The method, which assumes underlying normal distributions, is a combination of maximum likelihood and moments methods and uses the statistics of the genetic marker genotype samples for the quantitative trait to estimate the recombination frequency between the two loci and the means and variances of the genotypes of the quantitative trait locus. With this method, the genetic parameters of a locus affecting plant height linked to an electrophoretic marker for esterase were accurately estimated from a sample of 1596 F-2 progeny of a cross between two species of Lycopersicon (tomato). Linkage distance between the two loci was 38 map units and the effect of the quantitative trait locus was 1.6 phenotypic standard deviation units. Accurate estimates of the genetic parameters and linkage distance for populations of 2000 individuals simulated with a segregating codominant locus with an effect of 1.63 standard deviations linked to a genetic marker with . 2 recombination were also derived by this method. The method is not effective in distinguishing between complete and partial linkage in samples of only 500 individuals or for quantitative loci with effects less than a phenotypic standard deviation. The method is more effective for codominant than for dominant loci.
Gene × Abstinence Effects on Drug Cue Reactivity in Addiction: Multimodal Evidence

Functional polymorphisms in the dopamine transporter gene (DAT1 or SLC6A3) modulate responsiveness to salient stimuli, such that carriers of one 9R-allele of DAT1 (compared with homozygote carriers of the 10R-allele) show heightened reactivity to drug-related reinforcement in addiction. Here, using multimodal neuroimaging and behavioral dependent variables in 73 human cocaine-addicted individuals and 47 healthy controls, we hypothesized and found that cocaine-addicted carriers of a 9R-allele exhibited higher responses to drug cues, but only among individuals who had used cocaine within 72 h of the study as verified by positive cocaine urine screens (a state characterized by intense craving). Importantly, this responsiveness to drug cues was reliably preserved across multimodal imaging and behavioral probes: psychophysiological event-related potentials, self-report, simulated cocaine choice, and fMRI. Because drug cues contribute to relapse, our results identify the DAT1R 9R-allele as a vulnerability allele for relapse especially during early abstinence (e.g., detoxification).