Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Regulatory Pathways Controlling Gene Expression of Stress-Responsive Mitochondrial Proteins in Arabidopsis1[W][OA]

In this study we analyzed transcript abundance and promoters of genes encoding mitochondrial proteins to identify signaling pathways that regulate stress-induced gene expression. We used Arabidopsis (Arabidopsis thaliana) alternative oxidase AOX1a, external NADP H-dehydrogenase NDB2, and two additional highly stress-responsive genes, At2g21640 and BCS1. As a starting point, the promoter region of AOX1a was analyzed and functional analysis identified 10 cis-acting regulatory elements (CAREs), which played a role in response to treatment with H2O2, rotenone, or both. Six of these elements were also functional in the NDB2 promoter. The promoter region of At2g21640, previously defined as a hallmark of oxidative stress, shared two functional CAREs with AOX1a and was responsive to treatment with H2O2 but not rotenone. Microarray analysis further supported that signaling pathways induced by H2O2 and rotenone are not identical. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA), whereas the promoters of AOX1a and NDB2 were unresponsive to SA. Analysis of transcript abundance of these genes in a variety of defense signaling mutants confirmed that BCS1 expression is regulated in a different manner compared to AOX1a, NDB2, and At2g21640. These mutants also revealed a pathway associated with programmed cell death that regulated AOX1a in a manner distinct from the other genes. Thus, at least three distinctive pathways regulate mitochondrial stress response at a transcriptional level, an SA-dependent pathway represented by BCS1, a second pathway that represents a convergence point for signals generated by H2O2 and rotenone on multiple CAREs, some of which are shared between responsive genes, and a third pathway that acts via EDS1 and PAD4 regulating only AOX1a. Furthermore, posttranscriptional regulation accounts for changes in transcript abundance by SA treatment for some genes.
Rearrangement and expression of T cell receptor and immunoglobulin loci in immortalized CD4−CDS−T cell lines

Injection of newborn mice with mixtures of wild‐type moloney murine leukemia (Mo‐MuLV) virus and other recombinant retroviruses harboring the myc oncogene alone or in combination with the H‐ras oncogene resulted in a 100% incidence of lymphatic leukemias from which permanent cell lines could be established in vitro. These cells are immunoglobulin (Ig)−, Thy‐1+BP− and CD8−CD4− indicating that they are early thymocytes. Such transformed pre‐T lines lack retroviral myc and ras genes but occasionally possess proviral insertion near to their endogenous myc and pim genes. We show that both Ig heavy chain (Igh) and T cell receptor (TcR) genes are rearranged in most of these lines. In some cases, a primary recombination was followed by a secondary rearrangement at the same locus. We show that VTγ genes can rearrange outside of their known cluster suggesting that TcRγ diversification in such pre‐T cells may be different to that in more mature T cells. Ig D‐JH recombinations may precede TcR gene recombination in these early T cell lines, and some but not all express sterile Cu transcripts. Some of these lines express surface heterodimers that appear composed of α and β chains that can be immunoprecipitated with a monoclonal anti‐T3 antibody but not with the anti‐Vβ8 monoclonal antibody F23.1. This established pre‐T cell line represents novel biological material for the dissection of T cell development and function analogous to A‐MuLV transformed pre‐B cells.
ROBUST CONTROL FOR HAPTIC-BASED ROBOTIC TELEOPERATION

The paper deals with teleoperated robotic systems that are commanded by a human operator via interface that provides task feedback information. In order to successfully perform challenging tasks, not only visual, but also a haptic feedback is strongly desired. Thus, such teleoperator system has to be controlled bilaterally. The paper presents a bilateral control scheme which is designed based on modal decomposition to decouple force and position coordinates. The control algorithm is derived following the sliding mode control approach which guarantees robustness to model perturbation, parameters uncertainty and system disturbance. The proposed design also applies external force observer; thus, none external force sensor is required. The design was experimentally validated on a simple master-slave teleoperator with a 1-DoF robotic system.
A COGNITIVE BEHAVIOURAL FRAMEWORK FOR THE TREATMENT OF DISTRESSING VISUAL HALLUCINATIONS IN OLDER PEOPLE

This paper summarizes a recently developed model for understanding the genesis of visual hallucinations, shows how this can be incorporated into a cognitive behavioural framework, and then illustrates possible ways in which this may be used to successfully treat the emotional distress that some older people experience as a consequence of their hallucinations. These ideas have been developed as a model-based clinical response to patients distressed by their hallucinations. The purpose of this paper is to outline this approach in order to stimulate discussion and empirical evaluation.
Circulating Angiogenic Cells can be Derived from Cryopreserved Peripheral Blood Mononuclear Cells

Background Cell transplantation for regenerative medicine has become an appealing therapeutic method; however, stem and progenitor cells are not always freshly available. Cryopreservation offers a way to freeze cells as they are generated, for storage and transport until required for therapy. This study was performed to assess the feasibility of cryopreserving peripheral blood mononuclear cells (PBMCs) for the subsequent in vitro generation of their derived therapeutic population, circulating angiogenic cells (CACs). Methods PBMCs were isolated from healthy human donors. Freshly isolated cells were either analyzed immediately or cryopreserved in media containing 6% plasma serum and 5% dimethyl sulfoxide. PBMCs were thawed after being frozen for 1 (early thaw) or 28 (late thaw) days and analyzed, or cultured for 4 days to generate CACs. Analysis of the cells consisted of flow cytometry for viability and phenotype, as well as functional assays for their adhesion and migration potential, cytokine secretion, and in vivo angiogenic potential. Results The viability of PBMCs and CACs as well as their adhesion and migration properties did not differ greatly after cryopreservation. Phenotypic changes did occur in PBMCs and to a lesser extent in CACs after freezing; however the potent CD34+VEGFR2+CD133+ population remained unaffected. The derived CACs, while exhibiting changes in inflammatory cytokine secretion, showed no changes in the secretion of important regenerative and chemotactic cytokines, nor in their ability to restore perfusion in ischemic muscle. Conclusion Overall, it appears that changes do occur in cryopreserved PBMCs and their generated CACs; however, the CD34+VEGFR2+CD133+ progenitor population, the secretion of pro-vasculogenic factors, and the in vivo angiogenic potential of CACs remain unaffected by cryopreservation.
“Koe wai hoki koe?!”, or “Who are you?!”: Issues of trust in cross‐cultural collaborative research

Abstract Cross‐cultural research designs are increasingly employed in the New Zealand context to investigate a range of complex social and environmental issues. However, there is little guidance for researchers who work for mainstream organisations and hapū (subtribe(s)) and iwi (tribe(s)) on how to undertake cross‐cultural collaborative research. Trust is a key issue that makes cross‐cultural research possible and it is surprising that issues relating to trust have not featured widely in the literature. In this paper, we reflect on our experiences working cross‐culturally and collaboratively with a hapū in Northland, New Zealand. We discuss how a mainstream research organisation worked with a community health trust and developed a working relationship with a hapū, forming the basis of a community‐driven collaborative evaluation of a central government‐funded project. Key findings were the establishment of a tuākana‐tēina relationship (where teacher and learner are interchangeable) between the members of the collaborative research team and the employment of appropriate research methods to develop a research agenda that ensured everyone would benefit from the research.
Wavelet-based illumination normalization for face recognition

The appearance of a face image is severely affected by illumination conditions that hinder the automatic face recognition process. To recognize faces under varying illuminations, we propose a wavelet-based normalization method so as to normalize illuminations. This method enhances the contrast as well as the edges of face images simultaneously, in the frequency domain using the wavelet transform, to facilitate face recognition tasks. It outperforms the conventional illumination normalization method - the histogram equalization that only enhances image pixel gray-level contrast in the spatial domain. With this method, our face recognition system works effectively under a wide range of illumination conditions. The experimental results obtained by testing on the Yale face database B demonstrate the effectiveness of our method with 15.65% improvement, on average, in the face recognition system.
Send Orders of Reprints at Reprints@benthamscience.net Sensitivity of Different Early Developmental Periods of Baltic Herring (clupea Harengus) to Water-accommodated Fraction of Crude Oil

The probability for the oil accident to occur at the Gulf of Finland has been increasing last ten years and it is predicted to continue so. The risk is high based on the accident probability and the probable harm caused; some spawning areas of the Baltic herring (Clupea harengus membras) are located in the vicinity of ports and ship fairways with heavy traffic, so any oil spillage there could affect recruitment of this commercially important species. In this study, newly fertilized embryos, the older embryos and the hatched larvae of Baltic herring were exposed to water-accommodated fraction (WAF) made from crude oil. Oil exposure increased most the mortality of the hatched larvae, and larvae hatched during the exposure were more sensitive to the impacts of oil than larvae which were exposed after their hatching. The LC 50 value was 16 % of WAF-solution of crude oil for the exposed larvae. The most tolerant for the oil were the embryos in late embryonic stage (the LC 50 was 44 % of WAF-solution). During the exposure, some malformations i.e. a curving of the notochord were noticed. INTRODUCTION The part of the Baltic Sea most heavily used by oil tankers is the Gulf of Finland and it is predicted that by 2020 the amount of oil transported will be 170 million tons according to the slow growth scenario and 200 million tons with a strong growth scenario, which correspond the increase of 13 and 34%, respectively, compared to the year 2009 [1,2]. In the case of an accident, large and hazardous amounts of crude oil may be spilled into the sea. When oil is spilled, it starts to spread and mix with the water. Oil acts differently in the open sea and when it is dispersed by coastal rocks [3,4]. In the Gulf of Finland, some spawning areas of the Baltic herring are located in the vicinity of ports and ship fairways with heavy traffic [5], so any oil spillage there could affect recruitment of this commercially important species.
HOW IS THE COULOMB BLOCKADE SUPPRESSED IN HIGH-CONDUCTANCE TUNNEL JUNCTIONS?

We present a theory of the Coulomb blockade for a tunnel junction, with arbitrarily large tunnel conductance but with small channel transmissions, placed in a general electromagnetic environment containing no island. Our model, based on a self-consistent calculation of the complex admittance of the junction, predicts that high tunnel conductances wash out the Coulomb blockade and restore Ohmic behavior. We find quantitative agreement between predictions and measurements of the dc conductance of small metallic tunnel junctions in series with a resistor. [S0031-9007(98)05514-8]
An Inverted Index for Storing and Retrieving Grammatical Dependencies

Web count statistics gathered from search engines have been widely used as a resource in a variety of NLP tasks. For some tasks, however, the information they exploit is not fine-grained enough. We propose an inverted index over grammatical relations as a fast and reliable resource to access more general and also more detailed frequency information. To build the index, we use a dependency parser to parse a large corpus. We extract binary dependency relations, such as he-subj-say (he is the subject of say) as index terms and construct the index using publicly available open-source indexing software. The unit we index over is the sentence. The index can be used to extract grammatical relations and frequency counts for these relations. The framework also provides the possibility to search for partial dependencies (say, the frequency of he occurring in subject position), words, strings and a combination of these. One possible application is the disambiguation of syntactic structures.
Steatosis and liver cancer in transgenic mice expressing the structural and nonstructural proteins of hepatitis C virus.

BACKGROUND & AIMS The aim of this study was to determine whether expression of hepatitis C virus proteins alters hepatic morphology or function in the absence of inflammation. METHODS Transgenic C57BL/6 mice with liver-specific expression of RNA encoding the complete viral polyprotein (FL-N transgene) or viral structural proteins (S-N transgene) were compared with nontransgenic littermates for altered liver morphology and function. RESULTS FL-N transcripts were detectable only by reverse-transcription polymerase chain reaction, and S-N transcripts were identified in Northern blots. The abundance of viral proteins was sufficient for detection only in S-N transgenic animals. There was no inflammation in transgenic livers, but mice expressing either transgene developed age-related hepatic steatosis that was more severe in males. Apoptotic or proliferating hepatocytes were not significantly increased. Hepatocellular adenoma or carcinoma developed in older male animals expressing either transgene, but their incidence reached statistical significance only in FL-N animals. Neither was ever observed in age-matched nontransgenic mice. CONCLUSIONS Constitutive expression of viral proteins leads to common pathologic features of hepatitis C in the absence of specific anti-viral immune responses. Expression of the structural proteins enhances a low background of steatosis in C57BL/6 mice, while additional low level expression of nonstructural proteins increases the risk of cancer.
Quality costing: a management review

This paper relates a review of the English language literature on quality costing and traces its historical development; it provides authoritative reading on the subject. The review also has a focus on collection and use of quality-costing methods, quantitative cost data and the role and views of accountants in the task of quality-cost collection and reporting. Amongst the main findings is the preoccupation with the prevention – appraisal – failure categorization of quality costs and lack of guidance on definitions. The considerable impact of the American quality profession on the development of quality costing is pointed out along with the increasingly positive stance of accountants.
Improving accuracy through density correction in guided wave tomography

The accurate quantification of wall loss caused by corrosion is critical to the reliable life estimation of pipes and pressure vessels. Traditional thickness gauging by scanning a probe is slow and requires access to all points on the surface; this is impractical in many cases as corrosion often occurs where access is restricted, such as beneath supports where water collects. Guided wave tomography presents a solution to this; by transmitting guided waves through the region of interest and exploiting their dispersive nature, it is possible to build up a map of thickness. While the best results have been seen when using the fundamental modes A0 and S0 at low frequency, the complex scattering of the waves causes errors within the reconstruction. It is demonstrated that these lead to an underestimate in wall loss for A0 but an overestimate for S0. Further analysis showed that this error was related to density variation, which was proportional to thickness. It was demonstrated how this could be corrected for in the reconstructions, in many cases resulting in the near-elimination of the error across a range of defects, and greatly improving the accuracy of life estimates from guided wave tomography.
Multiobjective evolutionary algorithm-based soft subspace clustering

In this paper, a multiobjective evolutionary algorithm based soft subspace clustering, MOSSC, is proposed to simultaneously optimize the weighting within-cluster compactness and weighting between-cluster separation incorporated within two different clustering validity criteria. The main advantage of MOSSC lies in the fact that it effectively integrates the merits of soft subspace clustering and the good properties of the multiobjective optimization-based approach for fuzzy clustering. This makes it possible to avoid trapping in local minima and thus obtain more stable clustering results. Substantial experimental results on both synthetic and real data sets demonstrate that MOSSC is generally effective in subspace clustering and can achieve superior performance over existing state-of-the-art soft subspace clustering algorithms.
Beginning treatment for childhood acute lymphoblastic leukemia: insights from the parents' perspective.

PURPOSE/OBJECTIVES To report the perspective of parents during the initial stages of diagnosis and treatment for their children's acute lymphoblastic leukemia (ALL). DESIGN Descriptive and phenomenologic. SETTING Royal Children's Hospital, Brisbane, Australia. SAMPLE Parents (mothers, n = 12; fathers, n = 4) of 12 children (ages 0-10) undergoing treatment for ALL. METHODS Open-ended, audiotaped interviews were transcribed verbatim and analyzed. MAIN RESEARCH VARIABLES Parents' experiences of their children's initial diagnosis and treatment of ALL. FINDINGS The parents' insights provided a clear indication that the initial stage of treatment is highly stressful and parents may be overwhelmed by the experience. The situational stress translated into three potentially overwhelming emotional states: the stress of uncertainty, the shock of diagnosis, and a feeling of being trapped in an unpleasant emotional roller-coaster ride. Honesty from healthcare professionals, the opportunity to share feelings, and an affirmation of the harshness of the situation were reported as helpful in dealing with the sense of being overwhelmed. CONCLUSION Parents need honest information and sensitive emotional support to come to terms with the stresses associated with their children's diagnosis and initial treatment of ALL. Parents must have access to a safe environment where they can express their feelings and have the harsh reality of the initial stage of treatment affirmed. IMPLICATIONS FOR NURSING Parents need considerable emotional support to negotiate the initial stage of treatment for ALL. Parents of children diagnosed with ALL must have honest information about diagnosis and treatment, as much information as possible for planning their daily lives, an opportunity to express real feelings, access to moments of personal space where feelings can be processed, and compassionate understanding of the emotional difficulties associated with this difficult life journey.
Vacancy formation on C60/Pt (111): unraveling the complex atomistic mechanism

The interaction of fullerenes with transition metal surfaces leads to the development of an atomic network of ordered vacancies on the metal. However, the structure and formation mechanism of this intricate surface reconstruction is not yet understood at an atomic level. We combine scanning tunneling microscopy, high resolution and temperature programmed-x-ray photoelectrons spectroscopy, and density functional theory calculations to show that the vacancy formation in C60/Pt(111) is a complex process in which fullerenes undergo two significant structural rearrangements upon thermal annealing. At first, the molecules are physisorbed on the surface; next, they chemisorb inducing the formation of an adatom–vacancy pair on the side of the fullerene. Finally, this metastable state relaxes when the adatom migrates away and the vacancy moves under the molecule. The evolution from a weakly-bound fullerene to a chemisorbed state with a vacancy underneath could be triggered by residual H atoms on the surface which prevent a strong surface-adsorbate bonding right after deposition. Upon annealing at about 440 K, when all H has desorbed, the C60 interacts with the Pt surface atoms forming the vacancy-adatom pair. This metastable state induces a small charge transfer and precedes the final adsorption structure.
Similarity in targets with REST points to neural and glioblastoma related miRNAs

There are groups of genes that need coordinated repression in multiple contexts, for example if they code for proteins that work together in a pathway or in a protein complex. Redundancy of biological regulatory networks implies that such coordinated repression might occur at both the pre- and post-transcriptional level, though not necessarily simultaneously or under the same conditions. Here, we propose that such redundancy in the global regulatory network can be detected by the overlap between the putative targets of a transcriptional repressor, as identified by a ChIP-seq experiment, and predicted targets of a microRNA (miRNA). To test this hypothesis, we used publicly available ChIP-seq data of the neural transcriptional repressor RE1 silencing transcription factor (REST) from 15 different cell samples. We found 20 miRNAs, each of which shares a significant amount of predicted targets with REST. The set of predicted associations between these 20 miRNAs and the overlapping REST targets is enriched in known miRNA targets. Many of the detected miRNAs have functions related to neural identity and glioblastoma, which could be expected from their overlap in targets with REST. We propose that the integration of experimentally determined transcription factor binding sites with miRNA-target predictions provides functional information on miRNAs.