Miracle-dz/UniFAR-FTUs huggingface dataset:
SNAP-23 Is Not Cleaved by Botulinum Neurotoxin E and Can Replace SNAP-25 in the Process of Insulin Secretion*

The synaptosomal-associated protein of 25 kDa (SNAP-25) is expressed in neurons and endocrine cells. It has been shown to play an important role in the release mechanism of neurotransmitters and peptide hormones, including insulin. Thus, when insulin-secreting cells are permeabilized and treated with botulinum neurotoxin E (BoNT/E), SNAP-25 is hydrolyzed, and insulin secretion is inhibited. Recently SNAP-23, a more generally expressed isoform of SNAP-25, has been described. The functional role of SNAP-23 has not been investigated to date. It is now shown that SNAP-23 is resistant to cleavage by BoNT/E. It was therefore possible to test whether transfection of HIT (transformed pancreatic B-) cells with SNAP-23 reconstitutes insulin release from BoNT/E treated cells, in which SNAP-25 is inactivated by the toxin. The results show that SNAP-23 is able to replace SNAP-25 when it is overexpressed. While these results demonstrate that SNAP-23 is a functional homologue of SNAP-25, able to function in regulated exocytosis, they indicate that SNAP-23 may be inefficient in this process. This suggests that both isoforms may have their own specific binding partners and discrete, albeit mechanistically similar, functional roles within the cell.
Kernel Learning of Histogram of Local Gabor Phase Patterns for Face Recognition

This paper proposes a new face recognition method, named kernel learning of histogram of local Gabor phase pattern (K-HLGPP), which is based on Daugman's method for iris recognition and the local XOR pattern (LXP) operator. Unlike traditional Gabor usage exploiting the magnitude part in face recognition, we encode the Gabor phase information for face classification by the quadrant bit coding (QBC) method. Two schemes are proposed for face recognition. One is based on the nearest-neighbor classifier with chi-square as the similarity measurement, and the other makes kernel discriminant analysis for HLGPP (K-HLGPP) using histogram intersection and Gaussian-weighted chi-square kernels. The comparative experiments show that K-HLGPP achieves a higher recognition rate than other well-known face recognition systems on the large-scale standard FERET, FERET200, and CAS-PEAL-R1 databases.
Treadmill Pre-Training Ameliorates Brain Edema in Ischemic Stroke via Down-Regulation of Aquaporin-4: An MRI Study in Rats

Objective Treadmill pre-training can ameliorate blood brain barrier (BBB) dysfunction in ischemia-reperfusion injury, however, its role in ischemic brain edema remains unclear. This study assessed the neuroprotective effects induced by treadmill pre-training, particularly on brain edema in transient middle cerebral artery occluded model. Methods Transient middle cerebral artery occlusion to induce stroke was performed on rats after 2 weeks of treadmill pre-training. Magnetic resonance imaging (MRI) was used to evaluate the dynamic impairment of cerebral edema after ischemia-reperfusion injury. In addition, measurements of wet and dry brain weight, Evans Blue assay and Garcia scores were performed to investigate the cerebral water content, BBB permeability and neurologic deficit, respectively. Moreover, during ischemia-reperfusion injury, the expression of Aquaporin 4 (AQP4) was detected using immunofluorescence and Western bloting analyses. Results Treadmill pre-training improved the relative apparent diffusion coefficient (rADC) loss in the ipsilateral cortex and striatum at 1 hour and 2.5 hours after cerebral ischemia. In the treadmill pre-training group, T2W1 values of the ipsilateral cortex and striatum increased less at 7.5 hours, 1 day, and 2 days after stroke while the brain water content decreased at 2 days after ischemia. Regarding the BBB permeability, the semi-quantitative amount of contrast agent leakage of treadmill pre-training group significantly decreased. Less Evans Blue exudation was also observed in treadmill pre-training group at 2 days after stroke. In addition, treadmill pre-training mitigated the Garcia score deficits at 2 days after stroke. Immunofluorescence staining and Western blotting results showed a significant decrease in the expression of AQP4 after treadmill ischemia following pre-training. Conclusions Treadmill pre-training may reduce cerebral edema and BBB dysfunction during cerebral ischemia/reperfusion injury via the down-regulation of AQP4.
Extended Version of “ Expectation propagation for approximate inference in dynamic Bayesian networks ”

We consider inference in general dynamic Bayesian networks. We are especially interested in models in which exact inference becomes intractable, as, for example, in switching linear dynamical systems. We introduce expectation propagation as a straightforward extension of Pearl’s exact belief propagation. Expectation propagation, is a greedy algorithm, converges in many practical cases, but not always. Our goal is therefore to derive a message propagation scheme that can be guaranteed to converge. Following Minka, we therefore first derive a Bethe-free energy like functional, the fixed points of which correspond to fixed points of expectation propagation. We turn this primal objective into a dual objective in terms of messages or Lagrange multipliers. Approximate inference boils down to a saddle-point problem: maximization with respect to the difference between forward and backward messages, minimization with respect to the sum of the forward and backward messages. We derive several variants, ranging from a double-loop algorithm that guarantees convergence to the saddle point to a damped version of “standard” expectation propagation. We discuss implications for approximate inference in general, treestructured or even loopy, Bayesian networks. This technical report formed the basis of [12]: @inproceedings{Heskes_Zoeter_UAI2002, AUTHOR = "Heskes, T. and Zoeter, O. ", YEAR = 2002, TITLE = "Expectation propagation for approximate inference in dynamic {B}ayesian networks", BOOKTITLE = "Proceedings UAI-2002", EDITOR = "Darwiche, A. and Friedman, N. ", PAGES = "216--233", URL = "ftp://ftp.snn. kun.nl/pub/snn/pub/reports/Heskes.uai2002. ps.gz"} It is, however, not fully compatible. I tried to update it backwardly, but may not have completely succeeded. If possible, please refer to the published proceedings paper.
Models and Techniques for Network Tomography

A new approach to network tomography is pre- sented. This technique is not only useful for assessing the \health" of the network, but also useful for developing ad- vanced congestion control algorithms. The approach relies on sending data packets and receiving acknowledgments. Based on the acknowledgments, the state of the network along the path between the source and destination is de- termined. This work presents a framework for assessing the state, while it is expected that future work will focus on issues such as determining what the normal state of the network is and combining information about the state along several paths into a picture of the entire network.
Spirituality promotes better health outcomes and lowers anxiety about aging: The importance of spiritual dimensions for baby boomers as they enter older adulthood

ABSTRACT Baby boomers present unique challenges to aged care service provision. Like previous generations, baby boomers will face challenges of ageing. Spirituality in later life, understood largely as meaning in life, is crucial to well-being. Little has been studied about this dimension of ageing for baby boomers. This mixed methods study used survey and focus groups methods to investigate spirituality in a sample of baby boomers (N = 143). Participants comprised staff, children of adults in care, and Uniting Church congregational members. We examined associations between physical and mental health, and ageing anxiety with spirituality and whether baby boomer spirituality buffered the impact of negative life events. Focus groups revealed fears of future frailty, loss, and fears of dementia. Religious affiliation in study was lower, yet spirituality was important, even with those without religious affiliation. Closeness of association of staff with older people in their care seemed to account for lower levels of fear of older people amongst staff, but higher fears of future loss compared with the other groups. Higher levels of spirituality were related to better mental and physical health and lower anxiety about and fear of ageing, and buffered the impact of negative life events where they occurred.
Disruptionof Cell Polarity by Enteropathogenic Escherichia coli EnablesBasolateral Membrane Proteins To Migrate Apically and ToPotentiate PhysiologicalConsequences

ABSTRACT Enteropathogenic Escherichia coli (EPEC) disrupts the structure and barrier function of host intestinal epithelial tight junctions (TJs). The impact of EPEC on TJ “fence function,” i.e., maintenance of cell polarity, has not been investigated. In polarized cells, proteins such as β1-integrin and Na+/K+ ATPase are restricted to basolateral (BL) membranes. The outer membrane EPEC protein intimin possesses binding sites for the EPEC translocated intimin receptor (Tir) and β1-integrin. Restriction ofβ 1-integrin to BL domains, however, precludes opportunity for interaction. We hypothesize that EPEC perturbs TJ fence function and frees BL proteins such as β1-integrin to migrate to apical (AP) membranes of host cells, thus allowing interactions with bacterial adhesins such as intimin. The aim of this study was to determine whether EPEC alters the polar distribution of BL proteins, in particular β1-integrin, and if such redistribution contributes to pathogenesis. Human intestinal epithelial T84 cells and EPEC strain E2348/69 were used. Selective biotinylation of AP or BL membrane proteins and confocal microscopy showed the presence of β1-integrin and Na+/K+ ATPase on the AP membrane following infection. β1-Integrin antibody afforded no protection against the initial EPEC-induced decrease in transepithelial electrical resistance (TER) but halted the progressive decrease at later time points. While the effects of EPEC on TJ barrier and fence function were Tir dependent, disruption of cell polarity by calcium chelation allowed a tir mutant to be nearly as effective as wild-type EPEC. In contrast, deletion of espD, which renders the type III secretory system ineffective, had no effect on TER even after calcium chelation, suggesting that the putativeβ 1-integrin-intimin interaction serves to provide intimate contact, like that of Tir and intimin, making translocation of effector molecules more efficient. We conclude that the initial alterations of TJ barrier and fence function by EPEC are Tir dependent but that later disruption of cell polarity and accessibility of EPEC to BL membrane proteins, such asβ 1-integrin, potentiates the physiological perturbations.
A buffer replacement algorithm exploiting multi-chip parallelism in solid state disks

Solid State Disks (SSDs) are superior to magnetic disks from a performance point of view due to the favorable features of NAND flash memory. Furthermore, thanks to improvement on flash memory density and adopting a multi-chip architecture, SSDs replace magnetic disks rapidly. Most previous studies have been conducted for enhancing the performance of SSDs, but these studies have been worked on the assumption that the operation unit of a host interface is the same as the operation unit of NAND flash memory, where it is needless to give consideration to partially-filled pages. In this paper, we analyze the overhead caused by the partially-filled pages, and propose a buffer replacement algorithm exploiting multi-chip parallelism to enhance the write performance. Our simulation results show that the proposed algorithm improves the write performance by up to 30% over existing approaches.
In vitro engineering of heart muscle: artificial myocardial tissue.

INTRODUCTION Myocardial infarction followed by heart failure represents one of the major causes of morbidity and mortality, particularly in industrialized countries. Engineering and subsequent transplantation of contractile artificial myocardial tissue and, consequently, the replacement of ischemic and infarcted areas of the heart provides a potential therapeutic alternative to whole organ transplantation. METHODS Artificial myocardial tissue samples were engineered by seeding neonatal rat cardiomyocytes with a commercially available 3-dimensional collagen matrix. The cellular engraftment within the artificial myocardial tissues was examined microscopically. Force development was analyzed in spontaneously beating artificial myocardial tissues, after stretching, and after pharmacologic stimulation. Moreover, electrocardiograms were recorded. RESULTS Artificial myocardial tissues showed continuous, rhythmic, and synchronized contractions for up to 13 weeks. Embedded cardiomyocytes were distributed equally within the 3-dimensional matrix. Application of Ca(2+) and epinephrine, as well as electrical stimulation or stretching, resulted in enhanced force development. Electrocardiographic recording was possible on spontaneously beating artificial myocardial tissue samples and revealed physiologic patterns. CONCLUSIONS Using a clinically well-established collagen matrix, contractile myocardial tissue can be engineered in vitro successfully. Mechanical and biologic properties of artificial myocardial tissue resemble native cardiac tissue. Use of artificial myocardial tissues might be a promising approach to reconstitute degenerated or failing cardiac tissue in many disease states and therefore provide a reasonable alternative to whole organ transplantation.
Cache misses and energy-dissipation results for JPEG-2000 filtering

After its establishment as a new standard for still-image coding, JPEG-2000 is now in the stage of the exploration for efficient implementation in real-life systems. In this paper we focus on the implementation of the frontend part, i.e. the filtering processes performed by the discrete wavelet transform (DWT). The target platforms are programmable processors, since the modern evolution of their design positions them as good alternatives for efficient, flexible and fast time-to-market designs. As a result, to facilitate the incorporation of the new standard in such designs, we present experimental and theoretical results for the data-related cache misses that occur during the DWT, since it has been shown that these comprise the main bottleneck in this type of application. In addition to this, we also rank the presented designs with respect to the power efficiency, under a high-level power estimation scheme. To validate our models, apart from the simulation results, indicative experimental results are presented in superscalar and VLIW real-life architectures.
Monomer DJ-1 and Its N-Terminal Sequence Are Necessary for Mitochondrial Localization of DJ-1 Mutants

DJ-1 is a novel oncogene and also a causative gene for familial Parkinson’s disease (park7). DJ-1 has multiple functions that include transcriptional regulation, anti-oxidative reaction and chaperone and mitochondrial regulation. Mitochondrial dysfunction is observed in DJ-1-knockout mice and fry, and mitochondrial DJ-1 is more protective against oxidative stress-induced cell death. Although translocation of DJ-1 into mitochondria is enhanced by oxidative stress that leads to oxidation of cysteine 106 (C106) of DJ-1, the characteristics of mitochondrial DJ-1 and the mechanism by which DJ-1 is translocated into mitochondria are poorly understood. In this study, immunostaining, co-immunoprecipitation, cell fractionation and pull-down experiments showed that mutants of glutamine 18 (E18) DJ-1 are localized in mitochondria and do not make homodimers. Likewise, DJ-1 with mutations of two cysteines located in the dimer interface, C46S and C53A, and pathogenic mutants, M26I and L166P DJ-1, were found to be localized in mitochondria and not to make homodimers. Mutant DJ-1 harboring both E18A and C106S, in which C106 is not oxidized, was also localized in mitochondria, indicating that oxidation of C106 is important but not essential for mitochondrial localization of DJ-1. It should be noted that E18A DJ-1 was translocated from mitochondria to the cytoplasm when mitochondrial membrane potential was reduced by treatment of cells with CCCP, an uncoupler of the oxidative phosphorylation system in mitochondria. Furthermore, deletion or substitution of the N-terminal 12 amino acids in DJ-1 resulted in re-localization of E18A, M26I and L166P DJ-1 from mitochondria into the cytoplasm. These findings suggest that a monomer and the N-terminal 12 amino acids are necessary for mitochondrial localization of DJ-1 mutants and that conformation change induced by C106 oxidation or by E18 mutation leads to translocation of DJ-1 into mitochondria.
Fast Encoding Algorithm for Vector Quantization

In this paper, we present a new and fast encoding algorithm (FEA) for vector quantization. The magnitude (sum of the components of a vector) feature of the vectors is used in this algorithm to improve the efficiency of searching. Sorting of the magnitude values enhances the searching. As the values are sorted, the searching can be terminated in advance to reduce the time needed to locate the representative code vector. For a codebook of size M (M generally being 128/256/512/1024), M distortion calculations are performed. But in the proposed method, only 11 distortion computations are done irrespective of the size of the codebook. The time taken to locate the representative codevector is significantly reduced from 0.77 seconds to 0.07 seconds on an average. The experiments were carried over with codebooks of sizes 128, 256, 512 and 1024 with the standard images Lena, Boats, Cameraman and Bridge.
Revealing the density of encoded functions in a viral RNA

Significance Single-stranded RNA viruses self-assemble protective protein containers around their cognate genomes rapidly and efficiently at low concentrations. RNA encapsidation in vivo occurs preferentially with the cognate genome, in contrast to many in vitro reassembly experiments. We describe in molecular detail how this specificity and efficiency is accomplished using multiple contacts between coat proteins and dispersed packaging signals in the viral genome. The sequences and relative positioning of the packaging signals are important for this mechanism, creating a strong evolutionary constraint. Packaging signals overlap untranslated and coding regions ensuring assembly is in competition with other functions of the genome. Disrupting these contacts has deleterious consequences for capsid assembly identifying a novel antiviral drug target. We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.
A comparison of audio recordings and therapist's process notes in child and adolescent psychoanalytic psychotherapy

Therapistsʼ process notes - written descriptions of a session produced shortly afterwards from memory - hold a significant role in child and adolescent psychoanalytic psychotherapy. They are central in training, in supervision, and in developing oneʼs understanding through selfsupervision and forms of psychotherapy research. This thesis examines such process notes through a comparison with audio recordings of the same sessions. In so doing, it aims to generate theory that might illuminate the causes of significantly patterned discrepancies between the notes and recordings, in order to understand more about the processes at work in psychoanalytic psychotherapy and to explore the nature of process notes, their values and limitations. The literature searches conducted revealed limited relevant studies. All identified studies that compare process notes with recordings of sessions seek to quantify the differences between the two forms of recording. Unlike these, this thesis explores the meaning of the differences between process notes and recordings through qualitative data analysis. Using psychoanalytically informed grounded theory, in total nine sets of process notes and recordings from three different psychoanalytic psychotherapists are analysed. The analysis identifies eight core categories of findings. Initial theories are developed from these categories, most significantly concerning the role and influence of a ʻcore transference dynamicʼ between therapist and patient. Further theory is developed on the nature and function of process notes as a means for the therapistʼs conscious and unconscious processing of the session, as well as on the nature of the influence of the relationships – both internal and external – within which they are written. In the light of the findings, a proposal is made for a new approach for learning about the patient and clinical work, ʻthe comparison methodʼ (supervision involving a comparison of process notes and recordings), and, in particular, for its inclusion within the training of psychoanalytic psychotherapists. Further recommendations for research are also made.
High Capacity Neural Networks for Familiarity Discrimination

This paper presents two new novelty discrimination models for uncorrelated patterns based on neural modelling. The first model uses a single neuron with Hebbian learning and works well when the number of memorised patterns is less than 0.046N (N, the number of inputs). The second model is based on checking the value of the energy function of a Hopfield network. By sacrificing the ability to extract patterns - not needed for familiarity detection - an amazing jump from the normal capacity for retrieval of 0.145N to a capacity for novelty discrimination of 0.023N2 is achieved. In addition, both models give some insight on the effect of deja vu, since there is always a very small probability of detecting novel patterns as familiar.