Miracle-dz/UniFAR-FTUs huggingface dataset:
The Homeobox Protein MSX2 Interacts with Tax Oncoproteins and Represses Their Transactivation Activity*[boxs]

Bovine leukemia virus (BLV) tax is an essential gene involved in the transcriptional activation of viral expression. Tax is also believed to be implicated in leukemogenesis because of its ability to immortalize primary cells in vitro. To gain insight into the molecular pathways mediating the activities of this important gene, we identified cellular proteins interacting with Tax. By means of a two-hybrid approach, we show that Tax specifically interacts with MSX2, a general repressor of gene expression. GST pull-down experiments and co-immunoprecipitation assays further confirmed binding specificity. Furthermore, the N-terminal residues 1-79 of MSX2 are required for binding, whereas the C-terminal residues 201-267 of MSX2 do not play a critical role. Whereas the oncogenic potential of Tax in primary cells was only slightly affected by overexpression of MSX2, the other function of Tax, namely LTR-dependent transcriptional activation, was inhibited by MSX2 in human HeLa and bovine B-lymphoblastoid (BL3) cell lines. This MSX2 repression function can be counteracted by overexpression of transcription factors CREB2 and RAP74. The Tax/MSX2 interplay thus results in repression of viral transcriptional activation possibly acting as a regulatory feedback loop. Importantly, this viral gene silencing is not strictly associated with a concomitant loss of Tax oncogenicity as measured by its ability to immortalize primary cells. And interestingly, MSX2 also interacts with and inhibits the transactivation function of the related Tax1 protein encoded by the Human T-cell leukemia virus type 1 (HTLV-1).
Exploring the Role of 5’ Alternative Splicing and of the 3’-Untranslated Region of Cathepsin B mRNA

Abstract The cysteine peptidase cathepsin B is responsible for connective tissue breakdown in several diseases. The pathological expression of cathepsin B may depend on the structure of its mRNA. We investigated the translational efficiency of the cathepsin B mRNA untranslated regions (UTRs) using fusion constructs to green fluorescent protein (GFP) and luciferase. Transfection of fusion constructs with GFP and luciferase containing the full-length 5'-UTR, the variant lacking exon 2, and that lacking exons 2 and 3 into mammalian cells, resulted in modulation of the biosynthetic rate of cathepsin B in a cell-specific manner. Constructs missing these exons were biosynthetically more efficient than the full-length counterpart. Luciferase was cloned upstream of the 3'-UTR, downstream of the 5'- UTR, or sandwiched between the 5' and the 3'-UTR. The UTRs of cathepsin B downregulated luciferase biosynthesis moderately when present individually, with the 3'-UTR being more efficient than the 5'-UTR, and downregulated it even more when present simultaneously. A truncated cathepsin B-GFP chimeric product derived from the 5'-UTR missing exons 2 and 3 induced cell death. The increased biosynthetic rate and abnormal trafficking of cathepsin B observed in pathologies such as cancer and osteoarthritis may depend on alternative splicing of pre-mRNA.
Finding the Constrained Delaunay Triangulation and Constrained Voronoi Diagram of a Simple Polygon in Linear Time

In this paper, we present an $\Theta (n)$ time worst-case deterministic algorithm for finding the constrained Delaunay triangulation and constrained Voronoi diagram of a simple n-sided polygon in the plane. Up to now, only an O(n log n) worst-case deterministic and an O(n) expected time bound have been shown, leaving an O(n) deterministic solution open to conjecture.
Using dynamical downscaling to simulate rainfall for East Coast Low events

East Coast Lows (ECLs) are intense low-pressure systems which occur on average several times each year off the eastern coast of Australia, in particular southern Queensland, New South Wales (NSW) and eastern Victoria. East Coast Lows will often intensify rapidly overnight making them one of the more dangerous weather systems to affect and damage the eastern coast of Australia each year. They are also a major source of water for the reservoirs serving coastal communities and ECL events were identified as being responsible for most of the high inflow days in the NSW coastal catchments. In this study, four East Coast Low events, covering the various ECL categories, are simulated using the Weather Research and Forecasting (WRF) model in order to assess the model’s ability to capture the ECL events. By choosing various combinations of two Planetary Boundary Layer (PBL) schemes, two Cumulus (Cu) schemes, three microphysics (mp) schemes and three radiation (ra) schemes, a 36 member multi-physics ensemble is created and evaluated against observations. The uncertainties among the 36 ensemble members are analysed, rainfall probability assessment undertaken and the best estimation of the simulated rainfall are investigated. The results suggest that the Betts-Miller-Janjic cumulus scheme and the Yonsei University planetary boundary layer scheme can be chosen with some robustness to simulate rainfall pattern and the intensity and position of rainfall centres. Results further indicate that the selection of the cumulus scheme options has the largest impact on model performance during the more intensive rainfall events. The conclusions from the study can be applied to better estimate rainfall amount and its distribution from dynamical downscaling of climate change projections.
Development of finger-localization capacity in school children.

The ability to localize, either by pointing or naming, the fingers of one's own hands or those of another person is a perceptual skill of some clinical interest because impairment in the ability is related to the presence of cerebral injury or disease in both adults and children. "Finger agnosia" as a consequence of cerebral pathology was first described by Gerstmann (5) in 1924. Further study by him as well as other workers1 established the symptomatic significance of this rather distinctive behavioral deficit. Isolated impairment in finger-localization ability or, to use a term introduced by Strauss and Werner (6), in the appreciation of the "finger schema," is not a frequent finding in adult patients with cerebral disease. This is not altogether surprising when it is realized that the responsible lesion is almost invariably found to be in the dominant cerebral hemisphere. A frequent consequence of such a lesion is, of course, an aphasic disorder that is likely to interfere with the assessment of finger-localizing skill, a task which by its very nature involves some degree of symbol-understanding or symbolic response. Moreover, if a patient with gross sensory disturbances or profound impairment of the body-image is unable to localize his fingers, the deficit is not designated as a "finger-agnosia" because of the more basic disability. However, even when these factors are discounted, defective fingerlocalization, at least as conventionally measured, seems to be rather infrequently encountered in brain-injured adults. In contrast to the findings with adults, a significant proportion of braininjured and defective children appear to show impairment in finger-localization when their performances are compared with those of normal children of similar mental age. Thus, Benton, Hutcheon and Seymour (2) found in a preliminary study that four subjects (17 per cent) in a group of 23 1 See Critchley (4) for a review of the clinical literature since the publication of Gerstmann's classic paper.
Quality of work, well-being, and intended early retirement of older employees: baseline results from the SHARE Study.

BACKGROUND Given the challenge of a high proportion of older employees who retire early from work we analyse associations of indicators of a poor psychosocial quality of work with intended premature departure from work in a large sample of older male and female employees in 10 European countries. METHODS Baseline data from the 'Survey of Health, Ageing and Retirement in Europe' (SHARE) were obtained from 3523 men and 3318 women in 10 European countries. Data on intended early retirement, four measures of well-being (self-rated health, depressive symptoms, general symptom load, and quality of life), and quality of work (effort-reward imbalance; low control at work) were obtained from structured interviews and questionnaires. Country-specific and total samples are analysed, using logistic regression analysis. RESULTS Poor quality of work is significantly associated with intended early retirement. After adjustment for well-being odds ratios (OR) of effort-reward imbalance [OR 1.72 (1.43-2.08)] and low control at work [OR 1.51 (1.27-1.80)] on intended early retirement are observed. Poor quality of work and reduced well-being are independently associated with the intention to retire from work. CONCLUSION The consistent association of a poor psychosocial quality of work with intended early retirement among older employees across all European countries under study calls for improved investments into better quality of work, in particular increased control and an appropriate balance between efforts spent and rewards received at work.
New Steiglitz-McBride adaptive lattice notch filters

Two novel adaptive notch filters are presented. The updating algorithms are based on the Steiglitz-McBride error criterion minimization and the basic realizations of the notch filters are all-pass based lattice filters. The proposed realizations represent an extension of a previous ad-hoc scheme for adaptive notch filtering and avoid finding the roots of a high order polynomial to obtain the unknown frequencies of interest. Since the structure is based on the lattice realization, suitable properties with finite length precision realizations can be expected. Computer simulations are included to verify the adaptive filter performance when compared with alternative realizations. Keywords— Frequency estimation, lattice notch filter, Steiglitz-McBride method.
High-performance Implementation of Matrix-free High-order Discontinuous Galerkin Methods

Achieving a substantial part of peak performance on todays and future high-performance computing systems is a major challenge for simulation codes. In this paper we address this question in the context of the numerical solution of partial differential equations with finite element methods, in particular the discontinuous Galerkin method applied to a convection-diffusion-reaction model problem. Assuming tensor product structure of basis functions and quadrature on cuboid meshes in a matrix-free approach a substantial reduction in computational complexity can be achieved for operator application compared to a matrix-based implementation while at the same time enabling SIMD vectorization and the use of fused-multiply-add. Close to 60\% of peak performance are obtained for a full operator evaluation on a Xeon Haswell CPU with 16 cores and speedups of several hundred (with respect to matrix-based computation) are achieved for polynomial degree seven. Excellent weak scalability on a single node as well as the roofline model demonstrate that the algorithm is fully compute-bound with a high flop per byte ratio. Excellent scalability is also demonstrated on up to 6144 cores using message passing.
Transrectal ultrasound‐guided biopsy of prostate voxels identified as suspicious of malignancy on three‐dimensional 1H MR spectroscopic imaging in patients with abnormal digital rectal examination or raised prostate specific antigen level of 4–10 ng/ml

Results of the evaluation of transrectal ultrasound (TRUS) guided needle biopsy of voxels identified as suspicious of malignancy on magnetic resonance spectroscopic imaging (MRSI) in a large cohort of men (n = 83) with abnormal digital rectal examination (DRE) [prostate specific antigen (PSA) 0–4 ng/ml] or PSA less than 10 ng/ml, are reported. Three‐dimensional 1H MRSI was carried out at 1.5 T using a pelvic‐phased array coil in combination with an endorectal surface coil. Voxels were classified as suspicious of malignancy based on Cit/(Cho + Cr) metabolite ratio. TRUS‐guided biopsy of suspicious voxels was performed using the z‐ and x‐coordinates obtained from MR images and two to three cores were taken from the suspected site. A systematic sextant biopsy was also carried out. MRSI showed voxels suspicious of malignancy in 44 patients while biopsy revealed cancer in 11 patients (25%). Patients who were negative for malignancy on MRSI were also negative on biopsy. An overall sensitivity of 100%, specificity of 54%, negative predictive value of 100% and accuracy of 60% were obtained. The site of biopsy was confirmed (n = 20) as a hypo‐intense area on repeat MRI while repeat MRSI revealed high choline and low citrate. The overall success rate of MRI‐directed TRUS‐guided biopsy of 25% was higher compared with a 9% success rate achieved without MR guidance in another group of 120 patients. Our results indicate that TRUS‐guided biopsy of suspicious area identified as malignant from MRSI can be performed using the coordinates of the voxel derived from MR images. This increases the detection rate of prostate cancer in men with PSA level <10 ng/ml or abnormal DRE and also demonstrates the potential of MR in routine clinical practice. Copyright © 2006 John Wiley & Sons, Ltd.
Oosp1 encodes a novel mouse oocyte‐secreted protein

Summary: Oocyte‐somatic cell communication is necessary for normal ovarian function. However, the identities of the majority of oocyte‐secreted proteins remain unknown. A novel cDNA encoding mouse oocyte‐secreted protein 1 (OOSP1) was identified using a modified subtractive hybridization screen. The Oosp1 cDNA encodes a 202‐amino acid protein that contains a 21‐amino acid signal peptide sequence, 5 putative N‐linked glycosylation consensus sequences, and 6 cysteines that are predicted to form 3 disulfide bonds. OOSP1 shares amino acid identity with placental‐specific protein 1 (PLAC1), a secreted protein expressed in the placenta and the ectoplacental cone. The Oosp1 mRNA is approximately 1.0 kb and is present at high levels in the oocytes of adult ovaries and at lower levels in the spleen. The mouse Oosp1 gene is 5 exons, spans greater than 16.4 kb, and localizes to chromosome 19 at a position that shares synteny with human chromosome 11q12–11q13. The identification of OOSP1 as a new oocyte‐secreted protein permits future in vitro and in vivo functional analyses to define its role in ovarian folliculogenesis. genesis 31:105–110, 2001. © 2001 Wiley‐Liss, Inc.
Resorptive Response of rhBMP2 Simulating Infection in an Anterior Lumbar Interbody Fusion With a Femoral Ring

RhBMP-2 has been available for general use since July of 2002. No literature regarding its use with femoral ring allografts exists. This case demonstrates how a resorptive effect of rhBMP-2 with a femoral ring allograft on host bone at the interbody fusion site can easily be confused with infection. Spine surgeons should be aware of this effect to avoid unnecessary antibiotic use or additional surgery.
Structural model of human GAD65: Prediction and interpretation of biochemical and immunogenic features

The 65 kDa human isoform of glutamate decarboxylase, GAD65, plays a central role in neurotransmission in higher vertebrates and is a typical autoantigen in several human autoimmune diseases, such as insulin‐dependent diabetes mellitus (IDDM), Stiff‐man syndrome and autoimmune polyendocrine syndrome type I. In autoimmune diabetes, an attack of inflammatory cells to endocrine pancreatic β‐cells leads to their complete destruction, eventually resulting in the inability to produce sufficient insulin for the body's requirements. Even though the etiology of β‐cell destruction is still a matter of debate, the role and antigenic potency of GAD65 are widely recognized. Herein a model of GAD65 is presented, which is based on the recently solved crystal structures of mammalian DOPA decarboxylase and of bacterial glutamate decarboxylase. The model provides for the first time a detailed and accurate structure of the GAD65 subunit (all three domains) and of its dimeric quaternary assembly. It reveals the structural basis for specific antibody recognition to GAD65 as opposed to GAD67, the other human isoform, which shares 81% sequence similarity with GAD65 and is much less antigenic. Literature data on monoclonal antibody binding are perfectly consistent with the detailed features of the model, which allows explanation of several findings on GAD65 immunogenicity. Importantly, by analyzing the active site, we identified the residues most likely involved in catalysis and substrate recognition, paving the way for rational mutagenesis studies of the GAD65 reaction mechanism, specificity and inhibition. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Breaking the Curse of Dimensionality, Or How to Use SVD in Many Dimensions

For $d$-dimensional tensors with possibly large $d>3$, an hierarchical data structure, called the Tree-Tucker format, is presented as an alternative to the canonical decomposition. It has asymptotically the same (and often even smaller) number of representation parameters and viable stability properties. The approach involves a recursive construction described by a tree with the leafs corresponding to the Tucker decompositions of three-dimensional tensors, and is based on a sequence of SVDs for the recursively obtained unfolding matrices and on the auxiliary dimensions added to the initial “spatial” dimensions. It is shown how this format can be applied to the problem of multidimensional convolution. Convincing numerical examples are given.
Multioperand Parallel Decimal Adder: A Mixed Binary and BCD Approach

Decimal arithmetic has been revived in recent years due to the large amount of data in commercial applications. We consider the problem of multioperand parallel decimal addition with an approach that uses binary arithmetic, suggested by the adoption of binary-coded decimal (BCD) numbers. This involves corrections in order to obtain the BCD result or a binary-to-decimal (BD) conversion. We adopt the latter approach, which is particularly efficient for a large number of addends. Conversion requires a relatively small area and can afford fast operation. The BD conversion moreover allows an easy alignment of the sums of adjacent columns. We treat the design of BCD digit adders using fast carry-free adders and the conversion problem through a known parallel scheme using elementary conversion cells. Spreadsheets have been developed for adding several BCD digits and for simulating the BD conversion as a design tool.
A novel tuning approach for offset-free MPC

Since the beginnings in the chemical and process industry, model based predictive control strategies have become widely accepted. Often mentioned success factors for MPC are the use of optimization based on a plant model, the consideration of constraints, and an intuitive tuning. Indeed, if a nominal plant and overall objective are known, the tuning can become straightforward. However, as soon as disturbances have to be taken into account, the tuning effort increases and becomes less intuitive. Against this background, a novel strategy to address the issues with unknown disturbances is proposed. The idea is to separate the nominal tuning process and extend the control by an outer loop, which ensures offset-free control. The inner, nominal loop decouples the system and essentially leads to a first order response. This inner loop addresses the performance targets in the nominal case, and the outer loop provides offset-free control in case of unknown disturbances. The outer loop consists of feedback controllers adapting the reference, which due to the decoupling can be tuned by known guidelines. The proposed strategy is presented and evaluated using a simulated case study.
Multi-coupled-resonator dual-band bandpass microstrip filters with non-resonating nodes

This paper reports the application of non-resonating nodes to develop high-selectivity dual-passband microstrip filters. To this aim, these nodes are used as cross-coupling paths to increase the inter-resonator signal interactions. Thus, several transmission zeros can be created under signal-interference principles. Two alternative implementations for the non-resonating node, suitable for planar technologies, are shown. Moreover, they are validated through two different 1.1/1.4-GHz high-order dual-band bandpass filter examples designed at the coupling-matrix level. Simulation and measurement results of their associated manufactured proof-of-concept microstrip prototypes are also provided.
The study of the standards architecture and the standards attributes based on EMC standards and TEMPEST standards in computer system

Electromagnetic leakiness is so severe that reveal possibly the information contained in the signals with emissions. The standards on emission levels are classified into the EMC standards the TEMPEST standards. The paper discusses the standards architecture and the standards attributes based on the EMC standards and the TEMPEST standards in computer system. It presents the standards running at the same time should be serializability. The serializable standard means no conflicts on the specification of standards each other and so on. Every standard has a life cycle. It should be established and published on opportune moment. The architecture of standard exists so that can be named in nomenclature and demonstrated with systematical thinking approach. The research on the features of standards promotes the development of standards. The paper also reports the development of TEMPEST standards consistent with TEMPEST theories and products with analyzing of categorical data.
TGF‐β1 up‐regulates connexin43 expression: A potential mechanism for human trophoblast cell differentiation

Connexin43 (Cx43)‐mediated gap junctional intercellular communication (GJIC) are required for human trophoblast differentiation. To date, whether Cx43 mediates TGF‐β1‐induced trophoblast differentiation has not been determined. We showed that treatment with TGF‐β1 increased Cx43 expression and GJIC in HTR‐8/SVneo human trophoblast cells. In addition, Smad and ERK1/2 signaling pathways were involved in TGF‐β1‐induced up‐regulation of Cx43. Moreover, TGF‐β1 increased the expression of the syncytiotrophoblast marker, β‐hCG. Importantly, knockdown of Cx43 abolished the TGF‐β1‐induced up‐regulation of β‐hCG. Furthermore, overexpression of Cx43 up‐regulated β‐hCG expression. These results provide evidence that Cx43 and GJIC activity are up‐regulated by TGF‐β1 in human trophoblast cells, which subsequently contributes to TGF‐β1‐induced trophoblast differentiation. J. Cell. Physiol. 230: 1558–1566, 2015. © 2015 Wiley Periodicals, Inc., A Wiley Company
Multi-modal impedance spectroscopy device for simultaneous measurement of electrical and mechanical properties of cells

We demonstrate a novel microfluidic device based on electrical impedance spectroscopy (EIS) which independently measures the electrical properties of cells and simultaneously estimates their mechanical properties by measuring transit times across a mechanical constriction. The device also allows electrically probing the effect of mechanical squeezing on the cell. Compared to conventional EIS techniques that measures the electrical impedance of cells solely across a constriction, the proposed technique offers more versatility and enables multi-modal analysis of cellular properties.
A Method for Minimization of Quasidifferentiable Functions

In this paper, we propose a new method for the unconstrained minimization of a function presented as a difference of two convex functions. This method is based on continuous approximations to the Demyanov-Rubinov quasidifferential. First, a terminating algorithm for the computation of a descent direction of the objective function is described. Then we present a minimization algorithm and study its convergence. An implementable version of this algorithm is discussed. Finally, we report the results of preliminary numerical experiments.