Miracle-dz/UniFAR-FTUs huggingface dataset:
Antagonism between Nur77 and glucocorticoid receptor for control of transcription

Two important functions of glucocorticoids (Gc), namely, suppression of immune system function and feedback repression of the hypothalamo-pituitary-adrenal (HPA) axis, are mediated through repression of gene transcription. Previous studies have indicated that this repression is exerted in part through antagonism between the glucocorticoid receptors (GR) and the AP-1 family of transcription factors. However, this mechanism could not account for repression of the pro-opiomelanocortin (POMC) gene, an important regulator of the HPA axis. Our recent identification of the orphan nuclear receptor Nur77 as a mediator of CRH induction of POMC transcription led us, in the present work, to show that Gc antagonize this positive signal at two levels. First, Gc partly blunt the CRH induction of Nur77 mRNA, and second, they antagonize Nur77-dependent transcription. GR repression is exerted by antagonism of Nur77 action on the NurRE element of the POMC gene. Gc antagonism of NurRE activity was observed in response to physiological stimuli in both endocrine (CRH induction of POMC) and lymphoid (T-cell receptor activation) cells. In transfection experiments, transcriptional activation by Nur77 and the repressor activity of liganded GR titrated each other on their cognate DNA target. In vitro binding experiments as well as mutation analysis of GR suggest that the mechanism of GR antagonism of Nur77 is very similar to that of the antagonism between GR and AP-1. The convergence of positive signals mediated by Nur77 (and also probably by related family members) and negative signals exerted by GR appears to be a general mechanism for control of transcription, since it is active in both endocrine and lymphoid cells.
Using 2D finite element analysis in the calculation of current and force distributions for induction motors with broken bars

In this paper an ABC transient model of the three phase induction motor is developed that depends on self and mutual inductances calculation based on accurate finite element analysis (FEA). This model can represent both healthy and faulty motor conditions. The rotor broken bars faults are studied thoroughly including their effects on the rotor bar currents distribution, the forces exerted on the rotor bars, the motor speed and motor torque. It was observed that broken bar faults will cause fluctuations in the motor speed and torque. It was found that the non-uniform distribution of the rotor bar currents will lead to non-uniform radial forces affecting the bars. This will increase the mechanical stresses on the rotor shaft.
Content based Video Retrieval: A Survey

are a powerful and communicative media that can capture and present information. The rapidly expanding digital video information has motivated growth of new technologies for effective browsing, annotating and retrieval of video data. Content-based video retrieval has attracted wide research during the last 10 years. Users are more diverted to content based search rather than text based search. These lead to the process of selecting, indexing and ranking the database according to the human visual perception. This paper reviews the recent research in content based video retrieval system. This survey focusing on video structure analysis, like, shot boundary detection and key frame extraction, different feature extraction methods including SIFT, SURF, etc, similarity measure, video indexing, and video browsing. This system retrieves similar videos based on local feature descriptor called SURF (Speeded-Up Robust Feature). For image convolution SURF relies on integral images. In SURF we use Hessian matrix-based measure for the detector and a distribution-based descriptor. SURF can be computed and compared much faster with respect to repeatability, uniqueness and robustness. SURF is better than previous proposed methods as SIFT, PCA-SIFT, GLOH, etc. Finally the future scope in this system is specified.
Classical Mus musculus Igκ Enhancers Support Transcription but not High Level Somatic Hypermutation from a V-Lambda Promoter in Chicken DT40 Cells

Somatic hypermutation (SHM) of immunoglobulin genes is initiated by activation-induced cytidine deaminase (AID) in activated B cells. This process is strictly dependent on transcription. Hence, cis-acting transcriptional control elements have been proposed to target SHM to immunoglobulin loci. The Mus musculus Igκ locus is regulated by the intronic enhancer (iE/MAR) and the 3′ enhancer (3′E), and multiple studies using transgenic and knock-out approaches in mice and cell lines have reported somewhat contradictory results about the function of these enhancers in AID-mediated sequence diversification. Here we show that the M. musculus iE/MAR and 3′E elements are active solely as transcriptional enhancer when placed in the context of the IGL locus in Gallus gallus DT40 cells, but they are very inefficient in targeting AID-mediated mutation events to this locus. This suggests that either key components of the cis-regulatory targeting elements reside outside the murine Igκ transcriptional enhancer sequences, or that the targeting of AID activity to Ig loci occurs by largely species-specific mechanisms.
The refined topological vertex

We define a refined topological vertex which depends in addition on a parameter, which physically corresponds to extending the self-dual graviphoton field strength to a more general configuration. Using this refined topological vertex we compute, using geometric engineering, a two-parameter (equivariant) instanton expansion of gauge theories which reproduce the results of Nekrasov. The refined vertex is also expected to be related to Khovanov knot invariants.
Assessment of 3D inhomogeneous microstructure of highly alloyed aluminium foam via dual energy K-edge subtraction imaging

X-ray microtomography was used to evaluate the inhomogeneous characteristics of newly-developed Al–Zn–Mg foam. Using the synchrotron K-edge subtraction technique, a highly heterogeneous distribution of Zn was quantified three-dimensionally (3D) in the cell wall of as-cast foam. Time-resolved analysis of the concentration evolution revealed a tendency to a homogeneous Zn distribution as solution time prolonged. This was accompanied by a declined variation in hardness measurement. Other microstructural features after solution treatment, such as number and size distribution of micropores, were also characterised. By utilising various quenching rates, the inhomogeneities in microstructure and compression properties inside the foam were also clarified. Thus, element-sensitive tomography provides a novel solution for the 3D/4D analysis in the study of foams.
The primary pathway for lactate oxidation in Desulfovibrio vulgaris

The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species.
The Overtone Fiddle: an Actuated Acoustic Instrument

Overtone Fiddle is a new violin-family instrument that incorporates electronic sensors, integrated DSP, and physical actuation of the acoustic body. An embedded tactile sound transducer creates extra vibrations in the body of the Overtone Fiddle, allowing performer control and sensation via both traditional violin techniques, as well as extended playing techniques that incorporate shared man/machine control of the resulting sound. A magnetic pickup system is mounted to the end of the fiddle's fingerboard in order to detect the signals from the vibrating strings, deliberately not capturing vibrations from the full body of the instrument. This focused sensing approach allows less restrained use of DSP-generated feedback signals, as there is very little direct leakage from the actuator embedded in the body of the instrument back to the pickup.
Low Frequency of Germline TERT and MITF Mutations in Brazilian Melanoma-Prone Patients

Recent studies have reported rare germline mutations affecting the MITF gene, and the promoter of the TERT gene in melanoma families. Here we looked at the prevalence of these rare penetrant mutations in a series of 48 patients (either familial melanoma or multiple melanomas), all of them negative for CDKN2A and CDK4 mutations. A single mutation was detected in a multiple melanoma patient, who was a heterozygous carrier of the E318K MITF variant. However, this variant was also detected in 1 out of 125 controls. This preliminary data points to a low frequency of MITF and TERT mutations in this Brazilian group of melanoma-prone patients.
A hybrid method for real-time short-term predictions of traffic flows in urban areas

Short-term traffic forecasting is driven by an increasing need of new services for user information and new systems for dynamic control. Our research focuses on reproducing anticipated traffic conditions by means of statistical methods traditionally applied in artificial intelligence problems. Although we strongly believe that the effects of specific traffic events can only be predicted through transportation model based simulations in real-time, yet the fluctuations affecting the ordinary traffic conditions of a day-type can well be forecasted without.
Toll-like receptor 2 regulates the barrier function of human bronchial epithelial monolayers through atypical protein kinase C zeta, and an increase in expression of claudin-1

We investigated the role of Toll-like receptor (TLR) 2 in maintaining the integrity of the airway epithelial barrier using the human bronchial epithelial cell line Calu-3. Activation of TLR2 by its ligands, Pam3CysSK4 and Peptidoglycan showed a concentration dependent increase in epithelial barrier function, as measured by transepithelial electrical resistance (TEER). This was confirmed by a decrease in paracellular flux of fluorescein sodium. This TLR2 induced increase in TEER was significantly reduced by pretreatment with polyclonal anti-human TLR2-neutralizing antibody. TLR2 stimulation in Calu-3 cell monolayers resulted in an increased expression of the tight junction proteins claudin-1 and ZO-1, and a decreased expression of occludin, at both the mRNA and protein levels. A pseudosubstrate inhibitor to PKCζ significantly prevented the TLR2 mediated increase in barrier function. It also prevented the increase in claudin-1 in a concentration dependent manner up to 1 µM. TLR2 stimulation led to an increase in phosphorylation of atypical PKC ζ, which was prevented by the pseudosubstrate inhibitor in a concentration dependent manner. Taken together, our observations support a model whereby increased tight junction barrier function induced by activation of TLR2 occurs through increased expression of claudin-1, and through modulation of PKC ζ activity.
Design of multiple Gabor filters for texture segmentation

This paper presents a method for the design of multiple Gabor filters for segmenting multi-textured images. Although design methods for a single Gabor filter have been presented previously, the development of general multi-filter multi-texture design methods largely remains an open problem. Previous multi-filter design approaches required one filter per texture or were constrained to pairs of textures. Other approaches employed ad hoc banks of Gabor filters for texture segmentation, where the parameters of the constituent filters were restricted to fixed values and were not necessarily tuned for a specific texture-segmentation problem. The proposed method removes these restrictions on the number of filters and the number of textures. This offers the potential to improve the segmentation performance or to reduce the number of filters. Further, the development of the design method and mathematical models provide new insight into the design of multiple Gabor filters for texture segmentation. Results are presented that confirm the efficacy of our filter-design method and support underlying mathematical models.
Challenges in using an example-based MT system for a transnational digital government project

We describe ongoing efforts towards and challenges in using an Example-Based Machine Translation (EBMT) system in the context of a multinational, multi-university and multi-agency transnational digital government project. The project is aimed at applying information technology to the problem of collecting and sharing information securely in a multilingual context. We report on a number of issues encountered in obtaining and using language data for the EBMT system, discuss our current solutions, and briefly describe ongoing enhancements to the system to meet some of the technical and practical challenges posed by using this machine translation approach in the project domain.
Properties of the Schr̈odinger Theory of Electrons in Electromagnetic Fields

The Schr\"odinger theory of electrons in an external electromagnetic field can be described from the perspective of the individual electron via the `Quantal Newtonian' laws (or differential virial theorems). These laws are in terms of `classical' fields whose sources are quantal expectations of Hermitian operators taken with respect to the wave function. The laws reveal the following physics: (a) In addition to the external field, each electron experiences an internal field whose components are representative of a specific property of the system such as the correlations due to the Pauli exclusion principle and Coulomb repulsion, the electron density, kinetic effects, and an internal magnetic field component. (The response of the electron is described by the current density field.); (b) The scalar potential energy of an electron is the work done in a conservative field which is the sum of the internal and Lorentz fields. It is thus inherently related to the properties of the system. Its constituent property-related components are hence known. It is a known functional of the wave function; (c) As such the Hamiltonian is a functional of the wave function, thereby revealing the intrinsic self-consistent nature of the Schr\"odinger equation. This then provides a path for the determination of the exact wave function. (d) With the Schr\"odinger equation written in self-consistent form, the Hamiltonian now admits via the Lorentz field a new term that explicitly involves the external magnetic field. The new understandings are explicated for the stationary state case by application to a quantum dot in a magnetostatic field in both a ground and excited state. For the time-dependent case, the same states of the quantum dot in both a magnetostatic and a time-dependent electric field are considered.
Biological Feature Incorporated Alignment for Cross Species Analysis on Carbohydrate Binding Modules

Multiple sequence alignment is widely applied to discover core conserved regions among query sequences. However, the major deficiency is that alignment accuracy is extremely sensitive to primary sequence identity, which causes alignment of low identity sequences difficult. We propose a feature-integrated model called Feature-Incorporated Alignment (FIA) which integrates relevant biological characteristics including aromatic amino acids, hydrophilicity, β-stranded structure, and BLOSUM62 matrix to locate ligand-binding residue in carbohydrate binding modules (CBMs), a protein family with fairly low sequence identify but highly functional correlation. The results indicated that FIA can not only detect aromatic residues on the outer surface of structure, but also achieve better accuracy than ClustalW2 and DIALIGN-TX on entropy criterion in all three test datasets from CBMs. Computational analysis in CBMs can facilitate the discovery of crucial ligand-binding residues of carbohydrate-active enzymes.
Endoplasmic reticulum stress activates transglutaminase 2 leading to protein aggregation

Aberrant activation of transglutaminase 2 (TGase2) contributes to a variety of protein conformational disorders such as neurodegenerative diseases and age-related cataracts. The accumulation of improperly folded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR), which promotes either repair or degradation of the damaged proteins. Inadequate UPR results in protein aggregation that may contribute to the development of age-related degenerative diseases. TGase2 is a calcium-dependent enzyme that irreversibly modifies proteins by forming cross-linked protein aggregates. Intracellular TGase2 is activated by oxidative stress which generates large quantities of unfolded proteins. However, the relationship between TGase2 activity and UPR has not yet been established. In the present study, we demonstrated that ER stress activated TGase2 in various cell types. TGase2 activation was dependent on the ER stress-induced increase in the intracellular calcium ion concentration but not on the TGase2 protein expression level. Enzyme substrate analysis revealed that TGase2-mediated protein modification promoted protein aggregation concurrently with decreasing water solubility. Moreover, treatment with KCC009, a TGase2 inhibitor, abrogated ER stress-induced TGase2 activation and subsequent protein aggregation. However, TGase2 activation had no effect on ER stress-induced cell death. These results demonstrate that the accumulation of misfolded proteins activates TGase2, which further accelerates the formation of protein aggregates. Therefore, we suggest that inhibition of TGase2 may be a novel strategy by which to prevent the protein aggregation in age-related degenerative diseases.
Investigation of Tension-Compression Fatigue Behavior of a Unidirectional Metal Matrix Composite at Elevated Temperature.

Abstract : This study investigated the fatigue behavior in a unidirectional metal matrix composite under tension-compression loading conditions. Stress-strain responses, modulus and strain trends were monitored to characterize damage. Fractography and microscopy were used to characterize failure modes. Fatigue life curves were plotted base on different parameters such as stress and strain. Tension-compression fatigue life was shorter than the obtained under tension-tension fatigue cycling. Creep, observed in tension-tension. fatigue cycling, and the effects of the compressive load on the plastic zone around the crack tip explain shorter life under tension-compression fatigue loading.
Review of advanced methods for simulation output analysis

This paper reviews statistical methods for analyzing output data from computer simulations. First, it focuses on the estimation of steady-state system parameters. The estimation techniques include the replication/deletion approach, the regenerative method, the batch means method, and methods based on standardized time series. Second, it reviews recent statistical procedures to find the best system among a set of competing alternatives.
Bilingual Lexicon Construction from Comparable Corpora via Dependency Mapping

Bilingual lexicon construction (BLC) from comparable corpora is based on the idea that bilingual similar words tend to occur in similar contexts, usually of words. This, however, introduces noise and leads to low performance. This paper proposes a bilingual dependency mapping model for BLC which encodes a word’s context as a combination of its dependent words and their relationships. This combination can provide more reliable clues than mere context words for bilingual translation words. We further demonstrate that this kind of bilingual dependency mappings can be successfully generated and maximally exploited without human intervention. The experiments on BLC from English to Chinese show that, by mapping context words and their dependency relationships simultaneously when calculating the similarity between bilingual words, our approach significantly outperforms a state-of-the-art one by ~14 units in accuracy for frequently occurring noun pairs and similarly, though in a less degree, for nouns and verbs in a wide frequency range. This justifies the effectiveness of our dependency mapping model for BLC. TITLE AND ABSTRACT IN ANOTHER LANGUAGE, CHINESE 应用依存映射从可比较语料库中抽取双语词表 从可比较语料库中抽取双语词表的基本思想是,双语相似的词语出现在相同的语词上下文 中。 不过,这种方法引入了噪声,从而导致了低的抽取性能。 本文提出了一种用于双语词 表抽取的双语依存映射模型,在该模型中一个词语的上下文结合了依存词语及其依存关 系。 这种结合方法为双语词表构建提供了比单一的词语上下文更为可靠的信息。 我们还进 一步展示了在没有人工干预的情况下可以产生和利用这种双语依存关系。 从英文到中文的 双语词表构建实验表明,通过在计算双语词语相似度时同时映射词语及其依存关系,同目 前性能最好的系统相比,我们的方法显著提高了精度。 对于经常出现的名词,精度提高了 14个百分点;对于较大频率范围内的名词和动词,性能也提高了,尽管程度较小。 这说明 了依存映射模型对双语词表构建的有效性。
Integrative “Omics”-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses

Bacteria constantly face stress conditions and therefore mount specific responses to ensure adaptation and survival. Stress responses were believed to be predominantly regulated at the transcriptional level. In the phototrophic bacterium Rhodobacter sphaeroides the response to singlet oxygen is initiated by alternative sigma factors. Further adaptive mechanisms include post-transcriptional and post-translational events, which have to be considered to gain a deeper understanding of how sophisticated regulation networks operate. To address this issue, we integrated three layers of regulation: (1) total mRNA levels at different time-points revealed dynamics of the transcriptome, (2) mRNAs in polysome fractions reported on translational regulation (translatome), and (3) SILAC-based mass spectrometry was used to quantify protein abundances (proteome). The singlet oxygen stress response exhibited highly dynamic features regarding short-term effects and late adaptation, which could in part be assigned to the sigma factors RpoE and RpoH2 generating distinct expression kinetics of corresponding regulons. The occurrence of polar expression patterns of genes within stress-inducible operons pointed to an alternative of dynamic fine-tuning upon stress. In addition to transcriptional activation, we observed significant induction of genes at the post-transcriptional level (translatome), which identified new putative regulators and assigned genes of quorum sensing to the singlet oxygen stress response. Intriguingly, the SILAC approach explored the stress-dependent decline of photosynthetic proteins, but also identified 19 new open reading frames, which were partly validated by RNA-seq. We propose that comparative approaches as presented here will help to create multi-layered expression maps on the system level (“expressome”). Finally, intense mass spectrometry combined with RNA-seq might be the future tool of choice to re-annotate genomes in various organisms and will help to understand how they adapt to alternating conditions.