Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Proteomic Identification of MAZ as a Transcriptional Regulator of Muscle-Specific Genes in Skeletal and Cardiac Myocytes

ABSTRACT We identified a conserved sequence within the Muscle creatine kinase (MCK) promoter that is critical for high-level activity in skeletal and cardiac myocytes (MCK Promoter Element X [MPEX]). After selectively enriching for MPEX-binding factor(s) (MPEX-BFs), ICAT-based quantitative proteomics was used to identify MPEX-BF candidates, one of which was MAZ (Myc-associated zinc finger protein). MAZ transactivates the MCK promoter and binds the MPEX site in vitro, and chromatin immunoprecipitation analysis demonstrates enrichment of MAZ at the endogenous MCK promoter and other muscle gene promoters (Skeletal α-actin, Desmin, and α-Myosin heavy chain) in skeletal and cardiac myocytes. Consistent with its role in muscle gene transcription, MAZ transcripts and DNA-binding activity are upregulated during skeletal myocyte differentiation. Furthermore, MAZ was shown to bind numerous sequences (e.g., CTCCTCCC and CTCCACCC) that diverge from the GA box binding motif. Alternate motifs were identified in many muscle promoters, including Myogenin and MEF2C, and one motif was shown to be critical for Six4 promoter activity in both skeletal and cardiac myocytes. Interestingly, MAZ occupies and is able to transactivate the Six4 promoter in skeletal but not cardiac myocytes. Taken together, these findings are consistent with a previously unrecognized role for MAZ in muscle gene regulation.
A Simplified Adaptive Particle Swarm Optimization Algorithm

A new particle swarm optimization (PSO) algorithm is presented based on three methods of improvement in original PSO. First, the iteration formula of PSO is changed and simplified by removal of velocity parameter that is unnecessary during the course of evolution. Second, the dynamically decreasing inertia weight is employed to enhance the balance of global and local search of algorithm. Finally, the mutation operator is introduced to improve the search performance of algorithm. Experimental results show that the new algorithm not only outperforms standard PSO in terms of accuracy and convergence rate but also avoids effectively being trapped in local minima.
Abnormal brain structure in children with isolated clefts of the lip or palate.

OBJECTIVE To evaluate brain structure in a sample of children with isolated clefts of the lip and/or palate (ICLP). DESIGN Case-control study. SETTING Tertiary care center. PARTICIPANTS A large sample of 74 children aged 7 to 17 years with ICLP was compared with a healthy control group, matched by age and sex. MAIN EXPOSURE Isolated cleft lip and/or palate. OUTCOME MEASURES General measures of height and head circumference were obtained. Brain structure was evaluated using magnetic resonance imaging, generating both general and regional brain measures (volumes). RESULTS Height was significantly lower in the ICLP group (F = 4.83, P = .03). After controlling for this smaller body size, children with ICLP had abnormally small brains with both cerebrum (F = 4.47, P = .04) and cerebellum (F = 14.56, P <.001) volumes substantially decreased. Within the cerebrum, the frontal lobe was preferentially decreased (F = 7.22, P = .008) and subcortical nuclei were also substantially smaller (F = 4.18, P = .003). Tissue distribution of cortical gray matter and white matter within the cerebrum were abnormal in boys with ICLP (larger cortical volume, smaller volume of white matter) but proportional to controls in girls with ICLP. CONCLUSIONS Children with ICLP have abnormal brain structure, potentially due to abnormal brain development. The fact that the pattern of brain abnormalities in children with ICLP is dramatically different from the pattern of brain abnormalities seen in adults with ICLP suggests that brain growth and development trajectory is also abnormal in subjects with ICLP.
Multi-band antenna with enhanced gain for wireless applications

In this paper, a multi-band micro-strip patch antenna with uneven parallel slots and optimized gain is proposed. Two types of substrate such as air and FR4 are used in the design. A detail parametric study of the patch antenna are carried out with air substrate. Co-axial feeding is used for optimal antenna characteristics. Consequently air substrate is changed with FR4 substrate and microstrip line feeding is used for new design. This design shows the improvement of gain up to 6.9dB. This simulation is carried out by using HFSS.
The X-Ray-Radio Alignment in the z = 2.2 Radio Galaxy PKS 1138–262

We present high-resolution X-ray observations of the narrow-line radio galaxy PKS 1138-262 at z = 2.156 with the ACIS-S detector on the Chandra X-Ray Observatory. These observations show that the X-ray emission from 1138-262 is dominated by emission from the active galactic nucleus (AGN) with a 2-10 keV luminosity of 4 × 1045 ergs s-1. The relative X-ray and radio properties of the AGN in 1138-262 are similar to those seen for the AGN in the archetype powerful radio galaxy Cygnus A. Between 10% and 25% (depending on energy) of the X-ray emission from 1138-262 is spatially extended on scales of 10''-20''. The extended X-ray emission is elongated, with a major axis aligned with that of the radio source. While the X-ray and radio emissions are elongated on similar scales and position angles, there is no one-to-one correspondence between the radio and X-ray features in the source. The most likely origin for the extended X-ray emission in 1138-262 is thermal emission from shocked gas, although we cannot rule out a contribution from inverse Compton emission. If the emission is from hot gas, then the gas density is 0.05 cm-3 and the gas mass is 2.5 × 1012 M☉. The pressure in this hot gas is adequate to confine the radio-emitting plasma and the optical line-emitting gas. We set an upper limit of 1.5 × 1044 ergs s-1 to the (rest frame) 2-10 keV luminosity of any normal cluster atmosphere associated with 1138-262. No emission was detected from any of the Lyα-emitting galaxies in the (proto-) cluster around 1138-262, outside of the Lyα halo of 1138-262 itself, to a (rest frame) 2-10 keV luminosity limit of 1.2 × 1043 ergs s-1. Emission was detected from a z = 2.183 QSO located 2' west of 1138-262 with a luminosity of 1.8 × 1044 ergs s-1.
Building taxonomy of web search intents for name entity queries

A significant portion of web search queries are name entity queries. The major search engines have been exploring various ways to provide better user experiences for name entity queries, such as showing "search tasks" (Bing search) and showing direct answers (Yahoo! , Kosmix). In order to provide the search tasks or direct answers that can satisfy most popular user intents, we need to capture these intents, together with relationships between them. In this paper we propose an approach for building a hierarchical taxonomy of the generic search intents for a class of name entities (e.g., musicians or cities). The proposed approach can find phrases representing generic intents from user queries, and organize these phrases into a tree, so that phrases indicating equivalent or similar meanings are on the same node, and the parent-child relationships of tree nodes represent the relationships between search intents and their sub-intents. Three different methods are proposed for tree building, which are based on directed maximum spanning tree, hierarchical agglomerative clustering, and pachinko allocation model. Our approaches are purely based on search logs, and do not utilize any existing taxonomies such as Wikipedia. With the evaluation by human judges (via Mechanical Turk), it is shown that our approaches can build trees of phrases that capture the relationships between important search intents.
Classification of Web Services Using JForty Eight

– Web Services are emerging technologies that enable machine to machine communication and reuse of services over Web. They have innovative mechanism for rendering services over diversified environment. They promise to allow businesses to adapt rapidly to changes in the business environment and the needs of different customers. The rapid introduction of new web services into a dynamic business environment can adversely affect the service quality and user satisfaction. Consequently, assessment of the quality of web services is of paramount importance in selecting a web service for an application. In this paper, we employed well-known classification model decision tree (J48) to predict the quality of a web service based on a set of quality attributes. The experiments are carried out on the QWS dataset. We found that web-service relevance function is most significant attribute in determining quality of a web service. The experiments results shown in this paper are about classification accuracy, sensitivity and specificity. The results in the paper on this dataset also show that the efficiency and accuracy of J48.
Evolution of Symbiotic Bacteria in the Distal Human Intestine

The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.
Sweet and Bitter Tastes Evoked Different Neuronal Activation in the Rostral Portion of the Nucleus of the Solitary Tract of Developing Rats

The impact of the gustatory stimuli on the rostral portion of the nucleus of the solitary tract (rNST) was investigated in developing rats, by using c-fos immunohistochemical staining. Wistar male rats of 5, 15, and 25 days of age were isolated from the mother for 12 h, then stimulated via the intraoral route with quinine, sucrose, or NaCl, and sacrificed 90 min later. The water-stimulated group showed minimal c-fos-like immunoreactivity (FLI) compared with taste-stimulated groups that exhibited different FLI in the rNST at the different ages. At all ages the quinine-stimulated group induced FLI in the medial subfield, while sucrose induced FLI in the lateral subfield of the rNST. The intensity of FLI was highest at P15, and it declined at P25. These findings provide detailed insight into the anatomical basis of rNST activation that is involved in early food intake and the learning capacity of the newborn.
Spectral variations of the X-ray binary pulsar LMC X-4 during its long period intensity variation and a comparison with Her X-1

We present spectral variations of the binary X-ray pulsar LMC X-4 using the RXTE/PCA observations at different phases of its 30.5 day long super-orbital period. Only out of eclipse data were used for this study. During the high state of the super-orbital period of LMC X-4, the spectrum is well described by a high energy cut-off power-law with a photon index in the range of 0.7-1.0 and an iron emission line. In the low state, the spectrum is found to be flatter with power-law photon index in the range 0.5-0.7. A direct correlation is detected between the continuum flux in 7-25 keV energy band and the iron emission line flux, The equivalent width of the iron emission line is found to be highly variable during the low intensity state, whereas it remains almost constant during the high intensity state of the super-orbital period. It is observed that the spectral variations in LMC X-4 are similar to those of Her X- I (using RXTE/PCA data). These results suggest that the geometry of the region where the iron line is produced and its visibility with respect to the phase of the super-orbital period is similar in LMC X-4 and Her X-1. A remarkable difference between these two systems is a highly variable absorption column density with phase of the super-orbital period that is observed in Her X-1 but not in LMC X-4.
Molecular Epidemiology and Drug Resistance of Tuberculous Meningitis

Kiatichai Faksri1,3, Therdsak Prammananan2,3, Manoon Leechawengwongs3 and Angkana Chaiprasert3,4* 1Department of Microbiology, Faculty of Medicine, Khon Kaen University, 2National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 3Drug-Resistant Tuberculosis Research Fund, Siriraj Foundation, 4Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
Ultrastructural and Molecular Changes in the Developing Small Intestine of the Toad Bufo regularis

The ontogenetic development of the small intestine of the toad Bufo regularis was investigated using twofold approaches, namely, ultrastructural and molecular. The former has been done using transmission electron microscope and utilizing the developmental stages 42, 50, 55, 60, 63, and 66. The most prominent ultrastructural changes were recorded at stage 60 and were more evident at stage 63. These included the appearance of apoptotic bodies/nuclei within the larval epithelium, the presence of macrophages, swollen mitochondria, distorted rough endoplasmic reticulum, chromatin condensation, and irregular nuclear envelop, and the presence of large vacuoles and lysosomes. The molecular investigation involved examining DNA content and fragmentation. The results showed that the DNA content decreased significantly during the metamorphic stages 60 and 63 compared with both larval (50 and 55) and postmetamorphic (66) stages. The metamorphic stages (60 and 63) displayed extensive DNA laddering compared with stages 50, 55, and 66. The percentage of DNA damage was 0.00%, 12.91%, 57.26%, 45.48%, and 4.43% for the developmental stages 50, 55, 60, 63, and 66, respectively. In conclusion, the recorded remodeling of the small intestine represents a model for clarifying the mechanism whereby cell death and proliferation are controlled.
Cambios en la actividad cerebral en el envejecimiento normal en una tarea con interferencia valorados mediante magnetoencefalografía Magnetoencephalographic assessment of changes in brain activity in normal aging when performing a task under interference conditions

Objective: To determine whether performing a recognition task under interference conditions produces changes in brain activity pattern compared with the activity seen under conditions of passive interference. Population and methods: Twenty healthy elderly subjects were subjected to magnetoencephalography. In each patient we applied the Wechsler Memory Scale-III (WMS-III), the Wechsler Intelligence Scale, the Boston Naming Test, the verbal fluency test, the Wisconsin card classification test, the Trail Making Test and the colors and words test (STROOP). The recordings were made using a 148-channel magnetoencephalograph capable of measuring the magnetic activity generated within the entire cranial convexity. Results: Greater activation was recorded under active interference conditions in the medial temporal regions, visual cortex and anterior ventral area in the first 400 ms in the left hemisphere and only in the right hemisphere for the visual cortex, while under passive interference conditions, increased activation was obtained in the anterior ventral region during the 700-800 ms in the left hemisphere. Conclusion: The presentation of both types of interference, active and passive, modulates the fronto-temporal activation patterns in normal aging.
Attention, Attention Rating and Cognitive Assessment: A Review and a Study.

We begin with the suggestion that the definition of Attention Deficit Hyperactive Disorder (ADHD) still faces some challenges. Conceptually, inhibition of the Pavlovian kind preexisted the “behavioral inhibition” popular in the USA; the difference between them has to be understood in order to understand ADHD. The present project examines the relationship between a teacher rating scale for student attention and the Cognitive Assessment System’s measure of Attention in contrast to Planning. The participants were 82 Grade 3 and Grade 4 children from the First Nations community (Cree). Students were administered the Planning and Attention tests of the Cognitive Assessment System (CAS), while teachers rated their own students by using the Attention Checklist (ACL). Correlations between the ACL and the CAS Attention and Planning scores were positive and significant. However, based on the ACL, groups of low‐ and high‐ attention participants were contrasted on Attention and Planning scores; tests showed significant differences between the low‐ and high‐ attention participants in the Attention score but not in Planning.
The Multimedian Concert-Video Browser

The MultimediaN concert-video browser demonstrates a video interaction environment for efficiently browsing video registrations of pop, rock and other music concerts. The exhibition displays the current state of the project for developing an advanced concert-video browser in 2007. Three demos are provided: 1) a high-level content analysis methodology for modeling the "experience" of the concert at its different stages, and for automatically detecting and identifying semantically coherent temporal segments in concert videos, 2) a general-purpose video editor that associates semantic descriptions with the video segments using both manual and automatic inputs, and a video browser that applies ideas from information foraging theory and demonstrates patch-based video browsing, 3) the Fabplayer, specifically designed for patch-based browsing of concert videos by a dedicated user-group, making use of the results of automatic concert-video segmentation
RmpA2, an Activator of Capsule Biosynthesis in Klebsiella pneumoniae CG43, Regulates K2 cps Gene Expression at the Transcriptional Level

ABSTRACT The rmpA2 gene, which encodes an activator for capsular polysaccharide (CPS) synthesis, was isolated from a 200-kb virulence plasmid of Klebsiella pneumoniae CG43. Based on the sequence homology with LuxR at the carboxyl-terminal DNA-binding motif, we hypothesized that RmpA2 exerts its effect by activating the expression of cps genes that are responsible for CPS biosynthesis. Two luxAB transcriptional fusions, each containing a putative promoter region of the K. pneumoniae K2 cps genes, were constructed and were found to be activated in the presence of multicopy rmpA2. The activation is likely due to direct binding of RmpA2 to the cps gene promoter through its C-terminal DNA binding motif. Moreover, the loss of colony mucoidy in a K. pneumoniae strain deficient in RcsB, a regulator for cps gene expression, could be recovered by complementing the strain with a multicopy plasmid carrying rmpA2. The CPS production in Lon protease-deficient K. pneumoniae significantly increased, and the effect was accompanied by an increase of RmpA2 stability. The expression of the rmpA2 gene was negatively autoregulated and could be activated when the organism was grown in M9 minimal medium. An IS3 element located upstream of the rmpA2 was required for the full activation of the rmpA2 promoter. In summary, our results suggest that the enhancement of K2 CPS synthesis in K. pneumoniae CG43 by RmpA2 can be attributed to its transcriptional activation of K2 cps genes, and the expression level of rmpA2 is autoregulated and under the control of Lon protease.
Quantitative Evaluation of Related Web-Based Vulnerabilities

Current web application scanner reports contribute little to diagnosis and remediation when dealing with vulnerabilities that are related or vulnerability variants. We propose a quantitative framework that combines degree of confidence reports pre-computed from various scanners. The output is evaluated and mapped based on derived metrics to appropriate remediation for the detected vulnerabilities and vulnerability variants. The objective is to provide a trusted level of diagnosis and remediation that is appropriate. Examples based on commercial scanners and existing vulnerabilities and variants are used to demonstrate the framework’s capability.
Goal-based denial and wishful thinking

One of the aims of Affective Computing [19] is to design agents that behave according to models of human affective phenomena. Among these phenomena are the roles that emotions play on various cognitive processes, such as attention, reasoning, decision making, and belief selection. In this paper, we focus on an affective phenomenon that concerns belief selection.
An Overview of the Penman Text Generation System

The problem of programming computers to produce natural language explanations and other texts on demand is an active research area in artificial intelligence. In the past, research systems designed for this purpose have been limited by the weakness of their linguistic bases, especially their grammars, and their techniques often cannot be transferred to new knowledge domains. A new text generation system, Penman, is designed to overcome these problems and produce fluent multiparagraph text in English in response to a goal presented to the system. Penman consists of four major modules: a knowledge acquisition module which can perform domain-specific searches for knowledge relevant to a given communication goal; a text planning module which can organize the relevant information, decide what portion to present, and decide how to lead the reader's attention and knowledge through the content; a sentence generation module based on a large systemic grammar of English; and an evaluation and plan-perturbation module which revises text plans based on evaluation of text produced. Development of Penman has included implementation of the largest systemic grammar of English in a single notation. A new semantic notation has been added to the systemic framework, and the semantics of nearly the entire grammar has been defined. The semantics is designed to be independent of the system's knowledge notation, so that it is usable with widely differing knowledge representations, including both frame-based and predicate-calculus-based approaches.
Cosmic Dand DF-strings from D 3 D̄ 3 : Black Strings and BPS Limit

We study Dand DF-strings in a D3D̄3 system by using Dirac-Born-Infeld type action. In the presence of an electric flux from the transverse direction, we discuss gravitating thick D-string solutions of a spatial manifold, S2 ×R1, in which straight D-strings stretched along the R1 direction are attached to the south and north poles of the two-sphere. There is a horizon along its equator, which means the structure of black strings is formed. We also discuss the BPS limit for thin parallel Dand DF-strings in both flat and curved spacetime. We obtain the BPS sum rule for an arbitrarily-separated multi-string configuration with a Gaussian type tachyon potential. At the site of each thin BPS D(F)-string, the pressure takes a finite value. We find that there exists a maximum deficit angle π in the conical geometry induced by thin BPS Dand DF-strings.