Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and mutational analysis of E2 trans‐activating proteins of papillomaviruses reveals three distinct functional domains.

The E2 proteins of papillomaviruses are able to transactivate the viral enhancers by interacting with the sequence ACCGN4CGGT found in all papillomavirus long control regions. Analysis of the alignment of the amino acid sequences of 10 E2 proteins reveals three distinct regions: two partially conserved domains at the N and C termini of the proteins and a region variable in size and sequence in the middle. A computer prediction of the secondary structure of the 10 sequences outlines interesting conserved features, including two long amphiphilic alpha helices at the N terminus. To analyse the respective roles of the different segments of these proteins, we constructed a set of in‐frame deletion and insertion mutations in the E2 coding sequences of the bovine papillomavirus type 1 (BPV1) and cottontail rabbit papillomavirus (CRPV). The test of their capacity to trans‐activate or repress different viral constructs shows that the C‐terminal domain of the E2 proteins is involved exclusively in DNA binding whereas the N‐terminal domain is probably required for interaction with other components of the transcriptional machinery. The inner variable domain may confer flexibility to the protein such that it will facilitate contacts of the two others with their respective targets.
Production of high-amylose maize lines using RNA interference in sbe 2 a

To regulate the biosynthetic process of maize starch and produce high-amylose transgenic maize, RNA interference was used to inhibit the starch branching enzyme gene Sbe2. A construct with a 562 bp segment of Sbe2 (pRSBE2a) was cloned as inverted repeats. Highly efficient RNAi vector pRSBE2a was transferred to inbred maize line H99 by Agrobacterium tumefaciens mediated transformation. Two transgenic plants of the T1 generation were obtained with a single or double T-DNA copy number, and the interference segments were observed in transgenic T2 plants. The transcription of sbe2a and the activity of starch branching enzyme (SBE) were severely inhibited in transgenic plants, and SBE activity was decreased by up to 67.8%. The total starch content had no significant difference between the transgenic and control (wild type) plants, but the percentage of amylose was increased to approximately 66.8% versus the control. In conclusion, RNAi to silence endogenous gene sbe2a could produce high-amylose maize lines with a low T-DNA copy number, demonstrating that RNAi is an efficient method for the production of high-amylose maize lines.
The early embryonic pattern of internal vascularization of the mammalian cerebral cortex

His (1889) showed that the maturation of the hemispheric wall in proliferating neuroblasts was not simultaneous but progressed in a regular sequence, in the following manner. The first appearance of neuroblasts was in that part of the hemi-spheric wall which was continuous with the corpus striatum. The progression was then dorsal in the wall, and last in the medial wall. A similar progression existed from the rostra1 to the caudal end as the hemisphere developed.
Synthesis of broadband dispersive delay structures formed by commensurate C‐ and D‐sections

We propose an exact closed‐form synthesis method for the design of broadband dispersive delay structures (DDSs) formed by the series connection of commensurate all‐pass C‐ and D‐sections. In this method, the transfer function synthesis problem is converted into a Hurwitz polynomial generation problem, where the real roots correspond to C‐sections and the complex roots correspond to D‐sections. Several design examples are provided to illustrate the proposed synthesis method. A prototype is implemented in strip‐line configuration and fabricated in LTCC technology, and the measured response is in good agreement with the prescribed and full‐wave responses. © 2013 Wiley Periodicals, Inc. Int J RF and Microwave CAE 24:322–331, 2014.
Tyrosine phosphatases as regulators of skeletal development and metabolism

The protein tyrosine kinases (PTK) and the protein tyrosine phosphatases (PTPs) are enzymes which play an integral role in tyrosine phosphorylation‐dependent signaling cascades. By catalyzing the phosphorylation and dephosphorylation of cellular proteins, these enzymes direct the steady‐state levels of specific phosphoproteins and ultimately dictate the functional state of all cells. The importance of this type of signaling in the skeleton is accepted but poorly understood. The contribution of the PTKs to signaling events in bone has been well studied but, in contrast, the regulation by PTPs is poorly defined. The recent identification of 107 genes within the human genome which encode members of the PTP superfamily emphasizes the need to consider the importance of these proteins in skeletal tissue. In this prospective, we will summarize the present state of our knowledge regarding the function of this enzyme superfamily, illustrating its relevance to the development and maintenance of the skeleton and highlighting future directions that should improve our understanding of these critical signaling molecules. © 2005 Wiley‐Liss, Inc.
Involvement of abscisic acid and H2O2 in antioxidant enzyme activities mediated by nitric oxide synthase-like activity in maize

II DECLARATION.III ACKNOWLEDGEMENTS.VI LIST OF ABBREVIATION.V LIST OF FIGURES.VIII TABLE OF CONTENTS.IX CHAPTER 1.1 Literature Review.1 1.
Recognition of elephants in infrared images using clustering-based image segmentation

Object recognition is a challenging task in image processing and computer vision. This paper proposes a clustering-based image segmentation approach for elephant recognition. An appreciable recognition rate was achieved by k-means clustering technique followed by feature extraction and K nearest neighbour K-NN classifier. The k-means clustering algorithm employs the concept of fitness and belongingness to provide a more adaptive and better clustering process as compared to several conventional algorithms. Elephant shape features are extracted for the recognition. The recognition rate for each class is calculated for performance evaluation. The recognition rate for different K values in K-NN classifier is calculated to find a proper K value for the proposed design.
Genetic analysis of the Helicobacter pylori vacuoiating cytotoxin: structural similarities with the IgA protease type of exported protein

The human gastric bacterial pathogen Helicobacter pylori has been implicated in type B gastritis, peptic ulceration and gastric adenocarcinoma. Here we report on the cloning and genetic characterization of an H. pylori gene named vacA, which encodes the vacuolating cytotoxin VacA, a novel type of antigenic bacterial toxin that induces the formation of intracellular vacuoles in epithelial cells. The vacuolating cytotoxin activity is expressed by a subset of clinical isolates (Vac+), all of which produce the 87kDa cytotoxin antigen, but strains which produce neither the activity nor the cytotoxin protein (Vac−) also carry the gene, Isogenic H. pylori mutants in vacA generated by transposon shuttle mutagenesis produce neither the VacA antigen nor a vacuolating activity in a cell culture model. The vacA gene itself encodes a precursor protein of 139.6 kDa consisting of a 33‐amino acid signal sequence, the 87 kDa cytotoxin and a 50 kDa C‐termlnal domain with features typical of a bacterial outer membrane protein. The VacA precursor shows no significant primary sequence homology with any previously reported protein, but its structural organization closely resembles the IgA protease‐type of exoprotein produced by pathogenic Neisseriae and Haemophilus species. Our current data support a model for secretion of the cytotoxin through the two bacterial membranes which involves the 50 kDa domain for outer membrane translocation with subsequent proteolytic cleavage and release of the mature 87 kDa cytotoxin into the extracellular environment.
Requirement Change Management Process Models: Activities, Artifacts and Roles

Modern software-intensive systems are developed in a world where only constant thing is change. This results in continuously changing requirements. Failure to manage these changing requirements properly may result in failure of system. To manage these requirements, many requirements change management (RCM) process model has been proposed in the literature. Process models facilitate human understating and communication, support process improvement and process management. Coverage of process elements like activities, artifacts and roles has an affect on process model and its usage. This paper reports the current requirements change management process models in the literature on the basis of activities, artifacts and roles. Our survey highlights that there is lack of consensus on RCM process and it has not been described in sufficient detail for use of requirements engineers in the real world.
Characteristics of a Mesoporous Silicate Immobilized Trypsin Bioreactor in Organic Media

Mesoporous silicates (MPS) materials are attractive materials for immobilizing proteins/enzymes because of their well ordered structures, large surface areas (up to 1000 m2 g−1), narrow pore size distributions, large pore diameters, and pore volumes. MPS with average pore diameters ranging from 28 to 300 Å were prepared using cationic and nonionic surfactants. The influence of water content, pH, storage, and thermal treatment on the activity of trypsin immobilized onto MPS was investigated. In a range of solvents, the amidolytic activity of immobilized trypsin was higher than that of the lyophilized preparation. Significant increases in kcat/KM occurred in propanol, ethanol, methanol, and formamide of 90, 62, 45 and 26, respectively. The observed increases were primarily a result of substantial increases in kcat.
Integration of Inertial Navigation System with EM-log Using H-infinity Filter

This paper presents the integration of inertial navigation system (INS) with electromagnetic-log (EM-log) as an underwater navigation system using H-infinity filter for robustness from the uncertainty of the sea current model. In underwater environments, the electromagnetic signals are attenuated rapidly, so that the global navigation satellite system is not available in general. Thus, INS is usually chosen for underwater navigation, and other aiding sensors are also used to complement its accumulative errors, one of which is EM-log. Since an EM-log provides the relative velocity to seawater, the integrated navigation cannot be performed accurately unless the sea current speed is compensated properly. Generally, the INS and EM-log can be integrated using extended Kalman filter (EKF). However, EKF guarantees its performance when the stochastic properties of the system’s process and measurement noises are perfectly known. In other words, in the presence of sea current modelling errors, the integration using the EKF is not expected to show good performance. On the other hand, H-infinity filter is a robust filter which can tolerate such uncertainties. In this paper, the integration of INS and EM-log using H-infinity filter is studied. The performance is compared with that of the EKF case by proper computer simulation.
Structured-light 3D surface imaging: a tutorial

We provide a review of recent advances in 3D surface imaging technologies. We focus particularly on noncontact 3D surface measurement techniques based on structured illumination. The high-speed and high-resolution pattern projection capability offered by the digital light projection technology, together with the recent advances in imaging sensor technologies, may enable new generation systems for 3D surface measurement applications that will provide much better functionality and performance than existing ones in terms of speed, accuracy, resolution, modularization, and ease of use. Performance indexes of 3D imaging system are discussed, and various 3D surface imaging schemes are categorized, illustrated, and compared. Calibration techniques are also discussed, since they play critical roles in achieving the required precision. Numerous applications of 3D surface imaging technologies are discussed with several examples.
BIACORE: an affinity biosensor system for characterization of biomolecular interactions.

Oliver, H. NB. and Psalti, I . S. M. (1989) J. Am. Chem. Soc. 111, 9185-9189 6 Gao-Sheridan, H. S. , Pershad, H. R. , Armstrong, F. A. and Burgess, B. K. (1998) J. Biol. Chem. 273, 5514-5519 7 Guo, I,. €I. , Hill, 11. A. O. , Hooper, D. J., Lawrence, G. A. and Sanghera, G. S. (1989) J. Electroanal. Chem. 266, 379-390 8 Armstrong, F. A. , Ilill, H. A. 0. and Walton, N. J. (1987) ACC. Chem. Res. 21, 407-413 9 IIi11, 11. 11. 0. and IIunt, N. I . (1993) in Metallobiochemistry, Part D, Methods in Enzymology (Riordan, J. F. and Vallec, B. L,., eds.), 227, pp. 501-522, Academic Press, New York 10 Hirst, J., Ackrell, B. A. C. and Armstrong, F. A. (1997) Chem. Soc. Rev. 29, 169-175 11 Davis, G. , Hill, H. A. O. , Aston, W. J., Higgins, I. J. and Turner, A. P. F. (1983) Enzyme Microbial Technol. 5, 383-388
Wages or Fringes? Some Evidence on Trade-Offs and Sorting

The two key predictions of hedonic wage theory are that there is a trade-off between wages and nonmonetary rewards and that the latter can be used as a sorting device by firms to attract and retain the kind of employees they desire. We use the vignettes method to estimate individuals’ willingness-to-pay for fringe benefits and job amenities. We find negative wage-fringe trade-offs, considerable heterogeneity in willingness-to-pay for fringe benefits, and signs of sorting.
Prenatal experience and neonatal responsiveness to vocal expressions of emotion.

Newborn differentiation of emotion and the relevance of prenatal experience in influencing responsiveness to emotion was tested by examining newborn responses to the presentation of a range of vocal expressions. Differential responding was observed, as indicated by an increase in eye opening behavior in response to the presentation of happy speech patterns. More importantly, differential responding was observed only when the infants listened to emotional speech as spoken by speakers of their maternal language. No evidence of discrimination was found in the groups of infants listening to the same vocal expressions in a novel language. The results suggest that as a consequence of prenatal exposure to the distinctive prosodic maternal speech patterns that specify different emotions and to the temporally related stimuli created by distinctive maternal physiological concomitants of emotion, the fetus learns to differentiate those emotional speech patterns typical of the infant's maternal language.
A Tool for Diabetes Prediction and Monitoring Using Data Mining Technique

Data mining is the process of analyzing different aspects of data and aggregating it into useful information. Classification is a data mining task generally used in medical data mining. The goal here is to discover new and useful patterns to provide meaningful and useful information for the users about the diabetes. Here a diabetes prediction and monitoring system is designed and implemented using ID3 classification algorithm. The symptoms causing diabetes are identified and are applied to the prediction model based on which the prediction is done. The monitoring module analyzes the laboratory test reports of the blood sugar levels of the patient and provides proper awareness messages to the patient through mail and bar chart.
Fair and energy-efficient cooperative relaying with selfish nodes

Cooperative communication has been proven effective in enhancing the performance of wireless networks. In this paper, we propose an adaptive multi-relay selection with power allocation mechanism to offer energy fairness at each node for a cooperative network. Unlike traditional approaches where all nodes are considered to transmit in a collaborative manner, we explicitly consider the situation where each node exhibits some degree of selfishness behavior. By introducing novel concepts of the selfishness index and utility function which denote node's benefit from cooperation, we show that the proposed cooperation scheme can well balance the energy consumption among nodes as well as maximize the network lifetime. Theoretical analysis and extensive simulation results are supplemented to show advantages of the proposed approach in power saving and power allocation fairness.
Lisofylline decreases white cell adhesiveness and improves survival after experimental hemorrhagic shock.

OBJECTIVE Lisofylline is an enantiomer-specific, alkyl-substituted methylxanthine, which has specific and potent activity in down-regulating leukocyte activation. This study was designed to test the efficacy of lisofylline in the resuscitation of rats subjected to experimental hemorrhagic shock. DESIGN Prospective, randomized, and blinded survival studies were performed with two lisofylline dosing regimens added to fluid resuscitation in a shock model. In addition, white cell adhesiveness was measured to assess the effects of lisofylline. SETTING Animal laboratory. SUBJECTS Sixty Sprague-Dawley rats. INTERVENTIONS Lisofylline or placebo was added to the resuscitation regimen, either as a single dose or over 24 hrs. MEASUREMENTS AND MAIN RESULTS The 72-hr survival rate, white blood cell count, and platelet adhesiveness were determined. When a single 1-hr infusion of lisofylline was added to the initial resuscitation regimen, the 72-hr survival rate increased from 20% in controls to 50% (p < .009). When repeated doses of lisofylline were given over 24 hrs, the 72-hr survival rate increased from 40% in controls to 70% (p < .02). Control animals significantly increased leukocyte adhesiveness after shock and resuscitation. This increased adhesiveness was completely eliminated by lisofylline infusion. Platelet adhesiveness was not affected by lisofylline. CONCLUSIONS Lisofylline improves survival in this model of hemorrhagic shock. Its beneficial effect may be related to down-regulation of leukocyte adhesiveness.
ANALOGY-MAKING IN SITUATION THEORY

Analogy-making is finding analogies between different situations. In this paper, we provide a new model of computational analogy-making which uses Situation Theory as its formal background. Situation Theory is a semantic and logical theory which provides a naturalistic way to represent relations in situations. The system described in this paper is aimed at solving analogy problems made by basic geometric figures in a chessboard-like environment.
Phototransduction by Retinal Ganglion Cells That Set the Circadian Clock

Light synchronizes mammalian circadian rhythms with environmental time by modulating retinal input to the circadian pacemaker—the suprachiasmatic nucleus (SCN) of the hypothalamus. Such photic entrainment requires neither rods nor cones, the only known retinal photoreceptors. Here, we show that retinal ganglion cells innervating the SCN are intrinsically photosensitive. Unlike other ganglion cells, they depolarized in response to light even when all synaptic input from rods and cones was blocked. The sensitivity, spectral tuning, and slow kinetics of this light response matched those of the photic entrainment mechanism, suggesting that these ganglion cells may be the primary photoreceptors for this system.
Giant pituitary adenomas—An enigma revisited. Microsurgical treatment strategies and outcome in a series of 250 patients

Background. Giant pituitary adenomas (> 4 cm) are a surgical challenge. We present our experiences in surgical management of these tumors in a series of 250 patients. Methods. Two hundred and fifty patients with giant pituitary adenomas were managed surgically at our center over last 13 years. Majority (92%) of patients presented with visual deterioration. Non-functioning tumors were found in 136 patients (54.3%). Among functioning adenomas, 63 patients (25.4%) had prolactinomas and 45 patients (18%) had GH-secreting adenomas; while 3 patients each had LH and ACTH- secreting adenomas. The maximum tumor diameter varied from 4 to 10.5 cm, with mean diameter of 5.4 cm. The factors determining choice of operative approach and surgical outcomes in these tumors were analyzed. Results. Overall, 273 surgical procedures were performed in 250 patients. Of these, 110 were transsphenoidal, while 163 were transcranial approaches. A single surgical procedure was performed in 227 patients (89.2%). 23 patients (9.2%) underwent re-exploration either because of postoperative apoplexy or residual tumor. Overall, near total (>90%) tumor excision could be achieved in 74%, with improved vision in 53% and good outcome in 75% patients. The mortality and morbidity were 4.4% and 14%, respectively. Conclusions. The main goal of surgical treatment of giant pituitary adenoma is maximum possible tumor extirpation with minimal side effects, which can be achieved by careful preoperative planning of operative approach, based on directions of tumor extensions and invasiveness. Maximal surgical removal of giant adenomas offers best chances to control tumor growth when followed with adjuvant medical and radiation therapies.
Ultra-low noise nanoscale transistors for metrology of noise, energy harvesting and biosensing applications (Invited)

Flicker or 1/f noise in metal-oxide-semiconductor field-effect transistors (MOSFETs) has been identified as the main source of noise at low frequency. It often originates from an ensemble of a huge number of charges becoming trapped and de-trapped, or from mobility fluctuation. However, for nanoscale transistors, equations based on the density of traps are no more valid due to the small number of traps. Fluctuations at contacts can also be the dominant source of noise. Here, we summarize our results in this topic and show in addition that nanoscale transistors provide unique opportunities for metrological studies of noise. In particular, we propose an alternative to the criticized but widely used unified number and correlated mobility fluctuation model for MOSFETs, discuss the dielectric polarization/mobility noises as sources of 1/f noise for trap-free gate oxides and a model for Schottky-barrier-based nanoscale transistors. In a second part, we summarize our results for noise in liquid-gated nanoscale (0D) transistor sensors with applications in energy harvesting and biosensing.
Development of polymorphic microsatellite loci in the perennial herb Hepatica nobilis var. japonica (Ranunculaceae)1

Premise of the study: Microsatellite markers were developed and characterized in the vulnerable plant Hepatica nobilis var. japonica (Ranunculaceae) to investigate its genetic diversity, population structure, and gene flow. Methods and Results: Fourteen microsatellite markers were developed. The number of alleles per locus ranged from one to 12, and the expected heterozygosity per locus ranged from 0.043 to 0.855. Eleven markers were successfully amplified in the cultivar ‘Mego’ from Japan. Conclusions: These microsatellite markers can be used to investigate the genetic diversity, population structure, and gene flow of H. nobilis var. japonica.
Better Splitting Algorithms for Parallel Corpus Processing

Better Splitting Algorithms for Parallel Corpus Processing Each iteration of minimum error rate training involves re-translating a development set. Distributing this work across computational nodes can speed up translation time, but in practice some parts may take much longer to complete than others, leading to computational slack time. To address this problem, we develop three novel algorithms for distributing translation tasks in a parallel computing environment, drawing on research in parallel machine scheduling. We present results showing a substantial speedup in overall decoding time.