gebhart/patrepeval huggingface dataset:
Identification of Mcm2 Phosphorylation Sites by S-phase-regulating Kinases (2006)

Minichromosome maintenance 2-7 proteins play a pivotal role in replication of the genome in eukaryotic organisms. Upon entry into S-phase several subunits of the MCM hexameric complex are phosphorylated. It is thought that phosphorylation activates the intrinsic MCM DNA helicase activity, thus allowing formation of active replication forks. Cdc7, Cdk2, and ataxia telangiectasia and Rad3-related kinases regulate S-phase entry and S-phase progression and are known to phosphorylate the Mcm2 subunit. In this work, by in vitro kinase reactions and mass spectrometry analysis of the products, we have mapped phosphorylation sites in the N terminus of Mcm2 by Cdc7, Cdk2, Cdk1, and CK2. We found that Cdc7 phosphorylates Mcm2 in at least three different sites, one of which corresponds to a site also reported to be phosphorylated by ataxia telangiectasia and Rad3-related. Three serine/proline sites were identified for Cdk2 and Cdk1, and a unique site was phosphorylated by CK2. We raised specific anti-phosphopeptide antibodies and found that all the sites identified in vitro are also phosphorylated in cells. Importantly, although all the Cdc7-dependent Mcm2 phosphosites fluctuate during the cell cycle with kinetics similar to Cdc7 kinase activity and Cdc7 protein levels, phosphorylation of Mcm2 in the putative cyclin-dependent kinase (Cdk) consensus sites is constant during the cell cycle. Furthermore, our analysis indicates that the majority of the Mcm2 isoforms phosphorylated by Cdc7 are not stably associated with chromatin. This study forms the basis for understanding how MCM functions are regulated by multiple kinases within the cell cycle and in response to external perturbations.
Success and risk: Gene therapy for severe combined immunodeficiency (2008)

SCIDs are a group of inherited disorders characterized by profound defects in both cellmediated and humoral immunity (Figure 1). These diseases represent the most severe forms of primary immunodeficiencies, affecting approximately 1 child in every 75000 livebirths. The molecular pathology of these disorders has been deter mined for the majority of cases (Table 1), which typi cally present in the first few months of life with failure to thrive, chronic diarrhoea and recurrent infections. Conventional treatment for SCID is HSCT (haemo poietic stem cell transplantation) with high longterm survival rates for transplants from genotypically matched family donors. For the majority of patients for whom a matched family donor is unavailable, how ever, mismatched procedures offer a poorer prognosis and may be associated with incomplete recovery of immunity. Gene therapy therefore presents an attractive therapeutic alternative, and several features of SCIDs make these disorders particularly amenable to correc tion by this technology. First, as stated above, the molecular basis of the majority of SCID phenotypes has been defined and at tributed to defects in single genes (Table 1). Secondly, treatment by HSCT is curative, supporting the notion that correction of a patient's own bone marrow stem cells will lead to restoration of immunity. The target stem cells are easily accessible (allowing gene therapy to be performed ex vivo) and, furthermore, correction of the gene defect in these cells should confer a strong growth and survival advantage in the SCID setting. The gene therapy procedure can therefore be performed without or with minimal chemotherapeutic conditioning. This concept is supported by the partial immunological re constitution observed in two patients following spon taneous mutationreversion events and demonstrates that the correction of even a small number of lymphoid precursors may confer significant therapeutic benefit1,2.
Cubical S values for use with SPECT, PET, and autoradiographic imaging data in performing small-scale dosimetry (1996)

A traditional assumption made in nuclear medicine dosimetry methodologies such as the MIRD schema is that the activity in the source organ is uniformly distributed. Localization techniques such as quantitative SPEC and PET imaging allow one to dispense with this assumption and look at realistic nonuniform activity distributions in selected organs or organ regions. Therapy applications further emphasize the need for direct treatment of nonuniformities. Many researchers have relied upon elaborate computational techniques such as dose kernels to assess dose distributions in these regions. In this work, a simplified approach is proposed which allows direct use of the MIRD schema in conjunction with imaging data to rapidly assess organ dose distributions with minimal computational effort. The EGS4 radiation transportcode has been used with a cubical array of tissue voxel elements for a centrally located source cube of {sup 32}P, {sup 131}I, {sup 89}Sr, {sup 90}Y, and {sup 99m}Tc. Three sets of voxel dimensions are considered: 6 mm for SPECT images, 3 mm for PET images, and 50 {mu}m for autoradiography. Radionuclide S values are subsequently tabulated as a single function of the source-to-target voxel separation distance. Isodose contours are shown for (1) a mouse renal cell carcinoma with {sup 131}I-labeledmore » antibody, (2) a human colon adenocarcinoma with {sup 131}I-labeled antibody, and (3) various tumors directly injected With {sup 32}P.« less
<title>Understanding the echo clues used by dolphins to remotely identify the target characteristics of submerged elastic shells</title> (1996)

We have examined a large set of dolphin-emitted acoustic pulses (`echolocation clicks') which were reflected from various elastic shells that were suspended, underwater, 4.5 m in front of the animal in a large test site in Kaneohe Bay. A carefully instrumented analog-to-digital system continuously captured the emitted clicks and also the returned, backscattered, echoes (A/D conversion at 500 kHz). Using standard conditioning techniques and food reinforces, the dolphin is taught to push an underwater paddle when the `correct' target--the one he has been trained to identify--is presented to him. He communicates to us his consistently correct identifying choices in this manner. We have examined many echoes returned by three types of cylindrical shells in both the time and frequency domains. We will show exactly how specific features observable in these displays are directly related to the physical characteristics of the shells. Our processing uses certain fundamental resonance principles to show which echo- features contain information about the size, shape, wall-thickness, and material composition of both the shell and its filler substance. In the same fashion that these resonance features give us the identifying characteristics of each shell, we believe they also give them to the dolphin. These echo features may tell him the target properties without any need for computations. We claim that this may be the fundamental physical explanation of the dolphin's amazing target-ID feats, upon which they base their recognition choices. Our claim may be substantiated by the detailed analysis of many typical echoes returned by various shells, when they are interrogated by several dolphins. Thus far, this analysis of many echoes from many shells has only been carried out for a single dolphin.
Changing Software Engineers' Self-Efficacy with Bootcamps:A Research\n Proposal (2021)

In several areas of knowledge, self-efficacy is related to the perfomance of\nindividuals, including in Software Engineering. However,it is not clear how\nself-efficacy can be modified in training conducted by the industry.\nFurthermore, we still do not understand how self-efficacy can impact an\nindividual's team and career in the industry. This lack of understanding can\nnegatively impact how companies and individuals perceive the importance of\nself-efficacy in the field. Therefore, We present a research proposal that aims\nto understand the relationship between self-efficacy and training in Software\nEngineering. Moreover, we look to understand the role of self-efficacy at\nSoftware Development industry. We propose a longitudinal case study with\nsoftware engineers at Zup Innovation that participating of our bootcamp\ntraining. We expect to collect data to support our assumptions that\nself-efficacy can be related to training in Software Engineering. The other\nassumption is that self-efficacy at the beginning of training is higher than\nthe middle, and that self-efficacy at the end of training is higher than the\nmiddle. We expect that the study proposed in this article will motivate a\ndiscussion about self-efficacy and the importance of training employers in the\nindustry of software development.\n
Isolation and Characterization of a Chitinase from the Nine-Banded Armadillo, Dasypus novemcinctus (1998)

The insectivorous diet of the nine-banded armadillo, Dasypus novemcinctus, is abundant in the polysaccharide chitin. To detennine if armadillos produce a chitinase that aids in digestion of chitinous exoskeletons, armadillos were collected, and samples of their gastric and pancreatic tissues were removed. Tissues were lyophilized and stored at -20C until resuspended in appropriate buffers for studies of pH and temperature optima. Extract from resuspended tissues was assayed for chitinase activity using a colorimetric procedure that detected N-acetyl-D-glucosamine (NAG), the monomeric unit in chitin. Chitinase activity was present only in gastric tissues. Optimal pH for chitinase activity from gastric tissues of armadillo was 5.0, and optimal temperature was 50-60C. This chitinase was purified five-fold.
Estimation of membrane potentials of individual lymphocytes by flow cytometry. (1979)

The membrane potentials of individual cells can be estimated by flow cytometric quantitation of the cells' uptake of the fluorescent lipophilic cationic dye 3,3'-dihexyloxacarbocyanine iodide. Human lymphocytes separated from peripheral blood on Hypaque-Ficoll gradients are uniformly depolarized by gramicidin and hyperpolarized by valinomycin. Concanavalin A and phytohemagglutinin depolarize only a fraction of the lymphocytes. The flow cytometric technique allows precise detection of heterogeneous membrane potential responses to stimuli such as lectins; it could also provide a basis for sorting cells that respond differently to a given stimulus.
<title>Watermarking of MPEG-2 encoded video without decoding and reencoding</title> (1997)

Embedding information into multimedia data, also called watermarking, is a topic that has gained increased attention recently. For practical applications like authentication and labeling in pay-per-view television broad-casting, watermarking of video, and especially of already encoded video, is interesting. We present a scheme for robust watermarking of MPEG-2 encoded video. The watermark is embedded into the MPEG-2 bitstream, and can be retrieved from the decoded video. The scheme is robust and of much lower complexity that a complete decoding process followed by watermarking in the pixel domain and re-encoding. Although an existing MPEG-2 bitstream is partly altered, the scheme avoids drift by adding a drift compensation signal. The scheme has been implemented and the results confirm that a roust watermark can be embedded into MPEG encoded video which can be used to securely transmit arbitrary binary information at a data rate of several bytes/second. The scheme is also applicable to other hybrid coding schemes like MPEG-1, H.261 and H.263.
Expression of fibroblast growth factor receptor 3 in multiple myeloma causes II-6-independence and enhanced survival (1999)

Multiple myeloma (MM) is a common hematologic malignancy.A t(4;14) chromosomal translocation has been identified in 25% of multiple myeloma which results in dysregulated expression of fibroblast growth factor receptor 3 (FGFR.3)on der(l4) and an IgH-MMSET hybrid mRNA on der(4).Activating mutations of the translocated FGFR3 have been identified in MM cells suggesting that FGFR3 plays an important role in tumor development.In this thesis the potential role of FGFR3 in myeloma was investigated in an interleukin-6-dependent murine myeloma ce11 line.Overexpression of wild-type FGFR3 stimulated with ligand or mutant FGFR3 resulted in interleukin-6independence. decreased apoptosis in the absence of Uiterleukin-6 and an enhanced proliferative response to interleukin-6.These findings provide an explanation for the rnechanism by which f&3 contributes to both the viability and propagation of the myeloma clone and may provide a basis for the development of therapies targeting myeloma patients harbouring the t(4; 14) translocation.
Realistic ambient noise analysis for passive surveillance algorithm design (2011)

Passive surveillance algorithms are important for continuous monitoring of the offshore assets and the coastal regions to prevent unwanted intrusions by the adversary. The strategic shift of modern navies to the littoral waters presents great challenge for the algorithm designer as the underwater channel conditions in shallow waters leads to more complicated distortion effects and ambient noise characteristics. Typically, the ambient noise is assumed to be Gaussian. However, field experiments on ambient noise recordings and their characterization have established that it is predominantly non-Gaussian due to the various noise generating sources. In this work, the performance of a passive classification algorithm has been evaluated for Gaussian as well as realistic non-Gaussian noise models of the ambient noise in an underwater channel. The input data has been processed into spectrum and cepstrum domain features and the k-nearest neighbor pattern classification algorithm has been used. The performance evaluation is done in terms of percentage correct classification for three types of propulsion in marine vessels, namely diesel, gas turbine, and steam. The data analysis has been done for synthesized received signals and real signal recordings of marine vessels in shallow water conditions. It is observed that the passive sonar classifier is quite robust to varying ambient noise statistics.
Interactions between parasites and microbial communities in the human gut (2012)

The interactions between intestinal microbiota, immune system, and pathogens describe the human gut as a complex ecosystem, where all components play a relevant role in modulating each other and in the maintenance of homeostasis. The balance among the gut microbiota and the human body appear to be crucial for health maintenance. Intestinal parasites, both protozoans and helminths, interact with the microbial community modifying the balance between host and commensal microbiota. On the other hand, gut microbiota represents a relevant factor that may strongly interfere with the pathophysiology of the infections. In addition to the function that gut commensal microbiota may have in the processes that determine the survival and the outcome of many parasitic infections, including the production of nutritive macromolecules, also probiotics can play an important role in reducing the pathogenicity of many parasites. On these bases, there is a growing interest in explaining the rationale on the possible interactions between the microbiota, immune response, inflammatory processes, and intestinal parasites.
An in vitro study comparing a peripherally inserted central catheter to a conventional central venous catheter: no difference in static and dynamic pressure transmission (2010)

In vitro, no static or dynamic pressure differences were found between the PICC and a conventional CVP catheter. Clinical studies are required to assess whether the novel PICC has bedside equivalence to conventional catheters when measuring central venous pressures.
Operation of Two‐port On/Off and Off/On Planar Switches Using the Mutual Energy–Finite Element Method (2018)

A complete characterization of a one-port homogeneous circuit requires the solutions of one-port networks only. This chapter employs the mutual energy technique in conjunction with the finite element method to tackle an n-port problem. It includes the design of On-Off and Off-On two-port stripline switches using a commercial solver. The development of the open- or short-circuit parameters of a two-port planar circuit begins with the conservation of power immittance definitions. The admittance or impedance matrix of a circuit may be calculated once the electric fields due to the two one-port circuits defined by ports i and j are obtained. The mutual energy method may be used in conjunction with the finite element method to evaluate the frequency response of any n-port planar circuit. A two-port On/Off stripline junction may also be realized by replacing one of the two ferrite pucks by a metal plug.
Molecular Characterization of Multidrug-Resistant Isolates of Mycobacterium tuberculosis from Patients in North India (2002)

The World Health Organization has identified India as a major hot-spot region for Mycobacterium tuberculosis infection. We have characterized the sequences of the loci associated with multidrug resistance in 126 clinical isolates of M. tuberculosis from India to identify the respective mutations. The loci selected were rpoB (rifampin), katG and the ribosomal binding site of inhA (isoniazid), gyrA and gyrB (ofloxacin), and rpsL and rrs (streptomycin). We found known as well as novel mutations at these loci. Few of the mutations at the rpoB locus could be correlated with the drug resistance levels exhibited by the M. tuberculosis isolates and occurred with frequencies different from those reported earlier. Missense mutations at codons 526 to 531 seemed to be crucial in conferring a high degree of resistance to rifampin. We identified a common Arg463Leu substitution in the katG locus and certain novel insertions and deletions. Mutations were also mapped in the ribosomal binding site of the inhA gene. A Ser95Thr substitution in the gyrA locus was the most common mutation observed in ofloxacin-resistant isolates. A few isolates showed other mutations in this locus. Seven streptomycin-resistant isolates had a silent mutation at the lysine residue at position 121. While certain mutations are widely present, pointing to the magnitude of the polymorphisms at these loci, others are not common, suggesting diversity in the multidrug-resistant M. tuberculosis strains prevalent in this region. Our results additionally have implications for the development of methods for multidrug resistance detection and are also relevant in the shaping of future clinical treatment regimens and drug design strategies.
Characterization of Urbix Resources Natural Flake Graphite Material for Nuclear Applications (CRADA NFE-18-07340 Final Report) (2020)

Urbix Resources is a company specializing in graphite powder processing and purification. Urbix is looking to become the first domestic supplier of nuclear-grade graphite in the United States. This has led to a Cooperative Research and Development Agreement (CRADA) being established between the Oak Ridge National Laboratory (ORNL) and Urbix Resources, with the goal of characterizing a purified graphite feedstock supplied by Urbix Resources. The resulting data will then be used to determine the viability of a large-scale nuclear graphite production and qualification campaign. These characterization methods have been performed on the as-received graphite feedstock, a heat-treated batch of the feedstock, a milled batch of the feedstock, and a nuclear-grade graphite powder historically used in fuel production. The data from the heat-treated and milled feedstock will determine how different processing methods affect the powder’s physical properties, whereas the data from the nuclear grade graphite will provide information about the characteristics of a graphite previously accepted for nuclear applications. All of these powders have been characterized individually and as part of a resin-graphite blend (herein referred to as matrix) that has been used in past fuel experiments. The results of these experiments show that the Urbix powder and nuclear-grade graphite powder display notably different properties from one another in many cases, but this discrepancy may have been the result of the typical particle size of each powder. This hypothesis is supported by tests conducted on the milled powder, which showed a closer resemblance in properties to the nuclear-grade graphite than the as-received powder. The method for pressing the graphite matrix also had a noticeable effect on the measured properties.
Modified Virtual Reality for Intuitive Semantic Information Visualization (2008)

In order to make use of domain knowledge and thus to create less abstract visualizations of the available information, we propose to integrate information visualization techniques in 3D visualizations of the application subject. We describe a framework that is build on an ontology, an hierarchical visualization toolkit, and a modular concept of modeling 3D layouts. This allows us to integrate semantically related information directly in the scene. We achieve this integration by modifying the real world geometry in several ways. Our concept helps non-expert users to intuitively interact with the system and to understand what is going on.
SER Derivation and Power Optimization of a Two-Way MultiRelay Cooperative Communication System (2014)

In this paper, we consider Rayleigh fading based cooperative communication system with AaF (Amplify and Forward) relaying using multiple relays. We take spectrally efficient two-way model of cooperative communication terminals and formulate performance evaluation framework in terms of SER (Symbol Error Rate). We not only consider fading channel for this performance evaluation but also consider the effect of relay terminal location into our model which does not require any CSI (Channel State Information) at transmitting nodes. We have proposed power allocation framework for these nodes and analytically derived SER performance results. We have numerically evaluated this framework for power optimization as well as minimizing required SER. Significant performance improvement as compared with equal power sharing among the cooperating terminals is achieved using our proposed framework. It is shown that virtual cooperative antenna configurations is able to demonstrate up to 3dB gain as compared with co-located antenna configurations. Thus incorporating relay location information for performance evaluation results significant power savings
Entropy stable essentially non-oscillatory methods based on RBF reconstructions (2018)

To solve hyperbolic conservation laws on general grids we propose to use high-order essentially nonoscillatory methods based on radial basis functions. We introduce an entropy stable arbitrary high-order finite dierence method (RBF-TeCNOp) and an entropy stable second order finite volume method (RBF-EFV2) for one-dimensional problems. Thus, we show that such methods based on radial basis functions are as powerful as methods based on polynomial reconstruction. The main contribution is the construction of an algorithm and a smoothness indicator that ensures an interpolation function which fullls the sign-property.