gebhart/patrepeval huggingface dataset:
Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2 (2013)

The adaptive immunity of bacteria against foreign nucleic acids, mediated by CRISPR (clustered regularly interspaced short palindromic repeats), relies on the specific incorporation of short pieces of the invading foreign DNA into a special genomic locus, termed CRISPR array. The stored sequences (spacers) are subsequently used in the form of small RNAs (crRNAs) to interfere with the target nucleic acid. We explored the DNA-binding mechanism of the immunization protein Csn2 from the human pathogen Streptococcus agalactiae using different biochemical techniques, atomic force microscopic imaging and molecular dynamics simulations. The results demonstrate that the ring-shaped Csn2 tetramer binds DNA ends through its central hole and slides inward, likely by a screw motion along the helical path of the enclosed DNA. The presented data indicate an accessory function of Csn2 during integration of exogenous DNA by end-joining.
Online-estimation of road map elements using spline curves (2008)

Abstract—The basis for map assisted moving target tracking is a correct and up-to-date representation of the environment. In this contribution a method is proposed to model curved structures, e.g. roads or tracks, with cubic spline curves. The unknown model parameters are estimated based on corrupted measurements using a probabilistic approach. In particular, the method presented results in a linear formulation of the estimation problem, that offers itself to standard optimal estimation tech-niques. While the parameters are adapted to the measurements, the geometric progression of the curve is locally adjusted. The resulting representation provides information about the expected geometric run and the uncertainty of the estimated curve.
Diastereoselective Iodoamidation of 3-Acetoxybut-1-enylamines: Synthesis of 3-Acetoxy-4-iodo-2-(p-methoxybenzyl)pyrrolidines (2001)

3α-Acetoxy-4α-iodo-2α-(p-methoxybenzyl)pyrrolidine (2) and its enanti-omer (3) were synthesized via diastereoselective iodoamidation, starting from D-or L-tyrosine.The key step contains unfavorable 5-endo-trig cyclization and the diastereoselective addition of ethynylmagnesium bromide to aldehydes (9) by the chelation-controlled Cram cyclic model.The antibiotic (-)-anisomycin (1) possessing a pyrrolidine skeleton, which was isolated from various Streptomyces species, exhibits selective action against protozoa and several strains of fungi. 1 It also has been shown to act as an inhibitor of protein synthesis, 1 and it finds wide use in the treatment of trichomonas vaginitis and amebic dysentery. 2Because of its biological activity, many chemists have reported chiral synthesis of (-)-anisomycin (1) employing naturally occurring starting materials such as carbohydrates, 3 amino acids, 4 L-tartaric acis or its esters. 5In this paper, we wish to report synthetic route for preparation of 3α-acetoxy-4α-iodo-2α-(p-methoxybenzyl)pyrrolidine (2) and its enantiomer (3) through unfavorable 5-endo-trig cyclization, starting from D-or L-tyrosine.We also found the diastereoselective addition of ethynylmagnesium bromide to aldehyde by the chelation-controlled Cram cyclic model (Scheme 1).
"Change of mechanism" block copolymerizations: formation of block copolymers containing helical polyisocyanide and elastomeric polybutadiene segments (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT"Change of mechanism" block copolymerizations: formation of block copolymers containing helical polyisocyanide and elastomeric polybutadiene segmentsTimothy J. Deming and Bruce M. NovakCite this: Macromolecules 1991, 24, 19, 5478–5480Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/ma00019a043https://doi.org/10.1021/ma00019a043research-articleACS PublicationsRequest reuse permissionsArticle Views264Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Abundance and Depth of Origin of Neutral and Ionic Clusters Sputtered from a Liquid Gallium-Indium Eutectic Alloy (1994)

Neutral and positively charged clusters produced by 4 keV ${\mathrm{Ar}}^{+}$ ion bombardment of a liquid gallium-indium eutectic alloy have been studied by time-of-flight mass spectrometry coupled with single photon postionization of the neutrals. The abundance distributions for clusters with equal nuclearity are statistical. They confirm a strong indium surface segregation. An increasing gallium content, and, therefore, larger depth of origin, was found for increasing cluster size.
Cylindrical Ru-SrTiO/sub 3/-Ru capacitor technology for 0.11 μm generation DRAMs (2002)

We have developed a cylindrical Ru/ST/Ru capacitor for gigabit-scale DRAMs. Using cylindrical CVD-Ru as a storage node (SN), a new 2-step CVD-ST was employed to improve ST step coverage, surface morphology and to control composition at the Ru/ST interface. A SiO/sub 2/ equivalent thickness (t/sub eq/) of 0.6 nm and cell capacitance of 18 fF/cell with leakage current of 0.1 fA/cell at /spl plusmn/0.7 V applied voltage has been achieved on a 256K cylindrical Ru/ST/Ru capacitor array.
Large-Sample Learning of Bayesian Networks is NP-Hard (2012)

In this paper, we provide new complexity results for algorithms that learn discrete-variable Bayesian networks from data. Our results apply whenever the learning algorithm uses a scoring criterion that favors the simplest model able to represent the generative distribution exactly. Our results therefore hold whenever the learning algorithm uses a consistent scoring criterion and is applied to a sufficiently large dataset. We show that identifying high-scoring structures is hard, even when we are given an independence oracle, an inference oracle, and/or an information oracle. Our negative results also apply to the learning of discrete-variable Bayesian networks in which each node has at most k parents, for all k &gt; 3.
Alternative T-Cell Costimulatory Pathways in Transplant Rejection and Tolerance Induction: Hierarchy or Redundancy? (2003)

Since the original proposal of a two-signal model for lymphocyte activation (1), it has become firmly established that costimulatory signals mediated primarily via the conventional CD28-B7 and CD154-CD40 pathways, are necessary for full T-cell activation and play a crucial role in mediating allograft rejection (2). In several transplantation models, CD28-B7 or CD154-CD40 blockade has been shown to prevent acute rejection, induce long-term allograft survival and prevent the development and progression of chronic rejection.
Supplementary Table and Figures from Consumption of the Fish Oil High-Fat Diet Uncouples Obesity and Mammary Tumor Growth through Induction of Reactive Oxygen Species in Protumor Macrophages (2023)

&lt;p&gt;Tables show realtime PCR primers and compositions of diets. Figures show that n-3 EPA induce pro-tumor macrophage effects in the fish oil HFD-induced obese mouse models.&lt;/p&gt;
Prediction of thermal hydrolysis pretreatment on anaerobic digestion of waste activated sludge (2008)

Thermal hydrolysis is known for an efficient sludge disintegration capability to enhance biogas potential--but to which extent? Obviously, residual VSS concentration in digested sludge gives not sufficient information to predict additional biogas potential. In this paper, different types of waste activated sludge (WAS) were pre-hydrolysed by a full-scale Thermo-Pressure-Hydrolysis Process (Thermo-Druck-Hydrolyse, TDH) and break-down mechanisms on specific organic compounds were investigated. The IWA Anaerobic Digestion Model No.1 (ADM1) has been used for a systematic analysis of monitoring data gained from experimental work. The TDH process combined with anaerobic digestion can be well described by a modified ADM1 model that includes an X(P)-fraction (inactivated aerobic biomass and their decay products). More rapid and more complete degradation of TDH-treated sludge is represented by calibrated disintegration rate and disintegration factors, while biokinetic parameters of acetogenesis and methanogenesis show no sensitivity. TDH process impacts mainly biomass and decay products while inerts Xi already contained in the raw wastewater are hardly converted. Final concentration of soluble inerts in digestion effluent has been increased from 2% to 9% of influent COD due to thermal hydrolysis. An increase in biogas generation (ca. +80%) and in ammonia release (ca. +75%) can be explained by complete degradation of cell mass.
Hepatic arterial infusion chemotherapy with complete hepatic venous isolation and extracorporeal chemofiltration (1991)

When chemotherapeutic drugs with low liver extraction are used for hepatic arterial infusion (HAI), dosage limits are usually determined by systemic rather than hepatic toxicity. If such agents could be administered by HAI at dosages limited by hepatic toxicity, regional drug exposure and therapeutic efficacy might be significantly enhanced. We report herein a novel system that achieves complete hepatic venous isolation using a dual-balloon vena cava catheter that can be inserted percutaneously. This catheter is connected to a carbon filter in an extracorporeal venous bypass circuit to recover drug that is not absorbed by the liver after HAI. The hemodynamic response to this system was evaluated in six pigs. When the animals were placed on the extracorporeal circuit, we observed a 22% decrease in cardiac output that was well tolerated without significant change in blood pressure. When the filter was incorporated into the circuit, cardiac output was significantly reduced (50%); however, continuous infusion of phenylephrine rapidly normalized blood pressure, heart rate, cardiac output, and left ventricular filling pressures. Initial testing of chemofiltration efficacy was performed in four of the six animals, the remaining two animals being used only to assess hemodynamic response. One each of the four tested animals received either doxorubicin (3 or 9 mg/kg), mitomycin C (1 mg/kg), or cisplatin (1 mg/kg) by HAI. The filter removed over 90% of hepatic venous doxorubicin and mitomycin C and 65% of hepatic venous cisplatin. This feasibility study confirms that hepatic venous isolation with chemofiltration can significantly reduce systemic exposure to high-dose chemotherapeutic agents given by HAI.
Exploiting sequential dependencies for expert finding (2008)

\n Contains fulltext :\n 227805.pdf (Author’s version preprint ) (Open Access)\n
Deep-Learning Driven Acceleration of Multi-Parametric Quantitative Phase-Cycled bSSFP Imaging (2020)

Prominent asymmetries in the bSSFP frequency profile in tissues with distinct fiber pathways are known to be a confounding factor in the quantification of relaxation times from a series of phase-cycled scans. It has been demonstrated that the resulting bias can be eliminated by training artificial neural networks using gold standard relaxation times as target. Here, the ability of neural networks to not only provide gold standard brain tissue T1 and T2 values as well as field map estimates (B1, ∆B0) but also to highly accelerate the acquisition by reducing the number of phase-cycles is explored.
pyvista/pyvista: Under the hood Under the hood changes for VTK9 (2021)

Release 0.29: Under the hood changes for VTK9 This minor release of <code>pyvista==0.29.0</code> includes a variety of changes and new features. The most major is improving our load-time by only loading in the VTK libraries used through lazy loading or selective imports using `vtkmodules``. It was quite an overhaul and should improve load time, reduce memory usage, and potentially the size of the frozen package. Other new features and bug-fixes include: New Features add subdivision option to extract_surface (#1174) Add a silhouette parameter to add_mesh (#1211) add new colors (#1173) Add pickle support to DataObject (#1143) Add where_is in BasePlotter (#1175) Create an explicit structured grid (#1133) Documentation Fix and update some sphinx docs (#1149) :memo: Add new function to geometric.rst (#1170) Update what-is-a-mesh.rst (#1176) Fix docstring in add_point_labels (#1188) API Changes Improve PolyData Import (#1213) Use vtkTransformFilter in DataSet.transform() (#1166) Improve Exodus Reader (#1191) Add bounds in reset_camera (#1161) Add option to hide plane widget vector (#1150) add origin kwarg to plotter.add_legend (#1153) Expose start_xvfb (#1151) Add render=True in add_point_labels (#1152) add transforms3d (#1142) Bug Fixes Fix the "reset camera" effect when parallel projection is enabled/disabled (#1221) Wrap pyvista_ndarray (#1222) Fix vtk not defined (#1217) plot_over_line should fail if scalar name does not exist (#1214) Fix labels (#1201) remove faulthandler (#1187) Fix log scale in scalar bar (#1183) Fix bugs in enable_cell_picking (#1158) fix add_actor (#1182) Fix Binary Writer (#1148) Reimplement Light.copy to get around VTK8.1 bug (#1137) Update enable_cell_picking (#1157) Update the active scalar bar when cmap is changed (#1169) Fix scalar bar moving upward (#1171) Miscellaneous/Testing Minor fix of plot_over_line's test #525 (#1216) common --&gt; dataset (#1209) :art: Minor fix of format of the code. (#1199) Fix doctest failure in BasePlotter.where_is (#1192) Use vtkmodules (#1163) Move Common, DataObject to dataset.py, dataobject.py (#1160) Partially add type hints to /core/ (#1145) improve import speed (#1156) Contributors (alphabetical) @adeak @akaszynski @banesullivan @d-chambers @GuillaumeFavelier @JevinJ @Keou0007 @RichardScottOZ @rodrigomologni @tkoyama010 @whophil @yienyien
Incremental Loading of Object Databases (1996)

Object-oriented and object-relational databases (OODB) need to be able to load the vast quantities of data that OODB users bring to them. Loading OODB data is significantly more complicated than loading relational data due to the presence of relationships, or references, in the data. In our previous work, we presented algorithms for loading new objects that only share relationships with other new objects. However, it is frequently the case that new objects need to share relationships with objects already in the database. In this paper we propose using queries within the load data file to identify the existing objects and suggest using parameterized functions to designate similar queries. We then propose a novel evaluation strategy for the queries that defers evaluation until all the queries can be evaluated together. All of the instantiations of a single query function can then be treated as a join between the function parameters and the collection over which the function ranges, rathe...
Neutralization sensitivity and accessibility of continuous B cell epitopes of the feline immunodeficiency virus envelope (1996)

Antibodies elicited during natural infection of domestic cats by the feline immunodeficiency virus (FIV) recognize continuous epitopes in nine domains of the virus envelope glycoproteins. Whereas antibodies directed against the V3 envelope region can neutralize laboratory-adapted virus, neutralization of FIV has been shown to depend upon cellular substrate, and virus adaptation to laboratory cell lines may alter sensitivity to neutralizing antibodies. We therefore undertook a systematic analysis of the continuous B cell epitopes of the envelope of a primary FIV isolate, Wo. The capacity of feline antisera elicited against nine envelope domains to neutralize primary and laboratory-adapted virus was evaluated in feline peripheral blood mononuclear cells (PBMC). The laboratory-adapted strain Petaluma was used to compare neutralization in PBMC and Crandell feline kidney cells (CrFK). Antibodies specific for the V3 region neutralized both primary and laboratory-adapted virus whether residual infectivity was measured in CrFK or in feline PBMC. However, a large discrepancy in the efficiency of neutralization was observed in these ex vivo models of infection, perhaps reflecting diversity in the interaction between virus and different cellular targets. We also examined the accessibility of epitopes on the functional oligomeric envelope complex of FIV. Most of the epitopes were poorly exposed on native envelope glycoproteins at the surface of live infected cells. The most accessible domain was the only domain sensitive to neutralizing antibodies. These results suggest that inaccessibility on oligomeric envelope glycoproteins may frequently underlie the insensitivity of diverse lentivirus B cell epitopes to neutralization.
Nonlinear optics in doped fibers. Final report, May 1, 1992--April 30, 1996 (1996)

The main objective of this contract was to study a novel scheme to obtain very strong third-order optical nonlinearities in fibers doped with a suitable absorber in order to produce low-power all-optical fiber switches. In these devices, a signal is switched from a first fiber to a second fiber by the application of an optimal pump of wavelength different from that of the signal. The pump acts on the nonlinearity of the fiber, resulting from the dopant present in the fiber core, to modify the fiber index. The switch is made of a fiber interferometer which transforms this index modulation into an amplitude modulation. The signal is switched as long as the pump is applied, and it returns to the first fiber when the pump is turned off. The incentive was to develop switches exhibiting the following properties: (1) low switching power, (2) a short nonlinear fiber to be able to utilize a short and thus environmentally stable interferometer, (3) fast response time, (4) broad range of signal wavelengths, particularly around 1.55 and 1.32 {micro}m, (5) pump wavelengths readily available from diode lasers, and (6) low signal loss. This research also involved the study of various fiber interferometers to determine the best possible switch architectures, in terms of pump power requirement, stability against environmental temperature fluctuations and possible pump-induced heating of the fiber. Switches are strongly needed for a large number of important applications. The rest of this report is a summary of the most important tasks carried out, and of the major discoveries made, under this contract.
Command Processing in Java Swing Programs (2011)

This chapter discusses two issues with command processing in Java/Swing programs and introduces a lightweight and practical framework for dealing with both of them. With command processing we mean the execution of a piece of code upon request by the user, for example by pressing a button. The two issues under consideration are (1) exception handling and (2) support for undo/redo. We studied the problems in the context of graphical user
Expression of Dominant Negative Mutant SHPTP2 Attenuates Phosphatidylinositol 3′-Kinase Activity via Modulation of Phosphorylation of Insulin Receptor Substrate-1 (1996)

To clarify the role of protein-tyrosine phosphatase (PTPase) containing Src homology 2 regions (SHPTP2) in insulin signaling, either wild-type or mutant SHPTP2 (delta PTP; lacking full PTPase domain) was expressed in Rat 1 fibroblasts overexpressing human insulin receptors. In response to insulin, phosphorylation of insulin receptor substrate 1 (IRS-1), IRS-1-associated PTPase activities and phosphatidylinositol (PI) 3'-kinase activities were slightly enhanced in wild-type cells when compared with those in the parent cells transfected with hygromycin-resistant gene alone. In contrast, introduction of delta PTP inhibited insulin-induced association of IRS-1 with endogenous SHPTP2 and impaired both insulin-stimulated phosphorylation of IRS-1 and activation of PI 3'-kinase. Furthermore, decreased content of p85 subunit of PI 3'-kinase was also found in mutant cells. Consistently, the insulin-stimulated mitogen-activated protein kinase activities and DNA synthesis were also enhanced in wild-type cells, but impaired in mutant cells. Thus, the interaction of SHPTP2 with IRS-1 may be associated with modulation of phosphorylation levels of IRS-1, resulting in the changes of PI 3'-kinase and mitogen-activated protein kinase activity. Furthermore, an impaired insulin signaling in mutant cells may be partly reflected in a decreased content of p85 protein of PI 3'-kinase.
SELECTIVE INHIBITORY EFFECT OF PORCINE FOLLICULAR FLUID ON FOLLICLE STIMULATING HORMONE SECRETION IN ANTERIOR PITUITARY CELLS IN CULTURE (1979)

Incubation of rat anterior pituitary cells in culture with porcine follicular fluid (treated with charcoal to remove steroids) led to a marked inhibition of spontaneous FSH release while no effect was observed on basal LH secretion. The inhibitory effect of follicular fluid was, however, less specific on LHRH-induced gonadotropin release. Although more potent on FSH than LH release, a significant inhibition of LH release induced by the neurohormone was also observed. This inhibitory activity is mainly associated with material of MW greater than or equal to 10,000 daltons.
Subcutaneous isoproterenol: a convenient rat model for early detection of myocardial necrosis. [Early uptake of /sup 99m/Tc-pyrophosphate in isoproterenol-induced myocardial necrosis] (1978)

The uptake of Tc-99m pyrophosphate was studied in rat myocardial lesions produced by a single subcutaneous injection of isoproterenol (10 to 50 mg/kg of body weight). The uptake in the whole heart of treated rats is directly proportional to the isoproterenol dose. The Tc-99m PPi uptake measured at various times after lesion initiation parallels the myocardial calcium concentration changes. This model is useful for screening radiopharmaceuticals, and may also be suitable for studying early uptake in myocardial infarcts.
Three-Input-Three-Output Air Path Control System of a Heavy-Duty Diesel Engine (2016)

This paper was accepted for publication in the journal IFAC-Papers OnLine and the definitive published version is available at http://dx.doi.org/10.1016/j.ifacol.2016.08.088