gebhart/patrepeval huggingface dataset:
Variable selection for inferential models with relatively high-dimensional data: Between method heterogeneity and covariate stability as adjuncts to robust selection (2020)

Variable selection in inferential modelling is problematic when the number of variables is large relative to the number of data points, especially when multicollinearity is present. A variety of techniques have been described to identify 'important' subsets of variables from within a large parameter space but these may produce different results which creates difficulties with inference and reproducibility. Our aim was evaluate the extent to which variable selection would change depending on statistical approach and whether triangulation across methods could enhance data interpretation. A real dataset containing 408 subjects, 337 explanatory variables and a normally distributed outcome was used. We show that with model hyperparameters optimised to minimise cross validation error, ten methods of automated variable selection produced markedly different results; different variables were selected and model sparsity varied greatly. Comparison between multiple methods provided valuable additional insights. Two variables that were consistently selected and stable across all methods accounted for the majority of the explainable variability; these were the most plausible important candidate variables. Further variables of importance were identified from evaluating selection stability across all methods. In conclusion, triangulation of results across methods, including use of covariate stability, can greatly enhance data interpretation and confidence in variable selection.
An integrated symbolic and neural network architecture for machine learning in the domain of nuclear engineering (2002)

On top of FUELCON and NEL, two extant, successful projects in, respectively, expert systems for engineering, and neural networks, we have defined and designed a new phase, meant to greatly increase the significance, for AI, of the combined project with respect to the already recognized merits of the two seed-projects. The NEL symbolic-to-neural conversion schema and language is resorted to in NEURALIZER, a component meant to automatically revise a ruleset, iteration after iteration, within the operation cycle of FUELCON, a generator of families of configurations of fuel assemblies for reloading the core of nuclear reactors.
Immunotherapy of Superficial Bladder Cancer (1982)

No AccessJournal of UrologyReview Article1 Nov 1982Immunotherapy of Superficial Bladder Cancer Amos Shapiro, Dov Kadmon, William J. Catalona, and Timothy L. Ratliff Amos ShapiroAmos Shapiro More articles by this author , Dov KadmonDov Kadmon More articles by this author , William J. CatalonaWilliam J. Catalona More articles by this author , and Timothy L. RatliffTimothy L. Ratliff More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)53265-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1982 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited byCarballido J, Alvarez-Mon M, Solovera J, Menéndez-Ondina L and Durántez A (2018) Clinical Significance of Natural Killer Activity in Patients with Transitional Cell Carcinoma of the BladderJournal of Urology, VOL. 143, NO. 1, (29-33), Online publication date: 1-Jan-1990.Woolley J, Lau B, Ruckle H and Torrey R (2018) Phagocytic and Natural Killer Cytotoxic Responses of Murine Transitional Cell Carcinoma to Postsurgical ImmunochemotherapyJournal of Urology, VOL. 140, NO. 3, (660-663), Online publication date: 1-Sep-1988.Lamm D (2018) Editorial CommentJournal of Urology, VOL. 136, NO. 4, (823-824), Online publication date: 1-Oct-1986.Haaff E, Dresner S, Ratliff T and Catalona W (2018) Two Courses of Intravesical Bacillus Calmette-Guerin for Transitional Cell Carcinoma of the BladderJournal of Urology, VOL. 136, NO. 4, (820-823), Online publication date: 1-Oct-1986. Volume 128 Issue 5 November 1982 Page: 891-894 Advertisement Copyright & Permissions© 1982 by The American Urological Association Education and Research, Inc.Metrics Author Information Amos Shapiro More articles by this author Dov Kadmon More articles by this author William J. Catalona More articles by this author Timothy L. Ratliff More articles by this author Expand All Advertisement PDF downloadLoading ...
Role of the JAK/STAT signaling pathway in diabetic nephropathy (2006)

Excessive cellular growth is a major contributor to pathological changes associated with diabetic nephropathy. In particular, high glucose-induced growth of glomerular mesangial cells is a characteristic feature of diabetes-induced renal complications. Glomerular mesangial cells respond to traditional growth factors, although in diabetes this occurs in the context of an environment enriched in both circulating vasoactive mediators and high glucose. For example, the vasoactive peptide ANG II has been implicated in the pathogenesis of diabetic renal disease, and recent findings suggest that high glucose and ANG II activate intracellular signaling processes, including the polyol pathway and generation of reactive oxygen species. These pathways activate the Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling cascades in glomerular mesangial cells. Activation of the JAK/STAT signaling cascade can stimulate excessive proliferation and growth of glomerular mesangial cells, contributing to diabetic nephropathy. This review focuses on some of the key elements in the diabetic microenvironment, especially high glucose and the accumulation of advanced glycoxidation end products and considers their impact on ANG II and other vasoactive peptide-mediated signaling events in vitro and in vivo.
Regulation of Notch signaling by <i>Drosophila</i> heparan sulfate 3-<i>O</i> sulfotransferase (2004)

Heparan sulfate (HS) regulates the activity of various ligands and is involved in molecular recognition events on the cell surface and in the extracellular matrix. Specific binding of HS to different ligand proteins depends on the sulfation pattern of HS. For example, the interaction between antithrombin and a particular 3-O sulfated HS motif is thought to modulate blood coagulation. However, a recent study of mice defective for this modification suggested that 3-O sulfation plays other biological roles. Here, we show that Drosophila melanogaster HS 3-O sulfotransferase-b (Hs3st-B), which catalyzes HS 3-O sulfation, is a novel component of the Notch pathway. Reduction of Hs3st-B function by transgenic RNA interference compromised Notch signaling, producing neurogenic phenotypes. We also show that levels of Notch protein on the cell surface were markedly decreased by loss of Hs3st-B. These findings suggest that Hs3st-B is involved in Notch signaling by affecting stability or intracellular trafficking of Notch protein.
Degradation of the Peroxisome Proliferator-activated Receptor γ Is Linked to Ligand-dependent Activation (2000)

The nuclear hormone receptor peroxisome proliferator-activated receptor (PPAR) gamma is a ligand-activated transcription factor that regulates several crucial biological processes such as adipogenesis, glucose homeostasis, and cell growth. It is also the functional receptor for a new class of insulin-sensitizing drugs, the thiazolidinediones, now widely used in the treatment of type 2 diabetes mellitus. Here we report that PPARgamma protein levels are significantly reduced in adipose cells and fibroblasts in response to specific ligands such as thiazolidinediones. Studies with several doses of different ligands illustrate that degradation of PPARgamma correlates well with the ability of ligands to activate this receptor. However, analyses of PPARgamma mutants show that, although degradation does not strictly depend on the transcriptional activity of the receptor, it is dependent upon the ligand-gated activation function 2 (AF2) domain. Proteasome inhibitors inhibited the down-regulation of PPARgamma and ligand activation enhanced the ubiquitination of this receptor. These data indicate that, although ligand binding and activation of the AF2 domain increase the transcriptional function of PPARgamma, these same processes also induce ubiquitination and subsequent degradation of this receptor by the proteasome.
WiseNET: an ultralow-power wireless sensor network solution (2004)

A wireless sensor network consists of many energy-autonomous microsensors distributed throughout an area of interest. Each node monitors its local environment, locally processing and storing the collected data so that other nodes can use it. To optimize power consumption, the Swiss Center for Electronics and Microtechnology has developed WiseNET, an ultralow-power platform for the implementation of wireless sensor networks that achieves low-power operation through a careful codesign approach. The WiseNET platform uses a codesign approach that combines a dedicated duty-cycled radio with WiseMAC, a low-power media access control protocol, and a complex system-on-chip sensor node to exploit the intimate relationship between MAC-layer performance and radio transceiver parameters. The WiseNET solution consumes about 100 times less power than comparable solutions.
Computational methods for functional site identification suggest a substrate access channel in transaldolase. (2006)

The homozygous deletion of Serine 171 results in the catalytic inactivation of the human transaldolase. Since Ser171 is in an outside loop, whereas the catalytic site is inside of the alpha/beta-barrel of the protein at least 15 A away, the loss of activity is difficult to explain. Two distinct computational methods are used to elucidate the potential origin of inactivation. Computational solvent mapping, which moves small organic molecules as probes around a protein surface and finds favorable binding positions, identifies the region around Ser171 as an important binding site. Three-dimensional cluster analysis, based both on a reference structure and multiple sequence alignment, shows that a patch of functionally important residues extends from Ser171 toward the catalytic site. Based on the findings of these two methods, we propose a novel ligand access path connecting these specific sites to the enzyme's active site. We also suggest that this mechanism may be aided by a significant conformational change involving the separation of two helices, alphaD and alphaG, in order to create an easy-access channel between the Ser171-related site and the active site. Further experimental procedures will be necessary to examine the biological feasibility of this proposed ligand shuttling path.
Energy Levels in Cobalt Compensated Silicon (1970)

Measurements of the temperature dependence of resistivity and Hall coefficient in cobalt-doped silicon show a donor level 0.40 eV from the valence band and an acceptor level 0.53 eV from the conduction band. These levels appear to be due to different charge states of the same center. Absorption and photoconductivity measurements support these determinations. Closed tube diffusions of silicon wafers on which cobalt has been evaporated result in maximum concentrations of electrically active cobalt of about 3×1014 cm−3.
From Hyperglycemia to Diabetic Kidney Disease: The Role of Metabolic, Hemodynamic, Intracellular Factors and Growth Factors/Cytokines (2004)

At present, diabetic kidney disease affects about 15-25% of type 1 and 30-40% of type 2 diabetic patients. Several decades of extensive research has elucidated various pathways to be implicated in the development of diabetic kidney disease. This review focuses on the metabolic factors beyond blood glucose that are involved in the pathogenesis of diabetic kidney disease, i.e., advanced glycation end-products and the aldose reductase system. Furthermore, the contribution of hemodynamic factors, the renin-angiotensin system, the endothelin system, and the nitric oxide system, as well as the prominent role of the intracellular signaling molecule protein kinase C are discussed. Finally, the respective roles of TGF-beta, GH and IGFs, vascular endothelial growth factor, and platelet-derived growth factor are covered. The complex interplay between these different pathways will be highlighted. A brief introduction to each system and description of its expression in the normal kidney is followed by in vitro, experimental, and clinical evidence addressing the role of the system in diabetic kidney disease. Finally, well-known and potential therapeutic strategies targeting each system are discussed, ending with an overall conclusion.
Relationship of Clinical and Cognitive Variables with Brain Morphometric Abnormalities in Alzheimer’s Disease: a Voxel Based Morphometric Study Using 3-Tesla MRI (2013)

Alzheimer's disease (AD) is associated with widespread structural and functional brain alterations. The current study examined the gray matter (GM) voxel based morphometric (VBM) correlates of cognitive and clinical severity scores in patients with AD. The study included 34 patients with AD according to NINCDS/ADRDA AD criteria and 28 matched elderly controls. All subjects were clinically evaluated using Hindi Mental Status Examination (HMSE), Everyday Abilities Scale for India (EASI) and the Clinical Dementia Rating (CDR) scale. The structural Magnetic Resonance Imaging (MRI) data were acquired using a 3 Tesla MRI scanner and VBM analysis was performed using VBM5.1 toolbox. The patients with AD had significantly lower GM volume, white matter volume and total brain volume as compared to controls. The HMSE scores were positively correlated (p=0.009) and EASI (p=0.04) & CDR (p=0.0004) were negatively correlated with the total GM volumes in patients with AD. The VBM analysis revealed diffuse GM atrophy in patients with AD. Frontal& temporal GM volumes were positively correlated with the HMSE scores. Thus the results of the study replicate the previous observations of generalized GM atrophy, in an Indian sample with AD. The cognitive decline, clinical dementia severity and impairment in activities of daily living were correlated whole brain GM and WM volumes as well as with specific brain regional atrophy in AD. However further studies with larger samples & with more detailed cognitive evaluation are required for confirmation & validation of the relationship between regional morphometric abnormalities and cognitive deficits in AD.
Memory-efficient state lookups with fast updates (2000)

Routers must do a best matching prefix lookup for every packet; solutions for Gigabit speeds are well known. As Internet link speeds higher, we seek a scalable solution whose speed scales with memory speeds while allowing large prefix databases. In this paper we show that providing such a solution requires careful attention to memory allocation and pipelining . This is because fast lookups require on-chip or off-chip SRAM which is limited by either expense or manufacturing process. We show that doing so while providing guarantees on the number of prefixes supported requires new algorithms and the breaking down of traditional abstraction boundaries between hardware and software. We introduce new problem-specific memory allocators that have provable memory utilization guarantees that can reach 100%; this is contrast to all standard allocators that can only guarantee 20% utilization when the requests can come in the range [1 ... 32]. An optimal version of our algorithm requires a new (but feasible) SRAM memory design that allows shifted access in addition to normal word access. Our techniques generalize to other IP lookup schemes and to other state lookups besides prefix lookup.
Junctional Tachycardia (1973)

IN THE ABSENCE of functioning anomalous connection between atria and ventricles, the A-V junction serves as the only link between these structures, allowing the atrial impulse to be transmitted to the ventricles.The A-V junction may be defined as consisting of the atrial approaches to the A-V node, the A-V node itself, and the penetrating portion of the His bundle.Total transection of the A-V junction at any point should produce A-V block, and stimulation in the presence of a normal His-Purkinje system should produce a narrow QRS.The electrophysiologic function of the A-V junction is primarily that of conduction.However, in addition, the A-V junction possesses intrinsic automaticity, allowing it to serve as a subsidiary pacemaker in the event of failure of proximal impulse formation or propagation.Under pathologic conditions, the A-V junction can serve as an ectopic pacemaker, or as a site of reentry. Electrophysiologic ConsiderationsExperimental studies demonstrating automaticity in the A-V junction were extensively reviewed by Scherf and Cohen.1 Earlier workers produced A-V junctional escape rhythms after depressing sinus node function by various surgical, chemical, mechanical, and thermal maneuvers.In addition, experimental A-V junctional rhythms were pro- duced by increasing sympathetic tone or by warming specific areas in the A-V junction.The site of origin in the A-V junction was determined by noting the timing of atrial and ventricular contrac- tion, and also by noting the initial sites of negativity with direct recording.Zahn suggested classification into upper, middle, and lower A-V nodal rhythms.2In upper nodal rhythms, atrial contraction preceded
Polymerization of Styrene by n-Butyllithium. II. Effect of Lewis Acids and Bases<sup>1</sup> (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerization of Styrene by n-Butyllithium. II. Effect of Lewis Acids and Bases1F. J. WelchCite this: J. Am. Chem. Soc. 1960, 82, 23, 6000–6005Publication Date (Print):December 1, 1960Publication History Published online1 May 2002Published inissue 1 December 1960https://pubs.acs.org/doi/10.1021/ja01508a009https://doi.org/10.1021/ja01508a009research-articleACS PublicationsRequest reuse permissionsArticle Views679Altmetric-Citations73LEARN 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-Alertsclose Get e-Alerts
Site-Specific Nitration and Oxidative Dityrosine Bridging of the τ Protein by Peroxynitrite: Implications for Alzheimer's Disease (2005)

Alzheimer's disease (AD) is a progressive amnestic disorder typified by the pathological misfolding and deposition of the microtubule-associated τ protein into neurofibrillary tangles (NFTs). While numerous post-translational modifications influence NFT formation, the molecular mechanisms responsible for τ aggregation remain enigmatic. Since nitrative and oxidative injury have previously been shown to play a mechanistic role in neurodegeneration, we examined whether these events influence τ aggregation. In this report, we characterize the effects of peroxynitrite (ONOO-)-mediated nitration and oxidation on τ polymerization in vitro. Treatment of τ with ONOO- results in 3-nitrotyrosine (3-NT) immunoreactivity and the formation of heat-stable, SDS-insoluble oligomers. Using ESI-MS and HPLC with fluorescent detection, we show that these higher-order aggregates contain 3,3‘-dityrosine (3,3‘-DT). Tyrosine (Tyr) residues are critical for ONOO--mediated oligomerization, as τ proteins lacking all Tyr residues fail to generate oligomers upon ONOO- treatment. Further, τ nitration targets residues Y18, Y29, and to a lesser degree Y197 and Y394, and nitration at these sites inhibits in vitro polymerization. The inhibitory effect of nitration on τ polymerization is specific for the 3-NT modification, as pseudophosphorylation at these same Tyr residues does not inhibit τ assembly. Our results suggest that the nitrative and oxidative roles of ONOO- differentially affect τ polymerization and that ONOO--mediated cross-linking could facilitate τ aggregation in AD.
Structure of FabH and factors affecting the distribution of branched fatty acids in<i>Micrococcus luteus</i> (2012)

Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.
Efficient scheduling of task graph collections on heterogeneous resources (2009)

In this paper, we focus on scheduling jobs on computing grids. In our model, a grid job is made of a large collection of input data sets, which must all be processed by the same task graph or workflow, thus resulting in a collection of task graphs problem. We are looking for a competitive scheduling algorithm not requiring complex control. We thus only consider single-allocation strategies. In addition to a mixed linear programming approach to find an optimal allocation, we present different heuristic schemes. Then, using simulations, we compare the performance of our different heuristics to the performance of a classical scheduling policy in Grids, HEFT. The results show that some of our static-scheduling policies take advantage of their platform and application knowledge and outperform HEFT, especially under communication-intensive scenarios. In particular, one of our heuristics, DELEGATE, almost always achieves the best performance while having lower running times than HEFT.
Quadrupole Mass Filter Transmission in Island a of the First Stability Region with Quadrupolar Excitation (2002)

With quadrupolar excitation of ions by a small auxiliary RF field, the first stability region of the quadrupole mass filter splits into islands of stability. This study is of the first upper island, “A”. We calculate the location of this island for different values of the excitation parameter, q‘. Ion trajectory calculations are used to study the influence of the input fringing fields and the separation time. The Runge-Kutta–Nustrom–Dormand-Prince (RK–N–DP) method of order 6(7) is used for integration of the equations of ion motion. It is found that a weak auxiliary RF signal improves the peak shape for quadrupole mass filters that have weak field distortions.