gebhart/patrepeval huggingface dataset:
Programmable surface deformation: thickness-mode electroactive polymer actuators and their applications (2005)

Many different actuator configurations based on SRI International’s dielectric elastomer (DE) type of electroactive polymer (EAP) have been developed for a variety of applications. These actuators have shown excellent actuation properties including maximum actuation strains of up to 380% and energy densities of up to 3.4 J/g, using the planar mode of actuation. Recently, SRI has investigated different configurations of DE actuators that allow complex changes in surface shape and thus the creation of active surface texture. In this configuration, the “active” polymer film is bonded or coated with a thicker passive layer, such that changes in the polymer thickness during actuation of the DE device are at least partially transferred to (and often amplified by) the passive layer. Although the device gives out-of-plane motion, it can nonetheless be fabricated using two-dimensional patterning. The result is a rugged, flexible, and conformal skin that can be spatially actuated by subjecting patterned electrodes on a polymer substrate to an electric field. Using thickness-mode DE, we have demonstrated thickness changes of the order of 0.5 - 2 mm by laminating a passive elastomeric layer to a DE polymer that is only 60 &mu;m in thickness. Such thickness changes would otherwise require a very large number of stacked layers of the DE film to produce comparable surface deformations. Preliminary pressures of 4.2 kPa (0.6 psi) in a direction normal to the plane of the DE film have been measured. However, theoretical calculations indicate that pressures of the order of 100 kPa are feasible using a single layer of DE film. Stacking multiple layers of DE film can lead to a further increase in achievable actuation pressures. Even with current levels of thickness change and actuation pressures, potential applications of such surface texture change are numerous. A thin, compliant pad made from these actuators can have a massaging or sensory augmentation function, and can be incorporated into garments if desired. The bumps and troughs could act as valves or pumping elements in a fluidic or microfluidic system. Such a device could also be the basis of a smart skin that controls boundary-layer flow properties in a boat or airplane so as to reduce overall drag. The DE elements of the pad can also be used as sensors to make a touch-sensitive skin for recording human interaction with the environment. By driving a thin, compliant vibrating layer at resonant frequencies, one can also configure these devices as solid or fluidic conveyors that transport material on a macroscopic or microscopic scale.
Creating RNA Bulges:  Cleavage of RNA in RNA/DNA Duplexes by Metal Ion Catalysis (1996)

The manipulation of a single-stranded RNA target by forming different RNA/antisense hybrids demonstrates the possibility of cleaving the RNA strand within duplexes. This was achieved using the sequence composition of the antisense oligonucleotide, an approach that results in various bulges [unpaired base(s)] in the RNA target, which is then cleavable at these specific bulge sites under free metal ion or metal complex catalysis. RNA cleavages promoted by metal ions were performed under mild conditions and characterized by separating the RNA fragments carrying end label. The observed products result from intramolecular transesterification causing RNA strand scission. No detectable cleavage of the RNA was observed with either a fully complementary RNA/antisense hybrid or a bulged base in the antisense strand. A molecular modeling study of the RNA backbone suggests that the local conformation of the RNA backbone at a bulge in such hybrid duplexes greatly facilitates the metal-assisted catalytic cleavage. Endonucleolytic RNA cleavage within an RNA/antisense hybrid by metal complexes attached to the antisense oligonucleotide might lead to a new approach in antisense technology with artificial ribonucleases which operate with catalytic turnover.
Improving access to the international coverage of reports of controlled trials in electronic databases: a search of the Australasian Medical Index (2002)

The large proportion of trials found to be unique to the AMI database increases the pool of studies available to systematic reviewers, and helps ensure CCTR remains the most comprehensive source of trials.
Tumor Regression and Autoimmunity after Reversal of a Functionally Tolerant State of Self-reactive CD8+ T Cells (2003)

Many tumor-associated antigens are derived from nonmutated "self" proteins. T cells infiltrating tumor deposits recognize self-antigens presented by tumor cells and can be expanded in vivo with vaccination. These T cells exist in a functionally tolerant state, as they rarely result in tumor eradication. We found that tumor growth and lethality were unchanged in mice even after adoptive transfer of large numbers of T cells specific for an MHC class I-restricted epitope of the self/tumor antigen gp100. We sought to develop new strategies that would reverse the functionally tolerant state of self/tumor antigen-reactive T cells and enable the destruction of large (with products of perpendicular diameters of >50 mm2), subcutaneous, unmanipulated, poorly immunogenic B16 tumors that were established for up to 14 d before the start of treatment. We have defined three elements that are all strictly necessary to induce tumor regression in this model: (a) adoptive transfer of tumor-specific T cells; (b) T cell stimulation through antigen-specific vaccination with an altered peptide ligand, rather than the native self-peptide; and (c) coadministration of a T cell growth and activation factor. Cells, vaccination, or cyto-kine given alone or any two in combination were insufficient to induce tumor destruction. Autoimmune vitiligo was observed in mice cured of their disease. These findings illustrate that adoptive transfer of T cells and IL-2 can augment the function of a cancer vaccine. Furthermore, these data represent the first demonstration of complete cures of large, established, poorly immunogenic, unmanipulated solid tumors using T cells specific for a true self/tumor antigen and form the basis for a new approach to the treatment of patients with cancer.
Magnetic Alignment of Fluorescent Nanowires (2001)

Nickel nanowires prepared by electrochemical growth in alumina templates have been removed from their templates and functionalized with luminescent porphyrins. The nanowires response to magnetic fields was quantified using video microscopy. In viscous solvents, magnetic fields can be used to orient the nanowires; in mobile solvents, the nanowires form chains in a head-to-tail configuration when a small magnetic field is applied. The dynamics for chain formation have been quantitatively modeled. The results demonstrate a new approach for assembling nanowires.
mRNA Differential Display in a Microbial Enrichment Culture: Simultaneous Identification of Three Cyclohexanone Monooxygenases from Three Species (2003)

mRNA differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. Thirteen DNA fragments randomly amplified from the total RNA of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. Nine of these DNA fragments are part of genes encoding three distinct Baeyer-Villiger cyclohexanone monooxygenases from three different bacterial species present in the enrichment culture. In Arthrobacter sp. strain BP2 and Rhodococcus sp. strain Phi2, the monooxygenase is part of a gene cluster that includes all the genes required for the degradation of cyclohexanone, while in Rhodococcus sp. strain Phi1 the genes surrounding the monooxygenase are not predicted to be involved in this degradation pathway but rather seem to belong to a biosynthetic pathway. Furthermore, in the case of Arthrobacter strain BP2, three other genes flanking the monooxygenase were identified by differential display, demonstrating that the repeated sampling of bacterial operons shown earlier for a pure culture (D. M. Walters, R. Russ, H. Knackmuss, and P. E. Rouvière, Gene 273:305-315, 2001) is also possible for microbial communities. The activity of the three cyclohexanone monooxygenases was confirmed and characterized following their expression in Escherichia coli.
Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases (1999)

DNA sequence database search revealed that most of Tn5053/Tn402 family transposons inserted into natural plasmids were located in putative res regions upstream of genes encoding various resolvase-like proteins. Some of these resolvase genes belonged to Tn3 family transposons and were closely related to the tnpR genes of Tn1721 and a recently detected Tn5044. Using recombinant plasmids containing fragments of Tn1721 or Tn5044 as targets in transposition experiments, we have demonstrated that Tn5053 displays striking insertional preference for the res regions of these transposons: more than 70% of Tn5053 insertion events occur in clusters inside the target res regions, while most remaining insertion events occur no further than 200 base pairs away from both sides of the res regions. We demonstrate that Tn5053 insertions (both into and outside a res region of the target plasmid) require the presence of a functional cognate resolvase gene either in cis or in trans. To our knowledge, this is the first case when a site-specific recombination system outside a transposon has been shown to be involved in transposition.
Within‐ and between‐subject variations in pharmacokinetic parameters of ethanol by analysis of breath, venous blood and urine (2000)

The low within-subject variation of the key parameter Vss (only 2%) suggests that ethanol dilution analysed by the pharmacokinetic model applied here may be used as an index of the total body water. Breath samples yielded at least as good reproducibility in the model parameters as venous blood.
Gimme a brake: HPK1 regulates LFA-1 and neutrophil traction (2013)

In this issue of Blood, Jakob et al report that hematopoietic progenitor kinase 1 (HPK1) participates during signaling of neutrophil recruitment by acting as a regulator of the adhesiveness of the b2-integrin lymphocyte function-associated antigen 1 (LFA-1) during acute inflammation.
A Cell-based Model of Hemostasis (2001)

Based on our work and that of many other workers, we have developed a model of coagulation in vivo. Many workers have demonstrated mechanisms by which cells can influence the coagulation process. Nonetheless, the prevailing view of hemostasis remains that the protein coagulation factors direct and control the process with cells serving primarily to provide a phosphatidylserine containing surface on which the procoagulant complexes are assembled. By contrast, we propose a model in which coagulation is regulated by properties of cell surfaces. This model emphasizes the importance of specific cellular receptors for the coagulation proteins. Thus, cells with similar phosphatidylserine content can play very different roles in hemostasis depending on their complement of surface receptors. We propose that coagulation occurs not as a "cascade", but in three overlapping stages: 1) initiation, which occurs on a tissue factor bearing cell; 2) amplification, in which platelets and cofactors are activated to set the stage for large scale thrombin generation; and 3) propagation, in which large amounts of thrombin are generated on the platelet surface. This cell based model explains some aspects of hemostasis that a protein-centric model does not.
Penetration of Drugs through the Blood-Cerebrospinal Fluid/Blood-Brain Barrier for Treatment of Central Nervous System Infections (2010)

The entry of anti-infectives into the central nervous system (CNS) depends on the compartment studied, molecular size, electric charge, lipophilicity, plasma protein binding, affinity to active transport systems at the blood-brain/blood-cerebrospinal fluid (CSF) barrier, and host factors such as meningeal inflammation and CSF flow. Since concentrations in microdialysates and abscesses are not frequently available for humans, this review focuses on drug CSF concentrations. The ideal compound to treat CNS infections is of small molecular size, is moderately lipophilic, has a low level of plasma protein binding, has a volume of distribution of around 1 liter/kg, and is not a strong ligand of an efflux pump at the blood-brain or blood-CSF barrier. When several equally active compounds are available, a drug which comes close to these physicochemical and pharmacokinetic properties should be preferred. Several anti-infectives (e.g., isoniazid, pyrazinamide, linezolid, metronidazole, fluconazole, and some fluoroquinolones) reach a CSF-to-serum ratio of the areas under the curves close to 1.0 and, therefore, are extremely valuable for the treatment of CNS infections. In many cases, however, pharmacokinetics have to be balanced against in vitro activity. Direct injection of drugs, which do not readily penetrate into the CNS, into the ventricular or lumbar CSF is indicated when other effective therapeutic options are unavailable.
Leukemia diagnosis and testing of complement-fixing antibodies for bone marrow purging in acute lymphoid leukemia (1986)

In this paper a microplate method is described for diagnosing acute leukemia and for investigating the reactivity of monoclonal antibodies (MoAbs) against membrane antigens in combination with rabbit or murine antibodies to nuclear terminal transferase (TdT). The speed of this method facilitates the investigation of fresh leukemic cells from individual patients and assesses the cytolytic efficacy of the relevant MoAbs in the presence of complement (C'). Lymphoblasts (TdT+) are mixed in equal proportions with known numbers of “inert” cells, eg, RBC or nonleukemic bone marrow (BM). Following incubation with MoAbs and C' the ratio of residual TdT+ cells and inert cells is determined on cytospin preparations. Initially, percentages of TdT+ cells are counted in a unit volume of 5,000 inert cells, followed by the scanning of greater than 2 X 10(4) inert cells on entire slides. With this method more than 4 log cytoreduction of TdT + cells is detected. The method is also applicable for studying the cytolysis of malignant B cells by using mostly monoclonal lg expression rather than TdT for the identification of residual B cells. Ten representative patients selected from a group of greater than 100 are reported. In some cases cytoreduction of greater than 4 log with no identifiable residual TdT + cells is achieved by a single C'-fixing MoAb: anti-CD10 (RFAL3) in common acute lymphoid leukemia (ALL) and anti-CD7 (RFT2) in T cell ALL (T-ALL). Other cases require cocktails of anti-CD10, anti-CD19, and anti-CD24 in common ALL or anti-CD7 and anti-CD8 in T-ALL. In T-ALL a few TdT + cells remain that exhibit the features of normal TdT + BM cells (CD7-, HLA-DR+). This is particularly noticeable when patients are studied in partial remission or if nonleukemic BM is used as a source of inert cells. The methods described here contribute to establishing a range of MoAbs (ie, of IgM class) and techniques for efficient purging and to comparing the efficacy of “clean-up,” in remission, of common ALL, T-ALL, and B cell malignancies.
Scanned light pulse technique for the investigation of insulator–semiconductor interfaces (1983)

A new measurement method, scanned light pulse technique, for the investigation of the interface properties of metal–insulator–semiconductor (MIS) structures is introduced. The measured signal is the charge contents of current transients induced by light pulses applied to the investigated sample. This signal depends on surface potential, interface state density and voltage applied to the MIS structure. By analyzing the results of such measurements it is quantitatively demonstrated how insulator charge and interface state distribution influence the voltage dependence. By scanning a light spot across the surface of an MIS structure with transparent metal electrode it is further shown that pictures of the spatial variation of the surface potential and the interface state density can be obtained.
Role for Glycogen Synthase Kinase-3 in NK Cell Cytotoxicity and X-Linked Lymphoproliferative Disease (2005)

NK cells from individuals with X-linked lymphoproliferative (XLP) disease exhibit functional defects when stimulated through the NK receptor, 2B4 (CD244). These defects are likely a consequence of aberrant intracellular signaling initiated by mutations of the adaptor molecule SLAM-associated protein. In this report, we show that NK cells from individuals with XLP but not healthy individuals fail to phosphorylate and thereby inactivate glycogen synthase kinase-3 (GSK-3) following 2B4 stimulation. Lack of GSK-3 phosphorylation prevented the accumulation of the transcriptional coactivator beta-catenin in the cytoplasm and its subsequent translocation to the nucleus. Potential signaling pathways leading from 2B4 stimulation to GSK-3 phosphorylation were also investigated. Ligation of 2B4 resulted in the phosphorylation of the guanine nucleotide exchange factor, Vav-1, and subsequent activation of the GTP-binding protein Rac-1 (but not Ras) and the serine-threonine kinase Raf-1 in healthy but not XLP-derived NK cells. In addition, the activity of MEK-2 (but not MEK-1) was up-regulated, and Erk1/2 was phosphorylated in normal NK cells but not those from an individual with XLP suggesting that these proteins relay SLAM-associated protein-dependent signals from 2B4. Finally, inactivation of GSK-3 using a specific inhibitor of GSK-3beta increased the cytotoxicity and cytokine secretion of both healthy and XLP NK cells. These data indicate that the signaling of 2B4 in NK cells is mediated by GSK-3 and beta-catenin, possibly through a signal transduction pathway that involves Vav-1, Rac-1, Raf-1, MEK-2, and Erk1/2 and that this pathway is aberrant in individuals with XLP.
Cloning of monomeric human papillomavirus type 16 DNA integrated within cell DNA from a cervical carcinoma (1986)

We have molecularly cloned and characterized monomeric human papillomavirus type 16 DNA with flanking cell DNA sequences from a cervical carcinoma. Determination of nucleotide sequence around the junctions of human papillomavirus and cell DNAs revealed that at the site of integration within cell DNA the cloned viral DNA had a deletion between nucleotides 1,284 and 4,471 (numbering system from K. Seedorf, G. Krämmer, M. Dürst, S. Suhai, and W. G. Röwekamp, Virology 145:181-185, 1985), which includes the greater part of E1 gene and the entire E2 gene. In the remaining part of the E1 gene, three guanines were found at the location where two guanines at nucleotides 1,137 and 1,138 have been recorded. This additional guanine shifted the reading frame and erased an interruption in the E1 gene described by Seedorf et al. The data strongly suggest that, like other papillomaviruses, human papillomavirus type 16 has an uninterrupted E1 gene.
Low-loss 1.5% Δ arrayed waveguide grating with spot-size converters (2002)

We achieved a very low insertion loss of 0.7 dB in a 1.5% /spl Delta/ arrayed-waveguide grating by successfully fabricating spot-size converters that reduced single-mode fiber coupling loss from 1.6 to 0.2 dB/point.
Slepian-Wolf coding for nonuniform sources using turbo codes (2004)

The recently proposed turbo-binning scheme is shown to be both efficient and optimal for uniform source Slepian-Wolf coding problem (Z. Tu et al., 2003). This paper studies the case when sources are i.i.d. but nonuniformly distributed. It is firstly shown that any algebraic binning scheme based on linear codes is optimal for nonuniform sources only asymptotically. Next two modifications are proposed to improve the performance of the turbo-binning scheme for nonuniform sources. The first is to carefully design the constituent encoder structures to maximally match the turbo code to the nonuniform source distribution, and the second is to use variable-length syndrome sequences to index the bins. Simulations show that the combination of both strategies can lead to an improvement of as much as 0.22 bit/symbol in overall compression rate for highly nonuniform sources.
Microfabricated conductimetric pH sensor (1995)

A miniature conductimetric pH sensor has been developed, based on the measurement of the conductivity of a pH-responsive hydrogel. The microfabricated sensor is constructed by coating planar interdigitated electrode arrays with a photolithographically patterned hydrogel membrane. The hydrogel sensing layer swells or shrinks to a hydration determined by the pH of the solution in which it is immersed. This leads to a corresponding increase or decrease in the mobility of the ions partitioned by the gel. The sensitivity of ion mobility to small changes in hydration leads to sensor resistance changes as large as 45% per pH unit at physiological pH. Since the sensor operation is based on changes in ion mobility, the sensor operates in high ionic strength solutions, whereas most conductimetric sensors to date have been limited to use in solutions with low mobile ion content. The sensor response time is approximately five minutes, and appears to be limited by the protonation/deprotonation of the polybasic hydrogel. Devices have operated for more than six weeks with a 50% loss of sensitivity over three weeks.
An analysis of Bayesian classifiers (1992)

In this paper we present an average-case analysis of the Bayesian classifier, a simple probabilistic induction algorithm that fares remarkably well on many learning tasks. Our analysis assumes a monotone conjunctive target concept, Boolean attributes that are independent of each other and that follow a single distribution, and the absence of attribute noise. We first calculate the probability that the algorithm will induce an arbitrary pair of concept descriptions; we then use this expression to compute the probability of correct classification over the space of instances. The analysis takes into account the number of training instances, the number of relevant and irrelevant attributes, the distribution of these attributes, and the level of class noise. In addition, we explore the behavioral implications of the analysis by presenting predicted learning curves for a number of artificial domains. We also give experimental results on these domains as a check on our reasoning. Finally, we ...
Multicenter Standardized 18F-FDG PET Diagnosis of Mild Cognitive Impairment, Alzheimer's Disease, and Other Dementias (2008)

Standardized automated analysis of (18)F-FDG PET scans may provide an objective and sensitive support to the clinical diagnosis in early dementia.