gebhart/patrepeval huggingface dataset:
Evaluation of Tyro3 Expression, Gas6-Mediated Akt Phosphorylation, and the Impact of Anti-Tyro3 Antibodies in Melanoma Cell Lines (2013)

Tyro3, a member of the Tyro3/Axl/Mer (TAM) family of receptor tyrosine kinases, has emerged as a potential oncogene in melanoma. Here, we confirm that Tyro3 is specifically overexpressed in primary melanoma samples and show that Tyro3 is expressed at varying levels in numerous melanoma cell lines. Short hairpin RNA-mediated knockdown of Tyro3 led to significant cell death via apoptotic mechanisms in nearly all melanoma cell lines tested, regardless of the BRAF or NRAS mutation status or co-expression of Axl and/or Mer. We generated soluble and monomeric versions of the human Tyro3 extracellular domain and human Gas6 for affinity measurements and correlated these values with the level of Gas6 required to induce Tyro3 signaling in cellular assays. Calcium was critical for the correct folding of Gas6 and its binding to Tyro3. In melanoma cell lines, Gas6 induced Tyro3 phosphorylation and downstream Akt phosphorylation without apparent effects on Erk. We generated monoclonal antibodies (mAbs) against Tyro3 to examine their effect on survival signaling in melanoma cell lines. The mAbs generated against Tyro3 included nonligand blockers, partial blockers, and competitive ligand blockers. A number of weak and partial ligand blockers (all recognizing the Tyro3 Ig domains) were the most effective at blocking ligand-mediated downstream signaling of Tyro3. Overall, these data indicate that Tyro3 may confer increased survival signals in melanoma cells and can be stymied using inhibitory mAbs. These mAbs may be useful for further investigations of the role of Tyro3 in melanoma.
Epitope Recognition in Histone H1 by Sle Autoantibodies in the Presence of a Dna-Ligand (1992)

To investigate the specificity of anti HI antibodies peptides from the N- and C-domain of HI and the synthetic oligonucleotide (AT)6 were complexed. Circular dichroism (CD) spectroscopy indicated that the free peptides H1(1-16), H1(204-218) and C(121-210) in low salt buffer assume a random structure but become helical when bound to the oligonucleotide. The structured and unstructured HI fragments were then analyzed by enzyme linked immunosorbent assay (ELISA) with anti-Hl antibodies in sera from patients with systemic lupus erythematosis (SLE) and with the monoclonal anti-Hl antibody MRA-12 derived from MLR lpr/lpr autoimmune mice. Binding of these antibodies to HI(204-218) and C was inhibited to a level of 50% when these HI peptides were complexed with (AT)6. When the same antibody was tested with HI fragment GC(34-210), attachment to oligonucleotide (AT)6 did not influence antibody binding. Competition studies with liquid phase GC and C antigen against solid phase GC and C indicated that liquid phase GC was more efficient in displacing antibody binding reactivity than liquid phase C. The displacement effect of both liquid phase antigens was greatest against solid phase C. We conclude that anti-Hl autoantibodies are directed against an epitope located near the junction of the G- and C-domain which is exposed and not masked when HI is bound to DNA.
PEROXIDASE-LABELED ANTIBODY A NEW METHOD OF CONJUGATION (1974)

A new method of conjugating horseradish peroxidase with proteins was developed. The carbohydrate moiety of fluorodinitrobenzene-blocked peroxidase was oxidized with sodium periodate to form aldehyde groups. The peroxidase-aldehyde was then bound to free amino groups of proteins unidirectionally at high efficiencies. Peroxidase-labeled immunoglobulin retained its immunologic as well as enzymatic activities.
Ambient and Unobtrusive Cardiorespiratory Monitoring Techniques (2015)

Monitoring vital signs through unobtrusive means is a goal which has attracted a lot of attention in the past decade. This review provides a systematic and comprehensive review over the current state of the field of ambient and unobtrusive cardiorespiratory monitoring. To this end, nine different sensing modalities which have been in the focus of current research activities are covered: capacitive electrocardiography, seismo- and ballistocardiography, reflective photoplethysmography (PPG) and PPG imaging, thermography, methods relying on laser or radar for distance-based measurements, video motion analysis, as well as methods using high-frequency electromagnetic fields. Current trends in these subfields are reviewed. Moreover, we systematically analyze similarities and differences between these methods with respect to the physiological and physical effects they sense as well as the resulting implications. Finally, future research trends for the field as a whole are identified.
Leishmania EF-1α Activates the Src Homology 2 Domain Containing Tyrosine Phosphatase SHP-1 Leading to Macrophage Deactivation (2002)

The human leishmaniasis are persistent infections of macrophages caused by protozoa of the genus Leishmania. The chronic nature of these infections is in part related to induction of macrophage deactivation, linked to activation of the Src homology 2 domain containing tyrosine phosphatase-1 (SHP-1) in infected cells. To investigate the mechanism of SHP-1 activation, lysates of Leishmania donovani promastigotes were subjected to SHP-1 affinity chromatography and proteins bound to the matrix were sequenced by mass spectrometry. This resulted in the identification of Leishmania elongation factor-1alpha (EF-1alpha) as a SHP-1-binding protein. Purified Leishmania EF-1alpha, but not host cell EF-1alpha, bound directly to SHP-1 in vitro leading to its activation. Three independent lines of evidence indicated that Leishmania EF-1alpha may be exported from the phagosome thereby enabling targeting of host SHP-1. First, cytosolic fractions prepared from macrophages infected with [(35)S]methionine-labeled organisms contained Leishmania EF-1alpha. Second, confocal, fluorescence microscopy using Leishmania-specific antisera detected Leishmania EF-1alpha in the cytosol of infected cells. Third, co-immunoprecipitation showed that Leishmania EF-1alpha was associated with SHP-1 in vivo in infected cells. Finally, introduction of purified Leishmania EF-1alpha, but not the corresponding host protein into macrophages activated SHP-1 and blocked the induction of inducible nitric-oxide synthase expression in response to interferon-gamma. Thus, Leishmania EF-1alpha is identified as a novel SHP-1-binding and activating protein that recapitulates the deactivated phenotype of infected macrophages.
An Overview of Near Field UHF RFID (2007)

In this paper, an overview of near field UHF RFID is presented. This technology recently received attention because of its possible use for item-level tagging where LF/HF RFID has traditionally been used. We review the relevant literature, discuss basic theory of near and far field antenna coupling in application to RFID, and present some experimental measurements.
Transition from compensatory hypertrophy to dilated, failing left ventricles in Dahl salt-sensitive rats (1994)

To establish an experimental model for studying a specific transitional stage for compensatory hypertrophy to heart failure, we studied the pathophysiology of the left ventricle (LV) in Dahl salt-sensitive (DS) rats fed a high-salt diet. DS rats fed an 8% NaCl diet after the age of 6 wk developed concentric LV hypertrophy at 11 wk, followed by marked LV dilatation at 15-20 wk. During the latter stage, the DS rats showed labored respiration with LV global hypokinesis. All the DS rats died within 1 wk by massive pulmonary congestion. The dissected left ventricles revealed chamber dilatation and a marked increase in mass without myocardial necrosis. In contrast, corresponding Dahl salt-resistant (DR) rats fed the same diet showed neither mortality nor any of these pathological changes. The in vivo LV end-systolic pressure-volume relationship shifted to the right with a less steep slope in the failing DS rats compared with that in age-matched DR rats. Isometric contractions of LV papillary muscles isolated from these DS rats showed reduced tension development in the failing stage, but normal tension development in the hypertrophied stage. In conclusion, the DS rat fed a high-salt diet is a useful model showing rapidly developing congestive heart failure, in which the transition from compensatory hypertrophy to decompensatory dilatation of LV is easily and consistently manifested.
Scurfin (FOXP3) Acts as a Repressor of Transcription and Regulates T Cell Activation (2001)

We have recently identified and cloned Foxp3, the gene defective in mice with the scurfy mutation. The immune dysregulation documented in these mice and in humans with mutations in the orthologous gene indicates that the foxp3 gene product, scurfin, is involved in the regulation of T cell activation and differentiation. The autoimmune state observed in these patients with the immune dysregulation polyendocrinopathy, enteropathy, X-linked syndrome, or X-linked autoimmunity-allergic dysregulation syndrome also points to a critical role for scurfin in the regulation of T cell homeostasis. FOXP3 encodes a novel member of the forkhead family of transcription factors. Here we demonstrate that this structural domain is required for nuclear localization and DNA binding. Scurfin, transiently expressed in heterologous cells, represses transcription of a reporter containing a multimeric forkhead binding site. Upon overexpression in CD4 T cells, scurfin attenuates activation-induced cytokine production and proliferation. We have identified FKH binding sequences adjacent to critical NFAT regulatory sites in the promoters of several cytokine genes whose expression is sensitive to changes in SFN abundance. Our findings indicate that the ability of scurfin to bind DNA, and presumably repress transcription, plays a paramount role in determining the amplitude of the response of CD4 T cells to activation.
Isolation and characterization of two repetitive DNA fragments located near the centromere of the mouse X chromosome (1985)

Two repetitive DNA fragments located on the mouse X chromosome are described. The fragments were isolated from a lambda phage library enriched in X-chromosomal sequences by flow sorting. Both fragments, which are repeated 20 to 50 times in the genome, were mapped to the mouse X chromosome by Southern blot hybridization to DNA from hybrid cells retaining the mouse X chromosome, by dosage analysis, and by in situ hybridization to mouse chromosomes. In mouse strain C57BL/10BK, one fragment appeared to be located only on the X chromosome, while the other fragment had homologous sequences on chromosome 11 in addition to the X chromosome. The latter fragment showed DNA variants between mouse strains, which are potentially useful for mapping. Both fragments cross-hybridized to another mouse species: Mus caroli. In this species, each fragment appeared to be located on the X chromosome, indicating that some X-chromosome repetitive sequences are partially conserved. In addition, one fragment cross-hybridized to human DNA.
A unified formulation of the constant temperature molecular dynamics methods (1984)

Three recently proposed constant temperature molecular dynamics methods by: (i) Nosé (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.
Targeting E3 Ubiquitin Ligases for Cancer Therapy (2003)

E3 ubiquitin ligases are a large family of proteins that can be classified into three major structurally distinct types: N-end rule E3s, E3s containing the HECT (Homology to E6AP C-Terminus) domain, and E3s with the RING (Really Interesting New Gene) finger, including its derivatives, the U- Box and the PHD (Plant Homeo-Domain). E3 ubiquitin ligases exist as single polypeptide or multimeric complexes. Together with ubiquitin activating enzyme E1 and ubiquitin conjugating enzyme E2, E3 ubiquitin ligases catalyze the ubiquitination of a variety of protein substrates for targeted degradation via the 26S proteasome. E3 ubiqutin ligases, therefore, play an essential role in regulation of many biological processes. Furthermore, E3s are enzymes that determine the specificity of protein substrates; they represent a class of "drugable" targets for pharmaceutical intervention. In this review, I will mainly focus on E3 ubiquitin ligases as potential cancer targets and discuss three of the most promising E3s, Mdm2/Hdm2, IAPs, and SCF, for their target rationales, target validation, and critical issues associated with them. These E3 ligases or their components are overexpressed in many human cancers and their inhibition leads to growth suppression or apoptosis. In addition, I will evaluate two current methodologies available for the high throughput screening for small molecular weight chemical inhibitors of the E3 ubiquitin ligases. Although targeting E3 ubiquitin ligases is still in its infancy, speedy approval of the general proteasome inhibitor, Velcade (bortezomib) by the FDA for the treatment of relapsed and refractory multiple myeloma suggests the promise of specific E3 inhibitors in anti-cancer therapy. Emerging technologies, such as siRNA, will provide a better validation of many E3s. It is anticipated that E3 ubiquitin ligases will represent an important new target platform for future mechanism-driven drug discovery.
Construction and characterization of the hybrid bacteriophage lambda Charon vectors for DNA cloning (1979)

Twenty hybrid lambda phages especially designed for molecular cloning have been constructed and named Charon phages. These phages differ in the ranges of sizes of DNA fragments that may be inserted, by the selections and screens which may be used to isolate and detect the incorporation of cloned fragments, by the way transcription of the cloned fragment may be controlled, by the different restriction enzymes that can be used for cloning, by the phage immunities that may be employed for controlling replication and transcription, and by the biological safety features that they contain. The crosses used to produce the vectors are described, and their genealogy is discussed. The structure of each vector has been verified by genetic tests, by DNA length determinations, by electron micrographic analysis of DNA heteroduplexes, and by gel electrophoresis of restriction enzyme digests. In the course of these constructions, a new EcoRI site was found in a derivative of lambda Aam32Bam1 which maps very near the left cohesive end of lambda.
Hype, hope and hubris: the quest for the killer application in microfluidics (2009)

A graphical abstract is available for this content
Drop-off Detection with the Long Cane: Effects of Different Cane Techniques on Performance. (2009)

This study compared the drop-off detection performance with the two-point touch and constant contact cane techniques using a repeated-measures design with a convenience sample of 15 cane users with visual impairments. The constant contact technique was superior to the two-point touch technique in the drop-off detection rate and the 50% detection threshold. The findings may help an orientation and mobility instructor select an appropriate technique for a particular client or training situation.
StyleCam: Interactive, Stylized 3D Experiences using Integrated Spatial and Temporal Controls. (2003)

This thesis describes StyleCam, an approach for authoring 3D viewing experiences that incorporate stylistic elements which are not available in typical 3D viewers. StyleCam allows the author to tailor what the user sees and when they see it. The resulting viewing experience can approach the visual richness and pacing of highly authored visual content such as television commercials or feature films. StyleCam allows for a satisfying level of interactivity while avoiding the problems inherent in using unconstrained camera models. StyleCam&apos;s main components are camera surfaces which spatially constrain the viewing camera; animation clips that allow for appealing transitions between camera surfaces; and a simple, unified, interaction technique that permits the user to seamlessly and continuously move between spatial-control of the camera and temporal-control of the animated transitions. In addition to describing the conceptual model of StyleCam and its current implementation, we present the results of an evaluation involving real users.
Modification of hemoglobin with analogs of aspirin. (1980)

A variety of acyl esters of salicyclic acid and 3,5-dibromosalicylic acid have been prepared and examined for their ability to place the acyl group on hemoglobin. In general, short chain acyl groups (C2 and C3) are more reactive than longer chains (C4 to C10), but longer chains may be more effective with intact red cells because of their enhanced ability to permeate the erythrocyte membrane. The brominated salicyl esters also exhibit enhanced permeation of the membrane, as well as increased activity due to activation at the acyl site. Bis(salicyl) esters, nonbrominated and brominated, are more reactive than corresponding monoesters, and those from C4 dicarboxylic acids connect beta subunits by covalent bridges. These double-headed aspirins have the attractive features of being bound selectively by hemoglobin and of forming a covalent cross-link that may influence the conformation of the tetramer.
Comparison of MTT and ATP‐based assays for the measurement of viable cell number (1995)

Cell viability assays are widely used to assess the effect chemotherapeutic drugs and other agents on cell lines and have shown promise for the prediction of tumour chemosensitivity. In this study we have compared two viability assays using Daudi and CCRF-CEM cell lines over a range of 1500-100,000 cells/well of a microplate. The ATP assay was able to detect the lower limit of 1563 cells/well with luminescence values at least 100 x background readings, while the MTT assay could not detect less than 25,000 cells/well above background readings. The ATP assay also showed better reproducibility and sensitivity when cells were grown in microtitre plates over several days, and is particularly useful for the measurement of viability with low cell numbers.
Reversibly Crosslinked Nanocarriers for on-demand Drug Delivery in Cancer Treatment (2012)

Polymer micelles have proven to be one of the most versatile nanocarriers for anticancer drug delivery. However, the in vitro and in vivo stability of micelles remains a challenge due to the dynamic nature of these self-assembled systems, which leads to premature drug release and nonspecific biodistribution in vivo. Recently, reversibly crosslinked micelles have been developed to provide solutions to stabilize nanocarriers in blood circulation. Increased stability allows nanoparticles to accumulate at tumor sites efficiently via passive and/or active tumor targeting, while cleavage of the micelle crosslinkages, through internal or external stimuli, facilitates on-demand drug release. In this review, various crosslinking chemistries as well as the choices for reversible linkages in these nanocarriers will be introduced. Then, the development of reversibly crosslinked micelles for on-demand drug release in response to single or dual stimuli in the tumor microenvironment is discussed, for example, acidic pH, reducing microenvironment, enzymatic microenvironment, photoirradiation and the administration of competitive reagents postmicelle delivery.
Recombinant transforming growth factor beta 1 and beta 2 protect mice from acutely lethal doses of 5-fluorouracil and doxorubicin. (1994)

Transforming growth factor beta 1 (TGF-beta 1) and TGF-beta 2 can reversibly inhibit the proliferation of hematopoietic progenitor cells in vivo, leading us to hypothesize that such quiescent progenitors might be more resistant to high doses of cell cycle active chemotherapeutic drugs, thereby allowing dose intensification of such agents. Initial studies showed that whereas administration of TGF-beta 1 or TGF-beta 2 did not prevent death in normal mice treated with high doses of 5-fluorouracil (5-FU), those mice that received TGF-beta 2 did exhibit the beginning of a hematologic recovery by day 11 after administration of 5-FU, and were preferentially rescued by a suboptimal number of transplanted bone marrow cells. Subsequently, it was found that the administration of TGF-beta 2 protected recovering progenitor cells from high concentrations of 5-FU in vitro. This protection coincided with the finding that significantly more progenitors for colony-forming unit-culture (CFU-c) and CFU-granulocyte, erythroid, megakaryocyte, macrophage (GEMM) were removed from S-phase by TGF-beta in mice undergoing hematopoietic recovery than in normal mice. Further studies showed that the administration of TGF-beta protected up to 90% of these mice undergoing hematologic recovery from a rechallenge in vivo with high dose 5-FU, while survival in mice not given TGF-beta was < 40%. Pretreatment of mice with TGF-beta 1 or TGF-beta 2 also protected 70-80% of mice from lethal doses of the noncycle active chemotherapeutic drug, doxorubicin hydrochloride (DXR). These results demonstrate that TGF-beta can protect mice from both the lethal hematopoietic toxicity of 5-FU, as well as the nonhematopoietic toxicity of DXR. This report thus shows that a negative regulator of hematopoiesis can be successfully used systemically to mediate chemoprotection in vivo.
Sequencing and Comparative Analysis of Flagellin Genes fliC , fljB , and flpA from Salmonella (2004)

Salmonella isolates have traditionally been classified by serotyping, the serologic identification of two surface antigens, O-polysaccharide and flagellin protein. Serotyping has been of great value in understanding the epidemiology of Salmonella and investigating disease outbreaks; however, production and quality control of the hundreds of antisera required for serotyping is difficult and time-consuming. To circumvent the problems associated with antiserum production, we began the development of a system for determination of serotype in Salmonella based on DNA markers. To identify flagellar antigen-specific sequences, we sequenced 280 alleles of the three genes that are known to encode flagellin in Salmonella, fliC, fljB, and flpA, representing 67 flagellar antigen types. Analysis of the data indicated that the sequences from fliC, fljB, and flpA clustered by the antigen(s) they encode not by locus. The sequences grouped into four clusters based on their conserved regions. Three of the four clusters included multiple flagellar antigen types and were designated the G complex, the Z4 complex, and the alpha cluster. The fourth cluster contained a single antigen type, H:z(29). The amino acid sequences of the conserved regions within each cluster have greater than 95% amino acid identity, whereas the conserved regions differ substantially between clusters (75 to 85% identity). Substantial sequence heterogeneity existed between alleles encoding different flagellar antigens while alleles encoding the same flagellar antigen were homologous, suggesting that flagellin genes may be useful targets for the molecular determination of flagellar antigen type.