gebhart/patrepeval huggingface dataset:
Treatment of a glioblastoma patient by vaccination with autologous dendritic cells pulsed with allogeneic major histocompatibility complex class I–matched tumor peptides (2000)

Dendritic cells (DCs) are antigen-presenting cells that play a central role in the initiation and modulation of antitumor immune responses. In this pilot study, we investigated the ability of autologous DCs pulsed ex vivo with allogeneic major histocompatibility complex class I-matched glioblastoma peptides to stimulate host antitumor immune responses when injected as a vaccine. A patient with recurrent brainstem glioblastoma multiforme (GBM) received a series of three intradermal immunizations of antigen-pulsed DCs on an outpatient basis following surgical debulking of her posterior fossa tumor. Dendritic cell vaccination was well tolerated, and no clinical signs of autoimmunity or experimental allergic encephalomyelitis were detected. She developed a measurable cellular immune response against the allogeneic glioblastoma peptides used in her vaccine preparation, as demonstrated by in vitro T-cell proliferation assays. In addition, increased T-cell infiltration was noted within the intracranial tumor site in the biopsy sample obtained following DC vaccination. An objective clinical response, however, was not evident, and this patient eventually died 21 months after her disease was diagnosed. To our knowledge, this is the first patient with brain cancer ever to be treated with DC-based immunotherapy. This case illustrates that vaccination with DCs pulsed with acid-eluted glioblastoma peptides is feasible and can induce systemic antigen-specific immunity in a patient with recurrent GBM. Additional studies are necessary to determine the optimum DC doses and antigen loading conditions that may translate into clinical effectiveness and survival benefit for patients with brain tumors. Phase I trials for malignant glioma are currently underway.
Survival and neuritic growth of sympathoadrenal (chromaffin) precursor cells in vitro (1989)

Chromaffin precursor cells from embryonic rat adrenal glands were isolated at 16.3 and 20.3 days of gestation and purified by centrifugation on density gradients. Approximately 50% of the cells of both age groups that had attached to the culture substratum by 12 hr survived during a 4-day culture period in the absence of exogenous trophic factors. Nerve growth factor (NGF) and a C6 glioma-cell-conditioned medium (C6-CM) had no or a very moderate promoting effect on survival. The glucocorticoid dexamethasone (DEX) supported the survival of 70-80% of the cells that otherwise would have died. Spontaneous neuritic growth of the sympathoadrenal precursor cells was significantly more pronounced with cells isolated at embryonic day (E) 16.3 than at E20.3. NGF had a significantly smaller promoting effect on neurite ougrowth at E16.3 than at E20.3. C6-CM induced neurite outgrowth from 25% (E16.3) and 35% (E20.3) of the surviving cells. DEX (10(-6) M) completely abolished spontaneous neuritic growth and partially suppressed C6-CM-mediated fiber outgrowth. These data underscore the importance of glucocorticoids for the maintenance and development of an endocrine morphologic phenotype of sympathoadrenal precursors. They suggest that the cells may be initially driven by growth factors other than NGF into a neuronal direction and that they lack NGF-responsiveness and -dependence during the early stages of their development.
Left Ventricular Remodeling in Transgenic Mice With Cardiac Restricted Overexpression of Tumor Necrosis Factor (2001)

Our results suggest that progressive time-dependent changes in the balance between MMP activity and TIMP activity are responsible, at least in part, for the spectrum of TNF-induced changes in the myofibrillar collagen content that occur during LV structural remodeling in the MHCsTNF mice.
CpG DNA can induce strong Th1 humoral and cell-mediated immune responses against hepatitis B surface antigen in young mice (1998)

Successful neonatal immunization of humans has proven difficult. We have evaluated CpG-containing oligonucleotides as an adjuvant for immunization of young mice (1-14 days old) against hepatitis B virus surface antigen. The protein-alum-CpG formulation, like the DNA vaccine, produced seroconversion of the majority of mice immunized at 3 or 7 days of age, compared with 0-10% with the protein-alum or protein-CpG formulations. All animals, from neonates to adults, immunized with the protein-alum vaccine exhibited strong T helper (Th)2-like responses [predominantly IgG1, weak or absent cytotoxic T lymphocytes (CTL)]. Th2-type responses also were induced in young mice with protein-CpG (in 1-, 3-, and 7-day-old mice) and protein-alum-CpG (in 1- and 3-day-old mice) but immunization carried out at older ages gave mixed Th1/Th2 (Th0) responses. DNA vaccines gave Th0-like responses when administered at 1 and 7 days of age and Th1-like (predominantly IgG2a and CTL) responses with 14-day-old or adult mice. Surprisingly, the protein-alum-CpG formulation was better than the DNA vaccine for percentage of seroconversion, speed of appearance, and peak titer of the antibody response, as well as prevalence and strength of CTL. These findings may have important implications for immunization of human infants.
Amplification of a chromatin remodeling gene, Rsf-1/HBXAP, in ovarian carcinoma (2005)

A genomewide technology, digital karyotyping, was used to identify subchromosomal alterations in ovarian cancer. Amplification at 11q13.5 was found in three of seven ovarian carcinomas, and amplicon mapping delineated a 1.8-Mb core of amplification that contained 13 genes. FISH analysis demonstrated amplification of this region in 13.2% of high-grade ovarian carcinomas but not in any of low-grade carcinomas or benign ovarian tumors. Combined genetic and transcriptome analyses showed that Rsf-1 (HBXAPalpha) was the only gene that demonstrated consistent overexpression in all of the tumors harboring the 11q13.5 amplification. Patients with Rsf-1 amplification or overexpression had a significantly shorter overall survival than those without. Overexpression of Rsf-1 gene stimulated cell proliferation and transform nonneoplastic cells by conferring serum-independent and anchorage-independent growth. Furthermore, Rsf-1 gene knockdown inhibited cell growth in OVCAR3 cells, which harbor Rsf-1 amplification. Taken together, these findings indicate an important role of Rsf-1 amplification in ovarian cancer.
A Model of Rational Competitive Bidding (1969)

This paper presents a mathematical model of the bidding process that deals explicitly with the uncertainty of the bidders about the value of the subject of the auction. By dealing with this often ignored factor, it obtains equilibrium strategies and profits as a function of the number of bidders, the relative values they attach to the subject of the auction and their accuracy in estimating it. Models are developed for both highest-bid-wins and lowest-bid-wins auctions.
Slow light in fiber Bragg gratings (2011)

We demonstrate through numerical simulations that a fiber Bragg grating operated in transmission can support much slower light than previously anticipated. This is accomplished by increasing the grating's index modulation, reducing its loss, optimizing its length, and apodizing its index profile. With current fiber Bragg grating loss and index modulation, we predict that group velocities lower than <i>c</i>/1000 are attainable. We validate this concept with a record measured group index of 130 in a strong apodized grating (index modulation of ~1.1 10<sup>-3</sup>) with a nearly optimized length of 1.2 cm and an inferred loss coefficient of 1 m<sup>-1</sup>.
Reproduction and Feeding of the Electric Fish Brachyhypopomus gauderio (Gymnotiformes: Hypopomidae) and the Discussion of a Life History Pattern for Gymnotiforms from High Latitudes (2014)

The reproductive biology and feeding habits of the electric fish Brachyhypopomus gauderio were studied. The species has seasonal reproductive behavior, with breeding occurring during the Southern Hemisphere spring and summer, and having a positive relation with the photoperiod variation. Brachyhypopomus gauderio was defined as a fractional spawner, with low relative fecundity and high first maturation size. Sexual dimorphism was registered, males undergoing hypertrophy of the distal portion of caudal filament. The results on reproductive biology herein obtained are in agreement with data concerning gymnotiforms from Southern Brazil and Uruguay, pointing to an ecological pattern for the species from high latitudes, differing from species with tropical distribution. According to the analysis of the food items, B. gauderio feed mainly on autochthonous insects, likewise the other gymnotiforms previously investigated, leading to conclude that there is no variation on the diet of the species of the order related to climatic conditions or even to habitat of occurrence.
Intravascular micro active catheter for minimal invasive surgery (2002)

The authors have developed an intravascular micro active catheter system for microsurgery in human vascular systems, such as cerebrovascular and coronary arteries. Also this system can be applied to laparoscopical treatment. It consists of the micro active bending catheter and some functional catheters. The former is a tube-like catheter which has an outer-diameter of 3.0 mm, an inner-diameter of 2.0 mm and a length of 1000 mm. It's inner hole is a pathway for the functional catheters, such as conventional guide wire, balloon catheter, conventional suction tube, micro ultrasound probe catheter, fiber optics (angioscope), angioplatic devices and drug injection lines. This active bending catheter is actuated with three SMA (shape-memory-alloy) zigzag type springs-SMA wires are connected with plastic and brass connection links. This actuator can be bent to any direction with the PWM controlled electric current. The authors also developed a micro drug infusion catheter and a micro ultrasound probe catheter fitted to the inner hole of active bending catheter. All of these systems were evaluated with the human mock circulation system. They can be introduced through 90/spl deg/, 120/spl deg/, 180/spl deg/ crooked branches to the brachiocephalic artery, common carotid artery, subelavian artery and so on in the mock circulation system. Also, the authors tested this endoscope system in vivo by performing laparoscopical surgery on a pig. They could easily induce the catheter to the point they wanted in the pig ovary.
Robust Optimal Power Flow Solution Using Trust Region and Interior-Point Methods (2010)

A globally convergent optimization algorithm for solving large nonlinear optimal power flow (OPF) problems is presented. As power systems become heavily loaded, there is an increasing need for globally convergent OPF algorithms. By global convergence, one means the optimization algorithm being able to converge to an OPF solution, if at least one exists, for any choice of initial point. The globally convergent OPF presented is based on an infinity-norm trust region approach, using interior-point methods to solve the trust region subproblems. The performance of the proposed trust region interior-point OPF algorithm, when applied to the IEEE 30-, 57-, 118-, and 300-bus systems, and to an actual 1211-bus system, is compared with that of two widely used nonlinear interior-point methods, namely, a pure primal-dual and its predictor-corrector variant.
Evaluations of port performances from a seaborne cargo supply chain perspective (2013)

Abstract Previous research on port efficiency focuses primarily on the provider’s perspective and assumes that maximizing the output is always desirable. This paper recognizes that maximizing the final output does not necessarily guarantee an efficient system and the notion of port efficiency and service effectiveness needs to be considered from the perspectives of both the provider and the consumer of the port service. The paper proposes a network-DEA model to evaluate the performances of 30 seaports worldwide. The concurrent consideration of efficiency scores from the network-DEA model and the traditional DEA-CCR model will offer valuable insights to port operators on how to improve port performances as part of a seaborne cargo supply chain.
Elucidation of Control Mechanisms Discovered during Adaptive Manipulation of [Ru(dpb)3](PF6)2 Emission in the Solution Phase (2007)

To design methodologies that will allow researchers to directly correlate the results of adaptive control experiments with physiochemical control pathways in arbitrary complex molecular systems it is imperative that prototype systems are developed and that exigent control pathways are understood. We have been interested in the results of adaptive control experiments in our laboratory involving the maximization of a ratio of two experimental observables: (1) the thermalized emission from the solution-phase coordination complex [Ru(dpb)3](PF6)2 and (2) the second harmonic signal (a purely intensity-dependent phenomenon) of the shaped laser fields. Using a rational pulse shaping strategy, we have made a measurement of the ratio spectrum (in essence the two-photon absorption cross section) for the molecule [Ru(dpb)3](PF6)2 in a room temperature solution of acetonitrile. This spectrum is highly varied across the accessible two-photon power spectrum of our broad-band laser pulses and demonstrates the existence of a control pathway wherein a shaped laser field can manipulate excited-state population (with respect to SHG) by conforming to the second-order spectral response of the molecule in solution. We show that our adaptive control algorithm is capable of taking advantage of these control pathways using simulated adaptive control experiments. Finally, we measure second-harmonic spectra of shaped laser fields discovered during an adaptive control experiment and show that these agree with simulation. These results suggest that our adaptive control experiment can be understood in the context of the elucidated spectral control pathway.
Analysis of Edge-Detection Techniques for Crack Identification in Bridges (2003)

Bridge monitoring and maintenance is an expensive yet essential task in maintaining a safe national transportation infrastructure. Traditional monitoring methods use visual inspection of bridges on a regular basis and often require inspectors to travel to the bridge of concern and determine the deterioration level of the bridge. Automation of this process may result in great monetary savings and can lead to more frequent inspection cycles. One aspect of this automation is the detection of cracks and deterioration of a bridge. This paper provides a comparison of the effectiveness of four crack-detection techniques: fast Haar transform (FHT), fast Fourier transform, Sobel, and Canny. These imaging edge-detection algorithms were implemented in MatLab and simulated using a sample of 50 concrete bridge images (25 with cracks and 25 without). The results show that the FHT was significantly more reliable than the other three edge-detection techniques in identifying cracks.
Structural Determinants for Signal Sequence Function in the Mammalian Endoplasmic Reticulum (1999)

Signal sequences function in protein targeting to and translocation across the endoplasmic reticulum membrane. To investigate the structural requirements for signal sequence function, chimeras of the Escherichia coli LamB signal peptide and prolactin were prepared. The LamB signal peptide was chosen by virtue of the extensive biophysical and biological characterization of its activity. In vitro, nascent prolactin chains bearing the LamB signal peptide (LamB) were targeted in a signal recognition particle (SRP)-dependent manner to rough microsomes but remained protease- and salt-sensitive and translocated at low efficiency. Full translocation activity was obtained in a gain of function mutant (LamB*) in which three hydrophobic residues in the LamB hydrophobic core were converted to leucine residues. Cross-linking studies demonstrated that the LamB* signal sequence displayed markedly enhanced interactions with SRP and integral membrane proteins. In contrast, chemically denatured LamB and LamB*-precursors bound with identical efficiencies and in a salt-resistant manner to rough microsomes, suggesting that during de novo synthesis the signal sequence of LamB-bearing precursors assumes a conformation refractory to translocation. These data indicate that a leucine-rich signal sequence is necessary for optimal interaction with SRP and suggest that SRP, by maintaining the signal sequence in a conformation suitable for membrane binding, performs a chaperone function.
Stabilization of cell-free RNA in blood samples using a new collection device (2012)

The novel chemical cocktail contained in the new device allows for the stabilization of cfRNA in blood samples at room temperature, which potentially enhances the clinical utility of cfRNA.
Predictive Value of Biochemical Markers in Stroke (2007)

Biochemical markers of cerebral ischemia and subsequent inflammation represent a potential diagnostic and predictive modality in acute ischemic stroke. Measurement of these markers may improve clinical functions ranging from diagnosis of ischemic stroke to prediction of functional outcome at 3 months. Predictive models, using various biochemical markers, continue to be investigated.
Detecting Exosomes Specifically: A Multiplexed Device Based on Alternating Current Electrohydrodynamic Induced Nanoshearing (2014)

Exosomes show promise as noninvasive biomarkers for cancer, but their effective capture and specific detection is a significant challenge. Herein, we report a multiplexed microfluidic device for highly specific capture and detection of multiple exosome targets using a tunable alternating current electrohydrodynamic (ac-EHD) methodology, referred to as nanoshearing. In our system, electrical body forces generated by ac-EHD act within nanometers of an electrode surface (i.e., within the electrical layer) to generate nanoscaled fluid flow that enhances the specificity of capture and also reduce nonspecific adsorption of weakly bound molecules from the electrode surface. This approach demonstrates the analysis of exosomes derived from cells expressing human epidermal growth factor receptor 2 (HER2) and prostate specific antigen (PSA), and is also capable of specifically isolating exosomes from breast cancer patient samples. The device also exhibited a 3-fold enhancement in detection sensitivity in comparison to hydrodynamic flow based assays (LOD 2760 exosomes/μL for ac-EHD vs LOD 8300 exosomes/μL for hydrodynamic flow; (n = 3)). We propose this approach can potentially have relevance as a simple and rapid quantification tool to analyze exosome targets in biological applications.
Macrophage migration in fibrin gel matrices. (1986)

Macrophage migration has been extensively studied in vitro on artificial substrates but in vivo macrophages migrate through connective tissue and fibrin gel meshworks that comprise the stroma of many inflammatory reactions and solid tumors. Studies were therefore undertaken to investigate macrophage migration in this more biologically relevant matrix cast either with or without nitrocellulose filter support. Macrophage migration in fibrin gels depended on both fibrin and thrombin concentrations and on the nature of fibrin crosslinking. With gamma-chain crosslinking only, macrophage migration was enhanced as compared with untreated filters at fibrin concentrations of up to 5 mg/ml. However, when fibrin alpha-chains were also crosslinked, as occurs in vivo, macrophage migration was inhibited at approximately 3 mg/ml fibrin and was stopped altogether at 5 mg/ml. Thrombin concentrations of 1 unit/ml favored maximal macrophage migration. Depletion of contaminating fibronectin did not affect these results. The pore size of fibrin gels is well below the minimum that permits macrophage migration through nitrocellulose filters. Thus, to penetrate fibrin gels, macrophages could enlarge effective pore size by local fibrinolysis or by pushing apart fibrin strands. If fibrinolysis is responsible, this process must be highly localized because only small amounts of fibrinolysis accompanied extensive macrophage migration in fibrin gels; moreover, fibrinolysis inhibitors did not affect macrophage migration. We conclude that the fibrin deposited in inflammatory reactions and solid tumors is present in forms and concentrations that either facilitate or inhibit macrophage migration; fibrin may therefore regulate macrophage participation in these and other pathologic reactions.
Autoimmunity to the M(r) 32,000 subunit of replication protein A in breast cancer. (2002)

In view of the central role of RPA in DNA replication, recombination, and repair, we suggest that autoimmunity to RPA32 may reflect molecular changes involved in the process of tumorigenesis. The finding of antibodies to RPA32 before diagnosis and their prevalence in in situ carcinoma suggest that they are potentially useful markers of early disease.
A Low Phase Noise 10GHz Optoelectronic RF Oscillator Implemented Using CMOS Photonics (2007)

A mostly integrated 10.2GHz optoelectronic oscillator (OEO) using Si photonics monolithic integration technology is reported. The OEO is a chip-scale device manufactured using a standard 0.13mum SOI CMOS process, with phase noise of -112dBc/Hz at 10kHz carrier offset and RF power consumption of less than 800mW.
Straightforward Recursive Partitioning Model for Discarding Insoluble Compounds in the Drug Discovery Process (2008)

Poor aqueous solubility is one of the major issues in drug discovery and development, impacting negatively on all aspects of the research and development process. The pharmaceutical industry has realized that solubility issues need to be resolved at the discovery stage. We here present an innovative way to address this problem via a model designed to address the simple question, "Is the compound likely to be sufficiently soluble to provide interpretable data in biological screening assays?" A recursive partitioning (RP) method was applied to a set of 3563 molecules, with in house determined aqueous solubility values. Five models were generated on the basis of a small number of descriptors affording intuitive information regarding structural features influencing solubility. The final model was based on only two descriptors: the molecular weight (MW) and the aromatic proportion (AP). This model provided satisfactory values of accuracy (81%) and precision (75%) for a test set of 1200 compounds, suggesting that the model may add value in compound selection and library design during early drug discovery.
Nonstochastic Coexpression of Activation Receptors on Murine Natural Killer Cells (2000)

Murine natural killer cells (NK) express lectin-like activation and inhibitory receptors, including the CD94/NKG2 family of receptors that bind Qa-1, and the Ly-49 family that recognizes major histocompatibility complex class I molecules. Here, we demonstrate that cross-linking of NK cells with a new specific anti-Ly-49H mAb induced NK cell cytotoxicity and cytokine production. Ly-49H is expressed on a subset of NK cells and can be coexpressed with Ly-49 inhibitory receptors. However, unlike Ly-49 inhibitory receptors, Ly-49H is not detectable on naive splenic CD3(+) T cells, indicating that Ly-49H may be an NK cell-specific activation receptor. In further contrast to the stochastically expressed Ly-49 inhibitory receptors, Ly-49H is preferentially expressed with the Ly-49D activation receptor, and expression of both Ly-49H and Ly-49D is augmented on NK cells that lack receptors for Qa-1 tetramers. On developing splenic NK1.1(+) cells, Ly-49D and Ly-49H are expressed later than the inhibitory receptors. These results directly demonstrate that Ly-49H activates primary NK cells, and suggest that expression of Ly-49 activation receptors by NK cells may be specifically regulated on NK cell subsets. The simultaneous expression of multiple activation receptors by individual NK cells contrasts with that of T cell antigen receptors and is relevant to the role of NK cells in innate immunity.