gebhart/patrepeval huggingface dataset:
Abstract 1791: Targeting radiation-inducible cell surface GRP78 using GIRLRG peptide as a novel imaging and therapeutic strategy for tumors (2015)

Abstract Traditional radiation therapy is often associated with significant toxicity to normal cells that could limit the success of cancer therapy. The greater understanding in the molecular differences between cancer cells and normal cells has lead to targeted therapies in cancer treatment. We have discovered novel radiation-inducible antigens in cancer using phage-display peptide libraries. One such inducible-antigen is Glucose regulated protein 78kDa (GRP78) that was shown to bind the hexapeptide GIRLRG. GRP78 is known to regulate cellular stresses, including hypoglycemia, hypoxia and the ER stress response. It is over-expressed in different cancer subtypes and has been correlated to their poor prognosis. In this study, we evaluated the cell surface induction of GRP78 post irradiation (IR) on lung cancer (A549 and LLC), glioma (D54 and GL261) and endothelial (HUVEC and 3B11) cell lines using flow cytometry. Significantly higher surface expression of GRP78 was observed in all cell lines. We determined the specificity of GIRLRG to bind tumors in vivo using nano SPECT technology. GIRLRG was conjugated to a 40KDa PEG (for longer circulation time) and radiolabelled with 111Indium (111In) using diethylene triamine pentaacetic acid (DTPA) as the chelator. The A549 tumor bearing nude mice were irradiated (3Gy x 3 times) or sham irradiated prior to tail vein injections of 111In labeled GIRLRG. The mice were imaged 48h and 96h post injection using nano CT-SPECT imager. The SPECT images revealed that GIRLRG specifically bound to the irradiated A549 tumors while little or no binding was seen in the sham irradiated tumors. The post-SPECT imaging bio-distrubution also revealed maximum uptake in irradiated tumors. We further evaluated tumor binding of GIRLRG in Glioma (D54), esophageal cancer (OE33), cervical cancer (HT3), and pancreatic cancer (BxPC3). The nano-SPECT imaging showed that GIRLRG specifically bound to all the irradiated tumors tested. Phosphor images of the tumor sections showed that GIRLRG specifically bound to the tumors and not to normal tissues. In conclusion, GIRLRG peptide has high affinity to GRP78 in vitro and in vivo. Radiolabeled GIRLRG is a novel tool for imaging tumors and may be developed further as a therapeutic agent to deliver cancer specific drugs or therapeutic radioisotopes. Citation Format: Vaishali Kapoor, David Dadey, Kim Nguyen, Hua Li, Buck Rogers, Dinesh Thotala, Dennis Hallahan. Targeting radiation-inducible cell surface GRP78 using GIRLRG peptide as a novel imaging and therapeutic strategy for tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1791. doi:10.1158/1538-7445.AM2015-1791
Generation of Expressed Sequence Tags from Low-CO2 and High-CO2 Adapted Cells of Chlamydomonas reinhardtii (2000)

To characterize genes whose expression is induced in carbon-stress conditions, 12,969 and 13,450 5'-end expressed sequence tags (ESTs) were generated from cells grown in low-CO2 and high-CO2 conditions of the unicellular green alga, Chlamydomonas reinhardtii. These ESTs were clustered into 4436 and 3566 non-redundant EST groups, respectively. Comparison of their sequences with those of 3433 non-redundant ESTs previously generated from the cells under the standard growth condition indicated that 2665 and 1879 EST groups occurred only in the low-CO2 and high-CO2 populations, respectively. It was also noted that 96.2% and 96.0% of the cDNA species respectively obtained from the low-CO2 and high-CO2 conditions had no similar EST sequence deposited in the public databases. The EST species identified only in the low-CO2 treated cells included genes previously reported to be expressed specifically in low-CO2 acclimatized cells, suggesting that the ESTs generated in this study will be a useful source for analysis of genes related to carbon-stress acclimatization. The sequence information and search results of each clone will appear at the web site: http://www.kazusa.or.jp/en/plant/chlamy/EST/.
Characterization of a 3D optrode array for infrared neural stimulation (2012)

This paper characterizes the Utah Slant Optrode Array (USOA) as a means to deliver infrared light deep into tissue. An undoped crystalline silicon (100) substrate was used to fabricate 10 × 10 arrays of optrodes with rows of varying lengths from 0.5 mm to 1.5 mm on a 400-μm pitch. Light delivery from optical fibers and loss mechanisms through these Si optrodes were characterized, with the primary loss mechanisms being Fresnel reflection, coupling, radiation losses from the tapered shank and total internal reflection in the tips. Transmission at the optrode tips with different optical fiber core diameters and light in-coupling interfaces was investigated. At λ = 1.55μm, the highest optrode transmittance of 34.7%, relative to the optical fiber output power, was obtained with a 50-μm multi-mode fiber butt-coupled to the optrode through an intervening medium of index n = 1.66. Maximum power is directed into the optrodes when using fibers with core diameters of 200 μm or less. In addition, the output power varied with the optrode length/taper such that longer and less tapered optrodes exhibited higher light transmission efficiency. Output beam profiles and potential impacts on physiological tests were also examined. Future work is expected to improve USOA efficiency to greater than 64%.
Nonlinear observer design for stabilization of gliding robotic fish (2014)

Gliding robotic fish is a new type of underwater robots for aquatic environmental monitoring applications. The robot features both buoyancy-driven gliding and active tail-actuated swimming or maneuvering. In our previous work, a passivity-based controller was designed for stabilizing the glide motion. Estimation of the system states including the velocities, which is essential for the feedback control implementation, is challenging for such a low-speed and low-cost underwater robot with highly nonlinear dynamics. In this paper, a nonlinear model-based observer is proposed to estimate the system states. For comparison purposes, a linear observer based on linearized dynamics is also considered. The nonlinear observer proves to have better performance over the linear observer, especially in terms of the robustness against the measurement noise. The proposed nonlinear observer is then implemented in the passivity-based stabilization controller on a gliding robotic fish, and the experimental results are presented to support the effectiveness of both the controller and the observer.
Optical properties of human skin in the near infrared wavelength range of 1000 to 2200 nm (2001)

In this paper we present the absorption coefficient mu(a) and the isotropic scattering coefficient mu(s)(') for 22 human skin samples measured using a double integrating sphere apparatus in the wavelength range of 1000-2200 nm. These in vitro results show that values for mua) follow 70% of the absorption coefficient of water and values for mu(s)(') range from 3 to 16 cm(-1). From the measured optical properties, it was found that a 2% Intralipid solution provides a suitable skin tissue phantom.
A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses (1993)

Abstract We develop and test a new elementary Monte Carlo move for use in the efficient simulation of polymer systems. The move consists of a concerted rotation around up to seven adjacent skeletal bonds that leaves the rest of the chain unaffected. No assumption is made concerning the backbone geometry other than that bond lengths and bond angles are held constant during the elementary move. Special sampling techniques are needed because the new move involves a correlated change in seven degrees of freedom along the chain backbone. We use the new move in conjunction with reptation in an isothermal-isobaric Monte Carlo simulation of a bulk tetracosane melt system and find that it improves computational efficiency relative to a purely reptation-based Monte Carlo scheme. Comparisons are also made between a concerted rotation-based Monte Carlo simulation and a molecular dynamics simulation of an oligomer of atactic polypropylene.
Experience in reducing the hemolysis of an impeller assist heart. (1989)

Blood trauma has been one of the main problems of centrifugal pumps. The difficulties in reducing hemolysis are many, and all the factors causing excessive hemolysis always act together, making them difficult to discover and distinguish. Furthermore, error could occur at many points during hemolysis testing, making it difficult to repeat results. In developing the low hemolysis pulsatile and nonpulsatile impeller pumps the authors established an experimental method for investigating and searching for the hemolysis factors. In this study two pumps with only one differing factor were compared or only one factor on one pump was changed in the middle of the test period. In this way the effect of the individual factor on pump hemolysis could be seen and some factors have been thus confirmed as important reasons for hemolysis: 1) the drift of the pump output (including the volume and efficiency) from the design point; 2) impeller vane angles, i.e., the radial logarithmic spiral angle and the axial helical spiral angle; 3) roughness of vane surface and other blood contacting surfaces of the sealing box and pump housing; 4) vibration of the rotor resulting from dynamic disequilibrium; and 5) prerotation swirl at the inlet of the pump. The blood pressure to be pumped has been shown to have no influence on pump hemolysis. After eliminating the hemolysis factors, the blood trauma of the impeller heart has been reduced remarkably. The index of hemolysis of the nonpulsatile pump is 0.015, about one fifth of a clinically used roller made in Shanghai and two sevenths of one Sarns 7,000 Roller; the index of hemolysis of the pulstile pump is 0.020, about one sixth of a self-made diaphragm pump and one thirteenth of the Polystan pulsa tile pump.
IgE and T‐cell responses to high‐molecular weight allergens from bee venom (1999)

Although present in low amounts, high-molecular weight allergens from bee venom elicit strong IgE and T-cell responses, and may need to be considered as clinically relevant. Therefore, the development of peptide or recombinant protein-based immunotherapy for bee venom allergy may require careful characterization of such allergens.
Hepatocyte telomere shortening and senescence are general markers of human liver cirrhosis (2002)

Telomere shortening limits the number of cell divisions of primary human cells and might affect the regenerative capacity of organ systems during aging and chronic disease. To test whether the telomere hypothesis applies to human cirrhosis, the telomere length was monitored in cirrhosis induced by a broad variety of different etiologies. Telomeres were significantly shorter in cirrhosis compared with noncirrhotic samples independent of the primary etiology and independent of the age of the patients. Quantitative fluorescence in situ hybridization showed that telomere shortening was restricted to hepatocytes whereas lymphocytes and stellate cells in areas of fibrosis had significantly longer telomere reserves. Hepatocyte-specific telomere shortening correlated with senescence-associated beta-galactosidase staining in 84% of the cirrhosis samples, specifically in hepatocytes, but not in stellate cells or lymphocytes. Hepatocyte telomere shortening and senescence correlated with progression of fibrosis in cirrhosis samples. This study demonstrates for the first time that cell type-specific telomere shortening and senescence are linked to progression of human cirrhosis. These findings give a novel explanation for the pathophysiology of cirrhosis, indicating that fibrotic scarring at the cirrhosis stage is a consequence of hepatocyte telomere shortening and senescence. The data imply that future therapies aiming to restore regenerative capacity during aging and chronic diseases will have to ensure efficient targeting of specific cell types within the affected organs.
Hyperdiploid Acute Lymphoblastic Leukemia With 51 to 65 Chromosomes: A Distinct Biological Entity With a Marked Propensity to Undergo Apoptosis (1999)

To determine the cellular basis for the excellent clinical outcome of hyperdiploid acute lymphoblastic leukemia (ALL), defined by a modal chromosome number of 51 to 65, we assessed the growth potential of leukemic cells from 129 children with newly diagnosed ALL. Flow cytometric analysis was used to compare leukemic cell recoveries at the beginning and at the end of 7-day cultures on allogeneic bone marrow-derived stromal layers. The median percentage of cell recovery after culture was 91% (range, <1% to 550%). Among the 25 hyperdiploid cases, only two had cell recoveries above the median value, compared with 63 of 104 cases with different ploidies (P <.001); 21 had recoveries within the first quartile, in contrast to only 12 of the 104 other cases. Cell recoveries in the 16 cases with duplications of chromosomes 4 and 10, a feature previously associated with a superior outcome, were all within the first quartile. Flow cytometric studies indicated that rapid induction of apoptosis was the underlying cause of low cell recoveries in cases with hyperdiploidy. The demise of hyperdiploid cells on stroma was not due to failure to adhere with stromal elements (as shown by electron microscopy) or to deficiencies of interleukin-1 (IL-1), IL-2, IL-3, IL-4, IL-6, IL-7, IL-11, stem-cell factor, interferon- (IFN-), tumor necrosis factor- (TNF-), or to combinations of these cytokines. Inactivation of IL-4, IFN- and TNF-, which if secreted by stromal layers could be toxic to ALL cells, failed to improve the survival of hyperdiploid blasts. We conclude that leukemic cells bearing 51 to 65 chromosomes have a marked propensity to undergo apoptosis. The stringent survival requirements of these cells, together with their potentially higher sensitivity to antileukemic drugs, may well account for the high cure rates achieved in patients with this form of ALL.
Vertebrate head induction by anterior primitive endoderm (1997)

In vertebrates the antero-posterior organization of the embryonic body axis is thought to result from the activity of two separate centers, the head organizer and the trunk organizer, as operationally defined by Spemann in the 1920s. Current molecular studies have supported the existence of a trunk organizer activity while the presence of a distinct head inducing center has remained elusive. Mainly based on analyses of headless mutants in mice, it has been proposed that the anterior axial mesoderm plays a determining role in head induction. Recent gain- and loss-of-function studies in various organisms, however, provide compelling evidence that a largely ignored region, the anterior primitive endoderm, specifies rostral identity. In this review we discuss the emerging concept that the anterior primitive endoderm, rather than the prechordal plate mesoderm, induces head development in the vertebrate embryo.
Cell proliferation kinetics in human tumor xenografts measured with iododeoxyuridine labeling and flow cytometry: a study of heterogeneity and a comparison between different methods of calculation and other proliferation measurements. (1995)

The influence of overall treatment time in the results of fractionated radiation treatment was initially established in experimental tumors and, subsequently, in the clinic. The availability of techniques (antibodies against halogenated thymidine analogues and flow cytometry) which permit determinations of the duration of the synthesis phase, the labeling index, and the tumor potential doubling time (Tpot) in a short period of time and requiring only a small biopsy of tumor tissue, has expanded interest in the relationship between tumor cell proliferation and response to irradiation. A valuable tool in the study of this relationship are human tumor xenografts. Previous studies have shown a substantial intratumoral heterogeneity in the determinations of Tpot. Different methods of calculation of the kinetic parameters have been published. We have conducted a heterogeneity analysis and an evaluation of the different calculation methods in order to define the validity of Tpot as a proliferation rate measurement in human tumor xenografts. Results show the intertumoral variability in Tpot [between different types of human tumor xenografts systems (coefficient of variation = 88.2%)] to be greater than mean intratumoral variation (coefficient of variation = 30.8%); this suggests that this variation is potentially adequate to serve as a predictor of response. The diverse calculation methods provided significantly different absolute values but not different tumor ranking, probably because the time interval between labeling and sampling was maintained, for all the samples, between 6 and 8 h. Our study has found significant differences between the labeling index and the S-phase fraction determined with the DNA profile in 9 out of 10 tumor types. No correlation was found between the DNA index of the tumors in this series and their proliferation rate.
Sustainable Concepts in Olefin Metathesis (2007)

Ruthenium-catalyzed olefin metathesis reactions represent an attractive and powerful transformation for the formation of new carbon-carbon double bonds. This area is now quite familiar to most chemists as numerous catalysts are available that enable a plethora of olefin metathesis reactions. Nevertheless, with the exception of uses in polymerization reactions, only a limited number of industrial processes use olefin metathesis. This is mainly due to difficulties associated with removing ruthenium from the final products. In this context, a number of studies have been carried out to develop procedures for the removal of the catalyst or the products of catalyst decomposition, however, none are universally attractive so far. This situation has resulted in tremendous activity in the area dealing with supported or tagged versions of homogeneous catalysts. This Review summarizes the numerous studies focused on developing cleaner ruthenium-catalyzed metathesis processes.
Combining Interval, Probabilistic, and Fuzzy Uncertainty: Foundations, Algorithms, Challenges -- An Overview (2005)

Since the 1960s, many algorithms have been designed to deal with interval uncertainty. In the last decade, there has been a lot of progress in extending these algorithms to the case when we have a combination of interval and probabilistic uncertainty. We provide an overview of related algorithms, results, and remaining open problems.
The Clinical Benefit of Device Therapy for Meniere’s Disease in Adults: Systematic Review and Meta-Analysis (2019)

This study showed that the device therapy might reduce vertigo attacks and sick days in patients with MD. Additionally, the function level and hearing level may improve after the device therapy. In addition, the decrease in electrocochleographic parameters showed that inner ear electrophysiology improved after device therapy.
Multi-neuron intracellular recording in vivo via interacting autopatching robots (2018)

The activities of groups of neurons in a circuit or brain region are important for neuronal computations that contribute to behaviors and disease states. Traditional extracellular recordings have been powerful and scalable, but much less is known about the intracellular processes that lead to spiking activity. We present a robotic system, the multipatcher, capable of automatically obtaining blind whole-cell patch clamp recordings from multiple neurons simultaneously. The multipatcher significantly extends automated patch clamping, or 'autopatching', to guide four interacting electrodes in a coordinated fashion, avoiding mechanical coupling in the brain. We demonstrate its performance in the cortex of anesthetized and awake mice. A multipatcher with four electrodes took an average of 10 min to obtain dual or triple recordings in 29% of trials in anesthetized mice, and in 18% of the trials in awake mice, thus illustrating practical yield and throughput to obtain multiple, simultaneous whole-cell recordings in vivo.
Vehicle Black Box System (2008)

The main purpose of this paper is to develop a prototype of the vehicle black box system VBBS that can be installed into any vehicle all over the world. This prototype can be designed with minimum number of circuits. The VBBS can contribute to constructing safer vehicles, improving the treatment of crash victims, helping insurance companies with their vehicle crash investigations, and enhancing road status in order to decrease the death rate.
IFCC Reference System for Measurement of Hemoglobin A1c in Human Blood and the National Standardization Schemes in the United States, Japan, and Sweden: A Method-Comparison Study (2004)

There is a firm and reproducible link between the IFCC RM and DCM HbA(1c) values.
The space of human body shapes (2003)

We develop a novel method for fitting high-resolution template meshes to detailed human body range scans with sparse 3D markers. We formulate an optimization problem in which the degrees of freedom are an affine transformation at each template vertex. The objective function is a weighted combination of three measures: proximity of transformed vertices to the range data, similarity between neighboring transformations, and proximity of sparse markers at corresponding locations on the template and target surface. We solve for the transformations with a non-linear optimizer, run at two resolutions to speed convergence. We demonstrate reconstruction and consistent parameterization of 250 human body models. With this parameterized set, we explore a variety of applications for human body modeling, including: morphing, texture transfer, statistical analysis of shape, model fitting from sparse markers, feature analysis to modify multiple correlated parameters (such as the weight and height of an individual), and transfer of surface detail and animation controls from a template to fitted models.
Metal−Semiconductor Transition in Single-Walled Carbon Nanotubes Induced by Low-Energy Electron Irradiation (2005)

We report the effect of low-energy (1 keV) electron beam irradiation on gated, three-terminal devices constructed from metallic single-walled carbon nanotubes. Pristine devices, which exhibited negligible gate voltage response at room temperature and metallic single-electron transistor characteristics at low temperatures, when exposed to an electron beam, exhibited ambipolar field effect transistor (room temperature) and single-electron transistor (low temperature) characteristics. This metal-semiconductor transition is attributed to inhomogeneous electric fields arising from charging during electron irradiation.