gebhart/patrepeval huggingface dataset:
Antitumor Activity and Mechanism of Action of a Novel Stat3 Inhibitor, WP1066, Against Human B-Cell Non-Hodgkin’s Lymphoma and Multiple Myeloma. (2005)

Abstract B-cell non-Hodgkin’s lymphomas (B-NHL) have the highest incidence rates among all lymphomas, comprising more than 85% of malignant lymphomas worldwide. Multiple myeloma (MM) is a plasma cell malignancy that affects 14,000 patients per year. Although new therapies have recently been introduced to treat these malignancies, patient survival has not significantly improved, illustrating the need for additional agents that target and suppress this disease. B-cell malignancies over-express c-myc and frequently retain a constitutively activated Stat3, resulting in increased survival gene expression and apoptotic protection. Targeting these transcription factors may reduce apoptotic thresholds and suppress the growth and survival of these malignancies. In this study, we refined and tested the anti-tumor activity of a novel small MW compound discovered by screening a synthetic library for agents that bock Stat3 activation. WP1066, blocked IL-6 mediated Stat3 activation in numerous human B-NHL and MM tumor cells including the Mino, LP, MM-1 and OCI-My5 at low micromolar concentrations. This compound blocks Jak2-depedent cytokine signaling (IL-3, GM-CSF, IL-6) through the rapid (15 min) down-regulation of the upstream tyrosine kinase, Jak2. WP1066 also causes rapid reduction in c-myc in B-cell malignancies but other transcription factors and signaling kinases are not affected by WP1066. The apoptotic effects of WP1066 on B-NHL and MM cells parallel its Stat inhibitory, Jak2 down-regulatory activity. Jak2 down-regulation is not dependent on proteosomal processing but requires activation of a tyrosine phosphatase, suggesting a unique mechanism of WP1066 action. Based on activities described in vitro, we further examined the antitumor activity of WP1066 in a B-NHL xenograft tumor model. Mice were inoculated (i.p.) with 25 × 106 Mino cells (CB17 SCID mice, 4–5 weeks of age) and 13 days later were treated with 10, 20, or 40 mg/kg of WP1066 (i.p.) qd x 5/week for 2 weeks. WP1066 significantly decreased tumor burden and increased the survival of Mino tumor bearing mice treated with 20 or 40 mg/kg of WP1066. These results suggest that WP1066 reduces Stat activation through a unique mechanism and may have therapeutic potential for the treatment of human B-cell non-Hodgkin’s lymphomas and multiple myeloma.
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays (2009)

By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA (1993)

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.
Use of a Multiantigen Detection Algorithm for Diagnosis of Kaposi's Sarcoma-Associated Herpesvirus Infection (2006)

The ability to readily and accurately diagnose Kaposi's sarcoma-associated herpesvirus (KSHV, or human herpesvirus 8) infection in individuals remains a demanding task. Among the available diagnostic methods, sensitivities and specificities range widely, and many are inadequate for large-scale screening studies. We examined a serological algorithm for detecting KSHV in human sera having high sensitivity and specificity. This method uses previously described open reading frame (ORF) K8.1 and ORF65 peptide-based enzyme-linked immunosorbent assays and a novel purified recombinant full-length LANA1 protein. We generated two multiantigen algorithms: one that maximized sensitivity and one that maximized specificity. These serological algorithms were then used to evaluate seroprevalence rates among populations of clinical and epidemiological importance. The serological algorithms yielded sensitivities of 96% and 93% and specificities of 94% and 98% for the more sensitive and specific algorithms, respectively. Among kidney donors, seroprevalence was low, 4.0% (2/50), and similar to that of blood donors (P = 0.46; odds ratio [OR], 1.4; confidence interval [CI], 0.14 to 7.9) using the highly specific algorithm. Using the sensitive algorithm, 8.0% (4/50) were infected compared to 6.4% (16/250) observed among blood donors (OR, 1.3; CI, 0.41 to 4.0; P = 0.43). Among subjects requiring bone marrow transplantation, seroprevalence rates were not elevated compared to those of blood donors (OR, 2.0; 95% CI, 0.10 to 122.9; P = 0.50). Because the need for high-quality KSHV detection methods are warranted and because questions remain about the optimal methods for assessing KSHV infection in individuals, we propose a systematic approach to standardize and optimize the assessment of KSHV infection rates using a combination of established and novel serological assays and methods.
Synthesis, functionalization and bioimaging applications of highly fluorescent carbon nanoparticles (2011)

Highly fluorescent crystalline carbon nanoparticles (CNPs) have been synthesized by one step microwave irradiation of sucrose with phosphoric acid at 100 W for 3 min 40 s. This method is very simple, rapid and economical and hence can be used for large scale applications. The average particle sizes are 3 to 10 nm and they emit bright green fluorescence under the irradiation of UV-light. Therefore, the particles can be used as a unique material for bioimaging as well as drug delivery. To further increase the fluorescence property of the synthetic carbon nanoparticles we simply functionalized them by using different organic dyes, such as fluorescein, rhodamine B and α-naphthylamine; the maximum fluorescence intensity was observed for the particles functionalized with fluorescein. It is very interesting to note that all of those compounds show maximum fluorescence intensity at 225 nm excitation wavelength and for any excitation wavelength the peak positions are exactly same the position as that of CNPs itself, which is completely different from the individual precursors (dyes). All of the above compounds, including CNPs, have also been successfully introduced into the erythrocyte enriched fraction of healthy human blood cells with minimum cytotoxicity.
Virtual reality robotic telesurgery simulations using MEMICA haptic system (2001)

There is increasing realization that some tasks can be performed significantly better by humans than robots but, due to associated hazards, distance, etc., only a robot can be employed. Telemedicine is one area where remotely controlled robots can have a major impact by providing urgent care at remote sites. In recent years, remotely controlled robotics has been greatly advanced and the NASA Johnson Space Center's robotic astronaut, Robonaut, is one such example. Unfortunately, due to the unavailability of force and tactile feedback the operator must determine the required action by visually examining the remote site and therefore limiting the tasks that Robonaut can perform. There is a great need for dexterous, fast, accurate teleoperated robots with the operator's ability to feel the environment at the robot's field. The authors conceived a haptic mechanism called MEMICA (remote MEchanical MIrroring using Controlled stiffness and Actuators) that can enable the design of high dexterity, rapid response, and large workspace haptic system. The development of a novel MEMICA gloves and virtual reality models are being explored to allow simulation of telesurgery and other applications. The MEMICA gloves are being designed to provide intuitive mirroring of the conditions at a virtual site where a robot simulates the presence of a human operator. The key components of MEMICA are miniature electrically controlled stiffness (ECS) elements and Electrically Controlled Force and Stiffness (ECFS) actuators that are based on the use of Electro-Rheological Fluids (ERF). In this paper the design of the MEMICA system and initial experimental results are presented.
Erysipelas: Clinical and Bacteriologic Spectrum and Serological Aspects (1996)

The bacteriologic, serological, and clinical characteristics of 229 patients with erysipelas diagnosed during a 2-year period at a university hospital for infectious diseases in Sweden are presented. Beta-Hemolytic streptococci were detected in 34% of these patients. Group A was the dominant serogroup, but group G streptococci were found in about half as many cases. Bacteremia was present in 5%. A serological response with antistreptolysin O (ASO) and antideoxyribonuclease B (ADNase B) was seen primarily in patients harboring group A streptococci but also in those from whom no pathogen was isolated. ASO was also found in high titers in some patients with Group G streptococcal infection. The clinical course was usually benign, with few complications, but recurrences were common (occurring in 21% of the patients). No cases of streptococcal toxic shock were seen. Culture of skin biopsy specimens had low sensitivity; Beta-hemolytic were isolated from only two of 15 patients.
Bacteremia and Septic Arthritis Caused by Moraxella catarrhalis (1991)

Moraxella catarrhalis was isolated from blood from a 41-year-old man who had a 24-hour history of increasing pain in and swelling of the left knee. No history of trauma, arthropathy, fever, chills, cough, or chest pain was noted. What is believed to be the first case of bacteremia caused by M. catarrhalis that was associated with septic arthritis is described in this report. The case presented suggests the pathophysiology of this rare condition. One previous case of septic arthritis caused by M. catarrhalis without documented bacteremia has been reported.
Far Red Bioluminescence from Two Deep-Sea Fishes (1984)

Spectral measurements of red bioluminescence were obtained from the deep-sea stomiatoid fishes Aristostomias scintillans (Gilbert) and Malacosteus niger (Ayres). Red luminescence from suborbital light organs extends to the near infrared, with peak emission at approximately 705 nanometers in the far red. These fishes also have postorbital light organs that emit blue luminescence with maxima between 470 and 480 nanometers. The red bioluminescence may be due to an energy transfer system and wavelength-selective filtering.
Sub-Two Nanometer Single Crystal Au Nanowires (2008)

Ultrathin single crystal Au nanowires with diameter of approximately 1.6 nm and length of few micrometers were synthesized with high yield by simply mixing HAuCl 4 and oleylamine at room temperature. High resolution transmission electron microscopy studies revealed that all of these nanowires are single crystalline and grew along the [111] direction. The valency evolution of the gold species during the synthesis was studied by X-ray photoelectron spectroscopy, which showed a clear Au (3+) --> Au (+) --> Au stepwise reduction at different reaction stages. Small angle X-ray scattering and small-angle X-ray diffraction suggest mesostructure formation upon HAuCl 4 and oleylamine mixing. The slow in situ reduction of this mesostructure leads to the formation of ultrathin nanowires in solution. This novel nanowire growth mechanism relies on cooperative interaction, organization, and reaction between inorganic precursor salts and oleylamine.
<title>Charge transport in photochemically modified molecularly doped polymers</title> (1995)

Hole mobilities in p-diethylaminobenzaldehyde diphenylhydrazone (DEH) doped polycarbonate films are determined using the time-of-flight transient photocurrent technique. Measurements of hole transport parameters are determined over a range of electric fields before and after the samples are deliberately irradiated with UV light. UV irradiation of the hole transport molecule DEH results in the creation of a photoproduct, 1-phenyl-3-(4- diethylamino-1-phenyl)-1, 3-indazole with moderately high efficiency. Once formed, this photoproduct has been shown to act as a barrier to hole conduction. We exploit this photochemical reaction to examine the hole transport properties in a molecularly doped polymer system containing DEH doped polycarbonate. We propose that the increase in concentration of the photoproduct modifies the intrinsic order of the system and provides a unique probe to distinguish between the disorder formalism of Baessler and coworkers and models which propose polaron formation.
Neurosteroids—Endogenous Regulators of Seizure Susceptibility and Role in the Treatment of Epilepsy (2012)

Abstract Neurosteroids are endogenous modulators of neural excitability that are believed to have a role in the regulation of seizure susceptibility in the setting of preexisting epilepsy. Menstrual and stress-related fluctuations in seizures may in part be related to changes in brain neurosteroid levels. In addition, men with TLE who have suppression of the hypothalamic-pituitary-gonadal axis may have a reduction in testosterone-derived neurosteroids that could worsen seizures. Treatment with exogenously administered natural neurosteroids or synthetic analogs such as ganaxolone may be beneficial to treat partial seizures. Further studies are required to determine if neurosteroid replacement is a useful therapeutic approach for seizure exacerbations related to endogenous neurosteroid fluctuations, such as in catamenial epilepsy and stress. In the future, agents that influence the endogenous synthesis of neurosteroids, such as TSPO ligands, may find utility as an alternative to neurosteroids themselves in the treatment of epilepsy.24,131
Protein Degradation during Renal Passage in Normal Kidneys is Inhibited in Experimental Albuminuria (1997)

1. Tritium labelled proteins, namely bovine serum albumin ([3H]BSA), rat serum albumin ([3H]RSA), anionic horseradish peroxidase ([3H]aHRP) and immunoglobulin present in urine fractions from rat filtration studies in vivo and isolated perfused rat kidneys (IPKs) have been shown by gel chromatographic analysis to be severely degraded to small peptides. The degradation of RSA and BSA in vivo has been shown to be similar. 2. Degradation of proteins in the urine from IPK experiments was inhibited by including 150 mmol/l lysine in the perfusate. Similarly, [3H]BSA and [3H]aHRP excreted from rats with puromycin aminonucleoside nephrosis was again essentially intact for both IPK and in vivo experiments. 3. It appears that the degradation of proteins observed in urine obtained from control kidneys is due, in part, to proteolytic activity associated with the proximal tubule. Inhibition of proximal tubule function, which occurs for both lysine and puromycin aminonucleoside treatments (as calibrated by lysozyme uptake), results in inhibition of the degradation observed. Glomerular epithelial cells could also contribute to the degradation. 4. There was no generation of low-molecular-weight material in the perfusate or plasma arising from breakdown of circulating proteins or recycling of potential degradation products from the tubules.
A key functional role for the insulin-like growth factor 1 N-terminal pentapeptide (1989)

In order to elucidate the role of the N-terminus of insulin-like growth factor 1 (IGF-1) with respect to its biological properties, we chemically synthesized analogues of IGF-1 truncated by one to five amino acid residues from the N-terminus. In a bioassay that measured the stimulation of protein synthesis in rat L6 myoblasts, the concentrations required to produce a half-maximal response were: IGF-1, 13 ng/ml; des-(1)-IGF-1, 10 ng/ml; des-(1-2)-IGF-1, 13 ng/ml; des-(1-3)-IGF-1, 1.5 ng/ml; des-(1-4)-IGF-1, 5.1 ng/ml; des-(1-5)-IGF-1, 1200 ng/ml. When tested for their abilities to compete with 125I-IGF-1 binding to L6 myoblasts at 3 degrees C, the concentrations required for 50% competition were: IGF-1, des-(1)-IGF-1 and des-(1-2)-IGF-1, 20 ng/ml; des-(1-3)-IGF-1, 14 ng/ml; des-(1-4)-IGF-1, 40 ng/ml; des-(1-5)-IGF-1, greater than 1000 ng/ml. Receptor-binding experiments at 25 degrees C, however, gave results suggesting that the myoblasts were secreting a binding protein selective for the three longest peptides. This interpretation was confirmed by binding studies with medium conditioned by the L6 myoblasts as well as binding protein purified from MDBK-cell-conditioned medium. In both cases IGF-1, des-(1)-IGF-1 and des-(1-2)-IGF-1 competed for tracer IGF-1 binding at least 60-fold better than did the three shorter peptides. The results obtained account for the increased potency of des-(1-3)-IGF-1 and des-(1-4)-IGF-1, since their activities are not attenuated by the binding protein, and the relatively lower potency of des-(1-4)-IGF-1 is a consequence of this peptide binding less well to the L6-myoblast receptor.
Polymorphisms within the folate pathway predict folate concentrations but are not associated with disease activity in rheumatoid arthritis patients on methotrexate (2010)

Although RBC folate concentrations are associated with genetic polymorphisms within the folate pathway, these variants do not predict disease activity. To accurately evaluate whether any polymorphisms are reliable predictors of MTX efficacy or toxicity, large prospective clinical trials are required. Furthermore, application of a genome-wide association strategy is likely to uncover novel predictors of MTX response.
The Click modular router (1999)

Click is a new software architecture for building flexible and configurable routers. A Click router is assembled from packet processing modules called elements. Individual elements implement simple router functions like packet classification, queueing, scheduling, and interfacing with network devices. Complete configurations are built by connecting elements into a graph; packets flow along the graph's edges. Several features make individual elements more powerful and complex configurations easier to write, including pull processing, which models packet flow driven by transmitting interfaces, and flow-based router context, which helps an element locate other interesting elements.We demonstrate several working configurations, including an IP router and an Ethernet bridge. These configurations are modular---the IP router has 16 elements on the forwarding path---and easy to extend by adding additional elements, which we demonstrate with augmented configurations. On commodity PC hardware running Linux, the Click IP router can forward 64-byte packets at 73,000 packets per second, just 10% slower than Linux alone.
Introduction (1994)

Gunboat diplomacy is most familiar, but will never be employed in these pages, as a term of abuse, a metaphorical epithet for almost any kind of attempt by one government to exert an unwelcome influence on the policy of another. It is often applied to situations involving no threat or use of naval force, sometimes even to disputes in which the only pressures employed are economic or diplomatic.
Foundations of medical imaging (1994)

BASICS FOR MEDICAL IMAGING Mathematical Preliminaries for Image Processing Image Reconstruction from Projections in Two Dimensions Image Reconstruction from Projections True Three-Dimensions and Other Related Techniques IMAGING WITH IONIZING RADIATION Radiation Physics and Detectors X-Ray Computerized Tomography Nuclear Tomographic Imaging Single Photon Emission Computed Tomography Tomographic Nuclear Medical Imaging Positron Emission Tomography MAGNETIC RESONANCE IMAGING Nuclear Magnetic Resonance Physics and Instrumentation Magnetic Resonance Imaging: Mathematics and Algorithms Magnetic Resonance Imaging: Methods and Techniques Flow and Flow-Related Magnetic Resonance Imaging Chemical-Shift and Spectroscopic Imaging ULTRASOUND AND ULTRASONIC IMAGING Ultrasound Physics Ultrasonic Imaging BIOMAGNETIC IMAGING Neuromagnetic Imaging Index.
Synthesis and .alpha.-adrenergic activities of 2- and 4-substituted imidazoline and imidazole analogs (1992)

Seven analogues of medetomidine and naphazoline were synthesized and evaluated for their alpha 1 (aorta) and alpha 2 (platelet) activities. The analogues were composed of 2- and 4-substituted imidazoles and imidazolines attached through a methylene bridge to either the 1- or 2-naphthalene ring system. In general the 1-naphthalene analogues were the most potent inhibitors of epinephrine-induced platelet aggregation. Of considerable interest was the fact that the 1-naphthalene analogues (2, 5-7) were partial agonists while the 2-naphthalene analogues (3, 8, 9) were antagonists in an alpha 1-adrenergic system (aorta). Thus, appropriately substituted naphthalene analogues of medetomidine and naphthazoline provide a spectrum of alpha 1-agonist, alpha 1-antagonist, and alpha 2-antagonist activity.
First Comes Love, Then Comes Marriage, Then Comes Baby Carriage: Perspectives on Gay Parenting and Reproductive Technology (2007)

WHEN I WAS FIRST INVITED TO SPEAK ABOUT GAY PARENTING, I felt flattered and slightly flummoxed. What could I talk about? As the coordinator and moderator of a panel last year at the Boston Psychoan...
Scaling of Atrioventricular Transmission in Mammalian Species: An Evolutionary Riddle! (2002)

"Scaling deals with the structural and functional consequences of changes in size or scale among otherwise similar organisms." It plays a key role in all studies on comparative mammalian physiology and morphology. Heart weight is proportionally related to body weight and can be described by a straightforward, so-called allometric equation. We studied scaling of AV transmission times (PR intervals on the ECG) in 375 mammals of different dimensions and species. Scaling of AV transmission times versus heart length (third root of weight) is statistically best described by a S-shaped curve. This implies that AV transmission time in mammals is not linearly related to heart length and does not depend solely on the length of the AV transmission system. The AV node fine-tunes AV transmission times at rest and during exercise in individuals; it protects the ventricles against high-rate atrial arrhythmias such as atrial fibrillation; and it regulates basal AV transmission times in mammalian species of varying sizes. We call the "how" and "why" of the scaling of AV transmission time in mammals an evolutionary riddle that deserves further study.