gebhart/patrepeval huggingface dataset:
Immunizing Patients With Metastatic Melanoma Using Recombinant Adenoviruses Encoding MART-1 or gp100 Melanoma Antigens (1998)

Background: The characterization of the genes encoding melanoma-associated antigens MART-1 or gp100, recognized by T cells, has opened new possibilitiesfor the development of immunization strategies for patients with metastatic melanoma. With the use of recombinant adenoviruses expressing either MART-1 or gp100 to immunize patients with metastatic melanoma, we evaluated the safety, immunologic, and potential therapeutic aspects of these immunizations. Methods: In phase I studies, 54 patients received escalating doses (between 10 7 and 10 11 plaque-forming units) of recombinant adenovirus encoding either MART-1 or gp100 melanoma antigen administered either alone or followed by the administration of interleukin 2 (IL-2). The immunologic impact of these immunizations on the development of cellular and antibody reactivity was assayed. Results: Recombinant adenoviruses expressing MART-1 or gp100 were safely administered. One of 16 patients with metastatic melanoma receiving the recombinant adenovirus MART-1 alone experienced a complete response. Other patients achieved objective responses, but they had received IL-2 along with an adenovirus, and their responses could be attributed to the cytokine. Immunologic assays showed noconsistent immunization to the MART-1 or gp100 transgenes expressed by the recombinant adenoviruses. High levels of neutralizing anti-body were found in the pretreatment sera of the patients. Conclusions: High doses of recombinant adenoviruses could be safely administered to cancer patients. High levels of neutralizing anti-body present in patients' sera prior to treatment may have impaired the ability of these viruses to immunize patients against melanoma antigens.
Growth Dynamics for DNA-Guided Nanoparticle Crystallization* (2020)

Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices &lt;i&gt;via&lt;/i&gt; DNA-directed hybridization. Crystallities of SNA with various shapes emerge during the assembly process, which coalesce during coarsening, leading to polycrystalline materials. Here, we investigate the growth dynamics of SNAs into body-centered cubic superlattices and the coalescence of SNA aggregates using a colloidal model formulated from the competition of electrostatic core repulsions and localized DNA hybridization attractions. We find that the growth law of isolated SNA crystallities is well-described by the power law &lt;i&gt;t&lt;/i&gt;&lt;sup&gt;1/2&lt;/sup&gt;, in agreement with experimental observations. At later times, coalescence slows the growth dynamics considerably and is dependent on the orientational mismatch (misorientation angle) of the coalescing crystallites. Molecular dynamics simulations show that the misorientation angle decreases continually during the coalescence, which is a signature of the grain rotation induced coalescence mechanism. This mechanism is followed by the coarsening of a “neck” that develops at the boundary between the coalescing crystallites. Remarkably, we find faster coalescence dynamics for larger SNAs compared to smaller SNAs due to their enhanced surface diffusion, which more effectively reduces curvature at the boundary of two superlattices. These findings provide fundamental insight into the relationship between nanoparticle surface chemistry and its crystallite growth and coalescence.
Nice to Meet You, Mr. GFR! (2006)

Teleologically speaking kidney’s function is designed to maintain life parameters as close as possible to the normal level. Clearance is a tool to compare renal function among different individuals independently on urine flow, body size and solute concentration in blood. Since the tubulus manipulates the glomerular filtrate composition, for the computation of clearance as a surrogate of GFR, we need a molecule with ideal features: fully filtered by the glomerular membrane, absent reabsorption or secretion in the tubular part of the nephron and easily measurable. In a steady state condition the serum level of an endogenous marker is correlated to the reciprocal of the level of GFR making possible GFR estimation without urine collection. GFR can be estimated using different equations that include race, gender, age and body size. The MDRD equation, derived from the study carried out in 1999 resulted reasonably accurate and probably more precise than the previous Cockcroft-Gault equation developed in 1973 for patients with chronic kidney disease. Both equations however have been reported to be less accurate in patients without chronic kidney disease. In several conditions, estimated GFR (from MDRD formula) can result significantly lower than direct measurements of renal clearance potentially leading to a false positive diagnosis of chronic renal disease (GFR < 60 ml/min/1.73m2) with important consequences. This phenomenon is particularly evident in Europe compared to United States especially for a different calibration of serum creatinine assays among laboratories. A potential GFR underestimation from inaccurate serum creatinine measurements (or better, calibrations) could cause a “false epidemic” of mild chronic kidney. So, from one side we really encourage GFR monitoring in the general population and especially in the population at risk for kidney and cardiovascular disease; on the other side we must remind general practitionners that patients cannot be frightened with potentially false positive diagnoses of kidney dysfunction.
Interleukin-18 does not modulate the acute-phase response (2005)

IL-18 is a pro-inflammatory cytokine of the IL-1 family and it induces IL-1, TNF, and IL-6, all of which are endogenous pyrogens.The pyrogenic properties of recombinant IL-18 were studied in a rabbit model of fever.rIL-18 did not cause fever when injected intravenously into rabbits.Furthermore, the ability of rIL-18 to modulate other components of the acute-phase response was assessed.rIL-18 did not induce leukocytosis, or changes of circulating concentrations of lipoproteins and corticosterone in mice.In conclusion, rIL-18 is not able to induce a febrile response in rabbits and does not modulate the acute-phase response in mice.
Residue growth on metallic-hard mask after dielectric etching in fluorocarbon-based plasmas. I. Mechanisms (2010)

This work focuses on the formation of residues that grow on a metallic-hard mask after etching of porous low-k materials in fluorocarbon-based plasmas. The residue growth, which is dependent on the air exposure time after etching, causes line and via opens that strongly impact the yield performance. The different elements which could play a role in the chemical reactions have been clarified. The authors have demonstrated that in their experimental conditions, after fluorocarbon etching and air exposure, the oxidized titanium nitride reacts with fluorhydric acid to form metallic salts. This is a reaction between fluorine from the reactive layer formed on titanium nitride and hydrogen coming from the atmosphere. This reaction is all the more fast because the titanium nitride is oxidized.
Brief Report: Practicability and safety of amphotericin B deoxycholate as continuous infusion in neutropenic patients with hematological malignancies (2005)

Fungal infections are a major cause of morbidity and mortality in patients with hematological malignancies. Candida and Aspergillus species are the most important opportunistic fungal pathogens in this patient population. Amphotericin B is the treatment of choice, but its administration is often hampered by severe side-effects, which may be reduced by continuous infusion of this drug. We describe 17 consecutive patients with hematological malignancies, suffering from fever of unknown origin with possible fungal infections, treated with amphotericin B as continuous infusion compared with a control group of 10 patients treated with conventional rapid infusion of amphotericin B over 2 - 6 h. No acute side-effects or severe nephrotoxicity were observed during continuous infusion of amphotericin B. Target doses were reached faster in patients with continuous infusion of amphotericin B than in patients with rapid infusion. We conclude that continuous infusion of amphotericin B is safe in neutropenic patients with hematological malignancies.
Identification of mutagenic metabolites of indeno[1,2,3-cd]pyrene formed in vitro with rat liver enzymes. (1985)

Indeno[1,2,3-cd]pyrene (IP) is a major environmental pollutant which is carcinogenic on mouse skin and in rat lung. Unlike benzo(a)pyrene, IP is a nonalternant polycyclic aromatic hydrocarbon which is devoid of a bay region. IP was mutagenic in Salmonella typhimurium TA100 in the presence of a 9000 X g supernatant from the livers of Aroclor-pretreated rats. Using a similar activation system, the major metabolites of IP were isolated and identified by comparison with synthetic reference standards. trans-1,2-Dihydro-1,2-dihydroxy-IP, 8-, 9-, and 10-hydroxy-IP, 8- and 9-hydroxy-trans-1,2-dihydro-1,2-dihydroxy-IP, and IP-1,2-quinone are among the metabolites formed in vitro. The 1,2-epoxide of indeno[1,2,3-cd]pyrene is a potent direct-acting mutagen. 8- and 9-hydroxy-IP were mutagenic with metabolic activation. 1-,2-, and 6-hydroxy-IP and the trans-1,2-dihydrodiol had no significant mutagenic activity in S. typhimurium TA100 with metabolic activation. These data suggest that the K-region oxides of IP and of 8- and 9-hydroxy-IP are ultimately responsible for its mutagenic activity.
Mutagenesis by Insertion of Tn4001 into the Genome of Spiroplasma citri: Characterization of Mutants Affected in Plant Pathogenicity and Transmission to the Plant by the Leafhopper Vector Circulifer haematoceps (1997)

Two hundred and fifty-seven transposon Tn4001 mutants of Spiroplasma citri strain GII3 were used for transmission assays by the leafhopper vector Circulifer haematoceps into periwinkle (Catharanthus roseus) plants. Multiplication of the mutants in the two hosts, the leafhopper and the plant, as well as the symptom expression in the plant were studied. Two mutants, GMT 470 and GMT 553, caused no symptoms on plants. Tn4001 is inserted as a single copy in the genome of these mutants. Mutant GMT 470 did not multiply, or multiplied only poorly, in the leaf-hopper and was not transmitted by the insect to the plant, nor to culture medium through Parafilm membrane. The growth rate of GMT 470 in SP4 medium was twice as slow as that of wild-type strain GII3. Mutant GMT 553 multiplied in the leafhopper as well as the wild-type spiro-plasma, and was transmitted by the leafhoppers into the plants, where it reached the same titers as the wild-type strain but in approximately twice as much time. The plants containing high titers of mutant GMT 553 remained symptomless for several weeks. However, symptoms began to develop at a time when revertants that had lost the transposon were detected.
Studies of Cuticle Drugs from Natural Sources. IV. Inhibitory Effects of Some Arctostaphylos Plants on Melanin Biosynthesis. (1996)

The inhibitory effect of 50% ethanol extracts obtained from the leaves of six Arctostaphylos plants (A. patula, A. viscida, A. canescens, A. columbiana, A. nevadensis and A. uva-ursi) (Ericaceae) was tested on melanin biosynthesis. Among them, the extracts of A. patula and A. viscida showed potent inhibition against tyrosinase. The two extracts not only inhibited the production of melanin from dopachrome by autoxidation, but exhibited SOD (superoxide dismutase)-like activity and had a moderate absorbance in the UV-B area. These results suggest that the leaves of Arctostaphylos plants, especially A. patula and A. viscida can be applied to a whitening agent for the skin.
Adenosine 5′-Triphosphate Activates Nuclear Translocation of Mitogen-Activated Protein Kinases Leading to the Induction of Early Growth Response 1 and Raf Expression in Human Granulosa-Luteal Cells (2004)

With the stimulation of many types of cell surface receptors, MAPKs are activated. We have previously demonstrated an effect of extracellular ATP on ERKs and gonadotropin- induced progesterone secretion, implicating the significance of ATP in the regulation of ovarian function. However, little is known about the specific role of ATP in the subsequent MAPK-induced signaling cascade in human granulosa-luteal cells (hGLCs). The present study was designed to examine the effect of ATP on the activation of the MAPK signaling pathway, including nuclear translocation and the expression of the immediate early genes in hGLCs. Western blot analysis, using a monoclonal antibody, which detected the total and phosphorylated forms of ERK1 and ERK2 (p42(mapk) and p44 (mapk), respectively), demonstrated that exogenous ATP evoked ERKs in a dose- and time-dependent manner. In contrast, p38 and JNK were not significantly activated after ATP treatment. To examine the translocation of activated ERKs, fluorescein isothiocyanate-conjugated secondary antibody was used to detect the distribution of total and phosphorylated ERKs. Immunofluorescent staining revealed that phosphorylated ERKs were translocated from cytoplasm into nucleus subsequent to 10 microm ATP treatment. To study the gene(s) induced by exogenous ATP, mRNA was extracted from hGLCs in the presence or absence of 10 microm ATP. Gene array for 23 genes associated with members of the mitogenic pathway cascade and immediate early genes revealed that the expression of early growth response 1 and c-raf-1 was increased. To our knowledge, this is the first demonstration of the ATP-induced nuclear translocation of MAPKs in the human ovary. These results suggest that the MAPK signaling pathway plays a role in mediating ATP actions in the human ovary.
E2F decoy oligodeoxynucleotide ameliorates cartilage invasion by infiltrating synovium derived from rheumatoid arthritis (2006)

This study examined the ability of E2F decoy oligodeoxynucleotides (ODN) to inhibit proliferation of synovial fibroblasts derived from patients with rheumatoid arthritis (RA). The effect of E2F decoy ODN on cartilage invasion by RA synovium in a murine model of human RA was also investigated. E2F decoy ODN were introduced into synovial tissue and synovial fibroblasts derived from patients with RA using hemagglutinating virus of Japan (HVJ)-liposomes. The effect of E2F decoy ODN on synovial fibroblast proliferation was evaluated by MTT assay and by RT-PCR for the cell cycle regulatory genes proliferating-cell nuclear antigen (PCNA) and cyclin-dependent kinase 2 (cdk2). Changes in production of inflammatory mediators by RA synovial tissue following transfection with E2F decoy ODN were assessed by ELISA. Human cartilage and RA synovial tissue transfected with E2F decoy ODN were co-transplanted in severe combined immunodeficient (SCID) mice. After 4 weeks, the mice were sacrificed and the implants histologically examined for inhibition of cartilage damage by E2F decoy ODN. E2F decoy ODN resulted in significant inhibition of synovial fibroblast proliferation, corresponding with reduced expression of PCNA and cdk2 mRNA in synovial fibroblasts. The production of interleukin-1beta (IL-1beta), IL-6 and matrix metalloproteinase (MMP)-1 by synovial tissue was also significantly inhibited by the introduction of E2F decoy ODN. Further, in an in vivo model, cartilage that was co-implanted with RA synovial tissue transfected with E2F decoy ODN exhibited no invasive and progressive cartilage degradation. These data demonstrate that transfection of E2F decoy ODN prevents cartilage destruction by inhibition of synovial cell proliferation, and suggest that transfection of E2F decoy ODN may provide a useful therapeutic approach for the treatment of joint destruction in arthritis.
Support Vector Machine Detection of Peer-to-Peer Traffic (2006)

In this paper, we apply support vector machines to identify peer-to-peer p2p traffic in high-performance routers. Commercial networks limit user access bandwidth, either physically or logically. However, in research networks there are no individual bandwidth restrictions, since this would interfere with research tasks. User behavior in research networks has changed radically with the advent of p2p multimedia file transfers: many users take advantage of the huge bandwidth, e.g. compared to domestic DSL access to exchange movies and the like. This behavior may have a deep impact on research network utilization. Consequently, in the framework of the MOLDEIP project, we have proposed to apply support vector machine detection to identify those activities in high-performance research network routers. The results in this paper suggest that support vector machine detection of p2p traffic in high-performance routers is highly successful and outperforms recent approaches like 1
Discovery of Potent, Efficient, and Selective Inhibitors of Phosphoinositide 3-Kinase δ through a Deconstruction and Regrowth Approach (2018)

A deconstruction of previously reported phosphoinositide 3-kinase δ (PI3Kδ) inhibitors and subsequent regrowth led to the identification of a privileged fragment for PI3Kδ, which was exploited to deliver a potent, efficient, and selective lead series with a novel binding mode observed in the PI3Kδ crystal structure.
Effect of Thyroxine on Liver Tyrosine-glutamic Acid Transaminase (1956)

Thyroxine in concentrations as low as 5.10-5M has been shown to markedly inhibit transaminase-tautomerase activity of the liver tyrosine oxidase system. The transaminase enzyme appears to be the most directly involved in the inhibition as determined by difference studies. The authcr is indebted to Dr. J. B. Seilands for the use of his facilities and for stimulating discussions in the course of the work.
Actively Driven Fluctuations in a Fibrin Network (2021)

Understanding force propagation through the fibrous extracellular matrix can elucidate how cells interact mechanically with their surrounding tissue. Presumably, due to elastic nonlinearities of the constituent filaments and their random connection topology, force propagation in fiber networks is quite complex, and the basic problem of force propagation in structurally heterogeneous networks remains unsolved. We report on a new technique to detect displacements through such networks in response to a localized force, using a fibrin hydrogel as an example. By studying the displacements of fibers surrounding a two-micron bead that is driven sinusoidally by optical tweezers, we develop maps of displacements in the network. Fiber movement is measured by fluorescence intensity fluctuations recorded by a laser scanning confocal microscope. We find that the Fourier magnitude of these intensity fluctuations at the drive frequency identifies fibers that are mechanically coupled to the driven bead. By examining the phase relation between the drive and the displacements, we show that the fiber displacements are, indeed, due to elastic couplings within the network. Both the Fourier magnitude and phase depend on the direction of the drive force, such that displacements typically propagate farther, but not exclusively, along the drive direction. This technique may be used to characterize the local mechanical response in 3-D tissue cultures, and to address fundamental questions about force propagation within fiber networks.
Nehrke and Pieper Reply: (1996)

A Reply to the Comment by U. Staub.Received 9 May 1996DOI:https://doi.org/10.1103/PhysRevLett.77.4689©1996 American Physical Society
Towards Selective Cobalt Atomic Layer Deposition for Chip-to-Wafer 3D Heterogeneous Integration (2023)

The feasibility of a 3D bonding technology for ultra-dense input/output (I/O) interconnects using cobalt selective atomic layer deposition (Co ALD) is explored with a preliminary testbed. Steady-state thermal simulations benchmark the Co ALD bonding technology to investigate the potential thermal benefits compared to conventional bonding technologies such as microbumps <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(\boldsymbol{\mu}-\mathbf{bumps})$</tex> and hybrid bonds. Preliminary testbeds containing horizontal Cu/100 nm Gap/Cu structures are fabricated to show the feasibility of using Co ALD as a high-density Cu-Cu interconnect bonding technology. SEM and XPS are used to characterize the test structures, showing that after 400 cycles of Co ALD deposition, the 100 nm gap is filled between the aligned Cu pads.
Space between us (2011)

Work shown as part of the Erasure exhibition at Stoke City Museum and Art Gallery, January - May 2011. The theme of the exhibition focused on the idea of removing or erasing something, to create something new. 

'Space Between Us' is a graphic exposition of the spaces we construct in the built environment. The exhibition formed an open and participatory investigation into space and how it may relate to the human condition as lived within it.
Outdoor-to-indoor channel characteristics at 20 GHz (2016)

The next generation (5G) mobile communication system has been the focus of studies recently. One of the approaches to enable this system is utilizing the high-SHF band (over 6 GHz) and the EHF band (mainly 30–100 GHz). To design radio links with high accuracy and evaluate 5G system performances for various scenarios, channel characteristics must be clarified. In this paper, we clarify the channel characteristics of Outdoor-to-Indoor (O2I) propagation scenario at 20 GHz band based on the measurement using a channel sounder with a 50 MHz bandwidth. The propagation mechanism is also analyzed based on estimating single scattering positions of multipath.
Analogous responses in the nucleus accumbens and cingulate cortex to pain onset (aversion) and offset (relief) in rats and humans (2013)

In humans, functional magnetic resonance imaging (fMRI) activity in the anterior cingulate cortex (ACC) and the nucleus accumbens (NAc) appears to reflect affective and motivational aspects of pain. The responses of this reward-aversion circuit to relief of pain, however, have not been investigated in detail. Moreover, it is not clear whether brain processing of the affective qualities of pain in animals parallels the mechanisms observed in humans. In the present study, we analyzed fMRI blood oxygen level-dependent (BOLD) activity separately in response to an onset (aversion) and offset (reward) of a noxious heat stimulus to a dorsal part of a limb in both humans and rats. We show that pain onset results in negative activity change in the NAc and pain offset produces positive activity change in the ACC and NAc. These changes were analogous in humans and rats, suggesting that translational studies of brain circuits modulated by pain are plausible and may offer an opportunity for mechanistic investigation of pain and pain relief.
An A Priori Hysteresis Modeling Methodology for Improved Efficiency and Model Accuracy in Advanced PD SOI Technologies (2005)

An a priori hysteresis modeling methodology in partially depleted (PD) silicon-on-insulator (SOI) technologies is proposed that constitutes an essential part of an improved compact model extraction flow. By focusing on the parasitic currents, the capacitance network, the body effect, and fine-tuning the diode characteristics especially, the proposed methodology aims to closely capture the voltage and temperature dependences of hysteresis well before the full-fledged MOSFET model extraction begins. The resulting benefits, such as improved model extraction efficiency, relatively high fidelity to hardware data, and improved model accuracy, are demonstrated on a state-ofthe-art 90 nm PD SOI technology.
Abnormal glucose tolerance – a common risk factor in patients with acute myocardial infarction in comparison with population‐based controls (2004)

Abnormal glucose tolerance was almost twice as common amongst patients with acute myocardial infarction as in matched controls. Impaired glycaemic control accompanied by insulin resistance, dyslipidaemia, hypertension, together with increased plasma fibrinogen and proinsulin levels were main features characterizing patients.