gebhart/patrepeval huggingface dataset:
Adsorption of Sarin and Soman on Dickite:  An ab Initio ONIOM Study (2004)

The adsorption of sarin (GB), isopropyl methylphosphonofluoridate (C4H10FO2P), and soman (GD), 3,3-dimethyl-2-butyl methylphosphonoflouridate (C7H16FO2P), on the octahedral and tetrahedral surfaces of dickite was investigated using the ONIOM(B3LYP/6-31G(d,p):PM3) and ONIOM(B3LYP/6-31G(d,p):HF/3-21G) methods and the representative cluster models. In the case of adsorption on the octahedral sheet of dickite, the location of six hydrogen atoms of the outer −OH groups and the geometry of the adsorbed molecules were optimized. In the case of adsorption on the tetrahedral side of the dickite layer, the geometry of the mineral fragment was kept frozen. The location and orientation of GB and GD on the tetrahedral and octahedral surfaces of dickite were found. The adsorption on the surface of minerals occurs because of the formation of multiple hydrogen bonds between adsorbed GB and GD and the hydroxyl groups (the octahedral side) and the basal oxygen atoms (the tetrahedral side). This type of adsorption results in the polarization and the electron density redistribution of GB and GD on the surface of the mineral. The interaction energies of sarin and soman with the octahedral and tetrahedral surfaces corrected by the BSSE energy were found. The adsorption energies obtained at the ONIOM(B3LYP/6-31G(d,p):PM3) level of theory and using large models of the mineral for the adsorption systems of GB and GD on the octahedral surface of dickite are about −16 and −15 kcal/mol, respectively. In the case of adsorption on the tetrahedral surface, the interaction energies of adsorption systems with GB and GD are about −7.0 and −9.0 kcal/mol, respectively.
Topographical control of cell behaviour: I. Simple step cues (1987)

The photolithographic techniques of the microelectronics industry have allowed us to fabricate patterned plastic substrata to investigate contact guidance of animal tissue cells. The reactions of cells to single steps on a substratum were examined using time-lapse videorecording and scanning electron microscopy. BHK cells and chick embryonic neural cell processes exhibited gradual inhibition of crossing steps with a concomitant increase in alignment at steps dependent on increasing step height. Comparison of these cells' reactions, with those of chick heart fibroblasts and rabbit neutrophils, at a 5 micron step revealed that the influence of topography is also dependent on cell type, the neutrophils being relatively unaffected. The presence of an adhesive difference at a series of steps altered BHK cells' reactions such that the frequency of crossing was dependent on the direction of approach to a step. Although our data are consistent with Dunn & Heath's proposal (1976) that the inflexibility of the cytoskeleton of a moving cell's protrusion is the cellular property determining such reactions to topography, we have found that, on encountering a topographical feature, the response of a cell may be predictable on a probabilistic basis, i.e. the topographical feature reduces the probability of a cell making a successful protrusion and contact in a given direction, that even the largest features tested did not act as absolute barriers to cell locomotion since a small proportion of a population of cells were able to overcome them, and that other guidance cues could significantly alter a cell's response. Even in situations where it is not the primary cue in directing cell locomotion, topographical control may be an important factor during morphogenesis since it must, at the very least, influence the efficiency of other cues.
Naloxone's Pentapeptide Binding Site on Filamin A Blocks Mu Opioid Receptor–Gs Coupling and CREB Activation of Acute Morphine (2009)

Chronic morphine causes the mu opioid receptor (MOR) to switch its coupling from Gi/o to Gs, resulting in excitatory signaling via both Galphas and its Gbetagamma dimer. Ultra-low-dose naloxone (NLX) prevents this switch and attenuates opioid tolerance and dependence. This protective effect is mediated via a high-affinity interaction of NLX to a pentapeptide region in c-terminal filamin A (FLNA), a scaffolding protein interacting with MOR. In organotypic striatal slice cultures, we now show that acute morphine induces a dose-dependent Go-to-Gs coupling switch at 5 and 15 min that resolves by 1 hr. The acute Gs coupling induced by 100 microM morphine was completely prevented by co-treatment with 100 pM NLX, (+)NLX, or naltrexone (NTX), or their pentapeptide binding site (FLNA(2561-2565)), which we show can act as a decoy for MOR or bind to FLNA itself. All of these co-treatments presumably prevent the MOR-FLNA interaction. Since ultra-low-dose NTX also attenuates the addictive properties of opioids, we assessed striatal cAMP production and CREB phosphorylation at S(133). Correlating with the Gs coupling, acute morphine induced elevated cAMP levels and a several-fold increase in pS(133)CREB that were also completely blocked by NLX, NTX or the FLNA pentapeptide. We propose that acute, robust stimulation of MOR causes an interaction with FLNA that allows an initially transient MOR-Gs coupling, which recovers with receptor recycling but persists when MOR stimulation is repeated or prolonged. The complete prevention of this acute, morphine-induced MOR-Gs coupling by 100 pM NLX/NTX or 10 microM pentapeptide segment of FLNA further elucidates both MOR signaling and the mechanism of action of ultra-low-dose NLX or NTX in attenuating opioid tolerance, dependence and addictive potential.
Computer applications in facial plastic and reconstructive surgery (2007)

Computer-assisted facial reconstructive surgery is an area which continues to evolve. The current technology is best served in the repair of complex primary or secondary posttraumatic deformities. Congenital and oncologic reconstructive applications, however, are growing rapidly. While computer-aided surgery has historically been limited to tertiary care centers, easy access to intraoperative navigation systems and more user friendly software applications make these techniques more accessible to a greater number of surgeons.
The Josephson effect in superconductors and quantum gases (2009)

With the recent technical breakthroughs, physicists fully play with the beauty of quantum mechanics. In this theoretical work on the mesoscopic Josephson effect, we take advantage of the collaborations with experimentalists as well as the exchanges between the cold atoms and condensed matter communities. We consider various systems based on the Josephson junction, beginning with its quantum description in the underdamped regime. Using the Keldysh formalism, we obtain the current-voltage characteristics from the classical to the zero temperature regime and the quantum Smoluchowski equation in the quasi-classical limit. We then study the quantum dynamics of a phase qubit realized with a SQUID in a novel configuration where tunneling events occur through two quartic barriers. The escape rate in this camel-back potential, calculated with the instantons technique, allows us to describe the experiments. Circuit quantum electrodynamics predicts that a lasing effect appears when a qubit is coupled to a resonant cavity. We consider the case of a charge qubit and also that of a transmon which exploits the Purcell effect. With the Lindbladian we obtain the density matrix from which we derive the spectrum of the output field. Finally, we study a gas of cold atoms in a ring shape trap comprising a barrier, thus creating a Bose Josephson junction. The low energy physics is described through the correlation functions with the Luttinger liquid theory. We show that the quantum fluctuations in the ring induce a renormalization of the Josephson energy.
An alternative synthesis of the Corey prostaglandin aldehyde (1974)

This is a detailed description of 1 route to the chemical synthesis of PGs (prostaglandins) and their analogs in the laboratory. The chemical formula and chemical structure of each step in the chain is diagrammed. The aldehyde had served as intermediary in the synthesizing process in previous experiments. In this series of steps, the starting stage was the Prins reaction of norbornadiene and paraform-aldehyde in formic acid. Lactones were used as starting materials in the synthesis. Hydrolysis and oxidation were used to change 1 substance in the process into the next.
Plasmin-activated prodrugs for cancer chemotherapy. 2. Synthesis and biological activity of peptidyl derivatives of doxorubicin (1983)

We have synthesized peptidyl prodrugs of doxorubicin (Dox) designed to be selective substrates of plasmin. Such prodrugs might be locally activated by the elevated levels of plasmin produced near many solid tumors under the action of tumor-associated plasminogen activators. One such prodrug, 3'-(D-Val-Leu-Lys)-Dox, was obtained via a mixed-anhydride coupling with isobutyl chloroformate between the protected peptide Fmoc-D-Val-Leu-N epsilon-Fmoc-Lys-OH and doxorubicin, followed by removal of the Fmoc groups with anhydrous ammonia. Compared to doxorubicin, the prodrug showed about a 7-fold improved selective cytotoxicity against chicken embryo fibroblasts transformed with the Rous sarcoma virus (which produce high levels of plasminogen activator) compared to normal cells (which produce low levels of plasminogen activator). However, the prodrug was a very poor plasmin substrate, and although in vivo tests against the murine B16 melanoma showed that the prodrug was active, the maximum T/C obtained was less than that achieved by doxorubicin even at 25 times the molar concentration of prodrug. Qualitatively similar results were obtained for a far more hydrophobic prodrug, 3'-(Boc-Val-Leu-Lys)-Dox. These results demonstrate that peptidyl prodrugs of doxorubicin designed as plasmin substrates are more selective anticancer agents in vitro than doxorubicin itself but that the bulky anthracycline moiety probably prevents efficient plasmin-catalyzed conversion to the active parent drug, so that, in their present form, these drugs are not potent enough to allow a determination as to whether or not they are more selective in vivo.
Temporal expression of cytokines and chemokines in rat adjuvant-induced arthritis (2001)

We discuss the presence of anti-keratin antibodies (AKA) of the IgG class in patients with defined juvenile idiopathic arthritis (JIA). An indirect immunofluorescence test and rat oesophagus substrate was used for the detection and quantification of AKA antibodies in patients sera. Overall 33/60 patients with JIA had sera positive for AKA (55 %, P = 0,0001) ranging from 1:10 to 1:160 dilutions. Following idiopathic arthritis of childhood classification criteria AKA occurred in 2/7 patients with systemic disease (28,6 %), in 13/30 patients with RF negative polyarthritis (43,3 %, P = 0,008) and in 15/18 RF positive polyarthritis (83,3 %, P = 0,000002). AKA were also found in a small cohort of patients with oligoarthritis (1/3) and psoriatic arthritis (2/2). AKA positivity occurred in 3/26 healthy controls at a 1:20 dilution. The presence of AKA was correlated as well as with the severity of the disease. Our study revealed that AKA was present overall in 18/29 patients (62%) with severe JIA and in 12/26 patients (46,2 %) with non-severe disease, however this did not reach statistical significance (P = 0,18). We also observed that AKA remained positive regardless of disease activity. AKA were detectable in 55,6 % patients with active JIA and in 48,6 % patients in the complete or near remission.
Effects of Cord Blood Transfer on the Hematopoietic Recovery Following Sublethal Irradiation in MRL lpr/lpr Mice (1999)

The potential of cord blood (CB) to serve as a rich source of stem cells and stem cell factors is receiving increasing attention. In addition, perhaps because of the early ontogeny of these cells or the lack of surface antigens, cord blood stem cells do not appear to require close identity with the recipient. In the present pilot study, we investigated the presence of a hematopoiesis enhancing effect (HEE) by assaying the ability of human cord blood cells to augment hematopoiesis across a species barrier. For these experiments, autoimmune-prone MRL-lpr/lpr mice were exposed to sublethal levels of irradiation and cord blood administration to study the role of factors present in human cord blood in augmenting the rate of lymphopoiesis. This strain was chosen because of the increased presence of peripheral T and B subpopulations, namely the B-1 and CD4/CD8 double negative T-cell subpopulations, which do not arise directly from bone marrow precursors, but rather accumulate with age. MRL-lpr/lpr mice were sublethally irradiated and reconstituted with syngeneic bone marrow (BM) cells or with human cord blood cells or peripheral blood mononuclear cells (PBMC), or were left unreconstituted. At 2 weeks post-treatment, lymphoid populations in the spleen and lymph nodes were studied as a measure of hematopoiesis. Factors present in cord blood were able to augment hematopoiesis over that which occurred endogenously. At 2 weeks postirradiation, recipients of BM cells displayed the fastest rate of peripheral lymphoid recovery, nonreconstituted mice showed the slowest lymphoid recovery, and recipients of cord blood recovered their lymphoid populations at an intermediate rate. Similarly, myelopoiesis was increased in irradiated SJL/J recipients of human cord blood. Thus, human cord blood cells appear to produce/induce factors that may act as an adjunct to increase stem-cell activity.
Locating nearby copies of replicated Internet servers (1995)

In this paper we consider the problem of choosing among a collection of replicated servers, focusing on the question of how to make choices that segregate client/server traffic according to network topology. We explore the cost and effectiveness of a variety of approaches, ranging from those requiring routing layer support (e.g., anycast) to those that build location databases using application-level probe tools like traceroute. We uncover a number of tradeoffs between effectiveness, network cost, ease of deployment, and portability across different types of networks. We performed our experiments using a simulation parameterized by a topology collected from 7 survey sites across the United States, exploring a global collection of Network Time Protocol servers.
Synthesis of Convex Hexoctahedral Palladium@Gold Core–Shell Nanocrystals with {431} High-Index Facets with Remarkable Electrochemiluminescence Activities (2014)

Convex hexoctahedral nanocrystals have been synthesized through fast growth kinetics and the use of cetylpyridinium chloride as a capping agent. Monodisperse convex hexoctahedral Pd@Au core-shell nanocrystals with {431} high-index facets are obtained at high reaction rates by using high concentrations of ascorbic acid in the presence of cetylpyridinium chloride. In contrast, octahedral nanocrystals with {111} low-index facets and their {100}-truncated counterparts are formed at low ascorbic acid concentrations. The substitute of cetylpyridinium chloride with cetyltrimethylammonium chloride leads to the generation of concave trisoctahedral Pd@Au core-shell nanocrystals with {331} high-index facets, indicating that cetylpyridinium plays an important role in the formation of convex hexoctahedral nanocrystals. The as-prepared convex hexoctahedral Pd@Au core-shell nanocrystals exhibit remarkable catalytic performances toward electrochemiluminescence compared with truncated octahedral and concave trisoctahedral Pd@Au core-shell nanocrystals.
Suppression of experimental allergic encephalomyelitis by COP1--relevance to multiple sclerosis. (1989)

The evidence in this presentation clearly indicates that in the case of the model disease EAE, desensitization procedures are effective in suppressing the symptoms of the disease and in providing protection against it. The antigens used in our studies are all synthetic materials immunologically relevant to the myelin encephalitogenic protein, but not encephalitogenic themselves. The most effective of these materials is a random basic copolymer of alanine, glutamic acid, lysine and tyrosine, denoted COP 1. The finding that the suppressive polymers show immunological cross-reactivity with the encephalitogenic protein provides a logical basis for the explanation of their suppressive activity in terms of an immunological desensitization mechanism. Our studies suggest that the effectiveness of COP 1 in preventing EAE results from the production of antigen-suppressor T cells, and/or from blocking MBP-specific effector T cells. The results of the clinical trial presented here show demonstrable improvement in the COP 1-treated patients as compared with the placebo subjects, particularly for those patients with less severe MS at the start of the treatment. Thus, although the evidence supporting the antigenic role of MBP in MS is not strong, COP 1, a synthetic polypeptide simulating some of the properties of MBP, appears to be effective in altering the course of MS and is of potential value as a modality for the treatment of this disease.
Epigenetic Control of Circadian Clock Operation during Development (2012)

The molecular players of circadian clock oscillation have been identified and extensively characterized. The epigenetic mechanisms behind the circadian gene expression control has also been recently studied, although there are still details to be illucidated. In this review, we briefly summarize the current understanding of the mammalian clock. We also provide evidence for the lack of circadian oscillation in particular cell types. As the circadian clock has intimate interaction with the various cellular functions in different type of cells, it must have plasticity and specicity in its operation within different epigenetic environments. The lack of circadian oscillation in certain cells provide an unique opportunity to study the required epigenetic environment in the cell that permit circadian oscillation and to idenfify key influencing factors for proper clock function. How epigenetic mechansims, including DNA methylaiton and chromatin modifications, participate in control of clock oscillation still awaits future studies at the genomic scale.
Decentralized sensor fusion and support using multiple models (1997)

In an aircraft application there are a number of limitations (limited computational capability, limited data bus bandwidth...) on a sensor system as well as there are a number of requirements to fulfill to make the sensor system robust against jamming and other kinds of disturbances. We are presenting a new approach to decentralized sensor fusion and tracking, where `decentralized' means that there are a considerable amount of pre-computation performed in the sensors. The novelty of the approach lies in the way the information is fed back from the central fusion unit that is handling the information delivered by the sensors. The information is fed back to the sensors to enable an improved tracking performance and at the same time not contaminating the sensor in the case the central fusion information is distorted due to jamming. The algorithm is realized by using an extend version of the multiple models algorithm AFMM (same class of algorithms as the IMM), in combination with a decentralized Kalman filtering scheme. The extension of AFMM consists of a possibility to include externally hypotheses in the regular split and prune mechanism. This way the external information is treated the same way as a prior in a Kalman filtering scheme and thus the global track estimate is confronted with the sensor's view before accepted by the sensor. In the paper the performance of the tracking algorithm is evaluated in a system consisting of a Radar and an Infrared search and track sensor.
BMP signaling in the development of the mouse esophagus and forestomach (2010)

The stratification and differentiation of the epidermis are known to involve the precise control of multiple signaling pathways. By contrast, little is known about the development of the mouse esophagus and forestomach, which are composed of a stratified squamous epithelium. Based on prior work in the skin, we hypothesized that bone morphogenetic protein (BMP) signaling is a central player. To test this hypothesis, we first used a BMP reporter mouse line harboring a BRE-lacZ allele, along with in situ hybridization to localize transcripts for BMP signaling components, including various antagonists. We then exploited a Shh-Cre allele that drives recombination in the embryonic foregut epithelium to generate gain- or loss-of-function models for the Bmpr1a (Alk3) receptor. In gain-of-function (Shh-Cre;Rosa26(CAG-loxpstoploxp-caBmprIa)) embryos, high levels of ectopic BMP signaling stall the transition from simple columnar to multilayered undifferentiated epithelium in the esophagus and forestomach. In loss-of-function experiments, conditional deletion of the BMP receptor in Shh-Cre;Bmpr1a(flox/flox) embryos allows the formation of a multilayered squamous epithelium but this fails to differentiate, as shown by the absence of expression of the suprabasal markers loricrin and involucrin. Together, these findings suggest multiple roles for BMP signaling in the developing esophagus and forestomach.
Supramolecular Polymers from Linear Telechelic Siloxanes with Quadruple-Hydrogen-Bonded Units (1999)

Telechelic oligo- and poly(dimethylsiloxanes) 1 and 2, with two ureidopyrimidone (UPy) functional groups, have been prepared via a hydrosilylation reaction. The compounds have been characterized in solution by 1H NMR and viscometry and in the solid state by 1H NMR and 13C NMR, FTIR, and rheology measurements. The measurements show that the UPy groups of 1 and 2 are associated via quadruple hydrogen bonds in a donor−donor−acceptor−acceptor (DDAA) array. In many aspects, the materials behave like entangled, high molecular weight polymers. Compound 2 has a Tg at −119 °C and shows melting of microcrystalline domains of associated UPy units at −25 °C. Compound 1 has a crystalline form (Tm = 112 °C) and an amorphous modification with a Tg of 25 °C. Solid-state NMR was used to investigate the mobility of these phases. WISE spectra show a higher mobility of the UPy groups in the amorphous phase than in the crystals of 1. Amorphous 1 and 2 behave like entangled polymers. Their mechanical behavior is characterized by a rubbery plateau and a relatively high activation enthalpy for stress relaxation (ΔH = 127 kJ/mol for 1; ΔH = 54 kJ/mol for 2), which was derived from the temperature dependence of the zero-shear viscosity. Estimates for the degree of polymerization (DP) of 1 and 2, based on the mechanical properties, give DP > 100 for 1 and approximately 20 for 2. Like in condensation polymerization, the DP's of reversible supramolecular polymers are presumably limited by the presence of small amounts of monofunctional impurities.