gebhart/patrepeval huggingface dataset:
Perturbation of the fuchsone chromophore by 3,5-methyl substitution. Sterically crowded exocyclic double bond (1981)

Several 3,5-methyl substituted fuchsones have been synthesized and characterized by means of UV and NMR spectroscopy as well as dipole moment measurements. Two basic types of behaviour of the longest wavelength band have been found for these derivatives in comparison to 2,6-substituted analogues i.e. hypochromic effect and bathochromic shift. These effects can be attributed to a steric crowding of the C (4) -C (7) double bonds. The role of the steric interactions in the ground state and in the excited state is discussed.
Vascular Endothelial Growth Factor Signals Endothelial Cell Production of Nitric Oxide and Prostacyclin through Flk-1/KDR Activation of c-Src (1999)

Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mitogen that promotes angiogenesis, vascular hyperpermeability, and vasodilation by autocrine mechanisms involving nitric oxide (NO) and prostacyclin (PGI(2)) production. These experiments used immunoprecipitation and immunoassay procedures to characterize the signaling pathways by which VEGF induces NO and PGI(2) formation in cultured endothelial cells. The data showed that VEGF stimulates complex formation of the flk-1/kinase-insert domain-containing receptor (KDR) VEGF receptor with c-Src and that Src activation is required for VEGF induction of phospholipase C gamma1 activation and inositol 1,4,5-trisphosphate formation. Reporter cell assays showed that VEGF promotes a approximately 50-fold increase in NO formation, which peaks at 5-20 min. This effect is mediated by a signaling cascade initiated by flk-1/KDR activation of c-Src, leading to phospholipase C gamma1 activation, inositol 1,4,5-trisphosphate formation, release of [Ca(2+)](i) and nitric oxide synthase activation. Immunoassays of VEGF-induced 6-keto prostaglandin F(1alpha) formation as an indicator of PGI(2) production revealed a 3-4-fold increase that peaked at 45-60 min. The PGI(2) signaling pathway follows the NO pathway through release of [Ca(2+)](i), but diverges prior to NOS activation and also requires activation of mitogen-activated protein kinase. These results suggest that NO and PGI(2) function in parallel in mediating the effects of VEGF.
Design and evaluation of main memory hash join algorithms for multi-core CPUs (2011)

The focus of this paper is on investigating efficient hash join algorithms for modern multi-core processors in main memory environments. This paper dissects each internal phase of a typical hash join algorithm and considers different alternatives for implementing each phase, producing a family of hash join algorithms. Then, we implement these main memory algorithms on two radically different modern multi-processor systems, and carefully examine the factors that impact the performance of each method.
Photoregulation of a phytochrome gene promoter from oat transferred into rice by particle bombardment. (1989)

The regulatory photoreceptor phytochrome controls the transcription of its own phy genes in a negative feedback fashion. We have exploited microprojectile-mediated gene transfer to develop a rapid transient expression assay system for the study of DNA sequences involved in the phytochrome-regulated expression of these genes. The 5'-flanking sequence and part of the structural region of an oat phy gene have been fused to a reporter coding sequence (chloramphenicol acetyltransferase, CAT) and introduced into intact darkgrown seedlings by using high-velocity microprojectiles. Expression is assayable in less than 24 hr from bombardment. The introduced oat phy-CAT fusion gene is expressed and down-regulated by white light in barley, rice, and oat, whereas no expression is detected in three dicots tested, tobacco, cucumber, and Arabidopsis thaliana. In bombarded rice shoots, red/far-red light-reversible repression of expression of the heterologous oat phy-CAT gene shows that it is regulated by phytochrome in a manner parallel to that of the endogenous rice phy genes. These data indicate that the transduction pathway components and promoter sequences involved in autoregulation of phy expression have been evolutionarily conserved between oat and rice. The experiments show the feasibility of using high-velocity microprojectile-mediated gene transfer for the rapid analysis of light-controlled monocot gene promoters in monocot tissues that until now have been recalcitrant to such studies.
Optimization of tactical multimedia networks in the forward area (2002)

The US Army is investigating a Warfighter's Information Network (WIN) that includes the deployment of seamless multimedia voice, data and video services at the brigade level and below. Their intent is to leverage commercial PCS technology in the deployment of an autonomous network that supports fully distributed multimedia communications without the need for a commercial-type basestation infrastructure. The technology, necessary to support this concept, is being studied by the Focused Research Initiative team of Clemson University, ITT-A/CD and Techno-Sciences under a grant from the Army Research Office. We present the results of research at ITT with respect to the optimization of the network configuration, protocols and waveforms to increase the throughput, delay and reliability performance. This paper reports on a hierarchical network structure and signaling approach that eliminates cosite interference as a major obstacle to the network performance. The overall analysis at the physical and link protocol layers is based on the implementation and transmission of ATM-like packets over wireless links.
Hierarchical Patterns of Transgene Expression Indicate Involvement of Developmental Mechanisms in the Regulation of the Maize P1-rr Promoter (2000)

The maize P1-rr gene encodes a Myb-homologous transcription factor that regulates the synthesis of red flavonoid pigments. Maize plants transformed with segments of the P1-rr promoter driving a GUS reporter gene exhibit significant variation in transgene expression, both between independent transformation events and among sibling plants derived from a single event. Interestingly, variability in spatial expression is not random; rather, transgene activity occurs predominantly in five patterns that fit a hierarchy: expression is most common in kernel pericarp, with sequential addition of expression in cob glumes, husk, silk, and tassel. The hierarchical expression pattern of P-rr::GUS transgenes suggests a possible model for developmental regulation of the P1-rr gene. Our results demonstrate that variability in transgene expression, a common occurrence in transgenic plant studies, can be informative if adequately analyzed to uncover underlying patterns of gene expression.
Solvent-Promoted and -Controlled Aza-Michael Reaction with Aromatic Amines (2009)

1,4-Addition of anilines onto Michael acceptors proceeds easily in specific polar protic solvents, without any promoting agent. According to the solvent and to the electrophile, the selectivity of the reaction can be finely tuned. With methyl acrylate as electrophile, only monoaddition takes place in water, while the diadduct is yielded in hexafluoroisopropyl alcohol (HFIP). The use of methyl vinyl ketone as a partner affords the monoadduct in water, the diadduct in trifluoroethanol (TFE), and the quinoline in HFIP.
GENETICS OF COLON CANCER: Impact of Inheritance on Colon Cancer Risk (1995)

The genes that are mutated in two of the rare syndromes of hereditary colon cancer were recently identified, and genetic diagnosis is already possible in some cases. Acquired mutations of these same genes also appear to be important in sporadic colon cancers. Familial clustering of sporadic cases is common and may likewise arise from inherited susceptibility. Screening strategies for both the rare syndromes and the common cases of colon cancer with familial risk have been suggested. Certain clinical features allow stratification of colon cancer risk among common cases. It is anticipated that continued genetic investigation will result in more precise screening and improved diagnostic and therapeutic options for colon cancer.
Thermolytic Carbonates for Potential 5‘-Hydroxyl Protection of Deoxyribonucleosides (2003)

Thermolytic groups structurally related to well-studied heat-sensitive phosphate/thiophosphate protecting groups have been evaluated for 5'-hydroxyl protection of deoxyribonucleosides as carbonates and for potential use in solid-phase oligonucleotide synthesis. The spatial arrangement of selected functional groups forming an asymmetric nucleosidic 5'-O-carbonic acid ester has been designed to enable heat-induced cyclodecarbonation reactions, which would result in the release of carbon dioxide and the generation of a nucleosidic 5'-hydroxyl group. The nucleosidic 5'-O-carbonates 3-8, 10-15, and 19-21 were prepared and were isolated in yields ranging from 45 to 83%. Thermolytic deprotection of these carbonates is preferably performed in aqueous organic solvent at 90 degrees C under near neutral conditions. The rates of carbonate deprotection are dependent on the nucleophilicity of the functional group involved in the postulated cyclodecarbonation reaction and on solvent polarity. Deprotection kinetics increase according to the following order: 4 < 5 < 10 < 6 < 12 < 7 < 13 < 8 < 14 congruent with 19-21 and CCl4 < dioxane < MeCN < t-BuOH < MeCN:phosphate buffer (3:1 v/v, pH 7.0) < EtOH:phosphate buffer (1:1 v/v, pH 7.0). Complete thermolytic deprotection of carbonates 7, 8, 13, and 14 is achieved within 20 min to 2 h under optimal conditions in phosphate buffer-MeCN. The 2-(2-pyridyl)amino-1-phenylethyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups are particularly promising for 5'-hydroxyl protection of deoxyribonucleosides as thermolytic carbonates.
Fibroblast Growth Factor-23-mediated Inhibition of Renal Phosphate Transport in Mice Requires Sodium-Hydrogen Exchanger Regulatory Factor-1 (NHERF-1) and Synergizes with Parathyroid Hormone (2011)

Fibroblast growth factor-23 (FGF-23) inhibits sodium-dependent phosphate transport in brush border membrane vesicles derived from hormone-treated kidney slices of the mouse and in mouse proximal tubule cells by processes involving mitogen-activated protein kinase (MAPK) but not protein kinase A (PKA) or protein kinase C (PKC). By contrast, phosphate transport in brush border membrane vesicles and proximal tubule cells from sodium-hydrogen exchanger regulatory factor-1 (NHERF-1)-null mice were resistant to the inhibitory effect of FGF-23 (10(-9) m). Infection of NHERF-1-null proximal tubule cells with wild-type adenovirus-GFP-NHERF-1 increased basal phosphate transport and restored the inhibitory effect of FGF-23. Infection with adenovirus-GFP-NHERF-1 containing a S77A or T95D mutation also increased basal phosphate transport, but the cells remained resistant to FGF-23 (10(-9) m). Low concentrations of FGF-23 (10(-13) m) and PTH (10(-11) m) individually did not inhibit phosphate transport or activate PKA, PKC, or MAPK. When combined, however, these hormones markedly inhibited phosphate transport associated with activation of PKC and PKA but not MAPK. These studies indicate that FGF-23 inhibits phosphate transport in the mouse kidney by processes that involve the scaffold protein NHERF-1. In addition, FGF-23 synergizes with PTH to inhibit phosphate transport by facilitating the activation of the PTH signal transduction pathway.
Crystal Structures of Human MdmX (HdmX) in Complex with p53 Peptide Analogues Reveal Surprising Conformational Changes (2009)

p53 tumor suppressor activity is negatively regulated through binding to the oncogenic proteins Hdm2 and HdmX. The p53 residues Leu(26), Trp(23), and Phe(19) are crucial to mediate these interactions. Inhibiting p53 binding to both Hdm2 and HdmX should be a promising clinical approach to reactivate p53 in the cancer setting, but previous studies have suggested that the discovery of dual Hdm2/HdmX inhibitors will be difficult. We have determined the crystal structures at 1.3 A of the N-terminal domain of HdmX bound to two p53 peptidomimetics without and with a 6-chlorine substituent on the indole (which binds in the same subpocket as Trp(23) of p53). The latter compound is the most potent peptide-based antagonist of the p53-Hdm2 interaction yet to be described. The x-ray structures revealed surprising conformational changes of the binding cleft of HdmX, including an "open conformation" of Tyr(99) and unexpected "cross-talk" between the Trp and Leu pockets. Notably, the 6-chloro p53 peptidomimetic bound with high affinity to both HdmX and Hdm2 (K(d) values of 36 and 7 nm, respectively). Our results suggest that the development of potent dual inhibitors for HdmX and Hdm2 should be feasible. They also reveal possible conformational states of HdmX, which should lead to a better prediction of its interactions with potential biological partners.
P‐9: Numerical Analysis on Temperature Dependence of Characteristics of Amorphous In‐Ga‐Zn‐Oxide TFT (2009)

Abstract We fabricated inverted‐staggered amorphous In‐Ga‐Zn‐O (a‐IGZO) TFTs and measured temperature dependence of the TFT characteristics. A V th shift between 120°C and 180°C was as large as about 4 V. In the analysis with 2‐D numerical simulation, we could reproduce the measured result by assuming two kinds of donor‐like states as carrier generation sources.
New pathophysiological mechanisms in irritable bowel syndrome (2004)

Irritable bowel syndrome (IBS) is a functional, multifactorial disease characterized by abdominal pain and erratic bowel habit. Changes in gastrointestinal motor function, enhanced perception of stimuli arising from the gut wall and psychosocial factors are thought to be major contributors for symptom generation. In recent years, several additional factors have been identified and postulated to interact with these classical mechanisms. Reduced ability to expel intestinal gas with consequent gas trapping and bowel distension may contribute to abdominal discomfort/pain and bloating. Abnormal activation of certain brain regions following painful stimulation of the rectum suggests altered processing of afferent signals. An acute gastrointestinal infection is now a recognized aetiological factor for symptom development in a subset of IBS patients (i.e. post-infectious IBS), who are probably unable to down-regulate the initial inflammatory stimulus efficiently. Furthermore, low-grade inflammatory infiltration and activation of mast cells in proximity to nerves in the colonic mucosa may also participate in the frequency and severity of perceived abdominal pain in post-infectious and non-specific IBS. Initial evidence suggests the existence of changes in gut microflora, serotonin metabolism and a genetic contribution in IBS pathophysiology. These novel mechanisms may aid a better understanding of the complex pathophysiology of IBS and to develop new therapies.
Reciprocal subtraction differential RNA display: An efficient and rapid procedure for isolating differentially expressed gene sequences (1998)

A reciprocal subtraction differential RNA display (RSDD) approach has been developed that permits the rapid and efficient identification and cloning of both abundant and rare differentially expressed genes. RSDD comprises reciprocal subtraction of cDNA libraries followed by differential RNA display. The RSDD strategy was applied to analyze the gene expression alterations resulting during cancer progression as adenovirus-transformed rodent cells developed an aggressive transformed state, as documented by elevated anchorage-independence and enhanced in vivo oncogenesis in nude mice. This approach resulted in the identification and cloning of both known and a high proportion (>65%) of unknown sequences, including cDNAs displaying elevated expression as a function of progression (progression-elevated gene) and cDNAs displaying suppressed expression as a function of progression (progression-suppressed gene). Sixteen differentially expressed genes, including five unknown progression-elevated genes and six unknown progression-suppressed genes, have been characterized. The RSDD scheme should find wide application for the effective detection and isolation of differentially expressed genes.
Negative Differential Resistance in Transport through Organic Molecules on Silicon (2007)

Recent scanning tunneling microscopy studies of individual organic molecules on Si(001) reported negative differential resistance (NDR) above a critical applied field, observations explained by a resonant tunneling model proposed prior to the experiments. Here we use both density functional theory and a many-electron GW self-energy approach to quantitatively assess the viability of this mechanism in hybrid junctions with organic molecules on Si. For cyclopentene on p-type Si(001), the frontier energy levels are calculated to be independent of applied electric fields, ruling out the proposed mechanism for NDR. Guidelines for achieving NDR are developed and illustrated with two related molecules, aminocyclopentene and pyrroline.
Use of Positron Emission Tomography in Pharmacokinetic Studies to Investigate Therapeutic Advantage in a Phase I Study of 120-Hour Intravenous Infusion XR5000 (2003)

The recommended dose for XR5000 in phase II studies is 3,010 mg/m2/120 hours. PET studies with 11C-labeled drug were feasible and demonstrated in vivo distribution into tumors. Saturation of tumor exposure was not reached at the MTD.
Chimeric Antigen Receptor T Cells against CD19 for Multiple Myeloma (2015)

A patient with refractory multiple myeloma received an infusion of CTL019 cells, a cellular therapy consisting of autologous T cells transduced with an anti-CD19 chimeric antigen receptor, after myeloablative chemotherapy (melphalan, 140 mg per square meter of body-surface area) and autologous stem-cell transplantation. Four years earlier, autologous transplantation with a higher melphalan dose (200 mg per square meter) had induced only a partial, transient response. Autologous transplantation followed by treatment with CTL019 cells led to a complete response with no evidence of progression and no measurable serum or urine monoclonal protein at the most recent evaluation, 12 months after treatment. This response was achieved despite the absence of CD19 expression in 99.95% of the patient's neoplastic plasma cells. (Funded by Novartis and others; ClinicalTrials.gov number, NCT02135406.).
Stability analysis of even and odd waves of symmetric nonlinear planar optical waveguides (1993)

In terms of the known surface wave stability characteristics of the simpler single-interface problem, we have explained the known stability behavior of antisymmetric and symmetric solutions of a linear core sandwiched between two nonlinear media. Our method considers the lateral shift of the nonlinear surface wave on one interface caused by the wave on the second interface. The appearance of complex growth rates in the case of the antisymmetric solution is explained by using this method. We show that the antisymmetric wave is stable at high values of the propagation constant, in contrast to the symmetric wave. We give simple physical explanations for the difference in stability results for the symmetric and the antisymmetric states in terms of a general physical principle, according to which a particle combination with less energy than the sum of the energies of its constituent states is stable.
Anti-Galectin Compounds as Potential Anti-Cancer Drugs (2006)

Galectins form a family of carbohydrate-binding proteins defined by their affinity for beta-galactosides containing glycoconjugates. The carbohydrate recognition domain (CRD) is responsible for the specificity of galectins for saccharides. This binding may result in modulated cell proliferation, cell death and cell migration, three processes that are intimately involved in cancer initiation and progression. Galectins can also display protein-protein types of interactions with their binding partners. Certain galectins directly involved in cancer progression seem to be promising targets for the development of novel therapeutic strategies to combat cancer. Indeed, migrating cancer cells resistant to apoptosis still constitute the principal target for the cytotoxic drugs used to treat cancer patients. Reducing the levels of migration in apoptosis-resistant cancer cells can restore certain levels of sensitivity to apoptosis (and so to pro-apoptotic drugs) in restricted-migration cancer cells. Anti-galectin agents can restrict the levels of migration of several types of cancer cell and should therefore be used in association with cytotoxic drugs to combat metastatic cancer. We provide experimental proof in support of this concept. While the present review focuses on various experimental strategies to impair cancer progression by targeting certain types of galectins, it pays particular attention to glioblastomas, which constitute the ultimate level of malignancy in primary brain tumors. Glioblastomas form the most common type of malignant brain tumor in children and adults, and no glioblastoma patient has been cured to date.
Multimedia information interchange: Web forms meet data servers (2003)

The increasing use of Internet technology and of Web servers and services has pushed several organisations to automate the access to their services and their data collection processes by using HTML form-guided dialogs. A large part of the information collected by these HTML forms already exists in the information system of the Web client, but today's form filling procedures suppose to fill forms "by hand". We propose a generic middleware program located on the client side and dedicated to automatically fill the data fields of the HTML forms by picking up the required data from the local information system. A key feature of our middleware is that it runs without any prerequisite on the server side. We initially developed our approach for the medical assistance domain to support decision making for remote patients and to improve the continuity of care. This application domain however is not restrictive and our approach may be easily used in other domains.
α-Melanocyte-Stimulating Hormone Inhibits Allergic Airway Inflammation (2003)

Alpha-melanocyte-stimulating hormone (alpha-MSH) is a neuropeptide controlling melanogenesis in pigmentary cells. In addition, its potent immunomodulatory and immunosuppressive activity has been recently described in cutaneous inflammatory disorders. Whether alpha-MSH is also produced in the lung and might play a role in the pathogenesis of inflammatory lung conditions, including allergic bronchial asthma, is unknown. Production and functional role of alpha-MSH were investigated in a murine model of allergic airway inflammation. alpha-MSH production was detected in bronchoalveolar lavage fluids. Although aerosol challenges stimulate alpha-MSH production in nonsensitized mice, this rapid and marked stimulation was absent in allergic animals. Treatment of allergic mice with alpha-MSH resulted in suppression of airway inflammation. These effects were mediated via IL-10 production, because IL-10 knockout mice were resistant to alpha-MSH treatment. This study provides evidence for a novel function of alpha-MSH linking neuroimmune functions in allergic airway inflammation.
Rock perforation by pulsed Nd:YAG laser (2004)

In gas and oil well completion, perforation channels must be made through the steel casing wall and cement and into the rock formation in the production zone to allow formation fluid to enter the well. This paper will present study results on using a pulsed Nd:YAG laser to drill the perforation channels through reservoir rocks. With fiber optic cable delivery capability, an Nd:YAG laser beam has the potential to be delivered to deep oil production zones. Effects of laser pulse parameters, beam properties, and assistant gas purging on the perforating efficiency and rock permeability will be reported. Unlike the conventional explosive charge perforation that often causes great reduction of rock permeability, laser perforation would enhance the rock permeability, therefore increasing the oil or gas production rate of the well