gebhart/patrepeval huggingface dataset:
Role of head group structure in the phase behavior of amino phospholipids. 2. Lamellar and nonlamellar phases of unsaturated phosphatidylethanolamine analogs (1986)

Three types of analogues of unsaturated phosphatidylethanolamines (PE) have been prepared: phosphatidyl-omega-amino-1-alkanols, N-alkyl-PE's, and C2-alkyl-PE's, with alkyl substitution of carbon-2 of the ethanolamine head group. The physical properties of dioleoyl, dielaidoyl, and 1-palmitoyl-2-oleoyl phospholipids with these head groups have been examined by calorimetry, 31P NMR, freeze-fracture electron microscopy, and X-ray diffraction. N-Alkylation of PE, or substitution of the ethanolamine moiety by 3-amino-1-propanol or 4-amino-1-butanol, decreases the transition temperature of the hydrated gel phase (Tc) and considerably increases the temperature of the lamellar to hexagonal II transition (TH). The pattern of these effects for various PE analogues suggests that head group size and hydrophobicity as well as hydrogen bonding are important determinants of the phase behavior of these lipids. C2-Alkylated PE analogues exhibit several rather surprising properties, notably the ready formation of a quasi-crystalline "high-melting" solid phase even for di-cis-unsaturated species and substantially lower TH values than are observed for the parent PE species. The behavior of these compounds suggests that "hydration forces" can be more important than considerations of lipid "dynamic shape" in predicting the relative stabilities of lamellar vs. nonlamellar phases for at least some zwitterionic phospholipids.
Proteoglycans in health and disease: the multiple roles of syndecan shedding (2010)

Proteolytic processes in the extracellular matrix are a major influence on cell adhesion, migration, survival, differentiation and proliferation. The syndecan cell-surface proteoglycans are important mediators of cell spreading on extracellular matrix and respond to growth factors and other biologically active polypeptides. The ectodomain of each syndecan is constitutively shed from many cultured cells, but is accelerated in response to wound healing and diverse pathophysiological events. Ectodomain shedding is an important regulatory mechanism, because it rapidly changes surface receptor dynamics and generates soluble ectodomains that can function as paracrine or autocrine effectors, or competitive inhibitors. It is known that the family of syndecans can be shed by a variety of matrix proteinase, including many metzincins. Shedding is particularly active in proliferating and invasive cells, such as cancer cells, where cell-surface components are continually released. Here, recent research into the shedding of syndecans and its physiological relevance are assessed.
Suppression of cervical carcinoma cell growth by intracytoplasmic codelivery of anti-oncoprotein E6 antibody and small interfering RNA (2007)

Cervical cancer is caused by high-risk types of human papillomaviruses (HPV) that encode the E6 and E7 oncogenes. Silencing of E6 gene expression in HPV-positive cell lines by transfection of small interfering RNA (siRNA) with cationic lipids restores the dormant p53 tumor suppressor pathway. Because cationic lipids can also be used for intracytoplasmic delivery of proteins, we tested whether the delivery of monoclonal antibodies that bind to HPV16 E6 and neutralize its biological activity in vitro could restore p53 function in tumor cells. Here, we show that the 4C6 antibody is efficiently delivered into the cell cytoplasm using a lipidic reagent used for siRNA transfection. The delivery of 4C6 resulted in the nuclear accumulation of p53 protein in CaSki and SiHa cells but not in HeLa cells. Furthermore, the antibody-mediated p53 response was dramatically increased when a peptide corresponding to the 4C6 epitope and bearing a COOH-terminal cysteine residue was added to the transduction mixture. We found that a fraction of the added peptides were dimers that allowed the formation of antibody polymers adsorbed onto the lipidic matrix. With this system, the proliferation of CaSki and SiHa cells was strongly diminished, but no apoptosis was detectable. Remarkably, cell growth was almost totally suppressed by the addition of E6-specific siRNA to the transduction complex. The results indicate that the activity of E6 oncoprotein can be down-regulated in vivo by lipid-mediated antibody delivery and that antibodies and siRNA act synergistically when codelivered. This novel targeting strategy is simple to implement and may find therapeutic applications.
Potent and Selective Aurora Inhibitors Identified by the Expansion of a Novel Scaffold for Protein Kinase Inhibition (2005)

Potent and selective Aurora kinase inhibitors were identified from the combinatorial expansion of the 1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazole bi-cycle, a novel and versatile scaffold designed to target the ATP pocket of protein kinases. The most potent compound reported in this study had an IC(50) of 0.027 microM in the enzymatic assay for Aur-A inhibition and IC(50)s between 0.05 microM and 0.5 microM for the inhibition of proliferation of different tumor cell lines.
Reversal of P-glycoprotein is greatly reduced by the presence of plasma but can be monitored by an ex vivo clinical assay (1996)

The effects of nine reversers of P-glycoprotein on the uptake of daunomycin into MDR1-transfected P388 cells were quantitatively determined in undiluted human or mouse plasma and compared with their effects when measurements are made in a conventional cell culture medium (RPMI 1640) containing only 10% serum. Plasma diminished or greatly diminished the effectiveness of the reversers, reductions of up to 20-fold being found for reversers (cyclosporin A, prochlorperazine and amiodarone) that have been used in clinical trials, although quinidine was almost as effective in plasma as in cell culture medium containing 10% fetal calf serum. Human or bovine serum albumin could mimic the effect of whole plasma. When measurements of the effectiveness of the reverser cyclosporin A were made in an ex vivo assay, using these P388 cells, complete accord was found between such ex vivo determinations and cyclosporin A's effectiveness in vivo, as monitored by its ability to increase the accumulation of vinblastine in mouse kidney tissue. The ex vivo assay was shown to be suitable to monitor the effectivity of reversers present in plasma taken from patients receiving quinidine and cyclosporine A in routine clinical treatment.
Comparative molecular modeling and crystallization of P‐30 protein: A novel antitumor protein of Rana pipiens oocytes and early embryos (1992)

The P-30 protein (Onconase) of Rana pipiens oocytes and early embryos is homologous to members of the pancreatic ribonuclease superfamily and exhibits an antitumor activity in vitro and in vivo. It appears that the ribonucleolytic activity of P-30 protein may be required for its antitumor effects. A comparative molecular model of P-30 protein has been constructed based upon the known three-dimensional structure of bovine pancreatic RNase A in order to provide structural information. Functionally, these enzymes hydrolyze oligoribonucleotides to pyrimidine-3'-phosphate monoesters and 5'-OH ribonucleotides. In the modeling procedure, automated sequence alignments were revised based upon the inspection of the RNase A structure before the amino acids of the P-30 protein were assigned the coordinates of the RNase A template. The inevitable intermolecular steric clashes that result were relieved on an interactive graphics device through the adjustment of side chain torsion angles. This process was followed by energy minimization of the model, which served to optimize stereochemical geometry and to relieve any remaining unacceptably close contacts. The resulting model retains the essential features of RNase A as sequence insertions and deletions are almost exclusively found in exposed surface loops. The all atom superposition of active site residues of the P-30 protein model and an identically minimized RNase A structure has a root mean square deviation of 0.52 A. Though tentative, the model is consistent with a pyrimidine specificity.(ABSTRACT TRUNCATED AT 250 WORDS)
Survey and evaluation of query intent detection methods (2009)

User interactions with search engines reveal three main underlying intents, namely navigational, informational, and transactional. By providing more accurate results depending on such query intents the performance of search engines can be greatly improved. Therefore, query classification has been an active research topic for the last years. However, while query topic classification has deserved a specific bakeoff, no evaluation campaign has been devoted to the study of automatic query intent detection. In this paper some of the available query intent detection techniques are reviewed, an evaluation framework is proposed, and it is used to compare those methods in order to shed light on their relative performance and drawbacks. As it will be shown, manually prepared gold-standard files are much needed, and traditional pooling is not the most feasible evaluation method. In addition to this, future lines of work in both query intent detection and its evaluation are proposed.
Lanicemine: a low-trapping NMDA channel blocker produces sustained antidepressant efficacy with minimal psychotomimetic adverse effects (2013)

Ketamine, an N-methyl-D-aspartate receptor (NMDAR) channel blocker, has been found to induce rapid and robust antidepressant-like effects in rodent models and in treatment-refractory depressed patients. However, the marked acute psychological side effects of ketamine complicate the interpretation of both preclinical and clinical data. Moreover, the lack of controlled data demonstrating the ability of ketamine to sustain the antidepressant response with repeated administration leaves the potential clinical utility of this class of drugs in question. Using quantitative electroencephalography (qEEG) to objectively align doses of a low-trapping NMDA channel blocker, AZD6765 (lanicemine), to that of ketamine, we demonstrate the potential for NMDA channel blockers to produce antidepressant efficacy without psychotomimetic and dissociative side effects. Furthermore, using placebo-controlled data, we show that the antidepressant response to NMDA channel blockers can be maintained with repeated and intermittent drug administration. Together, these data provide a path for the development of novel glutamatergic-based therapeutics for treatment-refractory mood disorders.
DISCREPANCIES BETWEEN VENOGRAPHY AND REAL TIME B MODE ULTRASOUND IMAGING IN THE DIAGNOSIS OF DEEP VEIN THROMBOSIS (1987)

Methods : in this prospective study, real time B Mode ultrasound imaging (USI) was compared to bilateral ascending contrast venography, double blindly, in 430 patients suspected of deep vein thrombosis (DVT) or pulmonary embolism. A complete scan of the venous system from the inferior vena cava to the calf veins, was performed with a high resolution duplex system (DIASONICS DRF 400) and coupled systematically with a C.W. Doppler examination. The results obtained by USI were thus compared to the venograms performed on a total of 854 legs. Results : there are corresponding results in 95% of the legs (808/854). If we consider venography as the standard of reference, the sensitivity of USI is 98% (325/333) and the specificity 94% (483/514). Isolated calf vein thrombosis are detected in 91% (84/92) of the legs and proximal DVT in 100% (241/241) in this series whatever the topography and the extension of the thrombosis and whatever the degree of the obstruction of the vein. Discrepancies found in 46 legs are related to : - 8 DVT located in the calf (6 in the presumed healthy leg) diagnosed only by venography. - 27 DVT (18 distal, 9 femoral or iliac) detected only by USI - 9 doubtful examinations with USI not confirmed by venography - 2 doubtful venograms with negative USI test. Comments : Calf vein thrombosis especially located in the soleal sinuses and the gastrocnemius with in most cases the direct image of the thrombus are more often detected by USI provided that the technique and the equipment are appropriate. The absence of visualisation of venous segments with venography is not specific of venous thrombosis. These veins non affected by the thrombosis are not filled by the contrast medium when located above in occluded ilio-femoral or ilio-caval junction or when they are the site of extrinsic compression. The direct image of the vein and the surrounding structures obtained with USI enhances the diagnostic sensitivity and specificity and provides precision of the exact extension of the thrombosis. Due to these differences, can venography still be considered as the standard of reference in the diagnosis of DVT and their precise localisation ?
Gray Matter Density of Auditory Association Cortex Relates to Knowledge of Sound Concepts in Primary Progressive Aphasia (2012)

Long-term memory integrates the multimodal information acquired through perception into unified concepts, supporting object recognition, thought, and language. While some theories of human cognition have considered concepts to be abstract symbols, recent functional neuroimaging evidence has supported an alternative theory: that concepts are multimodal representations associated with the sensory and motor systems through which they are acquired. However, few studies have examined the effects of cortical lesions on the sensory and motor associations of concepts. We tested the hypothesis that individuals with disease in auditory association cortex would have difficulty processing concepts with strong sound associations (e.g., thunder). Human participants with the logopenic variant of primary progressive aphasia (lvPPA) performed a recognition task on words with strong associations in three modalities: Sound, Sight, and Manipulation. LvPPA participants had selective difficulty on Sound words relative to other modalities. Structural MRI analysis in lvPPA revealed gray matter atrophy in auditory association cortex, as defined functionally in a separate BOLD fMRI study of healthy adults. Moreover, lvPPA showed reduced gray matter density in the region of auditory association cortex that healthy participants activated when processing the same Sound words in a separate BOLD fMRI experiment. Finally, reduced gray matter density in this region in lvPPA directly correlated with impaired performance on Sound words. These findings support the hypothesis that conceptual memories are represented in the sensory and motor association cortices through which they are acquired.
Organic Synthesis with Anion-exchange Resins: Reaction of Imines with Active Methylene Compounds† (1998)

D. Konwar, D. Kumar Dutta and B. Nath Goswami, J. Chem. Res. (S), 1998, 342 DOI: 10.1039/A800951A
Application of Unscented Kalman Filter to a cable driven surgical robot: A simulation study (2012)

Cable driven power transmissions are used in applications such as haptic devices, surgical robots etc. The use of flexible cable based power transmission often causes relative motion between the motor actuator and mechanism joint during operation due to the elasticity of the cable. State-space control methods can be used to improve performance, but may require state estimates. For nonlinear systems, the Unscented Kalman Filter (UKF) provides a computationally efficient way to obtain state estimates. The UKF is applied here to a simulation of a minimially invasive surgical robot, to study the state estimation for a cable driven system with nonlinear dynamics. State estimates from the UKF are compared with the known states available from the simulation. These state estimates are also utilized by two different controllers interacting with the simulation to test the UKF performance under closed loop control. We tested the UKF performance with error perturbations in the system model's cable stiffness parameter.
Sobre la universalidad de la interpretación (2009)

En el articulo se defiende una concepcion de la interpretacion cuyo alcance constitutivo reside en el tipo de vinculacion que establece con el lenguaje que la expresa. Con ello, se busca satisfacer un doble proposito interrelacionado: indagar hasta que punto la interpretacion permite una redescripcion de la linguisticidad y, a la vez, como desde esta ultima se logra justificar el alcance irrebasable de aquella. En primer termino, se revisan algunas de las consecuencias en las descripciones del lenguaje como significado, luego se procede con el signo. A continuacion se propone un examen de cuno hermeneutico a partir de la obra de Paul Ricoeur para tratar con la lectura interpretativa de textos.
Pharmacological strategies for detoxification (2013)

Detoxification refers to the safe discontinuation from a substance of dependence and is distinct from relapse prevention. Detoxification usually takes between a few days and a few weeks to complete, depending on the substance being misused, the severity of dependence and the support available to the user. Psychosocial therapies alongside pharmacological treatments are essential to improve outcome. The dependencies considered in this overview are detoxification from opioids (with methadone, buprenorphine, α2-adrenoceptor agonists and adjunct medications), alcohol (with benzodiazepines, anti-glutamatergics and γ-aminobutyric acid (GABA)-ergic drugs), stimulants and cannabis (with no clear recommended pharmacological treatments), benzodiazepines (with dose tapering) and nicotine (with nicotine replacement therapy, antidepressants and partial agonists). Evidence is limited by a lack of controlled trials robust enough for review bodies, and more research is required into optimal treatment doses and regimes, alone and in combination.
Electrical Stimulation Enhances Migratory Ability of Transplanted Bone Marrow Stromal Cells in a Rodent Ischemic Stroke Model (2018)

These results suggest that electrical stimulation enhances migratory ability of transplanted BMSCs in ischemic stroke model of rats. If we can direct the implanted BMSCs to the site of interest, it may lead to a greater therapeutic effect.
Detection of N-RAS and K-RAS in their active GTP-bound form in acute myeloid leukemia without activatingRASmutations (2006)

RAS genes, predominantly N-RAS and K-RAS, have been implicated in the pathogenesis of acute myeloid leukemia (AML), due to activating RAS mutations detectable in approximately 20% of AML patients. In the present study, RAS proteins were detected in their activated, GTP-bound form, in AML patients (n = 10) not expressing mutated forms of H-RAS, K-RAS and N-RAS. Further analysis revealed the simultaneous presence of N-RAS and K-RAS proteins in the GTP-bound state in seven out of 10 AML samples. In four out of 10 samples the levels of RAS-GTP were comparable to an AML cell line (TF-1) with an activating N-RAS mutation (Q61P). The detection of RAS-GTP in AML patients without RAS mutations further supports a functional role of RAS proteins in the pathogenesis of AML and may explain the observed effects of RAS inhibitors in some AML patients in the absence of activating RAS mutations.
RNA Interference in Mammalian Cells by Chemically-Modified RNA (2003)

RNA interference (RNAi) is proving to be a robust and versatile technique for controlling gene expression in mammalian cells. To fully realize its potential in vivo, however, it may be necessary to introduce chemical modifications to optimize potency, stability, and pharmacokinetic properties. Here, we test the effects of chemical modifications on RNA stability and inhibition of gene expression. We find that RNA duplexes containing either phosphodiester or varying numbers of phosphorothioate linkages are remarkably stable during prolonged incubations in serum. Treatment of cells with RNA duplexes containing phosphorothioate linkages leads to selective inhibition of gene expression. RNAi also tolerates the introduction of 2'-deoxy-2'-fluorouridine or locked nucleic acid (LNA) nucleotides. Introduction of LNA nucleotides also substantially increases the thermal stability of modified RNA duplexes without compromising the efficiency of RNAi. These results suggest that inhibition of gene expression by RNAi is compatible with a broad spectrum of chemical modifications to the duplex, affording a wide range of useful options for probing the mechanism of RNAi and for improving RNA interference in vivo.
Cell Cycle Regulation in Plants (1994)

Plant Biology Laboratory’, The Salk lnstitute for Biological Studies, 10100 North Torrey Pines Road, La Jolla, California 92037 Cell division plays a crucial role during a11 phases of plant development. Continuing organogenesis and plastic growth responses to a changing environment require precise spatial, temporal, and developmental regulation of cell division activ- ity in meristems. The molecular analysis of cell division and its regulation in plants lags far behind such studies in yeast and animals. Since the cell theory was proposed by Schleiden and Schwann in 1838, many approaches have been taken to elucidate how cells divide, but insight into the molecular basis of division control developed only after the genetic analysis of cell division was initiated in yeast 25 years ago (Hartwell et al., 1970). Cell division cycle mutants in the yeasts
Machine Cell Formation using A Classification Neural Network (2004)

The machine cell formation problem is the problem to group machines into machine families and parts into part families so as to minimize bottleneck machines, exceptional parts, and inter-cell part movements in cellular manufacturing systems and flexible manufacturing systems. This paper proposes a new machine cell formation method based on the adaptive Hamming net which is a kind of neural network model. To show the applicability of the proposed method, it presents some experiment results and compares the method with other cell formation methods. From the experiments, we observed that the proposed method could produce good cells for the machine cell formation problem.
Designing a unified speech/audio codec by adopting a single channel harmonic source separation module (2008)

This paper propose a unified speech/audio codec by adopting a single channel harmonic separation module as a pre-processor. A modulation frequency analysis method is used for harmonic separation, and the separated components are first encoded by an appropriate codec, e.g. speech codec. The error between input and the encoded signal is recorded by another codec. Though any type of codec can be used for the purpose, we adopt two state-of-the-art international standards (AMR-WB and HE-AAC) to provide an interoperability option. The amount of allocated bits to each stage is controlled by a power ratio of separated harmonic componets to input signal. Subjective listening tests verify the consistency of the proposed method in speech, music and mixed signal inputs.
Novel self-planarizing CVD oxide for interlayer dielectric applications (2002)

This paper presents a highly-reliable interlayer dielectric process using a novel CVD method. The key to the process is a unique chemistry of SiH/sub 4/ and H/sub 2/O/sub 2/, which generates a liquid intermediate filling very narrow gaps and providing excellent planarity. Resistances of via-hole chains using this process are lower and more stable compared with those using P-TEOS and SOG process. This is due to a lower water content and a low absorption property of this self-planarizing CVD oxide.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>