gebhart/patrepeval huggingface dataset:
Holonomic quantum computing with cat-codes (2015)

Universal quantum computation on a space consisting of superpositions of $d$ well-separated coherent states can be achieved by two families of adiabatic holonomic gates. The first gate consists of moving a coherent state around a closed path in phase space, resulting in a relative Berry phase between that state and the other states. The second gate consists of colliding two coherent states, resulting in coherent population transfer between them. Such gates should be realizable via reservoir engineering of systems which support tunable nonlinearities, such as trapped ions and circuit QED.
On Ontology Alignment Experiments (2006)

Ontology Alignment is a process for finding related entities of different ontologies. This paper discusses the results of our research in this area. One of them is a formulation for a new structural measure which extends famous related works. In this measure with a special attention to the transitive properties, it is tried to increase recall with less harm on precision. Second contribution is a new method for compound measure creation without any need to the mapping extraction phase. Effectiveness of these ideas is discussed and quantitative evaluations are explained in this paper.
Purification of the 170- to 180-kilodalton membrane glycoprotein associated with multidrug resistance. 170- to 180-kilodalton membrane glycoprotein is an ATPase. (1988)

170-180-kDa membrane glycoprotein (P-glycoprotein) associated with multidrug resistance is involved in drug transport mechanisms across the plasma membrane of resistant cells. From sequence analysis of cDNAs of the P-glycoprotein gene, it is postulated that the active drug-efflux pump function may be attributable to the protein. However, purification of the P-glycoprotein while preserving its enzymatic activity has not been reported. In this study, we have purified the P-glycoprotein from the human myelogenous leukemia K562 cell line resistant to adriamycin (K562/ADM) by means of one-step immunoaffinity chromatography using a monoclonal antibody against P-glycoprotein. The procedure was simple and efficiently yielded an electrophoretically homogeneous P-glycoprotein sample. By solubilization with 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, the purified P-glycoprotein was found to have ATPase activity. This ATP hydrolysis may be coupled with the active efflux of anticancer drugs across the plasma membrane of multidrug-resistant cells.
Escherichia coli-Salmonella typhimurium hybrid nusA genes: identification of a short motif required for action of the lambda N transcription antitermination protein (1994)

The Escherichia coli nusA gene, nusAEc, encodes an essential protein that influences transcription elongation. Derivatives of E. coli in which the Salmonella typhimurium nusA gene, nusASt, has replaced nusAEc are viable. Thus, NusASt can substitute for NusAEc in supporting essential bacterial activities. However, hybrid E. coli strains with the nusASt substitution do not effectively support transcription antitermination mediated by the N gene product of phage lambda. We report the DNA sequence of nusASt, showing that the derived amino acid sequence is 95% identical to the derived amino acid sequence of nusAEc. The alignment of the amino acid sequences reveals scattered single amino acid differences and one region of significant heterogeneity. In this region, called 449, NusAEc has four amino acids and NusASt has nine amino acids. Functional studies of hybrid nusA genes, constructed from nusAEc and nusASt, show that the 449 region of the NusAEc protein is important for lambda N-mediated transcription antitermination. A hybrid that has a substitution of the four E. coli codons for the nine S. typhimurium codons, but is otherwise nusASt, supports the action of the N antitermination protein. The 449 region and, presumably, adjacent sequences appear to compose a functional domain of NusAEc important for the action of the N transcription antitermination protein of phage lambda.
Quorum sensing and virulence regulation inXanthomonas campestris (2008)

It is now clear that cell-cell communication, often referred to as quorum sensing (QS), is the norm in the prokaryotic kingdom and this community-wide genetic regulatory mechanism has been adopted for regulation of many important biological functions. Since the 1980s, several types of QS signals have been identified, which are associated commonly with different types of QS mechanisms. Among them, the diffusible signal factor (DSF)-dependent QS system, originally discovered from bacterial pathogen Xanthomonas campestris pv. campestris, is a relatively new regulatory mechanism. The rapid research progress over the last few years has identified the chemical structure of the QS signal DSF, established the DSF regulon, and unveiled the general signaling pathways and mechanisms. Particular noteworthy are that DSF biosynthesis is modulated by a novel posttranslational autoinduction mechanism involving protein-protein interaction between the DSF synthase RpfF and the sensor RpfC, and that QS signal sensing is coupled to intracellular regulatory networks through a second messenger cyclic-di-GMP and a global regulator Clp. Genomic and genetic analyses show that the DSF QS-signaling pathway regulates diverse biological functions including virulence, biofilm dispersal, and ecological competence. Moreover, evidence is emerging that the DSF QS system is conserved in a range of plant and human bacterial pathogens.
Endothelial Cell Seeding on Prosthetic Surfaces (2000)

Once thought to be a monolayer of passive cells lining the vasculature, endothelial cells are now known to be important regulators of normal vascular physiology. Unfortunately, these critically important cells are destroyed or removed by interventional and surgical procedures performed to recanalize or bypass vascular obstructions. The loss of these cells contributes to thrombosis and restenosis, the major complications observed after angioplasty, stent deployment, and prosthetic graft implantation. One approach to preventing these complications is the placement of endothelial cells on stents or prosthetic grafts prior to their placement in vivo in the hope that these cells will, after growth and maturation, release the factors necessary to inhibit thrombosis and intimal thickening. The purpose of this review paper is to provide an overview of the physiologic functions of normal and dysfunctional endothelial cells, and to discuss experiments in which endothelial cells have been placed on metallic stents and prosthetic grafts.
Novel Isolation of Alkaline Phosphatase‐Positive Subpopulation from Periodontal Ligament Fibroblasts (2003)

These results indicate that osteoblastic and/or cementoblastic PDLF subsets could be isolated from the PDLF populations using an immunomagnetic method. Magnetic isolation of PDLFs may be a useful tool to obtain the cells which will potentially induce mineralization on the root surface.
Progressive age‐related development of Alzheimer‐like pathology in APP/PS1 mice (2004)

Increasing evidence points to synaptic plasticity impairment as one of the first events in Alzheimer's disease (AD). However, studies on synaptic dysfunction in different transgenic AD models that overexpress familial AD mutant forms of amyloid precursor protein (APP) and/or presenilin (PS) have provided conflicting results. Both long-term potentiation (LTP) and basal synaptic transmission (BST) have been found to be both unchanged and altered in different models and under differing experimental conditions. Because of their more robust amyloid-beta (Abeta) deposition, double transgenic mice currently are used by several laboratories as an AD model. Here, we report that mice overexpressing APP (K670N:M671L) together with PS1 (M146L) have abnormal LTP as early as 3 months of age. Interestingly, reduced LTP paralleled plaque appearance and increased Abeta levels and abnormal short-term memory (working memory). BST and long-term memory (reference memory) are impaired only later (approximately 6 months) as amyloid burden increases. Abeta pathology across different ages did not correlate with synaptic and cognitive deficits, suggesting that Abeta levels are not a marker of memory decline. In contrast, progression of LTP impairment correlated with the deterioration of working memory, suggesting that percentage of potentiation might be an indicator of the cognitive decline and disease progression in the APP/PS1 mice.
Characteristics of HIV-1 Nef Regions Containing Multiple CD8+ T Cell Epitopes: Wealth of HLA-Binding Motifs and Sensitivity to Proteasome Degradation (2001)

First and foremost among the many factors that influence epitope presentation are the degradation of Ag, which results in peptide liberation, and the presence of HLA class I molecules able to present the peptides to T lymphocytes. To define the regions of HIV-1 Nef that can provide multiple T cell epitopes, we analyzed the Nef sequence and determined that there are 73 peptides containing 81 HLA-binding motifs. We tested the binding of these peptides to six common HLA molecules (HLA-A2, -A3, -A24, -B7, -B8, and -B35), and we showed that most of them were efficient binders (54% of motifs), especially peptides associating with HLA-A3, -B7/35, and -B8 molecules. Nef peptides most frequently recognized by T cells of HIV-1-infected individuals were 90-97, 135-143, 71-81, 77-85, 90-100, 73-82, and 128-137. The frequency of T cell recognition was not directly related to the strength of peptide-HLA binding. The generation of Nef epitopes is crucial; therefore, we investigated the digestion by the 20S proteasome of a large peptide, Nef(66-100). This fragment was efficiently cleaved, and NH(2)-terminally extended precursors of epitope 71-81 were recognized by T cells of an HIV-1-infected individual. These results suggest that a high frequency of T cell recognition may depend on proteasome cleavage.
The Performance of Orthogonal Wavelet Division Multiplexing (OWDM) in Flat Rayleigh Fading Channel (2008)

The aim of this paper is to investigate the effect of flat Rayleigh fading channel on the performance of the OWDM (Orthogonal Wavelet Division Multiplexing) system. This scheme is shown to be overall quite similar to Orthogonal Frequency Division Multiplexing (OFDM), but with some interesting additional features and improved characteristics. The system performance is investigated for various Doppler frequencies for a channel. OWDM system is compared with OFDM. A detailed analysis of the system's implementation complexity is also reported.
Biological effects of fulvestrant on estrogen receptor positive human breast cancer: short, medium and long‐term effects based on sequential biopsies (2015)

We report the first study of the biological effect of fulvestrant on ER positive clinical breast cancer using sequential biopsies through to progression. Thirty-two locally/systemically advanced breast cancers treated with first-line fulvestrant (250 mg/month) were biopsied at therapy initiation, 6 weeks, 6 months and progression and immunohistochemically-analyzed for Ki67, ER, EGFR and HER2 expression/signaling activity. This series showed good fulvestrant responses (duration of response [DoR] = 25.8 months; clinical benefit = 81%). Ki67 fell (p < 0.001) in 79% of tumours by 6 months and lower Ki67 at all preprogression time-points predicted for longer DoR. ER and PR significantly decreased in all tumours by 6 months (p < 0.001), with some declines in ER (serine 118) phosphorylation and Bcl-2 (p = 0.007). There were modest HER2 increases (p = 0.034, 29% tumours) and loss of any detectable EGFR phosphorylation (p = 0.024, 50% tumours) and MAP kinase (ERK1/2) phosphorylation (p = 0.019, 65% tumours) by 6 months. While ER remained low, there was some recovery of Ki67, Bcl-2 and (weakly) EGFR/MAPK activity in 45-67% patients at progression. Fulvestrant's anti-proliferative impact is related to DoR, but while commonly downregulating ER and indicators of its signaling and depleting EGFR/MAPK signaling in some patients, additional elements must determine response duration. Residual ER at fulvestrant relapse explains reported sensitivity to further endocrine therapies. Occasional modest treatment-induced HER2 and weakly detectable EGFR/HER2/MAPK signaling at relapse suggests targeting of such activity might have value alongside fulvestrant in some patients. However, unknown pathways must drive relapse in most. Ki67 has biomarker potential to predict fulvestrant outcome and as a quantitative measure of response.
DoMCoSAR:  A Novel Approach for Establishing the Docking Mode That Is Consistent with the Structure−Activity Relationship. Application to HIV-1 Protease Inhibitors and VEGF Receptor Tyrosine Kinase Inhibitors (2000)

DoMCoSAR is a novel approach for statistically determining the docking mode that is consistent with a structure-activity relationship. The approach establishes the binding mode for the compounds in a chemical series with the assumption that all molecules exhibit the same binding mode. It involves three stages. In the first stage all molecules that belong to a given chemical series are docked to the active site of the protein target. The only bias used in the docking at this stage involves the location of the protein binding site. Coordinates of the common substructure (CS) that results from the unbiased docking are then clustered to establish the major substructure docking modes. In the second stage all molecules are docked to the major docking modes (MDMs) with constraints based on the common substructure. The third stage generates, for the major docking modes, interaction-based descriptors that include electrostatic, VDW, strain, and solvation contributions. The problem of docking mode evaluation is now reduced to the question of which descriptor set is more predictive. To establish a quantitative comparison of the descriptor sets associated with the major docking modes, we use 50 instances of random 4-fold cross-validation. For each 4-fold cross-validation the predictive squared correlation coefficient (R(2)) is computed. t-Tests are applied to establish significance of the differences in mean R(2) for one docking mode versus another. We test the methodology on two test cases: HIV-1 protease inhibitors (Holloway et al. J. Med. Chem. 1995, 38, 305-317) and vascular endothelial growth factor (VEGF) receptor tyrosine kinase oxoindoles (Sun et al. J. Med. Chem. 1998, 41, 2588-2603). For both test cases there is statistically significant preference for the binding mode consistent with the X-ray structure. The appeal of this methodology is that researchers gain the objectivity of statistical justification for the selected docking mode. The methodology is relatively insensitive to subtle variations of the protein structure that include, but are not limited to, side chain and small backbone rearrangement during binding. In addition, predictive models that result from the approach can be used to further optimize chemical series.
Plant cannabinoids: a neglected pharmacological treasure trove (2005)

Most of the cannabinoids in Cannabis sativa L. have not been fully evaluated for their pharmacological activity. A publication in this issue presents evidence that a plant cannabinoid, Δ 9 ‐tetrahydrocannabivarin is a potent antagonist of anandamide, a major endogenous cannabinoid. It seems possible that many of the non‐psychoactive constituents of this plant will be of biological interest. British Journal of Pharmacology (2005) 146 , 913–915. doi: 10.1038/sj.bjp.0706415
Effects of Iloprost Inhalation on Exercise Capacity and Ventilatory Efficiency in Patients With Primary Pulmonary Hypertension (2000)

The present data show that iloprost inhalation exerts pulmonary vasodilatation and improves symptoms and exercise capacity in patients with PPH. The data also suggest that iloprost inhalation is a suitable treatment for PPH. Whether these effects are maintained during long-term treatment and are paralleled by improvement in prognosis remains to be determined.
Active phase of iron catalyst for alcohol formation in hydrogenation of carbon oxides (2000)

Hydrogenation of CO2 over iron catalysts has been carried out and compared with the activity obtained with CO. The rates of hydrocarbon and alcohol formation were higher in the reaction with CO. The rates of hydrocarbon and alcohol formation were suppressed by addition of steam to the reactant gas mixture of H2–CO x. Although no significant change in the structure of the catalyst was observed by the X-ray diffraction analyses, change in the oxidation state of the surface iron was detected by recording X-ray photoelectron spectroscopy of the catalysts. During the reaction with CO, the catalyst surface was further reduced even after the reduction at 500 °C, whereas it was oxidized in the reaction with CO2. A change in product distribution and the results of X-ray photoelectron spectroscopy analyses showed that the iron carbide is the active site for hydrocarbon formation and the oxygen species in iron hydroxide (OFeOH) may be relevant to the formation of MeOH. Copyright © 2000 John Wiley & Sons, Ltd.
Synthetic retinoids in dermatology. (1985)

The potential of vitamin A, or retinol, in the treatment of a variety of skin diseases has long been recognized, but because of serious toxic effects this substance generally could not be used. The recent development and marketing of two relatively non-toxic synthetic analogues, which are known as retinoids, has made it possible to treat some of the diseases that are resistant to standard forms of therapy. Isotretinoin is very effective in cystic and conglobate acne, while etretinate is especially useful in the more severe forms of psoriasis. Good results have also been obtained in other disorders of keratinization. Vitamin A and its derivatives apparently have an antineoplastic effect as well and may come to be used in both the prevention and the treatment of epithelial cancer. In many of these diseases the retinoids act by enhancing the normal differentiation and proliferation of epidermal tissues, but the exact mechanisms are not well understood. Their influence on the intracellular polyamines that control the synthesis of nucleic acids and proteins may be an important factor. Although the retinoids have few serious systemic effects, they are teratogenic, and because they persist in the body their use in women of childbearing potential is limited.
Synergistic Neuroprotective Effects of Lithium and Valproic Acid or Other Histone Deacetylase Inhibitors in Neurons: Roles of Glycogen Synthase Kinase-3 Inhibition (2008)

Lithium and valproic acid (VPA) are two primary drugs used to treat bipolar mood disorder and have frequently been used in combination to treat bipolar patients resistant to monotherapy with either drug. Lithium, a glycogen synthase kinase-3 (GSK-3) inhibitor, and VPA, a histone deacetylase (HDAC) inhibitor, have neuroprotective effects. The present study was undertaken to demonstrate synergistic neuroprotective effects when both drugs were coadministered. Pretreatment of aging cerebellar granule cells with lithium or VPA alone provided little or no neuroprotection against glutamate-induced cell death. However, copresence of both drugs resulted in complete blockade of glutamate excitotoxicity. Combined treatment with lithium and VPA potentiated serine phosphorylation of GSK-3 alpha and beta isoforms and inhibition of GSK-3 enzyme activity. Transfection with GSK-3alpha small interfering RNA (siRNA) and/or GSK-3beta siRNA mimicked the ability of lithium to induce synergistic protection with VPA. HDAC1 siRNA or other HDAC inhibitors (phenylbutyrate, sodium butyrate or trichostatin A) also caused synergistic neuroprotection together with lithium. Moreover, combination of lithium and HDAC inhibitors potentiated beta-catenin-dependent, Lef/Tcf-mediated transcriptional activity. An additive increase in GSK-3 serine phosphorylation was also observed in mice chronically treated with lithium and VPA. Together, for the first time, our results demonstrate synergistic neuroprotective effects of lithium and HDAC inhibitors and suggest that GSK-3 inhibition is a likely molecular target for the synergistic neuroprotection. Our results may have implications for the combined use of lithium and VPA in treating bipolar disorder. Additionally, combined use of both drugs may be warranted for clinical trials to treat glutamate-related neurodegenerative diseases.
Memory Suppressor Genes: Inhibitory Constraints on the Storage of Long-Term Memory (1998)

Synaptic plasticity, the ability of neurons to alter the strength of their synaptic connections with activity and experience, is thought to play a critical role in memory storage. Molecular studies of gene expression during long-lasting synaptic plasticity related to memory storage initially focused on the identification of positive regulators. More recent work has revealed that the establishment of long-lasting synaptic plasticity and long-term memory also requires the removal of inhibitory constraints. By analogy to tumor suppressor genes, which restrain cell proliferation, we propose that these inhibitory constraints of memory storage, which restrain synapse growth, be termed memory suppressor genes.
Content-based information retrieval for VRML 3D objects (2003)

Because of the interest of 3D images and the popularity of World Wide Web, the number of 3D scene/objects and model database throughout the world is growing both in number and in size. VRML (Virtual Reality Modeling Language) is used to model the 3D object of the Web page, and become as a standard for 3D information. Most content-based retrieval (CBR) techniques such as shape and color comparison among objects are for image and video. The mechanisms are designed based on 2D information. In this paper, we propose a new similarity method, based on 3D information extracted from a VRML object database. The system includes multiple subsystems, which are conducted in two main parts. The first part includes the VRML object parser system and the normalization system. The second part includes the comparison system, database management system and a friendly graphical user interface. The method is the first step of our project, which aims to incorporate feature extraction of virtual reality objects, such as chairs, car, and others in 3D space. House interior designers can use the proposed system. The user can select proper scenes and furniture in order to meet the requirement of potential customers.
The Lymphocytic Choriomeningitis Virus Envelope Glycoprotein Targets Lentiviral Gene Transfer Vector to Neural Progenitors in the Murine Brain (2004)

Feline immunodeficiency virus (FIV)-based lentiviral vectors can be targeted to restricted cell types by pseudotyping with envelopes from other viruses. An FIV vector expressing bacterial beta-galactosidase (beta-gal) and pseudotyped with lymphocytic choriomeningitis virus (LCMV) envelope glycoprotein was injected into postnatal mouse brain striatum to determine neural cell-type transduction. After 3 or 7.5 weeks, the beta-gal-expressing cells included astrocytes in the striatum and in the subventricular zone (SVZ), neuroblasts along the rostral migratory stream, and neurons in the olfactory bulb. This pattern was suggestive of transduction of neural stem cells/progenitors that reside in the SVZ and continually generate olfactory bulb neurons. To test for transduction of SVZ type B astrocyte/stem cells, LCMV-pseudotyped FIV encoding Cre recombinase driven by an astrocyte-specific promoter was injected into the striatum of ROSA26 Cre reporter mice. beta-Gal expression in these mice depends on Cre recombinase-mediated DNA recombination. beta-Gal-expressing neuroblasts and neurons were detected in the rostral migratory stream and olfactory bulb, respectively, indicating that these cells derived from an astrocytic-type stem cell. Thus, LCMV (WE54)-pseudotyped FIV provides a novel vector for transducing neural stem cells/progenitors in vivo and may prove valuable as a gene transfer vector for therapy of neurodegenerative diseases.