gebhart/patrepeval huggingface dataset:
Dichotomous effects of beta-chemokines on HIV replication in monocytes and monocyte-derived macrophages. (1998)

The role of beta-chemokines in the pathogenesis of HIV disease remains undefined. Given the potent capacities of these proteins to attract mononuclear cells to inflammatory sites, such as lymph nodes of patients with HIV disease, the effects of exposure of monocytes and monocyte-derived macrophages to beta-chemokines before HIV infection were compared with their effects when added either simultaneously with or after HIV infection. In this system, HIV replication was substantially increased in cells that had been exposed to beta-chemokines before HIV infection. These effects were pertussis toxin sensitive. By contrast, HIV replication was inhibited in cells that had been exposed to beta-chemokines either simultaneously with or after HIV infection. These effects were not pertussis toxin sensitive. In view of this potent capacity of beta-chemokines to stimulate HIV replication, treatment approaches for HIV disease based on the apparent inhibitory activity of these proteins on viral replication should be undertaken with caution.
Retinal Preconditioning and the Induction of Heat-Shock Protein 27 (2003)

These results provide evidence that the induction of Hsp27 is a gene-specific event associated with ischemic preconditioning in the retina. This increase in expression of Hsp27 occurs in both neuronal and non-neuronal retinal cells, and appears to be one component of the neuroprotective events induced by ischemic preconditioning in the retina.
The uptake of vitamin B12 by human lymphocytes and the relationships to the cell cycle. (1984)

The phase of the cell cycle permitting transcobalamin II (TC II) mediated entry of cobalamin (Cbl) into human lymphocytes was determined under several conditions. (1) Little was taken up by resting peripheral blood lymphocytes (PBL). (2) Uptake was enhanced by stimulation of PBL by culture with a mitogen. (3) This increase in capacity for uptake took place simultaneously during 3 days of culture with the increase in capacity to synthesize DNA. (4) Hydroxyurea inhibited both DNA synthesis and TC II-Cbl uptake. (5) As culture was prolonged and the cells passed beyond the phase of most active division, DNA synthesis and Cbl uptake declined sharply. (6) The increased capacity to take up Cbl after stimulation was determined, at least in part, by increased receptor activity for TC II-Cbl. (7) Internalization of the Cbl was also increased. (8) Simultaneously with the increasing DNA synthesis, the cells increased in the activity of the Cbl-dependent methionine synthetase (MS). (9) MS activity subsequently fell during longer culture. Thus PBL can take in Cbl only during a narrow "window" in the cell cycle. This window is associated with the period of most active DNA synthesis and at a time when one coenzyme of Cbl, MeCbl, is the most active.
Is Postmenopausal Osteoporosis Related to Pineal Gland Functions? (1991)

There is currently considerable interest in the pathogenesis of postmenopausal osteoporosis, which is the most common metabolic bone disease. Osteoporosis affects approximately 20 million persons in the United States, 90% of whom are postmenopausal women. Although there is evidence that estrogen deficiency is an important contributory factor, the pathogenesis of osteoporosis is multifactorial and presently poorly understood. There is evidence that pineal melatonin is an anti-aging hormone and that the menopause is associated with a substantial decline in melatonin secretion and an increased rate of pineal calcification. Animal data indicate that pineal melatonin is involved in the regulation of calcium and phosphorus metabolism by stimulating the activity of the parathyroid glands and by inhibiting calcitonin release and inhibiting prostaglandin synthesis. Hence, the pineal gland may function as a "fine tuner" of calcium homeostasis. In the following communication, we propose that the fall of melatonin plasma levels during the early stage of menopause may be an important contributory factor in the development of postmenopausal osteoporosis. Consequently, plasma melatonin levels taken in the early menopause could be used as an indicator or perhaps as a marker for susceptibility to postmenopausal osteoporosis. Moreover, light therapy, administration of oral melatonin (2.5 mg at night) or agents which induce a sustained release of melatonin secretion such as 5-methoxypsoralen, could be useful agents in the prophylaxis and treatment of postmenopausal osteoporosis. Finally, since application of external artificial magnetic fields has been shown to synchronize melatonin secretion in experimental animals and humans, we propose that treatment with artificial magnetic fields may be beneficial for postmenopausal osteoporosis.
Modified moving average analysis of T-wave alternans to predict ventricular fibrillation with high accuracy (2002)

T-wave alternans is a marker of cardiac electrical instability with the potential for arrhythmia risk stratification. The modified moving average method was developed to measure alternans in settings with artifacts, noise, and nonstationary data. Algorithms were developed and performance characteristics were validated with simulated electrocardiograms (ECGs). Experimental laboratory ECGs with dynamically changing alternans values were analyzed. Alternans values estimated by modified moving average analysis correlated strongly with input alternans values (r(2) = 0.9999). Rapidly changing alternans levels and phase reversals did not perturb the measurement. When heart rate was increased from 60 to 180 beats/min, with T-wave alternans apex moving from 237 to 103 ms after the R wave, the measured alternans peak varied <5% from input value. Simulated 50- to 1,000-microV motion artifact spikes typical of treadmill ECGs produced inaccuracies <2%. Alternans values in experimental laboratory study using standard electrodes tracked vulnerability to myocardial ischemia-induced ventricular fibrillation with 100% sensitivity and specificity at a cut point of 0.75 mV. Modified moving average analysis is a robust method that precisely measures T-wave alternans in settings with artifacts, noise, and nonstationary data typical of clinical ECGs and yields an accurate estimate of risk for ventricular fibrillation.
DNA Methyl Transferase Inhibiting Halogenated Monoterpenes from the Madagascar Red Marine Alga Portieria hornemannii (2006)

Three new halogenated monoterpenes, 2, 3, and 4, along with the known compounds halomon (1) and two analogues, 5 and 6, were isolated from the Madagascar red marine alga Portieria hornemannii. The structures of all three new compounds were determined by NMR spectroscopy in combination with mass spectrometric data analysis. Two of these monoterpenes (1 and 2) were low micromolar inhibitors of DNA methyl transferase-1.
Potentiation by L-cysteine of the bactericidal effect of hydrogen peroxide in Escherichia coli (1982)

Under anaerobic conditions an exponentially growing culture of Escherichia coli K-12 was exposed to hydrogen peroxide in the presence of various compounds. Hydrogen peroxide (0.1 mM) together with 0.1 mM L-cysteine or L-cystine killed the organisms more rapidly than 10 mM hydrogen peroxide alone. The exposure of E. coli to hydrogen peroxide in the presence of L-cysteine inhibited some of the catalase. This inhibition, however, could not fully explain the 100-fold increase in hydrogen peroxide sensitivity of the organism in the presence of L-cysteine. Of other compounds tested only some thiols potentiated the bactericidal effect of hydrogen peroxide. These thiols were effective, however, only at concentrations significantly higher than 0.1 mM. The effect of L-cysteine and L-cystine could be annihilated by the metal ion chelating agent 2,2'-bipyridyl. DNA breakage in E. coli K-12 was demonstrated under conditions where the organisms were killed by hydrogen peroxide.
Powered ankle-foot prosthesis for the improvement of amputee walking economy (2007)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2007.
Natural two-qubit gate for quantum computation using theXYinteraction (2003)

The two-qubit interaction Hamiltonian of a given physical implementation determines whether or not a two-qubit gate such as the controlled-NOT (CNOT) gate can be realized easily. It can be shown that, e.g., with the $\mathrm{XY}$ interaction more than one two-qubit operation is required in order to realize the CNOT operation. Here we propose a two-qubit gate for the $\mathrm{XY}$ interaction which combines the CNOT and SWAP operations. By using this gate quantum circuits can be implemented efficiently, even if only nearest-neighbor coupling between the qubits is available.
Integrating Automated Data Acquisition Technologies for Progress Reporting of Construction Projects (2009)

Integrating Automated Data Acquisition Technologies for Progress Reporting of Construction Projects Samir El-Omari, Osama Moselhi Pages 86-94 (2009 Proceedings of the 26th ISARC, Austin, USA, ISBN 978-0-578-02312-0, ISSN 2413-5844) Abstract: Controlling construction projects necessitates controlling their time and cost in an effort to meet the planned targets. Management needs timely data that represent the status of the project to take corrective actions, if needed. This paper presents a control model that integrates different automated data acquisition technology to collect data from construction sites required for progress measurement purposes. Current automated data acquisition technologies are described, and their suitability for use in tracking and controlling construction activities is assessed. This includes bar coding, Radio Frequency Identification (RFID) 3D laser scanning, photogrammetry, multimedia, and pen-based computers. The user can move with a tablet PC in the construction site and record, take snapshots and also hand written comments about activities on site. The proposed cost/schedule control model Integrates with the automated data acquisition technologies, a planning and scheduling software system, a relational database, and AutoCAD to generate progress reports that can assist project management teams in decision making. Keywords: 3D laser scanning, photogrammetry, RFID, Tablet PC, Bar Coding progress reporting, data acquisition, automation DOI: https://doi.org/10.22260/ISARC2009/0048 Download fulltext Download BibTex Download Endnote (RIS) TeX Import to Mendeley
[Immunoglobulin variable heavy chain region genetic constitution and mutation status in Chinese patients with chronic lymphocytic leukemia]. (2009)

There is significant difference in the frequency of the IGVH gene family in Chinese CLL patients compared to Western patients, suggesting the involvement of antigen selection in different ethnic and/or environmental factors in CLL disease initiation, and its prognostic significance needs further investigation.
Studies in spiro heterocycles. Part 4(1): Investigation of the reactions of fluorinated 3-aroylmethylene-indol-2-ones with hydrazine and phenylhydrazine and synthesis of spiro [indole-3,3'-pyrazol]-2-ones. (1985)

Reactions of various 3-aroylmethylene-indol-2-ones with hydrazine and phenylhydrazine under exactly similar conditions have been carried out. The reaction with phenylhydrazine has not been investigated earlier. It was found that although the reaction with hydrazine hydrate afforded a spiro derivative viz., spiro[3H-indole-3,3'-(3H)pyrazol]-2(1H)-one, that with phenylhydrazine yielded simply a hydrazone derivative. Representative spiro compounds have been screened for antifertility activity but none was found active at a dose of 10 mg/kg in adult female rats.
Tumor Antigen Escape from CAR T-cell Therapy (2018)

Emerging data from chimeric antigen receptor (CAR) T-cell trials in B-cell malignancies demonstrate that a common mechanism of resistance to this novel class of therapeutics is the emergence of tumors with loss or downregulation of the target antigen. Antigen loss or antigen-low escape is likely to emerge as an even greater barrier to success in solid tumors, which manifest greater heterogeneity in target antigen expression. Potential approaches to overcome this challenge include engineering CAR T cells to achieve multispecificity and to respond to lower levels of target antigen and more efficient induction of natural antitumor immune responses as a result of CAR-induced inflammation. In this article, we review the evidence to date for antigen escape and downregulation and discuss approaches currently under study to overcome these obstacles.<b>Significance:</b> Antigen escape and downregulation have emerged as major issues impacting the durability of CAR T-cell therapy. Here, we explore their incidence and ways to overcome these obstacles in order to improve clinical outcomes. <i>Cancer Discov; 8(10); 1219-26. ©2018 AACR.</i>
In Vivo Validation of In Silico Predicted Metabolic Engineering Strategies in Yeast: Disruption of α-Ketoglutarate Dehydrogenase and Expression of ATP-Citrate Lyase for Terpenoid Production (2015)

Stoichiometric metabolic network analysis can be used successfully as a metabolic prediction tool. However, this study highlights that kinetics, regulation and cultivation conditions may interfere, resulting in poor in vivo performance. Main sites of regulation need to be released and improved enzymes are essential to meet the required activities for an increased product formation in vivo.
Circulating ghrelin levels in patients with inflammatory bowel disease (2006)

Ghrelin, the gut-brain peptide recently identified as the natural endogenous ligand for growth hormone secretagogue receptors, exerts various endocrine and non-endocrine effects, including control of food intake and energy homeostasis.1 It could also play a role in modulating immune responses and inflammatory processes.1 Indeed, ghrelin exerts potent anti-inflammatory effects in vitro and in vivo,1–5 and high circulating ghrelin levels have been found in rats with septic shock, cysteamine induced duodenal ulcers, and adjuvant induced arthritis.4–6 Also, we have recently demonstrated that in patients with newly diagnosed coeliac disease, circulating ghrelin levels are abnormally high, correlate positively with intestinal mucosal lesion severity, and normalise in successfully gluten free diet treated patients.7 However, normal or even decreased ghrelin levels have been found in other inflammatory diseases, including rheumatoid arthritis and Helicobacter pylori associated …
High-Performance Electrocatalysts for Oxygen Reduction Derived from Polyaniline, Iron, and Cobalt (2011)

The prohibitive cost of platinum for catalyzing the cathodic oxygen reduction reaction (ORR) has hampered the widespread use of polymer electrolyte fuel cells. We describe a family of non-precious metal catalysts that approach the performance of platinum-based systems at a cost sustainable for high-power fuel cell applications, possibly including automotive power. The approach uses polyaniline as a precursor to a carbon-nitrogen template for high-temperature synthesis of catalysts incorporating iron and cobalt. The most active materials in the group catalyze the ORR at potentials within ~60 millivolts of that delivered by state-of-the-art carbon-supported platinum, combining their high activity with remarkable performance stability for non-precious metal catalysts (700 hours at a fuel cell voltage of 0.4 volts) as well as excellent four-electron selectivity (hydrogen peroxide yield <1.0%).
Correlation of patient immune responses with genetically characterized small round-structured viruses involved in outbreaks of nonbacterial acute gastroenteritis in the United States, 1990 to 1995 (1997)

Small round-structured viruses (SRSVs) are a genetically and antigenically diverse group of caliciviruses that are the most common cause of outbreaks of acute nonbacterial gastroenteritis. We have applied both molecular techniques to characterize SRSVs in fecal specimens and serologic assays using four different expressed SRSV antigens to examine the distribution of outbreak strains in the United States and determine if the immune responses of patients were strain specific. Strains from 23 outbreaks of SRSV gastroenteritis were characterized by reverse transcription-PCR and nucleotide sequencing of a 277-base region of the capsid gene. These strains segregated into two distinct genogroups, I and II, comprising four and six clusters of strains respectively, each representing a distinct phylogenetic lineage. Serum IgG responses in patients were measured by enzyme immunoassay using expressed capsid antigens of Norwalk virus (NV), Toronto virus (TV), Hawaii virus (HV), and Lordsdale virus (LV), representing four of the 10 clusters. While strains in genogroups I and II were antigenically distinct, within genogroups, the specificity of the immune response varied greatly. Patients infected with genogroup I strains which had as much as 38.5% aa divergence from NV demonstrated relatively homologous seroresponses to the single NV antigen. In contrast, in genogroup II, homologous seroresponses to TV and HV were only present when the infecting strains showed less than 6.5% aa divergence from these antigens. These results suggest that TV and HV represent not only separate genetic clusters in genogroup II but also separate antigenic groups, each of which is related but distinguishable. In addition, two genetically distinct SRSV strains were identified for which we have no homologous antigen. This study suggests that while current molecular diagnostics are capable of detecting the full range of SRSVs, additional expressed antigens will be required to detect an immune response to SRSV infection caused by all the antigenically diverse strains.
Early integrin binding to Arg-Gly-Asp peptide activates actin polymerization and contractile movement that stimulates outward translocation (2011)

Integrin-mediated adhesions are critical for stem cell differentiation, cancer metastasis, and the immune response [Hynes RO (2009) Science 326:1216-1219]. However, the mechanisms of early adhesion formation remain unclear, especially the effects of lateral clustering of integrins and the role of the Src family kinases. Using mobile Arg-Gly-Asp (RGD) peptide ligands on lipid bilayers with nano-fabricated physical barriers [Salaita K, et al. (2010) Science 327:1380-1385], we observe surprising long-range lateral movements of ligated integrins during the process of cell spreading. Initially, RGD-activated integrin clusters stimulate actin polymerization that radiates from the clusters. Myosin II contraction of actin from adjacent clusters produces contractile pairs that move toward each other against barriers. Force generated by myosin II stimulates a Src kinase-dependent lamellipodial extension and outward movement of clusters. Subsequent retraction by myosin II causes inward movement of clusters. The final cell spread area increases with the density of periodic barriers. Early integrin clustering recruits adhesion proteins, talin, paxillin, and FAK, irrespective of force generation. However, recruitment of vinculin is only observed upon contraction. Thus, we suggest that integrin activation and early clustering are independent of lateral forces. Clustering activates Src-dependent actin polymerization from clusters. Myosin contraction of clusters to lines stimulates active spreading with outward forces from actin polymerization followed by a second wave of contraction. Many of these early mechanical steps are not evident in cells spreading on immobilized matrices perhaps because of the low forces involved. These observations can provide new targets to control integrin-dependent adhesion and motility.
ChemInform Abstract: Synthesis, Oral Bioavailability Determination, and in vitro Evaluation of Prodrugs of the Antiviral Agent 9‐(2‐(Phosphonomethoxy)ethyl) adenine (PMEA). (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Organizing heterogeneous scene collections through contextual focal points (2014)

We introduce focal points for characterizing, comparing, and organizing collections of complex and heterogeneous data and apply the concepts and algorithms developed to collections of 3D indoor scenes. We represent each scene by a graph of its constituent objects and define focal points as representative substructures in a scene collection. To organize a heterogeneous scene collection, we cluster the scenes based on a set of extracted focal points: scenes in a cluster are closely connected when viewed from the perspective of the representative focal points of that cluster. The key concept of representativity requires that the focal points occur frequently in the cluster and that they result in a compact cluster. Hence, the problem of focal point extraction is intermixed with the problem of clustering groups of scenes based on their representative focal points. We present a co-analysis algorithm which interleaves frequent pattern mining and subspace clustering to extract a set of contextual focal points which guide the clustering of the scene collection. We demonstrate advantages of focal-centric scene comparison and organization over existing approaches, particularly in dealing with hybrid scenes, scenes consisting of elements which suggest membership in different semantic categories.
Scar Resurfacing with High-Energy, Short-pulsed and Flashscanning Carbon Dioxide Lasers (1998)

The high-energy, short-pulsed CO2 laser and the continuous wave CO2 laser with flash-scanning attachment are safe and effective as a treatment modality for scar revision. In general, elevated scars improve more dramatically than depressed scars.
An Exonuclease Induced by Bacteriophage λ (1967)

Abstract The deoxyribonucleic acid exonuclease induced by bacteriophage λ has been obtained in crystalline and physically homogeneous form. The purified preparation is free of detectable contamination by the endonuclease I, DNA polymerase, DNA phosphatase-exonuclease, alkaline phosphatase, 5'-nucleotidase, and ribonuclease activities known to be present in Escherichia coli; it may contain a trace (0.01%) of exonuclease I.
The Plasmodium falciparum Ca2+-ATPase PfATP6: insensitive to artemisinin, but a potential drug target (2011)

The disease malaria, caused by the parasite Plasmodium falciparum, remains one of the most important causes of morbidity and mortality in sub-Saharan Africa. In the absence of an efficient vaccine, the medical treatment of malaria is dependent on the use of drugs. Since artemisinin is a powerful anti-malarial drug which has been proposed to target a particular Ca2+-ATPase (PfATP6) in the parasite, it has been important to characterize the molecular properties of this enzyme. PfATP6 is a 139 kDa protein composed of 1228 amino acids with a 39% overall identity with rabbit SERCA1a (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 1a). PfATP6 conserves all sequences and motifs that are important for the function and/or structure of a SERCA, such as two high-affinity Ca2+-binding sites, a nucleotide-binding site and a phosphorylation site. We have been successful in isolating PfATP6 after heterologous expression in yeast and affinity chromatography in a pure, active and stable detergent-solubilized form. With this preparation, we have characterized and compared with the eukaryotic SERCA1a isoform the substrate (Ca2+ and ATP) -dependency for PfATP6 activity as well as the specific inhibition/interaction of the protein with drugs. Our data fully confirm that PfATP6 is a SERCA, but with a distinct pharmacological profile: compared with SERCA1a, it has a lower affinity for thapsigargin and much higher affinity for cyclopiazonic acid. On the other hand, we were not able to demonstrate any inhibition by artemisinin and were also not able to monitor any binding of the drug to the isolated enzyme. Thus it is unlikely that PfATP6 plays an important role as a target for artemisinin in the parasite P. falciparum.