gebhart/patrepeval huggingface dataset:
A simple method for reconstitution of CHO cell and human fibroblast acyl coenzyme A: cholesterol acyltransferase activity into liposomes. (1988)

A new method for reconstituting acyl coenzyme A: cholesterol acyltransferase (ACAT) activity from either Chinese hamster ovary (CHO) or human fibroblast cell extracts into cholesterol-phosphatidylcholine liposomes is described. The method is rapid (less than 60 min) and easy to perform. The procedure involves solubilizing the cell extracts with deoxycholate followed by dilution into preformed liposomes. Ficoll gradient analysis demonstrated that, after reconstitution, almost all of the detectable ACAT activity co-migrated with the liposomes. Exogenous cholesterol in the liposomes was absolutely necessary for providing ACAT activity, but not for incorporation of the ACAT enzyme into the vesicle bilayer. Human fibroblast cell extracts prepared from cells grown in medium containing 10% fetal calf serum were found to contain a 10-fold higher microsomal ACAT activity compared to extracts from cells grown in 10% delipidated fetal calf serum. In contrast, when the ACAT activity from these extracts was measured using the reconstitution assay, there was no difference in the specific activities. These results support our previous work (Doolittle, G. M., and T. Y. Chang. 1982. Biochim. Biophys. Acta. 713: 529-537; and Chang, C. C. Y., et al. 1986. Biochemistry. 25: 1693-1699), and suggest that cholesterol regulates ACAT activity in CHO cells and human fibroblasts by mechanism(s) other than modulation of the amount of enzyme.
Reducing uncertainties in data mining (2002)

Data mining, which is also referred to as knowledge discovery in databases, has attracted much research interest. Data mining among independently developed databases often involves uncertain information. These uncertainties can be generated during both processes of combining relations and merging tuples. We propose a framework in which uncertainties can be measured. The objective is to determine the best way to combine and merge tuples in multiple databases and avoid generating unexpected uncertainties. The Shannon entropy theory plays a key part in our approach to reduce uncertainties when merging related tuples in a combined relation. Detailed examples are provided to address key issues.
Characterisation of the temporal sequence of osteoblast gene expression during estrogen‐induced osteogenesis in female mice (2001)

Osteoblast differentiation under in vitro conditions is associated with increased expression of non-collagenous bone proteins including osteocalcin, osteopontin, and osteonectin, the exact function of which remain poorly understood. To determine whether these proteins play an important role in the formation of mineralised bone matrix by osteoblasts in vivo, we analysed the time-course of their expression during estrogen-induced osteogenesis in female mice, and compared this with the formation of new cancellous bone. Female mice were sacrificed prior to or following treatment with 17beta-estradiol for up to 32 days (500 microg/animal/week). Total RNA was extracted from femurs, and changes in expression of genes for a range of osteoblast-derived proteins assessed by Northern blot analysis. In parallel experiments, the time course of cancellous bone formation was determined by measuring bone mineral density (BMD) of the distal femur. Estrogen led to a rapid increase in BMD, which reached significance by Day 16. This was preceded by three-fold increases in expression of alkaline phosphatase (ALP) and type I collagen (COL I) at Days 8 and 12 respectively. In contrast, osteocalcin, osteopontin, and osteonectin expression showed no change during this initial period, although modest increases were observed at later times (i.e., Days 20 and 24). Our results suggest that osteocalcin, osteopontin, and osteonectin are not involved in the initial phase of the osteogenic response to estrogen, suggesting that these non-collagenous bone proteins do not play a direct role in the formation of mineralised bone matrix by osteoblasts in vivo.
Small-Pore Molecular Sieves SAPO-34 and SAPO-44 with Chabazite Structure: A Study of Silicon Incorporation (1994)

Two small-pore silicon-substituted molecular sieves SAPO-34 and SAPO-44 with varying amount of silicon have been synthesized and characterized by XRD, SEM, FT-IR spectroscopy, and thermal analyses. Their acidity has been measured quantitatively by temperature-programmed desorption of ammonia. The results of these studies along with solid-state MAS NMR results show that the major part of silicon substitutes isolated phosphorus atoms in the structure whereas some amount of it forms small silica patches. The extent of formation of such small patches is more noticeable in SAPO-34 than in SAPO-44.
Rituximab Efficiently Depletes Increased CD20-Expressing T Cells in Multiple Sclerosis Patients (2014)

In multiple sclerosis (MS), B cell-depleting therapy using monoclonal anti-CD20 Abs, including rituximab (RTX) and ocrelizumab, effectively reduces disease activity. Based on indirect evidence, it is generally believed that elimination of the Ag-presenting capabilities and Ag nonspecific immune functions of B cells underlie the therapeutic efficacy. However, a small subset of T lymphocytes (T cells) was shown to also express CD20, but controversy prevails surrounding the true existence of this T cell subpopulation. Using single-cell imaging flow cytometry and expression profiling of sorted lymphocyte subsets, we unequivocally demonstrate the existence of CD3(+)CD20(dim) T cells. We show that in MS patients, increased levels of CD3(+)CD20(dim) T cells are effectively depleted by RTX. The pathological relevance of this T cell subset in MS remains to be determined. However, given their potential proinflammatory functionality, depletion of CD20-expressing T cells may also contribute to the therapeutic effect of RTX and other mAbs targeting CD20.
Model of β-cell mitochondrial calcium handling and electrical activity. II. Mitochondrial variables (1998)

In the preceding article [Am. J. Physiol. 274 (Cell Physiol. 43): C1158-C1173, 1998], we describe the development of a kinetic model for the interaction of mitochondrial Ca2+ handling and electrical activity in the pancreatic beta-cell. Here we describe further results of those simulations, focusing on mitochondrial variables, the rate of respiration, and fluxes of metabolic intermediates as a function of D-glucose concentration. Our simulations predict relatively smooth increases of O2 consumption, adenine nucleotide transport, oxidative phosphorylation, and ATP production by the tricarboxylic acid cycle as D-glucose concentrations are increased from basal to 20 mM. On the other hand, we find that the active fraction of pyruvate dehydrogenase saturates, due to increases in matrix Ca2+, near the onset of bursting electrical activity and that the NADH/NAD+ ratio in the mitochondria increases by roughly an order of magnitude as glucose concentrations are increased. The mitochondrial ATP/ADP ratio increases by factor of < 2 between the D-glucose threshold for bursting and continuous spiking. According to our simulations, relatively small changes in mitochondrial membrane potential (approximately 1 mV) caused by uptake of Ca2+ are sufficient to alter the cytoplasmic ATP/ADP ratio and influence ATP-sensitive K+ channels in the plasma membrane. In the simulations, these cyclic changes in the mitochondrial membrane potential are due to synchronization of futile cycle of Ca2+ from the cytoplasm through mitochondria via Ca2+ uniporters and Na+/Ca2+ exchange. Our simulations predict steady mitochondrial Ca2+ concentrations on the order of 0.1 microM at low glucose concentrations that become oscillatory with an amplitude on the order of 0.5 microM during bursting. Abrupt increases in mitochondrial Ca2+ concentration > 5 microM may occur during continuous electrical activity.
Up‐regulation of crystallins is involved in the neuroprotective effect of wolfberry on survival of retinal ganglion cells in rat ocular hypertension model (2010)

Wolfberry (fruit of Lycium barbarum Linn) has been known for balancing 'Yin' and 'Yang' in the body, nourishing the liver and kidney, improving visual acuity for more than 2,500 years in oriental countries. The active components in wolfberry include L. barbarum polysaccharide (LBP), zeaxanthine, betaine, cerebroside and trace amounts of zinc, iron, and copper. Each of them confers distinct beneficial effects and together they help to explain widespread use of wolfberry in the eastern world. Earlier study reported the neuroprotective effects of LBP on retinal ganglion cell (RGC) in an experimental model of glaucoma and the underlying in vivo cellular mechanisms of LBP neuroprotection deserve further exploration. In this study, we adopted proteomics, functional genomics, to evaluate pharmacological effects of LBP on the neuronal survival pathways. Among the significantly changed proteins induced by LBP feeding on ocular hypertension (OH) retinas, only proteins in crystallin family were focused in this study. The proteomic results were further confirmed using the Western blotting of the retinas and immunohistochemical staining of the retinal sections. We demonstrated that neuroprotective effect of-wolfberry extract-LBP on the survival of RGCs may be mediated via direct up-regulation of neuronal survival signal betaB2-crystallin.
Perhalogenmethylthio‐Heterocyclen, VI: (Perchlorfluormethylthio)‐ und (Halogenformylthio)thiophene (1976)

Abstract Thiophen setzt sich mit Cl 3 ‐ n F n CSCl (n = 2, 3) bzw. ClC(O)SCl in Gegenwart katalytischer Mengen SnCl 4 zu 2‐substituierten Thiophenen 1a ‐ c um. Analog reagieren 2,5‐Dimethylthiophen bzw. 2‐Bromthiophen mit Cl 3 ‐ n F n CSCl zu 3 bzw. 2. Letztere sind auch durch Bromierung von 1a , b zugänglich. Durch Umsetzung von 2‐Thienylmagnesiumbromid mit Cl 3 ‐ n F n CSCl (n = 0, 1) bzw. FC(O)SCl sind weitere 2‐substituierte Thiophene 1d ‐ f synthetisiert worden. 2,5‐Disubstituierte Derivate 4a ‐ d werden aus 1a ‐ c und Cl 3 ‐ n F n CSCl(n =2,3)bzw. ClC(O)SCl in Anwesenheit von CF 3 SO 3 H bzw. C 4 F 9 SO 3 H erhalten; analog kann 3 höher substituiert werden. Die CF 3 S‐Gruppe wird durch H 2 O 2 in Eisessig zur CF 3 SO 2 ‐Gruppe oxidiert. Durch Fluor‐Chlor‐Austausch lassen sich CF 3 S‐in CCl 3 S‐Thiophenderivate ( 1f und 11 ) umwandeln. 1 H‐NMR‐und 19 F‐NMR‐Spektren werden angegeben.
The influence of Thomson effect on the maximum power output and maximum efficiency of a thermoelectric generator (1996)

Considering a thermoelectric generator as a heat engine cycle, the general differential equations of the temperature field inside thermoelectric elements are established by means of nonequilibrium thermodynamics. These equations are used to study the influence of heat leak, Joule’s heat, and Thomson heat on the performance of the thermoelectric generator. New expressions are derived for the power output and the efficiency of the thermoelectric generator. The maximum power output is calculated and the optimal matching condition of load is determined. The maximum efficiency is discussed by a representative numerical example. The aim of this research is to provide some novel conclusions and redress some errors existing in a related investigation.
Targeting of Antigens to B Lymphocytes via CD19 as a Means for Tumor Vaccine Development (2013)

Ab therapy against surface Ags on tumor cells has demonstrated significant efficacy for some cancers. However, it is costly and patients frequently develop acquired resistance over time. In cases of Ab therapy resistance, T cell responses have been shown to be essential in controlling disease progression. Thus, vaccination that generates a sustained Ab response as well as a T cell response may be more effective and economical. In this article, we have developed a vaccination strategy by targeting protein Ags to B cells via a CD19 single-chain variable fragment miniAb. Using the tumor-associated Ag her-2/neu extracellular domain, we showed that the coengagement of CD19 and BCR induced full B cell activation to produce a high titer of Abs and enhanced CD4 Th2 response and CD8 T cell activation and differentiation. These Abs competitively inhibited humanized her-2/neu Ab binding and were capable of activating the complement and inhibiting human breast cancer growth in vitro. Therapeutic efficacy was demonstrated in vivo using murine mammary carcinoma models. Furthermore, four different extracellular domains of her-2/neu could be targeted to B cells to generate Abs against particular domains with different antitumor properties. This approach may offer a new avenue for vaccine development with significantly lower cost, which may be of use not only for cancer therapy but also for infectious agents.
Visual saliency based on multiscale deep features (2015)

Visual saliency is a fundamental problem in both cognitive and computational sciences, including computer vision. In this paper, we discover that a high-quality visual saliency model can be learned from multiscale features extracted using deep convolutional neural networks (CNNs), which have had many successes in visual recognition tasks. For learning such saliency models, we introduce a neural network architecture, which has fully connected layers on top of CNNs responsible for feature extraction at three different scales. We then propose a refinement method to enhance the spatial coherence of our saliency results. Finally, aggregating multiple saliency maps computed for different levels of image segmentation can further boost the performance, yielding saliency maps better than those generated from a single segmentation. To promote further research and evaluation of visual saliency models, we also construct a new large database of 4447 challenging images and their pixelwise saliency annotations. Experimental results demonstrate that our proposed method is capable of achieving state-of-the-art performance on all public benchmarks, improving the F-Measure by 5.0% and 13.2% respectively on the MSRA-B dataset and our new dataset (HKU-IS), and lowering the mean absolute error by 5.7% and 35.1% respectively on these two datasets.
Heterogeneity of risk for melanoma and pancreatic and digestive malignancies (2004)

Familial heterogeneity testing in the study population did not improve the selection of high-risk families for genetic study. Even in a large case-control study, few families that had multiple members with melanoma were identified, and family members with pancreatic malignancies were rare.
A new mechanism involving cyclic tautomers for the reaction with nucleophiles of the water-soluble peptide coupling reagent 1-ethyl-3-(3'-(dimethylamino)propyl)carbodiimide (EDC) (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new mechanism involving cyclic tautomers for the reaction with nucleophiles of the water-soluble peptide coupling reagent 1-ethyl-3-(3'-(dimethylamino)propyl)carbodiimide (EDC)Andrew Williams and Ibrahim T. IbrahimCite this: J. Am. Chem. Soc. 1981, 103, 24, 7090–7095Publication Date (Print):December 1, 1981Publication History Published online1 May 2002Published inissue 1 December 1981https://pubs.acs.org/doi/10.1021/ja00414a011https://doi.org/10.1021/ja00414a011research-articleACS PublicationsRequest reuse permissionsArticle Views2975Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cytokines in the Treatment of Hematopoietic Failure (1998)

The Hematopoietic System: Principles of Therapy with Hematopoietically Active Cytokines, Hal E. Broxmeyer Graft Failure and Cytokines, John Nemunaitis Peripheral-Blood Progenitor Cell Transplantation, Stefan Scheding, Wolfram Brugger, and Lothar Kanz Acute Leukemia, Gernot Seipelt, Oliver G. Ottmann, Dieter Hoelzer, and Gerd Heil Clinical Use of Hematopoietic Growth Factors in Myelodysplastic Syndromes, Raoul Georg Geissler and Arnold Ganser Hematopoietic Growth Factors in the Pathophysiology and Treatment of Aplastic Anemia, Marcel P. Devetten and Neal S. Young Cytopenias Associated with HIV-1 and Other Infections, David T. Scadden Erythropoietin, Kai-Uwe Eckardt, Ulrich Frei, and Karl-Martin Koch Tumor-Associated Anemia, H. Ludwig and E. Fritz Use of Cytokines in the Neonate, Michael Obladen, Rolf F. Maier, and Christoph Buhrer Treatment of Thrombocytopenia with Cytokines, Ronald Hoffman Hematopoietic Growth Factors in Transfusion Medicine, Thomas H. Price and John W. Adamson Use of G-CSF and GM-CSF in the Treatment of Solid Tumors, Patrick Schoeffski, Thomas Weihkopf, and Arnold Ganser Severe Congenital Neutropenias, Cornelia Zeidler and Karl Welte
Phagocytosis by neutrophils induces an amino acid deprivation response in Saccharomyces cerevisiae and Candida albicans (2003)

The transcriptional profiles of yeast cells that have been phagocytosed by either human neutrophils or monocytes were compared by using whole genome arrays. After phagocytosis by neutrophils, both Saccharomyces cerevisiae and Candida albicans respond by inducing genes of the methionine and arginine pathways. Neither of these pathways is induced upon phagocytosis by monocytes. Both fungi show a similar induction of these pathways when transferred from amino acid-rich medium to amino acid-deficient medium. These data suggest that the internal phagosome of the neutrophil is an amino acid-deficient environment.
Microsatellite Instability of Endothelial Cell Growth and Apoptosis Genes Within Plexiform Lesions in Primary Pulmonary Hypertension (2001)

Primary pulmonary hypertension (PPH) is a frequently fatal disease whose pathobiology is poorly understood. Monoclonal endothelial cell growth is present within plexiform lesions of patients with PPH but not secondary PH because of congenital heart malformations. We hypothesized that endothelial cells within PPH plexiform lesions harbor mutations permissive for clonal cell growth. We found that endothelial cells in PPH plexiform lesions demonstrated microsatellite instability within the human MutS Homolog 2 gene (10 of 20 lesions) and displayed microsatellite site mutations and reduced protein expression of transforming growth factor-beta receptor type II (6 of 19 lesions) and Bax (4 of 19 lesions). These results suggest that, in PPH, proliferated endothelial cells have genetic alterations associated with microsatellite instability and concomitant perturbation of growth and apoptosis gene expression akin to neoplasia. The full text of this article is available at http://www.circresaha.org.
Functional consequences of altered blood oxygen affinity. (1981)

The effect of an acute left shift in the oxygen dissociation curve (ODC) was examined in several animal models. When combined with hemorrhagic shock, a left shift of the ODC produced diminished shock tolerance with evidence of increased sympathetic outflow and increased mortality. Perfusion of the isolated canine brain with low P50 blood produced major electroencephalographic abnormalities and a sharp decrease in cerebral oxygen consumption. Exchange transfusion of normal rats with low P50 blood resulted in a major increase in coronary and cerebral flow. The data suggest that an acute left shift of the ODC is capable of disturbing oxygen delivery significantly, particularly to the brain and probably to the heart. Normal animals appear to compensate for an acute increase in oxygen affinity by increasing blood flow to these organs. When oxygen affinity is increased in combination with a fixed rate of blood flow, hypoxia results.
Primate response to immunization with a homologous zona pellucida peptide. (1996)

Development of a contraceptive vaccine using zona pellucida (ZP) antigens has been hampered by the observation that the immune response to the antigens results in altered ovarian function and depletion of the follicular pool of oocytes. The amino acid sequences of many ZP proteins have been determined in the past decade allowing study of fully synthetic peptide immunogens based on these ZP sequences. Such immunogens permit a precisely targeted response. The non-human primate is the best model for predicting how women may respond to ZP peptide vaccines. Cynomolgus macaques (Macaca fascicularis) have been immunized with synthetic peptides comprising a human ZP3 epitope and a macaque homologue of the same epitope. In both studies, immune response to the peptides was initiated, and infertility was accompanied by normal ovarian function.
The Effect of Treating Forages with Fibrolytic Enzymes on its Nutritive Value and Lactation Performance of Dairy Cows (2000)

Forages (corn silage and alfalfa hay) were sprayed with liquid enzymes prior to combining with a concentrate to form a total mixed ration (50% forage:50% concentrate, dry matter basis) and fed to lactating cows. In the first year, treatments were 1) no enzymes, 2) an enzyme complex containing 3500 carboxymethyl cellulase (CMCase) and 16,000 xylanase units per kilogram of forage dry matter, or 3) an enzyme complex containing 8800 CMCase units and 40,000 xylanase units. In the second year, the treatments were 1) no enzymes, 2) an enzyme complex as in yr 1 containing 3700 CMCase and 14,000 xylanase units, or 3) an enzyme complex using an alternative cellulase and containing 3600 CMCase and 11,000 xylanase units. In the first year, cows fed diet 2 tended to produce more milk (39.5 kg/d) than those fed diet 1 (37.0 kg/d) or those fed diet 3 (36.2 kg/d). The high level of enzyme treatment in diet 3 decreased the output of milk protein and fat compared to the low level of enzyme treatment. In the second year, cows fed diet 3 produced more milk (35.4 kg/d) than did those fed diet 1 (32.9 kg/d) and numerically more than those fed diet 2 (33.6 kg/d). Milk fat and protein were similar among treatments but numerically lower for cows fed enzyme-treated forages. Dry matter intake (kg/d) was similar among treatments in both years. Spraying certain doses and combinations of enzymes directly onto forages prior to feeding can improve milk yields but enzyme sources and dose levels are of critical importance.
Circumventing tamoxifen resistance in breast cancers using antiestrogens that induce unique conformational changes in the estrogen receptor. (2001)

Tamoxifen inhibits estrogen receptor (ER) transcriptional activity by competitively inhibiting estradiol binding and inducing conformational changes in the receptor that may prevent its interaction with coactivators. In bone, the cardiovascular system, and some breast tumors, however, tamoxifen exhibits agonist activity, suggesting that the tamoxifen-ER complex is not recognized identically in all cells. We used phage display to demonstrate that the antiestrogen GW5638 induces a unique structural change in the ER. The biological significance of this conformational change was revealed in studies that demonstrated that tamoxifen-resistant breast tumor explants are not cross-resistant to GW5638. Because of these properties, this drug is currently being developed as a potential therapeutic for tamoxifen-resistant breast cancers.