gebhart/patrepeval huggingface dataset:
Genistein, the Dietary-Derived Angiogenesis Inhibitor, Prevents LDL Oxidation and Protects Endothelial Cells From Damage by Atherogenic LDL (1997)

There is now growing evidence that the oxidative modification of LDL plays a potential role in atherosclerosis. In this study, genistein, a compound derived from a soy diet with a flavonoid chemical structure (4',5,7-trihydroxyisoflavone), which was found to inhibit angiogenesis, has been evaluated for its ability to act as an LDL antioxidant and a vascular cell protective agent against oxidized LDL. The results showed that genistein was able to inhibit the oxidation of LDL in the presence of copper ions or superoxide/nitric oxide radicals as measured by thiobarbituric acid-reactive substance formation, alteration in electrophoretic mobility, and lipid hydroperoxides. Bovine aortic endothelial cell- and human endothelial cell-mediated LDL oxidation was also inhibited in the presence of genistein. The 7-O-glucoside of genistein, genistin, was much less effective in inhibiting LDL oxidation in the cell-free and cell-mediated lipoprotein-oxidating systems. Incubating human endothelial cells in the absence or presence of genistein and challenging the cells with already oxidized lipoprotein revealed that in addition to its antioxidative potential during LDL oxidating processes, genistein effectively protected the vascular cells from damage by oxidized lipoproteins. The tyrosine kinase inhibitor genistein was found to block upregulation of two tyrosine-phosphorylated proteins of 132 and 69 kDa in endothelial cells induced by oxidized LDL. Parallel experiments with the inactive analogue daidzein, however, showed that the cytoprotective effect of the isoflavones seems not to be dependent on tyrosine phosphorylation. Our findings will support the suggested and documented beneficial action of a soy diet in preventing chronic vascular diseases and early atherogenic events.
Deeply-Learned Feature for Age Estimation (2015)

Human age provides key demographic information. It is also considered as an important soft biometric trait for human identification or search. Compared to other pattern recognition problems (e.g., object classification, scene categorization), age estimation is much more challenging since the difference between facial images with age variations can be more subtle and the process of aging varies greatly among different individuals. In this work, we investigate deep learning techniques for age estimation based on the convolutional neural network (CNN). A new framework for age feature extraction based on the deep learning model is built. Compared to previous models based on CNN, we use feature maps obtained in different layers for our estimation work instead of using the feature obtained at the top layer. Additionally, a manifold learning algorithm is incorporated in the proposed scheme and this improves the performance significantly. Furthermore, we also evaluate different classification and regression schemes in estimating age using the deep learned aging pattern (DLA). To the best of our knowledge, this is the first time that deep learning technique is introduced and applied to solve the age estimation problem. Experimental results on two datasets show that the proposed approach is significantly better than the state-of-the-art.
Early Cystometrograms Can Predict the Response to Intravesical Instillation of Oxybutynin Chloride in Myelomeningocele Patients (1994)

Recent reported experiences with intravesical medications in neurogenic bladder patients prompted us to evaluate this form of therapy in 28 myelomeningocele patients who could not tolerate oral anticholinergic agents or did not have adequate control on these agents. A pretreatment cystometrogram was performed followed by intravesical administration of oxybutynin chloride, with a repeat cystometrogram 3 hours later. Patients then began twice daily intravesical oxybutynin for a minimum of 4 months. The mean bladder capacity increased by 41%, the mean intravesical pressure decreased by 47% and compliance improved. Five patients achieved continence and 62% had less wetting while on intravesical therapy. The immediate posttreatment cystometrogram was predictive of the response to intravesical therapy on followup studies. Unfortunately, patient compliance was poor, with only 13 of the 28 patients remaining on therapy for the duration of the study.
Involvement of receptor activator of nuclear factor κB ligand/osteoclast differentiation factor in osteoclastogenesis from synoviocytes in rheumatoid arthritis (2000)

RANKL/ODF expressed on synovial fibroblasts is involved in rheumatoid bone destruction by inducing osteoclastogenesis and would therefore be a good therapeutic target.
NEW PHOTOLABELING AND CROSSLINKING METHODS (1993)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Sacral Stress Fractures in Long-Distance Runners (2000)

The clinical presentation of runners with sacral stress fractures can mimic disk disease. However, stress fractures in athletes, especially long-distance runners, must be treated differently. The imaging characteristics appear as linear abnormal signal intensity paralleling the sacroiliac joint on MR imaging and linear sclerosis with cortical disruption on CT. Imaging with bone scintigraphy shows increased uptake that parallels the sacroiliac joint.
Individual-Initiated Public Policy (1992)

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Deuterium NMR studies of the effect of pulmonary surfactant SP-C on the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine headgroup: A model for transbilayer peptides in surfactant and biological membranes (1993)

Surfactant protein C (SP-C) was isolated from solvent extracts of porcine pulmonary surfactant by gel filtration chromatography. The surfactant protein was combined with dipalmitoylphosphatidylcholine deuterated at the alpha and beta positions of the choline headgroup (DPPC-d4) Deuterium nuclear magnetic resonance spectra were collected as a function of temperature for a series of protein concentrations. The splitting of the alpha-deuteron spectrum in the liquid-crystalline phase was insensitive to temperature but decreased with increasing protein concentration. The response of headgroup conformation to protein concentration was consistent with an interaction between the lipid headgroup dipole and the net positive surface charge associated with the protein. The observed effect per charge on the alpha splitting was less than that reported for singly-charged amphiphiles [Scherer, P. G., & Seelig, J. (1989) Biochemistry 28, 7720-7728] but was similar to that obtained using a multipled-charged amphiphilic polypeptide [Roux, M., Neumann, J.-M., Hodges, R. S., Devaux, P. F., & Bloom, M. (1989) Biochemistry 28, 2313-2321]. This comparison suggests that the charges on SP-C are located near the bilayer surface. The possibility that the headgroup response is sensitive to the degree of clustering of surface charge is discussed. The beta-deuteron splitting in the liquid-crystalline phase decreased with increasing temperature but was relatively insensitive to protein concentration, suggesting that the torsion angle about the C alpha-C beta bond might be sensitive to steric interactions between the lipid headgroup and the protein.
Turning single cells into microarrays by super-resolution barcoding (2012)

In this review, we discuss a strategy to bring genomics and proteomics into single cells by super-resolution microscopy. The basis for this new approach are the following: given the 10 nm resolution of a super-resolution microscope and a typical cell with a size of (10 µm)(3), individual cells contain effectively 10(9) super-resolution pixels or bits of information. Most eukaryotic cells have 10(4) genes and cellular abundances of 10-100 copies per transcript. Thus, under a super-resolution microscope, an individual cell has 1000 times more pixel volume or information capacities than is needed to encode all transcripts within that cell. Individual species of mRNA can be uniquely identified by labeling them each with a distinct combination of fluorophores by fluorescence in situ hybridization. With at least 15 fluorophores available in super-resolution, hundreds of genes in can be barcoded with a three-color barcode (3C15 = 455). These calculations suggest that by combining super-resolution microscopy and barcode labeling, single cells can be turned into informatics platforms denser than microarrays and that molecular species in individual cells can be profiled in a massively parallel fashion.
Biotin–Avidin as a Protease‐Responsive Cap System for Controlled Guest Release from Colloidal Mesoporous Silica (2009)

Tell your guests when it's time to go: When avidin caps are attached to biotinylated colloidal mesoporous silica, the four subunits of the protein avidin can each bind to a biotin moiety attached to the surface (see picture). The resulting material is a promising candidate for the design of smart detergents or drug-delivery systems. The caps can be opened to release guest molecules by controlled enzymatic hydrolysis of the protein.
Genome-wide RNAi screen of Ca 2+ influx identifies genes that regulate Ca 2+ release-activated Ca 2+ channel activity (2006)

Recent studies by our group and others demonstrated a required and conserved role of Stim in store-operated Ca(2+) influx and Ca(2+) release-activated Ca(2+) (CRAC) channel activity. By using an unbiased genome-wide RNA interference screen in Drosophila S2 cells, we now identify 75 hits that strongly inhibited Ca(2+) influx upon store emptying by thapsigargin. Among these hits are 11 predicted transmembrane proteins, including Stim, and one, olf186-F, that upon RNA interference-mediated knockdown exhibited a profound reduction of thapsigargin-evoked Ca(2+) entry and CRAC current, and upon overexpression a 3-fold augmentation of CRAC current. CRAC currents were further increased to 8-fold higher than control and developed more rapidly when olf186-F was cotransfected with Stim. olf186-F is a member of a highly conserved family of four-transmembrane spanning proteins with homologs from Caenorhabditis elegans to human. The endoplasmic reticulum (ER) Ca(2+) pump sarco-/ER calcium ATPase (SERCA) and the single transmembrane-soluble N-ethylmaleimide-sensitive (NSF) attachment receptor (SNARE) protein Syntaxin5 also were required for CRAC channel activity, consistent with a signaling pathway in which Stim senses Ca(2+) depletion within the ER, translocates to the plasma membrane, and interacts with olf186-F to trigger CRAC channel activity.
Applications of Foliar Fertilizers Containing Glycinebetaine Improve Wheat Yields (2001)

Nitrogen availability and drought influence wheat ( Triticum aestivum L.) grain yields in the semiarid and subhumid Pampas region of Argentina. The application of fertilizers containing osmoprotectants, such as glycinebetaine, to crop canopies might reduce crop losses caused by environmental stresses. The objectives of this study were (a) to determine the effects on wheat grain yields of the foliar application of a commercial fertilizer with glycinebetaine, and (b) to establish, under farmers’ field conditions, the relation between soil properties and the productivity of wheat crops treated with the same product. Two experiments were conducted in the north‐western part of the Buenos Aires province of Argentina on Typic Hapludolls and Entic Hapludolls. In the first, the treatments were N fertilization (0, 23 and 46 kg ha −1 ) and the foliar application to the wheat crop, in the vegetative stages, of a foliar fertilizer containing N, P, Zn and glycinebetaine (0 and 2.5 l ha −1 ). The second experiment was carried out on 10 farmers’ fields, for each of which the treatment was the foliar application to the wheat crop, in the vegetative stages, of the same foliar fertilizer (0 and 2.5 l ha −1 ). In both experiments, the grain yield, the individual grain weight, the number of grains per spike and the spike and plant density at the physiological maturity of the crops were determined. Soil organic matter (SOM) and available P were determined in each of the 10 fields of the second experiment. Wheat grain yields were increased by N fertilization and glycinebetaine treatment. The number of grains per spike was higher in the treatments with glycinebetaine application. In the farmers’ fields, the grain yields of the treatments with the application of the product with glycinebetaine were, on average, 18 % higher than those of the non‐treated plots, with greater responses at sites with low SOM levels. We conclude that, in subhumid regions with a dry period between the tillering and flowering stages of wheat, the foliar application of foliar fertilizers containing glycinebetaine at the vegetative stages of crop development enhances grain yields by increasing the number of grains per spike. This response is independent of the SOM level or the N fertilization rate.
THE EFFICIENCY OF SAND RAT METABOLISM IS RESPONSIBLE FOR DEVELOPMENT OF OBESITY AND DIABETES (1993)

Two separate lines--diabetic and partially diabetes-resistant--have been isolated from the sand rat (Psammomys obesus), each with different growth characteristics in response to diets of varying digestible caloric densities (high energy, HE, 2.93 kcal/g, or low energy, LE, 2.38 kcal/g). Over a two week period all animals consumed similar quantities (c. 125 g) irrespective of the diet consumed. Weight gains were as follows: diabetic line on HE diet - 59.7 g, on LE - 46.2 g; non-diabetic animals from the diabetes-resistant line on HE - 44 g. Only animals from the diabetic line, fed the HE diet, developed hyperinsulinemia, obesity and diabetes. The energy cost of weight gain for the diabetic line fed either HE or LE diets was 6.0 - 6.3 kcal/g whereas for the diabetes-resistant line on the HE diet, the cost of growth was 50% higher at 9.3 kcal/g. These differences could be due either to alterations in the content of tissue laid down or to differences in energy expenditure. It has already been established that diet-induced obesity and diabetes develop in the diabetic line with features typical of insulin resistance in the metabolism of the pancreas, liver and peripheral tissues. Some of the animals of the diabetes-resistant line may also develop diabetes over a long time period and go through a phase of transient hyperinsulinemia-normoglycemia. This may represent an intermediate stage in the development of the diabetic syndrome and serve as a model of type 2 diabetes in man.
Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells (2007)

Accumulating evidence suggests a role for microRNAs in human carcinogenesis as novel types of tumor suppressors or oncogenes. However, their precise biological role remains largely elusive. In the present study, we aimed to identify microRNA species involved in the regulation of cell proliferation. Using quantitative RT-PCR analysis, we demonstrated that miR-34a was highly up-regulated in a human colon cancer cell line, HCT 116, treated with a DNA-damaging agent, adriamycin. Transient introduction of miR-34a into two human colon cancer cell lines, HCT 116 and RKO, caused complete suppression of cell proliferation and induced senescence-like phenotypes. Moreover, miR-34a also suppressed in vivo growth of HCT 116 and RKO cells in tumors in mice when complexed and administered with atelocollagen for drug delivery. Gene-expression microarray and immunoblot analyses revealed down-regulation of the E2F pathway by miR-34a introduction. Up-regulation of the p53 pathway was also observed. Furthermore, 9 of 25 human colon cancers (36%) showed decreased expression of miR-34a compared with counterpart normal tissues. Our results provide evidence that miR-34a functions as a potent suppressor of cell proliferation through modulation of the E2F signaling pathway. Abrogation of miR-34a function could contribute to aberrant cell proliferation, leading to colon cancer development.
Dihydroxyacetone synthase from a methanol-utilizing carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803 (1997)

Acinetobacter sp. strain JC1 DSM 3803, a carboxydobacterium, grown on methanol was found to show dihydroxyacetone synthase, dihydroxyacetone kinase, and ribulose 1,5-bisphosphate carboxylase, but no hydroxypyruvate reductase and very low hexulose 6-phosphate synthase, activities. The dihydroxyacetone synthase was found to be expressed earlier than the ribulose 1,5-bisphosphate carboxylase. The dihydroxyacetone synthase was purified 19-fold in eight steps to homogeneity, with a yield of 9%. The final specific activity of the purified enzyme was 1.12 micromol of NADH oxidized per min per mg of protein. The molecular weight of the native enzyme was determined to be 140,000. Sodium dodecyl sulfate-gel electrophoresis revealed a subunit of molecular weight 73,000. The optimum temperature and pH were 30 degrees C and 7.0, respectively. The enzyme was inactivated very rapidly at 70 degrees C. The enzyme required Mg2+ and thiamine pyrophosphate for maximal activity. Xylulose 5-phosphate was found to be the best substrate when formaldehyde was used as a glycoaldehyde acceptor. Erythrose 4-phosphate, glycolaldehyde, and formaldehyde were found to act as excellent substrates when xylulose 5-phosphate was used as a glycoaldehyde donor. The Kms for formaldehyde and xylulose 5-phosphate were 1.86 mM and 33.3 microM, respectively. The enzyme produced dihydroxyacetone from formaldehyde and xylulose 5-phosphate. The enzyme was found to be expressed only in cells grown on methanol and shared no immunological properties with the yeast dihydroxyacetone synthase.
Gain spectra in GaAs double−heterostructure injection lasers (1975)

Gain spectra for GaAs double−heterostructure junction lasers have been obtained with high resolution. This is accomplished by using an automated data aquisition system to analyze the Fabry−Perot resonance modulation in the spontaneous emission spectra. For active regions doped with Ge at a level of 4×1017 cm−3, the gain in the TE polarization at a fixed wavelength increases linearly with current, below lasing threshold. However, the peak gain (at a variable wavelength) increases slightly faster than linearly with current. The photon energy at which gain is a maximum increases logarithmically with current. Gain in the TM polarization depicts the same general behavior as that for the TE case, except that it is slightly less than the TE gain. It is concluded that for this particular doping the spectral gain characteristics are intermediate between those for undoped and heavily doped active regions. Above the threshold for lasing in the TE mode the TE gain spectra are well saturated, with new fine details revealed in the saturated spectra. On the other hand, gain in the nonlasing TM polarization is not well saturated above threshold, with marked differences in gain between high and low photon energies relative to the TE lasing energy.
Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing (2012)

This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.
Characterization of PBSX, a defective prophage of Bacillus subtilis (1990)

PBSX, a defective Bacillus subtilis prophage, maps to the metA-metC region of the chromosome. DNA (33 kilobases) from this region of the chromosome was cloned and analyzed by insertional mutagenesis with the integrating plasmid pWD3. This plasmid had a promoterless alpha-amylase gene (amyL) that provided information on the direction and level of transcription at the site of integration. Transcription under the control of the PBSX repressor proceeded in the direction metA to metC over a distance of at least 18 kilobases. Electrophoretic analysis of proteins produced by different integrant strains upon PBSX induction and by fragments subcloned in Escherichia coli allowed the identification of early and late regions of the prophage. A set of contiguous fragments directing mutagenic integration suggested that the minimum size of an operon that encodes phage structural proteins is 19 kilobases. The adaptation of PBSX transcriptional and replicational functions to a chromosomally based, thermoinducible expression system is discussed.
Activation of long chain fatty acids with acyl carrier protein: demonstration of a new enzyme, acyl-acyl carrier protein synthetase, in Escherichia coli. (1976)

A soluble enzyme activity which catalyzes the synthesis of acyl-acyl carrier protein from acyl carrier proteins, a long chain fatty acid, and ATP has been demonstrated in E. coli. The reaction requires high concentrations of both Ca++ and Mg++ for activity, and cleaves ATP to AMP and PPi. The fatty acyl product has been identified as acyl-acyl carrier protein by its solubility, thioester linkage, molecular weight, charge, and biological activity. Several criteria indicate the enzyme is distinct from acyl-CoA synthetase. The fatty acid specificity of the enzyme suggests a role of acyl-acyl carrier protein synthetase in the incorporation of fatty acids into phospholipid.
Vectors--shuttle vehicles for gene therapy. (1997)

Gene therapy is being considered for the treatment of various inherited and acquired disorders. The basic premise of this new therapeutic modality is manipulation of gene expression towards a therapeutic end. The early development of the field focused on a technique called ex vivo gene therapy in which autologous cells are genetically manipulated in culture prior to transplantation. Recent advances have stimulated the development of in vivo gene therapy approaches based on direct delivery of the therapeutic gene to cells in vivo. The rate-limiting technologies of gene therapy are the gene delivery vehicles, called vectors, used to accomplish gene transfer. The most efficient vectors are based on recombinant versions of viruses with retroviral vectors serving as prototypes. This viral vector system has been exploited in ex vivo approaches of gene therapy in which cultured, dividing cells are transduced with the recombinant virus resulting in integration of the proviral DNA into the chromosomal DNA of the recipient cell. The use of retroviral vectors in gene therapy has been restricted to ex vivo approaches because of difficulties in purifying the virion and the requirement that the target cell is dividing at the time of transduction. More recently, vectors based on adenoviruses have been developed for in vivo gene therapy. These viruses can be grown in large quantities and highly purified. Importantly, they efficiently transduce the recombinant genome into non-dividing cells. Applications include in vivo gene delivery to a variety of targets such as muscle, lung, liver and the central nervous system. Clinical trials of in vivo delivery with adenoviruses have been undertaken for the treatment of cystic fibrosis.