gebhart/patrepeval huggingface dataset:
Microtiter assay for interferon: microspectrophotometric quantitation of cytopathic effect (1976)

This report describes an accurate, reproducible, and efficient microassay for human interferon, using a dye-uptake method to quantitate cytopathogenicity. The antiviral activity was measured by using a Gilford 300-N microsepctrophotometer, with the automatic programmer, sampler, and data lister. Two hundred interferon samples, each in a final volume of 1.0 ml, may be analyzed and recorded in 45 min. The reproducibility of a laboratory reference interferon and the human international reference B 69/19 on two different cell lines, using the model Q Oxford sampler, was found to be excellent, with the standard error of the log10 geometric mean of both references +/- 0.04 to 0.06.
Hyperfibrinolysis in a case of myelodysplastic syndrome with leukemic spread of mast cells (1999)

Mast cells (MC) are multipotent hemopoietic effector cells producing diverse mediators like histamine, heparin, or tissue type plasminogen activator. We report a 75-year-old male patient with myelodysplastic syndrome (MDS) of recent onset (3 months' history) associated with a massive leukemic spread of immature tryptase+ MC (tentative term: myelomastocytic leukemia). The patient presented with pancytopenia, bleeding, hypofibrinogenemia, and an increased cellular tryptase level. Moreover, an excessive elevation of plasmin-antiplasmin complexes (9,200 ng/ml; normal range: 10-150), an elevated D-dimer, and an increase in thrombin-antithrombin III complexes were found. The identity of the circulating MC was confirmed by immunophenotyping (CD117/c-kit+, CD123/IL-3R alpha-, CD11b/C3biR-), biochemical analysis (cellular ratio [ng:ng] of tryptase to histamine >1), and electron microscopy. Bone marrow (bm) examination showed trilineage dysplasia (17% blasts), 30% diffusely scattered MC, and a complex karyotype. No dense, compact MC infiltrates (mastocytosis) were detectable in bm sections. Despite hyperfibrinolysis and mediator syndrome (flushing, headache), the patient received remission induction polychemotherapy (DAV) followed by two cycles of consolidation with intermediate dose ARA-C (2 x 1 g/m2/day on days 1, 3, and 5). He entered complete remission after the first chemotherapy cycle without evidence of recurring MDS. Moreover, in response to chemotherapy, the hyperfibrinolysis and mediator syndrome resolved, and the circulating c-kit+ MC disappeared. We suggest consideration of polychemotherapy as a therapeutic option in patients with high-risk MDS of recent onset, even in the case of MC lineage involvement.
A New Approach for Dynamic Optimization of Waterflooding Problems (2006)

Abstract Technological advances have resulted in use of smart wells, which are typically equipped with remotely operated downhole chokes. We present an approach for controlling these chokes so that the water flooding is optimized. The optimization problem is done by maximizing either total cumulative oil production or net present value. The new methodology presented here avoids the limitations related to using optimal control as no adjoint equations are needed and the model equations are treated as a "black box". In the new approach the ensemble Kalman filter is used as an optimization routine, and the methodology is compared to the Partial Enumeration Method. We demonstrate the methodologies on a simple synthetic reservoir with five layers of different permeabilities. The conclusions from this work are that the ensemble Kalman filter approach is working robustly, and the results are in agreement with, or superior to, the results obtained with the Partial Enumeration Method and a reference solution.
AR Hale’s Best Jumbo, AR 5, and AR Topmark: Melon Aphid-resistant Muskmelon Breeding Lines (1984)

Abstract The melon (or cotton) aphid ( Aphis gossypii Glover), an economically important pest throughout the world (1), is an important vector of muskmelon viruses (6), and often causes damage by feeding large populations on this favored host (7). Resistance to the melon aphid was found in muskmelon PI 371795 from India (4).
Parathyroid hormone (PTH)–induced bone gain is blunted in SOST overexpressing and deficient mice (2009)

Intermittent parathyroid hormone (PTH) treatment is a potent bone anabolic principle that suppresses expression of the bone formation inhibitor Sost. We addressed the relevance of Sost suppression for PTH-induced bone anabolism in vivo using mice with altered Sost gene dosage. Six-month-old Sost overexpressing and 2-month-old Sost deficient male mice and their wild-type littermates were subjected to daily injections of 100 microg/kg PTH(1-34) or vehicle for a 2-month period. A follow-up study was performed in Sost deficient mice using 40 and 80 microg/kg PTH(1-34). Animals were sacrificed 4 hours after the final PTH administration and Sost expression in long bone diaphyses was determined by qPCR. Bone changes were analyzed in vivo in the distal femur metaphysis by pQCT and ex vivo in the tibia and lumbar spine by DXA. Detailed ex vivo analyses of the femur were performed by pQCT, microCT, and histomorphometry. Overexpression of Sost resulted in osteopenia and Sost deletion in high bone mass. As shown before, PTH suppressed Sost in wild-type mice. PTH treatment induced substantial increases in bone mineral density, content, and cortical thickness and in aging wild-type mice also led to cancellous bone gain owing to amplified bone formation rates. PTH-induced bone gain was blunted at all doses and skeletal sites in Sost overexpressing and deficient mice owing to attenuated bone formation rates, whereas bone resorption was not different from that in PTH-treated wild-type controls. These data suggest that suppression of the bone formation inhibitor Sost by intermittent PTH treatment contributes to PTH bone anabolism.
1,3-Diarilpropanos de Iryanthera paraensis e Iryanthera tricornis (1984)

Iryanthera paraensis e I. tricornis (Myristicaceae) contêm na madeira de seus troncos 1-(2', 4' - dihidroxifenil) -3- (4", 5"-metilenodoxi-2" -metoxifenil) -propano (1a 1-(2', 4' dihidroxifenil) -3-(3", 4" -metilenodioxifenil)-propano (1b) e 1-(4' -hidroxi -2'-metoxifenil) -3-(4"-hidroxi-3"-metoxifenil) -propano (1c). Apenas da primeira espécie se isolou adicionalmente 1-(2', 4'-dihidroxi-3' -metilfenil)-3-(4", 5"-metilenodioxi-2"- metoxifenil) -propano (1d) e 1-(2'-hidroxi-4'metoxifenil) -3-(3", 4"-metilenodioxifenil) -propano (1e). Dados espectroscópicos para a substância 1b, são descritos pela primeira vez.
Antiviral protection by vesicular stomatitis virus-specific antibodies in alpha/beta interferon receptor-deficient mice (1995)

The role of innate, alpha/beta interferon (IFN-alpha/beta)-dependent protection versus specific antibody-mediated protection against vesicular stomatitis virus (VSV) was evaluated in IFN-alpha/beta receptor-deficient mice (IFN-alpha/beta R0/0 mice). VSV is a close relative to rabies virus that causes neurological disease in mice. In contrast to normal mice, IFN-alpha/beta R0/0 mice were highly susceptible to infection with VSV because of ubiquitous high viral replication. Adoptive transfer experiments showed that neutralizing antibodies against the glycoprotein of VSV (VSV-G) protected these mice efficiently against systemic infection and against peripheral subcutaneous infection but protected only to a limited degree against intranasal infection with VSV. In contrast, VSV-specific T cells or antibodies specific for the nucleoprotein of VSV (VSV-N) were unable to protect IFN-alpha/beta R0/0 mice against VSV. These results demonstrate that mice are extremely sensitive to VSV if IFN-alpha/beta is not functional and that under these conditions, neutralizing antibody responses mediate efficient protection, but apparently only against extraneuronal infection.
Engineering Secondary Metabolism in Maize Cells by Ectopic Expression of Transcription Factors (1998)

Manipulation of plant natural product biosynthesis through genetic engineering is an attractive but technically challenging goal. Here, we demonstrate that different secondary metabolites can be produced in cultured maize cells by ectopic expression of the appropriate regulatory genes. Cell lines engineered to express the maize transcriptional activators C1 and R accumulate two cyanidin derivatives, which are similar to the predominant anthocyanin found in differentiated plant tissues. In contrast, cell lines that express P accumulate various 3-deoxy flavonoids. Unexpectedly, P-expressing cells in culture also accumulate phenylpropanoids and green fluorescent compounds that are targeted to different subcellular compartments. Two endogenous biosynthetic genes (c2 and a1, encoding chalcone synthase and flavanone/dihydroflavonol reductase, respectively) are independently activated by ectopic expression of either P or C1/R, and there is a dose-response relationship between the transcript level of P and the degree to which c2 or a1 is expressed. Our results support a simple model showing how the gene encoding P may act as a quantitative trait locus controlling insecticidal C-glycosyl flavone level in maize silks, and they suggest how p1 might confer a selective advantage against insect predation in maize.
Chiral Lewis Acid Catalyzed Ene-Reactions (2000)

This review covers recent progress in the use of chiral Lewis acid catalysts in ene-reactions which involve carbonyl and imine compounds as enophiles. Chiral Lewis acid catalysts containing aluminum, titanium, ytterbium and copper are critically reviewed. Synthetic applications of recent systems are specifically discussed.
The afferent pathways of discogenic low-back pain. Evaluation of L2 spinal nerve infiltration. (1996)

The afferent pathways of discogenic low-back pain have not been fully investigated. We hypothesised that this pain was transmitted mainly by sympathetic afferent fibres in the L2 nerve root, and in 33 patients we used selective local anaesthesia of this nerve. Low-back pain disappeared or significantly decreased in all patients after the injection. Needle insertion provoked pain which radiated to the low back in 23 patients and the area of skin hypoalgesia produced included the area of pre-existing pain in all but one. None of the nine patients with related sciatica had relief of that component of their symptoms. Our findings show that the main afferent pathways of pain from the lower intervertebral discs are through the L2 spinal nerve root, presumably via sympathetic afferents from the sinuvertebral nerves. Discogenic low-back pain should be regarded as a visceral pain in respect of its neural pathways. Infiltration of the L2 nerve is a useful diagnostic test and also has some therapeutic value.
Cure of Disseminated Cryptococcal Infection in a Renal Allograft Recipient After Addition of γ‐Interferon to Anti‐Fungal Therapy (2005)

The immunosuppressive regimens that are used in solid organ transplantation are potent inhibitors of Th0 as well as Th1 and Th2 cell-mediated immune responses. This predisposes patients to disseminated cryptococcal infections. Mortality in such patients remains very high despite advances in anti-fungal chemotherapy. We describe a case of disseminated cryptococcal disease in a renal allograft recipient that failed to respond to prolonged treatment with several anti-fungal drugs. However, addition of the immuno-modulator, interferon-gamma, resulted in the formation of granulomas and the resolution of his disease within 4-6 weeks. As we cannot find a similar example of combination therapy for disseminated cryptococcal disease in the solid organ transplant literature, we propose that interferon-gamma could be used in synergy with anti-fungal drugs to cure disseminated cryptococcal infections in solid organ transplant patients.
An intelligent dynamic simulation environment: an object-oriented approach (2003)

The authors present a prototype simulation environment for nuclear power plants which illustrate the application of object-oriented programming within a LISP environment to process simulation. Systems are modeled using this technique as a collection of objects which communicate via message passing. The environment allows users to build simulation models by selecting iconic representations of plant components from a menu and connecting them with the aid of a mouse. Models can be modified graphically at any time, even as the simulation is running, and the results can be observed immediately via real-time graphics. Advantages of an object-oriented approach to simulation include a high degree of modularity, the data abstraction afforded by classes, code reusability due to inheritance, and the ability to exploit the polymorphic nature of message passing to build very generic procedures. The interpretive nature of LISP eliminates the tedious compile-link-run cycle and allows dynamic, reconfigurable models to be built in a highly interactive manner.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of rat NK-2 (neurokinin A) receptor in E. coli. (1994)

With the goal of obtaining sufficient functional protein for structural analysis, rat neurokinin-2 receptor was produced in Escherichia coli by linking it to the periplasmic maltose-binding protein. As a first step, we present a biochemical and pharmacological investigation of the recombinant receptor. Western-blots showed that the fusion protein was associated with the membranes. The agonist [4,5-3H-Leu9]neurokinin A and the NK-2 antagonist [3H]SR48,968 bound to the receptor in a highly specific manner. Saturation binding of the [3H]agonist demonstrated a single class of receptors (KD = 10.5 nM, Bmax = 2.5 pmol/mg protein). The [3H]antagonist bound with higher affinity to a larger receptor population (KD = 0.2 nM, Bmax = 7.2 pmol/mg protein). Competition of [3H]agonist binding with other agonists demonstrated a potency order of: neurokinin A > [Nle10]NKA(4-10) = [beta-Ala8]NKA(4-10) >> substance P >>> senktide Against the [3H]antagonist, agonists were only partially inhibitory. Selective NK-2 antagonists inhibited binding of both [3H]ligands with an identical order of potency: SR48,968 >> R396 > MEN10,376, which is consistent with NK-2 receptor pharmacology in rat tissue.
Interspecific Hybridization within the Genus Cucurbita I, Fruit Set, Seed and Embryo Development (1963)

W. P. Bemis, J. M. Nelson, Interspecific Hybridization within the Genus Cucurbita I, Fruit Set, Seed and Embryo Development, Journal of the Arizona Academy of Science, Vol. 2, No. 3 (Feb., 1963), pp. 104-107
New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. (2001)

Amplification of the ERBB2 oncogene at 17q12 has been well documented in breast cancer and has been shown to contribute to a poor clinical outcome. However, systematic surveys of copy number and expression levels of all genes within the 17q12 region have not been performed. Here, we used cDNA and comparative genomic hybridization microarray technologies to undertake a broad survey of genes involved in the 17q12 amplification in breast cancer. A chromosomal region-specific cDNA microarray containing 217 expressed sequence tag (EST) clones from 17q12 was constructed and used for parallel analysis of gene copy numbers and expression levels in seven breast cancer cell lines allowing direct identification of genes whose expression is elevated because of an increase in copy number in this chromosomal region. The copy number and expression survey identified 12 transcripts that showed a consistent pattern of increased copy number and expression in three or more of the 17q12-amplified cell lines. As expected, these included ERBB2 as well as the GRB7 and MLN64 genes previously shown to be coamplified with ERBB2. In addition, five other known genes and four uncharacterized ESTs were also found to be consistently activated by amplification in these breast cancer cell lines. Amplicon mapping by fluorescence in situ hybridization revealed a minimal common region of amplification containing four highly expressed genes, ERBB2, GRB7, MLN64, and an uncharacterized EST 48582. Furthermore, several other genes, although not located in the minimal common region of amplification, showed a correlated pattern of amplification and expression indicating that they might play a role in breast cancers with the 17q12 amplification. In conclusion, parallel analysis of gene copy number and expression levels by cDNA microarray can be used to directly identify candidate target genes involved in amplifications. Our results show that the 17q12 amplification in breast cancer leads to the simultaneous elevation of expression levels of several genes.
DNA double-strand breaks and the RAD50-RAD57 genes in Saccharomyces. (1993)

The yeast Saccharomyces provides a powerful system for investigating the biological effects of ionizing radiation, and studies have identified double-strand breaks in DNA as probably of critical importance in determining lethality. These breaks are normally repaired by a recombinational mechanism, but in the absence of repair a single break may be lethal to the cell. Genetic and molecular analysis of the eight genes known as RAD50 to RAD57 has revealed much about recombinational repair. These genes are also of central importance in other processes including meiosis and may be of general significance in understanding radiation responses in eukaryotes.
High-Resolution Droplet-Based Fractionation of Nano-LC Separations onto Microarrays for MALDI-MS Analysis (2014)

We present a robust droplet-based device, which enables the fractionation of ultralow flow rate nanoflow liquid chromatography (nano-LC) eluate streams at high frequencies and high peak resolution. This is achieved by directly interfacing the separation column to a micro T-junction, where the eluate stream is compartmentalized into picoliter droplets. This immediate compartmentalization prevents peak dispersion during eluate transport and conserves the chromatographic performance. Subsequently, nanoliter eluate fractions are collected at a rate of one fraction per second on a high-density microarray to retain the separation with high temporal resolution. Chromatographic separations of up to 45 min runtime can thus be archived on a single microarray possessing 2700 sample spots. The performance of this device is demonstrated by fractionating the separation of a tryptic digest of a known protein mixture onto the microarray chip and subsequently analyzing the sample archive using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Resulting peak widths are found to be significantly reduced compared to standard continuous flow spotting technologies as well as in comparison to a conventional nano-LC-electrospray ionization-mass spectrometry interface. Moreover, we demonstrate the advantage of our high-definition nanofractionation device by applying two different MALDI matrices to all collected fractions in an alternating fashion. Since the information that is obtained from a MALDI-MS measurement depends on the choice of MALDI matrix, we can extract complementary information from neighboring spots containing almost identical composition but different matrices.
Adenoviral and AAV-Mediated Gene Transfer to the Inner Ear: Role of Serotype, Promoter, and Viral Load on In Vivo and In Vitro Infection Efficiencies (2009)

The lack of effective treatments for many forms of hearing and vestibular disorders has produced interest in virally mediated gene therapies. However, to develop a gene therapy strategy that would successfully treat inner ear disorders, appropriate viral vectors capable of transfecting cochlear and support cells must be identified. While virally mediated gene transfer into the inner ear has been accomplished using herpes simplex type I virus, vaccinia virus, retroviruses, adenovirus, and adeno-associated virus (AAV), we will restrict our discussion to AAV and adenoviral vectors. Issues such as vector toxicity and load, viral serotype and backbone, and promoter specificity are discussed and contrasted for both in vivo vs. in vitro inner ear gene transfer.
An aminopeptidase from Streptomyces sp. KK565 degrades beta amyloid monomers, oligomers and fibrils (2010)

The accumulation of beta amyloid (Aβ) has been a primary target for Alzheimer disease therapeutic strategies. Previously, we discovered an activity from Streptomyces sp. KK565 growth media that inhibits Aβ aggregation. The active component was an aminopeptidase and named Streptomyces sp. KK565 aminopeptidase (SKAP). SKAP cleaved N-terminal amino-acids of Aβ(1-42) monomer, inhibited formation of fibrils and protected Aβ(1-42)-induced neurotoxicity. Over-expression of a human homolog of SKAP, glutamate carboxypeptidase II (hGCPII) in Aβ-oversynthesizing cells dramatically reduced the Aβ levels. These findings suggest a possible role of M28 family peptidases in preventing Aβ deposits in mammalian brain.
Deep Convex Networks for Image and Speech Classification (2011)

 To overcome the scalability challenge associated with Deep Belief Network (DBN), we have designed a novel deep learning architecture, deep convex network (DCN). The learning problem in DCN is convex within each layer. Additional structure-exploited fine tuning further improves the quality of DCN. The full learning in DCN is batch-mode based instead of stochastic, naturally lending it amenable to parallel training that can be distributed over many machines. Experimental results on handwriting image recognition task (MNIST) and on phone state classification (TIMIT) demonstrate superior performance of DCN over DBN not only in training efficiency but also in classification accuracy. DCN gives the error rate of 0.83%, the lowest without the use of additional training data produced by elastic distortion. The corresponding error rate by the best DBN which we have carefully tuned is 1.06%. On the TIMIT task, DCN also outperforms DBN but with a relatively smaller percentage so far.
Microarray Analysis of Gene Expression in Fibrovascular Membranes Excised From Patients With Proliferative Diabetic Retinopathy (2015)

Our data indicate that extracellular matrix-related molecules such as POSTN, TNC, TGFβ, and angiogenic factors have important roles in promoting the development of FVMs associated with PDR.
As H5N1 Keeps Spreading, a Call to Release More Data (2006)

PARIS-- An impassioned call by a prominent Italian influenza scientist has renewed the debate about how to balance global health against scientists9 needs to publish and countries9 demands for secrecy. (Read more.)
Multiphase flows in microfluidics (2004)

Various aspects of microfluidic flows with different immiscible constituents are addressed. The fundamental physical characteristics are proposed, as well as the flow regimes which are determined by the wetting and surface tension properties. These fundamental aspects are followed by engineering applications that emerge in microfluidics, namely the creation of microbubbles or drops. Further applications are also discussed, such as the transfer of heat in bubbly flows, or the transport of colloids and emulsions.
Extraction of slant character candidates from maps using circular templates (2002)

The paper proposes a method for extracting slant characters from complicated background figures efficiently and rapidly. In this method, slant character candidates are extracted using the black pixel density features, that is, matching rate of two different sized circular templates, which are inscribing and circumscribing a target character, with an original image. In order to estimate performance of the proposed method, the method was applied to 41 topographic map images (512/spl times/512 pixels) involving 1032 slant characters. As a result, the average number of character candidates per character was reduced to about 41 candidates, and 94.3% of 1032 slant characters were extracted correctly.