gebhart/patrepeval huggingface dataset:
Neutralization of Infectivity of Diverse R5 Clinical Isolates of Human Immunodeficiency Virus Type 1 by gp120-Binding 2′F-RNA Aptamers (2003)

Human immunodeficiency virus type 1 (HIV-1) has evolved a number of strategies to resist current antiretroviral drugs and the selection pressures of humoral and cellular adaptive immunity. For example, R5 strains, which use the CCR5 coreceptor for entry and are the dominant viral phenotype for HIV-1 transmission and AIDS pathogenesis, are relatively resistant to neutralization by antibodies, as are other clinical isolates. In order to overcome these adaptations, we raised nucleic acid aptamers to the SU glycoprotein (gp120) of the R5 strain, HIV-1(Ba-L). These not only bound gp120 with high affinity but also neutralized HIV-1 infectivity in human peripheral blood mononuclear cells (PBMCs) by more than 1,000-fold. Furthermore, these aptamers were able to neutralize the infectivity of R5 clinical isolates of HIV-1 derived from group M (subtypes A, C, D, E, and F) and group O. One aptamer defined a site on gp120 that overlaps partially with the conserved, chemokine receptor-binding, CD4-induced epitope recognized by monoclonal antibody 17b. In contrast to the antibody, the site is accessible to aptamer in the absence of CD4 binding. Neutralizing aptamers such as this could be exploited to provide leads in developing alternative, efficacious anti-HIV-1 drugs and lead to a deeper understanding of the molecular interactions between the virus and its host cell.
On the mechanism of action of the antifungal agent propionate (2004)

Propionate is used to protect bread and animal feed from moulds. The mode of action of this short-chain fatty acid was studied using Aspergillus nidulans as a model organism. The filamentous fungus is able to grow slowly on propionate, which is oxidized to acetyl-CoA via propionyl-CoA, methylcitrate and pyruvate. Propionate inhibits growth of A. nidulans on glucose but not on acetate; the latter was shown to inhibit propionate oxidation. When grown on glucose a methylcitrate synthase deletion mutant is much more sensitive towards the presence of propionate in the medium as compared to the wild-type and accumulates 10-fold higher levels of propionyl-CoA, which inhibits CoA-dependent enzymes such as pyruvate dehydrogenase, succinyl-CoA synthetase and ATP citrate lyase. The most important inhibition is that of pyruvate dehydrogenase, as this affects glucose and propionate metabolism directly. In contrast, the blocked succinyl-CoA synthetase can be circumvented by a succinyl-CoA:acetate/propionate CoA-transferase, whereas ATP citrate lyase is required only for biosynthetic purposes. In addition, data are presented that correlate inhibition of fungal polyketide synthesis by propionyl-CoA with the accumulation of this CoA-derivative. A possible toxicity of propionyl-CoA for humans in diseases such as propionic acidaemia and methylmalonic aciduria is also discussed.
Acyltransferase domain substitutions in erythromycin polyketide synthase yield novel erythromycin derivatives (1997)

The methylmalonyl coenzyme A (methylmalonyl-CoA)-specific acyltransferase (AT) domains of modules 1 and 2 of the 6-deoxyerythronolide B synthase (DEBS1) of Saccharopolyspora erythraea ER720 were replaced with three heterologous AT domains that are believed, based on sequence comparisons, to be specific for malonyl-CoA. The three substituted AT domains were "Hyg" AT2 from module 2 of a type I polyketide synthase (PKS)-like gene cluster isolated from the rapamycin producer Streptomyces hygroscopicus ATCC 29253, "Ven" AT isolated from a PKS-like gene cluster of the pikromycin producer Streptomyces venezuelae ATCC 15439, and RAPS AT14 from module 14 of the rapamycin PKS gene cluster of S. hygroscopicus ATCC 29253. These changes led to the production of novel erythromycin derivatives by the engineered strains of S. erythraea ER720. Specifically, 12-desmethyl-12-deoxyerythromycin A, which lacks the methyl group at C-12 of the macrolactone ring, was produced by the strains in which the resident AT1 domain was replaced, and 10-desmethylerythromycin A and 10-desmethyl-12-deoxyerythromycin A, both of which lack the methyl group at C-10 of the macrolactone ring, were produced by the recombinant strains in which the resident AT2 domain was replaced. All of the novel erythromycin derivatives exhibited antibiotic activity against Staphylococcus aureus. The production of the erythromycin derivatives through AT replacements confirms the computer predicted substrate specificities of "Hyg" AT2 and "Ven" AT and the substrate specificity of RAPS AT14 deduced from the structure of rapamycin. Moreover, these experiments demonstrate that at least some AT domains of the complete 6-deoxyerythronolide B synthase of S. erythraea can be replaced by functionally related domains from different organisms to make novel, bioactive compounds.
High-Speed Imaging of Drops and Bubbles (2008)

This review presents recent technological advances in charge-coupled-device ultrahigh-speed video cameras and their applications in experimental fluid mechanics. Following a brief review of the various high-speed camera types, we point out the advantages of the new technology. Then we show examples of how these cameras are leading to new discoveries in the study of free-surface flows, emphasizing the dynamics of drops and bubbles. We specifically review work on the basic singularities occurring when liquid masses come into contact and coalesce, or break apart during the pinch-off of drops or bubbles from a vertical nozzle. We briefly discuss the imaging of cavitation bubbles and finish by outlining future prospects for these sensors.
Analysis of Adult Otitis Media: Polymerase Chain Reaction versus Culture for Bacteria and Viruses (1998)

Recent studies using the polymerase chain reaction (PCR) have identified bacterial and viral genomic sequences in culture-negative pediatric middle ear effusions. To evaluate this technique in adults, 19 effusions were analyzed to compare bacterial and viral culture and PCR detection of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and adenovirus. Effusions from 4 subjects positive for human immunodeficiency virus (HIV) were analyzed by PCR for HIV virus. Three of 19 effusions were culture-positive for bacteria, and 0 of 19 for viruses. Fifteen of 19 effusions were PCR-positive for bacterial genomic sequences, and 0 of 19 for adenovirus. Thirteen of 15 PCR-positive specimens demonstrated S pneumoniae, 5 of 15 H influenzae, and 0 of 13 M catarrhalis. All 4 effusions from HIV-positive subjects were PCR-positive for HIV. No effusion was culture-positive and PCR-negative. These results confirm that culture-negative middle ear effusions contain genomic sequences from bacterial pathogens. Finding of HIV RNA and DNA in effusion from HIV-positives suggests replicating virus in this fluid.
Double-Stranded DNA Diffusion in Slitlike Nanochannels (2006)

We present an experimental study of double-stranded DNA diffusion in slitlike channels. The channel heights span the regime from moderate confinement (height ∼ bulk radius of gyration of the DNA) to strong confinement (height ∼ persistence length). Scalings of diffusivity with channel height differ from blob model predictions. The diffusivity scales inversely with molecular weight when the channel height is smaller than the bulk radius of gyration. This scaling is indicative of hydrodynamic screening. A scaling analysis shows that the screening of hydrodynamic interactions arises from a combination of two mechanisms. After using a Zimm preaverage approximation, the unique symmetry of the thin-slit disturbance velocity and the isotropic nature of the polymer conformation together cause a cancellation of hydrodynamic interactions due to symmetry. We also find that the algebraic decay of the far-field velocity magnitude is sufficient to eliminate large-length scale hydrodynamic cooperativity in diffusion of quasi-two-dimensional polymers in good solvents.
Novel design procedure of broad-band multilayer antireflection coatings for optical and optoelectronic devices (1998)

A novel design procedure of broad-band multilayer antireflection (AR) coatings for optical and optoelectronic devices is proposed. The design algorithm is based on the optical admittance detuning, with the bandwidth of finite reflectivity as a new merit function. Coating structures consist of only two materials with nonquarter-wave thicknesses. Numerical mappings on the four-layer structure showed four optimizing regions where an optimized four-layer AR coating on 1.55 /spl mu/m GaInAs-AlGaInAs MQW semiconductor laser facet was predicted to have a broad bandwidth of 106 mm for a reflectivity of less than 10/sup -5/. TiO/sub 2/ and SiO/sub 2/ were electron-beam (EB) evaporated to form the four-layer AR coating on glass and InP substrates with an ion-beam assist and a real time in situ optical thickness monitor and experimentally verify its broad-band performance.
Neural network approximation of piecewise continuous functions: application to friction compensation (2002)

A new neural network (NN) structure is given for approximation of piecewise continuous (PC) functions of the sort that appear in friction, deadzone, backlash and other motion control actuator nonlinearities. The NN consists of neurons having a special class of nonsmooth activation functions termed 'jump approximation basis functions'. This 'jump approximation' NN plus a NN based on standard smooth sigmoidal activation functions can approximate any piecewise continuous function with discontinuities at a finite number of known points. Industrial motion device actuator nonlinearities are in this class of functions, therefore, the new NN structure is ideal for motion control applications in robotics and other industrial systems.
Production of Transgenic Rice (Oryza sativa subspecies japonica cv. Taipei 309) (1998)

Oryza sativa L. has three subspecies: indica, japonica, and javanica. Subsp. indica grows well in southern temperate and tropical regions; subsp. japonica grows well in cooler climates such as Japan; and subsp. javanica is grown mostly in the Americas and Europe. Several viruses infect rice, causing devastating losses in yield. Tungro disease is caused by an association of an RNA genome virus (rice tungro spherical virus) and a DNA genome virus (rice tungro bacilliform virus). Estimated annual yield losses caused by Tungro virus infection of rice exceed $1.5 billion (). Rice ragged stunt virus causes the second most important viral disease, with economic losses exceeding $140 million annually. Several tenuiviruses are also major pathogens in various rice-growing regions. These include rice grassy stunt virus, which is prevalent in the Philippines; rice stripe virus, which is often found in Japan; and rice hoja blanca virus, which is endemic in Latin America and occurs in sporadic but disastrous outbreaks. Novel biotechnological approaches for resistance, using various pathogen-derived genes, are being explored (). The production and thorough molecular analysis of transgenic plants by methods such as those described in this chapter and in Chapter 41 are vital toward evaluation of the efficacy of these new approaches.
Recovery of Bitumen From Tar Sand Deposits With the Radio Frequency Process (1986)

Summary The IIT Research Institute (IITRI) radio frequency (RF) process for tar sands consists of two steps: (1) the deposit is volumetrically heated with RF energy to lower the viscosity of the bitumen, and (2) the bitumen is produced by one of several petroleum recovery methods. The RF heating step is accomplished by inserting tubular electrodes into boreholes and by energizing them with an RF power source. The electrode pattern is designed so that the deposit between the electrodes is uniformly heated with a minimum energy loss. The operating frequency is selected on the basis of the electromagnetic characteristics of the deposit. The recovery techniques that we investigated include replacing the heated bitumen with sodium silicate solutions, by gravity drainage, and by autogenously developed steam and hydrocarbon gases. Two small-scale field experiments were conducted in the Asphalt Ridge tar sand deposit near Vernal, UT. About 25 m3 [33 cu yd] of the deposit was heated with RF energy, and about 35% of the total in-place bitumen was recovered during the 3-week test period.
Cytosolic Phospholipase A2 Is Required for Macrophage Arachidonic Acid Release by Agonists That Do and Do Not Mobilize Calcium (2000)

The 85-kDa cytosolic phospholipase A(2) (cPLA(2)) mediates agonist-induced arachidonic acid release and eicosanoid production. Calcium and phosphorylation on Ser-505 by mitogen-activated protein kinases (MAPKs) regulate cPLA(2). Arachidonic acid release and eicosanoid production induced by stimuli that do (A23187, zymosan) or do not (phorbol myristate acetate (PMA), okadaic acid) mobilize calcium were quantitatively suppressed in cPLA(2)-deficient mouse peritoneal macrophages. The contribution of MAPKs to cPLA(2)-mediated arachidonic acid release was investigated. Both extracellular signal-regulated kinases (ERKs) and p38 contributed to cPLA(2) phosphorylation on Ser-505. However, although ERK inhibition did not affect A23187-induced arachidonic acid release, it suppressed zymosan-, PMA-, and okadaic acid-induced arachidonic acid release under conditions where phosphorylation of cPLA(2) on Ser-505 was unaffected. This indicates an additional regulatory mechanism for the ERK pathway. A role for transcriptional regulation is suggested by data showing that cycloheximide and actinomycin D inhibited arachidonic acid release induced by zymosan, PMA and, okadaic acid but not by A23187. Our results show that MAPK pathways contribute to arachidonic acid release in macrophages through alternative mechanisms in addition to their ability to phosphorylate cPLA(2) on Ser-505 and suggest a role for new protein synthesis.
Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I-SceI (1991)

Journal Article Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I- Sce I Get access Agneè;s Thierry, Agneè;s Thierry Search for other works by this author on: Oxford Academic PubMed Google Scholar Arnaud Perrin, Arnaud Perrin Search for other works by this author on: Oxford Academic PubMed Google Scholar Jeanne Boyer, Jeanne Boyer Search for other works by this author on: Oxford Academic PubMed Google Scholar Cecile Fairhead, Cecile Fairhead Search for other works by this author on: Oxford Academic PubMed Google Scholar Bernard Dujon, Bernard Dujon Search for other works by this author on: Oxford Academic PubMed Google Scholar Bruno Frey, Bruno Frey 1Boehringer Mannheim GmbH, Biochemical Research Center, Department of Molecular BiologyNonnenwald 2, D-8122 Penzberg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Gudrun Schmitz Gudrun Schmitz 1Boehringer Mannheim GmbH, Biochemical Research Center, Department of Molecular BiologyNonnenwald 2, D-8122 Penzberg, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 1, 11 January 1991, Pages 189–190, https://doi.org/10.1093/nar/19.1.189 Published: 11 January 1991 Article history Received: 26 September 1990 Published: 11 January 1991
Axons arrest the migration of Schwann cell precursors (1994)

ABSTRACT The neural crest gives rise to a variety of cell types including Schwann cells of the peripheral nervous system. Schwann cell precursors begin to differentiate early and migrate along specific pathways in the embryo before associating with nerve trunks. To determine whether motor axons direct the migration of Schwann cell precursors along specific pathways, we tested the effect of ablating the ventral half of the neural tube, which contains motor neuron cell bodies. The ventral neural tube was removed unilaterally from lumbar regions of chicken embryos at stage 17, when neural crest cells are just beginning to migrate and before motor axons have extended out of the neural tube. At several stages after ventral tube ablation, sections of the lumbar region of these embryos were stained with anti-acetylated tubulin to label developing axons, HNK-1 to label migrating neural crest cells and 1E8 to label Schwann cell precursors. In many embryos the ablation of motor neurons was incomplete. The staining patterns in these embryos support the idea that some Schwann cells are derived from the neural tube. In embryos with complete motor neuron ablation, at stage 18, HNK-1-positive neural crest cells had migrated to normal locations in both control and ablated sides of the embryo, suggesting that motor axons or the ventral neural tube are not required for proper migration of neural crest cells. However, by stage 19, cells that were positive for HNK-1 or 1E8 were no longer seen in the region of the ventral root, nor ventral to the ventral root region. Because Schwann cell precursors require neural-derived factors for their survival in vitro, we tested whether neural crest cells that migrate to the region of the ventral root in ventral neural tube-ablated embryos then die. Nile Blue staining for dead and dying cells in ventral neural tube-ablated embryos provided no evidence for cell death at stage 18. These results suggest that motor axons arrest the migration of Schwann cell precursors during neural crest migration.
The androgen control of sebum production. Studies of subjects with dihydrotestosterone deficiency and complete androgen insensitivity. (1993)

To evaluate the androgen control of sebum, subjects with complete androgen insensitivity and male pseudohermaphrodites with inherited 5 alpha-reductase deficiency and decreased dihydrotestosterone (DHT) production had sebum production studied. A hydrophobic polymeric film applied to the forehead was used to measure sebum production through the use of air filled micropores. Sebum scores of normal preadrenarchal children (ages 2-6), and normal age-matched adult males and females, were studied as well as males treated with the 5 alpha-reductase inhibitor, finasteride, for benign prostatic hyperplasia who were studied at baseline and after drug therapy. Androgen insensitive subjects had no sebum production by this methodology, and the results were identical to preadrenarchal children. In contrast, adult male pseudohermaphrodites with 5 alpha-reductase deficiency and a selective decrease in DHT production had sebum production scores identical to normal age-matched males. Males with benign prostatic hyperplasia treated with the 5 alpha-reductase inhibitor, finasteride, to lower DHT levels did not decrease the sebum score from baseline values. The lack of demonstrable sebum in androgen-insensitive subjects clearly demonstrates the absolute androgen control of sebum production. The DHT dependency of the sebaceous gland, however, could not be demonstrated in this study. Two 5 alpha-reductase isoenzymes 1 and 2, have been described. 5 alpha-reductase-2 is the gene responsible for inherited 5 alpha-reductase deficiency. Although the degree of inhibition of DHT in utero and in adulthood in male pseudohermaphrodites with a defect in 5 alpha-reductase-2 enzyme activity caused severe impairment of external genital and prostate differentiation and decreased facial and body hair, it had no demonstrable effect on sebaceous gland development or function. Furthermore, lowering DHT levels in adulthood had no effect on sebum production. If the gland is rich in the enzyme 5 alpha-reductase-2, it is proposed that the sebaceous gland is either exquisitely sensitive to DHT, requiring only small amounts for normal development and function, or that male levels of testosterone compensate for DHT and maintain normal sebaceous gland activity throughout life. It is also possible that 5 alpha-reductase-1 is the enzyme of the sebaceous gland and is unaffected in the inherited condition and by finasteride.
Region-Based Convolutional Networks for Accurate Object Detection and Segmentation (2015)

Object detection performance, as measured on the canonical PASCAL VOC Challenge datasets, plateaued in the final years of the competition. The best-performing methods were complex ensemble systems that typically combined multiple low-level image features with high-level context. In this paper, we propose a simple and scalable detection algorithm that improves mean average precision (mAP) by more than 50 percent relative to the previous best result on VOC 2012-achieving a mAP of 62.4 percent. Our approach combines two ideas: (1) one can apply high-capacity convolutional networks (CNNs) to bottom-up region proposals in order to localize and segment objects and (2) when labeled training data are scarce, supervised pre-training for an auxiliary task, followed by domain-specific fine-tuning, boosts performance significantly. Since we combine region proposals with CNNs, we call the resulting model an R-CNN or Region-based Convolutional Network. Source code for the complete system is available at http://www.cs.berkeley.edu/~rbg/rcnn.
Tauroursodeoxycholic Acid Prevents Bax-Induced Membrane Perturbation and CytochromecRelease in Isolated Mitochondria (2003)

Bax is a potent pro-apoptotic member of the Bcl-2 protein family that localizes to the mitochondrial membrane during apoptosis. Tauroursodeoxycholic acid (TUDCA) modulates the apoptotic threshold, in part, by preventing Bax translocation both in vitro and in vivo. The mechanisms by which Bax induces and TUDCA inhibits release of cytochrome c are unclear. We show here that recombinant Bax protein induced cytochrome c release in isolated mitochondria without detectable swelling. Co-incubation with TUDCA prevented efflux of mitochondrial factors and proteolytic processing of caspases in cytosolic extracts. Spectroscopic analyses of mitochondria exposed to Bax revealed increased polarity and fluidity of the membrane lipid core as well as altered protein order, indicative of Bax binding, together with loss of spin-label paramagnetism, characteristic of oxidative damage. TUDCA markedly abrogated the Bax-induced membrane perturbation. In conclusion, our results indicate that Bax protein directly induces cytochrome c release from mitochondria through a mechanism that does not require the permeability transition. Rather, it is accompanied by changes in the organization of membrane lipids and proteins. TUDCA is a potent inhibitor of Bax association with mitochondria. Thus, TUDCA modulates apoptosis by suppressing mitochondrial membrane perturbation through pathways that are also independent of the mitochondrial permeability transition.
Lysogenization of Escherichia coli by bacteriophage Lambda: complementary activity of the host's DNA polymerase I and ligase and bacteriophage replication proteins Q and P (1976)

When bacteriophage lambda DNA replication is blocked by mutation in phage genes O or P, the efficiency of lysogenization drops to a very low value unless high multiplicities of infecting phage are used. Our results show that even at high multiplicity, lambda O or P mutants cannot efficiently lysogenize some hosts that are defective in either DNA polymerase I or DNA ligase. Covalent closure of infecting DNA molecules, a preliminary step for insertion according to Campbell's model and an obvious candidate for this lysogenization defect, appears to occur normally under our conditions. In addition, prophage excision as measured by the frequency of curing O- and P- lysogens seemed normal when tested in the poll- strain. These results suggest that the Escherichia coli enzymes DNA polymerase I and ligase, and phage proteins O and P, are able to provide some complementary activity whose function is required specifically for prophage integration.