gebhart/patrepeval huggingface dataset:
Antioxidant protection of phospholipid bilayers by alpha-tocopherol. Control of alpha-tocopherol status and lipid peroxidation by ascorbic acid and glutathione. (1986)

Factors affecting the balance between pro- and antioxidant effects of ascorbic acid and glutathione were studied in soybean phosphatidylcholine liposomes challenged with Fe2+/H2O2. Effective antioxidant protection by alpha-tocopherol appeared to be due to efficient reaction with lipid oxy-radicals in the bilayer rather than to interception of initiating oxygen radicals. At concentrations above a threshold level of approximately 0.2 mol % (based on phospholipid content), alpha-tocopherol completely suppressed lipid oxy-radical propagation, which was measured as malondialdehyde production. Both ascorbic acid and glutathione, alone or in combination, enhanced lipid oxy-radical propagation. Alpha-Tocopherol, incorporated into liposomes at concentrations above its threshold protective level, reversed the pro-oxidant effects of 0.1-1.0 mM ascorbic acid but not those of glutathione. Ascorbic acid also prevented alpha-tocopherol depletion. The combination of ascorbic acid and subthreshold levels of alpha-tocopherol only temporarily suppressed lipid oxy-radical propagation and did not maintain the alpha-tocopherol level. Glutathione antagonized the antioxidant action of the alpha-tocopherol/ascorbic acid combination regardless of alpha-tocopherol concentration. These observations indicate that membrane alpha-tocopherol status can control the balance between pro- and antioxidant effects of ascorbic acid. The data also provide the most direct evidence to date that ascorbic acid interacts directly with components of the phospholipid bilayer.
Antigen-specific immunotherapy for murine lung metastatic tumors expressing human papillomavirus type 16 E7 oncoprotein (1998)

An important goal of cancer immunotherapy is to prevent and treat tumor metastasis. We have previously reported a recombinant vaccinia-based vaccine (Sig/E7/LAMP-1) that demonstrated significant anti-tumor effect in a subcutaneous tumor challenge model. In this study, we investigated the potency of the Sig/E7/ LAMP-1 vaccine in preventing and treating metastatic tumors. A tumor metastasis model was generated by injecting human papillomavirus type 16 (HPV-16) E6/E7 expressing tumor cells, designated TC-1, into the tail vein of syngeneic C57BL/6 mice. All the naive mice injected with 1 x 10(6) TC-1 cells developed tumors confined exclusively to the lungs within 1 month. For in vivo tumor prevention experiments, mice were vaccinated with Sig/E7/ LAMP-1 followed by tumor challenge. While tumor growth was observed in all of the mice (10/10) in the control groups, 8 of 10 vaccinated mice (80%) remained tumor-free 2 months post-tumor challenge. For in vivo treatment experiments, mice were first inoculated with TC-1 cells and then vaccinated with Sig/E7/ LAMP-1. Treatment with Sig/E7/LAMP-1 was effective in eliminating preexisting tumor cells in 4 of 5 vaccinated mice. Most importantly, treatment with Sig/E7/LAMP-1 resulted in regression of fully established lung tumors in 10% (5/10) of vaccinated mice. Our data suggest that the Sig/E7/LAMP-1 vaccine is effective in controlling the hematogenous spread of TC-1 tumor cells. In addition, the TC-1 lung metastasis model can be used to test the efficacy of various E6/E7-specific vaccines and immunotherapeutic strategies.
Characterization of a Gene Encoding a DNA Binding Protein with Specificity for a Light-Responsive Element (1992)

Philip M. Gilmartin, Johan Memelink, Kazuyuki Hiratsuka, Steve A. Kay, Nam-Hai Chua, Characterization of a Gene Encoding a DNA Binding Protein with Specificity for a Light-Responsive Element, The Plant Cell, Vol. 4, No. 7 (Jul., 1992), pp. 839-849
SVM-Based Prediction of Propeptide Cleavage Sites in Spider Toxins Identifies Toxin Innovation in an Australian Tarantula (2013)

Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree) and developed an algorithm (SpiderP) for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM) framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor) from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP) is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html), a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the SpiderP website.
Preparation of unsaturated carbohydrates. A facile synthesis of methyl 4,6-O-Benzylidene-D-hex-2-enopyranosides (1968)

A simple method was explored for the preparation of methyl 4,6-O-benzylidene-hex-2-enopyranosides. Methyl 2,3-anhydro-4,6-O-benzylidene-D-hexopyranosides were converted to diaxial iodohydrins using sodium iodide in acetone which contained sodium acetate and acetic acid. Treatment of the iodohydrins with either methane- or p-toluenesulfonyl chloride in refluxing pyridine yielded the 2,3-unsaturated derivative in excellent yield. The four isomers for methyl 4,6-O-benzylidene-D-hex-2-enopyranoside were thus prepared. The rotations of the anomeric pairs followed Hudson's rules of isorotation. Evidence is provided that, in the absence of strong destabilizing interactions in the product, the epoxide ring of one of the above-mentioned 2,3-anhydroglycosides is opened by lithium iodide in ether to form the iodohydrin as the lithium alkoxide in high yield. This observation provides an explanation for the reduction of methyl 2,3-anhydro-4,6-O-benzylidene-α-D-allopyranoside to 4,6-O-benzylidene-D-allal. Reaction of methyl 4,6-O-benzylidene-2-deoxy-2-iodo-α-D-idopyranoside with methyl lithium provided 4,6-O-benzylidene-D-gulal. The conformational properties of a number of the compounds prepared and of acetylated methyl pentopyranosides, as derived from their nuclear magnetic resonance parameters, are discussed with particular reference to the role that geminal coupling constants may play in the determination of configuration and conformational equilibria.
Self‐Supporting Elastic Film without Covalent Linkages as a Hierarchically Integrated β‐Sheet Assembly (2003)

Hierarchic self-assembly: The formation of a self-supporting elastic film without the use of macromolecular materials is described. The film is prepared by using a peptide-containing amphiphile that has three or four consecutive leucinate residues. The amphiphile initially forms β-sheet structures, which stack in a fastenerlike fashion between the side chains of leucine within the different β-sheets (see picture).
Drug development in anaesthesia: industrial perspective (2006)

We consider the main reason for low activity is the perception in industry that there is little need for new drugs in anaesthesia because the needs are well addressed by existing agents. If this is not the case then anaesthesiologists need to be more effective in communicating their requirements.
TGF‐β receptors (1992)

The nature and role of cell surface proteins that bind members of the TGF-beta family has been investigated. TGF-beta, activins, and BMPs each bind to receptors of 55 kDa (type I) and 70 kDa (type II). In the TGF-beta system, these receptors are implicated in the mediation of multiple responses. A member of the type II receptor family has been cloned that encodes four alternatively spliced versions of a transmembrane serine/threonin kinase receptor related to the recently cloned mouse activin receptor and C-elegans daf-1 gene. Inhibitors of serine/threonine kinase activity block transcriptional and growth inhibitory responses to TGF-beta. In addition to the signaling receptors, many cell types express the TGF-beta binding proteoglycan betaglycan. Betaglycan has been purified, molecularly cloned, and shown to bind TGF-beta via its core protein and basic fibroblast growth factor via its heparan sulfate chains. In addition to receptors I and II and betaglycan, some cells express a newly identified set of membrane proteins that specifically bind either TGF-beta 1 or TGF-beta 2. Three of the four isoform-restricted binding proteins are bound to the membrane via phospholipid anchors. Like betaglycan, these proteins might function to regulate the interaction between TGF-beta and their target cells.
Stereoselektive Synthese von Alkoholen, VI1) Asymmetrische Synthesen von 4‐Penten‐2‐ol über Allylboronsäureester chiraler Glycole (1981)

Abstract Die Allylboronsäureester 3 substituierter Campherglycole 2 wurden mit Acetaldehyd zu 4‐Penten‐2‐ol ( 1 ) umgesetzt. Dabei ist die Substituentenwirkung auf die Größe der asymmetrischen Induktion annähernd additiv. Mit 2d als chiralem Hilfsstoff konnte Pentenol von 86% e.e. erhalten werden.
Group C adenovirus DNA sequences in human lymphoid cells (1986)

Human peripheral blood lymphocytes from healthy adults, cord blood lymphocytes, and lymphoblastoid cell lines were screened by hybridization for the presence of group C adenovirus DNA sequences. In 13 of 17 peripheral blood lymphocyte samples from adults, 1 of 10 cord blood samples, and seven of seven lymphoblastoid cell lines tested, results were positive for Group C adenovirus DNA (adenovirus 1 [Ad1], Ad2, Ad5, or Ad6). About 1 to 2% of the lymphocytes carried 50 to 100 viral genome copies per positive cell, as estimated by in situ hybridization. Infectious virus representing all members of group C were recovered, but cultivation in the presence of adenovirus antibody did not cure the cells of free viral genomes. Viral DNA was found in B, T, and N cells but only in 1 of 10 cord blood samples. The results suggest that group C adenovirus infections in childhood result in the persistence of the viral genome in circulating lymphocytes.
Salting-out Extraction of 3-Hydroxypropionic Acid with Reactive Extraction and Aqueous Two-phase Systems (2017)

3-Hydroxypropionic acid (3-HP) is an isomer of 2-hydroxypropionic acid (2-HP) and an important platform molecule. A biological production route of 3-HP has become of interest as a sustainable alternative to the chemical route. However, its hydrophilic property makes the separation of 3-HP from the fermentation broth difficult. In this study, reactive solvent extraction and an aqueous two phase system (ATPS) were utilized to extract 3-HP from an aqueous solution. In the reactive extraction system, synergism, which was found in the reactive extraction of 2-HP, was not observed with mixed extractants of TBP and TOA diluted in heptane. TOA diluted in 1-octanol gave the highest extractability in the reactive extraction system. There was little effect on the extractability of 3-HP by the addition of salt to the system. In an ATPS composed of alcohols and salts, binodal curves and tie lines were measured, and then 3-HP was extracted with the ATPS. The highest extractability and distribution ratio were obtained by using an ATPS composed of t-BuOH and Na2SO4. The maximum distribution ratios in both systems were similar.
Correlation of pathologic findings with progression after radical retropubic prostatectomy (1993)

The most likely explanation for the discrepancy between margins and progression is that some of these margins represented artifactually positive margins caused by the unique problems with handling and assessing radical prostatectomy specimens. Radical prostatectomy provided excellent local control, with only 8% of patients exhibiting local recurrence. Sixty-one percent of men with progression had an elevated serum prostate-specific antigen level as their only manifestation of progression. The significance of isolated elevated serum prostate-specific antigen levels is uncertain, and long-term morbidity and mortality will depend on whether these patients have local disease or occult distant metastases.
Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions (2009)

To perform transcript profiling studies on brains of the desert locust, the use of Sg-RP49, Sg-EF1a and Sg-ACT as reference genes is proposed for studies of fifth instar nymphs. In experiments with adult brains, however, the most preferred reference genes were Sg-GAPDH, Sg-Ubi and Sg-EF1a. These data will facilitate transcript profiling studies in desert locusts and provide a good starting point for the initial selection of genes for validation studies in other insects.
p38MAPK Acts in the BMP7-dependent Stimulatory Pathway during Epithelial Cell Morphogenesis and Is Regulated by Smad1 (2004)

Bone morphogenetic protein (BMP)-7 exerts dose-dependent stimulatory and inhibitory effects during renal branching morphogenesis. Previously, we identified an inhibitory role for activin-like kinase receptors and Smad1 in BMP-dependent inhibition (Piscione, T. D., Phan, T., and Rosenblum, N. D. (2001) Am. J. Physiol. 280, F19-F33). Here we demonstrate a novel role for p38 mitogen-activated kinase (p38(MAPK)) in BMP7-dependent stimulatory signaling. Stimulatory doses (0.25 nm) of BMP7 increased p38(MAPK) activity and stimulated phosphorylation of endogenous activating transcription factor 2 (ATF2) in a p38(MAPK)-dependent manner in murine inner medullary collecting duct (mIMCD-3) cells. In contrast, high doses (10 nm) of BMP7 inhibited p38(MAPK) activity and phosphorylation of endogenous ATF2. Treatment with BMP7 exerted no significant effect on the levels of the phosphorylated forms of endogenous SAPK/JNK or p44 and p42 (ERK1 and ERK2) protein kinases. To investigate the functional importance of p38(MAPK) signaling, we showed that SB203580, a p38(MAPK) inhibitor, blocked the stimulatory effect of BMP7 on mIMCD-3 cell morphogenesis but had no effect on BMP7-dependent inhibition in a three-dimensional culture model. To identify mechanisms by which BMP7-dependent inhibitory signaling suppresses p38(MAPK) activity, we measured p38(MAPK) activity in ligand independent mIMCD-3 models of enhanced and suppressed Smad signaling. Basal activity of p38(MAPK) was decreased in mIMCD-3 cells and in embryonic kidney tissue expressing a constitutively active activin-like kinase receptor, but was increased in mIMCD-3 cells stably expressing a dominant negative form of Smad1. We conclude that BMP7 stimulates renal epithelial cell morphogenesis via p38(MAPK) and that p38(MAPK) activity is negatively regulated by Smad1.
Optical Propagation Effects of an Underwater Laser Range-gated Imaging System (1996)

A report on the verification of a suite of mathematical models related to propagation of light in water. The developed models were assessed by comparison with experimental results for forward scattering and backscattering, in addition to image propagation, using the high performance underwater imaging system.
A direct in vivo comparison of the inflammatory properties of human C5a and C5a des Arg in human skin. (1988)

C5a is an 11,000-Da complement-derived inflammatory glycoprotein that has been shown to mediate inflammatory reactions in vitro as well as in vivo in human skin. The C5a degradation product, C5a des Arg, is rapidly formed after exposure of C5a to serum carboxypeptidase N and may represent the relevant C5-derived inflammatory peptide in vivo. To examine the biologic activity of human C5a des Arg in vivo and to compare it with that seen with human C5a, we purified and characterized homogeneous preparations of human C5a and C5a des Arg and injected them intradermally into seven normal volunteers. C5a des Arg exhibited biochemical and biologic properties in vitro that were different from those of C5a. When injected into human skin, C5a des Arg was less potent than C5a, in respect to both minimal dose eliciting wheal and flare reactions and maximal wheal and flare elicited at a given dose, but C5a des Arg still elicited cutaneous wheal and flare reactions at physiologically relevant concentrations. Histologically, C5a des Arg skin test sites showed dense polymorphonuclear neutrophil-rich infiltrates associated with leukocytoclasis, dermal mast cell degranulation, and endothelial cell swelling. These were virtually indistinguishable from reactions elicited by C5a and occurred with concentrations attainable in vivo. Cutaneous wheal and flare reactions elicited by either C5a or C5a des Arg were partially inhibited by H1 antihistamines but were unaffected by selected nonsteroidal anti-inflammatory agents.
Synthesis of application accelerators on Runtime Reconfigurable Hardware (2008)

Application accelerators are predominantly ASICs. The cost of ASIC solutions are order of magnitudes higher than programmable processing cores. Despite this, ASIC solutions are preferred when both high performance and low power is the target. ASICs offer no flexibility in terms of it being able to cater to application derivatives, unless this has been provisioned for at the time of design. In this paper we define the architecture of Runtime Reconfigurable Hardware (RRH) as the platform for application acceleration. The proposed RRH is a homogeneous fabric comprising computing, storage and communicating resources. We also propose a synthesis methodology to realize application written a high level language (HLL) on the RRH. Applications described in HLL is compiled into application substructures. For each application substructure a set of Compute Elements interconnected in a manner that closely matches the communication pattern within it, is allocated. CEs in such a configuration is called a hardware affine. Hardware Affines are carved out on the RRH at runtime. These hardware affines are defined at compile time, and are provisioned at runtime on the fabric. By virtue of the fact that these hardware affines are NOT instruction set processor cores or Logic Elements as in FPGAs, we bear the performance and power advantage of an ASIC, and the hardware reconfigurability/programmability of that of an FPGA/Instruction Set Processor.
Comparing and Combining Generative and Posterior Probability Models: Some Advances in Sentence Boundary Detection in Speech (2004)

We assessed prevalence of and risk factors for candidaemia following Clostridium difficile infection (CDI) using longitudinal population-based surveillance. Of 13 615 adults with CDI, 113 (0·8%) developed candidaemia in the 120 days following CDI. In a matched case-control analysis, severe CDI and CDI treatment with vancomycin + metronidazole were associated with development of candidaemia following CDI.
EmbeddedButtons (1992)

EmbeddedButtons is a library of routines and a runtime kernel that support the integration of buttons into document media, including text and graphics. Existing document editors can be modified to participate in this open architecture with the addition of a few simple routines. Unlike many button systems that insert special button objects into document media, this system supports turning existing document objects into buttons . As a consequence, buttons inherit all of the attributes of normal document objects, and the appearance of buttons can be edited using operations already familiar to users. Facilities are provided for linking buttons to application windows so that documents can serve as application control panels. Hence, user interface designers can lay out control panels using familiar document editors rather than special-purpose tools. Three classes of buttons have been implemented, including buttons that pop up a menu and buttons that store and display the value of a variable. New button classes, editors, and applications can be added at run time. Two editors, one for text and one for graphics, currently participate in the architecture.
Adiponectin inhibits palmitate-induced apoptosis through suppression of reactive oxygen species in endothelial cells: involvement of cAMP/protein kinase A and AMP-activated protein kinase (2010)

The present study examined whether adiponectin can inhibit palmitate-induced apoptosis, and also the associated mechanisms and signal transduction pathways in human umbilical vein endothelial cells. Cells treated with 500 μM palmitate for 48 h increased reactive oxygen species (ROS) generation and induced apoptosis. Treatment with antioxidant N-acetyl-L-cysteine (1 mM) and globular adiponectin (5 μg/ml) inhibited palmitate-induced ROS generation and apoptosis. The AMP-activated protein kinase (AMPK) activator 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR; 1 mM), and cAMP activators forskolin (10 μM) and cholera toxin (200 ng/ml) also displayed the same effects. The inhibitory effects of adiponectin on ROS generation and apoptosis were reversed by the AMPK inhibitor compound C (40 μM), cAMP inhibitor SQ22536 (50 μM), and protein kinase A (PKA) inhibitor H-89 (10 μM). The inhibitory effect of forskolin on palmitate-induced apoptosis was reversed by compound C, whereas the inhibitory effect of AICAR was not reversed by SQ22536 and H-89. AICAR and forskolin could not inhibit palmitate-induced apoptosis in cells treated with dominant-negative AMPK. Forskolin increased phosphorylated AMPK at both Thr-172 and Ser-485/491. These results suggest that adiponectin inhibits palmitate-induced apoptosis by suppression of ROS generation via both the cAMP/PKA and AMPK pathways. Interaction between cAMP/PKA and AMPK pathways may be involved.
The SIFT information dissemination system (1999)

Information dissemination is a powerful mechanism for finding information in wide-area environments. An information dissemination server accepts long-term user queries, collects new documents from information sources, matches the documents against the queries, and continuously updates the users with relevant information. This paper is a retrospective of the Stanford Information Filtering Service (SIFT), a system that as of April 1996 was processing over 40,000 worldwide subscriptions and over 80,000 daily documents. The paper describes some of the indexing mechanisms that were developed for SIFT, as well as the evaluations that were conducted to select a scheme to implement. It also describes the implementation of SIFT, and experimental results for the actual system. Finally, it also discusses and experimentally evaluates techniques for distributing a service such as SIFT for added performance and availability.