gebhart/patrepeval huggingface dataset:
Vascular endothelial growth factor: Direct neuroprotective effect in in vitro ischemia (2000)

Vascular endothelial growth factor (VEGF) is a hypoxia-inducible angiogenic peptide with recently identified neurotrophic effects. Because some neurotrophic factors can protect neurons from hypoxic or ischemic injury, we investigated the possibility that VEGF has similar neuroprotective properties. In HN33, an immortalized hippocampal neuronal cell line, VEGF reduced cell death associated with an in vitro model of cerebral ischemia: at a maximally effective concentration of 50 ng/ml, VEGF approximately doubled the number of cells surviving after 24 h of hypoxia and glucose deprivation. To investigate the mechanism of neuroprotection by VEGF, the expression of known target receptors for VEGF was measured by Western blotting, which showed that HN33 cells expressed VEGFR-2 receptors and neuropilin-1, but not VEGFR-1 receptors. The neuropilin-1 ligand placenta growth factor-2 failed to reproduce the protective effect of VEGF, pointing to VEGFR-2 as the site of VEGF's neuroprotective action. Two phosphatidylinositol 3'-kinase inhibitors, wortmannin and LY294002, reversed the neuroprotective effect of VEGF, implicating the phosphatidylinositol 3'-kinase/Akt signal transduction system in VEGF-mediated neuroprotection. VEGF also protected primary cultures of rat cerebral cortical neurons from hypoxia and glucose deprivation. We conclude that in addition to its known role as an angiogenic factor, VEGF may exert a direct neuroprotective effect in hypoxic-ischemic injury.
Binding between outer membrane proteins of nontypeable Haemophilus influenzae and human nasopharyngeal mucin (1996)

Bacterial colonization of the epithelial cells precedes infection. Mucins of the epithelial cell secretions modulate bacterial colonization. This study was designed to understand the mechanism of mucin-bacterial interactions and in particular binding between nontypeable Haemophilus influenzae and nasopharyngeal mucin(s). In an overlay assay, binding appears to be mediated by outer membrane proteins P2 and P5 of bacteria and sialic acid-containing oligosaccharides of mucin.
Purification and characterization of metabolically active capillaries of the blood-brain barrier (1991)

Microvessels were isolated from bovine and rat cerebral cortex by simple procedures involving mechanical homogenization, differential and density-gradient centrifugation, and chromatography on a column of glass beads. The preparations were composed of short capillaries with a diameter of 1-10 microns. Both purifications were monitored by assaying the activity of the marker enzyme gamma-glutamyl transpeptidase (gamma-GTase). The final bovine and rat preparations were enriched 20- and 14-fold over the homogenate respectively. gamma-GTase activity was measured in different fractions after bovine and rat membranes were solubilized with 0.5% and 0.3% Triton X-100 respectively. Measurement of 5'-nucleotidase and acetylcholinesterase activities indicated very low levels of contamination of the microvessel preparations by glial cells and neurons. The integrity of the capillary membranes was confirmed by the assay of a cytosolic marker enzyme, lactate dehydrogenase. Viability of the microvessels was demonstrated by the presence of detectable levels of adenylates and by tissue respiration induced by glucose and succinate. Comparison of the proteins of homogenized bovine and rat brain cortex with those of purified capillaries separated by SDS/PAGE revealed enrichment of at least three predominant proteins of 14, 16 and 18 kDa in the capillary preparations. It is concluded that these methods allow rapid isolation of small blood vessels of the blood-brain barrier which are suitable for metabolic and structural studies in vitro.
Dual Effect of Synthetic Aminoglycosides: Antibacterial Activity against Bacillus anthracis and Inhibition of Anthrax Lethal Factor (2004)

Defence against bioterrorism: Recent events have created an urgent need for therapeutic strategies to treat anthrax, an infectious disease caused by the toxigenic bacterium Bacillus anthracis. A new class of aminoglycosides (see picture) are powerful inhibitors under physiological conditions of the anthrax lethal factor, which has a major role in the disease, and function simultaneously as antibiotics against B. anthracis.
Role of the heavy and light chains of botulinum neurotoxin in neuromuscular paralysis. (1987)

Botulinum neurotoxin (NT) is synthesized by Clostridium botulinum in any of seven antigenically distinct forms called types A-G. NT, when fully active, is a dichain protein, composed of two polypeptides, a heavy (H) and a light (L) chain (approximately 100,000 and approximately 50,000 Da, respectively) that are held together by noncovalent bonds and at least one disulfide bond. Two types of dichain NT, A and B, and their respective H and L chains were applied to nerve-muscle (NM) preparations (phrenic nerve-hemidiaphragm of the mouse), in order to develop a broader, comparative understanding of the neuroparalytic actions of NT types. It was found that the paralysis induced by dichain NT was delayed or antagonized if NM preparations were incubated with isolated and purified H chain prior to, or during, incubation with the parent, dichain NT. NM preparations preincubated with H chain and then washed free of unbound H chain became paralyzed after subsequent incubation with L chain. Paralysis did not occur if NM preparations were incubated first with L chain, washed, and then incubated with H chain. These observations suggest that the H chain binds with specific sites on the nerve terminal. This binding appears to permit the L chain, or some combination of the L and H chain, to bring about neuroparalysis through a mechanism very similar to that of the parent, dichain NT.
A Review of Pharmacotherapy of Major Depression in Children and Adolescents (2000)

Tricyclic antidepressants are not superior to placebo for the treatment of child and adolescent major depressive disorder. Although two of three trials of second-generation antidepressants in this age group have had negative results, data suggest that these drugs may be more promising. It is too early in our investigation to know whether these agents will be effective in treating major depressive disorder in children and adolescents.
Changes in Microtubule Protofilament Number Induced by Taxol Binding to an Easily Accessible Site (1998)

We have investigated the accessibility of the Taxol-binding site and the effects of Taxol binding on the structures of assembled microtubules. Taxol and docetaxel readily bind to and dissociate from microtubules, reaching 95% ligand exchange equilibrium in less than 3 min under our solution conditions (microtubules were previously assembled from GTP-tubulin, GTP-tubulin and microtubule-associated proteins, or GDP-tubulin and taxoid). Microtubules assembled from purified tubulin with Taxol are known to have typically one protofilament less than with the analogue docetaxel and control microtubules. Surprisingly, Taxol binding and exchange induce changes in the structure of preformed microtubules in a relatively short time scale. Cryoelectron microscopy shows changes toward the protofilament number distribution characteristic of Taxol or docetaxel, with a half-time of approximately 0.5 min, employing GDP-tubulin-taxoid microtubules. Correspondingly, synchrotron x-ray solution scattering shows a reduction in the mean microtubule diameter upon Taxol binding to microtubules assembled from GTP-tubulin in glycerol-containing buffer, with a structural relaxation half-time of approximately 1 min. These results imply that microtubules can exchange protofilaments upon Taxol binding, due to internal dynamics along the microtubule wall. The simplest interpretation of the relatively fast taxoid exchange observed and labeling of cellular microtubules with fluorescent taxoids, is that the Taxol-binding site is at the outer microtubule surface. On the contrary, if Taxol binds at the microtubule lumen in agreement with the electron crystallographic structure of tubulin dimers, our results suggest that the inside of microtubules is easily accessible from the outer solution. Large pores or moving lattice defects in microtubules might facilitate the binding of taxoids, as well as of possible endogenous cellular ligands of the inner microtubule wall.
The R*-tree: an efficient and robust access method for points and rectangles (1990)

The R-tree, one of the most popular access methods for rectangles, is based on the heuristic optimization of the area of the enclosing rectangle in each inner node. By running numerous experiments in a standardized testbed under highly varying data, queries and operations, we were able to design the R*-tree which incorporates a combined optimization of area, margin and overlap of each enclosing rectangle in the directory. Using our standardized testbed in an exhaustive performance comparison, it turned out that the R*-tree clearly outperforms the existing R-tree variants. Guttman's linear and quadratic R-tree and Greene's variant of the R-tree. This superiority of the R*-tree holds for different types of queries and operations, such as map overlay, for both rectangles and multidimensional points in all experiments. From a practical point of view the R*-tree is very attractive because of the following two reasons 1 it efficiently supports point and spatial data at the same time and 2 its implementation cost is only slightly higher than that of other R-trees.
Antibacterial Nanocomposite with Calcium Phosphate and Quaternary Ammonium (2012)

Secondary caries is a frequent reason for restoration failure, resulting from acidogenic bacteria and their biofilms. The objectives of this study were to: (1) develop a novel nanocomposite containing nanoparticles of amorphous calcium phosphate (NACP) and quaternary ammonium dimethacrylate (QADM); and (2) investigate its mechanical and antibacterial durability. A spray-drying technique yielded NACP with particle size of 116 nm. The nanocomposite contained NACP and reinforcement glass fillers, with QADM in the resin. Two commercial composites were tested as controls. Composites were inoculated with Streptococcus mutans. After 180-day water-aging, NACP+QADM nanocomposite had flexural strength and elastic modulus matching those of commercial controls (p > 0.1). NACP+QADM nanocomposite reduced the biofilm colony-forming units (CFU) by 3-fold, compared with commercial composites (p < 0.05). Metabolic activity and lactic acid production of biofilms on NACP+QADM were much less than those on commercial composites (p < 0.05). The antibacterial properties of NACP+QADM were maintained after water-aging for 30, 90, and 180 d (p > 0.05). In conclusion, the novel NACP-QADM nanocomposite greatly decreased biofilm metabolic activity, CFU, and lactic acid, while matching the load-bearing capability of commercial composites without antibacterial properties. The NACP-QADM nanocomposite with strong and durable antibacterial properties, together with its previously reported Ca-PO(4) release capability, may render it useful for caries-inhibiting restorations.
Soft microorigami: self-folding polymer films (2011)

Fabrication of 3D objects using folding of thin films is a novel and very attractive research field. The manuscript overviews recent advances in development and application of polymer films, which are able to fold and form 3D structures.
A vaccinia virus-vectored Hantaan virus vaccine protects hamsters from challenge with Hantaan and Seoul viruses but not Puumala virus (1995)

To investigate the ability of a vaccinia virus-vectored vaccine expressing the M and the S segments of Hantaan (HTN) virus (C. S. Schmaljohn, S. E. Hasty, and J. M. Dalrymple, Vaccine 10:10-13, 1992) to elicit a protective immune response against other hantaviruses, we vaccinated hamsters with the recombinant vaccine and challenged them with HTN, Seoul (SEO), or Puumala (PUU) virus. Neutralizing antibodies to HTN virus were found in all vaccinated hamsters both before and after challenge. Neutralizing antibody titers to SEO virus were present at low levels or were undetectable after two immunizations with the vaccine but were positive in all vaccinated hamsters after challenge with SEO virus and were also positive in control animals that were not challenged. Neutralizing antibodies to PUU virus were observed only in hamsters previously challenged with PUU virus. To assay for virus in the blood and tissues of the hamsters, we developed a nested reverse transcriptase (RT)-PCR with cross-reactive outer primers and serotype-specific inner primers. The RT-PCR specifically detected as little as 1 PFU of virus in serum containing high-titer neutralizing antibodies and was more sensitive than immunofluorescent antibody staining for detecting virus in lung and kidney specimens of infected hamsters. By using the RT-PCR, we found that vaccinated hamsters, challenged with HTN or SEO virus, neither were viremic nor had evidence of virus in their lungs or kidneys. In contrast, vaccinated hamsters challenged with PUU virus were viremic and had PUU virus-specific nucleic acid in their organs.
DNA Binding Made Easy (2009)

A mechanism by which proteins of bacterial plant pathogens recognize and control the expression of host plant genes to promote infection is identified.
Vaccination with a Human High Molecular Weight Melanoma-Associated Antigen Mimotope Induces a Humoral Response Inhibiting Melanoma Cell Growth In Vitro (2005)

Peptide mimics of a conformational epitope that is recognized by a mAb with antitumor activity are promising candidates for formulations of anticancer vaccines. These mimotope vaccines are able to induce a polyclonal Ab response focused to the determinant of the mAb. Such attempts at cancer immunotherapy are of special interest for malignant melanoma that is highly resistant to chemotherapy and radiotherapy. In this study, we describe for the first time the design and immunogenicity of a vaccine containing a mimotope of the human high m.w. melanoma-associated Ag (HMW-MAA) and the biological potential of the induced Abs. Mimotopes were selected from a pVIII-9mer phage display peptide library with the anti-HMW-MAA mAb 225.28S. The mimotope vaccine was then generated by coupling the most suitable candidate mimotope to tetanus toxoid as an immunogenic carrier. Immunization of rabbits with this vaccine induced a specific humoral immune response directed toward the epitope recognized by the mAb 225.28S on the native HMW-MAA. The induced Abs inhibited the in vitro growth of the melanoma cell line 518A2 up to 62%. In addition, the Abs mediated 26% lysis of 518A2 cells in Ab-dependent cellular cytotoxicity. Our results indicate a possible application of this mimotope vaccine as a novel immunotherapeutic agent for the treatment of malignant melanoma.
The mitogenic response to tumor necrosis factor alpha requires c-Jun/AP-1. (1993)

In the present study, we addressed the role of the c-jun proto-oncogene in the mitogenic response of human fibroblasts and primary acute myelogenous leukemia blasts to tumor necrosis factor alpha (TNF-alpha). Our data indicate that TNF-alpha treatment of these cells is associated with transcriptional activation of c-jun, resulting in accumulation of c-jun mRNA and protein expression. In order to elucidate the role of c-Jun/AP-1 in TNF-mediated growth stimulation, the antisense (AS) technique was used. Uptake studies of oligonucleotides were performed with fibroblasts, demonstrating that incorporation of oligomers was maximal at 4 h. Oligodeoxynucleotides remained stable in these cells for up to 24 h. Treatment of fibroblasts with the AS oligonucleotide resulted in intracellular duplex formation followed by an efficient translation blockade of c-Jun/AP-1. In contrast, sense (S) and nonsense (NS) oligodeoxynucleotides failed to form intracellular duplexes and also did not interfere with translation of c-Jun/AP-1, suggesting specific elimination of c-Jun/AP-1 by the AS oligomer. Fibroblasts cultured in the presence of the AS oligonucleotide but not those cultured in the presence of the S or NS oligonucleotide failed to respond proliferatively to TNF-alpha. These findings could be confirmed by experiments with primary acute myelogenous leukemia blasts, which also demonstrated that TNF-induced growth stimulation required c-Jun/AP-1 function. Taken together, our results indicate that activation of c-Jun/AP-1 plays a pivotal role in the signaling cascade initiated by TNF, which leads to a proliferative response of its target cells.
Dual Angiotensin Converting Enzyme/Thromboxane Synthase Inhibitors (1994)

A variety of compounds were prepared to determine whether dual angiotensin converting enzyme (ACE)/thromboxane synthase (TxS) inhibition could be obtained in the same molecule. These compounds would be used to explore the concept that a dual inhibitor would have superior antihypertensive activity in the spontaneous hypertensive rat compared to an ACE inhibitor. Potent in vitro dual ACE and TxS inhibition was obtained in the same molecule with five series of compounds. Potent blood pressure lowering in the SHR was observed after oral administration of 8b and 11. However, a correlation between blood pressure lowering and the A1 pressor response inhibition was not observed. The blood pressure-lowering actions of enalapril were significantly potentiated by concurrent administration of 3, a thromboxane synthase inhibitor. Analysis of the area under the curve for 24 h showed nearly a doubling of the blood pressure-lowering effect.
Potential Applicability of Chymotrypsin-Susceptible Microcin J25 Derivatives to Food Preservation (2009)

Microcin J25 (MccJ25) is a 21-residue ribosomally synthesized lariat peptide antibiotic. MccJ25 is active against such food-borne disease-causing pathogens as Salmonella spp., Shigella spp., and Escherichia coli, including E. coli O157:H7 and non-O157 strains. MccJ25 is highly resistant to digestion by proteolytic enzymes present in the stomach and intestinal contents. MccJ25 would therefore remain active in the gastrointestinal tract, affecting normal intestinal microbiota, and this limits the potential use of MccJ25 as a food preservative. In the present paper, we describe a chymotrypsin-susceptible MccJ25 derivative with a mutation of Gly(12) to Tyr that retained almost full antibiotic activity and efficiently inhibited the growth of pathogenic Salmonella enterica serovar Newport and Escherichia coli O157:H7 in skim milk and egg yolk. However, unlike the wild-type MccJ25, the MccJ25(G12Y) variant was inactivated by digestive enzymes both in vitro and in vivo. To our knowledge, our results represent the first example of a rational modification of a microcin aimed at increasing its potential use in food preservation.
Mimicking the Silicon Surface: Reactivity of Silyl Radical Cations toward Nucleophiles (2011)

Radical cations of selected low molecular-weight silicon model compounds were obtained by photoinduced electron transfer. These radical cations react readily with a variety of nucleophiles, regularly used in monolayer fabrication onto hydrogen-terminated silicon. From time-resolved kinetics, it was concluded that the reactions proceed via a bimolecular nucleophilic attack to the radical cation. A secondary kinetic isotope effect indicated that the central Si-H bond is not cleaved in the rate-determining step. Apart from substitution products, also hydrosilylation products were identified in the product mixtures. Observation of the substitution products, combined with the kinetic data, point to an bimolecular reaction mechanism involving Si-Si bond cleavage. The products of this nucleophilic substitution can initiate radical chain reactions leading to hydrosilylation products, which can independently also be initiated by dissociation of the radical cations. Application of these data to the attachment of organic monolayers onto hydrogen-terminated Si surfaces via hydrosilylation leads to the conclusion that the delocalized Si radical cation (a surface-localized hole) can initiate the hydrosilylation chain reaction at the Si surface. Comparison to monolayer experiments shows that this reaction only plays a significant role in the initiation, and not in the propagation steps of Si-C bond making monolayer formation.
Rickettsial diseases: the typhus group of fevers—a review (2000)

Abstract Epidemic louse borne typhus has historically caused massive mortality in the wake of war, famine, and great migrations.1 In the four years from 1918 in Eastern Europe and Russia there were up to 30 million cases, and three million deaths. In the recent past in Burundi typhus has infected prison inmates before spreading to the wider community.2 It remains a risk among refugee populations in all parts of the world, despite its omission from a recent review of health care in refugee camps.3
STAT2 Is a Primary Target for Measles Virus V Protein-Mediated Alpha/Beta Interferon Signaling Inhibition (2008)

Measles virus, a member of the Morbillivirus family, infects millions of people each year despite the availability of effective vaccines. The V protein of measles virus is an important virulence factor that can interfere with host innate immunity by inactivating alpha/beta interferon (IFN-alpha/beta) and IFN-gamma signaling through protein interactions with signal transducer and activator of transcription proteins STAT1 and STAT2. Here we demonstrate that although STAT1 interference results from protein interactions within a V protein N-terminal region encompassed by amino acids 110 to 130, detection of STAT1 interaction and IFN-gamma signaling inhibition requires the presence of cellular STAT2. Cell-specific variability in STAT1 interference was observed to correlate with V protein expression level. A more direct target for measles virus V protein-mediated IFN-alpha/beta evasion is STAT2. Results indicate that the widely conserved C-terminal zinc finger domain of measles virus V protein is both necessary and sufficient to bind STAT2 and disrupt IFN-alpha/beta signal transduction. Mutagenesis and molecular modeling define a contact surface for STAT2 association that includes aspartic acid residue 248 as critical for STAT2 interference and IFN antiviral immune suppression. These findings clearly define the molecular determinants for measles virus IFN evasion and validate specific targets as candidates for therapeutic intervention.
Coaxial, Photon-Ion Technology Enables Direct Navigation to Buried Nodes on Planarized Surfaces, Including Silicon (2002)

Abstract The limitation of Focused Ion Beam (FIB) and all charged beam technologies are their insensitivity to the internal composition of materials relative to surface composition. For the most part, charged particle technology cannot provide the resolution at a depth necessary for locating traces either buried under passivation or through silicon. Before CMP planarization was utilized in the industry, it was possible to correlate passivation topography with buried metal traces and manually navigate to the correct x-y coordinates necessary for edit placement. There was still a level of difficulty and CAD navigation helped immensely. With the advent of CMP-planarized metallization, CAD navigation became a necessity, yet still required passivation topography for precise alignment. Current manufacturing processes now planarize all layers, including the passivation, increasing the overall difficulty of navigation. Techniques of drilling “seeker” holes or surface demarcation using FIB and lasers to establish reference fiducials are used extensively [1,2]. Seeker holes and optical-to-FIB image correlation have been useful workarounds for the navigation-related problems presented by advanced ICs. In this paper we will discuss the advantages of Real-Time Optical Imaging coaxially integrated into the FIB, providing non-invasive navigation to nodes for front side and backside applications.