gebhart/patrepeval huggingface dataset:
Alveolar neutrophils in endotoxin-induced and bacteria-induced acute lung injury in rats (1997)

Polymorphonuclear neutrophils (PMNs) are thought to play a major role in the pathogenesis of adult respiratory distress syndrome. Because the alveolar epithelium is a decisive factor in alveolo-capillary wall permeability, a toxic effect of emigrated PMNs in alveolar spaces is conceivable. We evaluated alveolar PMN function in two rat models of acute lung injury induced by alveolar instillation of endotoxin [lipopolysaccharide (LPS)] or live Pseudomonas aeruginosa (PYO). Alveolar PMNs were isolated from bronchoalveolar lavage fluid 4 and 24 h after the challenge. Hypoxemia was assessed based on the ratio arterial partial pressure of O2 (PaO2)/fraction of inspired O2 (FIO2) during mechanical ventilation. The severity of lung injury in the two models was clearly different, since PaO2/FIO2 were approximately 400 mmHg in PYO- and LPS-induced injuries, respectively. Both contrast, alveolar neutrophil influx, unstimulated oxygen metabolite production, and proteinase (elastase, gelatinase B) secretions of ex vivo alveolar PMNs were not larger in the PYO model. Thus the difference in severity was not associated with variations in alveolar neutrophil recruitment or activation. Moreover, gelatinase and leukocyte elastase activities were absent in bronchoalveolar fluid, indicating effective antiproteinase defense in alveolar spaces. We conclude that alveolar neutrophils are not sufficient to create severe respiratory failure.
Mandatory Leaf Node Prediction in Hierarchical Multilabel Classification (2014)

In hierarchical classification, the output labels reside on a tree- or directed acyclic graph (DAG)-structured hierarchy. On testing, the prediction paths of a given test example may be required to end at leaf nodes of the label hierarchy. This is called mandatory leaf node prediction (MLNP) and is particularly useful, when the leaf nodes have much stronger semantic meaning than the internal nodes. However, while there have been a lot of MLNP methods in hierarchical multiclass classification, performing MLNP in hierarchical multilabel classification is difficult. In this paper, we propose novel MLNP algorithms that consider the global label hierarchy structure. We show that the joint posterior probability over all the node labels can be efficiently maximized by dynamic programming for label trees, or greedy algorithm for label DAGs. In addition, both algorithms can be further extended for the minimization of the expected symmetric loss. Experiments are performed on real-world MLNP data sets with label trees and label DAGs. The proposed method consistently outperforms other hierarchical and flat multilabel classification methods.
DNA helicase associated with DNA polymerase .alpha.: Isolation by a modified immunoaffinity chromatography (1993)

We have developed a novel immunoaffinity method for isolating a DNA polymerase alpha-associated DNA helicase from the yeast Saccharomyces cerevisiae. Earlier we have reported the characterization of a DNA helicase activity associated with the multiprotein DNA polymerase alpha complex from yeast [Biswas, E. E., Ewing, C. M., & Biswas, S. B. (1993) Biochemistry 32, 3030-3027]. We report here the isolation of the DNA helicase from the DNA polymerase alpha (pol alpha) complex bound to an anti-pol alpha immunoaffinity matrix. The DNA helicase activity eluted at approximately 0.35 M NaCl concentration. The eluted ATPase/helicase peak was further purified by size-exclusion high-performance liquid chromatography (HPLC). At low ionic strength (50 mM NaCl), it remained associated with other proteins and eluted as a large polypeptide complex. At high ionic strength (500 mM NaCl), the helicase dissociated, and the eluted ATPase/helicase fraction contained 90-, 60-, and 50-kDa polypeptides. Photoaffinity cross-linking of helicase with ATP during the isolation process demonstrated a 90-kDa polypeptide to be the likely ATP binding component of the helicase protein. The DNA helicase has single-stranded DNA (ssDNA)-stimulated ATPase and dATPase activities. The ATPase activity was stimulated by yeast replication protein A (RPA). The DNA helicase activity was stimulated by Escherichia coli ssDNA binding protein and RPA. The DNA helicase migrated on a DNA template in the 5'-->3' direction which is also the overall direction of migration of pol alpha on the lagging strand of the replication fork.(ABSTRACT TRUNCATED AT 250 WORDS)
Degradation of plant pathogenic fungi by <i>Trichoderma harzianum</i> (1982)

Trichoderma harzianum excreted β-1, 3-glucanase and chitinase into the medium when grown on laminarin and chitin, respectively, or on cell walls of the pathogen Sclerotium rolfsii, as sole carbon source. Trichoderma harzianum also showed high activity of both enzymes when grown on homogenized S. rolfsii sclerotia. Glucanase activity increased by 67% when the fungus was grown on a mixture of laminarin and glucose (3:1, v/v). Similarly, high lytic activity was detected in wheat bran culture of the fungus and in soil inoculated with this culture. Protease and lipase activity were detected in the medium when the antagonist attacked mycelium of S. rolfsii.Isolates of T. harzianum were found to differ in the levels of hydrolytic enzymes produced when mycelium of S. rolfsii, Rhizoctonia solani, and Pythium aphanidermatum in soil was attacked. This phenomenon was correlated with the ability of each of the Trichoderma isolates to control the respective soilborne pathogens.
Fields of Ozone Applications (2009)

The powerful oxidative action of ozone provides basis for development of novel or improved technologies which are widely used in ecology and industry. Special attention is paid to purification of waste gases, water, and soils. The disinfection and cleaning of drinking and process water are considered in detail. Applications of ozone in chemical, pharmaceutical and perfume industries, cosmetics, cellulose, paper and sugar industries, flotation, microelectronics, and many others are also examined in the review
Actin Filament Stress Fibers in Vascular Endothelial Cells in Vivo (1983)

Fluorescence microscopy with 7-nitrobenz-2-oxa-3-diazole phallacidin was used to survey vertebrate tissues for actin filament bundles comparable to the stress fibers of cultured cells. Such bundles were found only in vascular endothelial cells. Like the stress fibers of cultured cells, these actin filament bundles were stained in a punctate pattern by fluorescent antibodies to both alpha-actinin and myosin. The stress fibers were oriented parallel to the direction of blood flow and were prominent in endothelial cells from regions exposed to high-velocity flow, such as the left ventricle, aortic valve, and aorta. Actin bundles may help the endothelial cell to withstand hemodynamic stress.
Sexual Orientation: Testing the Universality of International Human Rights Law (2004)

Until recently, the United States consistently opposed cultural relativism while embracing universalism in international human rights law.Relativists argue that understandings of right and wrong vary along cultural lines, and thus, definitions of human rights should vary accordingly.'Islamic states have argued for a Muslim conception of women's rights; 2 China has defended its treatment of political dissidents by invoking Confucian norms; 3 and numerous African states have sought to justify female circumcision' by upholding the practice's cultural sanctity.'Such assertions of cultural relativism have routinely elicited American criticism.At the 1993 World Conference on Human Rights, Secretary of State Warren Christopher proclaimed: "We cannot let cultural relativism become the last refuge of repression. 6Since then, Christopher's words have echoed in the United States's diplomatic relations and treaty negotiations.Thanks in part to American lobbying, universalism now underpins major human rights instruments such as the Universal Declaration of Human Rights (UDHR); the In-
HAVi Example By Example : Java Programming for Home Entertainment Devices (2001)

From the Book:
PrefaceWhat Is HAVi?
HAViHome Audio-Video Interoperabilityis a system architecture for the development of home network applications. The HAVi architecture is specified by an organization of consumer electronics and software companies. For HAVi, a home network is a group of connected AV (audio-video) devices within a home. This is sometimes called a home entertainment network or an AV cluster. Devices compliant with the HAVi specification implement a set of system services that allow them to interoperate over IEEE 1394 connections. IEEE 1394, also known as FireWire and i.LINK, is a high-speed serial bus used to connect devices into tree-shaped networks. HAVi specifies services to locate, query, control, and extend IEEE 1394 audio-video devices.
Who This Book Is For
This book is intended primarily for developers with an interest in home entertainment devices and services. Others who may find the book of interest include those studying networking and distributed systems, and designers of audio-video products. Basic knowledge of Java is useful, but some familiarity with programming is all that is needed to follow many of the examples.
Programming Aids
The HAVi by Example Web site is located at www.vividlogic.com/hbx. At this Web site you can find:

JavaDoc for HJA 1.1
source code examples, and
HAVi 1.1 SDK (Software Developers Kit).


To run the SDK you will need a Pentium-class PC with Linux 2.4.1 or later (this version of Linux has IEEE 1394 support), a JVM, and JDK 1.1.8 or later. If you want to control HAVi devices, you will need anIEEE 1394 port on your PC. See www.vividlogic.com/hbx/releaseNotes.txt for a list of supported IEEE 1394 cards.
Identification of key peptide-specific CD4+ T cell responses to human cytomegalovirus: implications for tracking antiviral populations (2006)

Human cytomegalovirus (CMV) infection is normally controlled effectively by the immune response, including CD4(+) T cells. Large numbers of these cells are present in healthy seropositive individuals but their loss in immunosuppression leads to reactivation and disease. Tracking such responses in vivo is hampered by poor definition of their peptide targets. In this study, we defined the key targets of the peptide-specific CD4(+) T cell responses to the CMV pp65 protein using functional assays and a peptide library. Despite a good deal of interindividual variation in the numbers of peptides recognized, responses to CMV pp65 were strikingly targeted at three key epitopes. A response to one or more of these three key peptides was seen in all individuals tested (P < 0.0001) and this finding was tested and reproduced in a second independent population. The most common response identified was that to a DR53 restricted epitope, aa281-295. HLA-DR1 restricted CMV pp65-specific populations, although reproducibly detected, were of low frequency ex vivo. However, it was possible to detect and phenotype these cells using an enrichment protocol and this revealed them to have 'effector memory' status although, in contrast to CD8(+) T cell responses, these were CD45RA(-). These data suggest that CD4(+) T cell responses to CMV can be identified reliably using a pool of just three peptides. This simple approach will provide a robust and reliable as well as economic method for tracking peptide specific populations in health and disease.
Physical Properties of Polypeptide Electrospun Nanofiber Cell Culture Scaffolds on a Wettable Substrate (2012)

Physical properties of poly(L-ornithine) (PLO), a polycation, poly(L-glutamic acid4-co-L-tyrosine) (PLEY), a polyanion, and electrospun fibers made of these polymers have been determined and compared. The polymers adopted random coil-like conformations in aqueous feedstocks at neutral pH and in dehydrated cast films and fibers on glass, and the fibers comprised numerous counterions, according to spectral analysis. Adsorption of model proteins and serum proteins onto hydrated and crosslinked fibers depended on the electrical charge of the proteins and the fibers. The surface charge density of the fibers will be comparable to, but less than, the charge density on the outer leaflet of the plasma membrane of usual eukaryotic cells. The present analysis thus advances understanding of cell behavior on electrospun fiber scaffolds, a topic of considerable current interest.
IMMUNOLOGICAL RELATIONSHIPS OF A FILTERABLE AGENT CAUSING A LEUKEMIA IN ADULT MICE (1959)

The antigenic character of a filterable agent which induces leukemia in adult mice has been investigated. Mice and rabbits injected with filtrate yielded sera which specifically neutralized infectivity of the agent. Normal sera, sera from mice with other neoplasms-including leukemias from which no causative agent has as yet been obtained,-and sera from leukemic human beings contained no such neutralizing antibody. A formalinized vaccine prepared from filtrates of leukemic spleens induced a significant degree of immunity against the agent, approximately 80 per cent of the vaccinated mice being immune on challenge with it.
Microstructures and mechanical properties of Ti5553 alloy processed by high-pressure torsion (2014)

In the present research, the effects of high-pressure torsion (HPT) processing on the microstructure and mechanical properties of Ti-5Al-5Mo-5V-3Cr (Ti5553) alloy were studied. HPT processing produced a white etching layer (WEL) in the middle section of the cross-section and numerous shear bands in the surface region of the cross-section. And the thickness of the WEL increased with increasing the HPT revolutions. TEM observation of the WEL revealed an ultrafine-grained structure with high degree of lattice distortions. The mechanical properties measurements showed that the hardness and ultimate tensile strength increased by HPT processing, accompanied with a decrease in the elongation to failure. It is considered that the mechanical properties of HPT processed Ti5553 alloy are mostly dominated by the shear banded region and the WEL where have the finest grain size and high density of dislocations.
Amniotic Fluid <scp>MMP</scp>‐9 and Neurotrophins in Autism Spectrum Disorders: An Exploratory Study (2012)

Evidence suggests that some developmental disorders, such as autism spectrum disorders (ASDs), are caused by errors in brain plasticity. Given the important role of matrix metalloproteinases (MMPs) and neurotrophins (NTs) in neuroplasticity, amniotic fluid samples for 331 ASD cases and 698 frequency-matched controls were analyzed for levels of MMP-9, brain-derived neurotrophic factor, NT-4 and transforming growth factor-β utilizing a Danish historic birth cohort and Danish nationwide health registers. Laboratory measurements were performed using an in-house multiplex sandwich immunoassay Luminex xMAP method, and measurements were analyzed using tobit and logistic regression. Results showed elevated levels of MMP-9 in ASD cases compared with controls (crude and adjusted tobit regression P-values: 0.01 and 0.06). Our results highlight the importance of exploring the biologic impact of MMP-9 and potential therapeutic roles of its inhibitors in ASD and may indicate that neuroplastic impairments in ASD may present during pregnancy.
The proteomic profile of hair damage (2012)

Applying proteomics to the study of congenital and acquired hair shaft disorders can deliver new insights into hair damage and novel strategies to strengthen hair.
A breathtaking feat (2011)

Salmonella is a common cause of food poisoning. However, after ingestion the pathogen has to compete with resident microbes that already occupy the intestinal lumen (microbiota), which poses a challenge for Salmonella to successfully colonize this niche. Recent data show that Salmonella elicits help from the host immune response to beat the competition. After arriving in the intestine, Salmonella elicits acute intestinal inflammation. The respiratory burst of neutrophils that transmigrate into the intestinal lumen during inflammation oxidizes endogenous sulfur compounds to generate a respiratory electron acceptor, tetrathionate. As a result, Salmonella can use tetrathionate respiration to outgrow the fermenting microbiota in the anaerobic environment of the gut, which promotes transmission of the pathogen. This principle might be used by other gut microbes and contribute to changes in the microbiota composition observed during inflammation.
Cyclophosphamide Allows for <i>In vivo</i> Dose Reduction of a Potent Oncolytic Virus (2005)

The success of cancer virotherapy depends on its efficacy versus toxicity profile in human clinical trials. Progress towards clinical trials can be hampered by the relatively elevated doses of oncolytic viruses administered in animal models to achieve an anticancer effect and by the even higher doses required in humans to approximate an animal bioequivalent dose. Such elevated doses of injected viral proteins may also lead to undesirable toxicities and are also very difficult to produce in a biotechnological setting. We report that a relatively potent herpes simplex virus type 1 oncolytic virus (rQNestin34.5) produces 45% survivors at a dose of 3 x 10(4) plaque-forming units (pfu) in a 9-day-old mouse model of human glioma. Unlike our previous findings with less potent oncolytic viruses, though, the preadministration of cyclophosphamide did not enhance this survival or affect oncolytic virus tumor distribution and tumor volume. However, when oncolytic virus doses were reduced (3 x 10(3) and 3 x 10(2) pfu), cyclophosphamide significantly enhanced both animal survival and oncolytic virus tumor distribution and also reduced tumor volumes. These findings thus show that cyclophosphamide allows for dose reduction of doses of a relatively potent oncolytic virus, a finding with implications for the development of clinical trials.
Phase estimates from slope-type wave-front sensors (1978)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Robert J. Noll, "Phase estimates from slope-type wave-front sensors," J. Opt. Soc. Am. 68, 139-140 (1978) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Resistance Determinants and Mobile Genetic Elements of an NDM-1-Encoding Klebsiella pneumoniae Strain (2014)

Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. Some β-lactamases are active on a broad spectrum of β-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-β-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight β-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses the two-step transposition mechanism of IS3. Robust genome-based phylogeny showed that a unified Klebsiella cluster contains Enterobacter aerogenes and Raoultella, suggesting the latter genus should be abandoned.
TGFBR3, a potential negative regulator of TGF‐β signaling, protects cardiac fibroblasts from hypoxia‐induced apoptosis (2010)

A lot of evidence indicates that cardiac fibroblasts are essential for maintaining the structure and function of heart. The present study examined whether TGFBR3 (transforming growth factor type III receptor, also known as betaglycan) could prevent hypoxia-induced injury in neonatal mice cardiac fibroblasts, if so, its possible molecular targets. MTT, electron microscopy and TUNEL assay were used to identify cell viability and apoptosis in neonatal mice cardiac fibroblasts. Results showed that hypoxia for 24 h markedly reduce cell viability by 49.8 ± 8.9%, largely via apoptosis. However, hypoxia-induced apoptosis in cardiac fibroblasts were almost completely prevented by overexpression of TGFBR3. In the present study, hypoxia also induced TGF-β1, p-Smad2/3 expression, TGFBR1-TGFBR2 complex formation and collagen production in cardiac fibroblasts, which were attenuated substantially by TGFBR3 overexpression. TGFBR3 also reversed Bax up-regulation, Bcl-2 down-regulation and Caspase-3 activation induced by hypoxia in cardiac fibroblasts. Hypoxia or TGF-β1 itself triggered an increase of [Ca(2+) ](i) in cardiac fibroblasts, which were both inhibited by TGFBR3 overexpression. Taken together, our results indicate that TGFBR3 may act as a protective factor in apoptotic process of cardiac fibroblasts by negative regulation of TGF-β signaling and represent a potential therapeutic target for heart remodeling after hypoxia injury.
Unraveling the plant microbiome: looking back and future perspectives (2014)

Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant's second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.