gebhart/patrepeval huggingface dataset:
An update on cytokines in the pathogenesis of insulin-dependent diabetes mellitus (1998)

Correlation studies between cytokines expressed in islets and autoimmune diabetes development in NOD mice and BB rats have demonstrated that beta-cell destructive insulitis is associated with increased expression of proinflammatory cytokines (IL-1, TNF alpha, and IFN alpha) and type 1 cytokines (IFN gamma, TNF beta, IL-2 and IL-12), whereas non-destructive (benign) insulitis is associated with increased expression of type 2 cytokines (IL-4 and IL-10) and the type 3 cytokine (TGF beta). Cytokines (IL-1, TNF alpha, TNF beta and IFN gamma) may be directly cytotoxic to beta-cells by inducing nitric oxide and oxygen free radicals in the beta-cells. In addition, cytokines may sensitize beta-cells to T-cell-mediated cytotoxicity in vivo by upregulating MHC class I expression on the beta-cells (an action of IFN gamma), and inducing Fas (CD95) expression on beta-cells (actions of IL-1, and possibly TNF alpha and IFN gamma). Transgenic expression of cytokines in beta-cells of non-diabetes-prone mice and NOD mice has suggested pathogenic roles for IFN alpha, IFN gamma, IL-2 and IL-10 in insulin-dependent diabetes mellitus (IDDM) development, and protective roles for IL-4, IL-6 and TNF alpha. Systemic administrations of a wide variety of cytokines can prevent IDDM development in NOD mice and/or BB rats; however, a given cytokine may retard or accelerate IDDM development, depending on the dose and frequency of administration, and the age and the diabetes-prone animal model studied (NOD mouse or BB rat). Islet-reactive CD4+ T-cell lines and clones that adoptively transfer IDDM into young NOD mice have a Th1 phenotype (IFN gamma-producing), but other islet-specific Th1 clones that produce TGF beta can adoptively transfer protection against IDDM in NOD mice. NOD mice with targeted deletions of IL-12 and IFN gamma genes still develop IDDM, albeit delayed and slightly less often. In contrast, post-natal deletions of IL-12 and IFN gamma, also IL-1, TNF alpha, IL-2, and IL-6--by systemic administrations of neutralizing antibodies, soluble receptors and receptor antagonists, and receptor-targeted cytotoxic drugs--significantly decrease IDDM incidence in NOD mice and/or BB rats. These cytokine deletion studies have provided the best evidence for pathologic roles for proinflammatory cytokines (IL-1, TNF alpha, and IL-6) and type 1 cytokines (IFN gamma, IL-2 and IL-12) in IDDM development.
Digital Single Event Transient Trends With Technology Node Scaling (2006)

We have measured the single-event-transient (SET) width as a function of cross-section over three CMOS bulk/epitaxial technology nodes (0.25, 0.18 and 0.13 mum) using an identically scaled programmable-delay temporal-latch technique. Both the maximum width of the SET pulse and the cross-section are shown to depend primarily on the supply voltage, with a substantial increase in transient width and cross-section with lower operating potentials
Weed problems in wheat and their control in the Indian subcontinent (1991)

Abstract The wheat crop suffers badly due to heavy weed infestation. Phalaris minor Retz., Chenopodium albam L., Avena fatua L., Melilotus alba Deser., Melilotus indica All., Anagallis arvensis L., Fumaria parviflora Lam. and Convolvulus arvensis L. are common weeds of wheat in the Indian subcontinent. Besides handhoeing and manual weeding, use of herbicides plays a lårge role in weed management. Minimum tillage has some positive effects on soil. Pre‐emergence application of pendimethalin, terbutryn, methabenzthiazuron, bifenox and oxyfluorfen renders excellent weed control in wheat. Isoproturon, methabenzthiazuron, metoxuron, terbutryn, tralkoxydim and fluroxypyr post‐emergence give effective weed kill. For Avena fatua L. control, triallate, difenzoquat and diclofop‐methyl show promising results. Herbicide mixtures give broad‐spectrum weed control. Integrated weed management performs better. Wheat cultivars Sonilika, WH‐147, WH‐2009 and HD‐2329 are tolerant to isoproturon. Moderately susceptible varieties are WH‐157, WH‐291, DWL‐5023 and HD‐2285. All these cultivars show tolerance to pendimethalin. Wheat herbicides now in use do not have residual persistence. In wheat cropping systems, pendimethalin and isoproturon meet the basic requirements
Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes (2000)

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.
Quantum Coin-Flipping-Based Authentication (2009)

Quantum cryptographic key distribution (QKD) is a promising candidate for achieving unconditional security, making the renowned one-time pad encryption technically feasible for building computer networks. However, although well-developed theoretical foundations perfectly ensure protection against eavesdropping, no natural mechanism is yet able to successfully repel an adversary sitting between Alice and Bob, performing QKD with both and re-encrypting each message after heaving read it in plain text. Authentication is hence of crucial importance, and normally applied to all messages that are related to the public discussion part of the QKD protocol. We present an analysis of a scenario, in which authentication is postponed until the end of the QKD protocol. This yields to reduced computational effort, as well as simple and tight bounds on the amount of pre-shared key material. Our solution relies on a combination of quantum key distribution and quantum coin-flipping, which ensures non- controllability of the QKD key. Based on this assumption, we can apply a standard fingerprint comparison for authentication, to guard the protocol against a person-in-the-middle attack.
Reexamining the Effects of Particle Size and Surface Chemistry on the Magnetic Properties of Iron Oxide Nanocrystals: New Insights into Spin Disorder and Proton Relaxivity (2008)

Superparamagnetic iron oxide nanocrystals are a class of nontoxic and biodegradable nanomaterials with broad applications in science, engineering, and medicine, but there is still considerable debate on how crystalline domain size and surface chemistry influence their properties for magnetic resonance imaging (MRI). Here we examine the effects of particle size and surface chemistry by comparing proton relaxivity data for two particle sizes and three surface coatings (6 combinations). These combinations are achieved by using both direct ligand exchange and indirect encapsulation methods to solubilize oleic-acid capped iron oxide nanocrystals. The results indicate that proton relaxivity depends on the particle size, the surface coating thickness and hydrophilicity, and the coordination chemistry of inner capping ligands. Nanocrystals coated with the hydrophilic ligand polyethylenimine (PEI) yield the highest proton relaxivity, whereas nanocrystals capped with oleic acid and amphiphilic polymers exhibit the strongest dependence on particle size. These effects arise from intrinsic surface spin disorders as well as from rapid exchange (diffusion) of water molecules between the bulk phase and the adjacent layer surrounding the particle surface.
Efflux-mediated antimicrobial resistance (2005)

Antibiotic resistance continues to plague antimicrobial chemotherapy of infectious disease. And while true biocide resistance is as yet unrealized, in vitro and in vivo episodes of reduced biocide susceptibility are common and the history of antibiotic resistance should not be ignored in the development and use of biocidal agents. Efflux mechanisms of resistance, both drug specific and multidrug, are important determinants of intrinsic and/or acquired resistance to these antimicrobials, with some accommodating both antibiotics and biocides. This latter raises the spectre (as yet generally unrealized) of biocide selection of multiple antibiotic-resistant organisms. Multidrug efflux mechanisms are broadly conserved in bacteria, are almost invariably chromosome-encoded and their expression in many instances results from mutations in regulatory genes. In contrast, drug-specific efflux mechanisms are generally encoded by plasmids and/or other mobile genetic elements (transposons, integrons) that carry additional resistance genes, and so their ready acquisition is compounded by their association with multidrug resistance. While there is some support for the latter efflux systems arising from efflux determinants of self-protection in antibiotic-producing Streptomyces spp. and, thus, intended as drug exporters, increasingly, chromosomal multidrug efflux determinants, at least in Gram-negative bacteria, appear not to be intended as drug exporters but as exporters with, perhaps, a variety of other roles in bacterial cells. Still, given the clinical significance of multidrug (and drug-specific) exporters, efflux must be considered in formulating strategies/approaches to treating drug-resistant infections, both in the development of new agents, for example, less impacted by efflux and in targeting efflux directly with efflux inhibitors.
Serological and Ecological Characteristics of a Nodule-Dominant Serotype from an Indigenous Soil Population of Rhizobium leguminosarum bv. trifolii (1994)

Although at least 13 antigenically distinct serotypes of Rhizobium leguminosarum bv. trifolii exist in an Abiqua silty clay loam soil, one serotype, AS6, occupies >/=50% of the root nodules formed on field-grown subclover and between 33 and 78% of the nodules formed on five annual clover species grown in the same soil under laboratory conditions. The dominance of subclover nodules by serotype AS6 was reproducible over a 4-year sampling period and throughout the entire 200- by 100-m pasture examined. Serotype AS6 was composed of three antigenically distinct subtypes (AS6-a, AS6-b, and AS6-c). Each subtype contributed about one-third of the AS6 isolates recovered from nodules of field-grown subclover plants and maintained similar population densities in nonrhizosphere and rhizosphere soil. Rhizobia with the AS6 antigenic signature accounted for from 20 to 100% of the soil populations of R. leguminosarum in arable and pasture soils under legumes throughout the state of Oregon. Over a 12-month period, the population densities of the serotype AS6 complex and three minor nodule-occupying serotypes (AG4, AP17, and AS21) were measured in the rhizospheres of field-grown subclover and orchard grass and in nonrhizosphere Abiqua soil. Regardless of season or serotype, the orchard grass rhizosphere effect was minimal, with the ratio between rhizosphere and nonrhizosphere serotype population densities ranging between 2.5 (midsummer) and 10.5 (spring). In contrast, the magnitude of the subclover rhizosphere effect varied seasonally and among serotypes. Between October and December the ratios for all serotypes were similar (12.5 to 25.5). However, in the spring (April and May), the magnitude of the rhizosphere effect varied among the indigenous serotypes (ratios, 10.5 to 442) and for minor nodule-occupying serotypes AS21 (ratio, 442) and AP17 (ratio, 47) was as great as, or even greater than, the magnitude of the rhizosphere effect observed with the AS6 complex (ratio, 65.5).
OSTEOGENIC ACTIVITY OF HUMAN MESENCHYMAL STEM CELLS IN VIVO ON CALCIUM PHOSPHATE CERAMICS (2000)

Purpose of Study: The combination of bone-forming cells and a matrix that supports bone growth, integration and remodeling is an attractive design for a bone graft substitute. Human mesenchymal stem cells (MSCs) on hydroxyapatite/β-tricalcium phosphate (HA/TCP) matrices have been shown to induce bone formation in large, long bone defects. However, full repair and function of the limb was limited due to poor remodeling of the 63/37 HA/TCP matrix. The rate of degradation or resorption of these biphasic calcium phosphate ceramics in vivo can be improved by increasing the amount of the more soluble phase, TCP. In order to design a matrix that supports bone formation and becomes fully replaced by bone, an optimum balance between the more stable phase of HA and the more soluble phase TCP must be achieved. In this study, we investigated the osteogenic activity of human MSCs on various HA/TCP compositions in vivo. Methods: Six calcium phosphate ceramic matrices were examined: 100% Hydroxyapatite (100 HA). 100% β-tricalcium phosphate (100 TCP) and four formulations of HA/TCP (76/24, 63/37, 56/44 and 20/80, ratio of HA/TCP. Biomatlante, France). All compositions had a porosity of 60%-70% and a pore size range of 300 to 600 μm. Bone marrow was collected from two male donors. Human MSCs were isolated, culture expanded and loaded onto matrices at 5 ± 106 cells/mL using existing methods. MSC-loaded matrices and cell-free matrices were implanted subcutaneously in SCID mice. Implants were harvested at 6 and 12 weeks and were processed for decalcified paraffin histology. Results: More bone formed within the pores of MSC-loaded 20/80 HA/TCP matrices than all other matrices at 6 weeks. By 12 weeks, both MSC-loaded 56/44 and 20/80 HA/TCP matrices demonstrated the greatest amount of bone. The least amount of bone formed within the pores of 100 TCP and 100 HA throughout the study. These results demonstrate the potential of using faster resorbing ceramics. 56/44 and 20/80 HA/TCP, in combination with MSCs for bone regeneration Future studies will test these results in more clinically relevant models.
Rap1GAP2 is a new GTPase-activating protein of Rap1 expressed in human platelets (2005)

The Ras-like guanine-nucleotide-binding protein Rap1 controls integrin alpha(IIb)beta3 activity and platelet aggregation. Recently, we have found that Rap1 activation can be blocked by the nitric oxide/cyclic guanosine monophosphate (NO/cGMP) signaling pathway by type 1 cGMP-dependent protein kinase (cGKI). In search of possible targets of NO/cGMP/cGKI, we studied the expression of Rap1-specific GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs) in platelets. We could detect mRNAs for a new protein most closely related to Rap1GAP and for postsynaptic density-95 discs-large and zona occludens protein 1 (PDZ)-GEF1 and CalDAG-GEFs I and III. Using 5'-rapid amplification of cDNA ends (RACE), we isolated the complete cDNA of the new GAP encoding a 715-amino acid protein, which we have termed Rap1GAP2. Rap1GAP2 is expressed in at least 3 splice variants, 2 of which are detectable in platelets. Endogenous Rap1GAP2 protein partially colocalizes with Rap1 in human platelets. In transfected cells, we show that Rap1GAP2 exhibits strong GTPase-stimulating activity toward Rap1. Rap1GAP2 is highly phosphorylated, and we have identified cGKI as a Rap1GAP2 kinase. cGKI phosphorylates Rap1GAP2 exclusively on serine 7, a residue present only in the platelet splice variants of Rap1GAP2. Phosphorylation of Rap1GAP2 by cGKI might mediate inhibitory effects of NO/cGMP on Rap1. Rap1GAP2 is the first GTPase-activating protein of Rap1 found in platelets and is likely to have an important regulatory role in platelet aggregation.
Brain Natriuretic Peptide and Cerebral Vasospasm in Subarachnoid Hemorrhage (2000)

In conclusion, our results show that BNP plasma levels are elevated shortly after SAH, although they increase markedly during the first week in patients with symptomatic CVS. The present findings suggest that secretion of BNP secretion after spontaneous SAH may exacerbate blood flow reduction due to arterial vasospasm.
Advances in Livestock Nuclear Transfer (2000)

Cloning and transgenic animal production have been greatly enhanced by the development of nuclear transfer technology. In the past, genetic modification in domestic animals was not tightly controlled. With the nuclear transfer technology one can now create some domestic animals with specific genetic modifications. An ever-expanding variety of cell types have been successfully used as donors to create the clones. Both cell fusion and microinjection are successfully being used to create these animals. However, it is still not clear which stage(s) of the cell cycle for donor and recipient cells yield the greatest degree of development. While for the most part gene expression is reprogrammed in nuclear transfer embryos, all structural changes may not be corrected as evidenced by the length of the telomeres in sheep resulting from nuclear transfer. Even after these animals are created the question of "are they really clones?" arises due to mitochondrial inheritance from the donor cell versus the recipient oocyte. This review discusses these issues as they relate to livestock.
Development and Characterization of a High-Throughput System for Assessing Cell-Surface Receptor−Ligand Engagement (2005)

A nonfouling interfacial interpenetrating polymer network (IPN) of poly(acrylamide-co-ethylene glycol/acrylic acid) [p(AAm-co-EG/AAc)] was grafted to polystyrene for use as a novel platform for the development of high-throughput assays for screening of specific bimolecular interactions (i.e., receptor-ligand engagement). For the development of the IPN, a water-soluble hydrogen-abstracting photoinitiator was investigated: (4-benzoylbenzyl)trimethylammonium chloride. IPN-modified polystyrene surfaces were characterized using XPS, contact angle goniometry, and protein adsorption analysis. These IPN surfaces minimized fibrinogen adsorption compared to tissue culture polystyrene (>96% reduction), prevented mammalian cell adhesion, and served as nonfouling surfaces to graft biological ligands. For bimolecular interaction studies, a model peptide ligand from bone sialoprotein (Ac-CGGNGEPRGDTYRAY-NH(2)) was grafted to p(AAm-co-EG/AAc) via a 3400 M(w) linear pEG spacer. Ligand density measurements, cell culture, and a centrifugal adhesion assay were used to study cell adhesion to peptide-modified IPNs (i.e., receptor-ligand engagement). Ligand density (Gamma) was controllable from approximately 1 to 20 pmol/cm(2) by modulating the peptide input concentration (0.02-20 microM). Cell adhesion was directly dependent on the ligand density. This technology creates a powerful high-throughput system to simultaneously probe a myriad of cell-surface receptor-ligand interactions.
Cloning and characterization of a sixth adenylyl cyclase isoform: types V and VI constitute a subgroup within the mammalian adenylyl cyclase family. (1992)

A sixth member of the mammalian adenylyl cyclase family has been isolated from a canine cardiac cDNA library. This isoform is more highly homologous to type V than to the other adenylyl cyclase types; sequence similarity is apparent even in the transmembrane regions where the greatest divergence among the types exists. Type VI mRNA expression is most abundant in heart and brain; however, unlike type V, a low level of expression is also observed in a variety of other tissues examined. Type VI adenylyl cyclase can be stimulated by NaF, guanosine 5'-[gamma-thio]triphosphate, and forskolin but not by Ca2+/calmodulin, whereas it is inhibited by adenosine and its analogues. Comparison of both their structural and biochemical properties suggests that types V and VI constitute a distinct subgroup of the mammalian adenylyl cyclase family.
Construction of a bovine yeast artificial chromosome (YAC) library (1998)

We have constructed a bovine yeast artificial chromosome (YAC) library to provide a common resource for bovine genome research. We used leukocytes of a Japanese black bull (Bos taurus) as the DNA source, AB1380 for the yeast host, and pYAC4 for the vector. The library consists of 24,576 clones arranged in 256 96-well microtiter plates. An average insert size estimated from the analysis of 251 randomly selected clones was 480 kb. The rate of chimeric YACs evaluated by fluorescence in situ hybridization (FISH) analysis of 44 randomly selected clones was 36.4%. To estimate the number of genome equivalents, PCR-based screening was performed with 48 primer pairs and isolated 3.2 clones on average. In order to provide broad access for the scientific community, this library has been incorporated into the Reference Library system which provides high density filters for colony hybridization screening and a common database of the library.
Calcium Cyanamide and other Artificial Fertilisers in the Treatment of Soil infected with Heterodera schachtii (1935)

During the course of experimental work on the factors governing the escape of larvae from the cysts of Heterodera schachtii , a preliminary series of experiments was carried out to determine whether the admixture of artificial fertilisers with infected soil modified in any way the rate of hatching of the larvae. It was thought possible, firstly, that some form of fertiliser might have a lethal effect on the cyst contents or on the larvae during their passage through the soil before they succeeded in entering the roots of the host; secondly, that the fertiliser or its break-down products in soil might neutralise or retard the action of potato-root excretion, which normally stimulates the larvae to escape from the cysts and attracts them towards the roots of the plant; or thirdly, that the larvae might be stimulated to hatch to some extent even in the absence of the host-plant.
Predator–prey interactions: olfactory adaptations of generalist and specialist predators (1999)

Summary 1 Olfactory responses of the Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae), a generalist predator, Podisus maculiventris (Say) (Hemiptera, Heteroptera: Pentatomidae) ( Pm ), and a specialist predator, Perillus bioculatus (F.) (Hemiptera, Heteroptera: Pentatomidae) ( Pb ) were investigated. Volatiles tested included 20 compounds emitted by undamaged potato plants ( Solanum tuberosum ), plants that had been artificially damaged, or plants damaged by feeding by CPB larvae. 2 Coupled gas chromatography/electroantennogram detector (GC/EAD) recordings revealed five compounds for which reliable responses were recorded from CPB antennae: ( E )‐2‐hexen‐1‐ol, ( Z )‐3‐hexen‐1‐ol, ( ± )‐linalool, nonanal, methyl salicylate, and indole. Both Pm and Pb responded selectively to the same compounds as the CPB with exceptions: (1) ( Z )‐3‐hexenyl butyrate elicited reliable responses for both Pm and Pb, and (2) ( E )‐2‐hexen‐1‐ol and ( Z )‐3‐hexen‐1‐ol were inactive for Pm and Pb under these conditions. Dose–response curves showed that CPB was at least 100 times more sensitive to ( E )‐2‐hexen‐1‐ol than were the predators. Both predators were more sensitive to each of the other compounds than were CPB. Both CPB and Pm were attracted to a five component blend comprising ( E )‐2‐hexen‐1‐ol, ( Z )‐3‐hexen‐1‐ol, ( ± )‐linalool, nonanal and methyl salicylate. However, attraction of CPB to the blend occurred only with lower doses of ( E )‐2‐hexen‐1‐ol and ( Z )‐3‐hexen‐1‐ol. 3 These results show that the herbivore (CPB) has olfactory receptors which are more sensitive to constitutive host plant volatiles, e.g. green leaf volatiles, while both generalist ( Pm ) and specialist ( Pb ) predators are more sensitive to systemic volatiles produced in response to prey feeding. Keywords Colorado potato beetle, constitutive compounds, host plant, induced compounds, olfaction, Perillus bioculatus , Podisus maculiventris , predator, prey, tritrophic.