gebhart/patrepeval huggingface dataset:
Multiple loci of Pseudomonas syringae pv. syringae are involved in pathogenicity on bean: restoration of one lesion-deficient mutant requires two tRNA genes (1997)

A mutational analysis of lesion-forming ability was undertaken in Pseudomonas syringae pv. syringae B728a, causal agent of bacterial brown spot disease of bean. Following a screen of 6,401 Tn5-containing derivatives of B728a on bean pods, 26 strains that did not form disease lesions were identified. Nine of the mutant strains were defective in the ability to elicit the hypersensitive reaction (HR) and were shown to contain Tn5 insertions within the P. syringae pv. syringae hrp region. Ten HR+ mutants were defective in the production of the toxin syringomycin, and a region of the chromosome implicated in the biosynthesis of syringomycin was deleted in a subset of these mutants. The remaining seven lesion-defective mutants retained the ability to produce protease and syringomycin. Marker exchange mutagenesis confirmed that the Tn5 insertion was causal to the mutant phenotype in several lesion-defective, HR+ strains. KW239, a lesion- and syringomycin-deficient mutant, was characterized at the molecular level. Sequence analysis of the chromosomal region flanking the Tn5 within KW239 revealed strong similarities to a number of known Escherichia coli gene products and DNA sequences: the nusA operon, including the complete initiator tRNA(Met) gene, metY; a tRNA(Leu) gene; the tpiA gene product; and the MrsA protein. Removal of sequences containing the two potential tRNA genes prevented restoration of mutant KW239 in trans. The Tn5 insertions within the lesion-deficient strains examined, including KW239, were not closely linked to each other or to the lemA or gacA genes previously identified as involved in lesion formation by P. syringae pv. syringae.
Characterization of Polarity-Based Asphaltene Subfractions (2004)

Structural and compositional characterization of asphaltenes that were extracted from unstable crude oils, stable crude oils, and organic solid deposits was performed to elucidate their similarities and differences. A fractionation technique that divided the asphaltenes into different subfractions, based on polarity, was used to characterize these asphaltene samples. The parameters affecting the stability of these asphaltene subfractions were elucidated. The asphaltenes that were extracted from unstable crude oils and from solid deposits contained substantially greater portions of the higher polar fractions and have a higher polarity, compared to the asphaltenes obtained from crude oils with no asphaltene stability problems in the field. The dielectric constant, solubility, and flocculation experiments showed that these higher-polarity fractions have a greater tendency to aggregate and are more difficult to remediate. These results suggested that the presence of a certain type of asphalteneparticularly, a high-polarity asphaltenehas a key role in the stability of asphaltene in crude oils.
Receptor effects of cetirizine. (1987)

First-generation H1-antagonist antihistamines such as hydroxyzine have a significant ability to cross the blood-brain barrier and cause sedation, which limits their usefulness in the treatment of allergic disorders. Cetirizine, a carboxylated metabolite of hydroxyzine, possesses the parent compound's antihistaminic activity but does not cause sedation. This lack of CNS effects may be due to cetirizine's greater selectivity or potency at H1 receptors in the brain, compared with its effects at the receptors involved in sedation, or it may result from the agent's relative exclusion from the CNS compartment. We compared cetirizine's activity at central H1 sites with the activity of hydroxyzine and terfenadine. We also compared the abilities of cetirizine and three other antihistamines to cross the blood-brain barrier. We found the drugs' potency at H1 receptors in the CNS to be similar to their activities in other tissues. However, their selectivity varied widely. Cetirizine, in fact, failed to bind at any of the receptors investigated except H1 sites, even at concentrations as high as 10 micron. Both hydroxyzine and D-chlorpheniramine crossed the blood-brain barrier in significant amounts. Terfenadine did so to a much lesser extent, and cetirizine passed into the CNS only half as readily as terfenadine. We suggest that cetirizine's reduced incidence of sedative side effects may stem partly from its selectivity for H1 receptors over sites involved in sedation, and partly from its relative exclusion from the CNS.
Analysis of Proteasome-Dependent Proteolysis in Haloferax volcanii Cells, Using Short-Lived Green Fluorescent Proteins (2004)

Proteasomes are energy-dependent proteases that are central to the quality control and regulated turnover of proteins in eukaryotic cells. Dissection of this proteolytic pathway in archaea, however, has been hampered by the lack of substrates that are easily detected in whole cells. In the present study, we developed a convenient reporter system by functional expression of a green fluorescent protein variant with C-terminal fusions in the haloarchaeon Haloferax volcanii. The levels of this reporter protein correlated with whole-cell fluorescence that was readily detected in culture. Accumulation of the reporter protein was dependent on the sequence of the C-terminal amino acid fusion, as well as the presence of an irreversible, proteasome-specific inhibitor (clasto-lactacystin beta-lactone). This inhibitor was highly specific for H. volcanii 20S proteasomes, with a Ki of approximately 40 nM. In contrast, phenylmethanesulfonyl fluoride did not influence the levels of fluorescent reporter protein or inhibit 20S proteasomes. Together, these findings provide a powerful tool for the elucidation of protein substrate recognition motifs and the identification of new genes which may be involved in the proteasome pathway of archaea.
Far-field RF powering system for RFID and implantable devices with monolithically integrated on-chip antenna (2010)

A fully integrated far-field powering system for RFID and implantable devices with monolithically fully integrated on-chip antenna in 0.18μm CMOS is presented. The chip receives power, clock and data wirelessly through RF signal at all the three ISM bands of 915 MHz, 2.45 GHz and 5.8 GHz. Measurements show a minimum input power of -19.41 dBm at 900MHz for chip operation, corresponding to 15.7 meter of operation range with an off-chip 0dB gain antenna. On the other hand, with its on-chip antenna at 5.8 GHz, the chip can be powered-up up to 7.5 cm distance. This is a huge improvement in terms of operation distance compared with other reported similar works with on-chip antenna as well as the off-chip antennas.
Wireless LAN Positioning with Mobile Devices in a Library Environment (2005)

This paper describes the issues involved in performing location tracking in a library environment using existing wireless LAN infrastructure and personal digital assistants. Limitations on computation power and operating systems support are considered in the experiment design and four mainstream location estimation algorithms: center of gravity, triangulation, smallest M-vertex polygon and fingerprinting, are being compared to facilitate location-aware computing.
Selective fading on LOS microwave links: classical and spread-spectrum measurement techniques (1988)

A survey is presented of techniques for measuring selective fading on line-of-sight (LOS) microwave links, particularly over a wide band. Classical pulse methods, including pulse compression, as well as the much used frequency-sweep approach are covered. Methods utilizing both frequency-hopping and direct-sequence spread-spectrum transmissions are also discussed. An analysis of this latter method (used by the US National Bureau of Standards and by the authors) is included and a relationship is established between the true channel transmittance and that estimated by this approach. The advantages and disadvantages of the various schemes are outlined with the aim of assisting an experimenter in the choice of technique in a given experimental context.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Clonal T cell responses in tumor infiltrating lymphocytes from both regressive and progressive regions of primary human malignant melanoma. (1996)

The T cell receptor (TCR) BV variable (V) gene repertoire of tumor infiltrating lymphocytes (TIL) found in progressive and regressive regions of the same primary human melanomas were characterized by reverse transcription coupled polymerase chain reaction (RT-PCR). After surgery, the tumors were divided into different parts which were judged as regressive or progressive regions by visual inspection. Subsequently this diagnosis was confirmed by histology. From a total of four primary melanomas analyzed, 2 were drawn to be HLA-A2+. Only relatively few BV-gene families were expressed at significant levels in each of the samples. Comparison of the BV-expression in regressive versus progressive regions of the same tumor revealed major differences in all cases examined. Direct sequencing of RT-PCR products indicated that highly expressed BV-gene families were of clonal origin in both the regressive and progressive regions. Together, these data strongly suggest the occurrence of clonal T cell responses in both regressive and progressive areas of the same primary tumor. The differences in expression of certain BV-genes may correlate with the functional activity of certain populations of tumor-infiltrating T cells.
Exploitation of a Rapid and Sensitive Assay to Analyse Transactivation of the Human Immunodeficiency Virus type 1 (HIV-1) Long Terminal Repeat (1990)

Transregulation of the promoter within the 5′ long terminal repeat (LTR) of the human immunodeficiency virus (HIV) provirus determines the level of replication of HIV in latently, persistently or acutely infected cells. To measure rapidly the degree of transactivation of the HIV-1 LTR by various cellular and viral effectors, stably transformed cell lines containing integrated copies of the HIV LTR promoter (−122 to +80, relative to the major mRNA cap site) linked to the Escherichia coli lac Z gene were prepared by co-selection for pSV2 neo-mediated G418 resistance. One cell clone, RS 3/7, containing about 40 integrated copies of the recombinant LTR- lacZ gene was analysed further. RS 3/7 cells expressed high levels of β-galactosidase in response to co-transfection with plasmids expressing the HIV-1 transactivator, tat, infection with low multiplicities of herpes simplex virus type 1 (HSV-1), transfection with a plasmid expressing the HSV-1 immediate-early (IE) protein, ICPO, and by incubation with medium containing sodium butyrate. β-galactosidase activity was also induced by incubation of RS 3/7 cells with medium containing full length tat polypeptide. The cysteine analogue, D-penicillamine, previously reported as a potent inhibitor of tat-mediated transactivation (Chandra et al., 1988), was of limited efficacy in RS 3/7 cells transfected with tat-expressing plasmids. This cell line will be of value in identifying additional transactivators of the HIV-1 LTR, and in the selection of inhibitors of such effectors.
Beta-amyloid-based immunotherapy as a treatment of Alzheimer'sdisease (2007)

The pathology of Alzheimer's disease shows a significant correlation between beta-amyloid peptide conformation and the clinical severity of dementia. For many years efforts have been focused on the development of inhibitors of beta-amyloid formation and its related neurotoxic effects. A new concept has been developed which shows that site-directed antibodies may modulate formation of beta-amyloid. The performance of anti-beta-amyloid antibodies in transgenic mice models of Alzheimer's disease showed that they are delivered to the central nervous system, preventing in vivo formation of beta-amyloid. Moreover, those antibodies dissolve beta-amyloid plaques and protect the mice from learning and age-related memory deficits. Experimental active immunization with beta-amyloid (1-42) in humans was stopped in phase II of their clinical trials. However, several new preparations, able to provide antibodies against beta-amyloid by either active or passive routes, have been formulated and have reached clinical testing. The data presented support the hypothesis that beta-amyloid peptide plays a central role in Alzheimer's disease, and antibodies which modulate beta-amyloid conformation may lead to immunotherapy of the disease.
Chemoenzymatic Probes for Detecting and Imaging Fucose-α(1-2)-galactose Glycan Biomarkers (2012)

The disaccharide motif fucose-α(1-2)-galactose (Fucα(1-2)Gal) is involved in many important physiological processes, such as learning and memory, inflammation, asthma, and tumorigenesis. However, the size and structural complexity of Fucα(1-2)Gal-containing glycans have posed a significant challenge to their detection. We report a new chemoenzymatic strategy for the rapid, sensitive detection of Fucα(1-2)Gal glycans. We demonstrate that the approach is highly selective for the Fucα(1-2)Gal motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of the motif on live cells, discriminating malignant from normal cells. This approach represents a new potential strategy for biomarker detection and expands the technologies available for understanding the roles of this important class of carbohydrates in physiology and disease.
RECOVERY OF SPECIFIC ACTIVITY AFTER COMPLETE UNFOLDING AND REDUCTION OF AN ANTIBODY FRAGMENT (1965)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Crystal structure of cholesterol oxidase complexed with a steroid substrate: implications for flavin adenine dinucleotide dependent alcohol oxidases. (1993)

Cholesterol oxidase from Brevibacterium sterolicum is a flavin-dependent enzyme that catalyzes the oxidation and isomerization of 3 beta-hydroxy steroids with a double bond at delta 5-delta 6 of the steroid ring backbone. The crystal structure of the free enzyme in the absence of a steroid substrate has previously been determined. In this paper we report the crystal structure of the complex of cholesterol oxidase with the steroid substrate dehydroisoandrosterone, refined at 1.8-A resolution. The final crystallographic R-value is 15.7% for all reflections between 10.0- and 1.8-A resolution. The steroid is buried within the protein in an internal cavity which, in the free enzyme crystal structure, was occupied by a lattice of water molecules. The conformations of a number of side chains lining the active-site cavity have changed in order to accommodate the steroid substrate. A loop region of the structure between residues 70 and 90 differs significantly between the substrate-free and substrate-bound forms of the enzyme, presumably to facilitate binding of the steroid. The hydroxyl group of the steroid substrate is hydrogen-bonded to both the flavin ring system of the FAD cofactor and a bound water molecule. FAD-dependent cholesterol oxidase shares significant structural homology with another flavoenzyme, glucose oxidase, suggesting that it might also be a member of the glucose-methanol-choline (GMC) oxidoreductase family. Although there is only limited sequence homology, a superposition of these two structures reveals a conserved histidine residue within hydrogen-bonding distance of the active-site water molecule.(ABSTRACT TRUNCATED AT 250 WORDS)
Transgenic sorghum plants via microprojectile bombardment. (1993)

Transgenic sorghum plants have been obtained after microprojectile bombardment of immature zygotic embryos of a drought-resistant sorghum cultivar, P898012. DNA delivery parameters were optimized based on transient expression of R and C1 maize anthocyanin regulatory elements in scutellar cells. The protocol for obtaining transgenic plants consists of the delivery of the bar gene to immature zygotic embryos and the imposition of bialaphos selection pressure at various stages during culture, from induction of somatic embryogenesis to rooting of regenerated plantlets. One in about every 350 embryos produced embryogenic tissues that survived bialaphos treatment; six transformed callus lines were obtained from three of the eight sorghum cultivars used in this research. Transgenic (T0) plants were obtained from cultivar P898012 (two independent transformation events). The presence of the bar and uidA genes in the T0 plants was confirmed by Southern blot analysis of genomic DNA. Phosphinothricin acetyltransferase activity was detected in extracts of the T0 plants. These plants were resistant to local application of the herbicide Ignite/Basta, and the resistance was inherited in T1 plants as a single dominant locus.
Context-dependent Regulation of the GLI Code in Cancer by HEDGEHOG and Non-HEDGEHOG Signals (2010)

A surprisingly large and unrelated number of human tumors depend on sustained HEDGEHOG-GLI (HH-GLI) signaling for growth. This includes cancers of the skin, brain, colon, lungs, prostate, blood and pancreas among others. The basis of such commonality is not obvious. HH-GLI signaling has also been shown to be active in and required for cancer stem cell survival and expansion in different cancer types, and its activity is essential not only for tumor growth but also for recurrence and metastatic growth, two key medical problems. Here we review recent data on the role of HH-GLI signaling in cancer focusing on the role of the GLI code, the regulated combinatorial and cooperative function of repressive and activating forms of all Gli transcription factors, as a signaling nexus that integrates not only HH signals but also those of multiple tumor suppressors and oncogenes. Recent data support the view that the context-dependent regulation of the GLI code by oncogenes and tumor suppressors constitutes a basis for the widespread involvement of GLI1 in human cancers, representing a perversion of its normal role in the control of stem cell lineages during normal development and homeostasis.
1858 Laws of Iowa: a Treatment Narrative (2010)

The article describes the treatment of Laws of Iowa, 7th G.A., 1858 performed by Iowa State University Library’s book conservator. ISU borrowed the volume from the Iowa State Archives to display during ISU’s sesquicentennial celebration. The volume contains the act which founded the college.
Differential expression profiles of apoptosis-affecting genes in HIV-infected cell lines and patient T cells (1999)

Objective: To clarify the molecular mechanisms of HIV-induced apoptosis. Design: The assessment of expression patterns for genes affecting the interrelated cell cycle and apoptosis processes in HIV-1LAI-infected T lymph oblastoid (CEM) cells, as well as CD4 and CD8 cells from HIV-infected individuals and controls. Methods: The kinetics of HIV infection in CEM cells were defined by flow cytometry of green fluorescent protein expression from a reporter vector. Apoptosis of CEM cells was measured by propidium iodine staining and flow cytometry. Gene expression levels were determined by a multiprobe RNase protection assay. Results: The infection and apoptosis of CEM cells were associated with enhanced expression of Bax, Bcl-2, Bcl-XL and caspase 1 (ICE). There was increased expression of Bcl-2 and caspase 1 and decreased expression of cyclin-dependent kinase inhibitor p21CIP1 in CD4 cells of HIV-infected individuals compared with uninfected controls. The CD8 cells of HIV-infected individuals exhibited increased expression of Bcl-2, Bcl-XL, Bax and caspase 1 but, in contrast to the CD4 subset, they showed elevated expression of p21CIP1 and p16INK4a compared with controls. Conclusions: The Bax increase in CEM cells appears to be a direct effect associated with a high frequency of infection and apoptosis, because it was not found in the CD4 cells of patients. In contrast, the increase of Bax in the CD8 cells of patients seems to be an indirect effect. Increases in Bcl-2, Bcl-XL and caspase 1 in HIV-infected CEM cells may be caused by both direct and indirect mechanisms, because they also occurred in CD4 and CD8 cells of HIV-infected individuals. In addition, the low expression of p21CIP1 in the CD4 subset of HIV-infected individuals could promote apoptosis, whereas the high expression of p21CIP1 and p16INK4a in the CD8 subset may lead to a state of anergy, akin to replicative senescence.
Postnatal Undernutrition (1984)

Rats were kept undernourished from birth to 24 days of age. At 17 days of age, the undernourished animals were divided into two groups and then injected with either saline or epidermal growth factor (EGF; 20 micrograms/kg) once a day for 7 days. They were killed 12-14 h after the last injection at which time the animals were 24 days old. During the experimental period the undernourished animals were prevented from weaning. A well-nourished group (weaned) which was injected with saline from 17 to 24 days of age, was also included. Undernutrition by itself significantly decreased body weight and the weight of the oxyntic gland area, antrum, and small intestine. This was also accompanied by a parallel reduction in DNA, RNA, and protein content in the oxyntic gland and small intestine. However, administration of EGF to undernourished rats resulted in a partial reversal of the situation. In undernourished rats, EGF caused significant enhancements in body weight as well as the weight of the gastrointestinal tissues and their protein and nucleic acid content when compared with the saline-treated undernourished controls. Furthermore, the magnitude of stimulation was found to be greater in the oxyntic gland than in the small intestine following EGF administration. The antral or serum gastrin levels were not affected by EGF. In both saline- and EGF-treated undernourished rats, lactase, sucrase, and alkaline phosphatase activities (expressed as total or specific activity) were found to be significantly higher than in the well-nourished animals.(ABSTRACT TRUNCATED AT 250 WORDS)
Angiotensin I‐converting enzyme insertion‐related genotypes and allele are associated with higher susceptibility of endometriosis and leiomyoma (2006)

Endometriosis and leiomyoma display features similar to malignancy, requiring neovascularization to proliferation and growth. Altered vascular-related genes might be related to the development of endometriosis and leiomyoma. Polymorphisms of the angiotensin-converting enzyme (ACE) insertion/deletion (I/D) genes have been linked with some vascular diseases. This study investigates whether ACE I/D gene polymorphisms could be used as markers of susceptibility in endometriosis and leiomyoma. Women were divided into three groups: (1) endometriosis (n = 125); (2) leiomyoma (n = 120); (3) normal controls (n = 128). Genomic DNA was obtained from peripheral leukocyte. ACE I/D gene polymorphisms in intron 16 were amplified by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) Genotypes and allelic frequencies in both groups were compared. We observed the genotype distribution and allele frequency of ACE I/D gene polymorphisms in both groups were significantly different. Proportions of ACE*I homozygote/heterozygote/D homozygote in both groups were: (1) 50.4/24/25.6%; (2) 25/23.33/51.67%; (3) 10.2/29.7/60.1%. Proportions of I/D alleles in each group were: (1) 62.4/37.6%; (2) 36.7/63.3%; (3) 25/75%. We concluded that ACE*I/D gene polymorphisms are associated with endometriosis and leiomyoma susceptibilities. ACE*I-related genotypes and allele are strongly related to the occurrence of endometriosis and moderately related to the occurrence of leiomyoma.