gebhart/patrepeval huggingface dataset:
Physiological role of tumor necrosis factor α in traumatic muscle injury (2002)

degenerative and regenerative roles of tumor necrosis factor alpha (TNF-alpha), a pro-inflammatory cytokine with pleiotropic functions, were investigated by using TNF receptor 1 and 2 double knockout (TNFR-DKO) and TNF-alpha antibody neutralized mice following traumatic freeze injury to the tibialis anterior muscle. In wild-type control mice, TNF-alpha mRNA transcripts and protein increased following injury and gradually returned to control (uninjured) levels by 13 days. A reduction in MyoD mRNA expression occurred in TNF-alpha-deficient mice, although there were no visible differences in MyoD immunostaining or histological characteristics in regenerating muscles. At 5 days post-injury, the reductions in isometric strength in TNFR-DKO and TNF-alpha-depleted mice did not differ from that of wild-type mice but by 13 days after injury, the TNFR-DKO and TNF-alpha-depleted mice exhibited strength deficits twice that of wild-type mice (i.e., 27-31% vs 13%). Muscle injury was also accompanied by increased expression of interleukin-6 (IL-6), but IL-6-deficient mice demonstrated MyoD expression and recovery of isometric strength similar to that of wild-type mice. These data indicate that TNF-alpha is involved in the recovery of muscle function after traumatic muscle injury, and this effect might be associated with modulation of muscle regulatory genes, including MyoD.
Autoreactive IgG memory antibodies in patients with systemic lupus erythematosus arise from nonreactive and polyreactive precursors (2008)

Persistent autoantibody production in patients with systemic lupus erythematosus (SLE) suggests the existence of autoreactive humoral memory, but the frequency of self-reactive memory B cells in SLE has not been determined. Here, we report on the reactivity of 200 monoclonal antibodies from single IgG+ memory B cells of four SLE patients. The overall frequency of polyreactive and HEp-2 self-reactive antibodies in this compartment was similar to controls. We found 15% of IgG memory B cell antibodies highly reactive and specific for SLE-associated extractable nuclear antigens (ENA) Ro52 and La in one patient with serum autoantibody titers of the same specificity but not in the other three patients or healthy individuals. The germ-line forms of the ENA antibodies were non-self-reactive or polyreactive with low binding to Ro52, supporting the idea that somatic mutations contributed to autoantibody specificity and reactivity. Heterogeneity in the frequency of memory B cells expressing SLE-associated autoantibodies suggests that this variable may be important in the outcome of therapies that ablate this compartment.
A Potent and Specific Morpholino Antisense Inhibitor of Hepatitis C Translation in Mice (2003)

Hepatitis C virus (HCV) is an RNA virus infecting one in every 40 people worldwide. Current treatments are ineffective and HCV is the leading cause of liver failure leading to transplantation in the United States and Europe. Translational control of HCV is a prime therapeutic target. We assessed the inhibitory potential of morpholino phosphoramidate antisense oligonucleotides (morpholinos) on HCV translation by codelivering them with reporter plasmids expressing firefly luciferase under the translational control of the HCV internal ribosome entry site (IRES) into the livers of mice. Real-time imaging of HCV IRES luciferase reporter messenger RNA (mRNA) translation in living mice showed that a 20-mer complementary to nucleotides 345-365 of the IRES inhibited translation by greater than 95% for at least 6 days and showed mismatch specificity. No significant nonspecific inhibition of a cap-dependent luciferase or encephalomyocarditis virus (EMCV) IRES luciferase reporter translation was observed. Inhibition by the 20-mer morpholino was dose dependent, with 1 nmol/mouse giving the highest inhibition. In conclusion, morpholino antisense oligonucleotides are potent inhibitors of HCV IRES translation in a preclinical mouse model; morpholinos have potential as molecular therapeutics for treating HCV and other viral infections. The in vivo model described is a broadly applicable, straightforward, and rapid readout for inhibitor efficacy. As such, it will greatly facilitate the development of novel therapeutic strategies for viral hepatitis. Notably, the level of antisense inhibition observed in this in vivo model is similar to the maximal inhibition we have obtained previously with RNA interference in mice.
Label-free imaging, detection, and mass measurement of single viruses by surface plasmon resonance (2010)

We report on label-free imaging, detection, and mass/size measurement of single viral particles in solution by high-resolution surface plasmon resonance microscopy. Diffraction of propagating plasmon waves along a metal surface by the viral particles creates images of the individual particles, which allow us to detect the binding of the viral particles to surfaces functionalized with and without antibodies. We show that the intensity of the particle image is related to the mass of the particle, from which we determine the mass and mass distribution of influenza viral particles with a mass detection limit of approximately 1 ag (or 0.2 fg/mm(2)). This work demonstrates a multiplexed method to measure the masses of individual viral particles and to study the binding activity of the viral particles.
<title>Fiber optic components and systems at Oregon State University</title> (1996)

Research efforts in our department include work on novel GaAs/AlGaAs laser structures and photodetectors which could be used in fiber optic sensor applications. Brief descriptions are given of three such components: a HEMT- compatible, very low threshold diode laser; a high-gain traveling-wave amplifier or high-power, broad linewidth LED; and a MODFET photoconductor. A senior/graduate level course is also taught on guided wave optics. In this lecture/laboratory course, students do design projects on either fiber optic sensors or fiber communication systems. Two examples of student fiber sensor projects will be given: a pressure sensor and an interferometric temperature sensor.
Large Germline Deletions of Mitochondrial Complex II Subunits SDHB and SDHD in Hereditary Paraganglioma (2004)

More than 30% of adrenal pheochromocytomas are hereditary. These neuroendocrine tumors are major components of three inherited cancer syndromes: multiple endocrine neoplasia type 2, von Hippel-Lindau disease (VHL), and pheochromocytoma/paraganglioma syndrome (PC/PGL). Germline mutations in RET; VHL; and SDHB, SDHC, and SDHD are associated with multiple endocrine neoplasia type 2, VHL, and PC/PGL, respectively. The majority (>70%) of hereditary extraadrenal PCs [catecholamine-secreting paragangliomas (PGL)] are accounted for by germline intragenic mutations in SDHB, SDHC, or SDHD. Therefore, a subset of hereditary PGL is not accounted for. Here we report two unrelated hereditary PGL families, one with a germline whole-gene deletion of SDHD (family 4194), the other a partial deletion of SDHB (family BRZ01). Although they were initially designated mutation negative for all of the PC-associated genes after PCR-based analysis, we suspected that a large deletion or rearrangement might be present. Genotyping around the PC-associated genes demonstrated that both families were consistent with linkage with one of these genes. Using fine structure genotyping and semiquantitative duplex PCR analysis, we identified an approximately 96-kb deletion spanning SDHD in family 4194 and an approximately 1-kb deletion involving the 5' end of SDHB in family BRZ01. Thus, including SDHB and SDHD deletion analysis could increase gene-testing sensitivity for PGL patients, which would aid in genetic counseling and management of patients and families.
Isolation of Viral IgY Antibodies from Yolks of Immunized Hens (1980)

Antibodies were isolated from the yolks of hens that were immunized with a variety of plant viruses by the use of polyethylene glycol (PEG). A concentration of 3.5% of the polymer caused the lipids and vitellin to separate, and the IgY was then precipitated with 12% PEG. The titre of the isolated antibody appears to remain at a high level after cessation of the course of immunization. Antibodies derived from the yolks of hens appear to have titres similar to those found in serum of rabbits immunized simultaneously. The observation made by several authors that a high salt concentration enhances fowl serum antibody precipitin titres could not be corroborated with 'yolk' antibodies directed against several plant viruses.
Moonlit Revelations: The Discourse of the End in Gina B. Nahai's 'Moonlight on the Avenue of Faith' (2006)

Young adult fiction often engages with what Derrida terms a discourse of the end, a paradoxical notion that is evident - yet hidden - in such fictions. For Derrida, a discourse of the end is the haunted existence that surrounds extreme events, where the presence of the end is the 'staging for the end of history' that we simultaneously comprehend, yet it is incomprehensible (1974, p.10). One aspect of the discourse of the end is the post-apocalyptic, which Berger describes as: 'Everything that follows the revelation is postapocalyptic' (Berger 1999, p.138). The post-apocalyptic is evident in the novel Moonlight on the Avenue of Faith (Nahai 1999) where the women have sensed the 'doom' that surrounds a daughter in each generation for the last 1000 years. Moonlight is written by an Iranian 'exile' (as Nahai puts it) living in America, and set in a Jewish Iranian culture in the midst of political upheaval and religious persecution. The narrative focuses on the matrilineal heritage of Lili, a teenage girl, and the role that prophecy has played in her family's lives. Particularly, the novel focuses on her mother (Roxanna) and the events leading to, and following, her disappearance when Lili was still a girl. In this paper, I first delve into the discourse of the end, and then comment on how this concept can bring the importance of the interwoven narration, the events of the story, and character constructions together into a post-apocalyptic understanding of the text. Although Moonlight has many potential avenues for exploration, I will be focusing on the role of the revelation by using concepts of hiddenness (Bull 1999), protention/portention (Derrida 1974), and the post-apocalyptic (Berger 1999). This combination of theoretical perspectives offers a new scholarly direction in the analysis of young adult fiction.
Regulation of Sperm Motility in Starfish. I. Initiation of Movement. (starfish sperm/seminal plasma/sperm propulsion/sperm best frequency) (1982)

Starfish seminal plasma has such characteristics as higher concentration of potassium ions, higher osmolality, and lower pH compared with those of sea water. These factors independently inhibited the movement of spermatozoa. Sperm movement was recorded by taking photographs of the swimming paths under a dark field microscope. Spermatozoa either did not move or swam with decreased beat frequency in isolated seminal plasma or in the presence of certain fractions of seminal plasma obtained by gel-filtration or by partitions. In normal sea water (containing calcium ions), a low pH of less than 6 resulted in a decrease in the number (%) of swimming spermatozoa, though the speed of propulsion and the beat frequency was not affected. On the other hand, in a calcium-free sea water, a large proportion of spermatozoa moved in both low and high pH conditions, but in low pH the speed of propulsion was reduced and many spermatozoa (31 %) swam in smaller circles.
PHR1 , a pH-Regulated Gene of Candida albicans , is Required for Morphogenesis (1995)

Candida albicans, like many fungi, exhibits morphological plasticity, a property which may be related to its biological capacity as an opportunistic pathogen of humans. Morphogenesis and alterations in cell shape require integration of many cellular functions and occur in response to environmental signals, most notably pH and temperature in the case of C. albicans. In the course of our studies of differential gene expression associated with dimorphism of C. albicans, we have isolated a gene, designated PHR1, which is regulated in response to the pH of the culture medium. PHR1 expression was repressed at pH values below 5.5 and induced at more alkaline pH. The predicted amino acid sequence of the PHR1 protein was 56% identical to that of the Saccharomyces cerevisiae Ggp1/Gas1 protein, a highly glycosylated cell surface protein attached to the membrane via glycosylphosphatidylinositol. A homozygous null mutant of PHR1 was constructed and found to exhibit a pH-conditional morphological defect. At alkaline pH, the mutant, unlike the parental type, was unable to conduct apical growth of either yeast or hyphal growth forms. This morphological aberration was not associated with defective cytoskeletal polarization or secretion. The results suggest that PHR1 defines a novel function required for apical cell growth and morphogenesis.
Binding of sugar ligands to Ca(2+)-dependent animal lectins. I. Analysis of mannose binding by site-directed mutagenesis and NMR. (1994)

The Ca(2+)-dependent carbohydrate-recognition domain (CRD) of rat serum mannose-binding protein has been subjected to site-directed mutagenesis to determine the importance of individual residues in ligation of mannose and related sugars. The effects of the mutations were assessed by direct binding assays, competition binding studies, partial proteolysis, and NMR analysis of sugar-CRD titrations. As suggested by the crystal structure of the mannose-binding CRD complexed with oligosaccharide ligand, asparagine and glutamic acid residues that interact with hydroxyl groups 3 and 4 of the sugar, as well as with one of the two bound Ca2+, are critical for ligand binding. In addition, the beta-carbon of His189 contributes substantially to the binding affinity, apparently through a van der Waals contact with C-4 of the sugar ligand. van der Waals contacts between the imidazole ring of His189 and the 2 hydroxyl group of mannose, and between Ile207 and C-6 of mannose, observed in the crystal structure, contribute less to stability of the ligand complex. The effects of changes at positions 189 and 207 on the ability of the CRD to distinguish between alpha-and beta-methyl L-fucosides suggest that fucose may bind in an alternative orientation compared to the arrangement originally proposed based on the mannose-CRD complex.
Enhancement of Complement Activation and Cytolysis of Human IgG3 by Deletion of Hinge Exons (1990)

The capacity to induce complement-mediated cell lysis is greatly enhanced by truncating the hinge of IgG3 through exon deletions. This was shown by establishing five new cell lines which secreted chimeric IgG3 molecules with specificity for the hapten 4-hydroxy-3-nitrophenacetyl (NP) and having 47,45,32,15, and 0 amino acid hinge regions (the wild-type IgG3 has 62 amino acids in the hinge). Efficient complement activation and complement-mediated cell lysis did not depend on a long total hinge or on a long 'upper' hinge (the stretch from the beginning of the hinge to the first inter-heavy chain S-S bond). On the contrary, the mutant having a 15 amino acid hinge element was up to 10 times more efficient in complement lysis than the wild type. Thus the complement-activation potential appeared to be down-regulated in the wild type. On the other hand, the mutant lacking the hinge altogether did not activate complement or induce complement-mediated cytolysis. These findings have to be taken into account when antibodies are designed for human therapy.
Dissolution of Xylose Metabolism in Lactococcus lactis (2000)

Xylose metabolism, a variable phenotype in strains of Lactococcus lactis, was studied and evidence was obtained for the accumulation of mutations that inactivate the xyl operon. The xylose metabolism operon (xylRAB) was sequenced from three strains of lactococci. Fragments of 4.2, 4.2, and 5.4 kb that included the xyl locus were sequenced from L. lactis subsp. lactis B-4449 (formerly Lactobacillus xylosus), L. lactis subsp. lactis IO-1, and L. lactis subsp. lactis 210, respectively. The two environmental isolates, L. lactis B-4449 and L. lactis IO-1, produce active xylose isomerases and xylulokinases and can metabolize xylose. L. lactis 210, a dairy starter culture strain, has neither xylose isomerase nor xylulokinase activity and is Xyl(-). Xylose isomerase and xylulokinase activities are induced by xylose and repressed by glucose in the two Xyl(+) strains. Sequence comparisons revealed a number of point mutations in the xylA, xylB, and xylR genes in L. lactis 210, IO-1, and B-4449. None of these mutations, with the exception of a premature stop codon in xylB, are obviously lethal, since they lie outside of regions recognized as critical for activity. Nevertheless, either cumulatively or because of indirect affects on the structures of catalytic sites, these mutations render some strains of L. lactis unable to metabolize xylose.
The hypothesis of a late Würm arctic ice sheet (1980)

Abstract On the basis of geomorphological and geological data as well as radiocarbon dates, the author rebuts the hypothesis of the existence during the Late Pleistocene and Early Holocene of an extensive ice sheet on the Barents and Kara shelves and the adjacent northern lowlands.
Positive magnetic susceptibility in polygonal nanotube tori (2005)

A type of large paramagnetic persistent current is revealed in polygonal carbon nanotube (CNT) tori through calculation of the persistent current-induced magnetic moment using a tight binding model. Polygonal CNT tori, constructed by apices formed at heptagonal and pentagonal defects on the inner and outer fringes, exhibit paramagnetism related to the semimetallic band structures of the periodic CNT junctions, despite the inherent diamagnetism of graphite. This type of persistent current differs from that originating from metallic band structures, and is caused by both magnetic flux in the inner hole (Aharonov-Bohm flux) and the magnetic flux penetrating the graphite plane directly (direct flux). This magnetic moment is close to that calculated based on the Aharonov-Bohm alone for a cross section that includes the region of direct flux.
Light Scattering Measurements of Subcellular Structure Provide Noninvasive Early Detection of Chemotherapy-Induced Apoptosis (2009)

We present a light scattering study using angle-resolved low coherence interferometry (a/LCI) to assess nuclear morphology and subcellular structure within MCF-7 cells at several time points after treatment with chemotherapeutic agents. Although the nuclear diameter and eccentricity are not observed to change, the light scattering signal reveals a change in the organization of subcellular structures that we interpret using fractal dimension (FD). The FD of subcellular structures in cells treated with paclitaxel and doxorubicin is observed to increase significantly compared with that of control cells as early as 1.5 and 3 hours after application, respectively. The FD is then found to decrease slightly at 6 hours postapplication for both agents only to increase again from 12 to 24 hours posttreatment when the observations ceased. The changes in structure appear over two time scales, suggesting that multiple mechanisms are evident in these early apoptotic stages. Indeed, quantitative image analysis of fluorescence micrographs of cells undergoing apoptosis verifies that the FD of 4',6-diamidino-2-phenylindole-stained nuclear structures does not change significantly in cells until 12 hours after treatment, whereas that of MitoTracker stained mitochondria is seen to modulate as early as 3 hours after treatment. In contrast, cells receiving an increased dose of paclitaxel that induced G(2)-M arrest, but not apoptosis, only exhibited the early change in subcellular structure but did not show the later change associated with changes in nuclear substructure. These results suggest that a/LCI may have utility in detecting early apoptotic events for both clinical and basic science applications.
Studies of Gastrointestinal Interactions (1974)

Lagerlöf, H. O., Johansson, C. & Ekelund, K. Studies of gastrointestinal interactions. VI. Intestinal flow, mean transit time, and mixing after composite meals in man. Scand. J. Gastroent. 1974, 9, 261-270.The postprandial flow in the jejunum was investigated with a multiple indicator dilution technique, by which the changes in transit times of the intestinal contents were considered. Two composite meals, which differed in their glucose content, were fed to 7 healthy subjects on different occasions. Despite a pronounced lower gastric emptying rate of the meal containing glucose, the flow volumes in jejunum were similar after the meals, owing to a dilution of the hypertonic meal during intestinal transit. A flow volume of about 500 ml had passed at the investigated jejunal level after 3 hours. Flow rates of about 2 ml per minute persisted after 2 hours. The transit times of the intestinal contents did not differ significantly between the meals, irrespective of the differences in gastric emptying rates. The mean transit time increased during the first hour after ingestion, and undulated thereafter between 20 to 40 minutes in the individual experiments. Based on the assumption of a constant velocity of the indicator particles, the transit of the indicator through the entire intestine could be estimated, as could the distribution of test meal marker in consecutive segments of the intestine.
Left Ventricular Function During Physiological Cardiac Pacing: Relation to Rate, Pacing Mode, and Underlying Myocardial Disease (1987)

The hemodynamic effects of cardiac pacing at different rates and in different modes were studied in 21 patients who were candidates for permanent pacemaker implantation. Nine of these had primary conduction disturbances (PCD), ten had ischemic heart disease (IHD), seven with additional cardiac failure (CHF), and two had hypertrophic cardiomyopathy (HCM). In patients with PCD, atrial (AOO) and AV sequential (DVI) pacing did not change systolic blood pressure and pulse pressure but ventricular (VVI) pacing caused a progressive fall in these measurements, especially as heart rate increased. Ventricular volume and stroke volume (counts) derived from radionuclide ventriculography (RVG) decreased progressively with higher pacing rates, especially during VVI pacing. Cardiac output was maintained during VVI pacing by the increase in heart rate; during AOO and DVI pacing, cardiac output increased. Similar but more marked differences were observed in patients with IHD and CHF and the changes were even greater in the patients with HCM. Left ventricular (LV) ejection fraction changed little with increasing heart rate in PCD but decreased progressively with the onset of ischemia in IHD and CHF. There was no difference in ejection fraction in the different pacing modes. Graphs related to LV contractility (end-systolic pressure-volume relations) showed that AOO pacing produced the highest and VVI pacing produced the lowest curves of myocardial contractility in all patient groups, except that at higher rates the AOO curve shifted down again in patients with IHD and CHF, presumably with the onset of myocardial ischemia. This study showed that physiological pacing produced the best hemodynamic results in all patient groups. Higher pacing rates should be avoided in patients with ischemic heart disease while VVI pacing should not be used in patients with HCM. Blood pressure and RVG studies during temporary pacing are useful in selecting the optimal pacing system in an individual patient when the clinical choice is not clear.