gebhart/patrepeval huggingface dataset:
Serum Antibodies Reactive with <i>Saccharomyces cerevisiae</i> in Inflammatory Bowel Disease: Is IgA Antibody a Marker for Crohn’s Disease? (1990)

Sera from patients with Crohn's disease (CD) and ulcerative colitis (UC) have been evaluated for antibodies reactive with Saccharomyces cerevisiae (anti-Sacc antibodies) using an enzyme-linked immunoassay (ELISA). IgG anti-Sacc antibodies were detected in 63% (25/40) of CD patients, compared with 15% (4/27) of UC patients (p less than 0.001) and 8% (5/60) healthy adult controls (p less than 0.001). Furthermore, the prevalence of detectable IgG anti-Sacc antibodies in adult patients with coeliac disease, dermatitis herpetiformis, irritable bowel syndrome or atopic eczema was not significantly different to controls. In comparison, the prevalence of detectable IgG anti-Escherichia coli antibodies was not significantly different between CD (75%) or UC (79%) patients. More particularly, elevated levels of serum IgA anti-Sacc antibodies were detected in 17/40 CD patients, but in none of the 27 UC patients. These data confirm that serum antibodies reactive with S. cerevisiae are strongly associated with CD and further show that serum IgA anti-Sacc antibodies may be specific for this disorder.
Neurotoxocarosis (2007)

Infection of humans with embryonated eggs of Toxocara canis (larva migrans) remains asymptomatic, or results in covert or common toxocarosis, visceral larva migrans syndrome, or ophthalmologic and neurologic impairment. Though neurological manifestations of Toxocara canis larvae are rare, toxocarosis remains an important differential diagnosis of various neurological disorders. Manifestations of the central nervous system are dementia, meningo-encephalitis, myelitis, cerebral vasculitis, epilepsy, or optic neuritis. Manifestations of the peripheral nervous system comprise radiculitis, affection of cranial nerves, or musculo-skeletal involvement. If toxocarosis is neglected, ignored, or refused as a differential of these abnormalities, it may be easily overlooked for years. Early recognition and treatment of the infection is, however, of paramount importance since it reduces morbidity and mortality and the risk of secondary superinfection. Like the visceral manifestations, neurological manifestations of toxocarosis are treated by benzimidazole components, most frequently albendazole, corticosteroids, or diethylcarbamazine. If detected and treated early, the prognosis of neurological manifestations of toxocarosis is favourable.
Synergistic Effect of Adrenal Steroids and Angiotensin II on Plasminogen Activator Inhibitor-1 Production1 (2000)

Recent data suggest an interaction between the renin-angiotensin-aldosterone system and fibrinolysis. Although previous work has focused on the effect of angiotensin II (Ang II) on plasminogen activator inhibitor (PAI-1) expression, the present study tests the hypothesis that aldosterone contributes to the regulation of PAI-1 expression. To test this hypothesis in vitro, luciferase reporter constructs containing the human PAI-1 promoter were transfected into rat aortic smooth muscle cells. Exposure of the cells to 100 nmol/L Ang II resulted in a 3-fold increase in luciferase activity. Neither 1 micromol/L dexamethasone nor 1 micromol/L aldosterone alone increased PAI-1 expression. However, both dexamethasone and aldosterone enhanced the effect of Ang II in a dose-dependent manner. This effect was abolished by mutation in the region of a putative glucocorticoid-responsive element. A similar interactive effect of Ang II and aldosterone was observed in cultured human umbilical vein endothelial cells. The time course of the effect of aldosterone on Ang II-induced PAI-1 expression was consistent with a classical mineralocorticoid receptor mechanism, and the effect of aldosterone on PAI-1 synthesis was attenuated by spironolactone. To determine whether aldosterone affected PAI-1 expression in vivo, we measured local venous PAI-1 antigen concentrations in six patients with primary hyperaldosteronism undergoing selective adrenal vein sampling. PAI-1 antigen, but not tissue plasminogen activator antigen, concentrations were significantly higher in adrenal venous blood than in peripheral venous blood. Taken together, these data support the hypothesis that aldosterone modulates the effect of Ang II on PAI-1 expression in vitro and in vivo in humans.
Human Feeder Layers for Human Embryonic Stem Cells1 (2003)

Human embryonic stem (hES) cells hold great promise for future use in various research areas, such as human developmental biology and cell-based therapies. Traditionally, these cells have been cultured on mouse embryonic fibroblast (MEF) feeder layers, which permit continuous growth in an undifferentiated stage. To use these unique cells in human therapy, an animal-free culture system must be used, which will prevent exposure to mouse retroviruses. Animal-free culture systems for hES cells enjoy three major advantages in the basic culture conditions: 1). the ability to grow these cells under serum-free conditions, 2). maintenance of the cells in an undifferentiated state on Matrigel matrix with 100% MEF-conditioned medium, and 3). the use of either human embryonic fibroblasts or adult fallopian tube epithelial cells as feeder layers. In the present study, we describe an additional animal-free culture system for hES cells, based on a feeder layer derived from foreskin and a serum-free medium. In this culture condition, hES cells maintain all embryonic stem cell features (i.e., pluripotency, immortality, unlimited undifferentiated proliferation capability, and maintenance of normal karyotypes) after prolonged culture of 70 passages (>250 doublings). The major advantage of foreskin feeders is their ability to be continuously cultured for more than 42 passages, thus enabling proper analysis for foreign agents, genetic modification such as antibiotic resistance, and reduction of the enormous workload involved in the continuous preparation of new feeder lines.
Stable Isotope Dilution Multidimensional Liquid Chromatography-Tandem Mass Spectrometry for Pancreatic Cancer Serum Biomarker Discovery (2009)

A novel approach to pancreatic cancer biomarker discovery has been developed, which employs a stable isotope labeled proteome (SILAP) standard coupled with extensive multidimensional separation coupled with tandem mass spectrometry (MS/MS). Secreted proteins from CAPAN-2 human pancreatic cancer derived cells were collected after conducting stable isotope labeling by amino acids in cell culture (SILAC). The resulting SILAP standard contained <0.5% of individual unlabeled proteins. Pooled sera from patients with early stage pancreatic cancer or controls were prepared, and an equal amount of the SILAP standard was added to each sample. Proteins were separated by isoelectric focusing (IEF) prior to two-dimensional liquid chromatography (2D-LC)-MS/MS analysis. A total of 1065 proteins were identified of which 121 proteins were present at 1.5-fold or greater concentrations in the sera of patients with pancreatic cancer. ELISA validation of these findings was successfully performed for two proteins, ICAM-1 and BCAM. Results of these studies have provided proof of principle that a SILAP standard derived from the CAPAN-2 secreted proteome can be used in combination with extensive multidimensional LC-MS/MS for the identification and relative quantitation of potential biomarkers of pancreatic cancer. This technique allows for the detection of low-abundance proteins, and focuses only on biologically relevant proteins derived from pancreatic cancer cells.
Multiparametric approach for the evaluation of lipid nanoparticles for siRNA delivery (2013)

Nanoparticle-mediated siRNA delivery is a complex process that requires transport across numerous extracellular and intracellular barriers. As such, the development of nanoparticles for efficient delivery would benefit from an understanding of how parameters associated with these barriers relate to the physicochemical properties of nanoparticles. Here, we use a multiparametric approach for the evaluation of lipid nanoparticles (LNPs) to identify relationships between structure, biological function, and biological activity. Our results indicate that evaluation of multiple parameters associated with barriers to delivery such as siRNA entrapment, pKa, LNP stability, and cell uptake as a collective may serve as a useful prescreening tool for the advancement of LNPs in vivo. This multiparametric approach complements the use of in vitro efficacy results alone for prescreening and improves in vitro-in vivo translation by minimizing false negatives. For the LNPs used in this work, the evaluation of multiple parameters enabled the identification of LNP pKa as one of the key determinants of LNP function and activity both in vitro and in vivo. It is anticipated that this type of analysis can aid in the identification of meaningful structure-function-activity relationships, improve the in vitro screening process of nanoparticles before in vivo use, and facilitate the future design of potent nanocarriers.
Rhizosphere Competitiveness of Trichloroethylene-Degrading, Poplar-Colonizing Recombinant Bacteria (2000)

Indigenous bacteria from poplar tree (Populus canadensis var. eugenei 'Imperial Carolina') and southern California shrub rhizospheres, as well as two tree-colonizing Rhizobium strains (ATCC 10320 and ATCC 35645), were engineered to express constitutively and stably toluene o-monooxygenase (TOM) from Burkholderia cepacia G4 by integrating the tom locus into the chromosome. The poplar and Rhizobium recombinant bacteria degraded trichloroethylene at a rate of 0.8 to 2.1 nmol/min/mg of protein and were competitive against the unengineered hosts in wheat and barley rhizospheres for 1 month (colonization occurred at a level of 1.0 x 10(5) to 23 x 10(5) CFU/cm of root). In addition, six of these recombinants colonized poplar roots stably and competitively with populations as large as 79% +/- 12% of all rhizosphere bacteria after 28 days (0.2 x 10(5) to 31 x 10(5) CFU/cm of root). Furthermore, five of the most competitive poplar recombinants (e.g., Pb3-1 and Pb5-1, which were identified as Pseudomonas sp. strain PsK recombinants) retained the ability to express TOM for 29 days as 100% +/- 0% of the recombinants detected in the poplar rhizosphere expressed TOM constitutively.
Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin (1986)

Seven cellular loci with acceptor sites for retroviral integrations have been mapped for the presence of DNase I-hypersensitive sites in chromatin. Integrations in three of these loci, chicken c-erbB, rat c-myc, and a rat locus, dsi-1, had been selected for in retrovirus-induced tumors. Of the remaining four, two, designated dsi-3 and dsi-4, harbored acceptor sites for apparently unselected integrations of Moloney murine leukemia virus in a Moloney murine leukemia virus-induced thymoma, and two, designated C and F, harbored unselected acceptor sites for Moloney murine leukemia virus integrations in a rat fibroblast cell line. Each acceptor site mapped to within 500 base pairs of a DNase I-hypersensitive site. In the analyses of the unselected integrations, six hypersensitive sites were observed in 39 kilobases of DNA. The four acceptor sites in this DNA were localized between 0.05 and 0.43 kilobases of a hypersensitive site. The probability of this close association occurring by chance was calculated to be extremely low. Hypersensitive sites were mapped in cells representing the lineage in which integration had occurred as well as in an unrelated lineage. In six of the seven acceptor loci hypersensitive sites could not be detected in the unrelated lineage. Our results indicate that retroviruses preferentially integrate close to DNase I-hypersensitive sites and that many of these sites are expressed in some but not all cells.
R-FCN: Object Detection via Region-based Fully Convolutional Networks (2016)

We present region-based, fully convolutional networks for accurate and efficient object detection. In contrast to previous region-based detectors such as Fast/Faster R-CNN that apply a costly per-region subnetwork hundreds of times, our region-based detector is fully convolutional with almost all computation shared on the entire image. To achieve this goal, we propose position-sensitive score maps to address a dilemma between translation-invariance in image classification and translation-variance in object detection. Our method can thus naturally adopt fully convolutional image classifier backbones, such as the latest Residual Networks (ResNets), for object detection. We show competitive results on the PASCAL VOC datasets (e.g., 83.6% mAP on the 2007 set) with the 101-layer ResNet. Meanwhile, our result is achieved at a test-time speed of 170ms per image, 2.5-20x faster than the Faster R-CNN counterpart. Code is made publicly available at: https://github.com/daijifeng001/r-fcn
Control of Early Viral and Bacterial Distribution and Disease by Natural Antibodies (1999)

Natural antibodies are often dismissed from immunological analysis as "background," but they may play an important role in conferring immunity against infections. In antibody-free mice infected with various viruses or with Listeria monocytogenes, viral or bacterial titers in peripheral organs, including the kidney and brain, were 10 to 100 times greater than in antibody-competent mice (and enhanced their susceptibility to some infections), and titers in secondary lymphoid organs were 10 to 100 times lower than in antibody-competent mice. Thus, natural antibodies play a crucial role by preventing pathogen dissemination to vital organs and by improving immunogenicity through enhanced antigen-trapping in secondary lymphoid organs.
Vagal afferent inhibition of spinothalamic cell responses to sympathetic afferents and bradykinin in the monkey. (1983)

Effects of stimulating the left thoracic vagus nerve on the responses of spinothalamic neurons to electrical stimulation of cardiopulmonary sympathetic afferent fibers and to intracardiac injections of bradykinin were determined. Experiments were performed on 39 monkeys (Macaca fascicularis) tranquilized with ketamine and anesthetized with alpha-chloralose. The 30 spinothalamic cells studied had the following characteristics. They were excited by manipulation of their somatic receptive fields, were excited by electrical stimulation of cardiopulmonary sympathetic afferent fibers, and exhibited viscerosomatic convergence. Responses of 15 of 19 cells to sympathetic afferent test stimuli were inhibited by conditioning stimuli applied to left thoracic vagus nerve. A conditioning-test interval of 40-50 msec resulted in maximal inhibition of responses to both A delta and C fiber sympathetic afferents. A long time course of inhibition was present to at least a conditioning-test interval of 200 msec. Left thoracic vagus nerve stimulation inhibited 14 of 14 cells responding to intracardiac injection of bradykinin. Entrainment of activity of five cells to the cardiac cycle occurred in response to bradykinin. In each case, left thoracic vagus nerve stimulation, in addition to reducing frequency of cell discharge, disrupted the cardiac related pattern of cell activity. Bilateral cervical vagotomy abolished all inhibitory effects of left thoracic vagus nerve stimulation. These results demonstrate that vagal afferents may participate in processing of information related to cardiac pain.
TLRs in Hepatic Cellular Crosstalk (2010)

Toll-like receptors (TLRs) are expressed on all major subsets of liver cells. Both exogenous ligands derived from pathogens, and endogenous ligands that are products of cellular injury, engage these receptors and activate aspects of innate immunity. These receptors play a role in viral and parasitic infections of the liver, in ischemia-reperfusion injury, and in toxic liver damage, promoting antipathogen immunity but also hepatocellular injury and fibrogenesis. However, TLRs may also participate in negative feedback that limits tissue injury. In the complex environment of the liver, TLRs participate in pathologic cascades involving multiple cell types, manifesting their effects both through cell-autonomous actions, and via cellular crosstalk. In this paper we survey the involvement of TLRs in these diverse processes.
Pharmacodynamics of subcutaneous recombinant human interleukin-10 in healthy volunteers* (1997)

Interleukin-10 inhibits T-lymphocyte activation and proliferation and lipopolysaccharide-induced monocyte production of proinflammatory cytokines. Fifty-four healthy volunteers received single doses of recombinant human interleukin-10 (1.0, 2.5, 5.0, 10, 25, or 50 micrograms/kg) or placebo by subcutaneous injection (randomized double-blind assignment). Clinical adverse events were infrequent at doses below 50 micrograms/kg (five of six subjects had mild flu-like syndrome). Mean serum interleukin-10 concentrations were dose related. The mean terminal-phase half-life ranged from 2.7 to 4.5 hours, and the apparent volume of distribution ranged from 0.70 to 1.35 L/kg. Hematologic changes included transient mild to moderate increases of neutrophil counts, decreases of lymphocyte counts, and a delayed decrease of platelet counts. Recombinant human interleukin-10 significantly suppressed production of the proinflammatory cytokines interleukin-1 beta and tumor necrosis factor-alpha by whole blood stimulated ex vivo with Escherichia coli lipopolysaccharide.
The web-DL environment for building digital libraries from the web (2003)

The Web contains a huge volume of unstructured data, which is difficult to manage. In digital libraries, on the other hand, information is explicitly organized, described, and managed. Community-oriented services are built to attend specific information needs and tasks. In this paper, we describe an environment, Web-DL, that allows the construction of digital libraries from the Web. The Web-DL environment will allow us to collect data from the Web, standardize it, and publish it through a digital library system. It provides support to services and organizational structure normally available in digital libraries, but benefiting from the breadth of the Web contents. We experimented with applying the Web-DL environment to the Networked Digital Library of Theses and Dissertations (NDLTD), thus demonstrating that the rapid construction of DLs from the Web is possible. Also, Web-DL provides an alternative as a largescale solution for interoperability between independent digital libraries.
Cyanoacrylate glue in the treatment of corneal ulcerations. (1990)

The application of tissue adhesives to treat different corneal diseases has been used extensively in recent years. Owing to the widespread application, it has been possible to establish the advantages and disadvantages of this method of treatment. Keeping in mind the disadvantages (primarily the toxicity of cyanoacrylate glue for the corneal endothelium and lens when it comes into direct contact with these structures), the application of cyanoacrylate glue was restricted to the treatment of progressive corneal ulcerations where the risk of corneal perforation was recognized. This method of treatment was applied in 30 patients with corneal melting in dry eye associated with rheumatoid arthritis (12), trophic postherpetic ulcerations of the cornea (9), chemical corneal burns (7), neurotrophic corneal ulceration (1) and Mooren's ulcer (1). The defect healed and anterior corneal surface epithelization occurred in 73.33% of patients in contrast to the additional treatment, most commonly penetrating keratoplasty, required in the remaining patients (26.67%).
Dark septate endophytes: a review of facultative biotrophic root‐colonizing fungi (1998)

Dark septate root endophytes (DSE) are conidial or sterile fungi (Deuteromycotina, Fungi Imperfecti) likely to be ascomycetous and colonizing plant roots. They have been reported for nearly 600 plant species representing about 320 genera and 100 families. DSE fungi occur from the tropics to arctic and alpine habitats and comprise a heterogeneous group that functionally and ecologically overlaps with soil fungi, saprotrophic rhizoplane‐inhabiting fungi, obligately and facultatively pathogenic fungi and mycorrhizal fungi. Numerous species of undescribed sterile and anamorphic taxa may also await discovery. Although DSE are abundant in washed root and soil samples from various habitats, and are easily isolated from surface‐sterilized roots of ecto‐, ectendo‐, endo‐ and non‐mycorrhizal host species, their ecological functions are little understood. Studies of DSE thus far have yielded inconsistent results and only poorly illustrate the role of DSE in their natural habitats. These inconsistencies are largely due to the uncertain taxonomic affinities of the strains of DSE used. In addition, because different strains of a single anamorph taxon seem to vary greatly in function, no clear generalizations on their ecological role have been drawn. This paper reviews the current literature on DSE and the ecology and discusses the need for and direction of future research.
Chapter 2 Isotope effect: Implications for pharmaceutical investigations (1997)

This chapter highlights isotope effect. It reviews aspects of the theoretical and empirical literature on kinetic isotope effect relevant to the design and performance of pharmaceutical investigations. The greater mass of the heavy isotope results in greater force bonding it to the other atom and a greater energy of activation to break the bond. In any reaction in which the breaking of this bond is the rate-limiting step, the reaction will proceed slower for the molecule with the heavy isotope because of this “kinetic isotope effect.” In addition to kinetic isotope effects, there are other (secondary) isotope effects because of differences in bond length and bond angle of bonds involving heavy and light isotopes. Kinetic isotope effects are modified during enzymatically mediated reactions following a set of rules. Kinetic isotope effect is proportional to the mass difference between different isotopes of the same atom. The greater strength of bonds involving heavy isotopes can change a number of properties of drug molecules, including bond length, bond angle, polarity, molar volume, electron donation, Vander Walls forces, dipole moment, lipophilicity, and enzyme binding kinetics.
Plasma lipoprotein metabolism in transgenic mice overexpressing apolipoprotein E. Accelerated clearance of lipoproteins containing apolipoprotein B. (1992)

We have reported that transgenic mice overexpressing rat apo E shows marked reduction of plasma cholesterol and triglyceride levels due to the disappearance of VLDL and LDL. In this study, we investigated the metabolism of plasma lipoproteins in transgenic mice. After intravenous injection, the rates of clearance of 125I-VLDL and 125I-LDL were 3.0- and 2.4-fold greater in transgenic mice than in controls, respectively. Furthermore, clearance of chylomicron remnants estimated by oral retinyl palmitate-loading test was markedly enhanced in transgenic mice. The hepatic expression of LDL receptors by immunoblot analysis was similar in both groups. These data suggest that elimination of lipoproteins containing apo B was due to enhanced clearance of these lipoproteins enriched with apo E through hepatic LDL receptors. When fed a high cholesterol diet, controls showed twofold elevation of plasma cholesterol levels with marked increases in VLDL and LDL cholesterol on gel filtration chromatography. In contrast, cholesterol-fed transgenic mice showed resistance against these increases. High cholesterol feeding decreased the activity of hepatic LDL receptors and had no effect on enhancement of chylomicron remnant clearance in transgenic mice. Thus, overexpression of apo E facilitates metabolism of lipoproteins containing apo B presumably primarily via the LDL receptor pathway and possibly through an interaction with the chylomicron remnant receptor.