gebhart/patrepeval huggingface dataset:
Vascular permeability, vascular hyperpermeability and angiogenesis (2008)

The vascular system has the critical function of supplying tissues with nutrients and clearing waste products. To accomplish these goals, the vasculature must be sufficiently permeable to allow the free, bidirectional passage of small molecules and gases and, to a lesser extent, of plasma proteins. Physiologists and many vascular biologists differ as to the definition of vascular permeability and the proper methodology for its measurement. We review these conflicting views, finding that both provide useful but complementary information. Vascular permeability by any measure is dramatically increased in acute and chronic inflammation, cancer, and wound healing. This hyperpermeability is mediated by acute or chronic exposure to vascular permeabilizing agents, particularly vascular permeability factor/vascular endothelial growth factor (VPF/VEGF, VEGF-A). We demonstrate that three distinctly different types of vascular permeability can be distinguished, based on the different types of microvessels involved, the composition of the extravasate, and the anatomic pathways by which molecules of different size cross-vascular endothelium. These are the basal vascular permeability (BVP) of normal tissues, the acute vascular hyperpermeability (AVH) that occurs in response to a single, brief exposure to VEGF-A or other vascular permeabilizing agents, and the chronic vascular hyperpermeability (CVH) that characterizes pathological angiogenesis. Finally, we list the numerous (at least 25) gene products that different authors have found to affect vascular permeability in variously engineered mice and classify them with respect to their participation, as far as possible, in BVP, AVH and CVH. Further work will be required to elucidate the signaling pathways by which each of these molecules, and others likely to be discovered, mediate the different types of vascular permeability.
Mercury in first-cut baby hair of children with autismversustypically-developing children (2008)

Children with autism were examined to determine amounts of mercury (Hg) in their baby hair and the factors that might affect Hg body burden. US children with autism (n = 78) and matched controls (n = 31) born between 1988 and 1999 were studied. Hg in first-cut baby hair was determined using cold vapor atomic fluorescence spectrometry (CVAFS). Twenty samples were split and also measured with Neutron Activation Analysis (NAA). Logistic regression analysis showed that compared to children with higher levels of mercury (above 0.55 mcg g−1), children with lower levels of mercury in their hair (below 0.55 mcg g−1) were 2.5-fold more likely to manifest with autism. Children with autism had similar mercury exposure as controls from maternal seafood and maternal dental amalgams. Children with autism also had 2.5-fold higher incidence of oral antibiotic use during their first 18 months of life. Their mothers were possibly more likely to use oral antibiotics during pregnancy or nursing. The amount of Hg in the baby hair of children with autism showed a significant correlation with the number of maternal dental amalgams. The lower level of Hg in the baby hair of children with autism indicates an altered metabolism of Hg, and may be due to a decreased ability to excrete Hg. This is consistent with usage of higher amounts of oral antibiotics, which are known to inhibit Hg excretion in rats due to alteration of gut flora, and may exert a similar effect in humans. Higher usage of oral antibiotics in infancy may also partially explain the high incidence of chronic gastrointestinal problems seen in individuals with autism.
Type 2 diabetes mellitus, cognitive impairment and dementia (1999)

Current classification structures for dementia may not be adequate in diabetes, where mixed pathogenesis is likely. Further research into the mechanisms of cognitive impairment in Type 2 DM may allow us to challenge the concept of dementia, at least in these patients, as an irremediable disease.
Tumour invasion and metastasis are promoted in mice deficient in tenascin‐X (2001)

TNX deficiency led to an increase in the production of MMPs, and the increased activity of MMPs may result in the degradation of laminin. Consequently, the melanoma cells inoculated in TNX-/- mice might facilitate invasion and metastasis. These results imply that TNX is required for impeding the invasion and metastasis of tumour cells.
Si bipolar 2-GHz 6-bit flash A/D conversion LSI (1988)

A gigahertz-sampling-rate flash A/D (analog/digital)-conversion LSI using high-speed Si bipolar technology (SST-1B) is investigated. To improve comparator speed, a circuit technology to minimize the comparator-speed limiting factors with minimum power is investigated and applied. To enhance the dynamic accuracy, speed mismatch among comparators is also minimized using this circuit technology. To improve encoder speed, a quasi-Gray code is adopted and glitch noise is reduced with this code. The LSI performance at 1-GHz sampling rate is measured with a gigahertz-operation data acquisition system developed with the SST MSI family, and effective bits of 5.8 at an input frequency of 100 MHz and 4.8 at 500 MHz are achieved. This LSI also demonstrates the feasibility of a single-chip flash A/D converter with a gigahertz sampling rate using Si bipolar technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In vitro activities of oxazolidinones U-100592 and U-100766 against penicillin-resistant and cephalosporin-resistant strains of Streptococcus pneumoniae (1996)

Two oxazolidinones and ceftriaxone, imipenem, rifampin, and vancomycin were tested against 162 penicillin-intermediate and 68 penicillin-resistant strains of pneumococci. U-100592 is two- to fourfold more active than U-100766 against penicillin-resistant pneumococci. The MICs of U-100592 at which 90% of the isolates were inhibited were 0.25 and 0.5 microgram/ml for penicillin-intermediate and -resistant strains, respectively, and 0.5 microgram/ml for ceftriaxone-susceptible, -intermediate, and -resistant strains. U-100592 MICs for 7 of 230 strains (2 from blood, 3 from middle-ear fluid, and 2 from the upper respiratory tract) were 1 microgram/ml.
Safety and immunogenicity of Staphylococcus aureus type 5 capsular polysaccharide-Pseudomonas aeruginosa recombinant exoprotein A conjugate vaccine in patients on hemodialysis. (1996)

Seventeen volunteers with ESRD on hemodialysis, negative for infection with HIV or hepatitis B and C and not receiving immunosuppressive therapy, were injected two times 6 wk apart with 25 micrograms of Staphylococcus aureus Type 5 capsular polysaccharide-Pseudomonas aeruginosa exoprotein A (rEPA) conjugate. Controls were healthy adults, 18 to 44 yr old, injected previously with the same vaccine. None of the patients had fever or significant elevations in their SGOT or SGPT attributable to the vaccine. Two vaccinees had transient induration > 1 cm in diameter at the injection site. The preimmunization geometric mean (GM) Type 5 antibody levels of the ESRD patients and controls were similar. Type 5 antibody levels of the three major immunoglobulin (lg) classes rose at 2 and 6 wk after immunization (P < 0.001 for lgG, P < 0.005 for lgM, and P = 0.0001 for lgA). Reimmunization at 6 wk did not elicit a booster response. At 6 months, the GM lgG level of the patients was approximately 50% of that of the healthy volunteers and 14 of 17 had a more than fourfold higher antibody level than the preimmune value. The GM lgM level, in contrast, declined to the preimmunization value. Vaccine-induced Type 5 antibodies had opsonophagocytic activity. There was a slight increase of lgG antibodies to the heterologous S. aureus Type 8 polysaccharide (P < 0.01) that was sustained at 6 months. The S. aureus Type 5-rEPA vaccine is safe and immunogenic in ESRD patients, and evaluation of its effectiveness against S. aureus bacteremia in this at-risk group is planned.
Monoclonal antibodies directed against human airway secretions. Localization and characterization of antigens. (1988)

Cellular mechanisms of normal airway mucus secretion and their alterations in chronic obstructive lung disease are poorly understood. To aid in their study, the authors have produced a panel of monoclonal antibodies directed against various constituents of human airway secretions. Two fusions yielded 401 hybridoma-containing cultures. Supernatants from 150 of these cultures stained human tracheal secretory cells by immunofluorescence. Twenty-nine hybridomas were selected for expansion because they selectively stained a single cell type or displayed another interesting distribution. Antigens were further characterized by their localization in glycol methacrylate sections of human trachea, sensitivity to periodate oxidations, selective affinity for fraction peaks obtained by Sepharose 4B chromatography, and reactivity with molecules of various sizes, as estimated by SDS-PAGE. These antibodies will be useful for 1) quantitative detection of antigens in sputum or lavage samples by immunoassay and 2) purification and biochemical characterization of molecular constituents of airway secretions in health and disease.
ChemInform Abstract: SYNTHESIS OF 2‐O‐α‐, 3‐O‐α‐, 3‐O‐β‐, AND 4‐O‐α‐L‐RHAMNOPYRANOSYL‐D‐GALACTOSE (1982)

Abstract Die Kondensation des Rhamnopyranosylbromids (II) mit den Galaktosiden (Ia), (Ib) bzw. (IX) unter Quecksilbersalzkatalyse ergibt hauptsächlich die α‐glycosidisch gebundenen Disaccharide (III), (V) bzw; (X).
<title>Warping of a computerized 3-D atlas to match brain image volumes for quantitative neuroanatomical and functional analysis</title> (1991)

We describe the implementation, experience and preliminary results obtained with a 3-D computerized brain atlas for topographical and functional analysis of brain sub-regions. A volume-of-interest (VOI) atlas was produced by manual contouring on 64 adjacent 2 mm-thick MRI slices to yield 60 brain structures in each hemisphere which could be adjusted, originally by global affine transformation or local interactive adjustments, to match individual MRI datasets. We have now added a non-linear deformation (warp) capability (Bookstein, 1989) into the procedure for fitting the atlas to the brain data. Specific target points are identified in both atlas and MRI spaces which define a continuous 3-D warp transformation that maps the atlas on to the individual brain image. The procedure was used to fit MRI brain image volumes from 16 young normal volunteers. Regional volume and positional variability were determined, the latter in such a way as to assess the extent to which previous linear models of brain anatomical variability fail to account for the true variation among normal individuals. Using a linear model for atlas deformation yielded 3-D fits of the MRI data which, when pooled across subjects and brain regions, left a residual mis-match of 6 - 7 mm as compared to the non-linear model. The results indicate a substantial component of morphometric variability is not accounted for by linear scaling. This has profound implications for applications which employ stereotactic coordinate systems which map individual brains into a common reference frame: quantitative neuroradiology, stereotactic neurosurgery and cognitive mapping of normal brain function with PET. In the latter case, the combination of a non-linear deformation algorithm would allow for accurate measurement of individual anatomic variations and the inclusion of such variations in inter-subject averaging methodologies used for cognitive mapping with PET.
More accurate tests for the statistical significance of result differences (2000)

Statistical significance testing of differences in values of metrics like recall, precision and balanced F-score is a necessary part of empirical natural language processing. Unfortunately, we find in a set of experiments that many commonly used tests often underestimate the significance and so are less likely to detect differences that exist between different techniques. This underestimation comes from an independence assumption that is often violated. We point out some useful tests that do not make this assumption, including computationally-intensive randomization tests.
Evaluation of cardiac function in active and hibernating grizzly bears (2003)

Cardiac function parameters in hibernating bears are opposite to the chronic bradycardic effects detected in nonhibernating species, likely because of intrinsic cardiac muscle adaptations during hibernation. Understanding mechanisms and responses of the myocardium during hibernation could yield insight into mechanisms of cardiac function regulation in various disease states in nonhibernating species.
N-Acetylgalactosamino Dendrons as Clearing Agents to Enhance Liver Targeting of Model Antibody-Fusion Protein (2013)

Dendrimer clearing agents represent a unique class of compounds for use in multistep targeting (MST) in radioimmunotherapy and imaging. These compounds were developed to facilitate the removal of excess tumor-targeting monoclonal antibody (mAb) prior to administration of the radionuclide to minimize exposure of normal tissue to radiation. Clearing agents are designed to capture the circulating mAb, and target it to the liver for metabolism. Glycodendrons are ideally suited for MST applications as these highly branched compounds are chemically well-defined, thus advantageous over heterogeneous macromolecules. Previous studies have described glycodendron 3 as a clearing agent for use in three-step MST protocols, and early in vivo assessment of 3 showed promise. However, synthetic challenges have hampered its availability for further development. In this report we describe a new sequence of chemical steps which enables the straightforward synthesis and analytical characterization of this class of dendrons. With accessibility and analytical identification solved, we sought to evaluate both lower and higher generation dendrons for hepatocyte targeting as well as clearance of a model protein. We prepared a series of clearing agents where a single biotin is connected to glycodendrons displaying four, eight, sixteen or thirty-two α-thio-N-acetylgalactosamine (α-SGalNAc) units, resulting in compounds with molecular weights ranging from 2 to 17 kDa, respectively. These compounds were fully characterized by LCMS and NMR. We then evaluated the capacity of these agents to clear a model (131)I-labeled single chain variable fragment antibody-streptavidin ((131)I-scFv-SAv) fusion protein from blood and tissue in mice, and compared their clearing efficiencies to that of a 500 kDa dextran-biotin conjugate. Glycodendrons and dextran-biotin exhibited enhanced blood clearance of the scFv-SAv construct. Biodistribution analysis showed liver targeting/uptake of the scFv-SAv construct to be 2-fold higher for compounds 1 to 4, as well as for the 500 kDa dextran, over saline. Additionally, the data suggest the glycodendrons clear through the liver, whereas the dextran through reticuloendothelial system (RES) metabolism.
Laboratory Assays for Diagnosis and Management of Hepatitis C Virus Infection (2002)

It was noted in 1974 that 75% of cases of transfusion-associated hepatitis were caused by NANBH, but 15 years passed before advances in molecular biology led to the cloning of the NANBH agent and anti-HCV assays were developed (2). In a little more than a decade, our knowledge of and ability to diagnose and treat HCV infections have increased dramatically. In 1990, mass screening of blood donors was implemented in the United States and was estimated to have prevented 40,000 HCV infections in the first year (2). Improvements in EIAs and the performance of NAT on donations prior to transfusion have further lowered the incidence of transfusion-transmitted HCV (39).

Although the incidence of new HCV infections in the United States has declined, the population of individuals infected for ≥20 years who are at risk for serious complications is projected to increase until about 2015 (19). Improvements in therapy have resulted in better virologic response rates, and molecular HCV tests have proved useful in making management decisions. As new therapeutic options evolve and laboratory assays change, the clinical relevance and use of laboratory testing for HCV will require frequent reassessments. Consensus conferences that include experts from a variety of disciplines provide an ideal environment where these issues can be debated (12, 29).
Cisplatin-based interferon gamma gene therapy of murine ovarian carcinoma. (1998)

Cis-diamminedichloroplatinum(II) increased in vivo lipofection efficiency of tumor cells with a target gene, interferon gamma (IFN gamma), in a murine metastatic ovarian carcinoma model. The expression of IFN gamma gene in ascitic tumors reached a peak at day 11 after cisplatin treatment and lasted over 1 week. A local increase in IFN gamma gene expression increased a local expression of inducible nitric oxide synthase (iNOS) and the tumor necrosis factor a gene. This treatment suppressed tumor growth (or killed tumor cells) and increased the long-term survival of animals (at least 80 days) without tumors, which was prevented by simultaneous treatment of iNOS inhibitor aminoguanidine. The results indicate that cisplatin-based IFN gamma gene therapy is an effective treatment protocol and nitric oxide may play a major part for tumor cell killing or growth.
Identification of N-Glycosylation Sites on Secreted Proteins of Human Hepatocellular Carcinoma Cells with a Complementary Proteomics Approach (2009)

N-linked glycosylation is prevalent in proteins destined for extracellular environments; nearly all secreted proteins are glycosylated. However, with respect to their glycosylation sites, little attention has been paid. Here, we report the analysis of N-glycosylation sites on secreted proteins of human hepatocellular carcinoma cells. For the enrichment of glycopeptides, capture methods with hydrophilic affinity (HA) and hydrazide chemistry (HC) were used complementarily. With the use of both methods in combination with nano-LC-ESI-MS/MS analysis, 300 different glycosylation sites within 194 unique glycoproteins were identified, and 172 glycosites have not been determined experimentally previously. A direct comparison between HA and HC methods was also investigated for the first time. In brief, in terms of selectivity for glycopeptides, HC is superior to HA (92.9% vs 51.3%); however, based on the number of glycosites identified, HA outweighs HC (265 vs 159). Furthermore, unavoidable contaminants such as actin and bovine serum albumin which are not N-glycosylated could be easily depleted by using this glycoproteomic strategy. As a consequence, more low-abundance and genuinely secreted proteins were identified. Among the glycoproteins identified, alpha-fetoprotein, CD44 and laminin have been reported to be implicated in HCC and its metastasis.
Building additional complexity to in vitro-derived intestinal tissues (2013)

Gastrointestinal (GI) disorders affect up to 25% of the US population. Common intestinal disorders include malabsorption, irritable bowel syndrome and fecal incontinence. Some GI disorders such as Hirschsprung's disease have a genetic basis and are associated with an absence or paucity of enteric nerves. Current treatment plans for GI disorders range from changes in diet to bowel resection, and there are very few drugs available that target the primary deficiencies in intestinal function such as controlled peristalsis. While animal models can recapitulate the broad range of intestinal pathologies of the GI tract, they are intrinsically complicated and of low throughput. Several in vitro systems have been established, and these range from epithelial enteroids to more complex organoids, which contain most intestinal cell types. One of the more complex organoid systems was derived from adult mouse intestines and contains functional enteric nerves and smooth muscle capable of peristalsis. Establishing an equivalent human intestinal system is challenging due to limited access and variable quality of human intestinal tissues. However, owing to recent advances, it is possible to differentiate human induced and embryonic pluripotent stem cells, collectively called pluripotent stem cells, into human intestinal organoids (HIOs) in vitro. Although HIOs contain a significant degree of epithelial and mesenchymal complexity, they lack enteric nerves and thus are unable to model the peristaltic movements of the gut. The goal of this review is to discuss approaches to generate complex in vitro systems that can be used to more comprehensively model common intestinal pathologies. New and more biologically complete human models of the intestine would allow for unprecedented studies of the cellular and molecular basis of normal and pathological gut function. Furthermore, fully functional HIOs could serve as a platform for preclinical drug studies to model absorption and efficacy.
Scattering of Ultrasound by Blood (1976)

The ultrasonic volumetric scattering cross section of the erythrocyte has been measured over a range of frequencies by comparing the rms value of the gated backscattered signal from the blood with that of a wave reflected from a flat reflector with known reflection coefficient. It is found to be proportional to the fourth power of the frequency predicted by the wave scattering theory for small particles in the frequency range from 5 MHz to 15 MHz. The relation between the scattering coefficient and the hematocrit is also examined up to a hematocrit of 45 percent. This coefficient is found to increase along with the hematocrit until it reaches a maximum around hematocrit = 26 percent and then decreases as the hematocrit increases. Twersky's wave scattering theory is applied to describe this result.
α-Synuclein Expression in Rat Substantia Nigra Suppresses Phospholipase D2 Toxicity and Nigral Neurodegeneration (2010)

We present genetic evidence that an in vivo role of α-synuclein (α-syn) is to inhibit phospholipase D2 (PLD2), an enzyme that is believed to participate in vesicle trafficking, membrane signaling, and both endo- and exocytosis. Overexpression of PLD2 in rat substantia nigra pars compacta (SNc) caused severe neurodegeneration of dopamine (DA) neurons, loss of striatal DA, and an associated ipsilateral amphetamine-induced rotational asymmetry. Coexpression of human wild type α-syn suppressed PLD2 neurodegeneration, DA loss, and amphetamine-induced rotational asymmetry. However, an α-syn mutant defective for inhibition of PLD2 in vitro also failed to inhibit PLD toxicity in vivo. Further, reduction of PLD2 activity in SNc, either by siRNA knockdown of PLD2 or overexpression of α-syn, both produced an unusual contralateral amphetamine-induced rotational asymmetry, opposite to that seen with overexpression of PLD2, suggesting that PLD2 and α-syn were both involved in DA release or reuptake. Finally, α-syn coimmunoprecipitated with PLD2 from extracts prepared from striatal tissues. Taken together, our data demonstrate that α-syn is an inhibitor of PLD2 in vivo, and confirm earlier reports that α-syn inhibits PLD2 in vitro. Our data also demonstrate that it is possible to use viral-mediated gene transfer to study gene interactions in vivo.