gebhart/patrepeval huggingface dataset:
Blockade of clearance of immune complexes by an anti-F(cγ) receptor monoclonal antibody (1986)

Clearance of immune complexes by the mononuclear phagocyte system is important for maintaining normal host defenses against bacterial and viral assault (1), but also contributes to the pathogenesis of a variety of immune- mediated diseases . For example, removal from the circulation of IgG-coated erythrocytes and platelets by the MPS is the sine qua non of immune-mediated cytopenias (2, 3). On the other hand, abnormally decreased removal by the MPS of smaller, soluble immune complexes may play a role in the pathogenesis of immune complex-mediated tissue damage found in such autoimmune diseases as SLE (4). Although the physicochemical nature and the size of immune complexes can influence rates of clearance and sites of deposition (reviewed in 5), interactions between immune complexes and the MPS in vivo are poorly understood. The inability to directly measure binding or internalization of immune complexes by cells in the liver and spleen has made the analysis of the molecular basis of immune complex clearance very difficult . Receptors for the Fc portion of IgG (FcgammaR) and for complement (CR) undoubtedly play a role in the removal of immune complexes, but the relative importance of these receptors is not known.
Data shaders (1993)

The process of visualizing a scientific data set requires an extensive knowledge of the domain in which the data set is created. Because an in-depth knowledge of all scientific domains is not available to the creator of visualization software, a flexible and extensible visualization system is essential in providing a productive tool to the scientist. This paper presents a shading language, based on the RenderMan shading language, that extends the shading model used to render volume data sets. Data shaders, written in this shading language, give the users of a volume rendering system a means of specifying how a volume data set is to be rendered. This flexibility is useful both as a visualization tool in the scientific community and as a research tool in the visualization community. >
Adaptive loop filter with temporal prediction (2012)

In this paper, we propose a method to improve adaptive loop filter (ALF) efficiency with temporal prediction. For one frame, two sets of adaptive loop filter parameters are adaptively selected by rate distortion optimization. The first set of ALF parameters is estimated by minimizing the mean square error between the original frame and the current reconstructed frame. The second set of filter parameters is the one that is used in the latest prior frame. The proposed algorithm is implemented in HM3.0 software. Compared with the HM3.0 anchor, the proposed method achieves 0.4%, 0.3% and 0.3% BD bitrate reduction in average for high efficiency low delay B, high efficiency low delay P and high efficiency random access configuration, respectively. The encoding and decoding time increase by 1% and 2% on average, respectively.
Preservation of hatchery waste by lactic acid fermentation. 2. Large-scale fermentation and feeding trial to evaluate feeding value (1997)

Two waste streams from a Leghorn hatchery were preserved and recycled by fermentation with a by-product carbohydrate and extrusion processing into new feed ingredients that were evaluated with broiler chickens. Cockerel chicks (CC) and a 60:40 ratio of CC:shell waste (CC:SW) were fermented in 189-L barrels for 21 d following grinding, then mixing with a liquid culture (0.2%) and carbohydrate source at 15 and 16.66%, respectively. At 2 wk, pH was 4.44 and 5.09 for the CC and CC:SW products compared with higher values of 6.54 and 6.98 for the raw ingredients at the onset. Negligible hydrogen sulfide and no ammonia gas were recorded during the fermentation period. At 21 d, the fermented CC and CC:SW were extruded, dried, and ground to meals containing CP and TMEn levels of 47.4%, 3,187 kcal/kg, and 33.1%, 2,696 kcal/kg, respectively. Broiler chickens were fed a control diet and the CC (5 and 10%) and CC:SW (2.5 and 5%) ingredient diets with corn and soybean meal for 6 wk to evaluate feeding value and carcass yield. Body weight, gain and feed conversion at 42 d for birds fed diets supplemented with CC or CC:SW at all levels were comparable to those of the control. Diets supplemented with hatchery by-product had no negative effect on carcass measurements except ready to cook carcass and wing yield, which were significantly greater for the 10% CC:SW birds than for the control. These data indicate that nutrient dense hatchery by-products can be preserved with fermentation up to 21 d and support broiler live performance and carcass yield as dietary ingredients equal to or better than a corn-soybean meal control.
Comparison of radiolabeled nucleoside probes (FIAU, FHBG, and FHPG) for PET imaging of HSV1-tk gene expression. (2002)

The in vitro and in vivo results (including the PET images) show that FIAU is a substantially more efficient probe than FHBG or FHPG for imaging HSV1-tk expression, with greater sensitivity and contrast as well as lower levels of abdominal background radioactivity at 2 and 24 h.
Direct Analysis of Single Nucleotide Variation in Human DNA and RNA Using In Situ Dot Hybridization (1989)

Using oligonucleotide hybridization, single and multiple nucleotide differences between alleles were detected directly in genomic DNA without electrophoretic separation. The DNA was immobilized in depressions in an agarose gel (in situ dots) and hybridized with radiolabeled, allele-specific oligonucleotide probes. An oligonucleotide complementary to a unique sequence region of the human major histocompatibility complex gene HLA-B27 only hybridized with genomic DNA from an HLA-B27-positive individual. Two other oligonucleotides complementary to the normal human beta-globin gene (beta A) and to the sickle cell globin gene (beta S) were synthesized. Using competition hybridization conditions which included the presence of a 10-fold molar excess of unlabeled oligonucleotide complementary to the other beta-globin allele, DNA from individuals homozygous for the normal beta-globin gene (beta A beta A) hybridized to the beta A probe exclusively, whereas DNA from individuals homozygous for the sickle cell globin gene (beta S beta S) hybridized only with the probe for the sickle cell gene. As expected, DNA from heterozygous individuals bound to both probes. Similar results were obtained with total human RNA immobilized in in situ dots. Possible applications of this methodology include genetic disease diagnosis, population carrier screening, HLA "DNA" typing, and DNA and RNA sequence polymorphism analysis.
Optimizing Schottky S/D offset for 25-nm dual-gate CMOS performance (2003)

For the first time, mixed mode simulation is used to optimize the design of ultrathin-body dual-gate metal source/drain 25-nm CMOS, showing an advantage for source/drain-to-gate underlap, rather than overlap. The effect of source/drain workfunction and silicon thickness on the optimal underlap, and on the resulting circuit speed, is examined. A substantial performance advantage versus doped source/drain is demonstrated.
Characterization of SMOC-1, a Novel Modular Calcium-binding Protein in Basement Membranes (2002)

We have isolated the novel gene SMOC-1 that encodes a secreted modular protein containing an EF-hand calcium-binding domain homologous to that in BM-40. It further consists of two thyroglobulin-like domains, a follistatin-like domain and a novel domain. Recombinant expression in human cells showed that SMOC-1 is a glycoprotein with a calcium-dependent conformation. Results from Northern blots, reverse transcriptase-PCR, and immunoblots revealed a widespread expression in many tissues. Immunofluorescence studies with an antiserum directed against recombinant human SMOC-1 demonstrated a basement membrane localization of the protein and additionally its presence in other extracellular matrices. Immunogold electron microscopy confirmed the localization of SMOC-1 within basement membranes in kidney and skeletal muscle as well as its expression in the zona pellucida surrounding the oocyte.
Nucleotide Sequence at Position 1081 of the Hemagglutinin-Neuraminidase Gene in Wild-Type Strains of Mumps Virus Is the Most Relevant Marker of Virulence (1998)

Mumps immunization has been effective at controlling epidemic mumps infection, but a high rate of vaccine-associated disease for Urabe AM9 has been documented ([6][1]). Since the mumps virus (MuV) hemmagglutinin-neuraminidase (HN) antigen is the major surface protein and an important candidate with
Vaccina treatment in some hospital infections. (1991)

Phenol-treated vaccine was prepared from the usual hospital strains and patients with colorectal cancer were immunized intramuscularly 7-10 days prior to the operation. The efficiency of the vaccine treatment was judged by the incidence of wound infections. The best results were obtained in patients whose previously estimated immunoreactivity was strong or normal. Immunospecificity could not be detected in the above treatment. The frequent and inappropriate use of antibiotics in hospitals increases the number of resistant hospital bacterial strains. Apart from Staphylococci and Streptococci, different Gram-negatives--such as Klebsiella, Serratia, Pseudomonas, Proteus and E. coli strains--have been found in the hospitals and in the patients. Due to the resistance, it is difficult to find antibiotics against them. This fact puts forward the possibility of immunization especially by vaccination.
Dynamic Viscoelasticity in Polyelectrolyte Multilayers:  Nanodamping (2006)

We report on the time-dependent viscoelastic response of nanoblended films of a polyelectrolyte complex prepared by the multilayering method. The ion-pairing interactions within polyelectrolyte multilayers (PEMUs) are reversibly broken by adding salt to the electrolyte in which the PEMU is immersed. Thus, the bulk modulus of these ultrathin films may be regulated without changing temperature. We have measured surprisingly effective mechanical damping exhibited by PEMUs. Compared to other hydrogel damping materials such as articular bovine cartilage and polyethyleneoxide−terephtalate/polybutylene−terephtalate networks, PEMUs provided enhancement in damping properties over the frequency range of 0.3−10 Hz. This was obtained when the multilayer dry thickness was orders of magnitude less than that of the hydrogels. The mechanism for enhanced damping may be related to the high proportion of ladder-like ion pairing between complexed polyelectrolytes.
Merosin, a tissue-specific basement membrane protein, is a laminin-like protein. (1990)

Merosin is a basement membrane-associated protein found in placenta, striated muscle, and peripheral nerve. A 3.6-kilobase merosin cDNA clone was isolated from a placental cDNA expression library. The clone contained a 3.4-kilobase open reading frame, the 3' portion of which includes protein sequences of proteolytic fragments of merosin. The deduced amino acid sequence of the merosin polypeptide was similar to that of the COOH-terminal region of the 400-kDa A chain of laminin. This part of laminin forms the large globule at the end of the long arm of the laminin cross and is thought to contain the neurite-promoting site and the major cell binding site(s) in laminin. The sequence identity between merosin and the laminin A chain in this region is nearly 40%. An antiserum against a synthetic peptide from the middle of the merosin cDNA sequence identified a 300-kDa polypeptide in placental extracts, indicating that the merosin polypeptide is similar in size to the laminin A chain. Intact merosin was isolated from placental extracts and shown to be covalently associated with the laminin B chains and to have a cross-like structure similar to that of laminin. The similarities between merosin and laminin show that both proteins are members of the same family of basement membrane proteins.
MLL1 and DOT1L cooperate with meningioma-1 to induce acute myeloid leukemia (2016)

Meningioma-1 (MN1) overexpression is frequently observed in patients with acute myeloid leukemia (AML) and is predictive of poor prognosis. In murine models, forced expression of MN1 in hematopoietic progenitors induces an aggressive myeloid leukemia that is strictly dependent on a defined gene expression program in the cell of origin, which includes the homeobox genes Hoxa9 and Meis1 as key components. Here, we have shown that this program is controlled by two histone methyltransferases, MLL1 and DOT1L, as deletion of either Mll1 or Dot1l in MN1-expressing cells abrogated the cell of origin-derived gene expression program, including the expression of Hoxa cluster genes. In murine models, genetic inactivation of either Mll1 or Dot1l impaired MN1-mediated leukemogenesis. We determined that HOXA9 and MEIS1 are coexpressed with MN1 in a subset of clinical MN1hi leukemia, and human MN1hi/HOXA9hi leukemias were sensitive to pharmacologic inhibition of DOT1L. Together, these data point to DOT1L as a potential therapeutic target in MN1hi AML. In addition, our findings suggest that epigenetic modulation of the interplay between an oncogenic lesion and its cooperating developmental program has therapeutic potential in AML.
The Geranylgeranyltransferase-I Inhibitor GGTI-298 Arrests Human Tumor Cells in G0/G1 and Induces p21WAF1/CIP1/SDI1 in a p53-independent Manner (1997)

Recently we have shown that in fibroblasts (NIH 3T3 and Rat-1 cells) inhibition of protein geranylgeranylation leads to a G0/G1 arrest, whereas inhibition of protein farnesylation does not affect cell cycle distribution. Here we demonstrate that in human tumor cells the geranylgeranyltransferase-I (GGTase-I) inhibitor GGTI-298 blocked cells in G0/G1, whereas the farnesyltransferase (FTase) inhibitor FTI-277 showed a differential effect depending on the cell line. FTI-277 accumulated Calu-1 and A-549 lung carcinoma and Colo 357 pancreatic carcinoma cells in G2/M, T-24 bladder carcinoma, and HT-1080 fibrosarcoma cells in G0/G1, but had no effect on cell cycle distribution of pancreatic (Panc-1), breast (SKBr 3 and MDAMB-231), and head and neck (A-253) carcinoma cells. Furthermore, treatment of Calu-1, Panc-1, Colo 357, T-24, A-253, SKBr 3, and MDAMB-231 cells with GGTI-298, but not FTI-277, induced the protein expression levels of the cyclin-dependent kinase inhibitor p21WAF. HT-1080 and A-549 cells had a high basal level of p21WAF, and GGTI-298 did not further increase these levels. Furthermore, GGTI-298 also induces the accumulation of large amounts of p21WAF mRNA in Calu-1 cells, a cell line that lacks the tumor suppressor gene p53. There was little effect of GGTI-298 on the cellular levels of another cyclin- dependent kinase inhibitor p27KIP as well as cyclin E and cyclin D1. These results demonstrate that GGTase-I inhibitors arrest cells in G0/G1 and induce accumulation of p21WAF in a p53-independent manner and that FTase inhibitors can interfere with cell cycle events by a mechanism that involves neither p21WAF nor p27KIP. The results also point to the potential of GGTase-I inhibitors as agents capable of restoring growth arrest in cells lacking functional p53.
The cGAS–cGAMP–STING pathway connects DNA damage to inflammation, senescence, and cancer (2018)

Detection of microbial DNA is an evolutionarily conserved mechanism that alerts the host immune system to mount a defense response to microbial infections. However, this detection mechanism also poses a challenge to the host as to how to distinguish foreign DNA from abundant self-DNA. Cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) is a DNA sensor that triggers innate immune responses through production of the second messenger cyclic GMP-AMP (cGAMP), which binds and activates the adaptor protein STING. However, cGAS can be activated by double-stranded DNA irrespective of the sequence, including self-DNA. Although how cGAS is normally kept inactive in cells is still not well understood, recent research has provided strong evidence that genomic DNA damage leads to cGAS activation to stimulate inflammatory responses. This review summarizes recent findings on how genomic instability and DNA damage trigger cGAS activation and how cGAS serves as a link from DNA damage to inflammation, cellular senescence, and cancer.
Bioadhesive Characteristics of Chitosan Microspheres to the Mucosa of Rat Small Intestine (2001)

Chitosan (Chi) microspheres were examined in vitro and in vivo in terms of their bioadhesive characteristics to the mucosa of rat small intestine. Chi was labeled with fluorescein isothiocyanate (FITC), and the microspheres (FTC-MS) were prepared by the dry-in-oil method using the obtained fluorescein thiocarbamyl-chitosan (FTC-Chi). FTC-MS with a mean diameter of 27 microm and size distribution of a few micrometers to several tens of micrometers was used for the bioadhesion experiment. FTC-MS exhibited a tendency to adhere to each part of the small intestine to a greater extent than dissolved FTC-Chi, and the ratio of adhering FTC-MS increased as the amount of added FTC-MS decreased. FTC-MS showed slower transit following intraduodenal injection than oral administration. Following the intraduodenal injection of FTC-MS, more than half remained in the upper or middle part of the small intestine for over 8 h. Further, insulin-containing chitosan microspheres with a mean diameter of 20 microm and size distribution of 5 microm to 45 microm were checked in situ for drug absorption, but intraduodenal or intraileal application hardly gave any decrease in plasma glucose level at a very high dose. The present chitosan microsphere system showed good adhesion to the intestinal mucosa, but scarcely facilitated absorption of insulin.
NONOPSONIC PHAGOCYTOSIS OF PSEUDOMONAS AERUGINOSA: INSIGHTS FROM AN INFANT WITH LEUKOCYTE ADHESION DEFICIENCY (2001)

Children with leukocyte adhesion deficiency type I are at risk for overwhelming infection because their neutrophils lack surface beta 2 integrins (CD18/CD11) that normally interact with endothelial cell adhesion molecules and mediate migration to sites of bacterial invasion. In vitro studies of phagocytic cells from an infant with leukocyte adhesion deficiency type I demonstrated that complement receptor 3 (CD18/CD11b) mediates nonopsonic phagocytosis of some Pseudomonas aeruginosa strains and might play a control role in the control of Pseudomonas infections at sites where there are low levels of opsonins.
Host Immune System Gene Targeting by a Viral miRNA (2007)

Virally encoded microRNAs (miRNAs) have recently been discovered in herpesviruses. However, their biological roles are mostly unknown. We developed an algorithm for the prediction of miRNA targets and applied it to human cytomegalovirus miRNAs, resulting in the identification of the major histocompatibility complex class I-related chain B (MICB) gene as a top candidate target of hcmv-miR-UL112. MICB is a stress-induced ligand of the natural killer (NK) cell activating receptor NKG2D and is critical for the NK cell killing of virus-infected cells and tumor cells. We show that hcmv-miR-UL112 specifically down-regulates MICB expression during viral infection, leading to decreased binding of NKG2D and reduced killing by NK cells. Our results reveal a miRNA-based immunoevasion mechanism that appears to be exploited by human cytomegalovirus.
GSK-3β Inhibition Attenuates LPS-Induced Death but Aggravates Radiation-Induced Death via Down-Regulation of IL-6 (2013)

Inhibition of GSK-3β conferred resistance to LPS shock but fostered death induced by ionizing radiation. Inhibition of GSK-3β was effective by reducing IL-6.
Clinical usefulness of three monoclonal antibody-defined tumor markers: CA 19-9, CA 50, and CA 125. (1986)

This article reviews the clinical usefulness of three monoclonal antibody-defined tumor markers: CA 19-9 or GICA, CA 50, and CA 125. These markers have been regarded as worthwhile tools for diagnosis and monitoring the management of patients with cancers in selected sites. The CA 19-9 test in combination with the CEA test is a useful adjunct for staging in some advanced cases and for monitoring therapy in the majority of patients with carcinoma of the stomach. Sensitivity of these assays performed concurrently is comparable to CEA alone in colorectal carcinoma. The CA 19-9 test alone is useful for staging and monitoring management of patients with carcinoma of the pancreas. In colorectal carcinoma the CA 19-9 test is redundant because of significantly lower sensitivity than that of the CEA assay; the latter remains the test of choice. The CA 50 test per se is redundant since the CA 19-9 antigen is the target for both the C50 MAb and the NS 19-9 MAb. The CA 125 test contributes to staging and is a useful adjunct for monitoring management of patients with non-mucinous carcinomas of the ovary. If positive after initial surgery and chemotherapy, this test provides evidence of the presence of residual or metastatic tumor and thus may obviate the need for second-look surgery. These conclusions are based on a review of recent relevant publications as well as on our own results obtained from preoperative evaluation and postoperative follow-up of about 600 patients with cancers in relevant sites.
A Fluorescent Carbazole Derivative:  High Sensitivity for Quadruplex DNA (2003)

We have synthesized a novel molecule, 3,6-bis(1-methyl-4-vinylpyridium)carbazole diiodide (BMVC), for recognizing specific quadruplex structures, particularly the quadruplex of human telomeric sequence d(T(2)AG(3))(4). The fluorescence intensity of the BMVC molecule increases from 1 to almost 2 orders of magnitude upon interacting with various DNAs. At a concentration of BMVC of 10 microM, fluorescence bands with different colors of BMVC in electrophoresis gels of various DNAs can be observed. The fluorescence of BMVC can be used to discriminate between duplex and quadruplex DNAs. At the low concentration of 0.1 microM BMVC in prestained gels, the fluorescence is observed in the presence of quadruplexes with anti-anti-anti-anti and anti-anti-syn-syn arrangements. However, no fluorescence band is detected upon interacting with duplexes and quadruplexes with anti-syn-anti-syn arrangement. Moreover, the sensitivity assays show that as little as 0.2 pmol of quadruplex of d(T(2)AG(3))(4) can be revealed by BMVC.
<title>Computerized lung nodule detection on thoracic CT images: combined rule-based and statistical classifier for false-positive reduction</title> (2001)

We are developing a computer-aided diagnosis (CAD) system for lung nodule detection on thoracic helical computed tomography (CT) images. In the first stage of this CAD system, lung regions are identified and suspicious structures are segmented. These structures may include true lung nodules or normal structures that consist mainly of vascular structures. We have designed rule-based classifiers to distinguish nodules and normal structures using 2D and 3D features. After rule-based classification, linear discriminant analysis (LDA) is used to further reduce the number of false positive (FP) objects. We have performed a preliminary study using CT images from 17 patients with 31 lung nodules. When only LDA classification was applied to the segmented objects, the sensitivity was 84% (26/31) with 2.53 (1549/612) FP objects per slice. When the LDA followed the rule-based classifier, the number of FP objects per slice decreased to 1.75 (1072/612) at the same sensitivity. These preliminary results demonstrate the feasibility of our approach for nodule detection and FP reduction on CT images. The inclusion of rule-based classification leads to an improvement in detection accuracy for the CAD system.