gebhart/patrepeval huggingface dataset:
The Application of Frye’s Theory to Lord of the Flies (2014)

Frye’s theory of archetypal meaning includes the apocalyptic and the demonic imagery. The apocalyptic and demonic imagery will be applied to William Golding’s Lord of the Flies, which is stuffed with symbols. Through the demonic imagery, the theme of the novel, people naturally revert to cruelty, savagery and barbarism is clearly revealed. The apocalyptic imagery gives us some hope, though.
Accuracy of RNA-Seq and its dependence on sequencing depth (2012)

We proposed a novel form of overdispersion guaranteeing that the accuracy improves with sequencing depth. We demonstrated that the new form provides a better fit to the data.
Human Fatal Zaire Ebola Virus Infection Is Associated with an Aberrant Innate Immunity and with Massive Lymphocyte Apoptosis (2010)

This work, the largest study to be conducted to date in humans, showed that fatal outcome is associated with aberrant innate immune responses and with global suppression of adaptive immunity. The innate immune reaction was characterized by a "cytokine storm," with hypersecretion of numerous proinflammatory cytokines, chemokines and growth factors, and by the noteworthy absence of antiviral IFNα2. Immunosuppression was characterized by very low levels of circulating cytokines produced by T lymphocytes and by massive loss of peripheral CD4 and CD8 lymphocytes, probably through Fas/FasL-mediated apoptosis.
Enhanced tumor MR imaging with gadolinium‐loaded polychelating polymer‐containing tumor‐targeted liposomes (2008)

The results support the feasibility of using such multifunctional nanoparticular liposome-based agents simultaneously providing prolonged circulation, heavy Gd load, and specific cancer cell recognition as a superior contrast for MR tumor imaging.
Leukocyte Interferon-Induced Tumor Regression in Human Metastatic Breast Cancer, Multiple Myeloma, and Malignant Lymphoma (1980)

Thirty-eight patients with advanced breast cancer, multiple myeloma, and malignant lymphoma were treated with partially purified (about 0.1%) leukocyte interferon. Patients were treated with a remission-induction schedule of 3 million to 9 million antiviral units daily intramuscularly for 4 to 26 weeks. Responding patients were maintained on a schedule of 3 million U three times weekly. Tumor regression was observed in seven of 17 patients with breast cancer. Six of 10 patients with multiple myeloma responded with a decrease of at least 50% in serum myeloma protein levels or Bence Jones protein excretion. Six of the 11 lymphoma patients achieved tumor regression. Complete remissions occurred in two patients. Of the 19 responding patients, five remain on study for 52 to 63 weeks. Toxicity included low-grade fever, fatigue, anorexia, and partial alopecia. Myelosuppression (lowest median leukocyte count, 2500/mm3; granulocytes, 1300/mm3) occurred in most patients. On the basis of this pilot study, we conclude that leukocyte interferon can induce tumor regression in patients with advanced cancer.
Ouabain interaction with cardiac Na/K-ATPase reveals that the enzyme can act as a pump and as a signal transducer. (2001)

Na/K-ATPase hydrolyzes ATP to maintain the transmembrane gradients of Na+ and K+ found in most mammalian cells and is inhibited specifically by cardiac glycosides such as ouabain. Recently, we have shown that partial inhibition of Na/K-ATPase by non-toxic concentrations of ouabain causes hypertrophic growth and transcriptional regulation of several growth-related marker genes in neonatal rat cardiac myocytes. These ouabain effects involve the activation of multiple signal transduction pathways, including the activation of Src kinase and tyrosine phosphorylation of the epidermal growth factor receptors and other proteins, followed by the activation of Ras, the Ras/Raf/MEK/MAPK cascade, and increased production of reactive oxygen species. The gene regulatory actions of ouabain, like its classical effect on cardiac contractility, are dependent on the net influx of Ca2+ and rise in [Ca2+]i, indicating that the latter is a shared second messenger for the ouabain effects on cardiac contractility and growth. Significantly, the effects of ouabain on several early signaling events including stimulation of tyrosine phosphorylation and production of reactive oxygen species are independent of changes in intracellular Na and Ca2+ concentrations. Taken together, these new findings have led us to propose that when ouabain binds to Na/K-ATPase, it converts the enzyme to a signal transducer and initiates multiple gene regulatory pathways through either direct or indirect interactions with tyrosine kinases in cardiac myocytes.
X-Linked Cone Dystrophy Caused by Mutation of the Red and Green Cone Opsins (2010)

X-linked cone and cone-rod dystrophies (XLCOD and XLCORD) are a heterogeneous group of progressive disorders that solely or primarily affect cone photoreceptors. Mutations in exon ORF15 of the RPGR gene are the most common underlying cause. In a previous study, we excluded RPGR exon ORF15 in some families with XLCOD. Here, we report genetic mapping of XLCOD to Xq26.1-qter. A significant LOD score was detected with marker DXS8045 (Z(max) = 2.41 [theta = 0.0]). The disease locus encompasses the cone opsin gene array on Xq28. Analysis of the array revealed a missense mutation (c. 529T>C [p. W177R]) in exon 3 of both the long-wavelength-sensitive (LW, red) and medium-wavelength-sensitive (MW, green) cone opsin genes that segregated with disease. Both exon 3 sequences were identical and were derived from the MW gene as a result of gene conversion. The amino acid W177 is highly conserved in visual and nonvisual opsins across species. We show that W177R in MW opsin and the equivalent W161R mutation in rod opsin result in protein misfolding and retention in the endoplasmic reticulum. We also demonstrate that W177R misfolding, unlike the P23H mutation in rod opsin that causes retinitis pigmentosa, is not rescued by treatment with the pharmacological chaperone 9-cis-retinal. Mutations in the LW/MW cone opsin gene array can, therefore, lead to a spectrum of disease, ranging from color blindness to progressive cone dystrophy (XLCOD5).
Deep learning methods for CT image-domain metal artifact reduction (2017)

Artifacts resulting from metal objects have been a persistent problem in CT images over the last four decades. A common approach to overcome their effects is to replace corrupt projection data with values synthesized from an interpolation scheme or by reprojection of a prior image. State-of-the-art correction methods, such as the interpolation- and normalization-based algorithm NMAR, often do not produce clinically satisfactory results. Residual image artifacts remain in challenging cases and even new artifacts can be introduced by the interpolation scheme. Metal artifacts continue to be a major impediment, particularly in radiation and proton therapy planning as well as orthopedic imaging. A new solution to the long-standing metal artifact reduction (MAR) problem is deep learning, which has been successfully applied to medical image processing and analysis tasks. In this study, we combine a convolutional neural network (CNN) with the state-of-the-art NMAR algorithm to reduce metal streaks in critical image regions. Training data was synthesized from CT simulation scans of a phantom derived from real patient images. The CNN is able to map metal-corrupted images to artifact-free monoenergetic images to achieve additional correction on top of NMAR for improved image quality. Our results indicate that deep learning is a novel tool to address CT reconstruction challenges, and may enable more accurate tumor volume estimation for radiation therapy planning.
Monoclonal antibodies specific for beta 7 integrin and mucosal addressin cell adhesion molecule-1 (MAdCAM-1) reduce inflammation in the colon of scid mice reconstituted with CD45RBhigh CD4+ T cells (1997)

Mucosal addressin cell adhesion molecule-1 (MAdCAM-1) is an adhesion protein expressed on endothelium in mucosal tissues that has been shown to play an important role in the selective homing of lymphocytes to intestinal mucosa and associated lymphoid tissue. To determine whether MAdCAM-1 or its ligand alpha 4 beta 7 would be appropriate targets for therapeutic intervention in gut-associated inflammation, we tested the ability of rat mAbs specific for beta 7 integrin and MAdCAM-1 to inhibit chronic colonic inflammation in scid mice reconstituted with CD4+ T cells enriched for the CD45RBhigh subpopulation. Abs specific for beta 7 and MAdCAM-1 blocked recruitment of lymphocytes to the colitic colon, and more importantly, these Abs significantly reduced the severity of colonic inflammatory disease in this animal model. Therefore, the adhesive interactions mediated by alpha 4 beta 7 and MAdCAM are intimately involved in leukocyte recruitment to gut in chronic inflammatory disease and may be relevant therapeutic targets for patients with inflammatory bowel disease.
Baseband signal processing (1991)

The baseband signal processing of the ALTAIR wireless in-building network (WIN) is described. The discussion covers the 19-GHz oscillator, burst processing, packet detection, symbol clock synchronization and gain and offset correction. The algorithms described are carried out in a single ASIC composed of 60000 active gates. The implemented procedures allow for parallel processing, which significantly reduces the computation time and therefore leads to preserving high bandwidth efficiency. The learning processes that acquire information about packet parameters and the adjustment operations in the receivers are executed in 3 mu s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phase I/II Study of Biweekly Paclitaxel and Radiation in Androgen-Ablated Locally Advanced Prostate Cancer (2008)

Concurrent biweekly paclitaxel with RT is feasible, with an MTD of 73.8 Gy. Recovery of gonadal function occurs in the majority of patients. These results encourage testing in a phase III setting.
Biodegradable Interference Screw Fixation Exhibits Pull-Out Force and Stiffness Similar to Titanium Screws (1998)

Recently, increased interest in biodegradable interference screws for bone-tendon-bone graft fixation has led to numerous screws becoming available. The implants are made from different polymers and have different designs, which might influence their mechanical properties. Several studies have reported a wide range of mechanical results for these screws using different biomechanical models. The aim of the present study is to compare reliable biomechanical data for six different biodegradable interference screws, consisting of five different polymers, with a conventional titanium screw in a standardized model. Seventy proximal calf tibias were used to determine maximal pull-out force, stiffness of fixation, and insertion torque for interference screw fixation of bone-tendon-bone grafts. Additionally, maximal torque at failure was determined. Data were analyzed with respect to aspects of screw design, such as drive and thread shape. Five of the six biodegradable screws provided initial pull-out force and stiffness of fixation comparable with that of a conventional titanium screw. Torque at failure can be greatly increased by adapting the drive design to the mechanical properties of the polymeric raw material. A correlation between pull-out force and thread height indicates that fixation rigidity depends on screw design, even in a biodegradable implant.
Approaches to the High-Throughput Synthesis of Analogues of Dihydroaeruginoic Acid (2000)

A solution-phase synthesis of dihydroaeruginoic acid (1) was identified for its application towards the high-throughput synthesis of analogues of dihydroaeruginoic acid (1). Development of a solid-phase synthesis of dihydroaeruginoic acid (1) was examined. Simple analogues (11a–f) of dihydroaeruginoic acid (1) were obtained by using solution-phase high-throughput synthesis.
Quorum sensing in Escherichia coli , Salmonella typhimurium , and Vibrio harveyi : A new family of genes responsible for autoinducer production (1999)

In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. Quorum-sensing bacteria produce, release, and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. In the marine bacterium Vibrio harveyi two parallel quorum-sensing systems exist, and each is composed of a sensor-autoinducer pair. V. harveyi reporter strains capable of detecting only autoinducer 1 (AI-1) or autoinducer 2 (AI-2) have been constructed and used to show that many species of bacteria, including Escherichia coli MG1655, E. coli O157:H7, Salmonella typhimurium 14028, and S. typhimurium LT2 produce autoinducers similar or identical to the V. harveyi system 2 autoinducer AI-2. However, the domesticated laboratory strain E. coli DH5alpha does not produce this signal molecule. Here we report the identification and analysis of the gene responsible for AI-2 production in V. harveyi, S. typhimurium, and E. coli. The genes, which we have named luxSV.h., luxSS.t., and luxSE.c. respectively, are highly homologous to one another but not to any other identified gene. E. coli DH5alpha can be complemented to AI-2 production by the introduction of the luxS gene from V. harveyi or E. coli O157:H7. Analysis of the E. coli DH5alpha luxSE.c. gene shows that it contains a frameshift mutation resulting in premature truncation of the LuxSE.c. protein. Our results indicate that the luxS genes define a new family of autoinducer-production genes.
High-risk thyroid cancer. Prolonged survival with early multimodality therapy. (1981)

Eleven patients with high-risk thyroid carcinoma of anaplastic or mixed anaplastic-differentiated histology were treated using an early multimodality approach. Patients were classified using the prognostic index for thyroid carcinoma developed by the EORTC. Therapy consisted of a four-drug chemotherapy combination, radioiodine (131I), and Bacille-Calmette-Guerin (BCG) immunotherapy. Treatment was designed to maximize effects against both anaplastic and differentiated tumor components. There has been prolonged disease-free survival (14+ to 73+ months) in patients with clear cell, small cell, and mixed anaplastic histologies. Currently five patients have been in complete remission for over 4 years. Treatment has been well tolerated. The long-term participation in care by a multispecialty team has produced promising results which we hope can be valuable as a basis for multicenter trials.
Rapid induction of Alzheimer A beta amyloid formation by zinc (1994)

A beta 1-40, a major component of Alzheimer's disease cerebral amyloid, is present in the cerebrospinal fluid and remains relatively soluble at high concentrations (less than or equal to 3.7 mM). Thus, physiological factors which induce A beta amyloid formation could provide clues to the pathogenesis of the disease. It has been shown that human A beta specifically and saturably binds zinc. Here, concentrations of zinc above 300 nM rapidly destabilized human A beta 1-40 solutions, inducing tinctorial amyloid formation. However, rat A beta 1-40 binds zinc less avidly and is immune to these effects, perhaps explaining the scarcity with which these animals form cerebral A beta amyloid. These data suggest a role for cerebral zinc metabolism in the neuropathogenesis of Alzheimer's disease.
Pharmacokinetic Considerations of Formulation: Extended-Release Metoprolol Succinate in the Treatment of Heart Failure (2003)

Extended-release (ER) metoprolol succinate is a controlled-release formulation designed to deliver metoprolol succinate at a near constant rate for approximately 20 h, independent of food intake and gastrointestinal pH. Once-daily dosing of ER metoprolol succinate 12.5-200 mg produces even plasma concentrations over a 24-h period, without the marked peaks and troughs characteristically observed with the immediate-release (IR) formulation. This leads to consistent beta1-blockade over 24 h, while maintaining cardioselectivity at doses up to 200 mg daily. Pharmacokinetic studies have also been performed in heart failure patients and have demonstrated that ER metoprolol succinate is associated with a more pronounced and even beta1-blockade over a 24-h period than the IR formulation. The efficacy and good tolerability of ER metoprolol succinate in heart failure patients has now been demonstrated in a large-scale clinical trial.
Induction of Experimental Autoimmune Encephalomyelitis in IL-12 Receptor-β2-Deficient Mice: IL-12 Responsiveness Is Not Required in the Pathogenesis of Inflammatory Demyelination in the Central Nervous System (2003)

Abstract IL-12 is thought to be involved in the susceptibility to experimental autoimmune encephalomyelitis (EAE), a Th1 cell-mediated autoimmune disorder of the CNS. IL-12 signals through a heterodimeric receptor (IL-12Rβ1/IL-12Rβ2), whose β2-chain is up-regulated on activated, autoreactive Th1 cells. Contrary to the expectation that the absence of IL-12Rβ2 would protect from EAE, we found that IL-12Rβ2-deficient mice developed earlier and more severe disease, with extensive demyelination and CNS inflammation. The inflammatory cells were mainly comprised of CD4+ T cells, monocyte/macrophages, and dendritic cells. Compared to wild-type mice, IL-12Rβ2-deficient mice exhibited significantly increased autoantigen-induced proliferative response and increased production of TNF-α, GM-CSF, IL-17, IL-18/IL-18Rα, and NO. In addition, we found significantly increased levels of IL-23p19 mRNA expression in spleen cells from immunized IL-12Rβ2−/− mice compared with wild-type mice. These findings indicate that IL-12 responsiveness is not required in the pathogenesis of inflammatory demyelination in the CNS, and that, in the absence of IL-12Rβ2, increased IL-23 and other inflammatory molecules may be responsible for increased severity of EAE.
Oct-4 Regulates Alternative Platelet-derived Growth Factor α Receptor Gene Promoter in Human Embryonal Carcinoma Cells (1996)

Expression of the platelet-derived growth factor alpha-receptor (PDGFalphaR) gene is tightly controlled in mammalian embryogenesis. A well established model system to study human embryogenesis is the embryonal carcinoma cell line Tera2. We have shown previously that retinoic acid-differentiated Tera2 cells express two PDGFalphaR transcripts of 6.4 kilobase pairs (kb) (encoding the full-length receptor) and 3.0 kb, respectively, whereas in contrast, undifferentiated Tera2 cells express PDFGalphaR transcripts of 1.5 kb and 5.0 kb. Here we show that this switch in PDGFalphaR expression pattern during differentiation of Tera2 cells results from alternative promoter use. In undifferentiated cells, a second promoter is used, which is located in intron 12 of the PDGFalphaR gene. Functional analysis shows that this promoter contains a consensus octamer motif, which can be bound by the POU domain transcription factor Oct-4. Oct-4 is expressed in undifferentiated Tera2 cells but not in retinoic acid-induced differentiated cells. Mutation of the octamer motif decreases promoter activity, while ectopic expression of Oct-4 in differentiated Tera2 cells specifically enhances the activity of this PDGFalphaR promoter. Therefore, we suggest that an important aspect in the maintenance of the undifferentiated state of human embryonal carcinoma cells results from Oct-4 expression, which thereupon activates this PDGFalphaR promoter.
Polyethersulfone Hollow Fiber Membranes for Hemodialysis (2011)

Polyethersulfone (PES) is one of the most important polymeric materials and is widely used in separation fields. PES and PES-based membranes show outstanding oxidative, thermal and hydrolytic stability as well as good mechanical and film-forming properties. PES membranes could endure many kinds of sterilized methods, including epoxy ethane gas, steam, and γ-ray. Furthermore, PES-based membranes show high permeability for low molecular weight proteins when used as hemodialysis membranes. Thus, PES membranes are also widely employed in biomedical fields such as artificial organs and medical devices used for blood purification, e.g., hemodialysis, hemodiafiltration, hemofiltration, plasmapheresis and plasma collection (Zhao et al., 2001; Tullis, et al., 2002; Samtleben et al., 2003; Werner et al., 1995), especially in recent years. However, when contacting with blood, proteins will be rapidly adsorbed onto the surface of PES membrane and the adsorbed protein layer may lead to further undesirable results, such as platelet adhesion, aggregation and coagulation. As a consequence, the blood compatibility of PES membrane is not adequate, and injections of anti-coagulants are needed during its clinical application (Liu et al., 2009). The main disadvantage is related to the relatively hydrophobic character of PES membrane. And many studies have concluded that membrane fouling (as caused by protein adsorption) is directly related to hydrophobicity as reviewed by Van der Bruggen (Van der Bruggen, 2009) and Khulbe et al. (Khulbe et al., 2010), although the opposite has also been reported (Yu et al., 2008). Membrane fouling is mainly caused by adsorption of nonpolar solutes, hydrophobic particles or bacteria (Van der Bruggen, 2009; Koh et al., 2005). It is a serious problem in membrane filtration, resulting in a higher energy demand, shorter membrane lifetime, and unpredictable separation performance (Agenson & Urase, 2007). Thus, PES hollow fiber membranes used in hemodialysis are usually modified by hydrophilic polymers. For the modification of PES membranes, there are three approaches: (1) bulk modification of PES material, and then to prepare modified membrane; (2) surface modification of prepared PES membrane; and (3) blending, which can also be regarded as a surface modification. The modification procedures allow finding a compromise between the hydrophobicity and hydrophilicity, and localize the hydrophilic material specifically in the membrane pores, where they have a positive effect on flux and fouling reduction, and on the membrane
Expression of normal and truncated forms of human endoglin (1999)

Endoglin is a transmembrane glycoprotein 633 residues in length expressed at the surface of endothelial cells as a disulphide-linked homodimer; the specific cysteine residues involved in endoglin dimerization are unknown. Mutations in the coding region of the endoglin gene are responsible for hereditary haemorrhagic telangiectasia type 1 (HHT1), a dominantly inherited vascular disorder. Many of these mutations, if translated, would lead to truncated forms of the protein. It is therefore of interest to assess the protein expression of different truncated forms of endoglin. Infections in vitro or in vivo with recombinant vaccinia virus, as well as transient transfections with expression vectors, were used to express normal and truncated forms of endoglin. Truncated mutants could be classified into three different groups: (1) those that did not produce stable transcripts; (2) those that produced stable transcripts but did not secrete the protein; and (3) those that secreted a soluble dimeric protein. This is the first time that a recombinant truncated form of endoglin has been found to be expressed in a soluble form. Because a chimaeric construct encoding the N-terminal sequence of platelet/endothelial cell adhesion molecule (PECAM-1) antigen fused to residues Ile281-Ala658 of endoglin also yielded a dimeric surface protein, these results suggest that cysteine residues contained within the fragment Cys330-Cys412 are involved in disulphide bond formation. Infection with vaccinia recombinants encoding an HHT1 mutation did not affect the expression of the normal endoglin, and did not reveal an association of the recombinant soluble form with the transmembrane endoglin, supporting a haploinsufficiency model for HHT1.