gebhart/patrepeval huggingface dataset:
[The receptor-mediated endocytosis of influenza viruses and low-density lipoproteins by tissue cells]. (1994)

The experimental data obtained by immunological, immunomorphological, biochemical, and virological methods are presented which substantiate a concept that various strains of influenza virus under study may penetrate tissue cells at sites of high affinity usually meant for low-density lipoproteins (LDLP) providing the cells with cholesterol for construction of outer and inner membranes. A computer analysis of a bank of data on the primary structure of proteins (the package of GENBER programme) revealed significant similarity of amino acid sequences between the area of viral hemagglutinin site attachment to cells and corresponding amino acids comprising apoB LDLP. The presented proofs are a convincing example of virus particles mimicry realized at the molecular level and give new concepts concerning the mechanisms of virus penetration into body cells which are important for the development of a principally new approach to creation of highly effective antiviral compounds. Moreover, the observed phenomenon may serve for explanation of the nature and mechanism of action of the so-called thermostable virus-neutralizing blood serum inhibitor.
DNA attenuates enterocyte Toll-like receptor 4-mediated intestinal mucosal injury after remote trauma (2011)

Intestinal mucosal injury occurs after remote trauma although the mechanisms that sense remote injury and lead to intestinal epithelial disruption remain incompletely understood. We now hypothesize that Toll-like receptor 4 (TLR4) signaling on enterocytes after remote injury, potentially through the endogenous TLR4 ligand high-mobility group box-1 (HMGB1), could lead to intestinal dysfunction and bacterial translocation and that activation of TLR9 with DNA could reverse these effects. In support of this hypothesis, exposure of TLR4-expressing mice to bilateral femur fracture and systemic hypotension resulted in increased TLR4 expression and signaling and disruption of the ileal mucosa, leading to bacterial translocation, which was not observed in TLR4-mutant mice. TLR4 signaling in enterocytes, not immune cells, was required for this effect, as adenoviral-mediated inhibition of TLR4 in enterocytes prevented these findings. In seeking to identify the endogenous TLR4 ligands involved, the expression of HMGB1 was increased in the intestinal mucosa after injury in wild-type, but not TLR4-mutant, mice, and administration of anti-HMGB1 antibodies reduced both intestinal mucosal TLR4 signaling and bacterial translocation after remote trauma. Strikingly, mucosal injury was significantly increased in TLR9-mutant mice, whereas administration of exogenous DNA reduced the extent of TLR4-mediated enterocyte apoptosis, restored mucosal healing, and maintained the histological integrity of the intestinal barrier after remote injury. Taken together, these findings identify a novel link between remote injury and enterocyte TLR4 signaling leading to barrier injury, potentially through HMGB1 as a ligand, and demonstrate the reversal of these adverse effects through activation of TLR9.
A new prostaglandin synthon from the 4-oxatricyclo[4.3.0.03,7]non-8-ene system. A total synthesis of (.+-.)-prostaglandin F2.ALPHA.. (1979)

The synthesis of a new prostaglandin synthon (14) from 5-trichloromethyl-4-oxatricyclo [4. 3. 0. 03, 7] non-8-ene (2) and its conversion to prostaglandin F2α (21) are described. Compound (2) was transformed into the acetylene derivative (5) which was then led to the C-9 acetylene lactone (14) via a 6-step, 8-stage reaction. A new synthesis of (±)-prostaglandin F2a (21) was completed through a 5-step reaction starting from the C-9 lactone (14).
Cloning of the Zymomonas mobilis structural gene encoding alcohol dehydrogenase I (adhA): sequence comparison and expression in Escherichia coli (1990)

Zymomonas mobilis ferments sugars to produce ethanol with two biochemically distinct isoenzymes of alcohol dehydrogenase. The adhA gene encoding alcohol dehydrogenase I has now been sequenced and compared with the adhB gene, which encodes the second isoenzyme. The deduced amino acid sequences for these gene products exhibited no apparent homology. Alcohol dehydrogenase I contained 337 amino acids, with a subunit molecular weight of 36,096. Based on comparisons of primary amino acid sequences, this enzyme belongs to the family of zinc alcohol dehydrogenases which have been described primarily in eucaryotes. Nearly all of the 22 strictly conserved amino acids in this group were also conserved in Z. mobilis alcohol dehydrogenase I. Alcohol dehydrogenase I is an abundant protein, although adhA lacked many of the features previously reported in four other highly expressed genes from Z. mobilis. Codon usage in adhA is not highly biased and includes many codons which were unused by pdc, adhB, gap, and pgk. The ribosomal binding region of adhA lacked the canonical Shine-Dalgarno sequence found in the other highly expressed genes from Z. mobilis. Although these features may facilitate the expression of high enzyme levels, they do not appear to be essential for the expression of Z. mobilis adhA.
Role of the Bone Marrow Microenvironment in Multiple Myeloma (2002)

On June 26-27, 2001, the Sixth Research Roundtable in Multiple Myeloma, entitled "The Role of the Bone Microenvironment in Multiple Myeloma," was held and focused on the biology of cell-to-cell interactions, the mediators of bone disease, and novel treatment strategies for myeloma. Studies on cell-cell interactions showed that vascular cell adhesion molecule 1, expressed by local endothelial and stromal cells, binds to tumor cell surface integrins in which expression may be increased by tumor cell-derived chemokines such as macrophage inflammatory protein (MIP) 1alpha. These adhesive interactions increase production and release of vascular endothelial growth factor (VEGF). Studies on myeloma bone disease showed the ligand for receptor activator of nuclear transcription factor-kappaB (RANKL) was expressed on tumor cells and stromal cells associated with myeloma cells and was critical for osteoclast-induced osteolysis. Blockade of RANKL suppressed osteoclast maturation, bone resorption, and tumor development. Bisphosphonates, in addition to reducing osteoclast mobility and inducing osteoclast apoptosis, also decreased tumor cell adhesion to stroma. Immunomodulatory drugs such as thalidomide analogues targeted these tumor cell-stromal cell interactions, blocking both secretion of cytokines and activation of intracellular signaling pathways required for tumor survival and growth. These agents induced tumor cell apoptosis, decreased neovascularization, and potentiated natural killer cell activity. The proteasome inhibitor PS-341 also prevented expression of adhesion molecules and cytokines and triggered tumor cell apoptosis, even in drug-resistant cell lines, while showing minimal activity in healthy cells. In addition, potential therapeutic agents under investigation, which included RANKL antagonists, protein prenylation inhibitors, and osteoblast growth factors, were discussed.
Evaluation of Commercially Prepared Vaccines for Experimentally Induced Type A/New Jersey/8/76 Influenza Virus Infections in Mice and Squirrel Monkeys (1977)

Mice and squirrel monkeys were vaccinated and subsequently challenged at selected times to evaluate the immunoprophylactic value of vaccines against influenza virus type A/New Jersey/76. Mice were challenged with virulent, homologous virus either 17 or 60 days after vaccination with 80 chick cell-agglutinating (CCA) units of whole-virus vaccine. Vaccinated mice showed minimal lesions and virus in lung tissue and had lower lung weights than unvaccinated controls. These mice had titers of hemagglutination-inhibiting (HAI) antibody in serum of greater than 1:400, but only traces of antibody were found in lung washes. Vaccinated squirrel monkeys had significantly less illness than unvaccinated controls when challenged with virulent virus 30 days after intramuscular immunization with 200 CCA units of whole virus or 400 CCA units of split virus given either once or twice (at 30-day intervals). Equal protection was observed in all monkeys despite the absence of serum HAI antibody in some monkeys after vaccination. Anamnestic reactions were observed only in monkeys vaccinated with whole virus. The possible roles of various immune factors and antibody to neuraminidase are discussed.
A Cohort Study of the Risk of Cervical Intraepithelial Neoplasia Grade 2 or 3 in Relation to Papillomavirus Infection (1992)

Cervical intraepithelial neoplasia is a common and apparently early manifestation of cervical infection by HPV, particularly types 16 and 18.
Defense Against Adversarial Attacks Using High-Level Representation Guided Denoiser (2018)

Neural networks are vulnerable to adversarial examples, which poses a threat to their application in security sensitive systems. We propose high-level representation guided denoiser (HGD) as a defense for image classification. Standard denoiser suffers from the error amplification effect, in which small residual adversarial noise is progressively amplified and leads to wrong classifications. HGD overcomes this problem by using a loss function defined as the difference between the target model's outputs activated by the clean image and denoised image. Compared with ensemble adversarial training which is the state-of-the-art defending method on large images, HGD has three advantages. First, with HGD as a defense, the target model is more robust to either white-box or black-box adversarial attacks. Second, HGD can be trained on a small subset of the images and generalizes well to other images and unseen classes. Third, HGD can be transferred to defend models other than the one guiding it. In NIPS competition on defense against adversarial attacks, our HGD solution won the first place and outperformed other models by a large margin.
Conjugation of Keto Fatty Acids to Glutathione in Plant Tissues. Characterization and Quantification by HPLC−Tandem Mass Spectrometry (2005)

Both biotic and abiotic stress activate the oxylipin pathway in plants. As reactive electrophile species (RES), some oxylipins are expected to bind cellular nucleophiles in a Michaël-type addition reaction. Using the HPLC-tandem mass spectrometry techniques, we have established the analytical basis for the investigation of oxylipin conjugation to glutathione (GSH) in plant extracts. The GSH adducts to the four keto fatty acid isomers issued from both linoleic and linolenic acids were first produced and their mass spectrometric features analyzed in the positive electrospray ionization mode. In all cases, the main fragmentation (MS2 mode) of the pseudomolecular ion leads to the neutral loss of a glutamyl moiety (-129 Da), affording an ion that gives structural information upon an additional fragmentation (MS3 mode). The glutamyl loss was confirmed by the analysis of other GSH adducts to oxylipin RES and appeared as being characteristic of GSH adducts. It is thus proposed to search GSH adducts in plant extracts by HPLC-MS/MS, using initially the neutral loss mode and then the MS2 mode to further characterize the identified compounds. This methodology was successfully applied to the analysis of GSH adducts upon infiltration into leaves of the four previous keto fatty acids at 5 mM, a concentration inducing cell death. The production of GSH adducts to oxylipin RES was observed for the first time in plant tissues. Furthermore, the levels of adduct production explain in part the observed GSH depletion. These results support the role of RES in altering protein activities and cellular redox balance of plant cells, via addition reactions to cellular nucleophiles.
Noninvasive reconstruction of the three-dimensional ventricular activation sequence during pacing and ventricular tachycardia in the rabbit heart (2011)

Ventricular arrhythmias represent one of leading causes for sudden cardiac death, a significant problem in public health. Noninvasive imaging of cardiac electric activities associated with ventricular arrhythmias plays an important role in better our understanding of the mechanisms and optimizing the treatment options. The present study aims to rigorously validate a novel three-dimensional (3-D) cardiac electrical imaging (3-DCEI) technique with the aid of 3-D intra-cardiac mapping during paced rhythm and ventricular tachycardia (VT) in the rabbit heart. Body surface potentials and intramural bipolar electrical recordings were simultaneously measured in a closed-chest condition in thirteen healthy rabbits. Single-site pacing and dual-site pacing were performed from ventricular walls and septum. VTs and premature ventricular complexes (PVCs) were induced by intravenous norepinephrine (NE). The non-invasively imaged activation sequence correlated well with invasively measured counterparts, with a correlation coefficient of 0.72 and a relative error of 0.30 averaged over all paced beats and NE-induced PVCs and VT beats. The averaged distance from imaged site of initial activation to measured site determined from intra-cardiac mapping was ∼5mm. These promising results suggest that 3-DCEI is feasible to non-invasively localize the origins and image activation sequence of focal ventricular arrhythmias.
Immunostimulatory CpG-Oligodeoxynucleotides Cause Extramedullary Murine Hemopoiesis (1999)

Bacterial DNA and the synthetic CpG-oligodeoxynucleotides (ODNs) derived thereof have attracted attention because they activate cells of the adaptive immune system (lymphocytes) and the innate immune system (APCs) in a sequence-dependent manner. Here, we addressed whether CpG-ODNs affect hemopoiesis. Challenging mice with immunostimulatory CpG-ODN sequences led to transient splenomegaly, with a maximum increase of spleen weight at day 6. The induction of splenomegaly by CpG-ODNs was sequence-specific, dose-dependent, and associated with an increase in splenic cell count, in numbers of granulocyte-macrophage CFUs (GM-CFUs), and early erythroid progenitors (burst-forming units-erythroid). The transfer of spleen cells from CpG-ODN-pretreated animals into lethally irradiated syngeneic mice yielded an increase of spleen CFUs. Furthermore, the challenge of sublethally irradiated mice with CpG-ODNs caused radioprotective effects, in that recovery of GM-CFUs and cytotoxic T cell function was enhanced. The increase in GM-CFU and CTL function correlated with an enhanced resistance to Listeria infection in irradiated mice. We conclude from these data that CpG-ODNs trigger extramedullary hemopoiesis, and that this finding could be of therapeutic relevance in myelosuppression.
A New Solids-Free Non-Damaging High Temperature Lost-Circulation Pill: Development and First Field Applications (2003)

Abstract Excessive loss of high-density brines into the formation has always been a major concern during completion operations, since it leads to formation damage and well control issues. The problem becomes more complex at high temperatures and when the treatment involves running gravel-pack assemblies and downhole sand screens. Typically, the fluidloss-control pills are composed of very high concentrations of crosslinked polymers with or without bridging particulates. The sealing mechanism of these pills is a combination of viscosity, solids bridging, and polymer filter-cake buildup on the porous rock. Due to the instability of polymers at high bottomhole temperatures, incompatibility with some divalent brines, and the necessity to cleanup with acid, a new solids-free lost-circulation pill that is stable for prolonged periods at high temperatures was developed. This paper introduces the development and the first field application of a new solids-free non-damaging viscoelastic surfactant-based fluid-loss pill (VES-PILL). The single-additive system forms a "gel" with most completion brines currently used in well operations. Laboratory data demonstrate that this pill could be used up to 375°F. The "gel" structure of this system sustains viscosity high enough to effectively control or stop brine-loss, while maintaining a safe differential pressure into the formation. Several "frac and pack" completions were performed for the first time in Saudi Arabia in the Pre-Khuff sweet-gas zones. The VES-PILL was used to prevent losses after perforating, fracturing and gravel-pack operations. The pill was used in the field up to 310°F, and brine-loss was effectively controlled for more than 3 days. The effectiveness of the pill was also demonstrated by a five-fold increase in surface pumping pressure during placement. The wells were produced at rates exceeding expectations without further remediation to cleanup the fluid-loss pill.
PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors (2014)

Adoptive transfer of tumor-infiltrating lymphocytes (TILs) can mediate regression of metastatic melanoma; however, TILs are a heterogeneous population, and there are no effective markers to specifically identify and select the repertoire of tumor-reactive and mutation-specific CD8⁺ lymphocytes. The lack of biomarkers limits the ability to study these cells and develop strategies to enhance clinical efficacy and extend this therapy to other malignancies. Here, we evaluated unique phenotypic traits of CD8⁺ TILs and TCR β chain (TCRβ) clonotypic frequency in melanoma tumors to identify patient-specific repertoires of tumor-reactive CD8⁺ lymphocytes. In all 6 tumors studied, expression of the inhibitory receptors programmed cell death 1 (PD-1; also known as CD279), lymphocyte-activation gene 3 (LAG-3; also known as CD223), and T cell immunoglobulin and mucin domain 3 (TIM-3) on CD8⁺ TILs identified the autologous tumor-reactive repertoire, including mutated neoantigen-specific CD8⁺ lymphocytes, whereas only a fraction of the tumor-reactive population expressed the costimulatory receptor 4-1BB (also known as CD137). TCRβ deep sequencing revealed oligoclonal expansion of specific TCRβ clonotypes in CD8⁺PD-1⁺ compared with CD8⁺PD-1- TIL populations. Furthermore, the most highly expanded TCRβ clonotypes in the CD8⁺ and the CD8⁺PD-1⁺ populations recognized the autologous tumor and included clonotypes targeting mutated antigens. Thus, in addition to the well-documented negative regulatory role of PD-1 in T cells, our findings demonstrate that PD-1 expression on CD8⁺ TILs also accurately identifies the repertoire of clonally expanded tumor-reactive cells and reveal a dual importance of PD-1 expression in the tumor microenvironment.
On Demand Network and Application Provisioning ThroughWeb Services (2007)

While most service-oriented solutions are developed for system integration or data integration, we propose a Web services-based solution, Eucalyptus, for provisioning applications and networks on demand. Eucalyptus is built on the power of the user-controlled lightpath provisioning (UCLP) tool, which pioneers a user-centric and service-oriented approach for creating and managing a private end-to-end optical network. As a first user of UCLP, Eucalyptus aims to construct an participatory environment for geographically distributed teams of architects and industrial designers with the with the support of configurable broadband switched networks, as well as the traditional routed IP networks. The contribution of Eucalyptus is to provide a proof-of-concept example on how Web service and service-oriented architecture (SoA) can effectively provide on-demand provisioning for heterogenous resources in hybrid networks. These resources can be provisioned, launched, monitored, terminated, and reserved through Web services. Eucalyptus is network and platform neutral. It offers a single point of entry for users to access resources ranging from video conference applications, rendering clusters, to the underlying networks. Each resource is configured through a resource-specific Web service. Eucalyptus also includes a set of generic management Web services to coordinate sessions, to manage resources and users, and to compose workflows, such that the network and the application are properly configured for the users engaging in a participatory design session.
Plasma miR-17-5p, miR-20a and miR-22 are down-regulated in women with endometriosis (2012)

Plasma microRNAs provide a promising opportunity for detection of endometriosis.
Age-Dependence of Flow Homeostasis in the Left Ventricle (2019)

<b>Background:</b> Intracardiac flow homeostasis requires avoiding blood stasis and platelet activation during its transit through the cardiac chambers. However, the foundations of intraventricular blood washout and its exposure to shear stresses have been poorly addressed. We aimed to characterize and quantify these features in a wide population of healthy subjects and assess the relationships of these indices with age. <b>Methods:</b> We used color-Doppler echocardiography and custom post-processing methods to study 149 healthy volunteers from 26 days to 80 years old. From the intraventricular flow-velocity fields we obtained personalized maps of (1) the residence time of blood in the LV, and (2) the shear index, a metric accounting for the strongest occurrence of shear stresses inside the chamber. From these maps we derived quantitative indices of the overall intraventricular blood washout and shear exposure. We addressed the age-dependence of these indices and analyzed their relationship with age-related changes in filling-flow. <b>Results:</b> The entire intraventricular blood pool was replaced before 8 cycles. Average residence time of blood inside the LV was <3 cycles in all subjects and followed an inverse U-shape relationship with age, increasing from median (IQR) of 1.0 (0.7 to 1.2) cycles in the 1st year of life to 1.8 (1.4-2.2) cycles in young adults (17-30 years old), becoming shorter again thereafter. Shear index showed no relation with age and was bounded around 20 dyn·s/cm<sup>2</sup>. Regions with the longest residence time and highest shear index were identified near the apex. Differences in the degree of apical penetration of the filling waves and the duration of the late-filling phase explained the age-dependence of residence time ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup><mml:mrow><mml:mtext>R</mml:mtext></mml:mrow> <mml:mrow><mml:mtext>adj</mml:mtext></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msubsup> </mml:math> = 0.48, <i>p</i> < 0.001). <b>Conclusions:</b> In average, blood spends 1 to 3 beats inside the LV with very low shear stress rates. The apical region is the most prone to blood stasis, particularly in mid-aged adults. The washout of blood in the normal LV is age-dependent due to physiological changes in the degree of apical penetration of the filling waves.
Cellular Mechanisms of Tissue Fibrosis. 7. New insights into the cellular mechanisms of pulmonary fibrosis (2014)

Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by severe and progressive scar formation in the gas-exchange regions of the lung. Despite years of research, therapeutic treatments remain elusive and there is a pressing need for deeper mechanistic insights into the pathogenesis of the disease. In this article, we review our current knowledge of the triggers and/or perpetuators of pulmonary fibrosis with special emphasis on the alveolar epithelium and the underlying mesenchyme. In doing so, we raise a number of questions highlighting critical voids and limitations in our current understanding and study of this disease.
Principles of Adsorption and Adsorption Processes (1984)

List of Symbols. Microporous Adsorbents. Physical Adsorption and the Characterization of Porous Adsorbents. Thermodynamics of Adsorption. Correlation, Analysis, and Prediction of Adsorption Equilibria. Diffusion in Porous Media. Kinetics of Sorption in Batch Systems. Flow Through Packed Beds. Dynamics of Adsorption Columns: Single--Transition Systems. Dynamics of Adsorption Columns: Multiple Transition Systems. Chromatographic Separation Processes. Adsorption Separation Processes: I. Cyclic Batch Systems. Adsorption Separation Processes: II. Continous Counter Current Systems. Appendixes. Index.