gebhart/patrepeval huggingface dataset:
PIM serine/threonine kinases in the pathogenesis and therapy of hematologic malignancies and solid cancers (2010)

The identification as cooperating targets of Proviral Integrations of Moloney virus in murine lymphomas suggested early on that PIM serine/threonine kinases play an important role in cancer biology. Whereas elevated levels of PIM1 and PIM2 were mostly found in hematologic malignancies and prostate cancer, increased PIM3 expression was observed in different solid tumors. PIM kinases are constitutively active and their activity supports in vitro and in vivo tumor cell growth and survival through modification of an increasing number of common as well as isoform-specific substrates including several cell cycle regulators and apoptosis mediators. PIM1 but not PIM2 seems also to mediate homing and migration of normal and malignant hematopoietic cells by regulating chemokine receptor surface expression. Knockdown experiments by RNA interference or dominant-negative acting mutants suggested that PIM kinases are important for maintenance of a transformed phenotype and therefore potential therapeutic targets. Determination of the protein structure facilitated identification of an increasing number of potent small molecule PIM kinase inhibitors with in vitro and in vivo anticancer activity. Ongoing efforts aim to identify isoform-specific PIM inhibitors that would not only help to dissect the kinase function but hopefully also provide targeted therapeutics. Here, we summarize the current knowledge about the role of PIM serine/threonine kinases for the pathogenesis and therapy of hematologic malignancies and solid cancers, and we highlight structural principles and recent progress on small molecule PIM kinase inhibitors that are on their way into first clinical trials.
Changes of interstitial fluid volume in superficial tissues detected by a miniature ultrasound device (2000)

We evaluated the changes of tissue layer thickness in circumscribed superficial tissue areas with a 10-MHz A-mode and a 20-MHz B-mode ultrasound device under alterations in body posture and plasma volume to detect fluid shifts between the different compartments. In 20 male volunteers, we measured tissue thickness by A mode and corium and subcutis thickness by B mode at the forehead before and 30 min after three procedures: change from upright to supine position (P1); change from upright to 30 degrees head-down-tilt position (P2); infusion of 10 ml/kg body wt of Ringer solution (P3). We found a significant correlation between baseline tissue thickness and the sum of corium and subcutis thicknesses (r = 0.75, P < 0.01). The changes of body posture and plasma volume resulted in significant increases of tissue thickness (P1, 2.9%; P2, 11.6%; P3, 5.8%) and corium thickness (P1, 4.7%; P2, 8.1%; P3, 9.1%) but not of the sum of chorium and subcutis thicknesses. We conclude that fluid shifts from the intravascular to the extravascular compartment are detectable by evaluating corium thickness with a B-mode, or more easily tissue thickness with an A-mode, ultrasound device.
Human CD4+ Cytolytic T Lymphocyte Responses to a Human Immunodeficiency Virus Type 1 gp160 Subunit Vaccine (1993)

The development of an effective vaccine against human immunodeficiency virus type 1 (HIV-1) may require immunization protocols that elicit cytolytic T lymphocytes (CTL) in addition to neutralizing antibodies. This report demonstrates that vaccination of 4 HIV-1-seronegative volunteers with a recombinant HIV-1 gp160 vaccine produced in mammalian cells elicited a CTL response in 3. The observed CTL activity was not mediated by classic CD8+ CTL but rather by cells of the CD4+ phenotype. The level of CTL activity varied over time, did not correlate with the proliferative response to gp160, and was not increased by repeated immunization. At the clonal level, the vaccine was shown to elicit a functionally heterogeneous CD4+ T cell response that included clones with antigen-specific, major histocompatibility complex-restricted cytolytic activity. These clones were capable of lysing target cells expressing the HIV-1 env gene and thus might be active against HIV-1-infected cells in vivo.
Defective protein tyrosine phosphorylation and altered levels of p59fyn and p56ick in CD4 T cells from HIV-1 infected patients (1994)

Early in HIV infection, CD4+ lymphocytes exhibit the properties of an anergic state characterized by unresponsiveness to mitogens or to TCR stimulation and by defective IL-2 production. As tyrosine phosphorylation is the earliest of the biochemical events initiated by stimulation of CD3-TCR, we studied protein tyrosine phosphorylation in purified CD4+ lymphocytes from 25 asymptomatic seropositive patients (CD4 T cells > 350/mm3) previously stimulated in vitro by immobilized anti-CD3 mAb or by co-immobilized anti-CD3 and anti-CD28 mAbs. Purified CD4+ lymphocytes from HIV-infected patients exhibited defective early protein tyrosine phosphorylation in response to CD3 activation when compared with normal subjects. This defect was observed mainly in patients in whom proliferative responses to immobilized anti-CD3 ranged from 2 to 50% of control values obtained in healthy donors, and was frequently associated with increased cellular levels of p59fyn and decreased cellular levels of p56lck. Interestingly, these defects appeared to correlate with the degree of impairment in thymidine incorporation. Since CD28 mAbs have been reported to enhance proliferative responses to the CD3-TCR pathway in cloned murine or human anergic models and to induce tyrosine phosphorylation in human T cells, we studied the role of CD28 mAb as a co-signal. Although anti-CD28 co-stimulation augmented the proliferative responses in both controls and HIV-infected patients, it failed to correct the tyrosine phosphorylation pattern in the latter. Our results suggest a relationship between defective early protein tyrosine phosphorylation and impairment of proliferative responses in CD4 T cells from HIV-infected patients, and evidence is provided that associated altered cellular levels of the fyn and lck tyrosine kinases might play an important role in the anergic response observed early during HIV infection.
Atrial remodelling in atrial fibrillation: CaMKII as a nodal proarrhythmic signal (2016)

CaMKII is a serine-threonine protein kinase that is abundant in myocardium. Emergent evidence suggests that CaMKII may play an important role in promoting atrial fibrillation (AF) by targeting a diverse array of proteins involved in membrane excitability, cell survival, calcium homeostasis, matrix remodelling, inflammation, and metabolism. Furthermore, CaMKII inhibition appears to protect against AF in animal models and correct proarrhythmic, defective intracellular Ca(2+) homeostasis in fibrillating human atrial cells. This review considers current concepts and evidence from animal and human studies on the role of CaMKII in AF.
Development of Controlled Matrix Heterogeneity on a Triphasic Scaffold for Orthopedic Interface Tissue Engineering (2006)

Biological fixation of orthopedic soft tissue grafts to bone poses a significant clinical challenge. The clinical success of soft tissue-based grafts for anterior cruciate ligament (ACL) reconstruction is limited by the lack of functional graft integration with subchondral bone. Soft tissues such as the ACL connect to subchondral bone via a complex interface whereby three distinct tissue regions (ligament, fibrocartilage, and bone) work in concert to facilitate load transfer from soft to hard tissue while minimizing stress concentration at the interface. Although a fibrovascular tissue forms at the graft-to-bone interface following surgery, this tissue is nonphysiologic and represents a weak link between the graft and bone. We propose that the re-establishment of the native multi-tissue interface is essential for biological graft fixation. In vivo observations and our in vitro monolayer co-culture results suggest that osteoblast-fibroblast interaction is important for interface regeneration. This study focuses on the design of a triphasic scaffold system mimicking the multi-tissue organization of the native ACL-to-bone interface and the evaluation of osteoblast-fibroblast interactions during three-dimensional co-culture on the triphasic scaffold. We found that the triphasic scaffold supported cell proliferation, migration and phenotypic matrix production while maintaining distinct cellular regions and phase-specific extracellular matrix deposition over time. This triphasic scaffold is designed to guide the eventual reestablishment of an anatomically oriented and mechanically functional fibrocartilage interfacial region directly on biological and synthetic soft tissue grafts. The results of this study demonstrate the feasibility of multi-tissue regeneration on a single scaffold, and the potential of interface tissue engineering to enable the biological fixation of soft tissue grafts to bone.
THE THREE DIMENSIONAL STRUCTURE OF SOOT AGGREGATES (1985)

Stereo technique was used to count the number of particles in the soot aggregates, a procedure made possible by being able to see the aggregates in three dimensions. The following relationship was established between the number of particles in an aggregate and its relative projected area: N = 1.9 (A/a)0-92 A simple computer model based on a random collision mechanism for the simulation of soot aggregates was also used. The results from the programme were used to construct real models containing 5, 10, 15, 20, 25, and 30 polystyrene balls.
Polarized cholesterol and phospholipid efflux in cultured gall-bladder epithelial cells: evidence for an ABCA1-mediated pathway (2002)

Gall-bladder epithelial cells (GBEC) are exposed to high concentrations of cholesterol in bile. Whereas cholesterol absorption by GBEC is established, the fate of this absorbed cholesterol is not known. The aim of this study was to determine whether ABCA1 (ATP-binding cassette transporter A1) mediates cholesterol efflux in GBEC. Polarized canine GBEC were cultured on porous membrane filters allowing separate access to apical (AP) and basolateral (BL) compartments. After AP loading of cells with model bile and [14C]cholesterol, cholesterol efflux was measured. Cholesterol loading together with 8-bromo-cAMP treatment, which increased ABCA1 expression, led to a significant increase in cholesterol efflux with apolipoprotein A-I (apoA-I) as the acceptor. Cholesterol efflux was observed predominantly into the BL compartment. Similar results were found for phospholipid efflux. Confocal immunofluorescence microscopy showed a predominantly BL ABCA1 localization. Interestingly, apoA-I added to either the AP or the BL compartments elicited BL lipid efflux with cAMP treatment. No paracellular or transcellular passage of 125I-apoA-I occurred. Ligands for the nuclear hormone receptors liver X receptor alpha (LXRalpha) and retinoid X receptor (RXR) elicited AP and BL cholesterol efflux, suggesting the involvement of both ABCA1- and non-ABCA1-mediated pathways. In summary, BL cholesterol/phospholipid efflux consistent with an ABCA1-mediated mechanism occurs in GBEC. This efflux pathway is stimulated by cAMP and by LXRalpha/RXR ligands, and in the case of the cAMP pathway appears to involve a role for biliary apoA-I.
Are Peripheral Opioid Antagonists the Solution to Opioid Side Effects? (2004)

The major analgesic effects of opioid medication are mediated within the brain and spinal cord. Many of the side effects of opioids are caused by activation of receptors outside these areas. Recently developed peripherally restricted opioid antagonists have the ability to block many opioid side effects without affecting analgesia.
Up-regulation of Inhibitory Natural Killer Receptors CD94/NKG2A with Suppressed Intracellular Perforin Expression of Tumor-Infiltrating CD8+ T Lymphocytes in Human Cervical Carcinoma (2005)

Inhibitory signals that govern the cytolytic functions of CD8(+) T lymphocytes have been linked to the expression of natural killer cell receptors (NKRs) on CTLs. There is limited knowledge about the induction of inhibitory NKR (iNKR) expression in vivo. Up-regulation of iNKRs has been linked to the modulation of the virus- and/or tumor-specific immune responses in animal models. In the present study, we directly examined the expression of various NKRs on tumor-infiltrating lymphocytes (TILs) derived from human cervical cancer. We found that in human cervical cancer, the percentage expression of immunoglobulin-like NKR(+)CD8(+) T lymphocytes were similar in gated CD8(+)-autologous TILs and peripheral blood mononuclear cells. On the contrary, cervical cancer-infiltrating CD8(+) T lymphocytes expressed up-regulated C-type lectin NKRs CD94/NKG2A compared with either peripheral blood CD8(+) T cells or normal cervix-infiltrating CD8(+) T lymphocytes. Dual NKR coexpression analyses showed that CD94 and NKG2A were mainly expressed on CD56(-)CD161(-)CD8(+) TILs within the cancer milieu. Immunohistochemical study showed that cervical cancer cells expressed abundant interleukin 15 (IL-15) and transforming growth factor-beta (TGF-beta). In kinetic coculture assay, cervical cancer cells can promote the expression of CD94/NKG2A on CD8(+) T lymphocytes. The cancer-derived effects can be reversed by addition of rIL-15Ralpha/Fc and anti-TGF-beta antibody. Functional analyses illustrated that intracellular perforin expression of CD8(+) T cells was minimal upon up-regulation of CD94/NKG2A. Kinetic cytotoxicity assays showed that up-regulated expressions of CD94/NKG2A restrain CD8(+) T lymphocyte cytotoxicity. Our study strongly indicated that cervical cancer cells could promote the expression of iNKRs via an IL-15- and possibly TGF-beta-mediated mechanism and abrogate the antitumor cytotoxicity of TILs.
Utilization of Kinetically Enhanced Monovalent Binding Affinity by Immunoassays Based on Multivalent Nanoparticle-Antibody Bioconjugates (2001)

The monovalent binding affinity of high binding site density nanoparticle-antibody bioconjugates is shown to exceed the intrinsic affinity of the original, monoclonal antibody. The nanoparticle-antibody bioconjugates were prepared by covalent coupling of antibodies to long-lifetime fluorescent, europium(III) chelate nanoparticles, 107 nm in diameter. Experiments were carried out in standard microtitration wells to determine solid-phase association and dissociation rate constants, nonspecific binding, and affinity constants of the various binding site density nanoparticle-antibody bioconjugates and the conventionally labeled monoclonal antibody. The affinity constant for monovalent binding of a high binding site density bioconjugate (5.4 x 10(10) M(-1)) was 8-fold higher than the intrinsic affinity of the antibody (6.6 x 10(9) M(-1)). The separately measured association (2.5 x 10(6) M(-1) s(-1)) and dissociation (3.7 x 10(-5) s(-1)) rate constants of the bioconjugate were 2-fold higher and 4-fold lower, respectively, compared to the antibody. The dependence of the association rate constant of the density of the binding sites enhanced the kinetics and the affinity of the high binding site density bioconjugates. The nanoparticle labels with high specific activity, low nonspecific binding, and enhanced binding affinity of the nanoparticle-antibody bioconjugates contribute to the design of the next generation immunoassays with extreme sensitivity.
The Effect of Alpha-2 Macroglobulin on the Healing of Ruptured Anterior Cruciate Ligament in Rabbits (2004)

To investigate the effect of modification of biological environmental conditions, one of the factors influencing the healing of anterior cruciate ligament rupture, we performed experimental anterior cruciate ligament ruptures on New Zealand rabbits. After experimental rupture, intra-articular alpha-2 macroglobulin was injected into the knees of the rabbits in the experiment group to prevent structural changes resulting from the enzymatic reactions in the ruptured anterior cruciate ligament. At the end of 10th day of the experiment, we observed that the anterior cruciate ligaments in the experiment group had retained their prerupture brightness and volume when compared with the control group in which intraarticular alpha-2 macroglobulin had not been injected. We also noted that the anterior cruciate ligaments in the experiment group had not retracted or swollen, the incision sites were regular and clean, and they did not show any signs of degeneration. In the histological examination, the anterior cruciate ligaments in the control groups showed disruption of the collagen network and a significant diminution in number of fibroblasts and fibrocytes (p <.001). At the end of this study, we concluded that the necessary conditions for the healing and repair of ruptured anterior cruciate ligament could exist if the enzymatic and biological environments were under control.
Glycoproteomics Analysis of Human Liver Tissue by Combination of Multiple Enzyme Digestion and Hydrazide Chemistry (2009)

The study of protein glycosylation has lagged far behind the progress of current proteomics because of the enormous complexity, wide dynamic range distribution and low stoichiometric modification of glycoprotein. Solid phase extraction of tryptic N-glycopeptides by hydrazide chemistry is becoming a popular protocol for the analysis of N-glycoproteome. However, in silico digestion of proteins in human proteome database by trypsin indicates that a significant percentage of tryptic N-glycopeptides is not in the preferred detection mass range of shotgun proteomics approach, that is, from 800 to 3500 Da. And the quite big size of glycan groups may block trypsin to access the K, R residues near N-glycosites for digestion, which will result in generation of big glycopeptides. Thus many N-glycosites could not be localized if only trypsin was used to digest proteins. Herein, we describe a comprehensive way to analyze the N-glycoproteome of human liver tissue by combination of hydrazide chemistry method and multiple enzyme digestion. The lysate of human liver tissue was digested with three proteases, that is, trypsin, pepsin and thermolysin, with different specificities, separately. Use of trypsin alone resulted in identification of 622 N-glycosites, while using pepsin and thermolysin resulted in identification of 317 additional N-glycosites. Among the 317 additional N-glycosites, 98 (30.9%) could not be identified by trypsin in theory because the corresponding in silico tryptic peptides are either too small or too big to detect in mass spectrometer. This study clearly demonstrated that the coverage of N-glycosites could be significantly increased due to the adoption of multiple enzyme digestion. A total number of 939 N-glycosites were identified confidently, covering 523 noredundant glycoproteins from human liver tissue, which leads to the establishment of the largest data set of glycoproteome from human liver up to now.
Is hemoglobin level alone a reliable predictor of outcome in the severely anemic surgical patient? (1992)

The relationship between outcome and hemoglobin (Hgb), oxygen extraction ratio (ER), history of cardiac, renal, pulmonary, and/or hepatic disease, diabetes, malignancy, sepsis, hypertension, and active bleeding was analyzed in 47 patients with severe anemia (Hgb less than 7.0 gm/dl, mean = 4.6 +/- .2 gm/dl) to evaluate the effect of Hgb on survival and to look for other predictors of outcome. All patients had refused blood transfusion on religious grounds and were participants in a randomized, controlled study of the blood substitute Fluosol DA-20 per cent. Patients were analyzed as a group and after stratifying by Hgb into four levels: (Hgb less than 3.0 gm/dl, N = 7; Hgb less than 3.5 gm/dl, N = 12; Hgb less than 4.0 gm/dl, N = 17; Hgb less than 4.5 gm/dl, N = 23) and by ER into two levels of less than 50 per cent and greater than 50 per cent. Only Hgb, ER, sepsis and active bleeding were predictors of outcome, with sepsis being the only significant, independent predictor of outcome at all levels (P less than .01). Active bleeding was a predictor for levels of Hgb below 4.0 gm/dl. Hgb level alone was a significant predictor only at levels below 3 gm/dl (P less than .05). Extraction ratio interacted with Hgb only below 3 gm/dl (P less than .05). Multiple independent factors influence outcome in the severely anemic patient, the strongest being sepsis and active bleeding. Prevention of sepsis and early intervention to stop bleeding should improve survival in the patient who refuses transfusion.
The Reliable Multicast Design Space for Bulk Data Transfer (2000)

The design space for reliable multicast is rich, with many possible solutions having been devised.However, application requirements serve to constrain this design space to a relatively small solution space.This document provides an overview of the design space and the ways in which application constraints affect possible solutions.
Quantification of Intermediate-Abundance Proteins in Serum by Multiple Reaction Monitoring Mass Spectrometry in a Single-Quadrupole Ion Trap (2006)

A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this single-quadrupole assay, the coefficients of variance based on 12 repeated measurements for each of the endogenous tryptic peptides were 17.0, 25.4, 24.2, and 14.0% for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively.