gebhart/patrepeval huggingface dataset:
Multivalent nanobodies targeting death receptor 5 elicit superior tumor cell killing through efficient caspase induction (2014)

Multiple therapeutic agonists of death receptor 5 (DR5) have been developed and are under clinical evaluation. Although these agonists demonstrate significant anti-tumor activity in preclinical models, the clinical efficacy in human cancer patients has been notably disappointing. One possible explanation might be that the current classes of therapeutic molecules are not sufficiently potent to elicit significant response in patients, particularly for dimeric antibody agonists that require secondary cross-linking via Fcγ receptors expressed on immune cells to achieve optimal clustering of DR5. To overcome this limitation, a novel multivalent Nanobody approach was taken with the goal of generating a significantly more potent DR5 agonist. In the present study, we show that trivalent DR5 targeting Nanobodies mimic the activity of natural ligand, and furthermore, increasing the valency of domains to tetramer and pentamer markedly increased potency of cell killing on tumor cells, with pentamers being more potent than tetramers in vitro. Increased potency was attributed to faster kinetics of death-inducing signaling complex assembly and caspase-8 and caspase-3 activation. In vivo, multivalent Nanobody molecules elicited superior anti-tumor activity compared to a conventional DR5 agonist antibody, including the ability to induce tumor regression in an insensitive patient-derived primary pancreatic tumor model. Furthermore, complete responses to Nanobody treatment were obtained in up to 50% of patient-derived primary pancreatic and colon tumor models, suggesting that multivalent DR5 Nanobodies may represent a significant new therapeutic modality for targeting death receptor signaling.
TRPV3 and TRPV4 Mediate Warmth-evoked Currents in Primary Mouse Keratinocytes (2004)

Recently, a family of temperature-activated ion channels has been identified in mammalian and nonmammalian species that appear to contribute to thermosensation. Two of these proteins, TRPV3 and TRPV4, are ion channels activated by modest increases in ambient temperature. Localization studies have indicated that both proteins, in addition to being expressed in sensory neurons, are also expressed in skin keratinocytes. These and other findings have suggested that keratinocytes might act in concert with sensory neurons to perceive our thermal environment. In this study, we demonstrate that primary keratinocytes isolated from mouse skin exhibit two distinct heat-evoked current responses to mild increases in ambient temperature. The more common of these response types bears considerable similarity to responses mediated by recombinant TRPV4, is absent in mice lacking this ion channel, and is restored upon TRPV4 reintroduction. The second, rarer response strongly resembles those mediated by recombinant TRPV3. Together, these findings demonstrate that keratinocytes can indeed act as thermosensory cells and that they do so via at least two distinct transduction mechanisms.
Supraventricular Tachycardia (1995)

Supraventricular tachycardia is any tachyarrhythmia that requires atrial or atrioventricular junctional tissue for its initiation and maintenance. Decades ago the term “paroxysmal atrial tachycardia” was coined to describe supraventricular tachycardia that began and ended abruptly. This term has become obsolete, however, since it is now clear that many such arrhythmias arise in the atrioventricular junction, not in atrial muscle itself. Much of our present knowledge about the sites of origin and mechanisms of supraventricular tachycardia has been derived from cellular electrophysiologic studies and from clinical electrophysiologic studies using the technique of programmed electrical stimulation.1,2 We have learned that such . . .
The Oncogenic TLS-ERG Fusion Protein Exerts Different Effects in Hematopoietic Cells and Fibroblasts (2005)

The oncogenic TLS-ERG fusion protein is found in human myeloid leukemia and Ewing's sarcoma as a result of specific chromosomal translocation. To unveil the potential mechanism(s) underlying cellular transformation, we have investigated the effects of TLS-ERG on both gene transcription and RNA splicing. Here we show that the TLS protein forms complexes with RNA polymerase II (Pol II) and the serine-arginine family of splicing factors in vivo. Deletion analysis of TLS-ERG in both mouse L-G myeloid progenitor cells and NIH 3T3 fibroblasts revealed that the RNA Pol II-interacting domain of TLS-ERG resides within the first 173 amino acids. While TLS-ERG repressed expression of the luciferase reporter gene driven by glycoprotein IX promoter in L-G cells but not in NIH 3T3 cells, the fusion protein was able to affect splicing of the E1A reporter in NIH 3T3 cells but not in L-G cells. To identify potential target genes of TLS-ERG, the fusion protein and its mutants were stably expressed in both L-G and NIH 3T3 cells through retroviral transduction. Microarray analysis of RNA samples from these cells showed that TLS-ERG activates two different sets of genes sharing little similarity in the two cell lines. Taken together, these results suggest that the oncogenic TLS-ERG fusion protein transforms hematopoietic cells and fibroblasts via different pathways.
Clinical and Financial Outcomes Due to Methicillin Resistant Staphylococcus aureus Surgical Site Infection: A Multi-Center Matched Outcomes Study (2009)

The attributable impact of S. aureus and methicillin-resistance on outcomes of surgical patients is substantial. Preventing a single case of SSI due to MRSA can save hospitals as much as $60,000.
Social Recognition Memory Test in Rodents (2016)

Social recognition memory is essential for the establishment and maintenance of a rodent colony. Recognition memory is important for social hierarchy, mate and offspring recognition, and interspecies recognition. Interspecies recognition is vital for recognizing frequent visitors to the animal’s habitat and whether or not the visitors pose a threat to the animals or colony (Macbeth et al., 2009; Noack et al., 2010). Here, we describe a protocol which effectively and reproducibly measures the social recognition for a juvenile male, a female, a mouse of another strain, and a rat. This task relies on the animal’s innate tendency to explore a novel social partner and decrease the exploration of a known familiar social partner (Thor et al., 1982). A significant decrease in the exploration of a partner from the training session to the recall session demonstrates a memory of the social partner. Also, we describe a social recognition procedure, the habituation-dishabituation paradigm that closely mimics typical short, frequent interactions between animals in a colony (Dantzer et al., 1987; Winslow and Camacho, 1995). Further, olfaction is a key component of social recognition, to test olfaction see Jacobs et al. (2016). In this protocol, we use transgenic NR2A overexpression mice to demonstrate how an impairment in social recognition memory may appear.
Dynamics of NF κB and IκBα Studied with Green Fluorescent Protein (GFP) Fusion Proteins (2000)

We investigated the dynamics of nuclear transcription factor kappaB (NF-kappaB) by using fusion proteins of the p65 subunit with mutants of green fluorescent protein (GFP). GFP-NF-kappaB chimeras were functional both in vitro and in vivo, as demonstrated by electrophoretic mobility shift assays and reporter gene studies. GFP-p65 was regulated by IkappaBalpha similar to wild type p65 and associated with its inhibitor even if both proteins were linked to a GFP protein. This finding was also verified by fluorescence resonance energy transfer (FRET) microscopy and studies showing mutual regulation of the intracellular localization of both GFP chimerae. Incubation of GFP-p65 with fluorescently labeled NF-kappaB-binding oligonucleotides also resulted in FRET. This effect was DNA sequence-specific and exhibited saturation characteristics. Application of stopped-flow fluorometry to measure the kinetics of FRET between GFP-p65 and oligonucleotides revealed a fast increase of acceptor fluorescence with a plateau after about 10 ms. The observed initial binding rate showed a temperature-dependent linear correlation with the oligonucleotide concentration. The association constant calculated according to pre-steady state kinetics was 3 x 10(6) m(-1), although equilibrium binding studies implied significantly higher values. This observation suggests that the binding process involves a rapid association with a rather high off-rate followed by a conformational change resulting in an increase of the association constant.
Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents (2014)

The cardiac action potential (AP) and the consequent cytosolic Ca(2+) transient are key indicators of cardiac function. Natural developmental processes, as well as many drugs and pathologies change the waveform, propagation, or variability (between cells or over time) of these parameters. Here we apply a genetically encoded dual-function calcium and voltage reporter (CaViar) to study the development of the zebrafish heart in vivo between 1.5 and 4 days post fertilization (dpf). We developed a high-sensitivity spinning disk confocal microscope and associated software for simultaneous three-dimensional optical mapping of voltage and calcium. We produced a transgenic zebrafish line expressing CaViar under control of the heart-specific cmlc2 promoter, and applied ion channel blockers at a series of developmental stages to map the maturation of the action potential in vivo. Early in development, the AP initiated via a calcium current through L-type calcium channels. Between 90 and 102 h post fertilization (hpf), the ventricular AP switched to a sodium-driven upswing, while the atrial AP remained calcium driven. In the adult zebrafish heart, a sodium current drives the AP in both the atrium and ventricle. Simultaneous voltage and calcium imaging with genetically encoded reporters provides a new approach for monitoring cardiac development, and the effects of drugs on cardiac function.
Cycle length dependence of human action potential duration in vivo. Effects of single extrastimuli, sudden sustained rate acceleration and deceleration, and different steady-state frequencies. (1988)

Using a new method for long-term recording of monophasic action potentials from the human heart, we studied in 17 patients the effects on ventricular action potential duration (APD) of three clinically pertinent cycle length perturbations: (1) single extrastimuli, (2) abrupt sustained rate acceleration and deceleration, and (3) different steady-state cycle lengths. Results were: (a) APD after single extrastimuli at progressively longer cycle lengths were related to the extrastimulus cycle length with a biphasic electrical restitution curve which after an initial steep rise and a subsequent transient descent rose again more gradually to a plateau at cycle lengths above 800-1,000 ms. (b) After a sustained step decrease in cycle length, the first APD shortened abruptly while final steady-state adaptation required up to several minutes. The transition between the rapid and slow phase of APD change was characterized by a variable alternans of APD which correlated inversely with the preceding diastolic interval. (c) In the steady state, APD correlated linearly with cycle length, increasing an average of 23 ms per 100 ms cycle length increase (r = 0.995). The divergence between steady-state and non-steady-state APD, and the slowness of steady-state adaptation, are important factors to be considered in clinical electrophysiologic studies and in rate correction algorithms of APD or QT intervals, respectively.
Antimicrobial Peptides Human β-Defensins and Cathelicidin LL-37 Induce the Secretion of a Pruritogenic Cytokine IL-31 by Human Mast Cells (2010)

In addition to their microbiocidal properties, human beta-defensins (hBDs) and cathelicidin LL-37 stimulate a number of mammalian cell activities, including migration, proliferation, and cytokine/chemokine production. Because hBDs and LL-37 cause mast cells to release pruritogens such as histamine and PGs, we hypothesized that these peptides would stimulate the secretion of a novel pruritogenic mediator IL-31, predominantly produced by T cells. hBDs and LL-37 enhanced IL-31 gene expression and IL-31 protein production and release in the human mast cell line LAD2, as well as in peripheral blood-derived cultured mast cells, suggesting that mast cells are another source of IL-31. Moreover, the expression of IL-31 was elevated in psoriatic skin mast cells, and hBD-2-4 and LL-37, but not hBD-1, enhanced its expression in vivo in rat skin mast cells. hBDs and LL-37 also induced the release of other pruritogenic mediators, including IL-2, IL-4, IL-6, GM-CSF, nerve growth factor, PGE(2), and leukotriene C(4), and increased mRNA expression of substance P. hBD- and LL-37-mediated IL-31 production/release was markedly reduced by pertussis toxin and wortmannin, inhibitors of G-protein and PI3K, respectively. As evidenced by the inhibitory effects of MAPK-specific inhibitors, hBD-2-4 and LL-37 activated the phosphorylation of MAPKs p38, ERK, and JNK that were required for IL-31 production and release. The ability of hBDs and LL-37 to stimulate the production and release of IL-31 by human mast cells provides a novel mechanism by which skin-derived antimicrobial peptides/proteins may contribute to inflammatory reactions and suggests a central role of these peptides in the pathogenesis of skin disorders.
Lysine 63-linked polyubiquitin potentially partners with p62 to promote the clearance of protein inclusions by autophagy (2008)

AbstractAlthough protein inclusions associated with neurodegenerative diseases are typically enriched with ubiquitin, it is currently unclear whether the topology of ubiquitin linkage plays a role in their biogenesis. In an attempt to clarify this, our recent work identified K63-linked polyubiquitin as a key regulator of inclusion dynamics. We found in the setting of ectopic overexpression of different ubiquitin species in cultured cells that K63-linked ubiquitination promotes the formation and autophagic clearance of protein inclusions linked to several major neurodegenerative diseases. Further supporting this, we report here a similar phenomenon in cells co-expressing Ubc13 and Uev1a but not those expressing UbcH7 or UbcH8. Notably, Ubc13 in association with Uev1a is known to promote K63-linked ubiquitination. In exploring how K63-linked ubiquitination could promote the clearance of inclusions by autophagy, we also found in our current study that K63-linked polyubiquitin interacts with p62, a ubiquitin-binding protein previously demonstrated by others to facilitate autophagy-mediated clearance of inclusions. Further, K63 ubiquitin-positive inclusions were found to be enriched with p62. Given the observed intimate relationship between p62 and K63 polyubiquitin, our results suggest that p62 and K63-linked polyubiquitin may function as key partners involved in directing clearance of protein inclusions by autophagy.Addendum to: Tan JMM, Wong ESP, Kirkpatrick DS, Pletnikova O, Ko HS, Tay S-P, Ho M.W.L., Troncoso J, Gygi SP, Lee MK, Dawson VL, Dawson TM, Lim K-L. Lysine 63-linked ubiquitination promotes the formation and autophagic clearance of protein inclusions associated with neurodegenerative diseases. Human Mol Genet; In press.
Avibactam is a covalent, reversible, non–β-lactam β-lactamase inhibitor (2012)

Avibactam is a β-lactamase inhibitor that is in clinical development, combined with β-lactam partners, for the treatment of bacterial infections comprising gram-negative organisms. Avibactam is a structural class of inhibitor that does not contain a β-lactam core but maintains the capacity to covalently acylate its β-lactamase targets. Using the TEM-1 enzyme, we characterized avibactam inhibition by measuring the on-rate for acylation and the off-rate for deacylation. The deacylation off-rate was 0.045 min(-1), which allowed investigation of the deacylation route from TEM-1. Using NMR and MS, we showed that deacylation proceeds through regeneration of intact avibactam and not hydrolysis. Other than TEM-1, four additional clinically relevant β-lactamases were shown to release intact avibactam after being acylated. We showed that avibactam is a covalent, slowly reversible inhibitor, which is a unique mechanism of inhibition among β-lactamase inhibitors.
Triple Negative Breast Cancer: From Molecular Portrait to Therapeutic Intervention (2010)

Triple negative breast cancer is a subtype of breast cancer that lacks expression of an estrogen receptor (ER), a progesterone receptor (PR), and HER2. It is characterized by its unique molecular profile, aggressive behavior, and distinct pattern of metastasis. Epidemiological studies show a high prevalence of triple negative breast cancer among younger women and those of African descent. Although sensitive to chemotherapy, early relapse is common, and a predilection for visceral metastasis, including brain metastasis, has been described. Gene-expression profiling approaches demonstrated that triple negative breast cancer is a heterogeneous group of diseases composed of different, molecularly distinct subtypes. Although not synonymous, the majority of triple negative breast cancers carry the "basal-like" molecular profile on gene-expression arrays. However, several studies have shown that triple negative breast cancer includes tumors with a non-basal expression profile and, in particular, the "normal-breast," the "multiple marker negative," and the recently identified "claudin-negative" subtypes. Target-based agents, including epidermal growth factor receptor (EGFR), vascular endothelial growth factor (VEGF), and poly-ADP-ribose polymerase (PARP) inhibitors, are currently in clinical trials and hold promise in the treatment of this aggressive disease.
Atrial natriuretic factor inhibits mitogen‐induced growth in aortic smooth muscle cells (2002)

Atrial natriuretic factor (ANF) is a polypeptide able to affect cardiovascular homeostasis exhibiting diuretic, natriuretic, and vasorelaxant activities. ANF shows antimitogenic effects in different cell types acting through R(2) receptor. Excessive proliferation of smooth muscle cells is a common phenomenon in diseases such as atherosclerosis, but the role of growth factors in the mechanism which modulate this process has yet to be clarified. The potential antimitogenic role of ANF on the cell growth induced by growth factors appears very intriguing. Aim of the present study was to investigate the possible involvement of ANF on rat aortic smooth muscle (RASM) cells proliferation induced by known mitogens and the mechanism involved. Our data show that ANF, at physiological concentration range, inhibits RASM cell proliferation induced by known mitogens such as PDGF and insulin, and the effect seems to be elicited through the modulation of phosphatidic acid (PA) production and MAP kinases involvement.
Liquid-Phase Synthesis of Naturally Occurring Peptides, II. Syntheses of Three Mast Cell Degranulating Tetradecapeptide Amides from Wasp Venoms (1981)

The liquid-phase synthesis of three tetradecapeptideamides corresponding to the amino acid sequences of the wasp venoms mastoparan, mastoparan X, and Polistes mastoparan is described. The 4-(aminomethyl)-3-nitrobenzoyl-amino-poly(ethylene glycol) monomethyl ether was employed as the soluble support, and the completed peptideamides were cleaved from it by photolysis at 350 nm. After removal of protecting groups, the free peptide amides were purified by column chromatography on Sephadex G-25, and found to have expected elemental and amino acid composition; a satisfactory recovery of tryptophan from synthetic Mastoparan X and Polistes Mastoparan suggests that no extensive destruction of its indole ring occurred during the photolysis. The peptideamides so obtained are active in degranulating the rat peritoneal mast cells.
Application of a Sol Particle Immunoassay to the Determination of Affinity Constants of Monoclonal Antibodies (1991)

The affinity constants (Ka) of monoclonal antibodies (MAb) for binding to their corresponding antigens (Ag), unlabelled and in buffered solution were determined by the following procedure: 1. Incubation of MAb (fixed concentration) with Ag (concentration dilution series). 2. Rapid bound/free separation by adding immobilized second antibody, followed by centrifugation. 3. Determination of free Ag in the supernatant using a gold sol particle agglutination immunoassay (SPIA) in a microtitration plate format. 4. Calculations and interpretation were based on Scatchard and Sips plots. Ka values found by this procedure were found to be similar to those obtained by a radio-immunoassay (RIA) procedure. The present method avoids possible artefacts in Ka values introduced by the procedure or chemical modification due to labelling of MAb or Ag. It enables rapid, simultaneous screening of a considerable number of different MAbs under non-specialized (i.e. RIA) laboratory conditions.
Robbins pathologic basis of disease (1989)

Robbins pathologic basis of disease , Robbins pathologic basis of disease , کتابخانه الکترونیک و دیجیتال - آذرسا
Mapping Fusarium solani and Aphanomyces euteiches Root Rot Resistance and Root Architecture Quantitative Trait Loci in Common Bean (2015)

ABSTRACT Root rot diseases of bean ( Phaseolus vulgaris L.) are a constraint to dry and snap bean production. We developed the RR138 RI mapping population from the cross of OSU5446, a susceptible line that meets current snap bean processing industry standards, and RR6950, a root rot resistant dry bean with small brown seeds. We evaluated the RR138 RI population beginning in the F 6 generation for resistance to Fusarium solani f. sp. phaseoli (Burk.) root rot in Oregon and Aphanomyces euteiches (Drechsler) root rot in Wisconsin. The population was evaluated for a set of root architecture traits at the Oregon location. Fusarium solani root rot resistance was evaluated in three seasons, whereas A. euteiches resistance was evaluated in two seasons. For each disease, RR6950 was resistant and OSU 5446 was susceptible. The recombinant inbred (RI) population was normally distributed for reaction to both diseases. We assembled a high‐density linkage map using 1689 single‐nucleotide polymorphisms (SNPs) from an Illumina 6000‐SNP BARCbean6K_3 Beadchip. The map spanned 1196 cM over 11 linkage groups at a density of one SNP per 1.4 cM. Three quantitative trait loci (QTL) associated with A. euteiches were identified, each accounting for 5 to 15% of the total genetic variation, and two QTL associated with F. solani resistance accounted for 9 and 22% of the total genetic variation. A QTL for taproot diameter (TD) and one QTL for basal root angle were identified. The QTL for resistance to the two diseases mapped to different genome locations indicating a different genetic control.