gebhart/patrepeval huggingface dataset:
Identification of c-Jun NH2-terminal Protein Kinase (JNK)-activating Kinase 2 as an Activator of JNK but Not p38 (1997)

c-Jun NH2-terminal protein kinase (JNK), a distant member of the mitogen-activated protein (MAP) kinase family, regulates gene expression in response to various extracellular stimuli. JNK is activated by JNK-activating kinase 1 (JNKK1), a dual specificity protein kinase that phosphorylates JNK on threonine 183 and tyrosine 185 residues. Here we show that JNKK2, a novel member of the MAP kinase kinase family, was phosphorylated and activated by MEKK1, a MAP kinase kinase kinase in the JNK signaling cascade. JNKK2 activity was also stimulated by constitutively active forms of Rac and Cdc42Hs, members of the Rho small GTP-binding protein family. Unlike JNKK1 that activates both JNK and p38 MAP kinases, JNKK2 stimulated only JNK. Transient transfection assays demonstrated that JNKK2 potentiated the stimulation of c-Jun transcriptional activity by MEKK1. The existence of multiple JNK-activating kinases may contribute to the specificity of the JNK signaling cascade.
Targeting KIT on Innate Immune Cells to Enhance the Antitumor Activity of Checkpoint Inhibitors (2016)

Innate immune cells such as mast cells and myeloid-derived suppressor cells are key components of the tumor microenvironment. Recent evidence indicates that levels of myeloid-derived suppressor cells in melanoma patients are associated with poor survival to checkpoint inhibitors. This suggests that targeting both the innate and adaptive suppressive components of the immune system will maximize clinical benefit and elicit more durable responses in cancer patients. Preclinical data suggest that targeting signaling by the receptor tyrosine kinase KIT, particularly on mast cells, may modulate innate immune cell numbers and activity in tumors. Here, we review data highlighting the importance of the KIT signaling in regulating antitumor immune responses and the potential benefit of combining selective KIT inhibitors with immune checkpoint inhibitors.
A mechanical analog thoracolumbar spine model for the evaluation of scoliosis bracing technology (2018)

The Scoliosis Analog Model was developed to provide first time measures of the multidirectional forces applied to the spine by a thoracolumbar brace. This test assembly could be used as a future design and testing tool for scoliosis brace technology.
A laboratory comparison of pathogen reduction technology treatment and culture of platelet products for addressing bacterial contamination concerns (2009)

The results from this work suggest that the riboflavin and UV light process may provide up to 98% protection against transfusion of bacterially contaminated units at the most clinically relevant contamination levels (<20 CFUs per product). This compares favorably to the 60% to 66% effectiveness of bacterial culture testing using a 48-hour quarantine period before product release.
Production and characterization of genetically engineered antibody molecules. (1988)

Expression of antibody heavy- and light-chain genes by transfection permits the production of monoclonal antibodies with improved biological and antigen-binding properties. The immunoglobulin genes are placed in vectors containing a gene for encoding a protein that provides a biochemically selectable function in eukaryotic cells; these vectors are transfected into myeloma and hybridoma cells. Selection of drug-resistant cells permits the efficient isolation of the rare cells that express the transfected DNA. By placing heavy and light chains on plasmids with different selectable markers, one can deliver heavy- and light-chain genes simultaneously to the same cell. The transfected immunoglobulin genes are efficiently expressed and the proteins produced are a faithful mirror of the genes that were introduced. Using the standard techniques of genetic engineering and gene transfection, we can now produce antibodies of widely varying structures, including chimeric antibodies with segments derived from different species. These antibodies provide useful reagents to study structure-function relationships within the antibody molecule. Ultimately it will be possible to produce a new generation of antibody molecules with improved antigen-binding properties and effector functions.
Heterogeneity of Endothelial Cells (1997)

During embryonic development, endothelial cells differentiate from a common precursor called angioblast and acquire organ-specific properties. One of the important determinants of endothelial cell differentiation is the local environment, and especially the interaction with surrounding cells. This interaction may occur through the release of soluble cytokines, cell-to-cell adhesion and communication, and the synthesis of matrix proteins on which the endothelium adheres and grows. The acquisition and maintenance of specialized properties by endothelial cells is important in the functional homeostasis of the different organs. For instance, in the brain, alteration of the blood-brain barrier properties may have important consequences on brain functional integrity. One of the major limitations to the study of endothelial cell heterogeneity is the fact that these cells are still difficult to isolate and culture from the microcirculation of different organs, and once in culture, they tend to lose their specialized properties. This finding suggests that we have to develop new culture systems, which possibly include coculture with other cell types. An important issue is to develop tools that can help in recognizing endothelial cells and their differentiated phenotype both in vivo and in tissue culture. In this review we give a short overview of the differentiated properties of the endothelium, considering a few examples of highly specialized endothelial cells, such as the brain or bone marrow microcirculation or high endothelial venules. We made a particular effort to list the most common markers of endothelial cell phenotypes. These molecules and related antibodies may be valuable tools for endothelial cell isolation and characterization.
Strongly phosphorescent platinum(ii) complexes supported by tetradentate benzazole-containing ligands (2015)

A family of rigid platinum(<sc>ii</sc>) complexes based on tetradentate benzazole-containing ligands has been prepared as efficient dopants for high performance phosphorescent green/yellow OLEDs.
Expression, purification and characterization of the recombinant kringle 2 and kringle 3 domains of human plasminogen and analysis of their binding affinity for ω‐aminocarboxylic acids (1994)

The kringle 2 (E161T/C162S/EEE[K2HPg/C169S]TT) and the kringle 3 (TYQ[K3HPg]DS) domains of human plasminogen (HPg) were expressed in Escherichia coli in an expression vector with the phage T5 promotor/operator element N250PSN250P29 and the cDNA sequence for a hexahistidine tail to facilitate the isolation of the recombinant protein. A coagulation factor Xa (FXa)-sensitive cleavage site was introduced to remove the N-terminal histidine tag. In r-K2, mutations E161T and C162S were introduced to enhance the FXa cleavage yield and C169S to replace the cysteine residue, participating in the inter-kringle disulfide bridge between kringles 2 and 3. Recombinant proteins were isolated by affinity chromatography on Ni(2+)-nitrilotriacetic acid/agarose and refolded under denaturing and reducing conditions followed by a non-denaturing and oxidising environment. The free thiol group in position 297 in r-K3 was selectively alkylated with iodoacetamide. The hexahistidine tail was successfully removed with FXa. The N-terminal sequence, the amino acid composition and the molecular mass analyses are in agreement with the expected data. The correct arrangement of the disulfide bonds was verified by sequence analysis of the corresponding thermolytic and subtilisin fragments. r-K2 exhibits weak binding to lysine-Bio-Gel. The weak binding affinity of r-K2 for omega-aminocarboxylic acids is confirmed by intrinsic fluorescence titration with 6-aminohexanoic acid (NH2C5COOH) indicating a Kd of approximately 401 microM. In contrast, r-K3 seems to be devoid of a binding affinity for omega-aminocarboxylic acids. Considering earlier determined Kd values of kringle 1, kringle 4 and kringle 5, the binding affinity of HPg kringle domains for NH2C5COOH is proposed to decrease in the following order, kringle 1 > kringle 4 > kringle 5 > kringle 2 > kringle 3.
QM/MM: what have we learned, where are we, and where do we go from here? (2006)

This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM.
Affinity Purification of DNA and RNA from Environmental Samples with Peptide Nucleic Acid Clamps (2000)

Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sediment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO(4), 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate [SDS]) a PNA clamp recovered significantly more target DNA than either PNA or DNA oligomers. The efficacy of PNA clamps and oligomers was generally enhanced in the presence of excess nontarget DNA and in a low-salt extraction-hybridization buffer. Under high-salt conditions (200 mM NaPO(4), 100 mM disodium EDTA, and 0.5% SDS), however, capture efficiencies with the DNA oligomer were significantly greater than with the PNA clamp and PNA oligomer. Recovery and detection efficiencies for target DNA concentrations of > or =100 pg were generally >20% but depended upon the specific probe, solution background, and salt condition. The DNA probe had a lower absolute detection limit of 100 fg of target (830 zM [1 zM = 10(-21) M]) in high-salt buffer. In the absence of exogenous DNA (e.g., soil background), neither the bis-PNA nor the PNA oligomer achieved the same absolute detection limit even under a more favorable low-salt hybridization condition. In the presence of a soil background, however, both PNA probes provided more sensitive absolute purification and detection (830 zM) than the DNA oligomer. In varied environmental samples, the rank order for capture probe performance in high-salt buffer was DNA > PNA > clamp. Recovery of 16S rRNA from environmental samples mirrored quantitative results for DNA target recovery, with the DNA oligomer generating more positive results than either the bis-PNA or PNA oligomer, but PNA probes provided a greater incidence of detection from environmental samples that also contained a higher concentration of nontarget DNA and RNA. Significant interactions between probe type and environmental sample indicate that the most efficacious capture system depends upon the particular sample type (and background nucleic acid concentration), target (DNA or RNA), and detection objective.
First FDA Approval Agnostic of Cancer Site — When a Biomarker Defines the Indication (2017)

In May 2017, the FDA approved pembrolizumab, a programmed death 1 inhibitor, for adult and pediatric patients with unresectable or metastatic, microsatellite-instability–high or mismatch-repair–deficient solid tumors, regardless of tumor site or histology.
Identified postnatal mesolimbic dopamine neurons in culture: morphology and electrophysiology (1992)

To examine the intrinsic properties of postnatal mesolimbic dopamine (DA) neurons, we dissociated the ventral tegmental area (VTA) from postnatal rats, enriched for DA neurons by microdissection or gradient purification, and grew the cells in culture. In these cultures, up to 50% of neurons were dopaminergic. DA neurons resembled their in vivo counterparts in soma shapes, and in showing two levels of tyrosine hydroxylase (TH) expression, axodendritic differentiation, two sizes of synaptic vesicles, nest-like synaptic arrangements with non-DA cells, and synaptic specializations. Electrophysiologically, however, they could not be distinguished from non-DA cells, which could be consistent with heterogeneity in cell properties. To examine a functional subset of VTA DA neurons, we retrogradely labeled VTA neurons projecting to the nucleus accumbens. These mesoaccumbens neurons were 86% TH positive, 56% cholecystokinin positive, and 0% neurotensin positive; they also displayed the soma shapes characteristic of DA neurons more generally and two levels of TH expression. Like their in vivo counterparts, mesoaccumbens cells generally fired single broad spikes that were triggered by slow depolarizations and had robust spike afterhyperpolarizations, low- and high-threshold Ca2+ spikes, rapid accommodation of firing, time-dependent anomalous rectification, and hyperpolarizing autoreceptor responses. Strikingly, the expression of these active properties did not change with time in culture. Mesoaccumbens DA cells could be identified by a distinctive subset of properties that made up an electrophysiological signature; however, unlike their in vivo counterparts, they were less often spontaneously active and never fired in bursts. These results suggest that most DA cell properties are intrinsic to the cells, including a significant heterogeneity that is maintained in postnatal culture; their level and mode of activity, however, appear to require afferent input. Culturing identified postnatal VTA DA neurons now makes possible examination of the impact of their individual properties on synaptic function.
Multipeptide vaccination in cancer patients (2009)

Since the identification of tumor associated antigens (TAA) in different tumor histotypes, many vaccination strategies have been investigated, including peptide-based vaccines. Results from the first decade of clinical experimentation, though demonstrating the feasibility and the good toxicity profile of this approach, provided evidence of clinical activity only in a minority of patients, despite inducing immunization in up to 50% of them. In this review, we discuss the different approaches recently developed in order to induce stronger peptide-induced immune-mediated tumor growth control, possibly translating into improved clinical response rates, with specific focus on multipeptide-based anti-cancer vaccines. This strategy offers many advantages, such as the possibility of bypassing tumor heterogeneity and selection of antigen (Ag)-negative clones escaping peptide-specific immune responses, or combining HLA class I- and class II-restricted epitopes, thus eliciting both CD4- and CD8-mediated immune recognition. Notably, advances in Ag discovery technologies permit further optimization of peptide selection, in terms of identification of tumor-specific and unique TAA as well as Ags derived from different tumor microenvironment cell components. With the ultimate goal of combining peptide selection with patient-specific immunogenic profile, peptide based anti-cancer vaccines remain a promising treatment for cancer patients, as attested by of pre-clinical and clinical studies.
Genetic instability in pancreatic cancer and poorly differentiated type of gastric cancer. (1993)

To examine genetic instability during carcinogenesis, we screened 171 carcinomas of the breast, liver, proximal colon, stomach, pancreas, uterine cervix, and ovary for replication error at four microsatellite marker loci on chromosome 2, 3, and 17. A significantly high incidence of genetic instability was observed in pancreatic (6 of 9 tumors) and gastric cancers (22 of 57 cases). In other types of carcinoma, the incidence of replication error-positive cases was relatively low (3-16%). Among gastric carcinomas, significantly more replication error-positive cases were observed in the poorly differentiated types (16 of 25 cases) than in well differentiated types (3 of 18) (P = 0.0023 by Fisher's exact test). Our results suggested that genetic instability is likely to play an important role in development of pancreatic and gastric cancers, particularly poorly differentiated adenocarcinomas.
Dynamic Range Control of Digital Audio Signals (1984)

Methodes numeriques pour controler la gamme dynamique des signaux sons numeriques en radiodiffusion. Controleurs destines a proteger l'equipement contre les surcharges et a des fins artistiques
Identification of Target Messenger RNA Substrates for the Murine Deleted in Azoospermia-Like RNA-Binding Protein1 (2002)

The murine autosomal deleted in azoospermia-like protein (mDAZL) is a germ cell-restricted RNA-binding protein essential for sperm production. Homozygous disruption of the mDAZL gene results in the absence of germ cells beyond the spermatogonial stage. Progress into the function of DAZL in spermatogenesis has been hampered without identification of the cognate mRNA substrates that it binds to and regulates. Using the isolation of specific nucleic acids associated with proteins (SNAAP) technique recently developed in our lab, we identified mRNAs from testis that were specifically bound by mDAZL. One mRNA encoded the Tpx-1 protein, a testicular cell adhesion protein essential for the progression of spermatogenesis. A 26-nucleotide region necessary and sufficient to bind mDAZL was found within additional mRNAs isolated by the screen. These included mRNA encoding Pam, a protein associated with myc; GRSF1, an mRNA-binding protein involved in translation activation, and TRF2, a TATA box-binding protein-like protein involved in transcriptional regulation. Each mRNA containing the mDAZL binding site was specifically bound by mDAZL. A similar sequence is also present in the Cdc25A mRNA, a threonine/tyrosine phosphatase involved in cell cycle progression. The mDAZL and Cdc25A homologues are functionally linked in Drosophila and are necessary for spermatogenesis. Our demonstration that Tpx-1 and Cdc25A mRNAs are bound by mDAZL suggests that mDAZL regulates a subset of mRNAs necessary for germ cell development and cell cycle progression. Understanding how mDAZL regulates the target mRNAs will provide new insights into spermatogenesis, strategies for therapeutic intervention in azoospermic patients, and novel approaches for male contraception.
Identification of Oct4-activating compounds that enhance reprogramming efficiency (2012)

One of the hurdles for practical application of induced pluripotent stem cells (iPSC) is the low efficiency and slow process of reprogramming. Octamer-binding transcription factor 4 (Oct4) has been shown to be an essential regulator of embryonic stem cell (ESC) pluripotency and key to the reprogramming process. To identify small molecules that enhance reprogramming efficiency, we performed a cell-based high-throughput screening of chemical libraries. One of the compounds, termed Oct4-activating compound 1 (OAC1), was found to activate both Oct4 and Nanog promoter-driven luciferase reporter genes. Furthermore, when added to the reprogramming mixture along with the quartet reprogramming factors (Oct4, Sox2, c-Myc, and Klf4), OAC1 enhanced the iPSC reprogramming efficiency and accelerated the reprogramming process. Two structural analogs of OAC1 also activated Oct4 and Nanog promoters and enhanced iPSC formation. The iPSC colonies derived using the Oct4-activating compounds along with the quartet factors exhibited typical ESC morphology, gene-expression pattern, and developmental potential. OAC1 seems to enhance reprogramming efficiency in a unique manner, independent of either inhibition of the p53-p21 pathway or activation of the Wnt-β-catenin signaling. OAC1 increases transcription of the Oct4-Nanog-Sox2 triad and Tet1, a gene known to be involved in DNA demethylation.
A non‐invasive tape absorption method for recovery of inflammatory mediators to differentiate normal from compromised scalp conditions (2002)

The Sebutape method has proven useful for distinguishing normal from diseased scalp conditions. The cytokines recovered from the scalp tape samples showed distinct patterns that differentiated dandruff, seborrheic dermatitis and normal scalp populations. These methods may also prove useful for monitoring the clinical efficacy of therapeutic actives for treating dandruff and seborrhea.
Therapeutic strategies for spinal muscular atrophy: SMN and beyond (2017)

Spinal muscular atrophy (SMA) is a devastating neuromuscular disorder characterized by loss of motor neurons and muscle atrophy, generally presenting in childhood. SMA is caused by low levels of the survival motor neuron protein (SMN) due to inactivating mutations in the encoding gene <i>SMN1</i> A second duplicated gene, <i>SMN2</i>, produces very little but sufficient functional protein for survival. Therapeutic strategies to increase SMN are in clinical trials, and the first <i>SMN2</i>-directed antisense oligonucleotide (ASO) therapy has recently been licensed. However, several factors suggest that complementary strategies may be needed for the long-term maintenance of neuromuscular and other functions in SMA patients. Pre-clinical SMA models demonstrate that the requirement for SMN protein is highest when the structural connections of the neuromuscular system are being established, from late fetal life throughout infancy. Augmenting SMN may not address the slow neurodegenerative process underlying progressive functional decline beyond childhood in less severe types of SMA. Furthermore, individuals receiving SMN-based treatments may be vulnerable to delayed symptoms if rescue of the neuromuscular system is incomplete. Finally, a large number of older patients living with SMA do not fulfill the present criteria for inclusion in gene therapy and ASO clinical trials, and may not benefit from SMN-inducing treatments. Therefore, a comprehensive whole-lifespan approach to SMA therapy is required that includes both SMN-dependent and SMN-independent strategies that treat the CNS and periphery. Here, we review the range of non-SMN pathways implicated in SMA pathophysiology and discuss how various model systems can serve as valuable tools for SMA drug discovery.
Protection from experimental autoimmune diabetes in the non‐obese diabetic mouse with soluble interleukin‐1 receptor (1994)

We have evaluated the effects of a treatment with soluble interleukin-1 receptor (sIL-1R) in the accelerated model of autoimmune diabetes induced by cyclophosphamide (CY) in the non-obese diabetic (NOD) mouse. Prior to the CY challenge (350 mgkg body weight), female euglycemic NOD mice were randomly divided into three groups (A-C). Groups B and C were treated daily from 1 day before to 13 days after the CY challenge with sIL-1R at doses of 0.2 and 2 mg/kg body weight. Group A was treated with PBS. By 2 weeks after CY administration, an acute form of autoimmune diabetes with glycosuria, hyperglycemia and severe insulitis occurred in the majority (13/20, 65%) of the control mice (group A). In contrast, repeated injections with sIL-1R protected NOD mice from insulin-dependent diabetes mellitus (IDDM) development in a dose-dependent fashion; the incidence of IDDM was 53.3% (8/15) in the mice treated with 0.2 mg/kg and only 6.7% (1/15) in those treated with 2 mg/kg. However, none of the doses of the sIL-1R reduced the extent of insulitis in NOD mice. Importantly, the anti-diabetogenic property of sIL-1R may not involve major T cell function impairment; accordingly, in parallel experiments, splenic lymphoid cells from NOD mice not challenged with CY, but treated with 2 mg/kg sIL-1R for 5 consecutive days showed a normal distribution of mononuclear cell subsets and maintained their capacity to secrete interferon-gamma and IL-2 and to proliferate in response to polyclonal mitogenic stimulation with concanavalin A.