gebhart/patrepeval huggingface dataset:
Role of the LFA3-CD2 interaction in human specific B cell differentiation. (1988)

We examined the role of the lymphocyte function-associated (LFA)3 molecule in human B cell response. A mAb to this molecule did not influence B cell proliferation induced by anti-mu antibody and IL. In contrast, the same mAb inhibited the specific T-dependent B cell response induced by a particulate Ag. In the same line, two anti-CD2 mAb (directed toward the T11-1 and T11-2 epitopes) inhibited this response, whether used alone or in association. These inhibitions took place at an early stage of the response, and anti-LFA3 and anti-CD2 mAb acted on B cells and T cells, respectively. In contrast, when T cell help was provided by exogenous IL-2, the B cell response was resistant to the inhibitory effect of anti-LFA3 mAb. Taken together, these results indicate that the LFA3-CD2 pair play a major role in the direct T-B interaction required for T cell help.
Effect of acidic pH on flow cytometric detection of bacteria stained with SYBR Green I and their distinction from background (2013)

Unspecific background caused by biotic or abiotic particles, cellular debris, or autofluorescence is a well-known interfering parameter when applying flow cytometry to the detection of microorganisms in combination with fluorescent dyes. We present here an attempt to suppress the background signal intensity and thus to improve the detection of microorganisms using the nucleic acid stain SYBR<sup>®</sup> Green I. It has been observed that the fluorescent signals from SYBR Green I are greatly reduced at acidic pH. When lowering the pH of pre-stained samples directly prior to flow cytometric analysis, we hypothesized that the signals from particles and cells with membrane damage might therefore be reduced. Signals from intact cells, temporarily maintaining a neutral cytosolic pH, should not be affected. We show here that this principle holds true for lowering background interference, whereas the signals of membrane-compromised dead cells are only affected weakly. Signals from intact live cells at low pH were mostly comparable to signals without acidification. Although this study was solely performed with SYBR<sup>®</sup> Green I, the principle of low pH flow cytometry (low pH-FCM) might hold promise when analyzing complex matrices with an abundance of non-cellular matter, especially when expanded to non-DNA binding dyes with a stronger pH dependence of fluorescence than SYBR Green I and a higher pK<sub>a</sub> value.
Impairment of lymphopoiesis and myelopoiesis in mice reconstituted with bone marrow–hematopoietic progenitor cells expressing SDF-1–intrakine (2000)

Both SDF-1 and CXCR4 disruption are lethal to mice at the embryonic stage and cause abnormalities in B lymphopoiesis, myelopoiesis, cardiogenesis, vasculogenesis, and cerebellar development. To investigate the role of SDF-1 and CXCR4 in hematopoiesis during the adult stage, mice reconstituted with bone marrow–derived hematopoietic progenitor cells transduced with either the SDF-1 or a genetically modified SDF-1–intrakine gene using a retroviral expression vector were analyzed. Flow cytometric (FCM) analysis showed a dramatic reduction of CXCR4 expression on the cells of intrakine-transduced mice, whereas CCR7 and CCR1 expression was unchanged or marginally decreased on splenocytes. Migration of splenocytes and bone marrow cells to SDF-1 was markedly suppressed in intrakine-transduced mice. FCM analysis of bone marrow cells of intrakine-transduced mice exhibited decreased numbers of pro-B (B220+ CD43+), pre-B (B220+CD43−), and immature B (B220+IgM+) cells and a decreased number of granulocytes/myeloid (Gr1+ CD11b+) cells. Impaired B lymphopoiesis and myelopoiesis in intrakine-transduced mice were confirmed by an in vitro colony-forming assay of bone marrow cells. In contrast, B lymphopoiesis and myelopoiesis were enhanced in SDF-1–transduced mice. Interestingly, T-cell maturation in the thymus was impaired both in intrakine- and SDF-1–transduced mice, suggesting that SDF-1 and CXCR4 play an important role in T lymphopoiesis as well as in B lymphopoiesis and myelopoiesis in adults. These results demonstrate an essential role of CXCR4 and its ligand SDF-1 in adult hematopoiesis, and they indicate the intrakine method as a powerful tool for functional analysis of chemokines/chemokine receptors in vivo and as a potential therapeutic approach for acquired immunodeficiency syndrome.
Glucose Stimulates Translocation of the Homeodomain Transcription Factor PDX1 from the Cytoplasm to the Nucleus in Pancreatic β-Cells (1999)

One of the mechanisms whereby glucose stimulates insulin gene transcription in pancreatic beta-cells involves activation of the homeodomain transcription factor PDX1 (pancreatic/duodenal homeobox-1) via a stress-activated pathway involving stress-activated protein kinase 2 (SAPK2, also termed RK/p38, CSBP, and Mxi2). In the present study we show, by Western blotting and electrophoretic mobility shift assay, that in human islets of Langerhans incubated in low glucose (3 mM) PDX1 exists as an inactive 31-kDa protein localized exclusively in the cytoplasm. Transfer of the islets to high (16 mM) glucose results in rapid (within 10 min) conversion of PDX1 to an active 46-kDa form that was present predominantly in the nucleus. Activation of PDX1 appears to involve phosphorylation, as shown by incorporation of 32Pi into the 46-kDa form of the protein. These effects of glucose could be mimicked by chemical stress (sodium arsenite), or by overexpression of SAPK2 in the beta-cell line MIN6. Overexpression of SAPK2 also stimulated PDX1-dependent transcription of a -50 to -250 region of the human insulin gene promoter linked to a firefly luciferase reporter gene. The effects of glucose were inhibited by the SAPK2 inhibitor SB 203580, and by wortmannin and LY 294002, which inhibit phosphatidylinositol 3-kinase, although the effects of stress (arsenite) were inhibited only by SB 203580. These results demonstrate that glucose regulates the insulin gene promoter through activation and nuclear translocation of PDX1 via the SAPK2 pathway.
Is Diabetes a Risk Factor for Patients Undergoing Open Abdominal Aortic Aneurysm Repair? (2002)

A number of studies have compared results after aortic procedures in diabetics vs nondiabetics but few have focused specifically on abdominal aortic aneurysm surgery. An analysis of prospective data was carried out in the Vascular Surgery Registry (Beth Israel Deaconess Medical Center, Boston, MA) and identified 421 patients (422 grafts) who underwent elective open repair of an abdominal aortic aneurysm between 1990 and 1999. The influence of diabetes mellitus on outcome was assessed by dividing the patients into two groups: 52 diabetic and 370 nondiabetic patients. Postoperative mortality was 1.7% overall (n = 7) and proportionally higher in the diabetic population, although this did not reach statistical significance (3.8% vs 1.4%, p = 0.19). However, cumulative survival at 1 year and 3 years was essentially identical for diabetic vs nondiabetic patients (91.0% vs 92.6% and 70.0% vs 73.5%, respectively) and did not diverge until 5 years after surgery (25.0% vs 50.9% respectively [p > 0.05]). Overall, major complications occurred in 11 diabetics (21.2%) vs 58 nondiabetics (15.7%, p = 0.32). Specific complications that were increased in the diabetic population included pancreatitis (5.8% vs 1.1%, p = 0.01) and pneumonia (11.5% vs 3.2%, p = 0.006). Notably, overall cardiac morbidity was not higher in patients with diabetes mellitus (1.9% vs 4.3%, p = 0.41). Our data suggest that after elective open abdominal aortic aneurysm repair, patients with diabetes mellitus may have a higher rate of certain complications when compared to patients without diabetes mellitus. These differences however, do not preclude the expectation of excellent results of open abdominal aortic aneurysm repair in patients with diabetes mellitus.
A new wavelet function for audio and speech processing (2007)

A new mother wavelet function is proposed, for audio and speech signal processing, which based on an inner ear model and a critical band concept that allows to emulate the ear behavior. When proposed wavelet function is used in pattern recognition applications, it performs the feature extraction of speech and audio segments, using signal decomposition similar to that taking place in the basilar membrane.
C-Glycoside Clustering on Calix[4]arene, Adamantane, and Benzene Scaffolds through 1,2,3-Triazole Linkers (2006)

A route has been paved toward the preparation of triazole glycocluster libraries via the copper(I)-catalyzed modern version of the classical Huisgen 1,3-dipolar cycloaddition of azides to alkynes. Up to four 1,4-disubstituted 1,2,3-triazole rings bearing carbon-linked glycosyl fragments were constructed on various scaffolds via multiple cycloadditions of suitably polyfunctionalized calix[4]arene, adamantane, and benzene derivatives with ethynyl and azidomethyl C-glycosides. Each cycloaddition occurred with high regioselectivity to give exclusively the 1,4-disubstituted triazole ring in very high yield up to an average value of 98%. The high degree of efficiency of this approach and its wide scope constitute a simple and practical means for the attachment of various sugar units to polyfunctionalized substrates.
Stem Cells in Wound Healing: The Future of Regenerative Medicine? A Mini-Review (2015)

The increased risk of disease and decreased capacity to respond to tissue insult in the setting of aging results from complex changes in homeostatic mechanisms, including the regulation of oxidative stress and cellular heterogeneity. In aged skin, the healing capacity is markedly diminished resulting in a high risk for chronic wounds. Stem cell-based therapies have the potential to enhance cutaneous regeneration, largely through trophic and paracrine activity. Candidate cell populations for therapeutic application include adult mesenchymal stem cells, embryonic stem cells and induced pluripotent stem cells. Autologous cell-based approaches are ideal to minimize immune rejection but may be limited by the declining cellular function associated with aging. One strategy to overcome age-related impairments in various stem cell populations is to identify and enrich with functionally superior stem cell subsets via single cell transcriptomics. Another approach is to optimize cell delivery to the harsh environment of aged wounds via scaffold-based cell applications to enhance engraftment and paracrine activity of therapeutic stem cells. In this review, we shed light on challenges and recent advances surrounding stem cell therapies for wound healing and discuss limitations for their clinical adoption.
Metastamir: The Field of Metastasis-Regulatory microRNA Is Spreading (2009)

Despite advancements in knowledge from more than a century of metastasis research, the genetic programs and molecular mechanisms required for cancer metastasis are still incompletely understood. Genes that specifically regulate the process of metastasis are useful tools to elucidate molecular mechanisms and may become markers and/or targets for antimetastatic therapy. Recently, several noncoding regulatory RNA genes, microRNA (miRNA), were identified, which play roles in various steps of metastasis, some without obvious roles in tumorigenesis. Understanding how these metastasis-associated miRNA, which we term metastamir, are involved in metastasis will help identify possible biomarkers or targets for the most lethal attribute of cancer: metastasis.
Restriction Map of Rachiplusia ou and Rachiplusia ou-Autographa californica Baculovirus Recombinants (1980)

The restriction sites of Rachiplusia ou nuclear polyhedrosis virus (RoMNPV) DNA were mapped for the endonucleases SmaI, KpnI, BamHI, SacI, XhoI, and EcoRI. Of the 60 DNA restriction sites of RoMNPV, 35 mapped in similar positions as compared to the restriction sites of Autographa californica nuclear polyhedrosis virus (AcMNPV) DNA. Two plaque-purified viruses, obtained from randomly picked plaques of a wild-type isolate of RoMNPV, were recombinants of RoMNPV and AcMNPV. The recombinants were shown to have RoMNPV and AcMNPV restriction fragments as well as structural polypeptides from each parental virus. Both recombinant viruses had a major RoMNPV capsid protein but were occluded in the AcMNPV polyhedrin protein.
Activation of the small GTPase Rac1 by a specific guanine‐nucleotide‐exchange factor suffices to induce glucose uptake into skeletal‐muscle cells (2008)

Collectively, Rac1 activation specifically in membrane ruffles by the GEF FLJ00068 is sufficient for insulin induction of glucose uptake into skeletal-muscle cells.
Hodgkin lymphoma requires stabilized NIK and constitutive RelB expression for survival (2012)

We have analyzed the role of the REL family members in Hodgkin lymphoma (HL). shRNA targeting of each REL member showed that HL was uniquely dependent on relB, in contrast to several other B-cell lymphomas. In addition, relA and c-rel shRNA expression also decreased HL cell viability. In exploring relB activation further, we found stable NF-κB inducing kinase (NIK) protein in several HL cell lines and that NIK shRNA also affected HL cell line viability. More importantly, 49 of 50 HL patient biopsies showed stable NIK protein, indicating that NIK and the noncanonical pathway are very prevalent in HL. Lastly, we have used a NIK inhibitor that reduced HL but not other B-cell lymphoma cell viability. These data show that HL is uniquely dependent on relB and that the noncanonical pathway can be a therapeutic target for HL. Furthermore, these results show that multiple REL family members participate in the maintenance of a HL phenotype.
Cellular Uptake of Arginine-Rich Peptides: Roles for Macropinocytosis and Actin Rearrangement (2004)

The use of membrane-permeable peptides as carrier vectors for the intracellular delivery of various proteins and macromolecules for modifying cellular function is well documented. Arginine-rich peptides, including those derived from human immunodeficiency virus 1 Tat protein, are among the representative classes of these vectors. The internalization mechanism of these vector peptides and their protein conjugates was previously regarded as separate from endocytosis, but more recent reevaluations have concluded that endocytosis is involved in their internalization. In this report, we show that the uptake of octa-arginine (R8) peptide by HeLa cells was significantly suppressed by the macropinocytosis inhibitor ethylisopropylamiloride (EIPA) and the F-actin polymerization inhibitor cytochalasin D, suggesting a role for macropinocytosis in the uptake of the peptide. In agreement with this we observed that treatment of the cells with R8 peptide induced significant rearrangement of the actin cytoskeleton. The internalization efficiency and contribution of macropinocytosis were also observed to have a dependency on the chain length of the oligoarginine peptides. Uptake of penetratin, another representative peptide carrier, was less sensitive to EIPA and penetratin did not have such distinct effects on actin localization. The above observations suggest that penetratin and R8 peptides have distinct internalization mechanisms.
Definitions of Measures of Effect Duration for Psoriasis Treatments (2005)

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Use of the Inactivated Intranasal Influenza Vaccine and the Risk of Bell's Palsy in Switzerland (2004)

This study suggests a strong association between the inactivated intranasal influenza vaccine used in Switzerland and Bell's palsy. This vaccine is no longer in clinical use.
Functional Neuroimaging of Major Depressive Disorder: A Meta-Analysis and New Integration of Baseline Activation and Neural Response Data (2012)

The meta-analytic results support an elegant and neuroanatomically viable model of the salience of negative information in major depressive disorder. In this proposed model, high baseline pulvinar activity in depression first potentiates responding of the brain's salience network to negative information; next, and owing potentially to low striatal dopamine levels in depression, this viscerally charged information fails to propagate up the cortical-striatal-pallidalthalamic circuit to the dorsolateral prefrontal cortex for contextual processing and reappraisal.
Delaying Brain Mitochondrial Decay and Aging with Mitochondrial Antioxidants and Metabolites (2002)

Mitochondria decay with age due to the oxidation of lipids, proteins, RNA, and DNA. Some of this decay can be reversed in aged animals by feeding them the mitochondrial metabolites acetylcarnitine and lipoic acid. In this review, we summarize our recent studies on the effects of these mitochondrial metabolites and mitochondrial antioxidants (alpha-phenyl-N-t-butyl nitrone and N-t-butyl hydroxylamine) on the age-associated mitochondrial decay of the brain of old rats, neuronal cells, and human diploid fibroblast cells. In feeding studies in old rats, these mitochondrial metabolites and antioxidants improve the age-associated decline of ambulatory activity and memory, partially restore mitochondrial structure and function, inhibit the age-associated increase of oxidative damage to lipids, proteins, and nucleic acids, elevate the levels of antioxidants, and restore the activity and substrate binding affinity of a key mitochondrial enzyme, carnitine acetyltransferase. These mitochondrial metabolites and antioxidants protect neuronal cells from neurotoxin- and oxidant-induced toxicity and oxidative damage; delay the normal senescence of human diploid fibroblast cells, and inhibit oxidant-induced acceleration of senescence. These results suggest a plausible mechanism: with age, increased oxidative damage to proteins and lipid membranes, particularly in mitochondria, causes a deformation of structure of enzymes, with a consequent decrease of enzyme activity as well as substrate binding affinity for their substrates; an increased level of substrate restores the velocity of the reaction and restores mitochondrial function, thus delaying mitochondrial decay and aging. This loss of activity due to coenzyme or substrate binding appears to be true for a number of other enzymes as well, including mitochondrial complex III and IV.
Down-regulation of c-MYC antigen expression in lymphocytes of Emu-c-myc transgenic mice treated with anti-c-myc DNA methylphosphonates. (1992)

In transgenic mice bearing a murine immunoglobulin enhancer/c-myc fusion transgene (Emu-myc), it was found that antisense DNA methylphosphonates targeted against c-myc mRNA inhibited production of c-MYC protein in peripheral lymphocytes. The decrease in protein was measured 3-4 h after i.v. administration of a 300-nmol dose. c-MYC was detected by immunofluorescence of fixed cells stained with an anti-c-MYC antiserum. In addition, DNA methylphosphonates did not induce acute toxicity following i.v. administration of a 300-nmol dose. An identically administered scrambled sequence oligomer did not decrease c-MYC protein or induce toxicity. Finally, recovery of DNA methylphosphonates from the blood plasma of treated mice indicated that the oligomers remained intact up to 3 h, while their concentrations decreased rapidly for the first h, then slowly decreased over the next 2 h. This is the first demonstration of sequence-specific antisense DNA methylphosphonate inhibition of gene expression in the bloodstream of an animal model.
Hydroxypropyl-Substituted β-Cyclodextrins: Influence of Degree of Substitution on the Thermodynamics of Complexation with Tauroconjugated and Glycoconjugated Bile Salts (2010)

The effect of the degree of substitution (DS) on the ability of hydroxypropylated β-cyclodextrin (HPβCD) to form inclusion complexes with six different bile salts, found within the intestinal tracts of rats, dogs, and humans, was studied by isothermal titration calorimetry. The composition and molecular structure of the cyclodextrin samples were characterized by MALDI-TOF mass spectrometry together with 1D and 2D-NMR, and some of the complexes were studied by 2D ROESY NMR. The stability and structure of the complexes were mainly determined by the position of hydroxyl groups on the bile salts and depended relatively little on the number of hydroxypropyl side chains on the CDs. The enthalpy and entropy of complexation exhibited a strong linear increase as the DS increased from 0 to 1, and a pronounced enthalpy-entropy compensation was observed. These observations are interpreted as an increased release of ordered water from the hydration shells of the bile salts, caused by the hydroxypropyl substituents on the rim of the CD. It is estimated that each CD hydroxypropyl substituent dehydrates a hydrophobic surface area of approximately 10 Å(2).
Activation of shallow, high-dose BF+2 implants into silicon by rapid thermal processing (1984)

Rapid thermal processing has been used to activate shallow p+ layers (∼0.1–0.15 μm) following BF+2 implantation (49 keV, 2–6×1015 cm−2) into amorphized silicon. For doses of 2×1015 cm−2, the shallow as-implanted boron profile was preserved, unlike the case of furnace annealing (900 °C, 30 min). Sheet resistance of 85 Ω/sq following rapid annealing was close to that calculated assuming 100% activation of dopants in their as-implanted distribution. At 6×1015 cm−2 dose, however, these same rapid annealing conditions (10–15 sec exposure to a 1250 °C heater) produce considerable dopant redistribution (≳2000 Å) with peak carrier concentration of ∼1020 cc−1, which is far below the as-implanted value of ∼1021 cc−1. A two-step anneal is described which permits shallow junctions of ∼1500 Å to be obtained for the 6×1015 cm−2 dose implants; however, maximum carrier concentration was still ≲1020 cc−1. The present data suggests that the concentration limit for activation of implanted boron encountered when furnace annealing is applicable even when annealing is carried out on a much shorter time scale of 10 sec versus 30 min.
REDUCTIVE AMINATION WITH SODIUM CYANOBOROHYDRIDE: N,N-DIMETHYLCYCLOHEXYLAMINE (1972)

Reductive Amination with Sodium Cyanoborohydride: N,N-Dimethylcyclohexylamine



product: N,N-dimethylcyclohexylamine




byproduct: cyclohexanol




product: Cyclohexylamine




product: N-Methylcyclohexylamine




product: α-Phenylethylamine




product: N-Methylphenethylamine




product: N-Isobutylaniline




product: N-Methylpiperidine





Keywords:

condensation, miscellaneous;
reduction, miscellaneous;
sodium cyanoborohydride