gebhart/patrepeval huggingface dataset:
Ageing and the circadian and homeostatic regulation of human sleep during forced desynchrony of rest, melatonin and temperature rhythms (1999)

1. The circadian timing system has been implicated in age-related changes in sleep structure, timing and consolidation in humans. 2. We investigated the circadian regulation of sleep in 13 older men and women and 11 young men by forced desynchrony of polysomnographically recorded sleep episodes (total, 482; 9 h 20 min each) and the circadian rhythms of plasma melatonin and core body temperature. 3. Stage 4 sleep was reduced in older people. Overall levels of rapid eye movement (REM) sleep were not significantly affected by age. The latencies to REM sleep were shorter in older people when sleep coincided with the melatonin rhythm. REM sleep was increased in the first quarter of the sleep episode and the increase of REM sleep in the course of sleep was diminished in older people. 4. Sleep propensity co-varied with the circadian rhythms of body temperature and plasma melatonin in both age groups. Sleep latencies were longest just before the onset of melatonin secretion and short sleep latencies were observed close to the temperature nadir. In older people sleep latencies were longer close to the crest of the melatonin rhythm. 5. In older people sleep duration was reduced at all circadian phases and sleep consolidation deteriorated more rapidly during the course of sleep, especially when the second half of the sleep episode occurred after the crest of the melatonin rhythm. 6. The data demonstrate age-related decrements in sleep consolidation and increased susceptibility to circadian phase misalignment in older people. These changes, and the associated internal phase advance of the propensity to awaken from sleep, appear to be related to the interaction between a reduction in the homeostatic drive for sleep and a reduced strength of the circadian signal promoting sleep in the early morning.
Characterization of the nature of granulocytic myeloid-derived suppressor cells in tumor-bearing mice (2011)

MDSCs are a group of cells with potent immune-suppressive activity. These cells accumulate in many pathologic conditions and play a major role in the regulation of immune responses. The nature of MDSC remains highly debatable. In cancer, most MDSCs are represented by cells with granulocytic phenotype and morphology, G-MDSC. The relationship between G-MDSCs and Neu remains unclear. In this study, we have found that G-MDSCs, from tumor-bearing, and Neu, from tumor-free, mice share a common morphology and phenotype. However, in contrast to Neu, a substantial proportion of G-MDSCs expressed M-CSFR and a CD244 molecule. Neu had significantly higher phagocytic activity, expression of lysosomal proteins, and TNF-α than corresponding G-MDSCs, which had significantly higher activity of arginase, MPO, and ROS. In contrast to G-MDSC, neither rested nor mobilized Neu suppressed T cells. G-MDSC survived 2 days in culture in the presence of GM-CSF and within 24 h, became phenotypic and functionally similar to Neu. Tumor-associated G-MDSC shared most characteristics of splenic G-MDSC, rather then Neu. These data suggest that in cancer, despite morphological and phenotypic similarities, G-MDSCs are functionally distinct from Neu and are comprised of pathologically activated precursors of Neu.
Biodegradation of TNT (2,4,6-trinitrotoluene) by Phanerochaete chrysosporium (1990)

Extensive biodegradation of TNT (2,4,6-trinitrotoluene) by the white rot fungus Phanerochaete chrysosporium was observed. At an initial concentration of 1.3 mg/liter, 35.4 +/- 3.6% of the [14C]TNT was degraded to 14CO2 in 18 days. The addition of glucose 12 days after the addition of TNT did not stimulate mineralization, and, after 18 days of incubation with TNT only, about 3.3% of the initial TNT could be recovered. Mineralization of [14C]TNT adsorbed on soil was also examined. Ground corncobs served as the nutrient for slow but sustained degradation of [14C]TNT to 14CO2 such that 6.3 +/- 0.6% of the [14C]TNT initially present was converted to 14CO2 during the 30-day incubation period. Mass balance analysis of liquid cultures and of soil-corncob cultures revealed that polar [14C]TNT metabolites are formed in both systems, and high-performance liquid chromatography analyses revealed that less than 5% of the radioactivity remained as undegraded [14C]TNT following incubation with the fungus in soil or liquid cultures. When the concentration of TNT in cultures (both liquid and soil) was adjusted to contamination levels that might be found in the environment, i.e., 10,000 mg/kg in soil and 100 mg/liter in water, mineralization studies showed that 18.4 +/- 2.9% and 19.6 +/- 3.5% of the initial TNT was converted to 14CO2 in 90 days in soil and liquid cultures, respectively. In both cases (90 days in water at 100 mg/liter and in soil at 10,000 mg/kg) approximately 85% of the TNT was degraded. These results suggest that this fungus may be useful for the decontamination of sites in the environment contaminated with TNT.
Multi-Task Deep Convolutional Neural Network for the Segmentation of Type B Aortic Dissection (2018)

Segmentation of the entire aorta and true-false lumen is crucial to inform plan and follow-up for endovascular repair of the rare yet life threatening type B aortic dissection. Manual segmentation by slice is time-consuming and requires expertise, while current computer-aided methods focus on the segmentation of the entire aorta, are unable to concurrently segment true-false lumen, and some require human interaction. We here report a fully automated approach based on a 3-D multi-task deep convolutional neural network that segments the entire aorta and true-false lumen from CTA images in a unified framework. For training, we built a database containing 254 CTA images (210 preoperative and 44 postoperative) obtained using various systems from 254 unique patients with type B aortic dissection. Slice-wise manual segmentation of the entire aorta and the true-false lumen for each 3-D CTA image was provided. Upon evaluation of another 16 CTA images (11 preoperative and 5 postoperative) with ground truth segmentation provided by experienced vascular surgeons, our method achieves a mean dice similarity score(DSC) of 0.910,0.849 and 0.821 for the entire aorta,true lumen and false lumen respectively.
Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH) (2005)

Chromosomal aberrations are a common cause of multiple anomaly syndromes that include growth and developmental delay and dysmorphism. Novel high resolution, whole genome technologies, such as array based comparative genomic hybridisation (array-CGH), improve the detection rate of submicroscopic chromosomal abnormalities allowing re-investigation of cases where conventional cytogenetic techniques, Spectral karyotyping (SKY), and FISH failed to detect abnormalities. We performed a high resolution genome-wide screening for submicroscopic chromosomal rearrangements using array-CGH on 41 children with idiopathic mental retardation (MR) and dysmorphic features. The commercially available microarray from Spectral Genomics contained 2600 BAC clones spaced at approximately 1 Mb intervals across the genome. Standard chromosome analysis (>450 bands per haploid genome) revealed no chromosomal rearrangements. In addition, multi-subtelomeric FISH screening in 30 cases and SKY in 11 patients did not detect any abnormality. Using array-CGH we detected chromosomal imbalances in four patients (9.8%) ranging in size from 2 to 14 Mb. Large scale copy number variations were frequently observed. Array-CGH has become an important tool for the detection of chromosome aberrations and has the potential to identify genes involved in developmental delay and dysmorphism. Moreover, the detection of genomic imbalances of clinical significance will increase knowledge of the human genome by performing genotype-phenotype correlation.
Chiral Oxazoline/Imidazoline-2-ylidene Complexes (1998)

N-Heterocyclic “carbene” ligands derived from imidazole are alternatives for the well-established phosphines in organometallic catalysis. In contrast to phosphines, they do not easily dissociate from transition metals (e.g., palladium, rhodium) so they seem suited for chiral modifications. This publication reports on the synthesis and coordination chemistry of novel bidentate ligands with both imidazoline-2-ylidene and oxazoline moieties. The synthesis follows straightforward routes, using N-functionalized imidazolium salts and 2-amino alcohols. The crystal structures of palladium and rhodium complexes are presented. With rhodium, the ligands show a chelating coordination mode.
Recent investigations of metal oxide/CdTe heterojunction solar cells (1978)

Recent investigations of the properties of ZnO and indium--tin oxide (ITO) films both on glass and as components of single crystal p-CdTe based heterojunction solar cells are described. It was shown that ZnO films deposited by rf sputtering or spray pyrolysis can be brought within the desired conductivity range for solar cell performance. First generation n-ZnO/p-CdTe solar cells show high values of J/sub sc/ = 19 mA/cm/sup 2/ and solar efficiency n/sub s/ = 4.6% (AM2 simulation). Heterojunctions of n-ITO/p-CdTe prepared by rf sputtering give V/sub oc/ = 0.82 V, J/sub sc/ = 14.5 mA/cm/sup 2/, and n/sub s/ = 8% but properties are very sensitive to preparation variables. Preliminary structural studies have been made on the ITO films in situ on CdTe substrates to elucidate this sensitivity. The results of heat-treatments on both ZnO and ITO cells are also discussed.
Niacin noncompetitively inhibits DGAT2 but not DGAT1 activity in HepG2 cells (2004)

Niacin is a widely used lipid-regulating agent in dyslipidemic patients. Previously, we have shown that niacin inhibits triacylglycerol synthesis. In this report, using HepG2 cells, we have examined the effect of niacin on the mRNA expression and microsomal activity of diacylglycerol acyltransferase 1 and 2 (DGAT1 and DGAT2), the last committed but distinctly different enzymes for triglyceride synthesis. Addition of niacin to the DGAT assay reaction mixture dose-dependently (0-3 mM) inhibited DGAT activity by 35-50%, and the IC(50) was found to be 0.1 mM. Enzyme kinetic studies showed apparent K(m) values of 8.3 microM and 100 microM using [(14)C]oleoyl-CoA and sn-1,2-dioleoylglycerol as substrates, respectively. A decrease in apparent V(max) was observed with niacin, whereas the apparent K(m) remained constant. A Lineweaver-Burk plot of DGAT inhibition by niacin showed a noncompetitive type of inhibition. Niacin selectively inhibited DGAT2 but not DGAT1 activity. Niacin inhibited overt DGAT activity. Niacin had no effect on the expression of DGAT1 and DGAT2 mRNA. These data suggest that niacin directly and noncompetitively inhibits DGAT2 but not DGAT1, resulting in decreased triglyceride synthesis and hepatic atherogenic lipoprotein secretion, thus indicating a major target site for its mechanism of action.
An anti–PR1/HLA-A2 T-cell receptor–like antibody mediates complement-dependent cytotoxicity against acute myeloid leukemia progenitor cells (2011)

PR1 (VLQELNVTV) is a human leukocyte antigen-A2 (HLA-A2)-restricted leukemia-associated peptide from proteinase 3 (P3) and neutrophil elastase (NE) that is recognized by PR1-specific cytotoxic T lymphocytes that contribute to cytogenetic remission of acute myeloid leukemia (AML). We report a novel T-cell receptor (TCR)-like immunoglobulin G2a (IgG2a) antibody (8F4) with high specific binding affinity (dissociation constant [K(D)] = 9.9nM) for a combined epitope of the PR1/HLA-A2 complex. Flow cytometry and confocal microscopy of 8F4-labeled cells showed significantly higher PR1/HLA-A2 expression on AML blasts compared with normal leukocytes (P = .046). 8F4 mediated complement-dependent cytolysis of AML blasts and Lin(-)CD34(+)CD38(-) leukemia stem cells (LSCs) but not normal leukocytes (P < .005). Although PR1 expression was similar on LSCs and hematopoietic stem cells, 8F4 inhibited AML progenitor cell growth, but not normal colony-forming units from healthy donors (P < .05). This study shows that 8F4, a novel TCR-like antibody, binds to a conformational epitope of the PR1/HLA-A2 complex on the cell surface and mediates specific lysis of AML, including LSCs. Therefore, this antibody warrants further study as a novel approach to targeting leukemia-initiating cells in patients with AML.
A Simple Method to Identify Sleep Apnea Using Holter Recordings (2003)

HR tachogram patterns derived from ambulatory ECGs provide a simple method for identifying sleep apnea syndrome and other sleep disturbances in patients without major autonomic dysfunction.
MEMS pressure sensors embedded into fiber composite airfoils (2014)

The paper describes the integration of pressure sensors into fiber composite in order to obtain flow sensing airfoils to be used in future aircrafts. First, the sensor design and working principle is described, followed by an embedding procedure for damage-free integration. Here the sensors are faced to stresses by vacuum and curing during the embedding process into fiber-reinforced plastic. The mechanical characteristics and the influence of external mechanical stresses on the integrated sensor are further investigated. Finally, a sensor design unsusceptible to external mechanical stresses parallel to the surface of the airfoil is proposed and verified by tensile stress tests.
Will the real phylogeneticists please stand up? (2011)

In a recently published commentary, Mooi &amp; Gill asserted that there is a crisis brewing in systematic ichthyology caused by a failure of investigators to apply the basic tenets of outgroup comparison to recover clades based solely on shared apomorphic characters. The result, they claim, is that many recent analyses disregard real synapomorphies and discover clades by phenetic rather than phylogenetic principles. We take the opportunity to refute this claim and assert that matrix-based analyses, whether parametric or nonparametric, satisfy the basic tenets of Hennig’s methods, resulting in monophyletic groups confirmed by synapomorphies.
Existence of High Abundance Antiproliferative mRNA's in Senescent Human Diploid Fibroblasts (1986)

Polyadenylated RNA isolated from senescent human diploid fibroblasts (HDF) inhibited DNA synthesis in proliferation-competent cells after microinjection, whereas polyadenylated RNA from young HDF had no inhibitory effect. Polyadenylated RNA from young cells made quiescent by removal of serum growth factors had a slight inhibitory effect on DNA synthesis. The abundance level of inhibitor messenger RNA (mRNA) from senescent cells was estimated at 0.8 and that of quiescent cells at 0.005 percent. These results demonstrate the existence of one or more antiproliferative mRNA's in nonproliferating normal human cells; these RNA's code for factors that either work antagonistically to initiators of DNA synthesis or regulate the expression of the initiators in some way. The abundance level of the inhibitory mRNA in senescent cells indicates the feasibility of developing a complementary DNA probe that will be useful in studying cell cycle control mechanisms.
MEK1 and the extracellular signal-regulated kinases are required for the stimulation of IL-2 gene transcription in T cells (1996)

TCR engagement stimulates the activation of the protein kinase Raf-1. Active Raf-1 phosphorylates and activates the mitogen-activated protein (MAP) kinase/extracellular signal-regulated kinase kinase 1 (MEK1), which in turn phosphorylates and activates the MAP kinases/extracellular signal regulated kinases, ERK1 and ERK2. Raf-1 activity promotes IL-2 production in activated T lymphocytes. Therefore, we sought to determine whether MEK1 and ERK activities also stimulate IL-2 gene transcription. Expression of constitutively active Raf-1 or MEK1 in Jurkat T cells enhanced the stimulation of IL-2 promoter-driven transcription stimulated by a calcium ionophore and PMA, and together with a calcium ionophore the expression of each protein was sufficient to stimulate NF-AT activity. Expression of MEK1-interfering mutants inhibited the stimulation of IL-2 promoter-driven transcription and blocked the ability of constitutively active Ras and Raf-1 to costimulate NF-AT activity with a calcium ionophore. Expression of the MAP kinase-specific phosphatase, MKP-1, which blocks ERK activation, inhibited IL-2 promoter and NF-AT-driven transcription stimulated by a calcium ionophore and PMA, and in addition, MKP-1 neutralized the transcriptional enhancement caused by active Raf-1 and MEK1 expression. We conclude that the MAP kinase signal transduction pathway consisting of Raf-1, MEK1, and ERK1 and ERK2 functions in the stimulation IL-2 gene transcription in activated T lymphocytes.
Detection of Y chromosome by in situ hybridization in combination with membrane antigens by two-color immunofluorescence. (1991)

Discrimination between donor and recipient peripheral blood cells through detection of the Y chromosome can be useful to document chimerism and engraftment after sex-mismatched bone marrow transplantation. Currently applied methods are hampered by the selection of cells (e.g., karyotyping of cells in metaphase) or by the fact that the detection of Y chromosome by in situ hybridization with specific probes does not allow further characterization of the cells. Although quinacrine staining of Y chromosomes can be performed on cells previously marked for membrane antigens, this staining is not fully discriminative between male and female cells. To circumvent this, a technique has been developed, in which mononuclear cells in suspension were stained for membrane antigens by the consecutive use of monoclonal antibodies and tetramethylrhodamine isothiocyanate conjugates. After the cells were spun down on slides and fixed with methanol/acetic acid and formaldehyde, in situ hybridization with a biotinylated Y-chromosome-specific DNA probe was performed. The probe was detected with avidin-fluorescein isothiocyanate and the signal was amplified by consecutive incubation with biotinylated anti-avidin and avidin-fluorescein isothiocyanate. The membrane staining for various antigens remained undisturbed during the hybridization procedure and the Y probe discriminated almost completely between male and female cells. Therefore, this approach allowed us to determine the chimerism within different subpopulations of unseparated mononuclear cells after sex-mismatched bone marrow transplantation with a sensitivity of 98% and a specificity of 100%.
Inhibitory effects of cembratriene-4,6-diol derivatives on the induction of Epstein-Barr virus early antigen by 12-O-tetradecanoylphorbol-13-acetate. (1987)

Wehave reported that a short-term in vitro assay system to test inhibitory effects on the induction of the early antigen (EA) of Epstein-Barr virus (EBV) in lymphoblastoid Raji cells which carried the EBV-genome is a very useful means of screening inhibitors of tumor pro-
Multiepitopic HLA-A*0201-Restricted Immune Response Against Hepatitis B Surface Antigen After DNA-Based Immunization (2000)

CTL together with anti-envelope Abs represent major effectors for viral clearance during hepatitis B virus (HBV) infection. The induction of strong cytotoxic and Ab responses against the envelope proteins after DNA-based immunization has been proposed as a promising therapeutic approach to mediate viral clearance in chronically infected patients. Here, we studied the CTL responses against previously described hepatitis B surface Ag (HBsAg)-HLA-A*0201-restricted epitopes after DNA-based immunization in HLA-A*0201 transgenic mice. The animal model used was Human Human D(b) (HHD) mice, which are deficient for mouse MHC class I molecules (beta(2)-microglobulin(-/-) D(b-/-)) and transgenic for a chimeric HLA-A*0201/D(b) molecule covalently bound to the human beta(2)-microglobulin (HHD(+/+)). Immunization of these mice with a DNA vector encoding the small and the middle HBV envelope proteins carrying HBsAg induced CTL responses against several epitopes in each animal. This study performed on a large number of animals described dominant epitopes with specific CTL induced in all animals and others with a weaker frequency of recognition. These results confirmed the relevance of the HHD transgenic mouse model in the assessment of vaccine constructs for human use. Moreover, genetic immunization of HLA-A2 transgenic mice generates IFN-gamma-secreting CD8(+) T lymphocytes specific for endogenously processed peptides and with recognition specificities similar to those described during self-limited infection in humans. This suggests that responses induced by DNA immunization could have the same immune potential as those developing during natural HBV infection in human patients.
Mesenchymal Stem Cells Reconditioned in Their Own Serum Exhibit Augmented Therapeutic Properties in the Setting of Acute Respiratory Distress Syndrome (2019)

Mesenchymal stem cells (MSCs) are a promising form of therapy for acute respiratory distress syndrome (ARDS). The objective of this study was twofold: (a) to characterize cytokine expression in serum from ARDS subjects receiving MSCs and (b) to determine MSC function following "preconditioning" with ARDS serum. In phase I, serum from three cohorts of animals (uninjured [no ARDS, n = 4], injured untreated [n = 5], and injured treated with approximately 6 million per kilogram MSCs [n = 7]) was analyzed for expression of inflammatory mediators. In phase II, the functional properties of bone marrow porcine MSCs were assessed following "preconditioning" with serum from the three cohorts. In phase III, the findings from the previous phases were validated using human bone marrow MSCs (hBM-MSCs) and lipopolysaccharide (LPS). Serum from injured treated animals had significantly lower levels of interferon-γ and significantly higher levels of interleukin (IL)-1 receptor antagonist (IL-1RA) and IL-6. Similarly, upon exposure to the injured treated serum ex vivo, the MSCs secreted higher levels of IL-1RA and IL-10, dampened the secretion of proinflammatory cytokines, exhibited upregulation of toll-like receptor 4 (TLR-4) and vascular endothelial growth factor (VEGF) genes, and triggered a strong immunomodulatory response via prostaglandin E2 (PGE<sub>2</sub> ). hBM-MSCs demonstrated a similar augmented therapeutic function following reconditioning in a LPS milieu. Administration of MSCs modulated the inflammatory milieu following ARDS. Exposure to ARDS serum ex vivo paralleled the trends seen in vivo, which appear to be mediated, in part, through TLR-4 and VEGF and PGE<sub>2</sub> . Reconditioning MSCs in their own serum potentiates their immunotherapeutic function, a technique that can be used in clinical applications. Stem Cells Translational Medicine 2019;8:1092-1106.