gebhart/patrepeval huggingface dataset:
Plant Uptake of Per- and Polyfluoroalkyl Substances at a Contaminated Fire Training Facility to Evaluate the Phytoremediation Potential of Various Plant Species (2017)

Fire training facilities and other areas suffer from serious per- and polyfluoroalkyl substance (PFAS) contamination in soil, surface water, and groundwater due to regular practices with PFAS-containing aqueous firefighting foams (AFFFs). Therefore, the uptake of 26 PFASs in plants and the contamination of soil and groundwater has been investigated at a fire training site at Stockholm Arlanda airport, Stockholm (Sweden) in 2016. Elevated ∑<sub>26</sub>PFAS levels were detected in soil and groundwater ranging from 16 to 160 ng g<sup>-1</sup> dry weight (dw) and 1200-34 000 ng L<sup>-1</sup>, respectively. Samples from different plant species and tissues (i.e., roots, trunk/cores, twigs, leaves/needles) of the local plant community were taken, namely silver birch (Betula pendula), Norway spruce (Picea abies), bird cherry (Prunus padus), mountain ash (Sorbus aucuparia), ground elder (Aegopodium podagraria), long beechfern (Phegopteris connectilis), and wild strawberry (Fragaria vesca). The plants showed a high variability of concentrations with highest ∑<sub>26</sub>PFAS concentrations in vegetative compartments with up to 97 ng g<sup>-1</sup> wet weight (ww) and 94 ng g<sup>-1</sup> ww in birch leaves and spruce needles, respectively. Annual ground cover plants such as long beechfern and ground elder, and bushes like bird cherry showed concentrations up to 6.9, 23, and 21 ng g<sup>-1</sup> ww, respectively. The bioconcentration factors (BCFs; plant/soil ratios) were highest in foliage, while the total tree burden of ∑<sub>26</sub>PFASs per tree was up to 11 mg for birch and 1.8 mg for spruce. Considering a shelterwood system with mixed stands of silver birch and spruce in combination with regular harvest of leaves and birch sap and an understory of ground elder, it is potentially feasible to remove 1.4 g of ∑<sub>26</sub>PFASs per year and hectare from (heavily) contaminated sites. An alternative approach is the coppicing of birch trees in combination with an understory of ground elder, potentially removing 0.65 g yr<sup>-1</sup> ha<sup>-1</sup> of ∑<sub>26</sub>PFASs, while a simple meadow with ground elder can remove 0.55 g yr<sup>-1</sup> ha<sup>-1</sup> ∑<sub>26</sub>PFASs.
Polymer‐Embedded Carbon Nanotube Ribbons for Stretchable Conductors (2010)

A transparent stretchable conductor, in which well-aligned CNT ribbons are embedded in poly(dimethylsiloxane) (PDMS) (CNT/PDMS film), is presented. Due to the good inter-tube contact and stable CNT arrangement in the CNT ribbons, the CNT/PDMS film can maintain stable conductivity under repetitive stretching to strains up to 100%.
Inactivation of Escherichia coli , F′ Episomes at Transfer, and Bacteriophage Lambda by Psoralen Plus 360-nm Light: Significance of Deoxyribonucleic Acid Cross-Links (1971)

We have investigated some biological consequences of light-induced psoralen-deoxyribonucleic acid (DNA) adducts and find that for several Escherichia coli functions (killing of strain AB2480 recA13 uvrA6, inactivation of phage lambda plaque-forming ability in wild type and uvrA6 hosts, loss of ability to transmit intact Flac(+) episomes), a light exposure sufficient for production of a single cross-link per DNA molecule correlates well with the biological consequence. Although one cross-link per genome is apparently lethal to recA13 uvr(-) strains, mutants carrying the recA13 or uvrA6 markers survive light exposures producing 6.7 and 16 cross-links per genome, respectively, and wild-type cells recover from 65 psoralen cross-links. Evidently, the excision and recombinational repair systems complement one another in reconstructing an intact genome from cellular DNA containing psoralen photoproducts. The above bacterial and phage strains, in which DNA repair processes are minimized, are also extremely sensitive to pyrimidine dimer-forming 254-nm UV light (without psoralen), and were expected to respond similarly to formation of psoralen-pyrimidine base monoadducts in their DNA. Since the biological inactivation by psoralen correlates well with cross-link formation, we suggest that the sensitizing action of this drug primarily derives from its ability to form DNA cross-links.
Induction of lethal experimental allergic encephalomyelitis in nonhuman primates and guinea pigs with human glioblastoma multiforme tissue (1981)

✓ The introduction of active specific immunotherapy as an adjunct to conventional therapy of the brain-tumor patient creates the risk of the concomitant induction of experimental allergic encephalomyelitis (EAE). The lack of resolution concerning the total group of central nervous system (CNS) antigens which may be encephalitogenic, and the lack of definition of the necessary conditions for the induction of an anti-CNS myelin response complicate the design of an immunotherapeutic regimen for brain-tumor patients. We report here the ready induction of EAE in four of four guinea pigs and both of two nonhuman primates (Macaca fascicularis) with human glioblastoma multiforme (GBM) tissue injected with either complete or incomplete Freund's adjuvant (CFA, IFA). Immunization protocols utilizing encephalitogenic GBM tissue and adjuvant which did not result in EAE induction were established in both of two macaques, and the production of significant levels of antibodies specifically reactive with immunizing GBM-derived cultured cell lines in all of 12 macaques without EAE induction was demonstrated. As the lower detection limit of the sodium dodecyl sulfate-polyacrylimide gel electrophoresis (SDS-PAGE) assay for human myelin basic protein (HBP) was 0.6 µg HBP/gel, and an extract prepared from WR-GBM tumor tissue contained less than 0.6 µg of detectable HBP/25 µg of pH 3 extractable protein, and as 100 to 1000 µg of purified human basic protein (HBP) failed to induce EAE in three of three macaques, it was hypothesized that 1) GBM tissue may act as an adjuvant and markedly lower myelin basic protein (MBP) threshold doses for EAE induction, that 2) MBP encephalitogenic fragments capable of EAE induction may be present in GBM tissue but difficult to quantitate in precipitates by in vitro methods, or that 3) secondary encephalitogenic antigens unrelated to MBP may be present in GBM tissue. The threat of EAE induction and the potential difficulty of its detection in the deteriorating brain-tumor patient receiving active specific immunotherapy warrants a biological screen in immunizing CNS material in experimental animals prior to administration to patients in immunotherapy protocols.
A Recently Evolved Novel Trophoblast-Enriched Secreted Form of fms-Like Tyrosine Kinase-1 Variant Is Up-Regulated in Hypoxia and Preeclampsia (2009)

sFlt1-e15a emerged as an alternate transcript of Flt1 late in evolution with the insertion of an AluSq sequence into the primate genome after the emergence of the simian infraorder about 40 million years ago. sFlt1-e15a is particularly abundant in human placenta and trophoblasts and is also highly expressed in nonhuman primate placenta. The expressed protein has a C-terminal polyserine tail and, like reference sequence sFlt1 (sFlt1-i13), is glycosylated and secreted. Consistent with a role in placental pathophysiology, hypoxia stimulates sFlt1-e15a expression in isolated cytotrophoblasts and a trophoblast cell line, and differentiation into syncytiotrophoblasts further enhances the effect of hypoxia. Placental levels of sFlt1-e15a and sFlt1-i13 transcripts are significantly elevated in patients with preeclampsia compared with normal pregnancies. We speculate that sFlt1-e15a may contribute to the pathophysiology of preeclampsia.
Thyroid Function and Cancer Risk: A Prospective Population Study (2009)

Thyrotropin levels suggestive of hyperthyroid function are associated with increased cancer risk, and specifically, with increased risk of lung and prostate cancer, whereas hypothyroid function does not seem to be associated with cancer risk.
Cancer Regression and Neurological Toxicity Following Anti-MAGE-A3 TCR Gene Therapy (2013)

Nine cancer patients were treated with adoptive cell therapy using autologous anti-MAGE-A3 T-cell receptors (TCR)-engineered T cells. Five patients experienced clinical regression of their cancers including 2 on-going responders. Beginning 1-2 days postinfusion, 3 patients (#'s 5, 7, and 8) experienced mental status changes, and 2 patients (5 and 8) lapsed into comas and subsequently died. Magnetic resonance imagining analysis of patients 5 and 8 demonstrated periventricular leukomalacia, and examination of their brains at autopsy revealed necrotizing leukoencephalopathy with extensive white matter defects associated with infiltration of CD3(+)/CD8(+) T cells. Patient 7, developed Parkinson-like symptoms, which resolved over 4 weeks and fully recovered. Immunohistochemical staining of patient and normal brain samples demonstrated rare positively staining neurons with an antibody that recognizes multiple MAGE-A family members. The TCR used in this study recognized epitopes in MAGE-A3/A9/A12. Molecular assays of human brain samples using real-time quantitative-polymerase chain reaction, Nanostring quantitation, and deep-sequencing indicated that MAGE-A12 was expressed in human brain (and possibly MAGE-A1, MAGE-A8, and MAGE-A9). This previously unrecognized expression of MAGE-A12 in human brain was possibly the initiating event of a TCR-mediated inflammatory response that resulted in neuronal cell destruction and raises caution for clinical applications targeting MAGE-A family members with highly active immunotherapies.
Meta-analysis of radiation therapy with and without adjuvant chemotherapy for malignant gliomas in adults (1993)

The authors concluded that chemotherapy is advantageous for patients with malignant gliomas and should be considered part of the standard therapeutic regimen. Additional randomized trials using optimal radiation and chemotherapy may still be needed to precisely define which subgroups of patients, based on prognostic variables, will benefit most from chemotherapy after radiation.
Multiple spliced and unspliced transcripts from human cytomegalovirus immediate-early region 2 and evidence for a common initiation site within immediate-early region 1 (1985)

Human cytomegalovirus immediate-early (IE) region 2 (0.732 to 0.740 map unit) begins 35 nucleotides downstream of IE region 1 (Stenberg et al., J. Virol. 49:190-199, 1984). A series of mRNAs that have different splicing patterns are transcribed from region 2. There is an unspliced 1,589-nucleotide exon present in minor amounts and two spliced exons (836 and 289 nucleotides) present in larger amounts. The IE region 2 exons were found to be spliced onto the first three exons of region 1. Therefore, under IE conditions the region 1 promoter-regulatory region can promote transcription of region 2. Promoter sequences (i.e., CAAT and TATA boxes) are found upstream of the 5' end of IE region 2 but presumably function poorly at IE times after infection. The transcriptional regulation of these IE genes and the possible functional roles of the proteins are discussed. We postulate that a series of unique but related proteins are made from the region 2 transcripts. Some of these proteins should contain the same 169 amino-terminal residues as the major IE 72-kilodalton protein encoded by IE region 1 (Stenberg et al., J. Virol. 49:190-199, 1984). Variations in the amino acid sequences of the region 2 proteins could occur at either the amino terminus, the carboxy terminus, or both termini.
Inside Cover: Improving Cell‐Free Protein Synthesis through Genome Engineering of Escherichia coli Lacking Release Factor 1 (ChemBioChem 5/2015) (2015)

The inside cover picture shows the development of a high-yielding bacterial cell-free protein synthesis by multiplex automated genome engineering. Disabling nuclease genes in the source strain stabilized DNA and mRNA templates, which enhanced the modified cell-free protein synthesis containing non-standard amino acids. For details, see the paper by M. C. Jewett and co-workers on p. 844 ff.
Platelet activating factor and inflammation in atherogenesis: Targets for drug development (1986)

Abstract There is substantial evidence that the pathogenesis of atherosclerosis has one or more inflammatory components. As arterial injury is a primary event in the disease initiation and progression, inflammatory agents which injure and thus increase permeability of the arterial endothelium may lead to the development of atherosclerosis. The actions of circulatory mediators of inflammation to increase endothelial permeability may consequently accelerate entry or infiltration of lipid and other plasma macromolecules into the vessel wall. Reviewed are the biological properties of platelet activating factor (PAF), a potent lipid mediator believed to play a role in such disease states as allergic asthma, inflammation, systemic shock, myocardial ischemia, and allograph rejection. Emphasized are the actions of PAF related to increased endothelial permeability, cardiovascular actions and pathological profiles which indicate a role in the development of atherosclerosis and heart disease.
Anti-Human Immunodeficiency Virus Type 1 Human Monoclonal Antibodies that Bind Discontinuous Epitopes in the Viral Glycoproteins Can Identify Mimotopes from Recombinant Phage Peptide Display Libraries (1997)

A phage display library screening approach was used to identify peptide sequences that could bind to anti-HIV-1 MAbs whose binding specificities are complex. Most of the antibodies used recognize discontinuous epitopes in gp120 and one recognizes gp41. Both a 15-mer and a 21-mer display library (each with a complexity of greater than 60 x 10[6]) and two constrained, V3 region-biased libraries, all expressed as recombinant pIII protein of filamentous phage, were used. The unmapped anti-gp120 human MAb A32 recognized a set of related linear sequences and repeatedly identified a single phage sequence that could form a cyclic disulfide structure. Selection methods were also developed so that phage could be obtained by competition selection in the presence of antibody bound to native, monomeric gp120 antigen (used with MAb IgG1b12 and the anti-gp120 V3 region MAb 447-52D) or gp120 variable region 3 synthetic peptides (used with anti-gp120 V3 region MAb 19b). The potent, virus-neutralizing MAb IgG1b12 recognized numerous sequences and, when used in competition with gp120, recognized only one sequence. These studies extend the range of antibody determinant studies that can be performed with display phage libraries, demonstrate a workable experimental strategy for use of competition ligands to discriminate among phage mimotopes, and provide a large number of mimotopes that bind potent virus-neutralizing MAbs for HIV-1 vaccine studies.
Brain mast cell degranulation regulates blood-brain barrier (1996)

Mast cells synthesize vasoactive agents and a number of neurotransmitters. They are particularly numerous in the medial habenular region of the epithalamus, the attachment site of the choroid plexus. The present study examined whether degranulation of brain mast cells alters the permeability of the blood-brain barrier (BBB). To this end, doves were injected intramuscularly with the mast cell degranulator, compound 48/80 (C40/80), followed by i.v. injection of Evans blue. The distribution of the dye in the parenchyma was examined using digital imaging. Three brain areas were analyzed: the medial habenula (which also contains mast cells), the paraventricular nucleus (PVN, which abuts the third ventricle, but has no mast cells), and the lateral septal organ (LSO, a circumventricular organ with fenestrated capillaries). Significantly more Evans blue tracer and fewer toluidine blue-positive mast cells were detected in the medial habenula of subjects treated with C48/80 compared to saline controls. Evans blue did not enter the PVN in either the experimental or control group, while it entered the LSO equally in both. Degranulation of mast cells after C48/80 treatment was confirmed histochemically and ultrastructurally. The results support the hypothesis that brain mast cell degranulation locally alters BBB permeability. Activation of brain mast cells may provide a mechanism for regulated opening of the BBB.
The neurobiological basis of ADHD (2010)

Attention-Deficit/Hyperactivity Disorder is not a single pathophysiological entity and appears to have a complex etiology. There are multiple genetic and environmental risk factors with small individual effect that act in concert to create a spectrum of neurobiological liability. Structural imaging studies show that brains of children with Attention-Deficit/Hyperactivity Disorder are significantly smaller than unaffected controls. The prefrontal cortex, basal ganglia and cerebellum are differentially affected and evidence indicating reduced connectivity in white matter tracts in key brain areas is emerging. Genetic, pharmacological, imaging, and animal models highlight the important role of dopamine dysregulation in the neurobiology of Attention-Deficit/Hyperactivity Disorder. To date, stimulants are the most effective psychopharmacological treatments available for Attention-Deficit/Hyperactivity Disorder. Currently only immediate release methylphenidate and atomoxetine are approved for the treatment of ADHD in Italy. Drug treatment should always be part of a comprehensive plan that includes psychosocial, behavioural and educational advice and interventions.
Inhibitors of protein kinase C. 3. Potent and highly selective bisindolylmaleimides by conformational restriction (1993)

The protein kinase inhibitor staurosporine has been used to design a series of selective bisindolylmaleimide inhibitors of protein kinase C (PKC). Guided by molecular graphics, conformational restriction of the cationic side chain has led to ATP competitive inhibitors of improved potency and selectivity. Two compounds have been further evaluated and were shown to inhibit PKC of human origin and prevent T-cell activation in a human allogeneic mixed lymphocyte reaction. One of these compounds was orally absorbed in mice and antagonized a phorbol ester induced paw edema in a dose-dependent manner. This compound also selectively inhibited the secondary T-cell mediated response in a developing adjuvant arthritis model in rats and provides evidence for the potential use of PKC inhibitors as therapeutic immunomodulators.
A GRISM-based probe for spectrally encoded confocal microscopy (2003)

Spectrally encoded confocal microscopy (SECM) is a novel approach for obtaining high resolution, depth-sectioned images of microstructure within turbid samples. By encoding one spatial dimension in wavelength, imaging probes can be greatly simplified compared to standard scanning confocal microscopes, potentially enabling endoscopic implementation. The use of a diffraction grating for spectral encoding, however, skews the optical axis through the probe, thus complicating the design of narrow diameter instruments. In this Letter, we describe a novel use of a single-optical-axis element based on high index-of-refraction prisms and a transmission holographic grating for the design of narrow diameter SECM devices. Confocal images obtained with a 10.0 mm probe demonstrate a transverse resolution of 1.1 microm and a field of view of 650 microm.
Evidence for specific binding and stimulatory effects of recombinant human erythropoietin on isolated adult rat Leydig cells (1992)

The presence of specific binding of recombinant human erythropoietin and its effect on testosterone production were evaluated in isolated intact adult rat Leydig cells. Maximal specific binding was observed after 135 min incubation at 34 degrees C. Scatchard analysis of the binding data revealed two distinct classes of binding sites for [125I]-recombinant human erythropoietin with dissociation constant of (Kd1) 1.9 x 10(-10) mol/l and (Kd2) 1.37 x 10(-8) mol/l respectively and binding capacity of (Bmax1) 12.3 fmol/10(6) cells and (Bmax2) 42.8 fmol/10(6) cells, respectively. GnRH, hCG, IGF-I and EGF did not induce any modification of recombinant human erythropoietin-specific binding. Recombinant human erythropoietin added to isolated adult rat Leydig cells exerted a stimulatory effect on testosterone production reaching its maximal effect at the dose of 10(-10) mol/l (testosterone production from 14.9 +/- 1.7 to 45.1 +/- 6.2 pmol/10(6) cells/3 h). Addition of anti-recombinant human erythropoietin serum completely blocked the recombinant human erythropoietin-stimulated testosterone production. These results show that purified adult rat Leydig cells possess recombinant human erythropoietin specific binding, and suggest that this glycoprotein directly influences rat Leydig steroidogenesis.
Cell adhesion promoting peptide GVKGDKGNPGWPGAP from the collagen type IV triple helix: cis/trans proline-induced multiple proton NMR conformations and evidence for a KG/PG multiple turn repeat motif in the all-trans proline state (1991)

Peptide GVKGDKGNPGWPGAPY (called peptide IV-H1), derived from the protein sequence of human collagen type IV, triple-helix domain residues 1263-1277, represents an RGD-independent, cell-specific, adhesion, spreading, and motility promoting domain in type IV collagen. In this study, peptide IV-H1 has been investigated by 1H NMR (500 MHz) spectroscopy. Cis-trans proline isomerization at each of the three proline residues gives rise to a number of slowly exchanging (500-MHz NMR time scale) conformation states. At least five such states are observed, for example, for the well-resolved A14 beta H3 group, and K3, which is six residues sequentially removed from the nearest proline, i.e., P9, shows two sets. The presence of more than two sets of resonances for residues sequentially proximal to a proline, e.g., A14-cis-P15 and A14-trans-P15, and more than one set for a residue sequentially well-removed from a proline, e.g., K3, indicates long range conformation interactions and the presence of preferred structure in this short linear peptide. Many resonances belonging to these multiple species have been assigned by using mono-proline-substituted analogues. Conformational (isomer) state-specific 2D 1H NMR assignments for the combination of cis and trans proline states have been made via analysis of COSY-type, HOHAHA, and NOESY spectra. Peptide IV-H1 in the all-trans proline state ttt exists in relatively well-defined conformation populations showing numerous short- and long-range NOEs and long-lived backbone amide protons and reduced backbone NH temperature coefficients, suggesting hydrogen-bonding, and structurally informative 3J alpha N coupling constants. The NMR data indicate significant beta-turn populations centered at K3-G4, K5-G6, P9-G10, and P12-G13, and a C-terminal gamma-turn within the A14-P15-Y16 sequence. These NMR data are supported by circular dichroic studies which indicate the presence of 52% beta-turn, 10% helix, and 38% random coil structural populations. Since equally spaced KG and PG residues are found on both sides of peptide IV-H1 in the native collagen type IV sequence, this multiple turn repeat motif may continue through a longer segment of the protein. Synthetic peptide IV-H1 overlapping sequence "walk throughs" indicate that the primary biological activity is localized in the GNPGWPGAP double beta-turn domain, which contains the backbone constraining proline residues. This proline-domain conformation may suggest a collagen type IV receptor-specific, metastatic cell adhesion promoting binding domain.