gebhart/patrepeval huggingface dataset:
Photostability of CdSe Quantum Dots Functionalized with Aromatic Dithiocarbamate Ligands (2013)

Organic ligands are widely used to enhance the ability of CdSe quantum dots (QDs) to resist photodegradation processes such as photo-oxidation. Because long alkyl chains may adversely affect the performance of QD devices that require fast and efficient charge transfer, shorter aromatic ligands are of increasing interest. In this work, we characterize the formation of phenyl dithiocarbamate (DTC) adducts on CdSe surfaces and the relative effectiveness of different para-substituted phenyl dithiocarbamates to enhance the aqueous photostability of CdSe QDs on TiO2. Optical absorption and photoluminescence measurements show that phenyl DTC ligands can be highly effective at reducing QD photocorrosion in water, and that ligands bearing electron-donating substituents are the most effective. A comparison of the QD photostability resulting from use of ligands bearing DTC versus thiol surface-binding groups shows that the DTC group provides greater QD photostability. Density functional calculations with natural bond order analysis show that the effectiveness of substituted phenyl DTC results from the ability of these ligands to remove positive charge away from the CdSe and to delocalize positive charge on the ligand.
Pediatric Traumatic Brain Injury: Past, Present and Future (2006)

Traumatic brain injury (TBI) is the leading cause of death and disability in children. Evidence-based guidelines for the management of this population are available; however, the data highlight significant deficiencies with few treatment standards or guidelines. Considering the limited availability of resources, it is necessary to define realistic goals. Attention should be given to injury prevention, developing standardized pediatric admission and outcome evaluations, increasing the utility and spectrum of physiological and biochemical testing, and defining the evolving role of imaging in TBI.
Determination of milk concentrations and pharmacokinetics of salicylic acid following acetylsalicylic acid (aspirin) administration in postpartum dairy cows (2022)

The objectives of this descriptive study were to (1) describe the pharmacokinetics of salicylic acid (SA) in the milk and plasma of postpartum dairy cattle following oral administration of acetylsalicylic acid (ASA; aspirin), (2) to estimate a recommended milk withdrawal period for dairy cattle treated with ASA, and (3) to determine the effect of ASA administration on plasma prostaglandin E<sub>2</sub> metabolite (PGEM) concentrations. Primiparous (n = 3) and multiparous (n = 7) postpartum Holstein dairy cows received 2 oral treatments with ASA at 200 mg/kg of body weight, 24 h apart. Concentrations of SA in plasma and milk from 0 h through 120 h after ASA administration were analyzed using ultra performance liquid chromatography triple quadrupole mass spectrometry and a milk withdrawal period was estimated using the United States Food and Drug Administration Milk Discard App in R. Two withdrawal periods were estimated: (1) a whole-herd treatment scenario with no dilution factor and (2) an individual animal treatment scenario with a bulk tank factor included in analysis. Plasma PGEM concentrations in samples from 0 h to 24 h after ASA administration were determined using a commercially available competitive ELISA. Milk SA concentrations were undetected in all cows by 48 h after the last ASA treatment. Secondary peaks were observed in plasma at 58 and 82 h after the last treatment and in milk at 87 h after the last treatment. In the absence of a tolerance for SA in milk, the estimated milk withdrawal periods were (1) 156 h for the whole-herd treatment scenario and (2) 120 h for the individual animal treatment scenario. Plasma PGEM concentrations were reduced compared with baseline for up to 12 h after ASA administration, with the greatest reduction observed at 2 h. Results from this study suggest that the current milk withhold recommendation for dairy cattle administered ASA may need revision to 120 h (5 d) and that ASA administration may mitigate postpartum inflammation through reduction in prostaglandin production for up to 12 h after treatment. Pharmacokinetic and milk withdrawal data from this study will inform future recommendations for extra-label use of aspirin in postpartum dairy cows. Further research is required to determine the basis for the secondary SA peaks and to elucidate the long-term effects of ASA administration on dairy cow health.
Phosphatides isolated from seeds of commercial and experimental safflower varieties (1971)

Abstract Studies on phosphatides from several safflower varieties show the following five major results. The total phosphatide contents of the various safflower seeds are quite similar (0.48% for a commercial and 0.58% for a brown‐striped variety). The same three major and one minor phosphatides were present in all varieties: phosphatidyl choline (PC), phosphatidyl ethanolamine (PE), phosphatidyl inositol (PI) and phosphatidyl serine (PS). The amounts of these lipids present in the crude phosphatide mixture were quite similar in all varieties tested (}36% for PC, }15% for PE, }23% for PI, and less than 2% for PS). The fatty acid composition of the phosphatides of UC‐1 high oleic safflower is very different from that of the other varieties, but it reflects the composition of the corresponding oil triglycerides as far as the major acid is concerned. All other safflower seed phosphatides investigated have linoleic acid as the major fatty acid constituent. A simple and very sensitive color test has been found which can differentiate phosphatides of the high linoleic from the high oleic type.
Persistent Helicobacter pullorum colonization in C57BL/6NTac mice: a new mouse model for an emerging zoonosis (2012)

Helicobacter pullorum, an enterohepatic Helicobacter species, is associated with gastroenteritis and hepatobiliary disease in humans and chickens. Recently, a novel H. pullorum outbreak in barrier-maintained rats and mice was described. In this study, persistence of infection and serological responses were further evaluated in H. pullorum-infected female C57BL/6NTac and C3H/HeNTac mice obtained from the barrier outbreak. C57BL/6NTac mice (n=36) aged 10-58 weeks were confirmed to be chronically infected with H. pullorum by PCR or culture of caecum, colon and faeces, with no evidence of hepatic infection; two of three C3H/HeNTac mice cleared H. pullorum infection by 26 weeks of age. A quantitative PCR (qPCR) assay based on the cdtB gene specific to H. pullorum demonstrated that colonization was high in the caecum and colon at 10(4)-10(6) c.f.u. equivalents per µg host DNA, and decreased by several logs from 32 to 58 weeks of age. Infected mice were seropositive by ELISA, and H. pullorum-specific IgG levels decreased as colonization was lost over time in selected mice. Consistent with the lack of pathology associated with chronic infection of C57BL/6 mice with other murine enteric helicobacters, C57BL/6NTac and C3H/HeNTac mice infected with H. pullorum did not develop gross or histological lesions of the liver or gastrointestinal tract. The cdtB-based qPCR assay can be used in screening animals, food sources and environmental samples for H. pullorum, as this food-borne pathogen has zoonotic potential. These findings will also allow future studies in murine models to dissect potential pathogenic mechanisms for this emerging pathogen.
Identification on Human CD36 of a Domain (155-183) Implicated in Binding Oxidized Low-Density Lipoproteins (Ox-LDL) (1996)

Uptake of oxidized LDL (oxLDL) by macrophages is one of the key events implicated in the initiation and perpetuation of atherosclerotic lesions. One of the major scavenging receptors, which binds modified LDL, on macrophages is CD36. The domain on CD36 implicated in the binding of oxLDL remains to be elucidated. In this study, COS cells transfected with human CD36 cDNA bound FITC-oxidized human LDL in a dose-dependent, saturable manner. This binding was inhibited by an excess of oxLDL but not by native LDL. Anti-CD36 monoclonal antibodies (mAbs) 10/5, FA6-152, and 8A6 (directed against domain 155-183), but not mAb 13/10 (directed against domain 30-76), completely inhibited oxLDL binding to human CD36-transfected COS cells. Cells transfected with a chimeric human CD36 construct (hmh 155-183), resulting from the swapping of human domain 155-183 with its murine counterpart, resulted in low binding of oxLDL. In contrast, cells transfected with a chimeric murine CD36 construct (mhm 155-183), resulting from the swapping of murine domain 155-183 with its human counterpart, resulted in high binding of oxidized human LDL. Binding of oxLDL to cells transfected by chimeric construct mhm 155-183 were only partially blocked by mAbs 10/5, FA6-152, and 8A6. In the present study we have identified, for the first time, an important functional domain (encompassing amino acids 155-183) on CD36 involved in the binding of oxLDL. In addition, the binding site for oxidized human LDL on murine CD36 seems to differ from its human counterpart.
Endoglin expression on human microvascular endothelial cells (2000)

Transforming growth factor-beta (TGF-beta) plays an important role in angiogenesis and vascular function. Endoglin, a transmembrane TGF-beta binding protein, is highly expressed on vascular endothelial cells and is the target gene for the hereditary haemorrhagic telangiectasia type I (HHT1), a dominantly inherited vascular disorder. The specific function of endoglin responsible for HHT1 is believed to involve alterations in TGF-beta responses. The initial interactions on the cell surface between endoglin and TGF-beta receptors may be an important mechanism by which endoglin modulates TGF-beta signalling, and thereby responses. Here it is shown that on human microvascular endothelial cells, endoglin is co-expressed and is associated with betaglycan, a TGF-beta accessory receptor with which endoglin shares limited amino acid homology. This complex formation may occur in either a ligand-dependent or a ligand-independent manner. In addition, the occurrence of three higher order complexes containing endoglin, type II and/or type I TGF-beta receptors, on these cells is demonstrated. Our findings suggest that endoglin may modify TGF-beta signalling by interacting with both betaglycan and the TGF-beta signalling receptors at physiological receptor concentrations and ratios.
Close encounters with apolipoprotein E receptors (1996)

Most of the LDL receptor family members recognize apolipoprotein E. The structures of the VLDL receptor, and recently identified apolipoprotein E receptor 2, closely resemble the LDL receptor. Recent studies have demonstrated that the VLDL receptor is responsible for the reproduction of premammalian species by mediating oogenesis. Despite the importance of the VLDL receptor in premammalian species, the biological role of the mammalian VLDL receptor is still unclear. Apolipoprotein E receptor 2 is structurally most closely related to the LDL receptor and expressed predominantly in brain. This newly identified receptor may play a role in the uptake of cholesterol in the central nervous system.
Abstract IA21: Tumor heterogeneity and cell-of-origin of mouse small cell and non-small cell lung cancer (2014)

Abstract Small cell lung cancer (SCLC) is one of the most lethal human malignancies, due to its high metastatic potential and chemo-resistance upon relapse. Using the Rbf/f;p53f/f mouse model for SCLC, we found that the tumors are often composed of phenotypically different cells, characterized by mesenchymal and neuroendocrine markers. These cells often share a common origin. Crosstalk between these cells can endow the neuroendocrine component with metastatic capacity, illustrating the potential relevance of tumor cell heterogeneity in dictating functional tumor properties. Also specific genetic lesions appear to be associated with metastatic potential. Interestingly, the two cell types can also interconvert raising the question of their cell-of-origin. To investigate this in more detail, we inactivated Trp53 and Rb1 in distinct cell types in the adult lung by targeting Cre-recombinase expression to Clara, neuroendocrine, and alveolar type II cells using adenoviral vectors. We could show that neuroendocrine cells serve as the predominant although not the exclusive cell of origin of SCLC. In contrast, mutant Kras-driven adenocarcinomas (one of the NSCLC subtypes) originates primarily from alveolar type II cells. However, in LSL-mutant-Kras;p53flox/flox mice also other cell types gave effectively rise to adenomas and adenocarcinomas. Our data indicate that both cell type specific features and the nature of the oncogenic lesion(s) are critical factors in determining the tumor initiating capacity of lung (progenitor) cells. Furthermore, the cell-of-origin appears to influence the malignant properties of the resulting tumors. Citation Format: Anton Berns. Tumor heterogeneity and cell-of-origin of mouse small cell and non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr IA21.
Immunomodulatory response to neoadjuvant nivolumab in non-metastatic clear cell renal cell carcinoma. (2023)

708 Background: Novel perioperative strategies are needed to reduce recurrence rates in patients undergoing nephrectomy for high-risk, non-metastatic clear cell renal cell carcinoma (ccRCC). We sought to (1) elucidate the effects of PD-1 inhibition on primary tumor-infiltrating and circulating immune cell populations in ccRCC and (2) correlate tumor microenvironment and circulating immune cell compositions with response to anti-PD-1 therapy. Methods: We conducted a prospective, phase I trial of neoadjuvant nivolumab prior to nephrectomy in 15 evaluable patients with non-metastatic ccRCC. We leveraged tissue from this cohort to elucidate the effects of PD-1 inhibition on immune cell populations in ccRCC and correlate the evolving immune milieu with anti-PD-1 response using fluorescence-activated cell sorting, bulk RNA sequencing with protein activity inference, and enzyme-linked immunosorbent assay for circulating cytokines. Results: We found that nivolumab durably promotes a pro-inflammatory state within the primary tumor, as evidenced by a sustained increase in the effector T cell phenotype and decreased representation of regulatory T cell subsets. Baseline immune infiltration within the primary tumor including T effector and myeloid enrichment along with angiogenic depletion correlates with nivolumab responsiveness. Nivolumab increases CTLA-4 expression in the primary tumor, and subsequent nephrectomy increases circulating concentrations of sPD-L1, sPD-L3 (sB7-H3), and s4-1BB. Conclusions: Our findings form the basis to consider neoadjuvant immune checkpoint inhibition (ICI) for high-risk ccRCC while the tumor remains in situ and provide the rationale for perioperative strategies of novel ICI combinations. Clinical trial information: NCT02575222 .
Deep 3D reconstruction of synchrotron X-ray computed tomography for intact lungs (2023)

Synchrotron X-rays can be used to obtain highly detailed images of parts of the lung. However, micro-motion artifacts induced by such as cardiac motion impede quantitative visualization of the alveoli in the lungs. This paper proposes a method that applies a neural network for synchrotron X-ray Computed Tomography (CT) data to reconstruct the high-quality 3D structure of alveoli in intact mouse lungs at expiration, without needing ground-truth data. Our approach reconstructs the spatial sequence of CT images by using a deep-image prior with interpolated input latent variables, and in this way significantly enhances the images of alveolar structure compared with the prior art. The approach successfully visualizes 3D alveolar units of intact mouse lungs at expiration and enables us to measure the diameter of the alveoli. We believe that our approach helps to accurately visualize other living organs hampered by micro-motion.
Restriction in IgM expression. III. Affinity analysis of monoclonal anti-lactose antibodies. (1981)

Abstract A clonal analysis has been made of the murine BALB/C response to lactose-containing immunogens with respect to the affinity restriction in IgM expression. Monoclonal IgM and IgG antibodies were prepared from antilactosyl hybridomas generated from mice immunized with p-aminophenyl-beta-lactoside (PAPL) coupled to BGG or with a vaccine of Streptococcus faecalis (Strain N). Association constants for the binding of monovalent derivatives of PAPL were measured by quenching fluorescence. These derivatives carried a probe (2,4-dinitrophenyl or 1-dimethylaminonaphthalene-5-sulfonyl) that served to quench the protein fluorescence when the ligand was complexed with the protein. The central finding was that with both immunogens a restriction in the affinity of IgM was demonstrated since the highest values exhibited by IgG antibody exceeded by at least a factor of 50 the highest comparable values of the association constants for IgM antibody. It is suggested that the hypothesis of germ-line restriction, previously proposed as the basis for the affinity restriction of IgM, may also be applicable to the T cell receptor since its distinctive properties parallel those of IgM antibody.
Regulation of the voltage-gated Ca 2+ channel Ca V α 2 δ-1 subunit expression by the transcription factor Egr-1 (2018)

It is well known that the Ca<sub>V</sub>α<sub>2</sub>δ auxiliary subunit regulates the density of high voltage-activated Ca<sup>2+</sup> channels in the plasma membrane and that alterations in their functional expression might have implications in the pathophysiology of diverse human diseases such as neuropathic pain. However, little is known concerning the transcriptional regulation of this protein. We previously characterized the promoter of Ca<sub>V</sub>α<sub>2</sub>δ, and here we report its regulation by the transcription factor Egr-1. Using the neuroblastoma N1E-115 cells, we found that Egr-1 interacts specifically with its binding site in the promoter, affecting the transcriptional regulation of Ca<sub>V</sub>α<sub>2</sub>δ. Overexpression and knockdown analysis of Egr-1 showed significant changes in the transcriptional activity of the Ca<sub>V</sub>α<sub>2</sub>δ promoter. Egr-1 also regulated the expression of Ca<sub>V</sub>α<sub>2</sub>δ at the level of protein. Also, functional studies showed that Egr-1 knockdown significantly decreases Ca<sup>2+</sup> currents in dorsal root ganglion (DRG) neurons, while overexpression of the transcription factor increased Ca<sup>2+</sup> currents in the F11 cell line, a hybrid of DRG and N18TG2 neuroblastoma cells. Studying the effects of Egr-1 on the transcriptional expression of Ca<sub>V</sub>α<sub>2</sub>δ could help to understand the regulatory mechanisms of this protein in both health and disease.
Human serum albumin as a cosolvent for parenteral drugs. (1989)

Diazepam, solubilized in human serum albumin and delivered i.p. to mice, neutralized seizures induced with Metrazole in a mouse epilepsy model. Diazepam-free albumin, injected immediately after the Metrazole, also reduced seizures; albumin binds Metrazole. Heat-denatured rabbit albumin failed to elicit precipitating antibodies in the rabbit. Albumin is a suitable cosolvent for some water-insoluble drugs but probably is not cost-effective.
Raman emission in porous silicon at 1.5 micron: a possible approach (2005)

In this paper, in order to generate radiation at 1.54 micron, an approach based on Raman scattering in porous silicon is presented. Experimental results, proving spontaneous Raman emission at 1.5 micron and tuning of the Stokes shift, are reported. Finally, we discuss about the possibility to enhance the Raman gain coefficient and to eliminate two photon absorption in porous silicon.
Merging environments for shared spaces in mixed reality (2018)

In virtual reality a real walking interface limits the extent of a virtual environment to our local walkable space. As local spaces are specific to each user, sharing a virtual environment with others for collaborative work or games becomes complicated. It is not clear which user's walkable space to prefer, or whether that space will be navigable for both users.
Fluorine‐18 labelling of PNAs functionalized at their pseudo‐peptidic backbone for imaging studies with PET (2004)

Abstract Peptide nucleic acids (PNAs) form a unique class of synthetic macromolecules, originally designed as ligands for the recognition of double‐stranded DNA, where the deoxyribose phosphate backbone of original DNA is replaced by a pseudo‐peptide N ‐(2‐aminoethyl)glycyl backbone, while retaining the nucleobases of DNA. We have previously developed an original method to label oligonucleotide‐based macromolecules with the short‐lived positron‐emitter fluorine‐18 ( t 1/2 : 109.8 min) using the N‐ (4‐[ 18 F]fluorobenzyl)‐2‐bromoacetamide reagent. Using this method, we herein report the fluorine‐18‐labelling of 13 decameric PNAs ( OLP_1‐13 ), of the same sequence (CTCATACTCT), but presenting selected modification of the pseudo‐peptidic backbone at two or three of the thymine residues (positions 2, 5 and 8). Structural characteristics of these backbone modifications include either an amino acid side chain ( L ‐Lys, L ‐Glu, L ‐Leu and L ‐Arg) or a glycosyl moiety (mannose, galactose, fucose, N ‐Ac‐galactosamine and N ‐Ac‐glucosamine) attached via an appropriate spacer. N ‐(4‐[ 18 F]fluorobenzyl)‐2‐bromoacetamide was synthesized in three radiochemical steps from 4‐cyano‐ N , N , N ‐trimethylanilinium trifluoromethanesulfonate and HPLC‐purified in 85–90 min (typical production: 3.7–4.8 GBq starting from a batch of 29.6–31.4 GBq of [ 18 F]fluoride). Conjugation of the fluorine‐18‐labelled bromoacetamide reagent with the PNAs was performed in a mixture of acetonitrile and HEPES buffer (0.1 M, pH 7.9) for 10 min at 60°C and gave the corresponding pure labelled conjugated PNAs ([ 18 F] c‐OLP_1‐13 ) after RP‐HPLC purification. The whole synthetic procedure, including the preparation of the fluorine‐18‐labelled reagent, provides up to 0.9 GBq (25 mCi) of HPLC‐purified [ 18 F] c‐OLP_1‐13 in 160 min with a specific radioactivity of 45–65 GBq/µmol (1.2–1.7 Ci/µmol) at the end of synthesis starting from 29.6 to 31.4 GBq (800–850 mCi) of [ 18 F]fluoride. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity (1992)

We have cloned fragments of DNA (up to 13 kb), from Pseudomonas putida AJ1, that code for two stereospecific haloalkanoate dehalogenases. These enzymes are highly specific for D and L substrates. The two genes, designated hadD and hadL, have been isolated and independently expressed in Escherichia coli and P. putida hosts by using broad-host-range vectors. They are closely adjacent and inducible in what appears to be an operon with an upstream open reading frame of unknown function. Nucleotide sequence determination of hadD predicts a mature, cytoplasmic protein of 300 amino acid residues (molecular weight of 33,601). This has no significant homology with the L-specific haloalkanoate dehalogenases from Pseudomonas sp. strain CBS3 (B. Schneider, R. Muller, R. Frank, and F. Lingens, J. Bacteriol. 173:1530-1535, 1991) nor with any other known DNA or protein sequences.
Plasma levels of lipopolysaccharide correlate with insulin resistance in HIV patients (2018)

Our results showed a clear correlation between plasma LPS and markers of insulin resistance, suggesting a relationship between LPS levels and metabolic alterations, particularly affecting lipids and insulin resistance in HIV patients.