gebhart/patrepeval huggingface dataset:
Biochemical Characterization of Endogenously Formed Eosinophilic Crystals in the Lungs of Mice (2000)

Crystals seldom form spontaneously within tissues of mammals, except in the urinary tract or in association with eosinophil-rich diseases in humans (Charcot-Leyden crystals). Endogenously formed eosinophilic crystals have been reported in respiratory tract and other tissues of several strains of mice, but the biochemical characterization of these crystals has not been reported. In this study, eosinophilic crystal formation was examined in homozygous C57BL/6J viable motheaten mice, lung-specific surfactant apoprotein C promoter/soluble human tumor necrosis factor p75 receptor type II fusion protein transgenic mice (C57BL/6NTac x Sv/129), and CD40L-deficient mice with spontaneous Pneumocystis carinii infection. In viable motheaten but not wild type mice, rapidly developing crystals represented a major feature of the fatal lung injury induced by macrophage dysregulation. Conversely, eosinophilic crystals did not form until 4-8 months of age in transgenic and CD40L-deficient mice and were present in 10-30% of age-matched wild type controls. Mass spectrometry analysis of proteins from bronchoalveolar lavage fluid identified the crystals as Ym1, sometimes referred to as T-lymphocyte-derived eosinophil chemotactic factor. The Ym1 sequence was homologous to chitinase, and enzymatic assays indicated a 3-5-fold increase in chitinase activity compared with control mice. Intracellular and extracellular crystals associated with epithelial damage suggested that the crystals may contribute to lung inflammation through mechanical damage and enzymatic degradation.
Expression of caveolin by bovine lymphocytes and antigen‐presenting cells (2002)

Caveolin is a generic term for a family of proteins that include caveolin-1, -2 and -3. Although the distribution of these proteins varies between cells, caveolin-1 and -2 are commonly found coating membrane invaginations known as caveolae. Studies on human and murine cells suggest that caveolin/caveolae can be found in neutrophils, macrophages and mast cells, in which they are involved in the uptake of pathogens, but not in lymphocyte cell lines. Expression of caveolin-1, -2 and -3 in bovine immune cells was investigated using confocal microscopy and Western blotting. Staining for caveolin-1 was evident in all peripheral blood mononuclear cells (PBMC) and in CD4+, CD8+ and CD21+ lymphocytes, monocytes, macrophages and monocyte-derived dendritic cells (DC). In addition, the caveolin-1 antibody detected a protein with a molecular weight of approximately 22[?]000 in all PBMC, macrophages and DC, as well as in bovine aortic endothelial (BAE)-1 cells and human endothelial cells by Western blotting. In macrophages and DC, caveolin co-localized with the endoplasmic reticulum--Golgi intermediate compartment (ERGIC) and to a lesser extent with Golgi, but not with endoplasmic reticulum. Staining was not seen on the plasma membrane in any bovine immune cells, suggesting the absence of caveolae, while in BAE-1 cells staining was predominantly on the cell membrane. Caveolin-2 could not be detected in any bovine cells by confocal microscopy or Western blotting, while caveolin-3 was detected in all bovine cells by Western blotting, but not by confocal microscopy. These data provide evidence for the presence of caveolin in bovine lymphocytes and antigen-presenting cells.
Bioreversible Derivatives of Phenol. 2. Reactivity of Carbonate Esters with Fatty Acid-like Structures Towards Hydrolysis in Aqueous Solutions (2007)

A series of model phenol carbonate ester prodrugs encompassing derivatives with fatty acid-like structures were synthesized and their stability as a function of pH (range 0.4 - 12.5) at 37 degrees C in aqueous buffer solutions investigated. The hydrolysis rates in aqueous solutions differed widely, depending on the selected pro-moieties (alkyl and aryl substituents). The observed reactivity differences could be rationalized by the inductive and steric properties of the substituent groups when taking into account that the mechanism of hydrolysis may change when the type of pro-moiety is altered, e.g. n-alkyl vs. t-butyl. Hydrolysis of the phenolic carbonate ester 2-(phenoxycarbonyloxy)-acetic acid was increased due to intramolecular catalysis, as compared to the derivatives synthesized from omega-hydroxy carboxylic acids with longer alkyl chains. The carbonate esters appear to be less reactive towards specific acid and base catalyzed hydrolysis than phenyl acetate. The results underline that it is unrealistic to expect that phenolic carbonate ester prodrugs can be utilized in ready to use aqueous formulations. The stability of the carbonate ester derivatives with fatty acid-like structures, expected to interact with the plasma protein human serum albumin, proved sufficient for further in vitro and in vivo evaluation of the potential of utilizing HSA binding in combination with the prodrug approach for optimization of drug pharmacokinetics.
Analysis of Human CYP7A1 mRNA Decay in HepG2 Cells by Reverse Transcription–Polymerase Chain Reaction (1998)

The conversion of cholesterol to bile acids is the major pathway through which cholesterol is removed from the body. The initial and rate-limiting step in this catabolic pathway is catalyzed by the liver-specific enzyme cholesterol 7alpha-hydroxylase (CYP7A1). The HepG2 cell line has been used as a model to study human CYP7A1. The levels of CYP7A1 mRNA, however, are quite low in this cell line and require the use of poly(A)+ mRNA for detection using standard Northern analysis. As an alternative, we established a reverse transcription-polymerase chain reaction (RT-PCR) assay that can be used to study CYP7A1 mRNA in HepG2 cells. Using RT-PCR, we analyzed the influence of cell culture conditions on CYP7A1 mRNA levels. We observed an increase in CYP7A1 mRNA levels as the density of the cell culture increased. This rise in CYP7A1 was accompanied by a reciprocal drop in the levels of the proto-oncogene c-myc. Since c-myc expression is strongly associated with cell growth status, this inverse relationship suggests that conditions that favor reduced cell proliferation result in higher levels of CYP7A1 expression. We also established the validity of using RT-PCR for the measurement of mRNA decay rates using c-myc and glyceraldehyde-3-phosphate dehydrogenase mRNAs as a model: The same half-life value was obtained for the c-myc mRNA using either Northern analysis or RT-PCR. Using our RT-PCR method we determined that human CYP7A1 mRNA decays with a half-life of 4.6 +/- 0.9 h (n = 8) in HepG2 cells. We show that the protein synthesis inhibitor cycloheximide prolonged the CYP7A1 mRNA half-life, suggesting that translation is required for mRNA decay. Dexamethasone treatment, however, did not alter CYP7A1 mRNA decay rate but it increased CYP7A1 steady-state mRNA levels, suggesting that the effect of this glucocorticoid in HepG2 cells may be transcriptional.
Mechanical Properties and Corrosion Behaviour of Nanostructured Cu-rich CuNi Electrodeposited Films. (2012)

Nanocrystalline Cu-rich CuNi alloy thin films (with copper content ranging from 22 to 97 at%) have been grown by electrodeposition, using galvanostatic conditions in an electrolytic bath containing Ni and Cu sulphates with a [Ni (II)]/[Cu (II)] molar ratio of 11. The Cu content is tuned by varying the applied current density during deposition. The nanoscrystalline nature of Cu-rich CuNi thin films has been achieved using saccharine as a grain refinement agent, although for high Cu content (> 90 at%) the refinement effect is less pronounced. Due to the nanocrystalline character of the films, low surface roughness, good compactness, and outstanding mechanical properties (e.g. nanoindentation hardness values of approximately 7 GPa) are obtained, particularly for Cu percentages below 70 at%. The presence of stacking faults also contributes to the observed high strength. The films show good corrosion protective behaviour in a 3.5 wt% NaCl medium, with corrosion potentials more positive than the bare substrate (pure-Cu) and lower corrosion current density values ranging from 1.8 to 5.4 μA/cm2.
Magnetic Resonance Imaging Findings of Portal Biliopathy (2005)

Purpose: We wanted to evaluate the MR imaging findings of portal biliopathy. Materials and Methods: We retrospectively reviewed the MR imaging of twelve patients having biliary abnormalities and portal cavernoma. Two radiologists working in consensus analyzed the presence of extrahepatic portal vein obstruction, cavernous transformation, portosystemic collaterals and bile ducts abnormalities that included irregular contour, stricture, ductal dilatation, wall thickening and enhancement of the ductal wall. Results: Extrahepatic portal vein obstruction was replaced by cavernous transformations in all patients. The cavernous transformations depicted on the MR scans were paracholedochal veins in 12 patients and epicholedochal veins in 6 patients. Three different types of biliary abnormalities were present: 1) the pseudocholangiocarcinoma type (3 patients) that resembled extrahepatic cholangiocarcinoma, 2) the varicoid type (6 patients) that was mainly distinguished by the multiple smooth extrinsic impressions along the common bile duct and 3) the mixed type (3 patients). The highly specific findings for the pseudocholangiocarcinoma type disease were thickening and delayed enhancement of the biliary ductal wall. Conclusion: The MR findings of portal biliopathy include cavernous transformation of the portal vein and morphological alterations of the biliary tracts such as irregular contour, biliary stricture with proximal ductal dilatation and thickening of the ductal wall with delayed enhancement. Recognition of these MR findings should facilitate the accurate diagnosis of portal biliopathy and prevent the misinterpretation or inappropriate management of this disease as malignancy or sclerosing chloangitis.
Sociability deficits after prenatal exposure to valproic acid are rescued by early social enrichment (2018)

We show that early social enrichment can specifically rescue social deficits in a mouse model of ASD. Our results identified the Pir as a structure affected by VPA-exposure and social enrichment, suggesting that it could be a key component of the social brain circuitry.
Syntenator: Multiple gene order alignments with a gene-specific scoring function (2008)

We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from http://www2.tuebingen.mpg.de/abt4/plone.
Planarized multi-layer fabrication technology for LTS large-scale SFQ circuits (2003)

We have been developing a 10 kA cm−2 Nb advanced fabrication process to make larger scale and higher speed SFQ circuits that have over 100k junctions. The main challenges in implementing this process are related to increasing the critical current density of junctions, decreasing design rules and increasing the number of Nb layers. We have proposed a planarized multi-layer structure, which consists of a Nb/AlOx/Nb junction layer, Nb wiring layers, Nb shield layers, a Nb layer for dc power, a Nb ground plane, SiO2 insulator layers and a Mo resistor layer. In fabricating this multi-layer structure, we have developed a new planarization technology which enables the flattening of the SiO2 insulator surface over the Nb wiring layer independent of the pattern sizes of the Nb wirings. This planarization technology consists of SiO2 bias sputtering, reactive ion etching with a reversal mask of the Nb wiring and mechanical polishing planarization. The SEM photographs showed excellent flatness for the planarized multi-layer structure.
Molecular epidemiology of human cancer risk: gene-environment interactions andp53 mutation spectrum in human lung cancer (1999)

The p53 tumour suppressor gene is at the crossroads of a network of cellular pathways including cell cycle checkpoints, DNA repair, chromosomal segregation, and apoptosis. These pathways have evolved to maintain the stability of the genome during cellular stress from DNA damage, hypoxia, and activated oncogenes. The high frequency of p53 mutations in human cancer is a reflection of the importance of p53 involvement in this network of pathways during human carcinogenesis. An electronic database containing p53 mutations from more than 9000 cancers (http:/(/)www.iarc.fr/p53/homepage.html) can be used to generate hypotheses for further clinical, epidemiological, and laboratory investigations. For example, one can hypothesize that (a) p53 mutations vary in their pathobiological significance; (b) cellular content influences the selection of p53 mutations in clonally derived cancers; (c) the location and type of mutation within the p53 gene provide clues to functional domains in the gene product; and (d) the p53 mutation spectrum can be a molecular link between aetiological agents and human cancer. This review will focus on the role of p53 and cancer susceptibility genes in the molecular pathogenesis and epidemiology of human lung cancer.
Polymer composites of rigid and flexible molecules: System of wholly aromatic and aliphatic polyamides (1980)

Abstract As an extension of reinforcing principles of composite materials in which macroscopic fibers are dispersed in a ductile matrix, rigid microfibrils of wholly aromatic polyamides such as poly(p-phenylene terephthalamide) (PPTA), poly-p-benzamide (PBA), and their block copolymers with blocks of nylon 6 or nylon 66 were dispersed in a matrix of nylon 6 or nylon 66. On blending polyaramides with aliphatic polyamides, the spherulitic texture disappeared and a locally birefringent homogeneous texture was obtained. Electron microscopy revelaed that microfibrils of PPTA with diameter of 15-30 nm were dispersed in a fractured surface of the polymer composite. Strong interaction between the fibril surface and the matrix was suggested by the fact that the crystallization of matrix polyamides was induced by the rigid polyaramides. Wide-angle x-ray diffraction intensity curves, DSC curves of cooling process from the melt, and isothermal crystallization curves indicated a marked tendency for induced crystallization with polyaramides. Viscoelastic relaxation curves indicated increased fraction of immobilized noncrystalline chains, increased modulus of the blend, and increased heat resistance of the blend as shown in retention of the blend modulus even at 200°C. By applying the modified Halpin-Tsai equation to the relationship between Young's modulus and the fraction of rigid molecules in the blend, the aspect ratio of microfibril was estimated at 15 to 25. Young's modulus and yield stress were remarkably improved by blending the polyaramides as low as 5%. With increasing molecular weight of PPTA, both modulus and yield strength systematically increased, while ultimate strength did not vary and ultimate elongation decreased. Blending the block copolymers of polyaramides and aliphatic nylon blocks with nylon matrix increased ultimate elongation compared with the physical blend of homopolyaramides and aliphatic polyamides. The orientation effect was very effective, as shown in the system of 3% PPTA and 97% nylon 6, in which the ultimate strength increased from 230 MPa of nylon 6 to 340 MPa of the blend. An ultimate strength of the PPTA microfibril of more than 4 GPa is realized in the blend, indicating full reinforcing effect of rigid fibrils at a supramolecular level.
Vβ-Specific Stimulation of Human T Cells by Staphylococcal Toxins (1989)

The staphylococcal toxins are responsible for a number of diseases in man and other animals. Many of them have also long been known to be powerful T cell stimulants. They do not, however, stimulate all T cells. On the contrary, each toxin reacts with human T cells bearing particular V beta sequences as part of their receptors for major histocompatibility complex protein-associated antigen. The specificity of these toxins for V beta s puts them in the recently described class of superantigens and may account for the differential sensitivity of different individuals to the toxic effects of these proteins.
Slow muscle induction by Hedgehog signalling in vitro (2000)

Muscles are composed of several fibre types, the precise combination of which determines muscle function. Whereas neonatal and adult fibre type is influenced by a number of extrinsic factors, such as neural input and muscle load, there is little knowledge of how muscle cells are initially determined in the early embryo. In the zebrafish, fibres of the slow twitch class arise from precociously specified myoblasts that lie close to the midline whereas the remainder of the myotome differentiates as fast myosin expressing muscle. In vivo evidence has suggested the Sonic Hedgehog glycoprotein, secreted from the notochord, controls the formation of slow twitch and fast twitch muscle fates. Here we describe an in vitro culture system that we have developed to test directly the ability of zebrafish myoblasts to respond to exogenous Sonic Hedgehog peptide. We find that Sonic Hedgehog peptide can control the binary cell fate choice of embryonic zebrafish myoblasts in vitro. We have also used this culture system to assay the relative activities of different Hedgehog-family proteins and to investigate the possible involvement of heterotrimeric G-proteins in Hedgehog signal transduction.
In the Right Light: Photodynamic Inactivation of Microorganisms Using a LED-Based Illumination Device Tailored for the Antimicrobial Application (2019)

Drug-resistant bacteria threaten the health of people world-wide and cause high costs to their health systems. According to Scientific American, the number of regrettable fatalities due to the bacteria that are resistant to conventional antibiotics will sum up to 300 million until 2050 if the problem is not tackled immediately. Photodynamic Inactivation (PDI) has proven effective against microorganisms irrespective of their resistance to conventional treatment, but for the translation into clinical practice, economic, homogenous and powerful light sources holding approval as medical devices are needed. In this study we present two novel light emitting diode (LED)-based lamps (Repuls7PDI-red and Repuls7PDI-blue) tailored for application in PDI and demonstrate their photodynamic efficiency upon using either methylene blue (MB), a photoactive compound widely used in PDI, or Sodium Magnesium Chlorophyllin (CHL), a water-soluble derivative of chlorophyll, which holds approval as food additive E140, against bacteria and fungi. Gram+ <i>Staphylococcus aureus</i>, Gram- <i>Escherichia coli</i> and the yeast <i>Candida albicans</i> serve as model systems. Repuls7PDI-red emits a wavelength of 635 nm and an intensity of 27.6 ± 2.4 mW·cm<sup>-2</sup> at a distance of 13.5 cm between the light source and the target, while the Repuls7PDI-blue allows an exposure at 433 nm (within the range of violet light) (6.4 ± 0.5 mW·cm<sup>-2</sup> at 13.5 cm). Methylene blue was photoactivated with the Repuls7PDI-red at 635 nm (25.6 J·cm<sup>-2</sup>) and allows for photokilling of <i>E. coli</i> by more than 6 log<sub>10</sub> steps at a concentration of 10 µM MB. Using equal parameters, more than 99.99999% of <i>S. aureus</i> (20 µM MB) and 99.99% of <i>C. albicans</i> (50 µM MB) were killed. If blue light (Repuls7PDI-blue, 433 nm, 6.6 J·cm<sup>2</sup>) is used to trigger the production of reactive oxygen species (ROS), a photoinactivation of <i>S. aureus</i> (5 µM CHL, CFU reduction > 7 log<sub>10</sub>) and <i>C. albicans</i> (>7 log<sub>10</sub>) below the detection limit is achieved. PDI based on CHL (10 µM) using red light activation reduces the number of viable <i>S. aureus</i> by more than 6 log<sub>10</sub>. Our data prove that both LED-based light sources are applicable for Photodynamic Inactivation. Their easy-to-use concept, high light output and well-defined wavelength might facilitate the translation of PDI into clinical practice.
Toxin-Antitoxin Systems Influence Biofilm and Persister Cell Formation and the General Stress Response (2011)

In many genomes, toxin-antitoxin (TA) systems have been identified; however, their role in cell physiology has been unclear. Here we examine the evidence that TA systems are involved in biofilm formation and persister cell formation and that these systems may be important regulators of the switch from the planktonic to the biofilm lifestyle as a stress response by their control of secondary messenger 3',5'-cyclic diguanylic acid. Specifically, upon stress, the sequence-specific mRNA interferases MqsR and MazF mediate cell survival. In addition, we propose that TA systems are not redundant, as they may have developed to respond to specific stresses.
Repeated PSMA-targeting radioligand therapy of metastatic prostate cancer with 131I-MIP-1095 (2017)

The first dose of RLT with <sup>131</sup>I-MIP-1095 presented with low side effects and could significantly reduce the tumor burden in a majority of patients. The second and third therapies were less effective and presented with more frequent and more intense side effects, especially hematologic toxicities and xerostomia.
Synthesis of [1,2,4]triazoloquinazolinones and imidazoquinazolinones (1986)

Abstract 4‐Quinazolinones have been cyclised to [1,2,4]triazoloquinazolinones and to imidazoquinazolinones. The direction of cyclisation has been proved by the unambiguous synthesis of their ethylation products.
Coordinated Expression of Noggin and Bone Morphogenetic Proteins (BMPs) During Early Skeletogenesis and Induction of Noggin Expression by BMP-7 (1999)

Coordinated regulation of the activities of bone morphogenetic protein (BMP) and its inhibitors is essential for skeletal development since loss-of-function experiments show that both BMPs and BMP inhibitory signals, such as noggin, are required to establish proper formation of skeletal tissues. In this paper, we asked how and when noggin would be functional to interact with BMPs during skeletogenesis in mammals. For this purpose, we first analyzed the spatial and temporal patterns of noggin, BMP-2, BMP-4, and BMP-7 expression during early skeletogenesis in mouse embryos. In situ hybridization study revealed that noggin expression was detected at a low level in limb mesenchyme, whereas BMP-7 was expressed at a high level throughout limb mesenchyme 10.5 days postcoitum (dpc) in mouse embryos. One day later, noggin mRNA was expressed at a high level in the prechondrogenic condensations in appendicular and axial skeletal primordia, where sox9 transcripts were also expressed. At this stage, noggin-expressing cells were surrounded by those expressing BMP-7. The chondrogenic cell condensation continued to express noggin transcripts in 12.5 dpc and 13.5 dpc embryos, and again the noggin-expressing cells within the cartilaginous tissue were surrounded by those expressing BMP-7. We further examined interaction of noggin and BMPs by using organ cultures of 11.5 dpc mouse forelimbs and found that implantation of carriers containing BMP-7 protein into the forelimb explants induced noggin expression in the limb mesenchyme. BMP-7 also induced type II collagen and sox9 mRNAs in the same cell population, indicating that noggin induction occurred in the chondrogenic precursor cells. BMP-7 effects on noggin expression were observed in a dose-dependent manner within a dose range of 10-100 ng/microliter. These results suggest that BMP-7 induced expression of noggin transcripts within skeletal cell condensation and that this noggin expression in turn could act antagonistically to attenuate BMP action in the early skeletogenesis.