gebhart/patrepeval huggingface dataset:
Cross-Linking of Lens Crystallins in a Photodynamic System: A Process Mediated by Singlet Oxygen (1980)

In a dye-sensitized photooxidation system, lens crystallin polypeptides become cross-linked, and a blue fluorescence that is associated with the proteins is produced. These changes are similar to those seen in vivo in the aging human lens. Evidence implicating singlet oxygen as the causative agent of the effects in vitro is presented, and the possibility that this species may play a role in aging and cataractogenesis in vivo is discussed.
All-trans-Retinoic Acid Inhibits Growth of Human Pancreatic Cancer Cell Lines (1996)

Retinoids are a class of molecules structurally related to vitamin A that have potent antiproliferative and differentiating effects on a variety of normal and neoplastic tissues. All-trans-retinoic acid (ATRA) has become a first-line chemotherapeutic agent in the treatment of certain leukemias; however, the effect of ATRA on pancreatic tumors is unknown. The purpose of this study was to determine the effect of ATRA on the growth characteristics of both exocrine and endocrine human pancreatic cancer cell lines. The in vitro growth of four cell lines was examined after treatment with a wide dose range of ATRA. The growth of all tumor cell lines was inhibited by ATRA in a dose-dependent fashion beginning at 0.1 microgram M. The in vivo growth of functioning human pancreatic carcinoid (BON) xenografts in Balb/c athymic mice was determined by treatment with several doses of ATRA over 1 month. The growth of BON tumors was inhibited in a dose-dependent fashion. These results suggest that ATRA exerts direct antiproliferative effects on both exocrine and endocrine human pancreatic cancers and may be useful in the chemotherapy of these tumors.
Postgenomic Analysis of Four Novel Antigens of Group A Streptococcus : Growth Phase-Dependent Gene Transcription and Human Serologic Response (2002)

Analysis of three group A Streptococcus genomes (serotypes M1, M3, and M18) recently identified four previously undescribed genes that encode extracellular proteins. Each of these genes encode proteins with an LPXTG amino acid motif that covalently links many virulence factors produced by gram-positive bacteria to the cell surface. Western immunoblot analysis of serum samples obtained from 80 patients with invasive infections, noninvasive soft tissue infections, pharyngitis, and rheumatic fever indicated that these four proteins are expressed in vivo. However, the level of gene transcript and the time of maximal gene transcription varied in representative serotype M1, M3, and M18 strains. Surface expression of two proteins was confirmed by flow cytometry. Studies using a mouse infection model suggest that antibodies specific for one of the proteins (Spy0843) may contribute to a protective host immune response against a serotype M1 infection. These results are additional evidence that postgenomic strategies provide new ways to identify and investigate novel bacterial proteins that may participate in host-pathogen interactions or serve as targets for therapeutics research.
Directed assembly of cell-laden hydrogels for engineering functional tissues (2010)

Tissue engineering aims to develop functionalized tissues for organ replacement or restoration. Biodegradable scaffolds have been used in tissue engineering to support cell growth and maintain mechanical and biological properties of tissue constructs. Ideally cells on these scaffolds adhere, proliferate, and deposit matrix at a rate that is consistent with scaffold degradation. However, the cellular rearrangement within these scaffolds often does not recapitulate the architecture of the native tissues. Directed assembly of tissue-like structures is an attractive alternative to scaffold-based approach for tissue engineering which potentially can build tissue constructs with biomimetic architecture and function. In directed assembly, shape-controlled microstructures are fabricated in which organized structures of different cell types can be used as tissue building blocks. To fabricate tissue building blocks, hydrogels are commonly used as biomaterials for cell encapsulation to mimic the matrix in vivo. The hydrogel-based tissue building blocks can be arranged in pre-defined architectures by various directed tissue assembly techniques. In this paper, recent advances in directed assembly-based tissue engineering are summarized as an emerging alternative to meet challenges associated with scaffold-based tissue engineering and future directions are addressed.
Inhibition of Integrin αvβ6, an Activator of Latent Transforming Growth Factor-β, Prevents Radiation-induced Lung Fibrosis (2007)

Alpha(v)beta6-mediated TGF-beta activation is required for radiation-induced lung fibrosis. Together with previous data, our results demonstrate a robust requirement for alpha(v)beta6 in distinct fibrosis models. Inhibition of alphavbeta6-mediated TGF-beta activation is a promising new approach for antifibrosis therapy.
Regulation of Glucose Transport and Glycogen Synthesis in L6 Muscle Cells during Oxidative Stress (1999)

We have investigated the cellular mechanisms that participate in reducing insulin sensitivity in response to increased oxidant stress in skeletal muscle. Measurement of glucose transport and glycogen synthesis in L6 myotubes showed that insulin stimulated both processes, by 2- and 5-fold, respectively. Acute (30 min) exposure of muscle cells to hydrogen peroxide (H(2)O(2)) blocked the hormonal activation of both these processes. Immunoblot analyses of cell lysates prepared after an acute oxidant challenge using phospho-specific antibodies against c-Jun N-terminal kinase (JNK), p38, protein kinase B (PKB), and p42 and p44 mitogen-activated protein (MAP) kinases established that H(2)O(2) induced a dose-dependent activation of all five protein kinases. In vitro kinase analyses revealed that 1 mM H(2)O(2) stimulated the activity of JNK by approximately 8-fold, MAPKAP-K2 (the downstream target of p38 MAP kinase) by approximately 12-fold and that of PKB by up to 34-fold. PKB activation was associated with a concomitant inactivation of glycogen synthase kinase-3. Stimulation of the p38 pathway, but not that of JNK, was blocked by SB 202190 or SB203580, while that of p42/p44 MAP kinases and PKB was inhibited by PD 98059 and wortmannin respectively. However, of the kinases assayed, only p38 MAP kinase was activated at H(2)O(2) concentrations (50 microM) that caused an inhibition of insulin-stimulated glucose transport and glycogen synthesis. Strikingly, inhibiting the activation of p38 MAP kinase using either SB 202190 or SB 203580 prevented the loss in insulin-stimulated glucose transport, but not that of glycogen synthesis, by oxidative stress. Our data indicate that activation of the p38 MAP kinase pathway plays a central role in the oxidant-induced inhibition of insulin-regulated glucose transport, and unveils an important biochemical link between the classical stress-activated and insulin signaling pathways in skeletal muscle.
Towards usefully secure email (2007)

We have built attribute based, usefully secure email (ABUSE), a system that leverages users by enabling them to build a decentralized, nonhierarchical public key infrastructure (PKI) to express their trust relationships with each other, and then use this PKI to manage their trust in people with whom they correspond via secure email. Our design puts humans into the system - to do things that humans are good at but machines are not - at both the creation of credentials as well as the interpretation of credentials. By doing so, we hope this system can overcome the failings of approaches based on standard PKI
A Protein‐Based Encapsulation System with Calcium‐Controlled Cargo Loading and Detachment (2018)

Protein-based encapsulation systems have a wide spectrum of applications in targeted delivery of cargo molecules and for chemical transformations in confined spaces. By engineering affinity between cargo and container proteins it has been possible to enable the efficient and specific encapsulation of target molecules. Missing in current approaches is the ability to turn off the interaction after encapsulation to enable the cargo to freely diffuse in the lumen of the container. Separation between cargo and container is desirable in drug delivery applications and in the use of capsids as catalytic nanoparticles. We describe an encapsulation system based on the hepatitis B virus capsid in which an engineered high-affinity interaction between cargo and capsid proteins can be modulated by Ca<sup>2+</sup> . Cargo proteins are loaded into capsids in the presence of Ca<sup>2+</sup> , while ligand removal triggers unbinding inside the container. We observe that confinement leads to hindered rotation of cargo inside the capsid. Application of the designed container for catalysis was also demonstrated by encapsulation of an enzyme with β-glucosidase activity.
Etching of porous and solid SiO2 in Ar∕c-C4F8, O2∕c-C4F8 and Ar∕O2∕c-C4F8 plasmas (2004)

C - C 4 F 8 -based plasmas are used for selective etching of high aspect ratio (HAR) trenches in SiO2 and other dielectrics for microelectronics fabrication. Additives such as Ar and O2 are often used to optimize the process. Understanding the fundamentals of these processes is critical to extending technologies developed for solid SiO2 to porous SiO2, as used in low-dielectric constant insulators. To investigate these issues, reaction mechanisms developed for etching of solid and porous SiO2 in fluorocarbon plasmas and for etching of organic polymers in O2 plasmas have been incorporated into a feature profile model capable of addressing two-phase porous materials. The reaction mechanism was validated by comparison to experiments for blanket etching of solid and porous SiO2 in Ar∕c-C4F8 and O2∕c-C4F8 plasmas using inductively coupled plasma reactors. We found that the blanket etch rates of both solid and porous SiO2 had maxima as a function of Ar and O2 addition to c-C4F8 at mole fractions corresponding to an optimum thickness of the overlying polymer layer. Larger Ar and O2 additions were required to optimize the etch rate for porous SiO2. Whereas etch stops occurred during etching of HAR features in solid and porous SiO2 using pure c-C4F8 plasmas, Ar and O2 addition facilitated etching by reducing the polymer thickness, though with some loss of critical dimensions. Mixtures of Ar∕O2∕c-C4F8 can be used to manage this tradeoff.
Fast LIDAR-based road detection using fully convolutional neural networks (2017)

In this work, a deep learning approach has been developed to carry out road detection using only LIDAR data. Starting from an unstructured point cloud, top-view images encoding several basic statistics such as mean elevation and density are generated. By considering a top-view representation, road detection is reduced to a single-scale problem that can be addressed with a simple and fast fully convolutional neural network (FCN). The FCN is specifically designed for the task of pixel-wise semantic segmentation by combining a large receptive field with high-resolution feature maps. The proposed system achieved excellent performance and it is among the top-performing algorithms on the KITTI road benchmark. Its fast inference makes it particularly suitable for real-time applications.
Synthesis, physicochemical properties, and biological evaluation of N-substituted 2-alkyl-3-hydroxy-4(1H)-pyridinones: orally active iron chelators with clinical potential (1993)

The synthesis of a range of novel bidentate ligands containing the chelating moiety 3-hydroxy-4(1H)-pyridinone is described. The pKa values of the ligands and the stability constants of their iron(III) complexes have been determined. The crystal structures of one of the ligands and one of the iron(III) complexes are presented. The distribution coefficients of the ligands are reported and are related to the ability of the ligands to remove iron from hepatocytes. The influence of 3-hydroxy-4(1H)-pyridinones on oxidative damage to cells is described. In contrast to the iron chelator in current therapeutic use, desferrioxamine-B, many of the bidentate ligands described in this study are orally active in iron-overloaded mice.
Nucleic Acid Engineering (2009)

This chapter contains sections titled: Introduction: Nucleic Acids DNA Nanotechnology DNA Materials DNA Aptamers and Nucleic Acid Enzymes Characterizations of Oligonucleic Acids Reference
Functional recovery after spinal cord hemisection in guinea pigs: The effects of applied electric fields (1990)

Right lateral hemisection of the lower thoracic spinal cord was performed in 216 adult guinea pigs. Animals that proved suitable for the study were divided into one control and two experimental groups. Experimental animals were implanted with intraperitoneal stimulators delivering regulated current of 35 or 50 microA through electrodes placed 1 cm rostral and caudal of the hemisection. The cathode was cranial to the lesion in one group (n = 67) and caudal in the other (n = 33). Control animals (n = 62) were implanted with sham stimulators and electrodes delivering no current. The functional status of the animals was measured by tactile stimulation of the back skin to elicit the cutaneus trunci muscle reflex, and by the vestibulospinal free-fall response. The cutaneous response ipsilateral and caudal to the lesion was lost following hemisection and did not recover in any of the control animals or in animals with cathode caudal to the lesion. Recovery of the response was found in 9 of 67 animals in the cathode rostral group, between 56 and 139 days after injury. Toe spreading recovered spontaneously in 80-90% of animals in all groups. Of the possible mechanisms of skin reflex recovery, most current evidence points to regrowth of ascending nerve fibers in the lateral funiculus of the spinal cord local to the lesion.
[A study on the long-term non-small cell lung cancer survivors in the Expand Access Program of gefitinib in China]. (2012)

A 250 mg dose of gefitinib offers good QoL and is safe for advanced NSCLC long-term survivors even after more than three years of treatment. According to the evaluation of the current tumor control statuses of patients, gefitinib demonstrates good efficacy in these active long-term survivors.
Identification of Semiochemicals in Adults and Nymphs of the Stink Bug Pallantia macunaima Grazia (Hemiptera: Pentatomidae) (2011)

The contents of the dorsal abdominal glands in nymphs and the metathoracic glands in adult males and females (10, 20 and 30 days old) were characterized and quantified for the stink bug, Pallantia macunaima. The major component for nymphs and adults was tridecane, with lesser amounts of other aliphatic hydrocarbons, aldehydes, oxo-alkenals and esters. The five nymphal instars showed significant differences in the proportions of compounds present, mainly between those of the first instar compared to the dorsal abdominal glands components of later instars. No significant differences were detected in the proportion of metathoracic gland components between the sexes but, between individuals of different ages, (E)-2-hexenal and (E)-2-decenyl acetate significantly decreased in adults from 10 to 20 days of age.
Physicochemical Studies on Reverse Micelles of Sodium Bis(2-ethylhexyl) Sulfosuccinate at Low Water Content (1996)

Studies on aggregation of sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in isooctane at low water content were carried out. The critical micelle concentration (cmc) thermodynamic parameters were determined at various temperatures. The observations suggested that the micellization process was endothermic in nature and that it is mainly an entropic process. The cmc was also determined at various R values (R < 3) and it was found that cmc increases with increasing R. The aggregation number was determined at the R value of 1.6. From the pyrene and ANS binding studies, the microviscosity and micropolarity changes on the onset of micellization are well characterized. Spectral studies with ANS indicate a decrease in microviscosity on increase in R value. ANS fluorescence was monitored in the presence of additives like acrylamide, KI3, and tetrabutylammonium iodide. The iodide-based additives lead to quenching of fluorescence of ANS with concomitant red shift in the λem suggesting decreased microviscosity and micropolarity. Acrylamide was shown to increase the polarity by the ANS spectral features. These findings led to the conclusions that the positive ΔHm° values arise mainly from the dismantling of hydrated ions in the quasi-lattice of AOT interior. With an increase in temperature, immobilized structured states of water get destructured, which ultimately leads to favoring the aggregation process.
Recent Progress in GM-CSF-Based Cancer Immunotherapy (2017)

Cancer immunotherapy is a growing field. GM-CSF, a potent cytokine promoting the differentiation of myeloid cells, can also be used as an immunostimulatory adjuvant to elicit antitumor immunity. Additionally, GM-CSF is essential for the differentiation of dendritic cells, which are responsible for processing and presenting tumor antigens for the priming of antitumor cytotoxic T lymphocytes. Some strategies have been developed for GM-CSF-based cancer immunotherapy in clinical practice: GM-CSF monotherapy, GM-CSF-secreting cancer cell vaccines, GM-CSF-fused tumor-associated antigen protein-based vaccines, GM-CSF-based DNA vaccines and GM-CSF combination therapy. GM-CSF also contributes to the regulation of immunosuppression in the tumor microenvironment. This review provides recommendations regarding GM-CSF-based cancer immunotherapy.
RAFT1 phosphorylation of the translational regulators p70 S6 kinase and 4E-BP1 (1998)

The complex of rapamycin with its intracellular receptor, FKBP12, interacts with RAFT1/FRAP/mTOR, the in vivo rapamycin-sensitive target and a member of the ataxia telangiectasia mutated (ATM)-related family of kinases that share homology with the catalytic domain of phosphatidylinositol 3-kinase. The function of RAFT1 in the rapamycin-sensitive pathway and its connection to downstream components of the pathway, such as p70 S6 kinase and 4E-BP1, are poorly understood. Here, we show that RAFT1 directly phosphorylates p70(S6k), 4E-BP1, and 4E-BP2 and that serum stimulates RAFT1 kinase activity with kinetics similar to those of p70(S6k) and 4E-BP1 phosphorylation. RAFT1 phosphorylates p70(S6k) on Thr-389, a residue whose phosphorylation is rapamycin-sensitive in vivo and necessary for S6 kinase activity. RAFT1 phosphorylation of 4E-BP1 on Thr-36 and Thr-45 blocks its association with the cap-binding protein, eIF-4E, in vitro, and phosphorylation of Thr-45 seems to be the major regulator of the 4E-BP1-eIF-4E interaction in vivo. RAFT1 phosphorylates p70(S6k) much more effectively than 4E-BP1, and the phosphorylation sites on the two proteins show little homology. This raises the possibility that, in vivo, an unidentified kinase analogous to p70(S6k) is activated by RAFT1 phosphorylation and acts at the rapamycin-sensitive phosphorylation sites of 4E-BP1.
Role of the Common Cytokine Receptor γ Chain in Cytokine Signaling and Lymphoid Development (1995)

To examine the role of gamma c in lymphoid development, we have analyzed mice in which the gamma c gene was specifically inactivated by homologous recombination. These mice also serve as an animal model of human X-linked severe combined immunodeficiency (XSCID). Interestingly, gamma c knockout mice exhibited a somewhat different phenotype than humans with XSCID. Absolute T-cell numbers are greatly diminished in young gamma c-/Y mice, but accumulate with age. gamma delta T cells and NK cells are absent in gamma c-/Y mice and conventional B cells are greatly diminished, yet substantial numbers of peritoneal B-1 cells are present. Since humans with XSCID have essentially no mature T cells, it is especially striking that T cells are readily apparent in gamma c-/Y mice. This observation indicates that in these mice, the gamma c-dependent block in T cell development is less severe than it is in humans. It is possible but unproven that thymic stromal derived lymphopoietin, TSLP, contributes to thymocyte development in these mice. Since B-cell numbers are normal in humans with XSCID, it is also striking that gamma c-/Y mice paradoxically exhibit greatly diminished numbers of B cells. This likely indicates that IL-7 signaling plays a critical role in pre-B cell maturation in mice but is less important in humans. Thus, the abnormalities observed in gamma c-/Y mice have provided clues to assist in dissecting the role of cytokines and their receptors in lymphoid development and have also identified interesting differences in the regulation of this process in mice and humans.
Wild-type p53 induces apoptosis in a Burkitt lymphoma (BL) line that carries mutant p53. (1993)

All Burkitt lymphoma (BL) biopsies and cell lines carry a c-myc/Ig translocation. The resulting constitutive activation of c-myc is regarded as an essential factor for the progressive growth of the tumor cells. At least 60% of BL cell lines carry a mutated p53 gene as well. It has been shown that the growth of mutant p53 carrying tumor cells could be inhibited by the introduction of wild-type p53. In order to examine whether this also applies to the presumably 'myc-driven' BL cell, we have transfected the Epstein-Barr virus (EBV) negative BL41 cell line with a temperature sensitive p53 mutant (p53-Val135) that expresses p53 with a largely mutant conformation at 37.5 degrees C and mostly wild-type conformation at 32 degrees C. At 37.5 degrees C, the p53-Val135 transfected cells behaved like the parental or neo transfected control cells. However, expression of exogenous wild-type p53 at 32 degrees C resulted in a rapid reduction of the number of viable cells while the parental and neo control cells remained unaffected. Cell death was due to apoptosis as shown by chromatin and nuclear condensation and specific DNA fragmentation. The first signs of apoptosis were evident after 10 h at 32 degrees C and after 3 days 90-100% of the cells had undergone apoptosis. These findings indicate an incompatibility between expression of wild-type p53 and progressive growth of BL cells if their neoplastic development has included a p53 mutation. The question whether apoptosis was induced in by the wild-type protein per se or by the contradictory signals of a constitutively activated c-myc and wild-type p53 needs further investigation.
Amperometric Glucose Sensor: Short-Term, In Vivo Test (1982)

The influence of selected physiologic coreactants on current-voltage scans of a (Pt-pvc) Pt electrode (the working electrode of the amperometric glucose sensor) was tested. It was shown that the electrode is sufficiently sensitive to glucose even in a case when a strong interference of tested substances was observed. On the basis of the preliminary in vivo measurements it was concluded that after the proper pretreatment, the amperometric glucose sensor can be used for short-term blood glucose monitoring.
Single-Cell Analysis in Biotechnology, Systems Biology, and Biocatalysis (2012)

Single-cell analysis (SCA) has been increasingly recognized as the key technology for the elucidation of cellular functions, which are not accessible from bulk measurements on the population level. Thus far, SCA has been achieved by miniaturization of established engineering concepts to match the dimensions of a single cell. However, SCA requires procedures beyond the classical approach of upstream processing, fermentation, and downstream processing because the biological system itself defines the technical demands. This review characterizes currently available microfluidics and microreactors for invasive (i.e., chemical) and noninvasive (i.e., biological) SCA. We describe the recent SCA omics approaches as tools for systems biology and discuss the role of SCA in genomics, transcriptomics, proteomics, metabolomics, and fluxomics. Furthermore, we discuss applications of SCA for biocatalysis and metabolic engineering as well as its potential for bioprocess optimization. Finally, we define present and future challenges for SCA and propose strategies to overcome current limitations.