gebhart/patrepeval huggingface dataset:
Comparative physiology of plant and arthropod land adaptation (1985)

Abstract Plants related to aquatic Charophycean green algae were probably terrestrial by the early to mid Silurian; these plants were the ancestors of the vascular plants that have dominated the Earth’s flora since the Devonian. The arthropods have been the major herbivores and carnivores in many terrestrial communities since the Devonian: they arose from a number of aquatic arthropod stocks which invaded the land from the Silurian onwards. The vascular plants and arthropods conduct their basic metabolism in the same way as their aquatic counterparts, but in the aerial environment which differs greatly from the aquatic in the exchange of materials, momentum and heat between organisms and their environment. Terrestrial organisms differ from their aquatic relatives in (inter alia) the water vapour loss attendant on the exchange of gases in photosynthesis and respiration; the potential for large and rapid changes in body temperature; and differences in the structural requirements for maintenance of posture and, in animals, locomotion. The (putatively) adaptive responses to these problems of terrestrial life show a number of im portant parallels between the vascular plants and arthropods, including internalization of gas-exchange surfaces, regulation of gas diffusion between the gas-exchange surfaces and the outside air, a wax layer over the general body surface which restricts non-respiratory and non-photosynthetic water loss, and the importance of rigid skeletal members (present in the ancestral aquatic arthropods, but not in algae). At the biochemical level many of the prerequisites for the special structures and functions found in terrestrial organisms can be traced in their algal and aquatic arthropod relatives. The seductive argument that increasing O2 levels in the atmosphere in the Siluro-Devonian were of great significance in permitting larger phototrophs (absence of restriction of plants to shaded habitats to avoid ultraviolet, and increased bulk of non-photosynthetic parts permitted by greater O2 availability) and larger and more active phagotrophs (as a result of greater O2 availability) is, alas, very difficult to test quantitatively.
Development of a Lectin Microarray for the Rapid Analysis of Protein Glycopatterns (2005)

Glycosylation plays a role in a wide variety of biological processes including bacterial pathogenesis, tumor cell metastasis and inflammation. Despite the importance of carbohydrates, few techniques exist for the rapid and systematic evaluation of protein glycosylation. This paper describes a lectin microarray for the rapid analysis of protein glycopatterns (see scheme). Supporting information for this article is available on the WWW under http://www.chembiochem.org or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mutations in FIE, a WD Polycomb Group Gene, Allow Endosperm Development without Fertilization (1999)

A fundamental problem in biology is to understand how fertilization initiates reproductive development. Higher plant reproduction is unique because two fertilization events are required for sexual reproduction. First, a sperm must fuse with the egg to form an embryo. A second sperm must then fuse with the adjacent central cell nucleus that replicates to form an endosperm, which is the support tissue required for embryo and/or seedling development. Here, we report cloning of the Arabidopsis FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) gene. The FIE protein is a homolog of the WD motif-containing Polycomb proteins from Drosophila and mammals. These proteins function as repressors of homeotic genes. A female gametophyte with a loss-of-function allele of fie undergoes replication of the central cell nucleus and initiates endosperm development without fertilization. These results suggest that the FIE Polycomb protein functions to suppress a critical aspect of early plant reproduction, namely, endosperm development, until fertilization occurs.
Increased death receptor 5 expression by chemotherapeutic agents in human gliomas causes synergistic cytotoxicity with tumor necrosis factor-related apoptosis-inducing ligand in vitro and in vivo. (2000)

The intractability of malignant gliomas to multimodality treatments plays a large part in their extremely poor prognosis. Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a novel member of the tumor necrosis factor (TNF) family that induces apoptosis preferentially in tumor cells through binding to its cognate death receptors, DR4 and DR5. Here we show that the DNA-damaging chemotherapeutic drugs, cis-diamminedichloroplatinum(II) (CDDP) and etoposide, elicited increased expression of DR5 in human glioma cells. Exposure of such cells in vitro to soluble human TRAIL in combination with CDDP or etoposide resulted in synergistic cell death that could be blocked by soluble TRAIL-neutralizing DR5-Fc or the caspase inhibitors, Z-Asp-CH2-DCB and CrmA. Moreover, systemic in vivo administration of TRAIL with CDDP synergistically suppressed both tumor formation and growth of established s.c. human glioblastoma xenografts in nude mice by inducing apoptosis without causing significant general toxicity. The combination treatment resulted in complete and durable remission in 29% of mice with the established s.c. xenografts and also significantly extended the survival of mice bearing intracerebral xenografts. These results provide preclinical proof-of-principle for a novel therapeutic strategy in which the death ligand, TRAIL, is safely combined with conventional DNA-damaging chemotherapy.
Human alpha-L-iduronidase. I. Purification and properties of the high uptake (higher molecular weight) and the low uptake (processed) forms. (1984)

Two major forms of human alpha-L-iduronidase have been individually purified over 175,000-fold to apparent homogeneity by sequential anion exchange, lectin affinity, and gel filtration chromatography. The two forms, initially designated as soluble and membrane-associated, were extracted from human lung in approximately equal amounts. Optimal solubilization of the membrane-associated form was facilitated by use of a non-ionic detergent or mannose 6-phosphate and saponin. Following detergent homogenization, the two forms were separated by anion exchange chromatography and then individually purified. The more electronegative form was membrane-associated, had a pI of approximately 5.9, and was selectively taken up (high uptake) by cultured Hurler syndrome fibroblasts; the more electropositive soluble form had a pI of about 6.6 and was incorporated into Hurler fibroblasts at a markedly lower rate (low uptake). After treatment with alkaline phosphatase, the pI values of both enzymes were about 7.8. Using 4-methylumbelliferyl-alpha-L-iduronide as substrate, the low and high uptake forms were each purified in milligram quantities to specific activities of 284,000 and 202,000 units/mg, respectively, with a combined yield greater than 35%. Each purified enzyme form migrated as a single protein band which also stained for enzymatic activity when electrophoresed in 7% native polyacrylamide disc gels at pH 4.3. By gel filtration, the high uptake form had an Mr = 85,000 whereas the Mr for the low uptake form was 68,000. Molecular weight estimates by analytical polyacrylamide gel electrophoresis were 82,000 and 70,000 for the high and low uptake forms, respectively. Rabbit anti-human low uptake alpha-L-iduronidase antibodies cross-reacted with the high uptake form as demonstrated by both immunotitration and Ouchterlony double immunodiffusion. Amino acid analysis revealed that the high uptake (higher molecular weight) form contained more arginine, glycine, alanine, glutamate or glutamine, leucine, isoleucine, histidine, and proline residues per molecule than the low uptake (lower molecular weight) form. Automated Edman degradation determined that the NH2-terminal residues of both forms were blocked. Both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and high performance liquid chromatography demonstrated that each purified form was composed of several components; each post-high performance liquid chromatographic component retained catalytic activity and was immunologically cross-reactive with antibodies against the low uptake form.(ABSTRACT TRUNCATED AT 400 WORDS)
Protective Immunity Does Not Correlate with the Hierarchy of  Virus-specific Cytotoxic T Cell Responses to Naturally Processed Peptides (1998)

Infection of C57BL/6 mice with lymphocytic choriomeningitis virus (LCMV) stimulates major histocompatibility complex class I–restricted cytotoxic T cells (CTLs), which normally resolve the infection. Three peptide epitopes derived from LCMV have been shown to bind the mouse class I molecule H-2 Db and to stimulate CTL responses in LCMV-infected mice. This report describes the identity and abundance of each CTL epitope after their elution from LCMV-infected cells. Based on this information, peptide abundance was found to correlate with the magnitude of each CTL response generated after infection with LCMV. Subsequent experiments, performed to determine the antiviral capacity of each CTL specificity, indicate that the quantitative hierarchy of CTL activity does not correlate with the ability to protect against LCMV infection. This report, therefore, indicates that immunodominant epitopes should be defined, not only by the strength of the CTL response that they stimulate, but also by the ability of the CTLs to protect against infection.
Influence of the Foundation Layer on the Layer-by-Layer Assembly of Poly-l-lysine and Poly(styrenesulfonate) and Its Usage in the Fabrication of 3D Microscale Features (2004)

The layer-by-layer (LBL) assembly of a polypeptide, poly-L-lysine (PLL), with poly(styrenesulfonate) sodium salt (PSS) on flat template-stripped gold (TSG) surfaces precoated with a self-assembled monolayer of alkanethiols terminated with positive (pyridinium), negative (carboxylic acid), and neutral [hexa(ethylene glycol)] groups is investigated. Both the topography and the rate of film thickness growth are found to be strongly dependent on the initial surface foundation layer. LBL assembly of PLL and PSS on patterned TSG surfaces produced by micro contact printing leads to structurally distinct microscale features, including pillars, ridges, and wells, whose height can be controlled with nanometer precision.
Optical biosensor assay (OBA) (1991)

We describe a new biosensor immunoassay involving optical diffraction to detect clinically important analytes in human body fluids. A silicon wafer is used as a support for immobilization of antigen or antibody. The protein-coated surface is illuminated through a photo mask to create distinct periodic areas of active and inactive protein. When the surface is incubated with a positive sample, antigen-antibody binding occurs only on the active areas. Upon illumination with a light source such as a laser, the resulting biological diffraction grating diffracts the light. A negative sample does not result in diffraction because no antigen-antibody binding occurs to create the diffraction grating. The presence or absence of a diffraction signal differentiates between positive and negative samples, and the intensity of the signal provides a quantitative measure of the analyte concentration. The technique is demonstrated with a quantitative assay of choriogonadotropin in serum.
Flow cytometric analysis of kappa and lambda light chain expression in evaluation of specimens for B-cell neoplasia (1996)

Analysis of light chain expression is one of the most important determinations in flow cytometric immunophenotyping of patient specimens. Numerous technical factors, such as antibody choice and cytophilic antibody artifact, impact a laboratory's ability to perform this test. There have been conflicting reports concerning the efficacy of polyclonal versus monoclonal antibodies, as well as methods of circumventing cytophilic antibodies, indicating that a consensus has not been reached on optimal methods for light chain determination. The authors have investigated methods for light chain analysis in 104 normal donors and 366 patient specimens, comparing different anti-light chain antibodies as well as strategies for analysis of specimens with low numbers of monoclonal B cells, admixed polyclonal B cells, or cytophilic antibodies. The patient specimens were either part of the initial diagnostic evaluation of patients with suspected lymphoma, or were performed for staging or assessment of treatment of patients with known B-cell neoplasia. No monoclonality was detected in control specimens, and there was no significant difference in staining with monoclonal verses polyclonal anti-light chain antibodies. In addition, cytophilic antibody did not obscure results in normal controls. Monoclonality was detected in 106 patient specimens, with 89 showing gross involvement with a predominant monoclonal B-cell process. However, in 43% of the grossly monoclonal specimens, there was failure to detect monoclonality with at least one light chain antibody set, with 8% of these cases showing failure with two anti-light chain sets. This indicates the importance of antibody choice in light chain analysis. Cytophilic antibody artifact in monoclonal specimens was easily overcome by appropriate antibody combinations, obviating the need for cytophilic antibody-shedding by incubation at 37 degrees C in fetal calf serum. In 27 patient specimens with low numbers of B cells or admixed polyclonal B cells, a clonal search based on FSC and CD19 or CD20 expression was performed. In 17 of the 27 cases (63%), a small monoclonal population was detected among admixed polyclonal B cells. The authors conclude that multiple strategies are necessary in flow cytometric analysis for B-cell monoclonality.
Asparagine synthetase: A new potential biomarker in ovarian cancer (2009)

L-Asparaginase (L-ASP) is an enzyme drug that has been an asset to leukemia treatment regimens for four decades. Variability in its clinical efficacy, however, has prompted the search for biomarkers capable of distinguishing responders from non-responders. In that regard, the NCI-60 cell line panel has served as a biomarker discovery platform and has led to the identification of a correlation between L-ASP efficacy and asparagine synthetase (ASNS) expression in cultured cells. The presence of that correlation in the ovarian subpanel of the NCI-60 has made a case for repositioning L-ASP to ovarian cancer. This review presents an overview of the biomarker development process, summarizes the efforts that have been invested thus far in developing ASNS as a biomarker for ovarian cancer treatment, highlights the role of RNAi and the limitations of the NCI-60 in that process, and addresses important considerations for next steps in the development of ASNS as a predictive biomarker.
Kinetics of Oleic Acid Esterification with Methanol in the Presence of Triglycerides (2005)

In the present work, the kinetics of oleic acid esterification with methanol has been studied by using an acid ion-exchange polymeric resin (Relite CFS) as the heterogeneous catalyst. The kinetics of the reaction has been studied by performing batch runs at different temperatures and in the presence of a certain amount of triglyceride for simulating an oil with a high content of free fatty acids, which is of great potential interest as a raw material in the biodiesel production process. The experimental data have been interpreted with a second-order, pseudo-homogeneous kinetic model, and a good agreement between the experimental data and the model has been obtained.
Abscopal effect of high-dose-rate brachytherapy on pelvic bone metastases from renal cell carcinoma: a case report (2019)

Radiation therapy is considered an optimal partner for immunotherapies. Several pre-clinical studies have demonstrated that regression of distant metastases, at remote non-irradiated sites of the body, termed the "abscopal effect", can be achieved by an appropriate timing and combination of radiation with immunotherapy. However, nearly all pre-clinical and clinical studies evaluating a combination of radiation and immunotherapies have used external beam radiation therapy. We present in this case report, the abscopal effect observed in a 30-year-old Japanese woman with metastatic renal cell carcinoma after the treatment with high-dose-rate interstitial brachytherapy combined with nivolumab. This is the first published report demonstrating an abscopal effect following brachytherapy for human malignancy. Our case indicates that immuno-oncology effects are not limited to external beam irradiation regimens as they can also be attained by brachytherapy.
509. Thionaphthencarboxylic acids (1957)

G. M. Badger, D. J. Clark, W. Davies, K. T. H. Farrer and N. P. Kefford, J. Chem. Soc., 1957, 2624 DOI: 10.1039/JR9570002624
Characterization of insulin-mediated phosphorylation of the insulin receptor in a cell-free system. (1983)

Insulin stimulates phosphorylation of both alpha- and beta- subunits of its own receptor in a cell-free system. A solubilized lectin-purified preparation of insulin receptors from rat liver membranes was preincubated with or without insulin at 4 degrees C and labeled for 10 min with Mn[gamma- 32P]ATP; the receptor subunits were isolated by specific immunoprecipitation with anti-receptor antibodies, followed by gel electrophoresis in sodium dodecyl sulfate. In gels run under reduced conditions, two bands (Mr = 135,000 and 95,000) were selectively labeled. These correspond exactly to the position of the alpha- and beta-subunits of the insulin receptor. Labeling of the Mr = 95,000 band was approximately 5-fold that of the Mr = 135,000 band. No labeled bands were detected when identical samples were immunoprecipitated in control serum. Phosphorylation of the receptor subunits required the presence of the divalent cation Mn2+ or Co2+; other cations such as Mg2+, Cr3+, Ca2+, and Zn2+ were ineffective. [gamma- 32P]ATP served as the 32P donor, whereas [gamma- 32P]GTP was ineffective. Phosphorylation of both subunits was stimulated 4-6-fold after a 60-min exposure to 10(-7) M pork insulin. Insulin-stimulated phosphorylation was half-maximal after 5 min of incubation with 10(-7) M insulin or after 18 h with 3 X 10(-10) M hormone. The enhanced phosphorylation was specific for insulin and its analogs; guinea pig insulin was about 2% as potent as pork insulin, whereas epidermal growth factor, adrenocorticotropic hormone, and glucagon, as well as cAMP, were ineffective. The rapidity and specificity of this reaction, as well as the presence of all necessary components in the plasma membrane, suggest that insulin-mediated receptor phosphorylation is one of the earliest biochemical steps following insulin binding.
New triple coaxial catheter system for carotid angioplasty with cerebral protection. (1990)

We previously reported an angioplasty technique involving temporary occlusion of the internal carotid artery to prevent cerebral embolization during manipulation of ulcerated plaques [18]. The present article describes a new triple coaxial catheter system (Schneider [Europe] AG, Zurich, Switzerland) (Fig. 1), which simplifies this technique and allows angioplasty with a «cerebral protection» based on the same concepts of distal temporary occlusion of the internal carotid artery
Determination of higher carboxylic acids in snow samples using solid-phase extraction and LC/MS-TOF (2008)

The objective of this work was to develop a method to determine the concentrations of higher organic acids in snow samples. The target species are the homologous aliphatic alpha,omega-dicarboxylic acids from C(5) to C(13), pinonic acid, pinic acid and phthalic acid. A preconcentration procedure utilizing solid phase extraction was developed and optimized using solutions of authentic standards. The influences of different parameters such as flow rate during extraction and the concentration of the eluent on the efficiency of the extraction procedure were investigated. The compounds of interest were separated by HPLC and detected by a quadrupole time-of-flight mass spectrometer (qTOF-MS). The recovery rate (extraction efficiency) of the extraction procedure was found to vary between 41% for tridecanedioic acid and 102% for adipic acid. The limits of detection were determined for all compounds and were between 0.9 nmol/L (dodecanedioic acid) and 29.5 nmol/L (pinonic acid). An exception is pinic acid, for which a considerably higher detection limit of 103.9 nmol/L was calculated. Snow samples were collected in December 2006 and January 2007 at the Fee glacier (Switzerland) from locations at heights from 3056 to 3580 m asl and from different depths within the snow layer. In total, the analysis of 61 single snow samples was performed, and the following compounds could be quantified: homologous aliphatic alpha,omega-dicarboxylic acids with 5-12 carbon atoms and phthalic acid. Tridecanedioic acid, pinonic and pinic acid were identified in the samples but were not quantified due to their low concentrations. The three most abundant acids found in the molten snow samples were glutaric acid (C(5)-di; 3.90 nmol/L), adipic acid (C(6)-di; 3.35 nmol/L) and phthalic acid (Ph; 3.04 nmol/L).
An Introduction to Fluorescence Imaging Techniques Geared Towards Biosensor Applications (2013)

After providing a brief overview of the basics of fluorescence and FRET, this chapter discusses the most commonly used methods to record FRET. Emphasis is on microscopy methods that are widely used for biosensor imaging. We cover choice of instruments, describe various ways to detect FRET based on intensity as well as on donor lifetime, and provide some guidelines to match particular recording methods with specific scientific experiments. We end with an extensive discussion on further practical considerations that may greatly affect the success of the experiments.
Myotubularin, a protein tyrosine phosphatase mutated in myotubular myopathy, dephosphorylates the lipid second messenger, phosphatidylinositol 3-phosphate (2000)

The lipid second messenger phosphatidylinositol 3-phosphate [PI(3)P] plays a crucial role in intracellular membrane trafficking. We report here that myotubularin, a protein tyrosine phosphatase required for muscle cell differentiation, is a potent PI(3)P phosphatase. Recombinant human myotubularin specifically dephosphorylates PI(3)P in vitro. Overexpression of a catalytically inactive substrate-trapping myotubularin mutant (C375S) in human 293 cells increases PI(3)P levels relative to that of cells overexpressing the wild-type enzyme, demonstrating that PI(3)P is a substrate for myotubularin in vivo. In addition, a Saccharomyces cerevisiae strain in which the myotubularin-like gene (YJR110w) is disrupted also exhibits increased PI(3)P levels. Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro, suggesting that this activity is intrinsic to all myotubularin family members. Mutations in the MTM1 gene that cause human myotubular myopathy dramatically reduce the ability of the phosphatase to dephosphorylate PI(3)P. Our findings provide evidence that myotubularin exerts its effects during myogenesis by regulating cellular levels of the inositol lipid PI(3)P.