gebhart/patrepeval huggingface dataset:
Polysaccharides Dissolved from Norway Spruce in Thermomechanical Pulping and Peroxide Bleaching (1994)

Abstract Methanolysis, followed by GC analysis, was used to determine the amount and composition of sugar units comprising the carbohydrates present in water samples from unbleached and peroxide bleached thermomechanical pulp (TMP). Circulation experiments were carried out in the laboratory to simulate white water system closure in mechanical pulp mills. Water samples from simulated “closed” water systems were fractionated to determine the composition of the neutral and anionic polysaccharides released from the TMP samples. Decreasing fresh water consumption from 100 to 10 m3/t, for both unbleached and peroxide bleached TMP, had little influence on the overall sugar composition of the carbohydrates in the water samples. Alkaline peroxide bleaching resulted in substantial changes in the sugar composition of the carbohydrates comprising the dissolved and colloidal substances (DCS) in the water samples. The polysaccharides released from unbleached TMP were comprised of neutral (88%) and anionic (12%) polysaccharides. The neutral polysaccharides were mostly O-acetyl-galactoglucomannans and the anionic polysaccharides were mostly arabinogalactans. The galactoglucomannans, partially acetylated when dissolved in the unbleached suspension, were deacetylated by the alkaline conditions of peroxide bleaching, thereby causing their substantial adsorption onto the TMP fibers. The anionic arabinogalactans probably originated from heartwood present in the TMP furnish. About half of the dissolved polysaccharides present after peroxide bleaching were neutral, probably comprised mostly of galactoglucomannans. Anionic galacturonans and arabino-(4-O-methylglucurono)xylans were released from the pulp in peroxide bleaching. Anionic arabinogalactans were also present after alkaline peroxide bleaching. Notes Phenyl superose technical bulletin, Pharmacia LKB Biotechnology AB, S-751 82 Uppsala, Sweden
Involvement of Cyclic AMP-Dependent Protein Kinases in the Signal Transduction Pathway for Interleukin-1 (1990)

Expression of a highly specific protein inhibitor for cyclic AMP-dependent protein kinases in interleukin-1 (IL-1)-responsive cells blocked IL-1-induced gene transcription that was driven by the kappa immunoglobulin enhancer or the human immunodeficiency virus long terminal repeat. This inhibitor did not affect protein kinase C-mediated gene transcription, suggesting that cyclic AMP-dependent protein kinases are involved in the signal transduction pathway for IL-1 in a number of responsive cell types.
Ultrasensitive techniques and protein misfolding amplification assays for biomarker-guided reconceptualization of Alzheimer’s and other neurodegenerative diseases (2021)

Ultrasensitive assays represent innovative solutions for blood-based assessments during the entire Alzheimer's disease (AD) biological and clinical continuum, for contexts of use (COU) such as prediction, detection, early diagnosis, and prognosis of AD. Moreover, cerebrospinal fluid (CSF)-based misfolding amplification assays show encouraging performance in detecting α-synucleinopathies in prodromal or at-high-risk individuals and may serve as tools for patients' stratification by the presence of α-synuclein pathology. Further clinical research will help overcome current methodological limitations, also through exploring multiple accessible bodily matrices. Eventually, integrative longitudinal studies will support precise definitions for appropriate COU across NDDs.
Unoprostone isopropyl rescues retinal progenitor cells from apoptosisin vitro (2004)

The unoprostone metabolite M1 protects retinal neuro-glial progenitor R28 cells from apoptosis induced by serum deprivation via the PI3K and PKG pathways.
Analysis of Tumor-Associated Alkyldiacylglycerols and Other Lipids During Radiation-Induced Thymic Leukemogenesis (1975)

Lipid composition of thymuses investigated during the development of thymic leukemogenesis induced by exposing C57BL/6J mice to gamma radiation led to the following conclusions. 1. Alkyldiacylglycerols, a class of lipids that are generally elevated in most neoplastic tissues, occurred only in small quantities (less than 1% of the total lipids) in the thymuses of both control and irradiated mice. However, we found a 3- to 8-fold increase in this fraction in thymic tumors of mice at 5 mo after irradiation when compared to controls of similar age. However, the small quantity of this lipid class in thymic leukemia and the fact that similar levels were found in some samples of involuted thymuses of mice 3 days after irradiation, suggests to us that the level of alkyldiacylglycerols is not sufficiently specific or sensitive for detecting early stages of thymic leukemogenesis. 2. Thymuses 3 days after irradiation and leukemic thymuses contain 2- to 3-fold greater quantities of cholesterol esters than control thymuses. No major differences were found in the distribution of acyl moieties in the cholesterol esters of the various thymus samples from the same aged mice except that in thymic tumors the quantity of 18:1 esters was increased by about 25% over that of the controls. The apparent lack of specificity of increased cholesterol esters for neoplasia indicates that its measurement would not provide a suitable indicator of early neoplastic transformation. 3. Acyl composition of the triacylglycerols of thymuses revealed an increase in the 18:1 and a decrease in the 18:2 acids at 3 days after irradiation when compared to the same aged controls. However, thymic tumors occurring at 5 mo after irradiation contained less 14:0, 16:0, and 16:1 acids and increased amounts of 18:1 and 18:2 acids esterified as triacylglycerols compared to controls. The fatty acid distribution in the phospholipid fraction of thymuses was not altered by the appearance of leukemia.
ChemInform Abstract: EINE NEUE CYCLOADDITION VON KETENIMINEN, DIE SYNTH. EINES 1,2‐OXATHIANS (1971)

Abstract Die Reaktion von Diphenylketen‐p‐tolylimin (I) mit Keten (II) und Schwefel= dioxid (III) führt zu einem Addukt der Struktur (IV), das zu (V) hydriert wird.
Bordetella pertussisFilamentous Hemagglutinin Enhances the Immunogenicity of Liposome-Delivered Antigen Administered Intranasally (1998)

In an attempt to increase the immunogenicity of mucosally delivered antigens, we incorporated the Bordetella pertussis filamentous hemagglutinin (FHA) adhesin into liposomes containing the glutathione S-transferase of Schistosoma mansoni (Sm28GST) as a model antigen. Outbred mice immunized twice intranasally with liposomes containing a constant suboptimal dose of Sm28GST and increasing doses of FHA produced anti-Sm28GST antibodies in a FHA dose-dependent manner. The addition of 3 microg of FHA to the liposomes induced more than 10-fold-higher anti-Sm28GST antibody titers, compared to those induced by liposomes without FHA. The presence of FHA did not alter the nature of the humoral immune response, and the sera contained anti-Sm28GST immunoglobulin G1 (IgG1), IgG2a, and IgG2b. However, anti-Sm28GST IgA was only detected when at least 3 microg of FHA was added to the preparation. These results show a promising potential for FHA to enhance the immunogenicity of mucosally administered antigens incorporated into liposomes.
Inheritance is not subtyping (1990)

In typed object-oriented languages the subtype relation is typically based on the inheritance hierarchy. This approach, however, leads either to insecure type-systems or to restrictions on inheritance that make it less flexible than untyped Smalltalk inheritance. We present a new typed model of inheritance that allows more of the flexibility of Smalltalk inheritance within a statically-typed system. Significant features of our analysis are the introduction of polymorphism into the typing of inheritance and the uniform application of inheritance to objects, classes and types. The resulting notion of type inheritance allows us to show that the type of an inherited object is an inherited type but not always a subtype.
Indocyanine Green is an Ideal Dye for Endoscopic Ultrasound-Guided Fine-Needle Tattooing of Pancreatic Tumors (2006)

Endoscopic ultrasound-guided fine-needle tattooing (EUS-FNT) is an ideal technique for preoperative marking of lesions detected on preoperative examination. Although India ink has been used for endoscopic tattooing, there have been numerous reports of complications associated with its use. This is the first report of EUS-FNT using indocyanine green (ICG) and describes its use for preoperative marking of a tumor in a 78-year-old man with multiple pancreatic tumors. There were no complications associated with the EUS-FNT procedure and it is suggested that ICG is a more suitable dye for tattooing of pancreatic lesions than India ink, being far less frequently associated with side effects.
Hydrolysis of Insoluble Collagen by Deseasin MCP-01 from Deep-sea Pseudoalteromonas sp. SM9913 (2008)

Collagens are the most abundant proteins in marine animals and their degradation is important for the recycling of marine nitrogen. However, it is rather unclear how marine collagens are degraded because few marine collagenolytic proteases are studied in detail. Deseasins are a new type of multidomain subtilases. Here, the collagenolytic activity of deseasin MCP-01, the type example of deseasins, was studied. MCP-01 had broad substrate specificity to various type collagens from terrestrial and marine animals. It completely decomposed insoluble collagen into soluble peptides and amino acids, and was more prone to degrade marine collagen than terrestrial collagen. Thirty-seven cleavage sites of MCP-01 on bovine collagen chains were elucidated, showing the cleavage is various but specific. As the main extracellular cold-adapted protease from deep-sea bacterium Pseudoalteromonas sp. SM9913, MCP-01 displayed high activity at low temperature and alkaline range. Our data also showed that the C-terminal polycystic kidney disease (PKD) domain of MCP-01 was able to bind insoluble collagen and facilitate the insoluble collagen digestion by MCP-01. Site-directed mutagenesis demonstrated that Trp-36 of the PKD domain played a key role in its binding to insoluble collagen. It is the first time that the structure and function of a marine collagenolytic protease, deseasin MCP-01, has been studied in detail. Moreover, the PKD domain was experimentally proven to bind to insoluble protein for the first time. These results imply that MCP-01 would play an important role in the degradation of deep-sea sedimentary particulate organic nitrogen.
Homogeneous nanocrystalline cubic silicon carbide films prepared by inductively coupled plasma chemical vapor deposition (2007)

Silicon carbide films with different carbon concentrations x(C) have been synthesized by inductively coupled plasma chemical vapor deposition from a SiH(4)/CH(4)/H(2) gas mixture at a low substrate temperature of 500 °C. The characteristics of the films were studied by x-ray photoelectron spectroscopy, x-ray diffraction, scanning electron microscopy, high-resolution transmission electron microscopy, Fourier transform infrared absorption spectroscopy, and Raman spectroscopy. Our experimental results show that, at x(C) = 49 at.%, the film is made up of homogeneous nanocrystalline cubic silicon carbide without any phase of silicon, graphite, or diamond crystallites/clusters. The average size of SiC crystallites is approximately 6 nm. At a lower value of x(C), polycrystalline silicon and amorphous silicon carbide coexist in the films. At a higher value of x(C), amorphous carbon and silicon carbide coexist in the films.
ChemInform Abstract: Cyclization of Disulfide‐Rich Conotoxins in Drug Design Applications (2016)

Abstract Review: [91 refs.
Cancer cells same as zombies reprogram normal cells via the secreted microenvironment (2023)

The cancer microenvironment plays a crucial role in promoting metastasis and malignancy even in normal cells. In the present study, the effect of acidic and conditioned media of cancer cells (MDA-MB-231), separately and in combination, was studied for the first time on the cell death mechanisms and DNA methylation of normal fibroblasts (NIH/3T3). Cell survival of conditioned media was rescued by the addition of acidic media to conditioned media, as shown by the results. Cell metabolic activity is deviated in a direction other than the Krebs cycle by acidic media The mitochondrial metabolic activity of all groups was enhanced over time, except for acidic media. Unlike the highest amount of ROS in conditioned media, its level decreased to the level of acidic media in the combination group. Furthermore, cells were deviated towards autophagy, rather than apoptosis, by the addition of acidic media to the conditioned media, unlike the conditioned media. Global DNA methylation analysis revealed significantly higher DNA hypomethylation in acidic media than in normal and combination media. Not only were cells treated with conditioned media rescued by acidic media, but also DNA hypomethylation and apoptosis in the combination group were decreased through epigenetic modifications. The acidic and conditioned media produced by cancer cells can remotely activate malignant signaling pathways, much like zombies, which can cause metabolic and epigenetic changes in normal cells.
Coherent Perfect Absorption in a Hybrid Silicon-Metal Photonic Circuit (2015)

Losses occurring in optical systems are either strongly desired or carefully avoided, depending on the specific subject of research. For instance, detectors and solar cells fall in the first category, whereas integrated optical elements such as waveguides and couplers usually belong to the second one. However, far from being an exhausted field of study, the analysis of absorption in linear optical systems recently attracted the researcher’s attention, mainly in connection with the non-trivial phenomenon known as coherent perfect absorption (CPA).
A domain mimic increases ΔF508 CFTR trafficking and restores cAMP-stimulated anion secretion in cystic fibrosis epithelia (2004)

The major disease-causing mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) is deletion of phenylalanine 508 (DeltaF508), which adversely affects processing and plasma membrane targeting of CFTR. Under conditions predicted to stabilize protein folding, DeltaF508 CFTR is capable of trafficking to the plasma membrane and retains cAMP-regulated anion channel activity. Overexpression is one factor that increases CFTR trafficking; therefore, we hypothesized that expression of a domain mimic of the first nucleotide-binding fold (NBF1) of CFTR, i.e., the site of F508, may be sufficient to overwhelm the quality control process or otherwise stabilize DeltaF508 CFTR and thereby restore cAMP-stimulated anion secretion. In epithelial cells expressing recombinant DeltaF508 human (h)CFTR, expression of wild-type NBF1 increased the amount of both core-glycosylated and mature protein to a greater extent than expression of DeltaF508 NBF1. Expression of wild-type NBF1 in the DeltaF508 hCFTR cells increased whole cell Cl(-) current density to approximately 50% of that in cells expressing wild-type hCFTR. Expression of NBF1 in polarized epithelial monolayers from a DeltaF508/DeltaF508 cystic fibrosis mouse (MGEF) restored cAMP-stimulated transepithelial anion secretion but not in monolayers from a CFTR-null mouse (MGEN). Restoration of anion secretion was sustained in NBF1-expressing MGEF for >30 passages, whereas MGEN corrected with hCFTR progressively lost anion secretion capability. We conclude that expression of a NBF1 domain mimic may be useful for correction of the DeltaF508 CFTR protein trafficking defect in cystic fibrosis epithelia.
Debugging (2009)

One of the fundamental truths of computer programming (and life) is that not everything works perfectly. No matter how much you plan, and no matter how long you've been programming, it's rare for an application you write to work perfectly the first time and forever under all circumstances and possible uses. Knowing how to properly architect your application and write well-formed code is important. Knowing how to find out why things aren't working the way they're supposed to, and fixing them, is equally important. This last part of the coding cycle, as you're probably well aware, is a process called debugging.KeywordsLine NumberGlobal VariableSnow LeopardVariable ListSource Code FileThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women (2016)

This GWAS meta-analysis of fractures in African American women identified a potentially novel locus in the supervillin gene, which encodes a platelet-associated factor and was previously associated with platelet thrombus formation in African Americans. If validated in other populations of African descent, these findings suggest potential new mechanisms involved in fracture that may be particularly important among African Americans.
The Amyloid β Peptide (Aβ1-40) Is Thermodynamically Soluble at Physiological Concentrations (2003)

Precipitation of the 39-43-residue amyloid beta peptide (Abeta) is a crucial factor in Alzheimer's disease (AD). In normal as well as in AD-afflicted brain, the Abeta concentration is estimated to be a few nanomolar. Here we show that Abeta(1-40) precipitates in vitro only if the dissolved concentration is >14 microM. Using fluorescence correlation spectroscopy, we further show that the precipitation is complete in 1 day, after which the size distribution of Abeta monomer/oligomers in the solution phase becomes stationary in time and independent of the starting Abeta concentration. Mass spectra confirm that both the solution phase and the coexisting precipitate contain chemically identical Abeta molecules. Incubation at 68 degrees C for 1 h reduces the solubility by <12%. Together, these results show that the thermodynamic saturation concentration (C(sat)) of Abeta(1-40) in phosphate-buffered saline (PBS) at pH 7.4 has a well-defined lower limit of 15.5 +/- 1 microM. Divalent metal ions (believed to play a role in AD) at near-saturation concentrations in PBS reduce C(sat) only marginally (2 mM Mg(2+) by 6%, 2.5 microM Ca(2+) by 7%, and 4 microM Zn(2+) by 11%). Given that no precipitation is possible at concentrations below C(sat), we infer that coprecipitant(s), and not properties of Abeta(1-40) alone, are key factors in the in vivo aggregation of Abeta.
The Biosynthesis and Function of Polysaccharide Components of the Plant Cell Wall (2014)

This chapter discusses the primary cell wall and the dynamic aspects of its major components, namely cellulose and matrix polysaccharides, in relation to its function. It describes the structural features of the cellulose microfibrils and two major matrix polysaccharides – pectin and hemicellulosel. The chapter then focuses on the general mechanisms of the synthesis of the two types of cell wall polysaccharides and how these polysaccharides are assembled into the dynamic architecture of the primary cell wall. It discusses the roles of XTH family enzymes and their specific substrates, xyloglucans, in determining cell shape in plants. Finally, the chapter focuses on pectin methylesterases (PMEs)-mediated modification of pectin and its biological significance in the determination of cell shape in plants.
The role of bradykinin B1 receptors in the maintenance of intra‐articular plasma extravasation in chronic antigen‐induced arthritis (1994)

1. The role of bradykinin B1 and B2 receptors in bradykinin- and des-Arg9-bradykinin-induced plasma extravasation in normal and inflamed rat knee joints was investigated by use of an antigen-induced model of chronic arthritis. A modification of an Evans blue extraction technique allowed the unstimulated (basal) plasma extravasation to be assessed in this model. The contributions of bradykinin B1 and B2 receptors towards basal synovial plasma extravasation were determined. 2. In normal knees, intra-articular injection of bradykinin (BK) induced plasma extravasation in a potent, dose-dependent manner with a threshold of 0.01 nmol and an ED50 of 0.1 nmol. In day 5 arthritic knees, basal plasma extravasation was substantially enhanced. Lower doses of BK had no demonstrable effect and increases above basal extravasation were first observed at 0.1 nmol. Thereafter the dose-response mirrored the response in normal knees and the maximal response was unaltered. 3. The B1 agonist, des-Arg9-BK, induced slight but significant plasma extravasation in normal knees but was less potent than bradykinin. This response was inhibited by the B1 receptor antagonist, des-Arg9, [Leu8]-BK. Lower doses of des-Arg9-BK bradykinin did not significantly increase basal extravasation in day 5 arthritic knees but, in contrast to BK, the maximal response was significantly enhanced. 4. The B2 antagonist, Hoe 140, inhibited BK-induced plasma extravasation in normal joints over a dose-range of 0.1-1.0 nmol but was relatively inactive in day 5 inflamed knees. The B1 receptor antagonist, des-Arg9, [Leu8]-BK, was relatively inactive in normal joints but showed increased potency against BK-induced plasma extravasation in day 5 arthritic joints.5. Hoe 140 and des-Arg9,[Leu8]-BK both inhibited basal extravasation in arthritic joints on days 1 and 5 post-challenge in a dose-dependent fashion. Whilst Hoe 140 was the more potent inhibitor on day 1, it was less potent than des-Arg9,[Leu8]-BK on day 5.6. Although the majority of responses to BK in normal tissue are mediated via B2 receptors, a small population of B1 receptors may exist in normal joint tissues. The data presented in this study suggest an evolving role for B1 receptors in the mediation of plasma extravasation in inflamed joint tissues. A role for BK antagonists in the treatment of arthritis is also suggested.
An Optical Analysis of Strain Energy Stored in a Viscoelastic Material (1973)

Many polymeric meterials such as rubbers and plastics show strong dependencies on strain rate and temperature, optically as well as mechanically. Therefore, it is difficult, in general, to perform the complete analysis of mechanical and optical behaviors of these materials mathematically.In this study, a method was proposed on the optical determination of strain energy stored in a linear viscoelastic material, based on the fact that the optical properties may be represented by such a spring-and-dashpot model, as the generalized Maxwell or Voigt model, in the same way as the mechanical properties. Then, the experimental strain energy analysis of polyurethane rubber under uniaxial tension was carried out by the use of both mechanical and optical coefficients.The results obtained from both experiments agreed qualitatively as well as quantitatively. Consequently, it is concluded that the optical method would be useful for the experimental determination of strain energy in the viscoelastic materials.