gebhart/patrepeval huggingface dataset:
Radicals in biological catalysis (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRadicals in biological catalysisJoAnne StubbeCite this: Biochemistry 1988, 27, 11, 3893–3900Publication Date (Print):May 31, 1988Publication History Published online1 May 2002Published inissue 31 May 1988https://pubs.acs.org/doi/10.1021/bi00411a001https://doi.org/10.1021/bi00411a001research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Toward Superlyophobic Surfaces (2010)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
A selective TrkB agonist with potent neurotrophic activities by 7,8-dihydroxyflavone (2010)

Brain-derived neurotrophic factor (BDNF), a cognate ligand for the tyrosine kinase receptor B (TrkB) receptor, mediates neuronal survival, differentiation, synaptic plasticity, and neurogenesis. However, BDNF has a poor pharmacokinetic profile that limits its therapeutic potential. Here we report the identification of 7,8-dihydroxyflavone as a bioactive high-affinity TrkB agonist that provokes receptor dimerization and autophosphorylation and activation of downstream signaling. 7,8-Dihydroxyflavone protected wild-type, but not TrkB-deficient, neurons from apoptosis. Administration of 7,8-dihydroxyflavone to mice activated TrkB in the brain, inhibited kainic acid-induced toxicity, decreased infarct volumes in stroke in a TrkB-dependent manner, and was neuroprotective in an animal model of Parkinson disease. Thus, 7,8-dihydroxyflavone imitates BDNF and acts as a robust TrkB agonist, providing a powerful therapeutic tool for the treatment of various neurological diseases.
Making and Using Antibodies (2006)

Antibodies Matthew R. Kaser and Gary C. Howard Antigens and Adjuvants Paul Algate, Jory Baldridge, and Sally P. Mossman Production of Polyclonal Antibodies Lon V. Kendall Purification and Characterization of Antibodies Joseph P. Chandler Production of Monoclonal Antibodies Kathleen C. F. Sheehan Quantitative Production of Monoclonal Antibodies David A. Fox and Elizabeth M. Smith Making Antibodies in Bacteria Frederic A. Fellouse and Sachdev S. Sidhu In Vitro Selection of Aptamers Tianjiao Wang, Xiangyu Cong, and Marit Nilsen-Hamilton Chemical and Proteolytic Modification of Antibodies George P. Smith Western Blots and Other Applications Lee Bendickson and Marit Nilsen-Hamilton Immunohistochemical Methods Jose A. Ramos-Vara Immunoelectron Microscopy Sara E. Miller and David N. Howell Flow Cytometry Steven B. McClellan ELISAs John Chen and Gary C. Howard Humanization of Antibodies Juan Carlos Almagro, Sreekumar Kodangattil, and Jian Li Antibodies in the Future: Challenges and Opportunities Gary C. Howard and Matthew R. Kaser Index
Nano-photosensitizer based on layered double hydroxide and isophthalic acid for singlet oxygenation and photodynamic therapy (2018)

Singlet oxygen has won a great deal of attention to catalysis and biological studies due to its strong oxidizing properties. However, the photosensitizers which require for the generation of singlet oxygen remain inadequate because of their lack of long-wavelength absorption, weak hydrophilicity, and poor biocompatibility. Here, we develop near-infrared laser activated supramolecular photosensitizers (isophthalic acid/layered double hydroxide nanohybrids) for efficient two-photon photodynamic therapy. The singlet oxygen quantum yield of nanohybrid is up to 0.74. Critically, in vitro tests verify the superior anti-cancer properties of nanohybrid with an IC<sub>50</sub> determine to be 0.153 μg mL<sup>-1</sup>. The nanohybrids take advantage of the superior tissue penetration of 808 nm laser irradiation and exhibit a dramatically strong ability to ablate tumors in vivo, with extremely low toxicity. This work provides the proof of concept that ultralong-lived triplet excitons can function as two-photon-activated photosensitizers for an effective singlet oxygen generation.
Isosorbide as a Renewable Platform chemical for Versatile Applications—Quo Vadis? (2011)

Isosorbide is a platform chemical of considerable importance for the future replacement of fossil resource-based products. Applications as monomers and building blocks for new polymers and functional materials, new organic solvents, for medical and pharmaceutical applications, and even as fuels or fuel additives are conceivable. The conversion of isosorbide to valuable derivatives by functionalization or substitution of the hydroxyl groups is difficult because of the different configurations of the 2- and 5-positions and the resulting different reactivity and steric hindrance of the two hydroxyl groups. Although a substantial amount of work has been published using exclusively the endo or exo derivatives isomannide and isoidide, respectively, as starting material, a considerable effort is still necessary to transfer and adapt these methods for the efficient conversion of isosorbide. This Minireview deals with all aspects of isosorbide chemistry, which includes its production by catalytic processes, special properties, and chemical transformations for its utilization in biogenic polymers and other applications of interest.
Embryonic Stem Cell-Derived Neurons Form Functional Networks In Vitro (2006)

Embryonic stem (ES) cells provide a flexible and unlimited source for a variety of neuronal types. Because mature neurons establish neuronal networks very easily, we tested whether ES-derived neurons are capable of generating functional networks and whether these networks, generated in vitro, are capable of processing information. Single-cell electrophysiology with pharmacological antagonists demonstrated the presence of both excitatory and inhibitory synaptic connections. Extracellular recording with planar multielectrode arrays showed that spontaneous bursts of electrical activity are present in ES-derived networks with properties remarkably similar to those of hippocampal neurons. When stimulated with extracellular electrodes, ES-derived neurons fired action potentials, and the evoked electrical activity spread throughout the culture. A statistical analysis indicated that ES-derived networks discriminated between stimuli of different intensity at a single trial level, a key feature for an efficient information processing. Thus, ES-derived neurons provide a novel in vitro strategy to create functional networks with defined computational properties.
A specific role of integrin Mac-1 in accelerated macrophage efflux to the lymphatics (2005)

In response to injury, monocytes migrate to the site of inflammation, where they differentiate into macrophages and participate in various biologic processes. However, their fate during the resolution of acute inflammation is not fully understood. Here, we show that inflammatory macrophages do not die locally by apoptosis; rather, they migrate across the peritoneal mesothelium to the lymphatics, through which they further migrate to the lymph nodes and to the blood circulation. Macrophage efflux is enhanced considerably on cell activation, and such accelerated macrophage migration is dependent specifically on integrin Mac-1, and can be blocked by addition of its antagonist. Thus, genetic inactivation of Mac-1 in mice inhibits the accelerated macrophage efflux from the inflammatory site to the lymphatics, but it does not compromise the accumulation of blood monocytes into the inflammatory site. Together, our study demonstrates that Mac-1 is involved specifically in the efflux of activated macrophages to the lymphatics, suggesting that Mac-1 may play an important role in the removal of local inflammatory macrophages and in their subsequent migration to the lymph nodes, a process that is critical to the development of the adaptive immunity.
A yeast TDP-43 proteinopathy model: Exploring the molecular determinants of TDP-43 aggregation and cellular toxicity (2008)

Protein misfolding is intimately associated with devastating human neurodegenerative diseases, including Alzheimer's, Huntington's, and Parkinson's. Although disparate in their pathophysiology, many of these disorders share a common theme, manifested in the accumulation of insoluble protein aggregates in the brain. Recently, the major disease protein found in the pathological inclusions of two of these diseases, amyotrophic lateral sclerosis (ALS) and frontal temporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), was identified as the 43-kDa TAR-DNA-binding protein (TDP-43), providing a molecular link between them. TDP-43 is a ubiquitously expressed nuclear protein that undergoes a pathological conversion to an aggregated cytoplasmic localization in affected regions of the nervous system. Whether TDP-43 itself can convey toxicity and whether its abnormal aggregation is a cause or consequence of pathogenesis remain unknown. We report a yeast model to define mechanisms governing TDP-43 subcellular localization and aggregation. Remarkably, this simple model recapitulates several salient features of human TDP-43 proteinopathies, including conversion from nuclear localization to cytoplasmic aggregation. We establish a connection between this aggregation and toxicity. The pathological features of TDP-43 are distinct from those of yeast models of other protein-misfolding diseases, such as polyglutamine. This suggests that the yeast model reveals specific aspects of the underlying biology of the disease protein rather than general cellular stresses associated with accumulating misfolded proteins. This work provides a mechanistic framework for investigating the toxicity of TDP-43 aggregation relevant to human disease and establishes a manipulable, high-throughput model for discovering potential therapeutic strategies.
[The clinical significance of Delphian lymph node metastasis in papillary thyroid cancer]. (2016)

<b>Objective:</b> To evaluate the clinical significance of Delphian lymph node (DLN) metastasis in papillary thyroid cancer (PTC). <b>Method:</b> A total of 505 cases with PTC confirmed pathologically in our hospital between January 2015 and December 2015 were retrospectively reviewed. 208 patients with DLN assessed separately by histopathologic examination who underwent primary surgery for PTC were included for the following analysis. <b>Results:</b> In 208 patients, the detection rate of DLN was 63.0% and the metastasis rate of DLN was 21.4%. DLN metastasis was correlated with PTC multifocality (<i>P</i>=0.038), tumor size over 1cm (<i>P</i>=0.001), <i>BRAF</i><sup>V600E</sup> mutation (<i>P</i>=0.017) and central neck node metastasis (<i>P</i><0.001). Tumor size over 1cm (95%<i>CI</i> 1.308-9.909, <i>OR</i>=3.600, <i>P</i>=0.013) and the number of node with central neck metastasis (95%<i>CI</i> 1.313-2.163, <i>OR</i>=1.685, <i>P</i><0.001) were independent risk factors for DLN metastasis. The presence of DLN metastasis was associated with an 8.8-fold higher frequency of central neck node metastasis compared to cases without DLN metastasis. Among patients with DLN metastases, central lymph node metastasis was more common in the cases with lateral neck node metastases compared to those without lateral neck node metastases (6.5±3.0 vs 1.5±0.7, <i>P</i>=0.009), and 5 of the 6 patients also presented with PTC multifocality and <i>BRAF</i><sup>V600E</sup> mutation. <b>Conclusion:</b> DLN metastasis implies a higher possibility of central neck lymph node metastasis. DLN should be assessed during operation to provide information for neck dissection, post-operative administration and follow-up strategy.
The Value of C-reactive Protein as a Marker of Bacterial Infection in Patients with Septicaemia/Endocarditis and Influenza (1989)

In order to evaluate the capacity of C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), white blood cell count (WBC) and polymorphonuclear neutrophils (PMNs) to differentiate between bacterial and viral infection we studied 176 patients with septicaemia/endocarditis (SE), 59 patients with uncomplicated influenza (UI) and 22 patients with complicated influenza (CI) retrospectively. All 4 parameters were significantly more elevated in SE and CI than in UI. Among patients with SE 10 176 had a CRP value less than 50 mg/l and in patients with UI 5/56 had a CRP value greater than 100 mg/l. Patients with SE caused by pneumococci had the highest CRP levels and patients with alfa-haemolytic streptococci the lowest. The sensitivity and specificity favours the use of CRP as an indicator of bacterial superinfection in influenza.
Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of alzheimer's amyloid β‐protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): Engineering of inhibitors with altered specificities (1997)

The crystal structures of the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) complexed to bovine chymotrypsin (C-APPI) and trypsin (T-APPI) and basic pancreatic trypsin inhibitor (BPTI) bound to chymotrypsin (C-BPTI) have been solved and analyzed at 2.1 A, 1.8 A, and 2.6 A resolution, respectively. APPI and BPTI belong to the Kunitz family of inhibitors, which is characterized by a distinctive tertiary fold with three conserved disulfide bonds. At the specificity-determining site of these inhibitors (P1), residue 15(I)4 is an arginine in APPI and a lysine in BPTI, residue types that are counter to the chymotryptic hydrophobic specificity. In the chymotrypsin complexes, the Arg and Lys P1 side chains of the inhibitors adopt conformations that bend away from the bottom of the binding pocket to interact productively with elements of the binding pocket other than those observed for specificity-matched P1 side chains. The stereochemistry of the nucleophilic hydroxyl of Ser 195 in chymotrypsin relative to the scissile P1 bond of the inhibitors is identical to that observed for these groups in the trypsin-APPI complex, where Arg 15(I) is an optimal side chain for tryptic specificity. To further evaluate the diversity of sequences that can be accommodated by one of these inhibitors, APPI, we used phage display to randomly mutate residues 11, 13, 15, 17, and 19, which are major binding determinants. Inhibitors variants were selected that bound to either trypsin or chymotrypsin. As expected, trypsin specificity was principally directed by having a basic side chain at P1 (position 15); however, the P1 residues that were selected for chymotrypsin binding were His and Asn, rather than the expected large hydrophobic types. This can be rationalized by modeling these hydrophilic side chains to have similar H-bonding interactions to those observed in the structures of the described complexes. The specificity, or lack thereof, for the other individual subsites is discussed in the context of the "allowed" residues determined from a phage display mutagenesis selection experiment.
A Variant of Recombinant Factor VIIa With Enhanced Procoagulant and Antifibrinolytic Activities in an In Vitro Model of Hemophilia (2007)

By increasing factor Xa generation, NN1731 promotes the formation of thrombin and a stable clot to a greater degree than rFVIIa.
Abiotic conversion of dihydrophloroglucinol to resorcinol (1993)

Chemical conversion of a dihydrophloroglucinol preparation (a mixture of the tautomers 1,3,5-trihydroxy-1,3-cyclohexadiene, 1,3-dioxo-5-hydroxycyclohexane, and 3,5-dihydroxy-3-cyclohexene-1-one) to resorcinol occurred during a 24-h extraction of an acidic (pH 2.0) aqueous dihydrophloroglucinol preparation into ethyl acetate. This conversion did not occur at neutral pH, nor did phloroglucinol (1,3,5-trihydroxybenzene)-induced or succinate-induced Penicillium simplicissimum enzyme extracts convert the dihydrophloroglucinol preparation to resorcinol at pH values of 5.5–8.0. The chemical structure of the dihydrophloroglucinol preparation was determined by gas chromatography - mass spectrometry, high resolution 13 C and 1 H nuclear magnetic resonance, Fourier-transformed infrared spectrometry, and ultraviolet spectrophotometry. Resorcinol (1,2-dihydroxybenzene) was detected by gas chromatography - mass spectrometry or thin-layer chromatography and ultraviolet spectrophotometry. A chemical mechanism for the conversion of the dihydrophloroglucinol preparation to resorcinol is proposed.Key words: dihydrophloroglucinol, chemical conversion, resorcinol.
Synthetic peptide libraries in the determination of T cell epitopes and peptide binding specificity of class I molecules (1992)

Major histocompatibility complex (MHC) class I molecules combine with short peptides of defined length and sequence. Here we describe an approach that may be used in the analysis of peptide preference of different allelic MHC class I molecules, and in the determination of T cell epitopes. We produced synthetic "peptide libraries" of limited complexity by standard peptide chemistry. Using these peptide mixtures we show that H-2 Kb molecules can accommodate both 8- and 9-residue peptides, whereas Db molecules are unable to combine with peptides shorter than 9 amino acids present in these libraries. When these peptide mixtures are used to provide "fingerprints" of Db molecules and mutants thereof, both loss and gain of the ability to combine with certain peptides is observed. For the Kbm1 mutant a strong influence of amino acid substitutions in class I molecules on the peptides selected is observed. In these synthetic peptide mixtures, the presence of a specific T cell epitope, known to be represented once, can be detected. This approach may be extended to the identification of new T cell epitopes from larger peptide libraries.
Entries in the Leiden Duchenne muscular dystrophy mutation database: An overview of mutation types and paradoxical cases that confirm the reading‐frame rule (2006)

The severe Duchenne and milder Becker muscular dystrophy are both caused by mutations in the DMD gene. This gene codes for dystrophin, a protein important for maintaining the stability of muscle-fiber membranes. In 1988, Monaco and colleagues postulated an explanation for the phenotypic difference between Duchenne and Becker patients in the reading-frame rule: In Duchenne patients, mutations induce a shift in the reading frame leading to prematurely truncated, dysfunctional dystrophins. In Becker patients, in-frame mutations allow the synthesis of internally deleted, but largely functional dystrophins. Currently, over 4700 mutations have been reported in the Leiden DMD mutation database, of which 91% are in agreement with this rule. In this study we provide an update of the mutational variability in the DMD gene, particularly focusing on genotype-phenotype correlations and mutations that appear to be exceptions to the reading-frame rule.
Antidepressant treatment of the depressed patient with insomnia. (1999)

Sleep disturbances are an integral part of depressive disorder. As such, they are a part of all contemporary sets of diagnostic criteria for major depression and of all major symptom-based rating scales for depression. Insomnia is a particularly frequent complaint, and it is reported by more than 90% of depressed patients. Although the "kindling" or "illness transduction" model of depression remains hypothetical, there is evidence that people with recurrent depression have more pronounced abnormalities of sleep neurophysiology than those experiencing a single or initial episode. Therefore, early relief of insomnia in a depressed patient, in addition to alleviating other symptoms, may increase adherence to treatment and increase daytime performance and overall functioning, while complete relief of insomnia may improve prognosis. Stimulation of serotonin-2 (5-HT2) receptors is thought to underlie insomnia and changes in sleep architecture seen with selective serotonin reuptake inhibitors (SSRIs) or serotonin-norepinephrine reuptake inhibitors (SNRIs). This is the reason why hypnotics or low-dose trazodone are commonly coprescribed at the initiation of the treatment with either the SSRIs or SNRIs. On the other hand, antidepressant drugs with 5-HT2 blocking properties, such as mirtazapine or nefazodone, alleviate insomnia and improve sleep architecture. In depressed patients, mirtazapine produces a significant shortening of sleep-onset latency, increases a total sleep time, and leads to a marked improvement in sleep efficiency. Antidepressants with preferential 5-HT2 blocking properties are therefore a good treatment option for depressed patients with marked insomnia.
SHORT-TERM ETHANOL EXPOSURE INCREASES THE EXPRESSION OF KUPFFER CELL CD14 RECEPTOR AND LIPOPOLYSACCHARIDE BINDING PROTEIN IN RAT LIVER (1999)

Gut-derived endotoxins (lipopolysaccharide, LPS) complexed to LPS-binding protein (LBP) activate liver Kupffer cells via their CD14 receptor. Pro-inflammatory cytokines are released and this is postulated to promote liver injury. We previously demonstrated enhanced expression of CD14 endotoxin receptor after 2 weeks of alcohol administration. A similar result, based on 6 weeks of ethanol treatment, was recently reported and suggested to correlate with alcohol-induced liver injury. To establish whether this occurs prior to or after the initiation of damage, we investigated the temporal effect of continuous ethanol exposure on the expression of CD14 and the associated LBP. In addition, we studied the effect of treatment with gadolinium chloride (GdCl3) that inactivates Kupffer cells and alleviates alcohol-induced liver damage. The amount of CD14 and LBP mRNA, as determined by reverse transcriptase-polymerase chain reaction (RT-PCR), was unchanged 4-8 h after intragastric ethanol administration. However, after 24-48 h of repeated ethanol administration, CD14 and LBP mRNA both increased significantly and reached a level similar to that observed after 6 weeks of ethanol exposure by liquid diet. Immunostaining experiments with ED2 antibody demonstrated that GdCl3 efficiently inactivated Kupffer cells. However, there was no concomitant reduction in the expression of CD14 mRNA, suggesting that compensatory infiltration by ED2-negative, but CD14-positive, macrophages had occurred. Our results demonstrate that soon after the initiation of ethanol exposure, i.e. within 24-48 h, the hepatic expression of both the CD14 receptor and LBP is increased. This suggests that these increases could contribute to the initiation of alcoholic damage rather than being a consequence of the injury.