gebhart/patrepeval huggingface dataset:
Structure−Activity Relations of Nanolipoblockers with the Atherogenic Domain of Human Macrophage Scavenger Receptor A (2009)

Oxidized low density lipoprotein (oxLDL) uptake by macrophages is mediated by scavenger receptors and leads to unregulated cholesterol accumulation. Micellar nanolipoblockers (NLBs) consist of alkyl chains and polyethylene glycol on mucic acid. NLBs functionalized with anionic groups inhibit oxLDL uptake via the scavenger receptor A (SR-A). Molecular modeling and docking approaches were used to understand the structure-activity relationship (SAR) between NLBs and SR-A. Six NLB models were docked to the SR-A homology model to investigate charge placement and clustering. NLB models with the most favorable binding energy were also the most effective oxLDL inhibitors in THP-1 macrophages. Mutant SR-A models were generated by replacing charged residues with alanine. All charged residues in the region were necessary, with Lys60, Lys63, and Lys66 having the greatest effect on binding. We hypothesize that structural studies aided by theoretical modeling and docking can be used to design promising NLB candidates with optimal binding properties.
Nicotinic cholinergic system involvement in eyeblink classical conditioning in rabbits. (1994)

A nicotinic cholinergic antagonist, mecamylamine (MEC), was administered to rabbits tested on eyeblink classical conditioning (EBCC) in the 750-ms delay paradigm for 10 90-trial sessions. Nicotinic receptors were measured in 3 brain regions in 5 treatment groups: paired conditioned stimulus-unconditioned stimulus (CS-US) presentations with (a) vehicle, young; (b) vehicle, older; (c) 0.5 mg/kg MEC, young; unpaired CS-US with (d) 0.5 mg/kg MEC, young; and (e) vehicle, young. Daily MEC injections disrupted acquisition in young rabbits (769 trials to learning criterion vs. 323 trials for vehicle-treated young rabbits). MEC-treated young rabbits learned similarly to older rabbits. Brain nicotinic receptors were not affected by 10 daily MEC injections. To our knowledge, this experimental protocol, using a low MEC dose to selectively inhibit nicotinic cholinergic receptors, is the first to demonstrate a role for nicotinic cholinergic receptors in EBCC.
N-methylisatin-beta-thiosemicarbazone derivative (SCH 16) is an inhibitor of Japanese encephalitis virus infection in vitro and in vivo (2008)

Only one of the 14 isatin derivatives -SCH 16 exhibited antiviral action on JEV and WNV virus infection in vitro. SCH 16 was also found to completely inhibit JEV replication in vivo in a mouse model challenged peripherally with 50LD50 of the virus. These results warrant further research and development on SCH 16 as a possible therapeutic agent.
The Potential Use of Allogeneic Platelet-Rich Plasma for Large Bone Defect Treatment: Immunogenicity and Defect Healing Efficacy (2013)

Autologous platelet-rich plasma (PRP) has been extensively investigated for large bone defect treatment, but its clinical application is harassed by controversial outcome, due to highly variable PRP quality among patients. Alternatively, allogeneic PRP from well-characterized donors cannot only generate more consistent and reliable therapeutic effect but also avoid harvesting large quantities of blood, an additional health burdens to patients. However, the use of allogeneic PRP for bone defect treatment is generally less investigated, especially for its immunogenicity in such application. Here, we meticulously investigated the immunogenicity of allogeneic PRP and evaluated its healing efficacy for critical-sized defect treatment. Allogeneic PRP contained 4.1-fold and 2.7- to 4.9-fold higher amount of platelets and growth factors than whole blood, respectively. The intramuscular injection of allogeneic PRP to rabbits did not trigger severe and chronic immunoresponse, evidenced by little change in muscular tissue microstructure and CD4⁺/CD8⁺ T lymphocyte subpopulation in peripheral blood. The implantation of allogeneic PRP/deproteinized bone matrix (DPB) constructs (PRP+DPB) successfully bridged 1.5-cm segmental radial defects in rabbits, achieving similar healing capacity as autologous MSC/DPB constructs (MSC+DPB), with greater bone formation (1.1-1.5×, p<0.05) and vascularization (1.3-1.6×, p<0.05) than DPB alone, shown by histomorphometric analysis, bone mineral density measurement, and radionuclide bone imaging. Furthermore, the implantation of both allogeneic PRP- and autologous MSC-mediated DPB constructs (PRP + MSC + DPB) resulted in the most robust bone regeneration (1.2-2.1×, p<0.05) and vascularization (1.3-2.0×, p<0.05) than others (PRP+DPB, MSC+DPB, or DPB alone). This study has demonstrated the promising use of allogeneic PRP for bone defect treatment with negligible immunogenicity, great healing efficacy, potentially more consistent quality, and no additional health burden to patients; additionally, the synergetic enhancing effect found between allogeneic PRP and autologous MSCs may shed a light on developing new therapeutic strategies for large bone defect treatment.
CALCIUM CHANNELS: Mechanisms of Selectivity, Permeation, and Block (1987)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Future medical applications of single-cell sequencing in cancer (2011)

Advances in whole genome amplification and next-generation sequencing methods have enabled genomic analyses of single cells, and these techniques are now beginning to be used to detect genomic lesions in individual cancer cells. Previous approaches have been unable to resolve genomic differences in complex mixtures of cells, such as heterogeneous tumors, despite the importance of characterizing such tumors for cancer treatment. Sequencing of single cells is likely to improve several aspects of medicine, including the early detection of rare tumor cells, monitoring of circulating tumor cells (CTCs), measuring intratumor heterogeneity, and guiding chemotherapy. In this review we discuss the challenges and technical aspects of single-cell sequencing, with a strong focus on genomic copy number, and discuss how this information can be used to diagnose and treat cancer patients.
Microsomal preparation from an animal tissue catalyzes release of carbon monoxide from a fatty aldehyde to generate an alkane. (1988)

Alkanes are widely distributed in nature and impaired alkane synthesis was implicated in certain neurological disorders. However, the mechanism of synthesis of alkanes in animals is unknown. Our search to find a convenient animal tissue to study alkane biosynthesis resulted in the finding that the uropygial gland (a modified sebaceous gland) of the eared grebe (Podiceps nigricollis) produces large amounts of alkanes. These alkanes, which constitute 35-41% of the total lipid produced, are mainly C21, C23, C25, and C27 n-alkanes. Cell free homogenates of this tissue synthesized alkanes from both fatty acid and aldehyde in the absence of O2. Differential centrifugation of the homogenates indicated that this activity was located in the microsomal fraction. With isolated microsomes conversion of fatty acid to alkane required CoA, ATP, and NADH whereas conversion of an aldehyde to alkane did not require the addition of cofactors. That the final step in alkane synthesis is a decarbonylation was shown by the stoichiometric production of heptadecane and CO from octadecanal. CO was identified by adsorption to RhCl [(C6H6)3P]3 and oxidation of the trapped CO to CO2 by watergas shift reaction. The enzyme preparation also catalyzed incorporation of 14C from 14CO into octadecanal showing the reversible nature of the decarbonylase. This decarbonylase had a sharp pH optimum at 7.0, a Kapp of 180 microM and a V1/2 of 90 rho mol/min/mg protein for octadecanal. The enzyme was inhibited by the metal chelators EDTA, O-phenanthroline, and 8-hydroxyquinoline, but not by KCN. It was stimulated nearly 3-fold by 5 microM 2-mercaptoethanol and inhibited by the presence of O2. During the conversion of [1-3H]octadecanal to heptadecane, 3H was lost to water and 3H from 3H2O was incorporated into the alkane generated from unlabeled octadecanal. The mechanism of the decarbonylation and the nature of the enzyme remain to be elucidated.
Transgene stacking in potato using the GAANTRY system (2019)

The 28.5 kilobase 10-stack T-DNA, was introduced into Lenape potato plants with a 32% transformation efficiency. Molecular and phenotypic characterization confirmed that six of the seven tested independent transgenic lines carried the entire desired construct, demonstrating that the GAANTRY 10-stack strain can be used can be used in a tissue culture-based callus transformation method to efficiently generate transgenic potato plants. Analysis using droplet digital PCR showed that most of the characterized events carry one or two copies of the 10-stack transgenes and that 'backbone' DNA from outside of the T-DNA was absent in the transgenic plants. These results demonstrate that the GAANTRY system efficiently generates high quality transgenic potato plants with a large construct of stacked transgenes.
Regulation of Calcitonin Gene‐Related Peptide Secretion From Trigeminal Nerve Cells by Botulinum Toxin Type A: Implications for Migraine Therapy (2004)

These data provide the first evidence that botulinum toxin type A can directly decrease the amount of calcitonin gene-related peptide released from trigeminal neurons. The results suggest that the effectiveness of botulinum toxin type A in the treatment of migraine may be due, in part, to its ability to repress calcitonin gene-related peptide release from activated sensory neurons.
Mannosylated <i><scp>N</scp></i>‐Aryl Substituted 3‐Hydroxypyridine‐4‐Ones: Synthesis, Hemagglutination Inhibitory Properties, and Molecular Modeling (2014)

Structural alterations of the aglycon portions of α-mannosides influence their inhibitory potency toward type 1-fimbriated Escherichia coli. The aim of our work was to prepare and explore inhibitory properties of novel mannosylated N-aryl-substituted 3-hydroxypyridine-4-ones because they possess needed structural characteristics as possible FimH antagonists. Hemagglutination inhibitory tests showed that the examined 3-hydroxypyridine-4-one α-mannosides exhibited better inhibitory activity than methyl α-d-mannopyranoside used as a reference compound. Molecular modeling studies revealed the specific interactions responsible for the observed binding activities toward the mannose-specific FimH lectin. The activity depends on the substituent in p-position on the aglycon aromatic ring.
Midwave (4 μm) infrared lasers and light-emitting diodes with biaxially compressed InAsSb active regions (1994)

Heterostructures with biaxially compressed, As-rich InAsSb are being investigated as active regions for midwave infrared emitters. InAs1−xSbx/In1−xGaxAs (x≊0.1) strained-layer sublattices (SLSs), nominally lattice matched to InAs, were grown using metalorganic chemical vapor deposition. An SLS light-emitting diode was demonstrated which emitted at 3.6 μm with 0.06% efficiency at 77 K. Optically pumped laser emission at 3.9 μm was observed in a SLS/InPSb heterostructure. The laser had a maximum operating temperature of approximately 100 K.
A new approach to random mutagenesis in vitro (2004)

Random mutagenesis is a powerful tool for studying the effects of a large number of permutations of a particular DNA sequence and its encoded products. Here we describe a new strategy of conducting in vitro random mutagenesis using ethyl methane sulfonate (EMS). The Bacillus aprN18 gene, coding for a serine protease with fibrinolytic activity, was used as a target gene. To study the mutations of the coding region, rather than the whole plasmid, the 1.4 kb gene fragment was cut out from an expression plasmid and treated with 10 mM EMS at 37 degrees C for 1 h. The treated fragment was then ligated back into the original expression vector and a library of random mutants was constructed in a protease-deficient Bacillus subtilis strain. A plate assay-based screening method was used to select for mutant clones with altered enzyme activity, and the change of activity was then confirmed by a semi-quantitative enzyme assay using liquid culture supernatant. The inserts of five clones with altered enzyme activity were randomly chosen for sequencing analysis. Among the point mutations detected, GC --> AT transition accounts for 42.1%, AT --> GC transition 34.2% and GC/CG transversion 23.7%, respectively. To our knowledge this is the first application of EMS for in vitro mutagenesis of a defined DNA sequence.
Web application security assessment by fault injection and behavior monitoring (2003)

As a large and complex application platform, the World Wide Web is capable of delivering a broad range of sophisticated applications. However, many Web applications go through rapid development phases with extremely short turnaround time, making it difficult to eliminate vulnerabilities. Here we analyze the design of Web application security assessment mechanisms in order to identify poor coding practices that render Web applications vulnerable to attacks such as SQL injection and cross-site scripting. We describe the use of a number of software-testing techniques (including dynamic analysis, black-box testing, fault injection, and behavior monitoring), and suggest mechanisms for applying these techniques to Web applications. Real-world situations are used to test a tool we named the Web Application Vulnerability and Error Scanner (WAVES, an open-source project available at http://waves.sourceforge.net) and to compare it with other tools. Our results show that WAVES is a feasible platform for assessing Web application security.
Reduced-order estimator for closed-looponline estimation of cross-directionalparameters in a plastics extrusion process (1997)

The paper addresses the problem of estimating the ‘effective’ actuator centre locations in a plastics extrusion process while the process is operating in closed loop. It shows that it is possible to use a lower-order model estimator and hence considerably reduce the complexity of the procedure. The estimator is described as a radial basis function network, where the basis functions in the hidden layer are defined using discrete Chebyshev polynomials. The problem is considered as a nonlinear optimisation problem and solved online using a recursive prediction error method.
Tritiated Thymidine Incorporation Does Not Measure DNA Synthesis in Ribavirin-Treated Human Cells (1981)

When the incorporation of tritiated thymidine into acid insoluble material was measured, ribavirin appeared to be a potent inhibitor of DNA synthesis in KB cells and human lymphocytes. Inhibition was nearly 100-fold less, however, when DNA synthesis was measured by incorporation of phosphorus-32-labeled phosphate or by DNA fluorescence. The potent inhibition detected by incorporation of tritiated thymidine into DNA actually was the result of a potent effect on the labeling of deoxythymidine triphosphate, not on the synthesis of DNA.
A controller-based architecture for information centric network construction and topology management (2018)

Information-Centric Networking (ICN) has recently emerged as a result of the increased demand to access contents regardless of their location in the network services. This new approach facilitates content distribution as a service of the network with lower delay and higher security in comparison with the current IP network. Applying ICN in current IP infrastructure leads to major complexities. One approach to deploy ICN with less complexity is to integrate ICN with Software Defined Networking (SDN). The SDN controller manages the content distribution, caching, and routing based on the users' requests. In this paper, we extend these context by addressing the ICN topology management problem over the SDN network to achieve an improved user experience as well as network performance. In particular, a centralized controller is designed to construct and manage the ICN overlay. Experimental results indicate that this adopted topology management strategy achieves high performance, in terms of low failure in interest satisfaction and reduced download time compared to a plain ICN.
Acylation and Alkoxycarbonylation of Oximes Through an Enzymatic Oximolysis Reaction (1993)

Ketone or benzaldehyde O-acyloximes and O-(tert-butoxycarbonyl)oximes can be prepared by reaction of oximes with vinyl esters and di-tert-butyl dicarbonate, respectively, using lipases as biocatalysts.
Immunochemical Studies on Blood Groups XXX. Cleavage of A, B, and H Blood-Group Substances by Alkali<sup>*</sup> (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImmunochemical Studies on Blood Groups XXX. Cleavage of A, B, and H Blood-Group Substances by Alkali*Gerald Schiffman, Elvin A. Kabat, and William ThompsonCite this: Biochemistry 1964, 3, 1, 113–120Publication Date (Print):January 1, 1964Publication History Published online1 May 2002Published inissue 1 January 1964https://pubs.acs.org/doi/10.1021/bi00889a018https://doi.org/10.1021/bi00889a018research-articleACS PublicationsRequest reuse permissionsArticle Views64Altmetric-Citations193LEARN 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
USEFULNESS OF INTRAOPERATIVE PHOTODYNAMIC DIAGNOSIS USING 5-AMINOLEVULINIC ACID FOR MENINGIOMAS WITH CRANIAL INVASION (2008)

To the best of our knowledge, this is the first case demonstrating the efficacy of PDD using 5-aminolevulinic acid for a meningioma with cranial invasion. Additional studies are warranted, as shown in cases of malignant gliomas.
Altered Fluid Transport Across Airway Epithelium in Cystic Fibrosis (1993)

In cystic fibrosis (CF), absence or dysfunction of a phosphorylation-regulated chloride channel [CF transmembrane conductance regulator (CFTR)] leads to the loss or reduction of chloride secretion into the airways. Active sodium absorption is also increased in CF, and both of these ion transport changes could alter fluid transport across the airways. Under baseline conditions, cultured human airway epithelia from normal individuals absorbed fluid, and this absorption was increased in epithelia from patients with CF. In normal and CF epithelial cultures fluid absorption was inhibited by amiloride. Adenosine 3',5'-monophosphate stimulated fluid secretion in normal epithelial cultures but not in cultures from individuals with CF. In contrast, fluid secretion induced by nucleotide triphosphates (uridine triphosphate or adenosine triphosphate) was unaltered in cultures of epithelia from patients with CF, suggesting an approach to the treatment of CF.
History and Physiology of Immune Privilege (2010)

Immune privilege is the condition in which selected immune responses are suppressed or excluded in certain organs, such as the eye. Immune privilege in the eye was described over 130 years ago, but its significance was not appreciated until the early 1950s. Investigations beginning in the 1970s ushered in a new era and revealed that ocular immune privilege is due to anatomical, physiological, and immunoregulatory processes that prevent the induction and expression of immune-mediated inflammation. It is widely believed that immune privilege is an adaptation for reducing immune-mediated injury to ocular cells that have limited or no capacity for regeneration.
Detection of DNA sequence polymorphisms in human genomic DNA by using denaturing gradient gel blots. (1992)

Denaturing gradient gel electrophoresis can detect sequence differences outside restriction-enzyme recognition sites. DNA sequence polymorphisms can be detected as restriction-fragment melting polymorphisms (RFMPs) in genomic DNA by using blots made from denaturing gradient gels. In contrast to the use of Southern blots to find sequence differences, denaturing gradient gel blots can detect differences almost anywhere, not just at 4-6-bp restriction-enzyme recognition sites. Human genomic DNA was digested with one of several randomly selected 4-bp recognition-site restriction enzymes, electrophoresed in denaturing gradient gels, and transferred to nylon membranes. The blots were hybridized with radioactive probes prepared from the factor VIII, type II collagen, insulin receptor, beta 2-adrenergic receptor, and 21-hydroxylase genes; in unrelated individuals, several RFMPs were found in fragments from every locus tested. No restriction map or sequence information was used to detect RFMPs. RFMPs can be used as genetic markers, because their alleles segregate in a Mendelian manner. Unlike most other methods for detecting DNA sequence polymorphisms, a genomic DNA blot made from one gel can be hybridized consecutively with many (30 or more) different probes.
Akt-Dependent Phosphorylation of Hepatic FoxO1 Is Compartmentalized on a WD40/ProF Scaffold and Is Selectively Inhibited by aPKC in Early Phases of Diet-Induced Obesity (2014)

Initiating mechanisms that impair gluconeogenic enzymes and spare lipogenic enzymes in diet-induced obesity (DIO) are obscure. Here, we examined insulin signaling to Akt and atypical protein kinase C (aPKC) in liver and muscle and hepatic enzyme expression in mice consuming a moderate high-fat (HF) diet. In HF diet-fed mice, resting/basal and insulin-stimulated Akt and aPKC activities were diminished in muscle, but in liver, these activities were elevated basally and were increased by insulin to normal levels. Despite elevated hepatic Akt activity, FoxO1 phosphorylation, which diminishes gluconeogenesis, was impaired; in contrast, Akt-dependent phosphorylation of glycogenic GSK3β and lipogenic mTOR was elevated. Diminished Akt-dependent FoxO1 phosphorylation was associated with reduced Akt activity associated with scaffold protein WD40/Propeller/FYVE (WD40/ProF), which reportedly facilitates FoxO1 phosphorylation. In contrast, aPKC activity associated with WD40/ProF was increased. Moreover, inhibition of hepatic aPKC reduced its association with WD40/ProF, restored WD40/ProF-associated Akt activity, restored FoxO1 phosphorylation, and corrected excessive expression of hepatic gluconeogenic and lipogenic enzymes. Additionally, Akt and aPKC activities in muscle improved, as did glucose intolerance, weight gain, hepatosteatosis, and hyperlipidemia. We conclude that Akt-dependent FoxO1 phosphorylation occurs on the WD/Propeller/FYVE scaffold in liver and is selectively inhibited in early DIO by diet-induced increases in activity of cocompartmentalized aPKC.