gebhart/patrepeval huggingface dataset:
Potent Thiophene Antagonists of Human Complement C3a Receptor with Anti-Inflammatory Activity (2020)

Structure-activity relationships for a series of small-molecule thiophenes resulted in potent and selective antagonism of human Complement C3a receptor. The compounds are about 100-fold more potent than the most reported antagonist SB290157. A new compound JR14a was among the most potent of the new antagonists in vitro, assessed by (a) inhibition of intracellular calcium release (IC<sub>50</sub> 10 nM) induced in human monocyte-derived macrophages by 100 nM C3a, (b) inhibition of β-hexosaminidase secretion (IC<sub>50</sub> 8 nM) from human LAD2 mast cells degranulated by 100 nM C3a, and (c) selectivity for human C3aR over C5aR. JR14a was metabolically stable in rat plasma and in rat liver microsomes and efficacious in rats when given orally to suppress rat paw inflammation, macrophage and mast cell activation, and histopathology induced by intraplantar paw administration of a C3aR agonist. Potent C3aR antagonists are now available for interrogating C3a receptor activation and suppressing C3aR-mediated inflammation in mammalian physiology and disease.
Effect of parameter variations on the current-voltage behavior of AlGaAs tunnel junction models (2008)

To optimize the design of multi-junction photovoltaic devices, robust models of the tunnel junctions connecting sub-cells are essential. In this paper, we describe the effects of varying key parameters in a model of an AlGaAs tunnel junction. We noted two peaks in the current-voltage behavior of the AlGaAs tunnel junction under consideration. We found that the effective Richardson constant scaling factors in the model primarily affected the magnitude of the main peak. The p++ doping concentration impacted the height of both peaks, while the n++ doping concentration changed the magnitude of the main peak and shifted the secondary peak.
New Insights into the Function of N-Terminal 11 Amino Acids of Band 3 from Structural and Functional Study of a Naturally Occuring Band 3 Variant. (2004)

Abstract The 911 amino acid human erythroid AE1 (eAE1) Cl-/HCO3- exchanger SLC4A1 (usually called band 3) is the major intrinsic membrane protein of red cells. The N-terminal cytoplasmic domain of AE1 represents the anchoring site for membrane-associated proteins such as ankyrin, protein 4.2, protein 4.1, glycolytic enzymes (including aldolase and glyceraldeyde-3-phosphate dehydrogenase (GAPDH) and hemoglobin. We identified marked band 3 deficiency in the second son of a consanguineous marriage with a life-threatening nonimmune hemolytic anemia. The patient was transfusion-dependent prior to splenectomy. SDS-PAGE and immunoblotting analysis of the proband red cell membrane proteins showed approximately 12±4% of band 3 and protein 4.2 compared to controls. Direct nucleotide sequence of SLC4A1 gene showed a single base substitution (T-&gt;C) at position +2 in the donor splice site of intron 2 (Band 3 Neapolis). Functionally, the mutation causes an altered splicing with the consequent formation of two different mature mRNAs, one including intron 2 and one skipping exon 2. While intron 2 retention leads to premature translation termination, exon 2 skipping causes the loss of the normal start site of eAE1 protein translation. The purification of mutant band 3 and its characterization by MALDI mass spectrometry demonstrated the lack of the first 11 amino acids due to the usage of second in frame start site. Real-time RT-PCR analyses of reticulocyte mRNA showed a marked decrement in band 3 transcription accounting for protein deficiency. The lack of the 11 N-terminal amino acids resulted in complete absence of membrane bound aldolase while other glycolitic enzymes (for example GAPDH) were membrane bound. Syk tyrosine kinase recognized the truncated band 3 as a substrate in vitro. In spite of this ability to be phosphorylated by Syk and to recruit Lyn tyrosine kinase in vitro, we were unable to demonstrate Tyr-phosphorylation of mutant band 3 in intact erythrocytes following stimulation by oxidative stress. This finding implies a requirement for the 11 N-terminal amino acids for the sequential Tyr-phosphorylation of band 3 in intact red cell membranes. The mutant band 3 was largely present in the high molecular weight aggregate fraction (about 5.2 fold higher than control), indicating its increased tendency to cluster in the membrane. The spontaneous clustering of truncated band 3 strongly suggests that the negatively charged N-terminal domain may regulate oligomeric state of band 3 in the membrane. Biophysical characterization showed that band 3 deficiency resulted in decreased cohesion between lipid bilyer and spectrin based membrane skeleton accounting for membrane loss. The structural and functional characterization of the naturally occuring mutant band 3 has enabled us to identify a significant role for the 11 N-terminal amino acids in band 3 function and in red cell membrane physiology.
Epigenetic plasticity in tumor biology (2022)

Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.
The Action Mechanism of the Myc Inhibitor Termed Omomyc May Give Clues on How to Target Myc for Cancer Therapy (2011)

Recent evidence points to Myc--a multifaceted bHLHZip transcription factor deregulated in the majority of human cancers--as a priority target for therapy. How to target Myc is less clear, given its involvement in a variety of key functions in healthy cells. Here we report on the action mechanism of the Myc interfering molecule termed Omomyc, which demonstrated astounding therapeutic efficacy in transgenic mouse cancer models in vivo. Omomyc action is different from the one that can be obtained by gene knockout or RNA interference, approaches designed to block all functions of a gene product. This molecule--instead--appears to cause an edge-specific perturbation that destroys some protein interactions of the Myc node and keeps others intact, with the result of reshaping the Myc transcriptome. Omomyc selectively targets Myc protein interactions: it binds c- and N-Myc, Max and Miz-1, but does not bind Mad or select HLH proteins. Specifically, it prevents Myc binding to promoter E-boxes and transactivation of target genes while retaining Miz-1 dependent binding to promoters and transrepression. This is accompanied by broad epigenetic changes such as decreased acetylation and increased methylation at H3 lysine 9. In the presence of Omomyc, the Myc interactome is channeled to repression and its activity appears to switch from a pro-oncogenic to a tumor suppressive one. Given the extraordinary therapeutic impact of Omomyc in animal models, these data suggest that successfully targeting Myc for cancer therapy might require a similar twofold action, in order to prevent Myc/Max binding to E-boxes and, at the same time, keep repressing genes that would be repressed by Myc.
[Performance profile of FDG-PET and PET/CT for cancer screening based on a Japanese nationwide survey]. (2007)

A total of 50,558 healthy subjects underwent an FDG-PET (including PET/CT) scan with or without combination of other tests for cancer screening in 46 PET centers during fiscal year of 2005 in Japan. Thorough examination was indicated for 9.8% of the cases due to positive findings suggesting possible cancer. On analyzing 43,996 cases from 38 PET centers, where detailed information was obtained, 500 cases of cancers (1.14%) were found, of which 0.90% was PET positive and 0.24% was PET negative, resulting in the relative sensitivity of PET being 79.0%. Cancers of thyroid, colon/rectum, lung and breast were most frequently found (107, 102, 79, 35 cases, respectively) with high PET sensitivity (88%, 90%, 80%, 92%). PET showed an overall positive predictive value of 29.0%. PET/CT had better detection rate, sensitivity, and positive predictive value than dedicated PET (p<0.01).
Raman scattering in single-crystal sapphire at elevated temperatures (2017)

Sapphire is a widely used high-temperature material, and this work presents thorough characterization of all the measurable Raman scattering modes in sapphire and their temperature dependencies. Here, Raman scattering in bulk sapphire rods is measured from room temperature to 1081°C and is illustrated as a method of noncontact temperature measurement. A single-line argon ion laser at 488 nm was used to excite the sapphire rods inside a cylindrical furnace. All the anti-Stokes peaks (or lines) were observable through the entire temperature range of interest, while Stokes peaks were observable until they were obscured by background thermal emission. Temperature measurements were found to be most reliable for A<sub>1g</sub> and E<sub>g</sub> modes using the peaks at ±418, ±379, +578, +645, and +750 cm<sup>-1</sup> (+ and - are designated for Stokes and anti-Stokes peaks, respectively). The 418 cm<sup>-1</sup> peak was found to be the most intense peak. The temperature dependence of peak position, peak width, and peak area of the ±418 and ±379 peaks is presented. For +578, +645, and +750, the temperature dependence of peak position is presented. The peaks' spectral positions provide the most precise temperature information within the experimental temperature range. The resultant temperature calibration curves are given, which indicate that sapphire can be used in high-temperature Raman thermometry with an accuracy of about 1.38°C average standard deviation over the entire >1000°C temperature range.
Highly Selective Dry Etching of GaN over AlGaN Using Inductively Coupled Cl2/N2/O2Plasmas (2003)

A systematic study of the selective etching of GaN over Al0.28Ga0.72N was performed using Cl2/N2/O2 inductively coupled plasmas (ICP). Highly selective etching at high GaN etch rate is realized by optimizing the O2 flow rate, the ICP power and the chamber pressure. Maximum etching selectivity of about 60:1 at a GaN etch rate of 320 nm/min has been demonstrated. X-ray photoelectron spectroscopy (XPS) analysis shows that the effective oxidation of AlGaN due to the addition of a small fraction of O2 is crucial to obtain highly selective etching at high GaN etch rate.
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences (2005)

International audience
The Future of Clinical Craniofacial Research: A Collaborative International Craniofacial Registry (2020)

George Washington School of Medicine, Children's National Hospital, Washington, DC. Address correspondence and reprint requests to Gary F. Rogers, MD, the George Washington School of Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC 20010; E-mail: [email protected] Received 31 July, 2020 Accepted 16 August, 2020 The author reports no conflicts of interest.
A Better Bound on the Variance (2000)

(2000). A Better Bound on the Variance. The American Mathematical Monthly: Vol. 107, No. 4, pp. 353-357.
Abstract 820: Analysis of potential mutagenic effects of World Trade Center dust on in vitro systems (2015)

Abstract Following the World Trade Center tragedy of September 11, 2001 rescue workers as well as New York City residents were exposed to thousands of tons of complex particulate matter that was inhaled and ingested over an extended period of time. Some of the immediate effects of these pollutants included “World Trade Center Cough,” a condition that resulted in increased coughing, respiratory pathway irritation, and decreases in lung function. Though there are several known carcinogens found within the heterogeneous mixture of particles that make up World Trade Center dust, there is has been no clearly defined link between World Trade Center dust inhalation and specific cancer development. This study investigated the physical and chemical properties of World Trade Center dust using in vitro methods. A sample of this dust from the tragic events was given for this research by Dr. Paul Lioy of Rutgers University in New Jersey, who was the leader of the 20+ scientists who analyzed and published information on the chemical contents of this particulate matter. Human lung fibroblast cells (MRC-5 and WI-38) were exposed to various concentrations of World Trade Center dust and controls to simulate the World Trade Center dust exposure in in vivo lung systems. Proliferation and apoptosis rates were measured in cells exposed to various concentrations of World Trade Center dust. Assays such as the Apo-Live Glo Multiplex Assay (Promega) utilizing the techniques of luminescence and fluorescence were read by 96 well plate reader. The goal was to elucidate any physical or chemical interactions between cells and particles that may decrease cell viability and induce injury or mutation in DNA. These studies indicate that there is a very specific timing and concentration of particulate matter exposure which leads to noticeable apoptotic events in cultured cells. Apoptosis occurs after 24 hours of incubation for cells exposed to 25 ppm, but likely occurs earlier in cells exposed to 50 ppm and greater. An Ames assay was also performed to further demonstrate possible mutagenic effects that various concentrations of World Trade Center dust may have on living systems. Mutations were incurred by Salmonella typhimurium cells and successfully point to the increased possibility that World Trade Center dust would be a definite mutagenic material. These studies conclude that analysis of proliferation and the timing of apoptosis in cells exposed to World Trade Center dust, in conjunction with Ames assay, allow for a better understanding of the future risks to be faced by personnel exposed to particulate matter pollution following the World Trade Center attack of 9-11. Citation Format: Barbara Soares, Kayla Cortese, Ann Marie DiLorenzo. Analysis of potential mutagenic effects of World Trade Center dust on in vitro systems. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 820. doi:10.1158/1538-7445.AM2015-820
Reconstitution of human shelterin complexes reveals unexpected stoichiometry and dual pathways to enhance telomerase processivity (2017)

The human shelterin proteins associate with telomeric DNA to confer telomere protection and length regulation. They are thought to form higher-order protein complexes for their functions, but studies of shelterin proteins have been mostly limited to pairs of proteins. Here we co-express various human shelterin proteins and find that they form defined multi-subunit complexes. A complex harboring both TRF2 and POT1 has the strongest binding affinity to telomeric DNA substrates comprised of double-stranded DNA with a 3' single-stranded extension. TRF2 interacts with TIN2 with an unexpected 2:1 stoichiometry in the context of shelterin (RAP1<sub>2</sub>:TRF2<sub>2</sub>:TIN2<sub>1</sub>:TPP1<sub>1</sub>:POT1<sub>1</sub>). Tethering of TPP1 to the telomere either via TRF2-TIN2 or via POT1 gives equivalent enhancement of telomerase processivity. We also identify a peptide region from TPP1 that is both critical and sufficient for TIN2 interaction. Our findings reveal new information about the architecture of human shelterin and how it performs its functions at telomeres.
Electroimmunoassay of rat apolipoproteins A-I, A-IV, and E. A procedure for sample treatment to increase the sensitivity in diluted fractions. (1985)

Methods for the quantitative determination of rat apolipoproteins A-I, A-IV, and E by electroimmunoassay are described. Apolipoproteins present in diluted samples of biological fluids (approx. 2 ml) were concentrated by precipitation with deoxycholate and trichloroacetic acid. The protein pellets were solubilized in 0.1 ml of 0.5 M NaOH and these samples were delipidated with tetramethylurea and assayed. This protocol enables the measurement of apolipoprotein concentrations that are at least 10 times lower than normally detectable; 0.2 micrograms of apolipoprotein A-IV, 0.2 micrograms of apolipoprotein A-I, and 0.8 micrograms of apolipoprotein E can be easily detected in samples of 2 ml.
A human canalicular multispecific organic anion transporter (cMOAT) gene is overexpressed in cisplatin-resistant human cancer cell lines with decreased drug accumulation. (1996)

By targeting the ATP binding conserved domain in three ATP binding cassette superfamily proteins (P-glycoprotein, multidrug resistance protein, and cystic fibrosis transmembrane regulator), we isolated the cDNA of a new ATP binding cassette superfamily that was specifically enhanced in a cisplatin-resistant human head and neck cancer KB cell line. A human clone homologous to rat canalicular multispecific organic anion transporter (cMOAT) was found and designated human cMOAT. Fluorescence in situ hybridization demonstrated the chromosomal locus of the gene on chromosome 10q24. The human cMOAT cDNA hybridized a 6.5-kb mRNA that was expressed 4- to 6-fold higher by three cisplatin-resistant cell lines derived from various human tumors exhibiting decreased drug accumulation. Human cMOAT may function as a cellular cisplatin transporter.
.alpha.,.beta.-Epoxy sulfoxides as useful intermediates in organic synthesis. 22. Stereospecific desulfinylation of sulfinylaziridines with alkylmetals: a novel synthesis including asymmetric synthesis of (Z)-N-arylaziridines and some mechanistic studies (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.alpha.,.beta.-Epoxy sulfoxides as useful intermediates in organic synthesis. 22. Stereospecific desulfinylation of sulfinylaziridines with alkylmetals: a novel synthesis including asymmetric synthesis of (Z)-N-arylaziridines and some mechanistic studiesTsuyoshi Satoh, Takahiko Sato, Teruhiko Oohara, and Koji YamakawaCite this: J. Org. Chem. 1989, 54, 16, 3973–3978Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://pubs.acs.org/doi/10.1021/jo00277a041https://doi.org/10.1021/jo00277a041research-articleACS PublicationsRequest reuse permissionsArticle Views334Altmetric-Citations85LEARN 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
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms (2009)

BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/.
Opsite Flexifix: An effective adjunct in the management of pain and hypersensitivity in the hand (2001)

Hand trauma commonly results in pain, swelling and stiffness. These sequelae of injury usually resolve uneventfully. In a small number of patients, however, pain will persist long after the initial trauma. Persisting pain has a significant impact on the patient’s ability to participate in the hand therapy programme; this, in turn, hinders restoration of hand function. Pain management strategies are numerous and draw from a wide variety of disciplines, including hand therapy (occupational therapy and physiotherapy), psychology, pharmacology and, occasionally, surgery. Opsite film has been used for a number of years in the management of pain associated with diabetic neuropathy. The types of symptoms experienced by patients with neuropathy are very similar to those described by some patients with hand injuries. For the past 12 months the authors have trialled Opsite Flexifix (Smith and Nephew) on 42 patients with varying diagnoses. Patient response to this pain‐relieving strategy has been very positive and the authors believe that inclusion of Opsite Flexifix in a pain management programme is indicated.
Divergent Selection for Heading Date in Barley (1986)

Abstract Divergent selection for heading time was performed in two F 2 barley population. Five populations were obtained for each cross: F 5 SSD (unselected control), 3E and 3L (from three cycles of selection for earliness or lateness), 2E1L and ZL1E (from two cycles of direct and one of reverse selection). These populations, together with corresponding parents and F 2 generations, were evaluated over two years. The response to selection was 5.6 and 6.5 days inane direction (earlier heading) and 7.7 and 6.7 clays in the other direction (later heading) in the two crosses, respectively. 3E and 3L populations were highly transgressive as compared to their parents. A sizeable amount of genetic variability was still present after two cycles of selection. Heading was probably controlled by a polygenic system with prevailing additive effects and alleles for earliness and earliness somewhat equally distributed in the parents. Selection fur heading time led to significant changes in plant height, yield and kernel weight. Early progenies were higher yielding than lace ones.
From the programmer's apprentice to human-robot interaction: thirty years of research on human-computer collaboration (2006)

The purpose of a Network Intrusion Detection System is to detect intrusive, malicious activities or policy violations in a host or host's network. In current networks, such systems are becoming more important as the number and variety of attacks increase along with the volume and sensitiveness of the information exchanged. This is of particular interest to Internet of Things networks, where an intrusion detection system will be critical as its economic importance continues to grow, making it the focus of future intrusion attacks. In this work, we propose a new network intrusion detection method that is appropriate for an Internet of Things network. The proposed method is based on a conditional variational autoencoder with a specific architecture that integrates the intrusion labels inside the decoder layers. The proposed method is less complex than other unsupervised methods based on a variational autoencoder and it provides better classification results than other familiar classifiers. More important, the method can perform feature reconstruction, that is, it is able to recover missing features from incomplete training datasets. We demonstrate that the reconstruction accuracy is very high, even for categorical features with a high number of distinct values. This work is unique in the network intrusion detection field, presenting the first application of a conditional variational autoencoder and providing the first algorithm to perform feature recovery.