gebhart/patrepeval huggingface dataset:
The emerging role of mRNA methylation in normal and pathological behavior (2017)

Covalent RNA modifications were recently rediscovered as abundant RNA chemical tags. Similarly to DNA epigenetic modifications, they have been proposed as essential regulators of gene expression. Here we focus on 3 of the most abundant adenosine methylations: N6-methyladenosine (m<sup>6</sup> A), N6,2'-O-dimethyladenosine (m<sup>6</sup> Am) and N1-methyladenosine (m<sup>1</sup> A). We review the potential role of these modifications on mature mRNA in regulating gene expression within the adult brain, nervous system function and normal and pathological behavior. Dynamic mRNA modifications, summarized as the epitranscriptome, regulate transcript maturation, translation and decay, and thus crucially determine gene expression beyond primary transcription regulation. However, the extent of this regulation in the healthy and maladapted adult brain is poorly understood. Analyzing this novel layer of gene expression control in addition to epigenetics and posttranslational regulation of proteins will be highly relevant for understanding the molecular underpinnings of behavior and psychiatric disorders.
Catheter Ablation of Paroxysmal Atrial Fibrillation Initiated by Non–Pulmonary Vein Ectopy (2003)

Ectopic beats initiating PAF can originate from the non-PV areas, and catheter ablation of the non-PV ectopy has a moderate efficacy in treatment of PAF.
Zero-Shot Learning via Semantic Similarity Embedding (2015)

In this paper we consider a version of the zero-shot learning problem where seen class source and target domain data are provided. The goal during test-time is to accurately predict the class label of an unseen target domain instance based on revealed source domain side information (\eg attributes) for unseen classes. Our method is based on viewing each source or target data as a mixture of seen class proportions and we postulate that the mixture patterns have to be similar if the two instances belong to the same unseen class. This perspective leads us to learning source/target embedding functions that map an arbitrary source/target domain data into a same semantic space where similarity can be readily measured. We develop a max-margin framework to learn these similarity functions and jointly optimize parameters by means of cross validation. Our test results are compelling, leading to significant improvement in terms of accuracy on most benchmark datasets for zero-shot recognition.
Luminescence : from theory to applications (2008)

"Adopting a didactical approach, Professor Ronda discusses all the underlying principles, such that both researchers as well as beginners in the field will profit from this book. The focus is on the inorganic side and the phenomena of luminescence behind the manifold applications illustrated here, including displays, LEDs, lamps, and medical applications." "Valuable reading for chemists and electrochemists, as well as materials scientists, those working in the optical and chemical industry, plus lamp and lighting manufacturers."--BOOK JACKET.
Independent formation of DnaseI hypersensitive sites in the murine β-globin locus control region (2000)

Mammalian β-globin loci are composed of multiple orthologous genes whose expression is erythroid specific and developmentally regulated. The expression of these genes both from the endogenous locus and from transgenes is strongly influenced by a linked 15-kilobase region of clustered DNaseI hypersensitive sites (HSs) known as the locus control region (LCR). The LCR encompasses 5 major HSs, each of which is highly homologous among humans, mice, and other mammals. To analyze the function of individual HSs in the endogenous murine β-globin LCR, we have used homologous recombination in embryonic stem cells to produce 5 mouse lines, each of which is deficient for 1 of these major HSs. In this report, we demonstrate that deletion of the conserved region of 5′HS 1, 2, 3, 4, or 5/6 abolishes HS formation at the deletion site but has no influence on the formation of the remaining HSs in the LCR. Therefore, in the endogenous murine locus, there is no dominant or initiating site whose formation must precede the formation of the other HSs. This is consistent with the idea that HSs form autonomously. We discuss the implications of these findings for current models of β-globin regulation.
A convergent approach to protein design. Metal ion-assisted spontaneous self-assembly of a polypeptide into a triple-helix bundle protein (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convergent approach to protein design. Metal ion-assisted spontaneous self-assembly of a polypeptide into a triple-helix bundle proteinM. Reza Ghadiri, Christopher Soares, and Chong ChoiCite this: J. Am. Chem. Soc. 1992, 114, 3, 825–831Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ja00029a004https://doi.org/10.1021/ja00029a004research-articleACS PublicationsRequest reuse permissionsArticle Views1510Altmetric-Citations183LEARN 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
POTENTIAL USE OF GENETICALLY MODIFIED PIGS AS ORGAN DONORS FOR TRANSPLANTATION INTO HUMANS (1999)

1. Transplantation is currently viewed as a successful treatment for end-stage organ failure. Its more widespread use is severely limited by a shortage of human organ donors. This has stimulated the scientific and medical communities to look at the potential use of animals to solve this problem. For a number of reasons, the pig appears to be the preferred species. 2. The initial immunological problem encountered in pig-to-primate transplantation is a process of hyperacute rejection, which is mediated by the binding of antibodies to the graft endothelium followed by the activation of the complement cascade. We have sought to overcome these initial immunological challenges by focusing our attention not only on the recipient of the graft but also on the donor. Therefore, we have generated transgenic animals with specific genetic modifications designed to inhibit the activation of the complement cascade. Upon transplantation to baboons of organs derived from these transgenic pigs, we have been able to demonstrate that hyperacute rejection can be prevented. We will discuss the generation of these and other transgenic animals and their potential role in clinical xenotransplantation.
Food-induced changes of lipids in rat neuronal tissue visualized by ToF-SIMS imaging (2016)

Time of flight secondary ion mass spectrometry (ToF-SIMS) was used to image the lipid localization in brain tissue sections from rats fed specially processed cereals (SPC). An IonTof 5 instrument equipped with a Bi cluster ion gun was used to analyze the tissue sections. Data from 15 brain samples from control and cereal-fed rats were recorded and exported to principal components analysis (PCA). The data clearly show changes of certain lipids in the brain following cereal feeding. PCA score plots show a good separation in lipid distribution between the control and the SPC-fed group. The loadings plot reveal that the groups separated mainly due to changes in cholesterol, vitamin E and c18:2, c16:0 fatty acid distribution as well as some short chain monocarboxylic fatty acid compositions. These insights relate to the working mechanism of SPC as a dietary supplement. SPC is thought to activate antisecretory factor (AF), an endogenous protein with regulatory function for inflammation and fluid secretion. These data provide insights into lipid content in brain following SPC feeding and suggest a relation to activating AF.
Protective response to subunit vaccination against intranasal Burkholderia mallei and B. pseudomallei challenge (2010)

<i>Burkholderia mallei</i> and <i>B. pseudomallei</i> are Gram-negative pathogenic bacteria, responsible for the diseases glanders and melioidosis, respectively. Furthermore, there is currently no vaccine available against these <i>Burkholderia</i> species. In this study, we aimed to identify protective proteins against these pathogens. Immunization with recombinant <i>B. mallei</i> Hcp1 (type VI secreted/structural protein), BimA (autotransporter protein), BopA (type III secreted protein), and <i>B. pseudomallei</i> LolC (ABC transporter protein) generated significant protection against lethal inhaled <i>B. mallei</i> ATCC23344 and <i>B. pseudomallei</i> 1026b challenge. Immunization with BopA elicited the greatest protective activity, resulting in 100% and 60% survival against <i>B. mallei</i> and <i>B. pseudomallei</i> challenge, respectively. Moreover, sera from recovered mice demonstrated reactivity with the recombinant proteins. Dendritic cells stimulated with each of the different recombinant proteins showed distinct cytokine patterns. In addition, T cells from immunized mice produced IFN-γ following <i>in vitro</i> re-stimulation. These results indicated therefore that it was possible to elicit cross-protective immunity against both <i>B. mallei</i> and <i>B. pseudomallei</i> by vaccinating animals with one or more novel recombinant proteins identified in <i>B. mallei</i>.
Interactions of selenium compounds with other antioxidants in DNA damage and apoptosis in human normal keratinocytes. (2001)

Selenite (SeL) or selenomethionine (SeM) are the most common selenium (Se) compounds taken as dietary antioxidants to reduce oxidative stress. Because the public may frequently supplement Se compounds at high doses, the possible pro-oxidant effect of Se becomes a concern. SeL and SeM have entirely different pharmacokinetic effects based on dose-related cytotoxicity. Our laboratory has shown previously that high doses of SeL resulted in cytotoxicity and induction of 8-hydroxydeoxyguanosine (8-OHdG) in DNA of primary human keratinocytes (NHK), compared with those treated with the same doses of SEM: Besides Se compounds, other dietary antioxidants, such as vitamin (Vit) C or Vit E, are often supplemented and taken together with Se compounds. However, the cellular effects of these interactions of Se with antioxidants are still unknown. In addition, copper is commonly present in drinking water, food, soil, or the environment to increase the possibility of subchronic toxicity. Copper has been shown to inhibit SeL-induced cytotoxicity and apoptosis in human colonic carcinoma cells. The present study was designed to investigate the interactive effects of SeL or SeM plus Vit C, trolox (a water-soluble Vit E), or copper sulfate (CuSO(4)) on cell viability and induction of 8-OHdG adduct formation in DNA of NHK. NHK cells were treated with no Se, SeL (126.6 microM Se), or SeM (316.6 microM Se) plus two doses each of Vit C (2.27 and 4.45 microM), trolox (40 and 80 microM), or CuSO(4) (7.85 and 15.7 microM) for 24 h. Coincubation of Vit C or CuSO(4) with SeL appeared to protect NHK against SeL-induced cytotoxicity. However, synergistic effects were observed between SeL and trolox resulting in enhanced cytotoxicity. On the other hand, SeM + Vit C, SeM + trolox, and SeM + CuSO(4) did not affect cell viability. In the absence of Se supplementation, Vit C, trolox, or CuSO(4) alone did not induce 8-OHdG adduct formation, regardless of dose. When NHK cells were coincubated with SeL (126.6 microM Se) and Vit C or CuSO(4), they protected NHK from SeL-induced DNA damage with a reduction in 8-OHdG generation. In contrast, treatment of SeL + trolox elevated generation of 8-OHDG: Furthermore, treatments of SeM plus trolox or CuSO(4) elevated 8-OHdG adduct formation. In terms of apoptosis measured as internucleosomal DNA fragmentation, copper protected NHK against SeL-induced apoptosis in cultured NHK. These data suggest that the use of CuSO(4) may play a protective role in SeL-induced cytotoxicity, DNA oxidative damage, and apoptosis and that there may be potentially deleterious interactions among common high-dose antioxidant supplements taken by the public.
Indexing algorithms for Z/sub n/, A/sub n/, D/sub n/, and D/sub n//sup ++/ lattice vector quantizers (2001)

This paper describes vector indexing algorithms valid for a large class of lattices (Z/sub n/, A/sub n/, D/sub n/, and D/sub n//sup ++/ including as special cases the Gosset (E/sub 8/) and Barnes-Wall (/spl Lambda//sub 16//sup n/) lattices), widely used in audio-visual signal compression. The indexing mechanism relies on reverse lexicographic ordering of the vectors, in classes of equivalence defined as sets of vectors obtained by "signed" permutations of the components of initial vectors called leaders. The approach makes it possible to trade the size of the lookup tables-or codebooks-for arithmetic operations. The reduction of codebook sizes leads in turn to reduced encoder and decoder complexities. Pursuing the goal of best tradeoff between storage requirements and arithmetic complexity, two algorithms, based on the proposed indexing mechanisms, allowing "on-the-fly" generation of adaptive portions of codebooks are then described. These algorithms make it possible to overcome the problems of lattice truncating usually encountered in lattice vector quantization (LVQ). Combined with product codes, these indexing techniques lead to increased compression performances.
Requirement for an Interaction of XRCC4 with DNA Ligase IV for Wild-type V(D)J Recombination and DNA Double-strand Break Repairin Vivo (1998)

The XRCC4 gene is required for the repair of DNA double-strand breaks in mammalian cells. Without XRCC4, cells are hypersensitive to ionizing radiation and deficient for V(D)J recombination. It has been demonstrated that XRCC4 binds and stimulates DNA ligase IV, which has led to the hypothesis that DNA ligase IV is essential for both of these processes. In this study deletion mutants of XRCC4 were tested for their ability to associate with DNA ligase IV in vitro and for their ability to reconstitute XRCC4-deficient cells in vivo. We find that a central region of XRCC4 from amino acids 100-250 is necessary for DNA ligase IV binding and that deletions within this region functionally inactivates XRCC4. Deletions within the C-terminal 84 amino acids neither affect DNA ligase IV binding nor the in vivo function of XRCC4. The correlation between the ability or inability of XRCC4 to bind DNA ligase IV and its ability or failure to reconstitute wild-type DNA repair in vivo, respectively, demonstrates for the first time that the physical interaction with DNA ligase IV is crucial for the in vivo function of XRCC4. Deletions within the N-terminal 100 amino acids inactivate XRCC4 in vivo but leave DNA ligase IV binding unaffected. This indicates further DNA ligase IV-independent functions of XRCC4.
A dissection of the cauliflower mosaic virus polyadenylation signal. (1991)

Mutagenesis analysis of the polyadenylation [poly(A)] signal from the cauliflower mosaic virus (CaMV), a plant pararetrovirus, revealed striking differences to known vertebrate poly(A) signals. Our results show that (1) the AATAAA sequence is necessary for efficient cleavage at the poly(A) site, although the requirement for an authentic AATAAA might be less stringent in plant than in vertebrate cells; (2) surprisingly and in contrast to the majority of vertebrate poly(A) signals, the sequences downstream of the CaMV poly(A) site do not influence processing efficiency drastically although they affect the precision of cleavage; and (3) deletion of sequences upstream of the CaMV AATAAA sequence decreased processing at the CaMV site dramatically, suggesting the presence of one or several positively acting upstream elements. An oligonucleotide consisting of CaMV upstream sequences could induce the recognition of a normally silent exogenous poly(A) signal when inserted upstream of its AATAAA motif.
Structural Analysis of α-Enolase (2000)

Myc-binding protein-1 (MBP-1) is a 37-kDa protein with sequence homology to the 3' portion of the alpha-enolase gene. alpha-Enolase is a 48-kDa protein, which plays a critical role in the glycolytic pathway. MBP-1 binds to the c-myc P2 promoter and down-regulates c-myc expression. We have investigated the role of alpha-enolase in regulation of the c-myc protooncogene. RNase protection assay shows that alpha-enolase is transcribed into a single RNA species in HeLa cells. A start codon, 400 base pairs downstream of the alpha-enolase ATG, corresponds to the MBP-1 ATG, suggesting that MBP-1 is an alternative translation initiation product of the alpha-enolase RNA. Domain mapping was performed using constructs containing truncations of the alpha-enolase gene. In vitro binding to the c-myc gene was abolished after deletion of the N-terminal portion of alpha-enolase. In order to determine the relationship between DNA binding activity and transcription inhibition, we performed co-transfection assays in HeLa cells. These studies confirmed that an N-terminal deletion of alpha-enolase is unable to down-regulate c-myc promoter activity. Our data suggest that alpha-enolase plays an important role in regulation of c-myc promoter activity in the form of an alternative translation product MBP-1, which is distinct from its role as a glycolytic enzyme.
High-Rate Solar Photocatalytic Conversion of CO2 and Water Vapor to Hydrocarbon Fuels (2009)

Efficient solar conversion of carbon dioxide and water vapor to methane and other hydrocarbons is achieved using nitrogen-doped titania nanotube arrays, with a wall thickness low enough to facilitate effective carrier transfer to the adsorbing species, surface-loaded with nanodimensional islands of cocatalysts platinum and/or copper. All experiments are conducted in outdoor sunlight at University Park, PA. Intermediate reaction products, hydrogen and carbon monoxide, are also detected with their relative concentrations underlying hydrocarbon production rates and dependent upon the nature of the cocatalysts on the nanotube array surface. Using outdoor global AM 1.5 sunlight, 100 mW/cm(2), a hydrocarbon production rate of 111 ppm cm(-2) h(-1), or approximately 160 microL/(g h), is obtained when the nanotube array samples are loaded with both Cu and Pt nanoparticles. This rate of CO(2) to hydrocarbon production obtained under outdoor sunlight is at least 20 times higher than previous published reports, which were conducted under laboratory conditions using UV illumination.
CCCLXXII.—The nitrosation of phenols. Part VII. Resorcinol monomethyl ether and m-cresol (1929)

H. H. Hodgson and H. Clay, J. Chem. Soc., 1929, 2775 DOI: 10.1039/JR9290002775
Oracle PL/SQL programming (1996)

From the Publisher:
The essential guide for every Oracle programmer,with new information on performance and tuning. 
Speak the Language of PL/SQL 8. 0 for Oracle8. 
Become fluent in the powerful Oracle8 development language and create applications that exude efficiency,reliability,and grace. This completely revised and updated book and CD-ROM package is your ticket to mastering PL/SQL in Oracle7 and Oracle8. 
An Oracle insider,Scott Urman presents up-to-date information on the best ways to develop,test,debug,and tune your Oracle7 and Oracle8 PL/SQL applications,with an emphasis on critical server-side techniques. Beginning with an overview of PL/SQL and general programming constructs,you'll receive valuable guidance so you can: 

Minimize the time spent learning PL/SQLget clear,concise examinations of the essential features that all Oracle developers,programmers,and DBAs must knowUnderstand how PL/SQL 8. 0 interacts with the new object relational database,Oracle8Become fluent in new,advanced PL/SQL 8. 0 features,such as large objects and abstract data typesFind solutions to your common business problems using real-world examples of PLSQL at workLearn how to expertly test and debug your PL/SQL code suing a variety of methods and tools,including Platinum's SQL-StationFind out how to use PL/SQL with third-party tools,and in such diverse environments as Oracle Developer/2000 and the Oracle Application Web ServerDiscover rich resources on the CD-ROM,including ready-to-use code from the book,and demo versions of Platinum's SQL-Station and Oracle's Web Server


Take your applications from specifications from specification to brilliantly workingcode in no time with Oracle8 PL/SQL Programming.
Epstein-Barr virus-encoded protein found in plasma membranes of transformed cells (1985)

We have developed monoclonal antibodies to a 63,000-molecular-weight protein (p63) which is the product of the most abundant messenger RNA in Epstein-Barr virus-transformed cells and shown that the protein is associated specifically with plasma membranes. It was also found to be associated with the other membrane fractions and was found in all Epstein-Barr virus-transformed cells tested. In addition, p63 was present in virions, resulting in transient, early appearance in newly infected cells. Newly synthesized p63 was detected at the time cells underwent blast transformation (48 to 72 h postinfection). The possible role of this protein in transformation and as a target for cell-mediated cytotoxicity is discussed.
<title>Electron Beam Testing And Its Application To Packaging Modules For Very Large Scale Integrated (VLSI) Chip Arrays</title> (1982)

Electron Beam techniques, which have been applied for VLSI testing, are also useful for contactless testing of packaging modules. A test system has been developed to detect electrical opens and shorts in multilayer network wiring using specimens of 100 x 100 x 6mm in size. Various physical effects including charging, discharging, secondary electron emission and others allow a complete test to be performed. The contrast mechanism of the detected signal is based on the secondary electron yield vs. the beam potential and will be discussed in detail. Other signal mechanisms were also applied. By coordinating a pulsed electron beam in a vector mode to predetermined network terminals, computer controlled experiments were carried out. Results on the present status of this new testing approach will be presented.
Multifunctional Vitrimer-Like Polydimethylsiloxane (PDMS): Recyclable, Self-Healable, and Water-Driven Malleable Covalent Networks Based on Dynamic Imine Bond (2019)

Vitrimer is a new class of polymeric materials which can be reprocessed to any shape while being permanently cross-linked. We designed and synthesized a catalyst-free network with poly(dimethylsiloxane)etherimide (PDMS-NH2), terephthalaldehyde (TA), and tri(2-aminoethyl)amine (TREA) through the condensation reaction between amino groups and aldehyde groups. As a result of the exchange reaction of the dynamic imine bond obtained, this PDMS network exhibits the nature of vitrimer-like material, which is examined by solubility and stress-relaxation experiments, and the relaxation time is as short as 64 s at 130 °C. In addition, the vitrimer-like PDMS is malleable and capable of self-healing, and the mechanical properties can be maintained even after three consecutive breaking/mold pressing cycles. Especially, besides heating, this vitrimer-like PDMS can also be recycled and reshaped at ambient temperature due to the exchange reaction of dynamic imine bond when immersed in water, which will potentially lead to green processing of the elastomers.