gebhart/patrepeval huggingface dataset:
The control region of the pdu/cob regulon in Salmonella typhimurium (1994)

The pdu operon encodes proteins for the catabolism of 1,2-propanediol; the nearby cob operon encodes enzymes for the biosynthesis of adenosyl-cobalamin (vitamin B12), a cofactor required for the use of propanediol. These operons are transcribed divergently from distinct promoters separated by several kilobases. The regulation of the two operons is tightly integrated in that both require the positive activator protein PocR and both are subject to global control by the Crp and ArcA proteins. We have determined the DNA nucleotide sequences of the promoter-proximal portion of the pdu operon and the region between the pdu and cob operons. Four open reading frames have been identified, pduB, pduA, pduF, and pocR. The pduA and pduB genes are the first two genes of the pdu operon (transcribed clockwise). The pduA gene encodes a hydrophobic protein with 56% amino acid identity to a 10.9-kDa protein which serves as a component of the carboxysomes of several photosynthetic bacteria. The pduF gene encodes a hydrophobic protein with a strong similarity to the GlpF protein of Escherichia coli, which facilitates the diffusion of glycerol. The N-terminal end of the PduF protein includes a motif for a membrane lipoprotein-lipid attachment site as well as a motif characteristic of the MIP (major intrinsic protein) family of transmembrane channel proteins. We presume that the PduF protein facilitates the diffusion of propanediol. The pocR gene encodes the positive regulatory protein of the cob and pdu operons and shares the helix-turn-helix DNA binding motif of the AraC family of regulatory proteins. The mutations cobR4 and cobR58 cause constitutive, pocR-independent expression of the cob operon under both aerobic and anaerobic conditions. Evidence that each mutation is a deletion creating a new promoter near the normal promoter site of the cob operon is presented.
Perceptual grouping (2013)

Modifying a digital sketch may require multiple selections before a particular editing tool can be applied. Especially on large interactive surfaces, such interactions can be fatiguing. Accordingly, we propose a method, called Suggero, to facilitate the selection process of digital ink. Suggero identifies groups of perceptually related drawing objects. These "perceptual groups" are used to suggest possible extensions in response to a person's initial selection. Two studies were conducted. First, a background study investigated participant's expectations of such a selection assistance tool. Then, an empirical study compared the effectiveness of Suggero with an existing manual technique. The results revealed that Suggero required fewer pen interactions and less pen movement, suggesting that Suggero minimizes fatigue during digital sketching.
Measures of Response: RECIST, WHO, and New Alternatives (2006)

RECIST (Response Evaluation Criteria in Solid Tumors) is a widely employed method introduced in 2000 to assess change in tumor size in response to therapy. The simplicity of the technique, however, contrasts sharply with the increasing sophistication of imaging instrumentation. Anatomically based imaging measurement, although supportive of drug development and key to some accelerated drug approvals, is being pressed to improve its methodologic robustness, particularly in the light of more functionally-based imaging that is sensitive to tissue molecular response such as fluorodeoxyglucose positron emission tomography. Nevertheless ready availability of computed tomography and magnetic resonance imaging machines largely assures anatomically based imaging a continuing role in clinical trials for the foreseeable future. Recent advances in image processing enabled by the computational power of modern clinical scanners open a considerable opportunity to characterize tumor response to therapy as a complement to image acquisition. Various alternative quantitative volumetric approaches have been proposed but have yet to gain wide acceptance by clinical and regulatory communities, nor have these more complex techniques shown incontrovertible evidence of greater reproducibility or predictive value of clinical events and outcome. Unless plans are created for clinical trials that incorporate the design needed to prove the added value and unique clinical utility of these novel approaches, any theoretical benefit of these more elaborate methods could remain unfulfilled.
Intravenous Erythropoietin (rHuEPO) Administration Increases Plasma Endothelin and Blood Pressure in Hemodialysis Patients (1993)

The correction of anemia in end stage renal disease with recombinant human erythropoietin (rHuEPO) is associated with hypertension in about a third of hemodialysis patients. In the present study, we investigated the role of endothelin (ET-1) on rHuEPO associated hypertension and the effect of the rHuEPO administration route on plasma ET-1 levels. We studied 50 stable chronic hemodialysis patients who were divided into three groups: 26 patients received rHuEPO intravenously (IV) and 21 subcutaneously (SC). The control group was nine patients who were treated with nandrolone decanoate (ND). Prehemodialysis ET-1 plasma levels were correlated with mean arterial pressure (MAP), hematocrit (Hct), time on dialysis, and rHuEPO doses. The antihypertensive therapeutic index (ATI) was used to determine the changes in blood pressure medication intake. We observed that the ET-1 levels were significantly higher in the IV group (19.3 +/- 2) than the SC (5.0 +/- 0.6) or ND groups (3.6 +/- 0.4 pg/mL) (P < 0.001, IV v SC or ND). After IV rHuEPO treatment, there were increases in both MAP (pre- v post-rHuEPO, P < .001) and in ATI (pre- v post-rHuEPO, P < .001). In the SC group, the increases in MAP and ATI were not significant. Only the IV group showed a significant correlation between MAP and ET-1 levels (r = .05, P = .02). To accomplish the same Hct, the IV group received higher rHuEPO doses than those of the SC (180 +/- 15 v 87 +/- 12 U/kg/week) (P < .001). No significant correlations were found between the plasma ET-1 levels and Hct, time on dialysis and rHuEPO doses.(ABSTRACT TRUNCATED AT 250 WORDS)
Bridging XML-schema and relational databases (2001)

Many organizations and enterprises establish distributed working environments, where different users need to exchange information based on a common model. XML is widely used to facilitate this information exchange. The extensibility of XML allows the creation of generic models that integrate data from different sources. For these tasks, several applications are used to import and export information in XML format from the data repositories. In order to support this process for relational repositories we developed the X-Database system. The base of this system is an XML-Schema file that describes the logical model of interchanged information. Initially, the system analyses the syntax of the XML-Schema file and generates the relational database. Then it handles the decomposition of valid XML files according to that Schema and the composition of XML documents from the information in the database. Finally the system offers a flexible mechanism for modifying and querying database contents using only valid XML documents, which are validated over the XML-Schema file's rules.
Evolution of trans-splicing plant mitochondrial introns in pre-Permian times (1997)

Trans-splicing in angiosperm plant mitochondria connects exons from independent RNA molecules by means of group II intron fragments. Homologues of trans-splicing introns in the angiosperm mitochondrial nad2 and nad5 genes are now identified as uninterrupted group II introns in the ferns Asplenium nidus and Marsilea drummondii. These fern introns are correctly spliced from the pre-mRNA at the sites predicted from their well-conserved secondary structures. The flanking exon sequences of the nad2 and nad5 genes in the ferns require RNA editing, including the removal of in-frame stop codons by U-to-C changes for correct expression of the genetic information. We conclude that cis-splicing introns like the ones now identified in ferns are the ancestors of trans-splicing introns in angiosperm mitochondria. Intron disruption is apparently due to a size increase of the structurally variable group II intron domain IV followed by DNA recombination in the plant mitochondrial genome.
Analysis of a Mathematical Model for Tumor Anti-Angiogenesis (2006)

Anti-angiogenic therapy is a novel treatment approach for cancer that aims at preventing a tumor from developing its own blood supply system that it needs for growth. In this paper we consider a mathematical model where the stimulation term in the dynamics is proportional to the number of endothelial cells. This model is an example from a class of mathematical models for anti-angiogenic treatment that were developed and medically validated by Hahnfeldt, Panigrahy, Folkman and Hlatky [8]. The problem how to schedule a given amount of angiogenic inhibitors to achieve a maximum reduction in the primary cancer volume is considered as an optimal control problem and it is shown that optimal controls are bang-bang of the type 0a0 with 0 denoting a trajectory corresponding to no treatment and a a trajectory with treatment at maximum dose along which all inhibitors are being exhausted.
The Mechanism of Dye Formation in Color Photography. VII. Intermediate Bases in the Deamination of Quinonediimines1 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Mechanism of Dye Formation in Color Photography. VII. Intermediate Bases in the Deamination of Quinonediimines1L. K. J. Tong, M. Carolyn Glesmann, and R. L. BentCite this: J. Am. Chem. Soc. 1960, 82, 8, 1988–1996Publication Date (Print):April 1, 1960Publication History Published online1 May 2002Published inissue 1 April 1960https://pubs.acs.org/doi/10.1021/ja01493a036https://doi.org/10.1021/ja01493a036research-articleACS PublicationsRequest reuse permissionsArticle Views289Altmetric-Citations25LEARN 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
17β-Estradiol Vaginal Tablet Versus Conjugated Equine Estrogen Vaginal Cream to Relieve Menopausal Atrophic Vaginitis (2000)

Treatment regimens with 25-microg 17beta-estradiol vaginal tablets and with 1.25-mg conjugated equine estrogen vaginal cream were equivalent in relieving symptoms of atrophic vaginitis. The vaginal tablets demonstrated a localized effect without appreciable systemic estradiol increases or estrogenic side effects. Vaginal tablet therapy resulted in greater patient acceptance and lower withdrawal rates compared with vaginal cream therapy.
Cloning, expression, and immunological characterization of recombinant Lolium perenne allergen Lol p II. (1993)

The molecular cloning of the cDNA encoding for an isoallergenic form of Lol p II, a major rye grass (Lolium perenne) pollen allergen, was performed by polymerase chain reaction amplification on mRNA extracted from pollen. The amino acid sequence derived from the cDNA was truncated by 4 and 5 residues at the NH2- and COOH-terminal ends, respectively, and differed only in one position from that previously reported. This cDNA was expressed in Escherichia coli by fusion to the carboxyl terminus of the human ferritin H-chain. The molecule was produced in high yields as a soluble protein and was easily purified. The protein retains the multimeric quaternary structure of ferritin, and it exposes on the surface the allergenic moiety, which can be recognized in Western blotting and in enzyme-linked immunosorbent assay experiments by specific IgE from allergic patients. The recombinant allergen was used to analyze the sera of 26 patients allergic to L. perenne compared with control sera. The results were in good agreement with the values obtained with the radioallergosorbent test assay. In addition, histamine release experiments in whole blood from an allergic patient and skin prick tests showed that the recombinant allergen retains some of the biological properties of the natural compound. These findings indicate that the availability of homogeneous recombinant allergens may be useful for the development of more specific diagnostic and therapeutic procedures. Moreover, this expression system may be of more general interest for producing large amounts of soluble protein domains in E. coli.
Development of the MPEG-H TV Audio System for ATSC 3.0 (2017)

A new TV audio system based on the MPEG-H 3D audio standard has been designed, tested, and implemented for ATSC 3.0 broadcasting. The system offers immersive sound to increase the realism and immersion of programming, and offers audio objects that enable interactivity or personalization by viewers. Immersive sound may be broadcast using loudspeaker channel-based signals or scene-based components in combination with static or dynamic audio objects. Interactivity can be enabled through broadcaster-authored preset mixes or through user control of object gains and positions. Improved loudness and dynamic range control allows tailoring the sound for best reproduction on a variety of consumer devices and listening environments. The system includes features to allow operation in HD-SDI broadcast plants, storage, and editing of complex audio programs on existing video editor software or digital audio workstations, frame-accurate switching of programs, and new technologies to adapt current mixing consoles for live broadcast production of immersive and interactive sound. Field tests at live broadcast events were conducted during system design and a live demonstration test bed was constructed to prove the viability of the system design. The system also includes receiver-side components to enable interactivity, binaural rendering for headphone, or tablet computer listening, a “3D soundbar” for immersive playback without overhead speakers, and transport over HDMI 1.4 connections in consumer equipment. The system has been selected as a proposed standard of ATSC 3.0 and is the sole audio system of the UHD ATSC 3.0 broadcasting service currently being deployed in South Korea.
The Nuclear Matrix from Cells of Different Origin (1990)

We compared the protein composition of the nuclear matrix isolated from several murine embryonal carci- noma cells and mature tissues by two-dimensional gel electrophoresis. Two nuclear matrix fractions were investigated: the “peripheral” nuclear matrix (matrix proteins that remain insoluble after reduction), and the “internal” nuclear matrix (matrix proteins released by reduction). The two subfractions have completely dif- ferent protein compositions. Although numerous dif- ferences in nuclear matrix protein composition among different cell types were observed, a limited set of polypeptides common to all mouse cell types was iden- tified. A majority of these common proteins was also present in cells from other mammalian species (i.e. rat and human). For this set of proteins, we coin the term “minimal matrix.” As expected, lamin B, known to be expressed throughout differentiation, is part of the common set of peripheral nuclear matrix proteins. Lamins A and C are not because these proteins were absent from undif- ferentiated embryonal carcinoma cells. Since these common nuclear matrix proteins occur in all mamma- lian nuclear matrices analyzed so far, it is likely that they have a basic role in nuclear organization and function. Recently, several authors have expanded on the idea that a proteinaceous network in the nucleus (the nuclear matrix) is involved in control and coordination of gene expression during differentiation (Blobel, 1985; Razin, 1987; Bodnar, 1988). It is thought that loops of chromatin are persistently as well as transiently attached to this network (Pienta and Coffey, 1984; Mirkovitch et al., 1984; Gassar and Laemmli (1987); Earn- shaw, 1988). It has been proposed that each chromatin loop constitutes an independent regulatory unit containing several genes. Processes such as DNA replication (Jackson et
Antithrombogenic Modification of Small-Diameter Microfibrous Vascular Grafts (2010)

Microfibrous vascular grafts with antithrombogenic microfibers can be used as small-diameter grafts, with excellent patency and remodeling capability.
Efficient Generation of Myostatin Knock-Out Sheep Using CRISPR/Cas9 Technology and Microinjection into Zygotes (2015)

While CRISPR/Cas9 technology has proven to be a valuable system to generate gene-targeted modified animals in several species, this tool has been scarcely reported in farm animals. Myostatin is encoded by MSTN gene involved in the inhibition of muscle differentiation and growth. We determined the efficiency of the CRISPR/Cas9 system to edit MSTN in sheep and generate knock-out (KO) animals with the aim to promote muscle development and body growth. We generated CRISPR/Cas9 mRNAs specific for ovine MSTN and microinjected them into the cytoplasm of ovine zygotes. When embryo development of CRISPR/Cas9 microinjected zygotes (n = 216) was compared with buffer injected embryos (n = 183) and non microinjected embryos (n = 173), cleavage rate was lower for both microinjected groups (P<0.05) and neither was affected by CRISPR/Cas9 content in the injected medium. Embryo development to blastocyst was not affected by microinjection and was similar among the experimental groups. From 20 embryos analyzed by Sanger sequencing, ten were mutant (heterozygous or mosaic; 50% efficiency). To obtain live MSTN KO lambs, 53 blastocysts produced after zygote CRISPR/Cas9 microinjection were transferred to 29 recipient females resulting in 65.5% (19/29) of pregnant ewes and 41.5% (22/53) of newborns. From 22 born lambs analyzed by T7EI and Sanger sequencing, ten showed indel mutations at MSTN gene. Eight showed mutations in both alleles and five of them were homozygous for indels generating out-of frame mutations that resulted in premature stop codons. Western blot analysis of homozygous KO founders confirmed the absence of myostatin, showing heavier body weight than wild type counterparts. In conclusion, our results demonstrate that CRISPR/Cas9 system was a very efficient tool to generate gene KO sheep. This technology is quick and easy to perform and less expensive than previous techniques, and can be applied to obtain genetically modified animal models of interest for biomedicine and livestock.
Synthesis and characteristics of interpenetrating polymer network hydrogel composed of chitosan and poly(acrylic acid) (1999)

Interpenetrating polymer network (IPN) hydrogels composed of chitosan and poly(acrylic acid) (PAAc) were synthesized by UV irradiation method, and their structure, crystallinity, swelling behavior, thermal property, and mechanical property were investigated. Chitosan/PAAc IPNs exhibited relatively high equilibrium water content and also showed reasonable sensitivity to pH. From the swelling behaviors at various pH's, Fourier transform infrared spectra at high temperature and thermal analysis confirmed the formation of polyelectrolyte complex due to the reaction between amino groups in chitosan and carboxyl groups in PAAc. For this reason, even at a swollen state, the present chitosan/PAAc IPNs possess good mechanical properties. Particularly, the CA-2 sample (with a weight ratio of chitosan/PAAc = 50/50, molar ratio [NH2]/[COOH] = 25/75) showed the lowest equilibrium water content and free water content, attributed to the more compact structure of the polyelectrolyte than CA-1 or CA-3 due to the high amount of interchain bond within the IPN. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 73: 113–120, 1999
Cancer therapy with bispecific antibodies: Clinical experience. (2010)

The binding of at least two molecular targets simultaneously with a single bispecific antibody is an attractive concept. The use of bispecific antibodies as possible therapeutic agents for cancer treatment was proposed in the mid-1980s. The design and production of bispecific antibodies using antibody- and/or receptor-based platform technology has improved significantly with advances in the knowledge of molecular manipulations, protein engineering techniques, and the expression of antigens and receptors on healthy and malignant cells. The common strategy for making bispecific antibodies involves combining the variable domains of the desired mAbs into a single bispecific structure. Many different formats of bispecific antibodies have been generated within the research field of bispecific immunotherapeutics, including the chemical heteroconjugation of two complete molecules or fragments of mAbs, quadromas, F(ab')2, diabodies, tandem diabodies and single-chain antibodies. This review describes key modifications in the development of bispecific antibodies that can improve their efficacy and stability, and provides a clinical perspective on the application of bispecific antibodies for the treatment of solid and liquid tumors, including the promises and research limitations of this approach.
Bovine Brain Microvessel Endothelial Cell Monolayers as a Model System for the Blood‐Brain Barriera (1987)

Investigation of blood-brain barrier permeability and metabolic processes, and their regulation by endogenous or exogenous factors, will be important for development of efficient and selective delivery of therapeutic agents to the central nervous system. Primary cultures of brain microvessel endothelial cells offer a potentially powerful tool for studying at the cellular level the biochemical mechanisms regulating BBB function. Using this in vitro model, our studies are directed at characterization of the BBB processes that might be exploited as new schemes for drug delivery to the central nervous system.
Address mappings (1981)

This memo describes the relationship between address fields used in the Internet Protocol (IP) [1] and several specific
Natural killer cells activated with interleukin 2 in vitro can be adoptively transferred and mediate hematopoietic histocompatibility‐1 antigen‐specific bone marrow rejection in vivo (1990)

An adoptive transfer model was developed for examining natural killer (NK) cell-mediated bone marrow cell (BMC) graft rejection. Homogeneous populations of NK cells were obtained by culturing spleen cells from mice with severe combined immune deficiency in the presence of recombinant interleukin 2 for 7 days. These cells maintained a phenotypic (CD3-CD4-CD8-NK-2.1+ and asialo GM1+) and lytic pattern consistent with that of activated NK cells. The cells were infused into lethally irradiated recipients whose own NK cells were depleted by anti-NK-1.1 antibody treatment and could no longer reject marrow allografts. The transferred NK cells restored the ability of the hosts to reject BMC in a hematopoietic histocompatibility-1 (Hh-1) antigen-specific manner. Immunogenetic studies demonstrated that the rejection was a function of the donor, not host, NK cells. These studies demonstrate that NK cells can be cultured in vitro with recombinant interleukin 2 and are capable of mediating Hh-1-specific BMC rejection in vivo in the absence of other immune cell types.
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is pyruvylated during 3-bromopyruvate mediated cancer cell death. (2009)

GAPDH pyruvylation by 3BrPA affects its enzymatic function and is the primary intracellular target in 3BrPA mediated cancer cell death.