gebhart/patrepeval huggingface dataset:
Capture of Volatile Iodine, a Gaseous Fission Product, by Zeolitic Imidazolate Framework-8 (2011)

Here we present detailed structural evidence of captured molecular iodine (I(2)), a volatile gaseous fission product, within the metal-organic framework ZIF-8 [zeolitic imidazolate framework-8 or Zn(2-methylimidazolate)(2)]. There is worldwide interest in the effective capture and storage of radioiodine, as it is both produced from nuclear fuel reprocessing and also commonly released in nuclear reactor accidents. Insights from multiple complementary experimental and computational probes were combined to locate I(2) molecules crystallographically inside the sodalite cages of ZIF-8 and to understand the capture of I(2) via bonding with the framework. These structural tools included high-resolution synchrotron powder X-ray diffraction, pair distribution function analysis, and molecular modeling simulations. Additional tests indicated that extruded ZIF-8 pellets perform on par with ZIF-8 powder and are industrially suitable for I(2) capture.
Drug discovery in renin–angiotensin system intervention: past and future (2016)

The renin-angiotensin system (RAS) plays a central role in the control of blood pressure in the body and the way this interacts with other systems is widely recognized. This has not always been the case and this review summarizes how our knowledge has evolved from the initial discovery of renin by Tigerstedt and Berman in 1898. This includes the identification of angiotensin in the 1950s to the proposed relationship between this system, hypertension and ultimately cardiovascular disease. While the RAS is far more complex than originally thought, much is now known about this system and the wide ranging effects of angiotensin in the body. This has enabled the development of therapies that target the various proteins in this pathway and hence are implicated in disease. The first of these treatments was the angiotensin converting enzyme inhibitors (ACE-Is), followed by the angiotensin receptor blockers (ARBs), and more recently the direct renin inhibitors (DRIs). Clinical outcome trials have shown these drugs to be effective, but as they act at contrasting points in the RAS, there are differences in their efficacy and safety profiles. RAS blockade is the foundation of modern combination therapy with a calcium channel blocker and/or a diuretic given to reduce blood pressure and limit the impact of RAS activation. Other options that complement these treatments may be available in the future and will offer more choice to clinicians.
On the Well-Posedness of the Rational Covariance Extension Problem (1997)

In this paper, we give a new proof of the solution of the rational covariance extension problem, an interpolation problem with historical roots in potential theory, and with recent application in speech synthesis, spectral estimation, stochastic systems theory, and systems identification. The heart of this problem is to parameterize, in useful systems theoretical terms, all rational, (strictly) positive real functions having a specified window of Laurent coefficients and a bounded degree. In the early 1980’s, Georgiou used degree theory to show, for any fixed “Laurent window”, that to each Schur polynomial there exists, in an intuitive systems-theoretic manner, a solution of the rational covariance extension problem. He also conjectured that this solution would be unique, so that the space of Schur polynomials would parameterize the solution set in a very useful form. In a recent paper, this problem was solved as a corollary to a theorem concerning the global geometry of rational, positive real functions. This corollary also asserts that the solutions are analytic functions of the Schur polynomials. After giving an historical motivation and a survey of the rational covariance extension problem, we give a proof that the rational covariance extension problem is well-posed in the sense of Hadamard, i.e a proof of existence, uniqueness and continuity of solutions with respect to the problem data. While analytic dependence on the problem data is stronger than continuity, this proof is much more streamlined and also applies to a broader class of nonlinear problems. The paper concludes with a discussion of open problems.
Signal estimation from modified short-time Fourier transform (1984)

In this paper, we present an algorithm to estimate a signal from its modified short-time Fourier transform (STFT). This algorithm is computationally simple and is obtained by minimizing the mean squared error between the STFT of the estimated signal and the modified STFT. Using this algorithm, we also develop an iterative algorithm to estimate a signal from its modified STFT magnitude. The iterative algorithm is shown to decrease, in each iteration, the mean squared error between the STFT magnitude of the estimated signal and the modified STFT magnitude. The major computation involved in the iterative algorithm is the discrete Fourier transform (DFT) computation, and the algorithm appears to be real-time implementable with current hardware technology. The algorithm developed in this paper has been applied to the time-scale modification of speech. The resulting system generates very high-quality speech, and appears to be better in performance than any existing method.
Sterically-hindered zinc porphyrins for solar-energy conversion (1987)

Zinc porphyrins (1) and (2), their triplet excited states and their triplet excited states and their cation and anion radicals, are remarkably stable in 1 M nitric acid: the consequences for photosensitised water reduction, oxidation, and the photogalvanic effect, are discussed.
Efficacy of .beta.-Ionone in the Chemoprevention of Rat Mammary Carcinogenesis (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEfficacy of .beta.-Ionone in the Chemoprevention of Rat Mammary CarcinogenesisSuzanne G. Yu, Peter J. Anderson, and Charles E. ElsonCite this: J. Agric. Food Chem. 1995, 43, 8, 2144–2147Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/jf00056a035https://doi.org/10.1021/jf00056a035research-articleACS PublicationsRequest reuse permissionsArticle Views144Altmetric-Citations35LEARN 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
Efficient Gene Targeting by Homologous Recombination in Rat Embryonic Stem Cells (2010)

The rat is the preferred experimental animal in many biological studies. With the recent derivation of authentic rat embryonic stem (ES) cells it is now feasible to apply state-of-the art genetic engineering in this species using homologous recombination. To establish whether rat ES cells are amenable to in vivo recombination, we tested targeted disruption of the hypoxanthine phosphoribosyltransferase (hprt) locus in ES cells derived from both inbred and outbred strains of rats. Targeting vectors that replace exons 7 and 8 of the hprt gene with neomycinR/thymidine kinase selection cassettes were electroporated into male Fisher F344 and Sprague Dawley rat ES cells. Approximately 2% of the G418 resistant colonies also tolerated selection with 6-thioguanine, indicating inactivation of the hprt gene. PCR and Southern blot analysis confirmed correct site-specific targeting of the hprt locus in these clones. Embryoid body and monolayer differentiation of targeted cell lines established that they retained differentiation potential following targeting and selection. This report demonstrates that gene modification via homologous recombination in rat ES cells is efficient, and should facilitate implementation of targeted, genetic manipulation in the rat.
The factor VIII Structure and Mutation Resource Site: HAMSTeRS version 4 (1998)

Since 1996 the HAMSTeRS (Haemophilia A Mutation, Search, Test and Resource Site) WWW site has provided an online resource for access to data on the molecular pathology of haemophilia A, replacing previous text editions of the Haemophilia A Database published in Nucleic Acids Research . This report describes the continued development of the site (version 4), and in particular the expansion of factor VIII (FVIII) structure-related features. Access to the mutation database itself, both for searching the listings and for submission of new mutations, is via custom-designed forms: more powerful Boolean searches of the point mutations in the database are also available. During 1997 a total of 22 novel missense mutations were reported, increasing the total number of unique variants now described to 252 (238 in exonic sequences and 14 at intronic splice junctions). Currently, a total of 586 individual reports with associated phenotypic data are available for searching by any category including phenotype. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequencies from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Our intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. The HAMSTeRS URL is http://europium.mrc.rpms.ac.uk
Characterization of Porins from the Outer Membrane of Salmonella typhimurium 1. Chemical Analysis (1979)

The three species of channel-forming outer membrane proteins, porins, have been purified to homogeneity from mutant strains of Salmonella typhimurium which produce single species of porin. Purification was by stepwise solubilization with dodecylsulfate or guanidine thiocyanate, gel filtration, and preparative gel electrophoresis. Amino acid compositions and tryptic peptide maps of the three species of porins showed close resemblance, but at the same time clear differences among them. The number of amino acid residues in the porins purified from the strains SH5551, SH6377 and SH6017 were 361, 354 and 345, and their calculated molecular weights 39800, 39300 and 38000, respectively. Amino-terminal and carboxyl-terminal amino acids in all three species of porins appeared to be alanine and phenylalanine, respectively. Neither half-cystine nor hexosamine was found in these preparation of porins. The isoelectric points of porins from the strains SH5551, SH6377 and SH6017, determined by isoelectric focusing, showed slight differences from each other. These results, and the genetic experiments from another laboratory, suggest that the three species of porins in Salmonella typhimurium are distinct polypeptides, probably coded for by distinct structural genes, which might have been derived from the same ancestral gene.
Neonatal Oral-Motor Assessment scale: a reliability study. (1993)

Feeding problems are frequently encountered in the neonatal intensive care unit as a result of the survival of greater numbers of preterm, medically fragile, and chronically ill infants. Such feeding problems have not, however, been well described. In an attempt to categorize the oral-motor patterns that underlie poor feeding in the neonatal period, a clinical assessment tool was devised that describes jaw and tongue function during nutritive sucking. The Neonatal Oral-Motor Assessment Scale separates 13 characteristics of jaw movement and 13 characteristics of tongue movement into categories of normal, disorganized, and dysfunctional. This scale was administered to 40 infants to establish interrater reliability, revise the scale as necessary based on the reliability, and attempt to further qualify and describe patterns of disorganized and dysfunctional sucking in the neonatal period.
Expression of mRNA for vascular endothelial growth factor transmembraneous receptors Flt1 and KDR, and the soluble recetor sflt in cycling human endometrium (1999)

The aim of this study was to quantify and localize the mRNA expression of the vascular endothelial growth factor (VEGF) receptors Flt1, KDR and sflt, in human endometrium throughout the menstrual cycle. Since neoangiogenesis is crucial during embryonic implantation, we postulate that endometrial receptivity to VEGF may be altered during the luteal phase in order to support implantation. Human endometrium was collected and specified as early proliferative (n = 3), mid-proliferative (n = 4), late proliferative (n = 3), early secretory (n = 2), mid-secretory (n = 4), and late secretory (n = 4). Competitive reverse transcription-polymerase chain reaction (RT-PCR) was performed to evaluate the mRNA values throughout the menstrual cycle. Additionally, four samples were separated into epithelial and stromal-enriched cell fractions and competitive RT-PCR was carried out to specify the distribution of the mRNA expression. While mRNA for the transmembraneous receptors Flt1 and KDR was shown to be present at almost constant values throughout the menstrual cycle, the soluble receptor, sflt, had a three-fold higher level of transcription during mid-proliferative and late proliferative when compared with early proliferative and the entire secretory phase. The expression of Flt1, KDR and sflt mRNA was detected in both isolated endometrial epithelial and stromal cell fractions. In conclusion, the down-regulation of sflt, which functions as a soluble antagonist, during the luteal phase may act to sensitize the maternal endothelial receptors to angiogenetic stimuli secreted by the implanting embryo.
<title>Raman microscopy of de-novo woven bone tissue</title> (2001)

The composition of the bone tissue initially formed during the early mineralization of calvarial bone is poorly understood. Calvarial de novo mineral deposition occurs rapidly; however, whether the mineral is first deposited as an amorphous calcium phosphate or some other calcium phosphate lattice is unclear. Raman microscopy offers the ability to distinguish differences in the mineral lattice through the positions and shifts in the bands of the bone tissue mineral constituents, particularly in the phosphate v<SUB>1</SUB> stretch vibration (950 - 963 cm<SUP>-1</SUP>). The ratios of the mineral and organic matrix constituents throughout the sampled region can also elucidate the type of bone tissue deposited. The ability to examine intact specimens at high spatial resolution, without interference from water, is an important feature of Raman microscopy. Using postnatal murine calvaria, we show that the earliest mineral detected is a carbonated hydroxyapatite with other phosphate environments present at lower levels as well. We discuss the mineral composition changes with respect to the age of the mouse over the time period of 2 weeks using a sequence of calvarial sections: postnatal days 3, 7 and 14. We use two different data analysis techniques, factor analysis and center of gravity calculations, to elucidate these discrete changes.
Biochemistry and Role of Sialic Acids (1995)

Sialic acids mainly occur as terminal components of cell surface glycoproteins and glycolipids, playing as such a major role in the chemical and biological diversity of glycoconjugates. Cell-type-specific expression of glycosyltransferases, particularly of sialyltransferases (Paulson and Colley, 1989; van den Eijnden and Joziasse, 1993), leads to specific sialylation patterns of oligosaccharides which can be considered as key determinants in the makeup of cells. Striking differences have been found in the sialoglycosylation patterns of cells during development, activation, aging, and oncogenesis. Research on the structures, metabolism, and molecular biology, as well as on the biological and clinical importance of sialic acids as components of these glycoconjugates, has therefore intensified during the past several years.
Protein folding in the endoplasmic reticulum: Lessons from the human chorionic gonadotropin β subunit (1996)

There have been few studies of protein folding in the endoplasmic reticulum of intact mammalian cells. In the one case where the in vivo and in vitro folding pathways of a mammalian secretory protein have been compared, the folding of the human chorionic gonadotropin beta subunit (hCG-beta), the order of formation of the detected folding intermediates is the same. The rate and efficiency with which multidomain proteins such as hCG-beta fold to native structure in intact cells is higher than in vitro, although intracellular rates of folding of the beta subunit can be approached in vitro in the presence of an optimal redox potential and protein disulfide isomerase. Understanding how proteins fold in vivo may provide a new way to diagnose and treat human illnesses that occur due to folding defects.
The translation initiation factor eIF-4B contains an RNA-binding region that is distinct and independent from its ribonucleoprotein consensus sequence. (1994)

eIF-4B is a eukaryotic translation initiation factor that is required for the binding of ribosomes to mRNAs and the stimulation of the helicase activity of eIF-4A. It is an RNA-binding protein that contains a ribonucleoprotein consensus sequence (RNP-CS)/RNA recognition motif (RRM). We examined the effects of deletions and point mutations on the ability of eIF-4B to bind a random RNA, to cooperate with eIF-4A in RNA binding, and to enhance the helicase activity of eIF-4A. We report here that the RNP-CS/RRM alone is not sufficient for eIF-4B binding to RNA and that an RNA-binding region, located between amino acids 367 and 423, is the major contributor to RNA binding. Deletions which remove this region abolish the ability of eIF-4B to cooperate with eIF-4A in RNA binding and the ability to stimulate the helicase activity of eIF-4A. Point mutations in the RNP-CS/RRM had no effect on the ability of eIF-4B to cooperate with eIF-4A in RNA binding but significantly reduced the stimulation of eIF-4A helicase activity. Our results indicate that the carboxy-terminal RNA-binding region of eIF-4B is essential for eIF-4B function and is distinct from the RNP-CS/RRM.
Metastatic colorectal cancer-past, progress and future (2007)

The clinical management of metastatic (stage IV) colorectal cancer (CRC) is a common challenge faced by surgeons and physicians. The last decade has seen exciting developments in the management of CRC, with significant improvements in prognosis for patients diagnosed with stage IV disease. Treatment options have expanded from 5-fluorouracil alone to a range of pharmaceutical and interventional therapies, improving survival, and providing a cure in selected cases. Enhanced understanding of the biologic pathways most important in colorectal carcinogenesis has led to a new generation of drugs showing promise in advanced disease. It is hoped that in the near future the treatment paradigm of metastatic CRC will be analogous to that of a chronic illness, rather than a rapidly terminal condition. This overview discusses the epidemiology of advanced CRC and currently available therapeutic options including medical, surgical, ablative and novel modalities in the management of metastatic colorectal cancer.
Implementation of the substring test by hashing (1971)

In a paper in the November 1970 Communications of the ACM, V.Y. Lum introduced a technique of file indexing named combined indices. This technique permitted decreased retrieval time at the cost of increased storage space. This paper examines combined indices under conditions of file usage with different fractions of retrieval and update. Tradeoff curves are developed to show minimal cost of file usage by grouping various partially combined indices.
Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy (2007)

The intracellular events on the recycling pathway that lead from sorting endosomes to exocytosis at the plasma membrane are central to cellular function. However, despite intensive study, these processes are poorly characterized in spatial and dynamic terms. The primary reason for this is that, to date, it has not been possible to visualize rapidly moving intracellular compartments in three dimensions in cells. Here, we use a recently developed imaging setup in which multiple planes can be simultaneously imaged within the cell in conjunction with visualization of the plasma membrane plane by using total internal reflection fluorescence microscopy. This has allowed us to track and characterize intracellular events on the recycling pathway that lead to exocytosis of the MHC Class I-related receptor, FcRn. We observe both direct delivery of tubular and vesicular transport containers (TCs) from sorting endosomes to exocytic sites at the plasma membrane, and indirect pathways in which TCs that are not in proximity to sorting endosomes undergo exocytosis. TCs can also interact with different sorting endosomes before exocytosis. Our data provide insight into the intracellular events that precede exocytic fusion.