gebhart/patrepeval huggingface dataset:
Characterization of the rcsA and rcsB genes from Salmonella typhi: rcsB through tviA is involved in regulation of Vi antigen synthesis (1996)

Synthesis of Vi antigen, a capsular polysaccharide expressed by Salmonella typhi, is controlled by the viaA and viaB chromosomal loci. It was previously shown that Vi antigen expression was regulated by a system similar to the rcs regulatory system involved in colanic acid synthesis in Escherichia coli. We have cloned the rcsA, rcsB, and rcsC genes from S. typhi. The predicted amino sequences of the RcsA and RcsB proteins showed a high degree of similarity to their E. coli homologs. The nucleotide sequence of the rcsC gene was partially determined and was shown to be homologous to that of its E. coli counterpart. Complementation experiments indicated that rcsB and rcsC were encompassed within the viaA locus. The RcsA protein was not involved in Vi antigen synthesis. In contrast, the RcsB protein acted as a positive regulator of Vi polysaccharide expression. By mRNA and gene fusion analyses, we studied the role of RcsB and TviA, a via-B-encoded regulatory protein characterized previously, in regulating Vi antigen synthesis. The transcriptional start point of tviA mRNA was not influenced by RcsB or TviA. In the absence of RcsB or TviA protein, transcription of tviA gave rise to only a monocistronic tviA-specific mRNA. The presence of RcsB and TriA not only increased the amount of monocistronic tviA-specific mRNA but also resulted in countranscription of tviA and tviB, which is located immediately downstream of tviA on the viaB locus. In addition, TviA protein did not appear to be subject to degradation by the Lon protease. These results strongly suggest that TviA might act in concert with RcsB at the tviA promoter to activate transcription of the genes involved in Vi polymer synthesis in S. typhi in a Lon-independent manner.
Computer-Aided Drug Design (1987)

Progress in genetic engineering has increased the need for, while advances in computational hardware have removed barriers impeding, the development of appropriate computational tools to assist in the understanding of molecular interactions. Advancements both in techniques and in broadening application have been clearly demonstrated. Further development requires progress in the fundamental aspects of theoretical chemistry as well as an increased base of experience in choosing the appropriate set of assumptions for a particular problem. Computer-aided drug design is a current reality, but one that, at its best, supplements an incomplete methodology with the traditional insight and wisdom of an experienced medicinal chemist. In the next few years progress in developing a sound theoretical foundation will make molecular design a realistic aid to the medicinal chemist and protein engineer.
Temporal anti-aliasing in computer generated animation (1983)

The desirability of incorporating temporal anti-aliasing, or motion blur, into computer generated animation is discussed and two algorithms for achieving this effect are described. The first approximates continuous object movement and determines intervals during which each object covers each pixel. Hidden surface removal is then performed, allowing the calculation of visible object intensity functions and subsequent filtering. The second form of algorithm detailed involves supersampling the moving image and then filtering the resulting intensity function to “multiply-expose” each output picture. The effects of filter types and the relationship of the algorithms to forms of spatial anti-aliasing are discussed.
Mixed culture of pericytes and endothelial cells from fetal microvessels of the human placenta. (1995)

To explore the role of perivascular cells in angiogenesis and vasomotricity, placental cultures of perivascular cells were performed from calibrated villi excised from term placentas. Microvessels were isolated using repeated digestion of villi by collagenase-dispase and purification by Percoll gradients. Plated on Petri dishes, the microvessels became adherent to the gelatin matrix permitting to cells to proliferate. Cells were harvested and subcultured. Endothelial and pericyte cell lines were identified by phase contrast microscopy. Pericyte number predominated rapidly, the endothelial cells remaining visible. After seven days, cells started to cluster, thus piled up and built numerous nodules. Medium-size oval endothelial cells were stained by anti-von Willebrand factor and anti-IgG coupled to fluorescein. Large cells with irregular border reacted to smooth muscle anti-alpha-actin and anti-IgG coupled to fluorescein. There was no cross-reaction of these two cell types with the antibodies. In contrast, nodules were stained by both immunostainings. Endothelial cells reacting to von Willebrand factor antibody were frequently associated to the nodule. The isolation of microvessels from the human placenta described in this study allowed the establishment of cultures of endothelial cells and pericytes that show: i) rapid predominance of pericytes over endothelial cells, ii) formation of nodules, iii) participation of endothelial cells and pericytes to nodules formation.
‘The glue that binds…’: articulating values in multidisciplinary public health (2004)

Public health in the UK has undergone major changes since 1997. One of the main debates has focused on the function and delivery of the broad task of health improvement. This is no longer the province of doctors alone but of a new cadre of professionals now termed the multidisciplinary workforce. Establishing the coherence and cohesion of the professionals and practitioners from different backgrounds and disciplines who are expected to carry out these tasks has been the concern of policy makers and professional bodies. The route to achieve this has been through the delineation and specification of public health functions and the regulation of its training and career structures. Little, if any, attention has been given to understanding the role of values and the part played by an explicitly articulated shared purpose in building a unified and harmonized workforce. The material for this paper draws from an exploratory project undertaken by London South Bank University, the King's Fund and the Office for Public Management and presented as a case study at the UKPHA conference in Cardiff 2003.
Diffusion of Nitric Oxide into Low Density Lipoprotein (2002)

A key early event in the development of atherosclerosis is the oxidation of low density lipoprotein (LDL) via different mechanisms including free radical reactions with both protein and lipid components. Nitric oxide (( small middle dot)NO) is capable of inhibiting LDL oxidation by scavenging radical species involved in oxidative chain propagation reactions. Herein, the diffusion of ( small middle dot)NO into LDL is studied by fluorescence quenching of pyrene derivatives. Selected probes 1-(pyrenyl)methyltrimethylammonium (PMTMA) and 1-(pyrenyl)-methyl-3-(9-octadecenoyloxy)-22,23-bisnor-5-cholenate (PMChO) were chosen so that they could be incorporated at different depths of the LDL particle. Indeed, PMTMA and PMChO were located in the surface and core of LDL, respectively, as indicated by changes in fluorescence spectra, fluorescence quenching studies with water-soluble quenchers and the lifetime values (tau(o)) of the excited probes. The apparent second order rate quenching constants of ( small middle dot)NO (k(NO)) for both probes were 2.6-3.8 x 10(10) m(-1) s(-1) and 1.2 x 10(10) m(-1) s(-1) in solution and native LDL, respectively, indicating that there is no significant barrier to the diffusion of ( small middle dot)NO to the surface and core of LDL. Nitric oxide was also capable of diffusing through oxidized LDL. Considering the preferential partitioning of ( small middle dot)NO in apolar milieu (6-8 for n-octanol:water) and therefore a larger ( small middle dot)NO concentration in LDL with respect to the aqueous phase, a corrected k(NO) value of approximately 0.2 x 10(10) m(-1) s(-1) can be determined, which still is sufficiently large and consistent with a facile diffusion of ( small middle dot)NO through LDL. Applying the Einstein-Smoluchowsky treatment, the apparent diffusion coefficient (D(')NO) of ( small middle dot)NO in native LDL is on average 2 x 10(-5) cm(2) s(-1), six times larger than that previously reported for erythrocyte plasma membrane. Thus, our observations support that ( small middle dot)NO readily traverses the LDL surface accessing the hydrophobic lipid core of the particle and affirm a role for ( small middle dot)NO as a major lipophilic antioxidant in LDL.
Reconstructing the pupil function of microscope objectives from the intensity PSF (2002)

The quality of high performance microscope objectives is usually verified by interferometric measurement of the wave front. However, a non-interferometric method might be preferable, when appropriate light sources of sufficient coherence length or an interferometric setup are difficult to realize. Under these circumstances, the complex pupil function of an optical system can also be determined from its intensity point spread function (PSF), i.e. from the image of a sub-resolution point object. We present a system that can determine the pupil function of high-NA microscope objectives from defocused images of an artificial point source. An extended version of the "Misell" algorithm is used, which utilizes 4 or more PSF images to overcome the Fourier phase ambiguity and which generally converges rapidly to the correct pupil function both in phase and amplitude. The algorithm can also compensate small errors in the x-, y- and z-positions of the images, which might be caused by vibrations, thermal drift or the limited accuracy of the z-drive.
Forkhead Box M1 Is Essential for Nuclear Localization of Glioma-associated Oncogene Homolog 1 in Glioblastoma Multiforme Cells by Promoting Importin-7 Expression (2015)

The transcription factors glioma-associated oncogene homolog 1 (GLI1), a primary marker of Hedgehog pathway activation, and Forkhead box M1 (FOXM1) are aberrantly activated in a wide range of malignancies, including glioma. However, the mechanism of nuclear localization of GLI1 and whether FOXM1 regulates the Hedgehog signaling pathway are poorly understood. Here we found that FOXM1 promotes nuclear import of GLI1 in glioblastoma multiforme cells and thus increases the expression of its target genes. Conversely, knockdown of FOXM1 expression with FOXM1 siRNA abrogated its nuclear import and inhibited the expression of its target genes. Also, genetic deletion of FOXM1 in mouse embryonic fibroblasts abolished nuclear localization of GLI1. We observed that FOXM1 directly binds to the importin-7 (IPO7) promoter and increases its promoter activity. IPO7 interacted with GLI1, leading to enhanced nuclear import of GLI1. Depletion of IPO7 by IPO7 siRNA reduced nuclear accumulation of GLI1. In addition, FOXM1 induced nuclear import of GLI1 by promoting IPO7 expression. Moreover, the FOXM1/IPO7/GLI1 axis promoted cell proliferation, migration, and invasion in vitro. Finally, expression of FOXM1 was markedly correlated with that of GLI1 in human glioblastoma specimens. These data suggest that FOXM1 and GLI1 form a positive feedback loop that contributes to glioblastoma development. Furthermore, our study revealed a mechanism that controls nuclear import of GLI1 in glioblastoma multiforme cells.
Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway (2006)

Three genes up-regulated after addition of EGF (serine (or cysteine) proteinase inhibitor, clade H, member 1 (Serpinh1), solute carrier family 2 (facilitated glucose transporter), member 10 (Slc2a10) and secreted acidic cysteine-rich glycoprotein (Sparc)) were selected for further analysis and characterization. Of the three genes, Serpinh1 and Slc2a10 have never been implicated in the hearing process.
Relationship Between Group B Streptococcal Serotypes and Cell Surface Hydrophobicity (1992)

Cell surface hydrophobicities of streptococci of serological group B were determined by the adherence of the bacteria to hexadecane droplets. A significant adherence to hexadecane was observed with the group B streptococcal type reference strains Ib, V, Ic, R and X, but not with those of serotype Ia, II, III and IV. Cultivation of the bacteria in microcapsule-inducing media reduced the hexadecane adherence properties. The adherence to hexadecane was not related to fibrinogen binding properties of the cultures. Screening a large number of group B streptococci isolated from humans and bovines revealed that those with polysaccharide type antigen alone were generally hydrophilic, those with protein antigen alone or with protein antigen in combination with polysaccharide antigen were mostly hydrophobic. Cultivation of the bacteria under microaerobic conditions or after a single mouse passage enhanced microcapsule production and correspondingly reduced the hexadecane adherence values. Treatment of the bacteria by guanidinium chloride or by neuraminidase enhanced the hexadecane adherence. The hydrophobic component on group B streptococcal surface appeared to be partly inactivated by heat or proteolytic treatment of the bacteria.
Activation of the Androgen Receptor N-terminal Domain by Interleukin-6 via MAPK and STAT3 Signal Transduction Pathways (2002)

The androgen receptor (AR) is a ligand-activated transcription factor that mediates the biological responses of androgens. However, non-androgenic pathways have also been shown to activate the AR. The mechanism of cross-talk between the interleukin-6 (IL-6) and AR signal transduction pathways was investigated in LNCaP human prostate cancer cells. IL-6 induced several androgen-response element-driven reporters that are dependent upon the AR, increased the phosphorylation of mitogen-activated protein kinase (MAPK), and activated the AR N-terminal domain (NTD). Inhibitors to MAPK and JAK decreased the IL-6-induced phosphorylation of MAPK and activation of the AR NTD. Immunoprecipitation and transactivation studies showed a direct interaction between amino acids 234-558 of the AR NTD and STAT3 following IL-6 treatment of LNCaP cells. These results demonstrate that activation of the human AR NTD by IL-6 was mediated through MAPK and STAT3 signal transduction pathways in LNCaP prostate cancer cells.
Rate Enhancement in Dilute Salt Solutions of Aqueous Ethanol: The Diels-Alder Reaction (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRate Enhancement in Dilute Salt Solutions of Aqueous Ethanol: The Diels-Alder ReactionChaitanya K. Pai and Michael B. SmithCite this: J. Org. Chem. 1995, 60, 12, 3731–3735Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://pubs.acs.org/doi/10.1021/jo00117a026https://doi.org/10.1021/jo00117a026research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations18LEARN 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
Fibroblast response to microtextured silicone surfaces: Texture orientation into or out of the surface (1994)

Previous studies suggested that surface topographic configurations of 1-3 microns influence cellular behavior and tissue response. They did not address which specific aspect of the configurations elicits the cellular response. We therefore investigated the effect of the orientation of several surface configurations. Seven different textures on polydimethyl siloxane (silicone; Dow Corning Silastic) specimens were used to test the question of whether orientation into (down) or out of the surface (up) affected cellular response to a material. The textures were smooth and photoetched configurations of 2 microns up, 2 microns down, 5 microns up, 5 microns down, 10 microns up, and 10 microns down. The response of cultured fibroblasts on these surfaces was compared with that of a standard tissue culture material, polyethylene terepthalate (Thermanox). The cell density was measured over a 12-day period with the use of a colorimetric assay. The uptake of methylene blue was measured daily and compared as an absorbance in a destaining agent. Cells on the 2 and 5 microns up arrays showed increased rates of proliferation and cell density as compared with their down counterparts. This would indicate that textures of 2 and 5 microns have a significant influence on cell growth, and that the surface with hills has a greater effect than the surface with wells. In contrast, the 10 microns up and 10 microns down arrays did not prove to be statistically different from smooth ones. This indicates that the orientation effect is related to the configuration size and that this configuration size is not viewed differently from smooth silicone by the cells. The presented data are in agreement with results of this laboratory and others that fibroblasts recognize the dimensions of surface configurations and react accordingly. Specifically, they appear to react to the uppermost surface area presented to them, but conclusive data can only be obtained from a study of the focal adhesions.
Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing (2009)

The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. "Candidatus Liberibacter asiaticus" was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of "Candidatus Liberibacter asiaticus" in symptomatic leaves. These data implicate "Candidatus Liberibacter asiaticus" as the pathogen responsible for HLB disease.
ReducedN-Alkyl Substituted Bis(imino)pyridine Cobalt Complexes: Molecular and Electronic Structures for Compounds Varying by Three Oxidation States (2010)

The stepwise 1-3 electron reduction of the N-alkyl substituted bis(imino)pyridine cobalt dichloride complexes, ((R)APDI)CoCl(2), was studied where (R)APDI = 2,6-(RN=CMe)(2)C(5)H(3)N, R = C(6)H(11) (Cy), CHMe(2) ((i)Pr). One electron reduction with either zinc metal or NaBEt(3)H furnished the bis(imino)pyridine cobalt monochloride compounds, ((R)APDI)CoCl. X-ray diffraction on the ((iPr)APDI)CoCl derivative established a distortion from square planar geometry where the chloride ligand is lifted out of the idealized cobalt-chelate plane. Superconducting Quantum Interference Device (SQUID) magnetometry on both compounds established spin crossover behavior with an S = 1 state being predominant at room temperature. Computational studies, in combination with experimental results, establish that the triplet spin isomer arises from a high spin Co(II) center (S(Co) = 3/2) antiferromagnetically coupled to a bis(imino)pyridine chelate radical anion, [PDI](-) (S(PDI) = 1/2). At lower temperatures, the Co(II) ion undergoes a spin transition to the low spin form (S(Co) = 1/2) and antiferromagnetic coupling gives rise to the observed diamagnetic ground state. Replacing the chloride ligand with a methyl group, namely ((R)APDI)CoCH(3), also yielded distorted compounds, albeit less pronounced, that are diamagnetic at room temperature. Two electron reduction of the ((R)APDI)CoCl(2) derivatives with excess 0.5% sodium amalgam or 2 equiv of NaBEt(3)H furnished the bis(chelate)cobalt complexes, ((R)APDI)(2)Co, while three electron reduction with 3 equiv of sodium naphthalenide yielded the cobalt dinitrogen anions, [Na(solv)(3)][((R)APDI)CoN(2)] (solv = THF, Et(2)O). Both bis(chelate) compounds were crystallographically characterized and determined to have S = 3/2 ground states by SQUID magnetometry and electron paramagnetic resonance (EPR) spectroscopy. Computational studies, in combination with metrical parameters determined from X-ray diffraction, establish a high spin (S(Co) = 3/2) cobalt(II) center with two bis(imino)pyridine chelate radical anions. Antiferromagnetic coupling between the two chelate centered radicals is mediated by a doubly occupied t(2g) cobalt orbital and gives rise to the observed overall quartet ground state.
Pediatric Traumatic Brain Injury : Present and Future Considerations in Management(<SPECIAL ISSUE>Traumatic Brain Injury: Recent Advances) (2010)

Traumatic brain injury is the leading cause of death and disability in children. Published evidence-based guidelines for the management of acute pediatric traumatic brain injury provide a guide to patient care using a multidisciplinary team approach by clinicians and researchers through an easily incorporated algorithm. While review of these guidelines highlights the considerable lack of data from well-designed, controlled studies resulting in few treatment standards, they do provide a starting point in our understanding and many opportunities for increasing the fund of knowledge in the area. Since the pediatric guidelines also included "key areas for future investigation" in each chapter, there exist already a potential roadmap for questions to be answered for future management.
Generation of interpretive and compiled instruction set simulators (1999)

Due to the large variety of different embedded processor types, retargetable software development tools, such as compilers and simulators, have received attention recently. Retargetability allows one to handle different target processors with a single tool. In this paper, we present a system for automatic generation of instruction set simulators for a class of embedded processors. Retargetability is achieved by automatic generation of simulators from processor descriptions, given as behavioral or RT-level HDL models. The presented system is capable of bit-true simulation for arbitrary processor word lengths, and it generates both interpretive or compiled simulators. Experimental results for different processors indicate comparatively high simulation speed.