gebhart/patrepeval huggingface dataset:
Mechanism of DNA elongation catalyzed by Escherichia coli DNA polymerase III, dnaZ protein, and DNA elongation factors I and III. (1976)

Elongation of a primed single-stranded DNA template catalyzed by E. coli DNA polymerase III (DNA nucleotidyltransferase, deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7) requires dnaZ protein and two other protein factors, DNA elongation factors I and III. The reaction occurs by the following mechanism: (i) dnaZ protein and DNA elongation factor III together catalyze the transfer of DNA elongation factor I to a primed DNA template. This transfer reaction requires ATP or dATP in addition to dnaZ protein, DNA elongation factors I and III, and primed template; it does not require DNA polymerase III. (ii) DNA polymerase III binds to the complex of DNA elongation factor I with primed template; it does not bind to primed template which is not complexed with DNA elongation factor I. This binding reaction proceeds in the absence of ATP or dATP as cofactor, dnaZ protein, and DNA elongation factor III and without additional DNA elongation factor I. (iii) The complex of DNA polymerase III, DNA elongation factor I, and primed template catalyzes DNA synthesis upon the addition of dNTPs.
Olfactory Reception in Invertebrates (1999)

Recent progress in understanding the principles and mechanisms in olfaction is the result of multidisciplinary research efforts that explored chemosensation by using a variety of model organisms. Studies on invertebrates, notably nematodes, insects, and crustaceans, to which diverse experimental approaches can be applied, have greatly helped elucidate various aspects of olfactory signaling. From the converging results of genetic, molecular, and physiological studies, a common set of chemosensory mechanisms emerges. Recognition and discrimination of odorants as well as chemo-electrical transduction and processing of olfactory signals appear to be mediated by fundamentally similar mechanisms in phylogenetically diverse animals. The common challenge of organisms to decipher the world of odors was apparently met by a phylogenetically conserved strategy. Thus, comparative studies should continue to provide important contributions toward an understanding of the sense of smell.
Quality of experience management in mobile content delivery systems (2010)

This study contributes towards the relatively new but growing discipline of QoE management in content delivery systems. The study focuses on the development of a QoE-based management framework for the construction of QoE models for different types of multimedia contents delivered onto three typical mobile terminals—a mobile phone, PDA and a laptop. A statistical modelling technique is employed which, correlates QoS parameters with estimates of QoE perceptions. These correlations were found to be dependent on terminals and multimedia content types. The application of the framework and prediction models in QoE management strategies are demonstrated using examples. We find that significant resource savings can be achieved with our approach by contrast to conventional QoS solutions.
Staphylococcus aureus Expresses a Major Histocompatibility Complex Class II Analog (1995)

Staphylococcus aureus expresses various surface proteins which specifically recognize and bind to different host molecules. We have previously identified a bacterial protein that exhibits a broad specificity and binds to several mammalian extracellular proteins. The gene encoding this bacterial component has now been cloned and sequenced. The deduced protein consists predominantly of six repeated domains of 110 residues. Each of the repeated domains contain a subdomain of 31 residues that share striking sequence homology with a segment in the peptide binding groove of the beta chain of the major histocompatibility complex (MHC) class II proteins from different mammalian species. The purified recombinant bacterial protein bound several mammalian proteins, including recombinant osteopontin, suggesting a protein-protein interaction and also specifically recognized a 15-amino acid residue synthetic peptide. Taken together, these results suggest that the bacterial protein resembles mammalian MHC class II molecules with respect to both sequence similarities and peptide binding capabilities.
The Peripheral Blood Transcriptome Identifies the Presence and Extent of Disease in Idiopathic Pulmonary Fibrosis (2012)

These results demonstrate that the peripheral blood transcriptome has the potential to distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted D(L)CO, but not FVC.
Porting HTM Models to the Heidelberg Neuromorphic Computing Platform (2015)

Hierarchical Temporal Memory (HTM) is a computational theory of machine intelligence based on a detailed study of the neocortex. The Heidelberg Neuromorphic Computing Platform, developed as part of the Human Brain Project (HBP), is a mixed-signal (analog and digital) large-scale platform for modeling networks of spiking neurons. In this paper we present the first effort in porting HTM networks to this platform. We describe a framework for simulating key HTM operations using spiking network models. We then describe specific spatial pooling and temporal memory implementations, as well as simulations demonstrating that the fundamental properties are maintained. We discuss issues in implementing the full set of plasticity rules using Spike-Timing Dependent Plasticity (STDP), and rough place and route calculations. Although further work is required, our initial studies indicate that it should be possible to run large-scale HTM networks (including plasticity rules) efficiently on the Heidelberg platform. More generally the exercise of porting high level HTM algorithms to biophysical neuron models promises to be a fruitful area of investigation for future studies.
Transcriptional mapping and nucleotide sequence of the Listeria monocytogenes hlyA region reveal structural features that may be involved in regulation (1989)

DNA sequence analysis of the regions adjacent to the hlyA gene, which encodes listeriolysin O, an essential virulence factor of Listeria monocytogenes, revealed the presence of two open reading frames (ORFs): ORF D located 304 base pairs downstream from hlyA, and ORF U located 224 base pairs upstream from and in opposite direction to hlyA. Promoter mapping performed with RNAs extracted from cells growing exponentially in rich medium showed that the three ORFs are independently transcribed. hlyA is transcribed from two promoters separated by 10 base pairs (P1 hlyA and P2 hlyA). ORF U is transcribed in the opposite direction from an adjacent promoter. These two promoter regions are separated by a palindromic sequence T-T-A-A-C-A-A/T-T-G-T-T-A-A. This palindrome was also found upstream from the ORF D promoter, suggesting that all three genes are similarly regulated.
Synthesis of optically active trifluorinated compounds: asymmetric Michael addition with hydrolytic enzymes (1986)

Syntheses of optically active compounds possessing a trifluoromethyl group, via enzymatic chiral Michael addition reaction of 2-(trifluoromethyl)propenoic acid and synthesis of trifluoromethylated heterocycles, have been under-taken.
Inhibition of vascular smooth muscle cell growth by endothelial cell-derived heparin. Possible role of a platelet endoglycosidase. (1982)

Bovine aortic endothelial cells release a heparin-like substance in the presence of 0.4% fetal calf serum. This substance inhibited the growth of smooth muscle cells in vitro by about 70%. Substitution of platelet-poor plasma for serum resulted in minimal liberation of inhibitory activity from the cells unless at least 10-fold higher concentrations of platelet-poor plasma were utilized. This suggested that a platelet product was involved in the release process. Therefore, we examined the ability of the platelet heparitinase described in the preceding communication to release heparin-like species from cultured endothelial cells. Our results show that when endothelial cells were exposed to serum-free medium containing 1 ng/ml of the purified platelet endoglycosidase, at least as much inhibitory activity was released as was obtained with 0.4% serum. Dose response experiments indicated that only 10 pg/ml of the enzyme were necessary to liberate 50% of the inhibitory activity from endothelial cells. The heparin-like nature of the inhibitory substance was demonstrated by its sensitivity to Flavobacterium heparinase. Utilizing appropriate controls, the release of heparin-like material by the endoglycosidase was shown to be enzyme-specific and was not due to artifacts of experimental manipulations. In addition, this enzyme did not convert prereleased material to an active component, but directly liberated the active heparin-like species from endothelial cells. A simple model describing the possible role of heparin-like components and the endoglycosidase in the normal and injured wall is presented.
The regulation of the protein kinase PKR by RNA (1996)

A model is presented for the regulation of the double-stranded RNA (dsRNA)-activated mammalian protein kinase PKR, which is involved in protein synthesis inhibition and the antiviral response in cells. A series of previous findings abut PKROs behavior are reviewed, including its effects on translation; the activation of its protein kinase activity; binding sites for PKR on RNA; PKROs protein domains, which include two double-stranded RNA binding motifs (dsRBMs); and the likelihood of PKR dimer formation. The model which emerges to account for many of these observations includes the suggestion that PKR dimers form which are stabilized and rearranged upon binding to dsRNA regions 60 bp or longer. The hypothesis includes protein conformational changes within each member of a PKR dimer bound to dsRNA which re-position an inhibitory polypeptide domain and thus allow kinase activation. Also considered are ways in which PKR interacts with imperfectly duplexed, highly structured RNA molecules.
Droplet-Based Microfluidics for Emulsion and Solvent Evaporation Synthesis of Monodisperse Mesoporous Silica Microspheres (2008)

A novel method for the fabrication of monodisperse mesoporous silica particles is suggested. It is based on the formation of well-defined equally sized emulsion droplets using a microfluidic approach. The droplets contain the silica precursor/surfactant solution and are suspended in hexadecane as the continuous oil phase. The solvent is then expelled from the droplets, leading to concentration and micellization of the surfactant. At the same time, the silica solidifies around the surfactant structures, forming equally sized mesoporous particles. The procedure can be tuned to produce well-separated particles or alternatively particles that are linked together. The latter allows us to create 2D or 3D structures with hierarchical porosity.
Synthesis and photophysical and electrochemical properties of new halotricarbonyl(polypyridine)rhenium(I) complexes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and photophysical and electrochemical properties of new halotricarbonyl(polypyridine)rhenium(I) complexesAlberto Juris, Sebastiano Campagna, Ilesh Bidd, Jean Marie Lehn, and Raymond ZiesselCite this: Inorg. Chem. 1988, 27, 22, 4007–4011Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/ic00295a022https://doi.org/10.1021/ic00295a022research-articleACS PublicationsRequest reuse permissionsArticle Views1893Altmetric-Citations224LEARN 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
Single photon emission computed tomography (SPECT) for low back pain induced by extension with no root sign. (2004)

SPECT was more sensitive and located more lesions than planar bone scintigraphy, especially when the lesions were located at posterior element of vertebrae. Most of the lesions were distributed at the 4 th and 5 th lumbar vertebral segments. There was no significant statistical difference of abnormal SPECT related to X-ray finding. The use of SPECT was the first choice among all image modalities when cause of low back pain was assumed to arise from bone and joint disorder at clinical evaluation.
Progress in Modeling of Protein Structures and Interactions (2005)

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.
Osteoporosis in the Japanese Population (2001)

The characteristic of osteoporosis in the Japanese population is different from that in the Caucasian population. The different incidence of vertebral and hip fracture may be related to both genetic and lifestyle factors. In the aspect of genetics, approximately 77% of the Japanese have the bb genotype of the vitamin D receptor gene, which is considered to be associated with higher bone mass and lower bone turnover than the Bb genotype. The incidence of vertebral fracture is significantly lower in the younger birth cohorts in both genders. However, the total number of hip fractures rapidly grows as the elderly population increases in Japan. It may be explained by some epidemiological studies that the traditional Japanese lifestyle may prevent hip fractures in the Japanese elderly. The knowledge of the differences of osteoporosis between Caucasian and Japanese people must contribute to the prevention of osteoporosis and its complications.
Metal−Ligand Charge-Transfer-Promoted Photoelectronic Bergman Cyclization of Copper Metalloenediynes:  Photochemical DNA Cleavage via C-4‘ H-Atom Abstraction (2003)

Metal-to-ligand charge-transfer (MLCT) photolyses (lambda > or = 395 nm) of copper complexes of cis-1,8-bis(pyridin-3-oxy)oct-4-ene-2,6-diyne (bpod, 1), [Cu(bpod)(2)]PF(6) (2), and [Cu(bpod)(2)](NO(3))(2) (3) yield Bergman cyclization of the bound ligands. In contrast, the uncomplexed ligand 1 and Zn(bpod)(2)(CH(3)COO)(2) compound (4) are photochemically inert under the same conditions. In the case of 4, sensitized photochemical generation of the lowest energy (3)pi-pi state, which is localized on the enediyne unit, leads to production of the trans-bpod ligand bound to the Zn(II) cation by photoisomerization. Electrochemical studies show that 1, both the uncomplexed and complexed, exhibits two irreversible waves between E(p) values of -1.75 and -1.93 V (vs SCE), corresponding to reductions of the alkyne units. Irreversible, ligand-based one-electron oxidation waves are also observed at +1.94 and +2.15 V (vs SCE) for 1 and 3. Copper-centered oxidation of 2 and reduction of 3 occur at E(1/2) = +0.15 and +0.38 V, respectively. Combined with the observed Cu(I)-to-pyridine(pi) MLCT and pyridine(pi)-to-Cu(II) ligand-to-metal charge transfer (LMCT) absorption centered near approximately 315 nm, the results suggest a mechanism for photo-Bergman cyclization that is derived from energy transfer to the enediyne unit upon charge-transfer excitation. The intermediates produced upon photolysis degrade both pUC19 bacterial plasmid DNA, as well as a 25-base-pair, double-stranded oligonucleotide. Detailed analyses of the cleavage reactions reveal 5'-phosphate and 3'-phosphoglycolate termini that are derived from H-atom abstraction from the 4'-position of the deoxyribose ring rather than redox-induced base oxidation.
Detection of Growth-Stimulating Activity in the Proximal Small Intestine during Weaning in the Suckling Rat (1991)

Adaptive changes in enzyme expression and cell proliferation occur in the small intestine of the suckling rat at the beginning of the 3rd postnatal week. This physiological adaptation can be modulated by factors including diet or glucocorticoids. We have previously described an intestinal growth-stimulating fraction derived from the remnant small bowel after resection and found that enteral nutrition is critical for its detection. In view of the similarity between the changes in cell proliferation that occur between 15 and 22 days postnatally and those immediately after resection, we sought to determine whether the small intestinal mucosa of the neonatal rat also contains a similar growth-stimulating fraction. Our results show that extracts of the proximal intestine prepared from 15-day-old rats do contain the growth-stimulating fraction. The activity was not detectable in maternal milk nor in the intestinal extract from 8-day-old rats. When the suckling rats were deprived of solid food, the activity was not detectable in the 15-day-old group. Gel filtration of the acidic extract on a G-25 Sephadex column revealed that the active component is made up of two molecular weight species (approximately 4,500 and 1,500 daltons) similar to that described in the proximal intestine of the postresectional model. These findings suggest that dietary factors may play a role in modulating the proliferative changes that occur at the time of weaning by way of the growth-stimulating fraction.
A comparative study of spirochaetes from the porcine alimentary tract (1981)

Strains of Treponema hyodysenteriae capable of inducing swine dysentery in specific pathogen-free pigs were compared with other spirochaetes from the porcine alimentary tract by biochemical and serological tests and by electrophoresis of their proteins. Carbohydrate fermentation and esculin hydrolysis were similar in all the spirochaetes. Indole was produced by T. hyodysenteriae and by some of the other spirochaetes. Analysis of the fatty acids produced from glucose showed a difference between T. hyodysenteriae and other spirochaetes only in the amount of n-butyric acid produced. The indirect fluorescent antibody test showed extensive cross-reactions between all the spirochaetes unless antisera were first absorbed. A microtitre agglutination test and a growth-inhibition test were both more specific; strains of T. hyodysenteriae could be distinguished from the other spirochaetes using unabsorbed sera. Both tests revealed some antigenic heterogeneity among strains of T, hyodysenteriae. The cell proteins of a single strain of T. hyodysenteriae gave an electrophoretic pattern distinct from those of the other spirochaetes. Two of the six spirochaetes not associated with swine dysentery, PWS/B and PWS/C, were indistinguishable serologically and electrophoretically. The other four strains were serologically distinct from one another and from PWS/B and PWS/C. Only two of these spirochaetes were examined electrophoretically, but each gave a different pattern from PWS/B and PWS/C. The diversity observed among spirochaetes not associated with swine dysentery indicates that their suggested inclusion in a single species, T. innocens, may prove to be unjustified.
Synthesis, Crystal Structure Analysis, and Pharmacological Characterization of Disila-bexarotene, a Disila-Analogue of the RXR-Selective Retinoid Agonist Bexarotene (2005)

Twofold sila-substitution (C/Si exchange) in the saturated ring of the tetrahydronaphthalene skeleton of the RXR-selective retinoid agonist bexarotene (1a) leads to disila-bexarotene (1b). Compound 1b was synthesized in a multistep synthesis, starting from 1,2-bis(chlorodimethylsilyl)ethane. The identity of 1b was established by elemental analyses and multinuclear NMR studies, and the C/Si analogues 1a and 1b (and an intermediate in the synthesis of 1b) were structurally characterized by single-crystal X-ray diffraction. Furthermore, 1a and 1b were studied for their interaction with retinoid X receptors. Although the twofold sila-substitution of 1a resulted in significant differences in the molecular structures of 1a and 1b, disila-bexarotene (1b) was shown to be a highly potent RXR agonist.
Robust Tuning of Cross-Directional Model Predictive Controllers for Paper-Making Processes (2017)

This paper studies automated tuning of cross-directional model predictive control for industrial paper-making processes under user-specified model parameter uncertainties. Automated parameter tuning algorithms are developed to reduce the variability of the actuator and measurement profiles in the spatial domain and to achieve satisfactory performance in terms of worst case settling times and worst case control signal overshoots in the temporal domain for given parametric uncertainties. Due to decoupling properties of the spatial and temporal frequency components, the controller design and parameter tuning can be realized separately. For the spatial design and parameter tuning in the presence of parametric uncertainties, the undesirable high-frequency components in the actuator profile are suppressed via an appropriate design of the weighting matrix S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> using the real-valued Fourier matrix approach. For the temporal design, a temporal filter is adopted to smooth the reference trajectory, where the parameter in the temporal filter is carefully tuned to achieve a tradeoff between the worst case settling time and the worst case control signal overshoot. Finally, the effectiveness of the proposed tuning algorithms is verified using a system model extracted from the pulp and paper industry.
A randomized scheduler with probabilistic guarantees of finding bugs (2010)

This paper presents a randomized scheduler for finding concurrency bugs. Like current stress-testing methods, it repeatedly runs a given test program with supplied inputs. However, it improves on stress-testing by finding buggy schedules more effectively and by quantifying the probability of missing concurrency bugs. Key to its design is the characterization of the depth of a concurrency bug as the minimum number of scheduling constraints required to find it. In a single run of a program with n threads and k steps, our scheduler detects a concurrency bug of depth d with probability at least 1/ nk d-1 . We hypothesize that in practice, many concurrency bugs (including well-known types such as ordering errors, atomicity violations, and deadlocks) have small bug-depths, and we confirm the efficiency of our schedule randomization by detecting previously unknown and known concurrency bugs in several production-scale concurrent programs.