gebhart/patrepeval huggingface dataset:
Systematic Investigation of<i>Saccharomyces</i><i>c</i><i>erevisiae</i>Enzymes Catalyzing Carbonyl Reductions (2004)

Eighteen key reductases from baker's yeast (Saccharomyces cerevisiae) have been overproduced in Escherichia coli as glutathione S-transferase fusion proteins. A representative set of alpha- and beta-keto esters was tested as substrates (11 total) for each purified fusion protein. The stereoselectivities of beta-keto ester reductions depended both on the identity of the enzyme and the substrate structure, and some reductases yielded both L- and D-alcohols with high stereoselectivities. While alpha-keto esters were generally reduced with lower enantioselectivities, it was possible in all but one case to identify pairs of yeast reductases that delivered both alcohol antipodes in optically pure form. Taken together, the results demonstrate not only that individual yeast reductases can be used to supply important chiral building blocks, but that GST-fusion proteins allow rapid identification of synthetically useful biocatalysts (along with their corresponding genes).
PHF5A represents a bridge protein between splicing proteins and ATP-dependent helicases and is differentially expressed during mouse spermatogenesis (2008)

PHF5A is a highly conserved protein from yeast to man, and based on studies in yeast, it was suggested that the homologous protein RDS3P in S. cerevisiae takes part in the organization of U2 snRNP particles. By using the yeast two-hybrid assay we could demonstrate that PHF5A interacted both with ATP-dependent helicases EP400 and DDX1 and with arginine-serine (RS)-rich domains of splicing factors U2AF1 and SFRS5 in mouse. Furthermore, domain interaction studies revealed that PHF5A interaction with EP400 and DDX1 is restricted to the N-terminal part of PHF5A, whereas the C-terminal region of PHF5A was found to be responsible for the association with U2AF1 and SFRS5. By using the yeast three-hybrid assay, we could further show that both EP400 and DDX1 interacted only indirectly with U2AF1 and SFRS5 proteins via the bridge protein PHF5A. The subcellular localization of a PHF5A-GFP fusion protein was predominantly observed in the nucleus and, in addition, PHF5A co-localized with both U2AF1 and SFRS5 proteins in nuclear speckles of NIH3T3 cells. Moreover, expression analyses demonstrated that PHF5A and U2AF1 gene expression coincided in spermatocytes during murine spermatogenesis and interaction between these proteins was also detectable in the spermatocyte-specific cell line GC-4spc by using in vivo co-immunoprecipitation studies. Taken together, our results indicate that PHF5A resembles a protein which interacts with splicing factors U2AF1 and SFRS5 and helicases EP400 and DDX1 and functions as a bridge protein between these proteins.
Error in Anatomic Pathology (2001)

Error in anatomic pathology is a topic that is currently making the difficult transition from a problem peculiar to a subset of poorly trained or otherwise inadequate pathologists to a problem shared by the specialty of pathology. This transition will involve a number of difficult steps, including sorting error from both inherent diagnostic uncertainty andfrom variations in practice patterns from which no evidence-based best practice has emerged. Identification of error will require scientifically valid diagnostic gold standards, and in those areas of diagnosis without such a standard, the identification of and response to error will continue to be heavily influenced by hindsight bias and subjective opinion. The pathologist, like other physicians, has limited options to "make things right" following a significant error The silver lining is that many errors have the potential to prompt changes that will prevent future patient harm. Unfortunately, a dysfunctional legal system that values punishment and transfer of assets over future improvements in health care has wrung much of the positive potential out of error, leaving only the damaged patient and damaged pathologist.
Subpopulations of chondrocytes from different zones of pig articular cartilage: Isolation, growth and proteoglycan synthesis in culture (1990)

Articular cartilage varies in ultrastructure and composition with distance from the articular surface. We have cultured chondrocytes from different zones of pig articular cartilage and investigated whether there are intrinsic differences in their behaviour that might account for the variation observed in intact tissue. On isolation, cells from the upper third of the cartilage were smaller than those of the lower third, but this difference was not maintained in culture. Upper zone cells attached and spread more slowly than lower zone cells; morphological differences between the two populations could be seen for several weeks. The growth rates of the two populations were similar, but upper zone cells reached a lower confluent density. Levels of protein synthesis were similar for both populations, but upper zone cells deposited less proteoglycan in the cell layer. On isolation, the percentage of upper zone cells that stained positive with MZ15, a monoclonal antibody to keratan sulphate, was smaller than the percentage of lower zone cells, but this difference was lost after several days in culture. Nevertheless, the keratan sulphate content of proteoglycan synthesised by lower zone chondrocytes at high density was greater than of that synthesised by upper zone cells. The proportion of nonaggregating proteoglycan was greater in upper than lower zone cartilage and this difference was also observed in long-term cultures. proteoglycans were further characterised by composite and polyacrylamide gel electrophoresis and by immunoblotting; differences detected in cartilage extracts were not, however, maintained in culture; instead, the small proteoglycans synthesised by both upper and lower zone cells varied with plating density. Finally, alkaline phosphatase, a marker of hypertrophic, calcifying cartilage, was only expressed in lower zone cultures. We conclude that some of the observed heterogeneity of articular cartilage reflects intrinsic differences between the cells of different zones, whereas some may reflect the response of chondrocytes to different environmental conditions.
Leukotrienes in Asthma (1996)

Recent advances in research have led to the identification of an inflammatory component to asthma. Although many endogenous mediators are involved in inflammation, leukotrienes appear to play an especially important role in asthma. The leukotrienes produce tissue edema, mucus secretion, and smooth-muscle proliferation, along with a powerful bronchoconstriction. In addition, antileukotriene drugs have emerged as potential therapeutic agents for asthma. This study was designed to review the current information on these new agents. In this review, full-length articles of antileukotriene agents are examined. These articles were found through MEDLINE under the following medical headings: asthma, inflammation, leukotriene, leukotriene-receptor antagonist, and leukotriene-synthesis inhibitor. Most clinical studies cited are placebo-controlled trials involving healthy individuals and patients with asthma. These studies indicate that antileukotriene agents improve lung function and reduce the symptoms of asthma and the need for additional medication. Drugs that inhibit leukotriene-receptor binding and leukotriene synthesis hold promise as new additions to the armamentarium of clinicians who treat asthma. Furthermore, these drugs have already helped to elucidate some details of the pathophysiological features of asthma.<i>Arch Intern Med. 1996;156:2181-2189</i>
VARIABILITY AND CORRELATION STUDIES FOR QUANTITATIVE TRAITS IN SPANISH BUNCH GROUNDNUT (ARACHIS HYPOGAEA L.) GENOTYPES (2005)

Groundnut is an important oil seed crop grown in Andhra Pradesh and India during khanf (rainfed) and post rainy (rabi-summer) seasons. Study of variability and correlation among yield and yield component traits and stem necrosis disease would help in selection of high yielding varieties with stem necrosis disease resistance. Twenty two genotypes were sown in randomized block design with three replications during rabi 2000–01. High genotypic and phenotypic variation was observed for final plant stand (730.40 and 1059.80), 100 pod weight (41.18 and 76.60). High genotypic and phenotypic coefficients of variation were recorded for pod yield per plant (23.06% and 33.20%) and plant stand maintained at harvest (22.75% and 27.41%). It indicates the presence of considerable amount of genetic variability for these characters. High heritability was observed for 100 pod weight (73.33%), plant stand maintained at harvest (68.92%) and PSND (63.61%). High genetic advance as percentage of mean was observed for plant stand maintained at harvest (38.91%), pod yield per plant (32.99%) and PSND incidence (20.90). The performance of additive genetic variance for plant stand maintained at harvest as showing high heritability, genetic advance and PSND incidence gives a lot of scope for improvement through selection. Moderate heritability and low genetic gain was observed for days to maturity and shelling out turn indicating the non-additive gene effects. Pod yield showed highly significant positive correlation with shelling out turn (0.272), kernel yield per plant (0.901) and weak negative correlation with peanut stem necrosis disease incidence (−0.063).
Familiarity, Complexity, and Team Performance in Geographically Distributed Software Development (2007)

While prior research has found that familiarity is beneficial to team performance, it is not clear whether different kinds of familiarity are more or less beneficial when the work has different types of complexity. In this paper, we theorize how task and team familiarity interact with task and team coordination complexity to influence team performance. We posit that task familiarity is more beneficial with more complex tasks (i.e., tasks that are larger or with more complex structures) and that team familiarity is more beneficial when team coordination is more difficult (i.e., for larger or geographically dispersed teams). Finally, we propose that the effects of task familiarity and team familiarity on team performance are complementary. Based on a field study of geographically distributed software teams, two of our hypotheses are disconfirmed: Our results show that the beneficial effects of task familiarity decline when tasks are more structurally complex and are independent of task size. Conversely, the hypotheses for team familiarity are confirmed as the benefit of team familiarity for team performance is enhanced when team coordination is more challenging—i.e., when teams are larger or geographically dispersed. Finally, surprisingly, we find that task and team familiarity are more substitutive than complementary in their joint effects on team performance: Task familiarity improves team performance more strongly when team familiarity is weak and vice versa. Our study contributes by revealing how different types of familiarity can enhance team performance in a real-world setting where the task and its coordination can be highly complex.
β‐Lactoglobulin binds retinol and protoporphyrin IX at two different binding sites (1990)

Measurement of tryptophan fluorescence quenching and the excitation energy transfer from tryptophanyl residues to the bound ligand indicates that beta-lactoglobulin binds tightly to hemin and protoporphyrin IX in a ligand-to-protein stoichiometric ratio. The apparent dissociation constants of hemin-beta-lactoglobulin and protoporphyrin IX-beta-lactoglobulin complexes are 2.5 x 10(-7) M and 4 x 10(-7) M, respectively. The addition of beta-lactoglobulin (final concentration = 10 microM, phosphate buffer 50 mM, pH 7.1) to the solution containing retinol and protoporphyrin IX triggers an energy transfer between beta-lactoglobulin tryptophan and protoporphyrin IX as well as between retinol and protoporphyrin IX. The efficiency of energy transfer depends on the distance between the donor (retinol) and the acceptor (protoporphyrin IX). Using the Förster theory, a retinolprotoporphyrin IX distance of 25 A was calculated. These results indicate that retinol and protoporphyrin IX are bound to the beta-lactoglobulin monomer at two different sites.
Stereochemistry of the peroxisomal branched-chain fatty acid α- and β-oxidation systems in patients suffering from different peroxisomal disorders (2002)

Phytanic acid (3,7,11,15-tetramethylhexadecanoic acid) is a branched-chain fatty acid derived from dietary sources and broken down in the peroxisome to pristanic acid (2,6,10,14-tetramethylpentadecanoic acid) via alpha-oxidation. Pristanic acid then undergoes beta-oxidation in peroxisomes. Phytanic acid naturally occurs as a mixture of (3S,7R,11R)- and (3R,7R,11R)-diastereomers. In contrast to the alpha-oxidation system, peroxisomal beta-oxidation is stereospecific and only accepts (2S)-isomers. Therefore, a racemase called alpha-methylacyl-CoA racemase is required to convert (2R)-pristanic acid into its (2S)-isomer. To further investigate the stereochemistry of the peroxisomal oxidation systems and their substrates, we have developed a method using gas-liquid chromatography-mass spectrometry to analyze the isomers of phytanic, pristanic, and trimethylundecanoic acid in plasma from patients with various peroxisomal fatty acid oxidation defects. In this study, we show that in plasma of patients with a peroxisomal beta-oxidation deficiency, the relative amounts of the two diastereomers of pristanic acid are almost equal, whereas in patients with a defect of alpha-methylacyl-CoA racemase, (2R)-pristanic acid is the predominant isomer. Furthermore, we show that in alpha-methylacyl-CoA racemase deficiency, not only pristanic acid accumulates, but also one of the metabolites of pristanic acid, 2610-trimethylundecanoic acid, providing direct in vivo evidence for the requirement of this racemase for the complete degradation of pristanic acid.
Scintillator geometry and surface treatment for readout by a small area silicon photomultiplier (2007)

New solid state photomultipliers (SSPM) allow small radiation detectors to be more easily realized. Their compact, rugged, and simple operation are inherent advantages over the traditional photomultiplier tube. Because the cost and dark counts of SSPMs scale with area, we are investigating scintillation light read out from a fraction of one face of a scintillating crystal. The Monte Carlo optical transport code DETECT2000 [1,2] was used to track optical photons within the scintillator volume. A MATLAB interface was developed for DETECT2000 to facilitate parametric simulations of complex geometries. We examined the reflectivity of a 3 M mirror film and found it to be comparable to Teflon tape for certain wavelengths. Large crystals can be read out by small photodetectors with some degradation in the light collected. For small changes in size, light is lost approximately in proportion to the crystal-to-SSPM length ratio. For dosimetry applications, an effective brightness parameter was proposed which integrates the collected light yield for a uniform distribution of incident energies. A crystal twice the length of a 3 times 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> SSPM was determined to be optimal for a 50 to 1500 keV radiation field normally incident on a Teflon-wrapped cubic LYSO crystal. By maximizing the photofraction and minimizing the photostatistical energy resolution, the optimal crystal-to- SSPM ratio was determined to vary with the energy of interest for spectroscopic applications.
Corrigan's Analogy or What We Will Do at NYU (1965)

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Advanced selective optical sensors based on periodically organized mesoporous hybrid silica thin films (2004)

Mesoporous thin films functionalized with silylated [small beta]-diketone compounds with symmetry mesostructure dependent on the probe quantity were used as fast uranyl species sensors with high selectivity and sensitivity.
Thin-film distributed-feedback laser fabricated by ion milling (1972)

Distributed feedback of a thin-film optical guided mode has been produced by a periodic perturbation of the guide height. Using photoresist and ion-milling techniques, gratings with a period of ∼0.2 μ and a peak-to-peak height of ∼0.1 μ have been formed on fused silica substrates. A film of polyurethane doped with Rhodamine 6G pumped by an N2 laser formed the gain medium. Data presented on the oscillation threshold of several lasers are in agreement with calculated feedback parameters. This technique is capable of producing high-resolution gratings in durable materials which can provide feedback in low-gain laser media.
Biofilm formation by <i>Propionibacterium acnes</i> on biomaterials <i>in vitro</i> and <i>in vivo</i>: Impact on diagnosis and treatment (2006)

Propionibacterium acnes is found increasingly as a cause of delayed infection, usually involving implanted biomaterials. Despite susceptibility to common antibiotics, such infections are very difficult to treat and usually require surgical removal of the device. Three clinical isolates of P. acnes were assessed for ability to adhere to titanium, surgical steel and silicone, with and without a plasma conditioning film. After adherence, the biomaterials were then incubated for a further 6 days and examined for biofilm development. All three isolates adhered to all three biomaterials similarly. Importantly, we were able to demonstrate biofilm formation, including production of exopolymer similar in appearance to the polysaccharide intercellular adhesin of Staphylococcus epidermidis. A case summary also demonstrated failure to eradicate P. acnes infection in a hydrocephalus shunt after prolonged treatment. The removed shunt showed obvious biofilm formation, initially obscured by exopolymer when viewed by environmental scanning electron microscopy. Biofilm development by P. acnes explains the difficulties encountered in clinical management of such infections.
Review of automatic document formatting (2009)

We review the literature on automatic document formatting with an emphasis on recent work in the field. One common way to frame document formatting is as a constrained optimization problem where decision variables encode element placement, constraints enforce required geometric relationships, and the objective function measures layout quality. We present existing research using this framework, describing the kind of optimization problem being solved and the basic optimization techniques used to solve it. Our review focuses on the formatting of primarily textual documents, including both micro- and macro-typographic concerns. We also cover techniques for automatic table layout. Related problems such as widget and diagram layout, as well as temporal layout issues that arise in multimedia documents are outside the scope of this review.
Short Communication: Short-Day Photoperiod During the Dry Period Decreases Expression of Suppressors of Cytokine Signaling in Mammary Gland of Dairy Cows (2005)

Suppressors of cytokine signaling (SOCS) are induced by prolactin and act through negative feedback to inhibit cytokine signaling. We hypothesized that lower prolactin concentrations in cows exposed to short-day photoperiod (SD; 8 h light:16 h dark) lead to decreased expression of SOCS, which mediate the effects of SD on mammary proliferation during the dry period. Multiparous Holstein cows were dried off 60 d before expected calving and were assigned to long-day photoperiod (LD; 16 h light:8 h dark) or SD during the dry period. Mammary biopsies were obtained at -40, -20, -10, and +10 d relative to expected calving, and expression of SOCS-1, SOCS-2, SOCS-3, and cytokine-inducible SH2-containing protein (CIS) mRNA was assessed by real-time, quantitative, reverse transcription-PCR. Expression of all SOCS increased over time and expression of SOCS-3, SOCS-2, and CIS mRNA was lower in mammary gland of SD cows. These data suggest that lower SOCS expression in cows exposed to SD during the dry period may enhance prolactin signaling to the mammary gland, thereby augmenting mammary development during pregnancy and milk production in the subsequent lactation. Changes in SOCS expression during pregnancy and lactation imply that SOCS may regulate mammary gland development and function in dairy cows.
Breast Cancer Stem Cell Potent Copper(II)–Non‐Steroidal Anti‐Inflammatory Drug Complexes (2016)

Abstract The breast cancer stem cell (CSC) potency of a series of copper(II)–phenanthroline complexes containing the nonsteroidal anti‐inflammatory drug (NSAID), indomethacin, is reported. The most effective copper(II) complex in this series, 4 , selectivity kills breast CSC‐enriched HMLER‐shEcad cells over breast CSC‐depleted HMLER cells. Furthermore, 4 reduces the formation, size, and viability of mammospheres, to a greater extent than salinomycin, a potassium ionophore known to selectively inhibit CSCs. Mechanistic studies revealed that the CSC‐specificity observed for 4 arises from its ability to generate intracellular reactive oxygen species (ROS) and inhibit cyclooxygenase‐2 (COX‐2), an enzyme that is overexpressed in breast CSCs. The former induces DNA damage, activates JNK and p38 pathways, and leads to apoptosis.
The Lack of the C-Terminal Domain of Adipose Triglyceride Lipase Causes Neutral Lipid Storage Disease through Impaired Interactions with Lipid Droplets (2008)

These findings indicate that the domain including the hydrophobic region of ATGL was essential for association with LDs.
Sending entanglement through noisy quantum channels (1996)

This paper addresses some general questions of quantum information theory arising from the transmission of quantum entanglement through (possibly noisy) quantum channels. A pure entangled state is prepared of a pair of systems R and Q, after which Q is subjected to a dynamical evolution given by the superoperator ${\mathit{E}}^{\mathit{Q}}$. Two interesting quantities can be defined for this process: the entanglement fidelity ${\mathit{F}}_{\mathit{e}}$ and the entropy exchange ${\mathit{S}}_{\mathit{e}}$. It turns out that neither of these quantities depends in any way on the system R, but only on the initial state and dynamical evolution of Q. ${\mathit{F}}_{\mathit{e}}$ and ${\mathit{S}}_{\mathit{e}}$ are related to various other fidelities and entropies and are connected by an inequality reminiscent of the Fano inequality of classical information theory. Some insight can be gained from these techniques into the security of quantum cryptographic protocols and the nature of quantum error-correcting codes. \textcopyright{} 1996 The American Physical Society.
A maximum-entropy analysis of the problem of the rotameric distribution for substituted biphenyls studied by 1H nuclear magnetic resonance spectroscopy in nematic liquid crystals (1991)

The statistical principle of maximum entropy is applied to the analysis of dipolar couplings from 1H NMR of nonrigid molecules dissolved in liquid-crystalline phases. A distribution function for the orientational and inter-ring angles is so obtained. The most probable internal angle φ is determined for 4,4′-dichlorobiphenyl (φ=34°) in the nematic phase of I52, 4-pentyl-4′-cyanobiphenyl (φ=32°) and 4′-Br-4-Cl-2,6-difluorobiphenyl (φ=42°) in EBBA. The physical reliability of the distributions determined is discussed. The maximum-entropy treatment seems to indicate a limit for the information on the internal motion obtainable from the experimental data.
Determining Optimum Price Promotion Quantities (1970)

How can a price “special” be made more profitable for the manufacturer? Is it possible to predict sales which will be generated through price promotion? These are two of the basic questions that are examined in this article. A methodology is presented for optimizing manufacturers’ shipment quantities for price promotions in cases where the duration of the promotion is fixed and the item to be promoted is fair-traded.