gebhart/patrepeval huggingface dataset:
Modulating Protein Structure with Fluorous Amino Acids:  Increased Stability and Native-like Structure Conferred on a 4-Helix Bundle Protein by Hexafluoroleucine (2005)

There has recently been much interest in exploiting the unusual properties associated with fluorocarbons to modulate the physicochemical properties of proteins. Here we present a detailed investigation into the effect on structure and stability of systematically repacking the hydrophobic core of a model protein with the extensively fluorinated (fluorous) amino acid l-5,5,5,5',5',5'-hexafluoroleucine (hFLeu). The starting point was a 27-residue peptide, alpha(4)-H, that adopts an antiparallel 4-alpha-helix bundle structure, and in which the hydrophobic core comprises six layers of leucine residues introduced at the "a" and "d" positions of the canonical heptad repeat. A series of peptides were synthesized in which the central two (alpha(4)-F(2))(,) four (alpha(4)-F(4)), or all six layers (alpha(4)-F(6)) of the core were substituted hFLeu. The free energy of unfolding increases by 0.3 (kcal/mol)/hFLeu on repacking the central two layers and by an additional 0.12 (kcal/mol)/hFLeu on repacking additional layers, so that alpha(4)-F(6) is approximately 25% more stable than the nonfluorinated protein alpha(4)-H. One-dimensional proton, two-dimensional (1)H-(15)N HSQC, and (19)F NMR spectroscopies were used to examine the effect of fluorination on the conformational dynamics of the peptide. Unexpectedly, increasing the degree of fluorination also appears to result in peptides that possess a more structured backbone and less fluid hydrophobic core. The latter only occurs in alpha(4)-F(4) and alpha(4)-F(6), suggesting that crowding of the hFLeu residues may restrict the amplitude and/or time scales for rotation of the side chains.
Genetic Dissection of itpr Gene Function Reveals a Vital Requirement in Aminergic Cells of Drosophila Larvae (2004)

Signaling by the second messenger inositol 1,4,5-trisphosphate is thought to affect several developmental and physiological processes. Mutants in the inositol 1,4,5-trisphosphate receptor (itpr) gene of Drosophila exhibit delays in molting while stronger alleles are also larval lethal. In a freshly generated set of EMS alleles for the itpr locus we have sequenced and identified single point mutations in seven mutant chromosomes. The predicted allelic strength of these mutants matches the observed levels of lethality. They range from weak hypomorphs to complete nulls. Interestingly, lethality in three heteroallelic combinations has a component of cold sensitivity. The temporal focus of cold sensitivity lies in the larval stages, predominantly at second instar. Coupled with our earlier observation that an itpr homozygous null allele dies at the second instar stage, it appears that there is a critical period for itpr gene function in second instar larvae. Here we show that the focus of this critical function lies in aminergic cells by rescue with UAS-itpr and DdCGAL4. However, this function does not require synaptic activity, suggesting that InsP(3)-mediated Ca(2+) release regulates the neurohormonal action of serotonin.
Prognostic significance of the PC10 index as a prospective assay for cervical cancer treated with radiation therapy alone (1992)

The monoclonal antibody PC10 recognizes proliferating cell nuclear antigen (PCNA) in conventionally fixed and processed histologic materials. Formaldehyde-fixed and paraffin-embedded specimens taken from 194 patients with Stage III squamous cell carcinoma of the cervix treated with radiation therapy alone were investigated for PC10 positivity using immunohistochemical methods. A few squamous epithelial cells in the basal layer and the deepest zone of the prickle cell layer were positive for PC10. Cancer cells also were positive for PC10, showing a diffuse or granular nuclear staining pattern. The multiple logistic regression model analysis and the Kaplan-Meier method indicate that a strong correlation exists between the PC10 index and prognosis (P less than 0.001). Thus, the PC10 index may be a predictive indicator for the prognosis of patients with squamous cell carcinoma of the cervix treated with radiation therapy alone.
Dissimilarity measure of concentration ratios (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDissimilarity measure of concentration ratiosHideo. Nishida, Sadao. Ikeda, Masaya. Miyai, and Shizuo. SuzukiCite this: Anal. Chem. 1981, 53, 11, 1576–1579Publication Date (Print):September 1, 1981Publication History Published online1 May 2002Published inissue 1 September 1981https://pubs.acs.org/doi/10.1021/ac00234a009https://doi.org/10.1021/ac00234a009research-articleACS PublicationsRequest reuse permissionsArticle Views27Altmetric-Citations1LEARN 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
Gelation behavior and properties of lead zirconate titanate gel-cast under an electric field (2009)

Lead zirconate titanate (PZT) piezoelectric ceramics are fabricated by gelcasting method. The effect of gelling additives on the gelation behavior was investigated in details with a focus on the fine control of incubation time before gelling. Gelcasting was also tried under the application of an electric field up to 10 kV/cm to investigate its effect on the physical properties of the ceramics after sintering. Dense ceramics with electrical properties comparable to that of conventional dry pressed ones were obtained using the gelcasting method. Initial experiments on the application of electric field during gelation indicated formation of a thin porous layer on the surface of the ceramic but, otherwise, no significant effect on the properties.
Condition, Reliability, and Resilience Assessment of Tunnels and Bridges (2011)

Proceedings of the GeoHunan International Conference II: Emerging Technologies for Design, Construction, Rehabilitation, and Inspection of Transportation Infrastructure, held in Hunan, China, June 9-11, 2011. This Geotechnical Special Publication contains 24 papers addressing contemporary geotechnical topics. These papers focus on condition, reliability, and resilience assessments of tunnels and bridges and offer field investigations, laboratory experiments, and theoretical studies from China, the United States, and Africa. Topics include: bridge monitoring; tunnel issues; and laboratory tests.
Multi-Focus Image Fusion via Boundary Finding and Multi-Scale Morphological Focus-Measure (2014)

Multi-focus image fusion is to extract the focused regions from the multiple images of the same scene and combine them together to produce one fully focused image. The key is to find the focused regions from the source images. In this paper, we transform the problem of finding the focused regions to find the boundaries between the focused and defocused regions in the source images, and propose a novel image fusion method via boundary finding and a multi-scale morphological focus-measure. Firstly, a morphological focus-measure, consisted of multi- scale morphological gradients, is proposed to measure the focus of the images. Secondly, a novel boundary finding method is presented, which utilizes the relations of the focus information of the source images. Thirdly, the found boundaries naturally segment the source images into regions with the same focus condition and the focused regions can be simply selected by comparing the focus-measures of the corresponding regions. Fourthly, the detected focused regions are reconstructed to obtain the decision map for the multi-focus image fusion. Finally, the fused image is produced according to the decision map and the given fusion rule. Experimental results demonstrate the proposed algorithm outperforms other spatial domain fusion algorithms.
Comment on ‘‘The Effect of Uncontrolled Factors in a Validated Liquid Chromatography–Tandem Mass Spectrometry Method Question Its Use As Reference Method for Marine Toxins: Major Causes for Concern’’ (2011)

ADVERTISEMENT RETURN TO ISSUEPREVCommentNEXTComment on ''The Effect of Uncontrolled Factors in a Validated Liquid Chromatography–Tandem Mass Spectrometry Method Question Its Use As Reference Method for Marine Toxins: Major Causes for Concern''Ana Gago-Martinez*† and James M. Hungerford‡View Author Information† University of Vigo, Vigo, Spain and EU-RLMB, Vigo, Spain‡ USFDA and AOAC Marine and Freshwater Toxins Task Force, Bothell, Washington, United States*E-mail: [email protected]Cite this: Anal. Chem. 2012, 84, 1, 475Publication Date (Web):October 19, 2011Publication History Published online15 December 2011Published inissue 3 January 2012https://pubs.acs.org/doi/10.1021/ac2020933https://doi.org/10.1021/ac2020933article-commentaryACS PublicationsCopyright © 2011 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views929Altmetric-Citations3LEARN 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 PDF (607 KB) Get e-AlertscloseSUBJECTS:Liquids,Mass spectrometry,Quality management,Toxins Get e-Alerts
Characteristics of microbial community and aroma compounds in traditional fermentation of Pixian broad bean paste as compared to industrial fermentation (2017)

Traditionally fermented Pixian broad bean paste (PBP) is a traditional condiment in China and is recognized to have superior quality than the industrially fermented. This work aimed to identify the dominant microbes and unique aroma compounds in traditionally fermented PBP with respect to those in the industrially fermented one. Results showed that several species of lactic acid bacteria, yeasts, Aspergillus, molds, and Staphylococcus were only detected in traditionally fermented PBP, namely, Leuconostoc lactis, Staphylococcus xylosus, S. succinus, Amylomyces rouxii, Mucor genevensis, Absidia corymbifera, Issatchenkia orientalis, basidiomycete yeast sp., and Metschnikowia pulcherrima. Furthermore, the traditionally fermented PBP contained more compounds that contribute to its aroma than those in industrially fermented PBP. A total of 28 aroma substances only were detected in the traditionally fermented PBP. Among these substances, seven were considered aroma-active compounds, namely, ethyl caprylate, hexadecanoic acid methyl ester, 2-methyl-pyrazine, 2,6-dimethyl- pyrazine, 2-pentyl furan, 2-acetyl furan, and hexadecanoic acid. This work provides useful information on the microbial composition and aroma compounds of PBP that can be used to upgrade the quality of industrially fermented PBP.
Many-Task Computing and Blue Waters (2012)

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware.
A maximum a posteriori algorithm for the reconstruction of dynamic SPECT data (2002)

A 4D ordered-subsets maximum a posteriori (OSMAP) algorithm for dynamic SPECT is described. It uses a temporal prior that constrains each voxel's behavior in time to obey a compartmental model. No a priori limitations on kinetic parameters are applied; rather, the parameter estimates evolve as the algorithm iterates to a solution. The estimated parameters are also used to model changes in the activity distribution as the camera rotates, avoiding artifacts due to data inconsistencies between angles. This allows for fewer, longer duration scans to be used. Initial evaluations of the algorithm are presented for dynamic cardiac SPECT imaging with teboroxime using a two compartment model. Canine study results demonstrated qualitative improvements for OSMAP compared to OSEM. In a simulation 100 noise realizations were reconstructed using both OSEM and OSMAP. Population means and standard deviations of regional kinetic parameters were compared: True values: k/sub 21/=0.8, k/sub 12/=0.4 min/sup -1/; OSEM: k/sub 21/=77/spl plusmn/06, k/sub 12/=41/spl plusmn/06; OSMAP: L/sub 21/=.76/spl plusmn/.04, k/sub 12/=.41/spl plusmn/.05. The OSMAP algorithm provided parameter estimates with significantly lower standard deviations than did OSEM at similar levels of bias. This algorithm may where potentially improve dynamic SPECT imaging through its implications for noise control, ability to accurately model and reconstruct data in which the activity distribution is changing, and the potential for accurate reconstruction and data analysis using fewer, longer duration scans.
GrACE: Generation using Associated Code Edits (2023)

Developers expend a significant amount of time in editing code for a variety of reasons such as bug fixing or adding new features. Designing effective methods to predict code edits has been an active yet challenging area of research due to the diversity of code edits and the difficulty of capturing the developer intent. In this work, we address these challenges by endowing pre-trained large language models (LLMs) of code with the knowledge of prior, relevant edits. The generative capability of the LLMs helps address the diversity in code changes and conditioning code generation on prior edits helps capture the latent developer intent. We evaluate two well-known LLMs, Codex and CodeT5, in zero-shot and fine-tuning settings respectively. In our experiments with two datasets, the knowledge of prior edits boosts the performance of the LLMs significantly and enables them to generate 29% and 54% more correctly edited code in top-1 suggestions relative to the current state-of-the-art symbolic and neural approaches, respectively.
Lactate dehydrogenase isoenzymes in diabetic patients. (1985)

Lactate dehydrogenase (LDH) isoenzyme profiles in human platelets and the sera of patients with type I and II diabetes mellitus and vascular complications, as well as normal subjects were measured utilizing a recently established, modified micromethod. LDH-3 was the predominating species in platelets (37.5 +/- 3.0%), with LDH-2, 1, 4 and 5 following in decreasing order of concentration. The LDH-3/LDH-4 ratio in platelets varied from 6.2 to 1.38. Type I and type II diabetic patients with vascular complications showed a significantly higher ratio for LDH-3/LDH-4 (3.99 +/- 1.20 for DM I, 2.16 +/- 0.25 for DM II patients) than the mean ratio for normal subjects (1.14 +/- 0.08). This platelet-specific LDH isoenzyme pattern may be the result of frequent in vivo platelet-vessel wall interactions in the diabetic patients whose platelets are known to be hyperaggregable in in vitro test systems. Since non-diabetic patients patients with vascular complications also displayed a similarly elevated LDH-3/LDH-4 ratio, a wider classification is preferable, although the measurement of the LDH isoenzyme pattern will be helpful in assessing diabetic vascular complications.
Highly Enantioselective Reduction of β,β-Disubstituted Aromatic Nitroalkenes Catalyzed by Clostridium sporogenes (2008)

This is the first report of the use of Clostridium sporogenes extracts for enantioselective reduction of CC double bonds of beta,beta-disubstituted (1) and alpha,beta-disubstituted nitroalkenes (3). Crude enzyme preparations reduced aryl derivatives 1a-e and 1h, in 35-86% yield with > or =97% ee. Reduction of (E)- and (Z)-isomers of 1c gave the same enantiomer of 2c (> or =99% ee). In contrast, alpha,beta-disubstituted nitroalkene 3a was a poor substrate, yielding (S)- 4a in low yield (10-20%), and the ee (30-70% ee) depended on NADH concentration. An efficient synthesis of a library of nitroalkenes 1 is described.
Syntheses of manganoan fluorophlogopites K(Mg, Mn)<SUB>3</SUB>Si<SUB>3</SUB>AlO<SUB>10</SUB>F<SUB>2</SUB> and the germanate equivalents K(Mg, Mn)<SUB>3</SUB>Ge<SUB>3</SUB>AlO<SUB>10</SUB>F<SUB>2</SUB> (1981)

A series of manganoan fluorophlogopites K(Mg, Mn)3Si3AlO10F2 and the corresponding germanate micas K(Mg, Mn)3Ge3AlO10F2 with various Mg/Mn ratios were synthesized from melts of mixtures of KF, MgF2, MnF2, MgO, MnO, Al2O3 and SiO2 or GeO2 in appropriate ratios. Products were examined mainly by the X-ray diffraction technique, and variations of structural parameters of the manganoan micas were estimated from unit cell parameters. In K(Mg, Mn)3Si3AlO10F2, the substitution of Mg2+ ions by Mn2+ decreases the tetrahedral rotation angle α, and the tetrahedral sheet is expected to have a nearly hexagonal form at the solubility limit. In K(Mg, Mn)3Ge3AlO10F2, the solubility range is more extended than that in the corresponding silicate micas as is expected form the large [Ge3AlO10] tetrahedral sheet. However, the Mn-rich end member KMn3Ge3AlO10F2 could not be synthesized, and the crystal still has a large α value at the solubility limit. It was shown that the substitution of larger cations at the octahedral sites decreases rapidly the thermal stability of K(Mg, Mn)3Ge3AlO10F2.
Correlation effects in the spectra of polyenes (1976)

A Hamiltonian of the Pariser–Parr–Pople form is employed to investigate the effect of correlation on the π-electron spectrum of polyenes. Two limiting cases for the electron–electron interaction (short- and long-range limit) are considered, and it is shown that they yield descriptions corresponding to the standard valence-bond (Dirac–Heisenberg) and molecular-orbital models, respectively. The intermediate, chemically most interesting, range is examined in detail by means of a full configuration-interaction treatment with an exponential model potential that includes a variable effective range parameter. It is shown that correlation effects become more important as the effective range of the interaction decreases. The states of polyenes are classified as covalent or noncovalent, and it is found that the former are much more sensitive to correlation than the latter. Configuration interaction through double excitations yields a qualitatively correct ordering for all states in the chemical range, but triple and quadruple excitations are required for quantitative results. Applications to butadiene, hexatriene, and benzene demonstrate that correlation effects in these molecules lead to an important lowering in energy of the manifold of covalent states relative to that of the noncovalent states; most important, the first covalent (1A−g) state of the polyenes is found to be near degenerate with the strongly allowed noncovalent (1B+u) state. Density correlation functions and the fluctuation potential are obtained for the polyenes and used to clarify the nature of the correlation correction. Configuration interaction including double excitations is performed for polyenes through C12H14 to exhibit the length dependence of the correlation effects. It is shown that with increasing chain length, an increasing number of covalent states appears in the energy range of the two usually observed excited 1B+u and 1A+g (cis peak) states.
Preventing HIV Infection in Women: A Global Health Imperative (2010)

Women account for approximately one-half of all human immunodeficiency virus (HIV) infections worldwide. Sexual transmission is the dominant mode of HIV transmission to women, and there is a concomitant associated epidemic of transmission to infants. The majority of HIV infections in women are in sub-Saharan Africa, with a disproportionate burden in young women <25 years of age. Acquisition and prevention of HIV infection in women is complex and influenced by biological, behavioral, and structural factors. Efforts to reduce the incidence of HIV infection among women in sub-Saharan African could play a substantial role in altering global trajectories of HIV infection. Increasing access to sexual and reproductive health services, addressing gender-based violence and social instability, reducing poverty and the need to engage in sex for survival, and encouraging greater male responsibility are critical short-to-medium-term interventions. Efforts to find a microbicide and HIV vaccine need to be matched with efforts to deepen understanding of acquisition of HIV in the female genital tract to inform development of targeted molecules for prevention of HIV infection.
Engineering Aspects of Industrial Applications of Model-Based Control Techniques and System Theory (1993)

This paper describes some main engineering aspects of the design of robust, high performance industrial control systems. The importance of accurate modelling of relevant process dynamics is outlined. An identification procedure is discussed that robustly results in compact accurate models of all relevant process dynamics. The models obtained from process identification are embedded in internal model based control systems. The techniques have been successfully applied to many different processes. Two examples of applications are discussed: the control of a binary distillation column and the control of a low pressure gasphase polymerization reactor.