gebhart/patrepeval huggingface dataset:
A low FODMAP diet is associated with changes in the microbiota and reduction in breath hydrogen but not colonic volume in healthy subjects (2018)

A low FODMAP diet reduces total bacterial count and gas production with little effect on colonic volume.
An Integration Method to Identify Whirl Responses of A Rub-Impacting Rotor System (2006)

This study introduces the concept of an integration method in order to observe the vibration response problem of a rub-impacting rotor system. The method is called the P integration method, which can be applied to determine the response patterns of the system correctly, and then to avoid the misjudgment of the system response. This paper contributes to the development of efficient integration method to analyze and identify the whirl responses of a rotor system with rub-impact. This integration method numerically integrates the distance between state trajectory and the origin with pre-determined starting times of integration and predicted intervals due to excitation periods. This identification process is based on the fact that the integration would be constant if the integration interval is equal to the response period. According to the result comparisons from the rub-impacting rotor system, it is inferred that during Poincare section method being applied to be analyzed the system response periods, the sampling points on Poincare section might be too close to cause disturbances to analyze if the system response is a high-order sub-harmonic vibration. Thus, the misjudgments for system response periods will be made. This integration method provides a quantitative characterization of periodic motion. It is a useful tool to observe the periodic motion which generally cannot be easily distinguished from either the orbit plot or the Poincare map.
Structural and Biochemical Characterization of Cinnamoyl-CoA Reductases (2016)

Cinnamoyl-coenzyme A reductase (CCR) catalyzes the reduction of hydroxycinnamoyl-coenzyme A (CoA) esters using NADPH to produce hydroxycinnamyl aldehyde precursors in lignin synthesis. The catalytic mechanism and substrate specificity of cinnamoyl-CoA reductases from sorghum (Sorghum bicolor), a strategic plant for bioenergy production, were deduced from crystal structures, site-directed mutagenesis, and kinetic and thermodynamic analyses. Although SbCCR1 displayed higher affinity for caffeoyl-CoA or p-coumaroyl-CoA than for feruloyl-CoA, the enzyme showed significantly higher activity for the latter substrate. Through molecular docking and comparisons between the crystal structures of the Vitis vinifera dihydroflavonol reductase and SbCCR1, residues threonine-154 and tyrosine-310 were pinpointed as being involved in binding CoA-conjugated phenylpropanoids. Threonine-154 of SbCCR1 and other CCRs likely confers strong substrate specificity for feruloyl-CoA over other cinnamoyl-CoA thioesters, and the T154Y mutation in SbCCR1 led to broader substrate specificity and faster turnover. Through data mining using our structural and biochemical information, four additional putative CCR genes were discovered from sorghum genomic data. One of these, SbCCR2, displayed greater activity toward p-coumaroyl-CoA than did SbCCR1, which could imply a role in the synthesis of defense-related lignin. Taken together, these findings provide knowledge about critical residues and substrate preference among CCRs and provide, to our knowledge, the first three-dimensional structure information for a CCR from a monocot species.
The Boncuklu Project: the spread of farming and the antecedents of Çatalhöyük (2012)

d'Athènes, Balkan Futures is an international network which supports original research by a new generation of scholars in the field of Balkan regional studies.Since his arrival in September 2011, Marc has invested much energy in increasing the dialogue between the foreign institutes in Ankara.One of the results of this superb effort is the birth of
GHB Free Acid: II. Isolation and Spectroscopic Characterization for Forensic Analysis (2006)

A reference standard for gamma-hydroxybutyric acid (GHB) free acid is not commercially available, making its analysis in forensic exhibits more difficult. GHB free acid is typically encountered in aqueous solution and in the presence of the lactone, gamma-butyrolactone (GBL), presenting difficulty in Fourier transform infrared (FT-IR) analysis. The strong infrared (IR) absorptivity of the GBL carbonyl band, the shifting of the GBL carbonyl band in aqueous solutions, and the position of the O-H bend for water can mask the main carbonyl band for GHB free acid. Model solutions of beta-hydroxybutyric acid (BHB) and GBL were studied in order to further understand the masking of the GHB free acid carbonyl band in FT-IR analysis. The use of second derivative FT-IR spectroscopy was shown to provide resolution of the free acid carbonyl band, and a presumptive test for GHB free acid was developed and applied. An extension of this work included preparing, for use as a standard reference material, small amounts (< or = 10 mg) of GHB free acid. Preparation was based on the instantaneous reaction of GHB's sodium salt with a stoichiometric amount of hydrochloric acid in aqueous solution, and subsequent isolation of the free acid in neat liquid form. Both FT-IR and proton nuclear magnetic resonance spectra of the neat reference material were obtained and used to verify its identity. The isolation of GHB free acid from actual forensic exhibits is also presented, with identity confirmation using FT-IR.
Combining functional genomics strategies identifies modular heterogeneity of breast cancer intrinsic subtypes (2014)

Overall, modular heterogeneity provides a framework with which to dissect cancer heterogeneity and better understand its underpinnings, thereby ultimately advancing our knowledge towards a more effective personalized cancer therapy.
Complete Genome Sequence of the Probiotic Strain Lactobacillus casei (Formerly Lactobacillus paracasei) LOCK919 (2013)

Lactobacillus casei is usually regarded as a bacterium that lives naturally in the human intestinal tract, where it can contribute to host health and well-being. We describe here the complete genome sequence of L. casei LOCK919, a strain with probiotic properties isolated from child feces. The genome consists of a 3.11-Mb chromosome and a 29,768-bp plasmid.
AIM: attentionally based interaction model for the interpretation of vascular angiography (1999)

We propose a model to interpret neurovascular X-ray angiogram (XRA) images interactively. This attentionally based interactive model (AIM) exploits human interaction as part of the solution. AIM posits two channels of interaction: context ("what to look for") and focus-of-attention ("where to look") as the locus of spatial information exchange between the user and the machine. In an AIM system, the user specifies a context (e.g., a carotid vessel) and directs the attentional spotlight to focus machine processing. AIM involves the user with the computer as integral partners and facilitates varying degrees of human intervention in the process. A hierarchy of context abstractions permits the system to function more autonomously (doing high-level tasks like extracting an arterial vessel) in routine interpretation and to require more user intervention (e.g., locating arterial wall boundaries) as the image complexity increases. This is especially important in medical imaging where the medical professional must have ultimate control and confidence in the system. Such technology can have a significant impact on the design of radiological systems.
Enabling large-scale scientific workflows on petascale resources using MPI master/worker (2012)

Computational scientists often need to execute large, loosely-coupled parallel applications such as workflows and bags of tasks in order to do their research. These applications are typically composed of many, short-running, serial tasks, which frequently demand large amounts of computation and storage. In order to produce results in a reasonable amount of time, scientists would like to execute these applications using petascale resources. In the past this has been a challenge because petascale systems are not designed to execute such workloads efficiently. In this paper we describe a new approach to executing large, fine-grained workflows on distributed petascale systems. Our solution involves partitioning the workflow into independent subgraphs, and then submitting each subgraph as a self-contained MPI job to the available resources (often remote). We describe how the partitioning and job management has been implemented in the Pegasus Workflow Management System. We also explain how this approach provides an end-to-end solution for challenges related to system architecture, queue policies and priorities, and application reuse and development. Finally, we describe how the system is being used to enable the execution of a very large seismic hazard analysis application on XSEDE resources.
Improved tetrahedron method for Brillouin-zone integrations (1994)

Several improvements of the tetrahedron method for Brillouin-zone integrations are presented. (1) A translational grid of k points and tetrahedra is suggested that renders the results for insulators identical to those obtained with special-point methods with the same number of k points. (2) A simple correction formula goes beyond the linear approximation of matrix elements within the tetrahedra and also improves the results for metals significantly. For a required accuracy this reduces the number of k points by orders of magnitude. (3) Irreducible k points and tetrahedra are selected by a fully automated procedure, requiring as input only the space-group operations. (4) The integration is formulated as a weighted sum over irreducible k points with integration weights calculated using the tetrahedron method once for a given band structure. This allows an efficient use of the tetrahedron method also in plane-wave-based electronic-structure methods.
Evaluating the Older Patient with Cancer: Understanding Frailty and the Geriatric Assessment (2010)

The majority of cancer incidence and mortality occurs in individuals aged older than 65 years, and the number of older adults with cancer is projected to significantly increase secondary to the aging of the US population. As such, understanding the changes accompanying age in the context of the cancer patient is of critical importance. Age-related changes can impact tolerance of anticancer therapy and can shift the overall risk-benefit ratio of such treatment. A challenge in implementing evidence-based approaches in older adults is the under-representation of this group in oncology clinical trials. In addition, although older adults are particularly vulnerable to the side effects of cancer therapy, few oncology studies to date have incorporated a measure of health status other than the Eastern Cooperative Oncology Group or Karnofsky performance scales. Novel metrics such as frailty indices or the geriatric assessment recognize heterogeneity among older adults, and may allow for risk-adapted approaches to therapy. It is increasingly recognized that several laboratory markers may predict morbidity and mortality in older adults; these biologic variables may further aid in stratifying this group of patients based on risk. This review describes key studies from the geriatric literature that provide principles for assessing health status in the older patient, and ways that these principles can be applied to oncology care in an older population are proposed.
A Flexible Method for the Conjugation of Aminooxy Ligands to Preformed Complexes of Nucleic Acids and Lipids (2008)

Attachment of targeted ligands to nonviral DNA or RNA delivery systems is a promising strategy that seeks to overcome the poor target selectivity generally observed in systemic delivery applications. Several methods have been developed for the conjugation of ligands to lipids or polymers, however, direct conjugation of ligands onto lipid- or polymer-nucleic acid complexes is not as straightforward. Here, we examine an oximation approach to directly label a lipoplex formulation. Specifically, we report the synthesis of a cationic diketo lipid DMDK, and its use as a convenient ligation tool for attachment of aminooxy-functionalized reagents after its complexation with DNA. We demonstrate the feasibility of direct lipoplex labeling by attaching an aminooxy-functionalized fluorescent probe onto pre-formed plasmid DNA-DMDK lipoplexes (luciferase, GFP). The results reveal that DMDK protects DNA from degradation on exposure to either DNase or human cerebral spinal fluid, and that simple mixing of DMDK lipoplexes with the aminooxy probe labels the complexes without sacrificing transfection efficiency. The biocompatibility and selectivity of this method, as well as the ease of bioconjugation, make this labeling approach ideal for biological applications.
Specific Detection of <scp>d</scp>-Glucose by a Tetraphenylethene-Based Fluorescent Sensor (2010)

A conceptually new "light-up" biosensor with a high specificity for d-glucose (Glu) in aqueous media has been developed. The emission from a tetraphenylethene (TPE)-cored diboronic acid (1) was greatly boosted when the fluorogen was oligomerized with Glu because of restriction of the intramolecular rotations of the aryl rotors of TPE by formation of the oligomer. Little change in the light emission was observed when 1 was mixed with D-fructose, D-galactose, or D-mannose, as these saccharides are unable to oligomerize with the fluorogen.
<sup>19</sup>F nuclear magnetic resonance imaging of drug distribution in vivo: The disposition of an antifolate anticancer drug in mice (1991)

The application of 19F nuclear magnetic resonance imaging to the study of drug distribution in vivo is discussed. CB3988 (C2-desamino-C2-methyl-N10-propargyl-2'-trifluoromethyl-5,8-dideazafolic acid) is a fluorinated representative of a class of quinazoline antifolates which act as inhibitors of thymidylate synthase and which are being evaluated for the treatment of human cancer. 19F images were obtained in vivo from the abdomen of mice following intravenous injection of CB3988 (500 mg/kg). Time resolutions of 4 and 20 min were achieved for two- and three-dimensional imaging, respectively. These images were consistent with the presence of high concentrations of drug (up to 26 mg/ml) in the gall bladder, urinary bladder, and small intestine, as confirmed ex vivo by extraction and HPLC analysis. The results indicate the potential value of 19F NMR imaging in pharmacokinetic studies.
Dapsone in the Treatment of Cutaneous Lupus erythematosus (1986)

Thirty-three patients with chronic discoid lupus erythematosus (DLE) who had received dapsone for 1-27 months were reviewed. The dapsone treatment gave excellent results in 8 patients (24%), some effect in 8 patients (24%), while no response was seen in 17 patients (52%). Of the patients who had earlier been treated with hydroxychloroquine (HCQ), 76% responded excellently to the treatment. Of 6 patients who received a combined dapsone and HCQ therapy, 2 responded well. Six patients (18%) terminated the dapsone treatment because of side effects, none of which were serious. It is concluded that dapsone might be an alternative or a supplement to HCQ in the treatment of DLE, when the latter causes adverse reactions or fails to be effective. However, we find that HCQ remains the drug of choice when systemic treatment is needed.
2.5 Gbit/s directly-modulated fibre grating laserfor WDM networks (1997)

Very low wavelength chirp (static < 0.07 GHz/mA and dynamic < 0.09 GHz/mA) was measured for a directly-modulated fibre grating laser with an angled facet semiconductor chip and a short fibre grating. Low-penalty transmission at 2.5 Gbit/s over 312 km of standard singlemode fibre has been demonstrated using this low-chirp device.
Financial Management: An Introduction (1999)

Part 1: The Scope and Environment of Financial Management 1. Introduction and Overview 2. Key Issues in Modern Financial Management 3. The Financial Environment 4. Capital Markets Part 2: The Core Concepts in Financial Management 5. The Time Value of Money 6. Risk and Return - Portfolio Theory 7. Risk and Return - The Capital Asset Pricing Model (CAPM) 8. The Central Concept of Value Case Study 1 Share Valuation Part 3: Financial Analysis and Performance Evaluation 9. Financial Analysis and Performance Evaluation Case Study 2 Part 4: Strategic Financial Decision-Making - The Investment Decision 10. Investment Appraisal Introduction 11. Investment Appraisal - Risk Analysis 12. The Cost of Capital Case Study 3 Part 5: Strategic Financial Decision Making - The Financial Decision 13. Capital Structure and Gearing 14. Dividend Policy Part 6: Financial Planning and Control 15. Financial Planning and Control Part 7 Short-Term Financial Management 16. Short-Term Financial Planning 17. Working Capital Management 1 18. Working Capital Management 2 19. Short and Medium Term Sources of Finance Case Study 4
Facile Synthesis of 1,4-Benzodiazepin-5-ones via Intramolecular Aza-Wittig Reaction<sup>1</sup> (1992)

A new and efficient synthetic method for 4-alkoxy-1,4-benzodiazepin-5-ones 4 has been developed by utilizing tandem Staudinger reaction and intramolecular aza-Wittig reaction of [N-(o-azidobenzoyl)]-α-amino esters 3.
Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells (2007)

Constitutive heterochromatin mainly consists of different classes of satellite DNAs and is defined as a transcriptionally inactive chromatin that remains compact throughout the cell cycle. The aim of this work was to investigate the level of condensation, methylation and transcriptional status of centromeric (alphoid DNA) and pericentromeric satellites (human satellite 3, HS3) in tissues (lymphocytes, placenta cells) and in cultured primary (MRC5, VH-10, AT2Sp) and malignant (A431) cells. We found that alphoid DNA remained condensed and heavily methylated in all the cell types. The HS3 of chromosome 1 (HS3-1) but not of chromosome 9 (HS3-9) was strongly decondensed and demethylated in A431 cells. The same observation was made for aged embryonic lung (MRC5) and juvenile foreskin (VH-10) fibroblasts obtained at late passages (32(nd) and 23(rd), respectively). Decondensation was also found in ataxia telangiectasia AT2Sp fibroblasts at the 16(th) passage. One of the manifestations of the disease is premature aging. The level of HS3-1 decondensation was higher in aged primary fibroblasts as compared to A431. The HS3-1 extended into the territory of neighbouring chromosomes. An RT-PCR product was detected in A431 and senescent MRC5 fibroblasts using primers specific for HS3-1. The RNA was polyadenylated and transcribed from the reverse chain. Our results demonstrate the involvement of satellite DNA in associations between human chromosomes and intermingling of chromosome territories. The invading satellite DNA can undergo decondensation to a certain level. This process is accompanied by demethylation and transcription.
Canola/Rapeseed Protein: Future Opportunities and Directions—Workshop Proceedings of IRC 2015 (2016)

At present, canola meal is primarily streamlined into the animal feed market where it is a competitive animal feed source owing to its high protein value. Beyond animal feed lies a potential game-changer with regards to the value of canola meal, and its opportunity as a high quality food protein source. An economic and sustainable source of protein with high bioavailability and digestibility is essential to human health and well-being. Population pressures, ecological considerations, and production efficiency underscore the importance of highly bioavailable plant proteins, both for the developed and developing world. Despite decades of research, several technologies being developed, and products being brought to large scale production, there are still no commercially available canola protein products. The workshop entitled "Canola/Rapeseed Protein-Future Opportunities and Directions" that was held on 8 July 2015 during the 14th International Rapeseed Congress (IRC 2015) addressed the current situation and issues surrounding canola meal protein from the technological, nutritional, regulatory and genomics/breeding perspective. Discussions with participants and experts in the field helped to identify economic barriers and research gaps that need to be addressed in both the short and long term for the benefit of canola industry.
Dynamics of collaborative document rating systems (2007)

The rise of social media sites, such as blogs, wikis, Digg and Flickr among others, underscores a transformation of the Web to a participatory medium in which users are actively creating, evaluating and distributing information. The social news aggregator Digg allows users to submit links to and vote on news stories. Like other social media sites, Digg also allows users to designate others as "friends" and easily track friends' activities: what new stories they submitted, commented on or liked. Each day Digg selects a handful of stories to feature on its front page. Rather than rely on the opinion of a few editors, Digg aggregates opinions of thousands of its users to decide which stories to promote to the front page. We construct a mathematical model to study how collaborative rating and promotion of news stories emerges from independent decisions made by many users. The model takes into account user behavior: e.g., whether they read stories on the front page or through the Friends interface. Solutions of the model qualitatively reproduce the observed dynamics of votes received by actual stories on Digg.
Differential response in allergen‐specific IgE, IgGs, and IgA levels for predicting outcome of oral immunotherapy (2016)

The response to OIT was associated with significant increases in serum allergen-specific IgG1 levels after rush phase and high baseline IgA levels, compared with small changes in immunoglobulin response in low-responders. The characteristic IgG1 changes and IgA levels in the responders could be potentially useful biomarkers for the prediction of positive clinical response to OIT.
Separation and Conversion Dynamics of Four Nuclear Spin Isomers of Ethylene (2005)

Molecules with three or more nuclei of nonzero spin exist as discrete spin isomers whose interconversion in the gas phase is generally considered improbable. We have studied the interconversion process in ethylene by creating a sample depleted in the B2u nuclear spin isomer. The separation was achieved through spatial drift of this isomer induced by resonant absorption of narrow-band infrared light. Evolution of the depleted sample revealed conversion between B2u and B3u isomers at a rate linearly proportional to pressure, with a rate constant of 5.5 (+/-0.8) x 10(-4) s(-1) torr(-1). However, almost no change was observed in the Ag isomer populations. The results suggest a spin conversion mechanism in C2H4 via quantum relaxation within the same inversion symmetry.
Computational algorithms for closed queueing networks with exponential servers (1973)

Methods are presented for computing the equilibrium distribution of customers in closed queueing networks with exponential servers. Expressions for various marginal distributions are also derived. The computational algorithms are based on two-dimensional iterative techniques which are highly efficient and quite simple to implement. Implementation considerations such as storage allocation strategies and order of evaluation are examined in some detail.