gebhart/patrepeval huggingface dataset:
Validation of a food frequency questionnaire to assess folate intake of Dutch elderly people (2007)

Folate is required for 1-carbon metabolism and deficiency in folate leads to megaloblastic anemia. Low levels of folate have been associated with increased risk of vascular disease. To investigate whether RDA of folate are met, habitual folate intake needs to be assessed reliably. We developed a FFQ to specifically measure folate intake over the previous 3 months in elderly people in the Netherlands. Major sources of folate intake, i.e. foods contributing to at least 80% of the average folate intake, were identified through an analysis of the second Dutch Food Consumption Survey for the sub-population of men and women aged 50-70. In 2000 and 2001, folate intake was estimated with this questionnaire in 1286 individuals aged 50-75 years. Concentrations of serum and erythrocyte folate served as biomarkers with which relative validity of the questionnaire was assessed. The same FFQ was repeated after 3 years in 803 subjects in order to assess long-term reproducibility. Mean folate intake was estimated to be 196 (SD 69) microg/d. Spearman correlation coefficients between folate intake and serum and erythrocyte concentrations were 0.14 (P < 0.01) and 0.05 (P = 0.06) respectively. Spearman correlations between folate intakes measured at baseline and after 3 years were 0.58 (P < 0.01). 47% of the participants were classified in the same quartiles on the two occasions. Our FFQ showed a weak correlation between folate intake and blood folate concentrations and reproducibility was acceptable. This FFQ is able to rank subjects according to their folate intake.
The grid protocol: a high performance scheme for maintaining replicated data (2002)

A protocol for maintaining replicated data that can provide both high data availability and low response time is presented. Existing protocols are designed primarily to achieve high availability by updating a large fraction of the copies, which provides some (although not significant) load sharing. In the new protocol, transaction processing is shared effectively among nodes storing copies of the data, and both the response time experienced by transactions and the system throughput are improved significantly. Also presented is an analysis of the availability of the new protocol and simulation is used to study the effect of load sharing on the response time of transactions. The new protocol is also compared with a voting-based scheme.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Amino‐terminal truncation of procalcitonin, a marker for systemic bacterial infections, by dipeptidyl peptidase IV (DP IV) (2000)

Increased concentrations of procalcitonin (PCT) are found in the plasma of patients with thermal injury and in patients with sepsis and severe infection, making this molecule important as a diagnostic and prognostic marker in these diseases. Interestingly, only the truncated form of PCT, PCT(3-116), is present in the plasma of these patients. The enzyme responsible for this truncation is unknown as yet. Here, using capillary zone electrophoresis, mass spectrometry and Edman sequence analysis, we demonstrate that dipeptidyl peptidase IV (DP IV, EC 3.4.14.5) is capable of catalyzing the hydrolysis of PCT(1-116), releasing the N-terminal dipeptide Ala-Pro. We hypothesize that PCT(3-116) is the result of the hydrolysis of PCT(1-116) by soluble DP IV of the blood plasma or by DP IV expressed on the surface of cells.
High-Speed InGaAs Photodetectors by Selective-Area MOCVD Toward Optoelectronic Integrated Circuits (2014)

We report selective-area growth of high-crystalline-quality InGaAs-based photodetectors with optimized InP/GaAs buffers on patterned (100)-oriented silicon-on-insulator (SOI) substrates by metal-organic chemical vapor deposition. The composite GaAs and InP buffer was grown using a two-temperature method. The island morphology of the low-temperature GaAs nucleation layer inside the growth well of the SOI substrate was optimized. A medium temperature GaAs layer was inserted prior to the typical high-temperature GaAs to further decrease the dislocation densities and antiphase boundaries. Both normal-incidence photodetectors and butt-coupled waveguide photodetectors were fabricated on the same substrate and showed a low dark current and high-speed performance. This result demonstrates a good potential of integrating photonic and electronic devices on the same Si substrate by direct epitaxial growth.
An efficient Escherichia coli expression system for the production of a functional N-terminal domain of the T1R3 taste receptor (2012)

Sweet taste is mediated by a dimeric receptor composed of two distinct subunits, T1R2 and T1R3, whereas the T1R1/T1R3 receptor is involved in umami taste perception. The T1R1, T1R2, and T1R3 subunits are members of the small family of class C G protein-coupled receptors (GPCRs). The members of this family are characterized by a large N-terminal domain (NTD), which is structurally similar to bacterial periplasmic-binding proteins and contains the primary ligand-binding site. In a recent study, we described a strategy to produce a functional dimeric human T1R3-NTD. Although the protein was expressed as inclusion bodies (IBs) using the Escherichia coli system, the conditions for the refolding of functional hT1R3-NTD were determined using a fractional factorial screen coupled to a binding assay. Here, we report that this refolding strategy can be used to produce T1R1- and T1R2-NTDs in large quantities. We also discuss that our findings could be more generally applicable to other class C GPCR-NTDs, including the γ-aminobutyric acid type B receptor (GABABR), the extracellular calcium-sensing receptor (CaSR) and the large family of pheromone (V2R) orphan receptors.
One-hand control of a speech synthesizer (2004)

The long-term objective of this research is the development of a one-hand-controlled speech synthesizer, to give laryngectomees and other speech-impaired persons a means of producing higher-quality speech with less effort than currently available methods such as an electrolarynx or a text-to-speech system. To demonstrate the feasibility of a one-hand-controlled speech synthesizer, a system was constructed using a hand-held device similar to a pen connected to an articulated arm for measuring six degrees of freedom (three Cartesian and three rotational dimensions) as the user interface to an HLsyn-based speech synthesizer. Through this interface, the user controls parameters for the first three formants, pitch, subglottal pressure, and glottal area. Parameter control was introduced progressively in that order to four participants who underwent training to produce synthesized speech composed of a subset of English phonemes: vowels, semivowels, diphthongs, /h/, and the glottal stop. The complexity of the synthesized speech targets also grew from monosyllabic utterances to short phrases over the training. After training, a separate group of four listeners compared the naturalness and intelligibility of the synthesized speech to the same utterances produced by the participants with a text-to-speech system. [Work supported by NIDCD Grant Number R43 DC006134-01.]
Acoustofluidics – changing paradigm in tissue engineering, therapeutics development, and biosensing (2023)

For more than 70 years, acoustic waves have been used to screen, diagnose, and treat patients in hundreds of medical devices. The biocompatible nature of acoustic waves, their non-invasive and contactless operation, and their compatibility with wide visualization techniques are just a few of the many features that lead to the clinical success of sound-powered devices. The development of microelectromechanical systems and fabrication technologies in the past two decades reignited the spark of acoustics in the discovery of unique microscale bio applications. Acoustofluidics, the combination of acoustic waves and fluid mechanics in the nano and micro-realm, allowed researchers to access high-resolution and controllable manipulation and sensing tools for particle separation, isolation and enrichment, patterning of cells and bioparticles, fluid handling, and point of care biosensing strategies. This versatility and attractiveness of acoustofluidics have led to the rapid expansion of platforms and methods, making it also challenging for users to select the best acoustic technology. Depending on the setup, acoustic devices can offer a diverse level of biocompatibility, throughput, versatility, and sensitivity, where each of these considerations can become the design priority based on the application. In this paper, we aim to overview the recent advancements of acoustofluidics in the multifaceted fields of regenerative medicine, therapeutic development, and diagnosis and provide researchers with the necessary information needed to choose the best-suited acoustic technology for their application. Moreover, the effect of acoustofluidic systems on phenotypic behavior of living organisms are investigated. The review starts with a brief explanation of acoustofluidic principles, the different working mechanisms, and the advantages or challenges of commonly used platforms based on the state-of-the-art design features of acoustofluidic technologies. Finally, we present an outlook of potential trends, the areas to be explored, and the challenges that need to be overcome in developing acoustofluidic platforms that can echo the clinical success of conventional ultrasound-based devices.
Exploiting nonlinear structure in hyperspectral coastal data (2006)

In this paper, we investigate the use of nonlinear structure to derive the physical characteristics of coastal data. In particular, we show how the physics of shallow water coastal regions lead to well defined nonlinear structures (manifolds) in the corresponding hyperspectral data. The exact form of this structure is determined by both the Inherent Optical Properties of the water column as well as the boundary conditions (bottom reflectance, depth). This structure is then used to develop efficient algorithms for searching large 'lookup tables' of precalculated spectra with known physical characteristics, which are used for estimating the various physical parameters (bathymetry, bottom type, etc.) of the scene. We assess our methods with data collected by the NRL PHILLS sensor at the Indian River Lagoon (IRL) in Florida. The IRL is a well-studied and characterized body of water that contains a number of different water and bottom types at various shallow (generally less than 8 meters, except in the shipping channel where depths can be as much as 18 m) depths. We show in particular that the search algorithm is able to produce valid results in a short amount of time, and compare our results with an IRL LIDAR bathymetry survey from early 2004.
Design of Thermoresponsive Polyamine Cross-Linked Perfluoropolyether Hydrogels for Imaging and Delivery Applications (2020)

Perfluorocarbons are versatile compounds with applications in <sup>19</sup>F magnetic resonance imaging (MRI) and chemical conjugation to drugs and pH sensors. We present a novel thermoresponsive perfluorocarbon emulsion hydrogel that can be detected by <sup>19</sup>F MRI. The developed hydrogel contains perfluoro(polyethylene glycol dimethyl ether) (PFPE) emulsion droplets that are stabilized through ionic cross-linking with polyethylenimine (PEI). Specifically, PFPE ester undergoes hydrolysis upon contact with aqueous PEI solution, resulting in an ionic bond between the PFPE acid and charged PEI amino groups. Due to the ionic nature of the PFPE/PEI bond, potassium buffer is required to preserve the hydrogel's pH and rheological and emulsion droplet stability. The presence of the surface cross-linked PFPE droplets does not affect the hydrogel's rheological behavior, drug loading, or drug release, and the hydrogel is nontoxic. We propose that the presented hydrogel can be adapted to a broad range of biomedical imaging and delivery applications.
Audio Interview: Covid-19 and Contact Tracing (2020)

Covid-19 and Contact Tracing In this audio interview conducted on August 19, 2020, the editors discuss the use of contact tracing to limit the spread of SARS-CoV-2 and the challenges posed by certa...
Surge-in-Place: Conversion of a Cardiac Catheterization Laboratory Into a COVID-19 Intensive Care Unit and Back Again (2020)

We describe our experience transforming our cardiac catheterization laboratories to accommodate an influx of COVID-19 patients so as to provide other hospitals with a potential blueprint. from Journal of Invasive Cardiology.
TH-E-110-03: Simultaneous Acquisition of Scatter and Image Data in CBCT Using a Novel Half Beam Blocker Method and a FDK Based Reconstruction Algorithm (2011)

Purpose: We propose a half blocker-based approach, in conjunction with a Feldkamp-Davis-Kress (FDK) algorithm, to correct scatter-induced shading artifacts by simultaneously acquiring image and scatter information from a single-rotation CBCT scan. Methods: A custom beam blocker, comprising of finely spaced lead strips, was mounted to the kV x-ray source of the Varian TrueBeam OBI system in a novel manner that enables image data acquisition on one side of the projection data and scatter data measurement on the other half side. Using the scatter distributions on strips, interpolation and extrapolation are applied to arrive at patient specific scatter information for the CBCT scan. The estimated scatter is subtracted from the image data of projection image acquired at the opposite view. To suppress the noise level produced by geometric errors between two opposed projections and interpolated scatter information, total variation regularization is applied by the minimization procedure based on the steepest gradient decent optimization. With half regions of all projections where subtraction and regularization steps are completed, a FDK algorithm based on cosine weighting function is performed to reconstruct CBCT volume. The experimental studies using Catphan504 phantom were carried out to evaluate the performance of the proposed scheme. Results: The scatter- induced shading artifacts were markedly suppressed in CBCT using the proposed scheme. Compared with CBCT without a blocker, the mean relative error and CT number errors in the regions of interest were significantly reduced to 2% and less than 20. Also, the proposed approach showed the contrast-to-noise ratio with spatial resolution comparable to images reconstructed with scatter-free projections acquired from narrow x- ray collimation. Conclusions: A half blocker-based FDK reconstruction algorithm has been established. The proposed scheme simultaneously reduces imaging dose at shaded regions and leads to complete volumetric information from current CBCT acquisition protocol without additional requirements such as prior images, dual scans, or moving strips. This work was supported in part by Mid-career Researcher Program (2009- 0085999) through NRF grant funded by the MEST and in part by the Industrial Strategic Technology Development Program (10035495) funded by the Ministry of Knowledge Economy (MKE, Korea).
Learning Graphical Model Parameters with Approximate Marginal Inference (2013)

Likelihood-based learning of graphical models faces challenges of computational complexity and robustness to model misspecification. This paper studies methods that fit parameters directly to maximize a measure of the accuracy of predicted marginals, taking into account both model and inference approximations at training time. Experiments on imaging problems suggest marginalization-based learning performs better than likelihood-based approximations on difficult problems where the model being fit is approximate in nature.
A Fresh Ruin & Recreate Implementation for the Capacitated Vehicle Routing Problem (2016)

Problems such as the Capacitated Vehicle Routing Problem (CVRP) attract both mathematical modellers and heuristic approaches. At present, exact mathematical approaches are capable of solving some CVRP instances with up to 360 customers. The excessive computation times incurred by such exact models does, however, severely limit their practical applicability within logistics and transportation sectors. By contrast, heuristic approaches are generally faster and easier to adapt to other problems, albeit at the expense of solution quality. Ruin & recreate represents one such heuristic approach. However, recent ruin & recreate heuristics, while being deployed for more and more problems, have been concomitant with an additive trend whereby the quantity of ruin methods and recreate methods has been systematically increasing. Essentially, improved ruin & recreate results regularly coincide with challenging to reproduce methods. This paper's approach (ASB-RR), by contrast, is formed of a single ruin method, adjacent string removal, and a single recreate method, greedy insertion with blinks. ASB-RR exhibits low computation times, robustness and yields a high number of improved benchmark solutions when compared against state of the art CVRP algorithms. Furthermore, the approach may be easily redeployed for similar problems within the field of vehicle routing.
Native Plants: The Preservation and Restoration of Native Plants in Designed Landscapes in Northwest Arkansas (2002)

A decline in Northwest Arkansas's native plant population has occurred over the past 50 years, as documented by the U.S. Forest Service in the Ozark-Ouachita Highlands Assessment. This decline has been caused by increased human development in natural areas and the replacement of native plants with exotic, non-native plants. As a result, a generation has grown up not knowing what an Ozark wake Robin trillium (Trillium pusillum var. ozarkanum) or Blood root (Sanguinaria canadensis) Look like, because these plants are difficult to find in nature, are not commonly grown in designed landscapes, and are Largely unavailable in garden centers. The loss of Arkansas's native plants has led to a second problem: the loss of the region's landscape identity. A proposed solution focuses on restoring the region's landscape identity by landscaping with native plants. The benefits of native plants include the following: the creation of native habitats, an increase in biodiversity, the conservation of natural resources, a reduction in long-term landscape costs and a decrease in landscape maintenance requirements and costs. Interviews with regional suppliers and users of native plants identified sources of information and methods of growing these plants. As a result, guidelines on how to incorporate native plants into designed landscapes were developed and are presented with a listing of native plant experts and nurseries, a partial listing of plants for Northwest Arkansas (organized by site conditions), a suggested reading and reference list, and a listing of public gardens that emphasize native plants
Primary functional brain connections associated with melancholic major depressive disorder and modulation by antidepressants (2020)

The limited efficacy of available antidepressant therapies may be due to how they affect the underlying brain network. The purpose of this study was to develop a melancholic MDD biomarker to identify critically important functional connections (FCs), and explore their association to treatments. Resting state fMRI data of 130 individuals (65 melancholic major depressive disorder (MDD) patients, 65 healthy controls) were included to build a melancholic MDD classifier, and 10 FCs were selected by our sparse machine learning algorithm. This biomarker generalized to a drug-free independent cohort of melancholic MDD, and did not generalize to other MDD subtypes or other psychiatric disorders. Moreover, we found that antidepressants had a heterogeneous effect on the identified FCs of 25 melancholic MDDs. In particular, it did impact the FC between left dorsolateral prefrontal cortex (DLPFC)/inferior frontal gyrus (IFG) and posterior cingulate cortex (PCC)/precuneus, ranked as the second 'most important' FC based on the biomarker weights, whilst other eight FCs were normalized. Given that left DLPFC has been proposed as an explicit target of depression treatments, this suggest that the limited efficacy of antidepressants might be compensated by combining therapies with targeted treatment as an optimized approach in the future.
Tumour inflammasome‐derived IL‐1β recruits neutrophils and improves local recurrence‐free survival in EBV‐induced nasopharyngeal carcinoma (2012)

Inflammasomes sense infection and cellular damage and are critical for triggering inflammation through IL-1β production. In carcinogenesis, inflammasomes may have contradictory roles through facilitating antitumour immunity and inducing oncogenic factors. Their function in cancer remains poorly characterized. Here we show that the NLRP3, AIM2 and RIG-I inflammasomes are overexpressed in Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC), and expression levels correlate with patient survival. In tumour cells, AIM2 and RIG-I are required for IL-1β induction by EBV genomic DNA and EBV-encoded small RNAs, respectively, while NLRP3 responds to extracellular ATP and reactive oxygen species. Irradiation and chemotherapy can further activate AIM2 and NLRP3, respectively. In mice, tumour-derived IL-1β inhibits tumour growth and enhances survival through host responses. Mechanistically, IL-1β-mediated anti-tumour effects depend on infiltrated immunostimulatory neutrophils. We show further that presence of tumour-associated neutrophils is significantly associated with better survival in NPC patients. Thus, tumour inflammasomes play a key role in tumour control by recruiting neutrophils, and their expression levels are favourable prognostic markers and promising therapeutic targets in patients.
A quantum lab in a beam (2022)

Advances in electron microscopy have revolutionized atomic-scale imaging, characterization, and manipulation of materials.
International European Respiratory Society/American Thoracic Society guidelines on severe asthma (2014)

From the authors: 

We thank J. Bousquet and colleagues for their concerns regarding exclusion of “untreated asthma” as a form of severe asthma, with respect to the recently published international European Respiratory Society (ERS)/American Thoracic Society (ATS) guidelines on severe asthma [1].

We do recognise this category of untreated asthma and agree that untreated asthma may result in serious exacerbations of disease and death, an issue that is not confined to developing countries alone. Indeed, everywhere in the world, untreated asthma can result from lack of access to medical care but can also result not only from nonadherence to therapy or of inadequately treated asthma. As emphasised in the ERS/ATS guideline definitions, these issues …
Figuring out the User in a Few Steps (2019)

Can a system discover what a user wants without the user explicitly issuing a query? A recommender system proposes items of potential interest based on past user history. On the other hand, active search incites, and learns from, user feedback, in order to recommend items that meet a user's current tacit interests, hence promises to offer up-to-date recommendations going beyond those of a recommender system. Yet extant active search methods require an overwhelming amount of user input, relying solely on such input for each item they pick. In this paper, we propose MF-ASC, a novel active search mechanism that performs well with minimal user input. MF-ASC combines cheap, low-fidelity evaluations in the style of a recommender system with the user's high-fidelity input, using Gaussian process regression with multiple target variables (cokriging). To our knowledge, this is the first application of cokriging to active search. Our empirical study with synthetic and real-world data shows that MF-ASC outperforms the state of the art in terms of result relevance within a budget of interactions.