gebhart/patrepeval huggingface dataset:
Correction: A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads (2013)

The advent of next-generation sequencing technologies has greatly promoted the field of metagenomics which studies genetic material recovered directly from an environment. Characterization of genomic composition of a metagenomic sample is essential for understanding the structure of the microbial community. Multiple genomes contained in a metagenomic sample can be identified and quantitated through homology searches of sequence reads with known sequences catalogued in reference databases. Traditionally, reads with multiple genomic hits are assigned to non-specific or high ranks of the taxonomy tree, thereby impacting on accurate estimates of relative abundance of multiple genomes present in a sample. Instead of assigning reads one by one to the taxonomy tree as many existing methods do, we propose a statistical framework to model the identified candidate genomes to which sequence reads have hits. After obtaining the estimated proportion of reads generated by each genome, sequence reads are assigned to the candidate genomes and the taxonomy tree based on the estimated probability by taking into account both sequence alignment scores and estimated genome abundance. The proposed method is comprehensively tested on both simulated datasets and two real datasets. It assigns reads to the low taxonomic ranks very accurately. Our statistical approach of taxonomic assignment of
Shortened onset of action of antidepressants in major depression using acetylsalicylic acid augmentation: a pilot open-label study (2006)

Based on our preclinical data showing a potential accelerating effect of acetylsalicylic acid (ASA) in combination with fluoxetine in an animal model of depression, we examined the effect of ASA augmentation therapy on selective reuptake inhibitors (SSRI) in major depressed non-responder patients. Twenty-four non-responder patients having received at least 4 weeks of an adequate SSRI treatment were included in a pilot open-label study. Participants were treated openly during 4 weeks with 160 mg/day ASA in addition to their current antidepressant treatment. The combination SSRI-ASA was associated with a response rate of 52.4%. Remission was achieved in 43% of the total sample and 82% of the responder sample. In the responder group, a significant improvement was observed within week 1 (mean Hamilton Depression Rating Scale-21 items at day 0=29.3+/-4.5, at day 7=14.0+/-4.1; P<0.0001) and remained sustained until day 28. Despite limitations due to the open nature of this study, our preliminary results confirm our preclinical findings and are in favour of an accelerating effect of ASA in combination with SSRIs in the treatment of major depression. Potential physiological and biochemical mechanisms may involve an anti-inflammatory and/or neurotrophic effect.
Organometallic Compounds. XXIII (). Matrix representation of octahedral and prismatic stereoisomers and of their interconversion reactions (1971)

Abstract Matrix representations are given to describe how octahedral and trigonal prismatic stereoisomers are converted into one another.
Interstitial Flow Promotes the Formation of Functional Microvascular Networks In Vitro through Upregulation of Matrix Metalloproteinase‐2 (2022)

Self-organized microvascular networks (MVNs) have become key to the development of many microphysiological models. However, the self-organizing nature of this process combined with variations between types or batches of endothelial cells (ECs) often lead to inconsistency or failure to form functional MVNs. Since interstitial flow (IF) has been reported to play a beneficial role in angiogenesis, vasculogenesis, and 3D capillary morphogenesis, we systematically investigated the role IF plays during neovessel formation in a customized single channel microfluidic chip for which IF has been fully characterized. Compared to static conditions, MVNs formed under IF have higher vessel density and diameters and greater network perfusability. Through a series of inhibitory experiments, we demonstrated that IF treatment improves vasculogenesis by ECs through upregulation of matrix metalloproteinase-2 (MMP-2). We then successfully implemented a novel strategy involving the interplay between IF and MMP-2 inhibitor to regulate morphological parameters of the self-organized MVNs, with vascular permeability and perfusability well maintained. The revealed mechanism and proposed methodology were further validated with a brain MVN model. Our findings and methods have the potential to be widely utilized to boost the development of various organotypic MVNs and could be incorporated into related bioengineering applications where perfusable vasculature is desired.
Mixing injector enables time-resolved crystallography with high hit rate at X-ray free electron lasers (2016)

Knowledge of protein structure provides essential insight into function, enhancing our understanding of diseases and enabling new treatment development. X-ray crystallography has been used to solve the structures of more than 100 000 proteins; however, the vast majority represent long-lived states that do not capture the functional motions of these molecular machines. Reactions triggered by the addition of a ligand can be the most challenging to detect with crystallography because of the difficulty of synchronizing reactions to create detectable quantities of transient states. The development of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) enables new approaches for solving protein structures following the rapid diffusion of ligands into micron sized protein crystals. Conformational changes occurring on millisecond timescales can be detected and time-resolved. Here, we describe a new XFEL injector which incorporates a microfluidic mixer to rapidly combine reactant and sample milliseconds before the sample reaches the X-ray beam. The mixing injector consists of bonded, concentric glass capillaries. The fabrication process, employing custom laser cut centering spacers and UV curable epoxy, ensures precise alignment of capillaries for repeatable, centered sample flow and dependable mixing. Crystal delivery capillaries are 50 or 75 μm in diameter and can contain an integrated filter depending on the demands of the experiment. Reaction times can be varied from submillisecond to several hundred milliseconds. The injector features rapid and uniform mixing, low sample dilution, and high hit rates. It is fully compatible with existing SFX beamlines.
A Hybrid Real-Time Correlation System Of Aerial Stereo Photographs (1988)

A digital-optical hybrid system composed of a computer and a coherent optical filtering system is successfully applied to perform a real-time correlation of aerial stereo photographs. A LOLV (Liquid Crystal Light Valve) as an incoherent-to-coherent convertor and a thermoplastic photoconductor material for holographic recording of MSF (Matched Spatial Filter) are used, and a sharp correlation peak with a good SNR is obtained.
Stability of fruit quality traits in diverse watermelon cultivars tested in multiple environments (2016)

Lycopene is a naturally occurring red carotenoid compound that is found in watermelon. Lycopene has antioxidant properties. Lycopene content, sugar content and hollowheart resistance are subject to significant genotype×environment interaction (G×E), which makes breeding for these fruit quality traits difficult. The objectives of this study were to (i) evaluate the influence of years and locations on lycopene content, sugar content and hollowheart resistance for a set of watermelon genotypes, and (ii) identify genotypes with high stability for lycopene, sugar, and hollowheart resistance. A diverse set of 40 genotypes was tested over 3 years and 8 locations across the southern United States in replicated, multi-harvest trials. Lycopene was tested in a subset of 10 genotypes. Data were analyzed using univariate and multivariate stability statistics (BLUP-GGE biplot) using SASGxE and RGxE programs. There were strong effects of environment as well as G×E interaction on watermelon quality traits. On the basis of stability measures, genotypes were classified as stable or unstable for each quality trait. 'Crimson Sweet' is an inbred line with high quality trait performance as well as trait stability. 'Stone Mountain', 'Tom Watson', 'Crimson Sweet' and 'Minilee' were among the best genotypes for lycopene content, sugar content and hollowheart resistance. We developed a stability chart based on marketable yield and average ranking generated from different stability measures for yield attributes and quality traits. The chart will assist in choosing parents for improvement of watermelon cultivars. See http://cuke.hort.ncsu.edu/cucurbit/wmelon/wmelonmain.html.
Synthesis of Colloidal Upconverting NaYF4 Nanocrystals Doped with Er3+, Yb3+ and Tm3+, Yb3+ via Thermal Decomposition of Lanthanide Trifluoroacetate Precursors (2006)

Upconverting lanthanide-doped nanocrystals were synthesized via the thermal decomposition of trifluoroacetate precursors in a mixture of oleic acid and octadecene. This method provides highly luminescent nanoparticles through a simple one-pot technique with only one preparatory step. The Er3+, Yb3+ and Tm3+, Yb3+ doped cubic NaYF4 nanocrystals are colloidally stable in nonpolar organic solvents and exhibit green/red and blue upconversion luminescence, respectively, under 977 nm laser excitation with low power densities.
Identification of the (+) and (−)-Ephedrine Used by THz-TDS (2012)

The (1R, 2S) and (1S,2R)-ephedrine hydrochloride are invested used by the THz-TDS from 0.5 ~1.8 THz at room temperature. Their different characteristic THz absorption peaks are detected, and can be used to identify themselves.
Semi-supervised bi-directional dimensionality reduction for face recognition (2010)

A novel method for face recognition called semi-supervised bi-directional dimensionality reduction (SSBDR) is proposed. Based on semi-supervised learning, domain knowledge in the form of pairwise constraints besides abundant unlabeled examples are available, which specifies whether a pair of instances belong to the same class or not. Compared to the semi-supervised dimensionality reduction (SSDR), it can not only preserve the intrinsic structure of the unlabeled data as well as both the must-link (the same class) and cannot-link constraints (different classes) defined on the labeled examples in the projected low-dimensional space, but also constructs two image covariance matrices directly by the original image matrix in two directions which can reduce the dimension of the original image matrix in two directions. The validity of this method can be verified by the experiments on ORL face database.
Laser cooling of rubidium atoms in a vapor cell (1994)

We have constructed a simplified setup for the demonstration of laser cooling and trapping of rubidium atoms. An external-cavity diode laser was swept across the F = 3 → F' = 2, 3, 4 resonances of the D2-line of 85Rb at 780 nm to resolve the saturated absorption features. Subsequently, the transition F = 3 → F' = 4 was used to cool rubidium atoms in a roomtemperature vapor cell. A cold cloud of trapped atoms with a diameter of approximately 1 mm was produced. The lifetime of the trap was measured to be 1 second.
Tunable Negative Refraction without Absorption using Electromagnetically Induced Chirality (2007)

We propose a novel approach that uses effects similar to EIT leading to resonantly enhanced chirality, negative refraction and suppression of absorption. The refractive index can be fine-tuned by means of external laser fields.
Effect of Alrestatin on Arginine-Induced Secretion of Glucagon and Insulin in the Rat (1978)

Alrestatin, a lens aldose reductase inhibitor, decreased i.v. arginine-induced glucagon levels and augmented arginine-stimulated insulin release in the ether anesthetized rat. Alrestatin may then be useful in the treatment of diabetes mellitus, due to its actions on insulin and glucagon, and its capacity to delay the onset of sugar-induced cataracts in the rat.
Spectral study of metabolism-based autofluorescence and white-light reflectance for endoscopic tumor imaging (2015)

Metabolism-based autofluorescence redox imaging is one of the promising options for non-invasive screening of digestive tumors. In this paper, autofluorescence from fluorescent coenzymes such as NADH and FAD related to cellular metabolism as well as total hemoglobin and oxygen saturation are analyzed based on a point spectrum. As a redox index based on the metabolism, the ratio of the 450nm-490nm fluorescence intensities for 365nm and 405nm excitation wavelengths (F365/F405) is used. Although F365/F405 is a good index in many samples, inversion and weakened contrast are observed. A Simplified models with and without collagen based on Lambert-Beer law are built to explain how F365/F405 depicts the tumor region.
Supplementary Figures 1 through 3 and Supplementary Tables 1 through 3 from OATP1A/1B Transporters Affect Irinotecan and SN-38 Pharmacokinetics and Carboxylesterase Expression in Knockout and Humanized Transgenic Mice (2023)

&lt;p&gt;PDF - 278KB, Supplemental figure 1. pH equilibrium between the lactone (closed ring) form and free carboxylic acid (open) form of irinotecan and SN-38. Supplemental Figure 2. Role of Oatp1a/1b uptake transporters in small intestinal (tissue plus content) exposure of irinotecan and SN-38 after intravenous administration of irinotecan (10 mg/kg) to female wild-type and Oatp1a/1b knockout mice. Supplemental Figure 3. Role of Oatp1a/1b uptake transporters in kidney exposure of irinotecan and SN-38 after intravenous administration of irinotecan (10 mg/kg) to female wild-type and Oatp1a/1b knockout mice. Supplemental Table 1. Overview of ΔCt values of the RT-PCR analysis of expression of several esterases in liver of female wild-type, Oatp1a/1b knockout (Slco1a/1b(-/-)) and OATP1B1/1B3 humanized mice. Supplemental Table 2. Overview of ΔCt values of the RT-PCR analysis of expression of several esterases in small intestine of female wild-type, Oatp1a/1b knockout (Slco1a/1b(-/-)) and OATP1B1/1B3 humanized mice. Supplemental Table 3. Overview of ΔCt values of the RT-PCR analysis of expression of several esterases in kidney of female wild-type, Oatp1a/1b knockout (Slco1a/1b(-/-)) and OATP1B1/1B3 humanized mice.&lt;/p&gt;
In vivo quantification of optical contrast agent dynamics in rat tumors by use of diffuse optical spectroscopy with magnetic resonance imaging coregistration (2003)

We present a study of the dynamics of optical contrast agents indocyanine green (ICG) and methylene blue (MB) in an adenocarcinoma rat tumor model. Measurements are conducted with a combined frequency-domain and steady-state optical technique that facilitates rapid measurement of tissue absorption in the 650-1000-nm spectral region. Tumors were also imaged by use of contrast-enhanced magnetic resonance imaging (MRI) and coregistered with the location of the optical probe. The absolute concentrations of contrast agent, oxyhemoglobin, deoxyhemoglobin, and water are measured simultaneously each second for approximately 10 min. The differing tissue uptake kinetics of ICG and MB in these late-stage tumors arise from differences in their effective molecular weights. ICG, because of its binding to plasma proteins, behaves as a macromolecular contrast agent with a low vascular permeability. A compartmental model describing ICG dynamics is used to quantify physiologic parameters related to capillary permeability. In contrast, MB behaves as a small-molecular-weight contrast agent that leaks rapidly from the vasculature into the extravascular, extracellular space, and is sensitive to blood flow and the arterial input function.
Summary Abstract: Growth and properties of ion-beam sputtered HgCdTe films (1986)

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Plasma chemistry in fluorocarbon film deposition from pentafluoroethane/argon mixtures (1999)

Plasma-enhanced deposition of fluorocarbon films was performed at 120 °C from a mixture of pentafluoroethane (CF3CHF2) and argon in a parallel plate plasma reactor. Mass spectrometry of the reactor effluent was used to gain an understanding of the plasma chemistry of this monomer. The monomer primarily dissociated into CF3• and CHF2• in the plasma. The results from mass spectrometry indicated that CHF2* was the primary precursor for deposition and that the fluorine radicals in the plasma were primarily scavenged as CF4 and HF. Monomer conversion (fraction of monomer fragmented) in the plasma was determined based on mass spectrometer partial pressure analysis of CH3CHF+ fragments (parent molecule: CF3CHF2) before and after plasma ignition. The conversion correlated directly with both the applied power and the deposition rate. The overall gas phase reactions did not change significantly with rf power within our range of operation, indicating a common reaction mechanism at all powers. No significant change in the composition of the deposited films was found, as measured by x-ray photoelectron spectroscopy (XPS), supporting the common mechanism conclusion. Further, XPS studies showed a fluorine-to-carbon ratio between 1.05 and 1.15 suggesting extensive crosslinking of the polymer. Infrared spectra of the deposited films showed negligible CHx concentration despite the presence of hydrogen in the monomer.
Thermodynamical Model for the Description of the Equilibrium of the SiCl4, O2, SF6, System in CVD Process (1990)

Article Thermodynamical Model for the Description of the Equilibrium of the SiCl4, O2, SF6, System in CVD Process was published on June 1, 1990 in the journal Journal of Optical Communications (volume 11, issue 2).
Higher-harmonics generation in tapping-mode atomic-force microscopy: Insights into the tip–sample interaction (2000)

We present an experimental analysis of the nonlinear tip–sample interaction in tapping-mode atomic-force microscopy by exploiting anharmonic contributions of the cantilever motion. Two aspects of a concept aiming at a full reconstruction of the tip–sample interaction are demonstrated: higher flexural eigenmode vibrations excited by the impact of the oscillating tip on the sample are used to measure the tip–sample interaction time; by imaging at higher harmonics of the driving frequency material contrast is obtained.
PNNLs Support to Homeland Security (2009)

This video describes how PNNL supports Homeland Security.
Studies on Bile Acids and Bile Alcohols. II.Separation of Bile Acids by Gas Liquid Chromatography (1965)

The separation of twenty-eight kinds of standard bile acids by gas liquid chromatography using QF-1, NGS, CNSi, SE-30 or SE-52 packing is discussed.
Performance Comparison of MIMO Techniques for Optical Wireless Communications in Indoor Environments (2013)

In this paper, we compare the performance of multiple-input-multiple-output (MIMO) techniques applied to indoor optical wireless communications (OWC) assuming line-ofsight (LOS) channel conditions. Specifically, several 4 × 4 setups with different transmitter spacings and different positions of the receiver array are considered. The following MIMO algorithms are considered: Repetition Coding (RC), Spatial Multiplexing (SMP) and Spatial Modulation (SM). Particularly, we develop a framework to analytically approximate the bit error ratios (BERs) of these schemes and verify the theoretical bounds by simulations. The results show that due to diversity gains, RC is robust to various transmitter-receiver alignments. However, as RC does not provide spatial multiplexing gains, it requires large signal constellation sizes to enable high spectral efficiencies. In contrast, SMP enables high data rates by exploiting multiplexing gains. In order to provide these gains, SMP needs sufficiently low channel correlation. SM is a combined MIMO and digital modulation technique. We show that SM is more robust to high channel correlation compared to SMP, while enabling larger spectral efficiency compared to RC. Moreover, we investigate the effect of induced power imbalance between the multiple transmitters. It is found that power imbalance can substantially improve the performance of both SMP and SM as it reduces channel correlation. In this context, we also show that blocking some of the links is an acceptable method to reduce channel correlation. Even though the blocking diminishes the received energy, it outweighs this degradation by providing improved channel conditions for SMP and SM. For example, blocking 4 of the 16 links of the 4 × 4 setup improves the BER performance of SMP by more than 20 dB, while the effective signal to noise ratio (SNR) is reduced by about 2 dB due to the blocking. Therefore, MIMO techniques can provide gains even under LOS conditions which provide only little channel differences.
Multiphysics modelling and experimental validation of an air-coupled array of PMUTs with residual stresses (2018)

In this paper a complete multiphysics modelling via the finite element method (FEM) of an air-coupled array of piezoelectric micromachined ultrasonic transducers (PMUT) and its experimental validation are presented. Two numerical models are described for the single transducer, axisymmetric and 3D, with the following features: the presence of fabrication induced residual stresses, which determine a non-linear initial deformed configuration of the diaphragm and a substantial fundamental mode frequency shift; the multiple coupling between different physics, namely electro-mechanical coupling for the piezo-electric model, thermo-acoustic-structural interaction and thermo-acoustic-pressure interaction for the waves propagation in the surrounding fluid. The model for the single transducer is enhanced considering the full set of PMUTs belonging to the silicon dye in a 4 x 4 array configuration. The results of the numerical multiphysics models are compared with experimental ones in terms of the initial static pre-deflection, of the diaphragm central point spectrum and of the sound intensity at 3.5 cm on the vertical direction along the axis of the diaphragm.
Sexual violence, HSV-2 and HIV are important predictors for infertility in Rwanda (2010)

Although temporal relationships are difficult to ascertain, history of sexual violence, HSV-2 infection and HIV infection are important predictors of infertility in Rwanda.
Knowledge and application of foot care : a study of diabetic patients in Mauritius (2013)

Mauritius has a high prevalence of diabetes mellitus. Diabetic patients are often unaware of injuries to their feet. Early intervention is vital to prevent small injuries from turning into non-healing ulcers that could potentially result in gangrene and amputation. The aim of this study was to determine the knowledge of diabetic patients in Mauritius about foot care, the prevention of foot problems and their application of foot care practices. A quantitative descriptive survey was done. A structured interview schedule was used to collect data from a convenience sample of 120 diabetic patients in five regional hospitals in Mauritius (n=120) during 2010. More than half of the respondents had not received any specific health education about foot care (62.5%; n=75). This could explain why many respondents did not adhere to basic precautions to prevent foot ulcerations such as checking water temperature, inspecting the soles of their feet, checking foot pulses and using moisturising cream. Of the respondents, 75.0% (n=90) were unaware that foot screening should be done annually while 46.7% (n=56) indicated that doctors did not inspect their feet during visits. Foot care education should be considered as an important component of diabetic health education and should be tailored according to the needs of the individual patients. It is the responsibility of all health professionals to determine whether patients understand what is being taught and to determine to what extent this knowledge is put into practice.