gebhart/patrepeval huggingface dataset:
Increased ethanol tolerance associated with the pntAB locus of Oenococcus oeni and Lactobacillus buchneri (2019)

Lactobacillus buchneri and Oenococcus oeni are two unique ethanol-tolerant Gram-positive bacteria species. Genome comparison analyses revealed that L. buchneri and O. oeni possess a pntAB locus that was absent in almost all other lactic acid bacteria (LAB) genomes. Our hypothesis is that the pntAB locus contributes to the ethanol tolerance trait of these two distinct ethanol-tolerant organisms. The pntAB locus, consisting of the pntA and pntB genes, codes for NADP(H) transhydrogenase subunits. This membrane-bound transhydrogenase catalyzes the reduction of NADP+ and is known as an important enzyme in maintaining cellular redox balance. In this study, the transhydrogenase operon from L. buchneri NRRL B-30929 and O. oeni PSU-1 were cloned and analyzed. The LbpntB shared 71.0% identity with the O. oeni (OopntB). The entire pntAB locus was expressed in Lactococcus lactis ssp. lactis IL1403 resulting in an increased tolerance to ethanol (6%), butanol (1.8%) and isopropanol (1.8%) when compared to the control strain. However, the recombinant E. coli cells carrying the entire pntAB locus did not show any improved ethanol tolerance. Independent expression of OopntB and LbpntB in recombinant E. coli BL21(DE3)pLysS host demonstrated higher tolerance to ethanol when compared with a control E. coli BL21(DE3)pLysS strain carrying pET28b vector. Ethanol tolerance comparison of E. coli strains carrying LbpntB and OopntB showed that LbpntB conferred higher ethanol tolerance (4.5%) and resulted in greater biomass, while the OopntB conferred lower ethanol tolerance (4.0%) resulted lower biomass. Therefore, the pntB gene from L. buchneri is a better choice in generating higher ethanol tolerance. This is the first study to uncover the role of pntAB locus on ethanol tolerance.
Exploration of inductor-based hybrid integrated voltage regulator architectures (2016)

Integrated voltage regulators (IVRs) fabricated and positioned close to the microprocessors can improve the energy conversion efficiency, power density and the output voltage regulation performance compared to discrete VRs. The highest cost in terms of space and volume in such IVRs corresponds to the bulky passive components needed for their operation. In this paper, two different hybrid architectures for IVRs are considered and evaluated. The proposed voltage regulators consist of a four-phase interleaved buck converter operated in Continuous Conduction Mode (CCM). The rated power of the considered converter is 1W, and nominal input and output voltages are constant and equal to V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in</sub> = 1.7V and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">out</sub> = 0.85V, respectively. In one case, inductors and deep trench capacitors are microfabricated in a silicon interposer underneath the CPU chip. In the second case, discrete off-the-shelf inductors and capacitors are assembled in the chip carrier laminate substrate. In both cases, the active components, i.e., the power switches and driving circuits for the buck converter in a half-bridge configuration (four phases) are fabricated using using 32nm CMOS process (IBM) in a power management IC (PMIC). This IC forms the test platform for the demonstration of the proposed hybrid integrated voltage regulator (HIVR), and also contains a CMOS programmable resistive load to emulate the CPU. The efficiency, power density and other performance metrics of both implementations are evaluated using modeling and simulations. Results from our design analyses show that while the laminate implementation fares well with regard to efficiency (≃ 93.5%), it cannot reach the high power densities attainable in the interposer implementations ≃ 0.95W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Ada (Trademark) Reusability Guidelines. (1985)

Abstract : This report presents guidelines for the use of Ada to produce reusable software, that can, with little or no modification, be used in a variety of application systems other than that for which it is originally developed. Reusability offers the potential for great cost savings in DoD systems development. The Ada language provides many features that support software reusability, but reusability can be greatly enhanced if the features are used in certain controlled ways. For example, reusable components must be exceptionally well-tested, and each reusable component must have its own documentation at the level currently required for a CPCI. Reusability also has implications for managers -- the additional cost of developing reusable software must be understood and developers must not be penalized. This report addresses the design, development, documentation, and management issues relating to reusability. The major motivation for development of this report was support for the acquisition of a highly-reusable Ada implementation of the JINTACCS Automated Message Preparation Systems (JAMPS).
Glucose, pyruvate, and lactate concentrations in the blastocoel cavity of rat and mouse embryos (1993)

The concentrations of glucose, pyruvate, and lactate have been measured in the blastocoel fluid of single rat and mouse blastocysts, using the technique of micropuncture combined with an ultramicrofluorescence assay. When cultured in the presence of 5.55 mM glucose, 11.5-12.5 mM L-lactate and 0.25-0.33 mM pyruvate, concentrations in the blastocoel fluid of mouse and rat were 2.30 and 2.75 mM glucose, 14.6 and 19.6 mM L-lactate, and 0.13 and 0.50 mM pyruvate, respectively. When cultured in the presence of 1.0 mM glucose and 1.0 mM L-lactate, concentrations in the blastocoel fluid were 0.50 and 0.59 mM glucose and 2.22 and 3.70 mM L-lactate, respectively. These results suggest that (1) the blastocyst is capable of maintaining considerable concentration gradients of substrates across the trophectoderm, (2) the microenvironment of the blastocoel is adequately supplied with energy substrates for the development of the inner cell mass, and (3) the inner cell mass is capable of developing in both high and low glucose and lactate concentrations.
Co3O4nanoparticles/cellulose nanowhiskers-derived amorphous carbon nanoneedles: sustainable materials for supercapacitors and oxygen reduction electrocatalysis (2015)

Amorphous carbon nanoneedles-supported Co<sub>3</sub>O<sub>4</sub>nanoparticles, materials that have electrocatalytic activity for ORR and the ability to store charges, are synthesized with nanoreactors using Co(<sc>ii</sc>) ions and cellulose nanowhiskers as precursor.
Oxide-confined verticle-cavity surface-emitting lasers, quantum dots, and the Purcell effect: can scaling the mode size improve laser performance? (1999)

The development of vertical-cavity surface -emitting lasers (VCSELs) has led to new types of low power, high efficiency light sources for data communication. The small size, low power, and surface-normal emission of VCSELs has enabled relatively dense 2D arrays for highly parallel data communication and optical signal processing. In this paper we examine the issues of device scaling on VCSEL performance. We look specifically at what benefits may be derived from continued scaling of the active volume down to minimum sized dimensions, and what device schemes may be required to obtain the dimensions, a significant improvement in modulation speed is predicted based on the radiative lifetime change due to the Purcell effect. However, several parasitic effects must be controlled in order to realize these benefits. Most important are control of the optical loss due to diffraction or scattering,and control of the electronic losses due to carrier diffusion and surface effects. Novel optical confinement schemes based on oxide- apertures, photonic bandgaps, and/or closely coupled 2D array may be useful for controlling optical loss, while self-assembled quantum dots are attractive for controlling electronic diffusion to dimensions within the minimum optical mode volume.
Supplementary Tables 1-5 from Nanobody-Based Targeting of the Macrophage Mannose Receptor for Effective <i>In Vivo</i> Imaging of Tumor-Associated Macrophages (2023)

&lt;p&gt;PDF file - 69K, This file contains Supplementary Tables Supplementary Table 1. Sequences of primers Supplementary Table 2. SPR kinetic and equilibrium parameters for anti-MMR Nanobodies and bivalent Nanobody cl1 derivatives. Supplementary Table 3. Uptake values of 99mTc-labeled anti-MMR Nb cl1, cl3 and Nb BCII10 in naive WT and MMR-KO mice, based on dissection at 1 hour post injection. Supplementary Table 4. Uptake values of 99mTc-labeled anti-MMR Nb in s.c. 3LL-R tumor-bearing WT or CCR2-KO mice, based on dissection at 3 hours post injection Supplementary Table 5. Uptake values of 99mTc-labeled bivalent anti-MMR Nbs in naive WT and MMR-KO mice, based on dissection at 1 hour post injection&lt;/p&gt;
Known Content Network (CN) Request-Routing Mechanisms (2003)

This document presents a summary of Request-Routing techniques that are used to direct client requests to surrogates based on various policies and a possible set of metrics. The document covers techniques that were commonly used in the industry on or before December 2000. In this memo, the term Request-Routing represents techniques that is commonly called content routing or content redirection. In principle, Request-Routing techniques can be classified under: DNS Request-Routing, Transport-layer Request-Routing, and Application-layer Request-Routing.
Bayesian Optimization for High-Speed Channel Equalization (2019)

Equalization methods are used to recover the signal attenuated by channel loss. Different optimization algorithms are applied to find the best tap coefficients for each equalization that will improve eye opening and reduce bit error rate. The goal function for most equalization optimization algorithms is to reduce the difference between input and output signals, which is a linear optimization problem and can be solved relatively easily. This indirectly will increase eye height and improve eye diagram. Directly optimizing eye height is a non-linear problem and cannot be solved with analytical method. We are proposing FFE and DFE combined equalization optimization algorithm that optimizes directly eye height using Bayesian Optimization (BO). The proposed algorithm can be generalized for multi-level signals.
Near real-time determination of B.1.1.7 in proportion to total SARS-CoV-2 viral load in wastewater using an allele-specific primer extension PCR strategy (2021)

Abstract The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed millions of lives to date. Antigenic drift has resulted in viral variants with putatively greater transmissibility, virulence, or both. Early and near real-time detection of these variants of concern (VOC) and the ability to accurately follow their incidence and prevalence in communities is wanting. Wastewater-based epidemiology (WBE), which uses nucleic acid amplification tests to detect viral fragments, is a faithful proxy of COVID-19 incidence and prevalence, and thus offers the potential to monitor VOC viral load in a given population. Here, we describe and validate a primer extension PCR strategy targeting a signature mutation in the N gene of SARS-CoV-2. This allows quantification of the proportional expression of B.1.1.7 versus non-B.1.1.7 alleles in wastewater without the need to employ quantitative RT-PCR standard curves. We show that the wastewater B.1.1.7 profile correlates with its clinical counterpart and benefits from a near real-time and facile data collection and reporting pipeline. This assay can be quickly implemented within a current SARS-CoV-2 WBE framework with minimal cost; allowing early and contemporaneous estimates of B.1.1.7 community transmission prior to, or in lieu of, clinical screening and identification. Our study demonstrates that this strategy can provide public health units with an additional and much needed tool to rapidly triangulate VOC incidence/prevalence with high sensitivity and lineage specificity.
The cholinergic nucleus basalis: A key structure in neocortical arousal (1989)

Single unit studies indicate that increased activity in the cholinergic nucleus basalis (NB) correlates with behavioral activation and neocortical desynchronization. Lesions of the NB result in neocortical slow delta waves, similar to the action of antimuscarinic drugs, and the lesion releases the oscillation of GABAergic neurons in the reticular nucleus of the thalamus, resulting in high voltage neocortical spindles. Extensive damage of the thalamus does not produce slowing of neocortical activity but it abolishes neocortical spindles. We suggest that the NB plays a key role in neocortical activation by a) blocking the afterhyperpolarizations and accommodation in neocortical pyramidal neurons and b) suppressing the rhythm generation in the reticular nucleus-thalamocortical circuitry. We further suggest that the NB system may serve as a structural basis for the concept of the generalized activation described by Moruzzi and Magoun (1949).
Engineered Nonviral Protein Cages Modified for MR Imaging (2023)

Diagnostic medical imaging utilizes magnetic resonance (MR) to provide anatomical, functional, and molecular information in a single scan. Nanoparticles are often labeled with Gd(III) complexes to amplify the MR signal of contrast agents (CAs) with large payloads and high proton relaxation efficiencies (relaxivity, <i>r</i><sub>1</sub>). This study examined the MR performance of two structurally unique cages, AaLS-13 and OP, labeled with Gd(III). The cages have characteristics relevant for the development of theranostic platforms, including (i) well-defined structure, symmetry, and size; (ii) the amenability to extensive engineering; (iii) the adjustable loading of therapeutically relevant cargo molecules; (iv) high physical stability; and (v) facile manufacturing by microbial fermentation. The resulting conjugates showed significantly enhanced proton relaxivity (<i>r</i><sub>1</sub> = 11-18 mM<sup>-1</sup> s<sup>-1</sup> at 1.4 T) compared to the Gd(III) complex alone (<i>r</i><sub>1</sub> = 4 mM<sup>-1</sup> s<sup>-1</sup>). Serum phantom images revealed 107% and 57% contrast enhancements for Gd(III)-labeled AaLS-13 and OP cages, respectively. Moreover, proton nuclear magnetic relaxation dispersion (<sup>1</sup>H NMRD) profiles showed maximum relaxivity values of 50 mM<sup>-1</sup> s<sup>-1</sup>. Best-fit analyses of the <sup>1</sup>H NMRD profiles attributed the high relaxivity of the Gd(III)-labeled cages to the slow molecular tumbling of the conjugates and restricted local motion of the conjugated Gd(III) complex.
Influence of acarbose on post-prandial insulin requirements in patients with Type 1 diabetes. (2000)

The primary objective of this double-blind, placebo-controlled, randomised cross-over study was to investigate the influence of acarbose on insulin requirement in patients with Type 1 diabetes (T1DM) following a standardised meal. In addition, the study assessed the effects of acarbose on post-prandial triglyceride, glucagon and gastrointestinal peptide levels, gastric emptying, and oxidative glucose metabolism. Following normalisation of their blood glucose, 10 patients received a standardised meal together with acarbose (100 mg) or placebo. Each patient was evaluated twice (separated by 10+/-3 days), and the cross-over study design ensured that they received both acarbose and placebo. The insulin requirement for maintenance of normoglycaemia was assessed using a closed-loop insulin infusion system (artificial pancreas, Biostator). Acarbose produced a statistically significant reduction in mean insulin requirement over a 3-hr period following the meal compared with placebo (5171.7+/-2282.6 mU vs 8074.5+/-3045.4 mU; p=0.003). The level of blood glucose control over the same period was similar in the two groups. Gastric inhibitory polypeptide levels also showed a statistically significant decrease with acarbose treatment compared with placebo for AUC (area under the curve; p=0.006) and Cmax (maximum plasma concentration; p=0.022), but not tmax (time to reach Cmax from the start of the standardised meal; p>0.05). Analysis of the other efficacy parameters revealed no statistically significant differences between acarbose treatment and placebo (p>0.05). These results indicate that acarbose decreases insulin requirement in patients with T1DM without affecting gastric emptying.
Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium (2020)

Classification of breast cancer into intrinsic subtypes has clinical and epidemiologic importance. To examine accuracy of immunohistochemistry (IHC)-based methods for identifying intrinsic subtypes, a three-biomarker IHC panel was compared to the clinical record and RNA-based intrinsic (PAM50) subtypes.
Integrative Analyses Reveal Novel Disease-associated Loci and Genes for Idiopathic Pulmonary Fibrosis (2021)

Abstract Background Although genome-wide association studies have identified many genomic regions associated with idiopathic pulmonary fibrosis (IPF), the causal genes and functions remain largely unknown. Many bulk and single-cell expression data have become available for IPF, and there is increasing evidence suggesting a shared genetic basis between IPF and other diseases. Methods By leveraging shared genetic information and transcriptome data, we conducted an integrative analysis to identify novel genes for IPF. We first considered observed phenotypes, polygenic risk scores, and genetic correlations to investigate associations between IPF and other traits in the UK Biobank. We then performed local genetic correlation analysis and cross-tissue transcriptome-wide association analysis (TWAS) to identify IPF genes. We further prioritized genes using bulk and single-cell gene expression data. Findings We identified 25 traits correlated with IPF on the phenotype level and seven traits genetically correlated with IPF. Using local genetic correlation, we identified 12 candidate genes across 14 genomic regions, including the POT1 locus (p-value = 4·1E-4), which contained variants with protective effects on lung cancer but increasing IPF risk. Using TWAS, we identified 36 genes, including 12 novel genes for IPF. Annotation-stratified heritability estimation and differential expression analysis of downstream-regulated genes suggested regulatory roles of two candidate genes, MAFK and SMAD2 , on IPF. Interpretation Our integrative analysis identified new genes for IPF susceptibility and expanded the understanding of the complex genetic architecture of IPF. Funding NIHR Leicester Biomedical Research Centre, Three Lakes Partners, the National Institutes of Health, the National Science Foundation, U01HL145567, and UH2HL123886.
Formation of Secondary Vortices in Turbulent Square-Duct Flow (2006)

A linear approach, inspired by hydrodynamic stability theory, is used to describe the formation of large-scale coherent vortices for the turbulent flow that develops in a duct of square cross section. A set of equations for small-amplitude coherent motion is derived and closed with a simple mixing-length strategy. The initial condition that maximizes a chosen functional (related to either the kinetic energy of the coherent motion or the rate of turbulence production) is found through a direct/adjoint numerical approach borrowed from optimal control theory. It is found that different kinds of secondary flows can appear in the duct cross section, sustained by the mean shear. Some of these optimal states display a symmetry about the bisectors and the diagonals of the duct, in agreement with experimental observations and direct numerical simulations.
Oil/Water‐Partitioning and Interfacial Behavior of Naphthenic Acids (2003)

Abstract Partitioning and dissociation constants for naphthenic acids from crude oils and several naphthenic acid model compounds are reported. The pK a for naphthenic acids from crude oil was found to be 4.9. The logarithm of the partition coefficients varies linearly vs. the number of carbons in the naphthenic acid molecules. The naphthenic acids with three rings were found to be more hydrophilic than acids with one or two rings. The data can be used to predict the content of different naphthenic acids in produced water at a given pH, given the acid content and mole weight distribution in the crude oil. By accounting for the dissociation in water and partitioning of undissociated acid a model for the total acid concentration in water was derived. Experiments with synthetic naphthenic acids were performed and the model proved to describe the experimental points at pH < 8. At higher pH there was a deviation between the model and the experimentally determined concentrations. This was suggested to be due to formation of ordinary and reversed micelles. The correlation between interfacial tension and pH was studied for several naphthenic acid systems. A decrease in interfacial tension was seen at high pH; this was explained by an increase in the total concentration of ionized naphthenic acids at the interface. The fraction of ionized naphthenic acids at the interface was lower than the fraction in the bulk phases. This effect is explained by the fact that interfacial pH is lower than the bulk pH due to electrical double layer effects.
Single-mode integrated out-of-plane meta beam shaper (2023)

Integration of metasurfaces with planar waveguide integrated circuits can provide unique functionalities for beam shaping. Recent works show vertical integration of independently designed planar sources and metalenses, however this is not trivial or scalable. Here, we demonstrate an inverse design approach to co-optimize and merge grating and metalens functions into an out-of-plane beam shaper within a single 240nm silicon nitride layer. To exemplify, we demonstrate a 240nm thick meta-beam shaper that focuses 473nm light into a diffraction-limited spot with sidelobe suppression over 10dB. This approach for inverse design is generalizable to arbitrary beam shapes, unlocking a wide variety of applications.
Transforming growth factor-β–induced protein (TGFBIp/β ig-h3) activates platelets and promotes thrombogenesis (2009)

Transforming growth factor-beta-induced protein (TGFBIp)/beta ig-h3 is a 68-kDa extracellular matrix protein that is functionally associated with the adhesion, migration, proliferation, and differentiation of various cells. The presence of TGFBIp in platelets led us to study the role of this protein in the regulation of platelet functions. Upon activation, platelet TGFBIp was released and associated with the platelets. TGFBIp mediates not only the adhesion and spread of platelets but also activates them, resulting in phosphatidylserine exposure, alpha-granule secretion, and increased integrin affinity. The fasciclin 1 domains of TGFBIp are mainly responsible for the activation of platelets. TGFBIp promotes thrombus formation on type I fibrillar collagen under flow conditions in vitro and induces pulmonary embolism in mice. Moreover, transgenic mice, which have approximately a 1.7-fold greater blood TGFBIp concentration, are significantly more susceptible to collagen- and epinephrine-induced pulmonary embolism than wild-type mice. These results suggest that TGFBIp, a human platelet protein, plays important roles in platelet activation and thrombus formation. Our findings will increase our understanding of the novel mechanism of platelet activation, contributing to a better understanding of thrombotic pathways and the development of new antithrombotic therapies.
Cyclopentadienone Synthesis by Rhodium(I)‐Catalyzed [3 + 2] Cycloaddition Reactions of Cyclopropenones and Alkynes. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.