gebhart/patrepeval huggingface dataset:
Regulation of waaH by PhoB during P i Starvation Promotes Biofilm Formation by Escherichia coli O157:H7 (2019)

In open environments such as water, enterohemorrhagic <i>Escherichia coli</i> O157:H7 responds to inorganic phosphate (P<sub>i</sub>) starvation by inducing the Pho regulon controlled by PhoB. This activates the phosphate-specific transport (Pst) system that contains a high-affinity P<sub>i</sub> transporter. In the Δ<i>pst</i> mutant, PhoB is constitutively activated and regulates the expression of genes in the Pho regulon. Here, we show that P<sub>i</sub> starvation and deletion of the <i>pst</i> system enhance <i>E. coli</i> O157:H7 biofilm formation. Among differentially expressed genes of EDL933 grown under P<sub>i</sub> starvation conditions and in the Δ<i>pst</i> mutant, we have found that a member of the PhoB regulon, <i>waaH</i>, predicted to encode a glycosyltransferase, was highly expressed. Interestingly, WaaH contributed to biofilm formation of <i>E. coli</i> O157:H7 during both P<sub>i</sub> starvation and in the Δ<i>pst</i> mutant. In the Δ<i>pst</i> mutant, the presence of <i>waaH</i> was associated with lipopolysaccharide (LPS) R3 core type modifications, whereas in <i>E. coli</i> O157:H7, <i>waaH</i> overexpression had no effect on LPS structure during P<sub>i</sub> starvation. Therefore, <i>waaH</i> participates in <i>E. coli</i> O157:H7 biofilm formation during P<sub>i</sub> starvation, but its biochemical role remains to be clarified. This study highlights the importance of the P<sub>i</sub> starvation stress response to biofilm formation, which may contribute to the persistence of <i>E. coli</i> O157:H7 in the environment.<b>IMPORTANCE</b> Enterohemorrhagic <i>Escherichia coli</i> O157:H7 is a human pathogen that causes bloody diarrhea that can result in renal failure. Outside of mammalian hosts, <i>E. coli</i> O157:H7 survives for extended periods of time in nutrient-poor environments, likely as part of biofilms. In <i>E. coli</i> K-12, the levels of free extracellular P<sub>i</sub> affect biofilm formation; however, it was unknown whether P<sub>i</sub> influences biofilm formation by <i>E. coli</i> O157:H7. Our results show that upon P<sub>i</sub> starvation, PhoB activates <i>waaH</i> expression, which favors biofilm formation by <i>E. coli</i> O157:H7. These findings suggest that WaaH is a target for controlling biofilm formation. Altogether, our work demonstrates how adaptation to P<sub>i</sub> starvation allows <i>E. coli</i> O157:H7 to occupy different ecological niches.
Aggregation Phenomena of Long α‐ and α,ω‐Substituted Oligothiophenes – the Effect of Branched vs. Linear End‐Groups (2007)

Abstract Five homologous series of α‐ and α,ω‐substituted oligothiophenes up to an undecamer with branched and linear alkyl chains, respectively, are presented. These series are compared with respect to self‐organisation in solution and in solid state. UV/Vis absorption data for the long disubstituted branched oligothiophenes indicate the formation of aggregates in solution, expressed by a bathochromic shift of the absorption maximum and the appearance of shoulders. These changes in the spectra are obtained by variation of the solvent quality and/or the temperature. Contrary, the linear disubstituted oligothiophenes exhibit the formation of H‐aggregates in solution indicated by a hypsochromic shift in the UV/Vis spectra. Results from fluorescence spectroscopy support the existence of aggregates. No aggregation phenomena were found for the monoalkylated branched oligothiophenes. In contrast, H‐aggregation is found for the monoalkylated linear oligomers. This unexpected influence of the branching of the alkyl end groups on the aggregation behaviour in solution is discussed with the aid of mixed substituted oligothiophenes. Further information on shape and size of the aggregates present in solution is found by AFM measurements revealing that the linear substituents rather provoke the formation of anisotropic structures whereas the branched alkyl chains lead to spherical nanoobjects. Investigations of the thermal behaviour in solid state show that some of the oligomers exhibit thermotropic liquid crystalline phases. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Eu concentration dependence of Eu doped GaN nanocolumns grown by RF-plasma-assisted molecular beam epitaxy (2016)

Eu doped GaN (GaN:Eu) shows a sharp line emission and thermal stability of the emission wavelength. To improve the optical properties, GaN:Eu nanocolumns were grown on GaN nanocolumn platform with high crystalline quality by rf-plasma-assisted molecular beam epitaxy. Although it was revealed that an increase of Eu concentration brought about the polycrystalline growth, photoluminescence (PL) intensity from Eu <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> monotonically increased with increasing Eu concentration without concentration quenching, which suggests that the nanocolumn crystal is a valuable way to develop the novel optical devices utilizing GaN:Eu.
Oseltamivir Prophylactic Regimens Prevent H5N1 Influenza Morbidity and Mortality in a Ferret Model (2008)

An increased dose of oseltamivir or twice-daily administration effectively protects ferrets against morbidity and mortality caused by H5N1 infection and does not interfere with the development of protective antibodies against subsequent H5N1 infection.
Test Level 4 Noise Wall for Attachment to Concrete Traffic Barriers (2006)

A new transparent noise barrier system was developed for use on rigid bridge railings and other rigid structures. The crashworthy noise barrier system incorporated specially designed, strategically located structural hardware into a noncrashworthy noise barrier system. The noise barrier system was anchored to the back face of a reinforced concrete parapet with vertical steel posts. Transparent sound panels surrounded by a metallic frame were dropped between the spaced posts to create a noise barrier. Three horizontal rails were used to prevent errant vehicles from penetrating into sound panels, snagging on the support posts, or both. The test installation consisted of a 34.56-m-long Paraglas Soundstop TL-4 noise barrier system supported by 18 steel posts. Two full-scale crash tests—one with a single-unit truck and one with a pickup truck—were conducted and reported in accordance with the requirements specified in NCHRP Report No. 350: Recommended Procedures for the Safety Performance Evaluation of Highway Features. The safety performance of the transparent noise barrier system was determined to be acceptable according to Test Level 4 evaluation criteria specified in NCHRP Report No. 350.
Time-domain compact macromodeling of linear photonic circuits via complex vector fitting (2019)

In this paper, a novel baseband macromodeling framework for linear passive photonic circuits is proposed, which is able to build accurate and compact models while taking into account the nonidealities, such as higher order dispersion and wavelength-dependent losses of the circuits. Compared to a previous modeling method based on the vector fitting algorithm, the proposed modeling approach introduces a novel complex vector fitting technique. It can generate a half-size state-space model for the same applications, thereby achieving a major improvement in efficiency of the time-domain simulations. The proposed modeling framework requires only measured or simulated scattering parameters as input, which are widely used to represent linear and passive systems. Three photonic circuits are studied to demonstrate the accuracy and efficiency of the proposed technique. (C) 2019 Chinese Laser Press
Assembly of Supramolecular Nanotubes from Molecular Triangles and 1,2-Dihalohydrocarbons (2014)

Precise control of molecular assembly is a challenging goal facing supramolecular chemists. Herein, we report the highly specific assembly of a range of supramolecular nanotubes from the enantiomeric triangular naphthalenediimide-based macrocycles (RRRRRR)- and (SSSSSS)-NDI-Δ and a class of similar solvents, namely, the 1,2-dihalo-ethanes and -ethenes (DXEs). Three kinds of supramolecular nanotubes are formed from the columnar stacking of NDI-Δ units with a 60° mutual rotation angle as a result of cooperative [C-H···O] interactions, directing interactions of the [X···X]-bonded DXE chains inside the nanotubes and lateral [X···π] or [π···π] interactions. They include (i) semiflexible infinite nanotubes formed in the gel state from NDI-Δ and (E)-1,2-dichloroethene, (ii) rigid infinite nonhelical nanotubes produced in the solid state from NDI-Δ and BrCH2CH2Br, ClCH2CH2Br, and ClCH2CH2I, and (iii) a pair of rigid tetrameric, enantiomeric single-handed (P)- and (M)-helical nanotubes formed in the solid state from the corresponding (RRRRRR)- and (SSSSSS)-NDI-Δ with ClCH2CH2Cl. In case (i), only the electron-rich C═C double bond of (E)-1,2-dichloroethene facilitates the gelation of NDI-Δ. In cases (ii) and (iii), the lengths of anti-DXEs determine the translation of the chirality of NDI-Δ into the helicity of nanotubes. Only ClCH2CH2Cl induces single-handed helicity into the nanotubes. The subtle interplay of noncovalent bonding interactions, resulting from the tiny structural variations involving the DXE guests, is responsible for the diverse and highly specific assembly of NDI-Δ. This research highlights the critical role that guests play in constructing assembled superstructures of hosts and offers a novel approach to creating supramolecular nanotubes.
Quantitative Trait Loci for Soybean Seed Yield in Elite and Plant Introduction Germplasm (2004)

Genetic improvement for yield in soybean [ Glycine max (L.) Merr.] has been accomplished by breeding within a narrow elite gene pool. Plant introductions (PIs) may be useful for obtaining additional increases in yield if unique and desirable alleles at quantitative trait loci (QTL) can be identified. The objectives of the study were to identify QTL for yield in elite and PI germplasm and to determine if the PIs possessed favorable alleles for yield. Allele frequencies were measured with simple sequence repeat (SSR) markers in three populations, designated AP10, AP12, and AP14, that differed in their percentage of PI parentage. AP10 had 40 PI parents, AP12 had 40 PI and 40 elite parents, and AP14 had 40 elite parents. Four cycles of recurrent selection for yield had been conducted in the three populations. Allele frequencies of the highest‐yielding C4 lines in the three populations were compared with the parents used to form the populations of the initial cycles. Allele flow was simulated to account for genetic drift. Fifty‐four SSRs were associated with 43 yield QTL. Seven of the QTL had been identified in previous research. Sixteen favorable marker alleles were unique to the PI parents. The genes associated with the unique PI alleles merit further investigation for their potential to increase yield of soybean cultivars.
Comprehensive Study on Ni- or Ir-Based Alloy Catalysts in the Hydrogenation of Olefins and Mechanistic Insight (2021)

Metal-alloyed atomic catalysts such as single-atom alloys have attracted much attention due to their high atom economy and their unique catalytic properties. Recently, we found that a SiO2-supported Ni-Ir alloy (Ni-Ir/SiO2) was an effective heterogeneous catalyst for the hydrogenation of styrene and that the isolated Ni atom surrounded by Ir metal atoms, an Ir-alloyed Ni single atom, in the Ni-Ir alloy was the main active site, showing much higher activity in comparison with the monometallic Ir/SiO2 and Ni/SiO2. Reports on such effective metal-alloyed non-noble-metal single-atom catalysts are limited, and their catalytic potential should be clarified. In this study, bimetallic catalysts composed of non-noble metals and noble metals were comprehensively scrutinized in the hydrogenation of styrene as a model reaction. Among various combinations, Ni-Ir/SiO2 (introduced Ni/Ir molar ratio 1) showed the largest rate enhancement (7-fold) in comparison with the monometallic counterpart catalysts, while a SiO2-supported Co-Ir alloy (Co-Ir/SiO2, introduced Co/Ir molar ratio 4) and Ni-Pt alloy (Ni-Pt/SiO2, introduced Ni/Pt molar ratio 0.25) were also effective. The activity orders were Co-Ir/SiO2 > Ir/SiO2 > Co/SiO2 and Ni-Pt/SiO2 > Pt/SiO2 > Ni/SiO2, and the (Co-Ir/SiO2)/(Ir/SiO2) and (Ni-Pt/SiO2)/(Pt/SiO2) activity ratios were 3.5 and 2.5, respectively. Moreover, Ni-Ir/SiO2 showed higher activity for the hydrogenation of various olefins in comparison to the monometallic Ir/SiO2 and Ni/SiO2. The reaction mechanism of styrene hydrogenation over the Ir-alloyed Ni single atom of Ni-Ir/SiO2 was proposed on the basis of spectroscopic studies such as FTIR, XPS, and XRD, kinetic studies such as the effect of substrate concentration and H2 pressure, the isotopic effect of hydrogen, and the effect of the reaction temperature, and DFT calculations. The rate-determining step is the second hydrogenation of the half-hydrogenated styrene adspecies on an Ni atom by H species on Ir atoms in the Horiuti–Polanyi mechanism. The single Ni atom in Ir metal atoms has two roles: (1) formation of the reactive half-hydrogenated styrene adspecies on Ni atom and (2) formation of the reactive H species on Ir atoms by the electron transfer from an Ni atom to Ir atoms. These roles resulted in a low activation energy, leading to a large rate enhancement in comparison to the monometallic counterpart catalysts.
Data from Epigenetic reversal of acquired resistance to 5-fluorouracil treatment (2023)

&lt;div&gt;Abstract&lt;p&gt;Acquired and intrinsic resistance still remains a limitation to the clinical use of 5-fluorouracil (5-FU). The contribution of epigenetic changes to the development of drug resistance remains to be elucidated. Several genes that are hypermethylated and silenced have been identified in colorectal cancer. Based on the findings described in the accompanying article, we hypothesized that acquired resistance to “pulse” 5-FU has an epigenetic origin and might be reversed. Here, we present a novel therapeutic approach to circumvent clinical resistance to bolus 5-FU, that is, treatment of bolus 5-FU-resistant colorectal cancer cells with low-dose 5-azadeoxycytidine (DAC), an inhibitor of DNA hypermethylation, restored sensitivity to 5-FU as well as 5-fluorouridine. Moreover, treatment of nude mice bearing a 5-FU-resistant tumor, characterized by decreased levels of UMP kinase (UMPK), with DAC overcame resistance to bolus 5-FU. DAC-mediated restoration of 5-FU sensitivity was associated with increases in UMPK levels. An increase in UMPK protein and mRNA levels following treatment with low-dose DAC was observed in cultured bolus 5-FU-resistant colorectal cancer cells (HCT-8) and in mice bearing these tumors. We conclude that DAC-mediated restoration of sensitivity to bolus 5-FU is mediated at least in part by increased UMPK levels and clinical resistance to 5-FU due to decreased UMPK in colorectal cancer may be overcome by including methylation inhibitors such as DAC. [Mol Cancer Ther 2009;8(5):1045–54]&lt;/p&gt;&lt;/div&gt;
Forest structure and landscape patterns in the subalpine lodgepole pine type: A procedure for quantifying past and present conditions. Forest Service general technical report (1993)

The report presents a method of quantitatively representing the mosaic of stand types on a small landscape in the subalpine lodgepole pine forest type. The method utilizes macroplots placed systematically on a transect grid. Structure and composition of both current and past stands are inventoried. Procedures for data analysis and interpretation are illustrated for a lodgepole pine landscape in Montana.
High-speed serial link challenges using multi-level signaling (2016)

The paper discusses challenges of high-speed serial links using multi-level signaling and gives comparison of the performance of the various channels with different lossy materials and equalization options. Advantages and problems of multi-level signaling are shown based on the test results.
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92 (2011)

Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas. Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain. Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, provides an in silico platform with which to investigate the metabolism of this important human pathogen.
Transductive Learning Models for Accurate Ambulatory Gait Analysis in Elderly Residents of Assisted Living Facilities (2022)

Instrumented footwear represents a promising technology for spatiotemporal gait analysis in out-of-the-lab conditions. However, moderate accuracy impacts this technology's ability to capture subtle, but clinically meaningful, changes in gait patterns that may indicate adverse outcomes or underlying neurological conditions. This limitation hampers the use of instrumented footwear to aid functional assessments and clinical decision making. This paper introduces new transductive-learning inference models that substantially reduce measurement errors relative to conventional data processing techniques, without requiring subject-specific labelled data. The proposed models use subject-optimized input features and hyperparameters to adjust the spatiotemporal gait metrics (i.e., stride time, length, and velocity, swing time, and double support time) obtained with conventional techniques, resulting in computationally simpler models compared to end-to-end machine learning approaches. Model validity and reliability were evaluated against a gold-standard electronic walkway during a clinical gait performance test (6-minute walk test) administered to N = 95 senior residents of assisted living facilities with diverse levels of gait and balance impairments. Average reductions in absolute errors relative to conventional techniques were -42.0% and -33.5% for spatial and gait-phase parameters, respectively, indicating the potential of transductive learning models for improving the accuracy of instrumented footwear for ambulatory gait analysis.
Response dynamics and directional properties of nonspiking local interneurons in the cockroach cercal system (1993)

The response properties and directional receptive fields of nonspiking local interneurons in the cercal system of the cockroach are described. Wind-evoked responses were recorded intracellularly, and then analyzed by means of the Wiener kernel method in which a Gaussian white noise signal was used as a stimulus. Cross-correlation between the response and the white noise signal produced first- (linear) and second-order (nonlinear) kernels that were used to define input-output characteristics of the interneurons. Three sets of interneurons were distinguished on the basis of kernel analysis. First, responses in interneurons 101, 107, 111, and 203 were characterized predominantly by a differentiating first-order kernel, which suggests a linear relationship to the stimulus. The amplitude and waveform of the kernel changed with the change in stimulus angle, indicating that these four cells are directionally sensitive. Second, responses in interneurons 102 and 103 were also directionally sensitive but highly nonlinear. The first-order kernel was biphasic, whereas the second-order kernel had an elongated depolarizing peak on the diagonal. The response dynamics were accounted for by a cascade of two filters, a linear band-pass filter and a static nonlinear filter, in which the nonlinearity is a signal compression (or a rectification). Third, responses in interneurons 104 and 201 consist largely of the second-order nonlinear component. The second-order kernel, which had an elongated depolarizing peak or a hyperpolarizing valley on the diagonal, did not show any directional preference. The second-order nonlinearity was dynamic, and could be modeled by a band-pass linear filter-static nonlinearity-low-pass linear filter cascade, where the static nonlinearity is a full-wave rectification. The band-pass filter would simply reflect the mechanical property of cercal hair sensilla, whereas the low-pass filter represents the transfer at synapses between the cercal afferents and the interneurons. The nonlinear response thus explains the difference in the directional sensitivity while the differentiating first-order kernel explains the velocity sensitivity of the interneurons. We show that 101 and 107 respond most preferentially to wind from the left versus right, whereas 102, 103, 111, and 203 respond to wind from the front versus rear. Thus, it is suggested that there are two subsystems responding maximally to wind displacement along two coordinate directions, one for the longitudinal direction and the other for the transverse direction. On the other hand, the full-wave-rectifier nonlinear interneurons are omnidirectional, and thus suggested to code simply the power of the wind displacement.
X-ray and Ellipsometric Studies of Self-Assembled Monolayers of Fluorinated Chlorosilanes (1994)

Results of X-ray and ellipsometric studies on self-assembled monolayer films of three fluorinated chlorosilanes are presented. By inferring an index of refraction, the monolayer thicknesses obtained from both these types of studies are self-consistent. The tilt of the molecules with respect to the layer normal is found to be strongly dependent on the functionality of (i.e. the number of chlorine atoms attached to) the terminal Si atom of the molecule.