gebhart/patrepeval huggingface dataset:
Growth and biofilm formation of Penicillium chrysogenum in simulated microgravity (2017)

Penicillium sp. are one of the main fungal genera detected on board the Russian Space Station (MIR) and the International Space Station (ISS), demonstrating its ability to grow on the space stations´ walls and to maintain growth under microgravity (1-3). As a spore-forming microorganism, Penicillium sp. poses a concern for planetary protection and to human/astronaut health, as its spores, associated with respiratory diseases, can be dispersed through the air (4). Fungal growth on the ISS has shown to promote biodegradation of the spacecraft materials, compromising their integrity. Biofilms are groups of organisms adhered to each other by self-synthesized extracellular polymeric substances, and are ubiquitous in industrial and natural environments (5). It has been reported that Penicillium sp. forms biofilms, which are associated with higher tolerance/resistance to adverse conditions (6). Therefore, biofilm formed on the ISS may have deleterious effects on astronaut’s health and/or on ISS materials. To gain valuable knowledge to control biofilm during long duration spaceflight missions, the NASA-funded project “Characterization of Biofilm Formation, Growth, and Gene Expression on Different Materials and Environmental Conditions in Microgravity” is currently being prepared. Pre-flight testing include: defining and optimizing the growth medium and culturing conditions of P. chrysogenum DSM 1075; characterizing the morphological response of P. chrysogenum growth under simulated microgravity; assessing biofilm formation by P. chrysogenum under different conditions. The study of this fungal strain represents the beginning of a new line of research on board ISS. The knowledge gained can be applicable to a) the safety and maintenance of crewed spacecraft, b) planetary protection, c) mitigation of biofilm-associated illnesses on the crew, as well as on the Earth. Besides, P. chrysogenum is of major medical and historical importance, as it presents the original and present-day industrial source of the antibiotic penicillin, and as an important producer of antifungal proteins and other relevant enzymes.
Two-stage L-band EDFA applying C/L-band wavelength-division multiplexer with the counterpropagating partial gain-clamping (2003)

A simple ring laser technique of two-stage gain-clamped long-wavelength band erbium-doped fiber amplifier is investigated. The ring laser light is excluded at the output end and noise-figure degradation can be reduced due to the counterpropagating partial gain-clamping in the second stage. The laser mechanism is achieved by the C/L-band wavelength-division multiplexer instead of a tunable bandpass filter and an optical circulator at the output end, which were often used in the previous counterpropagating ring laser architectures, and thus, this design is cost-effective. The gain-clamping of long-wavelength band (1559-1606.2 nm) in our configuration is demonstrated experimentally for the saturating tone (1587.6 nm) power up to -2 dBm.
Online Problems in Timetabling: Bus Priority at Signalised Junctions (2016)

We argue for the study of on-line problems in timetabling and given some novel examples thereof. The problem of prioritising delayed buses at signalised junctions underlies a timetabling competition held in conjunction with the International Conference on the Practice and Theory of Automated Timetabling.
Brillouin gain spectroscopy in glasses and crystals (1989)

Gain spectroscopy is a well established technique for the study of nonlinear scattering phenomena. Several capabilities of gain spectroscopy make the technique very powerful for frequency domain measurements of scattering processes. The use of gain spectroscopy is illustrated by the application of the technique to Brillouin measurements in solids. 21 refs., 2 figs.
Multiple radical additions: an expedient entry into complex frameworks (1988)

Irradiation of N-hydroxy-2-thiopyridone esters of suitable γ,δ-unsaturated carboxylic acids in the presence of an electron deficient alkene produces complex bicyclic systems by a multiple radical addition chain mechanism.
Endothelial MAPKs Direct ICAM-1 Signaling to Divergent Inflammatory Functions (2017)

Lymphocyte transendothelial migration (TEM) is critically dependent on intraendothelial signaling triggered by adhesion to ICAM-1. Here we show that endothelial MAPKs ERK, p38, and JNK mediate diapedesis-related and diapedesis-unrelated functions of ICAM-1 in cerebral and dermal microvascular endothelial cells (MVECs). All three MAPKs were activated by ICAM-1 engagement, either through lymphocyte adhesion or Ab-mediated clustering. MAPKs were involved in ICAM-1-dependent expression of TNF-α in cerebral and dermal MVECs, and CXCL8, CCL3, CCL4, VCAM-1, and cyclooxygenase 2 (COX-2) in cerebral MVECs. Endothelial JNK and to a much lesser degree p38 were the principal MAPKs involved in facilitating diapedesis of CD4<sup>+</sup> lymphocytes across both types of MVECs, whereas ERK was additionally required for TEM across dermal MVECs. JNK activity was critical for ICAM-1-induced F-actin rearrangements. Furthermore, activation of endothelial ICAM-1/JNK led to phosphorylation of paxillin, its association with VE-cadherin, and internalization of the latter. Importantly ICAM-1-induced phosphorylation of paxillin was required for lymphocyte TEM and converged functionally with VE-cadherin phosphorylation. Taken together we conclude that during lymphocyte TEM, ICAM-1 signaling diverges into pathways regulating lymphocyte diapedesis, and other pathways modulating gene expression thereby contributing to the long-term inflammatory response of the endothelium.
Synthesis of Nanostructured Bi2Te3 by Controlling Metal Species in Aqueous Solution (2013)

Abstract not Available.
Sero- and Subtypes of Group B Meningococci Causing Invasive Infections in Finland in 1976–87 (1989)

Neisseria meningitidis group B (MenB) strains isolated from 1976 to 1987 in Finland in 339 patients with invasive infection were sero/subtyped by whole cell enzyme immunoassay using monoclonal antibodies to class 1 and 2/3 outer membrane proteins. 66.7% of the strains could be serotyped (class 2/3) and 70.2% subtyped (class 1). No single phenotype was clearly predominant. The most common serotypes were 4 (18.6%) and 14 (17.4%) and the most common subtypes P1.16 (20.1%) and P1.2 (12.1%). The Norwegian phenotype B:15:P1.16 was seen only rarely (a total of 18 strains). Strains from Northern Finland did not differ from those from Southern Finland: no single phenotype caused the slight increase seen in the incidence of MenB infections in the end of 1970s in the North.
Pressure–Voltage Trap for DNA near a Solid-State Nanopore (2014)

We report the formation of a tunable single DNA molecule trap near a solid-state nanopore in an electrolyte solution under conditions where an electric force and a pressure-induced viscous flow force on the molecule are nearly balanced. Trapped molecules can enter the pore multiple times before escaping the trap by passing through the pore or by diffusing away. Statistical analysis of many individually trapped molecules yields a detailed picture of the fluctuation phenomena involved, which are successfully modeled by a one-dimensional first passage approach.
Distributed Microwave Wireless Power Transfer with Backscatter Feedback (2021)

In recent, microwave power transfer (MPT) for IoT devices has been studied. The distributed MPT can supply power efficiently by cooperate multiple transmit antenna arranged distributed in a relatively wide area. In this paper, we propose a method for distributed beam control by closed-loop with a backscatter signal from the receiver. The effectiveness of the proposed method will be demonstrated by lay-trace simulation and experiment.
Activity‐driven mobilization of post‐synaptic proteins (2009)

Synapses established during central nervous system development can be modified through synapse elimination and formation. These processes are, in part, activity dependent and require regulated trafficking of post-synaptic components. Here, we investigate the activity-driven remodeling of cultured rat hippocampal neurons at 14 days in vitro, focusing on the post-synaptic proteins PSD-95, Shank, neuroligin (NL)1 and actin. Using live imaging and photoconductive stimulation, we found that high-frequency activity altered the trajectory, but not velocity, of PSD-95-GFP and Shank-YFP clusters, whereas it reduced the speed and increased the number of NL1 clusters. Actin-CFP reorganized into puncta following activity and approximately 50% of new puncta colocalized with NL1 clusters. Actin reorganization was enhanced by the overexpression of NL1 and decreased by the expression of an NL1 mutant, NL1-R473C. These results demonstrate activity-dependent changes that may result in the formation of new post-synaptic sites and suggest that NL1 modulates actin reorganization. The results also suggest that a common mechanism underlies both the developmental and activity-dependent remodeling of excitatory synapses.
Automated analysis of meta‐analysis networks (2005)

The high information content in large data sets from voxel-based meta-analyses is complex, making it hard to readily resolve details. Using the meta-analysis network as a standardized data structure, network analysis algorithms can examine complex interrelationships and resolve hidden details. Two new network analysis algorithms have been adapted for use with meta-analysis networks. The first, called replicator dynamics network analysis (RDNA), analyzes co-occurrence of activations, whereas the second, called fractional similarity network analysis (FSNA), uses binary pattern matching to form similarity subnets. These two network analysis methods were evaluated using data from activation likelihood estimation (ALE)-based meta-analysis of the Stroop paradigm. Two versions of these data were evaluated, one using a more strict ALE threshold (P < 0.01) with a 13-node meta-analysis network, and the other a more lax threshold (P < 0.05) with a 22-node network. Java-based applications were developed for both RDNA and FSNA. The RDNA algorithm was modified to provide multiple subnets or maximal cliques for meta-analysis networks. Three different similarity measures were evaluated with FSNA to form subsets of nodes and experiments. RDNA provides a means to gauge importance of metanalysis subnets and complements FSNA, which provides a more comprehensive assessment of node similarity subsets, experiment similarity subsets, and overall node-to-factors similarity. The need to use both presence and absence of activations was an important finding in similarity analyses. FSNA revealed details from the pooled Stroop meta-analysis that would otherwise require separate highly filtered meta-analyses. These new analysis tools demonstrate how network analysis strategies can simplify greatly and enhance voxel-based meta-analyses.
Use of Underpotential Deposition for Evaluation of Overpotential Deposition Kinetics of Reactive Metals (2003)

The underpotential deposition (UPD) of Zn onto Pt is shown to produce an electrode surface which is suitable for the evaluation of Zn overpotential kinetics. The UPD of Zn onto polycrystalline Pt was characterized in acidic and neutral sulfate solutions using voltammetric charge measurements and X-ray photoelectron spectroscopy. The charge density for UPD Zn deposition on platinum from neutral sulfate solution was estimated to be consistent with a monolayer. The decrease in evolution rates provided further evidence of the formation of Zn UPD layer. Evidence for the formation of a Zn-Pt alloy, resulting from polarization of the Pt electrode at a potential between the Zn UPD and overpotential deposition potentials is also presented. The alloy was oxidized at the same potential as the Pt substrate, illustrating the large interaction between Zn and Pt due to the small crystallographic misfit. The alloy also decreased evolution rates, relative to the Pt substrate. The use of such a modified substrate for measurement of kinetic parameters for metal deposition is described and the results obtained are shown to compare favorably with the literature values. © 2003 The Electrochemical Society. All rights reserved.
Effects of Adsorbate Coverage and Bond‐Length Disorder on the d‐Band Center of Carbon‐Supported Pt Catalysts (2014)

Determination of the factors that affect the d-band center of catalysts is required to explain their catalytic properties. Resonant inelastic X-ray scattering (RIXS) enables direct imaging of electronic transitions in the d-band of Pt catalysts in real time and in realistic environmental conditions. Through a combination of in situ, temperature-resolved RIXS measurements and theoretical simulations we isolated and quantified the effects of bond-length disorder and adsorbate coverage (CO and H2) on the d-band center of 1.25 nm size Pt catalysts supported on carbon. We found that the decrease in adsorbate coverage at elevated temperatures is responsible for the d band shifts towards higher energies relative to the Fermi level, whereas the effect of the increase in bond-length disorder on the d-band center is negligible. Although these results were obtained for a specific case of non-interacting support and weak temperature dependence of the metal-metal bond length in a model catalyst, this work can be extended to a broad range of real catalysts.
Supplementary Table 3 from Intestinal Bacteria Modify Lymphoma Incidence and Latency by Affecting Systemic Inflammatory State, Oxidative Stress, and Leukocyte Genotoxicity (2023)

&lt;p&gt;PDF file - 551K, Relative Abundance of OTU of CM and RM Mice by Genotype and Intestinal Region.&lt;/p&gt;
Supplementary Table S2 from Genetic Variants Implicate Dual Oxidase-2 in Familial and Sporadic Nonmedullary Thyroid Cancer (2023)

&lt;p&gt;Supplemental Table 2. Hereditary cancer syndromes associated with increased non-medullary thyroid cancer risk&lt;/p&gt;
Water solublisation of single-walled carbon nanotubes using p-sulfonatocalix[4]arene (2009)

Single-walled carbon nanotubes (SWCNTs) are decorated with nanoparticles of p-sulfonatocalix[4]arene which render the nanotubes soluble in water. The nanocomposite was prepared by a solventless grinding method, followed by the additional of water then sonication. The non-covalently modified carbon nanotubes have been characterized using Raman, FTIR spectroscopy, fluorescence spectroscopy, transmission electron microscopy and thermogravimetric analysis.
Correction: A Novel Three-Phase Model of Brain Tissue Microstructure (2009)

In the Methods section, there was an error in the second equation in the fifth rule of the section titled Discrete First-Passage-Time Technique. The quantity in parentheses is incorrect. It should read 0.5(1-c). For the complete, correct equation, see here:
ChemInform Abstract: Synthesis of 1,3‐Diaryl‐Substituted Indazoles Utilizing a Suzuki Cross‐Coupling/Deprotection/N‐Arylation Sequence. (2010)

Abstract Substrate (I) is highly suitable for the title sequence which affords a broad spectrum of target compounds.
Higher-order oligomerization of Spc110p drives γ-tubulin ring complex assembly (2016)

The microtubule (MT) cytoskeleton plays important roles in many cellular processes. In vivo, MT nucleation is controlled by the γ-tubulin ring complex (γTuRC), a 2.1-MDa complex composed of γ-tubulin small complex (γTuSC) subunits. The mechanisms underlying the assembly of γTuRC are largely unknown. In yeast, the conserved protein Spc110p both stimulates the assembly of the γTuRC and anchors the γTuRC to the spindle pole body. Using a quantitative in vitro FRET assay, we show that γTuRC assembly is critically dependent on the oligomerization state of Spc110p, with higher-order oligomers dramatically enhancing the stability of assembled γTuRCs. Our in vitro findings were confirmed with a novel in vivo γTuSC recruitment assay. We conclude that precise spatial control over MT nucleation is achieved by coupling localization and higher-order oligomerization of the receptor for γTuRC.
Detection of Cracks in Turbomachinery Blades by Online Monitoring (2022)

Abstract The presence of a crack in a blade can change the natural frequencies of that blade. It has long been a goal to detect blade cracks by assessing the change in a measured vibration frequency of the blade over time. It has been found that prior frequency assessment methods can be less accurate than is desirable to reliably detect the relatively small frequency changes that are typically associated with blade crack sizes of practical interest. This paper describes a method in which potential temporal changes in the frequencies of individual blades are assessed by periodically analyzing complete rows of blades using mistuning analysis techniques that treat the blade rows as coupled systems, in contrast to other techniques that consider each blade individually in turn. This method, while computationally complicated and challenging, has been found to be capable of detecting blade root cracks that are much smaller than those that can be detected using other techniques. Moreover, this method has been demonstrated to detect cracks that are much smaller than the critical size for mechanical separation of the blade from the rotor. This improved frequency assessment technique has been used to identify more than 30 blades with frequency changes that were considered to be potential indicators of blade cracks. Subsequent inspections verified indications in all of those blades. In addition to providing operational guidance, the frequency change data were used to infer the time periods during which crack growth had occurred.
Figure from Somatic Epigenetic Silencing of <i>RIPK3</i> Inactivates Necroptosis and Contributes to Chemoresistance in Malignant Mesothelioma (2023)

&lt;p&gt;Restoration of RIPK3 expression triggers necroptosis in RIPK3-negative MM cells. A, Lentivirus expressing RIPK3-WT, RIPK3-KD, or empty vector only was used to transduce RIPK3-negative MM cells at MOI=5. Flow cytometry analysis of MM cells stained with AnnexinV and PI. B, Bar graphs depicting percentages of early apoptotic (AnnexinV only), later apoptotic (AnnexinV+PI), and necrotic (PI only) populations.&lt;/p&gt;
Antigenome of Helicobacter pylori: vaccination on the horizon? (2010)

Helicobacter pylori is the most prevalent human pathogen with about 50% of the world's population infected. Although, it remains silent in most individuals for lifetime, colonization may develop into severe gastric and duodenal conditions, such as peptic ulcer disease and gastric adenocarcinoma. Rapidly developing resistance to current antibiotic-based treatment regimes urgently calls for the development of effective vaccines. In these studies we determined the comprehensive antigenic profile (so called “ANTIGENome“) of two clinical isolates of H. pylori, KTH-Ca1 and KTH-Du that were derived from patients with gastric cancer and duodenal ulcer, respectively. With the aid of our whole genome-based bacterial surface display technology and disease-relevant human sera from well-characterized donors – including patients with clinically and microbiologically verified Helicobacter diseases and healthy adults – we identified 124 annotated ORFs and 54 non-annotated genomic regions coding for antigens. Through in vitro validation assays we selected the 20 most promising vaccine candidates. Importantly, two of the selected 20 candidates represent proteins that have been previously shown to provide protection in experimental models of H. pylori infection. One of the most frequently selected and conserved protein, the siderophore-dependent transporter HP1341, was confirmed to show high reactivity with human serum IgGs. These analyses provide the means to identify novel antigens for the selection of vaccine candidates, as well as disease associated biomarkers.
Application of VANET to Avoid Pedestrian Collision in Automotive Vehicles (2020)

Machines are playing a key role in most innovative industrial environments. These developments in terms of machinery can be improved by additional intelligence incorporated to the machines. Intelligent machines have the ability to help people in various scenarios of their day-to-day lives. For example, intelligent machines can be applied in various fields and situations, such as continuous monitoring and diagnosing patients, video surveillance, intelligent transportation system, communication between machines, and online education systems. In the near future, machinery will be the most integrated part of any company or organization for efficient and effective working. This chapter describes the modification to a special module for intelligent automobiles for safe driving on roads and also to avoid pedestrian collisions. Pedestrian protection is very important since there are many people who lose their lives in road accidents. An intelligent module should be developed to detect the presence of people crossing roads and then providing necessary alerts to the corresponding automobile in order to avoid collision and possible injury. One of the practical situations where the driver assistance system is compromised is in weather with heavy fog. In such scenarios, tracking the presence of pedestrians is a somewhat difficult task. To avoid this, we can introduce a specialized camera setup for clear vision information. The same pedestrian track information should be passed to 36the next adjacent vehicle that cannot view the presence of the approaching pedestrian. Such types of development improve safety measures and contributes to a comfortable lifestyle, even for physically challenged people in our society. This type of communication can be achieved by a special networking model called vehicular ad hoc network (VANET). These network models have no particular infrastructure and functionality. The features of automobile characteristics and its movements corresponding to the road conditions can be communicated to the neighboring vehicles by means of VANET.
Hypothalamic-Pituitary Axis Regulates Hydrogen Sulfide Production (2017)

Decreased growth hormone (GH) and thyroid hormone (TH) signaling are associated with longevity and metabolic fitness. The mechanisms underlying these benefits are poorly understood, but may overlap with those of dietary restriction (DR), which imparts similar benefits. Recently we discovered that hydrogen sulfide (H<sub>2</sub>S) is increased upon DR and plays an essential role in mediating DR benefits across evolutionary boundaries. Here we found increased hepatic H<sub>2</sub>S production in long-lived mouse strains of reduced GH and/or TH action, and in a cell-autonomous manner upon serum withdrawal in vitro. Negative regulation of hepatic H<sub>2</sub>S production by GH and TH was additive and occurred via distinct mechanisms, namely direct transcriptional repression of the H<sub>2</sub>S-producing enzyme cystathionine γ-lyase (CGL) by TH, and substrate-level control of H<sub>2</sub>S production by GH. Mice lacking CGL failed to downregulate systemic T<sub>4</sub> metabolism and circulating IGF-1, revealing an essential role for H<sub>2</sub>S in the regulation of key longevity-associated hormones.
Supplementary Tables 1-5, Figure Legends 1-3 from Taxol Increases the Amount and T Cell–Activating Ability of Self-Immune Stimulatory Multimolecular Complexes Found in Ovarian Cancer Cells (2023)

Supplementary Tables 1-5, Figure Legends 1-3 from Taxol Increases the Amount and T Cell–Activating Ability of Self-Immune Stimulatory Multimolecular Complexes Found in Ovarian Cancer Cells
Computational hair quality categorization in lower magnifications (2015)

We take advantage of human hair specific geometry to visualize sparse submicron cuticle peelings with highly oblique tip-side illumination. We show that the statistics of these features can directly estimate hair quality in much lower magnifications (down to 20<sup>x</sup>) with less powerful objectives when the features themselves are below the system resolution. Our technique has strong potential for lower cost, portable, and autonomous hair diagnostic apparatuses.