gebhart/patrepeval huggingface dataset:
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning (2012)

In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue-appropriate regulatory programs. A genome-scale analysis of DNA binding by Gli1 and Sox2, a pan-neural determinant, identified a set of shared regulatory regions associated with key factors central to cell fate determination and neural tube patterning. Functional analysis in transgenic mice validates core enhancers for each of these factors and demonstrates the dual requirement for Gli1 and Sox2 inputs for neural enhancer activity. Furthermore, through an unbiased determination of Gli-binding site preferences and analysis of binding site variants in the developing mammalian CNS, we demonstrate that differential Gli-binding affinity underlies threshold-level activator responses to Shh input. In summary, our results highlight Sox2 input as a context-specific determinant of the neural-specific Shh response and differential Gli-binding site affinity as an important cis-regulatory property critical for interpreting Shh morphogen action in the mammalian neural tube.
“Progress in Corneal Research and Practice in Japan and Abroad”: The 23rd Annual Meeting of the Kyoto Cornea Club, November 24 and 25, 2017 (2018)

Nishida, Kohji MD, PhD*; Sotozono, Chie MD, PhD†; Yamagami, Satoru MD, PhD‡; Shiraishi, Atsushi MD, PhD§; Saika, Shizuya MD, PhD¶; Fukushima, Atsuki MD, PhD‖; Hori, Yuichi MD, PhD** Author Information
Kidney Endothelial Dysfunction: Ischemia, Localized Infections and Sepsis (2011)

Endothelial cells play a key role in initiating and propagating the inflammatory response seen in ischemia, infections and sepsis. Situated in a key position between the epithelial cells and white blood cells (WBC), they interact and respond to signals from both cell types. Microvascular endothelial cells within the kidney mediate coagulation, WBC attachment, WBC migration into the interstitium, microvascular flow rates and permeability. Low regeneration potential and endothelial-mesenchymal transformation lead to fibrosis and subsequent microvascular dropout. This last event is in large part responsible for a chronic reduction in regional perfusion, subsequent increased vulnerability to recurrent acute kidney injury, and acceleration of chronic kidney disease progression to end-stage renal disease. Glomerular endothelial dysfunction may lead to preglomerular shunting of blood flow allowing kidney blood flow to remain close to normal while resulting in a reduction in glomerular filtration rate.
Supplementary Data from Multiparametric Photoacoustic Analysis of Human Thyroid Cancers <i>In Vivo</i> (2023)

&lt;p&gt;Supplementary movie 1. Boundary selection software&lt;/p&gt;
Heterocyclic structures useful in medicinal chemistry: the case of pyrazino[2,3-c][1,2,6]thiadiazine 2,2-dioxide. (1997)

Different aspects of a particular kind of heterocycle, namely pyrazino[2,3-c][1,2,6]thiadiazine 2,2-dioxide are discussed. These include synthesis, reactivity, tautomerism and acid-base properties, results of x-ray analysis and molecular orbital calcultations. Besides, some of the derivatives have shown interesting biological effects, among which are the diuretic properties which are also presented.
<title>Integrated force array: positioning drive applications</title> (1996)

Integrated Force Arrays (IFAs) are thin film membrane actuators that act as transfer devices for electrostatic force. They are capable of large amplitude motion and evidence significant energies per unit volume (eg. 8.2 erg/mm<SUP>3</SUP>). Devices which use IFAs as drivers to scan PZT acoustic imaging transducers are under development and will be discussed here.
Direct photo emission motion observation of current filaments in the IGBT under avalanche breakdown condition (2016)

Many recent studies have been reported that the current distribution has non-uniformity in IGBT under Unclamped inductive switching (UIS) condition. Those discussions are based on the calculation result performed using device simulators. And, the observation of thermal action of device has been reported by using the IR thermography. The non-uniform temperature distribution on chip and thermal map change at every several micro second periods. In this study, time resolved emission (TRE) microscopy was used to get highly precise data. The probability distribution of current in the IGBT under UIS condition was observed. Also, a change of current distribution dependent on the time and motion of current concentration were detected. These areas of high current density existence probability move along termination region of device 1.75μs after avalanche breakdown with damping. This is the first study to show the direct motion observation of photon emission from the current fllamentation in IGBT under avalanche breakdown condition.
Gene expression profiling of Gram-negative bacteria-induced inflammation in human whole blood: The role of complement and CD14-mediated innate immune response (2015)

Non-sterile pathogen-induced sepsis and sterile inflammation like in trauma or ischemia-reperfusion injury may both coincide with the life threatening systemic inflammatory response syndrome and multi-organ failure. Consequently, there is an urgent need for specific biomarkers in order to distinguish sepsis from sterile conditions. The overall aim of this study was to uncover putative sepsis biomarkers and biomarker pathways, as well as to test the efficacy of combined inhibition of innate immunity key players complement and Toll-like receptor co-receptor CD14 as a possible therapeutic regimen for sepsis. We performed whole blood gene expression analyses using microarray in order to profile Gram-negative bacteria-induced inflammatory responses in an ex vivo human whole blood model. The experiments were performed in the presence or absence of inhibitors of complement proteins (C3 and CD88 (C5a receptor 1)) and CD14, alone or in combination. In addition, we used blood from a C5-deficient donor. Anti-coagulated whole blood was challenged with heat-inactivated Escherichia coli for 2 h, total RNA was isolated and microarray analyses were performed on the Affymetrix GeneChip Gene 1.0 ST Array platform. The initial experiments were performed in duplicates using blood from two healthy donors. C5-deficiency is very rare, and only one donor could be recruited. In order to increase statistical power, a technical replicate of the C5-deficient samples was run. Subsequently, log2-transformed intensities were processed by robust multichip analysis and filtered using a threshold of four. In total, 73 microarray chips were run and analyzed. The normalized and filtered raw data have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible with GEO Series accession number GSE55537. Linear models for microarray data were applied to estimate fold changes between data sets and the respective multiple testing adjusted p-values (FDR q-values). The interpretation of the data has been published by Lau et al. in an open access article entitled "CD14 and Complement Crosstalk and Largely Mediate the Transcriptional Response to Escherichia coli in Human Whole Blood as revealed by DNA Microarray" (Lau et al., 2015).
Pepsin as a biomarker of reflux in patients presenting at a UK ENT voice clinic (2021)

Background: Gastro-esophageal reflux disease (GERD) is common and experienced by 40% of the population. Laryngopharyngeal reflux (LPR) is caused by gastric contents refluxing above the upper esophageal sphincter (UES). LPR diagnosis remains challenging. The aim of this study was to evaluate pepsin as a biomarker of reflux in symptomatic patients presenting at a secondary referral ENT voice clinic.Methods: All 331 patients and a group of 22 asymptomatic control subjects were recruited. Participants were instructed to provide three saliva samples. Patients provided samples on waking, post-prandial or post-symptom by an episodic or continuous symptom procedure. Saliva samples were analysed for the presence of pepsin using the lateral flow diagnostic device Peptest and the concentration of pepsin in ng/mL determined using the PepCube reader.Results: The 331 patients produced a total of 982 saliva samples with pepsin detected in 223 (67%) of patients. The greatest pepsin concentration was seen in the post-prandial samples (107.7 ng/mL) however, there was no significant difference between times of sample collection. Control subjects tested negative for pepsin. There was no significant difference in salivary pepsin concentration between genders and no difference in salivary pepsin concentration between patients presenting with episodic (97.5 ng/mL) or continuous symptoms (95.8 ng/mL). The majority of patients were aged between 51 to 80 years with older age tending to correlate with higher salivary pepsin concentrations.Conclusions: Pepsin was a good biomarker for detecting salivary pepsin in a large population of ENT patients and Peptest under clinical conditions was a reliable and rapid non-invasive diagnostic test.
CAT Scan Evaluation of Traumatic Hip Dislocations With Associated Posterior Acetabular Fractures (1983)

Computerized axial tomography (CAT scanning) was utilized in the evaluation and treatment of 11 patients with traumatic fracture dislocations of the hip. The results influenced the treatment of all patients studied, and demonstrated significant radiographic findings that were not apparent on standard plain radiographs and tomography. CAT scanning in fracture dislocations of the hip is an essential diagnostic tool in establishing adequate treatment regimens and prognosis for these severe injuries.
Lipophilic nano-bismuth inhibits bacterial growth, attachment, and biofilm formation (2013)

There is an urgent need for low-cost and low-toxicity antimicrobial agents for water treatment and medical applications. Current approaches utilize relatively expensive and corrosive chemicals and disinfectants to reduce, prevent or remove biofilms in technological systems. Nanoparticle-based approaches are sought increasingly to develop disinfection systems and self-cleaning surfaces that could ‘seek and destroy’ microorganisms. In this context, the authors have developed novel lipophilic bismuth dimercaptopropanol (BisBAL) nanoparticles using a simple aqueous reduction reaction with sodium borohydride at room temperature. The objective of this study was to assess the effect of BisBAL nanoparticles on growth, attachment and biofilm formation by Pseudomonas aeruginosa. Characterization of nanoparticles showed them to be very lipophilic, with a rhombohedral crystalline structure and crystallite size of approximately 18 nm. When introduced at or above the minimum inhibitory concentration (MIC = 12·5 µM), the growth of bacteria was completely inhibited for at least 30 d. The authors show that lipophilic BisBAL nanoparticles at the MIC inhibited bacterial attachment to track-etched polycarbonate membrane surfaces and lysed bacteria embedded in biofilms, within 1 h of exposure. The authors conclude that lipophilic bismuth nanoparticles are promising antimicrobial agents, that have the capability to inhibit growth, prevent bacterial attachment to surfaces or damage existing biofilms.
Aggregation of ligand-modified liposomes by specific interactions with proteins. I: Biotinylated liposomes and avidin (1996)

The aggregation of biotin-modified phospholipid vesicles (liposomes) induced by binding the protein avidin in solution is analyzed experimentally and theoretically. Avidin has four binding sites that can recognize biotin specifically, and is able to cross-link the liposomes to form large aggregates. The aggregation kinetics were followed using quasi-elastic light scattering (QLS) to measure the mean particle size, and by measuring the solution turbidity. The rate and extent of aggregation were determined as a function of vesicle concentration, protein concentration, and the biotin density on the surface of the liposomes. A model based on Smoluchowski kinetics, fractal concepts, and Rayleigh and Mie light scattering theory was developed to analyze the experimental observations. Small aggregates (<7800 A diameter) may be treated as globular; however, the fractal nature of larger particles must be taken into account. Parameters in the model are taken from molecular simulations, or fit to the experimental observations. The aggregation kinetics are primarily determined by the biotin density on the liposome surface, the stoichiometric ratio of avidin molecules to liposomes, and the liposome concentration. Good agreement is found between the model and the experimental results.
Long‐term follow‐up after radiofrequency ablation of ectopic atrial tachycardia in young patients (2019)

Abstract Aim Ectopic atrial tachycardia (EAT) is a common arrhythmia in children, adolescents, and young adults. Radiofrequency (RF) ablation is often considered the treatment of choice in this population. We sought to evaluate the long‐term follow‐up after RF ablation. Methods and Results We retrospectively analyzed 36 young patients (age range 8‐29 years), with clinical signs and symptoms suspected for EAT who underwent an electrophysiological study in our center. We evaluated the safety and acute success rate of ablation and the long‐term follow‐up. Ectopic foci were more frequently localized in the right atrium along the crista terminalis (28%) and EAT was successfully terminated in 97% of patients. At median follow‐up (38 months), the recurrence rate was 20% with mostly recurrences expressed within 6 months. Conclusions The study confirmed the safety and high acute success rate of EAT ablation in a population of children, adolescents, and young adults. Therefore, catheter ablation of EAT can be considered early in the course of treatment of these patients. The evidence of most recurrences within 6 months could be useful for advising patients on likely outcomes.
Loss Mechanisms Determining the Quality Factors in Quartz Tuning Forks Vibrating at the Fundamental and First Overtone Modes (2018)

Quartz tuning forks (QTFs) are piezo-transducers that have been implemented for numerous applications, such as chemical gas sensing, atomic force microscopy, rheology, and industrial process control. The most important parameter for QTFs' sensing application is the resonance quality factor (Q-factor). An experimental investigation and theoretical analysis of the influence of QTFs' geometries on the Q-factor of the flexural fundamental and first overtone resonance modes are reported. The resonance frequencies and related Q-factors for five different QTFs have been measured. The QTF response was recorded at different air pressures to investigate the influence of the surrounding medium on the Q-factor. A data analysis demonstrated that air viscous damping is the dominant energy dissipation mechanism for both flexural modes. Thermoelastic and support losses are additional contributions that depend on the QTF geometry. A study of the QTF damping mechanism dependence upon the prong geometry is also provided.
Metabolic syndrome is associated with poor response to rifaximin in minimal hepatic encephalopathy (2022)

Patients with cirrhosis may show minimal hepatic encephalopathy (MHE), for which rifaximin is effective. Metabolic syndrome may be associated with cognitive impairment. Our aims were to evaluate the influence of metabolic syndrome features on response to rifaximin for neurological and inflammatory alterations in MHE. A prospective cohort study was conducted in 63 cirrhotic patients and 30 controls from two tertiary centres recruited between 2015 and 2019. Metabolic syndrome was defined according to the Adult Treatment Panel-III. Patients were classified into 31 without and 32 with MHE according to the Psychometric Hepatic Encephalopathy Score (PHES). All participants performed specific psychometric tests, and inflammatory parameters were studied. Patients with MHE received rifaximin (400 mg/8 h). Response was evaluated by PHES at 3 and 6 months. Response according to metabolic syndrome manifestations was compared. The response rate was 66%. Older age (p = 0.012) and all metabolic syndrome diseases (p < 0.05) were associated with non-response, plus an increase in risk as the number of manifestations rose (p < 0.001). Patients with metabolic manifestations exhibited worse processing speed (p = 0.011), working memory (p = 0.005), visual coordination (p = 0.013) and lower proportion of activated CD4<sup>+</sup> lymphocytes (p = 0.039) at baseline, as well as worse concentration (p = 0.030), bimanual coordination (p = 0.004) and higher levels of intermediate monocytes (p = 0.026), CX3CL1 (p < 0.05), IL-17 (p = 0.022), AHR (p = 0.010) and IgG (p < 0.05) at 3 and/or 6 months of rifaximin. Patients with clinical signs of metabolic syndrome have poor response to rifaximin for MHE, with a higher proportion of neurological alterations associated with a pro-inflammatory environment.
Studies on the Catechin Constituents of Bark of <i>Cinnamomum sieboldii</i> (2023)

Screening for bioactivity related to anti-infective, anti-methicillin-resistant Staphylococcus aureus (MRSA) and anti-viral activity, led us to identify active compounds from a methanol extract of Litsea japonica (Thub.) Juss. and the hot water extract of bark of Cinnamomum sieboldii Meisn (also known as Karaki or Okinawa cinnamon). The two main components in these extracts were identified as the catechin trimers (+)-cinnamtannin B<sub>1</sub> and pavetannin B5. Moreover, these extracts exhibited anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity. The structures of these catechin trimers were previously determined by chemical and spectroscopic methods. Pavetanin B5 has never been reported to be isolated as a pure form and has been obtained as a mixture with another component. Although other groups have reported the putative structure of pavetannin B5, preparation of the methylated derivative of pavetannin B5 in this study allowed us to obtain the pure form for the first time as the undecamethyl derivative and confirm its exact structure. Commercially available (+)-cinnamtannin B<sub>1</sub> and aesculitannin B (C2'-epimer of cinnamtannin B<sub>1</sub>) both of which contained pavetannin B5 as a minor component, and C. sieboldii bark extract (approx. 5/2 mixture of (+)-cinnamtannin B<sub>1</sub>/pavetannin B5) were assessed for anti-SARS-CoV-2 activity. Both C. sieboldii bark extract and commercially available aesculitannin B showed viral growth inhibitory activity.
Radiating plasma species density distribution in EUV-induced plasma in argon: a spatiotemporal experimental study (2015)

In this contribution we experimentally study temporally and spatially resolved radiating plasma species density distribution in plasma induced by irradiating a low pressure argon gas with high energy photons with a wavelength of 13.5 nm, i.e. extreme ultraviolet (EUV). This is done by recording the optical emission spatially and temporally resolved by an iCCD camera as a function of the argon gas pressure. Our experimental results show that the emission intensity, i.e. density of radiating plasma species, depends quadratically on the gas pressure. The linear term is due to photoionization and simultaneous excitation by EUV photons, the quadratic term due to electron impact excitation by electrons generated by photoionization. The decay of radiating plasma species can be divided into two phases. At time scales shorter than 10 s (first phase), the decay is governed by radiative decay of radiating plasma species. At longer time scales (second phase, >10 s), the decay is dominated by diffusion and subsequent de-excitation at the wall. The experimental decay and expansion during this phase corresponds well with a simplified diffusion model. In order to gain more insight in this exotic type of plasma, we compare the electron density from previous measurements with the results obtained here.
Learning to Find Pictures of People (1998)

Finding articulated objects, like people, in pictures presents a particularly difficult object recognition problem. We show how to find people by finding putative body segments, and then constructing assemblies of those segments that are consistent with the constraints on the appearance of a person that result from kinematic properties. Since a reasonable model of a person requires at least nine segments, it is not possible to present every group to a classifier. Instead, the search can be pruned by using projected versions of a classifier that accepts groups corresponding to people. We describe an efficient projection algorithm for one popular classifier, and demonstrate that our approach can be used to determine whether images of real scenes contain people. 1 Introduction Several typical collections containing over ten million images are listed in [2]. There is an extensive literature on obtaining images from large collections using features computed from the whole image, including ...
Molecular control of excited cross-conjugated triene rearrangements. Exploratory and mechanistic organic photochemistry (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular control of excited cross-conjugated triene rearrangements. Exploratory and mechanistic organic photochemistryHoward E. Zimmerman and Donald R. DiehlCite this: J. Am. Chem. Soc. 1979, 101, 7, 1841–1857Publication Date (Print):March 1, 1979Publication History Published online1 May 2002Published inissue 1 March 1979https://pubs.acs.org/doi/10.1021/ja00501a035https://doi.org/10.1021/ja00501a035research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
20-GHz Bandwidth InGaAsP Lasers (1985)

Constricted mesa lasers use a mesa with an undercut region for optical, current and carrier confinement [1-3]. This label refers to undercut mesa lasers which may have no regrowth (sometimes called mushroom stripe [3]) or small amounts of LPE, VPE, MO-CVD or mass transported regrowth. The high speed characteristics of this structure have not been demonstrated, although 960 Mb/s modulation has been demonstrated [3]. In this paper, we describe modifications to the constricted mesa structure to allow very high frequency operation and describe small-signal and large-signal modulation of 1.3 μm InGaAsP constricted mesa lasers.