gebhart/patrepeval huggingface dataset:
Analysis of the Ligand-induced Assembling of the Type I Interferon Receptor (2001)

Type I interferons (IFNs) elicit antiviral, antiproliferative and immunmodulatory cellular response through binding to a cell surface receptor consisting of (at least) two transmembrane proteins, ifnar1 and ifnar2. Interestingly, different members of the family of type I IFNs (∼15 IFNa, 1 IFNb, 1 IFNw) induce different response patterns through binding to the same receptor components. Binding of interferons induces association of ifnar1 and ifnar2 on the cell surface, but neither stoichiometry nor orientation of the receptor components in the functional complex is known. While ifnar2 binds IFNs with high affinity (KD in the nanomolar range), the affinity of ifnar1 is very low (KD > 1 mM). It seems that the interaction between ifnar1 and IFNs play an important role for the response specificity. Our research aims to understand this differential recruitment of the receptor components by different IFNs. We have expressed and purified recombinant IFNa2 and the extracellular domain of ifnar2 (ifnar2-EC), and mapped the binding sites on these proteins in high resolution by mutational analysis using optical detection. The differences in the interaction of IFNa2 and IFNb with ifnar2 are only minor (Fig. 1, next page) and can hardly explain their differences in activity. To understand the IFN-induced cross-talk between the receptor components, the extracellular domains of the receptor are attached to supported lipid bilayers to mimic the properties on the cellular surface. Different strategies for attaching the lipid bilayers at the surface and for controlling their fluidity are investigated reflectometric detection and fluorescence recovery after photobleaching (FRAP). The interaction between the receptor components is monitored by fluorescence resonance energy transfer (FRET). This interaction will be investigated on a single molecule level by using a TIRF-microscope to identify possible different modes of interaction between the receptor components. The analysis of stoichiometry, dynamics and orientation during the interaction based on individual events will allow understanding the receptor assembling in detail and to identify the role its apparent promiscuity towards different IFNs.
Biofilm control in water by advanced oxidation process (AOP) pre-treatment: effect of natural organic matter (NOM) (2011)

The main goal of this study was to examine the influence of natural organic matter (NOM) on the efficiency of H₂O₂/UV advanced oxidation process (AOP) as a preventive treatment for biofilm control. Pseudomonas aeruginosa PAO1 biofilm-forming bacteria were suspended in water and exposed to various AOP conditions with different NOM concentrations, and compared to natural waters. H₂O₂/UV prevented biofilm formation: (a) up to 24 h post treatment - when residual H₂O₂ was neutralized; (b) completely (days) - when residual H₂O₂ was maintained. At high NOM concentrations (i.e. 25 mg/L NOM or 12.5 mg/L DOC) an additive biofilm control effect was observed for the combined H₂O₂/UV system compared to UV irradiation alone, after short biofilm incubation times (<24 h). This effect was H₂O₂ concentration dependent and can be explained by the high organic content of these water samples, whereby an increase in NOM could enhance (•)OH production and promote the formation of additional reactive oxygen species. In addition, maintaining an appropriate ratio of bacterial surviving conc.: residual H₂O₂ conc. post-treatment could prevent bacterial regrowth and biofilm formation.
Outcomes in Previously Healthy Cryptococcal Meningoencephalitis Patients Treated With Pulse Taper Corticosteroids for Post-infectious Inflammatory Syndrome (2020)

PCT in this small cohort of PIIRS was associated with improvements in CM-related complications with minimal toxicity in the acute setting.
Far-Field Control of Radiation from an Individual Optical Nanocavity: Analogue to an Optical Dipole (2008)

We demonstrate long-range control of the radiative lifetime of a silicon optical nanocavity using a metallic atomic force microscope probe. We extract changes in the radiative lifetime from changes in the cavity's transmittivity resulting from probe-cavity interaction over distances of several optical wavelengths. Analogous to atomic systems, the cavity acts as an individual radiating dipole with a radiative rate that is modified by a metallic interface.
Modeling the energy consumption of HEVC intra decoding (2013)

Battery life is one of the major limitations to mobile device use, which makes research on energy efficient soft- and hardware an important task. This paper investigates the energy required by a CPU when decoding compressed bitstream videos on mobile platforms. A model is derived that describes the energy consumption of the new HEVC decoder for intra coded videos. We show that the relative estimation error of the model is smaller than 3.2% and that the model can be used to build encoders aiming at minimizing decoding energy.
Bone marrow stromal cells as a genetic platformfor systemic delivery of therapeutic proteins in vivo: human factor IX model (2002)

These findings demonstrate that genetically modified BMSCs can continuously secrete biologically active hFIX from self-contained ectopic ossicles in vivo, and thus represent a novel delivery system for releasing therapeutic proteins into the circulation.
Outcome of infants with hypoxic ischemic encephalopathy treated with brain hypothermia (2014)

Infants with an Apgar score at 10 min ≥5, activity on electroencephalography on admission, and higher OEF during and after BHT were likely to have a favorable outcome.
Prediction of Relapse Risk by Day 100 BCR-ABL Quantification after Allogeneic Stem Cell Transplantation for Chronic Myeloid Leukaemia. (2005)

Abstract CML relapse after allogeneic SCT is a relatively frequent situation and is clearly correlated to disease status, time from diagnosis to transplant and T cell depletion. Defining other risk factors could help modulate post transplant immunosuppression. We evaluated the value of early minimal residual disease (MRD) quantification to predict relapse of CML patients receiving standard allogeneic SCT. MRD was analysed by RQ-PCR at Day 100 in 38 patients with a follow up after transplant &gt; 1 year and was expressed as BCR-ABL/ABL, qualified by objective evaluation of RNA amplifiability relative to local normal values for MRD samples (the Quality Index or QI). This QI allows objective evaluation of the degree of correction for positive results and modification of the limits of detection for negative results. Thirty six of 38 patients received conventional conditioning regimen with either BU/CY or TBI/CY and classical prevention of GVHD based on cyclosporin and methotrexate. The median time from diagnosis to transplant was 21 months and median follow up of the cohort was 76.8 months. Patients were allocated to two groups according to their Day 100 RQ PCR level. We compared the characteristics and evolution of the 14 patients with a high MRD level (Day 100 RQ PCR &gt;10−4) to that of the 24 patients with a low MRD level (Day 100 RQ PCR &lt;10−4). There were no significant differences in terms of disease status at transplant, median age at transplant, time from diagnosis to transplant, type of conditioning regimen, source of stem cells, sex mismatch, grade of acute GVHD or incidence of chronic GVHD between the two groups. We show that Day 100 BCR-ABL transcript levels &gt;10−4 by RQ-PCR represents an independent risk factor of relapse after conventional non T cell depleted SCT. These data should favour risk-adapted post transplant immunosuppression based on a single time point early evaluation of MRD.
<title>Smart optical waveguide sensors for cumulative damage assessment</title> (1999)

A strain gage is being developed, based on optical modulation that is capable of gage factors on the order of 500 for stains in excess of 2000 (mu) (epsilon) . The strain sensing element is a coated, hollow, glass waveguide of dimensions 0.5 mm ID X 1mm X OD X 100mm long. Since the geometry is compatible with standard telecommunication optical fiber such gages it can be readily incorporated into smart system arrays for damage assessment in structure such as buildings, roads and bridges. Optical fibers bring the excitation light signal to and the response signal for the sensing element. The small diameter glass tubes act as the substrate for a multiple thin film layers which can be optimized to provide the maximum dynamic range for a predetermined strain excursion. The sensor respond to bending strain by attenuation the optical intensity of the excitation signal. The gage elements exhibit little or no hysteresis and are insensitive to temperature. Also, they are environmentally stable and are not affected by factors such as corrosion or electromagnetic fields. The preliminary experimental result will be presented for this type of strain gage system operating to 2000 (mu) (epsilon) . Also, the model for the physical process will be discussed.
Secure Shell Transport Model for the Simple Network Management Protocol (SNMP) (2009)

This memo describes a Transport Model for the Simple Network
Management Protocol, using the Secure Shell protocol (SSH). This memo
also defines a portion of the Management Information Base (MIB) for
use with network management protocols in TCP/IP based internets. In
particular it defines objects for monitoring and managing the Secure
Shell Transport Model for SNMP.
Chiral Ru‐Based Complexes for Asymmetric Olefin Metathesis: Enhancement of Catalyst Activity Through Steric and Electronic Modifications. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
V‐sis induces Egr‐1 expression by a pathway mediated by c‐Ha‐ras (1994)

The early growth response gene, Egr-1, is up-regulated transiently by mitogens and many other stimuli in all cells tested. Using NIH3T3 cells conditionally expressing v-sis from a metallothionein promoter, we show that the addition of Zn2+ stimulates the production of PDGF-B (v-sis) and elicits the expression of Egr-1 in a dose-dependent and time-regulated manner. The signal is likely independent of protein kinase C, but depends on tyrosine kinase and other kinase activities and is mediated by c-Ha-Ras since the presence of dominant-negative mutants of Ras and Raf abrogates the induction of Egr-1 expression by Zn2+. Transiently activated Ras expression in NIH3T3 cells also stimulates the transient expression of Egr-1, but cells that constitutively express Ras do not have elevated levels of Egr-1. Transient assays also demonstrated that Zn2+ or activated Ras expression stimulate the activity of a 950 bp Egr-1 promoter-reporter gene construct and this is abrogated in the presence of mutant Ras and Raf. The accumulated data show that Egr-1 gene expression is regulated by multiple mechanisms, as would be needed for putative roles in cell proliferation, in suppression of transformation and in differentiation.
Detecting retinal neurodegeneration in people with diabetes: Findings from the UK Biobank (2021)

GC-IPL was thinner among participants with DM, compared to without DM. This difference persisted after adjusting for confounding variables and when considering only those with no/mild DR. This confirms that GC-IPL thinning occurs early in DM and can serve as a useful marker of DRN.
Bio-based building blocks from 5-hydroxymethylfurfural via 1-hydroxyhexane-2,5-dione as intermediate (2019)

The limits to the supply of fossil resources and their ever increasing use forces us to think about future scenarios for fuels and chemicals. The platform chemical 5-hydroxymethyl-furfural (HMF) can be obtained from biomass in good yield and has the potential to be converted in just a few steps into a multitude of interesting products. Over the last 20 years, the conversion of HMF to 1-hydroxyhexane-2,5-dione (HHD) has been studied by several groups. It is possible to convert HMF into HHD by hydrogenation/hydrolytic ring opening reaction in aqueous phase using various heterogeneous and homogeneous catalysts. This review addresses both the state of the art of HHD synthesis, including mechanistic aspects of its formation, as well as the recent progress in the application of HHD as a building block for many useful chemicals including pyrroles, cyclopentanone derivatives and triols.
Fractal Analysis of Small Peripheral Pulmonary Nodules in Thin-section CT: Evaluation of the Lung-nodule Interfaces (2002)

Fractal dimensions reflect the characteristics of the lung-nodule interfaces of small peripheral pulmonary nodules. The FD(2D)s revealed the irregularities of the contours. On the other hand, FD(3D)s revealed the complexities of the heterogeneous textures. With use of FD(2D) and FD(3D), it may be possible to distinguish bronchogenic carcinomas from benign pulmonary nodules. Moreover, FD(3D) may make it possible to distinguish between adenocarcinomas and squamous cell carcinomas.
9,9-Di-n-octyl-9H-fluorene (2005)

The title compound, C29H42, crystallizes from the melt as a triclinic crystal. The unit cell contains three crystallographically independent molecules. The three fluorene ring systems are oriented such that two non-equivalent ring systems related by a roto-translation are separated by a third ring system oriented orthogonally to them. The octyl chains of all three molecules are perpendicular to the fluorene ring system and force a 7.4 angstroms separation between the two coplanar molecules, thereby preventing molecular pi-stacking.
Hyperplastic Luschka Ducts (2011)

Ducts of Luschka are a developmental abnormality found within the gallbladder fossa in up to 10% of cholecystectomy specimens. They are most often encountered by surgeons when injured during laparoscopic or open cholecystectomy, leading to bile leakage and subsequent peritonitis. Histologically, they are typically composed of lobular aggregates of small ductules lined by bland, cuboidal-to-columnar biliary-type epithelium, associated with centrally located, larger ductules surrounded by concentric fibrosis. We have identified 6 cases of florid Luschka duct proliferation in which the ductules demonstrated irregular growth pattern, loss of characteristic concentric fibrosis, and epithelial atypia that strongly suggested the diagnosis of invasive pancreatobiliary adenocarcinoma or metastatic adenocarcinoma involving the gallbladder serosa. Two of the cases were initially diagnosed as invasive adenocarcinoma, whereas the other 4 were sent for consultation to rule out adenocarcinoma. All cases were associated with marked acute and chronic cholecystitis with mucosal ulceration, cholelithiasis, and thickening of the gallbladder wall. The ducts of Luschka were located within the rim of adherent liver in all 6 cases and the gallbladder serosa in 5 cases. Limited follow-up information was available for all patients with no documentation of progressive disease. Awareness and proper recognition of the anatomic location and histologic features are imperative in distinguishing florid ducts of Luschka from both non-neoplastic conditions and most importantly adenocarcinoma.
SearchBuddies: Bringing Search Engines into the Conversation (2021)

Although people receive trusted, personalized recommendations and auxiliary social benefits when they ask questions of their friends, using a search engine is often a more effective way to find an answer. Attempts to integrate social and algorithmic search have thus far focused on bringing social content into algorithmic search results. However, more of the benefits of social search can be preserved by reversing this approach and bringing algorithmic content into natural question-based conversations. To do this successfully, it is necessary to adapt search engine interaction to a social context. In this paper, we present SearchBuddies, a system that responds to Facebook status message questions with algorithmic search results. Via a three-month deployment of the system to 122 social network users, we explore how people responded to search content in a highly social environment. Our experience deploying SearchBuddies shows that a socially embedded search engine can successfully provide users with unique and highly relevant information in a social context and can be integrated into conversations around an information need. The deployment also illuminates specific challenges of embedding a search engine in a social environment and provides guidance toward solutions.
Detection sensitivity of field-resolved spectroscopy in the molecular fingerprint region (2017)

Summary form only given. Mid-infrared (MIR) vibrational spectroscopy is a versatile tool for identifying organic compounds (OC) in gases or liquids in a label-free manner due to their unique molecular fingerprint, promoting a large variety of applications in biology, chemistry, medicine or environmental monitoring. Although new technologies like quantum-cascade lasers are rapidly evolving, the workhorse in this field is still Fourier-transform infrared (FTIR) spectrometry based on thermal sources. Without pre-treatment of the sample and/or enrichment of the OC of interest, those techniques offer a limit of detection (LOD) for compounds in aqueous environments at ppm levels [1]. Pushing this limit to ppb levels is commonly hindered by the lack of broadband, stable and bright MIR sources as well as of low-noise, high-dynamic-range MIR detectors.Here, for the first time, we employ field-resolved spectroscopy (FRS) [2] in the molecular fingerprint region, as a time-domain method able to mitigate the above-mentioned limitations. A bright, broadband femtosecond MIR pulse is sent through the measurement cell for liquids and its resulting electric field is sampled in time with electro-optical sampling (EOS) [3, 4]. To test the performance of FRS for sensing applications, a glucose dilution series is measured and compared to the results obtained with a state-of-the-art FTIR (Bruker Vertex 70). An EOS trace of water (black) and 5000 ppm glucose solution (red) is shown in Fig 1a. The freeinduction decay (FID) of the glucose molecules can be efficiently separated in time from the main pulse propagating through the sample, which enables its detection in a background-free manner. This drastically reduces the negative influence of relative intensity noise on the LOD of the instrument. Fig. 1b,c show the Fourier transforms of the FRS signals after applying a high-pass time filter at t = 500 fs after the main pulse intensity maximum, for two different glucose concentrations. In both cases, the glucose fingerprint is clearly visible. Fig. 1d,e show the absorbance spectra obtained with FTIR for the same concentrations, revealing that at 150 ppm the glucose fingerprint is not discernible from noise anymore. Fig. 1f shows the glucose concentrations retrieved by fitting an ab-initio model to the measured data with error bars determined from multiple measurements. For a measurement time of 10 s (5 cm-1 resolution) we find an LOD of 120 ppm for the FTIR and 10 ppm for FRS (LOD defined as the concentration where the relative error of the retrieval is >100%). These measurements illustrate the potential of FRS for the detection of OC. An outlook on measurements with even higher sensitivity and a discussion of the specificity of FRS will be given at the conference.
Synthesis of Oxazocenones via Gold(I)-Catalyzed 8-Endo-Dig Hydroalkoxylation of Alkynamides (2015)

Several benzoxazocenones have been found to exhibit novel cellular activities. In the present study, we report a gold(I)-catalyzed 8-endo-dig hydroalkoxylation reaction of alkynamides to access analogous oxazocenone scaffolds. This methodology provided an advanced intermediate, which was elaborated to a des-benzo analog of a bioactive benzoxazocenone.
Safety and efficacy of human embryonic stem cell-derived astrocytes following intrathecal transplantation in SOD1G93A and NSG animal models (2018)

Our findings demonstrate the safety and potential therapeutic benefits of intrathecal injection of hES-AS for the treatment of ALS.
Table S3 from PP2A Inactivation Mediated by <i>PPP2R4</i> Haploinsufficiency Promotes Cancer Development (2023)

&lt;p&gt;Overview of cancer-associated PPP2R4 exome mutations found in COSMIC and cBioportal cancer databases.&lt;/p&gt;
Murine-leukemia-virus-related Cell-surface Antigens as Serological Markers of AKR Ecotropic, Xenotropic, and Dualtropic Viruses (1980)

Several systems of cell-surface antigens related to naturally occurring murine leukemia virus (MuLV) have been recognized serologically (Table 1). These antigens are defined by the conventional cytotoxic test (Old and Stockert 1978). Gross cell-surface antigen (GCSA) (Old et al. 1965) was recognized by sera of mice hyperimmunized with a spontaneous leukemia of the AKR strain; Gix antigen (Stockert et al. 1971) was recognized by sera of rats bearing transplants of a syngeneic leukemia induced originally by MuLV. More recently, cell-surface antigens G(RADA1) (Obata et al. 1978), G(ERLD) (Y. Obata et al., in prep.), and G(AKSL2) (Stockert et al. 1979) have been defined by normal mouse serum of selected F1 hybrids. Expression of antigen on other cells is determined by absorption of the typing antiserum followed by assay of residual cytotoxicity on the prototype target cell (see Table 1).
Diameter Enlargement of Single-Wall Carbon Nanotubes by Oxidation (2003)

The diameter of high-pressure CO (HiPco) single-wall carbon nanotubes (SWNTs) has been enlarged by treating them with nitric acid and oxygen, and the diameter enlargement is related to the nitric acid refluxing time. Raman spectra (exciting wavelength 488 nm) and transmission electron microscopy showed that the 0.8−1.2 nm diameter distribution of HiPco SWNTs could be narrowed to one centered around 1.2 nm when the nitric acid treatment time was 1 h. Significantly, SWNTs of 1.37−2.4 nm in diameter were discovered when the nitric acid treatment lasted more than 2 h.
A projector-camera system with real-time photometric adaptation for dynamic environments (2005)

Projection systems can be used to implement augmented reality, as well as to create both displays and interfaces on ordinary surfaces. Ordinary surfaces have varying reflectance, color, and geometry. These variations can be accounted for by integrating a camera into the projection system and applying methods from computer vision. The methods currently applied are fundamentally limited since they assume the camera, projector, and scene are static. In this paper, we describe a technique for photometrically adaptive projection that makes it possible to handle a dynamic environment. We begin by presenting a co-axial projector-camera system whose geometric correspondence is independent of changes in the environment. To handle photometric changes, our method uses the errors between the desired and measured appearance of the projected image. A key novel aspect of our algorithm is that we combine a physics-based model with dynamic feedback to achieve real time adaptation to the changing environment. We verify our algorithm through a wide variety of experiments. We show that it is accurate and runs in real-time. Our algorithm can be applied broadly to assist HCI, visualization, shape recovery, and entertainment applications.