gebhart/patrepeval huggingface dataset:
Memory T cell responses in survivors of the 2013–2016 West African Ebola outbreak (2018)

Abstract Primary infection with Ebola virus protects against subsequent challenge, thus an optimal vaccine should generate immune responses similar to those found in disease survivors. To this end, we characterized CD8 and CD4 T cell responses in Ebola survivors to uncover the immunogenicity of seven of eight Ebola virus proteins. T cell responses of 33 Sierra Leonean Ebola survivors were examined. Nearly all individuals studied harbored nucleoprotein (NP)-specific CD8 T cell responses. Moreover, NP-specific T cells responded more strongly and were more numerous in 65% of NP responders compared to responses to other EBOV proteins in the same individual. Conversely, we found glycoprotein (GP) CD8+ T cell responses in only 37% of EBOV responders. GP responses were also weaker and less numerous than other responses in the same individual. Specificity of the CD4+ T cell responses were more evenly distributed. Altogether, our data indicate that NP is among the most immunogenic EBOV proteins while only VP30 was less immunogenic than GP in our cohort of Sierra Leonean survivors. An optimal vaccine designed to elicit both humoral and cell mediated immune responses in a broad human population should contain both NP and the GP.
Intraindividual Comparison of 18F-PSMA-1007 with Renally Excreted PSMA Ligands for PSMA PET Imaging in Patients with Relapsed Prostate Cancer (2019)

<sup>18</sup>F-prostate-specific membrane antigen (PSMA)-1007 is excreted mainly through the liver. We benchmarked the performance of <sup>18</sup>F-PSMA-1007 against 3 renally excreted PSMA tracers. <b>Methods:</b> Among 668 patients, we selected 27 in whom PET/CT results obtained with <sup>68</sup>Ga-PSMA-11, <sup>18</sup>F-DCFPyL (2-(3-(1-carboxy-5-[(6-[<sup>18</sup>F]fluoro-pyridine-3-carbonyl)-amino]-pentyl)-ureido)-pentanedioic acid), or <sup>18</sup>F-JK-PSMA-7 (JK, Juelich-Koeln) were interpreted as equivocal or negative or as oligometastatic disease (PET-1). Within 3 wk, a second PET scan with <sup>18</sup>F-PSMA-1007 was performed (PET-2). The confidence in the interpretation of PSMA-positive locoregional findings was scored on a 5-point scale, first in routine diagnostics (reader 1) and then by an independent second evaluation (reader 2). Discordant PSMA-positive skeletal findings were examined by contrast-enhanced MRI. <b>Results:</b> For both readers, <sup>18</sup>F-PSMA-1007 facilitated the interpretability of 27 locoregional lesions. In PET-2, the clinical readout led to a significantly lower number of equivocal locoregional lesions (<i>P</i> = 0.024), and reader 2 reported a significantly higher rate of suspected lesions that were falsely interpreted as probably benign in PET-1 (<i>P</i> = 0.023). Exclusively in PET-2, we observed a total of 15 PSMA-positive spots in the bone marrow of 6 patients (22%). None of the 15 discordant spots had a morphologic correlate on the corresponding CT scan or on the subsequent MRI scan. Thus, <sup>18</sup>F-PSMA-1007 exhibits a significantly higher rate of unspecific medullary spots (<i>P</i> = 0.0006). <b>Conclusion:</b><sup>18</sup>F-PSMA-1007 may increase confidence in interpreting small locoregional lesions adjacent to the urinary tract but may decrease the interpretability of skeletal lesions.
ChemInform Abstract: Reactions of the (η3‐Allyl)iron Tricarbonyl Anion with Carbon Electrophiles. (1989)

Abstract A synthetic and mechanistic study is presented of the reaction of (I) with alkyl halides which leads to α,β‐ or β,γ‐unsaturated ketones.
Analysis of Hepatitis D Virus in Minor Salivary Gland of Sjögren’s Disease (2023)

Hepatitis delta virus (HDV) has been detected in the minor salivary gland (MSG) tissue of Sjögren's disease (SjD) patients in the absence of a hepatitis B virus (HBV) coinfection. Previous research has shown that HDV antigen (HDAg) expression can trigger an SjD-like phenotype in vivo, demonstrating a potential cause-and-effect relationship. We hypothesize that if HDV plays a role in the development of SjD, then HDV profiles may be correlated with disease manifestations. This retrospective study characterized HDV in a cohort of 48 SjD MSG samples collected between 2014 and 2021. Analyses of HDAg expression, including cell type and subcellular localization, in situ hybridization of HDV RNA, and comparative analyses with associated SjD and viral hepatitis clinical features, were conducted. HDAg was detected in MSG acinar, ductal, myoepithelial, and adipose cells and localized with the nuclei, cytoplasm, and mitochondria. In situ hybridization detected HDV genomic RNA localization in the MSG nuclei. A significant negative correlation was found between HDAg intensity and focal lymphocytic inflammation and in patients with both anti-SSA/Ro-52 and anti-SSA/Ro-60. In analyzing autoimmune disease comorbidities with SjD, it was found that SjD patients diagnosed with autoimmune thyroiditis and/or hypothyroidism were significantly more represented in the high HDAg intensity group compared to the negative and moderate HDAg intensity groups. No significant associations were detected between MSG-localized HDAg and liver enzymes or an evident HBV coinfection. This study has further confirmed that there is a nonhepatic reservoir for chronic HDV persistence in SjD-affected salivary gland tissue in a third independent SjD patient cohort. In addition, this study describes the unique colocalization of HDAg with mitochondria. The detection of HDV antigen and sequence within SjD-affected salivary gland tissue, and in the absence of an evident current or past HBV coinfection, warrants further investigation.
1886 Endoscopic Management of Tubulovillous Adenoma Within a Diverticulum: Report of a Case and Review of Literature (2019)

INTRODUCTION: Colonic polyps within a diverticulum are technically challenging to resect as the polyp might be difficult to access if it is buried within the diverticulum. There is also an increased risk of perforation upon endoscopic resection owing to the lack of muscularis propria in the wall of the diverticulum. We describe an endoscopic technique for management of a rare case of tubulovillous adenoma within a diverticulum with review of literature. CASE DESCRIPTION/METHODS: A 74-year-old male underwent screening colonoscopy which identified a 15 mm polyp within a sigmoid colon diverticulum. Attempted resection was unsuccessful despite sub-mucosal injection with saline and the use of multiple snares. Therefore, the endoscopist elected to use a variceal band ligator. The polyp was then suctioned into the band ligator cap and 2 bands were deployed which exposed a clearly defined 15 mm polyp. This was followed by endoscopic resection using hot snare polypectomy. Histopathology revealed a tubulovillous adenoma. Inspection of the resection site demonstrated a 3 mm perforation which was closed using 4 endoscopic clips. The patient was admitted overnight for observation and was discharged the following day without complications. DISCUSSION: Colonic polyps within a diverticulum are technically challenging to resect given that the majority of the polyp might be buried within the diverticulum. Suction over the polyp using a variceal banding device and deploying bands across the base was an effective method for exposing and resecting the entire polyp in this case. However, it was complicated by a small iatrogenic perforation likely due to the lack of a muscularis propria within the wall of the diverticulum. Review of literature revealed three other cases which reported endoscopic management of colonic polyps within a diverticulum. Two of the cases utilized an over the scope clip at the base of the suctioned polyp prior to resection with a hot snare to reduce the risk of iatrogenic perforation. The third case allowed for natural sloughing of the polyp to occur without tissue retrieval as a result of tissue ischemia from the band. In conclusion, colonic polyps within a diverticulum can be successfully removed by using a band ligator and/or over the scope clip to isolate the polyp. The polyp can then be resected using hot snare polypectomy to ensure tissue retrieval. However, an over the scope clip should be used prophylactically to prevent a perforation or a perforation can be closed with endoscopic clips.
Keeping an Eye on Your Neighbors: Agents Monitoring and Sanctioning One Another In a Common-Pool Resource Environment (2000)

The role of a specific institution in avoiding a "tragedy of the commons" situation in a common pool-resource environment is studied experimentally. The resource users privately decide their own exploitation level and then, once the group outcome is revealed, can choose to select other individuals for inspection. At a cost, the inspector can view the decision of any individual. If the inspected individual has exploited the resource excessively, relative to a publicly known amount, a fine is imposed and paid to the inspector. The rules, called Carte di Regola, were modeled after an historical case of self-governed rural communities. The impact of the rules is a dramatic increase in efficiency over the no rule case but still less than 100%. As part of an attempt to understand the nature of the impact of the rules the paper focuses on models of individual agent's choices. The patterns of results relative to the classical Nash model are similar to other experiments. The model does well, except for the fact that contributions to the public good are less than Nash equilibrium amount. However, when the environment is changed to allow sanctions, contributions above the Nash equilibrium are observed. This paradoxical "flip" in behavior is explained by a non classical model in which spite plays a role in preferences and in which agents are heterogeneous. The model of asymmetric, other regarding agents also does relatively well in predicting patterns of individual choices such as the choice to inspect and sanction others. Efficiency is improved along with the strength of sanctions and the patterns of individual choices are consistent with the non classical model.
Comparative studies on amniotic fluid and plasma fibronectins (1981)

Human fibronectin was isolated from second-trimester amniotic fluid, from amniotic fluid obtained at term and from adult plasma. The amniotic-fluid fibronectins had a slightly higher apparent molecular weight on sodium dodecyl sulphate/polyacrylamide-gel electrophoresis than the plasma fibronectin. Early- and late-amniotic-fluid fibronectin had 9.5 and 9.6% carbohydrate respectively, whereas plasma fibronectin had 5.8%. The amniotic-fluid fibronectins had similar mannose and sialic acid contents to plasma fibronectin, but greater amounts of glucosamine, galactosamine, galactose and fucose. There were no detectable differences in the amino-acid composition of amniotic-fluid and plasma fibronectins, and the patterns of peptides obtained after tryptic digestion of fibronectin from the two sources showed extensive similarities. Fibronectins from plasma and amniotic fluid were equally active in promoting cell attachment and were immunologically indistinguishable. These results show that fibronectin from amniotic fluid is more heavily glycosylated than plasma fibronectin or previously analysed fibronectins from cultured fibroblasts. The observed differences in glycosylation may be related to cell type and/or stage of development.
<title>Visible Human Slice Web Server: a first assessment</title> (1999)

The Visible Human Slice Server started offering its slicing services at the end of June 1998. From that date until the end of May, more than 280,000 slices were extracted from the Visible Man, by layman interested in anatomy, by students and by specialists. The Slice Server is based one Bi-Pentium PC and 16 disks. It is a scaled down version of a powerful parallel server comprising 5 Bi-Pentium Pro PCs and 60 disks. The parallel server program was created thanks to a computer-aided parallelization framework, which takes over the task of creating a multi-threaded pipelined parallel program from a high-level parallel program description. On the full blown architecture, the parallel program enables the extraction and resampling of up to 5 color slices per second. Extracting 5 slice/s requires to access the disks and extract subvolumes of the Visible Human at an aggregate throughput of 105 MB/s. The publicly accessible server enables to extract slices having any orientation. The slice position and orientation can either be specified for each slice separately or as a position and orientation offered by a Java applet and possible future improvements. In the very near future, the Web Slice Server will offer additional services, such as the possibility to extract ruled surfaces and to extract animations incorporating slices perpendicular to a user defined trajectory.
Adaptive underlay cognitive radios with imperfect CSI and probabilistic interference constraints (2011)

Efficient design of cognitive radios requires secondary users implementing adaptive resource allocation schemes that exploit knowledge of the channel state information (CSI), and limit interference to the primary system. In this paper, stochastic resource allocation algorithms are developed for underlay cognitive radios to maximize the sum-rate of secondary users while adhering to “average power” and “probability of interference” constraints. The latter guarantee that during most of the time the power interfering with primary receivers stays below a certain pre-specified level. Although the resultant optimization problem is non-convex, it exhibits zero-duality gap and can be efficiently solved. The optimal schemes are a function of the link quality of the secondary network, the activity of the primary users, and the Lagrange multipliers associated with the considered constraints. The focus is on developing algorithms that: i) employ stochastic approximation tools to estimate the multipliers; and ii) are able to cope with imperfections present in the CSI of the primary network.
Notch signaling modulates the electrical behavior of cardiomyocytes (2017)

Notch receptor signaling is active during cardiac development and silenced in myocytes after birth. Conversely, outward K<sup>+</sup> Kv currents progressively appear in postnatal myocytes leading to shortening of the action potential (AP) and acquisition of the mature electrical phenotype. In the present study, we tested the possibility that Notch signaling modulates the electrical behavior of cardiomyocytes by interfering with Kv currents. For this purpose, the effects of Notch receptor activity on electrophysiological properties of myocytes were evaluated using transgenic mice with inducible expression of the Notch1 intracellular domain (NICD), the functional fragment of the activated Notch receptor, and in neonatal myocytes after inhibition of the Notch transduction pathway. By patch clamp, NICD-overexpressing cells presented prolonged AP duration and reduced upstroke amplitude, properties that were coupled with reduced rapidly activating Kv and fast Na<sup>+</sup> currents, compared with cells obtained from wild-type mice. In cultured neonatal myocytes, inhibition of the proteolitic release of NICD with a γ-secretase antagonist increased transcript levels of the Kv channel-interacting proteins 2 (KChIP2) and enhanced the density of Kv currents. Collectively, these results indicate that Notch signaling represents an important regulator of the electrophysiological behavior of developing and adult myocytes by repressing, at least in part, repolarizing Kv currents. NEW & NOTEWORTHY We investigated the effects of Notch receptor signaling on the electrical properties of cardiomyocytes. Our results indicate that the Notch transduction pathway interferes with outward K<sup>+</sup> Kv currents, critical determinants of the electrical repolarization of myocytes.
Characterization of the crystalline A and B starch polymorphs and investigation of starch crystallization by high-resolution carbon-13 CP/MAS NMR (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of the crystalline A and B starch polymorphs and investigation of starch crystallization by high-resolution carbon-13 CP/MAS NMRR. P. Veregin, C. A. Fyfe, R. H. Marchessault, and M. G. TaylorCite this: Macromolecules 1986, 19, 4, 1030–1034Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/ma00158a016https://doi.org/10.1021/ma00158a016research-articleACS PublicationsRequest reuse permissionsArticle Views703Altmetric-Citations128LEARN 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
Anisotropic thermal expansion in pentacene and perfluoropentacene: Effects of molecular packing motif and fixation at the interface (2017)

Thermal expansion coefficients of molecular solids are typically significantly larger than those of inorganic materials. Since they are furthermore highly anisotropic, the molecular arrangement and consequently the intermolecular orbital overlap strongly depend on temperature, hence also affecting the energetics of optoelectronic excitations and the efficiency of charge transfer processes. Here, we report on the precise determination of the anisotropic thermal expansion coefficients of the organic semiconductor pentacene in its solid state. We compare the thermal expansion coefficients of three different pentacene polymorphs and observe distinct differences between both pentacene bulk polymorphs and the interface-stabilized thin film phase. By comparing epitaxial films with films prepared on weakly interacting, amorphous substrates, we identify a notable influence of the substrate fixation on the thermal expansion in thin pentacene films. Furthermore, the results for pentacene are compared to the thermal expansion of perfluoropentacene, where an exceptionally large vertical thermal expansion coefficient is found in the substrate-mediated π-stacked polymorph. The present study underlines the importance of thermal expansion for the interpretation of temperature-dependent spectroscopic measurements and device characterizations since the notable changes in the unit cell geometries severely affect the intermolecular coupling and thus the excitonic energetics.
Data from Identification of Recurrent <i>FGFR3–TACC3</i> Fusion Oncogenes from Lung Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Targetable oncogenic alterations are detected more commonly in patients with non–small cell lung cancer (NSCLC) who never smoked cigarettes. For such patients, specific kinase inhibitors have emerged as effective clinical treatments. However, the currently known oncogenic alterations do not account for all never smokers who develop NSCLC. We sought to identify additional oncogenic alterations from patients with NSCLC to define additional treatment options.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We analyzed 576 lung adenocarcinomas from patients of Asian and Caucasian ethnicity. We identified a subset of cancers that did not harbor any known oncogenic alteration. We performed targeted next-generation sequencing (NGS) assay on 24 patients from this set with &gt;75% tumor cell content.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt;&lt;i&gt;EGFR&lt;/i&gt; mutations were the most common oncogenic alteration from both Asian (53%) and Caucasian (41.6%) patients. No known oncogenic alterations were present in 25.7% of Asian and 31% of Caucasian tumor specimens. We identified a &lt;i&gt;FGFR3–TACC3&lt;/i&gt; fusion event in one of 24 patients from this subset using targeted NGS. Two additional patients harboring &lt;i&gt;FGFR3–TACC3&lt;/i&gt; were identified by screening our entire cohort (overall prevalence, 0.5%). Expression of &lt;i&gt;FGFR3–TACC3&lt;/i&gt; led to IL3 independent growth in Ba/F3 cells. These cells were sensitive to pan-fibroblast growth factor receptor (pan-FGFR) inhibitors but not the epidermal growth factor (EGFR) inhibitor gefitinib.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt;&lt;i&gt;FGFR3–TACC3&lt;/i&gt; rearrangements occur in a subset of patients with lung adenocarcinoma. Such patients should be considered for clinical trials featuring FGFR inhibitors. &lt;i&gt;Clin Cancer Res; 20(24); 6551–8. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Invariant Ser211 is involved in the catalysis of PD‐L4, type I RIP from Phytolacca dioica leaves (2007)

Multiple sequence alignment analysis of ribosome inactivating proteins (RIPs) has revealed the occurrence of an invariant seryl residue in proximity of the catalytic tryptophan. The involvement of this seryl residue in the catalytic mechanism of RIPs was investigated by site-directed mutagenesis in PD-L4, type 1 RIP isolated from Phytolacca dioica leaves. We show that the replacement of Ser211 with Ala apparently does not influence the N-beta-glycosidase activity on ribosomes (determined as IC(50) in a cell-free system), but it reduces the adenine polynucleotide glycosylase activity (APG), assayed spectrophotometrically on other substrates such as DNA, rRNA, and poly(A). The ability of PD-L4 to deadenylate polynucleotides appears more sensitive to the Ser211Ala replacement when poly(A) is used as substrate, as only 33% activity is retained by the mutant, while with more complex and heterogeneous substrates such as DNA and rRNA, its APG activity is 73% and 66%, respectively. While the mutated protein shows a conserved secondary structure by CD, it also exhibits a remarkably enhanced tryptophan fluorescence. This indicates that, although the overall protein tridimensional structure is maintained, removal of the hydroxyl group locally affects the environment of a Trp residue. Modelling and docking analyses confirm the interaction between Ser211 and Trp207, which is located within the active site, thus affecting RIP adenine polynucleotide glycosylase activity. Data accumulated so far confirm the potential involvement of Ser211 in the catalytic mechanism of type 1 RIP PD-L4 and a possible role in stabilizing the conformation of Trp207 side chain, which participates actively in the protein enzymatic activity.
ChemInform Abstract: Applications of Zeolites to Fine Chemicals Synthesis (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.