gebhart/patrepeval huggingface dataset:
Histologic Analysis of Idiopathic Pulmonary Fibrosis by Morphometric and Fractal Analysis (2023)

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic lung disorder, ultimately leading to respiratory failure and death. Despite great research advances in understanding the mechanisms underlying the disease, its diagnosis, and its treatment, IPF still remains idiopathic without known biological or histological markers able to predict disease progression or response to treatment. The histologic hallmark of IPF is usual interstitial pneumonia (UIP), with its intricate architectural distortion and temporal inhomogeneity. We hypothesize that normal lung alveolar architecture can be compared to fractals, such as the Pythagoras tree with its fractal dimension (<i>D<sub>f</sub></i>), and every pathological insult, distorting the normal lung structure, could result in <i>D<sub>f</sub></i> variations. In this study, we aimed to assess the UIP histologic fractal dimension in relationship to other morphometric parameters in newly diagnosed IPF patients and its possible role in the prognostic stratification of the disease. Clinical data and lung tissue specimens were obtained from twelve patients with IPF, twelve patients with non-specific interstitial pneumonia (NSIP), and age-matched "healthy" control lung tissue from patients undergoing lung surgery for other causes. Histology and histomorphometry were performed to evaluate <i>D<sub>f</sub></i> and lacunarity measures, using the box counting method on the FracLac ImageJ plugin. The results showed that <i>D<sub>f</sub></i> was significantly higher in IPF patients compared to controls and fibrotic NSIP patients, indicating greater architectural distortion in IPF. Additionally, high <i>D<sub>f</sub></i> values were associated with higher fibroblastic foci density and worse prognostic outcomes in IPF, suggesting that <i>D<sub>f</sub></i> may serve as a potential novel prognostic marker for IPF. The scalability of <i>D<sub>f</sub></i> measurements was demonstrated through repeated measurements on smaller portions from the same surgical biopsies, which were selected to mimic a cryobiopsy. Our study provides further evidence to support the use of fractal morphometry as a tool for quantifying and determining lung tissue remodeling in IPF, and we demonstrated a significant correlation between histological and radiological <i>D<sub>f</sub></i> in UIP pattern, as well as a significant association between <i>D<sub>f</sub></i> and FF density. Furthermore, our study demonstrates the scalability and self-similarity of <i>D<sub>f</sub></i> measurements across different biopsy types, including surgical and smaller specimens.
Lipid topology and linear cationic antimicrobial peptides: a novel mechanistic model (2017)

The dataset is a dedicated LabVIEW virtual instrument, for the analysis of dye-efflux dynamics. The instrument is capable of automatically extracting the apparent permeability from the leakage of encapsulated fluorescent markers, from within artificial cell systems.
Reactive Difunctional Siloxane Oligomers (1985)

Synthesis and characterization of well-defined, α,ω-terminated difunctional siloxane oligomers are discussed. Detailed procedures on the preparation of primary amine- and hydroxy-terminated oligomers are given. Control of the average molecular weight (Mn) and also the possible variations in the backbone structure and composition are explained. The effect of these variations on the physical, thermal and chemical properties of the resulting materials are discussed. Characterization of these oligomers by FT-IR, NMR and UV spectroscopy, potentiometric titration and DSC are summarized.
A Symbiont-Independent Endo-1,4-β-Xylanase from the Plant-Parasitic NematodeMeloidogyne incognita (2006)

Substituted xylan polymers constitute a major part of the hemicellulose fraction of plant cell walls, especially in monocotyledons. Endo-1,4-beta-xylanases (EC 3.2.1.8) are capable of hydrolyzing substituted xylan polymers into fragments of random size. Many herbivorous animals have evolved intimate relationships with endosymbionts to exploit their enzyme complexes for the degradation of xylan. Here, we report the first finding of a functional endo-1,4-beta-xylanase gene from an animal. The gene (Mi-xyl1) was found in the obligate plant-parasitic root-knot nematode Meloidogyne incognita, and encodes a protein that is classified as a member of glycosyl hydrolase family 5. The expression of Mi-xyl1 is localized in the subventral esophageal gland cells of the nematode. Previous studies have shown that M. incognita has the ability to degrade cellulose and pectic polysaccharides in plant cell walls independent of endosymbionts. Including our current data on Mi-xyl1, we show that the endogenous enzyme complex in root-knot nematode secretions targets essentially all major cell wall carbohydrates to facilitate a stealthy intercellular migration in the host plant.
Supplementary Figure S6 from Rapid Expansion of Highly Functional Antigen-Specific T Cells from Patients with Melanoma by Nanoscale Artificial Antigen-Presenting Cells (2023)

&lt;p&gt;Nano-aAPC expanded MART-1 Tet+ cells from patients pre- and post-PD-1 treatment.&lt;/p&gt;
Quality and Statistical Classification of Brazilian Vegetable Oils Using Mid-Infrared and Raman Spectroscopy (2012)

Palm oil, soy oil, sunflower oil, corn oil, castor oil, and rapeseed oil were analyzed with Fourier transform infrared (FT-IR) and FT-Raman spectroscopy. The quality of different oils was evaluated and statistically classified by principal component analysis (PCA) and a partial least squares (PLS) regression model. First, a calibration set of spectra was selected from one sampling batch. The qualitative variations in spectra are discussed with a prediction of oil composition (saturated, mono- and polyunsaturated fatty acids) from mid-infrared analysis and iodine value from FT-Raman analysis, based on ratioing the intensity of bands at given wavenumbers. A more robust and convincing oil classification is obtained from two-parameter statistical models. The statistical analysis of FT-Raman spectra favorably distinguishes according to the iodine value, while the mid-infrared spectra are most sensitive to hydroxyl moieties. Second, the models are validated with a set of spectra from another sampling batch, including the same oil types as-received and after different aging times together with a hydrogenated castor oil and high-oleic sunflower oil. There is very good agreement between the model predictions and the Raman measurements, but the statistical significance is lower for mid-infrared spectra. In the future, this calibration model will be used to check vegetable oil qualities before using them in polymerization processes.
Farview: Disaggregated Memory with Operator Off-loading for Database Engines (2021)

Cloud deployments disaggregate storage from compute, providing more flexibility to both the storage and compute layers. In this paper, we explore disaggregation by taking it one step further and applying it to memory (DRAM). Disaggregated memory uses network attached DRAM as a way to decouple memory from CPU. In the context of databases, such a design offers significant advantages in terms of making a larger memory capacity available as a central pool to a collection of smaller processing nodes. To explore these possibilities, we have implemented Farview, a disaggregated memory solution for databases, operating as a remote buffer cache with operator offloading capabilities. Farview is implemented as an FPGA-based smart NIC making DRAM available as a disaggregated, network attached memory module capable of performing data processing at line rate over data streams to/from disaggregated memory. Farview supports query offloading using operators such as selection, projection, aggregation, regular expression matching and encryption. In this paper we focus on analytical queries and demonstrate the viability of the idea through an extensive experimental evaluation of Farview under different workloads. Farview is competitive with a local buffer cache solution for all the workloads and outperforms it in a number of cases, proving that a smart disaggregated memory can be a viable alternative for databases deployed in cloud environments.
Electronic spectra of substituted cyanocobaltate(III) complexes (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic spectra of substituted cyanocobaltate(III) complexesVincent M. Miskowski and Harry B. GrayCite this: Inorg. Chem. 1975, 14, 2, 401–405Publication Date (Print):February 1, 1975Publication History Published online1 May 2002Published inissue 1 February 1975https://pubs.acs.org/doi/10.1021/ic50144a038https://doi.org/10.1021/ic50144a038research-articleACS PublicationsRequest reuse permissionsArticle Views108Altmetric-Citations38LEARN 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
Neuropilin‐1 is not a marker of human Foxp3+ Treg (2009)

Treg are immune cells that play a critical role in the regulation of the immune response. Although the transcription factor Foxp3 is widely accepted as the standard marker of Treg, specific surface markers are needed to better characterize these cells and decipher their mechanisms of action. Neuropilin-1 (Nrp-1), a membrane protein primarily involved in the nervous system, was identified as a specific marker of murine Treg, but its expression has not been rigorously investigated in human Treg. Here we show that in contrast to murine Treg and regardless of their origins (blood, thymus, spleen, lymph node or tonsil), human Foxp3(+) Treg do not specifically express Nrp-1. However, a population of Foxp3(-) Nrp-1(+) T cells can be detected in human secondary lymphoid organs, and Nrp-1 expression is induced on peripheral blood T lymphocytes upon in vitro activation. We conclude that Nrp-1 cannot be used as a specific marker of human Treg, but might represent a novel activation marker of human T cells both in vitro and in vivo.
Recovery Act: Alpena Biorefinery and Alpena Biorefinery Lignin Separation Final Technical Report (2016)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Antiviral Effect of Orally Administered (−)-β-d-2-Aminopurine Dioxolane in Woodchucks with Chronic Woodchuck Hepatitis Virus Infection (2007)

(-)-beta-D-2-Aminopurine dioxolane (APD) is a nucleoside prodrug that is efficiently converted to 9-(beta-D-1,3-dioxolan-4-yl)guanine (DXG). DXG has antiviral activity in vitro against hepatitis B virus (HBV) but limited aqueous solubility, making it difficult to administer orally to HBV-infected individuals. APD is more water soluble than DXG and represents a promising prodrug for the delivery of DXG. A placebo-controlled, dose-ranging efficacy and pharmacokinetic study was conducted with woodchucks that were chronically infected with woodchuck hepatitis virus (WHV). APD was efficiently converted to DXG after oral and intravenous administrations of APD, with serum concentrations of DXG being higher following oral administration than following intravenous administration, suggestive of a considerable first-pass intestinal and/or hepatic metabolism. APD administered orally at 1, 3, 10, and 30 mg/kg of body weight per day for 4 weeks produced a dose-dependent antiviral response. Doses of 3 and 10 mg/kg/day reduced serum WHV viremia by 0.4 and 0.7 log(10) copies/ml, respectively. The 30-mg/kg/day dose resulted in a more pronounced, statistically significant decline in serum WHV viremia of 1.9 log(10) copies/ml and was associated with a 1.5-fold reduction in hepatic WHV DNA. Individual woodchucks within the highest APD dose group that had declines in serum WHV surface antigen levels, WHV viremia, and hepatic WHV DNA also had reductions in hepatic WHV RNA. There was a prompt recrudescence of WHV viremia following drug withdrawal. Therefore, oral administration of APD for 4 weeks was safe in the woodchuck model of chronic HBV infection, and the effect on serum WHV viremia was dose dependent.
Identification of SNPs with high-resolution genotyping in the MHC region in Korean native chicken (2012)

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Characterizing Emerging Canine H3 Influenza Viruses (2020)

The continual emergence of novel influenza A strains from non-human hosts requires constant vigilance and the need for ongoing research to identify strains that may pose a human public health risk. Since 1999, canine H3 influenza A viruses (CIVs) have caused many thousands or millions of respiratory infections in dogs in the United States. While no human infections with CIVs have been reported to date, these viruses could pose a zoonotic risk. In these studies, the National Institutes of Allergy and Infectious Diseases (NIAID) Centers of Excellence for Influenza Research and Surveillance (CEIRS) network collaboratively demonstrated that CIVs replicated in some primary human cells and transmitted effectively in mammalian models. While people born after 1970 had little or no pre-existing humoral immunity against CIVs, the viruses were sensitive to existing antivirals and we identified a panel of H3 cross-reactive human monoclonal antibodies (hmAbs) that could have prophylactic and/or therapeutic value. Our data predict these CIVs posed a low risk to humans. Importantly, we showed that the CEIRS network could work together to provide basic research information important for characterizing emerging influenza viruses, although there were valuable lessons learned.
Multivariate Design for Mass Customization of Consumer Products (2009)

Abstract⎯In this paper, we propose a model and a solution procedure to minimize the cost associated with mass customizing consumer products in the presence of multivariate constraints. Three algorithms based on enumeration, steepest descent and Lagrange relaxation are used to solve the non-linear optimization problem and their performance is evaluated with numerical experiments. The sufficient and necessary conditions under which the optimal solution can be achieved are presented as well.
Application Of Halogenated Polymethylstyrenes To X-Ray Resists (1987)

A series of chlorinated polymethylstyrenes (CPMSs) and brominated polymethylstyrenes (BPMSs) were synthesized by anionic polymerization of methylstyrene followed by radical halogenation. Radiation chemistry of CPMSs and BPMSs were investigated using RhLa X-rays as a radiation source. Resist sensitivity of CPMSs and BPMSs increases with increases in molecular weight and halogen content up to 90 unit% of halogenation. In addition, CPMSs have higher sensitivity than BPMSs toward RhLa X-rays. Infrared spectroscopic studies of radiation induced chemical reactions of the polymers showed that X-ray radiation caused the dissociation of C-X (Cl or Br) bonds and that the dissociation was much faster for CPMSs than BPMSs in spite of lower mass absorption coefficients of CPMSs. CPMS-5 (Mw=49x104, Cl cont.=92 unit%) exhibits the highest sensitivity of 15 mJ/cm2 (Dg) while maintaining high contrast value of 1.3. The patterning tests of CPMS-5 were done with a MICRONIX MX-15 which had a palladium source. As a result, 0.6 &mu;m resist patterns were obtained despite its penumbral blurring being 0.35 &mu;m. It is confirmed that CPMS-5 is one of the best X-ray resists from a practical point of view.
Reaction of 5-substituted 2-methoxy-1,4-quinones with boron tribromide (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of 5-substituted 2-methoxy-1,4-quinones with boron tribromideMichael E. Garst and Janice D. FrazierCite this: J. Org. Chem. 1987, 52, 3, 446–448Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/jo00379a026https://doi.org/10.1021/jo00379a026research-articleACS PublicationsRequest reuse permissionsArticle Views152Altmetric-Citations8LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Asymmetric multilevel outphasing transmitter using class-E PAs with discrete pulse width modulation (2010)

We present a high-efficiency transmitter architecture based on asymmetric multilevel outphasing (AMO), but with a new method of generating discrete amplitude levels from the constituent amplifiers. AMO and multilevel LINC (ML-LINC) transmitters improve their efficiency over LINC by switching the supplies of the power amplifiers (PAs) among a discrete set of voltages. This allows them to minimize the occurrence of large outphasing angles. However, it is also possible to generate a discrete set of amplitudes by varying the duty cycle of the waveform that drives the PAs. The chief advantage of this discrete pulse width modulation (DPWM) is hardware simplicity, as it eliminates the need for a fast, low-loss switching network and a selection of power supply voltages. We demonstrate this concept with a 48-MHz, 20-W peak output power AMO transmitter using a four-level DPWM. At peak output power, the measured power-added efficiency is 77.7%. For a 16-QAM signal with a 6.5-dB peak-to-average power ratio, the AMO prototype improves the average efficiency from 17.1% to 36.5% compared to the standard LINC system.
Data for In vivo structural MRI-based atlas of human thalamic nuclei (2020)

This version fixes a bug in the atlasseg script in Version 1.0. Please use this. Data for the above titled paper being submitted to Scientific Data. <strong>MNI space (152 asymmetric 09b)</strong> MNIMaxProb_left.nii.gz and MNIMaxProb_right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in MNI space Note crop_mni_t1.nii.gz is the thalamus cropped MNI atlas provided for users for reference <strong>Custom template space</strong> Customtemplate.nii.gz - full size WMn MPRAGE custom (mean brain) template of 20 subjects (11 MS 9 healthy) CustomAtlasMaxProb_left.nii.gz and CustomAtlasMaxProb_right.nii.gz are the maximum probability (deterministic) thalamic nuclei atlas in custom template space for left and righ tthalamus CustomAtlasSpatialProbMap4D.nii.gz is the spatial probability map in custom template space for each of the 11 left and 11 right nuclei (4th dimension). See SpatialProbMap_descr.txt for the order and names of the nuclei CustomAtlas.ctbl is a color table file that can be used to standardize colors (read by Slicer,fsleyes etc). It also maps the labels to nuclei names (e.g. 2-AV 4-VA.... 14-MTT). For this atlas, only 2-14 are used. atlasseg is a tcsh script that can be used to segment your T1 data (see Notes below or atlas_README.txt for usage) Remaining files are used for atlas based segmentation (cropped custom template, mask used to crop the template etc). testdata.tgz is a set of 5 test cases (subset of what was used for testing the atlas). Details inside in the README file. Copyright Manojkumar Saranathan 2020 For research use only.
Reduction in plasma potential by applying negative DC cathode bias in RF magnetron sputtering (2016)

Abstract We applied a negative DC bias voltage to the cathode of an RF magnetron sputtering system and successfully reduced the plasma potential in both argon plasma and hydrogen-diluted argon plasma. The crystallinity of the deposited Ge films is improved by increasing the negative DC bias voltage. It is indicated that the reduction in plasma potential is effective for reducing the plasma damage on deposited materials, caused by the electric potential between the plasma and substrates. In addition, the deposition rate is increased by the increased electric potential between the plasma and the cathode owing to the negative DC bias voltage. The present method successfully gives us higher speed and lower damage sputtering deposition. The increased electric potential between the plasma and the cathode suppresses the evacuation of electrons from the plasma and also enhances the generation of secondary electrons on the cathode. These probably suppress the electron loss from the plasma and result in the reduction in plasma potential.
Left Atrial Appendage Occlusion for The Unmet Clinical Needs of Stroke Prevention in Nonvalvular Atrial Fibrillation (2019)

Oral anticoagulation is the dominant strategy for stroke prevention in patients with nonvalvular atrial fibrillation. However, lifelong oral anticoagulation is associated with major issues including inappropriate dosing, nonadherence, and adverse effects. Therefore, efforts have been made to develop site-specific therapy aimed to occlude the left atrial appendage, the anatomical site accountable for more than 90% of nonvalvular atrial fibrillation-related ischemic strokes. This review focuses on the growing literature to put into perspective the risk-balance ratio of left atrial appendage occlusion.