gebhart/patrepeval huggingface dataset:
Changes in the total knee joint moment in patients with medial compartment knee osteoarthritis over 5 years (2018)

Progression of medial compartment knee osteoarthritis (OA) has been associated with repetitive mechanical loading during walking, often characterized by the peak knee adduction (KAM) and knee flexion moments (KFM). However, the relative contributions of these components to the knee total joint moment (TJM) can change as the disease progresses since KAM and KFM are influenced by different factors that change over time. This study tested the hypothesis that the relative contributions of KAM, KFM, and the rotational moment (KRM) to the TJM change over time in subjects with medial compartment knee OA. Patients with medial compartment knee OA (n = 19) were tested walking at their self-selected speed at baseline and a 5-year follow-up. For each frame during stance, the TJM was calculated using the KAM, KFM, and KRM. The peaks of the TJM and the relative contributions of the moment components at the time of the peaks of the TJM were tested for changes between baseline and follow-up. The percent contribution of KFM to the first peak of the TJM (TJM1) significantly decreased (p < 0.001) and the percent contribution of KAM to TJM1 significantly increased (p < 0.001), while the magnitude of the TJM1 did not significantly change over the 5-year follow-up. These gait changes with disease progression appear to maintain a constant TJM1, but the transition from a KFM to a KAM dominance appears to reflect gait changes associated with progressing OA and pain. Thus, the TJM and its component analysis captures a comprehensive metric for total loading on the knee over time. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. 36:2373-2379, 2018.
Vectorial Control of Energy‐Transfer Processes in Metallocyclodextrin Heterometallic Assemblies (2003)

Shedding light on water wheels: Photoinduced energy transfer is demonstrated between metal centers by a RuII) cyclodextrin “wheel” assembled in water. Os- and Ir-complex guests with hydrophobic tails can be bound noncovalently in the cyclodextrin cavities. In such systems two-way communication is possible as energy transfer can occur from the Ru core to the outer metal centers (purple arrows) or from the outer metal units to the Ru core (white arrow).
Complement Activation by an Anti-Dengue/Zika Antibody with Impaired Fcγ Receptor Binding Provides Strong Efficacy and Abrogates Risk of Antibody-Dependent Enhancement (2023)

To combat infectious diseases, vaccines are considered the best prophylactic strategy for a wide range of the population, but even when vaccines are effective, the administration of therapeutic antibodies against viruses could provide further treatment options, particularly for vulnerable groups whose immunity against the viruses is compromised. Therapeutic antibodies against dengue are ideally engineered to abrogate binding to Fcγ receptors (FcγRs), which can induce antibody-dependent enhancement (ADE). However, the Fc effector functions of neutralizing antibodies against SARS-CoV-2 have recently been reported to improve post-exposure therapy, while they are dispensable when administered as prophylaxis. Hence, in this report, we investigated the influence of Fc engineering on anti-virus efficacy using the anti-dengue/Zika human antibody SIgN-3C and found it affected the viremia clearance efficacy against dengue in a mouse model. Furthermore, we demonstrated that complement activation through antibody binding to C1q could play a role in anti-dengue efficacy. We also generated a novel Fc variant, which displayed the ability for complement activation but showed very low FcγR binding and an undetectable level of the risk of ADE in a cell-based assay. This Fc engineering approach could make effective and safe anti-virus antibodies against dengue, Zika and other viruses.
Improving weak ad-hoc queries using wikipedia asexternal corpus (2007)

In an ad-hoc retrieval task, the query is usually short and the user expects to find the relevant documents in the first several result pages. We explored the possibilities of using Wikipedia's articles as an external corpus to expand ad-hoc queries. Results show promising improvements over measures that emphasize on weak queries.
Supplemental Figure S3 from Dendritic Cells in Irradiated Mice Trigger the Functional Plasticity and Antitumor Activity of Adoptively Transferred Tc17 Cells via IL12 Signaling (2023)

&lt;p&gt;Supplemental Figure S3. Effect of TBI on co-stimulatory ligand expression on myeloid cells in the tumor. A-B, Co-stimulatory ligand expression of CD11b+Ly6ChiLy6Glo MDSC-M (A), and CD11b+Ly6CCmidLy6Ghi MDSC-G (B) in the spleens of mice receiving 0, 5, or 9 Gy irradiation 1 day prior to spleen harvest; n=3 mice per group; * = p&lt;0.05, ** = p&lt;0.01, *** = p&lt;0.001, two tail t-test, error bars represent standard error.&lt;/p&gt;
Optimization of Duplex Stability and Terminal Asymmetry for shRNA Design (2010)

Prediction of efficient oligonucleotides for RNA interference presents a serious challenge, especially for the development of genome-wide RNAi libraries which encounter difficulties and limitations due to ambiguities in the results and the requirement for significant computational resources. Here we present a fast and practical algorithm for shRNA design based on the thermodynamic parameters. In order to identify shRNA and siRNA features universally associated with high silencing efficiency, we analyzed structure-activity relationships in thousands of individual RNAi experiments from publicly available databases (ftp://ftp.ncbi.nlm.nih.gov/pub/shabalin/siRNA/si_shRNA_selector/). Using this statistical analysis, we found free energy ranges for the terminal duplex asymmetry and for fully paired duplex stability, such that shRNAs or siRNAs falling in both ranges have a high probability of being efficient. When combined, these two parameters yield a approximately 72% success rate on shRNAs from the siRecords database, with the target RNA levels reduced to below 20% of the control. Two other parameters correlate well with silencing efficiency: the stability of target RNA and the antisense strand secondary structure. Both parameters also correlate with the short RNA duplex stability; as a consequence, adding these parameters to our prediction scheme did not substantially improve classification accuracy. To test the validity of our predictions, we designed 83 shRNAs with optimal terminal asymmetry, and experimentally verified that small shifts in duplex stability strongly affected silencing efficiency. We showed that shRNAs with short fully paired stems could be successfully selected by optimizing only two parameters: terminal duplex asymmetry and duplex stability of the hypothetical cleavage product, which also relates to the specificity of mRNA target recognition. Our approach performs at the level of the best currently utilized algorithms that take into account prediction of the secondary structure of the target and antisense RNAs, but at significantly lower computational costs. Based on this study, we created the si-shRNA Selector program that predicts both highly efficient shRNAs and functional siRNAs (ftp://ftp.ncbi.nlm.nih.gov/pub/shabalin/siRNA/si_shRNA_selector/).
A superconducting surprise comes of age (2015)

Seven years after the unexpected discovery of superconductivity in iron-based compounds, the study of these "surprise" superconductors is maturing. Hideo Aoki and the discoverer of the first iron-based superconductor, Hideo Hosono, review the field's status and prospects.
Rats with minimal hepatic encephalopathy show reduced cGMP-dependent protein kinase activity in hypothalamus correlating with circadian rhythms alterations (2015)

Patients with liver cirrhosis show disturbances in sleep and in its circadian rhythms which are an early sign of minimal hepatic encephalopathy (MHE). The mechanisms of these disturbances are poorly understood. Rats with porta-caval shunt (PCS), a model of MHE, show sleep disturbances reproducing those of cirrhotic patients. The aims of this work were to characterize the alterations in circadian rhythms in PCS rats and analyze the underlying mechanisms. To reach these aims, we analyzed in control and PCS rats: (a) daily rhythms of spontaneous and rewarding activity and of temperature, (b) timing of the onset of activity following turning-off the light, (c) synchronization to light after a phase advance and (d) the molecular mechanisms contributing to these alterations in circadian rhythms. PCS rats show altered circadian rhythms of spontaneous and rewarding activities (wheel running). PCS rats show more rest bouts during the active phase, more errors in the onset of motor activity and need less time to re-synchronize after a phase advance than control rats. Circadian rhythm of body temperature is also slightly altered in PCS rats. The internal period length (tau) of circadian rhythm of motor activity is longer in PCS rats. We analyzed some mechanisms by which hypothalamus modulate circadian rhythms. PCS rats show increased content of cGMP in hypothalamus while the activity of cGMP-dependent protein kinase was reduced by 41% compared to control rats. Altered cGMP-PKG pathway in hypothalamus would contribute to altered circadian rhythms and synchronization to light.
Stability improvement of Cu3(BTC)2 metal–organic frameworks under steaming conditions by encapsulation of a Keggin polyoxometalate (2011)

Cu(3)(BTC)(2) with an incorporated Keggin polyoxometalate was demonstrated to be stable under steaming conditions up to 483 K, while the isostructural HKUST-1 degrades and transforms into [Cu(2)OH(BTC)(H(2)O)](n)·2nH(2)O from 343 K onwards.
Estrogen Increases Galanin Immunoreactivity in Hyperplastic Prolactin-Secreting Cells in Fisher 344 Rats* (1990)

Galanin is a widely distributed regulatory peptide which modulates the pituitary secretion of PRL and GH. Estrogen administration strongly stimulates galanin gene expression in the rat anterior pituitary. In adult female Fischer 344 rats, estrogen also induces hyperplasia of lactotropes. We used immunocytochemical analysis to assess the effects of estrogen on galanin-like immunoreactivity (Gal-IR) in the rat pituitary and hypothalamus during sc diethylstilbestrol (DES) implantation and after its removal at 30 days. In the anterior pituitary, DES implantation increased the portion of Gal-IR-containing cells from less than 2% in the control rats to 18.3% after 3 days of DES and 36% after 30 days. These changes paralleled the lactotrope hyperplasia exhibited in response to DES exposure. Ten and 30 days after removal of the DES capsules, the percentage of Gal-IR-containing cells in the anterior pituitary decreased to 6.3% and 1.5%, respectively. Colocalization studies revealed that Gal-IR-containing cells were predominantly lactotropes. Immunoelectron microscopy demonstrated that Gal-IR was concentrated in the Golgi region of these hyperplastic lactotropes and suggests that little of the synthesized galanin is secreted. The distribution of Gal-IR in the hypothalamus, median eminence, and neurohypophysis was unaffected by DES treatment. These data demonstrate that galanin is synthesized by hyperplastic pituitary lactotropes of Fischer 344 rats and that peptide accumulation is dependent on the presence of circulating estrogens. In contrast, neuronal galanin synthesis in the hypothalamus does not appear to be regulated by estrogen.
Defective Glucagon-Like Peptide 1 Secretion in Prediabetes and Type 2 Diabetes Is Influenced by Weight and Sex. Chicken, Egg, or None of the Above? (2015)

Glucagon-like peptide 1 (GLP-1) is considered to be the primary incretin hormone, released in response to food ingestion and contributing to meal assimilation. GLP-1 is a powerful insulin secretagogue, stimulating insulin secretion and suppressing glucagon secretion in a glucose-dependent manner (1), and indeed, numerous pharmacologic agents use the GLP-1 pathway to produce effective glucose-lowering therapy (2). Given the antidiabetogenic actions of GLP-1, it is a reasonable question to wonder whether defects in GLP-1 secretion contribute to the pathogenesis of type 2 diabetes. Over the years, multiple studies have examined this question. However, the evidence to suggest decreased GLP-1 secretion in prediabetes and diabetes has been mixed at best, with decreased (3–5), normal (6,7), or increased (8) GLP-1 concentrations reported in subjects with prediabetes or type 2 diabetes.

Subsequently, Nauck et al. (9) undertook a meta-analysis of studies comparing active and total GLP-1 in people with diabetes and weight-matched control subjects and concluded that after an oral glucose challenge or after a mixed meal, the integrated, incremental concentrations of GLP-1 did not differ between patients with type 2 diabetes and control subjects. GLP-1 concentrations were unaffected by weight or age. In addition, we examined active and total GLP-1 concentrations in 165 …
Acquisition design for optimum amplitude accuracy (2001)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2001Acquisition design for optimum amplitude accuracyAuthors: A. W. F. VolkerG. BlacquièreA. J. BerkhoutA. W. F. VolkerDelft University of Technology, G. BlacquièreDelft University of Technology, and A. J. BerkhoutDelft University of Technologyhttps://doi.org/10.1190/1.1816696 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816696FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 2001ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2001 Pages: 2135 publication data© 2001 Copyright © 2001 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 03 Jan 2005 CITATION INFORMATION A. W. F. Volker, G. Blacquière, and A. J. Berkhout, (2001), "Acquisition design for optimum amplitude accuracy," SEG Technical Program Expanded Abstracts : 60-63. https://doi.org/10.1190/1.1816696 Plain-Language Summary PDF DownloadLoading ...
Complementary Roles for CD19 and Bruton’s Tyrosine Kinase in B Lymphocyte Signal Transduction (2002)

CD19 and Bruton's tyrosine kinase (Btk) may function along common signaling pathways in regulating intrinsic and B cell Ag receptor (BCR)-induced signals. To identify physical and functional interactions between CD19 and Btk, a CD19-negative variant of the A20 B cell line was isolated, and CD19-deficient (CD19(-/-)) and CD19-overexpressing mice with the X-linked immunodeficient (Xid; Btk) mutation were generated. In A20 cells, Btk physically associated with CD19 following BCR engagement. CD19 and Btk interactions were not required for initial Btk phosphorylation, but CD19 expression maintained Btk in an activated state following BCR engagement. In primary B cells, CD19 signaling also required downstream Btk function since CD19-induced intracellular Ca(2+) ([Ca(2+)](i)) responses were modest in Xid B cells. In addition, CD19 overexpression did not normalize the Xid phenotype and most phenotypic and functional hallmarks of CD19 overexpression were not evident in these mice. However, CD19 and Btk also regulate independent signaling pathways since their combined loss had additive inhibitory effects on BCR-induced [Ca(2+)](i) responses and CD19 deficiency induced a severe immunodeficiency in Xid mice. Thus, CD19 expression amplifies or prolongs Btk-mediated signaling, rather than serving as a required agent for Btk activation. Consistent with this, phosphatidylinositol 3-monophosphate kinase and Akt activation were normal in CD19(-/-) B cells following IgM engagement, although their kinetics of activation was altered. Thus, these biochemical and compound gene dosage studies indicate that Btk activation and [Ca(2+)](i) responses following BCR engagement are regulated through multiple pathways, including a CD19/Src family kinase-dependent pathway that promotes the longevity of Btk signaling.
Large-Scale Production of Bioactive Ingredients as Supplements for Healthy Human and Animal Nutrition (2011)

In this review, synthetic strategies and the development of environmentally benign methods for the production of economically important vitamins, carotenoids, and nutraceuticals used as food and feed supplements are illustrated by selected examples. The application of efficient catalytic transformations in multi-step chemical syntheses of such natural products enables technically feasible and cost-effective processes. For the preparation of fat-soluble (isoprenoid) vitamins A and E and the water-soluble vitamin (+)-biotin, homogeneous metal catalysis, including enantioselective transformations, heterogeneous and enzymatic catalysis serve as key methodologies. In the area of carotenoids, general building concepts and coupling methods for the total synthesis of beta-carotene and astaxanthin are discussed. Biotechnological methods and isolation from natural sources are also employed successfully, as exemplified for the xanthophyll lutein and the antioxidant (-)-epigallocatechin gallate. Lastly, key steps of the chemical synthesis of the polyphenol resveratrol are highlighted.
The use of a Temporary Extracochlear Electrode in Preoperative Testing of Permanent Implant Candidates (1986)

This paper describes hearing and speech perception in 9 post-lingually deaf adults fitted with a temporary single electrode, surgically positioned close to the round window niche. After baseline testing, unaided and aided binaurally with the high-power Phonic Ear PE 845, each subject was admitted to hospital for a period of 7 days. During each test session, stimuli were presented directly to the electrode lead by means of an isolation unit. Current thresholds, upper tolerable limits and gap detection were measured for various acoustical waveforms and stimulus frequencies. A laryngograph was used to test the discrimination of prelinguistic and suprasegmental speech features. The results indicated that the prosthesis could provide acoustic sensations of loudness, pitch and duration that changed with stimulus waveform, level of current and frequency, and a gap threshold less than 50 msec. Lipreading appeared to be a necessary adjunct for consonant discrimination.
Evidence for Specific Solvation of Two Halocarbene Amides (2004)

Laser flash photolysis (LFP, 308 nm) of endo-10-halo-10'-N,N-dimethylcarboxamidetricyclo[4.3.1.0]-deca-2,4-diene (1Cl and 1F) releases indan and halocarbene amide (2Cl and 2F). Although the carbenes are not UV-vis active, they react rapidly with pyridine to form ylides (4Cl, 4F), which are readily detected in LFP experiments (lambda(max) = 450 nm). Dioxane decreases the observed rate of carbene reaction with pyridine in CF(2)ClCFCl(2). Small amounts of THF decrease the observed rate of reaction of carbene 2F with pyridine but increase the rate of reaction of carbene 2Cl with pyridine. LFP (266 nm) of dienes 1Cl and 1F in CF(2)ClCFCl(2) with IR detection produces carbenes 2Cl and 2F with carbonyl vibrations at 1635 and 1650 cm(-1), respectively. In dioxane or THF solvent, LFP produces the corresponding ether ylides (5Cl, 5F) by capture of carbenes 2Cl and 2F. The ylides have broad carbonyl vibrations between 1560 and 1610 cm(-1). The addition of a small amount of dioxane in CFCl(2)CF(2)Cl extends the lifetime of the carbene. This observation, together with the ether-induced retardation of the rates of carbene capture by tetramethylethylene and pyridine, is evidence for solvation of the carbene by dioxane.
13C NMR and IR Evidence for the Two Types of Copper(I) and (II) Complexes with 5-Pyrido-1,4-benzodiazepin-2-ones (1994)

Abstract 5-Pyrido-1,4-benzodiazepin-2-onederivatives 1–9 are investigated as potential 1,4-N,N-bidentate ligands in copper(I) and (II) complexes. On the basis of 13C NMR and IR spectra two types of complexation are revealed. In the first ones, ligands 1–5behave as l,4-N,N-bidentates, whereas their 4,5-dihydro congeners 6–9 unexpectedly form N,O-bidentate complexes, engaging carbonyl oxygen and pyridine nitrogen as the coordination sites.
Characterization and Mechanisms of Action of Avocado Extract Enriched in Mannoheptulose as a Candidate Calorie Restriction Mimetic (2021)

Increased consumer interest in the avocado (<i>Persea americana</i> or <i>Persea gratissima</i>) has been attributed to established health benefits of this fruit associated with a wide range of ingredients. In search of effective calorie restriction mimetics (CRM), we present herein a consideration of possible health benefits of the rare sugar, mannoheptulose (MH), which acts as an intracellular glycolytic inhibitor and presents the highest concentration of this inhibitor in unripe avocados. A method for producing an extract of unripe avocado (AvX) to enrich concentrations of MH is described. Experiments using myocyte cultures demonstrated a pattern of CRM-like responses when treated with AvX. In vivo experiments confirmed that orally consumed AvX is bioavailable in both mice and dogs, as observed in urine and blood samples. Additional experiments in both these species demonstrated CRM-like improvements in glucose and insulin responses. In sum, the MH-enriched AvX exhibits promise as a CRM.
High Aspect Ratio CPW Fabricated Using a Micromachining Process Combining DRIE, Thermal Oxidation, Electroplating, and Planarization (2009)

A micromachining process has been developed to fabricate high aspect ratio CPW. The tall conductor sidewall created from the high aspect ratio process reduces the resistance per length of the transmission line which lowers the attenuation. The micromachining process combines Si DRIE, thermal oxidation, electroplating, and planarization to create tall CPW with Au conductors and SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> dielectrics. Transmission lines with characteristic impedances of 16-21 Omega have been fabricated on high resistivity Si. Transmission line characteristics were measured from 1-50 GHz and showed propagation loss of 1.1-1.3 dB/cm at 10 GHz.
A General and Mild Copper-Catalyzed Arylation of Diethyl Malonate (2002)

[reaction: see text] A general method for the synthesis of alpha-aryl malonates is described. The coupling of an aryl iodide and diethyl malonate in the presence of Cs(2)CO(3) and catalytic amounts of copper(I) iodide and 2-phenylphenol affords the alpha-aryl malonate in good to excellent yields. The mild reaction conditions and high levels of functional group compatibility make this an attractive synthetic alternative to previous methods.
Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution: a focus on aging and cancer (2019)

ABSTRACT Mitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation and motility as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. Importantly, mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method (ddMDM; droplet digital mitochondrial DNA measurement) to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 hours, is optimized for 96-well plates and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. Importantly, we show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.