gebhart/patrepeval huggingface dataset:
Mammalian Toll-like receptors: to immunity and beyond (2005)

Toll-like receptors (TLRs) constitute an archetypal pattern recognition system. Their sophisticated biology underpins the ability of innate immunity to discriminate between highly diverse microbial pathogens and self. However, the remarkable progress made in describing this biology has also revealed new immunological systems and processes previously hidden to investigators. In particular, TLRs appear to have a fundamental role in the generation of clonal adaptive immune responses, non-infectious disease pathogenesis and even in the maintenance of normal mammalian homeostasis. Although an understanding of TLRs has answered some fundamental questions at the host-pathogen interface, further issues, particularly regarding therapeutic modulation of these receptors, have yet to be resolved.
Genome‐wide association study of sleep duration in the Finnish population (2014)

Sleep duration is genetically regulated, but the genetic variants are largely unknown. We aimed to identify such genes using a genome-wide association study (GWAS) combined with RNA expression at the population level, and with experimental verification. A GWAS was performed in a Finnish sample (n = 1941), and variants with suggestive association (P < 5 × 10(-5) ) were tested in a follow-up sample from the same population with sleep duration (n = 6834) and time in bed (n = 1720). Variants with pointwise association of P < 0.05 in the follow-up sample were analysed further. First, we correlated genotypes with transcript expression levels with sleep duration (n = 207). The expression levels of significant transcripts were further studied in experimental sleep restriction. Of the 31 variants with P < 5 × 10(-5) in the discovery sample, three variants showed nominal allelic association (P < 0.05) in the follow-up sample: rs10914351, near PTPRU (P = 0.049), rs1037079 in PCDH7-CENTD1 (P = 0.011) and rs2031573 near KLF6 (P = 0.044). The risk alleles for shorter sleep (rs2031573 and rs1037079) were also associated with higher KLF6 and PCDH7 expression levels (P < 0.05). Experimental sleep restriction increased the expression of KLF6 (P < 0.01). These data suggest that rs2031573 near KLF6 or related loci and rs1037079 between PCDH7-CENTD1 or related loci may contribute to the regulation of sleep duration via gene expression. These results illustrate the utility of combining different analytical approaches to identify genetic determinants for traits related to sleep physiology. However, additional studies are needed in order to understand the roles of KLF6 and PCDH7 in sleep regulation.
ChemInform Abstract: Metabolic Glycoengineering with N‐Acyl Side Chain Modified Mannosamines (2016)

Abstract Review: 428 refs.
Analysis of reversible lipoprotein-cell interactions. (1982)

Quantitation and characterization of freely reversible ligand-receptor interactions in adherent cell lines grown in vitro have been technically difficult to perform. We report the growth of human fibroblasts on a microcarrier bead system which obviates the limitation of cell adherence in such determinations. This system has been applied to the reversible interaction of low density lipoproteins (LDL) with the fibroblast membrane receptors. Of the 125I-LDL specifically bound to filtered cells, 52.2 +/- 9.8% was reversibly bound. This reversible LDL-cell binding occurred in less than 1 h at 37 degrees C, was specific for LDL, and occurred without significant 125I-LDL degradation. Using these techniques, it is now possible to obtain direct measurement and characterization of lipoprotein-receptor interactions in adherent cell lines of normal subjects and patients with dyslipoproteinemia.
Photovoltage Mechanism for Room Light Conversion of Citrate Stabilized Silver Nanocrystal Seeds to Large Nanoprisms (2008)

We investigate the photoconversion of aqueous 8 nm Ag nanocrystal seeds into 70 nm single crystal plate nanoprisms. The process relies on the excitation of Ag surface plasmons. The process requires dioxygen, and the transformation rate is first-order in seed concentration. Although citrate is necessary for the conversion, and is consumed, the transformation rate is independent of citrate concentration. We propose a mechanism that accounts for these features by coupling the oxidative etching of the seed and the subsequent photoreduction of aqueous Ag(+). The reduced Ag deposits onto a Ag prism of specific size that has a cathodic photovoltage resulting from plasmon "hot hole" citrate photo-oxidation. This photovoltage mechanism also explains recent experimental results involving single and dual wavelength irradiation and the core/shell synthesis of Ag layers on Au seeds.
ECFCs from patients with PAH show a disturbed reaction to high fluid flow induced shear stress (2015)

In Pulmonary Arterial Hypertension (PAH) structural and functional abnormalities in the lung lead to an increased pulmonary vascular resistance and right heart failure. Dysfunction of the pressure-regulating endothelial cells (ECs) is thought to play an crucial role. Recently it was shown in our laboratory that lung biopsy derived microvascular ECs (MVECs) from PAH-patients are unable to align under 120h of high shear stress. As the availability of these cells is limited, a suitable alternative is needed. Our aim was to investigate ECFC as a substitute for MVECs regarding reaction to shear stress. ECFC are circulating ECs, easily obtainable from venous blood. ECFCs obtained form patients expressed EC markers CD31, VE-cadherin, VEGFR2, VWF, and were negative for α-SMA, CD14, CD45. For flow experiments, an unidirectional flow (25 dyn/cm<sup>2</sup>) was applied to ECFC for 120 hours. Allignment was quantified with phase contrast microscopy. When &gt;50% of cells aligned, this is called aligned. After 120 h 6 out of 6 control donors aligned, in the PAH group 4 out of 6 alligned. In addition we analyzed proliferation under flow. After 120 h, in the control group we count 37.25x10 cells/ cm<sup>2</sup>, in the PAH group 73,7x10/ cm<sup>2</sup> cells (multiple t-test, corrected by Holm Sidak method) p= 0.013551. In conclusion we show that out of ECFC from 8 PAH patients 4 donors are unable to align after 120h of high fluid flow induced shear stress. This is in line with with previous observations in PAH-MVECS. In addition we found that ECFC proliferate under flow. This makes it likely that ECFC play a role in disease progression, and strengthens the hypothesis for an intrinsic base for EC dysfunction in PAH.
[P4–357]: THE ASSOCIATION OF POST‐OPERATIVE COGNITIVE DECLINE AND POST‐OPERATIVE DELIRIUM (2017)

A substantial number of older patients experience acute cognitive decline following surgery. When acute fluctuating impairment in consciousness and/or attention is present, the disturbance is recognized as post-operative delirium (POD). Postoperative cognitive decline (POCD), on the other hand, is a subacute codition measured using changes in performance with serial cognitive assessment. While POD and POCD are both areas of interest for researchers and concern for older surgical patients, the relationship between these two conditions has not been well-examined. Participants were from the Successful Aging after Elective Surgery study, a prospective study of 560 older adults (≥70 years) without dementia at baseline who underwent elective surgery. Delirium was evaluated each postoperative day using the Confusion Assessment Method (CAM) supplemented with medical chart review. Cognition was assessed with a battery of neuropsychological tests. POCD was defined using the approach developed by the International Study of Postoperative Cognitive Dysfunction. POD occurred in nearly a quarter (n = 134, 24%) of patients. About 47% of patients satisfied criteria for POCD at 1 month following surgery, but this proportion was lower at months 2, 6 and 12 (23%, 16%, and 24%, respectively) following surgery. At each follow-up, the level of agreement (on the basis of a kappa agreement statistic) between post-operative delirium (POD) and POCD was poor (kappa < .08) and the (tetrachoric) correlations were small (r < .16). The risk for POCD was significantly elevated for patients with a history of POD at 1 month (RR = 1.4, 95% CI 1.2, 1.7, P < .001) but not at month 2 (RR = 1.1, P = .64), month 6 (RR = 0.95, P = .82), or month 12 (RR = 1.2, P = .40). POD does not appear to be a risk factor for POCD. The association of POD and POCD at 1 month likely reflects unresolved delirium. This study suggests that POD and POCD are distinct entities, raising the strong possibility that specific underlying causal mechanisms are at work. Distinct and targeted interventions may be required to improve the cognitive outcomes of older surgical patients.
Development of Highly Efficient Light Extraction Technology with Nano-structure for OLED Devices (2015)

Novel nano-structure for the improved light extraction efficiency of reduced evanescent mode OLED devices (REM OLED) was developed. The nano-structure was designed to have high transmittance especially over critical angle in order to achieve good combination with the light distribution pattern of the REM OLED devices. In this system, the wide angular substrate mode was efficiently converted into the external mode, and high efficacy green OLED with EQE of 54 % was obtained. Relative light extraction efficiency to a hemisphere lens system was 89 %.
MicroRNA-148/152 Impair Innate Response and Antigen Presentation of TLR-Triggered Dendritic Cells by Targeting CaMKIIα (2010)

MicroRNAs (miRNAs) are involved in the regulation of immunity, including the lymphocyte development and differentiation, and inflammatory cytokine production. Dendritic cells (DCs) play important roles in linking innate and adaptive immune responses. However, few miRNAs have been found to regulate the innate response and APC function of DCs to date. Calcium/calmodulin-dependent protein kinase II (CaMKII), a major downstream effector of calcium (Ca(2+)), has been shown to be an important regulator of the maturation and function of DCs. Our previous study showed that CaMKIIα could promote TLR-triggered production of proinflammatory cytokines and type I IFN. Inspired by the observations that dicer mutant Drosophila display defect in endogenous miRNA generation and higher CaMKII expression, we wondered whether miRNAs can regulate the innate response and APC function of DCs by targeting CaMKIIα. By predicting with software and confirming with functional experiments, we demonstrate that three members of the miRNA (miR)-148 family, miR-148a, miR-148b, and miR-152, are negative regulators of the innate response and Ag-presenting capacity of DCs. miR-148/152 expression was upregulated, whereas CaMKIIα expression was downregulated in DCs on maturation and activation induced by TLR3, TLR4, and TLR9 agonists. We showed that miR-148/152 in turn inhibited the production of cytokines including IL-12, IL-6, TNF-α, and IFN-β upregulation of MHC class II expression and DC-initiated Ag-specific T cell proliferation by targeting CaMKIIα. Therefore, miRNA-148/152 can act as fine-tuner in regulating the innate response and Ag-presenting capacity of DCs, which may contribute to the immune homeostasis and immune regulation.
Hierarchical Fe2O3@CNF fabric decorated with MoS2 nanosheets as a robust anode for flexible lithium-ion batteries exhibiting ultrahigh areal capacity (2018)

Hierarchical Fe<sub>2</sub>O<sub>3</sub>@CNF@MoS<sub>2</sub> fabric film was fabricated as robust anode for flexible LIBs exhibiting ultrahigh areal capacity.
GWAS of Dental Caries Patterns in the Permanent Dentition (2012)

The importance of susceptibility genes in the risk for dental caries has been clearly established. While many candidate caries genes have been proposed, to date, few of them have been rigorously validated through observational and experimental studies. Moreover, most genetic epidemiological studies have analyzed global caries phenotypes that ignore the possibility that genes may exert differential effects across tooth surfaces of the dentition. Therefore, we performed genome-wide association studies (GWAS) of 5 novel dental caries phenotypes (developed by clustering the permanent dentition into categories of tooth surfaces based on co-occurrence of caries) to nominate new candidate caries genes. GWAS was performed in 920 self-reported white participants, aged 18 to 75 years, with genotype data on 518,997 genetic variants. We identified a significant genetic association between dental caries of the anterior mandibular teeth and LYZL2 (p value = 9e-9), which codes a bacteriolytic agent thought to be involved in host defense. We also identified a significant genetic association between caries of the mid- dentition tooth surfaces and AJAP1 (p value = 2e-8), a gene possibly involved in tooth development. Suggestive genetic associations were also observed for ABCG2, PKD2, the dentin/bone SCPP sub-family, EDNRA, TJFBR1, NKX2-3, IFT88, TWSG1, IL17D, and SMAD7 (p values < 7e-6). We nominate these novel genes for future study.
Spectral derivative features for supervised classification of remote sensing data: An experimental evaluation (2012)

Derivatives of spectral reflectance signatures can capture salient features of different land-cover classes. This information is widely used for supervised classification of remote sensing data. In the paper, we study the issue when the derivatives of spectral reflectance work for supervised classification of remote sensing data and give an empirical conclusion in terms of a large amount of experimental evaluations.
Dynamic Software Testing of MPI Applications with Umpire (2000)

As evidenced by the popularity of MPI (Message Passing Interface), message passing is an effective programming technique for managing coarse-grained concurrency on distributed computers. Unfortunately, debugging message-passing applications can be difficult. Software complexity, data races, and scheduling dependencies can make programming errors challenging to locate with manual, interactive debugging techniques. This article describes Umpire, a new tool for detecting programming errors at runtime in message passing applications. Umpire monitors the MPI operations of an application by interposing itself between the application and the MPI runtime system using the MPI profiling layer. Umpire then checks the application’s MPI behavior for specific errors. Our initial collection of programming errors includes deadlock detection, mismatched collective operations, and resource exhaustion. We present an evaluation on a variety of applications that demonstrates the effectiveness of this approach.
Bilateral Oxford Meniscal Knee Arthroplasty (1985)

Thirty-two patients who underwent bilateral bicompartmental Oxford Meniscal Knee arthroplasty have been followed up prospectively for a mean period of 51 months from the time of their first operation. Pain relief was obtained in all but one knee; walking ability was improved in more than two-thirds. Overall patient satisfaction with the results was good. Two knees failed. The results demonstrate that bilateral knee arthroplasty can be expected to give good functional results.
26 Epstein-Barr Virus DNA Replication (1996)

Epstein-Barr virus (EBV) and its close relatives are the only known viruses that have two fully independent systems for replicating their genomes, one that supports virus production during active or “lytic” infection, and a second one that operates during latent stages of infection to allow the circular viral genomes to be duplicated during each cell division cycle. Although EBV’s system of lytic DNA replication is for the most part a heritage of the herpesvirus family, its system for replication during latency is entirely its own. During latent infection, while the genes required for lytic replication and virus production are silent, the circular EBV chromosome is replicated by the cell’s DNA replication machinery, apparently only once during each S phase. This arrangement of having the host cell replicate its genome during latency is probably related to the fact that EBV establishes latency in cells that are prone to divide. EBV appears to maintain its life-long infection of people by residing within B cells (Klein 1994; Miyashita et al. 1995), and, during the initial phase of latent infection of B cells, EBV expresses a small set of genes that together cause the cells to proliferate (Kieff and Leibowitz 1990; Miller 1990). EBV DNA replication during latency might also be important for the eventual productive infection of epithelial cells, because EBV appears to be most able to infect undifferentiated epithelial cells but to replicate lytically in differentiated cells (Sixbey 1989). EBV replication during latency relies almost entirely on the cell. A single EBV-encoded...
Totally extra-peritoneal repair for acute incarcerated femoral hernia with intestinal obstruction (2017)

This modification of the TEP repair technique for the acutely incarcerated and obstructed femoral hernia serves to minimise potential contamination by keeping the pre-peritoneal plane strictly separate from the intra-peritoneal space.
Identification of Two NF-κB Sites in Mouse CD95 Ligand (Fas Ligand) Promoter: Functional Analysis in T Cell Hybridoma (1998)

Abstract Fas ligand (FasL) gene expression is critically involved in peripheral T cell tolerance and lymphocyte homeostasis. Previous studies have suggested that nuclear translocation of NF-κB during T cell activation is a critical event for FasL gene activation. In the present study we have identified two NF-κB sites (designated FasL-κB1 and FasL-κB2) on the promoter (∼700 bp) of FasL. The NF-κB sites were identified by electrophoretic mobility shift assay. Transient transfection reporter analyses showed that the FasL promoter activity was comparable between a construct that contains both sites and a shorter construct (433 bp) that contains only the FasL-κB1 site. Furthermore, elimination of FasL-κB1 by site-directed mutagenesis significantly inhibited FasL promoter activity. These observations provide strong evidence that NF-κB directly binds to the FasL-κB1 site and up-regulates FasL gene expression.
Association of CDK4 amplification with duration of response to bevacizumab in glioblastoma. (2023)

2026 Background: Bevacizumab remains the standard second line therapy in glioblastoma (GBM) with reported improved progression free survival, but not overall survival. We investigated a large clinico-genomic database of GBM patients treated with bevacizumab for molecular alterations associated with treatment outcome. Methods: Molecular profiles of GBM were tested by next-generation sequencing (NGS) of DNA (592 genes, NextSeq or whole-exome sequencing, Novaseq) and RNA (whole transcriptome sequencing, NovaSeq) at Caris Life Sciences (Phoenix, AZ). Gene amplification was determined by NGS with a threshold of &gt; = 6 copies. Real-world survival information was obtained from insurance claims data. Time-on-treatment (TOT) of bevacizumab was calculated from start to finish of treatment while post-bevacizumab overall survival (bevOS) from start of bevacizumab to last day of contact. Short-term (ST) and long-term (LT) responders were defined as those with TOT ≤6 months and ≥1 year, respectively. Kaplan-Meier estimates were calculated and significance was determined as p values of &lt; 0.05. For molecular comparisons, Fisher’s exact tests and Mann-Whiney U were used when appropriate. Results: Among the total of 383 ST and 107 LT patients identified, no significant difference in gender or age were seen. The LT cohort had significantly longer bevOS compared to the ST cohort (HR 0.27, [95% CI: 0.28-0.35], p &lt; 0.0001). Interestingly, CDK4 amplification was seen in 23% (18/78) of LT patients but only 7% (21/300, p = 0.0002) of ST. When investigating the total cohort of 498 GBM treated with bevacizumab, CDK4 amplified patients demonstrated significantly improved TOT compared to non-amplified (HR: 0.639, [0.48-0.85, p = 0.002]). Conversely, the ST cohort had significantly more EGFR amplifications than the LT cohort (43%, 130/300 vs. 19%, 15/79, p &lt; 0.0001). In the total bevacizumab-treated cohort, EGFR-amplified GBM had significantly worse TOT on bevacizumab than non-EGFR amplified GBM (HR 1.387, [1.15-1.67], p &lt; 0.001). No associations were seen in other alterations explored including PIK3CA mutation (HR = 0.81 [0.587-1.113], p = 0.2), EGFR mutation (HR: 1.209, [0.977-1.495], p = 0.1) or RAF1 (HR: 0.647, [0.318-1.317], p = 0.2). Conclusions: Using a large clinical genomic database with GBM subjected to comprehensive molecular profiling, we demonstrated that amplification of CDK4 and EGFR were associated with long-term and short-term responses to bevacizumab, respectively. This warrants further investigation in independent cohorts controlled for age and other prognostic factors. If confirmed, a genetic basis for treatment optimization may provide meaningful clinical outcomes.
ChemInform Abstract: BA7(SI7O21).≅10BACL2 ‐ A COMPOUND WITH A NEW TYPE OF CYCLIC SILICATE ANIONS (1984)

Abstract Die Verbindung 2 BaO · 2 SiO 3 · 3 BaCl 2 (BaCO 3 : SiO 3 : BaCl 2 = 1:1:2, 1020°C, 1 h) wird mit Hilfe der Molybdatmethode, papierchromatographisch, durch hochauflösende Festkörper‐ 29 Si‐NMR‐Spektroskopie sowie die Trimethylsilylierungsmethode (gaschromatographische und MS‐Charakterisierung der Produkte) untersucht.
Neutrophil elastase enhances the proliferation and decreases apoptosis of leukemia cells via activation of PI3K/Akt signaling (2016)

Neutrophil elastase (NE) is a neutrophil‑derived serine proteinase with specificity for a broad range of substrates. NE has been reported to be associated with the pathogenesis of several conditions, particularly that of pulmonary diseases. Previous studies have shown that NE can cleave the pro‑myelocyte ‑ retinoic acid receptor‑alpha chimeric protein and is important for the development of acute pro‑myelocytic leukemia. To further elucidate the role of NE in acute pro‑myelocytic leukemia, the present study successfully constructed a lentiviral vector containing the NE gene (LV5‑NE), which was transfected into NB4 acute pro‑myelocytic leukemia cells. The effects of NE overexpression in NB4 cells were detected using a Cell-Counting Kit‑8 assay, flow cytometry and western blot analysis. The results showed that NE significantly promoted the proliferation of NB4 cells, inhibited cell apoptosis and apoptotic signaling, and led the activation of Akt. In an additional experiment, a vector expressing small hairpin RNA targeting NE was constructed to assess the effects of NE knockdown in U937 cells. Western blot analysis revealed that apoptotic signaling was increased, while Akt activation was decreased following silencing of NE. The results of the present study may indicate that NE activates the phosphoinositide-3 kinase/Akt signaling pathway in leukemia cells to inhibit apoptosis and enhance cell proliferation, and may therefore represent a molecular target for the treatment of pro‑myelocytic leukemia.