gebhart/patrepeval huggingface dataset:
PINK1-PARK2-mediated mitophagy in COPD and IPF pathogeneses (2018)

Mitochondria regulate not only cell functions through energy generation but also aging-associated cell phenotypes. Impaired mitochondrial structural and functional integrity accompanied by excessive mitochondrial reactive oxygen species (mtROS) production is associated with enhanced programmed cell death (PCD) and cellular senescence. Dysregulation of mechanisms for mitochondrial integrity, including mitophagy, induces accumulation of mitochondrial damage. Mitophagy is a highly conserved mechanism of selectively delivering damaged mitochondria for lysosomal degradation and is mainly governed by phosphatase and tensin homolog (PTEN)-induced putative protein kinase 1 (PINK1) and PARK2. Accumulating evidence suggests that PINK1-PARK2-mediated mitophagy has an important role in the pathogenesis of aging-associated pulmonary disorders, represented by chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). COPD characterized by progressive airflow limitation is mainly caused by cigarette smoke (CS) exposure, and accumulation of damaged mitochondria in bronchial epithelial cells (BEC) has been demonstrated. Intriguingly, both enhanced and impaired mitophagy have been implicated in COPD pathogenesis. Enhanced mitophagy induced by increased PINK1 expression has been associated with programmed necrosis, necroptosis. On the other hand, reduced PARK2 levels were linked to insufficient mitophagy, resulting in accelerated cellular senescence in BEC. Although dominant involvement of PCD and cellular senescence remains unclear, PINK1-PARK2-mediated mitophagy regulates mitochondrial ROS and cell fate during COPD pathogenesis. Involvement of insufficient mitophagy has been proposed in lung fibrosis development during IPF pathogenesis. Accumulation of dysmorphic mitochondria and increased ROS production linked to decrease in PINK1 expression were demonstrated in type II alveolar epithelial cells (AECIIs) in IPF lungs, which can be associated with enhanced apoptosis and cellular senescence. Furthermore, reduced PARK2 expression levels have been shown in myofibroblasts in IPF lungs. Insufficient mitophagy caused by PARK2 deficiency induced mtROS production with concomitantly activated platelet-derived growth factor receptor (PDGFR)/mammalian target of rapamycin (mTOR) signaling, resulting in increased myofibroblast differentiation and proliferation. Inappropriate PINK1-PARK2-mediated mitophagy appears to be mainly responsible for regulating cell fate, including PCD, cellular senescence, and myofibroblast differentiation during COPD and IPF pathogeneses. Modalities to achieve specific and appropriate levels of PINK1-PARK2-mediated mitophagy activation may be a promising therapeutic option to regulate the aging-associated pathology, COPD, and IPF.
Hepatitis C Virus: Assembly and Release of Virus Particles (2010)

Hepatitis C virus is a blood-borne virus that typically establishes a chronic infection in the liver, which often results in cirrhosis and hepatocellular carcinoma. Progress in understanding the complete virus life cycle has been greatly enhanced by the recent availability of a tissue culture system that produces infectious virus progeny. Thus, it is now possible to gain insight into the roles played by viral components in assembly and egress and the cellular pathways that contribute to virion formation. This minireview describes the key determining viral and host factors that are needed to produce infectious virus.
CD33 in Alzheimer’s Disease – Biology, Pathogenesis, and Therapeutics: A Mini-Review (2018)

Alzheimer's disease (AD) affects nearly 50 million people worldwide, and currently no disease-modifying treatment is available. With continuous failure of anti-amyloid-beta- or tau-based therapies, identification of new targets has become an urgent necessity for AD prevention and therapy. Recently, conventional genetic approaches and computational strategies have converged on immune-inflammatory pathways as key events in the pathogenesis of AD. A number of genes have been highly linked to the onset and development of late-onset sporadic AD, the most common form of AD. Strikingly, most of these genes are involved in microglial biology. Mutations and/or differential expression of microglial receptors such as TREM2, CD33, and CR3 have been strongly associated with an increased risk of developing AD. The mechanistic actions of these risk factors in AD etiology have been actively investigated since they were identified. Whether these genes can be targeted for a disease-modifying treatment is under hot debate. CD33 is one of the top-ranked AD risk genes identified by genome-wide association studies. This review summarizes the recently advanced biology of CD33 and its association with AD. It also provides insights from a drug discovery perspective into the druggability, therapeutic strategies, and challenges to target CD33 for treating this devastating disorder.
Studies on Production of Lipids in Fungi. V. (1982)

The amounts of squalene produced by various species of fungi have been studied by gas chromatographic technique. Some species of the order Mucorales were found to contain 0.3-0.6% of squalene to dry weight of cultivated mycellium.
Synthesis, antibacterial activity and structure-activity relationships of N-substituted 4-diazo-pyrazole-5-carboxamides. 2. (1991)

A series of 4-diazopyrazole-5-carboxamides 1 d-n has been synthesized and their antibacterial activity against a number of Gram-negative and Gram-positive strains has been tested. Some of the compounds resulted quite active and the whole set allowed to further study the SAR of the class. Substituents in position 5 affect Gram-negative and Gram-positive activities via bulk and electronic properties respectively; position 3 mostly affects the Gram-negative activity, while the presence of the charged diazo group in position 4 is crucial for both antibacterial activities.
Oxidative DNA Damage and Mammary Cell Proliferation by Alcohol-Derived Salsolinol (2013)

Drinking alcohol is a risk factor for breast cancer. Salsolinol (SAL) is endogenously formed by a condensation reaction of dopamine with acetaldehyde, a major ethanol metabolite, and SAL is detected in blood and urine after alcohol intake. We investigated the possibility that SAL can participate in tumor initiation and promotion by causing DNA damage and cell proliferation, leading to alcohol-associated mammary carcinogenesis. SAL caused oxidative DNA damage including 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), in the presence of transition metal ions, such as Cu(II) and Fe(III)EDTA. Inhibitory effects of scavengers on SAL-induced DNA damage and the electron spin resonance study indicated the involvement of H₂O₂, which is generated via the SAL radical. Experiments on scavengers and site specificity of DNA damage suggested ·OH generation via a Fenton reaction and copper-peroxide complexes in the presence of Fe(III)EDTA and Cu(II), respectively. SAL significantly increased 8-oxodG formation in normal mammary epithelial MCF-10A cells. In addition, SAL induced cell proliferation in estrogen receptor (ER)-negative MCF-10A cells, and the proliferation was inhibited by an antioxidant N-acetylcysteine and an epidermal growth factor receptor (EGFR) inhibitor AG1478, suggesting that reactive oxygen species may participate in the proliferation of MCF-10A cells via EGFR activation. Furthermore, SAL induced proliferation in estrogen-sensitive breast cancer MCF-7 cells, and a surface plasmon resonance sensor revealed that SAL significantly increased the binding activity of ERα to the estrogen response element but not ERβ. In conclusion, SAL-induced DNA damage and cell proliferation may play a role in tumor initiation and promotion of multistage mammary carcinogenesis in relation to drinking alcohol.
PI3Kα activates integrin α4β1 to establish a metastatic niche in lymph nodes (2013)

Lymph nodes are initial sites of tumor metastasis, yet whether the lymph node microenvironment actively promotes tumor metastasis remains unknown. We show here that VEGF-C/PI3Kα-driven remodeling of lymph nodes promotes tumor metastasis by activating integrin α4β1 on lymph node lymphatic endothelium. Activated integrin α4β1 promotes expansion of the lymphatic endothelium in lymph nodes and serves as an adhesive ligand that captures vascular cell adhesion molecule 1 (VCAM-1)(+) metastatic tumor cells, thereby promoting lymph node metastasis. Experimental induction of α4β1 expression in lymph nodes is sufficient to promote tumor cell adhesion to lymphatic endothelium and lymph node metastasis in vivo, whereas genetic or pharmacological blockade of integrin α4β1 or VCAM-1 inhibits it. As lymph node metastases accurately predict poor disease outcome, and integrin α4β1 is a biomarker of lymphatic endothelium in tumor-draining lymph nodes from animals and patients, these results indicate that targeting integrin α4β1 or VCAM to inhibit the interactions of tumor cells with the lymph node microenvironment may be an effective strategy to suppress tumor metastasis.
Effect of winding speed on the physical structure of as‐spun poly(ethylene terephthalate) fibers, including orientation‐induced crystallization (1978)

Abstract As‐spun fibers of poly(ethylene terephthalate), PET, made at winding speeds ranging from 2000 to 6000 m/min exhibit quite different physical structures. Yarns wound at relatively low speeds are amorphous, whereas those spun at high speeds contain well‐developed crystals of closely packed molecules. In this study the structures have been characterized by means of various techniques such as differential scanning calorimetry, x‐ray diffraction, density, and pulse propagation measurements. Based on the results obtained, an arrangement of the molecules in the various yarns is proposed. It is shown that these arrangements can account for the extreme wide variety in contraction behavior found experimentally. Finally, the results obtained are compared with those of other investigations into orientation‐induced crystallization.
Applied Wavelet Analysis with S-PLUS. (1997)

From the Publisher:
This book introduces applied wavelet analysis through the S-PLUS software system. Using a visual data analysis approach, wavelet concepts are explained in a way that is intuitive and easy to understand. Wavelets, as well as a whole range of related signal-processing techniques, such as wavelet packets, local cosine analysis, and matching pursuits are covered. Applications of wavelet analysis are illustrated, including nonparametric function estimation, digital image compressing, and time-frequency acoustic signal analysis.
Hyperglycemia in Acutely Ill Patients (2002)

MOST PHYSICIANS WILL ENcounter acutely ill patients who develop hyperglycemia. A third of all persons admitted to an urban general hospital had fasting glucose levels exceeding 126 mg/dL (7 mmol/L), or 2 or more random glucose levels exceeding 200 mg/dL (11.1 mmol/L); a third of those patients with hyperglycemia did not have a prior diagnosis of diabetes. Physicians often perceive hyperglycemia as a consequence of stress that runs parallel to the clinical course of an acute illness. Clinicians often start treatment of hyperglycemia only after glucose levels have exceeded 200 to 250 mg/dL (11-14 mmol/L). One reason for this is the perception that avoidance of hypoglycemia and its potential consequences is more important than glycemic control while patients are hospitalized. We discuss the evidence supporting the hyperglycemic milieu as a risk factor for adverse outcomes in the acutely ill patient with and without known diabetes, and we focus on the efficacy and safety of implementing tighter glycemic control for hospitalized patients.
Depressive symptoms during buprenorphine vs. methadone maintenance: findings from a randomised, controlled trial in opioid dependence (2004)

Research suggests that buprenorphine may possess antidepressant activity. The Beck Depression Inventory was completed at baseline and 3 months by heroin dependent subjects receiving either buprenorphine or methadone maintenance as part of a larger, pre-existing, double blind trial conducted by NDARC (Australia). Depressive symptoms improved in all subjects, with no difference between methadone and buprenorphine groups, suggesting no differential benefit on depressive symptoms for buprenorphine compared to methadone.
Differential Regulation of<i>Salmonella typhimurium</i>Type III Secreted Proteins by Pathogenicity Island 1 (SPI-1)-Encoded Transcriptional Activators InvF and HilA (1999)

Salmonella enterica encodes a type III protein secretion system within a pathogenicity island (SPI-1) that is located at centisome 63 of its chromosome. This system is required for the ability of these bacteria to stimulate cellular responses that are essential for their pathogenicity. Expression of components and substrates of this system is subject to complex regulatory mechanisms. These mechanisms involve the function of HilA and InvF, two transcriptional regulatory proteins encoded within SPI-1. In this study, we examined the functional relationship between these two regulatory proteins. We found that strains carrying loss-of-function mutations in either hilA or invF differ in their ability to stimulate cellular responses. An S. typhimurium hilA mutant strain retained considerable signaling capacity that resulted in significant levels of internalization into host cells. In contrast, introduction of a nonpolar loss-of-function mutation in invF rendered S. typhimurium significantly impaired in its ability to enter host cells. Consistent with these different phenotypes, we found that HilA and InvF control the expression of different genes. HilA regulates the expression of components of the type III secretion machinery, whereas InvF controls the expression of type III secreted proteins encoded outside of SPI-1. We also found that the expression of secreted proteins encoded within SPI-1 are under the control of both HilA and InvF. Our results therefore indicate that InvF and HilA differentially control the expression of components and substrates of the invasion-associated type III secretion system.
Augmented Reality Graph Visualizations (2019)

Three-dimensional node-link diagrams are an important class of visualization for immersive analysis. Yet, there is little knowledge on how to visualize edges to support efficient analysis. We present an exploration of the design space for edge styles and discuss the results of a user study comparing six different edge variants.
Chaotic mixing in microdroplets (2006)

We describe a general methodology for introducing thorough chaotic mixing in microdroplets. The mixing properties of fluid flows in microdroplets are governed by their symmetries, which give rise to invariant surfaces serving as barriers to transport. Complete three-dimensional mixing by chaotic advection requires destruction of all flow invariants. To illustrate this idea, we demonstrate that complete mixing can be obtained in a time-dependent flow produced by moving a microdroplet along a two-dimensional path. The theoretical predictions are confirmed by experiments that use the thermocapillary effect to manipulate microdroplets.
Preservation of endothelium-dependent vascular relaxation in cholesterol-fed rabbit by treatment with the calcium blocker PN 200110. (1986)

We tested the effects of low doses of a dihydropyridine calcium antagonist, PN 200110, on endothelium-dependent vascular relaxation in rabbits fed a 1% cholesterol diet. The drug was given orally, 1 mg/day, and control rabbits received placebo. Plasma total cholesterol after 10 weeks, was similar in the placebo- and PN 200110-treated groups. The respective values averaged 2140 +/- 116 (n = 14; mean +/- SEM) and 2012 +/- 115 mg/dl (n = 13). In placebo-treated rabbits, sudanophilic aortic lesions covered 52 +/- 5% of the intimal surface, and the aortic cholesterol concentration was 72 +/- 6 mg/g protein. Corresponding values in aortas from PN 200110-treated rabbits were significantly lower [36 +/- 5% (P less than 0.03) and 52 +/- 3 mg/g protein (P less than 0.03)]. Maximal endothelium-dependent cholinergic relaxation of aortic strips in untreated (n = 14) and treated cholesterol-fed rabbits (n = 13) differed significantly (P less than 0.01) and averaged 31 +/- 4% and 61 +/- 7% of the value in normocholesterolemic controls (n = 13). We conclude that cholesterol feeding suppresses endothelium-dependent relaxation evoked by acetylcholine, and that PN 200110 reduces the severity of atherosclerosis and impairment of endothelium-dependent relaxation.
Optimization of Chemical Processes by the Hydrodynamic Simulation Method (HSM) (2018)

We describe a hydrodynamic simulation method (HSM) that is based on hydrodynamic considerations in Batch and Semi Batch stirred reactor systems. The method combines hydrodynamic studies of the mixing procedure obtained from experiments in small and large scale stirred reactors together with process simulation by VisiMix software. We describe how this hydrodynamic simulation method can aid in process optimization and scale up. The use of the simulation method described in this article, will offer the user the possibility to achieve the best results during production stage, saving time and currency, and at the same time increasing the knowledge of the performed process. Several examples in the article demonstrate the benefits of the proposed method.
Structural, photophysical and lasing properties of pyrromethene dyes (2005)

The molecular structure and the photophysical properties of pyrromethene-BF2 (PM) dyes are studied with the aim of finding the best structural and environmental conditions which optimize the laser performance of these dyes. To this end, UV–Vis absorption and fluorescence spectra and fluorescence decay curves of several PM dyes are registered in a multitude of solvents with different physicochemical properties and in polymeric solid matrices. Quantum mechanical calculations at different levels are also applied in order to explain the photophysical behaviour of these dyes. The studied pyrromethenes incorporate alkyl (methyl, ethyl and tert-butyl), sulfonate, cyano, and acetoxy- and methacryloyloxy-polymethylene groups in different positions of the chromophore. In the last case, the presence of the polymerizable acryloyl group facilitates the covalent linkage of the chromophore to a polymeric chain, of special technological interest in the development of tunable dye lasers in the solid state. From the experimental results and the theoretical calculations, we discuss different mechanisms of internal conversion for PM dyes, such as the loss in the planarity of the chromophore, the electron flow through the delocalized π-system, the vibrational coupling and the formation of an intramolecular charge transfer state. The present work demonstrates the good correlation between the photophysical and the lasing properties of PM dyes with different structural (substituents) and environmental (solvents and polymers) conditions. Structural, photophysical and lasing properties of pyrromethene dyesAll authorsF. López Arbeloa, J. Bañuelos, V. Martínez, T. Arbeloa & I. López Arbeloahttps://doi.org/10.1080/01442350500270551Published online:22 February 2007Table Download CSVDisplay Table
Image Analysis, Classification, and Change Detection in Remote Sensing (2009)

Demonstrating the breadth and depth of growth in the field since the publication of the popular first edition, Image Analysis, Classification and Change Detection in Remote Sensing, with Algorithms for ENVI/IDL, Second Edition has been updated and expanded to keep pace with the latest versions of the ENVI software environment. Effectively interweav
The RXR ortholog USP suppresses early metamorphic processes in <i>Drosophila</i> in the absence of ecdysteroids (2000)

The steroid hormone 20-hydroxyecdysone (20E) initiates metamorphosis in insects by signaling through the ecdysone receptor complex, a heterodimer of the ecdysone receptor (EcR) and ultraspiracle (USP). Analysis of usp mutant clones in the wing disc of Drosophila shows that in the absence of USP, early hormone responsive genes such as EcR, DHR3 and E75B fail to up-regulate in response to 20E, but other genes that are normally expressed later, such as (&bgr;)-Ftz-F1 and the Z1 isoform of the Broad-Complex (BRC-Z1), are expressed precociously. Sensory neuron formation and axonal outgrowth, two early metamorphic events, also occur prematurely. In vitro experiments with cultured wing discs showed that BRC-Z1 expression and early metamorphic development are rendered steroid-independent in the usp mutant clones. These results are consistent with a model in which these latter processes are induced by a signal arising during the middle of the last larval stage but suppressed by the unliganded EcR/USP complex. Our observations suggest that silencing by the unliganded EcR/USP receptor and the subsequent release of silencing by moderate steroid levels may play an important role in coordinating early phases of steroid driven development.
Frequency of Smad gene mutations in human cancers. (1997)

Much excitement has recently been generated by the discovery of the Smad genes, encoding proteins that transduce signals from the transforming growth factor beta family of cytokines. Here, we report the completion of cloning of the six known human Smads, providing novel sequences for Smad5 and Smad6. Previously, Smad4 and Smad2 were shown to be mutated in human cancers. However, analysis of the other four Smad genes revealed no mutations in a total of 167 tumors, including those from colon, breast, lung, and pancreas. These results suggest that the various Smad genes have different functions and demonstrate that mutations in these four genes do not, in general, account for the widespread resistance to transforming growth factor beta that is found in human tumors.
Nosocomial Transmission of Extensively Drug-Resistant Tuberculosis in a Rural Hospital in South Africa (2012)

The XDR-tuberculosis epidemic in Tugela Ferry, South Africa, has been highly clonal. However, the epidemic is not the result of a point-source outbreak; rather, a high degree of interconnectedness allowed multiple generations of nosocomial transmission. Similar to the outbreaks of multidrug-resistant tuberculosis in the 1990s, poor infection control, delayed diagnosis, and a high HIV prevalence facilitated transmission. Important lessons from those outbreaks must be applied to stem further expansion of this epidemic.
Technetium-99m-sestamibi prone scintimammography to detect primary breast cancer and axillary lymph node involvement. (1995)

This preliminary study confirms the results of some previous reports, which showed the high diagnostic accuracy of scintimammography in detecting breast cancer. This study also shows the potential value of this procedure to detect axillary lymph node involvement as concomitant information.
Mutation detection in the alpha-1 antitrypsin gene (PI) using denaturing gradient gel electrophoresis (2001)

A method for mutation detection in the alpha-1 antitrypsin gene (protease inhibitor 1; PI) has been developed using denaturing gradient gel electrophoresis of PCR amplified gene fragments. Using this experimental approach, all common phenotypes and mutations could be detected. Denaturing gradient gel electrophoresis (DGGE) was compared with standard isoelectric focusing (IEF) in 20 potential alpha1-antitrypsin deficient patients and their relatives. The genotype determined by DGGE was found to be more reliable in some cases than IEF, which is essential for a proper diagnosis of alpha-1 antitrypsin malfunctioning.