gebhart/patrepeval huggingface dataset:
Fictive temperature-independent density and minimum indentation size effect in calcium aluminosilicate glass (2008)

Using the calcium aluminosilicate system a glass was developed that exhibits fictive temperature-independent density by creating an intermediate glass between normal and anomalous glasses. Normal glass, such as soda-lime silicate glass, exhibits decreasing density with increasing fictive temperature while anomalous glass, such as silica glass, exhibits increasing density with increasing fictive temperature. This intermediate glass composition was found to exhibit the minimum indentation size effect during indentation hardness testing. It appears that the indentation size effect is correlated with a deformation-induced fictive temperature increase, which is accompanied by a density change and hardness change in the vicinity of the indentation. It is suggested from these observations that indentation size effect originates from the energy required to create interfaces and defects such as shear bands, subsurface cracks, and point defects near the indenter-specimen boundary, which accompany the volume change.
High-Density Lipoproteins Induce Transforming Growth Factor-β 2 Expression in Endothelial Cells (2005)

Because TGF-beta possesses antiinflammatory properties and stabilizes the plaque, the results of the present work suggest a novel target for the antiatherosclerotic effect of HDL.
RIG-I and Other RNA Sensors in Antiviral Immunity (2018)

Pattern recognition receptors (PRRs) survey intra- and extracellular spaces for pathogen-associated molecular patterns (PAMPs) within microbial products of infection. Recognition and binding to cognate PAMP ligand by specific PRRs initiates signaling cascades that culminate in a coordinated intracellular innate immune response designed to control infection. In particular, our immune system has evolved specialized PRRs to discriminate viral nucleic acid from host. These are critical sensors of viral RNA to trigger innate immunity in the vertebrate host. Different families of PRRs of virus infection have been defined and reveal a diversity of PAMP specificity for wide viral pathogen coverage to recognize and extinguish virus infection. In this review, we discuss recent insights in pathogen recognition by the RIG-I-like receptors, related RNA helicases, Toll-like receptors, and other RNA sensor PRRs, to present emerging themes in innate immune signaling during virus infection.
<title>Development of short-wavelength near-infrared spectral imaging for grain color classification</title> (1999)

Color class of wheat is an important attribute for the identification of cultivars and the marketing of wheat, but is not always easy to measure in the visible spectral range because of variation in vitreosity and surface structure of the kernels. This work examines whether short-wavelength near IR imaging in the range 632-1098 nm can be used to distinguish different cultivars. The spectral characteristics of six hard white winter and hard red spring wheats were first studied by bulk-sample SW-NIR reflectance spectroscopy using regression analysis to select appropriate wavelengths and sets of wavelengths. Prediction of percent red wheat was better if C-H or O-H vibrational overtones were included in the models in addition to the tail from the visible chromophore absorbance, apparently because the vibrational bands make it possible to normalize the color measurement to the dry matter content of the samples. Next, a reflectance spectral image of 640 X 480 spatial pixels and 11 wavelengths was acquired for a mixture of the two contrasting wheat samples using a CCD camera and a liquid crystal tunable filter. The cultivars were distinguished in the image of principal component (PC) score number two that was calculated from the spectral image. The discrimination is due to the tail from the absorbance band that peaks in the visible. PC images 3 and 6 seem to arise mainly from O-H and C-H bands, respectively, and it is speculated that these spectral features will be important for generating multivariate models to predict the color class of grain. It is shown that the contrast between the red-wheat, white- wheat and background can be increased by applying histogram equalization and segmentation of the kernels in the images.
Towards Self-Tuning Parameter Servers (2020)

Recent years, many applications have been driven advances by the use of Machine Learning (ML). Nowadays, it is common to see industrial-strength machine learning jobs that involve millions of model parameters, terabytes of training data, and weeks of training. Good efficiency, i.e., fast completion time of running a specific ML training job, therefore, is a key feature of a successful ML system. While the completion time of a long-running ML job is determined by the time required to reach model convergence, that is also largely influenced by the values of various system settings. In this paper, we contribute techniques towards building self-tuning parameter servers. Parameter Server (PS) is a popular system architecture for large-scale machine learning systems; and by self-tuning we mean while a long-running ML job is iteratively training the expert-suggested model, the system is also iteratively learning which system setting is more efficient for that job and applies it online. Our techniques are general enough to various PS-style ML systems. Experiments on TensorFlow show that our techniques can reduce the completion times of a variety of long-running TensorFlow jobs from 1.4× to 18×.
Human apolipoprotein E: the Alzheimer's disease connection (1996)

Human apolipoprotein (apo) E, long known for its prominent role in cholesterol transport and plasma lipoprotein metabolism, has recently emerged as a major genetic risk factor for Alzheimer's disease, a neurodegenerative disorder. In a variety of populations worldwide, one of the three common alleles of apoE, apoE4, is overrepresented in Alzheimer's subjects compared with age- and sex-matched controls. The genetic and epidemiologic evidence suggests that apoE is a major susceptibility gene for Alzheimer's disease; it likely accounts for a major portion of the genetic heterogeneity in the disease. Although its role in the development of Alzheimer's disease is unknown, biochemical and cell biology studies are providing important insights into how apoE may be involved in neurodegenerative disorders. Based on an understanding of the structure and function of apoE in lipid transport and cellular metabolism, it is suggested that apoE is involved in a final common pathway of neuronal repair and remodeling: apoE3 (most common allele) supporting effective repair and remodeling after neuronal injury by noxious agents, and apoE4 being less effective in these processes.
Metastatic Renal Cell Carcinoma Presenting as a Skin Nodule: Case Report and Review of the Literature (1994)

Cutaneous metastasis from renal cell carcinoma is unusual. A patient is described who presented with a solitary skin metastasis 6 months after unilateral radical nephrectomy for renal cell carcinoma. In most instances, once cutaneous involvement is manifest the disease is widespread and has a poor prognosis. The skin should be examined during tumor evaluation as part of the physical examination and skin lesions in patients with renal cell carcinoma should be evaluated aggressively to rule out cutaneous metastasis.
Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase (2016)

The directed evolution of enzymes promises to eliminate the long-standing limitations of biocatalysis in organic chemistry and biotechnology—the often-observed limited substrate scope, insufficient activity, and poor regioselectivity or stereoselectivity. Saturation mutagenesis at sites lining the binding pocket with formation of focused libraries has emerged as the technique of choice, but choosing the optimal size of the randomization site and reduced amino acid alphabet for minimizing the labor-determining screening effort remains a challenge. Here, we introduce structure-guided triple-code saturation mutagenesis (TCSM) by encoding three rationally chosen amino acids as building blocks in the randomization of large multiresidue sites. In contrast to conventional NNK codon degeneracy encoding all 20 canonical amino acids and requiring the screening of more than 1015 transformants for 95% library coverage, TCSM requires only small libraries not exceeding 200–800 transformants in one library. The triple code utilizes structural (X-ray) and consensus-derived sequence data, and is therefore designed to match the steric and electrostatic characteristics of the particular enzyme. Using this approach, limonene epoxide hydrolase has been successfully engineered as stereoselective catalysts in the hydrolytic desymmetrization of meso-type epoxides with formation of either (R,R)- or (S,S)-configurated diols on an optional basis and kinetic resolution of chiral substrates. Crystal structures and docking computations support the source of notably enhanced and inverted enantioselectivity.
Local oestrogen for vaginal atrophy in postmenopausal women (2006)

Creams, pessaries, tablets and the oestradiol vaginal ring appeared to be equally effective for the symptoms of vaginal atrophy. One trial found significant side effects following cream (conjugated equine oestrogen) administration when compared to tablets causing uterine bleeding, breast pain and perineal pain. Another trial found significant endometrial overstimulation following use of the cream (conjugated equine oestrogen) when compared to the ring. As a treatment choice women appeared to favour the oestradiol-releasing vaginal ring for ease of use, comfort of product and overall satisfaction.
Protective role of tea catechins against oxidation‐induced damage of type 2 diabetic erythrocytes (2005)

1. Oxidative stress is recognized as a major contributing factor for the development of late complications of diabetes. 2. Tea contains polyphenolic compounds (catechins), which have many important biological properties, including strong anti-oxidant activity. 3. The present study was undertaken to evaluate the effect of tea catechins (epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC)) on markers of oxidative stress (malondialdehyde (MDA), reduced glutathione (GSH) and membrane -SH group) in erythrocytes from type 2 diabetics. 4. Oxidative stress was induced in normal and type 2 diabetic erythrocytes by incubating with tert-butyl hydroperoxide (t-BHP). 5. Diabetic erythrocytes have higher MDA and decreased GSH and membrane -SH groups compared with normal erythrocytes. 6. Our results show that tea catechins protect erythrocytes from t-BHP-induced oxidative stress, the effect being more pronounced in diabetic erythrocytes. The relative effectiveness of individual catechins are in the order of EGCG>ECG>EGC>EC. 7. We hypothesise that a higher intake of catechin-rich food by diabetic patients may provide some protection against the development of long-term complications of diabetes.
Vascular dementia (1993)

Criteria for the diagnosis of vascular dementia (VaD) that are reliable, valid, and readily applicable in a variety of settings are urgently needed for both clinical and research purposes. To address this need, the Neuroepidemiology Branch of the National Institute of Neurological Disorders and Stroke (NINDS) convened an International Workshop with support from the Association Internationale pour la Recherche et l'Enseignement en Neurosciences (AIREN), resulting in research criteria for the diagnosis of VaD. Compared with other current criteria, these guidelines emphasize (1) the heterogeneity of vascular dementia syndromes and pathologic subtypes including ischemic and hemorrhagic strokes, cerebral hypoxic-ischemic events, and senile leukoencephalopathic lesions; (2) the variability in clinical course, which may be static, remitting, or progressive; (3) specific clinical findings early in the course (eg, gait disorder, incontinence, or mood and personality changes) that support a vascular rather than a degenerative cause; (4) the need to establish a temporal relationship between stroke and dementia onset for a secure diagnosis; (5) the importance of brain imaging to support clinical findings; (6) the value of neuropsychological testing to document impairments in multiple cognitive domains; and (7) a protocol for neuropathologic evaluations and correlative studies of clinical, radiologic, and neuropsychological features. These criteria are intended as a guide for case definition in neuroepidemiologic studies, stratified by levels of certainty (definite, probable, and possible). They await testing and validation and will be revised as more information becomes available.
Heparin binding to protein C inhibitor. (1992)

Protein C inhibitor is a plasma protein whose ability to inhibit activated protein C, thrombin, and other enzymes is stimulated by heparin. These studies were undertaken to further understand how heparin binds to protein C inhibitor and how it accelerates proteinase inhibition. The region of protein C inhibitor from residues 264-283 was identified as the heparin-binding site. This differs from the putative heparin-binding site in the related proteins antithrombin and heparin cofactor. The glycosaminoglycan specificity of protein C inhibitor was relatively broad, including heparin and heparan sulfate, but not dermatan sulfate. Non-sulfated and non-carboxylated polyanions also enhanced proteinase inhibition by protein C inhibitor. Heparin accelerated inhibition of alpha-thrombin, gamma T-thrombin, activated protein C, factor Xa, urokinase, and chymotrypsin, but not plasma kallikrein. The ability of glycosaminoglycans to accelerate proteinase inhibition appeared to depend on the formation of a ternary complex of inhibitor, proteinase, and glycosaminoglycan. The optimum heparin concentration for maximal rate stimulation varied from 10 to 100 micrograms/ml and was related to the apparent affinity of the proteinase for heparin. There was no obvious relationship between heparin affinity and maximum inhibition rate or degree of rate enhancement. The affinity of the resultant protein C inhibitor-proteinase complex was also not related to inhibition rate enhancement, and the results showed that decreased heparin affinity of the complex is not an important part of the catalytic mechanism of heparin. The importance of protein C inhibitor as a regulator of the protein C system may depend on the relatively large increase in heparin-enhanced inhibition rate for activated protein C compared to other proteinases.
Novel DNA materials and their applications (2010)

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.
On the Front Line: Quantitative Virus Dynamics in Honeybee (Apis mellifera L.) Colonies along a New Expansion Front of the Parasite Varroa destructor (2014)

Over the past fifty years, annual honeybee (Apis mellifera) colony losses have been steadily increasing worldwide. These losses have occurred in parallel with the global spread of the honeybee parasite Varroa destructor. Indeed, Varroa mite infestations are considered to be a key explanatory factor for the widespread increase in annual honeybee colony mortality. The host-parasite relationship between honeybees and Varroa is complicated by the mite's close association with a range of honeybee viral pathogens. The 10-year history of the expanding front of Varroa infestation in New Zealand offered a rare opportunity to assess the dynamic quantitative and qualitative changes in honeybee viral landscapes in response to the arrival, spread and level of Varroa infestation. We studied the impact of de novo infestation of bee colonies by Varroa on the prevalence and titres of seven well-characterised honeybee viruses in both bees and mites, using a large-scale molecular ecology approach. We also examined the effect of the number of years since Varroa arrival on honeybee and mite viral titres. The dynamic shifts in the viral titres of black queen cell virus and Kashmir bee virus mirrored the patterns of change in Varroa infestation rates along the Varroa expansion front. The deformed wing virus (DWV) titres in bees continued to increase with Varroa infestation history, despite dropping infestation rates, which could be linked to increasing DWV titres in the mites. This suggests that the DWV titres in mites, perhaps boosted by virus replication, may be a major factor in maintaining the DWV epidemic after initial establishment. Both positive and negative associations were identified for several pairs of viruses, in response to the arrival of Varroa. These findings provide important new insights into the role of the parasitic mite Varroa destructor in influencing the viral landscape that affects honeybee colonies.
The lipofuscin fluorophore A2E mediates blue light-induced damage to retinal pigmented epithelial cells. (2000)

These studies implicate A2E as an initiator of blue light-induced apoptosis of RPE cells.
Medical Corpora Comparison Using Topic Modeling (2020)

Free-form texts from electronic medical records are often used to build predictive models for medical and healthcare processes. In different medical centers, treatment of patients and other healthcare processes can occur in different ways according to the hospital's internal protocols, which affects the structure of electronic medical records and the style of free-form texts. The paper aim is to compare two medical corpora in content to understand whether trained models of the first corpora apply to the second corpora. The approach contains topic modeling, topic segmentation, topic cross-segmentation and specific metric Topic Segmentation Collation to compare cross-segmentation results. Also, the results of the word-level analysis for both corpora are provided. We conclude each of the corpora needs different word-level processing and has a specific set of descriptions, which limits the use of predictive models for some diseases.
The Talin Head Domain Binds to Integrin β Subunit Cytoplasmic Tails and Regulates Integrin Activation (1999)

The beta subunit cytoplasmic domains of integrin adhesion receptors are necessary for the connection of these receptors to the actin cytoskeleton. The cytoplasmic protein, talin, binds to beta integrin cytoplasmic tails and actin filaments, hence forming an integrin-cytoskeletal linkage. We used recombinant structural mimics of beta(1)A, beta(1)D and beta(3) integrin cytoplasmic tails to characterize integrin-binding sites within talin. Here we report that an integrin-binding site is localized within the N-terminal talin head domain. The binding of the talin head domain to integrin beta tails is specific in that it is abrogated by a single point mutation that disrupts integrin localization to talin-rich focal adhesions. Integrin-cytoskeletal interactions regulate integrin affinity for ligands (activation). Overexpression of a fragment of talin containing the head domain led to activation of integrin alpha(IIb)beta(3); activation was dependent on the presence of both the talin head domain and the integrin beta(3) cytoplasmic tail. The head domain of talin thus binds to integrins to form a link to the actin cytoskeleton and can thus regulate integrin function.
Halftone to continuous-tone conversion of error-diffusion coded images (1993)

The problem of reconstructuring a continuous-tone (cotone) image from its error-diffused halftoned version is presented. The authors present a POCS (projection onto convex sets)-based iterative nonlinear algorithm for this problem, and show simulation results that compare the performance of the algorithm with that of conventional linear lowpass filtering. It is found that the proposed technique results in subjectively superior reconstruction. As there is a natural relationship between error diffusion and sigma-delta modulation, the proposed reconstruction algorithm can also be applied to the decoding problem for sigma-delta modulators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heat shock protein 60 enhances CD4+ CD25+ regulatory T cell function via innate TLR2 signaling (2006)

CD4+CD25+ Tregs regulate immunity, but little is known about their own regulation. We now report that the human 60-kDa heat shock protein (HSP60) acts as a costimulator of human Tregs, both CD4+CD25int and CD4+CD25hi. Treatment of Tregs with HSP60, or its peptide p277, before anti-CD3 activation significantly enhanced the ability of relatively low concentrations of the Tregs to downregulate CD4+CD25- or CD8+ target T cells, detected as inhibition of target T cell proliferation and IFN-gamma and TNF-alpha secretion. The enhancing effects of HSP60 costimulation on Tregs involved innate signaling via TLR2, led to activation of PKC, PI3K, and p38, and were further enhanced by inhibition of ERK. HSP60-treated Tregs suppressed target T cells both by cell-to-cell contact and by secretion of TGF-beta and IL-10. In addition, the expression of ERK, NF-kappaB, and T-bet by downregulated target T cells was inhibited. Thus, HSP60, a self-molecule, can downregulate adaptive immune responses by upregulating Tregs innately through TLR2 signaling.
How a Cytokine Is Chaperoned through the Secretory Pathway by Complexing with Its Own Receptor: Lessons from Interleukin-15 (IL-15)/IL-15 Receptor α (2008)

While it is well appreciated that receptors for secreted cytokines transmit ligand-induced signals, little is known about additional roles for cytokine receptor components in the control of ligand transport and secretion. Here, we show that interleukin-15 (IL-15) translocation into the endoplasmic reticulum occurs independently of the presence of IL-15 receptor alpha (IL-15R alpha). Subsequently, however, IL-15 is transported through the Golgi apparatus only in association with IL-15R alpha and then is secreted. This intracellular IL-15/IL-15R alpha complex already is formed in the endoplasmic reticulum and, thus, enables the further trafficking of complexed IL-15 through the secretory pathway. Just transfecting IL-15R alpha in cells, which transcribe but normally do not secrete IL-15, suffices to induce IL-15 secretion. Thus, we provide the first evidence of how a cytokine is chaperoned through the secretory pathway by complexing with its own high-affinity receptor and show that IL-15/IL-15R alpha offers an excellent model system for the further exploration of this novel mechanism for the control of cytokine secretion.