gebhart/patrepeval huggingface dataset:
Urine Cytokines as biomarkers in COVID‐19 Patients (2021)

Introduction COVID‐19 pandemic has been one of the main global health concerns in 2020, and many aspects of the disease remain enigmatic. While some patients infected with the disease‐causing virus SARS‐CoV2 have no or mild symptoms, others experience severe symptoms requiring hospitalization. Of these more severe patients, some remain stable while others experience cytokine storm syndrome or an exaggerated immune response that has been correlated with disease severity and progression of acute respiratory deterioration. It is currently unknown why some patients with COVID‐19 demonstrate this response and others do not. In light of the apparent prominent role of the inflammatory mediators (i.e. cytokines) in COVID‐19 pathogenesis, the ability to identify screening tools not only for the SARS‐CoV2 virus but also for cytokines is important. The present investigation was designed to identify the urinary cytokine signature in COVID‐19 patients. Methods The study enrolled 17 COVID‐19 patients and 10 control subjects (SARS‐CoV‐2 negative) 18 years or older with glomerular filtration rate of &gt; 60mL/min. Urine samples were collected and cytokines quantitated using the Luminex multiplex assay. The cytokines analyzed were growth‐regulated oncogene (GRO), interleukin‐8 (IL‐8), and interleukin‐6 (IL‐6). Results The levels of GRO and IL‐6 were significantly elevated in urine samples obtained from COVID‐19 patients compared to controls (mean 16.8 pg/ml vs. 9.2 pg/ml ± 2.39, p &lt; 0.0171 and mean 16.8 pg/ml vs 9.2 pg/ml ± 2.42, p &lt; 0.0157, respectively). Conversely, IL‐8 level was similar between COVID‐19 patients and controls (15.6 pg/ml vs 11.3 pg/ml ± 1.3, p&lt;0.1833). Conclusion The present investigation found that the levels of urinary cytokines GRO and IL‐6 were significantly elevated in COVID‐19 patients compared to controls and may serve as urinary biomarkers of disease progression. Furthermore, IL‐8 although elevated in COVID‐19 patients, did not reach statistical significance in our population sample. The findings of this proof of concept study underscore that the urinary cytokines may serve as prognostic and diagnostic accessible biomarkers in COVID‐19.
Recognizing Sights, Smells, and Sounds with Gnostic Fields (2013)

Mammals rely on vision, audition, and olfaction to remotely sense stimuli in their environment. Determining how the mammalian brain uses this sensory information to recognize objects has been one of the major goals of psychology and neuroscience. Likewise, researchers in computer vision, machine audition, and machine olfaction have endeavored to discover good algorithms for stimulus classification. Almost 50 years ago, the neuroscientist Jerzy Konorski proposed a theoretical model in his final monograph in which competing sets of "gnostic" neurons sitting atop sensory processing hierarchies enabled stimuli to be robustly categorized, despite variations in their presentation. Much of what Konorski hypothesized has been remarkably accurate, and neurons with gnostic-like properties have been discovered in visual, aural, and olfactory brain regions. Surprisingly, there have not been any attempts to directly transform his theoretical model into a computational one. Here, I describe the first computational implementation of Konorski's theory. The model is not domain specific, and it surpasses the best machine learning algorithms on challenging image, music, and olfactory classification tasks, while also being simpler. My results suggest that criticisms of exemplar-based models of object recognition as being computationally intractable due to limited neural resources are unfounded.
ChemInform Abstract: Total Synthesis of 3‐Chloro‐3‐deoxy‐1‐O‐(1,2‐di‐O‐palmitoyl‐sn‐glycero‐ 3‐phospho)‐D‐myo‐inositol. A Potential Mechanistic Probe for Phosphoinositide Signal Transduction Pathways. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Concurrent design and analysis of the Navigator wearable computer system: the thermal perspective (1995)

This paper describes the concurrent design of a wearable computer, called the Navigator, developed and built at Carnegie Mellon University in a multidesigner, multidomain environment. The design effort for the Navigator involved nineteen designers, representing the disciplines of electrical engineering, industrial design, mechanical engineering, software engineering, and human-computer interaction. The concurrent design framework developed by the Navigator design team is outlined and the parallel activities within each design phase are described, including the synchronization and interactions among all design disciplines at the phase boundaries. The evolution of the interdisciplinary design of the Navigator wearable computer is presented, with particular emphasis placed upon the role of the thermal design group in the overall design process. Furthermore, the particular challenges associated with the concurrent thermal management of wearable computer systems are outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Neue Materialien für Flüssigkristallanzeigen: Struktur‐Eigenschafts‐Beziehungen bei 2‐Fluorpyridinen (1994)

Die Synergie von Theorie und Experiment besteht auch bei Flüssigkristallen . Durch vergleichsweise einfache Rechungen kann der unerwartete Einfluß einer Alkoxygruppe auf das Dipolmoment eines Flüssigkristalle bildenden Moleküls wie 1 erklärt werden. Damit ist zugleich der Weg zu effizienten Synthesen neuer Materialien für Flüssigkristallanzeigen gewiesen. magnified image
Surface magnetic structure of epitaxial magnetite thin films grown on MgO(001) (2009)

The crystallographic structure of antiphase domain boundaries (APBs) and the magnetic structure of large domains of magnetite (Fe3O4) thin films, which were epitaxially grown on MgO(001) substrates and annealed in an ambient condition, were investigated by scanning tunneling microscopy (STM), transmission electron microscopy (TEM), magnetic force microscopy (MFM), and scanning electron microscopy with polarization analysis (SEMPA). STM and TEM showed the morphology of the APBs in film surfaces and the bulk, whereas MFM and SEMPA showed the magnetic structure of the surfaces. As in previous paper reported by another group, STM and TEM observations revealed the antiphase domains on a scale from tens of nanometers to a few hundred nanometers. Also MFM measurement showed the magnetic domains on a scale of a few hundred nanometers and large-scale undulations of a few micrometers. Our SEMPA observations of the films displayed large-scale magnetic structures on a scale of a few hundred nanometers to a few micrometers. These large-scale magnetic structures are expected to be induced by the enlargement of magnetic domains that contain magnetic moments aligned along a magnetic easy axis. These moments have in-plane components that make the SEMPA images visible. An air-annealing process is needed to change magnetic couplings in APBs and to form large-scale magnetic ordering.
Front Cover: Organellar Omics – A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell (2018)

DOI: 10.1002/pmic.201700113 The cover art represents the experimental workflow to analyse the biomolecular composition of purified plasma membranes and lysosomes. The methodology is based on the use of superparamagnetic iron oxide nanoparticles (SPIONs) with different functionalized groups. Aminolipid-coated SPIONs are targeted to the cell surface while DMSA-coated SPIONs are taken up by cells and chased to lysosomes. Magnetically isolated compartments are compatible for subsequent proteome and lipidome analysis. In their review, article number 1700113, Tharkeshwar, Gevaert and Annaert go more deep into the different available strategies for subcellular omics analysis.
Multi‐information source Bayesian optimization of culture media for cellular agriculture (2022)

Culture media used in industrial bioprocessing and the emerging field of cellular agriculture is difficult to optimize due to the lack of rigorous mathematical models of cell growth and culture conditions, as well as the complexity of the design space. Rapid growth assays are inaccurate yet convenient, while robust measures of cell number can be time-consuming to the point of limiting experimentation. In this study, we optimized a cell culture media with 14 components using a multi-information source Bayesian optimization algorithm that locates optimal media conditions based on an iterative refinement of an uncertainty-weighted desirability function. As a model system, we utilized murine C2C12 cells, using AlamarBlue, LIVE stain, and trypan blue exclusion cell counting assays to determine cell number. Using this experimental optimization algorithm, we were able to design media with 181% more cells than a common commercial variant with a similar economic cost, while doing so in 38% fewer experiments than an efficient design-of-experiments method. The optimal medium generalized well to long-term growth up to four passages of C2C12 cells, indicating the multi-information source assay improved measurement robustness relative to rapid growth assays alone.
Association between early carotid artery plaque presence, vascular strain imaging features and traditional cardiovascular risk factors in HIV infected individuals (2021)

A machine learning classification model was used to discriminate subjects with and without carotid artery plaques in a population of HIV -positive and -negative individuals with low-to-intermediate cardiovascular risks. The aim was to identify associations between the presence of plaques and features consisting of traditional cardiovascular risk factors and strain elastography in normal sections of the common carotid artery. One hundred and two HIV-infected and 84 age-matched control subjects were recruited from a prospective, controlled cohort study (mean age 57 years ± 8 years; 159 men). Plaques, defined as an intima-media thickness (IMT) greater than 1 mm, were identified on ultrasound images in longitudinal views of the common and internal carotid arteries. A classification task of identifying subjects with presence of plaque was defined using a random forests model. Six strain features on normal CCA in addition to 21 clinical biomarkers and clinical ultrasound imaging features* were selected as inputs in the classification model. The 5 most discriminant combinations of features had ROC-AUCs between 0.76 and 0.80.
IL-21 Receptor signaling by B-cells is essential for BXSB-Yaa pathogenesis (99.39) (2009)

Abstract IL-21 is a member of the IL-2 cytokine family that exerts potent biological effects on multiple hemopoietic cell types. It is produced by activated CD4 T cells, while its receptor, IL-21R, is found on cells including NK cells, dendritic, T cells and B cells. To investigate the role of IL-21 signaling in autoimmune disease, we addressed whether this cytokine contributes to the severe systemic lupus erythematosus (SLE)-like syndrome developed by BXSB-Yaa mice. We show that BXSB-Yaa CD4 T cells produce IL-21 but lack discriminative T follicular helper cell markers. We also show that BXSB-Yaa mice completely lacking the IL-21R or Igh6 are remarkably resistant to multiple aspects of the prototypic BXSB-Yaa autoimmune disease. Finally, we show that mixed bone marrow chimeric BXSB-Yaa mice lacking IL-21R specifically in the B-cell compartment are similarly resistant. These results suggest that IL-21 produced by a novel population of BXSB-Yaa CD4 T-cells acts through B-cells to evoke multiple features characteristic of severe SLE. The results indicate that IL-21 signaling through B-cells is an essential step in the pathogenesis of this SLE-like autoimmune disease and potentially others. Funded by an Arthritis Foundation grant to JB.
Helicity (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
Local Immune Control of Latent Herpes Simplex Virus Type 1 in Ganglia of Mice and Man (2021)

Herpes simplex virus type 1 (HSV-1) is a prevalent human pathogen. HSV-1 genomes persist in trigeminal ganglia neuronal nuclei as chromatinized episomes, while epithelial cells are typically killed by lytic infection. Fluctuations in anti-viral responses, broadly defined, may underlay periodic reactivations. The ganglionic immune response to HSV-1 infection includes cell-intrinsic responses in neurons, innate sensing by several cell types, and the infiltration and persistence of antigen-specific T-cells. The mechanisms specifying the contrasting fates of HSV-1 in neurons and epithelial cells may include differential genome silencing and chromatinization, dictated by variation in access of immune modulating viral tegument proteins to the cell body, and protection of neurons by autophagy. Innate responses have the capacity of recruiting additional immune cells and paracrine activity on parenchymal cells, for example <i>via</i> chemokines and type I interferons. In both mice and humans, HSV-1-specific CD8 and CD4 T-cells are recruited to ganglia, with mechanistic studies suggesting active roles in immune surveillance and control of reactivation. In this review we focus mainly on HSV-1 and the TG, comparing and contrasting where possible observational, interventional, and <i>in vitro</i> studies between humans and animal hosts.
Flexible and Cognitive Radio Access Technologies for 5G and Beyond (2020)

Standards for 5G and beyond will require communication systems with a much more flexible and cognitive design to support a wide variety of services including smart vehicles, smart cities, smart homes, IoTs, and remote health. Although future 6G technologies may look like an extension of their 5G counterparts, new user requirements, completely new applications and use-cases, and networking trends will bring more challenging communication engineering problems. New communication paradigms in different layers will be required, in particular in the physical layer of future wireless communication systems. This comprehensive book is intended to be both a tutorial on flexible and cognitive radio access technologies for 5G and beyond and an advanced overview for technical professionals and managers in the communications industry, as well as researchers in academia and industry. The authors cover enabling radio access technologies for 5G and beyond, not only from a standard specific angle (like 5G) but also by considering future trends beyond 5G. Rather than specific standard implementations, the book covers a wide variety of technologies and their uses. The presentations are both descriptive and mathematical in nature to cater to readers who need mathematical description as well as readers who do not. The book is written at a level suited to readers who already have a background in electrical engineering and basic wireless communications.
Existe-t-il encore une gestion municipale « de droite » et « de gauche » ? (Interview) (2014)

Premier paragraphe :\nQuelle grande ville aujourd’hui n’a pas son tramway, son centre piéton, ses vélos en libre-service ou encore son « écoquartier » ?\nSi les clivages politiques continuent à peser sur les élections municipales, la gestion des communes, elle, est marquée par le pragmatisme des élus et une uniformisation des pratiques.
A Survey of Feature Set Reduction Approaches for Predictive Analytics Models in the Connected Manufacturing Enterprise (2019)

The broad context of this literature review is the connected manufacturing enterprise, characterized by a data environment such that the size, structure and variety of information strain the capability of traditional software and database tools to effectively capture, store, manage and analyze it. This paper surveys and discusses representative examples of existing research into approaches for feature set reduction in the big data environment, focusing on three contexts: general industrial applications; specific industrial applications such as fault detection or fault prediction; and data reduction. The conclusion from this review is that there is room for research into frameworks or approaches to feature filtration and prioritization, specifically with respect to providing quantitative or qualitative information about the individual features in the dataset that can be used to rank features against each other. A byproduct of this gap is a tendency for analysts not to holistically generalize results beyond the specific problem of interest, and, related, for manufacturers to possess only limited knowledge of the relative value of smart manufacturing data collected.
On the Three-Finger Protein Domain Fold and CD59-Like Proteins in Schistosoma mansoni (2013)

Our results suggest that this group of proteins belongs to the TFPD superfamily. Their expression is associated to intra-host stages, present in the tegument surface, and also in intra-parasite tissues. Three distinct approaches using SmCD59 proteins to inhibit complement strongly suggested that these proteins are not complement inhibitors and their function in schistosomes remains to be determined.
Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data (2009)

miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex.
High Interrupting Capacity Equipment for Hazardous Locations (1997)

There are numerous methods of handling high fault currents in the modern industrial facility. When it comes to hazardous locations, however, questions abound as to the equipment and systems required to survive these conditions without causing ignition of the surrounding atmosphere. Many opinions, and in some cases misconceptions, exist over what actually is suitable for such an application. Two alternatives are presented here; one using a system approach, the other regarding explosion-proof equipment designed for this application.
An in vivo model of degenerative disc disease (2002)

Although the precise etiology of low back pain is disputed, degeneration of the intervertebral disc is believed to play an important role. Many animal models have been described which reproduce the changes found in degenerative disc disease, but none allow for efficient, large-scale testing of purported therapeutic agents. The purpose of this study was to develop a simple animal model resembling degenerative disc disease using the intervertebral discs found in the tails of rats. The proximal two intervertebral discs in the tails of 20 rats were injected with either chondroitinase ABC or control (phosphate buffered saline, PBS). The tails were harvested at 2 weeks, and measurements were made of intervertebral disc height (measured radiographically and histologically), biomechanics (stiffness, hysteresis, and residual deformation), and histologic appearance. Treatment with chondroitinase ABC resulted in a significant loss in intervertebral disc height (radiographic intervertebral disc height, p=0.001; histologic intervertebral disc height, p<0.001) and significant increases in all biomechanical parameters (stiffness, p<0.001; hysteresis, p=0.006; residual deformation, p=0.004) compared to PBS controls. Intervertebral discs treated with chondroitinase ABC had significantly lower histologic grades for each grading category (nucleus pulposus (NP), annulus fibrosus, and proteoglycan staining) compared to controls. The results of injury with chondroitinase ABC were similar to the findings in degenerative disc disease: reduced intervertebral disc height, diminished proteoglycan content, loss of NP cells, and increased stiffness of the disc. Thus, the model appears to be a reasonable tool for the preliminary in vivo evaluation of proposed treatments for degenerative disc disease.
Novel liver-specific TORC2 siRNA corrects hyperglycemia in rodent models of type 2 diabetes (2009)

The transcription factor TORC2 [transducer of regulated cAMP-responsive element-binding protein (CREB) activity 2] is a major regulator of hepatic gluconeogenesis and is increased in hyperglycemic rodent models. Because chronic hyperglycemia and increased hepatic glucose production, via increased gluconeogenesis, is a key feature of type 2 diabetes, an effective in vivo method to efficiently knock down TORC2 could provide a potential therapy for treating hyperglycemia and type 2 diabetes. To assess this, primary mouse hepatocytes, high-fat diet (HFD)-fed mice, and Zucker diabetic fatty (ZDF) rats were treated with a siRNA against TORC2 (siTORC2), which was delivered via a novel lipid nanoparticle system, or control siRNA (siCON). Compared with siCON, administration of siTORC2 resulted in highly efficient, sustained (1-3 wk) knockdown of TORC2 and its gluconeogenic target genes phosphoenolpyruvate carboxykinase and glucose-6-phophatase in primary mouse hepatocytes and in the livers of HFD-fed mice. In mice, this knockdown was specific to the liver and did not occur in kidney, skeletal muscle, or adipose tissue. In HFD-fed mice, siTORC2 reduced in vivo gluconeogenic capacity, fasting hepatic glucose production, and hyperglycemia, and led to improved hepatic and skeletal muscle insulin sensitivity. siTORC2 treatment also improved systemic hyperglycemia in ZDF rats. In conclusion, these results demonstrate the importance of TORC2 in modulating HGP in vivo and highlight a novel, liver-specific siRNA approach for the potential treatment of hyperglycemia and type 2 diabetes.
Copper-Mediated Selective Removal of Nitrification Inhibitors from Industrial Wastewaters (1998)

Current efforts to upgrade wastewater treatment plants focus on biological N and P removal. N removal is often limited by the rate of nitrification, which is sensitive to low concentrations of specific inhibitors present in industrial effluents. Many known nitrification inhibitors act by complexing the copper enzyme ammonium monooxygenase and can be counteracted via Cu(II) addition. We found here, using both a batch inhibition test and bench-scale semi-continuous activated sludge reactors, that the inhibition of nitrification with four industrial wastewaters was greatly reduced when Cu(II) was added and that Cu(I) or even particulate Cu(0) were at times the most effective forms. Conventional remedial additives, such as activated carbon or zeolite, were not effective. Because direct Cu(II) addition would lead to undesirable contamination of waste-activated sludge, a pretreatment process using reusable surface-immobilized forms of copper was sought. Surface-immobilized copper [e.g., particulate Cu(0), Cu(II)-loaded chelating resins] was more efficient than soluble Cu(II) in detoxifying an industrial effluent and model inhibitor solution; XPS analysis suggests a surface complexation mechanism. The immobilized copper phases can be reused repeatedly in a pretreatment contact unit and regenerated upon saturation.
Charge Density Dependent Mobility of Organic Hole‐Transporters and Mesoporous TiO2 Determined by Transient Mobility Spectroscopy: Implications to Dye‐Sensitized and Organic Solar Cells (2013)

Transient mobility spectroscopy (TMS) is presented as a new tool to probe the charge carrier mobility of commonly employed organic and inorganic semiconductors over the relevant range of charge densities. The charge density dependence of the mobility of semiconductors used in hybrid and organic photovoltaics gives new insights into charge transport phenomena in solid state dye sensitized solar cells.