gebhart/patrepeval huggingface dataset:
Omics Driven Understanding of the Intestines of Parasitic Nematodes (2019)

The biological and molecular complexity of nematodes has impeded research on development of new therapies for treatment and control. We have focused on the versatility of the nematode intestine as a target for new therapies. To that end, it is desirable to establish a broad and deep understanding of the molecular architecture underlying intestinal cell functions at the pan-Nematoda level. Multiomics data were generated to uncover the evolutionary principles underlying both conserved and adaptable features of the nematode intestine. Whole genomes were used to reveal the functional potential of the nematodes, tissue-specific transcriptomes provided a deep assessment of genes that are expressed in the adult nematode intestine, and comparison of selected core species was used to determine a first approximation of the pan-Nematoda intestinal transcriptome. Differentially expressed transcripts were also identified among intestinal regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. Profiling intestinal miRNAs targeting these genes identified the conserved intestinal miRNAs. Proteomics of intestinal cell compartments assigned proteins to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). Finally, advanced bioinformatic approaches were used to predict intestinal cell functional categories of seminal importance to parasite survival, which can now be experimentally tested and validated. The data provide the most comprehensive compilation of constitutively and differentially expressed genes, predicted gene regulators, and proteins of the nematode intestine. The information provides knowledge that is essential to understand molecular features of nematode intestinal cells and functions of fundamental importance to the intestine of many, if not all, parasitic nematodes.
Overexpression of Par‐4 enhances thapsigargin‐induced apoptosis via down‐regulation of XIAP and inactivation of Akt in human renal cancer cells (2007)

The prostate-apoptosis-response-gene-4 (Par-4) protein has been shown to function as an effector of cell death in response to various apoptotic stimuli that trigger mitochondria and membrane receptor-mediated cell death pathways. We found that overexpressing Par-4 by stable transfection sensitizes Caki cells to induction of apoptosis by TRAIL and drugs that induce endoplasmic reticulum (ER) stress [thapsigargin (TG), tunicamycin (TU) and etoposide]. Ectopic expression of Par-4 is associated with decreased levels of XIAP protein in TG-treated cells, caused in part by XIAP protein instability and caspase activation. Levels of phospho-Akt are decreased in Caki/Par-4 cells to a significantly greater extent than in Caki/Vector cells by treatment with TG, and this is in turn associated with decreased levels of phospho-PDK1, the kinase upstream of Akt. In conclusion, we provide evidence that ectopic expression of Par-4 sensitizes Caki cells to TG and that XIAP protein instability and inactivation of Akt are important in cellular pathways affected by Par-4.
ChemInform Abstract: The First Formal Asymmetric Synthesis of Phorbol. (1997)

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.
Effect of Bupivacaine on Cultured Tenocytes (2009)

Proliferation of cultured human fibroblasts and other types of cells has been shown to be hindered by exposure to local anesthetics, which are widely used in musculoskeletal medicine for their use in regional anesthesia, selective nerve blocks, bursography, and brisement. We hypothesized that bupivacaine would decrease cell proliferation and production of extracellular matrix components collagen and proteoglycan in healthy human tenocytes in culture. Primary human tenocyte cultures were prepared from samples of normal tendons obtained from healthy tissue that would otherwise have been discarded during lower extremity tendon transfer surgery. Samples were obtained from 6 patients, 5 women and 1 man with an average age of 69 years (range, 17-73 years). Five flexor digitorum longus tendon samples and 1 peroneus longus tendon sample were used. Harvested tendon tissues (5 mm(3)) were used as explants for primary cell cultures. To measure the proliferative response to bupivacaine, seeded cells were exposed to saline control or to various concentrations of bupivacaine in 1% fetal bovine serum DMEM/F12 or 10% fetal bovine serum DMEM/F12. The 1% fetal bovine serum medium demonstrated the pure bupivacaine effect, and 10% fetal bovine serum more closely approximated the in vivo environment. Seeded cells were starved of fetal bovine serum for 12 hours before exposure to phosphate-buffered saline (control group) and 500 microM bupivacaine (experimental group). This concentration of bupivacaine was selected because it was found to significantly hinder proliferation in both the 1% and 10% fetal bovine serum groups in our proliferation assay. Tenocyte proliferation and extracellular matrix component production were significantly lower (P<or=.05) at >or=1 time points up to 6 days in bupivacaine-treated groups as compared with controls.
Adapting the innate immune system to develop long-lived vaccines to bacterial pathogens (2017)

Abstract There is an urgent need to develop vaccines against bacteria due to the rise of Multi-drug resistant (MDR &amp; XDR) organisms. To date, it has been difficult to produce protective vaccines against bacterial pathogens; there is a danger of outgrowth of fast growing attenuated bacterial strains while polysaccharide cell walls are poorly immunogenic and subunit vaccines are ineffective, generating TI (T-independent) immune responses, characterized by low affinity, short lived, non-class switched IgM antibodies. We are developing technologies for generating vaccines in mice against multiple pathogen species, including bacterial; MDR E. coli, MRSA, MTb LAM, Viral; HIV gp120, parasitic; P. falciparum and fungal; C. albicans. We capture pathogens using FcMBL Opsonin technology (which binds more than 90 different pathogen species), and present the killed pathogens in an immune modulating biomaterial system. This lyophilized product provides long-lasting protection with a single dose through a novel self-boosting mechanism of action. Our vaccines can protect mice against MDR strains of E. coli which are lethal within 12 hours. We have raised antibodies with titers which are sustained beyond 90 days (to date) with a single vaccination (the biomaterial system has demonstrated titers beyond 1 year in other indications). Using this opsonin and immune modulating technology, E. coli can be captured from the blood and tissues of one animal and used to vaccinate other animals.
S-049 (2012)

Gribble, Matthew O; Howard, Barbara V; Umans, Jason G; Shara, Nawar M; Francesconi, Kevin A; Walter, Goessler; Crainiceanu, Ciprian; Silbergeld, Ellen K; Guallar, Eliseo; Navas-Acien, Ana Author Information
"Sometime" is sometimes "not never" (1980)

Pnueli [15] has recently introduced the idea of using temporal logic [18] as the logical basis for proving correctness properties of concurrent programs. This has permitted an elegant unifying formulation of previous proof methods. In this paper, we attempt to clarify the logical foundations of the application of temporal logic to concurrent programs. In doing so, we will also clarify the relation between concurrency and nondeterminism, and identify some problems for further research.In this paper, we consider logics containing the temporal operators "henceforth" (or "always") and "eventually" (or "sometime"). We define the semantics of such a temporal logic in terms of an underlying model that abstracts the fundamental concepts common to almost all the models of computation which have been used. We are concerned mainly with the semantics of temporal logic, and will not discuss in any detail the actual rules for deducing theorems.We will describe two different temporal logics for reasoning about a computational model. The same formulas appear in both logics, but they are interpreted differently. The two interpretations correspond to two different ways of viewing time: as a continually branching set of possibilities, or as a single linear sequence of actual events. The temporal concepts of "sometime" and "not never" ("not always not") are equivalent in the theory of linear time, but not in the theory of branching time -- hence, our title. We will argue that the logic of linear time is better for reasoning about concurrent programs, and the logic of branching time is better for reasoning about nondeterministic programs.The logic of linear time was used by Pnueli in [15], while the logic of branching time seems to be the one used by most computer scientists for reasoning about temporal concepts. We have found this to cause some confusion among our colleagues, so one of our goals has been to clarify the formal foundations of Pnueli's work.The following section gives an intuitive discussion of temporal logic, and Section 3 formally defines the semantics of the two temporal logics. In Section 4, we prove that the two temporal logics are not equivalent, and discuss their differences. Section 5 discusses the problems of validity and completeness for the temporal logics. In Section 6, we show that there are some important properties of the computational model that cannot be expressed with the temporal operators "henceforth" and "eventually", and define more general operators.
State estimation and parameter identification of flexible manipulators based on visual sensor and virtual joint model (2002)

When we control a flexible manipulator based on a dynamic model, we need to estimate the state variables with accuracy. In the case of rigid manipulators, the state variables consist of joint angles and their velocities which are measured easily by encoders, potentiometers, tachometers, and so on. In the case of flexible manipulators, however, the state variables also include elastic deformations and their velocities due to flexibility. Here we focus on visual sensor to measure distributed state variables of flexible manipulators. First, we discuss a distributed state estimation method which uses discrete position information of markers attached on flexible links. Second, when we apply the virtual joint model to flexible manipulators, elastic deformations are expressed by virtual passive joint angles which are lumped. So we have to correspond the real elastic deformations to the virtual joint angles. We also discuss this transformation. Third, when we estimate the lumped state variables by the proposed method, it is possible to identify physical parameters of the dynamic model. Finally, some experiments were carried out to verify the effectiveness of the proposed method.
RNA sequencing of a large number of psoriatic patients identifies 131 novel miRNAs and 11 miRNAs associated with disease severity (2021)

Abstract Background MicroRNAs are small regulatory molecules that are dysregulated in psoriasis. Despite previous efforts, much is unknown about the regulatory mechanisms of psoriasis genetics and their contributions to disease development and activity. Objectives To globally characterize the miRNAome of psoriatic skin in a large sample of psoriatic cases and controls for increased understanding of psoriasis pathophysiology. Methods Skin biopsies from psoriatic cases (n=75) and non-psoriatic controls (n=57) were RNA sequenced. Count data was meta-analyzed with a previously published dataset (cases, n=24, controls, n=20), increasing the number of psoriatic cases four-fold from previously published studies. Differential expression analyses were performed comparing lesional psoriatic (PP), non-lesional psoriatic (PN) and control (NN) skin. Further, functional enrichment and cell specific analyses were performed. Results We identified 439 significantly differentially expressed miRNAs (DEMs), of which 131 were novel and 11 were related to disease severity. Meta-analyses identified 20 DEMs between PN and NN, suggesting an inherent change in all psoriatic skin. By integrating the miRNA transcriptome with mRNA target interactions, we identified several functionally enriched terms, including ‘thyroid hormone signaling’, ‘insulin resistance’ and various infectious diseases. Cell specific expression analyses revealed that the upregulated DEMs were enriched in epithelial and immune cells. Conclusions We have provided the most comprehensive overview of the miRNome in psoriatic skin to date and identified a miRNA signature related to psoriasis severity. Our results may represent molecular links between psoriasis and related comorbidities and have outlined potential directions for future functional studies to identify biomarkers and treatment targets.
Vectorial adaptive optics: correction of polarization and phase (2020)

Adaptive optics normally concerns correction of phase aberrations; this has certainly been the case in microscopy. However, the performance of certain forms of microscope is also sensitive to polarization errors. We present the concept of vectorial adaptive optics (V-AO) to extend compensation techniques into the vectorial beam domain by including polarization. Full polarization and phase control are implemented based on a combined spatial light modulator (SLM) and deformable mirror (DM) system. We demonstrate that V-AO can manipulate/improve the point spread function (PSF) of microscopes and micro-endoscopes. We explore methods of control of such systems to enable feedback correction of polarization and/or phase aberrations. Widely-used high numerical aperture (NA) objective lenses and GRIN rod endoscope lenses based systems are used for testing. Comparisons of the performance using V-AO and without V-AO are demonstrated alongside a specific case of GRIN rod endoscope lenses based vectorial imaging. The enhancement of the normal/vectorial imaging of the samples validated that our technique may solve numerous residual optics error issues in various microscopic/endoscopic systems. This may pave the way for further application directions. It should be noted that the applications of V-AO are not confined to microscopes, may also find use such other areas of optics.
Pharmacokinetics and Pharmacodynamics of T-Cell Bispecifics in the Tumour Interstitial Fluid (2021)

The goal of this study is to investigate the pharmacokinetics in plasma and tumour interstitial fluid of two T-cell bispecifics (TCBs) with different binding affinities to the tumour target and to assess the subsequent cytokine release in a tumour-bearing humanised mouse model. Pharmacokinetics (PK) as well as cytokine data were collected in humanised mice after iv injection of cibisatamab and CEACAM5-TCB which are binding with different binding affinities to the tumour antigen carcinoembryonic antigen (CEA). The PK data were modelled and coupled to a previously published physiologically based PK model. Corresponding cytokine release profiles were compared to in vitro data. The PK model provided a good fit to the data and precise estimation of key PK parameters. High tumour interstitial concentrations were observed for both TCBs, influenced by their respective target binding affinities. In conclusion, we developed a tailored experimental method to measure PK and cytokine release in plasma and at the site of drug action, namely in the tumour. Integrating those data into a mathematical model enabled to investigate the impact of target affinity on tumour accumulation and can have implications for the PKPD assessment of the therapeutic antibodies.
Nanosecond burst mode X-ray imager development at Sandia National Laboratories. (2020)

Abstract not provided.
Three-dimensional spinal bone imaging with medical ultrasound for epidural anesthesia guidance (2011)

Epidural anesthesia procedures are performed in approximately 75 percent of all childbirths in the United States; however, failure rates for these procedures are as high as 40 percent across all cases and 70 percent in the obese population. Due to the limitations associated with X-ray-based fluoroscopy, including exposure to ionizing radiation and lack of portability, the standard of care is to perform epidurals using palpation - i.e. without medical imaging. High-quality 3D imaging of spinal bone surfaces, obtained using a portable ultrasound device, could potentially overcome these challenges and offer physicians a safe imaging tool to increase success rates. A 4-channel handheld ultrasound system with custom 0.95 cm diameter piston transducers focused at 5 cm were designed and fabricated. The system was then used to image an excised lumbar spine in a water bath over a mechanically scanned 90 mm × 50 mm 2D plane. Positional information regarding the surface of the lumbar spine bone at each point across the 2D plane was estimated in MATLAB by detecting the position of maximum envelope-detected signal above the noise level. 3D topographical images were rendered and qualitatively compared to photographs of the actual spine. Additionally, 3D printed models of anatomically accurate lumbar vertebrae were fabricated and embedded in a graphite gelatin phantom. Imaging was conducted with a mechanically scanned 5 MHz piston transducer, 3D images were formed, and the correlation between the known surfaces and ultrasound estimated surfaces was computed. Images of the excised spine using the handheld ultrasound system yielded excellent correlation to optical images. Automated measurements (performed in MATLAB) of spinous process and epidural gap dimensions across the axis of the spine were within 0.5 mm of the actual dimensions. 3D images of the printed spine model produced a 0.88 correlation coefficient between estimated and true spine surface locations. Results in this paper demonstrate the feasibility of a handheld ultrasound device for low-cost, safe, and portable imaging of spinal bone anatomy in 3D, which possesses the potential for improving the success rates of epidural anesthesia procedures.
Mechanism of isomerization of a .beta.-keto sulfide (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of isomerization of a .beta.-keto sulfideRichard B. SilvermanCite this: J. Org. Chem. 1981, 46, 23, 4789–4791Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/jo00336a035https://doi.org/10.1021/jo00336a035research-articleACS PublicationsRequest reuse permissionsArticle Views132Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
22‐1: Invited Paper: Latest Evolution of Small Molecule Based Emissive Layers for Ink Jet Printed OLED Displays (2021)

This article reviews the current performance of inkjet printed OLEDs. Recent progress on the crucial parameter of blue sub‐pixel lifetime is shown, achieved by improving the stability of the emissive material. By adjusting the charge balance towards highest efficiency, an external quantum efficiency of 11% can be achieved. Further progress on efficiency is also illustrated for red devices. Within latest R&amp;D type material, a significant efficiency increase can be observed by an improvement of the horizontal orientation of the emissive material. Prospectively, this will close the gap between evaporated and printed red devices.
Engineering of efficient phosphorescent iridium cationic complex for developing oxygen-sensitive polymeric and nanostructured films (2007)

In this study, a novel phosphorescent Ir(III) complex [Ir(2-phenylpyridine)2(4,4'-bis(2-(4-N,N-methylhexylaminophenyl)ethyl)-2-2'-bipyridine)Cl] (for convenience, the complex was given the synonym N-948) has been designed and synthesized, to be used as an oxygen probe. It was characterized by spectroscopic and analytical methods when incorporated in a polystyrene and nanostructured metal oxide support. N-948 is the first Ir complex in the literature with a luminescence emission at a wavelength higher than 650 nm (665 nm), with a quantum yield higher than 0.50 (0.58 +/- 0.05) and an extremely long phosphorescence lifetime (102 micros) which has been used for developing oxygen-sensitive films. In addition, the new complex shows a Stern-Volmer constant which is 20 times higher than that of other Ir complexes known from the literature when they are immobilized in polystyrene. The sensing film shows long-term stability (up to 12 months), complete reversibility of the signal quenched by oxygen and a quick response time to various oxygen concentrations (<2 s changing from 10 vol% pO2 to 90 vol% pO2). Thus, it is an interesting and promising complex for developing oxygen-selective sensors for gas analysis and the analysis of dissolved oxygen.
The space of accessibility and universal design (2023)

Accessibility is a compensatory strategy conceived to prevent discrimination while universal design seeks to change the consciousness of those who create the built environment to address a broader conception of the human body. Both concepts are united by the common goal of social inclusion, and both are necessary to achieve that goal. The Convention on the Rights of People with Disabilities (CRPD) explicitly emphasizes the former but implicitly acknowledges the value of the latter. The physical environment is a dynamic and charged reality incorporating and integrating conceptions of space, perceptions of space, and the lived experience space. A case study of the implementation of accessibility and universal design in the United States helps to understand how these three aspects of space contribute to the production of disability and the realization of social inclusion. The main lesson from the case study is that space, such as disability, is culturally determined and thus the path toward social inclusion will vary from one cultural context to another.