gebhart/patrepeval huggingface dataset:
Association between donor corneal endothelial cell counts and infectious agent reactivity: an eye bank database analysis (2019)

Background: To evaluate the association between corneal central endothelial cell count (CECC) with reactivity for hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), human T-lymphotropic virus-1 (HTLV1), and syphilis from an eye bank database. Methods: Eye bank data included 19,159 donors and 38,318 corneas screened for HBV, HCV, HIV, HTLV1, and syphilis from July 2007–May 2015. Linear and binary mixed effects models were used to determine the adjusted marginal effect a positive viral screening test had on CECC and morphology, respectively. The models were adjusted for age, race, gender, lens status, and death to preservation. Eyes with missing data were excluded from the analysis. Statistical significance was defined as P values <0.05. Results: A total of 18,097 donors and 35,136 corneas were included in the final analysis. Average CECC for eyes with negative viral screening was 2,597±436 while the average CECC for eyes screening positive for syphilis, HBV, HCV, HIV, and HTLV1 were 2,638±392 (P=0.073), 2,569±419 (P=0.815), 2,603±363 (P=0.207), 2,615±360 (P=0.733), and 2,625±436 (P=0.362) respectively. Conclusions: The presence of HBV, HCV, HIV, HTLV1, and syphilis display no association with a statistically significant difference in CECC when compared to normal non-diseased donors.
Pharmabiotic beads with improved encapsulation and gut survival for management of colonic inflammation associated gut derangements (2020)

Encapsulation techniques and materials, explored for addressing compromised probiotic gut survival, report significant production losses resulting in <10% entrapment. Presently, we report three-time enhanced entrapment (30 ± 1.2%) of <i>Lactobacillus acidophilus</i> (LAB) in calcium-alginate beads, by modifying process parameters and employing polyethylene glycol (PEG). Water-loving, viscolysing and osmotic-building effects of PEG create numerous, fine voids in the alginate gel allowing efficient diffusion of crosslinking calcium ions, resulting in less leaky beads. Eudragit S100 overcoat improved LAB survival by 690 times in simulated GIT stresses.In DMH-DSS induced colitis and precancerous lesions in rats, while free LAB failed to show any protection, pharmabiotic beads significantly (<i>p</i> < .05) reduced lipid peroxidation, increased antioxidant levels; decreased serum inflammatory burden; downregulated <i>COX-2</i>, <i>iNOS</i>, and <i>c-Myc</i> expression; elevated levels of the selected gut bacteria and SCFAs especially butyrate, all of which add up to antioxidant, anti-inflammatory, balanced gut biota, and ultimately anticancer effects.
Crystalline Adducts of Urea with Linear Aliphatic Compounds (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystalline Adducts of Urea with Linear Aliphatic CompoundsW. J. Zimmerschied, R. A. Dinerstein, A. W. Weitkamp, and Robert F. MarschnerCite this: Ind. Eng. Chem. 1950, 42, 7, 1300–1306Publication Date (Print):July 1, 1950Publication History Published online1 May 2002Published inissue 1 July 1950https://pubs.acs.org/doi/10.1021/ie50487a018https://doi.org/10.1021/ie50487a018research-articleACS PublicationsRequest reuse permissionsArticle Views395Altmetric-Citations81LEARN 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 options Get e-Alerts
Bayesian reconstruction of functional images using anatomical information as priors (1993)

Proposes a Bayesian method whereby maximum a posteriori (MAP) estimates of functional (PET and SPECT) images may be reconstructed with the aid of prior information derived from registered anatomical MR images of the same slice. The prior information consists of significant anatomical boundaries that are likely to correspond to discontinuities in an otherwise spatially smooth radionuclide distribution. The authors' algorithm, like others proposed recently, seeks smooth solutions with occasional discontinuities; the contribution here is the inclusion of a coupling term that influences the creation of discontinuities in the vicinity of the significant anatomical boundaries. Simulations on anatomically derived mathematical phantoms are presented. Although computationally intense in its current implication, the reconstructions are improved (ROI-RMS error) relative to filtered backprojection and EM-ML reconstructions. The simulations show that the inclusion of position-dependent anatomical prior Information leads to further improvement relative to Bayesian reconstructions without the anatomical prior. The algorithm exhibits a certain degree of robustness with respect to errors in the location of anatomical boundaries.
Identification of Potent and Selective Mechanism-Based Inhibitors of the Cysteine Protease Cruzain Using Solid-Phase Parallel Synthesis (2001)

Targeted libraries of ketone-based cysteine protease inhibitors were synthesized and screened against cruzain, a cysteine protease implicated in Chagas' disease. A number of single digit nanomolar, low molecular weight inhibitors were identified and optimized for solubility and potency. Specifically, the best inhibitors identified have K(i) values of 0.9-10 nM and molecular weights between 499 and 609 Da. The most effective inhibitor was also found to be greater than 1000-fold selective for cruzain relative to cathepsin B and 100-fold selective for cruzain relative to cathepsin L.
Mine haul road maintenance management systems (2003)

In surface mining operations, ultra-heavy trucks operate on haul road networks which are typically from 10-40km in length. These road networks are often not optimally designed and maintained and as a result, identifying and remediating road functional defects is problematic. Most surface mine operators agree good roads are desirable, but find it difficult to translate this into an effective road maintenance system. This paper presents a haul road maintenance management system which utilises an assessment of rolling resistance based on a functional performance evaluation of a haul road, together with mine haul truck operating cost models to derive the optimal frequency of road maintenance. A typical application is presented which illustrates the potential of the technique to manage maintenance as and where needed with resultant reduction in total road user costs and an improvement in service provided for the road user.
Poster Abstract: ProSe - A Programming Tool for Rapid Prototyping of Sensor Networks (2007)

ProSe hides low-level details from the designer. ProSe also preserves fault-tolerance properties of original program during transformation. Based on our results from [11], [17] on prototyping target tracking and power management protocols with ProSe, we expect ProSe to enable domain experts design sensor network protocols rather than <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">experts</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sensor</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">networks</i> .
First clinical pilot study with intravascular polarization sensitive optical coherence tomography(Conference Presentation) (2016)

Polarization sensitive (PS) OCT measures the polarization states of the light backscattered by tissue and provides measures of tissue birefringence and depolarization in addition to the structural OCT signal. Ex vivo studies have demonstrated that birefringence is increased in tissue rich in collagen and with elevated smooth muscle cell content. Preliminary data further suggests that depolarization can identify regions of macrophage infiltration, lipid, and irregularly arranged collagen fibers. These are important aspects of the mechanical integrity and vulnerability of atherosclerotic plaques. To evaluate the potential of PS-OCT in the clinical setting, we combined our custom PS-OCT system with commercially available OCT catheters (Fastview, Terumo Corporation) and performed a pilot study in 30 patients, scheduled to undergo percutaneous coronary intervention (PCI) on the grounds of stable or unstable angina. A total of 82 pullbacks in 39 vessels were performed, either in the native coronary arteries or post procedure. Comparing consecutive pullbacks of the same coronary artery, we found excellent agreement between the polarization features in the repeat pullbacks, validating the repeatability and robustness of PS-OCT in the clinical in vivo setting. In addition we observed that the birefringence and depolarization features vary significantly across lesions with identical structural OCT appearance, suggesting morphological subtypes. This first human pilot study proved the feasibility and robustness of intravascular PS-OCT. PS-OCT achieves improved tissue characterization and may help in identifying high-risk plaques, with the potential to ultimately improve risk stratification and help guiding PCI.
Therapeutic arteriogenesis in peripheral arterial disease: combining intervention and passive training (2011)

The prevalence of peripheral arterial disease (PAD) is on the rise in an aging population, significantly affecting quality of life, morbidity and mortality. Besides medical treatment and surgical or interventional revascularization, supervised exercise programs are a primary treatment modality for PAD. Training may significantly increase pain-free walking time (+ 180 %) while avoiding the associated complications of (repeated) invasive revascularization. Training effects rely on an improvement of risk factor management, muscle function, economy of movement, hemorheology, vascular growth and collateral vessel growth. Exercise training upregulates pulsatile fluid shear stress on the vascular endothelium, prompting an improvement of endothelial function (eNOS, NO) and an outgrowth of preexistent collaterals (arteriogenesis) to functional conductance arteries outside the ischemic area at risk. However, the necessary intense minimum training intervals compromise patient compliance, and the impaired functional status of many PAD patients limits active exercise training. Strategies are necessary to a) increase training compliance, b) make the benefits of exercise training available to patients unable to exercise actively and c) therapeutically enhance the adaptive growth of biological bypasses (arteriogenesis). A modified form of passive exercise training derived from enhanced external counterpulsation (low-pressure ECP) which was originally developed for the therapy of heart failure, may prove to be an option for this group of patients. Therefore, this review article suggests a tailored combination therapy, consisting of a facilitating revascularization procedure to restore arterial inflow, succeeded by supervised exercise training, which has yielded promising therapeutic results in clinical trials. Further studies, using appropriate imaging methods and controls, are under way to (a) establish the efficacy of low-pressure EECP in PAD patients and (b) to directly correlate training-induced improvements of collateral flow to the functional improvements seen with exercise training.
One-step synthesis of 3,8-methano-1-aza[10]annulene derivatives via Diels-Alder reaction of benzocyclopropene with 1,2,4-triazines (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOne-step synthesis of 3,8-methano-1-aza[10]annulene derivatives via Diels-Alder reaction of benzocyclopropene with 1,2,4-triazinesJohn C. Martin and Joseph M. MuchowskiCite this: J. Org. Chem. 1984, 49, 6, 1040–1043Publication Date (Print):March 1, 1984Publication History Published online1 May 2002Published inissue 1 March 1984https://pubs.acs.org/doi/10.1021/jo00180a017https://doi.org/10.1021/jo00180a017research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations24LEARN 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
RoomNet: End-to-End Room Layout Estimation (2017)

This paper focuses on the task of room layout estimation from a monocular RGB image. Prior works break the problem into two sub-tasks: semantic segmentation of floor, walls, ceiling to produce layout hypotheses, followed by an iterative optimization step to rank these hypotheses. In contrast, we adopt a more direct formulation of this problem as one of estimating an ordered set of room layout keypoints. The room layout and the corresponding segmentation is completely specified given the locations of these ordered keypoints. We predict the locations of the room layout keypoints using RoomNet, an end-to-end trainable encoder-decoder network. On the challenging benchmark datasets Hedau and LSUN, we achieve state-of-the-art performance along with 200× to 600× speedup compared to the most recent work. Additionally, we present optional extensions to the RoomNet architecture such as including recurrent computations and memory units to refine the keypoint locations under the same parametric capacity.
Ferric Uptake Regulator and Its Role in the Pathogenesis of Nontypeable Haemophilus influenzae (2013)

Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the human nasopharynx, and yet is also an opportunistic pathogen of the upper and lower respiratory tracts. Host microenvironments influence gene expression patterns, likely critical for NTHi persistence. The host sequesters iron as a mechanism to control microbial growth, and yet iron limitation influences gene expression and subsequent production of proteins involved in iron homeostasis. Careful regulation of iron uptake, via the ferric uptake regulator Fur, is essential in multiple bacteria, including NTHi. We hypothesized therefore that Fur contributes to iron homeostasis in NTHi, is critical for bacterial persistence, and likely regulates expression of virulence factors. Toward this end, fur was deleted in the prototypic NTHi clinical isolate, 86-028NP, and we assessed gene expression regulated by Fur. As expected, expression of the majority of genes that encode proteins with predicted roles in iron utilization was repressed by Fur. However, 14 Fur-regulated genes encode proteins with no known function, and yet may contribute to iron utilization or other biological functions. In a mammalian model of human otitis media, we determined that Fur was critical for bacterial persistence, indicating an important role for Fur-mediated iron homeostasis in disease progression. These data provide a profile of genes regulated by Fur in NTHi and likely identify additional regulatory pathways involved in iron utilization. Identification of such pathways will increase our understanding of how this pathogen can persist within host microenvironments, as a common commensal and, importantly, as a pathogen with significant clinical impact.
Optical corral using a standing-wave Bessel beam (2018)

Here we create a series of optical corrals and calculate their potential energy profile. A standing-wave Bessel beam is used to form traps in 1D (along the optical axis) and corrals in 2D, in planes perpendicular to the optical axis at the antinodal regions of the standing waves. These optical corrals are formed by an axicon-generated Bessel beam that is retro-reflected back onto itself. We report on Mie calculations of the 2D optical corrals and then compare the resulting probability distributions to those observed for latex particles of diameters 100, 200, and 300&#x00A0;nm. The experimental radial probability density function of tracked particles closely mimics the theoretical optical structure of a Bessel standing-wave corral. The Bessel standing-wave corrals we have characterized are being developed to measure rotational diffusion and torques on micro- and nanorods to help understand microfluidic behavior. The maximum forces on our small beads in the diffraction-free central zone of the Bessel beam standing wave are F||=0.5&#x2009;&#x2009;pN and F&#x22A5;=0.1&#x2009;&#x2009;pN.
An integrative biology approach for analysis of drug action in models of human vascular inflammation (2004)

Unexpected drug activities discovered during clinical testing establish the need for better characterization of compounds in human disease-relevant conditions early in the discovery process. Here, we describe an approach to characterize drug function based on statistical analysis of protein expression datasets from multiple primary human cell-based models of inflammatory disease. This approach, termed Biologically Multiplexed Activity Profiling (BioMAP), provides rapid characterization of drug function, including mechanism of action, secondary or off-target activities, and insights into clinical phenomena. Using three model systems containing primary human endothelial cells and peripheral blood mononuclear cells in different environments relevant to vascular inflammation and immune activation, we show that BioMAP profiles detect and discriminate multiple functional drug classes, including glucocorticoids; TNF-alpha antagonists; and inhibitors of HMG-CoA reductase, calcineurin, IMPDH, PDE4, PI-3 kinase, hsp90, and p38 MAPK, among others. The ability of cholesterol lowering HMG-CoA reductase inhibitors (statins) to improve outcomes in rheumatic disease patients correlates with the activities of these compounds in our BioMAP assays. In addition, the activity profiles identified for the immunosuppressants mycophenolic acid, cyclosporin A, and FK-506 provide a potential explanation for a reduced incidence of posttransplant cardiovascular disease in patients receiving mycophenolic acid. BioMAP profiling can allow integration of meaningful human biology into drug development programs.
Akt Forms an Intracellular Complex with Heat Shock Protein 90 (Hsp90) and Cdc37 and Is Destabilized by Inhibitors of Hsp90 Function (2002)

Hsp90 is a chaperone required for the conformational maturation of certain signaling proteins including Raf, cdk4, and steroid receptors. Natural products and synthetic small molecules that bind to the ATP-binding pocket in the amino-terminal domain of Hsp90 inhibit its function and cause the degradation of these client proteins. Inhibition of Hsp90 function in cells causes down-regulation of an Akt kinase-dependent pathway required for D-cyclin expression and retinoblastoma protein-dependent G(1) arrest. Intracellular Akt is associated with Hsp90 and Cdc37 in a complex in which Akt kinase is active and regulated by phosphatidylinositol 3-kinase. Functional Hsp90 is required for the stability of Akt in the complex. Occupancy of the ATP-binding pocket by inhibitors is associated with the ubiquitination of Akt and its targeting to the proteasome, where it is degraded. This results in a shortening of the half-life of Akt from 36 to 12 h and an 80% reduction in its expression. Akt and its activating kinase, PDK1, are the only members of the protein kinase A/protein kinase B/protein kinase C-like kinase family that are affected by Hsp90 inhibitors. Thus, transduction of growth factor signaling via the Akt and Raf pathways requires functional Hsp90 and can be coordinately blocked by its inhibition.
Kinetics of cell division in epidermal maintenance (2007)

The rules governing cell division and differentiation are central to understanding the mechanisms of development, aging, and cancer. By utilizing inducible genetic labeling, recent studies have shown that the clonal population in transgenic mouse epidermis can be tracked in vivo. Drawing on these results, we explain how clonal fate data may be used to infer the rules of cell division and differentiation underlying the maintenance of adult murine tail-skin. We show that the rates of cell division and differentiation may be evaluated by considering the long-time and short-time clone fate data, and that the data is consistent with cells dividing independently rather than synchronously. Motivated by these findings, we consider a mechanism for cancer onset based closely on the model for normal adult skin. By analyzing the expected changes to clonal fate in cancer emerging from a simple two-stage mutation, we propose that clonal fate data may provide a novel method for studying the earliest stages of the disease.
Thermal Modeling of Directly Cooled Electric Machines Using Lumped Parameter and Limited CFD Analysis (2013)

This paper presents a practical approach to model thermal effects in directly cooled electric machines. The main focus is put on modeling the heat transfer in the stator winding and to the cooling system, which are the two critical parts of the studied machines from a thermal point of view. A multisegment structure is proposed that divides the stator, winding, and cooling system into a number of angular segments. Thereby, the circumferential temperature variation due to the nonuniform distribution of the coolant in the cooling channels can be predicted. Additionally, partial computational fluid dynamics (CFD) simulations are carried out to model the coolant flow in the cooling channels and also on the outer surface of the end winding bodies. The CFD simulation results are used as input to the analytical models describing the convective heat transfer to the coolant. The modeling approach is attractive due to its simplicity since CFD simulations of the complete machine are avoided. The proposed thermal model is evaluated experimentally on two directly cooled induction machines where the stator winding is impregnated using varnish and epoxy, respectively. A good correspondence between the predicted and measured temperatures under different cooling conditions and loss levels is obtained.