gebhart/patrepeval huggingface dataset:
Keeping Multiple Views Consistent: Constraints, Validations, and Exceptions in Visualization Authoring (2017)

Visualizations often appear in multiples, either in a single display (e.g., small multiples, dashboard) or across time or space (e.g., slideshow, set of dashboards). However, existing visualization design guidelines typically focus on single rather than multiple views. Solely following these guidelines can lead to effective yet inconsistent views (e.g., the same field has different axes domains across charts), making interpretation slow and error-prone. Moreover, little is known how consistency balances with other design considerations, making it difficult to incorporate consistency mechanisms in visualization authoring software. We present a wizard-of-oz study in which we observed how Tableau users achieve and sacrifice consistency in an exploration-to-presentation visualization design scenario. We extend (from our prior work) a set of encoding-specific constraints defining consistency across multiple views. Using the constraints as a checklist in our study, we observed cases where participants spontaneously maintained consistent encodings and warned cases where consistency was overlooked. In response to the warnings, participants either revised views for consistency or stated why they thought consistency should be overwritten. We categorize participants' actions and responses as constraint validations and exceptions, depicting the relative importance of consistency and other design considerations under various circumstances (e.g., data cardinality, available encoding resources, chart layout). We discuss automatic consistency checking as a constraint-satisfaction problem and provide design implications for communicating inconsistencies to users.
Correlation between immune and vascular activities of xanthenone acetic acid antitumor agents. (1994)

To determine whether xanthenone acetic acid (XAA) analogues of flavone acetic acid (FAA) have similar ischemic and nonischemic mechanisms of antitumor action to FAA, a series of such compounds was evaluated in vivo and in vitro. Necrotising activity and changes in tumor blood flow were measured in Colon 38 tumors, and morphological changes assessed in immune cell-infiltrated EMT6 tumor cell spheroids, after treatment with FAA, XAA and its derivatives (5-methyl XAA, 5,6-dimethyl XAA, 3-O-methyl XAA, 8-methyl XAA and xanthenone-4,5-diacetic acid). FAA, XAA and the 5-methyl and 5,6-dimethyl analogues of XAA were active in inducing tumor necrosis, falls in tumor perfusion and characteristic morphological changes in multicellular spheroids. The other XAA analogues lacked these activities. 5-methyl XAA and 5,6-dimethyl XAA were more potent than FAA or XAA. The results suggest that XAA and its analogues have the same mechanisms of action as FAA, and that both the vascular and the immune effects of these compounds are mediated via a common biochemical receptor.
Bioactivation of tegafur to 5-fluorouracil is catalyzed by cytochrome P-450 2A6 in human liver microsomes in vitro. (2000)

Tegafur is a prodrug of 5-fluorouracil (5-FU) consisting of a new class of oral chemotherapeutic agents, tegafur/uracil and S-1, which are classified as dihydropyrimidine dehydrogenase inhibitory fluoropyrimidines. It is bioactivated to 5-FU via 5'-hydroxylation mediated by cytochrome P-450 (CYP). However, which isoform(s) of CYP is responsible for the bioactivation process of tegafur remains unclear. The purpose of the present study was to identify the human CYP isoform(s) involved in the metabolic activation of tegafur using human liver microsomes and cDNA-expressed human CYPs. The formation of 5-FU from tegafur in human liver microsomes showed biphase kinetics with Km and Vmax values for the high-affinity component of 0.43 +/- 0.05 mM and 4.02 +/- 1.70 nmol/mg/min (mean +/- SD, n = 4), respectively. In the correlation study using a panel of 10 human liver microsomes, the formation of 5-FU from tegafur showed a significant correlation (r = 0.98; P < 0.001) with coumarin 7-hydroxylation, a marker activity of CYP2A6. In addition, a specific substrate of CYP2A6 and anti-CYP2A6 antibody inhibited the formation of 5-FU by 90% in human liver microsomes. Moreover, cDNA-expressed CYP2A6 showed the highest activity for the formation of 5-FU among 10 cDNA-expressed CYPs, with a Km value similar to that found for the high-affinity component in human liver microsomes. These findings clearly suggest that CYP2A6 is a principal enzyme responsible for the bioactivation process of tegafur in human liver microsomes. However, to what extent the bioactivation of tegafur by CYP2A6 accounts for the formation of 5-FU in vivo remains unclear, because the formation of 5-FU from tegafur is also catalyzed by the soluble fraction of a 100,000 x g supernatant and also derived from spontaneous degradation of tegafur.
H5N1 Virus Attachment to Lower Respiratory Tract (2006)

Highly pathogenic avian influenza virus (H5N1) may cause severe lower respiratory tract (LRT) disease in humans. However, the LRT cells to which the virus attaches are unknown for both humans and other mammals. We show here that H5N1 virus attached predominantly to type II pneumocytes, alveolar macrophages, and nonciliated bronchiolar cells in the human LRT, and this pattern was most closely mirrored in cat and ferret tissues. These findings may explain, at least in part, the localization and severity of H5N1 viral pneumonia in humans. They also identify the cat and the ferret as suitable experimental animals based on this criterion.
A Theoretical Study of Performance of an Orthogonal Multiplexing Data Transmission Scheme (1968)

This paper presents a theoretical analysis of the performance of an orthogonal multiplexing data transmission scheme (parallel transmission scheme) subject to a number of degrading factors normally encountered by a practical operating system. The factors considered jointly are sampling time error, carrier phase offset, and nonideal phase characteristics of transmitting and receiving filters. Performance is measured by the familiar criterion of eye opening of the received data signal. A closed-form expression for the eye opening is obtained. It is shown that the lengthy nonlinear functions in the solution can be closely approximated by simple piecewise linear functions for parameter values of interest. The optimum settings of the sampling time and the carrier phase are determined for given filter phase distortion. Also, considering all factors, simple formulas are developed for computing interchannel interferences, intersymbol interference, and the resulting eye opening. Simple relationships between the eye opening and filter phase distortion are explored, and a concept of parametric eye is introduced to aid in filter design. An illustrative example is considered which shows that the impairment of the system performance is not excessive for a reasonable range of system design parameters.
The PASTA server for protein aggregation prediction (2007)

Many different proteins aggregate into amyloid fibrils characterized by cross-beta structure. beta-strands contributed by distinct protein molecules are generally found in a parallel in-register alignment. Here, we describe the web server for a novel algorithm, prediction of amyloid structure aggregation (PASTA), to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. PASTA was previously shown to yield results in excellent agreement with available experimental observations, when tested on both natively unfolded and structured proteins. The web server and downloadable source code are freely accessible from the URL: http://protein.cribi.unipd.it/pasta/.
The effect of heart rate reduction by ivabradine on collateral function in patients with chronic stable coronary artery disease (2013)

NCT01039389.
Learning deep representations by mutual information estimation and maximization (2018)

In this work, we perform unsupervised learning of representations by maximizing mutual information between an input and the output of a deep neural network encoder. Importantly, we show that structure matters: incorporating knowledge about locality of the input to the objective can greatly influence a representation's suitability for downstream tasks. We further control characteristics of the representation by matching to a prior distribution adversarially. Our method, which we call Deep InfoMax (DIM), outperforms a number of popular unsupervised learning methods and competes with fully-supervised learning on several classification tasks. DIM opens new avenues for unsupervised learning of representations and is an important step towards flexible formulations of representation-learning objectives for specific end-goals.
Labeling of eukaryotic messenger RNA 5' terminus with phosphorus -32: use of tobacco acid pyrophosphatase for removal of cap structures. (1981)

In recent years, there has been a growing appreciation of the potential applications of 5'-32P-end-labeled mRNA, not only for screening recombinant clones and mapping gene structure, but also for revealing possible nucleotide sequence and structural signals within mRNA molecules themselves, which may be important for eukaryotic mRNA processing and turnover and for controlling differential rates of translational initiation. Three major problems, however, have retarded progress in this area, lack of methods for efficient and reproducible removal of m7G5ppp5'-cap structures, which maintain the integrity of an RNA molecule; inability to generate a sufficient amount of labeled mRNA, owing to the limited availability of most pure mRNA species; and the frequent problem of RNA degradation during in vitro end-labeling owing to RNAse contamination. The procedures presented here permit one to decap and label minute quantities of mRNA, effectively. Tobacco acid pyrophosphatase is relatively efficient in removing cap structures from even nanogram quantities of available mRNA, and enough radioactivity can be easily generated from minute amounts ofintact mRNA with very high-specific-activity [gamma-32P]ATP and the inhibition of ribonuclease contamination with diethylpyrocarbonate. These procedures can be modified and applied to almost any other type of RNA molecule as well. In Section III of this volume, we explore in detail how effectively 5'-end-labeled mRNA can be used not only for nucleotide sequence analysis, but also for mapping mRNA secondary structure.
Clinicians' pocket guide to chronic wound repair (1999)

This thoroughly updated edition addresses the most current issues directly impacting wound care -- including the work of leading clinicians and researchers from multiple disciplines. Contents include wound repair, patient and wound evaluation, documentation and staging of wounds, microbiology, nutrition, skin and the aging process, incontinence care, pressure ulcers, lower extremity ulcers, vascular testing, skin tears, extravasation sites, dehisced surgical wounds, fistulas, radiation burns, wound management, support surfaces, and wound care products.
Image-Based Modeling of Urban Buildings Using Aerial Photographs and Digital Maps (2006)

A VR (virtual reality) simulator which is used for helicopter simulations requires a virtual environment of real world urban areas. However, real urban environments are continuously changing. It is necessary to develop a modeling method that makes direct use of GIS (geographical information system) data which is updated periodically. A flight simulation needs to visualize not only buildings in the near distance but also a large number of buildings in the far distance. We propose a method for modeling urban environments from aerial images and digital maps with relatively little manual work. An image-based method is applied to the urban modeling that considers the characteristics of Korean cities. Buildings in the distance can be presented without creating a large number of polygons. The proposed method consists of a pre-processing stage that prepares the model from the GIS data and a modeling stage that creates the virtual urban environment. The virtual urban environment utilizes the height map of buildings.
Stimuli-responsive surfaces for bio-applications (2008)

The development of surfaces that have switchable properties, also known as smart surfaces, have been actively pursued in the past few years. The recent surge of interest in these switchable systems stems from the widespread number of applications to many areas in science and technology ranging from environmental cleanup to data storage, micro- and nanofluidic devices. Moreover, the ability to modulate biomolecule activity, protein immobilisation, and cell adhesion at the liquid-solid interface is important in a variety of biological and medical applications, including biofouling, chromatography, cell culture, regenerative medicine and tissue engineering. Different materials have been exploited to induce such changes in surface biological properties that are mostly based on self-assembled monolayers or polymer films. This critical review focuses on the recent progress in the preparation of these switchable surfaces, and highlights their applications in biological environments. The review is organized according to the external stimuli used to manipulate the properties of the substrate-chemical/biochemical, thermal, electric and optical stimuli. Current and future challenges in the field of smart biological surfaces are addressed (189 references).
Virtual Reality Without Vision: A Haptic and Auditory White Cane to Navigate Complex Virtual Worlds (2020)

Current Virtual Reality (VR) technologies focus on rendering visuospatial effects, and thus are inaccessible for blind or low vision users. We examine the use of a novel white cane controller that enables navigation without vision of large virtual environments with complex architecture, such as winding paths and occluding walls and doors. The cane controller employs a lightweight three-axis brake mechanism to provide large-scale shape of virtual objects. The multiple degrees-of-freedom enables users to adapt the controller to their preferred techniques and grip. In addition, surface textures are rendered with a voice coil actuator based on contact vibrations; and spatialized audio is determined based on the progression of sound through the geometry around the user. We design a scavenger hunt game that demonstrates how our device enables blind users to navigate a complex virtual environment. Seven out of eight users were able to successfully navigate the virtual room (6x6m) to locate targets while avoiding collisions. We conclude with design consideration on creating immersive non-visual VR experiences based on user preferences for cane techniques, and cane material properties.
Stress granules as crucibles of ALS pathogenesis (2013)

Amyotrophic lateral sclerosis (ALS) is a fatal human neurodegenerative disease affecting primarily motor neurons. Two RNA-binding proteins, TDP-43 and FUS, aggregate in the degenerating motor neurons of ALS patients, and mutations in the genes encoding these proteins cause some forms of ALS. TDP-43 and FUS and several related RNA-binding proteins harbor aggregation-promoting prion-like domains that allow them to rapidly self-associate. This property is critical for the formation and dynamics of cellular ribonucleoprotein granules, the crucibles of RNA metabolism and homeostasis. Recent work connecting TDP-43 and FUS to stress granules has suggested how this cellular pathway, which involves protein aggregation as part of its normal function, might be coopted during disease pathogenesis.
Effect of Low Dose Dexmedetomidine on Emergence Delirium and Recovery Profile following Sevoflurane Induction in Pediatric Cataract Surgeries (2015)

This randomized trial was conducted to assess the efficacy and recovery profile of low dose intravenous dexmedetomidine in prevention of post-sevoflurane emergence delirium in children undergoing cataract surgery. Sixty-three children aged 1–6 years were included. Anesthesia was induced with sevoflurane and airway was maintained with LMA. They were randomized to group D 0.15 (received intravenous dexmedetomidine 0.15 μ g/kg), group D 0.3 (received dexmedetomidine 0.3 μ g/kg), or group NS (received normal saline). The incidence of emergence delirium, intraoperative haemodynamic variables, Aldrete scoring, pain scoring, rescue medication, and discharge time were recorded. Emergence delirium was significantly reduced in dexmedetomidine treated groups with incidence being 10% in group D 0.15, none in group D 0.3, and 35% in the NS group (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.002</mml:mn></mml:math>). Significantly lower PAED scores were observed in D 0.15 and D 0.3 group compared to the NS group (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mi>p</mml:mi><mml:mo>=</mml:mo><mml:mn>0.004</mml:mn></mml:math>). Discharge time was significantly prolonged in the NS group compared to D 0.15 and D 0.3 (45.1 min ± 4.4 versus 36.8 min ± 3.8 versus 34.4 min ± 4.6), <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mi>p</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>0.02</mml:mn></mml:math>. Intravenous dexmedetomidine in low doses (0.3 and 0.15 μ g/kg) was found to be effective in reducing emergence delirium in children undergoing unilateral cataract surgery.
Scavenger Receptor CD163 and Its Biological Functions (2009)

CD163 is a member of scavenger receptor super family class B of the first subgroup. It is mapped to the region p13 on chromosome 12. Five different isoforms of CD163 have been described, which differ in the structure of their cytoplasmic domains and putative phosporylation sites. This scavenger receptor is selectively expressed on cells of monocytes and macrophages lineage exclusively. CD163 immunological function is essentially homeostatic. It also has other functions because participates in adhesion to endothelial cells, in tolerance induction and tissues regeneration. Other very important function of CD163 is the clearance of hemoglobin in its cell-free form and participation in anti-inflammation in its soluble form, exhibiting cytokine-like functions. We review the biological functions of CD163 which have been discovered until now. It seems apparent from this review that CD163 scavenger receptor can be used as biomarker in different diseases and as a valuable diagnostic parameter for prognosis of many diseases especially inflammatory disorders and sepsis.
Effects of nerve growth factor on visual cortical plasticity require afferent electrical activity (1999)

It is known that administration of nerve growth factor (NGF) prevents the ocular dominance shift induced by monocular deprivation in the rat. To determine whether electrical activity in the visual afferent pathway is required for NGF effects on ocular dominance, we infused NGF into the cortex of animals subjected to complete monocular blockade of retinal discharges. Rats at the peak of the critical period received intravitreal tetrodotoxin (TTX) injections to silence activity in one eye for a period of 6-7 days; NGF was concurrently delivered into the visual cortex by means of osmotic minipumps. At the end of the treatment period, the ocular dominance distribution of cortical neurons was assessed by single-cell recordings. The results demonstrate that while infusion of NGF is effective in preventing the ocular dominance shift in lid-sutured rats, virtually no rescue can be observed in TTX-injected animals. Identical results were obtained when a specific agonist of the NGF receptor TrkA, the bivalent anti-rat TrkA IgG (RTA), was infused into the cortex in place of NGF. We conclude that NGF signalling via the TrkA receptor must be coupled to afferent electrical activity to produce its effects on the eye preference of cortical neurons. This suggests a generalized mechanism in which high-affinity neurotrophin receptor activation and afferent discharge interact to modulate neuronal plasticity in the developing visual cortex.
Small Intestinal Submucosa: A Rapidly Resorbed Bioscaffold for Augmentation Cystoplasty in a Dog Model (1998)

The extracellular matrix (ECM) of porcine small intestinal submucosa (SIS) has been shown to serve as a resorbable scaffold for tissue repair and remodeling in several body locations including the urinary bladder. The rate of resorption and extent of SIS degradation are unknown. Nine dogs were divided into three equal groups. Approximately 40% of the anterior dome of the urinary bladder was resected in each dog and replaced with porcine SIS. One group of dogs was sacrificed at each of 4, 8, and 12 weeks after surgery and the fate of the implanted SIS determined by immunohistochemical methods using a monoclonal antibody specific for porcine-derived SIS. By 4 weeks after surgery, only scattered remnants of SIS were present in the remodeled urinary bladder and these positively staining foci were surrounded by an extensive new host derived ECM and neovascularization. There was a continuous layer of transitional epithelium on the luminal surface by 4 weeks. No evidence for the originally implanted SIS could be found at either 8 or 12 weeks and bundles of organized smooth muscle cells were present at the operative site. In summary, SIS is rapidly and extensively degraded when used as a bioscaffold for augmentation cystoplasty in the dog model.
Core Glycosylation of Collagen Is Initiated by Two β(1-O)Galactosyltransferases (2008)

Collagen is a trimer of three left-handed alpha chains representing repeats of the motif Gly-X-Y, where (hydroxy)proline and (hydroxy)lysine residues are often found at positions X and Y. Selected hydroxylysines are further modified by the addition of galactose and glucose-galactose units. Collagen glycosylation takes place in the endoplasmic reticulum before triple-helix formation and is mediated by beta(1-O)galactosyl- and alpha(1-2)glucosyltransferase enzymes. We have identified two collagen galactosyltransferases using affinity chromatography and tandem mass spectrometry protein sequencing. The two collagen beta(1-O)galactosyltransferases corresponded to the GLT25D1 and GLT25D2 proteins. Recombinant GLT25D1 and GLT25D2 enzymes showed a strong galactosyltransferase activity toward various types of collagen and toward the serum mannose-binding lectin MBL, which contains a collagen domain. Amino acid analysis of the products of GLT25D1 and GLT25D2 reactions confirmed the transfer of galactose to hydroxylysine residues. The GLT25D1 gene is constitutively expressed in human tissues, whereas the GLT25D2 gene is expressed only at low levels in the nervous system. The GLT25D1 and GLT25D2 enzymes are similar to CEECAM1, to which we could not attribute any collagen galactosyltransferase activity. The GLT25D1 and GLT25D2 genes now allow addressing of the biological significance of collagen glycosylation and the importance of this posttranslational modification in the etiology of connective tissue disorders.
Gene Silencing in Cancer in Association with Promoter Hypermethylation (2003)

This article reviews the mechanisms of gene silencing in cancer and clinical applications of this phenomenon. The silencing of genes, especially tumor-suppressor genes, is a key event in the development of cancer. The silencing can be effected by a disabling mutation or by a shutting down of the promoter region, the site at which transcription of the gene begins.