gebhart/patrepeval huggingface dataset:
Self-heated thermistor measurements of perfusion (1992)

A microcomputer-based control system applies a combination of steady state and sinusoidal power to a thermistor probe which is inserted into the tissue of interest. The steady-state temperature response is an indication of the effective thermal conductivity (keff), which includes a component due to intrinsic conduction plus a convective component due to the tissue blood flow near the probe. By careful choice of the excitation frequency, the sinusoidal temperature response can be used to measure intrinsic thermal conductivity (km) in the presence of blood flow. Optimal sinusoidal heating frequency depends on the thermistor size. Experimental results in the alcohol-fixed canine kidney cortex show that perfusion is linearly related to the difference keff minus km. The instrument can measure tissue thermal conductivity with an accuracy of 2%. The instrument can resolve changes in perfusion of 10 mL/100g-min with a Thermometrics P60DA102M thermistor. The maximum error in measured perfusion is about 30%. When tissue trauma due to probe insertion is minimized, the self-heated thermistor method gives a reliable indication of local tissue blood flow.
Automatic Segmentation of Specular Reflections for Endoscopic Images Based on Sparse and Low-Rank Decomposition (2014)

Endoscopy is a minimally invasive medical diagnostic procedure that is used to provide a realistic view of the surfaces of organs inside human body. Images taken during such procedures largely show tissues of human organs. Due to the presence of mucosa of the gastrointestinal tract or other characteristics of the human body, these surfaces usually have a glossy appearance showing specular reflections. For many image analysis algorithms, these distinct and bright visual mark can be a significant source of error. On other hand, these features can also be useful for image restoration and for the construction of 3D model of the organs. In this article, we propose a segmentation method of the specular regions based on sparse and low-rank decomposition using a robust PCA via accelerated proximal gradient algorithm. In contrast to the existing approaches, the proposed segmentation works without using colour image thresholds. Moreover, the proposed method presents more precise segmentation results represented by grayscale masks instead of binary masks.
An experimental study of in-furnace processes and dynamic behaviour of a 235 MWe CFB boiler (2004)

In a project funded by the 5th Framework Programme of the European Union, a 235 MWe Circulating Fluidized Bed (CFB) boiler is investigated with respect to in-furnace processes and dynamic response to load changes. The purpose of the project is to assess the insufficiently known features of large-scale CFB boilers. The furnace of the boiler has a cross-section of 21 x 10 meters and a height of 44 meters. The boiler is located in Turow, Poland, and is operated on a local brown coal.The project is unique in that several measurement ports were opened in the walls of the large CFB furnace for measurements in various locations inside the furnace. Also, a number of techniques were employed with new probes developed for this type of measurements to form a basis for studies of hydrodynamic processes as well as local variations in gas components (such as O2, CO, THC) and solid bed materials. The paper describes the measurement techniques and provides examples of results obtained from the in-situ measurements and from the dynamic response study.
CloudRidAR (2014)

Mobile augmented reality (MAR) has exploded in popularity on mobile devices in various fields. However, building a MAR application from scratch on mobile devices is complicated and time-consuming. In this paper, we propose CloudRidAR, a framework for MAR developers to facilitate the development, deployment, and maintenance of MAR applications with little effort. Despite of advance in mobile devices as a computing platform, their performance for MAR applications is still very limited due to the poor computing capability of mobile devices. In order to alleviate the problem, our CloudRidAR is designed with cloud computing at the core. Computational intensive tasks are offloaded on cloud to accelerate computation in order to guarantee run-time performance. We also present two MAR applications built on CloudRidAR to evaluate our design.
Hepatocyte‐specific γ‐catenin deletion lacks an overt phenotype (649.6) (2014)

We have previously shown that β‐catenin loss in hepatocytes led to an increase in γ‐catenin at the adherens junctions (AJ) where γ‐catenin complexed with E‐cadherin in the absence of β‐catenin. γ‐Catenin (also known as Plakoglobin), is normally a major component of the desmosomes and its role in liver biology remains unexplored. Intriguingly both tumor suppressive as well as tumor promoter roles of γ‐catenin have been suggested in hepatocellular cancer (HCC). In the current study we conditionally deleted γ‐catenin in hepatocytes by interbreeding albumin‐cre and γ‐catenin floxed mice. We successfully deleted γ‐catenin genetically and at the protein level in mouse hepatocytes using this strategy in the γ‐catenin knockout mice (KO). These mice lacked any overt phenotype up to 3 months of age so far. However, male KO displayed larger size of liver that appeared softer in texture, although no change in liver weight/body weight ratio was evident. No change in basal cell proliferation, apoptosis or fibrosis was evident in KO mice. Additional histological analysis of KO was unremarkable. There was also no obvious difference in serum biochemistry between the WT and KO mice. Molecular analysis using whole cell lysates reveals comparable levels of E‐cadherin but showed marginally increased β‐Catenin. There were some changes in levels of key desmosomal proteins. Thus γ‐catenin loss in hepatocytes appears to be well‐tolerated in an unchallenged mice.
Star graphics (1982)

The XEROX Star 8010 Information System features an integrated text and graphics editor. The Star hardware consists of a processor, a large bit-mapped display, a keyboard and a pointing device. Star's basic graphic elements are points, lines, rectangles, triangles, graphics frames, text frames and bar charts. The internal representation is in terms of idealized objects that are displayed or printed at resolutions determined by the output device. This paper describes the design and implementation of a graphics editor using an object-oriented technique based on a Star-wide subclassing method called the Trait Mechanism.
Variables Associated With Administration of Nurse-initiated Analgesia in Pediatric Triage (2020)

TNIA yielded a short time to analgesia, but rates of any analgesia and opioid analgesia were low. Several variables associated with the provision of any analgesia and opioid analgesia were identified. Our findings provide evidence to guide future educational programs in this area.
The Skin Microbiome: Is It Affected by UV-induced Immune Suppression? (2016)

Human skin apart from functioning as a physical barricade to stop the entry of pathogens, also hosts innumerable commensal organisms. The skin cells and the immune system constantly interact with microbes, to maintain cutaneous homeostasis, despite the challenges offered by various environmental factors. A major environmental factor affecting the skin is ultraviolet radiation UV-R from sunlight. UV-R is well known to modulate the immune system, which can be both beneficial and deleterious. By targeting the cells and molecules within skin, UV-R can trigger the production and release of antimicrobial peptides (AMPs), affect the innate immune system and ultimately suppress the adaptive cellular immune response. This can contribute to skin carcinogenesis and the promotion of infectious agents such as herpes simplex virus and possibly others. On the other hand, a UV-established immunosuppressive environment may protect against the induction of immunologically mediated skin diseases including some of photodermatoses such as polymorphic light eruption. In this article, we share our perspective about the possibility that UV-induced immune suppression may alter the landscape of the skin's microbiome and its components. Alternatively, or in concert with this, direct UV-induced DNA and membrane damage to the microbiome may result in pathogen associated molecular patterns (PAMPs) that interfere with UV-induced immune suppression.
SOFIA's Choice: Automating the Scheduling of Airborne Observations (1999)

This paper describes the problem of scheduling observations for an airborne telescope. Given a set of prioritized observations to choose from, and a wide range of complex constraints governing legitimate choices and orderings, how can we efficiently and effectively create a valid flight plan which supports high priority observations? This problem is quite different from scheduling problems which are routinely solved automatically in industry. For instance, the problem requires making choices which lead to other choices later, and contains many interacting complex constraints over both discrete and continuous variables. Furthermore, new types of constraints may be added as the fundamental problem changes. As a result of these features, this problem cannot be solved by traditional scheduling techniques. The problem resembles other problems in NASA and industry, from observation scheduling for rovers and other science instruments to vehicle routing. The remainder of the paper is organized as follows. In 2 we describe the observatory in order to provide some background. In 3 we describe the problem of scheduling a single flight. In 4 we compare flight planning and other scheduling problems and argue that traditional techniques are not sufficient to solve this problem. We also mention similar complex scheduling problems which may benefit from efforts to solve this problem. In 5 we describe an approach for solving this problem based on research into a similar problem, that of scheduling observations for a space-borne probe. In 6 we discuss extensions of the flight planning problem as well as other problems which are similar to flight planning. In 7 we conclude and discuss future work.
Preserving omnidirectionality in optimized asymmetric transformation optics designs (2016)

Optimization techniques are efficient methods to simplify the design of transformation optics devices. Asymmetric devices obtained through these methods typically lose omnidirectionality and perform well only when illuminated from a finite set of directions. We present here an optimization approach that results in simplified, omnidirectional designs of fairly large bandwidths. The method leverages a class of coordinate transformations that result in transformation media whose material parameters follow identical isocontours. We show that discretizing these media in a finite number of layers that follow the common isocontours and optimizing the material parameters inside each layer is an effective way to significantly simplify the design complexity while preserving most of the original performance including omnidirectionality.
Radiation Damage Effects and Operation of the LHCb Vertex Locator (2018)

Vertex locator (VELO) is a silicon microstrip detector situated around the interaction point in the large Hadron Collider beauty (LHCb) spectrometer at the Large Hadron Collider. The LHCb experiment is dedicated to studying charge conjugation and parity symmetry violation in the heavy flavor sector and rare decays of B mesons. The precise reconstruction of both the primary and secondary vertices, obtained by the VELO, is crucial in the selection of signal events containing b and c quarks and lifetime measurements. VELO consists of two retractable parts that operate at 8 mm from the interaction region. Its proximity to proton beams makes the LHCb VELO a place for studying radiation damage effects in silicon detectors in proton-proton and heavy-ion collisions. The latest results from radiation damage studies and their impact on the operation of the LHCb VELO after the first data-taking period (Run I) and the ongoing Run II are presented in this paper. The main macroscopic parameters, influenced by particle fluence, are described along with selected methods of their monitoring. All the results show that VELO sustains the impact of high fluence of radiation, and its performance will not change significantly until the end of Run II.
Chemical Structure Data File For A. Kois's Thesis, "Synthetic approaches to heliangolide sesquiterpenes." (2020)

This Structure Data File (SDfile) is associated with the thesis: Kois, A. Synthetic approaches to heliangolide sesquiterpenes. and http://library.ua.edu/vwebv/holdingsInfo?bibId=741315 It is distributed by the University of Alabama Libraries. The SDfile is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). Chemical Structure Data Files can be viewed/processed with most cheminformatics toolkits and stand-alone software packages: See https://en.wikipedia.org/wiki/Cheminformatics_toolkit. Note that this is the archived non-standardized chemical substance data. If you are looking for the standardized see the UA Libraries PubChem Data Source: https://pubchem.ncbi.nlm.nih.gov/source/15645. The specific substances associated with this data set are indicated by the local DATSOURCE_REGID identifiers within the SDfile. These identifiers can be used to cross-reference the data within PubChem. Moreover, additional information about the structure data compiling workflow is available on the UA Libraries GitHub Chemical Structures Project Page: https://github.com/ualibweb/UALIB_ChemStructures
Lower tacrolimus exposure and time in therapeutic range increase the risk of de novo donor-specific antibodies in the first year of kidney transplantation (2017)

De novo donor-specific antibodies (dnDSAs) have been associated with reduced graft survival. Tacrolimus (TAC)-based regimens are the most common among immunosuppressive approaches used in in clinical practice today, yet an optimal therapeutic dose to prevent dnDSAs has not been established. We evaluated mean TAC C<sub>0</sub> (tacrolimus trough concentration) and TAC time in therapeutic range for the risk of dnDSAs in a cohort of 538 patients in the first year after kidney transplantation. A mean TAC C<sub>0</sub> < 8 ng/mL was associated with dnDSAs by 6 months (odds ratio [OR] 2.51, 95% confidence interval [CI] 1.32-4.79, P = .005) and by 12 months (OR 2.32, 95% CI 1.30-4.15, P = .004), and there was a graded increase in risk with lower mean TAC C<sub>0</sub> . TAC time in the therapeutic range of <60% was associated with dnDSAs (OR 2.05, 95% CI 1.28-3.30, P = .003) and acute rejection (hazard ratio [HR] 4.18, 95% CI 2.31-7.58, P < .001) by 12 months and death-censored graft loss by 5 years (HR 3.12, 95% CI 1.53-6.37, P = .002). TAC minimization may come at a cost of higher rates of dnDSAs, and TAC time in therapeutic range may be a valuable strategy to stratify patients at increased risk of adverse outcomes.
Mercaptoimidazolylpropionic acid hydrobromide. Inhibition of tadpole collagenase and related properties (1978)

A mercapto analogue of histidine (1), (RS)-2-mercapto-3-(5-imidazolyl)propionic acid (2), was prepared by treatment of (RS)-2-bromo-3-(5-imidazolyl)propionic acid with trithiocarbonate. Decomposition of the resulting intermediate with hydrochloric acid followed by Sephadex G-15 chromatography permitted isolation of 2 as a hydrobromide complex having unusual stability and properties as evidenced by IR and 1H NMR data. The potency of this complex in inhibiting tissue (Rana catesbiana) collagenase was estimated by radial diffusion assay. The amount of 2 required to produce 50% inhibition was 3.8 +/- 1.5 mM compared to 8.7 +/- 2.5 mM for cysteine. Preliminary tests of oxygen susceptibility, mutagenicity, and toxicity suggest that this substance may warrant study as a therapeutic agent for control of collagenase-linked corneal ulcerations.
Our experience in developing and operating the Airway Intervention Registry for Recurrent Respiratory Papillomatosis (AIR-RRP): national data collection (2023)

Recurrent respiratory papillomatosis (RRP) is characterised by benign wart-like growths in the respiratory tract caused by the human papillomavirus (HPV). These warts vary in size and grow quickly, causing voice changes and airway obstruction. Whilst the condition is rare, RRP is more common and aggressive in children. There is currently no curative treatment for HPV, therefore RRP is managed by maintaining a safe airway and a serviceable voice by repeated surgery to remove the growths. A lack of specific diagnostic codes prevents reliable case ascertainment of RRP from routine administrative databases such as Hospital Episode Statistics. In 2017 a cross-sectional survey identified 918 RRP patients in the UK, half of whom had received surgical intervention for RRP in the previous 12 months with 16 different interventions. Randomised controlled trials for RRP interventions are difficult due to the rarity of the disease, variation in severity and progression and non-standard care across the NHS. Consequently, there is a lack of definitive efficacy and safety evidence. The only national guidance for RRP interventions is "Radiofrequency cold ablation for respiratory papillomatosis" (NICE IPG434, 2017) which recommended further data collection due to lack of evidence. However, due to the wide variation in RRP management across the NHS, clinical opinion favoured that any data collection should include a comparison of safety and efficacy of all RRP interventions in order to advise which improved patient outcomes and quality of life. To address lack of evidence, and inform the future care of RRP patients, we developed a registry and used it to collect real-world data from patients receiving treatment for RRP in NHS hospitals across the UK. The purpose of this paper is to share lessons learned from this national data collection exercise to inform future clinical registry development.
Computational quest for understanding the role of astrocyte signaling in synaptic transmission and plasticity (2012)

The complexity of the signaling network that underlies astrocyte-synapse interactions may seem discouraging when tackled from a theoretical perspective. Computational modeling is challenged by the fact that many details remain hitherto unknown and conventional approaches to describe synaptic function are unsuitable to explain experimental observations when astrocytic signaling is taken into account. Supported by experimental evidence is the possibility that astrocytes perform genuine information processing by means of their calcium signaling and are players in the physiological setting of the basal tone of synaptic transmission. Here we consider the plausibility of this scenario from a theoretical perspective, focusing on the modulation of synaptic release probability by the astrocyte and its implications on synaptic plasticity. The analysis of the signaling pathways underlying such modulation refines our notion of tripartite synapse and has profound implications on our understanding of brain function.
A src family tyrosine kinase inhibits neurotransmitter release from neuronal cells (2001)

Tyrosine kinases are expressed in many tissues, particularly in the central nervous system, and regulate various cellular functions. We report here that a src family tyrosine kinase-specific inhibitor, PP2, enhances neurotransmitter release from PC12 cells and primary cultured neurons. PP2 enhances only Ca(2+)-dependent release; it does not affect basal release. These effects result from an enhancement of vesicular exocytosis and not from the reuptake or refilling of neurotransmitters because Ca(2+)-dependent secretion of an exogenously expressed reporter protein, the human growth hormone (hGH), is also enhanced by PP2. Overexpression of constitutive active v-src, but not of a kinase-inactive mutant, suppressed Ca(2+)-dependent release. In PP2-treated cells, Pyk2, paxillin, and some other proteins showed a decrease in tyrosine phosphorylation, and the enhancement of tyrosine phosphorylation of these proteins in response to Ca(2+) influx was also reduced. Electron and fluorescence microscopy showed that PP2 treatment induced morphological change and decreased phalloidin reactivity at the filopodium-like structures on the processes of PC12 cells. Interestingly, inhibition of actin polymerization with cytochalasin D and latrunculin A enhanced Ca(2+)-dependent, but not basal, release. It is possible that a src family tyrosine kinase, through the regulation of actin dynamics, has an inhibitory function to regulate neurotransmitter release.
Metabolic alterations and distribution of five-carbon precursors in jasmonic acid-elicited Catharanthus roseus cell suspension cultures (2015)

In Catharanthus roseus cell cultures, the terpenoid moiety is considered as the limiting factor in terpenoid indole alkaloid (TIA) production. The pathway of terpenoidal precursors in TIA is strongly linked with other terpenoid pathways, suggesting that TIA production might be limited by competition for the five-carbon (C5) precursors. This raises the question whether the stimulation of TIA production by certain signal molecules is due to a redistribution of C5 precursors between the associated terpenoid pathways and/or to a total increase of the precursor availability. To investigate the effect of a TIA-increasing signal molecule on C5 distribution, the cell suspension cultures of C. roseus were elicited with jasmonic acid (JA) and the metabolic changes of different terpenoid pathways were evaluated targeting on TIA (monoterpenoid; C10), carotenoids (tetraterpenoid; C40), and phytosterols (triterpenoid; C30). The chromatographic analyses showed that TIA and carotenoid levels almost doubled upon JA elicitation, while phytosterol levels remained constant if compared to the controls. Apparently, both TIA and carotenoid routes benefit from an increased C5 flow in the methyl-erythritol phosphate pathway, and potential export of C5 precursors to the cytosolic terpenoid routes, e.g., towards the phytosterols is minimal. However, the relative composition of individual compounds within each group remains similar when comparing elicited and control cells. This suggests that the increased production of TIA and carotenoid upon JA elicitation is predominantly caused by an increase of the precursor availability rather than due to a redistribution of C5 precursors between the associated terpenoid pathways. Furthermore, NMR-based metabolomics analysis showed a discrimination of JA-elicited and control cells between 24 and 72 h after treatments with significant changes in levels of strictosidine, malic acid, and sucrose. This study portrays metabolic alterations upon JA elicitation and channeling of C5 precursors in different terpenoid biosynthetic pathways, which provides a knowledge platform for developing strategies to engineer fluxes in a complex biosynthetic network in order to obtain high TIA-producing C. roseus cell lines.
Relative Stability of Formamidine and Carbamate Groups in the Bifunctional Pesticide Formetanate Hydrochloride (2007)

Formetanate hydrochloride is a bifunctional pesticide with remarkable solubility, high toxicity, and potential mobility in aqueous environments. The relative stability of the formamidine and carbamate groups in this compound can be used to predict the identity of its degradation products in water. The reported NMR and UV-vis spectroscopic studies revealed that the formamidine group is more labile than the carbamate group under strongly basic conditions, as well as under predetermined field conditions. The half-life of the formamidine group was determined to be 3.9 h under strongly basic conditions (pH 12.6) and 14.4 h under mildly basic conditions (pH 7.6). The longevity of the carbamate group may exceed 6 months due its resistance to base-promoted degradation. These results may be used in the design of more specific remediation technology for formetanate-contaminated surface water.