gebhart/patrepeval huggingface dataset:
Adrenal blood flow and secretory relationships during hypoxia in anesthetized dogs (1989)

To evaluate whether hypoxia-induced increases in adrenal cortical (CQ) and medullary (MQ) blood flow (radiolabeled microspheres) occur secondary to hypoxia-induced secretory activity, pentobarbital-anesthetized ventilated dogs were pretreated with dexamethasone (DEX) to prevent adrenocorticotropic hormone (ACTH) and corticosteroid secretory changes or underwent unilateral adrenal denervation to prevent adrenal catecholamine secretory responses. In nonsurgically stressed dogs, DEX completely prevented increases in ACTH or corticosteroid levels during reduction of arterial oxygen content to 8 vol% but had no effect on hypoxia-induced doubling of CQ. In dogs in which adrenal oxygen consumption (VO2) was measured, DEX reduced VO2 by 50% without altering CQ. Unilateral adrenal denervation prevented hypoxia-induced increases in adrenal catecholamine secretion and MQ but had no effect on the CQ response. These results suggest that hypoxia-induced medullary vasodilation is associated with adrenal catecholamine secretory activity but that increases in CQ occur independent of secretory activity and likely represent direct vascular effects of hypoxia.
Genome Sequence of the Plant-Pathogenic Bacterium Dickeya dadantii 3937 (2011)

Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria.
Gain Anisotropy Analysis in Green Semipolar InGaN Quantum Wells with Inhomogeneous Broadening (2010)

Polarization switching phenomena in semipolar (1122)-oriented InGaN quantum wells (QWs) were theoretically investigated by a newly formulated model considering the effect of In compositional fluctuation. The theoretical model successfully reproduced the reported polarization switching phenomena for both the emission wavelength and the excitation density in blue-green (1122) QWs, and this showed the importance of inhomogeneous broadening effects to understand polarization properties of semipolar quantum wells. Then, the model was applied for pure-green (1122) QWs, and we predicted that optical polarization was kept in the [1123] direction up to the carrier density high enough to create population inversion in such long-wavelength QWs. These results support the possibility for semipolar-oriented pure green InGaN laser diodes with cleaved facet cavity mirrors.
A Two-Time-Scale Design for Edge-Based Detection and Rectification of Uncooperative Flows (2006)

Existing Internet protocols rely on cooperative behavior of end users. We present a control-theoretic algorithm to counteract uncooperative users which change their congestion control schemes to gain larger bandwidth. This algorithm rectifies uncooperative users; that is, forces them to comply with their fair share, by adjusting the prices fed back to them. It is to be implemented at the edge of the network (e.g., by ISPs), and can be used with any congestion notification policy deployed by the network. Our design achieves a separation of time-scales between the network congestion feedback loop and the price-adjustment loop, thus recovering the fair allocation of bandwidth upon a fast transient phase
Evidence of a leading role for VEGF inBartonella henselae-induced endothelial cell proliferations (2001)

Bartonella henselae causes the vasculoproliferative disorders bacillary angiomatosis (BA) and bacillary peliosis (BP). The pathomechanisms of these tumorous proliferations are unknown. Our results suggest a novel bacterial two-step pathogenicity strategy, in which the pathogen triggers growth factor production for subsequent proliferation of its own host cells. In fact, B. henselae induces host cell production of the angiogenic factor vascular endothelial growth factor (VEGF), leading to proliferation of endothelial cells. The presence of B. henselae pili was associated with host cell VEGF production, as a Pil- mutant of B. henselae was unable to induce VEGF production. In turn, VEGF-stimulated endothelial cells promoted the growth of B. henselae. Immunohistochemistry for VEGF in specimens from patients with BA or BP revealed increased VEGF expression in vivo. These findings suggest a novel bacteria-dependent mechanism of tumour growth.
Charged and strange hadron elliptic flow inCu+Cucollisions atsNN=62.4and 200 GeV (2010)

We present the results of an elliptic flow, ${v}_{2}$, analysis of $\mathrm{Cu}+\mathrm{Cu}$ collisions recorded with the solenoidal tracker detector (STAR) at the BNL Relativistic Heavy Ion Collider at $\sqrt{{s}_{\mathit{NN}}}=62.4$ and $200$ GeV. Elliptic flow as a function of transverse momentum, ${v}_{2}$(${p}_{T}$), is reported for different collision centralities for charged hadrons ${h}^{\ifmmode\pm\else\textpm\fi{}}$ and strangeness-ontaining hadrons ${K}_{S}^{0}$, $\ensuremath{\Lambda}$, $\ensuremath{\Xi}$, and $\ensuremath{\phi}$ in the midrapidity region $|\ensuremath{\eta}|&lt;1.0$. Significant reduction in systematic uncertainty of the measurement due to nonflow effects has been achieved by correlating particles at midrapidity, $|\ensuremath{\eta}|&lt;1.0$, with those at forward rapidity, $2.5&lt;|\ensuremath{\eta}|&lt;4.0$. We also present azimuthal correlations in $p+p$ collisions at $\sqrt{s}=200$ GeV to help in estimating nonflow effects. To study the system-size dependence of elliptic flow, we present a detailed comparison with previously published results from $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{{s}_{\mathit{NN}}}=200$ GeV. We observe that ${v}_{2}$(${p}_{T}$) of strange hadrons has similar scaling properties as were first observed in $\mathrm{Au}+\mathrm{Au}$ collisions, that is, (i) at low transverse momenta, ${p}_{T}&lt;2 \mathrm{GeV}/c$, ${v}_{2}$ scales with transverse kinetic energy, ${m}_{T}\ensuremath{-}m$, and (ii) at intermediate ${p}_{T}$, $2&lt;{p}_{T}&lt;4 \mathrm{GeV}/c$, it scales with the number of constituent quarks, ${n}_{q}$. We have found that ideal hydrodynamic calculations fail to reproduce the centrality dependence of ${v}_{2}$(${p}_{T}$) for ${K}_{S}^{0}$ and $\ensuremath{\Lambda}$. Eccentricity scaled ${v}_{2}$ values, ${v}_{2}/\ensuremath{\varepsilon}$, are larger in more central collisions, suggesting stronger collective flow develops in more central collisions. The comparison with $\mathrm{Au}+\mathrm{Au}$ collisions, which go further in density, shows that ${v}_{2}/\ensuremath{\varepsilon}$ depends on the system size, that is, the number of participants ${N}_{\mathrm{part}}$. This indicates that the ideal hydrodynamic limit is not reached in $\mathrm{Cu}+\mathrm{Cu}$ collisions, presumably because the assumption of thermalization is not attained.
Cell wall evolution and diversity (2012)

Plant cell walls display a considerable degree of diversity in their compositions and molecular architectures. In some cases the functional significance of a particular cell wall type appears to be easy to discern: secondary cells walls are often reinforced with lignin that provides durability; the thin cell walls of pollen tubes have particular compositions that enable their tip growth; lupin seed cell walls are characteristically thickened with galactan used as a storage polysaccharide. However, more frequently the evolutionary mechanisms and selection pressures that underpin cell wall diversity and evolution are unclear. For diverse green plants (chlorophytes and streptophytes) the rapidly increasing availability of transcriptome and genome data sets, the development of methods for cell wall analyses which require less material for analysis, and expansion of molecular probe sets, are providing new insights into the diversity and occurrence of cell wall polysaccharides and associated biosynthetic genes. Such research is important for refining our understanding of some of the fundamental processes that enabled plants to colonize land and to subsequently radiate so comprehensively. The study of cell wall structural diversity is also an important aspect of the industrial utilization of global polysaccharide bio-resources.
Recombinant adeno-associated virus preferentially transduces human, compared to mouse, synovium: implications for arthritis therapy (2004)

Despite a number of published reports, including from our own laboratory, suggesting that adeno-associated virus (AAV) transduces mouse synovium, a careful analysis demonstrated transduction predominantly of the subsynovial muscle tissue, while the synovial lining is poorly transduced. To investigate the potential of AAV to transduce human synovium, three human rheumatoid arthritis (RA) and two murine collagen-induced arthritis (CIA) synovial cell lines were infected with recombinant AAV (rAAV) vectors encoding either mouse IL-10 or IL-4. Low-level transgene expression was observed. However, either Γ-irradiation or the addition of a low-titer E1-, E3-deleted recombinant adenovirus resulted in up to a 100-fold increase in transgene product in the human, but not the mouse, cell lines. RA synovial tissues implanted subcutaneously in severe combined immunodeficiency (SCID) mice, which were subsequently infected with rAAV, showed marked increases in transgene expression when co-infected with adenovirus. To our knowledge, this is the first study to show that intact human synovial tissues can be transduced by rAAV, and it suggests that murine arthritis may not be an optimal model to study rAAV as a gene transfer vector. Further studies to elucidate the mechanisms limiting gene transduction in human synovium may allow optimization of this vector for the treatment of arthritis.
Amorphous Active Pharmaceutical Ingredients in Preclinical Studies: Preparation, Characterization, and Formulation (2008)

A large number of the new pharmaceutical small molecules under development today are found to have poor water solubility. This in turn may lead to low bioavailability, which can have a significant impact on the development of the compound. Compounds with low bioavailability pose a greater challenge in early preclinical work involving animal studies, where obtaining maximum exposure is the primary goal especially in toxicology studies designed to establish the safe dose. From the standpoint of maximizing exposure, the amorphous phase is of great interest as pharmaceutical materials since it is the most metastable state and as such offers the potential of higher solubility and better bioavailability. However, the amorphous approach is not actively pursued in preclinical work owing to the tendency of the amorphous phase to crystallize thereby neutralizing the solubility advantage. This review focuses on (i) methods to generate the amorphous phase, (ii) methods to estimate the degree of crystallinity of the amorphous phase, (iii) methods to predict the stability of the amorphous phase against crystallization, and (iv) choice of polymers carrier and formulation of the amorphous phase for preclinical studies.
Prospective evaluation of relationships between radiotherapy dose to masticatory apparatus and trismus (2018)

Higher mean radiation doses to the ipsilateral block, LP and M were significantly associated with deterioration in trismus. Limiting dose to these structures to ≤40 Gy for tumors not invading the masticatory muscles may improve treatment-related sequelae. The ipsilateral block, LP and M should be studied further as possible alternative avoidance structures in radiotherapy treatment planning.
An online evolving framework for advancing reinforcement-learning based automated vehicle control (2020)

In this paper, an online evolving framework is proposed to detect and revise a controller's imperfect decision-making in advance. The framework consists of three modules: the evolving Finite State Machine (e-FSM), action-reviser, and controller modules. The e-FSM module evolves a stochastic model (e.g., Discrete-Time Markov Chain) from scratch by determining new states and identifying transition probabilities repeatedly. With the latest stochastic model and given criteria, the action-reviser module checks validity of the controller's chosen action by predicting future states. Then, if the chosen action is not appropriate, another action is inspected and selected. In order to show the advantage of the proposed framework, the Deep Deterministic Policy Gradient (DDPG) w/ and w/o the online evolving framework are applied to control an ego-vehicle in the car-following scenario where control criteria are set by speed and safety. Experimental results show that inappropriate actions chosen by the DDPG controller are detected and revised appropriately through our proposed framework, resulting in no control failures after a few iterations.
Nonlinear observer design for fuel processing reactors in fuel cell power systems (2004)

This work presents nonlinear observer designs for the catalytic partial oxidation (CPO) and the water gas shift (WGS) reactors in fuel cell power systems. The observers make use of available temperature and total pressure measurements and estimate the mole fractions of each species in the reactors. Estimation of H/sub 2/ and CO fractions is particularly useful for monitoring and control of the fuel processor. An advantage of our designs is that they are based on the reaction invariants and do not rely on knowledge of reaction rate expressions.
Cerebrospinal Fluid Neurotransmitter Changes During the Perioperative Period in Patients Undergoing Total Knee Replacement (2011)

In the perioperative period, the concentration changes of the 4 spinal neurotransmitters have a distinct time course. CSF substance P seems to increase very rapidly with surgical intervention, whereas the CSF norepinephrine concentration tends to decrease. At clinical doses, pregabalin does not seem to modulate these spinal neurotransmitter concentrations.
HCIR 2011 (2012)

This report describes the 2011 Workshop on Human-Computer Interaction and Information Retrieval. Now in its fifth year, the workshop was held in October, in Mountain View, CA. The event brings together researchers from academia, industry, and government and a range of disciplines for in-depth discussions in an informal atmosphere. The workshop continues to grow, with around 100 attendees this year. We continued the HCIR Challenge, this time focusing on the problem of information availability, with four in-depth system demonstrations, and audience selection of a challenge winner.
ANTI-CD40L TRANSIENTLY SUPPRESSES PRODUCTION OF ANTI-GAL IgG BUT NOT IgM IN α1,3GALACTOSYLTRANSFERASE KNOCK-OUT MICE IMMUNIZED WITH PIG KIDNEY MEMBRANES. (2000)

1Cardiovascular-Thoracic Surgery, Rush University, Chicago, IL;2Surgery, Rush University, Chicago, IL.
Individual genomic variations as determinants for DNA methylation and gene expression changes in cancer (2013)

This work was supported by the German Ministery for Education and Science winthin the e:Bio programme (EPITREAT, 0316190A) and the EU Seventh Framework Programme (PREDICT, 283775) Driven by the advance of high throughput sequencing (HTS) technology, several new technologies for whole (epi)genome analysis have been developed in recent years. Thanks to these methods, genetic variants, gene expression, and DNA methylation is now reliably detectable at a genome wide scale. Alteration of DNA methylation is a hallmark of cancer. It is thought to locally influence the regulatory potential of DNA, leading to changes in gene expression during development and disease. This correlation has been shown for selective cases, but general relations are not yet known.
Association of Bone Morphogenetic Protein 6 With Exocrine Gland Dysfunction in Patients With Sjögren's Syndrome and in Mice (2013)

In addition to identifying BMP-6 expression in association with xerostomia and xerophthalmia in primary SS, the present results suggest that BMP-6-induced salivary and lacrimal gland dysfunction in primary SS is independent of the autoantibodies and immune activation associated with the disease.
HBx and c-MYC Cooperate to Induce URI1 Expression in HBV-Related Hepatocellular Carcinoma (2019)

Unconventional prefoldin RNA polymerase II subunit 5 interactor (URI1) has emerged as an oncogenic driver in hepatocellular carcinoma (HCC). Although the hepatitis B virus (HBV) represents the most common etiology of HCC worldwide, it is unknown whether URI1 plays a role in HBV-related HCC (HCC-B). In the present study, we investigated URI1 expression and its underlying mechanism in HCC-B tissues and cell lines. URI1 gene-promoter activity was determined by a luciferase assay. Human HCC-B samples were used for a chromatin immunoprecipitation assay. We found that c-MYC induced URI1 expression and activated the <i>URI1</i> promoter through the E-box in the promoter region while the HBx protein significantly enhanced it. The positivity of URI1 expression was significantly higher in HCC-B tumor tissues than in non-HBV-related HCC tumor tissues, suggesting that a specific mechanism underlies URI1 expression in HCC-B. In tumor tissues from HCC-B patients, a significantly higher level of c-MYC was recruited to the E-box than in non-tumor tissues. These results suggest that HBx and c-MYC are involved in URI1 expression in HCC-B. URI1 expression may play important roles in the development and progression of HCC-B because HBx and c-MYC are well-known oncogenic factors in the virus and host, respectively.
Broadband antireflective surface-relief structure for THz optics (2007)

The requirements for a broadband antireflective structure in the THz spectral region are derived. Optimized structural parameters for a surface-relief grating adapted to the spectrum of an intended THz pulse are deduced. The effect of a structure fabricated into Topas((R)) by a single-point diamond-turning process is demonstrated.
Advanced modeling and simulation to design and manufacture high performance and reliable advanced microelectronics and microsystems. (2007)

An interdisciplinary team of scientists and engineers having broad expertise in materials processing and properties, materials characterization, and computational mechanics was assembled to develop science-based modeling/simulation technology to design and reproducibly manufacture high performance and reliable, complex microelectronics and microsystems. The team's efforts focused on defining and developing a science-based infrastructure to enable predictive compaction, sintering, stress, and thermomechanical modeling in ''real systems'', including: (1) developing techniques to and determining materials properties and constitutive behavior required for modeling; (2) developing new, improved/updated models and modeling capabilities, (3) ensuring that models are representative of the physical phenomena being simulated; and (4) assessing existing modeling capabilities to identify advances necessary to facilitate the practical application of Sandia's predictive modeling technology.
Optical Analysis on the Mixture Preparation and Combustion Behavior of Small Two-Stroke SI Engines Fueled with Alcohol-Blends (2017)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Small gasoline engines are used in motorcycles and handheld machinery, because of their high power density, low cost and compact design. The reduction of hydrocarbon emissions and fuel consumption is an important factor regarding the upcoming emission standards and operational expenses. The scavenging process of the two-stroke engine causes scavenging losses [&lt;span class="xref"&gt;1&lt;/span&gt;]. A reduction in hydrocarbon emissions due to scavenging losses can be achieved through a better understanding of the inner mixture formation. The time frame for fuel vaporization is limited using two-stroke SI engines by the high number of revolutions. With crank angle resolved optical methods it is possible to analyze the mixture formation behavior and combustion. A topic of these investigations is the use of alternative fuels such as alcohol- or butanol-blends and the analysis of their impact on the engine behavior. These fuels show high potential for further reduction of exhaust emissions while simultaneously increasing the engine power output.&lt;/div&gt;&lt;/div&gt;
A Bayesian-optimized spline representation of the electrocardiogram (2013)

We introduce an implementation of a novel spline framework for parametrically representing electrocardiogram (ECG) waveforms. This implementation enables a flexible means to study ECG structure in large databases. Our algorithm allows researchers to identify key points in the waveform and optimally locate them in long-term recordings with minimal manual effort, thereby permitting analysis of trends in the points themselves or in metrics derived from their locations. In the work described here we estimate the location of a number of commonly-used characteristic points of the ECG signal, defined as the onsets, peaks, and offsets of the P, QRS, T, and R' waves. The algorithm applies Bayesian optimization to a linear spline representation of the ECG waveform. The location of the knots—which are the endpoints of the piecewise linear segments used in the spline representation of the signal—serve as the estimate of the waveform's characteristic points. We obtained prior information of knot times, amplitudes, and curvature from a large manually-annotated training dataset and used the priors to optimize a Bayesian figure of merit based on estimated knot locations. In cases where morphologies vary or are subject to noise, the algorithm relies more heavily on the estimated priors for its estimate of knot locations. We compared optimized knot locations from our algorithm to two sets of manual annotations on a prospective test data set comprising 200 beats from 20 subjects not in the training set. Mean errors of characteristic point locations were less than four milliseconds, and standard deviations of errors compared favorably against reference values. This framework can easily be adapted to include additional points of interest in the ECG signal or for other biomedical detection problems on quasi-periodic signals.
Induction of stress by the swimbladder nematode Anguillicola crassus in European eels, Anguilla anguilla, after repeated experimental infection (2001)

The purpose of this study was to determine under laboratory conditions over a period of 311 days if infection with the nematode Anguillicola crassus induces stress in European eels (Anguilla anguilla), and stimulates the endocrine stress axis as measured by serum cortisol levels. Eels were experimentally infected with 3rd-stage larvae (L3) in different doses to simulate natural conditions with varying infection pressures. Blood samples were drawn from the caudal vein every 2 weeks and serum cortisol concentrations were determined by radioimmunoassay (RIA). The results showed that the application of L3 resulted in a significant increase in the cortisol levels. The period of time at which elevated cortisol values were observed was consistent with the time of larval development and the appearance of adult A. crassus. Thus, there is a stress response to the larval and young adult stages, but no chronic response to older adults. Therefore, it is likely that infection of eels under natural conditions especially with a high number of larvae may be a considerable stressor, in combination with different environmental factors like water temperature, pH, oxygen concentration, pollution and interindividual relationships.