gebhart/patrepeval huggingface dataset:
Changes in protein conformation and dynamics upon complex formation of brain‐derived neurotrophic factor and its receptor: Investigation by isotope‐edited Fourier transform IR spectroscopy (2002)

The interactions of brain-derived neurotrophic factor (BDNF) with the extracellular domain of its receptor (trkB) are investigated by employing isotope-edited Fourier transform IR (FTIR) spectroscopy. The protein secondary structures of individual BDNF and trkB in solutions are compared with those in their complex. The temperature dependence of the secondary structures of BDNF, trkB, and their complex is also investigated. Consistent with the crystal structure, we observe by FTIR spectroscopy that BDNF in solution contains predominantly beta strands (approximately 53%) and relatively low contents of other secondary structures including beta turns (approximately 16%), disordered structures (approximately 12%), and loops (approximately 18%) and is deficient in alpha helix. We also observe that trkB in solution contains mostly beta strands (52%) and little alpha helix. Conformational changes in both BDNF and trkB are observed upon complex formation. Specifically, upon binding of BDNF, the conformational changes in trkB appear to involve mostly beta turns and disordered structures while the majority of the beta-strand conformation remains unchanged. The IR data indicate that some of the disordered structures in the loop regions are likely converted to beta strands upon complex formation. The FTIR spectral data of BDNF, trkB, and their complex indicate that more amide NH groups of trkB undergo H-D exchange within the complex than those of the ligand-free receptor and that the thermal stability of trkB is decreased slightly upon binding of BDNF. The FT-Raman spectra of BDNF, trkB, and their complex show that the six intramolecular disulfide bonds of trkB undergo significant conformational changes upon binding of BDNF as a result of changes in the tertiary structure of trkB. Taken together, the FTIR and Raman data are consistent with the loosening of the tertiary structure of trkB upon binding of BDNF, which leads to more solvent exposure of the amide NH group and decreased thermal stability of trkB. This finding reveals an intriguing structural property of the neurotrophin ligand-receptor complex that is in contrast to other ligand-receptor complexes such as a cytokine-receptor complex that usually shows protection of the amide NH group and increased thermal stability upon complex formation.
Analysis and Design using MaSE and agentTool (2001)

This paper provides an overview of the work being done at the Air Force Institute of Technology on the Multiagent Systems Engineering methodology and the associated agentTool environment.Our research is focused on discovering methods and techniques for engineering practical multiagent systems.It uses the abstraction provided by multiagent systems for developing intelligent, distributed software systems.
Calibration of the medical display (2009)

In order to provide doctors with stable and uniform medial diagnosis image,the medical display must be calibrated.The usefulness of sensor is to keeps the monitor at the ideal brightness level under all lighting conditions,in which the lightness of monitor can be adjusted accordingly to the surrounding variation.The lightness compensation function can stabilize the brightness of the medical display within shortest period after starting up,check up and compensate the variation of background lightness,temperature of the LCD and surrounding temperature.There are two ways of calibration,which are inlay automatic and outlay manual brillmeter calibration respectivly.
Propofol Reverses Surgery-Induced Neuroinflammation and Cognitive Impairment in Aged Mice via α5-GABA A Receptors (2022)

Abstract Surgery may lead to long-lasting cognitive deficits that are referred to as perioperative neurocognitive disorder (NCD), particularly in elderly patients. Currently, no interventions are routinely employed in clinical practice to prevent perioperative NCD. Here we show that perioperative chronic intermittent administration of propofol to aged mice undergoing laparotomy under isoflurane anesthesia effectively blocks the surgery-induced increase in nitrosative stress, increased expression of proapoptotic proteins, microglial activation, and cognitive deficits. By contrast, in the absence of surgery and anesthesia, propofol had little effect on biochemical parameters and led to cognitive improvement only in a subset of behavioral paradigms. The actions of propofol were largely absent in mice lacking the GABA A receptor α5-subunit, indicating that they are mediated by α5-containing GABA A receptors. These results demonstrate that propofol – via α5-containing GABA A receptors that are redistributed to the cell surface membranes in a sustained manner – can attenuate surgery-induced neuroinflammation and postsurgical cognitive deficits.
Hard X-ray scanning transmission microscopy with a 2Dpixel array detector (2009)

X-ray microscopy is an invaluable tool for the characterization of life and materials science samples on the submicron length scale. Particularly in case of hard X-rays, it combines high penetration power with elemental, chemical, and magnetic specificity. However, contrast decreases drastically at higher photon energies, and imaging modalities beyond mere absorption measurements become increasingly attractive. We discuss the use of a fully pixelated detector for hard X-ray scanning microscopy of a biological specimen in absorption, phase contrast, and dark-field imaging mode. © 2009 IOP Publishing Ltd.
Линзовый корректор волнового фронта для изучения плоских поверхностей (2021)

The method of manufacturing and the results of studies of a lens corrector that converts a spherical diverging front into a plane one and is intended for studying flat surfaces as part of an interferometer with a diffraction comparison wave is described. A feature of the corrector is the use of an aspherical convex surface with a maximum deviation of ∼200 μm from the nearest sphere. The first experimental results are presented, indicating the prospects for using ion-beam processing to improve the quality of the wavefront. After the procedure of ion-beam processing, the aberrations over the entire aperture of the corrector decreased by more than 4 times and amounted to the parameter of the height difference PV = 207 nm (∼λ/3) and RMS = 19.2 nm (∼λ /33). On an area with a diameter of 80%, the aberrations fell to the nanometer level: PV = 65 nm (∼λ/10) and RMS = 8.3 nm (∼λ/76).
Production of Al/Al<SUB>3</SUB>Ti Composites by Low Pressure Casting-Combustion Synthesis Process (1998)

In order to get net-shape metal-matrix-composites, the LCCS process which is the combination of low pressure casting and combustion synthesis has been proposed. By this process, net-shape Al/Al3Ti MMCs, which contain few cavities, have been produced. Microstructures and mechanical properties of the produced samples were examined. The effective infiltration of molten Al into the Al-Ti mixed powders was observed at the Al mixing ratios higher than 50 at%. On the other hand, the Al mixing ratios less than 50 at% prevents the infiltration of molten Al. The critical mixing ratio, at which the infiltration can complete, is calculated by using a simple formula as a function of the relative density of Al-Ti mixed powders. In the mixing ratio of Ti powder less than the critical mixing ratio, the volume fraction of Al3Ti in the MMC increases with increasing Ti powder content.
Development and applications of diffuse correlation spectroscopy for non-invasive measurement of blood flow in clinics (2016)

Over the last decade, diffuse correlation spectroscopy (DCS) emerged as a promising tool for the non-invasive measurement of blood flow. I describe the clinical applications of DCS and outline future directions.
Effects of bandwidth on joint estimation performance of direction-of-departure and direction-of-arrival in ultra-wideband MIMO radar (2014)

In direction estimation applications, several angle estimation algorithms in multiple-input multiple-output (MIMO) radars were proposed, including joint estimation of direction-of-departure (DOD) and direction-of-arrival (DOA). Nevertheless, these reports were mainly based on narrowband signal assumption. Target localization using the narrowband signal, however, was unstable due to radar cross section fluctuation. The authors proposed a joint DOD and DOA estimation in an ultra-wideband (UWB) MIMO radar system (Pasya et al., IEEE Radio Wireless Symposium 2014, to be published). The proposed scheme utilized a two-way MUSIC algorithm to estimate the respective DOD and DOA at each frequency component. Among these angle estimations, wideband DOD and DOA were then estimated by majority decisions. This report studies the effects of signal bandwidth on the performance of the proposed angle estimation scheme.
Ionic Mechanisms Underlying the Positive Chronotropy Induced by β1-Adrenergic Stimulation in Guinea Pig Sinoatrial Node Cells: a Simulation Study (2008)

Positive chronotropy induced by beta1-adrenergic stimulation is achieved by multiple interactions of ion channels and transporters in sinoatrial node pacemaker cells (SANs). To investigate the ionic mechanisms, we updated our SAN model developed in 2003 and incorporated the beta1-adrenergic signaling cascade developed by Kuzumoto et al. (2007). Since the slow component of the delayed rectifier K+ current (IKs) is one of the major targets of the beta1-adrenergic cascade, we developed a guinea pig model with a large IKs. The new model provided a good representation of the experimental characteristics of SANs. A comparison of individual current during diastole recorded before and after beta1-adrenergic stimulation clearly showed the negative shift of the L-type Ca2+ current (ICaL) takeoff potential, enlargement of the sustained inward current (I st), and the hyperpolarization-activated nonselective cation current (Iha) played major roles in increasing the firing frequency. Deactivation of IKs during diastole scarcely contributed to the time-dependent decrease in membrane K+ conductance, which was the major mechanism for slow diastolic depolarization, as indicated by calculating the instantaneous equilibrium potential (lead potential). This was because the activation of IKs during the preceding action potential was negligibly small. However, IKs was important in counterbalancing the increase in ICaL and the Na+/Ca2+ exchange current (INaCa), which otherwise compromised the positive chronotropic effect by elongating the action potential duration. Enhanced Ca2+ release from the sarcoplasmic reticulum failed to induce an obvious chronotropic effect in our model.
INVERSE EMULSION POLYMERIZATION OF ACRYLAMIDE: POLYMERIZATION KINETICS AND PROCESS DEVELOPMENT (1984)

ABSTRACT Inverse emulsion polymerization confers the benefits of emulsion polymerization kinetics — rapid polymerization rates combined with high polymer molecular weights — on water-soluble polymers, particularly polyacrylamide and its copolymers and derivatives, and allows easy dissolution of the polymer in water by inversion of the latex. The mechanism and kinetics of the inverse emulsion polymerization of acrylamide in o-xylene containing Tetronic 1102 emulslfier and benzoyl peroxide initiator are described, particularly the formation of 10-200nm multiple emulsion droplets resulting from the particulate emulsifier, and their effect on the polymerization process
Universal Parameter Evaluating SiO<sub>2</sub>/SiC Interface Quality Based on Scanning Nonlinear Dielectric Microscopy (2017)

Oxidized both silicon-face (Si-face) and carbon-face (C-face) wafers with various post-oxidation-annealing conditions were measured by scanning nonlinear dielectric microscopy (SNDM) and method for evaluating SiO 2 /SiC interface quality using SNDM was investigated. We found that the normalized standard deviation of SNDM image was good parameter to evaluate SiO 2 /SiC interface of Si and C-face. SNDM measurement does not need electrode fabrication to measure C - V curve, but needs just scan on the oxidized wafer with conductive tip, which is easier and quicker. This technique enables us to quickly examine the effect of variation of process parameters in MOS fabrication and to effectively reduce the time needed for R&amp;D cycle.
Reliable prediction of clinical outcome in patients with chronic HCV infection and compensated advanced hepatic fibrosis: a validated model using objective and readily available clinical parameters (2014)

Prognosis of patients with chronic HCV infection and compensated advanced liver disease can be accurately assessed with risk scores including readily available objective clinical parameters.
Ensembles of Support Vector Data Description for Active Learning Based Annotation of Affective Corpora (2015)

The present work aims primary at developing an approach to detect irregular and spontaneous facial gestures in video sequences. The developed approach should help a system distinguish between neutral facial expressions characterized by the absence of facial gestures and facial events characterized by the presence of observable facial gestures in video sequences. For this purpose, an active learning approach is proposed in order to avoid the task of annotating an entire video sequence before proceeding with the classification. It is well known that the annotation task is hard, expensive and error prone. Each video sequence is segmented into smaller segments that are then to be investigated and annotated based on the absence or presence of facial gestures. The approach consists in first selecting a set of samples classified as uncharacteristic through the majority vote of a committee of support vector data description (SVDD) models generated randomly. The base learner then focuses on the selected outliers and not on the whole annotated corpus. Different query strategies are used to select the most informative samples among the selected outliers. Those samples are then annotated by the user and added to a pool of annotated samples. The latter is subsequently used to train the base learner again before the next iteration can take place. Experiments suggest that the proposed active learning approach performs as well as a system trained on a fully annotated corpus, while dramatically reducing the cost of annotation.
Correction: Characterization of Spontaneous and TGF-β-Induced Cell Motility of Primary Human Normal and Neoplastic Mammary Cells In Vitro Using Novel Real-Time Technology (2013)

The clinical complications derived from metastatic disease are responsible for the majority of all breast cancer related deaths. Since cell migration and invasion are a prerequisite for metastasis their assessment in patient cancer cells in vitro may have prognostic value for the tumor's metastatic capacity. We employed real-time cell analysis (RTCA) on the xCELLigence DP system to determine in vitro motility of patient-derived primary human breast cancer epithelial cells (HBCEC). Initially, the RTCA assay was validated using established human breast cancer cell lines with either an invasive (MDA-MB-231, MDA-MB-435s) or a non-invasive phenotype (MCF-7, MDA-MB-468), and primary NSCLC cells (Tu459). Previous standard assays of cell migration/invasion revealed that only MDA-MB-231, 2435s, and Tu459 cells exhibited spontaneous and TGF-b1-stimulated migration and invasion through a Matrigel barrier. In the present study, the TGF-b1stimulated activities could be blocked by SB431542, a potent kinase inhibitor of the TGF-b type I receptor ALK5. Application of the RTCA assay to patient-derived tumor cells showed that 4/4 primary HBCEC and primary NSCLC cells, but not normal human mammary epithelial cells (HMEC), displayed high spontaneous migratory and invasive activity which correlated with higher MMP-2 expression and uPA protein levels in HBCEC compared to HMEC. Upon treatment with TGF-b1, HBCEC exhibited morphologic and gene regulatory alterations indicative of epithelial-to-mesenchymal transition. However, exclusively the invasive but not the migratory activity of HBCEC was further enhanced by TGF-b1. This indicates the requirement for molecular, e.g. integrin interactions with Matrigel components in HBCEC in order to become responsive to pro-invasive TGF-b effects. Together, these results show for the first time that tumorigenic HBCEC but not normal HMEC possess a strong basal migratory as well as a basal and TGF-b1-inducible invasive potential. These findings qualify the RTCA assay as an in vitro migration/invasion testing system for patient-specific primary breast cancer cells.
Preferência de Diabrotica speciosa (Germar) (Coleoptera: Chrysomelidae) para oviposição em diferentes tipos e umidade de solos (2000)

Foi estudada a preferência de oviposição de Diabrotica speciosa (Germar, 1824), em relação a diferentes tipos de solo e diferentes umidades, em teste de livre escolha. Os experimentos foram realizados em laboratório à temperatura de 25 ± 2ºC, UR de 60 ± 10% e fotofase de 14h. Os resultados evidenciaram uma acentuada preferência de oviposição por solo tipo Terra Roxa Estruturada Distrófica de cor escura, com umidade variando entre 26 a 63%.
Transformation Networks for Target-Oriented Sentiment Classification (2018)

Target-oriented sentiment classification aims at classifying sentiment polarities over individual opinion targets in a sentence. RNN with attention seems a good fit for the characteristics of this task, and indeed it achieves the state-of-the-art performance. After re-examining the drawbacks of attention mechanism and the obstacles that block CNN to perform well in this classification task, we propose a new model to overcome these issues. Instead of attention, our model employs a CNN layer to extract salient features from the transformed word representations originated from a bi-directional RNN layer. Between the two layers, we propose a component to generate target-specific representations of words in the sentence, meanwhile incorporate a mechanism for preserving the original contextual information from the RNN layer. Experiments show that our model achieves a new state-of-the-art performance on a few benchmarks.
Clinical patterns and treatment outcome of elderly patients in clinical stage IB/II non‐small cell lung cancer (2004)

These above observations suggest that radiotherapy is an alternative strategy for patients who cannot undergo surgery, especially with adenocarcinoma.
Stages of sleep pathology in spinocerebellar ataxia type 2 (SCA2) (2006)

Progressive loss of dream recall in spinocerebellar ataxia type 2 was found and correlated with stages of REM more than non-REM pathology in video-polysomnography. These stages correspond to the progressive atrophy from the pons, nigrostriatal projection, and locus ceruleus to the thalamus.
Generation and persistence of human tissue-resident memory T cells in lung transplantation (2019)

Tissue-resident memory T cells (T<sub>RM</sub>) maintain immunity in diverse sites as determined in mouse models, whereas their establishment and role in human tissues have been difficult to assess. Here, we investigated human lung T<sub>RM</sub> generation, maintenance, and function in airway samples obtained longitudinally from human leukocyte antigen (HLA)-disparate lung transplant recipients, where donor and recipient T cells could be localized and tracked over time. Donor T cells persist specifically in the lungs (and not blood) of transplant recipients and express high levels of T<sub>RM</sub> signature markers including CD69, CD103, and CD49a, whereas lung-infiltrating recipient T cells gradually acquire T<sub>RM</sub> phenotypes over months in vivo. Single-cell transcriptome profiling of airway T cells reveals that donor T cells comprise two T<sub>RM</sub>-like subsets with varying levels of expression of T<sub>RM</sub>-associated genes, whereas recipient T cells comprised non-T<sub>RM</sub> and similar T<sub>RM</sub>-like subpopulations, suggesting de novo T<sub>RM</sub> generation. Transplant recipients exhibiting higher frequencies of persisting donor T<sub>RM</sub> experienced fewer adverse clinical events such as primary graft dysfunction and acute cellular rejection compared with recipients with low donor T<sub>RM</sub> persistence, suggesting that monitoring T<sub>RM</sub> dynamics could be clinically informative. Together, our results provide spatial and temporal insights into how human T<sub>RM</sub> develop, function, persist, and affect tissue integrity within the complexities of lung transplantation.
Video fluorescein imaging of the skin: description of an overviewing technique for functional evaluation of regional cutaneous blood perfusion in occlusive arterial disease of the limbs (1997)

In peripheral arterial occlusive disease (PAOD), and particularly in critical limb ischaemia, fluorescence recording of the skin after i.v. injection of sodium fluorescein provides an overviewing functional imaging of regional blood perfusion as revealed by a continuous, almost geographical, mapping of changes in the dynamic fluorescence pattern. Based on the previously used technique of rapid sequence flash photography introduced by Lund and Lund in 1973, a new video fluorescence imaging (VFI) technique has been developed and used in clinical routine. VFI has a broad versatility with non-touch access to areas of different size, such as the feet, hands or larger limb areas. Examples of application are the diagnosis of small artery disease, predictive prognosis of critical limb ischaemia, evaluation of distal outflow in connection with arterial reconstruction or pharmacotherapy of non-reconstructable critical ischaemia, as well as in decisions on amputation and assessment of amputation level. Thanks to its overviewing qualities with reproducible mapping of blood perfusion in standardized examination conditions, VFI would seem to have a well-justified role in angiology and above all in PAOD in both research and clinical routine work.
NO alters cell shape and motility in aortic smooth muscle cells via protein tyrosine phosphatase 1B activation (1999)

Cell motility is an important determinant of vascular disease. We examined mechanisms underlying the effect of nitric oxide (NO) on motility in cultured primary aortic smooth muscle cells from newborn rats. The NO donor S-nitroso-N-acetyl-penicillamine (SNAP) increased the activity of protein tyrosine phosphatase 1B (PTP-1B). This effect was mimicked by a cGMP analog and blocked by the guanyl cyclase antagonist 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, indicating the involvement of cGMP. Treatment of cells with antisense, but not control oligodeoxynucleotide (ODN), against PTP-1B attenuated the inhibitory effect of NO on cell motility. Cell shape and adhesion are important determinants of cell motility. We report that SNAP induced cell rounding and reduced adhesion and caused dissociation of actin stress fibers. Moreover, SNAP reduced phosphotyrosine levels in focal adhesion proteins, paxillin, and focal adhesion kinase. The PTP inhibitor phenylarsine oxide or decrease of PTP-1B protein levels via the use of antisense ODN prevented NO-induced cell-shape change, altered adhesion, and migration. These results indicate that NO regulates cell shape, adhesion, and migration by dephosphorylation of focal adhesion proteins via a mechanism that requires PTP-1B activity.