gebhart/patrepeval huggingface dataset:
The Death of Human Cancer Cells Following Photodynamic Therapy: Apoptosis Competence is Necessary for Bcl‐2 Protection but not for Induction of Autophagy<sup>†</sup> (2007)

Photodynamic therapy (PDT) is an efficient inducer of apoptosis in many types of cells, except in cells deficient in one or more of the factors that mediate apoptosis. Recent reports have identified autophagy as a potential alternative cell death process following PDT. Here we investigated the occurrence of autophagy after PDT with the photosensitizer Pc 4 in human cancer cells that are deficient in the pro-apoptotic factor Bax (human prostate cancer DU145 cells) or the apoptosis mediator caspase-3 (human breast cancer MCF-7v cells) and in apoptosis-competent cells (MCF-7c3 cells that stably overexpress human pro-caspase-3 and Chinese hamster ovary CHO 5A100 cells). Further, each of the cell lines was also studied with and without stably overexpressed Bcl-2. Autophagy was identified by electron microscopic observation of the presence of double-membrane-delineated autophagosomal vesicles in the cytosol and by immunoblot observation of the Pc 4-PDT dose- and time-dependent increase in the level of LC3-II, a component of the autophagosomal membrane. Autophagy was observed in all of the cell lines studied, whether or not they were capable of typical apoptosis and whether or not they overexpressed Bcl-2. The presence of stably overexpressed Bcl-2 in the cells protected against PDT-induced apoptosis and loss of clonogenicity in apoptosis-competent cells (MCF-7c3 and CHO 5A100 cells). In contrast, Bcl-2 overexpression did not protect against the development of autophagy in any of the cell lines or against loss of clonogenicity in apoptosis-deficient cells (MCF-7v and DU145 cells). Furthermore, 3-methyladenine and wortmannin, inhibitors of autophagy, provided greater protection against loss of viability to apoptosis-deficient than to apoptosis-competent cells. The results show that autophagy occurs during cell death following PDT in human cancer cells competent or not for normal apoptosis. Only the apoptosis-competent cells are protected by Bcl-2 against cell death.
Tunable multimode interference coupler (2007)

An electrically tunable multimode interference (MMI) coupler/splitter is demonstrated. The device operates by modifying the phase of the multiple self-images that are formed around the midpoint of the MMI structure. This provides a simple way to fine-tune the 50∶50 output power split ratio or other arbitrary ratio.
Detecting and Sonifying Temporal Patterns of Body Segments When Batting (2018)

To improve skill in sport activities it is essential to discern the temporal patterns of one’s own movements. Our previous motion capture experiment involving elite female softball players identified key differences in the temporal body movements between the top players and young players against fastballs/change-ups. In this paper, we found that key features could be extracted from the rotation of the pelvis and we developed a sonification feedback system with two nine-axes inertial sensors. Rotation patterns are converted into two synthesized sounds to represent the time at peak trunk rotation speed and impact time. We conducted a pilot experiment with this feedback proposal using expert and novice batters, male and female whether the participants can pace of the rotational motion in batting. As a result, this feedback approach may allow the user to alter the time of peak trunk rotation speed to more closely match the cue provided by the training sound.
Mucosal host immune response predicts the severity and duration of herpes simplex virus-2 genital tract shedding episodes (2010)

Herpes simplex virus-2 (HSV-2) shedding episodes in humans vary markedly in duration and virologic titer within an infected person over time, an observation that is unexplained. To evaluate whether host or virological factors more closely accounted for this variability, we combined measures of viral replication and CD8(+) lymphocyte density in genital biopsies, with a stochastic mathematical model of HSV-2 infection. Model simulations reproduced quantities of virus and duration of shedding detected in 1,003 episodes among 386 persons. In the simulations, local CD8(+) lymphocyte density in the mucosa at episode onset predicted peak HSV DNA copy number and whether genital lesions or subclinical shedding occurred. High density of CD8(+) T cells in the mucosa correlated with decreased infected cell lifespan and fewer infected epithelial cells before episode clearance. If infected cell lifespan increased by 15 min because of CD8(+) lymphocyte decay, then there was potential for a thousandfold increase in the number of infected cells. The model suggests that the rate of containment of infected cells by the peripheral mucosal immune system is the major driver of duration and severity of HSV-2 reactivation in the immunocompetent host.
Combination of ultimate magnetization and ultrahigh uniaxial anisotropy in CoFe exchange-coupled multilayers (2005)

CoFe exchanged-coupled multilayers are studied versus the thickness of the ferromagnetic (F) layer (eF) and the thickness of the antiferromagnetic (AF) layer (eAF). The F layer consists in Co90Fe10, Co50Fe50, and Co35Fe65, respectively. The AF layer is Ni50Mn50. Very high saturation magnetization (4πMs) are reported with 18.5, 23, and 24kG, respectively, combined with excellent soft rotational behaviors. The AF–F–AF multilayers cumulate top and bottom interfacial exchange coupling and show very high effective energy densities (Jex) of 1.01, 0.81, and 0.98ergcm−2, respectively. Jex increases with eAF up to a maximum for eAF⩾500Å. This leads to a strong bias field (Hex) with a classical 1∕eF dependence, which translates into a large uniaxial anisotropy (Hk) at 90° from the pinning direction. Typically, for eF=150Å, Hk is 741, 650, and 642Oe, respectively. However, this translation is rather complex and eF and 1∕eAF dependences of the ratio Hk∕Hex suggest a contribution of an intrinsic CoFe anisotropy. For all CoFe, it is shown that a ferromagnetic resonance frequency (fFMR) of 10GHz is achievable. Co35Fe65 mulilayers exhibit the highest eF×μ′ product, μ′ being very close to the theoretical ultimate permeability. Finally, the soft rotational behavior is shown unchanged over an angular range of ±30° from the pinning direction which is very unusual.
Tissue Transglutaminase and the Progression of Human Renal Scarring (2003)

Experimental renal scarring indicates that tissue transglutaminase (tTg) may be associated with the accumulation of extracellular matrix (ECM), both indirectly via TGF-beta1 activation and directly by the formation of epsilon(gamma-glutamyl) lysine dipeptide bonds within the ECM. The latter potentially accelerates deposition and confers the ECM with resistance to proteolytic digestion. Studied were 136 human renal biopsy samples from a range of chronic renal diseases (CRD) to determine changes in tTg and epsilon(gamma-glutamyl) lysine crosslinking. Immunofluorescence for insoluble tTg showed a 14-fold increase in the kidneys of CRD patients (5.3 +/- 0.5 versus 76 +/- 54 mV/cm(2)), which was shown to be active by a similar 11-fold increase in the epsilon(gamma-glutamyl) lysine crosslink (1.8 +/- 0.2 versus 19.3 +/- 14.2 mV/cm(2)). Correlations were obtained with renal function for tTg and crosslink. In situ hybridization for tTg mRNA showed that tubular epithelial cells were the major source of tTg; however, both mesangial and interstitial cells also contributed to elevated levels in CRD. This mRNA pattern was consistent with immunohistochemistry for soluble tTg. Changes in renal tTg and its product, the epsilon(gamma-glutamyl) lysine crosslink, occur in progressive renal scarring in humans independently of the original etiology and in a similar manner to experimental models. tTg may therefore play a role in the pathogenesis of renal scarring and fibrosis in patients with CRD and can therefore be considered a potential therapeutic target.
Lipoprotein lipaseBethesda: a single amino acid substitution (Ala-176----Thr) leads to abnormal heparin binding and loss of enzymic activity. (1990)

The molecular defect that leads to a deficiency of lipoprotein lipase (LPL) activity in the proband from a Bethesda kindred has been identified. The pre- and post-heparin plasma LPL mass in the proband was elevated when compared to controls; however, there was no detectable LPL activity, indicating the presence of a defective enzyme (termed LPLBethesda). Analysis of the patient's post-heparin plasma by heparin-Sepharose affinity chromatography demonstrated that the mutant LPL had an altered affinity for heparin. Southern blot hybridization of the gene for LPLBethesda revealed no major rearrangements. Northern blot analysis of LPLBethesda mRNA from patient monocyte-derived macrophages revealed normal-sized mRNAs (3.4 and 3.7 kilobases) as well as normal cellular mRNA levels when compared to control macrophages. Sequence analysis of polymerase chain reaction-amplified LPL cDNA revealed a G----A substitution at position 781 of the normal LPL gene that resulted in the substitution of an alanine for a threonine at residue 176 and the loss of an SfaNI site present in the normal LPL gene. Amplification of cDNA by the PCR followed by digestion with SfaNI established that the patient was a true homozygote for the mutation. Expression of LPL cDNA in COS-7 cells resulted in the synthesis of a nonfunctional LPL enzyme establishing that the Ala----Thr substitution was the mutation responsible for the inactive LPL. The identification of this mutation in the LPL gene defines a region of the LPL enzyme, at Ala-176, that is essential for normal heparin-binding and catalytic activity. We propose that an amino acid substitution in this critical region of LPLBethesda results in the synthesis of a nonfunctional enzyme that leads to the chylomicronemia syndrome expressed in this proband.
5-(3-Methoxyphenethyl)-4-(2-methoxyphenyl)-4<i>H</i>-1,2,4-triazol-3-ol (2008)

In the mol-ecule of the title compound, C(18)H(19)N(3)O(3), the triazole ring is oriented with respect to the 3-methoxy-phenyl and 2-methoxy-phenyl rings at dihedral angles of 11.79 (3) and 89.22 (3)°, respectively. The dihedral angle between the two benzene rings is 85.95 (3)°. In the crystal structure, inter-molecular O-H⋯N and C-H⋯O hydrogen bonds link the mol-ecules. There is a π-π contact between the triazole and 3-methoxy-phenyl rings [centroid-centroid distance = 3.916 (3) Å]. There is a π-π contact between the triazole and one of the 3-methoxy-phenyl rings [centroid-centroid distance = 3.916 (3) Å ]. C-H⋯π contacts are also found between the benzene ring and the methyl groups of their 3-methoxy-substituents.
Multi-stimuli responsive chromism with tailorable mechanochromic sensitivity for versatile interactive sensing under ambient conditions (2019)

A 3D integration strategy is applied to fabricate multi-stimuli responsive chromic devices that respond to UV, temperature, and mechanical stretching.
High-Resolution Doppler Lidar for Boundary Layer and Cloud Research (2001)

The high-resolution Doppler lidar (HRDL) was developed to provide higher spatial, temporal, and velocity resolution and more reliable performance than was previously obtainable with CO2-laser-based technology. The improved performance is needed to support continued advancement of boundary layer simulation models and to facilitate high-resolution turbulent flux measurements. HRDL combines a unique, eye-safe, near-IR-wavelength, solid-state laser transmitter with advanced signal processing and a high-speed scanner to achieve 30-m range resolution and a velocity precision of ∼10 cm s−1 under a variety of marine and continental boundary layer conditions, depending on atmospheric and operating conditions. An attitude-compensating scanner has been developed to facilitate shipboard marine boundary layer observations. Vertical velocities, fine details of the wind profile near the surface, turbulence kinetic energy profiles, and momentum flux are measurable with HRDL. The system is also useful for cloud studies. The HRDL technology, capabilities, and field performance are discussed.
The role of actin, fimbrin and endocytosis in growth of hyphae in <i>Aspergillus nidulans</i> (2008)

Filamentous fungi are ideal systems to study the process of polarized growth, as their life cycle is dominated by hyphal growth exclusively at the cell apex. The actin cytoskeleton plays an important role in this growth. Until now, there have been no tools to visualize actin or the actin-binding protein fimbrin in live cells of a filamentous fungus. We investigated the roles of actin (ActA) and fimbrin (FimA) in hyphal growth in Aspergillus nidulans. We examined the localization of ActA::GFP and FimA::GFP in live cells, and each displayed a similar localization pattern. In actively growing hyphae, cortical ActA::GFP and FimA::GFP patches were highly mobile throughout the hypha and were concentrated near hyphal apices. A patch-depleted zone occupied the apical 0.5 microm of growing hypha. Both FimA::GFP and Act::GFP also localize transiently to septa. Movement and later localization of both was compromised after cytochalasin treatment. Disruption of fimA resulted in delayed polarity establishment during conidium germination, abnormal hyphal growth and endocytosis defects in apolar cells. Endocytosis was severely impaired in apolar fimA disruption cells. Our data support a novel apical recycling model which indicates a critical role for actin patch-mediated endocytosis to maintain polarized growth at the apex.
A dark yellow fluorescent protein (YFP)-based Resonance Energy-Accepting Chromoprotein (REACh) for Förster resonance energy transfer with GFP (2006)

Förster resonance energy transfer (FRET) microscopy is a powerful technique that enables the visualization of signaling intermediates, protein interactions, and protein conformational and biochemical status. With the availability of an ever-increasing collection of fluorescent proteins, pairs of spectrally different variants have been used for the study of FRET in living cells. However, suitable spectral overlap, necessary for efficient FRET, is limited by the requirement for proper emission separation. Currently used FRET pairs represent compromises between these opposing spectral demands that reduce the maximally attainable FRET sensitivity. We present a previously undescribed FRET acceptor, a nonfluorescent yellow fluorescent protein (YFP) mutant called REACh (for Resonance Energy-Accepting Chromoprotein). REACh allows the use of the photophysically superior FRET donor EGFP, with which it exhibits optimal spectral overlap, which obviates the need for narrow spectral filtering and allows additional fluorescent labels to be used within the same cell. The latter allows the generation of sophisticated bioassays for complex biological questions. We show that this dark acceptor is ideally suited for donor fluorescence lifetime imaging microscopy (FLIM) and confirm these measurements with an independent intensity-based donor fluorescence quenching resonance energy transfer (FqRET) assay. REACh also can be used in donor photobleaching kinetics-based FRET studies. By detecting FRET between a GFP-tagged ubiquitination substrate and REACh-labeled ubiquitin, we imaged the active ubiquitination machinery inside cells. This assay therefore can be used to study proteins whose function is regulated by ubiquitination.
C- versus N-terminally linked melittin-polyethylenimine conjugates: the site of linkage strongly influences activity of DNA polyplexes (2005)

The high potency of C-mel-PEI to destabilize membranes at neutral pH is presumably due to a reported destabilization mechanism proceeding through membrane insertion of the peptide. In contrast, N-mel-PEI is supposed to induce lysis by insertion-independent pore formation according to the toroidal pore model.
The UK D-MAC/packet standard for DBS (1988)

The United Kingdom standard for direct broadcasting by satellite (DBS) is described. A multiplexed analog component (MAC) vision format was devised to overcome the inherent limitations of PAL. The resulting D-MAC/packet system offers improved pictures compared to PAL, together with rugged high-quality digital sound, secure encryption, the flexibility to provide widescreen pictures and, in the future, higher definition. The system is evolutionary in concept, and can be used in conjunction with existing television displays. The single-wire baseband format of D-MAC/packet takes up a bandwidth of approximately 8.5 MHz. It consists of time-compressed components of the luminance and color-difference vision signals, together with a 20.25 Mb/s digital data burst in duobinary form. Frequency modulation is applied for satellite transmission, while for distribution on cable networks, vestigial sideband amplitude modulation can be used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Surface polaritons on metallic wire gratings studied via power losses (1996)

Surface polaritons on metallic wire gratings have been investigated by studying power losses at the grating surface. The dispersion, exhibiting gaps of energy and momentum, respectively, has been obtained from calculated power losses for various grating materials and periods. The propagation mechanism of surface polaritons along this nonadjacent periodic interface and the energy gaps in the dispersion are explained by means of the Kronig-Penney model. The power losses at gold-wire gratings with different profiles have been measured by means of photoacoustic spectroscopy. The experimental results agree with the theoretical predictions. The position of the maximum surface polariton excitation yields interesting information for the characterization of the grating profile. \textcopyright{} 1996 The American Physical Society.
Monoclonal Antibody–Mediated Toxicity in<i>Cryptococcus neoformans</i>Infection: Mechanism and Relationship to Antibody Isotype (1999)

Antibody reagents represent an alternative for the therapy of human cryptococcosis, and monoclonal antibody 18B7 (IgG1) is a candidate for phase I trial in humans with cryptococcosis. However, antibody administration to mice with established Cryptococcus neoformans infection has been reported to produce acute lethal toxicity (ALT). The present study confirmed this phenomenon and investigated the mechanism of ALT. ALT was associated with hemoconcentration, hypotension, and circulatory collapse; however, toxicity could be prevented by platelet-activating factor inhibitor, rat antibody to Fc receptor, or IgM before IgG1. Significant isotype-specific differences were found in ALT, which can be interpreted as consistent with the hypothesis that there are distinct Fc receptors for murine IgG1 and IgG3. The IgM and IgG3 isotype preference in antibody responses to polysaccharide antigens in mice may translate to a lack of toxicity of antigen-antibody complexes during the course of infections with encapsulated pathogens.
Effects of 5-hydroxytamine and its antagonists on hepatic stellate cells. (2006)

HSC expresses 5-hydroxytamine receptors. 5-Hydroxytamine could effect the biological characteristics of HSC through its receptor mediation, and may play a role in the pathogenesis of liver cirrhosis and portal hypertension.
Recent developments in the redox-switched binding of organic compounds (2002)

This review summarizes and puts into context recent advances in the field of redox-switched binding processes, with particular reference to the interaction between redox-active compounds and organic compounds, both charged and neutral. Simple homogeneous, two-component systems are discussed at first as a precursor to sections on more advanced systems (e.g. multi-component and multi-pole) and binding processes involving components attached to a surface.
Learning robot behaviors by evolving genetic programs (2002)

A method for evolving behavior-based robot controllers using genetic programming is presented. Due to their hierarchical nature, genetic programs are useful representing high-level knowledge for robot controllers. One drawback is the difficulty of incorporating sensory inputs. To overcome the gap between symbolic representation and direct sensor values, the elements of the function set in genetic programming is implemented as a single-layer perceptron. Each perceptron is composed of sensory input nodes and a decision output node. The robot learns proper behavior rules based on local, limited sensory information without using an internal map. First, it learns how to discriminate the target using single-layer perceptrons. Then, the learned perceptrons are applied to the function nodes of the genetic program tree which represents a robot controller. Experiments have been performed using Khepera robots. The presented method successfully evolved high-level genetic programs that control the robot to find the light source from sensory inputs.
Stimulation of Proliferation of Rat Hepatic Stellate Cells by Galectin-1 and Galectin-3 through Different Intracellular Signaling Pathways (2003)

We found that the expression of galectin-1 and galectin-3 was significantly up-regulated in hepatic stellate cells (HSCs) both in the course of their transdifferentiation into myofibroblasts, a process of "self-activation," and in the fibrosis of liver tissues. Recombinant galectin-1 and galectin-3 stimulated the proliferation of cultured HSCs via the MEK1/2-ERK1/2 signaling pathway. However, galectin-3 utilized protein kinases C and A to induce this process, whereas galectin-1 did not. We also found that thiodigalactoside, a potent inhibitor of beta-galactoside binding, attenuated the effects of both galectins. In addition, galectin-1, but not galectin-3, promoted the migration of HSCs. Thus, it appears that galectin-1 and galectin-3, generated by activated HSCs, could participate in beta-galactoside binding and induce different intracellular signaling pathways leading to the proliferation of HSCs.
1-Chloro-2-deoxy-3,5-di-<u>p</u>-toluoyl-D-<u>erythro</u>-pentosyl Chloride - A Versatile Synthetic Intermediate (1991)

Abstract Syntheses of 1b-d is described using 1-chloro-2-deoxy-3,5-di-p-toluoyl-D-erythro-pentosyl chloride.
An Airplane Fuel Measurement System by Using Optic Fiber Sensors (2012)

A new type optic fiber pressure sensor is designed by using the mechanism of optical fiber macro-bend loss, which is used in the airplane fuel measurement system to obtain fuel level and density. The ratio method of pressure is adopted in the airplane fuel measurement system to reduce the influence factors, which include the vertical acceleration of a plane, fuel density, the pressure in the tank, etc. A pressure demodulation circuit of high precision and a data processing algorithm of high reliability are designed for measurement system. The experiment shows that the fuel measurement system has the characters of stability, reliability and high accuracy.
A Neural Network for Detailed Human Depth Estimation from a Single Image (2019)

This paper presents a neural network to estimate a detailed depth map of the foreground human in a single RGB image. The result captures geometry details such as cloth wrinkles, which are important in visualization applications. To achieve this goal, we separate the depth map into a smooth base shape and a residual detail shape and design a network with two branches to regress them respectively. We design a training strategy to ensure both base and detail shapes can be faithfully learned by the corresponding network branches. Furthermore, we introduce a novel network layer to fuse a rough depth map and surface normals to further improve the final result. Quantitative comparison with fused `ground truth' captured by real depth cameras and qualitative examples on unconstrained Internet images demonstrate the strength of the proposed method. The code is available at https://github.com/sfu-gruvi-3dv/deep_human.
A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers (2011)

The Jellyfish software is written in C++ and is GPL licensed. It is available for download at http://www.cbcb.umd.edu/software/jellyfish.