gebhart/patrepeval huggingface dataset:
HEARTS LACKING DONOR-TYPE ANTIGEN PRESENTING CELLS DEVELOP CARDIAC ALLOGRAFT VASCULOPATHY (1998)

145 Background: Previous studies have shown that depletion of donor-type bone marrow-derived antigen presenting cells (APCs) from rat renal allografts leads to prolonged survival. However, these studies have not examined grafts histologically for the presence of graft vasculopathy. We have depleted donor-type APCs from rat hearts using both “organ parking” and bone marrow transplantation (BMT) and we have confirmed APC replacement using flow cytometry, mixed lymphocyte response (MLR), immunohistochemistry, and reverse transcriptase polymerase chain reaction(RT-PCR). The goal of this study was to use chimeric hearts to test whether donor APC depletion prevents cardiac allograft vasculopathy (CAV). Methods: PVG hearts were depleted of PVG APCs by two methods: DA→PVG BMT and “parking” of PVG hearts in cyclosporine-treated DA recipients. APC replacement was ≥ 99.9% as assessed by two-color flow cytometry, MLR, immunohistochemistry and RT-PCR. Chimeric PVG hearts or PVG hearts bearing PVG APCs were transplanted heterotopically into DA rats. Recipients received no immunosuppression. Rejection was assessed by palpation. Rejected hearts and those surviving >100 days were examined histologically in a blinded fashion. Results: All PVG hearts bearing PVG APCs (n=21) were acutely rejected, whereas PVG hearts lacking PVG APCs (n=23) had significantly(p<.00001, Breslow) prolonged survival. However all long surviving PVG grafts had histologic evidence of moderate to severe CAV.TableConclusion: Depletion of donor APCs in rat heart grafts leads to prolonged survival, but does not prevent cardiac allograft vasculopathy (CAV). This finding lends credence to the hypothesis that CAV is a consequence of indirect allorecognition, since the lack of donor-type APCs prevents the direct pathway.
Protein microarrays using liquid phase fractionation of cell lysates (2003)

We describe an approach in which protein microarrays are produced using a two-dimensional (2-D) liquid phase fractionation of cell lysates. The method involves a pI-based fractionation using chromatofocusing in the first dimension followed by nonporous reversed-phase high-performance liquid chromatography (HPLC) of each pI fraction in the second dimension. This allows fractionation of cellular proteins in the liquid phase that could then be arrayed on nitrocellulose slides and used to study humoral response in cancer. Protein microarrays have been used to identify potential serum biomarkers for prostate cancer. It is shown that specific fractions are immunoreactive against prostate cancer serum but not against serum from healthy individuals. These proteins could serve as sero-diagnostic markers for prostate cancer. Importantly, this method allows for use of post-translationally modified proteins as baits for detection of humoral response. Proteins eliciting an immune response are identified using the molecular mass and peptide sequence data obtained using mass spectrometric analysis of the liquid fractions. The fractionation of proteins in the liquid phase make this method amenable to automation.
Direct Method of Search for Optimal Xenon Oscillation Control Based on New Concept of Axial Offsets (1992)

A new concept for control of Xe oscillations is applied to solve an optimal control problem. The concept is based on two additional newly defined axial offsets, AOi and AOx together with the conventional axial offset AOP of axial power distribution. The AOi and AOx are the axial offsets of power distributions which would give the current I and Xe distributions under equilibrium condition, respectively. Using these three AOs the necessary condition for a Xe oscillation to be controlled or suppressed can be clearly and simply expressed. In other words, when these three AOx meet together that is the point that the Xe oscillation dies out. Using this simple requirement as the target for Xe oscillation control, the solutions of some optimal problems can also be obtained quite straightforwardly. An example is presented to solve the shortest control time problem known as bang-bang control.
Identification of a hard surface contact‐induced gene in Colletotrichum gloeosporioides conidia as a sterol glycosyl transferase, a novel fungal virulence factor (2002)

Hard surface contact has been known to be necessary to induce infection structure (appressorium) formation in many phytopathogenic fungi. However, the molecular basis of this requirement is unknown. We have used a differential display approach to clone some of the genes induced in the conidia by hard surface contact. We report that one of the genes induced by hard-surface contact of the conidia of Colletotrichum gloeosporioides, chip6, encodes a protein with homology to sterol glycosyl transferases. chip6 expressed in E. coli catalyses glucosyl transfer from UDP-glucose to cholesterol. Disruption of chip6 causes a marked decrease in the transferase activity and a drastic reduction in virulence on its natural host, avocado fruits, although the mutant is capable of normal growth and appressorium formation. The requirement for sterol glycosyl transferase for pathogenicity suggests a novel biological function for this transferase.
Molecular and functional characterization of an Ih‐channel from lobster olfactory receptor neurons (2005)

We isolated a cDNA named PAIH encoding a member of the I(h)-channel family expressed in olfactory receptor neurons (ORNs) of the spiny lobster Panulirus argus. Functional expression of recombinant PAIH in HEK293 cells generated a slowly activating, noninactivating inward current under whole-cell voltage-clamp to hyperpolarizing voltage steps, the amplitude and activation rate of which increase with increasing hyperpolarization. The channel is weakly selective for K+. Intracellular cAMP or cGMP shifts activation of the current to less negative potentials in a concentration-dependent manner. Finally, the channel is blocked by the I(h)-channel blocker ZD7288. An I(h)-channel sharing the properties of the recombinant channel occurs in cultured lobster ORNs. PAIH immunoreactivity localizes the protein to the transduction compartment of the ORNs in situ, and selectively applying the blocker to the transduction compartment reduces spontaneous activity in the ORN. Collectively, these results implicate for the first time a functional role for an I(h)-channel in olfactory signal transduction.
The adaptive potential of a survival artist: characterization of thein vitrointeractions ofToxoplasma gondiitachyzoites with di-cationic compounds in human fibroblast cell cultures (2011)

The impact of di-cationic pentamidine-analogues against Toxoplama gondii (Rh- and Me49-background) was investigated. The 72 h-growth assays showed that the arylimidamide DB750 inhibited the proliferation of tachyzoites of T. gondii Rh and T. gondii Me49 with an IC(50) of 0·11 and 0·13 μM, respectively. Pre-incubation of fibroblast monolayers with 1 μM DB750 for 12 h and subsequent culture in the absence of the drug also resulted in a pronounced inhibiton of parasite proliferation. However, upon 5-6 days of drug exposure, T. gondii tachyzoites adapted to the compound and resumed proliferation up to a concentration of 1·2 μM. Out of a set of 32 di-cationic compounds screened for in vitro activity against T. gondii, the arylimidamide DB745, exhibiting an IC(50) of 0·03 μM and favourable selective toxicity was chosen for further studies. DB745 also inhibited the proliferation of DB750-adapted T. gondii (IC(50)=0·07 μM). In contrast to DB750, DB745 also had a profound negative impact on extracellular non-adapted T. gondii tachyzoites, but not on DB750-adapted T. gondii. Adaptation of T. gondii to DB745 (up to a concentration of 0·46 μM) was much more difficult to achieve and feasible only over a period of 110 days. In cultures infected with DB750-adapted T. gondii seemingly intact parasites could occasionally be detected by TEM. This illustrates the astonishing capacity of T. gondii tachyzoites to adapt to environmental changes, at least under in vitro conditions, and suggests that DB745 could be an interesting drug candidate for further assessments in appropriate in vivo models.
Supplementary Methods, Figure Legends from IDH1 Mutations Alter Citric Acid Cycle Metabolism and Increase Dependence on Oxidative Mitochondrial Metabolism (2023)

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OSCAR is an FcRγ-associated receptor that is expressed by myeloid cells and is involved in antigen presentation and activation of human dendritic cells (2004)

We have isolated a novel cell surface molecule, the human homolog of osteoclast-associated receptor (OSCAR). Unlike mouse OSCAR, hOSCAR is widely transcribed in cells of the myeloid lineage. Notably, hOSCAR is expressed on circulating blood monocytes and CD11c(+) dendritic cells but not on T and B cells. hOSCAR is continually expressed during differentiation of CD14(+) monocytes into dendritic cells and maintained after maturation. hOSCAR associates with the FcRgamma as shown by translocation of FcRgamma to the cell surface in presence of hOSCAR and coimmunoprecipitation from transfected cell lines and ex vivo cells. Engagement of hOSCAR with specific mAb leads to Ca(2+) mobilization and cytokine release, indicators of cellular activation. Endocytosis of the receptor in dendritic cells was observed, followed by passage of the internalized material into Lamp-1(+) and HLA-DR(+) compartments, suggesting a role in antigen uptake and presentation. Dendritic cells were able to stimulate a T-cell clone specific for an epitope of mouse IgG1 after uptake and processing of the hOSCAR-specific antibody, demonstrating the capacity of this receptor to mediate antigen presentation. hOSCAR thus represents a novel class of molecule expressed by dendritic cells involved in the initiation of the immune response.
P6C-10 Evaluation of the Structure Factor Size Estimator (SFSE) with Simulated Ultrasonic Backscattered Signals from Blood (2007)

Ultrasonic backscattered signals from blood contain frequency-dependent information that can be used to obtain quantitative parameters reflecting the aggregation state of red blood cells (RBCs). Recently, the structure factor size estimator (SFSE) was developed to solve for two parameters: the packing factor W and mean gyration radius of aggregates R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> , expressed in number of RBCs (Yu and Cloutier 2007, J. Acoust. Soc. Am. 122 645-656). Herein, the SFSE is assessed by computer simulations where deterministic rheology parameters, such as the hematocrit, number of RBCs per aggregate, and mean gyration radius of aggregates, are known. RBC aggregation was simulated at 40% hematocrit and mean gyration radii of clusters ranged from 1.6 (quasi-disaggregated RBCs) to 6.4. US frequencies were varied between 20 and 42 MHz, and the insoniflcation angle was fixed to 90deg (perpendicular to the flow). For the quasi-disaggregated RBCs, the packing factor W evaluated with the SFSE from the simulated signals matched those expected from theory: W was similar to the Perkus Yevick packing factor. For aggregating RBCs, good correlation was obtained between the gyration radii evaluated with the SFSE model and those expected (r <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.96). To conclude, this study shows the SFSE ability to estimate blood backscattering properties at a physiological hematocrit of 40% and open the way to parametric imaging (using the SFSE) in abnormal blood conditions promoting thrombosis.
Femtosecond pulse propagation in air: Variational analysis (2000)

We use a variational method to study the phenomenon of intense femtosecond pulse propagation in air. This method allows us to obtain a semianalytical solution to the problem in which a wide range of initial conditions can be studied. In addition, it provides a simple physical interpertation, where the problem is reduced to an analogous problem of a particle moving in a potential well. Different types of possible solutions are considered, with focus upon the main physical interpretations. The results recapture at least qualitatively some of the major experimental observations, and previous numerical simulations.
Transceiver Design in Full-Duplex MIMO Cognitive Radios Under Channel Uncertainties (2016)

In this paper, the operation of a full-duplex (FD) multiple-input multiple-output (MIMO) underlay cognitive radio (CR) network is studied. Each pair of secondary users (SUs) operate in FD mode, and each SU communicates with its peer within the coverage area of multiple primary users (PUs). Each SU suffers from self-interference, along with interference created by all other SUs and, in its turn, generates interference towards the PU. We assume that the channel-state-information (CSI) of the interference links between the SUs and the PU is imperfectly known and the channel estimation errors are norm bounded. Under such channel uncertainties, we address the problem of robust minimization of the aggregate mean-squared-error (MSE) of all estimated symbols, subject to a set of transmit power constraints, as well as interference constraints, with the aim of protecting PU communication. It is shown that the problem can be cast as a semidefinite programming problem and the optimal precoding matrices can be obtained via an iterative algorithm. By means of simulation, the proposed FD precoding scheme is shown to outperform the standard half-duplex scheme.
Finite-dimensional methods for computing the information state in nonlinear robust control (2002)

In nonlinear output robust control and in nonlinear risk-sensitive partially observed stochastic control, the optimal control is a memoryless function of the information state. The information state dynamics are directly influenced by the control performance metric, thus displaying a direct linkage between control objectives and sufficient statistics for control. It has been observed in several examples that by modifying the control performance metric one can render the dynamics of the information state finite dimensional. In linear robust control, it is well known that the information state can be computed by a simple finite-dimensional formula. Using the Lie theory for transformations of this basic solution, we show how the information state for certain nonlinear control problems can also be obtained using finite-dimensional calculations, e.g. via the solution of systems of ODE. This is explained using fundamental results on the invariance groups of the equations involved. An intuitive interpretation of the significance of the result is also provided.
Interstellar: Using Halide's Scheduling Language to Analyze DNN Accelerators (2018)

We show that DNN accelerator micro-architectures and their program mappings represent specific choices of loop order and hardware parallelism for computing the seven nested loops of DNNs, which enables us to create a formal taxonomy of all existing dense DNN accelerators. Surprisingly, the loop transformations needed to create these hardware variants can be precisely and concisely represented by Halide's scheduling language. By modifying the Halide compiler to generate hardware, we create a system that can fairly compare these prior accelerators. As long as proper loop blocking schemes are used, and the hardware can support mapping replicated loops, many different hardware dataflows yield similar energy efficiency with good performance. This is because the loop blocking can ensure that most data references stay on-chip with good locality and the processing units have high resource utilization. How resources are allocated, especially in the memory system, has a large impact on energy and performance. By optimizing hardware resource allocation while keeping throughput constant, we achieve up to 4.2X energy improvement for Convolutional Neural Networks (CNNs), 1.6X and 1.8X improvement for Long Short-Term Memories (LSTMs) and multi-layer perceptrons (MLPs), respectively.
Selective Inclusion of Electron‐Donating Molecules into Porphyrin Nanochannels Derived from the Self‐Assembly of Saddle‐Distorted, Protonated Porphyrins and Photoinduced Electron Transfer from Guest Molecules to Porphyrin Dications (2007)

A doubly protonated hydrochloride salt of a saddle-distorted dodecaphenylporphyrin (H2DPP), [H4DPPP]Cl2, forms a porphyrin nanochannel (PNC). X-ray crystallography was used to determine the structure of the molecule, which revealed the inclusion of guest molecules within the PNC. Electron-donating molecules, such as p-hydroquinone and p-xylene, were selectively included within the PNC in sharp contrast to electron acceptors, such as the corresponding quinones, which were not encapsulated. This result indicates that the PNC can recognize the electronic character and steric hindrance of the guest molecules during the course of inclusion. ESR measurements (photoirradiation at lambda>340 nm at room temperature) of the PNC that contains p-hydroquinone, catechol, and tetrafluorohydroquinone guest molecules gave well-resolved signals, which were assigned to cation radicals formed without deprotonation based on results from computer simulations of the ESR spectra and density functional theory (DFT) calculations. The radicals are derived from photoinduced electron transfer from the guest molecules to the singlet state of H4DPP2+. Transient absorption spectroscopy by femtosecond laser flash photolysis allowed us to observe the formation of 1(H4DPP2+)*, which is converted to H4DPP+. by electron transfer from the guest molecules to 1(H4DPP2+)*, followed by fast disproportionation of H4DPP+., and charge recombination to give diamagnetic species and the triplet excited state 3(H4DPP2+)*, respectively.
SPDT RF MEMS switch using a single bias voltage and based on dual series and shunt capacitive MEMS switches (2005)

A coplanar waveguide (CPW) single-pole double-throw (SPDT) X-band RF MEMS switch that can be actuated between states by applying a single voltage is introduced. Since a signal can be transmitted to one of the output ports without biasing, this has the potential to reduce the complexity of the required biasing network. The switch consists of a series and a shunt capacitive MEMS switch separated by a quarter wavelength transmission line. The shunt switch section was fabricated and measured separately and shown to have an insertion loss of 0.25 dB and isolation of 33 dB at 10 GHz. A SPDT 3-port switch was fabricated and port isolations of about 15 dB and an insertion loss of 1 dB were obtained in the up-state. In the down-state, 40 dB of isolation with a 1 dB insertion loss were measured. The actuation voltage was 35 V.
Supplementary Figure 9 from Genomic Alterations of Anaplastic Lymphoma Kinase May Sensitize Tumors to Anaplastic Lymphoma Kinase Inhibitors (2023)

Supplementary Figure 9 from Genomic Alterations of Anaplastic Lymphoma Kinase May Sensitize Tumors to Anaplastic Lymphoma Kinase Inhibitors
Stochastic Recurrent Dynamics of Complex Systems of Solitons (2010)

We study networks made up of interacting solitons (solitonets), and find that their dynamics exhibits stochastic recurrent behavior, independent of the topology, where the interaction rule at the single-node level can be used to predict the dynamics of the entire network. The ideas are general, not specific to solitonets: they apply to many kinds of networks whose dynamics converges to a recurrent structure.
Three-Phase Two-Phase-Clamped Boost-Buck Unity Power Factor Rectifier Employing Novel Variable DC Link Voltage Input Current Control (2018)

Battery chargers supplied from the three-phase mains are typically realized as two-stage systems consisting of a three-phase PFC boost-type rectifier with an output DC link capacitor followed by a DC/DC buck converter if boost and buck functionality is required. In this paper, a new modulation scheme for this topology is presented, where always only one out of three rectifier half-bridges is pulse width modulated, while the remaining two phases are clamped and therefore a higher efficiency is achieved. This modulation concept with a minimum number of active half-bridges, denoted as 1/3 rectifier, becomes possible if in contrast to other modulation schemes the intermediate DC link voltage is varied in a six-pulse voltage fashion, while still sinusoidal grid currents in phase with their corresponding phase voltages and a constant battery output voltage are obtained. In this paper, a detailed description of the novel 1/3 rectifier's operating principle and the corresponding control structure are presented and the proper closed loop operation is verified by means of a circuit simulation. Finally, the performance gain of the 1/3 rectifier control scheme compared to conventional modulation schemes is evaluated by means of a virtual prototype system.
Mechanisms of Desensitization and Resensitization of Proteinase-activated Receptor-2 (1996)

Proteinase-activated receptor-2 (PAR-2) is a G-protein-coupled receptor that is expressed by intestinal epithelial cells, which are episodically exposed to pancreatic trypsin in the intestinal lumen. Trypsin cleaves PAR-2 to expose a tethered ligand, which irreversibly activates the receptor. Thus, PAR-2 may desensitize and resensitize by novel mechanisms. We examined these mechanisms in kidney epithelial cells, stably expressing human PAR-2, and intestinal epithelial cells, which naturally express PAR-2. Trypsin stimulated a prompt increase in [Ca2+]i, due to mobilization of intracellular Ca2+, followed by a sustained plateau, due to influx of extracellular Ca2+. Repeated application of trypsin caused marked desensitization of this response, which is due in part to (a) irreversible cleavage of the receptor by trypsin and (b) protein kinase C-mediated termination of signaling. Trypsin exposure resulted in internalization of PAR-2 into early endosomes and then lysosomes; but endocytosis was not the mechanism of rapid desensitization. Thus, activated PAR-2 is endocytosed and degraded. The Ca2+ response to trypsin resensitized by 60-90 min. Brefeldin A, which disrupted Golgi stores of PAR-2, and cycloheximide, which inhibited protein synthesis, markedly attenuated resensitization. Thus, PAR-2-mediated Ca2+ mobilization desensitizes by irreversible receptor cleavage, protein kinase C-mediated termination of signaling, and PAR-2 targeting to lysosomes. It resensitizes by mobilization of large Golgi stores and synthesis of new receptors.
Recent Development in Chemical Reaction Engineering Utilizing Light and Active Species. (1999)

沿面コロナ放電装置を用いた直結型と分離型の2つの異なるイオン化CVD装置を製作した.直結型イオン化CVD装置でTEOS/O3-APCVD膜をsi基板上に形成したところ, 膜が沈着する箇所としない箇所がmm間隔で交互にでき, その結果沈着部分は等高線のような模様を描いた.これはイオンが基板に沈着したことによるチャージアップが原因と考えられる.分離型イオン化CVD装置では, ほぼ厚さの均一な膜が基板の全面を覆った.この装置では, イオン化により1hあたりの成膜量が1.3～1.5倍増加した.また, 膜の表面形状は沿面放電を行わなかったときには, 等方成長を示し流動性が見られないのに対し, イオン化をした場合には反応管内の全ての位置において高い流動性が確認された.また, イオン化しないときにガス中に発生するナノメーターサイズの粒子は, イオン化によりその発生が抑制された.
Fingerprint Representation Using Localized Texture Features (2006)

Fingerprint representations can be broadly divided into three categories: image level, texture features and minu- tiae features. Both image based and texture based repre- sentations require accurate alignment before comparison. This presents a problem since accurate registration of fin- gerprints is challenging. On the other hand, minutiae based matchers are invariant to changes in orientation and posi- tion, but completely ignore the rich visual content in the image. In this paper, we present a localized texture based representation scheme that relies solely on visual content for identification and at the same time does not require ab- solute alignment. We outline techniques to efficiently com- pute these features and also propose an algorithm to per- form identification based on these features. Our experimen- tal evaluations over database of several sizes show that the proposed features are both accurate and scalable.