gebhart/patrepeval huggingface dataset:
Excited State Potential Energy Surfaces of Polyenes and Protonated Schiff Bases (2009)

The potential energy surface of the (1)Bu and (1)A' states of all-trans-polyenes and the corresponding protonated Schiff bases have been studied at density functional theory and coupled cluster levels. Linear polyenes and protonated Schiff bases with 4 to 12 heavy atoms have been investigated. The calculations show remarkable differences in the excited state potential energy surfaces of the polyenes and the protonated Schiff bases. The excited states of the polyenes exhibit high torsion barriers for single-bond twists and low torsion barriers for double-bond twists. The protonated Schiff bases, on the other hand, are very flexible molecules in the first excited state with low or vanishing torsion barriers for both single and double bonds. Calculations at density functional theory and coupled cluster levels yield qualitatively similar potential energy surfaces. However, significant differences are found for some single-bond torsions in longer protonated Schiff bases, which indicate a flaw of the employed time-dependent density functional theory methods. The close agreement between the approximate second and third order coupled cluster levels indicates that for these systems calculations at second order coupled cluster level are useful in the validation of results based on time-dependent density functional theory.
Identifying SS reflections in conventional onshore multicomponent data (2021)

This work addresses the possible presence of pure S wave reflections (SS-waves) generated by conventional explosive sources in land multicomponent data. These reflections have been rarely observed, although their occurrence has been theoretically shown. Multicomponent surveys are intended to obtain just PP and PS reflections. In this work real data from a conventional 3C survey, were used to explore the possibility of using SS reflections. From arrival time estimation of reflections based on velocity from well-logs, it was found that SS-waves arrive embedded inside the ground roll cone, which explains the elusive character of these events. We applied noise attenuation for strong events related to ground roll such as surface waves, taking care of preserving the expected SS-waves. The resulting data after filtering show energy corresponding to the SS-events arrival time on both radial and transversal components. The S-wave source static correction is required, and no standard method is available. A couple of experiments to this purpose were carried out, with reasonable results. A basic velocity analysis allowed us to obtain an SS stack section, which shows events with the expected SS arrival time, and that correspond to events on a PS stack section previously obtained. Therefore, the experiment shows a feasible SS image, and appears a promising resource for obtaining additional elastic wave information from conventional land multicomponent data.
Acute Cardiac Allograft Rejection: Involvement of Apoptotic Cell Death and Proteolytic Bcl-2 Degradation (1999)

504 Despite of improvements in immunosuppressive therapy, acute allograft rejection remains one of the major obstacles of long-term success of organ transplantation. T cell directed responses are primarily responsible for acute cardiac allograft rejection. The role of induction of apoptosis by this lymphocyte-directed immune response has not yet been fully defined. Therefore, the aim of our study was to assess the role of apoptosis in the rejection cascade leading to acute allograft loss. LEW rats were challenged with WF cardiac allografts, which are rejected in an acute fashion within 6.9±2.1 days (n=15). At the time of graft loss, the anti-donor CTL generation/function displayed significant donor specific cell lysis as well as marked host cell proliferative response (MLR) in LEW recipients of WF cardiac allografts. Immunohistochemical analysis of acutely rejected cardiac allografts revealed dense infiltration with monocytes, macrophages (ED1), MHC class II bearing cells and T cells (R73). Apoptosis of cardiomyocytes and lymphocytes was demonstrated by TUNEL assay and confirmed by detection of typical DNA-laddering only in acutely rejected cardiac allografts (day 7), whereas it was not detectable in isografts and naive controls. Western blot analysis revealed complete loss of expression of the survival gene Bcl-2 in rejected allografts, in comparison to naive and isograft hearts, whereas Bax protein levels were upregulated about three-fold. RNase protection assay disclosed no alteration of Bcl-2 family members on mRNA level. A Bcl-2 cleavage product, about 17kD, could be detected, indicating posttranslational degradation of Bcl-2 as regulatory mechanism. To demonstrate the in vivo significance of Bcl-2 degradation in the course of acute rejection, well functioning grafts on day 7 after Cyclosporine A or CTLA4-Ig treatment were analyzed for Bcl-2 protein expression. These well functioning grafts displayed Bcl-2 protein expression at the time point of acute rejection (day 7). p53 levels did not vary significantly between rejected grafts, isografts and naive hearts, suggesting that p53 might not be involved at a transcriptional level in the regulation of bcl-2/bax expression. Thus, the induction of apoptosis by loss of Bcl-2 activity may play an integral part in the host rejection cascade leading to acute allograft loss. Inhibiting Bcl-2 proteolysis in order to prevent apoptosis induction may provide a novel target for immunosuppressive therapy.
Efficient multiple triplet quantum well structures in organic light-emitting devices (2009)

We demonstrate the multiple quantum well (MQW) structures with the charge control layers (CCLs) to produce highly efficient red phosphorescent organic light-emitting devices (OLEDs). Various triplet quantum well devices from a single to five quantum wells are realized using wide band-gap hole and electron transporting layers, narrow band-gap host and dopant materials, and CCLs. Triplet energies in such MQW devices are confined at the emitting layers. The maximum external quantum efficiency of 14.8% with a two quantum well device structure is obtained. The described MQW device concept has been proposed to be very useful to future OLED display and lighting applications.
Physiological control of NKT cell activation by extracellular adenosine via A2B adenosine receptor (138.27) (2010)

Abstract Negative regulatory mechanism of immune responses is essential to prevent excessive inflammatory tissue injury. Adenosine involves in physiological down-regulation of inflammation via A2A adenosine receptor (A2AR). In this study, we provide evidence that A2B adenosine receptor (A2BR) is also important in the physiological control of hepatic inflammation. Acute hepatitis induced by intravenous concanavalin A (Con A) injection was significantly more severe in A2BR-/- mice than in wild-type mice. The exaggerated inflammation in A2BR-/- mice accompanied higher levels of IL-4 from NKT cells suggesting A2BR-mediated suppression of NKT cell activation. In vitro activation of NKT cells by α-galactosylceramide (α-GalCer) showed that stimulation of A2BR is inhibitory to NKT cell activation. Furthermore, injection of α-GalCer induced higher serum cytokine levels and stronger liver damage in A2BR-/- mice. These results show that the lack of A2BR diminished negative regulatory mechanism of NKT cells by endogenously produced adenosine and, therefore, caused more severe acute hepatitis. Indeed, transfer of A2BR-/- NKT cells into RAG2-/- mice resulted in stronger Con A-induced liver injury than wild-type NKT cells. There have been controversial reports regarding the role of A2BR in inflammation. Our results demonstrate that NKT cell-mediated immune responses are under the physiological control of extracellular adenosine through A2BR signaling.
La condition animale : Places, statuts et représentations des animaux dans la société (2013)

« S’il n’existait point d’animaux la nature de l’homme serait encore plus incompréhensible. »Georges Louis Leclerc de Buffon, Discours sur la nature des animaux, 1753 « Die moderne Gleichgültigkeit gegenüber der Natur ist in der Tat nur eine Variante der pragmatischen Einstellung, die für die abendländische Zivilisation insgesamt typisch ist. Die Formen sind verschieden. Der frühe Trapper sah in den Prärien und Bergen nur die Aussicht auf gute Jagd ; der moderne Geschäftsmann sieht in der Lan...
Effect of Deglycosylation of Cellobiose Dehydrogenases on the Enhancement of Direct Electron Transfer with Electrodes (2012)

Cellobiose dehydrogenase (CDH) is a monomeric extracellular flavocytochrome composed of a catalytic dehydrogenase domain (DH(CDH)) containing flavin adenine dinucleotide (FAD), a cytochrome domain (CYT(CDH)) containing heme b, and a linker region connecting the two domains. In this work, the effect of deglycosylation on the electrochemical properties of CDH from Phanerochaete chrysosporium (PcCDH) and Ceriporiopsis subvermispora (CsCDH) is presented. All the glycosylated and deglycosylated enzymes show direct electron transfer (DET) between the CYT(CDH) and the electrode. Graphite electrodes modified with deglycosylated PcCDH (dPcCDH) and CsCDH (dCsCDH) have a 40-65% higher I(max) value in the presence of substrate than electrodes modified with their glycosylated counterparts. CsCDH trapped under a permselective membrane showed similar changes on gold electrodes protected by a thiol-based self-assembled monolayer (SAM), in contrast to PcCDH for which deglycosylation did not exhibit any different electrocatalytical response on SAM-modified gold electrodes. Glycosylated PcCDH was found to have a 30% bigger hydrodynamic radius than dPcCDH using dynamic light scattering. The basic bioelectrochemistry as well as the bioelectrocatalytic properties are presented.
Phase-Contrast CT: Qualitative and Quantitative Evaluation of Atherosclerotic Carotid Artery Plaque (2014)

The results of this study indicate that ex vivo phase-contrast CT can help identify and quantify atherosclerotic plaque components, with excellent correlation to histopathologic findings. Although not yet applicable in vivo, phase-contrast CT may become a valuable tool to monitor atherosclerotic disease process noninvasively.
Reconfigurable Designs for Radiosity (2005)

We develop reconfigurable designs to support radiosity, a computer graphics algorithm for producing highly realistic images of artificial scenes, but which is computationally expensive. We implement radiosity using stochastic raytracing, which affords both instruction-level and data parallelism. Our designs are parameterisable by bitwidth, allowing trade-offs between image quality and computation speed. We measure the speed of our designs for a Xilinx XC2V6000 device in the Celoxica RC2000 platform: at 53 MHz it can run up to five times faster than a software implementation on an Athlon MP 2600+ processor at 2.1 GHz. We estimate that retargeting our design for a Virtex-4 XCVSX55 device can result in over 160 times software speed, while a Spartan-3 XC3S5000 device can run more than 40 times faster than the software implementation.
The importance of imaging strategies for pre-clinical and clinical in vivo distribution of oncolytic viruses (2018)

Abstract: Oncolytic viruses (OVs) are an emergent and unique therapy for cancer patients. Similar to chemo- and radiation therapy, OV can lyse (kill) cancer cell directly. In general, the advantages of OVs over other treatments are primarily: a higher safety profile (as shown by less adverse effects), ability to replicate, transgene(s) delivery, and stimulation of a host’s immune system against cancer. The latter has prompted successful use of OVs with other immunotherapeutic strategies in a synergistic manner. In spite of extended testing in pre-clinical and clinical setting, using biologically derived therapeutics like virus always raises potential concerns about safety (replication at non-intended locations) and bio-availability of the product. Recent advent in in vivo imaging techniques dramatically improves the convenience of use, quality of pictures, and amount of information acquired. Easy assessing of safety/localization of the biotherapeutics like OVs became a new potential weapon in the physician’s arsenal to improve treatment outcome. Given that OVs are typically replicating, in vivo imaging can also track virus replication and persistence as well as precisely mapping tumor tissues presence. This review discusses the importance of imaging in vivo in evaluating OV efficacy, as well as currently available tools and techniques. Keywords: oncolytic virus, mouse imaging, NIS virus, viral efficacy, clinical trial
The Impact of a Boosting Immunogen on the Differentiation of Secondary Memory CD8 + T Cells (2007)

While recent studies have demonstrated that secondary CD8+ T cells develop into effector-memory cells, the impact of particular vaccine regimens on the elicitation of these cells remains poorly defined. In the present study we evaluated the effect of three different immunogens--recombinant vaccinia, recombinant adenovirus, and plasmid DNA--on the generation of memory cellular immune responses. We found that vectors that induce the rapid movement of CD8+ T cells into the memory compartment during a primary immune response also drive a rapid differentiation of these cells into effector-memory CD8+ T cells following a secondary immunization. In contrast, the functional profiles of both CD8+ and CD4+ T cells, assessed by measuring antigen-stimulated gamma interferon and interleukin-2 production, were not predominantly shaped by the boosting immunogen. We also demonstrated that the in vivo expression of antigen by recombinant vectors was brief following boosting immunization, suggesting that antigen persistence has a minimal impact on the differentiation of secondary CD8+ T cells. When used in heterologous or in homologous prime-boost combinations, these three vectors generated antigen-specific CD8+ T cells with different phenotypic profiles. Expression of the memory-associated molecule CD27 on effector CD8+ T cells decreased following heterologous but not homologous boosting, resulting in a phenotypic profile similar to that seen on primary CD8+ T cells. These data therefore suggest that the phenotype of secondary CD8+ T cells is determined predominantly by the boosting immunogen whereas the cytokine profile of these cells is shaped by both the priming and boosting immunogens.
Design and Analysis of Dynamic Multithreaded Algorithms (2004)

Dynamic multithreaded languages provide low-overhead fork-join primitives to express parallelism. One such language is Cilk [3, 5], which was developed in the MIT Laboratory for Computer Science (now the MIT Computer Science and Artificial Intelligence Laboratory). Cilk minimally extends the C programming language to allow interactions among computational threads to be specified in a simple and high-level fashion. Cilk’s provably efficient runtime system dynamically maps a user’s program onto available physical resources using a randomized “work-stealing” scheduler, freeing the programmer from concerns of communication protocols and load balancing.
Histological transformation to diffuse large B‐cell lymphoma in patients with Waldenström macroglobulinemia (2016)

Histological transformation to diffuse large B-cell lymphoma (DLBCL) rarely occurs in patients with Waldenström Macroglobulinemia (WM). We identified 20 patients out of a cohort of 1,466 WM patients who experienced histologic transformation. The 5, 10, and 15-year cumulative incidence rates were 1, 2.4, and 3.8%, respectively. Approximately half of the patients were naive to nucleoside analogues, and a quarter were previously untreated for WM at the time of transformation. More than 80% of patients presented with extranodal involvement, 65% with high IPI scores. DLBCL cells did not express CD10 but expressed BCL6 and BCL2. All patients were treated with chemoimmunotherapy. The median survival from histological transformation was 2.7 years. The median overall survival was shorter for transformed patients versus those who did not transform (estimated 9 vs. 16 years; P = 0.09). Histological transformation to DLBCL is rare, and is associated with inferior survival in WM. Am. J. Hematol. 91:1032-1035, 2016. © 2016 Wiley Periodicals, Inc.
Fast method for correcting image misregistration due to organ motion in time‐series MRI data (2003)

Abstract Time‐series MRI data often suffers from image misalignment due to patient movement and respiratory and other physiologic motion during the acquisition process. It is necessary that this misalignment be corrected prior to any automated quantitative analysis. In this article a fast and automated technique for removing in‐plane misalignment from time‐series MRI data is presented. The method is computationally efficient, robust, and fine‐tuned for the clinical setting. The method was implemented and tested on data from 21 human subjects, including myocardial perfusion imaging, renal perfusion imaging, and blood‐oxygen level‐dependent cardiac T imaging. In these applications 10‐fold or better reduction in image misalignment is reported. The improvement after registration on representative time–intensity curves is shown. Although the method currently corrects translation motion using image center of mass, the mathematical framework of our approach may be extended to correct rotation and other higher‐order displacements. Magn Reson Med 49:506–514, 2003. © 2003 Wiley‐Liss, Inc.
Band-Engineered Low PMOS V<inf>T</inf> with High-K/Metal Gates Featured in a Dual Channel CMOS Integration Scheme (2007)

Using strained SiGe on Si, the threshold voltage of high κ PMOS devices is reduced by as much as 300 mV. The 80 nm devices exhibit excellent short channel characteristics such as DIBL and GIDL. For the first time a dual channel scheme using standard activation anneal temperature is applied that allows La <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> capping in NMOS and SiGe channel in PMOS to achieve acceptable values of threshold voltage for high κ and metal gates for 32nm node and beyond.
Final Results of a Phase I/II Trial of the Combination Bendamustine and Rituximab With Temsirolimus (BeRT) in Relapsed Mantle Cell Lymphoma and Follicular Lymphoma (2020)

In this phase I/II study, we explored the combination of Temsirolimus with Bendamustine and Rituximab (BeRT) in patients with relapsed or refractory (r/r) follicular lymphoma (FL) or mantle cell lymphoma (MCL). Patients with 1 to 3 previous therapies received Bendamustine (90 mg/m<sup>2</sup>, day 1 + 2) and Rituximab (375 mg/m<sup>2</sup>, day 1) with Temsirolimus in doses from 25 to 75 mg in phase I and 50 mg Temsirolimus in phase II, added on day 1, 8, 15 of a 28 days cycle. The primary endpoint of the phase II was ORR at the end of treatment. Overall, 39 (29 MCL, 10 FL) patients were included. Median age was 71 years and median pretreatment number was 2. Grade 3/4 non-hematologic adverse events were rare and included hyperglycemia in 3 patients (7%) and angioedema in 2 patients (5%). Infectious complications grade 3/4 were observed in 9 patients (23%). Hematologic grade 3/4 events included leukopenia in 22 (56%), neutropenia in 18 (46%), lymphopenia in 16 (41%) and thrombocytopenia in 14 patients (36%). An objective response (best response) was observed in 33/39 patients (89%; 24 MCL (89%) and 9 FL (90%)), including 14 CR (38%; 12 MCL (36%) and 2 FL (20%)). Median PFS is 1.5y for MCL and 1.82 years for FL, and median OS has not been reached for either entity. This data demonstrates promising efficacy of Temsirolimus in r/r MCL and FL with acceptable toxicity. The BeRT regimen may be used as a treatment option for both entities.
NLOS Links Detection Algorithm for Improved 5G NR Indoor Positioning (2021)

In this paper we derive a signal processing algorithm for NLOS links detection and propose a reliability function that can be used in the positioning equations to perform correct weighting of the measurements. It is shown that the measurements may suffer from the NLOS propagation phenomenon, specifically in indoor environments, that causes an excess delay relative to the LOS transmission time. The proposed algorithm performs a binary hypothesis testing between the LOS and NLOS channel hypothesis to identify the link type. It uses an average NLOS channel power, estimated per subcarrier basis in the frequency domain to perform links classification. The provided simulation results demonstrate the validity of presented analytical formulation and the feasibility to achieve a submeter level positioning accuracy in application to the Industrial Internet of Things (I-IoT) use case.
Platelet membrane glycoprotein IIb heavy chain forms a complex with glycoprotein IIIa that binds Arg-Gly-Asp peptides (1989)

Platelet membrane GPIIb is comprised of a disulfide-linked heavy chain (GPIIb(H)) and light chain (GPIIb(L)). We have examined the role of the two chains of GPIIb in the maintenance of the GPIIb-IIIa heterodimer and Arg-Gly-Asp (RGD) peptide-binding function. Lysates of surface radioiodinated platelets were treated with 1% 2-mercaptoethanol for 18 hours at 4 degrees C. Reduction of the interchain disulfide in GPIIb was followed by immunoprecipitation with antipeptide antibodies specific for GPIIb(H) or GPIIb(L). In addition to the GPIIb-IIIa complex, a polypeptide of 120 Kd was precipitated by anti-GPIIb(H) and a polypeptide of 23 Kd was precipitated by anti-GPIIb(L) from reduced platelet lysates. To determine whether GPIIb(H) or GPIIb(L) remained complexed with GPIIIa, reduced platelet lysates were immunoprecipitated with AP3, a monoclonal anti-GPIIIa antibody, resulting in the coimmunoprecipitation of GPIIb(H) but not GPIIb(L). Conversely, the monoclonal anti-GPIIb(H) antibody PMI-1 immunoprecipitated GPIIIa with GPIIb(H). Thus GPIIb(H) maintains its association with GPIIIa. Furthermore, the GPIIb(H)-IIIa complex retains its reactivity with AP2, a monoclonal antibody (MoAb) specific for the nondissociated GPIIb-IIIa complex. Affinity chromatography of reduced platelet lysates on immobilized KYGRGDS resulted in binding and specific elution of the GPIIb(H)-IIIa complex. These findings indicate that GPIIb(H) contains sufficient information for maintenance of a complex with GPIIIa and support of the binding of the heterodimer to RGD peptides.