gebhart/patrepeval huggingface dataset:
Anti-CD20 Antibody Rituximab and Anti-CD23 Antibody IDEC-152 Induce Apoptosis of Malignant B-Cells in Combination with Chemical Antagonists of XIAP. (2004)

Abstract We tested the effects of Rituximab (anti-CD20) and IDEC-152 (anti-CD23) on apoptosis of B-cell malignancies, using established non-Hodgkin’s B-Cell lymphoma cell lines and freshly isolated Chronic Lymphocytic Leukemia (CLL) B-cells. We used monolayers of stably transfected CHO-cells expressing FcRγIII-A to present antibody to B-cells and promote crosslinking. Established B-cell lymphomas (n = 3) were cultured in the presence of FcRγIIIA-expressing CHO monolayer with or without MAbs and apoptosis was measured by annexin V/propidium iodide staining at various times thereafter. Both antibodies induced time-dependent apoptosis of B-cell lymphoma cell lines. After 48 hrs of treatment with either Rituximab or IDEC-152, the majority of the malignant B-cells were apoptotic (remaining viable cells = 28.7% ± 0.2137% for Rituximab and 30.87% ± 0.7332% for IDEC-152). Rituximab and IDEC-152 also induced marked increases in caspase activity in B-cell lymphoma cell lines, with fold-increases above baseline control cells of 25 ± 0.9031 and 24 ± 0.3839, respectively. In contrast, neither Rituximab nor IDEC-152 induced striking effects on primary CLL B-cells (n = 6). We therefore tested the combination of Rituximab or IDEC-152 with other agents that target anti-apoptotic proteins, exploring whether more efficient induction of apoptosis can be achieved. We cultured lymphoma cell lines and primary CLL specimens with chemical antagonists of XIAP (Schimmer, et al. Cancer Cell5: 25, 2004), an anti-apoptotic protein that inhibits effector caspases. When used at concentrations where XIAP antagonists alone were non-apoptotic (approximately 2.5 μM), a significant increase in apoptosis was achieved in cultures of lymphoma and CLL cells treated with either Rituximab or IDEC-152. These findings suggest that Rituximab or IDEC-152 may more efficiently induce apoptosis of malignant B-cells when combined with an apoptosis-sensitizing agent. (Supported by CA-81534; CA-78040; and an unrestricted grant from Genentech, Inc.).
Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive protection across divergent subgroups (2022)

Multivalent antigen display is a fast-growing area of interest towards broadly protective vaccines. Current nanoparticle-based vaccine candidates demonstrate the ability to confer antibody-mediated immunity against divergent strains of notably mutable viruses. In coronaviruses, this work is predominantly aimed at targeting conserved epitopes of the receptor-binding domain. However, targeting other conserved non-RBD epitopes could further limit the potential for antigenic escape. To further explore new potential targets, we engineered protein nanoparticles displaying CoV_S-2P trimers derived from MERS-CoV, SARS-CoV-1, SARS-CoV-2, hCoV-HKU1, and hCoV-OC43 and assessed their immunogenicity in mice. Monotypic SARS-1_S-2P nanoparticles elicited cross-neutralizing antibodies against MERS_S and protected against MERS-CoV challenge. MERS and SARS-I53_dn5 nanoparticles elicited S1-focused antibodies, revealing a conserved site on the NTD. Moreover, mosaic nanoparticles co-displaying distinct CoV_S-2P trimers elicited antibody responses to distant cross-group antigens while protecting against MERS challenge despite diminished valency of MERS_S-2P. Our findings will inform further efforts towards the development of pan-coronavirus vaccines.
SARS-CoV-2 Interference of Influenza Virus Replication in Syrian Hamsters (2021)

In hamsters, SARS-CoV-2 infection at the same time as or before H3N2 influenza virus infection resulted in significantly reduced influenza virus titers in the lungs and nasal turbinates. This interference may be correlated with SARS-CoV-2-induced expression of MX1.
The Topological Analysis of Compliant Mechanisms (1994)

Abstract Following the topological synthesis of mechanisms, a topological analysis constitutes the second phase of the type-synthesis process. Topological analysis involves investigating distinct ways of specifying inputs, outputs and joint types to satisfy the functional requirements. For compliant mechanisms, the number of possible input combinations is typically much greater than for their rigid-body counterparts. Therefore, a systematic approach to input specification is required. This paper deals primarily with the development of a systematic input specification procedure for compliant mechanisms, while building on the rigid-body type-synthesis techniques and the terminology previously established for compliant elements. The techniques developed are straightforward and may be easily automated.
Analysis of focus errors in lithography using phase-shift monitors (2002)

We present here a procedure to characterize focus behavior on a first generation prototype 193-nm scanner using phase-shift focus monitors, which clearly identifies the influence of full field dynamic effects and that of the wafer topography and flatness. These results are used to correct the systematic errors due to incorrect tool set-up and show that proposed procedure has capability to identify focus errors and on this basis to construct a focus budget for all components: reticle, wafer, tool. We also present results using a new focus monitor based on phase gratings, which is more sensitive than the traditional phase-shift focus monitor.
1025 Multi-echo dixon fat and water separation method for detecting fibro-fatty infiltration in the myocardium (2008)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Differences in Peripheral Blood Lymphocytes between Brand-Name and Generic Tacrolimus Used in Stable Liver Transplant Recipients (2017)

The level of CD4+Foxp3+ T cells was higher in the brand-name tacrolimus group than in the generic tacrolimus group after transplantation. This finding showed that brand-name tacrolimus could have more potential immunosuppressive activity than generic tacrolimus regarding the contribution of CD4+Foxp3+ T cells to graft tolerance in liver transplant recipients.
HIGH CURRENT MULTI-FILAMENT PHOTOCONDUCTIVE SEMICONDUCTOR SWITCHING. (2016)

Abstract not provided.
Similarity regularized sparse group lasso for cup to disc ratio computation (2017)

Automatic cup to disc ratio (CDR) computation from color fundus images has shown to be promising for glaucoma detection. Over the past decade, many algorithms have been proposed. In this paper, we first review the recent work in the area and then present a novel similarity-regularized sparse group lasso method for automated CDR estimation. The proposed method reconstructs the testing disc image based on a set of reference disc images by integrating the similarity between testing and the reference disc images with the sparse group lasso constraints. The reconstruction coefficients are then used to estimate the CDR of the testing image. The proposed method has been validated using 650 images with manually annotated CDRs. Experimental results show an average CDR error of 0.0616 and a correlation coefficient of 0.7, outperforming other methods. The areas under curve in the diagnostic test reach 0.843 and 0.837 when manual and automatically segmented discs are used respectively, better than other methods as well.
Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain protein (2005)

The papillomavirus E2 protein functions in viral transcriptional regulation, DNA replication, and episomal genome maintenance. Viral genomes are maintained in dividing cells by attachment to mitotic chromosomes by means of the E2 protein. To investigate the chromosomal tethering function of E2, plasmid stability assays were developed in Saccharomyces cerevisiae to determine whether the E2 protein could maintain plasmids containing the yeast autonomous replication sequence replication element but with the centromeric element replaced by E2-binding sites. E2 expression was not sufficient to maintain such plasmids, but plasmid stability could be rescued by expression of the mammalian protein Brd4. In the presence of both Brd4 and E2 proteins, plasmids with multiple E2-binding sites were stable without selection. S. cerevisiae encodes a homolog of Brd4 named Bdf1 that does not contain the C-terminal domain that interacts with the E2 protein. A fusion protein of Bdf1 and the Brd4 C-terminal "tail" could support E2-mediated plasmid maintenance in yeast. Using a panel of mutated E2 proteins, we determined that plasmid stability required the ability of E2 to bind DNA and to interact with Brd4 and mammalian mitotic chromosomes but did not require its replication initiation and transactivation functions. The S. cerevisiae-based plasmid maintenance assays described here are invaluable tools for dissecting mechanisms of episomal viral genome replication and screening for additional host protein factors involved in plasmid maintenance.
Superlattice electron wave optics (1988)

Starting from fundamental principles, quantitative analogies between electron waves in semiconductor materials and electromagnetic waves in dielectrics are presented. This in turn suggests a new class of electron wave optical devices such as narrowband superlattice interference filters. Phase effects associated with an electron wave are incorporated using the electron wave vector, which is proportional to the square root of the product of the effective mass and the electron kinetic energy. It is shown that the amplitude of a free electron wave is analogous to the electric field of a TE polarized electromagnetic wave in a dielectric. Amplitude effects associated with an electron wave are incorporated, using an effective amplitude refractive index that is proportional to the square root of the ratio of the kinetic energy to the effective mass. A simple expression for the critical angle for total internal reflection of an electron wave is developed. By analogy to the electromagnetic optical case, the overall electron transmissivity and reflectivity of a semiconductor superlattice are determined.
Magnetic resonance assessment of myocardial perfusion via catheter‐based ventricle–coronary vein bypass in porcine myocardial infarction model (2005)

VPASS implant with simultaneous AIV and LAD occlusion allows perfusion of oxygenated blood to the distal AIV, which in the setting of an acute myocardial infarction model was capable of rescuing most of the myocardium at risk.
Heterogeneity of CD34 and CD38 expression in acute B lymphoblastic leukemia cells is reversible and not hierarchically organized (2016)

The existence and identification of leukemia-initiating cells in adult acute B lymphoblastic leukemia (B-ALL) remain controversial. We examined whether adult B-ALL is hierarchically organized into phenotypically distinct subpopulations of leukemogenic and non-leukemogenic cells or whether most B-ALL cells retain leukemogenic capacity, irrespective of their immunophenotype profiles. Our results suggest that adult B-ALL follows the stochastic stem cell model and that the expression of CD34 and CD38 in B-ALL is reversibly and not hierarchically organized.
Supplementary File 13 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer (2023)

Supplementary File 13 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer
400-Gb/s direct modulation using a DFB+R laser (2020)

We demonstrate a direct-modulation and direct-detection system with a back-to-back line rate of 411.6 (net bit rate of 337.5) Gb/s using a 65 GHz DFB+R laser. The O-band laser with a chirp parameter of 0.6 supports dispersion-tolerant transmissions up to 15 km without an optical amplifier.
Orientation of 3 Component Rig-Source VSPs (2015)

About 75% of commercial borehole seismic operations are zero-offset VSPs, or “Rig-VSPs”. They are recorded before total completion in low deviated holes, with a deep open hole interval and a single casing, then multiple casing depth intervals above. Three components of geophones are recorded, with excellent mechanical tool coupling to the borehole wall, but usually the VSP tool cannot be oriented into geographical coordinates. Therefore only the Z-axis component is processed, or a near vertical component computed from the 3 recorded components, resulting in a reduction of the geological information derived from rig-VSPs. APS and IFPEN propose to implement current and future generations of VSP tools with cost effective fluxgates and inclinometers to improve the present situation.
Longevity and Age Exaggeration in Vilcabamba, Ecuador (1979)

Systematic age exaggeration was found after age 70 in an Equadorian population noted for extreme longevity. Extreme ages (over 100 years) were either incorrect or unsubstantiated. There was no evidence of increased longevity in the Vilcabamba population.
Wide-viewing angle IPS-LCD for TV applications using optical compensation technology (2006)

The viewing angle performance in IPS-LCDs has been greatly improved, by using two technologies. One is optical compensation technology using a biaxial film. The other is the newly developed IPS-Pro cell structure with its higher transmission efficiency. These technologies have been successfully introduced into the fabrication of 32-inch IPS-LCDs with a minimum contrast ratio of over three times that of the conventional and with a color saturation (area ratio to NTSC at CIE1931 xy chromaticity coordinates) of over 70 % at almost all viewing angles.
A linear matrix inequality approach to the general mixed ℋ/sub 2//ℋ/sub ∞/ control problem (2005)

This paper presents a solution method to the general mixed /spl Hscr//sub 2///spl Hscr//sub /spl infin//, problem, minimizing the /spl Hscr//sub 2/ norm of a closed-loop system subject to an /spl Hscr//sub /spl infin// norm constraint on another closed-loop system. It is shown that the true infimum over all internally stabilizing controllers can be approximated arbitrary closely by solving a sequence of globally convergent finite dimensional convex optimization problems over linear matrix inequalities. Numerical examples are provided to demonstrate the effectiveness of this approach.
Abstract B28: Signaling by PDGF-CC in the maintenance of a protumorigenic breast cancer microenvironment (2013)

Abstract It is increasingly appreciated that cancer results from the concerted performance of genetically altered tumor cells interacting with ostensibly normal cells in the microenvironment. As the cancer progresses, the surrounding stroma co-evolves into an activated state through continuous paracrine communication, thus creating a dynamic signaling circuitry that promotes cancer initiation and growth, and ultimately leads to a fatal disease. We aim to molecularly map the support functions performed by the various cell types comprising the tumor stroma. Specifically we will focus on, cancer-associated fibroblasts (CAFs), which are known to support many aspects of tumor progression. Based on our previous finding that paracrine signaling by Platelet-derived growth factor (PDGF)-CC serves to recruit CAFs into tumors we have generated Pdgfc-deficient genetically engineered mouse models of breast cancer. Our results show a significant reduction in the tumor burden followed by prolonged survival in the absence of PDGF-CC, in agreement with the recent finding that PDGF-CC expression is an indicator of poor prognosis for breast cancer patients. Upon transplantation of small tumor pieces from wildtype and Pdgfc-deficient tumors respectively into the mammary fatpad of wildtype mice, Pdgfc-deficient tumors show substantial growth retardation with massive hemorrhage and necrosis, indicative of malfunctional vessels and insufficient blood supply. qPCR arrays on total RNA from wildtype and Pdgfc-deficient tumors respectively, suggest that lack of PDGF-CC causes perturbed differentiation yielding a less advanced tumor. Furthermore, we are currently investigating the differences observed in the recruited fibroblasts and/or MSCs in wildtype and Pdgfc-deficient tumors, by performing proteomics on isolated PDGFR-α positive cells. Tumor morphology in combination with proteomics suggests that the lack of PDGF-CC causes an impaired migration and/or guidance of the recruited fibroblasts from the periphery of the tumor. Thus, our studies suggest a novel role for PDGF-CC in creating a pro-tumorigenic microenvironment and identify PDGF-CC as a valid and promising therapeutic target in breast cancer. Citation Format: Pernilla Roswall, Kristian Haller, Annika Petersson, Charlotte Anderberg, Hong Li, Jens-Henrik Norum, Rune Toftgård, Ulf Eriksson, Kristian Pietras. Signaling by PDGF-CC in the maintenance of a protumorigenic breast cancer microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B28.
Intrastriatal transplantation of neurotrophic factor-secreting human mesenchymal stem cells improves motor function and extends survival in R6/2 transgenic mouse model for Huntington's disease (2012)

Stem cell-based treatment for Huntington's disease (HD) is an expanding field of research. Although various stem cells have been shown to be beneficial in vivo, no long standing clinical effect has been demonstrated. To address this issue, we are developing a stem cell-based therapy designed to improve the microenvironment of the diseased tissue via delivery of neurotrophic factors (NTFs). Previously, we established that bone marrow derived human mesenchymal stem cells (MSCs) can be differentiated using medium based cues into NTF-secreting cells (NTF+ cells) that express astrocytic markers. NTF+ cells were shown to alleviate neurodegeneration symptoms in several disease models in vitro and in vivo, including the model for excitotoxicity. In the present study, we explored if the timing of intrastriatal transplantation of hNTF+ cells into the R6/2 transgenic mouse model for HD influences motor function and survival. One hundred thousand cells were transplanted bilaterally into the striatum of immune-suppressed mice at 4.5, 5.5 and 6.5 weeks of age. Contrary to our expectations, early transplantation of NTF+ cells did not improve motor function or overall survival. However, late (6.5 weeks) transplantation resulted in a temporary improvement in motor function and an extension of life span relative to that observed for PBS treated mice. We conclude that late transplantation of NTF+ cells induces a beneficial effect in this transgenic model for HD. Since no transplanted NTF+ cells could be detected in vivo, we suspect that the temporary nature of the beneficial effect is due to poor survival of transplanted cells. In general, we submit that NTF+ cells should be further evaluated for the therapy of HD.
Extraction of proteins from plant tissues for two‐dimensional electrophoresis analysis (2003)

To increase the number of proteins detectable by two-dimensional electrophoresis (2-DE) in plants, we present a new procedure for extracting total proteins from plant tissue. This method avoids any loss of proteins in the course of sample preparation and results in two different fractions, one comprising mainly the cytoplasmatic proteins, the other one containing predominantly structure bond proteins. 2-DE patterns obtained from these two fractions show that the total number of different protein spots detected exceeds the degree of resolution commonly reported for plant proteins threefold.
Performance Analysis of General P4 Forwarding Devices with Controller Feedback (2022)

Software-Defined Networking (SDN) lays the foundation for the operation of future networking applications. The separation of the control plane from the programmable data plane increases the flexibility in network operation. One of the most used languages for describing the packet behavior in the data plane is P4. It allows protocol and hardware independent programming. With the expanding deployment of P4 programmable devices, it is of utmost importance to understand their performance behavior and limitations in order to design a network and provide Quality of Service (QoS) guarantees. One of the most important performance metrics is the packet mean sojourn time in a P4 device. While previous works already modeled the sojourn time in P4 devices with controller feedback, those models were rather simplified and could not capture the system behavior for general cases, resulting in a potential highly inaccurate performance prediction. To bridge this gap, in this paper, we consider the system behavior of P4 devices for the general case, i.e., under general assumptions. To that end, we model the behavior with a queueing network with feedback. As it is impossible to provide closed-form solutions, we consider different approximations for the mean sojourn time. We validate our results against extensive realistic simulations, capturing different behaviors in the data and control planes. Results show that the most accurate approximation in almost all cases is the one in which the queues are decoupled and considered as independent despite the fact that there are dependencies. The level of discrepancy in the worst case does not exceed 18.2% for service times distributions with a coefficient of variation not greater than 1.
Determinants of Embolic Risk During Angioplasty and Stenting (2010)

These findings suggest that the presence of preprocedural neurologic symptoms and a history of CAD are associated with increased embolization during CAS. Therefore, the benefit of carotid stenting should be tempered by the potential for increased perioperative events in both symptomatic and CAD patients.
Nitric oxide synthase mediates cerebellar dysfunction in mice exposed to repetitive blast-induced mild traumatic brain injury (2020)

We investigated the role of nitric oxide synthase (NOS) in mediating blood-brain barrier (BBB) disruption and peripheral immune cell infiltration in the cerebellum following blast exposure. Repetitive, but not single blast exposure, induced delayed-onset BBB disruption (72 hours post-blast) in cerebellum. The NOS inhibitor N(G)-nitro-L-arginine methyl ester (L-NAME) administered after blast blocked BBB disruption and prevented CD4<sup>+</sup> T-cell infiltration into cerebellum. L-NAME also blocked blast-induced increases in intercellular adhesion molecule-1 (ICAM-1), a molecule that plays a critical role in regulating blood-to-brain immune cell trafficking. Blocking NOS-mediated BBB dysfunction during this acute/subacute post-blast interval (24-71 hours after the last blast) also prevented sensorimotor impairment on a rotarod task 30 days later, long after L-NAME cleared the body. In postmortem brains from Veterans/military Servicemembers with blast-related TBI, we found marked Purkinje cell dendritic arbor structural abnormalities, which were comparable to neuropathologic findings in the blast-exposed mice. Taken collectively, these results indicate that blast provokes delayed-onset of NOS-dependent pathogenic cascades that can later emerge as behavioral dysfunction. These results also further implicate the cerebellum as a brain region vulnerable to blast-induced mTBI.