gebhart/patrepeval huggingface dataset:
Computational design and crystal structure of an enhanced affinity mutant human CD8 αα coreceptor (2007)

Human CD8 is a T cell coreceptor, which binds to pHLA I and plays a pivotal role in the activation of cytotoxic T lymphocytes. Soluble recombinant CD8 alphaalpha has been shown to antagonize T cell activation, both in vitro and in vivo. However, because of a very low affinity for pHLA I, high concentrations of soluble CD8 alphaalpha are required for efficient inhibition. Based upon our knowledge of the wild-type CD8/pHLA I structure, we have designed and produced a mutated form of soluble CD8 alphaalpha that binds to pHLA I with approximately fourfold higher affinity. We have characterized the binding of the high affinity CD8 mutant using surface plasmon resonance and determined its structure at 2.1 A resolution using X-ray crystallography. The analysis of this structure suggests that the higher affinity is achieved by providing a larger side chain that allows for an optimal contact to be made between the HLA alpha3 loop and the mutated CDR-like loops of CD8.
Ad hoc network metrics: Which is best? (2012)

The area of wireless ad hoc networks has attracted much attention and gained great popularity in the last few years. Yet researchers are still investigating several metrics to evaluate ad hoc network performance. Furthermore, to our knowledge, no work has been published to address the comparison of different network metrics. In this paper, we analyze and compare several distinct network metrics including transport capacity, transmission capacity and network diameter, which quantify ad hoc network performance from different perspectives. We also evaluate the network metrics via simulation for two “extreme” routing strategies: “nearest neighbor” (NN) and “shortest path” (SP). Main conclusions are that the transport capacity and the transmission capacity are generally inversely related in ad hoc networks; SP routing can achieve larger transport capacity and smaller network diameter than NN routing, whereas NN routing results in larger transmission capacity than SP routing. Ultimately, the best network metric among these three depends upon application; more research is needed in this important area.
High temperature NMR observation of mobile phases up to 1500°C (1995)

A new high temperature Nuclear Magnetic Resonance device using double laser heating system has been developed for NMR experiments up to 1500°C. Different systems have been investigated, both of theoritical and applied interest. We report here three examples, where the appearance and the role of mobile species are characterized by 27 Al, 23 Na and 19 F NMR signal evolution with temperature : solid - liquid transition in cryolite Na3 AlF6 , β-α alumina transformation with fluoride mineralizer, and the effects of mineralizer CaF2 on the high temperature reactions in the clinker formation.
Diagnostics of induction machines using the zero sequence voltage (2004)

Diagnostics of induction machines using the zero sequence voltage is presented in this paper. Both stator-winding fault and broken rotor bar detection are covered. Faults in the stator windings or damaged rotor bar cause asymmetries in the phase impedances of the machine, which give rise to zero sequence voltage components. The measured zero sequence voltage is shown to contain reliable information on the condition of the machine, with little influence from the operating point or imbalances in the phase voltages. The method will be shown to be valid both for line-connected machines and inverter-fed machines.
Lesions of the retrosplenial cortex produce deficits in reversal learning of the rabbit nictitating membrane response: Implications for potential interactions between hippocampal and cerebellar brain systems. (1986)

The effect of bilateral lesions of the retrosplenial cortex on discrimination reversal learning of the rabbit nictitating membrane response was examined. Results showed that animals with such lesions were not impaired in their ability to acquire a cross-modality discrimination, but were severely impaired in their ability to reverse the discrimination once it was learned. All animals failed at the reversal phase of the task because they displayed high levels of conditioned responding to both the CS+ and the CS-. Thus bilateral damage to the retrosplenial cortex results in deficits in reversal learning that are highly similar to those observed after bilateral hippocampectomy. These findings are interpreted within a conceptual framework that characterizes multisynaptic projections from the hippocampus to the retrosplenial cortex, and ultimately to the cerebellum, as responsible for the behavioral expression of learning-related changes in hippocampal pyramidal cell activity.
Hemoglobin–albumin clusters as an artificial O2 carrier: Physicochemical properties and resuscitation from hemorrhagic shock in rats (2022)

A bovine hemoglobin (HbBv) or human adult hemoglobin (HbA) wrapped covalently by human serum albumins (HSAs), hemoglobin-albumin clusters (HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> ), are artificial O<sub>2</sub> carriers used as a red blood cell substitute. This article describes the physicochemical properties of the HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> solutions, and their abilities to restore the systemic condition after resuscitation from hemorrhagic shock in anesthetized rats. The HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> , which have high colloid osmotic activity, showed equivalent solution characteristics and O<sub>2</sub> binding parameters. Shock was induced by 50% blood withdrawal. Rats exhibited hypotension and significant metabolic acidosis. After 15 min, the rats were administered shed autologous blood (SAB), HbBv-HSA<sub>3</sub> , HbA-HSA<sub>3</sub> , or Ringer's lactate (RL) solution. Survival rates, circulation parameters, hematological parameters, and blood gas parameters were monitored during the hemorrhagic shock and for 6 h after administration. All rats in the SAB, HbBv-HSA<sub>3</sub> , and HbA-HSA<sub>3</sub> groups survived for 6 h. The HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> groups restored mean arterial pressure after the resuscitation. No remarkable difference was observed in the time courses of blood gas parameters in any resuscitated group except for the RL group. Serum biochemical tests showed increases in aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in the HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> groups compared to the SAB group. Therefore, we observed other rats awakened after resuscitation with HbA-HSA<sub>3</sub> for 7 days. The blood cell count, AST, and ALT recovered to the baseline values by 7 days. All the results implied that HbBv-HSA<sub>3</sub> and HbA-HSA<sub>3</sub> clusters provide restoration from hemorrhagic shock as an alternative material for SAB transfusion.
Abstract 1311: High order drug combinations are required to effectively kill colorectal cancer cells (2016)

Abstract Tumors are complex biological systems that often retain proliferative capacity even when challenged with drug treatment. Given this resiliency, drug combinations may provide greater therapeutic benefit, however, which molecules to combine and how many to include in combinations for effective responses is not clear yet. Using image-based proliferation and apoptosis assays in colorectal cancer cell lines we systematically investigated combinations that ranged in number from two to six drugs and targeted critical oncogenic pathways. Drug pairs targeting key signaling pathways resulted in synergies across a broad spectrum of genetic backgrounds, but often yielded only cytostatic responses. Enhanced cytotoxicity was observed when additional processes including apoptosis and cell cycle were targeted as part of the combination. In many cases, where cell lines were resistant to two- and three-way drug combinations, increased expression of anti-apoptotic proteins was observed and induction of cytotoxic responses required up to fourth-order combinations. Our results demonstrate that high-order drug combinations might be needed to kill cancers and show how systematic drug combination screening together with a molecular understanding of drug responses can guide their identification. Citation Format: Thomas Horn, Stephane Ferretti, Nicolas Ebel, Angela Tam, Samuel Ho, Fred Harbinski, Ali Farsidjani, Matt Zubrowski, William R. Sellers, Robert Schlegel, Dale Porter, Erick Morris, Jens Wuerthner, Sebastien Jeay, Joel Greshock, Ensar Halilovic, Levi A. Garraway, Giordano Caponigro, Joseph Lehar. High order drug combinations are required to effectively kill colorectal cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1311.
REJECTION OF TUMOR ALLOGRAFTS BY MOUSE SPLEEN CELLS SENSITIZED IN VITRO (1971)

This paper reports a model system of cellular immunity in which allosensitization of mouse spleen cells is induced in vitro. Allosensitization was achieved by culturing spleen cells upon monolayers of allogeneic fibroblasts. The ability of the spleen cells to inhibit the growth of tumor allografts in vivo served as a functional assay of sensitization. We found that unsensitized spleen cells or spleen cells sensitized against unrelated fibroblast antigens had no inhibitory effect on the growth of allogeneic fibrosarcoma cells when they were injected together into irradiated recipients. In contrast, spleen cells which were specifically allosensitized in vitro were found to be highly effective in inhibiting the growth of an equal number of allogeneic tumor cells. Several times more spleen cells from mice sensitized in vivo were required to produce a similar immune effect. This confirms the findings of previous studies which indicate that sensitization in cell culture can promote the selection of specifically sensitized lymphocytes. Preincubating sensitizing fibroblasts with allo-antisera blocked the allosensitization of spleen cells. This suggests that antibodies binding to fibroblasts may inhibit the induction of sensitization by competing with lymphocytes for antigenic sites. Mouse spleen cells which were able to recognize and reject tumor allografts in vivo were unable to cause lysis of target fibroblasts in vitro. Such fibroblasts, however, were susceptible to lysis by rat lymphoid cells sensitized by a similar in vitro method. These findings indicate that the conditions required for lymphocyte-mediated lysis of target cells may not be directly related to the processes of antigen recognition and allograft rejection in vivo.
Electron paramagnetic resonance studies of the neutral nitrogen vacancy in diamond (2008)

Despite the numerous experimental and theoretical studies on the negatively charged nitrogen vacancy center $({\mathrm{NV}}^{\ensuremath{-}})$ in diamond and the predictions that the neutral nitrogen vacancy center $({\mathrm{NV}}^{0})$ should have an $S=\frac{1}{2}$ ground state, ${\mathrm{NV}}^{0}$ has not previously been detected by electron paramagnetic resonance (EPR). We report new EPR data on a trigonal nitrogen-containing defect in diamond with an $S=\frac{3}{2}$ excited state populated via optical excitation. Analysis of the spin Hamiltonian parameters and the wavelength dependence of the optical excitation leads to assignment of this $S=\frac{3}{2}$ state to the $^{4}A_{2}$ excited state of ${\mathrm{NV}}^{0}$. This identification, together with an examination of the electronic structure of the NV centers in diamond, provides a plausible explanation for the lack of observation (to date) of an EPR signal from the ${\mathrm{NV}}^{0}$ ground state.
Selective histone deacetylase inhibition augments melanoma immunotherapy. (2016)

e14521 Background: Histone deacetylases (HDACs) are epigenetic modulators and regulate gene expression. The impact of the HDAC6 selective inhibitor ACY1215 was explored on immune cell biology, with novel implications for the treatment of melanoma patient T cells ex vivo prior to adoptive transfer. Methods: T cells were obtained from peripheral blood mononuclear cells of healthy donors and melanoma patients. Tumor infiltrating lymphocytes (TILs) were isolated from surgical biopsies. Cells were treated ex vivo with ACY1215 or DMSO control. Viability was addressed by MTS colorimetric assay. Cytokine levels were evaluated by Luminex. Expression of T cell markers and IFNγ/CD107a production were assessed by flow cytometry. T cell cytotoxicity was determined by co-culture of TILs and melanoma and analysis of annexin V and propidium iodide. Affymetrix based microarray was performed on TILs for gene expression analysis. Statistical significance of DMSO vs ACY1215 treated T cells was based on paired, two-tailed, student’s t-test. Results: ACY1215 was unique among pan and selective HDAC inhibitors in modulating T cell function, with minimal impact on viability. Treatment of melanoma patient-derived T cells reduced Th2 cytokine production (IL-4, IL-6, IL-10; p < 0.01) and maintained Th1 effector cytokine levels (IFNγ, IL-2). ACY1215 increased expression of the activation/costimulatory markers CD69 and ICOS (p < 0.05), and enhanced a central memory phenotype expressed by healthy and melanoma patient CD4 and CD8 T cells during ex vivo expansion (p < 0.05), as determined by expression of CD45RO, CD45RA, CD62L and CCR7. In fact, ACY1215 increased central memory TILs derived from multiple cell preparations (e.g. pre and post rapid in vitro expansion; p < 0.05). ACY1215 treated TILs exhibited higher levels of IFNγ/CD107a expressing CD8 T cells (50% vs 35%, p < 0.05), and enhanced cytotoxicity (50% vs 70% killing of HLA matched targets with DMSO vs ACY1215 treated TILs). Microarray analysis revealed increased expression of genes associated with an inflammatory response and T cell memory in ACY1215 treated TILs. Conclusions: ACY1215 augmented T cell proliferation and function during ex vivo expansion, with possible translatable clinical implications.
Reconfigurable Intelligent Surface-Assisted Massive MIMO: Favorable propagation, channel hardening, and rank deficiency [Lecture Notes] (2022)

Massive multiple-input multiple-output (MIMO) and reconfigurable intelligent surface (RIS) are two promising technologies for 5G-and-beyond wireless networks, capable of providing large array gain and multiuser spatial multiplexing. Without requiring additional frequency bands, those technologies offer significant improvements in both spectral and energy efficiency by simultaneously serving many users. The performance analysis of an RIS-assisted massive MIMO system as a function of channel statistics relies heavily on fundamental properties, including favorable propagation, channel hardening, and rank deficiency. The coexistence of both direct and indirect links results in aggregated channels, whose properties are the main concerns of this “Lecture Notes” article. For practical systems with a finite number of antennas and engineered scattering elements of the RIS, we evaluate the corresponding deterministic metrics, with Rayleigh fading channels as a typical example.
REMPI, SEP and MATI on laser desorbed diphenyl-amine (1995)

Mass‐selective spectroscopic techniques have been applied to unravel the vibrational structure of laser‐desorbed jet‐cooled diphenyl‐amine (DPA) in the first electronically excited singlet state and in the electronic ground state of the neutral molecule as well as in the electronic ground state of the cation. A large change in geometry upon electronic excitation and subsequent ionization is inferred from these spectra.
Admission Control for URLLC Traffic with Computation Requirements in 5G and Beyond (2023)

One of the three types of services supported by 5G networks are Ultra-Reliable Low-Latency Communications, which are characterized by the stringent requirement to deliver packets within a very short time with a high reliability. Besides being successfully transmitted/received, these data need to be processed as well. To satisfy these strict requirements, one needs to determine both the required data rate and the processing rate, given the channel conditions and traffic intensity of the service. Moreover, with constraints on both the Radio Access Network and edge computing resources as well as with the competition between an ever-increasing number of users in cellular networks, a very important question which arises is that of admission control. This guarantees users will not suffer from deteriorating performance. In this paper, using analytical modeling, we derive admission control policies for both homogeneous and heterogeneous types of users, taking into account the delay incurred by the RAN part of the network and that caused by the finite computing capability at the edge. We validate theoretical outcomes and provide additional insights on a 5G dataset. Results show that the number of admitted users depends on the worst channel conditions, the deadline by which the data must be processed and the available resources. There is an almost linear increase in the number of admitted users with the decrease in latency.
Co-operating STAT5 and AKT signaling pathways in chronic myeloid leukemia and mastocytosis: possible new targets of therapy (2014)

Chronic myeloid leukemia and systemic mastocytosis are myeloid neoplasms sharing a number of pathogenetic and clinical features. In both conditions, an aberrantly activated oncoprotein with tyrosine kinase activity, namely BCR-ABL1 in chronic myeloid leukemia, and mutant KIT, mostly KIT D816V, in systemic mastocytosis, is key to disease evolution. The appreciation of the role of such tyrosine kinases in these diseases has led to the development of improved therapies with tyrosine kinase-targeted inhibitors. However, most drugs, including new KIT D816V-blocking agents, have failed to achieve long-lasting remissions in advanced systemic mastocytosis, and there is a similar problem in chronic myeloid leukemia, where imatinib-resistant patients sometimes fail to achieve remission, even with second- or third-line BCR-ABL1 specific tyrosine kinase inhibitors. During disease progression, additional signaling pathways become activated in neoplastic cells, but most converge into major downstream networks. Among these, the AKT and STAT5 pathways appear most critical and may result in drug-resistant chronic myeloid leukemia and systemic mastocytosis. Inhibition of phosphorylation of these targets has proven their crucial role in disease-evolution in both malignancies. Together, these observations suggest that STAT5 and AKT are key drivers of oncogenesis in drug-resistant forms of the diseases, and that targeting STAT5 and AKT might be an interesting approach in these malignancies. The present article provides an overview of our current knowledge about the critical role of AKT and STAT5 in the pathophysiology of chronic myeloid leukemia and systemic mastocytosis and on their potential value as therapeutic targets in these neoplasms.
Experimental Results of an E-Field Probe Using Variable Resistors to Improve Performance (2015)

In this letter, experimental results are shown for an E-field probe using variable chip resistor values to improve performance. The E-field probe consists of three small orthogonal dipoles with a diode and a lossy transmission line. Since the transmission line does not receive transmitted signals directly or indirectly, a high impedance value of the transmission line is required. To achieve such a high impedance value, chip resistors are inserted in the transmission line. In this letter, variable resistors are used in the transmission line to improve probe performance of such areas as sensitivity and isotropy. Finally, probes with identical and variable resistance values are fabricated, performance levels are measured, and characteristics are compared.
Apigenin inhibits STAT3/CD36 signaling axis and reduces visceral obesity (2019)

Visceral obesity is the excess deposition of visceral fat within the abdominal cavity that surrounds vital organs. Visceral obesity is directly associated with metabolic syndrome, breast cancer and endometrial cancer. In visceral obese subjects, signal transducer and activator of the transcription 3 (STAT3) in adipocytes is constitutively active. In this study, we aimed to screen for dietary herbal compounds that possess anti-visceral obesity effect. Apigenin is abundant in fruits and vegetables. Our data show that apigenin significantly reduces body weight and visceral adipose tissue (VAT), but not subcutaneous (SAT) and epididymal adipose tissues (EAT), of the high fat diet (HFD)-induced obese mice. Mechanistic studies show that HFD increases STAT3 phosphorylation in VAT, but not in SAT and EAT. Further studies suggest that apigenin binds to non-phosphorylated STAT3, reduces STAT3 phosphorylation and transcriptional activity in VAT, and consequently reduces the expression of STAT3 target gene cluster of differentiation 36 (CD36). The reduced CD36 expression in adipocytes reduces the expression of peroxisome proliferator-activated receptor gamma (PPAR-γ) which is the critical nuclear factor in adipogenesis. Our data show that apigenin reduces CD36 and PPAR-γ expressions and inhibits adipocyte differentiation; overexpression of constitutive active STAT3 reverses the apigenin-inhibited adipogenesis. Taken together, our data suggest that apigenin inhibits adipogenesis via the STAT3/CD36 axis. Our study has delineated the mechanism of action underlying the anti-visceral obesity effect of apigenin, and provide scientific evidence to support the development of apigenin as anti-visceral obesity therapeutic agent.
Hermetic Encapsulation of Nanoenergetic Porous Silicon Wafer by Parylene (2014)

Abstract : Parylene film is attractive for hermetic encapsulation of porous surfaces, including energetic materials, and for the protection of integrated circuits on large-diameter silicon substrates. Achieving uniformity and repeatability of chemical vapor deposited (CVD) parylene film on large-diameter wafers in a batch system is challenging. The difficulties are related to improper selection of the wafer attachment apparatus in the chamber, and the poor coating repeatability from run to run is attributed to wafer volume changes in the CVD chamber. We discuss hardware modifications and preparation methods that improve the predictability, uniformity, and adhesion of the parylene film on nanoporous silicon surfaces. Atomic force microscopy (AFM) can determine surface roughness and distinguish differences in nanoporous silicon etched surfaces. Energetic materials that are hygroscopic in nature need to be protected from the environment during storage to improved ignition lifetime. Parylene film is an effective moisture barrier for nanoporous-scale material applications. We tested the adequacy and lifetime of parylene protection layer for a nanoenergetic device and found the shelf life can be extended in environments with greater than 80% humidity.