gebhart/patrepeval huggingface dataset:
Characterization of NY-ESO-1 gene expression in gastric cancer (GC). (2022)

4046 Background: Tumor specific antigens, such as NY-ESO-1 , are emerging as key tumor immune modulating factors with great potential to be used as therapeutic targets to enhance immunotherapy efficacy and expand treatment options for GC. We sought to compare GC tumors expressing high vs low levels of NY-ESO-1 in terms of immune cell abundance in the tumor microenvironment (TME) as well as distinct molecular features and immune biomarkers. Methods: 1967 tumor samples tested with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) by Caris Life Sciences (Phoenix, AZ) were retrospectively reviewed. The top quartile of transcripts per million was considered high while the bottom quartile was considered low NY-ISO-1 expression. Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous mutations. Mismatch repair deficiency/microsatellite instability (dMMR/MSI) status was evaluated by a combination of IHC, fragment analysis and NGS of known MSI loci. Gene fusions were detected based on WTS. X 2 , Fisher-exact, and Mann Whitney tests were used for comparison and significance adjusted for multiple testing by Benjamini-Hochberg correction ( q &lt; 0.05). Cell infiltration in the TME was estimated by quanTIseq. Gene expression profiles were analyzed for a transcriptional signature predictive of response to immunotherapy (T cell-inflamed signature: TIS). Results: The analysis was focused on primary tumors (N = 1323) in this initial study. Expression of NY-ESO-1 was lower in primary/local than metastases (Fold Change FC met vs primary: 1.60, q &lt; 0.05). NY-ESO-1 expression did not appear to be strongly associated with distinct gene mutation profiles in GC. There were no significant differences between low and high expression of NY-ESO-1 with regards to well established immuno-oncology markers (dMMR/MSI, TMB, PD-L1). However, high NY-ESO-1 expression was positively associated with immune related gene expression including CD274, CD80, CD86, CTLA4, HAVCR2, IDO1, IFNG, LAG3, PDCD1, and PDCD1LG2 (FC low vs high: 0.56 to 0.79, q &lt; 0.0001). High NY-ESO-1 expression was also positively associated with cell abundance in the TME including NK cells (FC = 0.87, q &lt; 0.0001), monocytes (FC = 0.29, q &lt; 0.05), myeloid dendritic cells (FC = 0.66, q &lt; 0.0001), CD4+ non-reg T cells (FC = 0.54, q &lt; 0.0001), and CD8+ T cells (FC = 0.73, q &lt; 0.05). Similarly, tumors with high NY-ESO-1 expression were associated with higher TIS scores ( q &lt; 0.0001). Conclusions: In our large cohort of GC, tumors expressing high NY-ESO-1 displayed a distinct landscape of immune cells in the TME and were associated with high expression of immune related genes, as well as high TIS score, which has been reported to predict benefit from anti-PD-1 treatment. The results of our analysis support an association between a more immunologically active tumor microenvironment and NY-ESO-1 gene expression which may have relevant implications on immunotherapy treatment for GC.
Supplementary Figure 2 from Nuclear Translocation of Hand-1 Acts as a Molecular Switch to Regulate Vascular Radiosensitivity in Medulloblastoma Tumors: The Protein uPAR Is a Cytoplasmic Sequestration Factor for Hand-1 (2023)

&lt;p&gt;PDF file - 2038K, Supplementary Fig.2. Hand-1-mediated negative regulation of HIF-1A.&lt;/p&gt;
Synthesis and immunological evaluation of peptide-based vaccine candidates against malaria (2016)

Introduction Malaria is considered as one of the most prevalent diseases in developing countries. It causes about one million deaths annually and is a major health problem worldwide [1,2]. People living in areas where rainfall and temperature favour the growth of Plasmodium parasites are at the highest risk [3]. Four Plasmodium
RELIGION AND EDUCATION—HOME AND ABROAD (1935)

RELIGION AND EDUCATION—HOME AND ABROAD Get access ALBERT EDWARD BAILEY ALBERT EDWARD BAILEY PROFESSOR Search for other works by this author on: Oxford Academic Google Scholar Journal of the American Academy of Religion, Volume 3, Issue 1, 1935, Pages 25-c–28, https://doi.org/10.1093/jaarel/3.1.25-c Published: 01 March 1935
Labeling pharmaceuticals with radioactive isotopes. Annual progress report, June 1, 1973--February 28, 1974 (1974)

Potentially useful radiopharmaceuticals labeled with /sup 18/F or /sup 131/I may be prepared by either homogeneous or heterogeneous halogen interachange procedures, giving amino acid analog compounds where an I-for-methyl or F-for-H substitution has taken place. These radio-labeled compounds will be evaluated for potential clinical utility via specific organ localization. Progress is reported in developing a suitable /sup 18/F source, free of carrier fluorine as well as of chemical and radionuclidic contaminants; preparation of surfaces and matrices for halogen interchange; initial testing of /sup 18/F-labeled surfaces with model compounds; identification and removal of tritium-containing organic compounds found in clinical /sup 18/F preparations, and preparation of several compounds which, after halogen interchange, can be used to produce I-formethyl amino acid analogs. (auth)
A Scalable, Out-of-Band Diagnostics Architecture for International Space Station Systems Support (2002)

The computational infrastructure of the International Space Station (ISS) is a dynamic system that supports multiple vehicle subsystems such as Caution and Warning, Electrical Power Systems and Command and Data Handling (C&DH), as well as scientific payloads of varying size and complexity. The dynamic nature of the ISS configuration coupled with the increased demand for payload support places a significant burden on the inherently resource constrained computational infrastructure of the ISS. Onboard system diagnostics applications are hosted on computers that are elements of the avionics network while ground-based diagnostic applications receive only a subset of available telemetry, down-linked via S-band communications. In this paper we propose a scalable, out-of-band diagnostics architecture for ISS systems support that uses a read-only connection for C&DH data acquisition, which provides a lower cost of deployment and maintenance (versus a higher criticality readwrite connection). The diagnostics processing burden is off-loaded from the avionics network to elements of the on-board LAN that have a lower overall cost of operation and increased computational capacity. A superset of diagnostic data, richer in content than the configured telemetry, is made available to Advanced Diagnostic System (ADS) clients running on wireless handheld devices, affording the crew greater mobility for troubleshooting and providing improved insight into vehicle state. The superset of diagnostic data is made available to the ground in near real-time via an out-of band downlink, providing a high level of fidelity between vehicle state and test, training and operational facilities on the ground.
Supplementary Data from Phase I/II Multicenter Trial of a Novel Therapeutic Cancer Vaccine, HepaVac-101, for Hepatocellular Carcinoma (2023)

Supplementary Data from Phase I/II Multicenter Trial of a Novel Therapeutic Cancer Vaccine, HepaVac-101, for Hepatocellular Carcinoma
Tunable, dual wavelength and self-Q-switched Alexandrite laser using crystal birefringence control (2019)

We present a red-diode-pumped Alexandrite laser with continuous wavelength tunability, dual wavelength and self-Q-switching in an ultra-compact resonator containing only the gain medium. Wavelength tuning is obtained by varying the geometrical path length and birefringence by tilting a Brewster-cut Alexandrite crystal. Two crystals from independent suppliers are used to demonstrate and compare the performance. Wavelength tuning between 750 and 764 nm is demonstrated in the first crystal and between 747 and 768 nm in the second crystal. Stable dual wavelength operation is also obtained in both crystals with wavelength separation determined by the crystal free spectral range. Temperature tuning was also demonstrated to provide finer wavelength tuning at a rate of -0.07 nm K <sup>-1</sup>. Over a narrow tuning range, stable self-Q-switching is observed with a pulse duration of 660 ns at 135 kHz, which we believe is the highest Q-switched pulse rate in Alexandrite to date. Theoretical modelling is performed showing good agreement with the wavelength tuning and dual wavelength results.
Modal instability-suppressing, single-frequency photonic crystal fiber amplifier with 811  W output power (2014)

An acoustic- and gain-tailored Yb-doped polarization-maintaining photonic crystal fiber is used to demonstrate 811 W single-frequency output power with near diffraction-limited beam quality. The fiber core is composed of 7 individually doped segments arranged to create three distinct transverse acoustic regions; including one region that is Yb-free. The utility of the Yb-free region is to reduce coupling between the LP01 and LP11 modes to mitigate the modal instability. The application of thermal gradients is utilized in conjunction with the transverse acoustic tailoring to suppress stimulated Brillouin scattering. To the best of our knowledge, the 811 W output represents the highest power ever reported from a near diffraction-limited single-frequency fiber laser.
Studies of Fabrication Procedure of 9-cell SRF Cavity for ILC Mass-production at KEK. (2014)

We had been constructing a new facility for the fabrication of superconducting RF cavity at KEK from 2009 to 2011. In the facility, we have installed a deep-drawing machine, a half-cup trimming machine, an electron-beam welding machine, and a chemical etching room in one place. We started the studies on the fabrication of 9-cell cavity for International Linear Collier (ILC) using this facility. The studies are focusing on the cost reduction with keeping high performance of cavity, and the goal is the establishment of mass-production procedure for ILC. We already finished the fabrication of two 9-cell cavities in this facility. This article reports the current status of the studies.
A soft microfabricated capacitive sensor for high dynamic range strain sensing (2016)

This work demonstrates an all-elastomer MEMS capacitive strain sensor with high dynamic range (5000:1), and features an inexpensive molding microfabrication process. The sensor is comprised of conductive elastometric comb capacitors embedded in a dielectric. Two different sensor designs, lateral combs (LC) and transverse combs (TC), were developed to evaluate sensor sensitivity as a function of load orientation. Both sensors have combs with a gap of 30 μm, length of 4 mm, and depth of 65 μm. A linear elastic analytical model was developed to predict change in capacitance as a function of strain, and experimental results show a reasonable agreement with the theoretical predictions. The observed strain responses have high linearity and dynamic range, and negligible hysteresis. The strain resolution of the LC and TC sensors is 100 μstrain and 500 μstrain, respectively, tested up to 50% strain.
ChemInform Abstract: Enolates of α‐Allenyl Ketones: Formation and Aldol Reactions of Cumulenolates. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Submarine towed communication antennas: past, present and future (2002)

Submarine antennas can be divided into two broad categories: mast and towed systems. In a mast system, a set of antennas is erected from the ship's sail to enable communication; several typical antennas used in a mast configuration are shown. A towed system, in contrast, is trailed behind the submerged vessel. The towed antenna system is probably the more complex design challenge of the two categories mentioned above, since issues such as buoyancy, mitigation of signal outages due to seawater wash-over, physical robustness and stealth must be simultaneously addressed if the system is to be used effectively in coastal warfare scenarios. Therefore, this paper focuses on submarine towed antenna design.
Biomass gasification hot gas cleanup demonstration program status (1994)

In support of the U.S. Department of Energy`s Biomass Power Program, Westinghouse Electric has been conducting research and development of a hot gas cleaning system compatible with a pressurized fluidized bed biomass gasifier and the operation of a gas turbine. The hot gas cleanup system must be capable of filtering out the flyash particulates at gasifier operating conditions, dealing with the feedstock`s inherent tars and oils, and removing excessive levels of alkali. The Westinghouse led team consisting of the Institute of Gas Technology, Gilbert/Commonwealth, and the Pacific International Center for High Technology Research began work in April 1993 on this 30 month program. Status of the program is: hot gas cleanup (HGCU) requirements and system evaluation have been completed; the hot gas cleanup filter system has been designed, fabricated and installed in the 10 ton-per-day process development unit (PDU) at IGT in Chicago, IL; a tar cracker has been designed, fabricated and installed in the PDU; the testing plan has been developed; PDU modifications have been completed along with complete facility shakedown; and testing of the cleanup system is in process. This paper discusses the status of each of the major program elements described above.
Cattle Mammary Bioreactor Generated by a Novel Procedure of Transgenic Cloning for Large-Scale Production of Functional Human Lactoferrin (2008)

Large-scale production of biopharmaceuticals by current bioreactor techniques is limited by low transgenic efficiency and low expression of foreign proteins. In general, a bacterial artificial chromosome (BAC) harboring most regulatory elements is capable of overcoming the limitations, but transferring BAC into donor cells is difficult. We describe here the use of cattle mammary bioreactor to produce functional recombinant human lactoferrin (rhLF) by a novel procedure of transgenic cloning, which employs microinjection to generate transgenic somatic cells as donor cells. Bovine fibroblast cells were co-microinjected for the first time with a 150-kb BAC carrying the human lactoferrin gene and a marker gene. The resulting transfection efficiency of up to 15.79 x 10(-2) percent was notably higher than that of electroporation and lipofection. Following somatic cell nuclear transfer, we obtained two transgenic cows that secreted rhLF at high levels, 2.5 g/l and 3.4 g/l, respectively. The rhLF had a similar pattern of glycosylation and proteolytic susceptibility as the natural human counterpart. Biochemical analysis revealed that the iron-binding and releasing properties of rhLF were identical to that of native hLF. Importantly, an antibacterial experiment further demonstrated that rhLF was functional. Our results indicate that co-microinjection with a BAC and a marker gene into donor cells for somatic cell cloning indeed improves transgenic efficiency. Moreover, the cattle mammary bioreactors generated with this novel procedure produce functional rhLF on an industrial scale.
Glutathione Peroxidase-1 Deficiency Potentiates Dysregulatory Modifications of Endothelial Nitric Oxide Synthase and Vascular Dysfunction in Aging (2013)

Recently, we demonstrated that gene ablation of mitochondrial manganese superoxide dismutase and aldehyde dehydrogenase-2 markedly contributed to age-related vascular dysfunction and mitochondrial oxidative stress. The present study has sought to investigate the extent of vascular dysfunction and oxidant formation in glutathione peroxidase-1-deficient (GPx-1(-/-)) mice during the aging process with special emphasis on dysregulation (uncoupling) of the endothelial NO synthase. GPx-1(-/-) mice on a C57 black 6 (C57BL/6) background at 2, 6, and 12 months of age were used. Vascular function was significantly impaired in 12-month-old GPx-1(-/-) -mice as compared with age-matched controls. Oxidant formation, detected by 3-nitrotyrosine staining and dihydroethidine-based fluorescence microtopography, was increased in the aged GPx-1(-/-) mice. Aging per se caused a substantial protein kinase C- and protein tyrosine kinase-dependent phosphorylation as well as S-glutathionylation of endothelial NO synthase associated with uncoupling, a phenomenon that was more pronounced in aged GPx-1(-/-) mice. GPx-1 ablation increased adhesion of leukocytes to cultured endothelial cells and CD68 and F4/80 staining in cardiac tissue. Aged GPx-1(-/-) mice displayed increased oxidant formation as compared with their wild-type littermates, triggering redox-signaling pathways associated with endothelial NO synthase dysfunction and uncoupling. Thus, our data demonstrate that aging leads to decreased NO bioavailability because of endothelial NO synthase dysfunction and uncoupling of the enzyme leading to endothelial dysfunction, vascular remodeling, and promotion of adhesion and infiltration of leukocytes into cardiovascular tissue, all of which was more prominent in aged GPx-1(-/-) mice.
Commentary: Isolated Stem Cells—Patentable as Cultural Artifacts? (2007)

This article argues that an isolated embryonic stem cell basically represents a cultural artifact that has no equivalent to cells of the embryo, and that it is likely that the isolation of adult stem cells has a similar consequence. An isolated stem cell could thus be distinguished as something other than the stem cell existing as part of a human body. Since isolation of stem cells implies modification, product patents should, where the results carry enough novelty, inventive step, and potential for industrial application, as a matter of principle be a viable option for patent authorities. Questions of morality, which may affect the patentability, should also be viewed in light of the distinction between isolated result and body part. At the same time, it is essential that patent authorities do not accept broad patent claims that will be detrimental to research. Disclosure of potential conflicts of interest is found at the end of this article.
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site (2021)

ABSTRACT The Internal R ibosome E ntry S ite (IRES) RNA of B ovine v iral d iarrhea v irus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modeling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA forms in solution a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are engaged in tertiary interactions to form an H-type pseudoknot. Computational modeling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
Biomaterials for polynucleotide delivery to anchorage-independent cells (2017)

Anchorage-independent cells possess morphological features and cell membrane compositions that are distinct from adherent cells. They display minimal surface area, have a low rate of endocytosis and generally possess few proteoglycans which make it a challenge to deliver nucleic acids into them. Wide ranges of methods and materials have been developed to tackle the delivery obstacles for the polynucleotide-based therapeutics in modifying non-adherent cells. This article summarizes the techniques and biomaterials that have been utilized for transfection of anchorage-independent cells. First, physical techniques are briefly described along with particular applications for which they are well-suited. The structure-activity relationship of various biomaterial carriers of polynucleotides are then discussed with strategies employed to enhance their capability to transfect anchorage-independent cells. In conclusion, the authors' perspectives on different methods for polynucleotide delivery to primary human cells are compared, along with a discussion of their progression towards clinical trials.
The flexible C‐terminal arm of the Lassa arenavirus Z‐protein mediates interactions with multiple binding partners (2010)

The arenavirus genome encodes for a Z-protein, which contains a RING domain that coordinates two zinc ions, and has been identified as having several functional roles at various stages of the virus life cycle. Z-protein binds to multiple host proteins and has been directly implicated in the promotion of viral budding, repression of mRNA translation, and apoptosis of infected cells. Using homology models of the Z-protein from Lassa strain arenavirus, replica exchange molecular dynamics (MD) was used to refine the structures, which were then subsequently clustered. Population-weighted ensembles of low-energy cluster representatives were predicted based upon optimal agreement of the chemical shifts computed with the SPARTA program with the experimental NMR chemical shifts. A member of the refined ensemble was identified to be a potential binder of budding factor Tsg101 based on its correspondence to the structure of the HIV-1 Gag late domain when bound to Tsg101. Members of these ensembles were docked against the crystal structure of human eIF4E translation initiation factor. Two plausible binding modes emerged based upon their agreement with experimental observation, favorable interaction energies and stability during MD trajectories. Mutations to Z are proposed that would either inhibit both binding mechanisms or selectively inhibit only one mode. The C-terminal domain conformation of the most populated member of the representative ensemble shielded protein-binding recognition motifs for Tsg101 and eIF4E and represents the most populated state free in solution. We propose that C-terminal flexibility is key for mediating the different functional states of the Z-protein.