gebhart/patrepeval huggingface dataset:
Prognostic impact of cancer/testis antigen expression in advanced stage multiple myeloma patients. (2008)

This study aims to analyze the expression of 14 cancer/testis (CT) antigens in multiple myeloma (MM) to identify possible prognostic markers and therapeutic targets. The expression of MAGEA1, MAGEA2, MAGEA3/6, MAGEA4, MAGEA10, MAGEA12, BAGE1, MAGEC1/CT7, the GAGE family, LAGE-1, PRAME, NY-ESO-1, SPA17 and SSX1 was studied by RT-PCR in 15 normal tissues, a pool of 10 normal bone marrow samples, 3 normal tonsils and bone marrow aspirates from 6 normal donors, 3 monoclonal gammopathies of undetermined significance (MGUS), 5 solitary plasmacytomas, 39 MM samples (95% advanced stage) and the MM cell line U266. MAGEC1/CT7 was expressed in bone marrow aspirates from one MGUS and one plasmacytoma. The frequencies at which CT antigen were found to be expressed in MM patients were MAGEC1/CT7 77%, LAGE-1 49%, MAGEA3/6 41%, MAGEA2 36%, GAGE family 33%, NY-ESO-1 33%, BAGE-1 28%, MAGEA1 26%, PRAME 23%, SSX-1 26%, MAGEA12 20.5%, MAGEA4 0%, and MAGEA10 0%. Cox's regression model showed that GAGE family expression and having >6 CT antigens expressed were independent prognostic factors when all patients were analyzed. However, MAGEC1/CT7 expression was the only independent prognostic factor when non-transplanted patients where analyzed. Based on our findings, MAGEC1/CT7, MAGEA3/6 and LAGE-1 are good candidates for immunotherapy, since together they cover 85% of our MM cases. Furthermore, expression of the GAGE family, >6 CT antigens and MAGEC1/CT7 seem to have impact on MM prognosis.
Supplemental Table 1 from Adenosine A<sub>2A</sub> Receptors Intrinsically Regulate CD8<sup>+</sup> T Cells in the Tumor Microenvironment (2023)

&lt;p&gt;Table summarizing the sources, properties and dilutions of antibodies used in this study.&lt;/p&gt;
Impact of long-term measures of glucose and blood pressure on the retinal microvasculature (2020)

Retinopathy and retinal microvascular abnormalities are common in adult populations, yet few long-term predictors have been identified. We therefore examined the association between systolic blood pressure (SBP) and fasting plasma glucose, assessed over 18 years, with retinopathy and retinal vascular caliber in 2,066 Carotid MRI participants, an Atherosclerosis Risk in Communities ancillary study.
Dosimetric properties of MgAl2O4 transparent ceramics doped with Ce (2022)

Abstract Ce-doped MgAl 2 O 4 transparent ceramics were fabricated by the spark plasma sintering method. The 0.01% Ce-doped MgAl 2 O 4 exhibited photoluminescence (PL) peaking at 410 nm upon the excitation of 310 nm. On the other hand, the 0.1%, 0.5%, and 1% Ce-doped MgAl 2 O 4 showed different PL excitation peaks. The PL peak at 410 nm was attributed to 5d-4f transitions of Ce 3+ ions with a decay time of a few nanoseconds. Thermally stimulated luminescence (TSL) glow curves were mainly composed of three glow peaks. When Ce-doped MgAl 2 O 4 was heated at 300 °C, three TSL emission peaks were observed at around 410, 520 and 700 nm in TSL spectra, originating from Ce 3+ ions, Mn 2+ impurities, and Mg 2+ vacancies, respectively. The normalized TSL intensity declined to 95% for the first 24 h and did not change in 1–5 d within the measurement error. The minimum detectable dose of the 0.5% Ce-doped MgAl 2 O 4 was 0.5 μ Gy.
Introduction to the Issue on Optical Interconnects for Data Centers (2013)

The authors are pleased to introduce the IEEE Journal of Selected Topics in Quantum Electronics (JSTQE) Issue on "Optical Interconnects for Data Centers." This issue signifies the first JSTQE issue dedicated to the emerging important roles photonics are playing in data centers. The issue showcases the significant research progress being made toward integrating optical interconnect technology (monolithically or multichip module) with CMOS computing logic to meet the challenges in achieving the high performance and energy efficiency needed for both high-performance computing and data centers. This issue contains 20 papers, including seven invited and 13 contributed papers, authored by some of the leading photonics research groups in the world. The papers in this issue cover the broad scope of research representative of this growing field.
Spontaneous Remission in Experimental Autoimmune Labyrinthitis (1992)

We investigated the time course of hearing impairment and cellular infiltration into the inner ear after systemic sensitization of guinea pigs with a single intradermal injection of bovine inner ear antigen (IEAg) in complete Freund's adjuvant (CFA). Lymphocytes and polymorphonucleocytes appeared mainly in the scala tympani on days 7 to 14, and in addition there was thickening and cellular infiltration of the round window membrane at day 14. These cellular infiltrations resolved after day 28. The auditory brain stem response thresholds from IEAg-sensitized animals were significantly elevated after day 7. Some sensitized animals (n = 5) had spontaneous remissions after day 28; however, the hearing thresholds did not completely recover. These results demonstrate that experimental autoimmune labyrinthitis can be induced by a single inoculation of IEAg-CFA and that remission, as evidenced by clearing of the cochlear cellular infiltration and improved hearing thresholds, can occur spontaneously.
Associations between Antimicrobial Resistance Genes in Fecal Generic Escherichia coli Isolates from Cow-Calf Herds in Western Canada (2008)

The objective of this study was to examine associations among the genetic determinants of antimicrobial resistance (AMR) in 207 fecal generic Escherichia coli isolates obtained from 77 cow-calf herds in western Canada. Twenty-three resistance genes corresponding to six different antimicrobial families were assessed using DNA hybridization and PCR. The most common resistance genes in the study sample (207 isolates) were sul2 (48.3%), tet(B) (45.4%), and ant(3'')-Ia (aadA1) (19.3%). Several statistically significant associations between the examined resistance genes were detected. The strongest associations observed were those between genes for resistance to chloramphenicol (catI) and trimethoprim (dhfrI) (odds ratio [OR] = 214; P = 0.0001), sulfonamide (sul1) and chloramphenicol (catI) (OR = 96.9; P = 0.0001), streptomycin [ant(3'')-Ia (aadA1)] and trimethoprim (dhfrI) (OR = 96.2; P = 0.0001), sulfonamide (sul1) and streptomycin [ant(3'')-Ia (aadA1)] (OR = 79.3; P = 0.0001), and tetracycline [tet(B)] and sulfonamides (sul2) (OR = 25.7; P = 0.0001). At least one of the resistance genes corresponding to each nonaminoglycoside family of antimicrobials examined in this study was associated with the two aminoglycoside resistance genes ant(3'')-Ia (aadA1) and aph(3')-Ia. The multiple, strong associations between genes and the diverse nature of the associations described in this study demonstrate the complexity of resistance gene selection in cow-calf herds and should be considered in the planning of AMR control practices for cow-calf operations.
Measurement of the single top quark and antiquark production cross sections in the t channel and their ratio in proton-proton collisions at s=13TeV (2019)

Measurements of the cross sections for the production of single top quarks and antiquarks in the t channel, and their ratio, are presented for proton-proton collisions at a center-of-mass energy of 13 TeV. The data set used was recorded in 2016 by the CMS detector at the LHC and corresponds to an integrated luminosity of 35.9 fb -1 . Events with one muon or electron are selected, and different categories of jet and b jet multiplicity and multivariate discriminators are applied to separate the signal from the background. The cross sections for the t-channel production of single top quarks and antiquarks are measured to be 130 1(stat) 19(syst) pb and 77 1(stat) 12(syst) pb, respectively, and their ratio is 1.68 0.02(stat) 0.05(syst). The results are in agreement with the predictions from the standard model.
Drift-free magnetic geometries in adiabatic motion (1975)

There exist magnetic fields in which particles bouncing between mirror points experience no net first-order guiding center drift. In such fields, even though the instantaneous gradient and curvature drifts are not zero, their total effect integrated over any bounce period vanishes, so that particles merely wobble back and forth around fixed field lines. A class of two-dimensional drift-free fields, somewhat resembling the configuration found in the geomagnetic tail, is described; several proofs of the drift-free property are given, including some that suggest that the property of vanishing net drift might extend to nonadiabatic orbits. A general criterion for identifying drift-free fields is developed, and a case of motion in a nearly drift-free field is also investigated. The theory is applied to the plasma sheet in the earth's magnetotail, and observational evidence is presented suggesting that the magnetic field there indeed approaches a drift-free configuration.
A comprehensive model for breakdown mechanism in HfO/sub 2/ high-κ gate stacks (2005)

Based on physical analysis results, a model describing the breakdown (BD) mechanism of HfO/sub 2//polysilicon gate stack is proposed. Due to the high mechanical strength and the polycrystalline nature of annealed HfO/sub 2/ dielectrics, and a very complicated BD induced thermo-chemical reaction and self-healing process, the BD mechanism and transient evolution in HfO/sub 2/ gate stacks are different from that of ultrathin SiO/sub x/N/sub y/. The formation of a percolation path is probably assisted by grain boundaries and/or enhanced electric field strength near the poly-Si edge. Besides polarity-dependent dielectric-BD-induced epitaxy (DBIE), due to the BD induced thermo-chemical reactions among HfO/sub 2/, SiO/sub x/ (i.e. IL oxide), Hf-compounds and Si, the formation of a dielectric-based "clog" which is HfSi/sub x/ O/sub y/-rich, termed as dielectric-BD-induced self-healing insulating cap (SHIC), is proposed. The microstructures of DBIE and SHIC are responsible for the leakage current evolution during a BD event in HfO/sub 2/ gate stacks.
Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins (2022)

Abstract Streptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each host environment. Consequently, an in-depth understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA-seq data sets of S. pyogenes serotype M1, and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, and changed bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify interpretation of noisy bacterial transcriptome at the infection site.
Organization-wide adoption of computerized provider order entry systems: a study based on diffusion of innovations theory (2009)

Qualifications for CPOE adoption as defined by three attributes of diffusion of innovation theory were not satisfied in the study setting. CPOE systems are introduced as a response to the present limitations in paper-based systems. In consequence, user expectations are often high on their relative advantages as well as on a low level of complexity. Building CPOE systems therefore requires designs that can provide rather important additional advantages, e.g. by preventing prescription errors and ultimately improving patient safety and safety of clinical work. The decision-making process leading to the implementation and use of CPOE systems in healthcare therefore has to be improved. As any change in health service settings usually faces resistance, we emphasize that CPOE system designers and healthcare decision-makers should continually collect users' feedback about the systems, while not forgetting that it also is necessary to inform the users about the potential benefits involved.
Evaluation of ab Initio Charge Determination Methods for Use in Continuum Solvation Calculations (2003)

Application of continuum electrostatic calculations to molecular modeling requires an accurate description of molecular charge distributions, typically as partial atomic charges. While for some systems, such as biological macromolecules, sets of charges have been parametrized on the basis of experimental data, for many other cases, ab initio methods of charge determination may be preferred. Presented here is a comprehensive evaluation of the performance of numerous methods for the ab initio determination of partial atomic charges in continuum electrostatic calculations. Charges were computed using several methods based both on fitting electrostatic potentials and on population analysis, and using various levels of theory ranging from semiempirical quantum mechanical methods through relatively high level ab initio quantum mechanical methods. All charge distributions were evaluated in terms of their ability to reproduce experimental free energies of solvation in the context of a continuum solvation model. Two sets of test molecules were used, one derived from the groups seen in proteins, and the other a more diverse set of neutral organic molecules. The results indicate that there are clearly preferred methods for determining charges and, conversely, that there are highly unsuitable methods. The agreement with experiment does not increase monotonically with increasingly accurate levels of theory, although the lowest level methods do perform particularly poorly. None of the methods performed uniformly well across all molecule types; the top performing methods tended to give charge magnitudes in the middle of the observed range, but both the under- and overpolarized charge distributions perform better for certain systems. The frequently used HF/6-31G* level of quantum mechanics did very well, ranking among the top methods, particularly when coupled with the Merz−Singh−Kollman charge fitting scheme or a restrained fit based on this scheme. For methods at a relatively high level of theory, the charges derived from B3LYP/6-311G*+ potentials performed the best, while the computationally inexpensive B3LYP/4-31G derived charges provided the best performance for a fairly low level method.
Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer (2018)

Advanced prostate cancer initially responds to androgen deprivation therapy (ADT), but the disease inevitably recurs as castration-resistant prostate cancer (CRPC). Although CRPC initially responds to abiraterone and enzalutamide, the disease invariably becomes nonresponsive to these agents. Novel approaches are required to circumvent resistance pathways and to extend survival, but the mechanisms underlying resistance remain poorly defined. Our group previously showed the histone lysine-<i>N</i>-methyltransferase EZH2 to be overexpressed in prostate cancer and quantitatively associated with progression and poor prognosis. In this study, we screened a library of epigenetic inhibitors for their ability to render CRPC cells sensitive to enzalutamide and found that EZH2 inhibitors specifically potentiated enzalutamide-mediated inhibition of proliferation. Moreover, we identified antisense oligonucleotides (ASO) as a novel drug strategy to ablate EZH2 and androgen receptor (AR) expression, which may have advantageous properties in certain settings. RNA-seq, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing demonstrated that EZH2 inhibition altered the AR cistrome to significantly upregulate AR signaling, suggesting an enhanced dependence of CRPC cells on this pathway following inhibition of EZH2. Combination treatment with ASO targeting EZH2 and AR transcripts inhibited prostate cancer cell growth <i>in vitro</i> and <i>in vivo</i> better than single agents. In sum, this study identifies EZH2 as a critical epigenetic regulator of ADT resistance and defines ASO-based cotargeting of EZH2 and AR as a promising strategy for the treatment of CRPC.<b>Significance:</b> Simultaneous targeting of lysine methyltransferase EZH2 and the AR with ASO proves a novel and effective therapeutic strategy in patients with CRPC. <i>Cancer Res; 78(20); 5731-40. ©2018 AACR</i>.
3D-Cell Control Technology for Frequency Sharing between HAPS and Terrestrial Systems (2022)

The high-altitude platform station (HAPS) is a promising solution for extreme coverage extension in the Fifth Generation (5G) Evolution and Sixth Generation (6G) eras. By providing radio waves from the stratosphere using HAPS, mobile communications can be made available in all locations that are not adequately covered by conventional mobile communications networks. It is desirable that the HAPS and terrestrial system share a frequency to actualize a direct access service in which terminals connected to the terrestrial International Mobile Telecommunications (IMT) network at 2.7 GHz or less can directly connect to the HAPS. In this paper, we propose a 3D-cell control technology as a load balancing and interference avoidance mechanism when HAPS and terrestrial network share a frequency. Evaluation results based on a 6G system-level simulator show that the load balance and interference-to-noise ratio characteristics are improved in the 2 GHz band.
Antigen‐specific proliferation of porcine CD8αα cells to an extracellular bacterial pathogen (2000)

A vaccine inducing protective immunity to a spirochaete-induced colitis of pigs predominantly stimulates expansion of CD8+ cells in vivo and in antigen-stimulated lymphocyte cultures. CD8+ cells, however, are rarely considered necessary for protection against extracellular bacterial pathogens. In the present study, pigs recovering from colitis resulting from experimental infection with Brachyspira (Serpulina) hyodysenteriae had increased percentages of peripheral blood CD4- CD8+ (alphaalpha-expressing) cells compared with non-infected pigs. CD8alphaalpha+ cells proliferated in antigen-stimulated cultures of peripheral blood mononuclear cells from B. hyodysenteriae-vaccinated pigs. Proliferating CD8alphaalpha+ cells consisted of CD4-, CD4+ and gammadelta T-cell receptor-positive cells. CD4- CD8alphabeta+ cells from vaccinated or infected pigs did not proliferate upon in vitro antigen stimulation. Of the CD8alphaalpha cells that had proliferated, flow cytometric analysis indicated that the majority of the CD4+ CD8+ cells were large (i.e. lymphoblasts) whereas the CD4- CD8+ cells were predominantly small. Addition of monoclonal antibodies (mAb) specific for either porcine major histocompatibility complex (MHC) class I or class II antigens diminished B. hyodysenteriae-specific proliferative responses whereas addition of mAb to porcine MHC II, but not porcine MHC I, reduced the CD8alphaalpha response. In vitro depletion of CD4+ cells by flow cytometric cell sorting diminished, but did not completely abrogate, the proliferative response of cells from vaccinated pigs to B. hyodysenteriae antigen stimulation. These results suggest that CD8alphaalpha cells are involved in recovery and possibly protection from a spirochaete-induced colitis of pigs; yet, this response appears to be partially dependent upon CD4+ cells.
Images of the early universe from the BOOMERanG experiment (2001)

The CMB is the fundamental tool to study the properties of the early universe and of the&#13;\nuniverse at large scales. In the framework of the Hot Big Bang model, when we look to&#13;\nthe CMB we look back in time to the end of the plasma era, at a redshift ~ 1000, when&#13;\nthe universe was ~ 50000 times younger, ~ 1000 times hotter and ~ 10^9 times denser&#13;\nthan today. The image of the CMB can be used to study the physical processes there, to&#13;\ninfer what happened before, and also to study the background geometry of our Universe.&#13;\n
Thermally stable photoaligned p-cyanoazobenzene moieties in polymer thin films (1998)

Poly(4-cy ano-4'-methacryloyloxy azobenzene) displayed a slow E-to-Z photoisomerization rate and a low Z-isomer content at a photostationary state in a film. Linearly polarized 436 nm light irradiation resulted in the gradual generation of dichroism due to the reorientation of the azobenzene chromophores. The photodichroism was enhanced markedly by heating the film and not deteriorated even at 240 °C. Discussion was made on the thermally enhanced photodichroism of the polymer with p-cy anoazobenzene side chains in respect to its semi-crystallinity.
Table S2 from Genetic Alterations in the PI3K/AKT Pathway and Baseline AKT Activity Define AKT Inhibitor Sensitivity in Breast Cancer Patient-derived Xenografts (2023)

&lt;p&gt;Genomic alterations in PDX by IMPACT-MSKCC platform or exome-sequencing&lt;/p&gt;
Effects of Mitragynine and its Active Metabolites on the Reinforcing Effects of Remifentanil and Cocaine in Rats Self‐Administering Remifentanil (2022)

Kratom is being developed as a pharmacotherapy to mitigate withdrawal symptoms from opioids; however, the presence of active metabolites of the primary kratom alkaloid mitragynine (MG) at mu‐opioid receptors [(MORs), 7‐hydoxymitragynine (7‐OH‐MG) and mitragynine pseudoindoxyl (MG‐P)] may limit effectiveness due to their abuse potential. Yue et al (2018) indicated specificity of the antagonizing effects of MG for the reinforcing effects of the MOR agonist heroin relative to the non‐opioid methamphetamine. Using an intravenous drug self‐administration assay, the present study compared abuse potential of MG and its metabolites, and assessed specificity of MG to antagonize the reinforcing effects of the MOR agonist remifentanil and the non‐opioid cocaine in rats. In rats self‐administering remifentanil (0.1‐3.2 µg/kg/injection), reference MOR agonists (methadone and buprenorphine) and the dopamine uptake inhibitor cocaine maintained self‐administration responding above extinction (no injection) levels whereas antagonists at MOR (naltrexone and naloxone) did not. Self‐administration responding above extinction was maintained by 7‐OH‐MG (1.0‐10 µg/kg/injection) and MGP (0.32 µg/kg/injection), but not MG (up to 3.2 mg/kg/injection) when substituted for remifentanil. Self administration of remifentanil, cocaine, 7‐OH‐MG, and MG‐P was decreased by naltrexone (3.2 mg/kg, i.p.). Self administration of remifentanil was also decreased by MG, 7‐OH‐MG, and MG‐P (ED 50 values: 34.5, 4.35, and 2.66 mg/kg, respectively). Self administration of cocaine was also decreased by MG, 7‐OH‐MG, and MG‐P (ED 50 values: 59.2, 5.12, and 5.17 mg/kg, respectively). Despite the abuse potential of active metabolites of MG, these results suggest less abuse potential of MG than that of its metabolites in rats. The lack of obvious reinforcing effects of MG also suggests if any low contribution of 7‐OH‐MG and MGP to the in vivo MOR activity of MG in rats. Though MG was least potent to decrease the reinforcing effects of remifentanil and cocaine, the comparable ED 50 values per compound suggest a lack of specificity of the antagonizing effects of MG and its metabolites in rats with opioid history. These results also indicate that drug history could affect the antagonizing effects of MG on the reinforcing effects of stimulants.