gebhart/patrepeval huggingface dataset:
Improved biodistribution of 125I-labeled anti-Tac disulfide-stabilized Fv fragment by blocking its binding to the alpha subunit of the interleukin 2 receptor in the circulation with preinjected humanized anti-Tac IgG. (1997)

Animal studies using radiolabeled anti-Tac disulfide-stabilized Fv (dsFv) monoclonal antibody have shown formation of complexes in serum with the soluble alpha subunit of the interleukin 2 receptor alpha (sIL-2R alpha). In this study, we improved the targeting of 125I-labeled anti-Tac dsFv to receptor-positive tumors in the presence of circulating receptor by preinjecting unlabeled humanized anti-Tac IgG antibody (HuTac IgG). We used mice bearing SP2/Tac tumor xenografts that express the IL-2R alpha. A positive correlation was seen between tumor size and the concentration of circulating receptor. Tumor-bearing mice were injected with 125I-labeled anti-Tac dsFv (400 ng), either alone or 15 min after injection of HuTac IgG. The 125I-labeled anti-Tac dsFv formed high molecular weight complexes with the sIL-2R alpha. The fraction of the dsFv present in the complexes increased as tumor size increased (greater sIL-2R alpha levels). The fractions of dsFv in the complexes were 9.9- to 11.6-fold higher when sIL-2R alpha was not blocked with preinjected HuTac IgG. The administration of a 12-fold molar excess of HuTac IgG over sIL-2R alpha resulted in >80% of the 125I activity present as the dsFv rather than in the complexes. Furthermore, the biodistribution of 125I-labeled anti-Tac dsFv was improved by blocking its binding to sIL-2R alpha by preinjecting HuTac IgG. Specifically, in the preinjected group, at 15 min postinjection, the 125I-labeled anti-Tac dsFv levels in tumor increased to 10.8% compared to 5.6% injected dose per gram in the non-preinjected group. In summary, our studies showed that preinjection of HuTac IgG can block the formation of complexes of circulating sIL-2R alpha and 125I-labeled anti-Tac dsFv. This blockade is associated with faster blood clearance, higher tumor uptake, and greater tumor:nontumor ratios of the radiolabeled antibody fragment.
Simulation of a Centrifugal Pump Based on a Lagrangian Particle Solver (2022)

Abstract A three-dimensional full-scale centrifugal pump is simulated using the moving particle semi-implicit (MPS) method. The generic smoothed wall (GSW) boundary is used and extended to three dimensions to address complicated wall shapes and thin-walled structures such as blades in turbomachines. The nonsurface detection technique (NSD) based on conceptual particles is introduced to avoid the loss of the particle-number-density near wall boundaries. A generic approach that can transfer arbitrary CAD models to wall-particle models is established by utilizing the nodal information of the shell mesh. An adaptative resolution technique is proposed by using fine and coarse particles to model the wall boundary with complex geometry. Fine and coarse particles are applied to curved and flat surfaces, respectively, to reduce the computational cost while maintaining high discretizing precision. A criterion based on the normal smooth angle (NSA) is defined to evaluate the local or global precision of established models and provide instructions for refinement. A fully-developed velocity inflow boundary based on 3D inlet rings and pressure outflow boundary based on the moving virtual wall is implemented. Three typical cases including hydrostatic cases with a typical geometry, flow over a two-dimensional backward-facing step, and flow over a three-dimensional tube are tested to verify the proposed models. A particle-based framework to simulate incompressible fluid machines, in which flow fields can be integrally discretized and solved within a single coordinate system, is established. The results are compared with those of the fine volume method and satisfactory agreements are observed.
Ten-year all-cause mortality according to smoking status in patients with severe coronary artery disease undergoing surgical or percutaneous revascularization (2020)

SYNTAX: ClinicalTrials.gov reference: NCT00114972; SYNTAX Extended Survival. ClinicalTrials.gov reference: NCT03417050.
FCRAO Millimeter Continuum Observations of Comet Hale-Bopp (C/1995 O1) (1997)

The number distribution of millimeter-size dust particles in cometary comae is difficult to establish by optical/IR means alone. However, millimeter wave continuum radio observations are sensitive to these large particles that may control the total dust coma mass. The dust/gas mass ratio derived by combining dust and spectral line observations provides very important and basic information about the physical nature of comets. In late February 1997, FCRAO expanded its intensive comet Hale-Bopp (C/1995 O1) spectral line mapping campaign with a program of millimeter wave bolometry observations of Hale-Bopp's dust coma. The observations were taken with the SuZIE multielement bolometer mounted on the FCRAO 14m radio telescope. This bolometer is capable of taking data simultaneously at wavelengths of 1.1, 1.4, and 2.1mm. Initial results from late February 1997 indicate that the equivalent blackbody cross section at 1.4mm was (6.1 +/- 0.2) x 10(4) km, implying a dust mass of M = 1.7 x 10(12) kg in the coma at the time of observation, and a dust mass production rate dM/dt = 3.2 x 10(5) kg s(-1) . For log[Q(OH)] = 30.35, this gives a dust/gas mass ratio of approximately 3.5. The slope of the continuum emission spectrum corresponds to an opacity index of beta = 1.36 +/- 0.30, intermediate between the values of beta for circumstellar dust disks and the ISM. This may be interpreted as a consequence of an evolving dust particle size distribution as the dust grains expanded outwards into the coma of comet Hale-Bopp.
A Simple WDM-PON Architecture to Simultaneously Provide Triple-play Services by Using One Single Modulator (2008)

Simple WDM-PON testbed with centralized-lightwave using single-arm IM to provide 10 Gb/s data and 2.5 Gb/s digital video downstream and 2.5 Gb/s upstream data has been demonstrated. After 20 km SSMF, power-penalty for all channels is less than 0.5dB.
Resonance Couplings in Si@MoS2 Core–Shell Architectures (2022)

Heterostructures of transition metal dichalcogenides and optical cavities that can couple to each other are rising candidates for advanced quantum optics and electronics. This is due to their enhanced light-matter interactions in the visible to near-infrared range. Core-shell structures are particularly valuable for their maximized interfacial area. Here, the chemical vapor deposition synthesis of Si@MoS<sub>2</sub> core-shells and extensive structural characterization are presented. Compared with traditional plasmonic cores, the silicon dielectric Mie resonator core offers low Ohmic losses and a wider spectrum of optical modes. The magnetic dipole (MD) mode of the silicon core efficiently couples with MoS<sub>2</sub> through its large tangential component at the core surface. Using transmission electron microscopy and correlative single-particle scattering spectroscopy, MD mode splitting is experimentally demonstrated in this unique Si@MoS<sub>2</sub> core-shell structure. This is evidence for resonance coupling, which is limited to theoretical proposals in this particular system. A coupling constant of 39 meV is achieved, which is ≈1.5-fold higher than previous reports of particle-on-film geometries with a smaller interfacial area. Finally, higher-order systems with the potential to tune properties are demonstrated through a dimer system of Si@MoS<sub>2</sub> , forming the basis for emerging architectures for optoelectronic and nanophotonic applications.
An immunodominant SSX-2–derived epitope recognized by CD4+ T cells in association with HLA-DR (2004)

Ectopic gene expression in tumors versus normal somatic tissues provides opportunities for the specific immunotargeting of cancer cells. SSX gene products are expressed in tumors of different histological types and can be recognized by tumor-reactive CTLs from cancer patients. Here, we report the identification of an SSX-2-derived immunodominant T cell epitope recognized by CD4(+) T cells from melanoma patients in association with HLA-DR. The epitope maps to the 37-58 region of the protein, encompassing the sequence of the previously defined HLA-A2-restricted immunodominant epitope SSX-2(41-49). SSX-2(37-58)-specific CD4(+) T cells were detected among circulating lymphocytes from the majority of melanoma patients analyzed and among tumor-infiltrating lymphocytes, but not in healthy donors. Together, our data suggest a dominant role of the 37-58 sequence in the induction of cellular CD4(+) T cell responses against SSX antigens and will be instrumental for both the onset and the monitoring of upcoming cancer-vaccine trials using SSX-derived immunogens.
Ultra-Sensitive Infrared Spectroscopy of Proteins with Collective Excitations of Nanoplasmonic Arrays (2010)

Short interaction lengths limit the application of infrared absorption spectroscopy to the study monolayer thickness films. We employ periodic infrared antenna arrays to obtain 104–105 enhancement of protein absorption signals corresponding to zepto-mole sensitivity.
Nutzen von Biologika in der Therapie der schweren chronischen Rhinusinusitis mit Polypen (CRSwNP)- Ergebnisse nach einem Jahr (2022)

Einleitung Die schwere chronische Rhinosinusitis mit Polyposis führt zu einer starken Einschränkung der Lebensqualität. Wenn eine Therapie mit konservativen als auch operativen Maßnahmen zu keiner Symptombesserung führt, stellen Biologika eine neue Therapieoption dar. Es wurde bereits in Zulassungsstudien eine Abnahme der Polypengröße, eine Verbesserung des Riechvermögens und der Lebensqualität bewiesen. Bisher wurden Dupilumab und Omalizumab als Add-on Therapie zu topischen Kortikoiden in Deutschland bei der schweren CRSwNP zugelassen. Wir berichten über Ergebnisse nach einem Jahr der Behandlung mit Dupilumab.
Synergy between c-di-GMP and quorum-sensing signaling in Vibrio cholerae biofilm morphogenesis (2022)

Abstract Transitions between individual and communal lifestyles allow bacteria to adapt to changing environments. Bacteria must integrate information encoded in multiple sensory cues to appropriately undertake these transitions. Here, we investigate how two prevalent sensory inputs converge on biofilm morphogenesis: quorum sensing, which endows bacteria with the ability to communicate and coordinate group behaviors, and second messenger c-di-GMP signaling, which allows bacteria to detect and respond to environmental stimuli. We use Vibrio cholerae as our model system, the autoinducer AI-2 to modulate quorum sensing, and the polyamine norspermidine to modulate NspS-MbaA-mediated c-di-GMP production. Individually, AI-2 and norspermidine drive opposing biofilm phenotypes, with AI-2 repressing and norspermidine inducing biofilm formation. Surprisingly, however, when AI-2 and norspermidine are simultaneously detected, they act synergistically to elevate biofilm formation. We show that this effect is caused by quorum-sensing-mediated activation of nspS - mbaA expression, which increases the levels of NspS and MbaA, and in turn, c-di-GMP biosynthesis, in response to norspermidine. Increased MbaA-synthesized c-di-GMP activates the VpsR transcription factor, driving elevated expression of genes encoding key biofilm matrix components. Thus, in the context of biofilm formation in V. cholerae , quorum-sensing regulation of c-di-GMP-metabolizing receptor levels connects changes in cell population density to detection of environmental stimuli. Importance The development of multicellular communities, known as biofilms, facilitates beneficial functions of gut microbiome bacteria and makes bacterial pathogens recalcitrant to treatment. Understanding how bacteria regulate the biofilm lifecycle is fundamental to biofilm control in industrial processes and in medicine. Here, we demonstrate how two major sensory inputs – quorum-sensing communication and second messenger c-di-GMP signaling – jointly regulate biofilm morphogenesis in the global pathogen Vibrio cholerae . We characterize the mechanism underlying a surprising synergy between quorum-sensing and c-di-GMP signaling in controlling biofilm development. Thus, the work connects changes in cell population density to detection of environmental stimuli in a pathogen of clinical significance.
Small Molecule Catalysts for Harvesting Methane Gas (2016)

As the average temperature of the earth increases the impact of these changes are becoming apparent. One of the most dramatic changes to the environment is the melting of arctic permafrost. The disappearance of the permafrost has resulted in release of streams of methane that was trapped in remote areas as gas hydrates in ice. Additionally, the use of fracking has also increased emission of methane. Currently, the methane is either lost to the atmosphere or flared. If these streams of methane could be brought to market, this would be an abundant source of revenue. A cheap conversion of gaseous methane to a more convenient form for transport would be necessary to economical. Conversion of methane is a difficult reaction since the C-H bond is very stable (104 kcal/mole). At the industrial scale, the Fischer-Tropsch reaction can be used to convert gaseous methane to liquid methanol but is this method is impractical for these streams that have low pressures and are located in remote areas. Additionally, the Fischer-Tropsch reaction results in over oxidation of the methane leading to many products that would need to be separated.
Brain sterol dysregulation in sporadic AD and MCI: relationship to heme oxygenase‐1 (2009)

The objective of this study was to ascertain the impact of aging and Alzheimer's disease (AD) on brain cholesterol (CH), CH precursors, and oxysterol homeostasis. Altered CH metabolism and up-regulation of heme oxygenase-1 (HO-1) are characteristic of AD-affected neural tissues. We recently determined that HO-1 over-expression suppresses total CH levels by augmenting liver X receptor-mediated CH efflux and enhances oxysterol formation in cultured astroglia. Lipids and proteins were extracted from postmortem human frontal cortex derived from subjects with sporadic AD, mild cognitive impairment (MCI), and no cognitive impairment (n = 17 per group) enrolled in the Religious Orders Study, an ongoing clinical-pathologic study of aging and AD. ELISA was used to quantify human HO-1 protein expression from brain tissue and gas chromatography-mass spectrometry to quantify total CH, CH precursors, and relevant oxysterols. The relationships of sterol/oxysterol levels to HO-1 protein expression and clinical/demographic variables were determined by multivariable regression and non-parametric statistical analyses. Decreased CH, increased oxysterol and increased CH precursors concentrations in the cortex correlated significantly with HO-1 levels in MCI and AD, but not no cognitive impairment. Specific oxysterols correlated with disease state, increasing neuropathological burden, neuropsychological impairment, and age. A model featuring compensated and de-compensated states of altered sterol homeostasis in MCI and AD is presented based on the current data set and our earlier in vitro work.
Emergence of RTK/RAS/PI3K pathway alterations in trastuzumab-refractory HER2-positive esophagogastric (EG) tumors. (2016)

11608 Background: Up to 30% of EG adenocarcinomas harbor ERBB2 (HER2) gene amplification or oncoprotein over-expression. While trastuzumab prolongs survival in patients with Stage IV HER2+ EG tumors, responses are rarely complete and resistance invariably develops, possibly through the emergence of additional genomic alterations. Methods: We reviewed clinical and pathologic data of patients with metastatic HER2+ (IHC 3+ or FISH >2.0) EG adenocarcinoma undergoing trastuzumab/chemotherapy treatment at MSKCC. Archival formalin fixed paraffin embedded (FFPE) samples were analyzed using a cancer-associated gene bait capture, next generation sequencing (NGS) assay (MSK-IMPACT). Results: 80 patients with Stage IV HER2+ EG adenocarcinoma (59 IHC 3+, 20 IHC2+/FISH+, 1 NGS) treated with trastuzumab/chemotherapy. Median progression free survival on 1st line trastuzumab-based therapy 23 mos [95% CI: 17-32 mos], median overall survival 30 mos [95% CI: 25-29 mos]. NGS was completed on 71 pre-trastuzumab, 38 post-trastuzumab samples, including matched samples for 28 of 80 patients. Loss of HER2 was noted in 21% (8 of 38) post-progression samples by IHC/FISH (4 IHC 0/1, 4 FISH-). We also observed an overall increase in alterations in other receptor tyrosine kinases as well as KRAS, PI3-kinase pathway genes, and SMAD4 (Table 1). In paired post-T samples, we observed loss of HER2 amplification in four patients, and new amplifications of MET (n=2), EGFR (n=1), IGF1R (n=1), as well as mutations in ERBB4 (n=4), KRAS (n=3), PIK3CA (n=2), MTOR (n=2), and loss of function of PTEN (n=3). The KRAS and PIK3CA mutations were known activating, the ERBB4 and MTOR mutations were of unknown significance. Conclusions: We identified loss of HER2 and frequent secondary alterations in the RTK/RAS/PI3K pathway in HER+ EG adenocarcinoma treated with trastuzumab, suggesting mechanisms of resistance. These data suggest the need for repeat biopsies to accurately determine appropriate use of second-line HER2 directed therapy. Gene % pre-T % post-T EGFR amp 9.9 13.2 ERBB4 mut 4.2 15.8 IGF1R amp 2.8 13.2 KRAS amp / mut 8.5 18.4 MET amp 2.8 13.2 MTOR mut 2.8 7.9 PIK3CA mut 5.6 10.5 PTEN mut / homdel 1.4 10.5 SMAD4 mut / homdel 9.9 31.6
Fast computation of physical optics scattering in the near field (2013)

A fast algorithm for the computation of the physical optical back scattering integral is presented. The algorithm employs a multilevel evaluation scheme based on optimal sampling and restoration of partial contributions on grids tailored for near- and far-fields. Reduction of the asymptotic computational complexity by 2 polynomial orders is achieved.
Crystallization behavior of PA‐6 clay nanocomposite hybrid (2002)

Abstract Polyamide‐6 (PA‐6)/clay (modified montmorillonite) hybrid was synthesized by melt blending at high shear stress. 27 Al‐NMR of solid state shows that the clay is not modified after melt blending. Using wide‐line 1 H‐NMR and TEM, it is demonstrated that the nanocomposite exhibits mainly an exfoliated structure. It is shown that the modified montmorillonite induces the crystallization of PA‐6 predominantly in γ‐form. The presence of clay in PA‐6 increases the polymer crystallization temperature, and decreases its melting point. These phenomena show that a certain number of interactions develop near the reinforcing material, and that the latter plays a particular role of nucleating agent. However, the crystallization is not spherulitic and the assumption of macromolecular orientation in the vicinity of the clay is demonstrated by the observations carried out in DSC and AFM. These particular properties of orientation will have a particular importance on the mechanical behavior of the nanocomposite material. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 2416–2423, 2002
Global Profiling in Vestibular Schwannomas Shows Critical Deregulation of MicroRNAs and Upregulation in Those Included in Chromosomal Region 14q32 (2013)

Our results suggest that several miRNAs are involved in tumor formation and/or maintenance and that global upregulation of the 14q32 chromosomal site contains miRNAs that may represent a therapeutic target for this neoplasm.
Inactivation of Tumor Suppressor Genes by Promoter Methylation is Important in the Pathogenesis of Pancreatic Cancer (2002)

No Abstract AvailableCommentary to:Title: Aberrant Methylation of the 5' CpG Island of TSLC1 Is Common in Pancreatic Ductal Adenocarcinoma and Is First Manifest in High-Grade PanINsAuthors: Marnix Jansen, Noriyoshi Fukushima, Christophe Rosty, Kim Walter, Renee Altink, Tjarda van Heek, Ralph Hruban, Johan G Offerhaus and Michael Goggins Page Numbers: 293-296
Volcanism in the Younger Dharwar Rocks Near Medur Dharwar District, Karnataka (1978)

Abstract Andesite lavas are associated with pyroclastics and a few sheet-like porphyritic flows. The volcanism is considered to have been of mixed eruptions indicating sufficient fluidity and low gas content. The andesitic lavas are characterised by well developed pillow structure. They are interlayered with pyritiferous and carbonaceous argillites indicating volcanic eruption under submarine condition. The lavas occupy the central part of a major refolded antiformal anticline plunging to the west. They have undergone metamorphism only up to the green-schist facies of regional metamorphism. Carbonatisation of lavas is a common feature, particularly in andesite.
HSUPA Scheduling Algorithms Utilizing RoT Measurements and Interference Cancellations (2008)

This paper discusses several important aspects in the HSUPA scheduling algorithms. First, it clearly demonstrates the benefit of explicitly utilizing the directly measured Rise-over- Thermal(RoT) values in term of capacity and robustness improvement. This paper also briefly presents the RoT measurement schemes designed specifically for the asynchronous systems such as WCDMA/HSUPA. If pilot and traffic interference cancellation (IC) schemes are implemented at the Node B receiver, this paper presents a scheduling algorithm that attains IC benefit in such a way that the capacity enhancement is maximized while fairness and link budget are maintained. The presented algorithm defines the effective RoT by monitoring the IC performance in real time and adjusts its grants accordingly. In addition, the user priority function used here optimizes the sum utility functions and provides multi-user diversity.
Supplementary Figure 3 from Lowering Bone Mineral Affinity of Bisphosphonates as a Therapeutic Strategy to Optimize Skeletal Tumor Growth Inhibition <i>In vivo</i> (2023)

Supplementary Figure 3 from Lowering Bone Mineral Affinity of Bisphosphonates as a Therapeutic Strategy to Optimize Skeletal Tumor Growth Inhibition &lt;i&gt;In vivo&lt;/i&gt;
Applying Machine Learning to the Choice of Size Modifiers (2011)

People use different size modifiers to refer to different object sizes; “the long table ” is likely to be a different table from “the small table”. However, the details influencing the selec-tion of size modifier have not yet been uncovered. When is something “long”, and when is something “small”? We in-troduce a connection between the visible dimensions of ob-jects and the kinds of language people use to refer to them. First, we conduct an experiment to elicit size-denoting modi-fiers from images of real world objects. We find that we are able to effectively model the relationship between dimensional features and modifier choice using decision trees. The images are then used as input to an object segmentation algorithm, and we compare how well we can predict speakers ’ behavior using the real world measurements of the pictured objects and the image pixel-based measurements. We find that real world measurements are the best predictors of modifier choice, sug-gesting that people infer real world size features from images. However, automatically extracted pixel measurements do per-form relatively well at predicting modifier choice, offering a potential connection between computer vision and natural lan-guage. When speaker identity is taken into account, modifier choice can be predicted with even greater accuracy (around 75%), and the difference between automatically extracted and real world measurements is no longer significant.