gebhart/patrepeval huggingface dataset:
Mutational landscape of gastric adenocarcinoma in Chinese: Implications for prognosis and therapy (2015)

Gastric cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with three primary tumors and two matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC). The HiC subtype of intratumoral heterogeneity was associated with older age, TP53 (tumor protein P53) mutation, enriched C > G transition, and significantly shorter survival, whereas the LoC subtype was associated with younger age, ARID1A (AT rich interactive domain 1A) mutation, and significantly longer survival. Phylogenetic tree analysis of whole-genome sequencing data from multiple samples of two patients supported the clonal evolution of GC metastasis and revealed the accumulation of genetic defects that necessitate combination therapeutics. The most recurrently mutated genes, which were validated in a separate cohort of 216 cases by targeted sequencing, were members of the homologous recombination DNA repair, Wnt, and PI3K-ERBB pathways. Notably, the drugable NRG1 (neuregulin-1) and ERBB4 (V-Erb-B2 avian erythroblastic leukemia viral oncogene homolog 4) ligand-receptor pair were mutated in 10% of GC cases. Mutations of the BRCA2 (breast cancer 2, early onset) gene, found in 8% of our cohort and validated in The Cancer Genome Atlas GC cohort, were associated with significantly longer survivals. These data define distinct clinicogenetic forms of GC in the Chinese population that are characterized by specific mutation sets that can be investigated for efficacy of single and combination therapies.
Innovative Technology for an Inertial Electrostatic Confinement (IEC) Fusion Propulsion Unit (1994)

An Inertial Electrostatic Confinement (IEC) fusion power source has the potential to support a very efficient nuclear propulsion system. High power‐to‐weight ratios, necessary for manned travel beyond our moon, are obtainable with an IEC power source because of the grid structure is relatively light weight. A preliminary design study of a system using an IEC power source has been done by integrating an IEC device, designed to burn d‐3He, with a Direct Energy Converter (DEC), an electrical system, and an electrical thruster unit. (Miley 1993a) Further investigation of this design will be presented. These subsequent studies were aimed at addressing several key issues which arose during the course of the original design work. The most important result is the discovery that a pulsed power version of the IEC offers a high fusion energy gain, giving an improved specific power for the design.
Using Synchrotron Radiation Microtomography to Investigate Multi-scale Three-dimensional Microelectronic Packages (2016)

Synchrotron radiation micro-tomography (SRµT) is a non-destructive three-dimensional (3D) imaging technique that offers high flux for fast data acquisition times with high spatial resolution. In the electronics industry there is serious interest in performing failure analysis on 3D microelectronic packages, many which contain multiple levels of high-density interconnections. Often in tomography there is a trade-off between image resolution and the volume of a sample that can be imaged. This inverse relationship limits the usefulness of conventional computed tomography (CT) systems since a microelectronic package is often large in cross sectional area 100-3,600 mm(2), but has important features on the micron scale. The micro-tomography beamline at the Advanced Light Source (ALS), in Berkeley, CA USA, has a setup which is adaptable and can be tailored to a sample's properties, i.e., density, thickness, etc., with a maximum allowable cross-section of 36 x 36 mm. This setup also has the option of being either monochromatic in the energy range ~7-43 keV or operating with maximum flux in white light mode using a polychromatic beam. Presented here are details of the experimental steps taken to image an entire 16 x 16 mm system within a package, in order to obtain 3D images of the system with a spatial resolution of 8.7 µm all within a scan time of less than 3 min. Also shown are results from packages scanned in different orientations and a sectioned package for higher resolution imaging. In contrast a conventional CT system would take hours to record data with potentially poorer resolution. Indeed, the ratio of field-of-view to throughput time is much higher when using the synchrotron radiation tomography setup. The description below of the experimental setup can be implemented and adapted for use with many other multi-materials.
ChemInform Abstract: Synthesis and Progesterone Receptor Binding Affinity of Substituted 1‐Phenyl‐7‐benzyl‐4,5,6,7‐tetrahydro‐1H‐indazoles. (1998)

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.
Genomic Alterations in Sporadic Synchronous Primary Breast Cancer Using Array and Metaphase Comparative Genomic Hybridization (2007)

Synchronous primary breast cancer describes the occurrence of multiple tumors affecting one or both breasts at initial diagnosis. This provides a unique opportunity to identify tissue-specific genomic markers that characterize each tumor while controlling for the individual genetic background of a patient. The aim of this study was to examine the genomic alterations and degree of similarity between synchronous cancers. Using metaphase comparative genomic hybridization and array comparative genomic hybridization (aCGH), the genomic alterations of 23 synchronous breast cancers from 10 patients were examined at both chromosomal and gene levels. Synchronous breast cancers, when compared to their matched counterparts, were found to have a common core set of genetic alterations, with additional unique changes present in each. They also frequently exhibited features distinct from the more usual solitary primary breast cancers. The most frequent genomic alterations included chromosomal gains of 1q, 3p, 4q, and 8q, and losses of 11q, 12q, 16q, and 17p. aCGH identified copy number amplification in regions that are present in all 23 tumor samples, including 1p31.3-1p32.3 harboring JAK1. Our findings suggest that synchronous primary breast cancers represent a unique type of breast cancer and, at least in some instances, one tumor may give rise to the other.
Development of 3.6 Gbps RF Transceiver for Wireless Nomadic Local Area Networks (2010)

We present high data rate wideband transceiver design and experimental evaluation for 3.62 Gbps wireless transmission systems in this paper. The present system provides high definition moving picture and contents in a real-time wireless environment at home, offices or class rooms of universities. Also, the present platform provides a test platform for the Giga level high throughput wireless communication system using the OFDM method and the multiple antennas.
Azimuthally-differential pion femtoscopy relative to the third harmonic event plane in Pb–Pb collisions at sNN=2.76TeV (2018)

Azimuthally-differential femtoscopic measurements, being sensitive to spatio-temporal characteristics of the source as well as to the collective velocity fields at freeze out, provide very important information on the nature and dynamics of the system evolution. While the HBT radii oscillations relative to the second harmonic event plane measured recently reflect mostly the spatial geometry of the source, model studies have shown that the HBT radii oscillations relative to the third harmonic event plane are predominantly defined by the velocity fields. In this Letter, we present the first results on azimuthally-differential pion femtoscopy relative to the third harmonic event plane as a function of the pion pair transverse momentum kT for different collision centralities in Pb–Pb collisions at sNN=2.76 TeV . We find that the Rside and Rout radii, which characterize the pion source size in the directions perpendicular and parallel to the pion transverse momentum, oscillate in phase relative to the third harmonic event plane, similar to the results from 3+1D hydrodynamical calculations. The observed radii oscillations unambiguously signal a collective expansion and anisotropy in the velocity fields. A comparison of the measured radii oscillations with the Blast-Wave model calculations indicate that the initial state triangularity is washed-out at freeze out.
Multifunctional Nanoagent for Thrombus-Targeted Fibrinolytic Therapy (2012)

The applicability of a FXIIIa-targeted thrombolytic nanoagent in the treatment of thromboembolism was demonstrated in vitro and in vivo. Future studies are planned to investigate the safety profile and overall efficacy of this class of nanoagents.
Quantification of Exosomes (2016)

Exosomes are released by cells as self-contained vesicles with an intact lipid bilayer that encapsulates a small portion of the parent cell. Exosomes have been studied widely as information-rich sources of potential biomarkers that can reveal cellular physiology. We suggest that quantification is essential to understand basic biological relationships between exosomes and their parent cells and hence the underlying interpretation of exosome signals. The number of methods for quantifying exosomes has expanded as interest in exosomes has increased. However, a consensus on proper quantification has not developed, making each study difficult to compare to another. Overcoming this ad hoc approach will require widely available standards that have been adequately characterized, and multiple comparative studies across platforms. We outline the current status of these technical approaches and our view of how they can become more coherent. J. Cell. Physiol. 232: 1587-1590, 2017. © 2016 Wiley Periodicals, Inc.
Secure Parallel Computation on Privately Partitioned Data and Applications (2022)

Parallel computation is an important aspect of multi-party computation, not only in terms of improving efficiency, but also in terms of providing privacy for computation involving conditional branching based on private data. While applying multi-party computation in parallel over several sets of input data is straightforward if the partitioning of the input data into sets is publicly known, the problem becomes much more challenging when this partitioning is private. This setting is relevant to broad class of secure computations, in particular to secure graph and database analysis in which the underlying data (graph or database) is private. In this paper, we consider a general class of functions which can be expressed via the iterative evaluation of a binary associative operation, and propose efficient protocols for evaluating such functions in parallel over privately partitioned input data. Our protocols are optimal in terms of the required number of evaluations of the underlying binary operation (i.e.\ N-1 evaluations for total input size N), while simultaneously achieving a round complexity which is only logarithmic in the total size of the input data (i.e.\ O(łog N)).
Analog Coding in Emerging Memory Systems (2020)

Exponential growth in data generation and large-scale data science has created an unprecedented need for inexpensive, low-power, low-latency, high-density information storage. This need has motivated significant research into multi-level memory devices that are capable of storing multiple bits of information per device. The memory state of these devices is intrinsically analog. Furthermore, much of the data they will store, along with the subsequent operations on the majority of this data, are all intrinsically analog-valued. Ironically though, in the current storage paradigm, both the devices and data are quantized for use with digital systems and digital error-correcting codes. Here, we recast the storage problem as a communication problem. This then allows us to use ideas from analog coding and show, using phase change memory as a prototypical multi-level storage technology, that analog-valued emerging memory devices can achieve higher capacities when paired with analog codes. Further, we show that storing analog signals directly through joint coding can achieve low distortion with reduced coding complexity. Specifically, by jointly optimizing for signal statistics, device statistics, and a distortion metric, we demonstrate that single-symbol analog codings can perform comparably to digital codings with asymptotically large code lengths. These results show that end-to-end analog memory systems have the potential to not only reach higher storage capacities than discrete systems but also to significantly lower coding complexity, leading to faster and more energy efficient data storage.
Island model in ActoDatA (2021)

In this paper, we make a first assessment of the performance of ActoDatA, a novel actor-based software library for distributed data analysis and machine learning in Java that we have recently developed. To do so we have implemented an evolutionary machine learning application based on a distributed island model. The model implementation is compared to an equivalent implementation in ECJ, a popular general-purpose evolutionary computation library that provides support for distributed computing.
Search for new phenomena in events with three charged leptons ats=7  TeVwith the ATLAS detector (2013)

A generic search for anomalous production of events with at least three charged leptons is presented. The search uses a $pp$-collision data sample at a center-of-mass energy of $\sqrt{s}=7\text{ }\text{ }\mathrm{TeV}$ corresponding to $4.6\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$ of integrated luminosity collected in 2011 by the ATLAS detector at the CERN Large Hadron Collider. Events are required to contain at least two electrons or muons, while the third lepton may either be an additional electron or muon, or a hadronically decaying tau lepton. Events are categorized by the presence or absence of a reconstructed tau-lepton or $Z$-boson candidate decaying to leptons. No significant excess above backgrounds expected from Standard Model processes is observed. Results are presented as upper limits on event yields from non-Standard-Model processes producing at least three prompt, isolated leptons, given as functions of lower bounds on several kinematic variables. Fiducial efficiencies for model testing are also provided. The use of the results is illustrated by setting upper limits on the production of doubly charged Higgs bosons decaying to same-sign lepton pairs.
Primary structure of human plasma fibronectin. Characterization of a 38 kDa domain containing the C-terminal heparin-binding site (Hep III site) and a region of molecular heterogeneity (1987)

The primary structure of a 38 kDa heparin-binding domain from human plasma fibronectin has been determined. This domain contains 380 residues arranged in three type-III homology regions of approx. 90 residues each, and a 67-amino-acid C-terminal segment. This segment has been shown to be encoded by certain mRNA species only, due to alternative splicing [Kornblihtt, Vibe-Pedersen & Baralle (1984) Nucleic Acids Research 12, 5853-5868], and therefore represents a region of heterogeneity in fibronectin. Our data indicate that at least one of the constituent polypeptide chains contains this region.
New Approaches for Synthesizing γIII‐CoOOH by Soft Chemistry. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
HIV-1-associated dementia: a basic science and clinical perspective. (2002)

HIV-1 associated dementia (HAD) is a metabolic encephalopathy induced by viral infection and fueled by immune activation of brain mononuclear phagocytes (perivascular and parenchymal macrophages and microglia). These same cells serve as reservoirs for persistent infection and sources for soluble neurotoxins. Neurologic impairments are manifested by cognitive, behavioral, and motor abnormalities that occur years after viral exposure and are associated with depletion of CD4+ T lymphocytes and high viral loads. Improvements in antiretroviral and adjunctive therapies have decreased HAD incidence, but cognitive dysfunction remains a cause of morbidity in many infected persons.
Glucocorticoids increase amylase mRNA levels, secretory organelles, and secretion in pancreatic acinar AR42J cells. (1985)

Previous studies have suggested a role for glucocorticoids in the differentiation of the acinar pancreas. We have now used the rat tumor cell line AR42J, derived from the acinar pancreas, to directly study this effect of glucocorticoids in vitro. The steroid hormones dexamethasone, corticosterone, aldosterone, and progesterone, but not estrogen, increased both the amylase content and the number of secretory granules of these cells. The potencies of the steroids were directly related to their effectiveness as glucocorticoids; dexamethasone was the most potent hormone and gave maximal effects at 100 nM. Morphometric analyses revealed that dexamethasone increased the volume density of granules 5.5-fold from 0.20 +/- 0.08 to 1.10 +/- 0.20% (n = 4) of the cytoplasmic volume. Dexamethasone treatment also increased the volume density of rough endoplasmic reticulum 2.4-fold from 1.20 +/- 0.09 to 2.86 +/- 0.30% (n = 5) of the cytoplasmic volume. After 48 h of dexamethasone treatment the cellular content of amylase increase eightfold from 2.8 +/- 0.4 to 22.6 +/- 3.8 U/mg protein (n = 6). This effect of dexamethasone was discernible after 12 h of incubation and approached maximal stimulation after 72 h of incubation. The increases in cellular amylase content were due to increased amylase synthesis as shown by specific immunoprecipitation of [35S]methionine-labeled proteins. Moreover, in vitro translation of cellular mRNA indicated that dexamethasone treatment increased amylase mRNA. Dexamethasone treatment also led to increased secretion of amylase in response to the secretagogue cholecystokinin. These data indicate, therefore, that glucocorticoids induce a more highly differentiated phenotype in AR42J pancreatic cells, and they suggest that glucocorticoids act via the enhanced transcription of specific mRNAs for acinar cell proteins.
Significant stabilization of palladium by gold in the bimetallic nanocatalyst leading to an enhanced activity in the hydrodechlorination of aryl chlorides (2015)

The stabilization effect of Au towards Pd changed the reactivity of Pd in Au/Pd bimetallic nanoclusters, altering the reaction mechanism from homogeneous to heterogeneous in dechlorination reaction of aryl chlorides. This phenomenon was illustrated by the observed enhancement of the rate of reaction by in situ generated Au-rich bimetallic Au/Pd nanoclusters.
Improvement in Outcomes After Cardiac Arrest and Resuscitation by Inhibition of S-Nitrosoglutathione Reductase (2019)

CA and CPR activated GSNOR and reduced the number of S-nitrosylated proteins in the brain. Pharmacological inhibition or genetic deletion of GSNOR prevented ischemic brain injury and improved survival rates by restoring S-nitrosylated protein levels in the brain after CA/CPR in mice. Our observations suggest that GSNOR is a novel biomarker of postarrest brain injury as well as a molecular target to improve outcomes after CA.
Geodesic distances for web document clustering (2011)

While traditional distance measures are often capable of properly describing similarity between objects, in some application areas there is still potential to fine-tune these measures with additional information provided in the data sets. In this work we combine such traditional distance measures for document analysis with link information between documents to improve clustering results. In particular, we test the effectiveness of geodesic distances as similarity measures under the space assumption of spherical geometry in a 0-sphere. Our proposed distance measure is thus a combination of the cosine distance of the term-document matrix and some curvature values in the geodesic distance formula. To estimate these curvature values, we calculate clustering coefficient values for every document from the link graph of the data set and increase their distinctiveness by means of a heuristic as these clustering coefficient values are rough estimates of the curvatures. To evaluate our work, we perform clustering tests with the k-means algorithm on the English Wikipedia hyperlinked data set with both traditional cosine distance and our proposed geodesic distance. The effectiveness of our approach is measured by computing micro-precision values of the clusters based on the provided categorical information of each article.
Related Articles from Enhancing Cancer Vaccine Efficacy via Modulation of the Tumor Microenvironment (2023)

Related Articles from Enhancing Cancer Vaccine Efficacy via Modulation of the Tumor Microenvironment
Metabolic Flux Estimation in Mammalian Cell Cultures (2013)

Metabolic flux analysis with its ability to quantify cellular metabolism is an attractive tool for accelerating cell line selection, medium optimization, and other bioprocess development activities. In the stoichiometric flux estimation approach, unknown fluxes are determined using intracellular metabolite mass balance expressions and measured extracellular rates. The simplicity of the stoichiometric approach extends its application to most cell culture systems, and the steps involved in metabolic flux estimation by the stoichiometric method are presented in detail in this chapter. Specifically, overdetermined systems are analyzed since the extra measurements can be used to check for gross measurement errors and system consistency. Cell-specific rates comprise the input data for flux estimation, and the logistic modeling approach is described for robust-specific rate estimation in batch and fed-batch systems. A simplified network of mammalian cell metabolism is used to illustrate the flux estimation procedure, and the steps leading up the consistency index determination are presented. If gross measurement errors are detected, a technique for determining the source of gross measurement error is also described. A computer program that performs most of the calculation described in this chapter is presented, and references to flux estimation software are provided. The procedure presented in this chapter should enable rapid metabolic flux estimation in any mammalian cell bioreaction network by the stoichiometric approach.