gebhart/patrepeval huggingface dataset:
Phase 1 study of AG-881, an inhibitor of mutant IDH1/IDH2, in patients with advanced IDH-mutant solid tumors, including glioma. (2018)

2002 Background: Isocitrate dehydrogenase 1 and 2 mutations (mIDH1/2) occur in solid tumors including glioma, and result in production of the oncometabolite 2-hydroxyglutarate (2-HG), promoting tumorigenesis. AG-881 is an oral, potent, brain-penetrant inhibitor of mIDH1/2 that reduces 2-HG by up to 98% in glioma models. Methods: Patients (pts) with recurrent/progressive mIDH1/2 glioma (G) and non-glioma (NG) solid tumors were eligible to receive AG-881 daily in continuous 28-day cycles. Dose escalation cohorts for G and NG solid tumors enrolled using a Bayesian logistic regression model (BLRM) escalation guided by the overdose control (EWOC). Blood and tumor samples were evaluated for pharmacokinetics (PK)/pharmacodynamics (PD). Dose-limiting toxicity (DLT) was defined as a Grade (Gr) ≥3 AG-881-related event in Cycle 1 or by sponsor designation. Results: As of 1Dec2017, 93 pts had received AG-881 (G: 52; NG: 41) and 20 remain on AG-881 (G: 19, NG: 1). Demographics: M/F = 40/53; median age = 51; median no. prior systemic therapies = 3 (range 1–7). Seven initial dose levels were tested: 25mg QD (n = 10); 50mg QD (n = 12); 100mg QD (n = 21); 200mg QD (n = 22); 200mg BID (n = 5); 300mg QD (n = 5) and 400mg QD (n = 6). To further assess safety and PK in the G cohort, a 10mg dose level was tested (n = 6) and 6 additional pts enrolled in the 50mg cohort. PK showed less than dose-proportional plasma exposure with a mean effective half-life of 71±54 hrs. Common adverse events (AEs) across all pts regardless of attribution: fatigue (38.7%), nausea (35.5%), ALT/AST increase (34.4% each). Elevated ALT/AST AEs were dose-dependent (n = 0 at 10mg, n = 7 at ≤50mg, n = 10 at 100mg, n = 20 at > 100mg). Five G pts experienced DLTs at 100mg and above: Gr ≥2 ALT/AST which resolved to Gr ≤1 with dose modification (n = 4) or discontinuation (n = 1). The MTD or RP2D were not reached by BLRM with EWOC. Conclusions: AG-881 was associated with a favorable safety profile at doses < 100mg in pts with glioma and non-glioma solid tumors. No ALT/AST AEs Gr > 2 were observed at 10mg and 50mg. These doses are being explored in an ongoing perioperative glioma study. Updated safety, PK/PD, and efficacy data will be presented. Clinical trial information: NCT02481154.
PCR detection of DNA specific for Aspergillus species in serum of patients with invasive aspergillosis (1996)

We investigated the possible presence of DNA specific for Aspergillus species in serum samples of patients with invasive aspergillosis (IA) by the nested PCR method. Fourteen strains of fungi including 5 strains of Aspergillus species and 10 strains of common bacteria were used for examination of specificity and sensitivity of the nested PCR. Two sets of oligonucleotide primers were derived from the sequence of the variable regions V7 to V9 of the 18S rRNA genes of Aspergillus fumigatus. The specific fragment was amplified from five strains of Aspergillus species in the single and nested PCR but not from other microorganisms. Target DNA was detected by the nested PCR with as little as 50 fg of the extracted DNA of A. fumigatus. We investigated the detection of DNA specific for Aspergillus species in serum samples of a murine model of aspergillosis and 20 patients with IA. The specific fragment was detected by the nested PCR in 71% of serum samples of infected mice and 70% of serum samples of patients with IA, while galactomannan antigen was detected in 43 and 60% of samples, respectively. The high sensitivity and specificity of the nested PCR indicate that the assay can provide early diagnosis with sufficient accuracy to be clinically useful for immunocompromised patients with IA.
Current and Developing Technologies for Monitoring Agents of Bioterrorism and Biowarfare (2005)

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.
Detector performance analysis of watermark-based error concealment in image communications (2005)

In this work, the detector performance of a watermark-based error concealment (WEC) system proposed in C.B. Adsumilli is mathematically analyzed. The spread spectrum based WEC algorithm embeds a low resolution version of an image in itself during encoding. At the receiver, this embedded watermark is extracted and used as a reference to conceal the transmission losses in the reconstructed image. For the application of error concealment, the detector modelling varies from the conventional watermark detectors due to the fact that we use a full frame DCT to embed the watermark data and vary the strength of the watermark in accordance with the embedding coefficients to reduce the standard deviation of the resulting distribution. We further approximate the full frame DCT coefficients to follow a generalized Gaussian distribution (GGD) like in the case of modelling block-based DCT coefficients and consequently, we provide a comparison between the performance of this system and conventional block-based embedding strategies for various packet loss probabilities. Both analytical and simulation results show that our system of full frame DCT embedding is more effective for error concealment in detecting the embedded bits with lesser probability of error.
Feridex labeling of mesenchymal stem cells inhibits chondrogenesis but not adipogenesis or osteogenesis (2004)

Magnetic resonance (MR) tracking of superparamagnetic iron oxide (SPIO)-labeled cells is a relatively new technique to non-invasively determine the biodistribution and migration of transplanted stem cells. A number of studies have recently reported encouraging results in the use of bone marrow-derived mesenchymal stem cells (MSCs) for repair of a variety of tissues. For MR tracking of SPIO-labeled MSCs, it is important to determine the effect that the magnetic labeling procedure may have on the differentiation capacity of labeled MSCs. Human MSCs were labeled with poly-L-lysine (PLL)-coated Feridex, with Feridex being an FDA-approved SPIO formulation in an off-label application, and assayed for cellular differentiation using five different assays. As compared with unlabeled controls, labeled MSCs exhibited an unaltered viability, proliferated similarly, and underwent normal adipogenic and osteogenic differentiation. However, there was a marked inhibition of chondrogenesis. The blocking of chondrogenic activity was mediated by the Feridex, rather than by the transfection agent (PLL). This is the first report showing Feridex blocking of cellular differentiation down a specific pathway (while not affecting viability and proliferation), and caution should thus be exercised when using Feridex-labeled MSCs for chondrogenic MR tracking studies. On the other hand, no detrimental effects of Feridex-labeling are anticipated for MR-guided osteogenic or adipogenic transplantation studies.
Quantitative interpretation of major planes from microseismic event locations with application in production prediction (2010)

We present a fracture mapping from microseismic event locations, that is both quantitative and repeatable, using a probabilistic framework to evaluate the number and location of major planes within the event clouds. The method can be applied automatically, handles the inherent ambiguity in interpretations consistently, and generates production predictions based on data directly available at the wellsite. Through a case study on a well in the Wildcat field (Bakken Shale, North Dakota), we demonstrate that this technique can provide reliable estimates of future production.
Dual-neodymium magnet-based microfluidic separation device (2019)

Microfluidic-based separation methods have been highlighted for a number of biological applications, such as single cell analysis, disease diagnostics, and therapeutics. Although a number of previous studies have been carried out to minimize the physical damage and chemical deformations of the sample during the separation process, it still remains a challenge. In this paper, we developed a microfluidic device with dual-neodymium magnet-based negative magnetophoresis for the separation of the microparticles and cells. The poly(ethylene oxide) (PEO) was added to the solution to increase the viscoelasticity of the medium which could assist the sorting of the microparticles in the microfluidic device even at low flow rates, while minimizing damage to the cells and microparticles. Following this method, it was possible to separate 10 and 16 μm microparticles with high efficiency of 99 ± 0.1%, and 97 ± 0.8%, respectively. We also demonstrated the separation of glioblastoma cancer cells and neural stem cells (NSCs) in the microfluidic device.
Tunable microdoublet lens array (2004)

We report a tunable microdoublet lens capable of creating dual modes of biconvex or meniscus lens. The microdoublet lens consists of a tunable liquid-filled lens and a solid negative lens. It can be tuned either by changing the shape of the liquid-filled lens into biconvex or meniscus or by changing a filling media with different refractive index. The microfabrication is based on photopolymer microdispensing and elastomer micromolding methods. The microdoublet lens can provide a solution for minimizing optical aberrations and maximizing the tunability of focal length or field of view by controlling variable and fixed lens curvatures.
Upregulation of cytokine receptors sTNF-R55, sTNF-R75, and sIL-2R in psoriatic arthritis synovial fluid. (1998)

In PsA SF sTNF-R55, sTNF-R75, and sIL-2R are upregulated compared to OA SF but are lower than in RA SF. Our results for TNF-R agree with recent findings in PsA, since TNF-alpha, an important stimulator for TNF-R, is also significantly lower in PsA than in RA. The upregulation of the cytokine receptors in PsA reconfirms its inflammatory nature, but indicates the more benign course of disease compared with RA.
Electronically Selective Chemical Functionalization of Carbon Nanotubes:  Correlation between Raman Spectral and Electrical Responses (2005)

Single-walled carbon nanotubes (SWNTs) demonstrate remarkable electronic and mechanical properties useful in developing areas such as nanoelectromechanical systems and flexible electronics. However, the highly inhomogeneous electronic distribution arising from different diameters and chirality in any given as-synthesized SWNT samples imposes severe limitations. Recently demonstrated selective chemical functionalization methods may provide a simple scalable means of eliminating metallic tubes from SWNT transistors and electronic devices. Here, we report on combined electron transport and Raman studies on the reaction of 4-bromobenzene diazonium tetrafluoroborate directly with single and networks of SWNT transistors. First, Raman studies are carried out on isolated individual SWNTs grown on SiO2/Si substrates by chemical vapor deposition with and without metal contacts. Metallic tubes are found to have, on average, higher reactivity toward diazonium reagents. However, a considerable degradation of electrical properties of semiconducting tubes occurs if the reaction is carried out to the point where the conductivity of metallic tubes is significantly suppressed. Insights from single-tube studies are then applied to elucidate the electrical and the Raman responses of SWNT random network transistors of different channel lengths to chemical functionalization.
Membranes for Hydrogen Separation (2007)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTADDITION / CORRECTIONThis article has been corrected. View the notice.Membranes for Hydrogen SeparationNathan W. Ockwig and Tina M. NenoffView Author Information Geochemistry, and Surface and Interface Sciences, Sandia National Laboratories, P.O. Box 5800, M.S. 1415, Albuquerque, New Mexico 87185 Cite this: Chem. Rev. 2007, 107, 10, 4078–4110Publication Date (Web):October 10, 2007Publication History Received27 November 2006Published online10 October 2007Published inissue 1 October 2007https://pubs.acs.org/doi/10.1021/cr0501792https://doi.org/10.1021/cr0501792research-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views20631Altmetric-Citations912LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alloys,Diffusion,Hydrogen,Membranes,Selectivity Get e-Alerts
Abstract 430: MiRNA profiling of prostate cancer cell-derived large oncosomes identifies a signature of invasion and metastasis (2012)

Abstract Introduction: We recently demonstrated that amoeboid prostate cancer (PCa) cells shed large (1-10µm diameter), bioactive membrane particles, representing a new class of tumor microvesicles termed large oncosomes (LO). LO can transfer oncogenic signals horizontally within the tumor microenvironment, as demonstrated by activation of phospho-tyrosines and Akt in recipient cells. Methods: We used differential ultracentrifugation and immuno-flow cytometry with size beads to isolate oncosomes in the 1-10µm diameter range. The method was applied to culture medium as well as to the plasma of mice with prostate cancer. In order to identify oncosome miRNAs relevant to metastasis, we performed a GeneChip® miRNA 2.0 Array screen of oncosomes shed by tumorigenic RWPE-2 PCa cells. Non-tumorigenic RWPE-1 cells were also analyzed. Results: LO contained protease and significantly stimulated migration of tumor and endothelial cells. LO also contained Caveolin-1, the GTPase ARF6 and other proteins that we used as markers to identify them in the circulation of mice with PCa, and in murine and human tissues with metastatic disease. Oncosomes also contained RNA. The miRNA profile of the oncosomes was compared to the miRNA profile of the cells of origin. While the miRNA profile of RWPE-2 almost completely matched the profile of RWPE-1 cells, the profiles differed significantly between LO isolated from the two cell lines. In particular, RWPE-2-derived LO contained miR-1228*, miR-150*, miR-373*, miR-135a*, miR-34b and miR-491-3p, which have been implicated in cancer cell proliferation and migration. In particular, the miRNAs miR-135a* and miR-373* target and inhibit the focal adhesion kinase (FAK), which plays a role in promoting a mesenchymal to amoeboid transition. miR-135a* and miR-373* have also been demonstrated to stimulate cell invasion, and are up-regulated in metastatic prostate and breast cancer. Target prediction analysis identified members of pathways involved in metabolic deregulation, and in oncogenic intercellular signaling and cell-cell interaction specifically in the LO purified from the tumorigenic cell line. Conclusions: Collectively, our results indicate that tumor cells can use oncosome formation to actively export pro-oncogenic miRNAs and that oncosomes therefore serve as a potential source of biomarkers of tumor progression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 430. doi:1538-7445.AM2012-430
Amiodarone as Paradigm for Developing New Drugs for Atrial Fibrillation (2008)

Introduced as an anti-anginal compound in 1962, amiodarone emerged in the 1970s as a uniquely effective antiarrhythmic and antifibrillatory drug with a multiplicity of properties, the most striking being the lengthening of the repolarization in the atria and ventricles associated with bradycardia but without a significant propensity for inducing torsade de pointes. Amiodarone is now the most frequently used agent for maintaining sinus rhythm in patients with AF. Its effectiveness for maintaining sinus rhythm remains unrivalled. Although the drug has few absolute contraindications to its use as an antiarrhythmic agent, limiting side effects such as thyroid dysfunction, pulmonary fibrosis, dermatological changes, and myriad lesser adverse effects often limit the use of the drug long-term in a proportion of patients. Thus, the idea has arisen that amiodarone might serve as a model for the synthesis and development of newer and novel antiarrhythmic agents devoid of organ toxicity. Amiodarone is an iodinated compound, and the possibility that its molecule may be modified with or without elimination of the iodine is being tested. The deletion of the iodine radical, substituting ethyl with butyl in the side chain of the aromatic ring, and adding a methylsulphonyl radical to the benzofuran component of the molecule leads to the loss of thyroid and pulmonary effects. The resulting compound, dronedarone, is in advanced clinical development. It is likely the first amiodarone congener that will be used in the control of atrial fibrillation. Others are in earlier phases of development.
The Monoshunt: a new intracoronary shunt design to avoid distal endothelial dysfunction during off-pump coronary artery bypass (OPCAB) (2003)

Insertion of intracoronary shunts during off-pump coronary artery bypass surgery can induce a severe endothelial dysfunction. The purpose of this study was to propose a new intracoronary shunt design called Monoshunt, to avoid distal endothelial damage of the target artery in a porcine model. The use of the Monoshunt avoids distal endothelial denudation and allows distal coronary perfusion.
Synthesis of monodisperse sub-3 nm RE2O3and Gd2O3:RE3+nanocrystals (2007)

Monodisperse, colloidally stable, sub-3 nm europium sesquioxide (Eu2O3), terbium sesquioxide (Tb2O3), and Eu3+-doped gadolinium sesquioxide (Gd2O3:Eu3+) nanocrystals have been synthesized via a hot solution-phase technique. The oleic acid concentration facilitated the production of the nanocrystals in a range of sizes from sub-2 nm up to 5.0 nm. The Eu2O3 and Gd2O3:Eu3+ nanocrystals exhibit new luminescence peaks at 620 nm, which correspond to modulation of the 7F2 transition of the Eu3+ ion. The Tb2O3 nanocrystals express a new luminescence feature at 548 nm, which corresponds to modulation of the 7F5 transition of the Tb3+ ion.
Generation of potent neutralizing human monoclonal antibodies against cytomegalovirus infection from immune B cells (2008)

The technology described has proven to be more reproducible, efficient and rapid than previously reported techniques, and can be adopted at low overall costs by any cell biology laboratory for the development of fully human mAbs for immunotherapeutic uses.
The R-type lipopolysaccharides of Neisseria meningitidis (1980)

The lipopolysaccharides of all the different serogroups of Neisseria meningitidis are of the "R" type despite the morphologically smooth appearance and the demonstrated virulence of the organisms from which they were derived. This was confirmed when each of the lipopolysaccharides was found to be devoid of detectable O-antigen side chains, giving only a low "molecular" weight core oligosaccharide when subjected to mild acid hydrolysis. The cores were modified by dephosphorylation and subjected to sugar and methylation analysis by gas-liquid chromatography. Although all the different cores contained identical components (glucose, galactose, glucosamine, heptose, and 2-keto-3-deoxyoctonate) they could be separated into three distinct categories according to their galactose:glucose ratios. These categories are typified by the cores obtained from groups A, C, and 29-e which have galactose:glucose ratios of 1:2, 2:2, and 2:1, respectively. The modified cores were methylated and analyzed by gas chromatography--mass spectrometry and on the basis of differences in the derived methylated sugars the cores could again be divided into the same three categories as above. This structural diversity also results in some serological specificity as demonstrated by the complete serogroup specificity of the group A lipopolysaccharide.
High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy‐neutral loss of heterozygosity and copy number alterations that target single genes (2010)

A multiplatform approach, including conventional cytogenetic techniques, BAC array comparative genomic hybridization, and Affymetrix 500K SNP arrays, was applied to the study of the tumor genomes of 25 follicular lymphoma biopsy samples with paired normal DNA samples to characterize balanced translocations, copy number imbalances, and copy-neutral loss of heterozygosity (cnLOH). In addition to the t(14;18), eight unique balanced translocations were found. Commonly reported FL-associated copy number regions were revealed including losses of 1p32-36, 6q, and 10q, and gains of 1q, 6p, 7, 12, 18, and X. The most frequent regions affected by copy-neutral loss of heterozygosity were 1p36.33 (28%), 6p21.3 (20%), 12q21.2-q24.33 (16%), and 16p13.3 (24%). We also identified by SNP analysis, 45 aberrant regions that each affected one gene, including CDKN2A, CDKN2B, FHIT, KIT, PEX14, and PTPRD, which were associated with canonical pathways involved in tumor development. This study illustrates the power of using complementary high-resolution platforms on paired tumor/normal specimens and computational analysis to provide potential insights into the significance of single-gene somatic aberrations in FL tumorigenesis.