gebhart/patrepeval huggingface dataset:
Pilot study of T cells redirected to EGFRvIII with a chimeric antigen receptor in patients with EGFRvIII+ glioblastoma. (2016)

2067 Background: We have developed an autologous T cell product directed to the EGFR variant III mutation via lentiviral transduction of a chimeric antigen receptor (CAR), and opened an IND. We have initiated a pilot study enrolling patients with recurrent EGFRvIII-positive glioblastoma (GBM). Methods: Patients with recurrent GBM have their tumors screened for the presence of the EGFRvIII mutation by a next-generation sequencing based assay. Eligible patients undergo leukapheresis for collection of autologous T cells, which are genetically modified ex vivo to express the EGFRvIII CAR, expanded, and then cryopreserved for infusion. Results: We report results on the nine patients we have treated. To date, we have found that infusion of 1-5x108 CART-EGFRvIII cells is feasible to manufacture and infusion is safe, without evidence of off-tumor toxicity or cross-reactivity to wild type EGFR. No clinical or laboratory signs of systemic cytokine release syndrome have been observed, though elevations in serum IL-6 occur concurrently with CART-EGFRvIII expansion in the peripheral blood. One patient developed non-convulsive status epilepticus nine days after CART-EGFRvIII infusion, which resolved with standard treatment and anti-cytokine therapy. All patients have had significant expansion of CART-EGFRvIII cells between 7-10 days post-infusion, as measured by flow cytometry and quantitative PCR in peripheral blood samples. Five patients have undergone surgical resection of tumor between 6-120 days after infusion, and pathologic evaluation has demonstrated infiltration of activated CAR T cells, recruitment of new T cells (as assessed by next generation T cell receptor deep sequencing), and specific EGFRvIII target antigen loss in GBM cells in some cases. Conclusions: These findings provide evidence that CART-EGFRvIII cells are safe, without evidence of off-target toxicity or cytokine release syndrome, and are immunologically active. The data also suggest a mechanism of antigen editing by activated CART-EGFRvIII cells that track to specific EGFRvIII GBM cells. Clinical trial information: NCT02209376.
2021. An Ultra-Rapid Host Response Assay to Discriminate Between Bacterial and Viral Infections Using Quantitative Isothermal Gene Expression Analysis (2018)

Accurate diagnosis and treatment of bacterial infection is critical for improving patient outcomes. However, over-prescription of antibiotics has contributed to C. difficile-infections and to the emergence of antimicrobial resistance. As assessing bacterial infection by culture is slow and molecular pathogen detection is limited in scope, an unmet need remains for a rapid test to differentiate between viral and bacterial infections. We have previously identified a set of 7 host response biomarkers demonstrating an AUROC of 0.91–0.93 for separating bacterial from viral infections across multiple independent cohorts. A clinical in-vitro diagnostic test (IVD) using these markers must be very fast to integrate with physician workflows. Loop-mediated isothermal amplification (LAMP) represents a rapid amplification solution with the potential to meet these needs. We describe an ultra-rapid LAMP assay designed to quantitate these markers for applications in point-of-care decision making. LAMP primers for gene expression analysis of selected markers with a housekeeping control were designed for mRNA specificity by targeting FIP primers to splice junctions. Assay specificity, sensitivity and linear dynamic range were evaluated using serial dilution of control material. RNA extracted from preserved patient samples was evaluated by LAMP for concordance with NanoString® nCounter® data (nCounter). Iterative optimization of primer design resulted in RT-LAMP assays that selectively amplify target mRNA. Assays demonstrate a linear dynamic range spanning 6 orders of magnitude and a quantitative LOD of about 103 copies. Quantitation of relative expression levels showed good concordance with nCounter data in 10 healthy, 6 viral and 6 bacterial patient samples, with average threshold times of <15 minutes. Accurate discrimination of bacterial and viral infection can be achieved on a true point-of-care timescale using our LAMP strategy. This assay could be run on a standard thermal cycler, or any quantitative molecular instrument that allows to measure at least eight targets. An IVD test distinguishing between bacterial and viral infections could aid in antimicrobial treatment decisions and thereby minimize over-prescription of antibiotics. D. Rawling, Inflammatix Inc.: Employee, Salary. W. Nie, Inflammatix Inc.: Employee, Salary. M. Remmel, Inflammatix Inc.: Employee, Salary. M. Eshoo, Inflammatix Inc.: Employee, Salary. J. Romanowsky, Inflammatix Inc.: Employee, Salary. O. Liesenfeld, Inflammatix Inc.: Employee, Salary. T. Sweeney, Inflammatix Inc.: Employee, Salary.
Trans-cutaneous electrogastrographic study of gastric myoelectric activity in transposed intrathoracic stomach after esophagectomy (2007)

We examined the feasibility of trans-cutaneous electrogastrography (EGG) in recording myoelectric activity of the transposed thoracic stomach after esophagectomy. Nineteen patients who had Ivor-Lewis esophagectomy were studied. The EGG signal was recorded using cutaneous electrodes placed over the lower sternum. Eleven patients who underwent total gastrectomy served as controls. Normal rhythm pattern (2.4-3.6 cpm > or = 70%) and power ratio (PR > or = 2) was observed in five and 12 patients, respectively, after esophagectomy. The observation of normal gastric rhythm was more frequent in the postprandial period in the esophagectomy group (median 42.6%vs. 7.4%, P = 0.01), and the PR was significantly higher (median 2.27 vs. 1.38, P = 0.013) than the gastrectomy group. Feeding further increased the prevalence of normal gastric slow wave in the esophagectomy group (median 14.8% to 42.6%, P = 0.002) and improved the stability of dominant frequency (median 78% to 67%, P = 0.015). We conclude that gastric myoelectric activities of thoracic transposed stomach can be detected from cutaneous sternal electrodes. This represented a preservation of gastric motility even when the stomach is pulled up to the thorax as a substitute for the esophagus.
Functional ablation of the mouseLdb1gene results in severe patterning defects during gastrulation (2003)

The LIM domain-binding protein 1 (Ldb1) is found in multi-protein complexes containing various combinations of LIM-homeodomain, LIM-only, bHLH, GATA and Otx transcription factors. These proteins exert key functions during embryogenesis. Here we show that targeted deletion of the Ldb1 gene in mice results in a pleiotropic phenotype. There is no heart anlage and head structures are truncated anterior to the hindbrain. In about 40% of the mutants, posterior axis duplication is observed. There are also severe defects in mesoderm-derived extraembryonic structures, including the allantois, blood islands of the yolk sack, primordial germ cells and the amnion. Abnormal organizer gene expression during gastrulation may account for the observed axis defects in Ldb1 mutant embryos. The expression of several Wnt inhibitors is curtailed in the mutant, suggesting that Wnt pathways may be involved in axial patterning regulated by Ldb1.
Role of Guest Materials in the Lower Stability of Solution-Coated versus Vacuum-Deposited Phosphorescent OLEDs (2022)

Utilizing different phosphorescent materials as emitter guests, this work investigates the root causes of the lower electroluminescence (EL) stability of solution-coated (SOL) organic light-emitting devices (OLEDs) relative to their vacuum-deposited (VAC) counterparts. The results show that emitter guest molecules aggregate under electrical stress, leading to the emergence of new longer-wavelength bands in the EL spectra of the devices over time. However, the intensity of these aggregation emission bands is much stronger in the case of SOL host:guest systems than that of their VAC counterparts, indicating that guest aggregation occurs much faster in the former. The results reveal that the phenomenon arises from differences in the initial morphologies and are likely associated with the use of solvents in the solution-coating process. Moreover, although excitons can drive this aggregation in the case of SOL emissive layer (EML) devices, the coexistence of excitons and polarons accelerates this phenomenon significantly. The results uncover one of the main causes of the lower stability of OLEDs made by solution coating and reveal the importance of adopting new molecular designs that make them less susceptible to aggregation for the development of SOL OLEDs with high performance.
Simultaneous Measurement of Reactive and Inelastic Scattering: Differential Cross Section of the H+HD→HD(v' , j' )+H Reaction (2013)

The protection of Egyptian reinforcing concrete infrastructures from corrosion is a pressing and critical task for construction engineering and industry, particularly in coastal locations. The primary aim of this case study is to integrate the advantages of both sacrificial anode cathodic protection (SACP) and impressed current cathodic protection (ICCP) in a single cathodic protection (CP) system and to use the new system in Alamein New Place near the Mediterranean sea (Egypt). The results showed that the new cathodic protection system is running very well to protect the concrete iron bars from corrosion. With the passage of time, the protective system’s efficiency and stability improve. During 30 days, the zinc anode’s potentials remain much more negative, indicating that the zinc anode can retain strong electrochemical activity for an extended length of time. The application of the CP method decreases the corrosion rate of rebar steel in concrete samples over time, according to electrochemical impedance spectroscopy (EIS).
Stress memorization in high-performance FDSOI devices with ultra-thin silicon channels and 25nm gate lengths (2006)

We report for the first time, the effect of stress memorization (SM), and the combined effects of SM and dual stress liner (DSL) on high performance fully-depleted ultra-thin channel devices with a raised source/drain architecture and channel thickness of 18nm. SM results in significant drive current and mobility enhancement, comparable to that obtained using the DSL approach. Stress transfer to the channel during SM likely occurs through the poly-gate, becoming more effective as the body is thinned. Combining SM and DSL results in a net gain that is substantially larger than that obtained using each technique separately
Ultrasound, CT and colonoscopy of colonic cancer. (1999)

Barium enema and colonoscopy are commonly used for the investigation of suspected colonic cancer. These techniques are relatively invasive and both the investigation and the preceding bowel preparation are demanding, particularly in the elderly. A prospective, blinded trial was conducted to compare ultrasound (US) and CT with colonoscopy. CT and colonoscopy were performed on 50 patients with symptoms suggesting colonic cancer. Both radiological investigations were performed prior to the bowel preparation for colonoscopy. US was performed without any preparation and oral contrast medium was the only preparation used for CT. Colonoscopy detected six cancers, all of which were diagnosed by both US and CT. In addition, US and CT diagnosed a further cancer not seen on colonoscopy due to an incomplete study. US had a sensitivity and specificity of 100% and CT a sensitivity of 100% and a specificity of 84%. US and CT were poor at diagnosing polyps. If the detection of polyps greater than 2 cm is included then US sensitivity falls to 67% and CT sensitivity falls to 89% and specificity rises to 88%. In conclusion, both US and CT are possible alternatives to colonoscopy in the investigation of symptomatic patients with suspected colonic cancer. The use of these techniques could markedly reduce the need for colonoscopy in this patient population with attendant cost savings. Non-invasive imaging has particular advantages in the elderly who cope poorly with both the bowel preparation and the procedure.
Historical Perspective and Future Direction of Blood Vessel Developments (2017)

Over the past 40 years, remarkable advances have been made in our understanding of successful blood vessel regeneration, starting with the failures of early tissue-engineered vascular grafts designed using isolated components or molecules, such as collagen gels. The vascular tissue engineers are today better educated and have steered ongoing research developments toward clinical developments of more complete vascular grafts that replicate the multitude of specialized arterial aspects required for function.
Fixation of molecular nitrogen byMethanosarcina barkeri (1985)

Methanosarcina barkeri cells were observed in ammonia-free anaerobic acetate enrichments for sulfate-reducing bacteria. The capacity of Methanosarcina to grow diazotrophicaUy was proved with a pure culture in mineral media with methanol. The cell yields with N 2 or NH~ ions as nitrogen source were 2.2 g and 6.1 g dry weight, respectively, per mol of methanol. Growth experiments with 15N 2 revealed that 84% of the cell nitrogen was derived from N 2. Acetylene was highly toxic to Methanosarcina and only reduced at concentrations lower than 100/tmol dissolved per 1 of medium. Assimilation of N 2 and reduction of acetylene were inhibited by NH~" ions. The experiments show that N 2 fixation occurs not only in eubacteria but also in archaebacteria. The ecological significance of diazotrophic growth of Methanosarcina is discussed.
Macrophage Inflammatory Protein-1β Induces Migration and Activation of Human Thymocytes (1998)

The CC chemokine macrophage inflammatory protein 1beta (MIP-1beta), has been shown to be a chemoattractant preferentially activating CD4(+) CD45RA+ T lymphocytes. Further analysis of chemokine action on lymphocytic cells has shown the potent migration-promoting capacity of MIP-1beta on human thymocytes. The responding cells were the CD4(+) and CD8(+) single-positive (SP), as well as the CD4(+) CD8(+) double-positive (DP) populations, with little if any migratory activity on the double-negative (DN) population. The activation of thymocytes by MIP-1beta appeared to be a direct, receptor-mediated event as evidenced by the rapid mobilization of intracellular calcium, increase in proteins phosphorylated on tyrosine, and activation of the mitogen-activated protein kinase (MAPK) pathway. Radioligand binding analyses showed specific and displaceable binding of MIP-1beta to thymocytes with a Kd of approximately 1 nmol/L, a profile that was comparable with MIP-1beta binding to CCR-5-transfected NIH 3T3 cells. In addition, CCR-5 mRNA was detected in total thymocyte populations indicating that activation of thymocytes by MIP-1beta may occur through binding to CCR-5. Further dissection of the subpopulations showed that only the DP and CD8(+) SP populations expressed CCR-5 and expression data on these two populations was confirmed using anti-CCR-5 monoclonal antibody. These data may be suggestive of a role for MIP-1beta in human thymocyte activation, and show a potential route for HIV infectivity in the developing immune system.
Correction: Publisher Correction: In vivo single-molecule imaging of syntaxin1A reveals polyphosphoinositide- and activity-dependent trapping in presynaptic nanoclusters (2018)

This corrects the article DOI: 10.1038/ncomms13660.
Novel electrophilic species equivalent to .alpha.-keto cations. Reactions of 0,0-diprotonated nitro olefins with benzenes yield arylmethyl ketones (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNovel electrophilic species equivalent to .alpha.-keto cations. Reactions of 0,0-diprotonated nitro olefins with benzenes yield arylmethyl ketonesKazuaki Okabe, Tomohiko Ohwada, Toshiharu Ohta, and Koichi ShudoCite this: J. Org. Chem. 1989, 54, 4, 733–734Publication Date (Print):February 1, 1989Publication History Published online1 May 2002Published inissue 1 February 1989https://pubs.acs.org/doi/10.1021/jo00265a001https://doi.org/10.1021/jo00265a001research-articleACS PublicationsRequest reuse permissionsArticle Views452Altmetric-Citations32LEARN 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 Get e-Alerts
Simulations of the static and dynamic molecular conformations of xyloglucan. The role of the fucosylated sidechain in surface‐specific sidechain folding (1991)

The hemicellulosic polysaccharide xyloglucan binds with a strong affinity to cellulosic cell wall microfibrils, the resulting heterogeneous network constituting up to 50% of the dry weight of the cell wall in dicotyledonous plants. To elucidate the molecular details of this interaction, we have performed theoretical potential energy calculations of the static and dynamic equilibrium conformations of xyloglucan using the GEGOP software. In particular, we have evaluated the preferred sidechain conformations of hexa-, octa-, deca- and heptadecasaccharide model fragments of xyloglucan for molecules with a cellulose-like, flat, glucan backbone, and a cellobiose-like, twisted, glucan backbone conformation. For the flat backbone conformation the determination of static equilibrium molecular conformations revealed a tendency for sidechains to fold onto one surface of the backbone, defined here as the H1S face, in the fucosylated region of the polymer. This folding produces a molecule that is sterically accessible on the opposite face of the backbone, the H4S face. Typically, this folding onto the H1S surface is significantly stabilized by favorable interactions between the fucosylated, trisaccharide sidechain and the backbone, with some stabilization from adjacent terminal xylosyl sidechains. In contrast, the trisaccharide sidechain folds onto the H4S face of xyloglucan fragments with a twisted backbone conformation. Preliminary NMR data on nonasaccharide fragments isolated from sycamore suspension-cultured cell walls are consistent with the hypothesis that the twisted conformation of xyloglucan represents the solution form of this molecule. Metropolis Monte Carlo (MMC) simulations were employed to assess sidechain flexibility of the heptadecasaccharide fragments. Simulations performed on the flat, rigid, backbone xyloglucan indicate that the trisaccharide sidechain is less mobile than the terminal xylosyl sidechains. MMC calculations on a fully relaxed molecule revealed a positive correlation between a specific trisaccharide sidechain orientation and the 'flatness' of the backbone glucosyl residues adjacent to this sidechain. These results suggest that the trisaccharide sidechain may play a role in the formation of nucleation sites that initiate the binding of these regions to cellulose. Based on these conformational preferences we suggest the following model for the binding of xyloglucan to cellulose. Nucleation of a binding site is initiated by the fucosylated, trisaccharide sidechain that flattens out an adjacent region of the xyloglucan backbone. Upon contacting a cellulose microfibril this region spreads by step-wise flattening of successive segments of the backbone. Self-association of xyloglucan molecules in solution may be prevented by the low frequency of formation of these nucleation sites and the geometry of the molecules in solution.
An accessory portal for posterior cruciate ligament tibial insertion visualization (2004)

Posterior cruciate ligament (PCL) reconstruction is infrequently performed, technically challenging, and has less predictable results compared with its anterior cruciate ligament (ACL) counterpart. Creation of a transtibial tunnel has been associated with catastrophic neurovascular complications, as well as tunnel malpositioning. This technical note reports the use of the femoral PCL tunnel to visually access the posterior slope for tibial tunnel creation. This technique modification allows concurrent placement of instruments through an inferomedial and/or posteromedial portal to facilitate PCL insertional debridement, placement of the tibial aimer, and creation of the tunnel. We feel that this technical modification provides superior visualization of this anatomic area.
Crystallization of Aluminophosphate VPI-5 Using Magic Angle Spinning NMR Spectroscopy (1990)

Variable temperature Magic Angle Spinning Nuclear Magnetic Resonance spectroscopy was used for the first time to study the crystallization process of the aluminophosphate, VPI-5. The results of these in-situ NMR experiments were compared to results obtained for VPI-5 synthesized by conventional methods in teflon lined autoclaves. The excellent agreement between the experiments demonstrate that in-situ Magic Angle Spinning Nuclear Magnetic Resonance spectroscopy can be used to monitor the entire crystallization process of VPI-5 and possibly other molecular sieves.
Self-interference cancellation in multi-hop full-duplex networks via structured signaling (2011)

This paper discusses transmission strategies for dealing with the problem of self-interference in multi-hop wireless networks in which the nodes communicate in a full duplex mode. An information theoretic study of the simplest such multi-hop network: the two-hop source-relay-destination network, leads to a novel transmission strategy called structured self-interference cancellation (or just "structured cancellation" for short). In the structured cancellation strategy the source restrains from transmitting on certain signal levels, and the relay structures its transmit signal such that it can learn the residual self-interference channel, and undo the self interference, by observing the portion of its own transmit signal that appears at the signal levels left empty by the source. It is shown that in certain nontrivial regimes, the structured cancellation strategy outperforms not only half-duplex but also full-duplex schemes in which time-orthogonal training is used for estimating the residual self-interference channel.
Analysis of Postdeployment Serum Samples Identifies Potential Biomarkers of Exposure to Burn Pits and Other Environmental Hazards (2019)

We identify a potential signature of exposure to open burn pits, and provide a framework for using postexposure sera to identify exposures when contemporaneous monitoring was inadequate.