gebhart/patrepeval huggingface dataset:
Linking laboratory and clinical research: the development of molecularly targeted therapeutics inside the national cancer institute center for cancer research. (2003)

Understanding the molecular basis of the pathways regulating the cancer cell promises to revolutionize clinical practice. The results of genomic- an proteomic-based studies at the National Cancer Center Institute Center for Cancer Research (NCI CCR) include the indentation of a molecular biomarker for ovarian cancer based on serum proteomic patterns that permits early detection and a new method for the diagnostic and prognostic assessment of subclasses of diffuse large B-cell lymphoma based on molecular criteria. The biological informativeness of molecularly based diagnostic categories confers the additional clinical advantage of identifying molecular pathways that can be selectively targeted for treatment. Molecular profiling of clear cell renal carcinoma, eg, has revealed that it responds to antiangiogenic agents. Moreover, targeted immunomodulatory interventions are proving effective against many cancers. The discovery and development of molecularly based means for detecting, diagnosis, and treating cancer are central priorities of the NCI CCR, which provides an interactive environment encouraging multidisciplinary collaborations, especially among basic and clinical investigators. Its infrastructure supports the iterative flow of information from the bench to the bedside and from the bedside to the bench, expediting the delivery of molecularly based therapeutics to cancer patients.
RET/Papillary Thyroid Cancer Rearrangement in Nonneoplastic Thyrocytes: Follicular Cells of Hashimoto’s Thyroiditis Share Low-Level Recombination Events with a Subset of Papillary Carcinoma (2006)

Low-level RET/PTC recombination occurs in nonneoplastic follicular cells in HT and in a subset of papillary thyroid carcinomas. RET/PTC expression variability should be taken into account for the molecular diagnosis of thyroid lesions. Overlapping molecular mechanisms may govern early stages of tumor development and inflammation in the thyroid.
<title>Video coding with adaptive quantization and rate control</title> (1992)

Adaptive quantization and rate-control are key components in the performance of video coding schemes. Within the framework of ongoing second phase of Motion Picture Experts Group (MPEG-2), various improvements in adaptive quantization and rate control concepts developed for MPEG-1 based coding are possible. In this paper, we first review the adaptive quantization schemes developed so far for MPEG based coding. We then analyze performance of one such scheme and compare its behavior with that expected from a good adaptive quantization scheme. Next, we propose several modifications that have the potential for substantially improving the performance of this scheme.
MFN2 Influences Amyotrophic Lateral Sclerosis Pathology (2021)

Abstract Objective To better understand the pathology of amyotrophic lateral sclerosis, we used sequence data from patients seen at the University of Utah to identify novel disease-associated loci. We utilized both in vitro and in vivo studies to determine the biological effect of patient mutations in MFN2 . Method Sequence data for a total of 140 patients were run through VAAST and Phevor to determine genes that were more burdened with rare, nonsynonymous variants compared to control longevity cohort. Variants identified in MFN2 were expressed in Mfn2 knockout cells to determine if mutant MFN2 could rescue mitochondrial morphology defects. We identified additional rare, nonsynonymous variants in MFN2 in ALSdb that were expressed in knockout mouse embryonic fibroblasts (MEFs). Membrane potential was measured to quantify mitochondrial health upon mutant MFN2 expression. mfn2 knockout zebrafish were used to examine movement compared to wildtype and protein aggregation in brain. Results MFN2 mutations identified in ALS patients from our University of Utah cohort and ALSdb were defective in rescuing morphological defects in Mfn2 knockout MEFs. Selected mutants showed decreased membrane potential compared to wildtype MFN2 expression. Zebrafish heterozygous and homozygous for loss of mfn2 showed increased TDP-43 levels in their hindbrain and cerebellum. Conclusion In total, 21 rare, deleterious mutations in MFN2 were tested in Mfn2 knockout MEFs. Mutant MFN2 expression was not able to rescue the knockout phenotype, though at differing degrees of severity. Decreased membrane potential also argues for inhibited mitochondrial function. Increased TDP-43 levels in mutant zebrafish illustrates MFN2’s function in ALS pathology. MFN2 variants influence ALS pathology and highlight the importance of mitochondria in neurodegeneration.
Variational blind deconvolution of multi‐channel images (2005)

Abstract The fundamental problem of denoising and deblurring images is addressed in this study. The great difficulty in this task is due to the ill‐posedness of the problem. We analyze multi‐channel images to gain robustness and regularize the process by the Polyakov action, which provides an anisotropic smoothing term that uses inter‐channel information. Blind deconvolution is then solved by an additional anisotropic regularization term of the same type for the kernel. It is shown that the Beltrami regularizer leads to better results than the total variation (TV) regularizer. An analytic comparison to the TV method is carried out and results on synthetic and real data are demonstrated. © 2005 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 15, 56–63, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.20038
Identification of morphological and biochemical changes in keratin‐8/18 knock‐down cells using Raman spectroscopy (2017)

Accurate understanding of cellular processes and responses to stimuli is of paramount importance in biomedical research and diagnosis. Raman spectroscopy (RS), a label-free and nondestructive spectroscopic method has the potential to serve as a novel 'theranostics' tool. Both fiber-optic and micro-Raman studies have demonstrated efficacy in diagnostics and therapeutic response monitoring. In the present study, we have evaluated the potential of micro-Raman spectroscopic maps in identifying changes induced by loss of K8/18 proteins in a tongue cancer cell line. Furthermore, we also evaluated the efficacy of less expensive and commercially available fiber probes to identify K8/18 wild and knock-down cell pellets, in view of the utility of cell pellet-based studies. The findings suggest that major differences in the cellular morphology and biochemical composition can be objectively identified and can be utilized for classification using both micro-Raman and fiber-probe-based RS. These findings highlight the potential of fiber-optic probe-based RS in noninvasive cellular phenotyping for diagnosis and therapeutic response monitoring, especially in low-resource settings.
Statistical investigation of sol-gel lead titanate (PT) processing (1992)

There are three stages involved in the successful application of a thin film sol-gel oxide, (1) solution synthesis, (2) application, and (3) post application treatments. Each stage contains many processing steps that can be varied in order to optimize the thin film for various applications. This work entails a statistical investigation of a thin film sol-gel PT process for use in memory applications. Statistical experimental design yields a maximum amount of information for a minimum amount of effort. Candidate controllable variables (factors) and responses are first identified. A screening experiment is then conducted to identify the most important factors based on the identified responses. A full-factorial experiment is then conducted to further evaluate the important factors. Finally, a response surface analysis is performed in order to optimize the important factors. Responses such as switching charge (2Pr), endurance and dielectric measurements are used to analyze the sol-gel lead titanate.
Multicomputer-based neural networks for imaging in random media (2002)

The authors describe a novel technique for imaging in random media using a neural network approach based on a modified backpropagation algorithm. Simulation results indicate that it is possible to produce images of simple structures in 2-D media with a reasonable computation time. The present approach is computation-intensive and for this reason the authors have developed a machine architecture and a machine, Kilonode, which is well suited to this class of computing problems, and which can ultimately be produced at a cost which is suitable for commercial application of the neural network algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Predicting Patient's Trajectory of Physiological Data using Temporal Trends in Similar Patients: A System for Near-Term Prognostics. (2010)

Providing near-term prognostic insight to clinicians helps them to better assess the near-term impact of their decisions and potential impending events affecting the patient. In this work, we present a novel system, which leverages inter-patient similarity for retrieving patients who display similar trends in their physiological time-series data. Data from the retrieved patient cohort is then used to project patient data into the future to provide insights for the query patient. The proposed approach and system were tested using the MIMIC II database, which consists of physiological waveforms, and accompanying clinical data obtained for ICU patients. In the experiments we report the effectiveness of the inter-patient similarity measure and the accuracy of the projection of patients' data. We also discuss the visual interface that conveys the near-term prognostic decision support to the user.
Intrasphincteric Botulinum Toxin for the Treatment of Achalasia (1995)

Injection of botulinum toxin into the lower esophageal sphincter is an effective, safe, and simple method of treatment for achalasia, with results that are sustained for several months.
Application of port-access-rejection probabilitytheory for integrated N -port memory architecture optimisation (1998)

Area-efficient architectures for integrated N-port memories employ blocks of one port memory cells and dynamic port-to-block connections. The authors determine the block number M necessary to achieve a target port-access-rejection probability for a given port number N and best-case/worst-case conflict-resolve algorithms, by applying stochastic probability theory.
Robust variance estimation and inference for causal effect estimation (2023)

Abstract We present two novel approaches to variance estimation of semi-parametric efficient point estimators of the treatment-specific mean: (i) a robust approach that directly targets the variance of the influence function (IF) as a counterfactual mean outcome and (ii) a modified non-parametric bootstrap-based approach. The performance of these approaches to variance estimation is compared to variance estimation based on the sample variance of the empirical IF in simulations across different levels of positivity violations and treatment effect sizes. In this article, we focus on estimation of the nuisance parameters using correctly specified parametric models for the treatment mechanism in order to highlight the challenges posed by violation of positivity assumptions (distinct from the challenges posed by non-parametric estimation of the nuisance parameters). Results demonstrate that (1) variance estimation based on the empirical IF may provide highly anti-conservative confidence interval coverage (as reported previously), (2) the proposed robust approach to variance estimation in this setting provides conservative coverage, and (3) the proposed modified bootstrap maintains close to nominal coverage and improves power. In the appendix, we (a) generalize the robust approach of estimating variance to marginal structural working models and (b) provide a proof of the consistency of the targeted minimum loss-based estimation bootstrap.
Characterized Chondrocyte Implantation Results in Better Structural Repair when Treating Symptomatic Cartilage Defects of the Knee in a Randomized Controlled Trial versus Microfracture (2008)

One year after treatment, characterized chondrocyte implantation was associated with a tissue regenerate that was superior to that after microfracture. Short-term clinical outcome was similar for both treatments. The superior structural outcome may result in improved long-term clinical benefit with characterized chondrocyte implantation. Long-term follow-up is needed to confirm these findings.
Hepatic cell encapsulation for applications in tissue engineering (2011)

"Hepatic cell encapsulation for applications in tissue engineering." Computer Methods in Biomechanics and Biomedical Engineering, 14(sup1), pp. 271–272Keywords: liverbioreactorencapsulationtissue engineering Acknowledgements Special thanks for G. Défarge from ISTO-University Orleans, for the cryo-SEM analysis. The FEDER programme and the Picardy Region, France provides financial support to this project. Notes 1. N-M Tran and S. Capone contributed equally to this work. Additional informationNotes on contributorsN. M. Tran1S. Capone1
1101. Rapid and Long-Term Protection Against Anthrax Lethal Toxin (2006)

Any delay in the treatment of anthrax significantly affects the chances of survival, therefore, an ideal vaccine or therapy for Bacillus anthracis would not only provide persistent protection but also act rapidly. We have addressed the requirement for rapid protection with a human adenovirus (Ad)-based vector (AdαPAscAb) encoding a single chain antibody that neutralizes protective antigen (PA; a critical component of B. anthracis lethal toxin; Kasuya et al. Molecular Therapy 2005; 11:237–244), and the requirement for long-term protective immunity with an Ad-based vector encoding PA (AdsechPA; Tan et al, Hum Gene Ther. 2003; 14:1673). The present study evaluates two strategies for the induction of both short-term and long-term protective immune responses, one combining 2 Ad vectors, and one using an AAV vector. For the combined Ad vector strategy, two Ad-based vectors were co- administered to mice: (1) AdαPAscAb, encoding a neutralizing anti- PA single chain antibody, to elicit short-term passive immunity; and (2) AdsechPA, encoding PA, to elicit active immunity and thus long- term protective immunity. Mice immunized with AdαPAscAb alone had detectable serum anti-lethal toxin neutralizing antibodies (NAb) by 3 days post-administration that dropped to the assay limit of detection by day 28, while mice immunized with AdsechPA alone had measurable anti-lethal toxin NAb titers by 14 days post-administration that continued to increase through 6 wk. Co- immunizing with both vectors led to circulating anti-lethal toxin NAb titers from 3 d through 6 wk post-administration. Mice immunized with AdαPAscAb alone were fully protected (100%) against a lethal toxin challenge at 3 days post-immunization, 20% at day 14, and 0% at 28 days. Mice immunized with AdsechPA alone were completely susceptible to lethal toxin challenge (0% survival) at 3 d post-immunization, but were fully protected (100% survival) at 14 and 28 days post-immunization. Importantly, mice co- immunized with AdαPAscAb and AdsechPA had rapid and long term protection, with complete protection against a lethal toxin challenge from 3 days through 28 days post-administration (100% survival). The 2nd strategy to induce rapid and protective immunity is based on the delivery of a non-human primate serotype (rh10) adeno-associated virus (AAV) vector encoding a single chain antibody that neutralizes PA (AAVαPAscAb). Animals immunized with AAVαPAscAb had circulating serum anti-lethal toxin NAb from 2 wk through at least 10 wk post-administration. At 11 wk post- administration, 100% of the immunized animals survived a lethal toxin challenge. These data demonstrate that co-administration of Ad vectors inducing passive and active immunity, respectively or an AAV vector coding for inducing passive immunity, will satisfy the requirement for rapid and persistent protective immune responses against B. anthracis, a fundamental requirement for an effective anti-bioterrorism vaccine.
Heterologous Production of Dihomo-γ-Linolenic Acid in Saccharomyces cerevisiae (2007)

To make dihomo-gamma-linolenic acid (DGLA) (20:3n-6) in Saccharomyces cerevisiae, we introduced Kluyveromyces lactis Delta12 fatty acid desaturase, rat Delta6 fatty acid desaturase, and rat elongase genes. Because Fad2p is able to convert the endogenous oleic acid to linoleic acid, this allowed DGLA biosynthesis without the need to supply exogenous fatty acids on the media. Medium composition, cultivation temperature, and incubation time were examined to improve the yield of DGLA. Fatty acid content was increased by changing the medium from a standard synthetic dropout medium to a nitrogen-limited minimal medium (NSD). Production of DGLA was higher in the cells grown at 15 degrees C than in those grown at 20 degrees C, and no DGLA production was observed in the cells grown at 30 degrees C. In NSD at 15 degrees C, fatty acid content increased up until day 7 and decreased after day 10. When the cells were grown in NSD for 7 days at 15 degrees C, the yield of DGLA reached 2.19 microg/mg of cells (dry weight) and the composition of DGLA to total fatty acids was 2.74%. To our knowledge, this is the first report describing the production of polyunsaturated fatty acids in S. cerevisiae without supplying the exogenous fatty acids.
Effect of completeness of revascularization on long-term outcome of patients with three-vessel disease undergoing coronary artery bypass surgery. A report from the Coronary Artery Surgery Study (CASS) Registry. (1992)

Complete revascularization (grafts to three or more vessels) in patients with three-vessel coronary disease appears to most benefit those with severe angina and left ventricular dysfunction.
IMCT-15PILOT STUDY OF T CELLS REDIRECTED TO EGFRvIII WITH A CHIMERIC ANTIGEN RECEPTOR IN PATIENTS WITH EGFRvIII+ GLIOBLASTOMA (2015)

We have initiated a first-in-human pilot study of intravenous delivery of autologous T cells re-directed to the EGFR variant III mutation by means of a lentiviral vector encoding a chimeric antigen receptor (CAR). Patients with recurrent or incompletely resected glioblastoma (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 then manufactured to form CART-EGFRvIII T cell products. We report preliminary results on the first six patients we have treated. We targeted a challenging subset of GBM patients, with multi-focal recurrent, residual, progressive disease refractory to standard and experimental therapies, including chemotherapy, radiation, bevacizumab and prior immunotherapy. To date, we have found that infusion of CART-EGFRvIII cells is safe, without evidence of off-tumor toxicity such as cross-reactivity to wild type EGFR. No clinical or laboratory signs of systemic cytokine release syndrome have been observed. One patient developed a seizure and non-convulsive status epilepticus nine days after CART-EGFRvIII infusion. Seizures resolved with anti-epileptic medications, and the patient was treated with steroids and anti-IL6 cytokine therapy. All patients have had significant expansion of CART-EGFRvIII cells as measured by flow cytometry and quantitative PCR in peripheral blood samples, despite the use of steroids in two patients. In one of two patients who had operative resection of presumed residual tumor, pathologic evaluation demonstrated inflammation, T cell infiltration, and EGFRvIII antigen loss. In total, two of six heavily pretreated patients are clinically stable three months post-CART infusion. These findings provide preliminary evidence that CART-EGFRvIII cells are safe, without evidence of off-target toxicity and without evidence of cytokine release syndrome, and that these are active T cell products that expand in the blood.
Evaluating a novel formula for noninvasive estimation of arterial carbon dioxide during post‐resuscitation care (2020)

This novel formula appears to provide an accurate, continuous, and noninvasive estimation of arterial carbon dioxide.
Nabpaclitaxel plus gemcitabine in subjects with advanced pancreatic cancer who have cholestatic hyperbilirubenemia secondary to bile duct obstruction. (2016)

e15717Background: The combination of nabpaclitaxel/gemcitabine (AG) is one standard of care treatment for patients (pts) with advanced pancreatic adenocarcinoma (APC). Only insufficient data accord...
Consciousness by the lights of logic and commonsense (1997)

I urge return by the lights of logic and commonsense to a dialectical tabula rasa – according to which: (1) consciousness, in the ordinary pre-analytic sense of the term, is identified with P-consciousness, and “A-consciousness” is supplanted by suitably configured terms from its Blockian definition; (2) the supposedly fallacious Searlean argument for the view that a function of P-consciousness is to allow flexible and creative cognition is enthymematic and, when charitably specified, quite formidable.
Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems (2023)

Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.