gebhart/patrepeval huggingface dataset:
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer (2012)

Abstract Next‐generation sequencing is making sequence‐based molecular pathology and personalized oncology viable. We selected an individual initially diagnosed with conventional but aggressive prostate adenocarcinoma and sequenced the genome and transcriptome from primary and metastatic tissues collected prior to hormone therapy. The histology‐pathology and copy number profiles were remarkably homogeneous, yet it was possible to propose the quadrant of the prostate tumour that likely seeded the metastatic diaspora. Despite a homogeneous cell type, our transcriptome analysis revealed signatures of both luminal and neuroendocrine cell types. Remarkably, the repertoire of expressed but apparently private gene fusions, including C15orf21:MYC, recapitulated this biology. We hypothesize that the amplification and over‐expression of the stem cell gene MSI2 may have contributed to the stable hybrid cellular identity. This hybrid luminal‐neuroendocrine tumour appears to represent a novel and highly aggressive case of prostate cancer with unique biological features and, conceivably, a propensity for rapid progression to castrate‐resistance. Overall, this work highlights the importance of integrated analyses of genome, exome and transcriptome sequences for basic tumour biology, sequence‐based molecular pathology and personalized oncology. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.
TRPV1 ligands with hyperthermic, hypothermic and no temperature effects in rats (2015)

Transient receptor potential vanilloid 1 (TRPV1) is a multifunctional ion channel playing important roles in a numerous biological processes including the regulation of body temperature. Within distinct and tight chemical space of chromanyl ureas TRPV1 ligands were identified that exhibit distinctive pharmacology and a spectrum of thermoregulatory effects ranging from hypothermia to hyperthermia. The ability to manipulate these effects by subtle structural modifications of chromanyl ureas may serve as a productive approach in TRPV1 drug discovery programs addressing either side effect or desired target profiles of the compounds. Because chromanyl ureas in the TRPV1 context are generally antagonists, we verified observed partial agonist effects of a subset of compounds within that chemotype by comparing the in vitro profile of Compound 3 with known partial agonist 5'-I-RTX.
Intratumoral immunotherapy relies on B and T cell collaboration (2022)

Antitumor T cell responses are the primary mediators of cancer immunotherapy. However, many other components of the immune system are needed for efficient T cell responses to be generated. Here, we developed a combinatorial approach where a Toll-like receptor 9 agonist (CpG) and Fc-fused IL-12 protein were injected together into just one of several tumor sites in a mouse. This combination led to body-wide (abscopal) therapeutic responses in multiple cancer models. These systemic responses were dependent not only on T cells but also on B cells. B cells were activated by the treatment and were required for optimal T cell activation. This cross-talk was dependent on MHC and was tumor antigen specific. The addition of an agonistic antibody against OX40 further enhanced T cell activation and therapeutic responses. Our data suggest that the combination of CpG, anti-OX40, and IL-12Fc may have success in patients with cancer and that B and T cell collaboration is crucial for the efficacy of this combination immunotherapy.
Cold molecular beam electronic spectrum of C6 and C7 (1991)

The electronic spectra of supersonically cooled C60 and C70 have been observed in a molecular beam by two-photon ionization spectroscopy in the regions 375 to 415 nm and 595 to 640 nm. Clear spectral features are observed in both regions for C60 and in the long wavelength region for C70. Neither molecule is responsible for the diffuse interstellar bands.
Changes in liver protein abundance in inbred alcohol‐preferring rats due to chronic alcohol exposure, as measured through a proteomics approach (2006)

This study compares the total liver proteome of inbred alcohol-preferring line (iP) rats exposed to alcohol with iP rats without alcohol experience. Rat liver proteins were extracted using a three-step procedure. Each of the three solutions solubilizes a different set of proteins. The extracted proteins were separated by 2-DE. Scanned gels of two sample groups, alcohol-exposed iP and alcohol-naïve iP, were compared, revealing many protein spots with significantly higher or lower densities. These spots were cut from the gel, destained, and subjected to trypsin digestion and subsequent identification by LC-MS/MS. Twenty-four individual rats, 12 alcohol-naïve, and 12 alcohol-exposed, were used in this study. Two groups, each containing six naïve and six exposed animals, were created for statistical comparison. For the first group, 64 spots were observed to have statistically significant intensity differences upon alcohol exposure across all three extracts while 118 such spots were found in the second group. There were 113 unique proteins in both groups together. The majority of these proteins were enzymes. Significant changes are observed for three major metabolic pathways: glycolysis, gluconeogenesis, and fatty acid beta-oxidation. In addition, enzymes involved in protein synthesis and antioxidant activity show significant changes in abundance in response to alcohol exposure.
New Synthetic Approaches to Estrogen Receptor Modulators: Imidazo[1,2‐a]pyridines. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Environmental pollution control devices based on novel forms of carbon (1996)

The use of carbonaceous cathodes is an effective means to remove heavy metal contaminants from aqueous streams. By increasing the surface area of exisitng cathode materials or by using new high surface area materials, improvements in the removal efficiencies are obtained without a vast increase in electrode volume. By careful selection of the appropriate experimental parameters, selective removal and recovery of these metal ions is feasible.
Alterations in the establishment and maintenance of epithelial cell polarity as a basis for disease processes. (1990)

Polarized epithelial cells play fundamental roles in the vecto- rial movement of ions, water, and macromolecules between biological compartments. These vectorial processes include absorption (enterocytes and renal proximal tubule cells), se- cretion (hepatocytes, endocrine and exocrine cells), and ex- change (alveolar cells and capillary endothelium). The ability to conduct these vectorial processes is dependent on the struc- tural and functional organization of epithelial cells into: (a) structurally, biochemically, and physiologically distinct apical and basolateral plasma membrane domains that contain different ion channels, transport proteins, enzymes, and lipids; and (b) cell-cell junctional complexes that integrate cells into a monolayer forming a cellular barrier between biological com- partments.
Supplementary Figure 1 from Heparin-Binding EGF-Like Growth Factor Is a Promising Target for Ovarian Cancer Therapy (2023)

Supplementary Figure 1 from Heparin-Binding EGF-Like Growth Factor Is a Promising Target for Ovarian Cancer Therapy
Rotating projection based localizer radiograph for which enables multiple pre-scan function for CT (2020)

In a modern CT system, the localizer radiograph (LR), which makes a visualized scan range planning and provides information for individual patient oriented automatic exposure control, is now a standard procedure before a major diagnostic scan. We proposed a rotating projection based localizer radiograph (RPLR), in contrast to current realization as static tube positioned scanning. With this approach, the localizer Radiograph can be realized to improve the whole clinical workflow by providing no geometry deformation from multiple viewing directions within one scan, with balanced image performance and controllable x-ray dose, . Somehow with this feasibility check on current 16-row CT gantry, the scanned dose is still higher than traditional situation, but with dedicated dose reduction techniques proposed with the RPLP, the exposure dose for the scanning can be dramatically decreased.
Reliable Online Stroke Recovery from Offline Data with the Data-Embedding Pen (2011)

In this paper we propose a complete system for online stroke recovery from offline data. The key idea of our approach is to use a novel pen device which is able to embed meta information into the ink during writing the strokes. This pen-device overcomes the need to get access to any memory on the pen when trying to recover the information, which is especially useful in multi-writer or multi-pen scenarios. The actual data-embedding is achieved by an additional ink dot sequence along a handwritten pattern during writing. We design the ink-dot sequence in such a way that it is possible to retrieve the writing direction from a scanned image. Furthermore, we propose novel processing steps in order to retrieve the original writing direction and finally the embedded data. In our experiments we show that we can reliably recover the writing direction of various patterns. Our system is able to determine the writing direction of straight lines, simple patterns with crossings (e.g., "x" and "II"), and even more complex patterns like handwritten words and symbols.
Compressive single-pixel snapshot x-ray diffraction imaging (2013)

We present a method for realizing snapshot, depth-resolved material identification using only a single, energy-sensitive pixel. To achieve this result, we employ a coded aperture with subpixel features to modulate the energy spectrum of coherently scattered photons and recover the object properties using an iterative inversion algorithm based on compressed sensing theory. We demonstrate high-fidelity object estimation at x-ray wavelengths for a variety of compression ratios exceeding unity.
Using Public Engagements to Provide Input and Insights into Policy, Legal, Ethical, and Other Impacts of Science (2011)

A scholarly article by authors Lisa M. PytlikZillig, Alan J. Tomkins, and Peter Muhlberger, Rosevelt L. Pardy, Thomas Jack Morris, Yuris A. Dzenis, Joseph A. Turner, Timothy P. Collins published in The International Journal of Science in Society
High-Rate Optimized Recursive Vector Quantization Structures Using Hidden Markov Models (2007)

This paper examines the design of recursive vector quantization systems built around Gaussian mixture vector quantizers. The problem of designing such systems for minimum high-rate distortion, under input-weighted squared error, is discussed. It is shown that, in high dimensions, the design problem becomes equivalent to a weighted maximum likelihood problem. A variety of recursive coding schemes, based on hidden Markov models are presented. The proposed systems are applied to the problem of wideband speech line spectral frequency (LSF) quantization under the log spectral distortion (LSD) measure. By combining recursive quantization and random coding techniques, the systems are able to attain transparent quality at rates as low as 36 bits per frame
Real time multicomponent echo particle image velocimetry technique for opaque flow imaging (2006)

This letter reports on a contrast-based ultrasonic particle imaging technique (echo PIV) for measuring multicomponent velocity vectors in opaque flows with excellent temporal (up to 0.5ms) and spatial (up to 0.4mm) resolution. Ultrasound contrast microbubbles are used as flow tracers, and digitally acquired rf data are converted into B-mode images for PIV analysis. Here, velocity fields from various flow patterns (including rotating and transient vortex flows) that are difficult to measure using other opaque flow methods such as ultrasound Doppler or magnetic resonance imaging are measured using echo PIV. This nonintrusive technique should be a promising addition to opaque flow diagnostics.
Prognostic and therapeutic impact of RPN2-mediated tumor malignancy in non-small-cell lung cancer (2015)

RNA interference (RNAi) is a powerful gene-silencing platform for cancer treatment. Previously, we demonstrated that ribophorin II (RPN2), which is part of the N-oligosaccharyl transferase complex, regulates docetaxel sensitivity and tumor lethal phenotypes in breast cancer. However, the molecular functions and clinical relevance of RPN2 in non-small-cell lung cancer (NSCLC) remain unknown. Here, we examined RPN2 expression in tumor specimens from recurrent NSCLC patients after resection (n = 32 and = 177) and assessed the correlation between RPN2 expression and various clinical features. We also investigated whether RPN2 affects cancer malignancy in vitro and tumor growth and drug resistance in vivo. Our data show that RPN2 expression confers early and distant recurrence as well as poor survival in NSCLC patients. Furthermore, RPN2 silencing suppressed cell proliferation and invasiveness, and increased the sensitivity to chemotherapeutic drugs in vitro. Remarkably, we found that intrinsic apoptosis signaling is the mechanism of cell death involved with RPN2 knockdown. Strikingly, RPN2 silencing repressed tumorigenicity and sensitized the tumors to cisplatin treatment, which led to the longer survival of NSCLC-bearing mice. In conclusion, these data suggest that RPN2 is involved in the regulation of lethal cancer phenotypes and represents a promising new target for RNAi-based medicine against NSCLC.
Phosphodiesterase Type 5 is Not Upregulated by Tadalafil in Cultures of Human Penile Cells (2006)

Long-term incubation of human penile cells with tadalafil at concentrations above the in vitro IC50, and around the in vivo Cmax utilized in the clinical setting, did not upregulate PDE5A expression nor decrease cGMP levels. These data suggest that PDE5 upregulation is unlikely to occur in vivo on long-term tadalafil treatment.
Multivariate Analysis of Vibrational Spectra in Industrial Research (2014)

Interpreting large and complex data sets in relatively short periods of time is a significant challenge in vibrational spectroscopy. We will show some of the multivariate analysis approaches that our lab uses to manage this problem in the context of industrial research.
LSM-YSZ Cathodes with Reaction-Infiltrated Nanoparticles - eScholarship (2006)

LBNL-58757 LSM-YSZ CATHODES WITH REACTION-INFILTRATED NANOPARTICLES Chun Lu 1 , Tal Z. Sholklapper 1, 2 , Craig P. Jacobson 1 , Steven J. Visco 1 , and Lutgard C. De Jonghe 1, 2 Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720 and Materials Science and Engineering Department University of California at Berkeley Berkeley CA 94720 ABSTRACT To improve the LSM-YSZ cathode performance of intermediate temperature solid oxide fuel cells (SOFCs), Sm 0.6 Sr 0.4 CoO 3-δ (SSC) perovskite nanoparticles are incorporated into the cathodes by a reaction-infiltration process. The SSC particles are ~20 to 80nm in diameter, and intimately adhere to the pore walls of the pre-formed LSM-YSZ cathodes. The SSC particles dramatically enhance single-cell performance with a 97%H 2 +3%H 2 O fuel, between 600 o C and 800 o C. Consideration of a simplified TPB (triple phase boundary) reaction geometry indicates that the enhancement may be attributed to the high electrocatalytic activity of SSC for electrochemical reduction of oxygen in a region that can be located a small distance away from the strict triple phase boundaries. The implication of this work for developing high-performance electrodes is also discussed.
Story Time for the 21st Century (2010)

Family Story Play is an interactive book-reading system designed for two-to-four-year-olds that couples videoconferencing with paper books and interactive content to support grandparents reading together with their grandchildren over the Internet. The Story Play system is designed to improve the amount and quality of interaction between children and distant grandparents by shifting interactions from conversation to shared activities. Ethnographic methods provide a rich understanding of current family practices. Findings from this research help the authors articulate the design rationale behind Story Play and express opportunities in a broader design space for family communication.
120 Hz-frame-rate SUPER Hi-VISION Capture and Display Devices (2012)

NHK has been researching and developing SUPER Hi-VISION, with 33 megapixels (7,680-pixel by 4,320-line of resolution), as the next-generation ultra-high definition television (UHDTV) broadcast system. Last year, NHK reported that it had decided to double the frame rate of SUPER Hi-VISION video to 120 Hz to improve its motion portrayal quality. This UHDTV system has been standardized as Recommendation ITU-R BT.2020. — We report on 120-Hz SUPER Hi-VISION devices that we have developed in this paper. One is a 120-Hz SUPER Hi-VISION image-capture device that uses three 120-Hz, 33-megapixel CMOS image sensors. The sensor uses 12-bit ADCs and operates at a data rate of 51.2 Gbit/s. We have also used three 8-megapixel LCOS chips and e-shift technology to develop a 120-Hz SUPER Hi-VISION projector. These 120-Hz SUPER Hi-VISION devices were exhibited at our open house in May 2012 and demonstrated superb picture quality with less motion blur.
Mitochondrial Dynamics and Bioenergetic Alteration During Inflammatory Activation of Astrocytes (2020)

Mitochondria are essential cellular organelles that act as metabolic centers and signaling platforms and have been identified as an important subcellular target in a broad range of neuropathologies. Studies on the role of mitochondria in neurological disorders have primarily focused on neurons. However, dysfunctional mitochondria in glial cells, particularly astrocytes, have recently gained research attention due to their close involvement in neuroinflammation and metabolic and neurodegenerative disorders. Furthermore, alterations in mitochondrial energy metabolism in astrocytes have been reported to modulate cellular morphology and activity and induce the release of diverse proinflammatory mediators. Moreover, emerging evidence suggests that dysregulation of mitochondrial dynamics characterized by aberrant fission and fusion events in glial cells is closely associated with the inflammatory activation of glia. In this mini-review, we cover the recent advances in the molecular aspects of astrocytic mitochondrial dynamics and their metabolic changes under the pathological conditions of the central nervous system (CNS).
Nanocomposites and polyethylene blends: two potentially synergistic strategies for HVDC insulation materials with ultra-low electrical conductivity (2020)

Among the various requirements that high voltage direct current (HVDC) insulation materials need to satisfy, sufficiently low electrical conductivity is one of the most important. The leading commercial HVDC insulation material is currently an exceptionally clean cross-linked low-density polyethylene (XLPE). Previous studies have reported that the DC-conductivity of low-density polyethylene (LDPE) can be markedly reduced either by including a fraction of high-density polyethylene (HDPE) or by adding a small amount of a well dispersed, semiconducting nanofiller such as Al2O3 coated with a silane. This study demonstrates that by combining these two strategies a synergistic effect can be achieved, resulting in an insulation material with an ultra-low electrical conductivity. The addition of both HDPE and C8–Al2O3 nanoparticles to LDPE resulted in ultra-insulating nanocomposites with a conductivity around 500 times lower than of the neat LDPE at an electric field of 32 kV/mm and 60–90 °C. The new nanocomposite is thus a promising material regarding the electrical conductivity and it can be further optimized since the polyethylene blend and the nanoparticles can be improved independently.
Identification of members of the Bex gene family as olfactory marker protein (OMP) binding partners (2003)

Olfactory marker protein (OMP) expression is a hallmark of mature vertebrate olfactory receptor neurons (ORNs). Evidence for OMP function derives from altered behavioral and electrophysiological activities of OMP-KO mice. The molecular basis for the altered phenotype following the deletion of OMP is still unclear. Recent structural studies predict the involvement of OMP in protein-protein interaction. Here we report the identification of an OMP partner, Bex2, by phage-display screening of an olfactory mucosal cDNA-library. In situ hybridization demonstrates cellular co-localization of OMP mRNA with mRNAs for Bex1, Bex2, and Bex3 in ORNs of olfactory tissue of the mouse. The OMP/Bex interaction has been confirmed by demonstrating the chemical cross-linking of recombinant rat OMP with a synthetic peptide derived from the Bex amino acid sequence. The subcellular localization of Bex and OMP proteins was evaluated in transfected HEK293 cells. Bex is visualized in the nucleus and cytoplasm. Following co-transfection we observed the unexpected presence of some OMP in the nucleus along with Bex. Together, these data argue convincingly that we have identified Bex as an OMP partner whose further characterization will provide insight to the role of OMP and to the mechanism of the OMP/Bex interaction in ORN differentiation and function.
IRONING OUT YOUR SYSTEM: REMOVAL OF FERRIHYDRITE PRECIPITATES FROM MINING INFLUENCED WATER PIPELINES (2008)

Iron hydroxide coatings are responsible for the failure of some mining influenced water (MIW) treatment systems. Iron hydroxide coatings can reduce the effectiveness of limestone drains, clog vertical flow reactors and bioreactors, and reduce the hydraulic efficiency of pipelines and hydraulic control structures. Physical disruption of iron hydroxide coatings is not always possible. Strong acids are effective at dissolving iron hydroxide precipitates but are not safe for field application. We examined the dissolution of iron hydroxide coatings using various combinations of slightly alkaline citrate, bicarbonate and dithionite solutions in batch laboratory tests. Iron hydroxide coatings were collected from a pipeline transporting iron-containing MIW. Solutions of citrate alone and citrate plus bicarbonate were effective at partially dissolving the iron hydroxide precipitates. A solution of citrate, bicarbonate and dithionite (CBD) completely dissolved the iron hydroxide coating in laboratory tests. In November 2007, 170-L of the CBD solution was applied to a clogged field pipeline that had originally supported a flow of over 30 liters per minute (lpm) to two bioreactors in October 2006. However, the flow to both bioreactors had reduced to less than one-lpm by November 2007, which was not enough to provide at least one-lpm to each bioreactor. After the initial application, the flow increased to three-lpm. Subsequent field applications of the CBD solution in November and December 2007 increased the flow to five-lpm. This paper presents the results of the laboratory investigation and the field application of the CBD solution. The CBD solution is a safe and user-friendly method to remove iron hydroxide coatings from a broad range of MIW treatment systems and hydraulic structures.
Rapid Single-Exposure Fabrication of 2D and 3D Custom-Modified Interference Patterns by Pattern-Integrated Interference Lithography (2017)

The Pattern-Integrated Interference Lithography (PIIL) exposure system is analyzed. Experimental results of custom-modified interference patterns show good agreement with simulations, thus validating the modeling and fabrication methods employed.