gebhart/patrepeval huggingface dataset:
The taxane-enhancer STA-4783 induces Hsp70 expression and apoptosis via an oxidative stress mechanism (2007)

14107 Background: STA-4783 is an inducer of Hsp70 expression and apoptosis that recently completed a successful Phase II clinical trial in melanoma. In a double-blind, randomized, controlled trial in patients with Stage IV disease, STA-4783 plus paclitaxel doubled progression-free survival compared to paclitaxel alone (Perspectives in Melanoma X and the Third International Melanoma Research Congress, 2006). The mechanism by which STA-4783 synergizes with paclitaxel is not fully understood. To identify the major pathway modulated by STA- 4783 in vitro, a transcriptional profiling analysis of drug-treated melanoma cells was performed. Methods: Transcriptional profiling was performed on Hs294T and MDA-MB-435 melanoma cell lines treated with STA-4783. The induction of Hsp70 RNA and other human genes was monitored by Real Time-PCR (RT-PCR) analysis. Measurement of reactive oxygen species (ROS) was performed in human cells using the Carboxy-H 2 DCFDA probe. Levels of apoptotic cell death were determined by flow cytometry analysis using an Annexin V specific probe. Results: Transcriptional profiling revealed that STA-4783 induced the expression of numerous gene families known to be regulated by oxidative stress, including heat shock proteins and metallothioneins. STA-4783 induced the generation of ROS in cells resulting in the oxidation and activation of the Carboxy-H 2 DCFDA fluorescent probe. The antioxidants N-Acetyl Cysteine (NAC) and Tiron potently blocked the induction of Hsp70 RNA and apoptotic cell death. Conclusions: STA-4783 induces oxidative stress in cells resulting in Hsp70 induction and apoptotic cell death. Although STA-4783 initially induced a transient protective response, apoptotic cell death occurred due to sustained oxidative stress. Cancer cells produce more ROS than normal cells and are thus more sensitive to insults that induce oxidative stress. The induction of ROS in melanoma cells by STA-4783 may therefore enhance the efficacy of paclitaxel in vivo. STA-4783 belongs to a novel class of anticancer agents that induce cell death by pushing the cancer cell beyond its oxidative stress breaking point. [Table: see text]
Photodynamic Ablation of Lymphatic Vessels and Intralymphatic Cancer Cells Prevents Metastasis (2011)

The dissemination of tumor cells to sites far from the primary tumor (metastasis) is the principal cause of death in cancer patients. Tumor-associated lymphatic vessels are a key conduit for metastatic tumor cells, which typically first colonize the lymph nodes. Although the primary tumor and affected lymph nodes can be removed during surgery, tumor cells inside lymphatic vessels are left behind. Here, we show that in-transit tumor cells inside lymphatic vessels in mice bearing mouse melanomas or human lung tumors give rise to metastases. Using photodynamic therapy with the benzoporphyrin derivative verteporfin, we selectively destroyed lymphatic vessels in mice and pigs. Destruction of tumor-associated lymphatic vessels also eradicated intralymphatic tumor cells and prevented metastasis of mouse melanoma cells and subsequent relapse. Photodynamic therapy, when combined with anti-lymphangiogenic therapy, prevented further tumor invasion of lymphatic vessels. These findings highlight the potential of targeting in-transit tumor cells in patients.
Donor Conjugated Polymers with Polar Side Chain Groups: The Role of Dielectric Constant and Energetic Disorder on Photovoltaic Performance (2018)

Abstract To better understand the correlation of the dielectric properties with the photovoltaic response in conjugated polymer:fullerene bulk heterojunction materials, the concept of introducing minimal structural change is employed to increase the polymer dielectric constant via polar cyano groups added to the end of butyl or octyl side chains in the poly(dithienosilole‐thienopyrrolodione) system. Density functional theory calculations confirm that the polar groups do not affect the polymer electronic structure but can lead to an increase in overall dipole moment depending on the polymer chain conformation. Despite the increased dielectric constant (from 2.7 to 4.3 for cyano‐octyl side chains and from 2.7 to 3.2 for the cyano‐butyl analogues), the device characteristics employing the cyano‐containing polymers are inferior to those of the devices made with unfunctionalized alkyl chains. It is found that the hole mobilities for the cyano‐containing polymers are two orders of magnitude lower compared to those for the parent polymers and suggest this is due to an increase in energetic disorder caused by the strong local permanent dipoles associated with the cyano groups. The study highlights the complexity in the relationship between the dielectric constant of organic materials, the morphologies that are induced, and their photovoltaic performance.
CHARACTERIZATION OF TURBIDITIC OIL RESERVOIRS BASED ON GEOPHYSICAL MODELS OF THEIR FORMATION (2005)

This report talks about characterization of Turbiditic Oil Reservoirs Based on Geophysical Models of Their Formation
Canonical transient receptor potential channel subtype 3‐mediated hair cell Ca2+ entry regulates sound transduction and auditory neurotransmission (2013)

The physiological significance of canonical transient receptor potential (TRPC) ion channels in sensory systems is rapidly emerging. Heterologous expression studies show that TRPC3 is a significant Ca(2+) entry pathway, with dual activation via G protein-coupled receptor (GPCR)-phospholipase C-diacylglycerol second messenger signaling, and through negative feedback, whereby a fall in cytosolic Ca(2+) releases Ca(2+) -calmodulin channel block. We hypothesised that the latter process contributes to cochlear hair cell cytosolic Ca(2+) homeostasis. Confocal microfluorimetry with the Ca(2+) indicator Fluo-4 acetoxymethylester showed that, when cytosolic Ca(2+) was depleted, Ca(2+) re-entry was significantly impaired in mature TRPC3(-/-) inner and outer hair cells. The impact of this disrupted Ca(2+) homeostasis on sound transduction was assessed with the use of distortion product otoacoustic emissions (DPOAEs), which constitute a direct measure of the outer hair cell transduction that underlies hearing sensitivity and frequency selectivity. TRPC3(-/-) mice showed significantly stronger DPOAE (2f1 - f2 ) growth functions than wild-type (WT) littermates within the frequency range of best hearing acuity. This translated to hyperacusis (decreased threshold) measured by the auditory brainstem response (ABR). TRPC3(-/-) and WT mice did not differ in the levels of temporary and permanent threshold shift arising from noise exposure, indicating that potential GPCR signaling via TRPC3 is not pronounced. Overall, these data suggest that the Ca(2+) set-point in the hair cell, and hence membrane conductance, is modulated by TRPC3s through their function as a negative feedback-regulated Ca(2+) entry pathway. This TPRC3-regulated Ca(2+) homeostasis shapes the sound transduction input-output function and auditory neurotransmission.
Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR (2015)

Magic-angle spinning (MAS) NMR is a powerful tool for studying molecular structure and dynamics, but suffers from its low sensitivity. Here, we developed a novel helium-cooling MAS NMR probe system adopting a closed-loop gas recirculation mechanism. In addition to the sensitivity gain due to low temperature, the present system has enabled highly stable MAS (vR=4-12 kHz) at cryogenic temperatures (T=35-120 K) for over a week without consuming helium at a cost for electricity of 16 kW/h. High-resolution 1D and 2D data were recorded for a crystalline tri-peptide sample at T=40 K and B0=16.4 T, where an order of magnitude of sensitivity gain was demonstrated versus room temperature measurement. The low-cost and long-term stable MAS strongly promotes broader application of the brute-force sensitivity-enhanced multi-dimensional MAS NMR, as well as dynamic nuclear polarization (DNP)-enhanced NMR in a temperature range lower than 100 K.
Titelbild: All‐Solid‐State Rechargeable Air Batteries Using Dihydroxybenzoquinone and Its Polymer as the Negative Electrode (Angew. Chem. 30/2023) (2023)

Rechargeable air batteries utilize oxygen from the atmosphere as the active material in the positive electrode and have high potential as next-generation energy devices owing to their high energy density. In their Research Article (e202304366), Kenji Miyatake, et al. design all-solid-state rechargeable air batteries, in which the negative electrode is free from metals and consists of a redox-active molecular compound or its polymer to achieve high discharge capacity, rate characteristics, and cyclability.
The automatic generation of sparse primitives (1998)

Primitives in mathematical software are usually written and optimized by hand. With the implementation of a “sparse compiler” that is capable of automatically converting a dense program into sparse code, however, a completely different approach to the generation of sparse primitives can be taken. A dense implementation of a particular primitive is supplied to the sparse compiler, after which it can be converted into many different sparse versions of this primitive. Each version is specifically tailored to a class of sparse matrices having a specific nonzero structure. In this article, we discuss some of our experiences with this new approach.
Dementia diagnosis using similar and dissimilar retrieval items (2011)

Image-based disease diagnosis often requires radiologists' qualitative interpretations that are highly dependent on their levels of expertise, and physical and mental status. Automated image analysis tools can help radiologists increase the diagnosis accuracy by providing quantitative measures. Accordingly, this paper presents an automated method for dementia diagnosis using search and retrieval of brain MR (magnetic resonance) images. The main contributions of the method are 1) its generic decision-making based on similar and dissimilar cases retrieved from a database that can be used to diagnose various brain disorders, 2) it realizes dementia diagnosis utilizing a tailored version of histogram of oriented gradients (HOGs) as features, and 3) it achieves high performance in dementia diagnosis that is independent of the database size. Comprehensive experiments with real data showed that combining information from similar and dissimilar cases leads to improved diagnostic accuracy than using similar or dissimilar cases alone, accuracy diminishes with extreme quantization of the HOGs and with small databases, and our method achieves high performance with comparable sensitivity score to the most skilled experts at better specificity figures.
Supplementary File 3 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets (2023)

&lt;p&gt;Supplementary File 3. Detailed plots of the data used for phylogenetic inference in each case. The description for the plots in Supplementary File 3 can be found in the Legend of Supplementary Figure S13-S17.&lt;/p&gt;
Analytical Chemistry Laboratory progress report for FY 1984 (1985)

Technical and administrative activities of the Analytical Chemistry Laboratory (ACL) are reported for fiscal year 1984. The ACL is a full-cost-recovery service center, with the primary mission of providing a broad range of technical support services to the scientific and engineering programs at ANL. In addition, ACL conducts a research program in analytical chemistry, works on instrumental and methods development, and provides analytical services for governmental, educational, and industrial organizations. The ACL is administratively within the Chemical Technology Division, the principal user, but provides technical support for all of the technical divisions and programs at ANL. The ACL has three technical groups - Chemical Analysis, Instrumental Analysis, and Organic Analysis. Under technical activities 26 projects are briefly described. Under professional activities, a list is presented for publications and reports, oral presentations, awards and meetings attended. 6 figs., 2 tabs.
Effect of Electron Blocking Layer Doping and Composition on the Performance of 310 nm Light Emitting Diodes (2017)

The effects of composition and p-doping profile of the AlGaN:Mg electron blocking layer (EBL) in 310 nm ultraviolet B (UV-B) light emitting diodes (LEDs) have been investigated. The carrier injection and internal quantum efficiency of the LEDs were simulated and compared to electroluminescence measurements. The light output power depends strongly on the temporal biscyclopentadienylmagnesium (Cp 2 Mg) carrier gas flow profile during growth as well as on the aluminum profile of the AlGaN:Mg EBL. The highest emission power has been found for an EBL with the highest Cp 2 Mg carrier gas flow and a gradually decreasing aluminum content in direction to the p-side of the LED. This effect is attributed to an improved carrier injection and confinement that prevents electron leakage into the p-doped region of the LED with a simultaneously enhanced carrier injection into the active region.
Targeted tumor dual mode CT/MR imaging using multifunctional polyethylenimine-entrapped gold nanoparticles loaded with gadolinium (2018)

We report the construction and characterization of polyethylenimine (PEI)-entrapped gold nanoparticles (AuNPs) chelated with gadolinium (Gd) ions for targeted dual mode tumor CT/MR imaging in vivo. In this work, polyethylene glycol (PEG) monomethyl ether-modified PEI was sequentially modified with Gd chelator and folic acid (FA)-linked PEG (FA-PEG) was used as a template to synthesize AuNPs, followed by Gd(III) chelation and acetylation of the remaining PEI surface amines. The formed FA-targeted PEI-entrapped AuNPs loaded with Gd (FA-Gd-Au PENPs) were well characterized in terms of structure, composition, morphology, and size distribution. We show that the FA-Gd-Au PENPs with an Au core size of 3.0 nm are water dispersible, colloidally stable, and noncytotoxic in a given concentration range. Thanks to the coexistence of Au and Gd elements within one nanoparticulate system, the FA-Gd-Au PENPs display a better X-ray attenuation property than clinical iodinated contrast agent (e.g. Omnipaque) and reasonable r<sub>1</sub> relaxivity (1.1 mM<sup>-1</sup>s<sup>-1</sup>). These properties allow the FA-targeted particles to be used as an efficient nanoprobe for dual mode CT/MR imaging of tumors with excellent FA-mediated targeting specificity. With the demonstrated organ biocompatibility, the designed FA-Gd-Au PENPs may hold a great promise to be used as a nanoprobe for CT/MR dual mode imaging of different FA receptor-overexpressing tumors.
BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology (2018)

Mass Spectrometry Imaging (MSI) holds significant promise in augmenting digital histopathologic analysis by generating highly robust big data about the metabolic, lipidomic and proteomic molecular content of the samples. In the process, a vast quantity of unrefined data, that can amount to several hundred gigabytes per tissue section, is produced. Managing, analysing and interpreting this data is a significant challenge and represents a major barrier to the translational application of MSI. Existing data analysis solutions for MSI rely on a set of heterogeneous bioinformatics packages that are not scalable for the reproducible processing of large-scale (hundreds to thousands) biological sample sets. Here, we present a computational platform (pyBASIS) capable of optimized and scalable processing of MSI data for improved information recovery and comparative analysis across tissue specimens using machine learning and related pattern recognition approaches. The proposed solution also provides a means of seamlessly integrating experimental laboratory data with downstream bioinformatics interpretation/analyses, resulting in a truly integrated system for translational MSI.
Making the Most of 3D Electron Diffraction: Best Practices to Handle a New Tool (2023)

Along with the adoption of three-dimensional electron diffraction (3D ED/MicroED) as a mainstream tool for structure determination from sub-micron single crystals, questions about best practices regarding each step along the workflow, from data collection to structure solutions, arise. In this paper, we discuss three particular aspects of a 3D ED/MicroED experiment which, after hundreds of structures solved in Rigaku’s laboratories, we have found to be important to consider carefully. First, for a representative model system of a hydrated compound (trehalose dihydrate), we show that cryo-transfer of the sample into the diffractometer is an effective means to prevent dehydration, while cooling of the sample without cryo-transfer yields a marginal improvement only. Next, we demonstrate for a small (tyrosine) and a large (clarithromycin) organic compound, how a simplified and fast workflow for dynamical diffraction calculations can determine absolute crystal structures with high confidence. Finally, we discuss considerations and trade-offs for choosing an optimal effective crystal-to-detector distance; while a long distance is mandatory for a protein (thaumatin) example, even a small molecule with difficult diffraction behavior (cystine) yields superior results at longer distances than the one used by default.
Bevacizumab Therapy and Multimodal Ultrawide-Field Imaging in Immunogammopathy Maculopathy Secondary to Waldenström’s Macroglobulinemia (2015)

Waldenström's macroglobulinemia (WM) is associated with retinal findings of hyperviscosity, such as venous dilation, and findings of immunogammopathy maculopathy, such as serous macular detachment. This report describes a case of bilateral serous macular detachment with intraretinal schisis-like fluid in a patient with WM. Enhanced depth imaging optical coherence tomography revealed a thickened choroid with hyperreflective accumulations in the retinal pigment epithelium layer. Ultrawide-field fundus autofluorescence demonstrated a central area of hyperautofluorescence corresponding to the area of serous macular detachment. Ultrawide-field fluorescein angiography was characteristically silent. Intravitreal bevacizumab therapy resulted in significant reduction in intraretinal fluid but minimal change in subretinal fluid. Long-term follow-up demonstrated alterations in retinal architecture and improved serous detachments.
Channel Confinement of Aromatic Petrochemicals via Aryl–Perfluoroaryl Interactions With a B←N Host (2019)

We report channel confinement properties of an electron-deficient boron host derived from the orthogonal B←N interaction between a boronic ester and <i>trans</i>-pentafluorostilbazole. The boron host forms one-dimensional channels in the crystalline solid state when crystallized with common electron-rich aromatic petrochemicals (i.e., benzene, toluene, <i>o</i>-xylene) to form solvates and a cocrystal with stilbene. Molecular confinement of the electron-rich molecules in the solids is achieved through a combination of aryl-perfluoroaryl interactions (π-π<sub>F</sub>) and hydrogen bonds.
Towards real-time wide-field fluorescence lifetime imaging of 5-ALA labeled brain tumors with multi-tap CMOS cameras (2020)

Fluorescence guided neurosurgery based on 5-aminolevulinic acid (5-ALA) has significantly increased maximal safe resections. Fluorescence lifetime imaging (FLIM) of 5-ALA could further boost this development by its increased sensitivity. However, neurosurgeons require real-time visual feedback which was so far limited in dual-tap CMOS camera based FLIM. By optimizing the number of phase frames required for reconstruction, we here demonstrate real-time 5-ALA FLIM of human high- and low-grade glioma with up to 12 Hz imaging rate over a wide field of view (11.0 x 11.0 mm). Compared to conventional fluorescence imaging, real-time FLIM offers enhanced contrast of weakly fluorescent tissue.
Dual Dynamic Inference: Enabling More Efficient, Adaptive, and Controllable Deep Inference (2020)

State-of-the-art convolutional neural networks (CNNs) yield record-breaking predictive performance, yet at the cost of high-energy-consumption inference, that prohibits their widely deployments in resource-constrained Internet of Things (IoT) applications. We propose a dual dynamic inference (DDI) framework that highlights the following aspects: 1) we integrate both input-dependent and resource-dependent dynamic inference mechanisms under a unified framework in order to fit the varying IoT resource requirements in practice. DDI is able to both constantly suppress unnecessary costs for easy samples, and to halt inference for all samples to meet hard resource constraints enforced; 2) we propose a flexible multi-grained learning to skip (MGL2S) approach for input-dependent inference which allows simultaneous layer-wise and channel-wise skipping; 3) we extend DDI to complex CNN backbones such as DenseNet and show that DDI can be applied towards optimizing any specific resource goals including inference latency and energy cost. Extensive experiments demonstrate the superior inference accuracy-resource trade-off achieved by DDI, as well as the flexibility to control such a trade-off as compared to existing peer methods. Specifically, DDI can achieve up to 4 times computational savings with the same or even higher accuracy as compared to existing competitive baselines.
Structure and localization of genes encoding aberrant and normal epidermal growth factor receptor RNAs from A431 human carcinoma cells. (1985)

A431 cells have an amplification of the epidermal growth factor (EGF) receptor gene, the cellular homolog of the v-erb B oncogene, and overproduce an aberrant 2.9-kilobase RNA that encodes a portion of the EGF receptor. A cDNA (pE15) for the aberrant RNA was cloned, sequenced, and used to analyze genomic DNA blots from A431 and normal cells. These data indicate that the aberrant RNA is created by a gene rearrangement within chromosome 7, resulting in a fusion of the 5' portion of the EGF receptor gene to an unidentified region of genomic DNA. The unidentified sequences are amplified to about the same degree (20- to 30-fold) as the EGF receptor sequences. In situ hybridization to chromosomes from normal cells and A431 cells show that both the EGF receptor gene and the unidentified DNA are localized to the p14-p12 region of chromosome 7. By using cDNA fragments to probe DNA blots from mouse-A431 somatic cell hybrids, the rearranged receptor gene was shown to be associated with translocation chromosome M4.