gebhart/patrepeval huggingface dataset:
The Bcl-2 repertoire of mesothelioma spheroids underlies acquired apoptotic multicellular resistance (2011)

Three-dimensional (3D) cultures are a valuable platform to study acquired multicellular apoptotic resistance of cancer. We used spheroids of cell lines and actual tumor to study resistance to the proteasome inhibitor bortezomib in mesothelioma, a highly chemoresistant tumor. Spheroids from mesothelioma cell lines acquired resistance to bortezomib by failing to upregulate Noxa, a pro-apoptotic sensitizer BH3-only protein that acts by displacing Bim, a pro-apoptotic Bax/Bak-activator protein. Surprisingly, despite their resistance, spheroids also upregulated Bim and thereby acquired sensitivity to ABT-737, an inhibitor of anti-apoptotic Bcl-2 molecules. Analysis using BH3 profiling confirmed that spheroids acquired a dependence on anti-apoptotic Bcl-2 proteins and were 'primed for death'. We then studied spheroids grown from actual mesothelioma. ABT-737 was active in spheroids grown from those tumors (5/7, ∼70%) with elevated levels of Bim. Using immunocytochemistry of tissue microarrays of 48 mesotheliomas, we found that most (33, 69%) expressed elevated Bim. In conclusion, mesothelioma cells in 3D alter the expression of Bcl-2 molecules, thereby acquiring both apoptotic resistance and sensitivity to Bcl-2 blockade. Mesothelioma tumors ex vivo also show sensitivity to Bcl-2 blockade that may depend on Bim, which is frequently elevated in mesothelioma. Therefore, mesothelioma, a highly resistant tumor, may have an intrinsic sensitivity to Bcl-2 blockade that can be exploited therapeutically.
Functional changes in hippocampal synaptic signaling in offspring survivors of a mouse model of intrauterine inflammation (2017)

These results offer a mechanistic explanation for the cognitive and behavioral deficits observed in survivors of preterm birth caused by intrauterine inflammation.
Detection of Lymph Node Metastases in Human Colorectal Cancer by Using 5-Aminolevulinic Acid-Induced Protoporphyrin IX Fluorescence with Spectral Unmixing (2013)

Accurate evaluation of metastatic lymph nodes (LNs) is indispensable for adequate treatment of colorectal cancer (CRC) patients. Here, we demonstrate detection of metastases of human CRC in removed fresh LNs using 5-aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence. A spectral unmixing method was employed to reduce the overlap of collagen autofluorescence on PpIX fluorescence. A total of 17 surgery patients with advanced CRC were included in this study. After 5-ALA at a dose of 15 mg/kg of body weight was applied orally 2 h prior to surgery, 87 LNs were subjected to spectral fluorescence imaging and histopathological diagnosis, and statistical analysis was performed. No apparent side effect was observed to be associated with 5-ALA administration. The spectral unmixing fluorescence intensity of PpIX in metastatic LNs was 10.2-fold greater than that in nonmetastaic LNs. The receiver-operating-characteristic (ROC) analysis showed that the area under the curve (AUC) was calculated as 0.95. Our results show the potential of 5-ALA-induced PpIX fluorescence processed by spectral unmixing for detecting metastases in excised fresh LNs from patients with CRC, suggesting that this rapid and feasible method is applicable to gross evaluation of resected LN samples in pathology laboratories.
Next Generation No Compromise Battery Chargers (2003)

 Support for batteries up to 28V at charge rates up to 4A with efficien cies higher than 95%.  Typical charging voltage and current accuracy is 0.8% and 4% respectively.  The PWM controller is a 300kHz synchronous architecture capable of achieving 98% maximum duty cycle for excellent low dropout performance and continuous switching down to zero charge current. The PWM controller is designed to be stable with and suppress the audible noise from ceramic input/output capacitors while also allowing the use of popular 10µH inductors for small size at high currents.  A low current sense voltage allows the use of small size and low value current sense resistors. Small IC size, low external part count and the use of small external components result in a very small circuit board footprint.  An overvoltage comparator protects against battery over voltage conditions and suspends PWM activity at logic speeds. Input current limiting automatically reduces charge current to prevent overloading the power adapter. A series input MOSFET also provides power adapter protection from reverse battery
On identifiability, maximum-likelihood, and novel HOS based criteria (1990)

Considers estimation and classification problems for a stretch of stationary data containing a non-Gaussian linear process and additive Gaussian noise of unknown covariance (AGN/UC). To allow general noncausal and nonminimum phase (NC/NMP) ARMA models, and develop estimation and classification schemes which are immune to AGN/UC higher-order statistics (HOS) are resorted to. Time-domain optimality criteria are discussed which employ a finite set of sample cumulant lags, while the frequency-domain criteria involve sample polyspectral lags.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High-Throughput Amenable MALDI-MS Detection of RNA and DNA with On-Surface Analyte Enrichment Using Fluorous Partitioning (2020)

High-throughput matrix-assisted laser desorption/ionization mass spectrometry (HT-MALDI-MS) has garnered considerable attention within the drug discovery industry as an information-rich alternative to assays using light-based detection methods. To date, these efforts have been primarily focused on assays using protein or peptide substrates. Methods for RNA or DNA analysis by HT-MALDI-MS have not been extensively reported due to the challenges associated with MALDI-MS of oligonucleotides, including the propensity to form multiple salt adducts, low ionization potential, and ease of fragmentation. The objective of this work was to develop a platform suitable for HT-MS analysis of RNA and DNA substrates that overcomes these hurdles by combining on-surface sample preparation with soft ionization. This has been accomplished through the selective immobilization of fluorous-tagged oligonucleotides on a fluorous-modified MS target plate, followed by on-surface enrichment, matrix addition, and direct laser desorption/ionization, a process dubbed fluorous HT-MS (F-HT-MS). The work has resulted in methods by which RNA and DNA substrates can be detected at nanomolar concentrations from a typical assay buffer system using procedures that are amenable to full automation. The protocols were applied to an miRNA biogenesis assay, demonstrating its potential for RNA processes and thereby filling a prominent gap in RNA drug discovery: the paucity of in vitro functional assays.
Plasmacytoid urothelial carcinoma: a rapid autopsy case report with unique clinicopathologic and genomic profile (2019)

The sheet-like growth pattern of PUC makes early phases of disease spread much more difficult to capture on cross-sectional imaging. Alternative forms of surveillance may be required for detection of recurrent PUC, and providers may need to treat based on symptoms and clinical suspicion.
Clarification of the introduction to the communication "New polymerization methodology: synthesis of thiophene-based poly(arylene ether ketones)" (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTClarification of the introduction to the communication "New polymerization methodology: synthesis of thiophene-based poly(arylene ether ketones)"J. M. DeSimone and V. V. ShearesCite this: Macromolecules 1993, 26, 10, 2642Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ma00062a042https://doi.org/10.1021/ma00062a042research-articleACS PublicationsRequest reuse permissionsArticle Views64Altmetric-Citations6LEARN 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
OFDM carrier frequency offset correction based on Type-2 control loop (2012)

In this paper, we propose a robust data-aided carrier frequency offset (CFO) tracking algorithm for orthogonal frequency division multiplexing (OFDM) system. The problem is solved as a sequence of estimation and correction steps. We find the major contributors to the CFO measurement uncertainty are the additive white noise together with the inter-carrier interference (ICI). Our derivation results show the noise variance can be reduced via averaging while the ICI introduced uncertainty can be decreased by iterative CFO compensations. These considerations lead us to a Type-2 correction loop. Theoretical analysis and simulation results show our proposed algorithm is robust and able to compensate and track comparably large CFO.
Conformal PEDOT Coating Enables Ultra-High-Voltage and High-Temperature Operation for Single-Crystal Ni-Rich Cathodes (2022)

Single-crystal Ni-rich Li[Ni<sub><i>x</i></sub>Mn<sub>y</sub>Co<sub>1-x-<i>y</i></sub>]O<sub>2</sub> (SC-NMC) cathodes represent a promising approach to mitigate the cracking issue of conventional polycrystalline cathodes. However, many reported SC-NMC cathodes still suffer from unsatisfactory cycling stability, particularly under high charge cutoff voltage and/or elevated temperature. Herein, we report an ultraconformal and durable poly(3,4-ethylenedioxythiophene) (PEDOT) coating for SC-NMC cathodes using an oxidative chemical vapor deposition (oCVD) technique, which significantly improves their high-voltage (4.6 V) and high-temperature operation resiliency. The PEDOT coated SC LiNi<sub>0.83</sub>Mn<sub>0.1</sub>Co<sub>0.07</sub>O<sub>2</sub> (SC-NMC83) delivers an impressive capacity retention rate of 96.7% and 89.5% after 100 and 200 cycles, respectively. Significantly, even after calendar aging at 45 °C and 4.6 V, the coated cathode can still retain 85.3% (in comparison with 59.6% for the bare one) of the initial capacity after 100 cycles at a 0.5 C rate. Synchrotron X-ray experiments and interface characterization collectively reveal that the conformal PEDOT coating not only effectively stabilizes the crystallographic structure and maintains the integrity of the particles but also significantly suppresses the electrolyte's corrosion, resulting in improved electrochemical/thermal stability. Our findings highlight the promise of an oCVD PEDOT coating for single-crystal Ni-rich cathodes to meet the grand challenge of high-energy batteries under extreme conditions.
Structural transition and antibody binding of Ebola GP and Zika E proteins from pre-fusion to fusion-initiation states (2018)

Abstract Membrane fusion proteins are responsible for viral entry into host cells– a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion initiation structures, and, despite differences in viral genomes and disease etiology, many fusion proteins are arranged as trimers. Structural information for both pre-fusion and fusion initiation states is critical for understanding virus neutralization by the host immune system. In the case of Ebola glycoprotein (GP) and Zika envelope protein (Zika E), pre-fusion state structures have been identified experimentally, but only partial structures of fusion initiation states have been described. While the fusion initiation structure is in an energetically unfavorable state that is difficult to solve experimentally, the existing structural information combined with computational approaches enabled the modeling of fusion initiation state structures of both proteins. These structural models provide an improved understanding of four different neutralizing antibodies in the prevention of viral host entry.
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats (2011)

In most cheminformatics workflows, chemical information is stored in files which provide the necessary data for subsequent calculations. The correct interpretation of the file formats is an important prerequisite to obtain meaningful results. Consistent reading of molecules from files, however, is not an easy task. Each file format implicitly represents an underlying chemical model, which has to be taken into consideration when the input data is processed. Additionally, many data sources contain invalid molecules. These have to be identified and either corrected or discarded. We present the chemical file format converter NAOMI, which provides efficient procedures for reliable handling of molecules from the common chemical file formats SDF, MOL2, and SMILES. These procedures are based on a consistent chemical model which has been designed for the appropriate representation of molecules relevant in the context of drug discovery. NAOMI's functionality is tested by round robin file IO exercises with public data sets, which we believe should become a standard test for every cheminformatics tool.
Power and Energy Perspectives of Nonvolatile Memory Technologies (2010)

Discrete and embedded nonvolatile memory (NVM) technologies have been an integral part of electronic systems for the past 25 years. In recent years, the proliferation of personal media devices such as multimedia-enabled cell phones, personal music players, and digital cameras has accelerated the adoption of silicon-based solid state storage cards in consumer markets. Despite the expanded use of nonvolatile memory technologies in a variety of integrated systems, little has changed with respect to the core technology and cells that hold the data when power has been turned off. Today, floating gate (FG) or oxide-nitride-oxide trapped charge (ONO) cell structures dominate as the core technology behind all NVM devices and embedded blocks. All of the nonvolatile memory devices in production today based on these technologies require high voltage in excess of 5-8 V to operate primarily due to the fundamental nature of core cells and the physics of charge storage mechanisms. These are huge overvoltage requirements considering that the transistors in the logic block require substantially lower voltages (e.g., sub-65 nm logic CMOS operate at less than 1 V). Integrating such high-voltage operation in advanced logic processes such as 65 nm or below logic CMOS process is yet another challenge limiting the exploitation of NVM for low-power embedded applications. The high voltage requirement for operation of these core cells has put strains on the continued scaling of today's discrete and embedded NVM technologies. Furthermore, future ultralow-power and subthreshold CMOS applications such as energy starved electronics require operations at sub-500 mV which clearly set forth significant challenges in integrating today's NVM technologies as nonvolatile storage elements for such systems. Several emerging technologies are competing to become the building blocks of next-generation nonvolatile memory solutions. Each of these emerging technologies has unique characteristics in terms of physical scaling, voltage scaling, cost, performance, and power features which differ from today's FG and ONO based technologies. This paper reviews the fundamental characteristics of current nonvolatile memory technologies as well as several promising emerging technologies from energy and power perspectives and specifically discusses the suitability of each one for use in ultralow-power and subthreshold CMOS applications.
Identification of Distorted RF Components via Deep Multi-Task Learning (2022)

High-quality radio frequency (RF) components are imperative for efficient wireless communication. However, these components can degrade over time and need to be identified so that either they can be replaced or their effects can be compensated. The identification of these components can be done through observation and analysis of constellation diagrams. However, in the presence of multiple distortions, it is very challenging to isolate and identify the RF components responsible for the degradation. This paper highlights the difficulties of distorted RF components’ identification and their importance. Furthermore, a deep multi-task learning algorithm is proposed to identify the distorted components in the challenging scenario. Extensive simulations show that the proposed algorithm can automatically detect multiple distorted RF components with high accuracy in different scenarios.
Institut Pasteur and Satellite Institutes (2003)

Abstract The Institut Pasteur is a French private institution devoted to research in the biomedical sciences and a renowned postgraduate teaching institution. Its research focuses on microbes with emphasis on parasitic, bacterial and viral genomics and pathogenesis and host–microbe relationships; developmental biology and neurobiology are newer fields of research at the institute.
Antibiotics from Basidiomycetes. XXXI. Aleurodiscal: An antifungal sesterterpenoid from Aleurodiscus mirabilis (Berk. & Curt.) Hoehn. (1989)

Aleurodiscal, an antifungal antibiotic has been isolated from mycelial cultures of Aleurodiscus mirabilis (Berk. & Curt.) Höhn. It causes abnormal apical branchings of Mucor miehei hyphae at very low concentrations. The structure and absolute configuration of the antibiotic has been determined by a single crystal X-ray analysis and hydrolysis to D-(+)-xylose. Aleurodiscal is a hydroxysesterterpene aldehyde beta-D-xyloside with a novel carbon skeleton.
Relationship of large hepatitis B surface antigen polypeptide to human serum albumin (1980)

A significant proportion (20 to 40%) of highly purified 22-nm hepatitis B surface antigen (HBsAg) particles contain human serum albumin (HSA) as demonstrated by specific precipitation of radioiodinated particles by anti-HSA. Preparations of the isolated major HBsAg polypeptides (P-1, P-2, and P-6) were iodinated and analyzed by radiommunoprecipitation for reactivity with rabbit antisera to human plasma proteins. Only the P-6 fraction (molecular weight, 68,000) was precipitated and only by anti-HSA; specific precipitation was observed with guinea pig antisera to P-6 and native HBsAg and goat or rabbit antisera to HSA. Coprecipitation of P-6 with antiserum to HBsAg and with anti-HSA, compared to precipitation with each antiserum alone, indicated that the HBsAg and HSA determinants were on separate molecules. The P-6 polypeptide may represent a precursor protein of the hepatitis B virion.
Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells (2008)

We conclude that LSR may impair bladder cancer cells from gaining invasive properties.
Human interleukin 4 down‐regulates the surface expression of CD5 on normal and leukemic B cells (1989)

CD5 is a pan-T cell antigen which is expressed on a minor subset of normal B lymphocytes and on most chronic lymphocytic leukemia B cells (B-CLL). In this study, it is demonstrated that interleukin (IL) 4 down-regulates the surface expression of CD5 on tonsil B cells and B-CLL cells, but not on T cells. IL 4 inhibits both the spontaneous and the phorbol myristate acetate (PMA)-induced hyperexpression of CD5 on tonsil B cells. In contrast, IL 4 only suppresses the PMA-induced hyperexpression of CD5 on B-CLL, whereas the spontaneous CD5 expression is essentially unaffected. The IL 4 concentrations required to down-regulate CD5 are the same as those required to up-regulate CD23. The IL 4-mediated down-regulation of CD5 is an intrinsic property of this IL, since an anti-IL 4-neutralizing antiserum blocks this effect. Interferon (IFN)-gamma, which inhibits the IL 4 induced CD23 expression, does not block the IL 4-induced down-regulation of CD5. Recombinant IL 1 alpha, IL 2, IL 3, IL 5, IL 6, tumor necrosis factor (TNF)-alpha, IFN-gamma and granulocyte macrophage colony-stimulating factor neither inhibit nor stimulate CD5 expression on B cells, therefore suggesting that the capacity to down-regulate CD5 expression on B cells is specific to IL 4.
Supplementary Figure 3 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells (2023)

Supplementary Figure 3 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells
Effect of Chemical Solution on the Stability of Low-k Films (2005)

The compatibility of chemical solutions with different pH is studied on microporous silica-based (SiOCH) and mesoporous methylsilsesquioxane (MSQ) based low-k materials. The surface and bulk properties of as-deposited and O2/CF4 plasma-treated low-k films have been studied after several wet treatments.
Wavelet entropy based fault detection approach for MMC-HVDC lines (2015)

Since the grounding mode, line parameters, and thus the transient performance of MMC-HVDC are quite different from those of LCC-HVDC system and AC system, fault detection strategies used in LCC-HVDC are no longer applicable to MMC-HVDC. In this paper, a wavelet entropy based fault detection approach for MMC-HVDC is proposed to detect DC line faults and distinguish AC area fault. This method does not use the magnitude of the current but evaluate the wavelet entropy of the current signal to detect the fault. Firstly, the factors which affect fault transient performance of MMC-HVDC are analyzed. Then the wavelet entropy theory and its role in the detection of non-stationary signals are outlined. The proposed fault detection mechanism using wavelet energy entropy and wavelet time entropy to process fault current signals is described in detail. Finally, the computer simulations are carried out. The results show that the proposed method can detect the pole to ground fault and the pole to pole fault in MMC-HVDC accurately and can satisfy the time requirement.
The gadonanotubes: structural origin of their high-performance MRI contrast agent behavior (2013)

We present an X-ray absorption spectroscopy study of the local structure around the Gd<sup>3+</sup> ions loaded within ultra-short carbon nanotubes (US-tubes). For this material, called gadonanotubes (GNTs), detailed modeling and analyses of the X-ray absorption near edge structure (XANES) and extended fine structure (EXAFS) data have helped decipher the structural origin of their exceedingly high-performance MRI contrast agent behavior. Analysis revealed that the Gd<sup>3+</sup> ions are surrounded by ∼9 oxygen ions in the first coordination sphere with ∼3 O<sup>2-</sup> ions and ∼6 O<sup>2-</sup> ions, respectively, centered around 2.24 Å and 2.41 Å and that the Gd<sup>3+</sup>-ion sites in the GNTs are small. These sites are proton decorated once in solution through formation of the -(OH) and/or -(OH<sub>2</sub>) ligands. A large hydration number due to small Gd<sup>3+</sup>-ion sites and short Gd-O bonds, and thus short Gd-H distances, are the essential structural details pertinent to the high proton relaxivity observed for GNTs suspended in water.