gebhart/patrepeval huggingface dataset:
Long wavelength vertical-cavity semiconductor optical amplifiers (2001)

This paper overviews the properties and possible applications of long wavelength vertical-cavity semiconductor optical amplifiers (VCSOAs). A VCSOA operating in the 1.3-/spl mu/m wavelength region is presented. The device was fabricated using wafer bonding; it was optically pumped and operated in reflection mode. The reflectivity of the VCSOA top mirror was varied in the characterization of the device. Results are presented for 13 and 12 top mirror periods. By reducing the top mirror reflectivity, the amplifier gain, optical bandwidth, and saturation output power were simultaneously improved. For the case of 12 top mirror periods, rye demonstrate 13-dB fiber-to-fiber gain, 0.6 nm (100 GHz) optical bandwidth, a saturation output power of -3.5 dBm and a noise figure of 8.3 dB. The switching properties of the VCSOA are also briefly investigated. By modulating the pump laser, we have obtained a 46-dB extinction ratio in the output power, with the maximum output power corresponding to 7-dB fiber-to-fiber gain. All results are for continuous wave operation at room temperature.
A Noise Preserving Sharpening Filter for CT Image Enhancement (2022)

There is growing interest in employing deep neural networks (DNN) for image sharpening. However, sharpening medical computed tomography (CT) images is challenging because sharpening substantially amplifies high-frequency noise. Alternatively, sharpening algorithms that are also designed to denoise produce images lacking texture. Most importantly, radiologists strongly prefer reading images at a consistent level of noise. Hence it is preferable that a sharpening algorithm not substantially change the noise energy or texture.In this work, we propose a noise preserving sharpening filter (NPSF) to sharpen CT images while keeping the noise energy and texture in the result similar to that of the input. We achieve this by adding appropriately scaled noise while training. Furthermore, the NPSF is characterized by three user-adjustable parameters which give flexibility to achieve a desired level of sharpness and noise. Our experiments show that the NPSF can sharpen noisy images while producing desired noise level and texture.
Supplementary Figures 1-4, Supplementary Tables 1-4 from Immunization against HIF-1α Inhibits the Growth of Basal Mammary Tumors and Targets Mammary Stem Cells <i>In Vivo</i> (2023)

&lt;p&gt;Supplementary Table 1. Th1/Th2 for eleven epitopes derived from the HIF-1α protein; Supplementary Table 2. Number of tumorigenic implants in the Sca-1positive or Sca-1negative Population; Supplementary Table 3. Complete blood count (median and range) for the indicted immunization. n=4 mice/group; Supplementary Table 4. Serum chemistries (median and range) for the indicted immunization; Supplementary Figure 1. Sca-1positive cells exhibit several stem cell/EMT markers; Supplementary Figure 2. HIF-1α epitope-specific Th respond to naturally processed HIF-1α protein; Supplementary Figure 3. Sca-1positive cells have increased estrogen receptor-alpha (ER-α) gene expression; Supplementary Figure 4. The HIF-1α vaccine does not induce tissue toxicities.&lt;/p&gt;
Data from Rhabdoid Tumors Are Sensitive to the Protein-Translation Inhibitor Homoharringtonine (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Rhabdoid tumors are devastating pediatric cancers in need of improved therapies. We sought to identify small molecules that exhibit &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; efficacy against preclinical models of rhabdoid tumor.&lt;/p&gt;Experimental Design:&lt;p&gt;We screened eight rhabdoid tumor cell lines with 481 small molecules and compared their sensitivity with that of 879 other cancer cell lines. Genome-scale CRISPR–Cas9 inactivation screens in rhabdoid tumors were analyzed to confirm target vulnerabilities. Gene expression and CRISPR–Cas9 data were queried across cell lines and primary rhabdoid tumors to discover biomarkers of small-molecule sensitivity. Molecular correlates were validated by manipulating gene expression. Subcutaneous rhabdoid tumor xenografts were treated with the most effective drug to confirm &lt;i&gt;in vitro&lt;/i&gt; results.&lt;/p&gt;Results:&lt;p&gt;Small-molecule screening identified the protein-translation inhibitor homoharringtonine (HHT), an FDA-approved treatment for chronic myelogenous leukemia (CML), as the sole drug to which all rhabdoid tumor cell lines were selectively sensitive. Validation studies confirmed the sensitivity of rhabdoid tumor to HHT was comparable with that of CML cell lines. Low expression of the antiapoptotic gene &lt;i&gt;BCL2L1&lt;/i&gt;, which encodes Bcl-XL, was the strongest predictor of HHT sensitivity, and HHT treatment consistently depleted Mcl-1, the synthetic-lethal antiapoptotic partner of Bcl-XL. Rhabdoid tumor cell lines and primary-tumor samples expressed low &lt;i&gt;BCL2L1&lt;/i&gt;, and overexpression of &lt;i&gt;BCL2L1&lt;/i&gt; induced resistance to HHT in rhabdoid tumor cells. Furthermore, HHT treatment inhibited rhabdoid tumor cell line and patient-derived xenograft growth &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;Conclusions:&lt;p&gt;Rhabdoid tumor cell lines and xenografts are highly sensitive to HHT, at least partially due to their low expression of &lt;i&gt;BCL2L1&lt;/i&gt;. HHT may have therapeutic potential against rhabdoid tumors.&lt;/p&gt;&lt;/div&gt;
Laser-Induced Linear-Field Particle Acceleration in Free Space (2017)

Linear-field particle acceleration in free space (which is distinct from geometries like the linac that requires components in the vicinity of the particle) has been studied for over 20 years, and its ability to eventually produce high-quality, high energy multi-particle bunches has remained a subject of great interest. Arguments can certainly be made that linear-field particle acceleration in free space is very doubtful given that first-order electron-photon interactions are forbidden in free space. Nevertheless, we chose to develop an accurate and truly predictive theoretical formalism to explore this remote possibility when intense, few-cycle electromagnetic pulses are used in a computational experiment. The formalism includes exact treatment of Maxwell’s equations and exact treatment of the interaction among the multiple individual particles at near and far field. Several surprising results emerge. We find that electrons interacting with intense laser pulses in free space are capable of gaining substantial amounts of energy that scale linearly with the field amplitude. For example, 30 keV electrons (2.5% energy spread) are accelerated to 61 MeV (0.5% spread) and to 205 MeV (0.25% spread) using 250 mJ and 2.5 J lasers respectively. These findings carry important implications for our understanding of ultrafast electron-photon interactions in strong fields.
Structure-Based Characterization and Optimization of Novel Hydrophobic Binding Interactions in a Series of Pyrrolidine Influenza Neuraminidase Inhibitors (2005)

The structure-activity relationship (SAR) of a novel hydrophobic binding interaction within a subsite of the influenza neuraminidase (NA) active site was characterized and optimized for a series of trisubstituted pyrrolidine inhibitors modified at the 4-position. Previously, potent inhibitors have targeted this subsite with hydrophilic substituents such as amines and guanidines. Inhibitor-bound crystal structures revealed that hydrophobic substituents with sp(2) hybridization could achieve optimal interactions by virtue of a low-energy binding conformation and favorable pi-stacking interactions with the residue Glu119. From a lead methyl ester, investigation of five-membered heteroaromatic substituents at C-4 produced a 3-pyrazolyl analogue that improved activity by making a targeted hydrogen bond with Trp178. The SAR of substituted vinyl substituents at C-4 produced a Z-propenyl analogue with improved activity over the lead methyl ester. The C-1 ethyl ester prodrugs of the substituted C-4 vinyl analogues gave compounds with excellent oral bioavailability (F > 60%) when dosed in rat.
Abstract 166: MicroRNA profiling analysis identify new signature of tumor-promoting M2-type macrophages (2011)

Abstract M2-type macrophages are a major inflammatory component in prostate cancer and are associated with cancer cell growth, survival, and metastasis. Since recent findings have demonstrated the importance of microRNAs in the differentiation of human cells, we hypothesize that microRNAs are involved in regulating monocytic differentiation into M2-type macrophages and we aim to identify the microRNAs involved. Methods: Human CD14+ PBMCs were isolated from healthy donors and stimulated with cytokines known to promote differentiation into the M2-type macrophages (IL4, IL13, IL6, and MCSF). As controls, we also treated cells with media only and with INFγ, a cytokine known to promote M1-type polarization. Cells were collected at 48 hours post-stimulation and sent for microRNA profiling by microarray. Microarray findings were then confirmed by qRT-PCR. Results: Microarray profiling of cytokine-stimulated M2-type macrophages demonstrated an altered miRNA expression compared to M1-type macrophages and untreated monocytic cells. Specifically, of the 858 microRNAs that were profiled, miR-135a, miR-193b, miR-203, miR-302, miR-375, miR-452, miR-511, miR-603, miR-622, miR-654, miR-938 and miR-1238 were found to be up-regulated by greater than 2 folds. Furthermore, qRT-PCR analysis confirmed the microarray results. When the qRT-PCR analysis was repeated for cells treated with cytokines for 6 hours, 18 hours and 24 hours, we noticed that the overexpression in these microRNAs could already be observed at 6 hours post-treatment, although the expression levels were noticeably greater at later timepoints. Flow cytometric analysis showed the surface expression of CD206 (mannose receptor: the well characterized surface marker of M2-type macrophages) in both MCSF and IL-4-treated cells but only after at least 18 hours of stimulation. Conclusions: MicroRNA expression in PBMCs is altered when they are stimulated by M2-type promoting cytokines and the change in microRNA expression preceded the expression of the M2-specific CD206 surface marker. This change in microRNA expression can therefore be used as a marker for M2-polarized macrophages and may play critical roles in the regulation of macrophage differentiation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 166. doi:10.1158/1538-7445.AM2011-166
Serologic analysis of human tumor antigens. II. Reactivity of sera from eleven osetogenic sarcoma patients against autologous and allogeneic tumor cells. (1979)

Sera from eleven patients bearing osteogenic sarcomas were tested for reactivity against autologous and allogeneic normal and tumor cells using a sensitive microcytotoxicity assay. Following absorption with human fetal tissue cultured lines, sera from all 11 patients lost reactivity to autologous and allogeneic normal fibroblasts in culture. However, sera from four patients retained reactivity against both autologous and allogeneic osteogenic sarcoma, sera from five patients retained reactivity to allogeneic but not autologous tumor, and sera from two patients lost all reactivity to tumor. Sera from nine normal individuals did not react with either normal or osteogenic sarcoma cells after fetal cell absorption. Thus it appears that nine of 11 patients bearing osteogenic sarcoma contained antibody to a common tumor-associated antigen. This tumor-associated antigen appears to be expressed on tumor cells and not normal cultured cells, and reactivity to it is present in tumor-bearing but not normal individuals.
ANTICANCER ACTIVITY OF SOME MEDICINAL PLANTS FROM HIGH ALTITUDE EVERGREEN ELEMENTS OF INDIAN WESTERN GHATS (2007)

Traditional medicine has a long history of serving peoples all over the world. India is without doubt a herbal hub. Medicinal plants that are native to India and their use in various traditional systems of medicine are indeed awe-inspiring. The ethnobotany and ubiquitous plants provide a rich resource for natural drug research and development. In recent years, the use of traditional medicine information on plant research received considerable interest. In the present study, twenty one plant extracts of different species used by Indian traditional healers for the treatment of ulcers, cancers, tumors, warts, and other diseases, were tested in vitro for their potential anticancer (antiproliferative and cytotoxic) activity. The ethanolic extracts were tested against six human cancer cell lines using MTT 3-(4,5-dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide. colorimetric assay and the cytotoxicity was confirmed by Soft agar colony forming 'Clonogenic assay'. Seven out of the 21 extracts (33%) showed remarkable cytotoxic potential. The highest activity was found in the leaf/stem ethanol extracts from Plectranthus urticioides and Garcinea morella against all the six human cancer cell lines screened. The present finding may pave the way for the bioactivity guided fractionation and isolation of important moieties for the anticancer chemotherapy and in part help to minimize the serious lacuna in scientific validation of these herbs.
New organic nitrates. I. Synthesis of 1,3‐benzoxazine‐2,4‐dione, 1,3‐benzoxazine‐2‐thion‐4‐one, 1,3‐benzothiazine‐2,4‐dione and quinazoline‐2,4‐dione derivatives (1994)

Abstract The preparation and the physico‐chemical characterization of new heterocyclic organic nitrates containing 1,3‐benzoxazine‐2,4‐dione, 1,3‐benzoxazine‐2‐thion‐4‐one, 1,3‐benzothiazine‐2,4‐dione and quinazo‐line‐2,4‐dione moieties, are reported.
Microwave Plasma Synthesis of Nanostructured γ‐Al 2 O 3 Powders (2003)

Nanostructured Al 2 O 3 powders have been synthesized by combustion of aluminum powder in a microwave oxygen plasma, and characterized by X‐ray diffraction and electron microscopy. The main phase is γ‐Al 2 O 3 , with a small amount of δ‐Al 2 O 3 . The particles are truncated octahedral in shape, with mean particle sizes of 21–24 nm. The effect of reaction chamber pressure on the phase composition and the particle size was studied. The γ‐alumina content increases and the mean particle size decreases with decreasing pressure. No α‐Al 2 O 3 appears in the final particles. Electron microscopy studies find that a particle may contain more than one phase.
A Cell-to-Cell Battery Equalizer With Zero-Current Switching and Zero-Voltage Gap Based on Quasi-Resonant <italic>LC</italic> Converter and Boost Converter (2014)

In conventional equalizers, the facts of bulky size and high cost are widespread. Particularly, the zero-switching loss and zero-voltage gap (ZVG) between cells are difficult to implement due to the high-frequency hard switching and the voltage drop across power devices. To overcome these difficulties, a direct cell-to-cell battery equalizer based on quasi-resonant LC converter (QRLCC) and boost dc-dc converter (BDDC) is proposed. The QRLCC is employed to gain zero-current switching, leading to a reduction of power losses. The BDDC is employed to enhance the equalization voltage gap for large balancing current and ZVG between cells. Moreover, through controlling the duty cycle of the BDDC, the topology can online adaptively regulate the equalization current according to the voltage difference, which not only effectively prevents overequalization but also abridges the overall balancing time. Instead of a dedicated equalizer for each cell, only one balancing converter is employed and shared by all cells, reducing the size and implementation cost. Simulation and experimental results show the proposed scheme exhibits outstanding balancing performance, and the energy conversion efficiency is higher than 98%. The validity of the proposed equalizer is further verified by a quantitative and systematic comparison with the existing active balancing methods.
The chromatin accessibility signature of human immune aging stems from CD8+ T cells (2017)

Aging is linked to deficiencies in immune responses and increased systemic inflammation. To unravel the regulatory programs behind these changes, we applied systems immunology approaches and profiled chromatin accessibility and the transcriptome in PBMCs and purified monocytes, B cells, and T cells. Analysis of samples from 77 young and elderly donors revealed a novel and robust aging signature in PBMCs, with simultaneous systematic chromatin closing at promoters and enhancers associated with T cell signaling and a potentially stochastic chromatin opening mostly found at quiescent and repressed sites. Combined analyses of chromatin accessibility and the transcriptome uncovered immune molecules activated/inactivated with aging and identified the silencing of the <i>IL7R</i> gene and the IL-7 signaling pathway genes as potential biomarkers. This signature is borne by memory CD8<sup>+</sup> T cells, which exhibited an aging-related loss in binding of NF-κB and STAT factors. Thus, our study provides a unique and comprehensive approach to identifying candidate biomarkers and provides mechanistic insights into aging-associated immunodeficiency.
Violacein-Induced Chaperone System Collapse Underlies Multistage Antiplasmodial Activity (2021)

Antimalarial drugs with novel modes of action and wide therapeutic potential are needed to pave the way for malaria eradication. Violacein is a natural compound known for its biological activity against cancer cells and several pathogens, including the malaria parasite, <i>Plasmodium falciparum</i> (Pf). Herein, using chemical genomic profiling (CGP), we found that violacein affects protein homeostasis. Mechanistically, violacein binds <i>Pf</i> chaperones, <i>Pf</i>Hsp90 and <i>Pf</i>Hsp70-1, compromising the latter's ATPase and chaperone activities. Additionally, violacein-treated parasites exhibited increased protein unfolding and proteasomal degradation. The uncoupling of the parasite stress response reflects the multistage growth inhibitory effect promoted by violacein. Despite evidence of proteotoxic stress, violacein did not inhibit global protein synthesis via UPR activation-a process that is highly dependent on chaperones, in agreement with the notion of a violacein-induced proteostasis collapse. Our data highlight the importance of a functioning chaperone-proteasome system for parasite development and differentiation. Thus, a violacein-like small molecule might provide a good scaffold for development of a novel probe for examining the molecular chaperone network and/or antiplasmodial drug design.
Topologically Constrained Manganese(III) and Iron(III) Complexes of Two Cross-Bridged Tetraazamacrocycles (2001)

A family of Mn3+ and Fe3+ complexes of 4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane (1) and 4,10-dimethyl-1,4,7,10-tetraazabicyclo[5.5.2]tetradecane (2) has been prepared by the chemical oxidation of the divalent manganese and iron analogues. The ligands are ethylene cross-bridged tetraazamacrocycles derived from cylam and cyclen, respectively. The synthesis and characterization of these complexes, including X-ray crystal structure determinations, are described. The structural evidence demonstrates that the tetradentate ligands enforce distorted octahedral geometries on the metal ions, with two cis sites occupied by labile ligands. Magnetic measurements reveal that the complexes are high spin with typical magnetic moments. Cyclic voltammetry shows reversible redox processes for the Fe3+/Fe2+ couples of the iron(III) complexes, while Mn3+/Mn2+ and Mn4+/Mn3+ couples were observed for the complexes with manganese(III). The manganese chemistry of 1 was studied in depth. The dichloro manganese(III) cation of 1 undergoes facile ligand substitution reactions at the labile, monodentate sites, for example substituting azide for chloride ligands. Air oxidation of the dichloro complex of Mn (1)2+ in basic solution does not give the expected mu-oxo dimeric product common to manganese. Instead, an unusual manganese(III)-OH complex has been isolated from this reaction and structurally characterized. A similar reaction under slightly different conditions gives a putative MnIII(OH)2 complex that metathesizes to MnIII(OMe)2 upon recrystallization from methanol.
Micromirror-based Scan Range Enhancement in Fourier-Domain Optical Coherence Tomography (2006)

This paper reports on a micromirror-based superresolution technique that can increase the depth scan range of Fourier-domain optical coherence tomography by improving the spectral resolution of grating-based spectrometers with pixelated image sensors
Intraparenchymal drug delivery via positive-pressure infusion: experimental and modeling studies of poroelasticity in brain phantom gels (2002)

We have used agarose gel to develop a robust model of the intraparenchymal brain tissues for the purpose of simulating positive-pressure infusion of therapeutic agents directly into the brain. In parallel with that effort, we have synthesized a mathematical description of the infusion process on the basis of a poroelastic theory for the swelling of the tissues under the influence of the infusate's penetration into the interstitial space. Infusion line pressure measurements and video microscopy determinations of infusate volume of distribution within the gel demonstrate a good match between theory and experiment over a wide range of flow rates (0.5-10.0 microliters/min) and have clinical relevance for the convection-enhanced delivery of drugs into the brain without hindrance by the blood-brain barrier. We have put the brain phantom gel and the infusion measurement system into routine use in determining performance characteristics of novel types of neurosurgical catheters. This approach simplifies the catheter design process and helps to avoid some of the costs of in vivo testing. It also will allow validation of the elementary aspects of treatment planning systems that predict infusion distribution volumes on the basis of theoretical descriptions such as those derived from the poroelastic model.
Microwave-Assisted Synthesis of Medicinally Relevant Indoles (2011)

Indoles represent an important structural class in medicinal chemistry with broad spectrum of biological activities. The synthesis of indoles, therefore, has attracted enormous attention from synthetic chemists. Microwave methods for the preparation of indole analogs have been developed to speed up the synthesis, therefore, microwave assisted organic synthesis (MAOS) in controlled conditions is an invaluable technique for medicinal chemistry. In this review, indole forming classical reactions such as Fischer, Madelung, Bischler-Mohlau, Batcho-Leimgruber, Hemetsberger-Knittel, Graebe-Ullmann, Diels-Alder and Wittig type reactions using microwave radiation has been summarized. In addition, metal mediated cyclizations along with solid phase synthesis of indoles have been discussed.
Field-theoretic simulations of block copolymers : design and solvent annealing. (2012)

Abstract Not Provided