gebhart/patrepeval huggingface dataset:
The Broad Spectrum HDAC Inhibitor PCI-24781 Induces Caspase- and ROS-Dependent Apoptosis and is Synergistic with Bortezomib in Lymphoma (2008)

Abstract We investigated the cytotoxicity and biology of the novel broad-spectrum hydroxamic acid-based histone deacetylase inhibitor (HDACi), PCI-24781. PCI-24781 was studied alone and combined with bortezomib in Hodgkin lymphoma (L428) and non-Hodgkin's lymphoma cell lines (Ramos, HF1, SUDHL4). PCI-24781 induced dose-dependent apoptosis that was associated with prominent G0/G1 arrest, decreased S-phase, increased p21 protein expression, and production of reactive oxygen species (ROS). Furthermore, PCI-24781-induced apoptosis was shown to be ROS- and caspase-dependent. Combined PCI-24781 and bortezomib exposure resulted in strong synergistic apoptosis in all cell lines (combination indices 0.19-0.6). Furthermore, compared to either agent alone, PCI-24781/bortezomib resulted in increased caspase cleavage, mitochondrial depolarization, and histone hyperacetylation. Microarray analyses showed that PCI-24781 alone significantly downregulated several antioxidant genes, proteasome components, and NF-kappaB pathway genes, effects which were enhanced further with bortezomib. RT-PCR confirmed downregulation of NF-kappaB targets NF-kappaB1 (p105), c-Myc, and IkappaB-kinase subunits, while gel-shift showed decreased NF-kappaB DNA-binding activity. Taken together, these results suggest that increased oxidative stress and NF-kappaB inhibition, leading to caspase activation and apoptosis, are likely responsible for the activity of PCI-24781 as well as the observed synergy with bortezomib. These data indicate that PCI-24781 has potential therapeutic value in lymphoma as a single-agent and combined with bortezomib.
Impact of type 2 targeting biologics on acute exacerbations of chronic rhinosinusitis (2021)

<b>Background:</b> Acute exacerbations of chronic rhinosinusitis (AECRS) are associated with significant morbidity and decreased quality of life. There are sparse data assessing the real-world impact of biologics on AECRS. <b>Objectives:</b> We sought to determine the impact of type 2-targeting biologics on the frequency of medication use for AECRS episodes. <b>Methods:</b> Antibiotic and/or systemic corticosteroid courses for AECRS were identified in a retrospective study from November 2015 to February 2020, at a single academic health system. The estimated yearly rates for antibiotic and corticosteroid courses were evaluated before and after initiation of type 2 biologics. <b>Results:</b> One-hundred and sixty-five patients with chronic rhinosinusitis (CRS) had received either omalizumab (n = 12), mepolizumab (n = 42), benralizumab (n = 44), dupilumab (n = 61), or reslizumab (n = 6). Seventy percent had CRS with nasal polyps, and 30% had CRS without nasal polyps. All the patients had asthma. When all the biologics were combined, the estimated yearly rate for antibiotics for AECRS decreased from 1.34 (95% confidence interval [CI], 1.12-1.59) to 0.68 (95% CI, 0.52-0.88) with biologic use (49% reduction, <i>p</i> < 0.001). Those with frequent AECRS (three or more courses of antibiotics in the 1 year before biologic use) had a larger degree of reduction, with an estimated yearly rate of 4.15 (95% CI, 3.79-4.55) to 1.58 (95% CI, 1.06-2.35) with biologic use (n = 27; 62% reduction; p < 0.001). Within the total cohort, the estimated yearly rate for systemic corticosteroids for AECRS decreased from 1.69 (95% CI, 1.42-2.02) to 0.68 (95% CI, 0.53-0.88) with biologic use (60% reduction; p < 0.001). <b>Conclusion:</b> Type 2-targeting biologics reduced medication use for AECRS. This suggested that biologics may be a therapeutic option for patients with frequent AECRS.
Table S1 from PD-1 Blockade and CD27 Stimulation Activate Distinct Transcriptional Programs That Synergize for CD8<sup>+</sup> T-Cell–Driven Antitumor Immunity (2023)

&lt;p&gt;List of genes represented in the heatmap&lt;/p&gt;
Identification and Control of Taylor-Go-yen;rtler Vortices in Turbulent Curved Channel Flow (2003)

Direct numerical simulations of turbulent flows in a curved channel are performed. The drifting Taylor-Gortler vortices are identified by applying a conditional averaging. A new algorithm is proposed for identifying the drifting Taylor-Gortler vortices based on the wavelet transform of wall information. A continuous wavelet transform with Marr wavelets is employed to decompose the flow signals at a chosen length scale. An active cancellation is applied to attenuate the Taylor-Gortler vortices and to reduce the wall skin friction
Intranephron distribution of creatine content in rats. (1994)

Creatine is a high energy phosphate donor and play an important role not only in muscle contraction, but also in buffering intracellular energy storage. In this study, we have identified the creatine content in microdissected nephron segments with an ultramicromethod. All nephron segments tested contained creatine, however the distribution was not uniform. Glomerulus, cortical thick ascending limb of Henle's loop and distal tubule possessed comparatively large amounts of creatine when calculated as pM/micrograms tissue protein. When calculation was made as pM/mm tubule length, the first segment of the proximal tubule and the distal tubule were the highest. These results suggest the existence of heterogeneity in creatine content along the nephron as one of the biochemical characteristics in individual nephron segments.
Hyaluronic Acid Conjugates as Vectors for the Active Targeting of Drugs, Genes and Nanocomposites in Cancer Treatment (2014)

Hyaluronic acid (HA) is a naturally-occurring glycosaminoglycan and a major component of the extracellular matrix. Low levels of the hyaluronic acid receptor CD44 are found on the surface of epithelial, hematopoietic, and neuronal cells; it is overexpressed in many cancer cells, and in particular in tumor-initiating cells. HA has recently attracted considerable interest in the field of developing drug delivery systems, having been used, as such or encapsulated in different types of nanoassembly, as ligand to prepare nano-platforms for actively targeting drugs, genes, and diagnostic agents. This review describes recent progress made with the several chemical strategies adopted to synthesize conjugates and prepare novel delivery systems with improved behaviors.
Effects of ionizing radiation on deoxyribonucleic acid and related systems. Part 1. The rôle of oxygen (1984)

Exposure of aqueous solutions of calf-thymus DNA to 60Co γ-rays at 77 K results in the formation of equal yields of G+ and T– centres, detected by e.s.r. spectroscopy. In the presence of oxygen, O2– ions are also formed at the expense of T–, the primary yield of G+ centres being unaffected. On annealing above 77 K the e.s.r. features for O2– ions were initially modified as a result of changes in solvation, and then, at ca. 193 K, they were lost irreversibly. A large growth in signals due to RO2· radicals was observed simultaneously. These radicals are formed from T– anions or the protonated form, TH, and probably also indirectly from G+ radicals. In parallel experiments, under comparable conditions, we have analysed for single and double stand breaks using plasmid DNA (pBR 322). Both single and double strand breaks persist under conditions in which G+ and T– are the only detectable primary radical products. The presence of oxygen causes only a slight increase in damage to DNA.
Poster abstract (2010)

Wireless multicast is an important service primitive for emerging applications such as live video, streaming audio and content telecasts. Transmission rate in such a link layer multicast is bottlenecked by the rate of the weakest client, leading to channel under-utilization. Attempts to increase the data rate results in lower reliability (due to higher bit error rate) and higher unfairness. This poster utilizes smart beamforming antennas to improve multicast performance in wireless LANs. The main idea is to satisfy majority of the (strong) clients with a high-rate omnidirectional transmission, followed by high-rate directional transmission(s) to cover the weaker ones. By selecting an optimal transmission strategy, we show that the multicast throughput can be maximized while achieving a desired delivery ratio at all the clients. We use testbed measurements to verify our main assumptions. We simulate our protocol in Qualnet, and observe consistent performance improvements over a wide range of client topologies and time-varying channel conditions.
Reactive astrocytes secrete lcn2 to promote neuron death (2013)

Glial reaction is a common feature of neurodegenerative diseases. Recent studies have suggested that reactive astrocytes gain neurotoxic properties, but exactly how reactive astrocytes contribute to neurotoxicity remains to be determined. Here, we identify lipocalin 2 (lcn2) as an inducible factor that is secreted by reactive astrocytes and that is selectively toxic to neurons. We show that lcn2 is induced in reactive astrocytes in transgenic rats with neuronal expression of mutant human TAR DNA-binding protein 43 (TDP-43) or RNA-binding protein fused in sarcoma (FUS). Therefore, lcn2 is induced in activated astrocytes in response to neurodegeneration, but its induction is independent of TDP-43 or FUS expression in astrocytes. We found that synthetic lcn2 is cytotoxic to primary neurons in a dose-dependent manner, but is innocuous to astrocytes, microglia, and oligodendrocytes. Lcn2 toxicity is increased in neurons that express a disease gene, such as mutant FUS or TDP-43. Conditioned medium from rat brain slice cultures with neuronal expression of mutant TDP-43 contains abundant lcn2 and is toxic to primary neurons as well as neurons in cultured brain slice from WT rats. Partial depletion of lcn2 by immunoprecipitation reduced conditioned medium-mediated neurotoxicity. Our data indicate that reactive astrocytes secrete lcn2, which is a potent neurotoxic mediator.
Total aberrations compensation in digital holographic microscopy with a reference conjugated hologram (2006)

In this paper we present a new method to achieve quantitative phase contrast imaging in Digital Holographic Microscopy (DHM) that allows to compensate for phase aberrations and image distortion by recording of a single reference hologram.We demonstrate that in particular cases in which the studied specimen does not have abrupt edges, the specimen's hologram itself can be used as reference hologram. We show that image distortion and phase aberrations introduced by a lens ball used as microscope objective are completely suppressed with our method. Finally the concept of self-conjugated reference hologram is applied on a biological sample (Trypanosoma Brucei) to maintain a spatial phase noise level under 3 degrees.
Through-The-Coating Fabrication of Fiber Bragg Grating Relative Humidity Sensors Using Femtosecond Pulse Duration Infrared Lasers and a Phase Mask (2023)

Fiber Bragg grating (FBG) relative humidity (RH) sensors are fabricated in commercially available polyimide (PI)-coated optical fibers with diameters of 50 and 125 μm. Infrared (800 nm) femtosecond pulse duration laser pulses and a phase mask are used to inscribe Type-I and Type-II FBGs directly through the protective polyimide coatings of both 50 and 125 μm diameter fibers without typical fiber processing such as hydrogen loading, cryogenic storage, stripping, recoating or annealing. The devices are then evaluated for their performance as humidity sensors. At telecom wavelengths, the 50 μm diameter fiber devices with a 10 μm thick PI coating had a wavelength shift of the Bragg resonance at a constant temperature of 2.7 pm/%RH, whereas the 125 μm diameter fiber devices with a 17 μm thick PI coating had a wavelength shift of 1.8 pm/%RH. The humidity sensors in the 50 µm diameter fiber demonstrated a more rapid response time to small changes in humidity and a weaker hysteresis when compared to the 125 µm diameter fiber devices. No modification to the PI coatings was observed during fabrication. No difference in RH sensitivity was observed for Type-I devices when compared with Type-II devices with the same fiber. The applicability of this approach for fabricating distributed RH sensing arrays with hundreds of sensing elements on a single fiber is discussed.
Steady state anisotropy two-photon microscopy resolves multiple, spectrally similar fluorophores, enabling in vivo multilabel imaging (2014)

The use of spectrally distinguishable fluorescent dyes enables imaging of multiple targets. However, in two-photon microscopy, the number of fluorescent labels with distinct emission spectra that can be effectively excited and resolved is constrained by the confined tuning range of the excitation laser and the broad and overlapping nature of fluorophore two-photon absorption spectra. This limitation effectively reduces the number of available imaging channels. Here, we demonstrate that two-photon steady state anisotropy imaging (2PSSA) offers the capability to resolve otherwise unresolvable fluorescent tracers both in live cells and in mouse tumor models. This approach expands the number of biological targets that can be imaged simultaneously, increasing the total amount of information that can be obtained through imaging.
Geometry Manipulation by Automatic Parameterization (GMAP) (2008)

The GMAP Mesh application is a program for parameterizing and morphing engineering analysis models using a simple abstraction called Morphing Tools. Morphing Tools allow complex geometry changes to be boiled down to a few simple design variables, allowing analysis models to be modified with ease in a parametric trade study or optimization study. Using GMAP Mesh allows one to set up multidisciplinary optimization systems that are completely automated once they have been started, providing time savings over systems that require a “man in the loop.”
AlGaN-Free Blue III–Nitride Laser Diodes Grown onc-Plane GaN Substrates (2010)

We report on the fabrication of InGaN-based multiple-quantum-well laser diodes (LDs) emitting at 420 nm. Structures with standard claddings (p-and n-AlGaN), asymmetric claddings (p-GaN and n-AlGaN), and AlGaN-free claddings were grown by metal organic vapor phase epitaxy on polar c-plane free-standing GaN substrates. Electrical and optical properties of each LD are presented. Thanks to an optimized design of the InGaN waveguide and active region, cw lasing of a completely AlGaN-free laser diode is demonstrated, with a threshold current density &lt; 5 kA/cm(2) and a differential efficiency per facet of similar to 0.4 W/A without high-reflection coatings. (c) 2010 The Japan Society of Applied Physics
Effective induction of protective systemic immunity with nasally administered vaccines adjuvanted with IL-1 (2021)

IL-1α and IL-1β were evaluated for their ability to provide adjuvant activity for the induction of serum antibody responses when nasally-administered with protein antigens in mice and rabbits. In mice, intranasal (i.n.) immunization with pneumococcal surface protein A (PspA) or tetanus toxoid (TT) combined with IL-1β induced protective immunity that was equivalent to that induced by parenteral immunization. Nasal immunization of awake (i.e., not anesthetized) rabbits with IL-1-adjuvanted vaccines induced highly variable serum antibody responses and was not as effective as parenteral immunization for the induction of antigen-specific serum IgG. However, i.n. immunization of deeply anesthetized rabbits with rPA + IL-1α consistently induced rPA-specific serum IgG ELISA titers that were not significantly different than those induced by intramuscular (IM) immunization with rPA + alum although lethal toxin neutralizing titers induced by nasal immunization were lower than those induced by IM immunization. Gamma scintigraphy demonstrated that the enhanced immunogenicity of nasal immunization in anesthetized rabbits correlated with an increased nasal retention of i.n. delivered non-permeable radio-labeled colloidal particles. Our results demonstrate that, in mice, IL-1 is an effective adjuvant for nasally-administered vaccines for the induction of protective systemic immunity and that in non-rodent species, effective induction of systemic immunity with nasally-administered vaccines may require formulations that ensure adequate retention of the vaccine within the nasal cavity.
Destruction of a first-order transition by dimensional crossover (1981)

The q=3-state Potts model undergoes a first-order transition in three dimensions, and a continuous one in two dimensions. For a system of finite thickness L, the transition will be either first order (for L>Lx) or continuous (for L<Lx). For some particular thickness Lx, the tricritical three-state Potts behaviour is obtained. An experimental system is proposed for which an external magnetic field plays the role of temperature, and physical temperature in turn corresponds to variation of the effective thickness. The system may provide the first experimental values for three-state Potts tricritical exponents in two dimensions.
Model-driven Design (2015)

DNA reveals the past, and predicts the future. Get used to it, learn how to read it, and use it practically– Henrik Wegener
Plant Lectin Can Target Receptors Containing Sialic Acid, Exemplified by Podoplanin, to Inhibit Transformed Cell Growth and Migration (2012)

Cancer is a leading cause of death of men and women worldwide. Tumor cell motility contributes to metastatic invasion that causes the vast majority of cancer deaths. Extracellular receptors modified by α2,3-sialic acids that promote this motility can serve as ideal chemotherapeutic targets. For example, the extracellular domain of the mucin receptor podoplanin (PDPN) is highly O-glycosylated with α2,3-sialic acid linked to galactose. PDPN is activated by endogenous ligands to induce tumor cell motility and metastasis. Dietary lectins that target proteins containing α2,3-sialic acid inhibit tumor cell growth. However, anti-cancer lectins that have been examined thus far target receptors that have not been identified. We report here that a lectin from the seeds of Maackia amurensis (MASL) with affinity for O-linked carbohydrate chains containing sialic acid targets PDPN to inhibit transformed cell growth and motility at nanomolar concentrations. Interestingly, the biological activity of this lectin survives gastrointestinal proteolysis and enters the cardiovascular system to inhibit melanoma cell growth, migration, and tumorigenesis. These studies demonstrate how lectins may be used to help develop dietary agents that target specific receptors to combat malignant cell growth.
microRNA-221 and microRNA-18a identification in stool as potential biomarkers for the non-invasive diagnosis of colorectal carcinoma (2014)

Stool-based miR-221 can be used as a non-invasive biomarker for the detection of CRC.
Supplementary Figures S1-S7 from Single-Cell Analysis Reveals a Preexisting Drug-Resistant Subpopulation in the Luminal Breast Cancer Subtype (2023)

&lt;p&gt;Figure S1. Schematic representation of workflow for single-cell isolation and sc-qPCR. Figure S2. Violin plot of each individual gene expression along drug resistance acquisition. Figure S3. Correlation of several genes expressed at the single-cell level, separated by cell type as represented by the color of each dot. Figure S4. Lef1, Vim and Cav1 protein expression in several Luminal breast cancer cell lines. Figure S5. Larger visual fields showing immunostaining in tissue samples. Figure S6. Clinical information regarding the role of Lef1 in stained tissue samples. Figure S7. Comparison of Lef1 protein levels in MCF7 and derivatives.&lt;/p&gt;
Proposal for nanoscale cascaded plasmonic majority gates for non-Boolean\n computation (2017)

Surface-plasmon-polariton waves propagating at the interface between a metal\nand a dielectric, hold the key to future high-bandwidth, dense on-chip\nintegrated logic circuits overcoming the diffraction limitation of photonics.\nWhile recent advances in plasmonic logic have witnessed the demonstration of\nbasic and universal logic gates, these CMOS oriented digital logic gates cannot\nfully utilize the expressive power of this novel technology. Here, we aim at\nunraveling the true potential of plasmonics by exploiting an enhanced native\nfunctionality - the majority voter. Contrary to the state-of-the-art plasmonic\nlogic devices, we use the phase of the wave instead of the intensity as the\nstate or computational variable. We propose and demonstrate, via numerical\nsimulations, a comprehensive scheme for building a nanoscale cascadable\nplasmonic majority logic gate along with a novel referencing scheme that can\ndirectly translate the information encoded in the amplitude and phase of the\nwave into electric field intensity at the output. Our MIM-based 3-input\nmajority gate displays a highly improved overall area of only 0.636 {\\mu}m$^2$\nfor a single-stage compared with previous works on plasmonic logic. The\nproposed device demonstrates non-Boolean computational capability and can find\ndirect utility in highly parallel real-time signal processing applications like\npattern recognition.\n
A Desymmetrization Approach to the Enantiopure syn/anti‐1,5‐Diols via Hydrolytic Kinetic Resolution (HKR) of Functionalized meso‐Bis‐Epoxides: Further Elaboration to syn/syn‐1,3,5‐Triols and Application to the Formal Synthesis of Cryptocarya Diacetate (2013)

Abstract A new approach has been developed for the synthesis of enantiopure syn / anti ‐1,5‐diols by desymmetrization of functionalized meso ‐bis‐epoxides using hydrolytic kinetic resolution (HKR). The usage of this protocol was demonstrated by converting syn ‐1,5‐diols into syn / syn ‐1,3,5‐triols and its subseqent application to the formal synthesis of cryptocarya diacetate.
A Novel Electrolyte for the Sodium/Iron Chloride Battery (1991)

In this study, a low melting temperature organic chloroaluminate salt was mixed with AlCl 3 -NaCl to form a low melting temperature mixture. The organic chloroaluminate salt utilized was a mixture of AlCl 3 and 1-methyl-3-ethylimidazolium chloride (MEICl), resulting in AlCl 3 -MEICl. The electrolyte for this investigation is a combination of AlCl 3 -NaCl and AlCl 3 -MEICl salts, resulting in the ternary AlCl 3 -MEICl-NaCl system