gebhart/patrepeval huggingface dataset:
Structural features of CD4 required for binding to HIV. (1989)

A soluble form of the human CD4 glycoprotein (sCD4), the cellular receptor for human HIV, was treated with various physical, chemical, and enzymic regimens and tested over a range of concentrations for its capacity to inhibit the binding of HIV to CD4+ T cells. Reduction of disulfide bonds and alkylation in denaturing buffer (8 M urea) destroyed the inhibitory activity of sCD4, whereas reduction and alkylation in PBS had no effect. Derivatization or digestion of carbohydrate groups by periodate oxidation or by glycolytic enzyme digestion did not affect sCD4 inhibitory capacity. Digestion with trypsin or endoproteinase Glu-C destroyed activity. A limited digestion of sCD4 with endoproteinase Glu-C resulted in a mixture of fragments, however, and the mixture had inhibitory activity equivalent to that of intact sCD4. Within this mixture, a fragment of 23 kDa was identified that binds to HIV. Although sCD4 can be digested to yield fully active fragments, the requirement for intrachain disulfide bonding indicates that the minimum sized portion of CD4 that will retain full affinity for HIV will have to be formulated with a proper tertiary structure.
Abstract B27: Epigenetic regulation of stem cell fate in leukemic subpopulations. (2015)

Abstract Leukemia often displays substantial intratumor heterogeneity, comprising subpopulations of cells with different self-renewing and leukemia initiation capacities. Epigenetic mechanisms have been implicated in stem cell fate regulation during normal hematopoiesis. Although aberrant epigenetic changes have been well documented in hematological malignancies, the role epigenetic mechanisms play in governing stem-like properties, such as leukemia initiating capacity, and possible cell fate transitions between stem-like and non-stem-like leukemia subpopulations is unclear. Using next-generation sequencing and microarray technologies, we conducted an integrated analysis of DNA methylation, histone modifications and transcriptional profiles to investigate the epigenomic differences between experimentally characterized CD34-positive (CD34pos) leukemia-initiating and CD34-negative (CD34neg) non-leukemia-initiating subpopulations in a human acute myelogenous leukemia (AML) cell line. We demonstrated that multiple normal and leukemic stem cell gene signatures are significantly enriched in CD34pos leukemia initiating cells as opposed to CD34neg AML cells. We also observed concordant chromatin state transitions at the promoters of stem cell signature genes. The stem-like state of CD34pos leukemia initiating cells is also characterized by a number of genes with bivalent histone modifications at their promoters. Many genes undergoing bivalent domain resolution and transcriptional activation in CD34neg AML cells are involved in differentiation-related pathways. Most importantly, epigenomic analysis showed that treatment with epigenetic modifying agents, such as 5-aza-2'-deoxycytidine, appeared to facilitate cell fate transitions, induce marked changes in chromatin configurations, and reverse the enrichments of stem cell signatures in CD34pos leukemia-initiating cells. This provides an important molecular basis for the diminished in vitro clonogenecity and in vivo leukemogenecity of AML cells after 5-aza-2'-deoxycytidine treatment in our previous studies. Our data supports the important role of epigenetic mechanisms in underpinning cell fate and functional properties of leukemia subpopulations. The epigenetic regulation of leukemic stem-like properties might differ from that of normal hematopoietic stem cell state since the same 5-aza-2'-deoxycytidine treatment did not seem to negatively affect clonogenecity of normal hematopoietic cells. Understanding the dynamics of epigenetic state transitions between leukemia subpopulations may offer novel targets for leukemia treatment, and facilitate development of epigenetic therapy targeting leukemia initiating cells. Citation Format: Hsing-Chen Tsai, Hariharan Easwaran, Stephen B. Baylin. Epigenetic regulation of stem cell fate in leukemic subpopulations. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr B27.
Clinical comparison of air-puff and Goldmann tonometers. (1991)

Intraocular pressures (IOPs) as measured with the Topcon CT-10, Reichert XPERT and NCT II, and Keeler PULSAIR air-puff tonometers were compared to the Goldmann IOPs for 452 eyes ranging in pressure from 6-40 mmHg. For eyes with pressures in the 10-20 mmHg range, the CT-10 read consistently too high. The XPERT and the NCT II read too high in the lower part of this range and too low in the higher part. The PULSAIR read too low across the entire range. At higher pressures, all of the tonometers read too high except the PULSAIR which again read too low. CT-10, XPERT, and NCT II and PULSAIR pressures were within 4.0 mmHg of Goldmann readings for 81, 85, 89 and 72 percent of the eyes, respectively. Subjects selected the XPERT as the most preferred tonometer and the NCT II was the least preferred mainly because of perceived air-puff intensity.
MICROWAVE-VACUUM DRYING OF CRANBERRIES: PART I. ENERGY USE AND EFFICIENCY (1996)

Microwave-vacuum drying was investigated as a potential method for drying cranberries. Cranberries were pretreated with either 30°B or 60°B high fructose corn syrup solution for 24 h. They were dried using a laboratory-scale microwave-vacuum oven operating either in continuous or pulsed mode until the final moisture content reached 15% (wet basis). In the continuous mode, two levels of microwave power (250, 500 W) and absolute pressure (5.33, 10.67 kPa) were applied. In the pulsed mode, microwave power of 250 W and two levels of pressure (5.33, 10.67 kPa) were used with two levels of power-on time (30, 60s) and three levels of power-off time (60, 90, 150s). Pulsed application of microwave energy was more efficient than continuous application. In both cases, drying efficiency improved when lower pressure (5.33 kPa) was applied. Shorter power-on time and longer power-off time provided more favorable drying efficiency in pulsed mode. Power-on time of 30 s and power-off time of 150 s was the most suitable setting for maximum drying efficiency.
Effect of Crystallization Inhibitors on Vascular Calcifications Induced by Vitamin D A Pilot Study in Sprague-Dawley Rats (2007)

The present study found that phytate acted as a vascular calcification inhibitor. Thus, the action of polyphosphates could be important in protecting against vascular calcification.
Resistance to Vesicular Stomatitis Virus Infection Requires a Functional Cross Talk between the Eukaryotic Translation Initiation Factor 2α Kinases PERK and PKR (2004)

Phosphorylation of the alpha (alpha) subunit of the eukaryotic translation initiation factor 2 (eIF2) leads to the inhibition of protein synthesis in response to diverse stress conditions, including viral infection. The eIF2alpha kinase PKR has been shown to play an essential role against vesicular stomatitis virus (VSV) infection. We demonstrate here that another eIF2alpha kinase, the endoplasmic reticulum-resident protein kinase PERK, contributes to cellular resistance to VSV infection. We demonstrate that mouse embryonic fibroblasts (MEFs) from PERK(-/-) mice are more susceptible to VSV-mediated apoptosis than PERK(+/+) MEFs. The higher replication capacity of VSV in PERK(-/-) MEFs results from their inability to attenuate viral protein synthesis due to an impaired eIF2alpha phosphorylation. We also show that VSV-infected PERK(-/-) MEFs are unable to fully activate PKR, suggesting a cross talk between the two eIF2alpha kinases in virus-infected cells. These findings further implicate PERK in virus infection, and provide evidence that the antiviral and antiapoptotic roles of PERK are mediated, at least in part, via the activation of PKR.
Encapsulation of Magnetic Nanoparticles with Biopolymer for Biomedical Application (2006)

Magnetite nanoparticles were synthesized by coprecipitation of Fe <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> and Fe <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> with NH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> OH using spinning disc processing (SDP). Chitosan was then coated on the surface of magnetite nanoparticles using SDP. FTIR study and zeta potential measurement confirmed the absorption of chitosan unto the surface of magnetite nanoparticles. Transmission electron microscope (TEM) image showed that the particle sizes are in the range 10-200 nm
Mitigating Temporal-Drift: A Simple Approach to Keep NER Models Crisp (2021)

Performance of neural models for named entity recognition degrades over time, becoming stale. This degradation is due to temporal drift, the change in our target variables' statistical properties over time. This issue is especially problematic for social media data, where topics change rapidly. In order to mitigate the problem, data annotation and retraining of models is common. Despite its usefulness, this process is expensive and timeconsuming, which motivates new research on efficient model updating. In this paper, we propose an intuitive approach to measure the potential trendiness of tweets and use this metric to select the most informative instances to use for training. We conduct experiments on three state-of-the-art models on the Temporal Twitter Dataset. Our approach shows larger increases in prediction accuracy with less training data than the alternatives, making it an attractive, practical solution. 1
Performance prediction of message passing SIMD multiprocessor systems (2003)

The paper focuses on two points: (1) the prediction of the execution signature of massively parallel applications prior to execution/implementation based on a more informative characterization of the workload, and (2) the definition of a more general form of speedup and efficiency. The systems considered are of SIMD message passing paradigm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Di-μ-acetone-κ2 O:O-bis[(acetone-κO)aqualithium(I)] di-μ-acetone-κ2 O:O-bis[diaqualithium(I)] tetrakis{[phthalocyaninato(2−)-κ4 N,N′,N′′,N′′′]lithiate(I)} (2006)

The crystals of the title compound, [Li 2 (C 3 H 6 O) 4 (H 2 O) 2 ][Li 2 (C 3 H 6 O) 2 (H 2 O) 4 ] [Li(C 32 H 16 N 8 )] 4 , were obtained by a recrystallization of dilithium phthalocyanine from an acetone/water/toluene solution. The title structure consists of two independent Li–phthalocyanine complexes along with acetone-bridged lithium dimers. The lithium dimers are located on inversion centers. The crystal structure is stabilized by a network of hydrogen bonds.
Depth image-based rendering with spatio-temporally consistent texture synthesis for 3-D video with global motion (2012)

Depth image-based rendering (DIBR) techniques are advanced tools in 3-D video (3DV) applications that are used to synthesize a number of additional views in a multiview-video-plus-depth (MVD) representation. The MVD format consists of video and depth sequences for a limited number of original camera views of the same scene. An inherent problem of the view synthesis concept is given by image information that is occluded in the original views and becomes visible, in the extrapolated views. To handle these disoc-clussions, we propose a DIBR algorithm with advanced inpainting methods. Our renderer enhances visual experience by taking spatial and temporal texture consistency problems into account. In order to compensate the global motion in a sequence, image registration is incorporated into the framework. The proposed method shows objective and subjective gains compared to the state-of-the-art.
Evaluating real-time audio localization algorithms for artificial audition in robotics (2009)

Although research on localization of sound sources using microphone arrays has been carried out for years, providing such capabilities on robots is rather new. Artificial audition systems on robots currently exist, but no evaluation of the methods used to localize sound sources has yet been conducted. This paper presents an evaluation of various real-time audio localization algorithms using a medium-sized microphone array which is suitable for applications in robotics. The techniques studied here are implementations and enhancements of steered response power - phase transform beamformers, which represent the most popular methods for time difference of arrival audio localization. In addition, two different grid topologies for implementing source direction search are also compared. Results show that a direction refinement procedure can be used to improve localization accuracy and that more efficient and accurate direction searches can be performed using a uniform triangular element grid rather than the typical rectangular element grid.
Charge plasma diode - a novel device concept (2008)

We propose a new device concept called charge plasma (CP) diode [1]. The diodes are with metal/silicided contacts of different workfunctions and thin intrinsic region in between. The workfunctions and layer thicknesses are chosen such that an electron plasma is formed on one side of the silicon body and a hole plasma on the other, i.e. a CP p-n diode is formed. The main advantages of these devices are low temperature budget and no dopant implantation is necessary in thin silicon layers [2,3,4]. We begin by discussing some important results from our silicon p-i-n diodes before moving on to the novel device concept of CP diodes.
Characterisation of heterogeneity and spatial autocorrelation in phase separating mixtures using Moran’s I (2017)

In complex colloidal systems, particle-poor regions can develop within particle-rich phases during sedimentation or creaming. These particle-poor regions are overlooked by 1D profiles, which are typically used to assess particle distributions in a sample. Alternative methods to visualise and quantify these regions are required to better understand phase separation, which is the focus of this paper. Magnetic resonance imaging has been used to monitor the development of compositional heterogeneity in a vesicle-polymer mixture undergoing creaming. T<sub>2</sub> relaxation time maps were used to identify the distribution of vesicles, with vesicle-poor regions exhibiting higher T<sub>2</sub> relaxation times than regions richer in vesicles. Phase separated structures displayed a range of different morphologies and a variety of image analysis methods, including first-order statistics, Fourier transformation, grey level co-occurrence matrices and Moran's I spatial autocorrelation, were used to characterise these structures, and quantify their heterogeneity. Of the image analysis techniques used, Moran's I was found to be the most effective at quantifying the degree and morphology of phase separation, providing a robust, quantitative measure by which comparisons can be made between a diverse range of systems undergoing phase separation. The sensitivity of Moran's I can be enhanced by the choice of weight matrices used.
Isomer effects on transport properties of polyesters based on bisphenol‐A (1993)

Abstract Pure gas sorption and transport properties of polyesters based on bisphenol‐A and both pure isophthalic and pure terephthalic acid chloride were obtained for He, N 2 , O 2 , CH 4 , and CO 2 at 35°C. The polymers were synthesized in our laboratory and amorphous films were prepared with a specialized solvent casting procedure. The polymer containing m‐phenylene groups shows higher permselectivity for most of the gas pairs. The ideal selectivity of O 2 /N 2 was increased by 33% when p‐phenylene units were replaced by m‐phenylene ones. On the other hand, the polyester containing only p ‐phenylene groups, shows higher permeability to all the gases studied. The polymer based on pure terephthalic acid chloride has a 75% higher oxygen permeability and a 1.1‐fold higher carbon dioxide permeability than the isophthalic acid derivative. The polyester containing meta ‐phenylene units has lower T g , higher permselectivity, lower permeability, lower fractional free volume (FFV), and lower d ‐spacing. The values of FFV, and lower d ‐spacing. The values of FFV and d ‐spacing were only slightly different between the two isomers. Moreover, for the sub‐ T g γ transition the maximum in tan δ occured at essentially the same temperature (−55°C). The polymer with a higher concentration of p ‐phenylene units shows somewhat larger area under the γ‐peak, indicating slightly more sub‐ T g motion. The Distribution of FFV is considered to be the determining factor for the differences in transport properties observed. © 1993 John Wiley &amp; Sons, Inc.
Tunable quantum dot lasers grown directly on silicon (2019)

Tunable semiconductor lasers are often listed in critical technology road maps for future dense-wavelength-division-multiplexing (DWDM) systems and high-performance computing systems, and they are increasingly demanded in long-haul, metropolitan, and access networks. The capability to produce such lasers directly on silicon (Si) could boost the use of Si photonics and facilitate the adoption of optical data transmission even at the chip scale. Moreover, just the use of Si as a cheap and large-diameter substrate for device production is very advantageous, as the fabrication can take advantage of the highly optimized processing techniques and economy of scale enabled by decades of development in Si microelectronics. Here, we report a tunable single-wavelength quantum dot (QD) laser directly grown on Si. The high carrier confinement and a real dot density of QDs provide reduced sensitivity to crystalline defects, which allows for exceptional lasing performance even in lattice-mismatched material systems. The discrete density of states of dots yields unique gain properties that show promise for improved device performance and new functionalities relative to the quantum well counterparts, including high temperature stability, low threshold operation, reduced sidewall recombination, and isolator-free stability. We implement a simple, integrable architecture to achieve over 45 dB side-mode-suppression-ratio without involving regrowth steps or subwavelength grating lithography. Under continuous-wave electrical injection at room temperature, we achieved a 16 nm tuning range with output powers of over 2.7 mW per tuning wavelength. This work represents a step towards using III–V/Si epitaxy to form efficient, easily manufacturable on-chip Si light sources for not only DWDM networks, but also spectroscopy, biosensors, and many other emerging applications.
Data from Inhibition of GSK-3 Induces Differentiation and Impaired Glucose Metabolism in Renal Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Glycogen synthase kinase-3 (GSK-3), a constitutively active serine/threonine kinase, is a key regulator of numerous cellular processes ranging from glycogen metabolism to cell-cycle regulation and proliferation. Consistent with its involvement in many pathways, it has also been implicated in the pathogenesis of various human diseases, including type II diabetes, Alzheimer disease, bipolar disorder, inflammation, and cancer. Consequently, it is recognized as an attractive target for the development of new drugs. In the present study, we investigated the effect of both pharmacologic and genetic inhibition of GSK-3 in two different renal cancer cell lines. We have shown potent antiproliferative activity of 9-ING-41, a maleimide-based GSK-3 inhibitor. The antiproliferative activity is most likely caused by G&lt;sub&gt;0&lt;/sub&gt;–G&lt;sub&gt;1&lt;/sub&gt; and G&lt;sub&gt;2&lt;/sub&gt;–M phase arrest as evident from cell-cycle analysis. We have established that inhibition of GSK-3 imparted a differentiated phenotype in renal cancer cells. We have also shown that GSK-3 inhibition induced autophagy, likely as a result of imbalanced energy homeostasis caused by impaired glucose metabolism. In addition, we have demonstrated the antitumor activity of 9-ING-41 in two different subcutaneous xenograft renal cell carcinoma tumor models. To our knowledge, this is the first report describing autophagy induction due to GSK-3 inhibition in renal cancer cells. &lt;i&gt;Mol Cancer Ther; 13(2); 285–96. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
3,4-Propylenedioxypyrrole-Based Conjugated Oligomers via Pd-Mediated Decarboxylative Cross Coupling (2010)

An effective decarboxylative cross-coupling involving a 3,4-dioxypyrrole is reported. Several conjugated oligomers were synthesized in high yields using various aryl bromides. No copper salt or other transmetalating agent was required. The reaction conditions employed displayed relatively low sensitivity toward the presence of water.
Oxygen partial pressure dependence of surface space charge formation in donor-doped SrTiO3 (2017)

In this study, we investigated the electronic surface structure of donor-doped strontium titanate. Homoepitaxial 0.5 wt. % donor-doped SrTiO3 thin films were analyzed by in situ near ambient pressure X-ray photoelectron spectroscopy at a temperature of 770 K and oxygen pressures up to 5 mbar. Upon exposure to an oxygen atmosphere at elevated temperatures, we observed a rigid binding energy shift of up to 0.6 eV towards lower binding energies with respect to vacuum conditions for all SrTiO3 core level peaks and the valence band maximum with increasing oxygen pressure. The rigid shift is attributed to a relative shift of the Fermi energy towards the valence band concomitant with a negative charge accumulation at the surface, resulting in a compensating electron depletion layer in the near surface region. Charge trapping effects solely based on carbon contaminants are unlikely due to their irreversible desorption under the given experimental conditions. In addition, simple reoxygenation of oxygen vacancies can be ruled out as the high niobium dopant concentration dominates the electronic properties of the material. Instead, the negative surface charge may be provided by the formation of cation vacancies or the formation of charged oxygen adsorbates at the surface. Our results clearly indicate a pO2-dependent surface space charge formation in donor-doped SrTiO3 in oxidizing conditions.
Prodrug strategies for improved efficacy of nucleoside antiviral inhibitors (2013)

Prodrug strategies can address the issues of poor oral bioavailability and delivery of active metabolites to the targeted cells. Additionally, NAPs demonstrate potential for improving deficiencies in oral absorption, metabolism, tissue distribution, cellular accumulation, phosphorylation, and overall potency, in addition to diminishing potential for in-vivo selection of resistant viruses. NAPs continue to be the backbone for the treatment of HIV and HBV, herpesviruses, and adenovirus infections because their active forms are potent, have long intracellular half-lives and are relatively safe with high barrier to resistance.