gebhart/patrepeval huggingface dataset:
Data from Application of Oligonucleotide Microarrays to Assess the Biological Effects of Neoadjuvant Imatinib Mesylate Treatment for Localized Prostate Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Neoadjuvant administration of antineoplastic therapies is used to rapidly assess the clinical and biological activity of novel systemic treatments. To assess the feasibility of using microarrays to assess molecular end points following targeted treatment in a heterogeneous tumor, we measured global gene expression in localized prostate cancer before and following neoadjuvant treatment with imatinib mesylate.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Patients and Methods:&lt;/b&gt; Patients with intermediate-risk to high-risk prostate cancer were treated for 6 weeks with 200 to 300 mg of oral imatinib mesylate. Frozen tissue was obtained from pretreatment ultrasound-guided biopsies and posttreatment radical prostatectomy specimens. Oligonucleotide microarray analysis following laser capture microdissection (LCM) and RNA amplification was used to assess gene expression changes associated with imatinib mesylate therapy. Immunohistochemistry was used to measure protein expression of MKP1 and CD31 and to assess cellular apoptosis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Of the 11 patients enrolled, high-quality microarray data was obtained from both biopsies (&lt;i&gt;n&lt;/i&gt; = 7) and radical prostatectomy specimens (&lt;i&gt;n&lt;/i&gt; = 9). Technically introduced intrasample gene expression variability was found to be significantly less than intertumor biological variability. Large gene expression differences were observed, and the gene with the most consistent differential expression (&lt;i&gt;MKP1&lt;/i&gt;) was validated by immunohistochemistry. Gene set enrichment analysis suggests that imatinib mesylate therapy results in apoptosis of microvascular endothelial cells, an observation anecdotally supported by immunohistochemistry.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study shows that high-quality microarray data can be generated using LCM and RNA amplification to discover potential mechanisms of targeted therapy in cancer.&lt;/p&gt;&lt;/div&gt;
Effect of growth temperature on the thermal stability of 1.3&#x03BC;m InAs/InGaAs/GaAs quantum dot structures (2008)

The effects of growth temperature on the optical properties of InAs/InGaAs/GaAs quantum dot (QD) structure were investigated at the important temperature range of 25degC to 80degC. Results from QD samples grown at low growth temperature of 450degC suggest better thermal stability as compared to that grown at 510degC. This work suggests the feasibility of obtaining better thermal stability at a low growth temperature for InAs/InGaAs/GaAs QD structures.
Synthesis and Characterization of Polyether Adducts of Barium and Strontium Carboxylates and Their Use in the Formation of MTiO3 Films (1996)

The synthesis, characterization, and reactivity of new polyether adducts of strontium and barium carboxylates of general composition M(O(2)CCF(3))(n)()(L) (M = Ba, L = 15-crown-5, (1); M = Ba (2), Sr (3), respectively, with L = tetraglyme are reported. The compounds were synthesized by reaction of BaCO(3) or MH(2) (M = Sr or Ba) with organic acids in the presence of the polyether ligands. These compounds have been characterized by IR and (13)C and (1)H NMR spectroscopies, elemental analyses, and thermogravimetric analysis. The species Ba(2)(O(2)CCF(3))(4)(15-crown-5)(2) (1) and [Ba(2)(O(2)CCF(3))(4)(tetraglyme)](infinity) (2), were also characterized by single-crystal X-ray diffraction. Ba(2)(O(2)CCF(3))(4)(15-crown-5)(2) (1) crystallizes in the orthorhombic space group Cccm with cell dimensions of a = 13.949(1) Å, b = 19.376(2) Å, c = 16.029(1) Å, and Z = 8. [Ba(2)(O(2)CCF(3))(4)(tetraglyme)](infinity) (2) crystallizes in the monoclinic space group C2/c with cell dimensions of a = 12.8673(12) Å, b = 16.6981(13) Å, c = 15.1191(12) Å, beta = 99.049(8) degrees, and Z = 4. Compounds 1-3 thermally decompose at high temperatures in the solid state to give MF(2). However, solutions of compounds 1-3 dissolved in ethanol with Ti(O-i-Pr)(4) give crystalline perovskite phase MTiO(3) films, or in the case of mixtures of 2 and 3, Ba(1)(-)(x)()Sr(x)()TiO(3) films below 600 degrees C when spin coated onto silicon substrates and thermally treated. The crystallinity, purity, and elemental composition of the films was determined by glancing angle X-ray diffraction and Auger electron spectroscopy.
ONO charging at different stages of microFlash/sup /spl reg// process flow (2004)

In-process ultraviolet (UV) stimulated charging of ONO (oxide-nitride-oxide) stack is observed in fieldless microFlash (NROM) memory arrays. This problem is solved by introducing a UV blocking layer into the D1 dielectric. In this paper we discuss an alternative approach to the solution of charging problem. A micropartitioning technique is described that allows to screen out the operations responsible for ONO charging and corresponding equipment.
ChemInform Abstract: SUBSTITUENT EFFECTS IN THE CYCLOADDITION REACTIONS OF REISSERT HYDROFLUOROBORATE SALTS WITH ALKENES (1981)

Abstract Aus den 2‐Aroyl‐1,2‐dihydro‐isochinaldonitrilen (I) entstehen mit den Zimtsäureestern (II) die Addukte (III) und (IV), deren Anteile in Relation zu den Substituenten bestimmt werden.
CINR difference analysis of optimal combining versus maximal ratio combining (2005)

The statistical gain differences between two common spatial combining algorithms: optimum combining (OC) and maximal ratio combining (MRC) are analyzed using a gain ratio method. Using the receive carrier-to-interference plus noise ratio (CINR), the gain ratio ClNR/sub OC/ /CINR/sub MRC/ is evaluated in a flat Rayleigh fading communications system with multiple interferers. Exact analytical solutions are derived for the probability density function (PDF) and the average gain ratio with one interferer. When more than one interferer is present, the PDF of the gain ratio is illustrated using Monte Carlo simulations and its mean value is shown in basic integral form. An upper bound to the gain ratio is derived providing a simple means to determine when OC will exhibit significant gains over MRC.
Mapping Networks of Protein‐Mediated Physical Interactions Between Chromatin Elements (2010)

Understanding of transcriptional regulation has advanced in recent years in part due to development of technologies which allow determination of physical proximities between interacting chromatin regions at a resolution beyond that offered by conventional microscopy techniques. However, these methods do not specifically identify the protein component(s) that might mediate such interactions. This unit provides a detailed protocol for Combined 3C-ChIP-Cloning (6C) technology, which combines multiple techniques to simultaneously identify physical proximities between chromatin elements as well as the proteins that mediate these interactions. The unit further explores how the 6C assay can be combined with other techniques for a complete, cell-type-specific mapping of all inter- and intrachromosomal interactions mediated by specific proteins. Thus, the 6C assay provides a useful tool to address the role of specific proteins in nuclear organization and to advance our understanding about the relation of chromatin higher-order organization and transcriptional regulation.
Gain-scheduled H/sub /spl infin// loop-shaping controller for automated guidance of tractor-semitrailer combination vehicles (2000)

Deals with the robust, gain-scheduled, lateral control problem for tractor-semitrailer combination vehicles (TSCVs) using an observer-structured H/sub /spl infin// loop-shaping controller. Vehicle longitudinal speed is chosen as the scheduling parameter since variations of speeds dramatically change system dynamics in different frequency ranges. By utilizing the vehicle speed as the scheduling parameter, the controller minimizes the effect of uncertainties and nonlinearities, which depends mainly on the velocity. Two scheduling techniques are applied to evaluate the effectiveness of the proposed controller. Simulation shows that the gain-scheduled controller generally sustains a larger robustness region than the fixed-gain linear controller under the uncertainties of varying road adhesion coefficients and cargo loads in the trailer.
Vaccinology: The art of putting together the right ingredients (2016)

Historically vaccines were produced using whole attenuated or killed pathogens and still a large proportion of current vaccines utilizes such procedure. However, for safety and quality reasons the development of novel vaccines is preferentially based on the selection and use of specific pathogen components which alone are capable of eliciting protective immune responses against the pathogens they derived from. The big challenge for vaccinologists is how to select the right antigens and to combine them with proper immune stimulatory components (adjuvants) in order to induce protective immunity. This Commentary outlines the authors' view on the current and future strategies for the efficient and rapid identification of the most effective protective antigens and adjuvants. Since efficacious subunit-based vaccines against recalcitrant pathogens are likely to require more than one antigen and/or immune stimulator, this poses the problem of how to make such vaccines economically acceptable. In this regard, the authors also present their view of how bacterial Outer Membrane Vesicles (OMVs) could become a promising platform for the development of future vaccines. The unique properties of OMVs might be exploited in the field of infectious diseases and oncology.
Spin-orbit coupling routes and OLED performance: studies of blue-light emitting Ir(III) and Pt(II) complexes (2007)

In this study, detailed spectroscopic investigations of the blue emitting compounds Ir(4,6-dFppy)<sub>2</sub>(pic) and Pt(4,6- dFppy)(acac) are presented. Due to spin-orbit coupling (SOC) of the emitting triplet state with higher lying singlet states both complexes show an intense phosphorescence and are utilized as emitters in organic light emitting diodes (OLEDs). Distinct differences with respect to important photophysical properties are found for the two compounds. For example, the (distorted) octahedral Ir(4,6-dFppy)<sub>2</sub>(pic) complex exhibits a shorter emission decay time and shows a larger zero-field splitting (ZFS) than the (distorted) square planar Pt(4,6-dFppy)(acac) complex (&tau;(Ir) = 0.4 &mu;s and &tau;(Pt) = 3.6 &mu;s of the respective shortest-lifed triplet substate; &Delta;(ZFS, Ir) = 67 cm<sup>-1</sup>, &Delta;E(ZFS, Pt) = 8 cm<sup>-1</sup>). This behaviour is connected with the extent of metal-to-ligand charge transfer (MLCT, d&pi;*) character in the emitting triplet state. High MLCT character usually results in a high emission decay rate and indicates a good suitability as OLED emitter material. Of crucial importance in this respect is the effectiveness of SOC. In this study it is shown that the SOC routes depend on the coordination geometry of the emitter compound. In particular, the couplings can be more effective in (distorted) octahedral than in (distorted) square planar compounds. Hence, the photophysical differences of Ir(4,6-dFppy)<sub>2</sub>(pic) compared to Pt(4,6-dFppy)(acac) can be rationalized. Moreover, this investigation shows that the analysis of SOC paths provides general guidelines for the design of efficient emitters for OLED applications.
Noise, Artifact, and Oversensing Related Inappropriate ICD Shock Evaluation: ALTITUDE NOISE Study (2012)

External noise and lead/connector noise were the primary causes, while T-wave oversensing was the least common cause of NAO resulting in ICD shock. Noise/artifact decreased immediately after a shock in nearly half of episodes. The specific ICD lead type did not impact the likelihood of NAO.
A robot system that observes and replicates grasping tasks (2002)

To alleviate the problem of overwhelming complexity in grasp synthesis and path planning associated with robot task planning, we adopt the approach of teaching the robot by demonstrating in front of it. The system has four components: the observation system, the grasping task recognition module, the task translator and the robot system. The observation system comprises an active multibaseline stereo system and a dataglove. The data stream recorded is then used to track object motion; this paper illustrates how complimentary sensory data can be used for this purpose. The data stream is also interpreted by the grasping task recognition module, which produces higher levels of abstraction to describe both the motion and actions taken in the task. The resulting information are provided to the task translator which creates commands for the robot system to replicate the observed task. In this paper we describe how these components work with special emphasis on the observation system. The robot system that we use to perform the grasping tasks comprises the PUMA 560 arm and the Utah/MIT hand.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Continuous renal replacement therapy: evolution in technology and current nomenclature. (1998)

The evolution of technology and biomaterials has permitted a parallel development of renal replacement therapies in the acute, critically ill patient. From the original description of continuous arteriovenous hemofiltration (CAVH), new techniques such as continuous venous venous hemofiltration (CVVH), hemodiafiltration (HDF) and high flux dialysis (HFD) have been developed and clinically utilized. A parallel improvement in efficiency has been achieved with daily clearances of urea as high as 50 liters or more. The use of special highly permeable dialyzers has also permitted increases in the clearances of larger solutes, thus leading to significant removals of chemical substances involved the acute inflammation and sepsis. In this field, recent observations have suggested the use of hemofiltration with high volumes of fluid exchange. The hardware and software of the newer continuous renal replacement therapy (CRRT) systems are certainly the key points in achieving these results and in safely performing such challenging techniques.
Bacterial persistence increases as environmental fitness decreases (2012)

Since persister cells cause chronic infections and since Escherichia coli toxin MqsR increases persisters, we used protein engineering to increase the toxicity of MqsR to gain insights into persister cell formation. Through two amino acid replacements that increased the stability of MqsR, toxicity and persistence were increased. A whole-transcriptome study revealed that the MqsR variant increased persistence by repressing genes for acid resistance, multidrug resistance and osmotic resistance. Corroborating these microarray results, deletion of rpoS, as well as the genes that the master stress response regulator RpoS controls, increased persister formation dramatically to the extent that nearly the whole population became persistent. Furthermore, wild-type cells stressed by prior treatment to acid or hydrogen peroxide increased persistence 12 000-fold. Whole-transcriptome analyses of persister cells generated by two different methods (wild-type cells pretreated with hydrogen peroxide and the rpoS deletion) corroborated the importance of suppressing RpoS in persister cell formation. Therefore, the more toxic MqsR increases persistence by decreasing the ability of the cell to respond to antibiotic stress through its RpoS-based regulation of acid resistance, multidrug resistance and osmotic resistance systems.
Design and synthesis of macroporous polymeric separation media based on substituted phenols (1990)

The suspension copolymerization of several t-butoxycarbonyl (t-BOC) protected 4-vinyl phenols with divinylbenzene has been studied to produce high porosity 10 μm bead materials with surface areas of 200–300 m2/g for use as separation media. The choice and amount of porogen is critical for the control of porosity and surface area while particle size and size distribution is controlled by other reaction variables. The t-BOC protecting groups of the polymers are easily removed by thermolysis and the deprotected beads are useful in the separation of amines. The relationship between polymer structure and separation ability in h.p.l.c. has been explored and the effect of alkyl substituents located ortho to the phenolic groups is discussed.
Evidence for an oscillating intramolecular ligand exchange mechanism due to an alternation between two identically strong aliphatic hydrogen to palladium interactions (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEvidence for an oscillating intramolecular ligand exchange mechanism due to an alternation between two identically strong aliphatic hydrogen to palladium interactionsMichele Postel, Michel Pfeffer, and Jean G. RiessCite this: J. Am. Chem. Soc. 1977, 99, 17, 5623–5627Publication Date (Print):August 1, 1977Publication History Published online1 May 2002Published inissue 1 August 1977https://pubs.acs.org/doi/10.1021/ja00459a015https://doi.org/10.1021/ja00459a015research-articleACS PublicationsRequest reuse permissionsArticle Views60Altmetric-Citations16LEARN 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
The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection (2021)

Venezuelan Equine Encephalitis Virus (VEEV) is a major biothreat agent that naturally causes outbreaks in humans and horses particularly in tropical areas of the western hemisphere, for which no antiviral therapy is currently available. The host response to VEEV and the cellular factors this alphavirus hijacks to support its effective replication or evade cellular immune responses are largely uncharacterized. We have previously demonstrated tremendous cell-to-cell heterogeneity in viral RNA (vRNA) and cellular transcript levels during flaviviral infection using a novel virus-inclusive single-cell RNA-Seq approach. Here, we used this unbiased, genome-wide approach to simultaneously profile the host transcriptome and vRNA in thousands of single cells during infection of human astrocytes with the live-attenuated vaccine strain of VEEV (TC-83). Host transcription was profoundly suppressed, yet "superproducer cells" with extremely high vRNA abundance emerged during the first viral life cycle and demonstrated an altered transcriptome relative to both uninfected cells and cells with high vRNA abundance harvested at later time points. Additionally, cells with increased structural-to-nonstructural transcript ratio exhibited upregulation of intracellular membrane trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral activities in both vaccine and virulent VEEV infections among the products of transcripts that positively or negatively correlated with vRNA abundance, respectively. Lastly, comparison with single cell transcriptomic data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the VEEV (TC-83)-host interplay, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.
Functionalized azamacrocyclic compounds as Ca2+ sensitive contrast agents for MR imaging (2005)

The ability to non-invasively observe changes in Ca2+ concentration is important for neuroscience. We have therefore developed a series of gadolinium chelate complexes based on DO3A (Scheme 1), which is hypothesized to change relaxivity in magnetic resonance experiments dynamically with Ca2+ concentration. Different lengths of the phosphonate side chains are expected to lead to different binding constants of the phosphonate - gadolinium bonds. The latter property can be exploited for fine-tuning the sensitivity of the agent to calcium ion concentration.
Controlled formation of dipyranoside derivatives through C6 and O4. Pyranosidic homologation. VII (1987)

A procedure has been developed for pyranosidic homologation of methyl α-D-glucopyranoside via C4 and C6. Reaction of the aldehydo group of compound 2 with the Wittig–Bestmann reagent, Ph 3 P=CHCH(OEt) 2 , gave an E/Z mixture of acetals, 4, which cyclizes under the specific catalysis of pyridinium p-toluenesulfonate and in the presence of alcohols to give anomerically pure olefinic bipyranosides, 6a–d. A general procedure for epoxidation of the latter involves osmium tetroxide hydroxylation, followed by reaction with phosgene iminium chloride (Viehe's salt) to give chlorocarbamates 12 and 13, which are then subjected to the action of sodium methoxide. This allows for the formation of a single series of diastereomeric epoxides, 7, and controlled cleavage of the latter with nucleophiles then follows well-established precedents. Selective access to the "ends" of the bipyranosides 7c and d can be obtained by oxidative removal of the activated benzyl glycosides with DDQ.
Photocatalyst Z-scheme system composed of a linear conjugated polymer and BiVO 4 for overall water splitting under visible light (2020)

A Z-scheme of a linear conjugated polymer photocatalyst and a metal oxide is able to facilitate overall water splitting without non-scalable sacrificial reagents showing potential for sustainable hydrogen production.
Monoclonal antibodies recognizing a putative immunodominant epitope in the hemagglutinin stalk do not enhance influenza A virus mediated fusion activity (VIR5P.1156) (2015)

Abstract The discovery of broadly neutralizing antibodies (Abs) which bind to the conserved hemagglutinin (HA) stalk has led to renewed interest in the development of a universal influenza virus vaccine. In swine, there have been isolated reports of vaccine-induced enhancement of disease in heterologous vaccination and challenge studies. It has been suggested that Abs recognizing the HA stalk promote virus fusion activity, contributing to pathology in pigs. Given that robust data in mouse and ferret models suggests a protective role for stalk Abs, here we examined the relationship between HA-stalk binding Abs and fusion. We generated mouse monoclonal Abs C4 and C6, which recognize a previously identified minimal epitope in the HA stalk. These Abs lack hemagglutination inhibition activity and did not inhibit or enhance virus-mediated fusion in vitro.In a mouse challenge model, we assessed the consequences of pre-exposure administration of a C4/C6 cocktail. No significant differences were observed in animals receiving C4/C6 in morbidity and mortality relative to naïve and isotype controls. We also probed the sera from a cohort of individuals who received an H5N1 vaccine. Although we detected baseline levels of Abs to the minimal stalk epitope associated with increased fusion activity in swine, titers did not increase post-vaccination. Together, our data suggests that stalk Abs do not enhance virus-mediated fusion and thus should not impede progress toward a universal influenza vaccine.