gebhart/patrepeval huggingface dataset:
miR-181a modulates acute myeloid leukemia susceptibility to natural killer cells (2015)

Although daunorubicin (DNR) is the most widely used anthracycline to treat acute myeloid leukemia (AML), resistance to this drug remains a critical problem. The aim of this study was to investigate the relationship between AML resistance to daunorubicin and susceptibility to natural killer (NK) cell-mediated cell lysis, and the putative expression of miRs. For this purpose, we used the parental AML cell lines U-937 and KG-1 and their equivalent resistant U937(R) and KG-1(R) cell lines. We demonstrate for the first time that the acquisition of resistance to DNR by the parental cell lines resulted in the acquisition of cross-resistance to NK cell-mediated cytotoxicity. miR microarray analysis revealed that this cross-resistance was associated with miR-181a downregulation and the subsequent regulation of MAP3K10 and MAP2K1 tyrosine kinases and the BCL<sup>-</sup>2 (BCL<sup>-</sup>2 and MCL<sup>-</sup>1) family. Overexpression of miR-181a in AML blasts resulted in the attenuation of their resistance to DNR and to NK-cell-mediated killing. These data point to a determinant role of miR-181a in the sensitization of leukemic resistant cells to DNR and NK cells and suggest that miR-181a may provide a promising option for the treatment of immuno- and chemo-resistant blasts.
Optimization of optical properties of silicon-based anti-reflective spin-on hardmask materials (2008)

In the current semiconductor industry, hardmasks have become essential for successful patterning in many applications. Silicon-based anti-reflective spin-on hardmask (Si-SOH), which can be built by spin-on coating, is desirable in terms of mass production throughput and cost of ownership. As the design rule shrinks, the thickness of photoresist also becomes thinner, which forces the thickness of Si-SOH to be thinner resulting in a tighter thickness margin. In this case, controlling of optical properties of Si-SOH is important in order to obtain low reflectivity in the exposure process. Previously, we reported papers on silicon-based anti-reflective spin-on hardmask materials for 193 nm lithography and immersion ArF lithography. In this paper, the technique for optimization of optical properties, especially n and k values, of Si-SOH is described. To control n and k values, several chromophores were screened and the ratio among them was optimized. Although the amount of chromophores increased and the silicon contents decreased, our etch resistance enhancement technique allowed Si-SOH to have sufficient etch resistance. Characterization of this Si-SOH and lithographic performance using these materials are described in detail.
The Statistics of Sensitivity Analyses (2015)

Suppose one wishes to estimate a causal parameter given a sample of observations. This requires making unidentifiable assumptions about an underlying causal mechanism. Sensitivity analyses help investigators understand what impact violations of these assumptions could have on the causal conclusions drawn from a study, though themselves rely on untestable (but hopefully more interpretable) assumptions. Díaz and van der Laan (2013) advocate the use of a sequence (or continuum) of interpretable untestable assumptions of increasing plausibility for the sensitivity analysis so that experts can have informed opinions about which are true. In this work, we argue that using appropriate statistical procedures when conducting a sensitivity analysis is crucial to drawing valid conclusions about a causal question and understanding what assumptions one would need to make to do so. Conducting a sensitivity analysis typically relies on estimating features of the unknown observed data distribution, and thus naturally leads to statistical problems about which optimality results are already known. We present a general template for efficiently estimating the bounds on the causal parameter resulting from a given untestable assumption. The sequence of assumptions yields a sequence of confidence intervals which, given a suitable statistical procedure, attain proper coverage for the causal parameter if the corresponding assumption is true. We illustrate the pitfalls of an inappropriate statistical procedure with a toy example, and apply our approach to data from the Western Collaborative Group Study to show its utility in practice.
The Design and Development of Palladium-Catalyzed Aerobic Oxidative Transformations (2005)

Oxidation is a fundamental process in chemistry and biology. In synthetic chemistry, several developments have been made in catalytic asymmetric oxidative transformations that involve a heteroatom transfer from a reagent to a substrate (e.g., epoxidations, dihydroxylations). Enantioselective oxidations that do not involve a heteroatom transfer have been relatively less explored. These types of oxidative transformations were investigated using a general palladium(II) catalyst system. A palladium-catalyzed oxidative kinetic resolution of secondary alcohols was developed. This catalytic system utilizes (–)-sparteine as the chiral ligand and molecular oxygen as the sole stoichiometric oxidant. Benzylic and allylic alcohols can be resolved to high enantiomeric excesses in excellent yields. The same selective process has been applied to the desymmetrization of meso diols. This general palladium(II) oxidative system was applied to intramolecular Wacker oxidations to form a variety of heterocycles. Lactones, lactams, tetrahydrofurans, dihydrobenzofurans, and dihydrobenzopyrans were all accessed by this methodology. Importantly, this work provided entry into the development of asymmetric variants. Highly enantioselective cyclizations of phenolic substrates were realized with a palladium-sparteine catalyst, analogous to the kinetic resolution chemistry. The heterocyclization chemistry was employed in the context of the total synthesis of the Cephalotxaxus alkaloids. Oxidative annulations for the synthesis of carbocycles were developed utilizing this general palladium system. Indoles with pendant olefin tethers were oxidatively cyclized under palladium(II) catalysis to form annulated indoles. Electron-rich aromatic systems were also investigated, culminating in the syntheses of benzofurans and dihydrobenzofurans. These reactions were demonstrated to proceed by an initial C-H bond functionalization event, followed by olefin insertion and beta-hydride elimination. Enantioselective heterocyclizations using the general oxidative system were further explored. Promising results were realized in the heterocyclizations of sulfonamide-based compounds. Key experiments allowed for a firmer understanding of how the reaction was progressing, and specifically, how enantioselectivity was being induced by the palladium catalyst.
Compartmentalisation‐based design automation method for power grid (2017)

Power grid design and maintenance are conducted to solve the problems caused by load growth over time and to stay within the constraints of voltage drop, power factor, etc. Typically, solutions to these problems are optimised individually. Considering multiple problems simultaneously and applying different solutions require vast design space exploration. This exclusively needs advanced algorithms and complex global optimisation methods which are not easily‐applicable in different scenarios. In the state‐of‐the‐art methods, for solving multiple problems simultaneously, these individually optimised solutions are applied sequentially to the power grid. In this so‐called uncoordinated method, the final solution may not be optimal solution considering all the variables, since it is considering the overlapping effect of the solutions on the power grid. To validate the compartmentalisation method, a detailed distribution grid has been modeled. After analysing the possible solutions and optimisation, power loss was reduced 45% and total cost decreased by 71%, compared to the uncoordinated method.
AB075. SOH22ABS110. Gender affirmation surgery: increases in demand requires urgent service planning (2022)

Background: According to the Irish National Gender Service, there has been a 7-fold increase in demand for gender affirmation surgery over the past decade. Since no reconstructive service currently exists, the Internet remains a key and ever-evolving source of information for these patients. We aimed to assess the quality and readability of online information available to patients in relation to gender affirmation surgery. Methods: We investigated the first 200 websites that appear on the search engine Google when the term ‘gender affirmation surgery’ is searched. Websites were then sorted into eight categories: commercial, government, health portal, news, non-profit, professional, scientific journal and others. Criteria for website exclusion include inaccessible websites, websites containing <1 sentence, articles >15 years old and duplicates. Website quality was assessed using the JAMA Benchmarks and inter-rater reliability was quantified using Cohen’s kappa. Results: There was a critical lack of information regarding indications, suitability, pre-operative assessments, risks and potential complications, and expected quality of life outcomes. Quality of information was often less than satisfactory as evidenced by a median JAMA score of less than 3. The highest score achieved by any website was 3. Of concern, fifty percent of these websites were categorised as professional with a paucity of scientific journal publications. Conclusions: The increased demand for gender affirmation surgery should be married with accurate, high-quality information available to both prospective patients and their treating physicians. Increases in demand for gender affirmation surgery need to be matched with funding to develop reconstructive services. To guide us in producing an accurate and readable patient information resource we are currently undertaking a survey of this patient cohort to assess the needs of this population.
Programmable group-delay module using binary polarization switching (2003)

We demonstrate the first programmable group-delay module based on polarization switching. With a unique binary tuning mechanism, the device can generate any differential group delay value from -45 to +45 ps with a resolution of 1.40 ps, or any true-time-delay value from 0 to 45 ps with a resolution of 0.7 ps. The delay varying speeds for both applications are under 1 ms and can be as fast as 0.1 ms. We evaluate both the dynamic and static performances of the device while paying special attention to its dynamic figures of merit for polarization-mode dispersion emulation and compensation applications. Our experiment shows that the device exhibits a negligible transient-effect induced power penalty (<0.2 dB) in a 10-Gb/s nonreturn-to-zero system.
ChemInform Abstract: Biomimetic Total Synthesis of Pseudotabersonine: A Novel Oxindole‐ Based Approach to Construction of Aspidosperma Alkaloids. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
VI. The Newer Enteroviruses (1962)

VI. The Newer Enteroviruses Karl M. Johnson, Henry H. Bloom, Robert M. Chanock, Maurice A. Mufson, and Vernon Knight CopyRight https://doi.org/10.2105/AJPH.52.6.933 Published Online: August 29, 2011
Supplementary Table 1 from Methylation Markers for <i>CCNA1</i> and <i>C13ORF18</i> Are Strongly Associated with High-Grade Cervical Intraepithelial Neoplasia and Cervical Cancer in Cervical Scrapings (2023)

Supplementary Table 1 from Methylation Markers for &lt;i&gt;CCNA1&lt;/i&gt; and &lt;i&gt;C13ORF18&lt;/i&gt; Are Strongly Associated with High-Grade Cervical Intraepithelial Neoplasia and Cervical Cancer in Cervical Scrapings
Cholesteric liquid crystals in applied electric fields: structural transformations and applications (1998)

The color change electrooptic effect in dual frequency addressable cholesteric liquid crystals (LCs) with an initial planar orientation was investigated. A field induced increase of the pitch was observed for the switching between low and high frequency fields. The investigations allow new conclusions on the origin of blue and red shift observed in an electric field applied parallel to the helix axis. In cholesteric LCs and polymer-dispersed cholesteric LCs with positive dielectric anisotropy, a colored texture with unusual properties was observed for pitch values of P approximately 0.8 micrometers and under certain conditions. This texture appears after the reduction of the electric field during the transition from the homeotropic nematic structure into the cholesteric one. The angular and the electrified dependencies of the spectral characteristics indicate that this state possesses diffractive grating properties. A voltage controlled color shift and a laser beam deflection were investigated.
Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides (2016)

Formation of correct disulfide bonds in the endoplasmic reticulum is a crucial step for folding proteins destined for secretion. Protein disulfide isomerases (PDIs) play a central role in this process. We report a previously unidentified, hypervariable family of PDIs that represents the most diverse gene family of oxidoreductases described in a single genus to date. These enzymes are highly expressed specifically in the venom glands of predatory cone snails, animals that synthesize a remarkably diverse set of cysteine-rich peptide toxins (conotoxins). Enzymes in this PDI family, termed conotoxin-specific PDIs, significantly and differentially accelerate the kinetics of disulfide-bond formation of several conotoxins. Our results are consistent with a unique biological scenario associated with protein folding: The diversification of a family of foldases can be correlated with the rapid evolution of an unprecedented diversity of disulfide-rich structural domains expressed by venomous marine snails in the superfamily Conoidea.
Levels of plasma fibulin-3 and accuracy of identifying patients with malignant pleural mesothelioma. (2014)

e18543 Background: Molecular markers for malignant pleural mesothelioma (MPM) are lacking, limiting early detection. Fibulin-3 was recently described as a highly sensitive and specific marker present in both plasma and pleural effusions from MPM patients. We sought to confirm this result in two independent sample series. Methods: Plasma samples from 63 MPM patients treated in Sydney (Royal Prince Alfred and Strathfield Private Hospitals) between 2010 and 2013, or Vienna (Medical University of Vienna) between 2011 and 2013 were included. Additional samples consisted of healthy individuals and patients with reactive pleuritis, other thoracic malignancies, or coronary artery disease collected over the same period. Blood samples were collected at the time of diagnosis for the various patients, were processed to plasma and stored at -80°C. Levels of fibulin-3 were measured using the Fibulin-3 ELISA kit (USCN Life Sciences) according to the manufacturer’s instructions. Statistical analyses were performed using SPSS21 (IBM). Results: Plasma fibulin-3 concentrations in samples from patients at both Institutes were 13.5 ± 1.5 ng/mL (n=63), compared with 10.6 ± 1.8 ng/mL in controls (n=45). This difference was not statistically significant (p=0.21). In the Sydney series, the mean fibulin-3 concentration in MPM patients was 15.4 ± 1.7 ng/ml (n=42) and 10.6 ± 1.8 ng/mL in controls (n=27). This difference did not reach statistical significance (p=0.07). Values in the Vienna series were 9.8 ± 2.7 ng/mL in MPM patients (n=21) and 10.6 ± 3.7 ng/mL in controls (n=18). These values are all within the range of those previously reported for plasma samples from asbestos-exposed but healthy individuals (13.9 ± 1.2 ng/mL), but do not reach the high levels reported for MPM patients (66.4 to 112.9 ng/mL). At a cut-off of 10.51 ng/mL, the sensitivity and specificity of fibulin-3 for discriminating MPM patients was 55.6 and 66.2 %, respectively. Conclusions: Our assessment of plasma fibulin-3 in two independent samples series suggests that fibulin-3 levels are neither specific nor sensitive enough to aid in the diagnostic process. Further studies are required to understand why these discrepancies in fibulin-3 levels in similar series exist.
Contrast induced nephropathy - cardiologist perspective (2014)

Use of contrast media for cardiovascular intervention is associated with risk of contrast induced nephropathy. Contrast induced nephropathy is associated with increased morbidity, prolonged hospitalization, potential need for dialysis and increased mortality rate. Although the consequences of contrast induced nephropathy are well known, the prospective identification of patient at risk for nephropathy has been inconsistent. The mechanism of contrast induced nephropathy is complex and not fully understood. Direct tubular toxicity and disturbances of renal hemodynamic with altered glomerular filtration and renal medullary ischemia are the most important path-physiological mechanism. Prevention of contrast induced nephropathy is address in numerous studies. The most attractive agents include hydration, N-acetylcysteine, and infusion of sodium bicarbonate. This review focuses on the definition, pathophysiology and prevention of contrast induced nephropathy. Nepalese Heart Journal | Volume 10 | No.1 | November 2013| Pages 30-37 DOI: http://dx.doi.org/10.3126/njh.v10i1.9745
Abstract C96: A novel polyclonal antibody library for expression profiling of poorly characterized membrane and secreted human proteins. (2011)

Abstract The YOMICS™ antibody library (http://www.yomics.com/) presented in this article is a new collection of 1559 murine polyclonal antibodies specific for 1287 distinct human proteins. This antibody library is designed to target marginally characterized membrane-associated and secreted proteins. It was generated against human proteins annotated as transmembrane or secreted in GenBank, EnsEMBL, Vega and Uniprot genome databases, described in no or very few dedicated PubMed-linked publications. The selected proteins/protein regions were expressed in E. coli, purified and used to raise antibodies in the mouse. The capability of YOMICS™ antibodies to specifically recognize their target proteins either as recombinant form or as expressed in cells and tissues was confirmed through several experimental approaches, including Western blot, confocal microscopy and immunohistochemistry (IHC). Moreover, to show the applicability of the library for biomarker investigation by IHC, five antibodies against proteins either known to be expressed in some cancers or homologous to tumor-associated proteins were tested on tissue microarrays carrying tumor and normal tissues from breast, colon, lung, ovary and prostate. A consistent differential expression in cancer was observed. Our results indicate that the YOMICS™ antibody library is a tool for systematic protein expression profile analysis that nicely complements the already available commercial antibody collections. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr C96.
A 2.535 GHz fully integrated Doherty power amplifier in CMOS 65nm with constant PAE in backoff (2013)

A fully integrated Doherty power amplifier at 2.535 GHz is presented in 65 nm CMOS technology with constant PAE over a 8.75dB backoff. The amplifier has 23.4 dBm output power and both PAE peaks have the same level in 25%. Both sub-amplifiers have a single-ended cascode topology and optimized input and output networks to reduce losses and correctly balance their behavior.
SRPerf: a Performance Evaluation Framework for IPv6 Segment Routing (2021)

Segment Routing (SR) is a form of loose source routing. It provides the ability to include a list of instructions, called segments, in the packet header. The SR architecture has been first implemented with the MPLS (SR-MPLS) data plane and then, quite recently, with the IPv6 data plane (SRv6). SRv6 is a promising solution to support advanced services such as Traffic Engineering, Service Function Chaining and Virtual Private Networks. The SRv6 data plane is supported in many different software forwarding engines including the Linux kernel and the Vector Packet Processor (VPP), as well as in hardware devices. In this paper, we present SRPerf, a performance evaluation framework for software and hardware implementations of SRv6. SRPerf is able to perform different benchmarking tests such as throughput and latency. The architecture of SRPerf can be easily extended to support new benchmarking methodologies as well as different SRv6 implementations. We have used SRPerf to evaluate the performance of two SRv6 implementations: Linux kernel and VPP. SRPerf is a valuable tool in the context of modern forwarding engines where new features can be added at fast pace, as it helps experimenters to validate their work. In this work, we have leveraged SRPerf to validate the implementation of some SRv6 behaviors in the Linux kernel and we have discovered and fixed some implementation flaws, making available the fixed code.
A group-delivered self-management program reduces spasticity in people with multiple sclerosis: A randomized, controlled pilot trial (2017)

Participation in STC improved self-reported impact of spasticity more than UC and provided encouraging improvements in other measures.
Synthetic Peptides to Target Stringent Response-Controlled Virulence in a Pseudomonas aeruginosa Murine Cutaneous Infection Model (2017)

Microorganisms continuously monitor their surroundings and adaptively respond to environmental cues. One way to cope with various stress-related situations is through the activation of the stringent stress response pathway. In <i>Pseudomonas aeruginosa</i> this pathway is controlled and coordinated by the activity of the RelA and SpoT enzymes that metabolize the small nucleotide secondary messenger molecule (p)ppGpp. Intracellular ppGpp concentrations are crucial in mediating adaptive responses and virulence. Targeting this cellular stress response has recently been the focus of an alternative approach to fight antibiotic resistant bacteria. Here, we examined the role of the stringent response in the virulence of <i>P. aeruginosa</i> PAO1 and the Liverpool epidemic strain LESB58. A Δ<i>relA</i>/Δ<i>spoT</i> double mutant showed decreased cytotoxicity toward human epithelial cells, exhibited reduced hemolytic activity, and caused down-regulation of the expression of the alkaline protease <i>aprA</i> gene in stringent response mutants grown on blood agar plates. Promoter fusions of <i>relA</i> or <i>spoT</i> to a bioluminescence reporter gene revealed that both genes were expressed during the formation of cutaneous abscesses in mice. Intriguingly, virulence was attenuated <i>in vivo</i> by the Δ<i>relA</i>/Δ<i>spoT</i> double mutant, but not the <i>relA</i> mutant nor the Δ<i>relA</i>/Δ<i>spoT</i> complemented with either gene. Treatment of a cutaneous <i>P. aeruginosa</i> PAO1 infection with anti-biofilm peptides increased animal welfare, decreased dermonecrotic lesion sizes, and reduced bacterial numbers recovered from abscesses, resembling the phenotype of the Δ<i>relA</i>/Δ<i>spoT</i> infection. It was previously demonstrated by our lab that ppGpp could be targeted by synthetic peptides; here we demonstrated that <i>spoT</i> promoter activity was suppressed during cutaneous abscess formation by treatment with peptides DJK-5 and 1018, and that a peptide-treated <i>relA</i> complemented stringent response double mutant strain exhibited reduced peptide susceptibility. Overall these data strongly indicated that synthetic peptides target the <i>P. aeruginosa</i> stringent response <i>in vivo</i> and thus offer a promising novel therapeutic approach.