gebhart/patrepeval huggingface dataset:
Thioredoxin interacting protein is a novel mediator of retinal inflammation and neurotoxicity (2011)

Elevated TXNIP expression contributed to retinal neurotoxicity by three different mechanisms, inducing release of inflammatory mediators such as TNF-α and IL-1β, altering antioxidant status and disrupting the Trx-ASK-1 inhibitory complex leading to activation of the p38 MAPK/JNK apoptotic pathway. Targeting TXNIP expression is a potential therapeutic target for retinal neurodegenerative disease.
All-in-One Single-Print Additively Manufactured Electroanalytical Sensing Platforms (2021)

This manuscript provides the first report of a fully additively manufactured (AM) electrochemical cell printed <i>all-in-one</i>, where all the electrodes and cell are printed as one, requiring no post-assembly or external electrodes. The three-electrode cell is printed using a standard non-conductive poly(lactic acid) (PLA)-based filament for the body and commercially available conductive carbon black/PLA (CB/PLA, ProtoPasta) for the three electrodes (working, counter, and reference; WE, CE, and RE, respectively). The electrochemical performance of the cell is evaluated first against the well-known near-ideal outer-sphere redox probe hexaamineruthenium(III) chloride (RuHex), showing that the cell performs well using an AM electrode as the <i>pseudo</i>-RE. Electrochemical activation of the WE via chronoamperometry and NaOH provides enhanced electrochemical performances toward outer-sphere probes and for electroanalytical performance. It is shown that this activation can be completed using either an external commercial Ag|AgCl RE or through simply using the internal AM CB/PLA <i>pseudo</i>-RE and CE. This <i>all-in-one</i> electrochemical cell (AIOEC) was applied toward the well-known detection of ascorbic acid (AA) and acetaminophen (ACOP), achieving linear trends with limits of detection (LODs) of 13.6 ± 1.9 and 4.5 ± 0.9 μM, respectively. The determination of AA and ACOP in real samples from over-the-counter effervescent tablets was explored, and when analyzed individually, recoveries of 102.9 and 100.6% were achieved against UV-vis standards, respectively. Simultaneous detection of both targets was also achieved through detection in the same sample exhibiting 149.75 and 81.35% recoveries for AA and ACOP, respectively. These values differing from the originals are likely due to electrode fouling due to the AA oxidation being a surface-controlled process. The cell design produced herein is easily tunable toward different sample volumes or container shapes for various applications among aqueous electroanalytical sensing; however, it is a simple example of the capabilities of this manufacturing method. This work illustrates the next step in research synergising AM and electrochemistry, producing operational electrochemical sensing platforms in a single print, with no assembly and no requirements for exterior or commercial electrodes. Due to the flexibility, low-waste, and rapid prototyping of AM, there is scope for this work to be able to span and impact a plethora of research areas.
An application-driven perspective on wireless sensor network security (2006)

Wireless sensor networks (WSNs) have recently attracted a lot of interest due to the range of applications they enable. Unfortunately, WSNs are exposed to numerous security threats that can adversely affect the success of important applications. Securing WSNs is challenging due to their unique nature as an application and a network, and due to their limited capabilities. In this paper, we argue that the WSN security research generally considers mechanisms that are modeled after and evaluated against abstract applications and WSN organizations. Instead, we propose that an effective solution for WSNs must be sensitive to the application and infrastructure. We propose an application-specific security context as the combination of a potential attacker's motivation and the WSN vulnerability. The vulnerability is a function of factors such as the sensor field, the WSN infrastructure, the application, protocols and system software, as well the accessibility and the observability of the WSN. To reduce the vulnerability, we argue that WSN design must balance traditional objectives such as energy efficiency, cost, and application level performance with security to a degree proportional to the attacker's motivation. We illustrate this argument via two example applications
RNA Virus-Encoded miRNAs: Current Insights and Future Challenges (2021)

MicroRNAs are small non-coding RNAs that regulate eukaryotic gene expression at the post-transcriptional level and affect a wide range of biological processes. Over the past two decades, numerous virus-encoded miRNAs have been identified. Some of them are crucial for viral replication, whereas others can help immune evasion. Recent sequencing-based bioinformatics methods have helped identify many novel miRNAs, which are encoded by RNA viruses. Unlike the well-characterized DNA virus-encoded miRNAs, the role of RNA virus-encoded miRNAs remains controversial. In this review, we first describe the current knowledge of miRNAs encoded by various RNA viruses, including newly emerging viruses. Next, we discuss how RNA virus-encoded miRNAs might facilitate viral replication, immunoevasion, and persistence in their hosts. Last, we briefly discuss the challenges in the experimental methodologies and potential applications of miRNAs for diagnosis and therapeutics.
Interaction of tetraiodofluorescein with a modified form of aspartate transcarbamylase. (1977)

Low concentrations of the dye tetraiodofluorescein activate native aspartate transcarbamylase (aspartate carbomoyltransferase, carbomoylphosphate:L-aspartate carbomoyltransferase, EC 2.1.3.2), while high concentrations inhibit the enzyme's activity [Jacobsberg, L. B., Kantrowitz, E. R. & Lipscomb, W. N. (1975) J. Biol. Chem. 250, 9238-9249]. This dye is now shown to produce similar effects upon a modified form of aspartate transcarbamylase produced by Escherichia coli grown in a culture medium supplemented with thiouracil. Significantly, the ATP-induced activation is reduced in the modified form of the enzyme to the same extent as is the tetraiodofluorescein-induced activation. Thus, a relationship is demonstrated between the internal mechanisms by which ATP and tetraiodofluorescein activate aspartate transcarbamylase.
Excited-State Triplet-Triplet Absorption in αNPO (1987)

Time-resolved excited-state triplet-triplet absorption measurements in αNPO solutions were performed. A concentration quenching effect on the excited absorption and fluorescence spectra, due to excimer formation, was seen. A numerical analysis of the results yielded the rate constants for intersystem crossing, triplet quenching by O 2 , triplet self-quenching, and excimer formation.
Enantio- and diastereoselective synthesis of β-substituted-δ-aminoboronic esters from nitriles (2013)

The first stereocontrolled synthesis of the title δ-aminoboronic esters—proceeding from commercially available nitriles—via a reduction, Brown’s ‘allyl’ boration reaction, a Boc-protection, a hydroboration, an oxidative elimination of α-pinene, and an esterification reaction, has been reported in excellent enantio- and diastereoselectivities.
Nutrition in the intensive care unit — you must breathe what you eat (2016)

The imprecision in prescribing of enteral nutrition in critically ill patients must result in occasions of overfeeding as well as underfeeding. Overfeeding could cause increased CO<sub>2</sub> production and thus increased work of breathing and prolonged ventilator dependence. This possibility is supported by the limited relevant literature. We examined this possibility mathematically using the data in The Augmented versus Routine Approach to Giving Energy Trial (TARGET) feasibility study and in its main study protocol. Patients in the energy-dense feeding arm will receive 50% more calories and produce 52% more CO<sub>2</sub> than patients in the standard feeding arm. The full TARGET study is ideally positioned to answer the practical clinical question of whether increased feeding in critically ill patients can be delivered without prolonging ventilator dependence.
In vitro assessment of the inflammatory breast cancer cell line SUM 149: Discovery of two single nucleotide polymorphisms in the RNase L gene. (2011)

196 Background: Inflammatory breast cancer (IBC) is a rare, aggressive form of breast cancer, accounting for 5% of breast cancers diagnosed annually in the United States. Understanding the distinct biology of IBC could help provide novel treatment targets. We sought to evaluate whether or not the IBC cell lines SUM 149 and SUM 190 demonstrated evidence of viral infection. Methods: We performed single nucleotide polymorphism (SNP) genotyping for 2 variants of the ribonuclease (RNase) L gene that have been correlated with the risk of prostate cancer due to a possible viral etiology. We also performed proliferation assays; developed dose response curves to assess the treatment effect of interferon-alpha (IFN-a); and assayed for evidence of the putative human mammary tumor virus (HMTV, which has been implicated but not definitively associated with IBC,) in the DNA and RNA of SUM 149 cells. Results: According to our allelic discrimination SNP assay, 2/2 IBC cell lines were homozygous for the 462 and 541 variants, whereas 0/10 non-IBC cell lines were homozygous positive for the 462 variant (p = 0.015) and 2/10 non-IBC cell lines contained homozygous alleles for the 541 variant (p = 0.52). We also found a dose and time-dependent decrease in the proliferation of SUM 149 IBC cells treated with IFN-a. In contrast, non-IBC cell lines did not show a dose-response decrease in cell proliferation. Our reverse transcriptase polymerase chain reaction (RT-PCR) and Southern blot analysis for the env/LTR and late LTR sequences of the putative HMTV revealed no evidence of the putative viral genome. Conclusions: We discovered 2 SNPs, in the 462 and 541 variants of the RNase L gene, that were homozygously mutated in IBC cell lines but the 462 variant was absent in non-IBC lines. Our discovery of these mutated SNPs present in IBC cell lines suggests a possible genetic risk factor for IBC. In our study, the IBC cell line SUM 149 demonstrated a direct and specific response to treatment with IFN-a, an antiviral agent. We noted no evidence of HMTV infection in that cell line. Further studies of the prevalence and significance of the RNase L 462 and 541 variants in human IBC tissue specimens are warranted to validate our in vitro findings.
Synthetic Self-Localizing Ligands That Control the Spatial Location of Proteins in Living Cells (2013)

Small-molecule ligands that control the spatial location of proteins in living cells would be valuable tools for regulating biological systems. However, the creation of such molecules remains almost unexplored because of the lack of a design methodology. Here we introduce a conceptually new type of synthetic ligands, self-localizing ligands (SLLs), which spontaneously localize to specific subcellular regions in mammalian cells. We show that SLLs bind their target proteins and relocate (tether) them rapidly from the cytoplasm to their targeting sites, thus serving as synthetic protein translocators. SLL-induced protein translocation enables us to manipulate diverse synthetic/endogenous signaling pathways. The method is also applicable to reversible protein translocation and allows control of multiple proteins at different times and locations in the same cell. These results demonstrate the usefulness of SLLs in the spatial (and temporal) control of intracellular protein distribution and biological processes, opening a new direction in the design of small-molecule tools or drugs for cell regulation.
A survey of stroke-based rendering (2003)

This tutorial describes several stroke-based rendering (SBR) algorithms. SBR is an automatic approach to creating nonphotorealistic imagery by placing discrete elements such as paint strokes or stipples.
Fuzzy logic systems for engineering: a tutorial (1995)

A fuzzy logic system (FLS) is unique in that it is able to simultaneously handle numerical data and linguistic knowledge. It is a nonlinear mapping of an input data (feature) vector into a scalar output, i.e., it maps numbers into numbers. Fuzzy set theory and fuzzy logic establish the specifics of the nonlinear mapping. This tutorial paper provides a guided tour through those aspects of fuzzy sets and fuzzy logic that are necessary to synthesize an FLS. It does this by starting with crisp set theory and dual logic and demonstrating how both can be extended to their fuzzy counterparts. Because engineering systems are, for the most part, causal, we impose causality as a constraint on the development of the FLS. After synthesizing a FLS, we demonstrate that it can be expressed mathematically as a linear combination of fuzzy basis functions, and is a nonlinear universal function approximator, a property that it shares with feedforward neural networks. The fuzzy basis function expansion is very powerful because its basis functions can be derived from either numerical data or linguistic knowledge, both of which can be cast into the forms of IF-THEN rules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Input-Output Stability Design of an Ammonium Based Aeration Controller for Wastewater Treatment (2018)

Ammonium feedback is commonly used for controlling the aeration in wastewater treatment plants having biological nitrogen removal. The paper proposes the use of a PI controller tuning method based on a simplified identified model with Hammerstein structure. The Hammerstein model accounts for the delay of the process caused by the settler, the multiple bioreactors dynamics and the main nonlinear process effects. The controller tuning method exploits the Popov inequality for a pre-computation of (a subset of) the stability region of the closed loop system as a function of the PI-controller parameters, quantified in terms of the maximum loop delay of the system. The controller parameters are selected in the computed stability region. In the numerical study, the plant is identified as a Hammerstein model using a recently published method, here extended to identify multiple bioreactor tank dynamics. The identification data is obtained from a high fidelity simulator, which is also used for evaluation of the proposed controller tuning method. The results show that the proposed procedure results in a PI-controller tuning with predictable stability properties and a good performance.
Stereotactic Device for Gamma Knife Radiosurgery in Experimental Animals: Technical Note (2006)

The modified animal stereotactic frame described herein can be used for both the production of experimental animal models and for performing radiosurgery with a common apparatus.
Supplementary Table S2 from Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes (2023)

&lt;p&gt;Tumor percentages estimated from H&amp;E images and comparison between HR, ovaHRDScar and Telli2016 status.&lt;/p&gt;
Synthesis and characterization of bactericidal oligopeptides designed on the basis of an insect anti-bacterial peptide (1999)

Defensin from a beetle, Allomyrina dichotoma, is known to have anti-bacterial activity against Gram-positive bacteria. This peptide, which comprises 43 amino acid residues, was effective against methicillin-resistant Staphylococcus aureus. We identified the active site of beetle defensin by measuring anti-bacterial activity against S. aureus of 64 overlapping 12-mer peptides with either a free carboxylate or a free amide group at their C-termini. An LCAAHCLAIGRR-NH2 (19L-30R-NH2) fragment showed the greatest activity of the synthetic oligopeptides. The 19L-30R-NH2 fragment was effective against both Gram-positive and Gram-negative bacteria. CD spectra showed that the 19L-30R-NH2 fragment formed an alpha-helical structure in the lipidic environment. The anti-bacterial effect of the 19L-30R-NH2 fragment was due to its interaction with bacterial membranes, judging from the leakage of liposome-entrapped glucose. Its anti-bacterial activity was increased when certain amino acid residues were replaced. Truncated peptides having had some amino acids removed from the N-terminus of the 19L-30R-NH2 fragment (8-10-mer peptides) still had strong anti-bacterial activity. Deleting some amino acids from the C-terminal region of the fragment dramatically reduced activity, indicating that the C-terminal region of the 19L-30R-NH2 fragment, i.e. RR-NH2, is important for exerting anti-bacterial activity. The AHCLAIGRR-NH2 (22A-30R-NH2) fragment and its analogues exhibited about 3-fold and 9-12-fold higher activity against S. aureus than did the 19L-30R-NH2 fragment, and these analogues were effective against methicillin-resistant S. aureus and Pseudomonas aeruginosa isolated from patients. These oligopeptides showed no haemolytic activity and did not inhibit the growth of murine fibroblast cells.
Tacrine–Trolox Hybrids: A Novel Class of Centrally Active, Nonhepatotoxic Multi-Target-Directed Ligands Exerting Anticholinesterase and Antioxidant Activities with Low In Vivo Toxicity (2015)

Coupling of two distinct pharmacophores, tacrine and trolox, endowed with different biological properties, afforded 21 hybrid compounds as novel multifunctional candidates against Alzheimer's disease. Several of them showed improved inhibitory properties toward acetylcholinesterase (AChE) in relation to tacrine. These hybrids also scavenged free radicals. Molecular modeling studies in tandem with kinetic analysis exhibited that these hybrids target both catalytic active site as well as peripheral anionic site of AChE. In addition, incorporation of the moiety bearing antioxidant abilities displayed negligible toxicity on human hepatic cells. This striking effect was explained by formation of nontoxic metabolites after 1 h incubation in human liver microsomes system. Finally, tacrine-trolox hybrids exhibited low in vivo toxicity after im administration in rats and potential to penetrate across blood-brain barrier. All of these outstanding in vitro results in combination with promising in vivo outcomes highlighted derivative 7u as the lead structure worthy of further investigation.
Laparoscopic and robotic radical prostatectomy (2006)

Radical retropubic prostatectomy is the current gold standard for surgical removal of the prostate gland. Recently, laparoscopic radical prostatectomy has been developed in an attempt to decrease surgical morbidity, and the technical difficulty of laparoscopy has been countered with the development of the da Vinci robotic interface. Studies that have compared the minimally invasive approaches with the traditional open approach have reported comparable perioperative outcomes. While long-term oncological data are available for open prostatectomy, there are only short-term studies available for laparoscopic prostatectomy. Functional outcomes, including urinary continence and sexual function, appear to be similar between the surgical approaches in the short term. However, currently, costs appear to favor open surgery, with the da Vinci-assisted prostatectomy having the highest expenses. Longer-term data are required to confidently determine the optimal balance between morbidity, oncological efficacy, functional outcomes and cost among the differing surgical approaches.
Distributed-directory scheme: Stanford distributed-directory protocol (1990)

The Stanford distributed-directory (SDD) cache-coherence protocol, based on a singly linked list of distributed directories, is examined. Sharing-list additions and removals are explained diagramatically. Reads, writes, pending signals, replacement, and synchronization are discussed. Replacing lines linked in a list is done by invalidating the lower part of the list. A doubly linked list may be used to patch the list in case of replacements. However, in practice, performance improvement depends on the list lengths and access patterns. A distributed-directory cache-coherence protocol allows efficient implementation of locks at minimal extra cost. The SDD protocol allows a lock implementation that minimizes network traffic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Domain reversal and nonstoichiometry in lithium tantalate (2001)

Recent studies have shown that lithium nonstoichiometry has a tremendous influence on domain reversal characteristics in ferroelectric lithium tantalate. This work presents a systematic study of the domain reversal characteristics such as threshold coercive fields for domain reversal, domain stabilization times, “backswitching” phenomena, domain switching and wall pinning times, and sideways wall mobility in near-stoichiometric LiTaO3 with Li/(Li+Ta)∼0.498. These properties are contrasted with those of congruent LiTaO3 [Li/(Li+Ta)∼0.485]. A qualitative model is proposed based on nonstoichiometric dipolar defects to explain the dependence of threshold coercive field on defect density, and on repeated field cycling, the origin of domain backswitching, and domain stabilization times.
Technical Considerations for the Use of REBOA in the Management of Placenta Accreta Spectrum (2022)

In recent years, the use of resuscitative endovascular balloon occlusion of the aorta (REBOA) has become popular to prevent or treat massive bleeding due to placenta accreta spectrum (PAS). There are multiple variations in the use of REBOA in this context, and although the experience of vascular surgeons with aortic balloons is extensive, there are particularities in the management of these devices in the obstetric population that deserve to be discussed. We discuss some technical considerations or “lessons learned” in our center that may be useful for other groups starting to use REBOA for PAS. Although REBOA is a useful strategy to prevent or treat massive bleeding due to PAS, its incorporation into management protocols must be carried out in a programmed and supervised manner.
Analyzing microarray data using cluster analysis (2003)

As pharmacogenetics researchers gather more detailed and complex data on gene polymorphisms that effect drug metabolizing enzymes, drug target receptors and drug transporters, they will need access to advanced statistical tools to mine that data. These tools include approaches from classical biostatistics, such as logistic regression or linear discriminant analysis, and supervised learning methods from computer science, such as support vector machines and artificial neural networks. In this review, we present an overview of another class of models, cluster analysis, which will likely be less familiar to pharmacogenetics researchers. Cluster analysis is used to analyze data that is not a priori known to contain any specific subgroups. The goal is to use the data itself to identify meaningful or informative subgroups. Specifically, we will focus on demonstrating the use of distance-based methods of hierarchical clustering to analyze gene expression data.