gebhart/patrepeval huggingface dataset:
Graphene oxide for electrochemical sensing applications (2011)

By exploiting the presence of abundant carboxylic groups (–COOH) on graphene oxide (GO) and using EDC–NHS (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride–N-hydroxysuccinimide) chemistry to covalently conjugate protein molecules, we demonstrate a novel electrochemical immunosensor for detection of antibody–antigen (Rabbit IgG–AntiRabbit IgG) interactions. The interactions were verified using Electrochemical Impedance Spectroscopy (EIS). Although GO is known to be a poor conductor, the charge transfer resistance (RP) of a GO modified glassy carbon electrode (GCE) was found to be as low as 1.26 Ω cm2. This value is similar to that obtained for reduced graphene oxide (RGO) or graphene and an order of magnitude less than bare GCE. The EIS monitored antibody–antigen interactions showed a linear increase in RP and the overall impedance of the system with increase of antibody concentration. Rabbit IgG antibodies were detected over a wide range of concentrations from 3.3 nM to 683 nM with the limit of detection (LOD) estimated to be 0.67 nM. The sensor showed high selectivity towards Rabbit IgG antibody as compared to non-complementary myoglobin. RGO modified GCE showed no sensing properties due to the removal of carboxylic groups which prevented subsequent chemical functionalization and immobilization of antigen molecules. The sensitivity and selectivity achievable by this simple label free technique hint at the possibility of GO becoming the electrode material of choice for future electrochemical sensing protocols.
Improvements in the Tolerability Profile of 2′- <i>O</i> -Methoxyethyl Chimeric Antisense Oligonucleotides in Parallel with Advances in Design, Screening, and Other Methods (2021)

The development process of antisense oligonucleotides (ASOs) as therapeutic agents in humans has advanced through the implementation of chemical compound modifications as well as increasingly sophisticated toxicological preclinical screening techniques. The Ionis Integrated Safety Database was utilized to determine if advances in ASO screening and clinical lead identification methods have improved the tolerability profiles of 2'-<i>O</i>-methoxyethyl (2'MOE)-modified ASOs as a class, relative to the first 2'MOE ASO approved for use in humans, mipomersen. Tolerability was assessed by the incidence and percentage of subcutaneous doses leading to adverse events at the injection site or flu-like reactions (FLRs), as well as by the incidence of dose discontinuations due to these events. In randomized placebo-controlled phase 1 and phase 2 trials, the incidence of each measure of tolerability was lower in the test group of 12 ASOs (713 ASO-treated subjects) compared with the reference, mipomersen (266 ASO-treated subjects); with the most marked reduction in the incidence of FLRs (0.6% vs. 9.4%). A similar reduction in the incidence of dose discontinuation due to FLRs was also observed (0.2% vs. 0.9%). When compared with mipomersen, 8 of 12 ASOs showed significant improvements in their respective mean percentage of doses leading to adverse events at the injection site, whereas 7 ASOs showed a significant improvement in mean percentage of doses leading to FLRs. These results support an overall improvement in the tolerability profile in 2'MOE ASOs that entered development after mipomersen, in parallel with advances in the drug discovery screening process as well as the gains in clinical experience during development of each ASO.
Enhanced AP-1 and NF-κB activities and stability of interleukin 8 (IL-8) transcripts are implicated in IL-8 mRNA superinduction in lung epithelial H292 cells (1998)

Inhibition of protein synthesis may result in superinduction of short-lived transcripts and has been attributed variably to stabilization of transcripts and/or increased gene transcription. Little is known about the kinetics of these processes and relevant transcriptional elements have not been identified. In this study, we describe superinduction of interleukin 8 (IL-8) mRNA, an important inflammatory mediator, in lung epithelial-like H292 cells and identify the underlying molecular mechanisms and their kinetics. Cycloheximide (CHI, 10 microg/ml), an inhibitor of protein synthesis, maximally increased IL-8 mRNA levels 30-fold in H292 cells. Tumour necrosis factor alpha (TNF-alpha), which induced IL-8 mRNA 3-fold, synergized with CHI causing a 150-fold increase at 6 h. CHI early on increased the stability of IL-8 mRNA (from 40 min in cells cultured with medium to more than 4 h with CHI). CHI also increased transcription as shown by transfection with IL-8 promoter constructs. Truncated and mutated constructs identified NF-kappaB and AP-1 binding sites as primary cis-acting elements in IL-8 gene transcription and IL-8 mRNA superinduction. Electrophoretic mobility shift assays indicated that CHI increased NF-kappaB and prolonged AP-1 DNA-binding activities and that the synergism of TNF-alpha and CHI on IL-8 mRNA expression was paralleled by a further increase of AP-1 DNA-binding activity. This synergism was still noticed when 4 h elapsed between the addition of CHI and that of TNF-alpha. Taken together, our results indicate that CHI interferes with both post-transcriptional and transcriptional repressive mechanisms of IL-8 mRNA expression.
The use of acoustical test fixtures for the measurement of hearing protector attenuation. Part I: Review of previous work and the design of an improved test fixture (1986)

This paper gives a comprehensive progress report on the development of objective methods for measuring the attenuation of hearing protection devices (HPD's), and focuses on the use of acoustic test fixtures (ATF's), i.e., artificial heads. While there are many publications on ATF's for the evaluation of circumaural HPD's (earmuffs), only one serious attempt to construct an ATF for the evaluation of intra-aural HPD's (earplugs) could be found. Consequently, no ATF for testing earplugs has been standardized so far, while two standardized ATF's currently exist for testing earmuffs [see ANSI S3.19-1974 (1975) and ISO/DIS 6290 (1983)]. Both ATF's are suited, however, only for production testing and are not designed for HPD-type testing. It is believed that both ATF's do not provide sufficiently high accuracy for HPD-type testing. A new ATF with appropriate circumaural and intra-aural flesh simulations was constructed, including a suitable ear simulator and a cast of an average pinna. Objectives for design and construction of the new ATF are discussed. The effect of using artificial flesh on the insertion loss of earmuffs (max. 5 dB at 125 and/or 250 Hz) and the effect of using a pinna (max. 12 dB lower insertion loss at 2 kHz) were evaluated.
Data Driven Authentication: On the Effectiveness of User Behaviour Modelling with Mobile Device Sensors (2014)

We propose a lightweight, and temporally and spatially aware user behaviour modelling technique for sensor-based authentication. Operating in the background, our data driven technique compares current behaviour with a user profile. If the behaviour deviates sufficiently from the established norm, actions such as explicit authentication can be triggered. To support a quick and lightweight deployment, our solution automatically switches from training mode to deployment mode when the user's behaviour is sufficiently learned. Furthermore, it allows the device to automatically determine a suitable detection threshold. We use our model to investigate practical aspects of sensor-based authentication by applying it to three publicly available data sets, computing expected times for training duration and behaviour drift. We also test our model with scenarios involving an attacker with varying knowledge and capabilities.
A multi-modal sweat sensing patch for cross-verification of sweat rate, total ionic charge, and Na<sup>+</sup> concentration (2019)

Sweat sensors introduced in recent years have targeted a variety of sweat features and biomarkers for non-invasive health monitoring. Amongst these targets, reliable monitoring of sweat rate is crucial due to its modulation of sweat analyte concentrations and its intrinsic significance to numerous medical and physiological health conditions. Here we present a sweat rate sensor structure comprising of electrodes with interdigitated fingers in a microfluidic channel. Each time the accumulating sweat impinges on an electrode finger, the sensor reports a jump in admittance that can be simply and efficiently counted to estimate sweat rate, overcoming selectivity limitations of previously reported sweat rate sensors. We further integrate an impedimetric sensor for measuring total ionic charge concentration and an electrochemical Na<sup>+</sup> sensor, together creating a multi-modal system for analyzing fluid and electrolyte secretion. We demonstrate how low analyte diffusion rates through this microfluidic device allow for multi-purpose sensor function, including utilizing the sweat rate sensor signal to corroborate total ionic sensor measurements. This cross-verification capability ensures data integrity in real time, satisfying a vital consideration for personalized healthcare technologies. We use the presented patch for continuous analysis of sweat rate, total ionic charge concentration, and Na<sup>+</sup> concentration during exercise, while demonstrating how multi-modal cross-verification brings new trust to sensor readings.
Stem Cells and Mesothelioma (2012)

Stem cells are self-renewing cells with the potential to differentiate into other cell types. Physiologically stem cells participate in hematopoiesis, wound healing, neuroregeneration, and many other important biological processes. It has been hypothesized that stem cells play a role in carcinogenesis. Although controversial, stem cell origin of cancers such as breast and prostate carcinomas and glioblastoma have been reported (Al-Hajj, 2003; Collins, 2005; Singh, 2004). In addition, stem cells are reported to be in the tumor microenvironment and potentially contribute to the tumorigenic process (Bergfeld & DeClerck, 2010). Such findings offer potentially new targets for tumor therapy.
Machinery for the Re-Education of a Delinquent Dictator (1983)

Other| December 01 1983 Machinery for the Re-Education of a Delinquent Dictator Doug Hall Doug Hall Search for other works by this author on: This Site PubMed Google Scholar Afterimage (1983) 11 (5): 28–29. https://doi.org/10.1525/aft.1983.11.5.28a Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Doug Hall; Machinery for the Re-Education of a Delinquent Dictator. Afterimage 1 December 1983; 11 (5): 28–29. doi: https://doi.org/10.1525/aft.1983.11.5.28a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentAfterimage Search This content is only available via PDF. © 1983 by The Regents of the University of California1983 Article PDF first page preview Close Modal You do not currently have access to this content.
Chronic Alcoholism Impedes the Recovery of Renal Function following Renal Ischemia (1991)

The recovery of renal function following renal ischemia was studied using rats fed for 1-, 3-, and 5-week periods with an alcoholic diet (ethanol provided 36% of total calories). Renal ischemia was produced by clamping the renal artery and vein for 20 min. Renal function was determined 24 hr after the ischemia. In the absence of ischemic insult, the renal function of rats fed with an alcoholic diet for 1, 3, and 5 weeks was not significantly different from those of nonalcoholic rats. In nonalcoholic rats, renal function (24 hr postischemia) were: glomerular filtration rate (GFR) 430.4 +/- 29.6 microliters/min/g KW (kidney weight), renal plasma flow rate (RPFR) 1.4 +/- 0.17 ml/min/g KW, and fractional sodium excretion (FENa) 2.0 +/- 0.04% (mean +/- SE). Postischemic renal function of rats on 1- and 3-week alcoholic diets were essentially the same as that of the control rats. However, the 24-hr postischemic renal function of 5-week alcoholic diet rats was significantly depressed. The values were only 117.2 +/- 35.2 microliters/min/g KW (p less than 0.05) for GFR, 0.31 +/- 0.12 ml/min/g KW (p less than 0.05) for RPFR, and 7.46 +/- 3.59% for FENa. The present results demonstrate that the rat kidney subjected to prolonged alcohol ingestion was more susceptible to renal insult than a nonalcoholic kidney.
Inferring spatial layout from a single image via depth-ordered grouping (2008)

Inferring the 3D spatial layout from a single 2D image is a fundamental visual task. We formulate it as a grouping problem where edges are grouped into lines, quadrilaterals, and finally depth-ordered planes. We demonstrate that the 3D structure of planar objects in indoor scenes can be fast and accurately inferred without any learning or indexing.
Transgenerational epigenetic effects of the endocrine disruptor vinclozolin on pregnancies and female adult onset disease (2008)

Endocrine disruptor exposure during gonadal sex determination was previously found to induce male rat adult onset transgenerational disease (F1-F4 generation), and this was associated with an alteration in the epigenetic (i.e., DNA methylation) programming of the male germ line. The current study was designed to characterize the transgenerational disease phenotypes of the female adult offspring. Pregnant rats (F0 generation) were treated transiently with vinclozolin (i.e., fungicide with anti-androgenic activity) on embryonic (E) days E8-E14 of gestation. F1 control and vinclozolin generation offspring from different litters were mated to produce F2 offspring, and similarly F2 generation animals produced F3 generation offspring. Observations demonstrated that 9 out of 105 pregnant rats (8.6%) from the vinclozolin F1-F3 generations exhibited uterine hemorrhage and/or anemia late in pregnancy. None (0 out of 82) of the control F1-F3 generation females had similar pregnancy problems. Complete blood cell counts and serum chemistry profiles demonstrated that selected vinclozolin generation animals, but not controls, exhibited marked regenerative anemia in late pregnancy. Examination of kidney histology revealed moderate or severe glomerular abnormalities in 67% of the vinclozolin F2 and F3 generation adult females compared with 18% of the controls. Adult female vinclozolin generation animals also developed various types of tumors in 6.5% of the animals (11 out of 170), while 2% of control-line animals (3 out of 151) developed mammary tumors. Observations demonstrate that vinclozolin exposure during gonadal sex determination promotes a transgenerational increase in pregnancy abnormalities and female adult onset disease states.
An Analytic and Empirical Evaluation of Return-on-Investment-Based Active Learning (2015)

Return-on-Investment (ROI) is a costconscious approach to active learning (AL) that considers both estimates of cost and of benefit in active sample selection. We investigate the theoretical conditions for successful cost-conscious AL using ROI by examining the conditions under which ROI would optimize the area under the cost/benefit curve. We then empirically measure the degree to which optimality is jeopardized in practice when the conditions are violated. The reported experiments involve an English part-of-speech annotation task. Our results show that ROI can indeed successfully reduce total annotation costs and should be considered as a viable option for machine-assisted annotation. On the basis of our experiments, we make recommendations for benefit estimators to be employed in ROI. In particular, we find that the more linearly related a benefit estimate is to the true benefit, the better the estimate performs when paired in ROI with an imperfect cost estimate. Lastly, we apply our analysis to help explain the mixed results of previous work on these questions.
Correlation Clustering of Stable Angina Clinical Care Patterns for 506 Thousand Patients (2017)

Though clinical guidelines provide a uniform regulation for medical decisions, doctors have great freedom in daily clinical practice. This freedom leads to regional preferences of certain clinical pathways, the intercenter professional links, and geographical locality and coupled with quantifiable consequences in terms of care costs and periprocedural risk of patients.
Graph Database Applications and Concepts with Neo4j (2013)

Graph databases (GDB) are now a viable alternative to Relational Database Systems (RDBMS). Chemistry, biology, semantic web, social networking and recommendation engines are all examples of applications that can be represented in a much more natural form. Comparisons will be drawn between relational database systems (Oracle, MySQL) and graph databases (Neo4J) focusing on aspects such as data structures, data model features and query facilities. Additionally, several of the inherent and contemporary limitations of current offerings comparing and contrasting graph vs. relational database implementations will be explored.
Improved specificity for detection of Mycobacterium bovis in fresh tissues using IS6110 real-time PCR (2011)

The IS6110_T assay provides a PCR based assay system that is compatible with current diagnostic protocols for the detection of M. bovis in the USA and compliments current testing strategies.
Statistical approach for detection and localization of a fluorescing mouse tumor in Intralipid (2005)

We present a method for detecting and localizing a fluorescing tumor obscured underneath several millimeters of a multiply scattering, homogeneous medium from fluorescence measurements made above the surface. Using a statistical model of the measurement system, we develop approaches for detection by use of a binary hypothesis testing approach and localization by use of maximum-likelihood estimation. We also compute the probability of tumor detection and the Cramér-Rao lower bound for the localization estimate error, which are performance metrics that could potentially be optimized in an experimental design. We validate the methods in an experimental study involving an excised mouse tumor tagged with a new folate-indocyanine dye and obscured under a tissue-simulating lipid suspension.
Screening for Bipolar Disorder in a Primary Care Practice (2005)

In an urban general medicine clinic, a positive screen for bipolar disorder appears to be common, clinically significant, and underrecognized. Because of the risks associated with treating bipolar disorder with antidepressant monotherapy, efforts are needed to educate primary care physicians about the screening, management, and pharmacotherapy of bipolar disorders.
Mechanical Characteristics of Male Urethral Catheterization: Simulator and Cadaveric Donor Study (2019)

University of Minnesota M.S.M.E. thesis.January 2019. Major: Mechanical Engineering. Advisor: Timothy Kowalewski. 1 computer file (PDF); viii, 68 pages.
Optimization of Displacements in Porous Media Using Rate Control (2001)

Abstract In many applications involving the injection of a fluid in a porous medium to displace another, a main objective is the maximization of the displacement efficiency. For a fixed arrangement of injection and production wells, such optimization is possible by controlling the injection rate policy. This paper is an abbreviated version of Ref. [1], where we described a fundamental approach based on optimal control theory, for the simplified case when the fluids are miscible, of equal viscosity and in the absence of dispersion and gravity effects. Both homogeneous and heterogeneous porous media are considered. The optimal injection policy that maximizes the displacement efficiency at the time of arrival of the injected fluid, is of the "bang-bang" type, namely where the rates take their extreme values in the range allowed. This result applies to both homogeneous and heterogeneous media. Examples in simple geometries and for various constraints are shown. In the heterogeneous case, the effect of the permeability heterogeneity, particularly its spatial correlation structure, on diverting the flow paths, is analysed. "Bang-bang" injection remains the optimal approach, compared to constant rate, if they were both designed under the assumption that the medium was homogeneous.
DNA Vaccines for Immunodeﬁciency Viruses (2002)

HIV-1, ﬁrst recognized in 1983, now scourges the world as the fourth leading cause of death. Most HIV-1 infections strike sexually active young adults, depleting both developed and developing countries of innovators, breadwinners, and parents. Why has this emergent epidemic so devastated populations, and why, with the tools of modern biology, has it been so hard to develop a vaccine. Within 4 years of the ability to culture polio virus, the Salk vaccine was reaching the public. We have been able to grow HIV-1 and have known the complete sequence of its genome for 15 years, yet are still without a vaccine. What is it about this virus that so challenges our ability to imprint an immune system with a protective memory response?
Novel Supramolecular Block Copolymer: A Polyrotaxane Consisting of Many Threaded α- and γ-Cyclodextrins with an ABA Triblock Architecture (2009)

10.1021/ma900302x
Sequence Diversity of <i>Pseudomonas aeruginosa</i> : Impact on Population Structure and Genome Evolution (2000)

Comparative sequencing of Pseudomonas aeruginosa genes oriC, citS, ampC, oprI, fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes of Salmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle of P. aeruginosa.
Methods for protein delivery into cells: from current approaches to future perspectives (2020)

The manipulation of cultured mammalian cells by the delivery of exogenous macromolecules is one of the cornerstones of experimental cell biology. Although the transfection of cells with DNA expressions constructs that encode proteins is routine and simple to perform, the direct delivery of proteins into cells has many advantages. For example, proteins can be chemically modified, assembled into defined complexes and subject to biophysical analyses prior to their delivery into cells. Here, we review new approaches to the injection and electroporation of proteins into cultured cells. In particular, we focus on how recent developments in nanoscale injection probes and localized electroporation devices enable proteins to be delivered whilst minimizing cellular damage. Moreover, we discuss how nanopore sensing may ultimately enable the quantification of protein delivery at single-molecule resolution.
A General Method for the Separation of Enantiomeric<i>trans</i>-2-Substituted Cyclohexanols (1990)

An number of different racemic trans-2-substituted cyclohexanols has been prepared in high optical purity by optical resolution of the respective 2′-substituted cyclohexyl butanoates with the aid of commercially available lipases.