gebhart/patrepeval huggingface dataset:
Sonoporation Delivery of Interleukin-27 Gene Therapy Efficiently Reduces Prostate Tumor Cell Growth In Vivo (2011)

We have examined the potential of a novel cytokine, interleukin-27 (IL-27), for gene therapy of prostate cancer. IL-27 is the most recently characterized member of the family of heterodimeric IL-12-related cytokines and has shown promise in halting tumor growth and mediating tumor regression in several cancer models. In the present study, we examined the efficacy of a new mode of gene delivery to prostate tumors: low-frequency ultrasound irradiation or "sonoporation." We also examined the potential of IL-27 gene delivery by sonoporation to treat and reduce the growth of prostate cancer in vivo. We used three models of immune-competent prostate adenocarcinoma and characterized the tumor-growth reduction, gene-profile expression, and effector cellular profiles. Our results suggest that IL-27 can be effective in reducing tumor growth and can help enhance accumulation of effector cells in prostate tumors in vivo. These results are promising, because they are potentially relevant to developing novel therapies that can be translated by using the novel and effective sonoporation gene-therapy delivery strategy.
105 Burning Heart - An Animal Model of Chronic Heart Failure Following Severe Burn Injury (2023)

Abstract Introduction Our clinical research unveiled chronic heart failure with preserved ejection fraction (HFpEF) as a long-term sequel in survivors of severe pediatric burn injury due to a yet unknown molecular pathomechanism. Applying a standardized rat model, we systematically determined the pathophysiological impact of burn injury on long-term cardiac performance to uncover systemic and molecular pathomechanisms that may cause post-burn HFpEF development. Methods Male adolescent SD-rats were subjected to a 60 % total body surface area (TBSA) full-thickness burn- or sham-trauma and subsequently characterized after burn-injury by serial transthoracic echocardiography, bulk myocardial next-generation sequencing and proteomics as well as RT-PCR, immuno-blotting (IB), histology and plasma proteomics for cardiac performance and molecular alterations, respectively, at 3, 7, 30 and 90days. Results In comparison to the sham-group (SG), animals from the burn-group (BG) recapitulated typical post-burn clinical traits, such as significant loss in body weight (BG 27 % less than SG at 30d, p&amp;lt; 0.05) or skeletal muscle wasting (27 % less at 30d, p&amp;lt; 0.05) in accord with elevated molecular atrophy markers. We show post-burn cardiac muscle wasting (BG 22 % less at 30d, p&amp;lt; 0.05) and persistent markers of cardiac dysfunction in accord with significant histological cardiomyocyte hypotrophy (BG -8 % at 30d, p&amp;lt; 0.05) and significantly diminished left ventricular (LV) global longitudinal strain and isovolumic relaxation time in BGs, while LV-EF remained unchanged. Weighted gene network correlation analysis from bulk myocardial NGS and clinical traits related activation of immunological and pro-fibrotic pathways in post-burn injury hearts to cardiac dysfunction in BGs. Subsequent RT-PCR and histology confirmed significant myocardial accumulation of cardio-depressive damage associated molecular patterns (i.e., S100A8 and A9) and infiltration by granulocytes and monocytes as well as significant LV fibrosis. Serial plasma proteomic analysis indicated elevated plasma levels of S100A8 and A9 and other heart failure markers that mirrored similar changes in human post-burn plasma samples. Conclusions Here we report the development of HFpEF as a novel systemic consequence of severe burn injury in a rodent model, which warrants further mechanistic and translational studies. Cardiac inflammation and fibrosis are known to negatively impact cardiac performance and may be mechanistic key findings that will guide further therapeutic studies and subsequent validation of post-burn heart failure biomarkers Applicability of Research to Practice This model is part of a translational and interdisciplinary experimental and clinical effort to inform pathophysiology and mechanistics of long-term heart failure in burn patients. Echocardiographic data and parameters from this model are currently being used to evaluate adult survivors of severe burn injury for signs of HFpEF.
Proportionally constantquantitative transmission ofnucleolin andprotein B23in cycling cancercells (1995)

Objective-To investigate whetherandto whatextentthetwomajorAgNOR proteins, nucleolin andprotein B23,aremaintainedafterone celldivisionin proliferating cells. Design-Usingthree asynchronously growinghuman cancercelllines, TG, SJNKP,andCHP 212cells, nucleolin and protein B23werefirst identified onSDSpolyacrylamide separated nucleolar proteins, transferred tonitrocellulose and silverstainedfor AgNOR proteins. Measurement ofdoubling timeindicated aperiod veryclose to24hforeachofthe celllines. Toquantify thepercentage of nucleolin andprotein B23maintained in daughter cells after duplication, cells were labelled with[35S]-methionine anda 24h coldchaseperformed. Nucleolin andproteinB23labelling wasevaluated bydensitometric analysis on nitrocellulose autoradiograms.
Automated memory analysis: improving the design and implementation of iterative algorithms (2005)

Historically, iterative solvers have been designed to achieve the best numerical accuracy for a given number of floating-point operations. However, this approach ignores the cost of memory access, which has not seen nearly as rapid of an improvement as floating-point costs. To reduce the time to solution, we need to address both the numerical efficiency and memory efficiency of an iterative algorithm. We contend that it is possible to evaluate the memory efficiency of an iterative algorithm during the design process. There are two techniques for a priori evaluation of memory efficiency: manual and automated memory analysis. Manual memory analysis, which involves the derivation of analytical expression for data movement, is a laborious, error-prone process that is too complex to perform on a regular basis. Automated memory analysis is possible through the use of the Sparse Linear Algebra Memory Model (SLAMM) language processor. The SLAMM language processor accepts as input Matlab code and outputs a suitably transformed Matlab source that contains blocks of code that predict data movement. We demonstrate that the SLAMM language processor accurately predicts the amount of data loaded from the memory hierarchy to the L1 cache (Mbytes L1) to within 20% error for numerous small kernels and complete iterative algorithms on three different compute platforms. SLAMM reduces the time to perform memory analysis from as long as several days to 20 minutes. SLAMM provides the ability to rapidly evaluate the memory efficiency of particular design choices during the design phase of an iterative algorithm. Additionally, we demonstrate how SLAMM is used to improve the memory efficiency of a pre-existing solver.
Brain Disorders Due to Lysosomal Dysfunction (2016)

Recent studies of autophagic and lysosomal pathways have significantly changed our understanding of lysosomes; once thought to be simple degradative and recycling centers, lysosomes are now known to be organelles capable of influencing signal transduction, via the mammalian target of rapamycin complex 1 (mTORC1), and regulating gene expression, via transcription factor EB (TFEB) and other transcription factors. These pathways are particularly relevant to maintaining brain homeostasis, as dysfunction of the endolysosomal and autophagic pathways has been associated with common neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Huntington's, and lysosomal storage disorders, a group of inherited disorders characterized by the intralysosomal buildup of partially degraded metabolites. This review focuses on the cellular biology of lysosomes and discusses the possible mechanisms by which disruption of their function contributes to neurodegeneration. We also review and discuss how targeting TFEB and lysosomes may offer innovative therapeutic approaches for treating a wide range of neurological conditions.
Ellipsometer With Adjustable Wavelength Capability (400 To 2000 Nm) (1988)

Coatings of optical surfaces for certain laser applications are designed to have very specific polarization characteristics. The polarization angle, psi, and the phase shift angle, delta, define the polarization characteristics of a surface at a given wavelength and at a given angle of incidence. Both psi and delta can vary greatly with wavelength and full characterization of the polarization of a coated surface requires the measurement of both psi and delta over a range of wavelengths and not just at single laser wavelengths. An ellipsometer has been built which is capable of expediently measuring both psi and delta at any selected wavelength from 400 to 2000 nanometers at any selected angle of incidence from 45 to 75 degrees. The ellipsometer uses an incanaescent lamp, a mono-chromator, and a silicon or a lead sulfide detector. The operation of the instrument is based on fixed angle settings and signal amplitude readings rather than on null settings and precision angle readings as in most common ellipsometers. Eight digitized signal level readings from a lock-in amplifier are needed for each measurement. A simple calculation gives the values for psi and delta. The ellipsometer is, in its present form, a manually operated prototype. Its construction would lend itself well to full automation and a true wavelength scanning ellipsometer could readily be built. The instrument is described and examples of ellipsometric scans of coatings designed for specific polarization characteristics are shown.
Mutanase from Paenibacillus sp. MP-1 produced inductively by fungal α-1,3-glucan and its potential for the degradation of mutan and Streptococcus mutans biofilm (2010)

Laetiporus sulphureus is a source of α-1,3-glucan that can substitute for the commercially-unavailable streptococcal mutan used to induce microbial mutanases. The water-insoluble fraction of its fruiting bodies from 0.15 to 0.2% (w/v) induced mutanase activity in Paenibacillus sp. MP-1 at 0.35 μ ml(-1). The mutanase extensively hydrolyzed streptococcal mutan, giving 23% of saccharification, and 83% of solubilization of glucan after 6 h. It also degraded α-1,3-polymers of biofilms, formed in vitro by Streptococcus mutans, even after only 3 min of contact.
Synthesis of a Silica-Based Heterogeneous Second Generation Grubbs Catalyst (2002)

The synthesis of a second generation Grubbs catalyst immobilized onto non-porous silica is described. For this purpose, a polymerizable cationic NHC precursor, 1,3-bis(1-mesityl)-4-{[(bicyclo[2.2.1]hept-5-en-2-ylcarbonyl)oxy]methyl}-4,5-dihydro-1H-imidazol-3-ium tetrafluoroborate (5) was prepared and characterized by X-ray analysis. Oligomers were prepared therefrom using both the well-defined Schrock initiator Mo(N-2,6-i-Pr2C6H3)(CHCMe2Ph)[OCMe(CF3)2]2 and the first generation Grubbs catalyst Cl2Ru(CHPh)(PCy3)2. Ru-initiated oligomerizations were terminated with ethyl vinyl ether, Mo-initiated oligomerizations were terminated by addition of (EtO)3SiCH2CH2CH2NCO. (EtO)3Si-terminated oligomers obtained by the Wittig-like reaction between the Mo-containing oligomer and the isocyanate were used for the immobilization of the NHC-precursor containing oligomers on non-porous silica. Both oligomerizations were characterized by quantitative consumption of the corresponding initiator. This allowed the controlled synthesis of oligomers via stoichiometry. Using both non-porous and porous silica, degrees of derivatization of 0.04 and 0.02 mmol, respectively, of cationic NHC precursor/g silica were obtained. These precursors were converted into the corresponding NHC's by standard procedures and used for the generation of a heterogeneous second-generation Grubbs catalyst. Ruthenium loadings of 5.3 and 1.3 μmol/g, corresponding to 0.5 and 0.1 weight-% of catalyst were realized. Additionally, coating techniques were applied, where C18-derivatized silica-60 was loaded with oligo-5. Conversion into the corresponding heterogeneous catalyst revealed 4.1 μmol/g, corresponding to 0.4 weight-% of catalyst. All supported catalysts prepared by this approach were successfully used in RCM in slurry type reactions.
Mycotoxin Determination in Foods Using Advanced Sensors Based on Antibodies or Aptamers (2016)

Mycotoxin contamination threatens health and life of humans and animals throughout the food supply chains. Many of the mycotoxins have been proven to be carcinogens, teratogens and mutagens. The reliable and sensitive sensing methods are requested to monitor mycotoxin contamination. Advanced sensors based on antibodies or aptamers boast the advantages of high sensitivity and rapidity, and have been used in the mycotoxin sensing. These sensors are miniaturized, thereby lowering costs, and are applicable to high-throughput modes. In this work, the latest developments in sensing strategies for mycotoxin determination were critically discussed. Optical and electrochemical sensing modes were compared. The sensing methods for single mycotoxin or multiple mycotoxins in food samples were reviewed, along with the challenges and the future of antibody or aptamer-based sensors. This work might promote academic studies and industrial applications for mycotoxin sensing.
Supplementary Figure from Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma (2023)

Supplementary Figure from Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma
β-Synuclein Reduces Proteasomal Inhibition by α-Synuclein but Not γ-Synuclein (2005)

The accumulation of aggregated alpha-synuclein is thought to contribute to the pathogenesis of Parkinson's disease. Recent studies indicate that aggregated alpha-synuclein binds to S6', a component of the 19 S subunit in the 26 S proteasome and inhibits 26 S proteasomal degradation, both ubiquitin-independent and ubiquitin-dependent. The IC(50) of aggregated alpha-synuclein for inhibition of the 26 S ubiquitin-independent proteasomal activity is approximately 1 nm. alpha-Synuclein has two close homologues, termed beta-synuclein and gamma-synuclein. In the present study we compared the effects of the three synuclein homologues on proteasomal activity. The proteasome exists as a 26 S and a 20 S species, with the 26 S proteasome containing the 20 S core and 19 S cap. Monomeric alpha- and beta-synucleins inhibited the 20 S and 26 S proteasomal activities only weakly, but monomeric gamma-synuclein strongly inhibited ubiquitin-independent proteolysis. The IC(50) of monomeric gamma-synuclein for the 20 S proteolysis was 400 nm. In monomeric form, none of the three synuclein proteins inhibited 26 S ubiquitin-dependent proteasomal activity. Although beta-synuclein had no direct effect on proteasomal activity, co-incubating monomeric beta-synuclein with aggregated alpha-synuclein antagonized the inhibition of the 26 S ubiquitin-independent proteasome by aggregated alpha-synuclein when added before the aggregated alpha-synuclein. Co-incubating beta-synuclein with gamma-synuclein had no effect on the inhibition of the 20 S proteasome by monomeric gamma-synuclein. Immunoprecipitation and pull-down experiments suggested that antagonism by beta-synuclein resulted from binding to alpha-synuclein rather than binding to S6'. Pull-down experiments demonstrated that recombinant monomeric beta-synuclein does not interact with the proteasomal subunit S6', unlike alpha-synuclein, but beta-synuclein does bind alpha-synuclein and competes with S6' for binding to alpha-synuclein. Based on these data, we hypothesize that the alpha- and gamma-synucleins regulate proteasomal function and that beta-synuclein acts as a negative regulator of alpha-synuclein.
Surface Stress Effects on Indentation Fracture Sequences (1990)

Ion exchange was used to introduce surface compression in soda‐lime‐silica glass (SLS) and aluminosilicate glass (ALS). In situ observations of the indentation cracking sequences on the modified surfaces were made and compared with those on the base glasses. The initiation point for each crack type formed during the loading and unloading cycle was monitored on the indenter load‐displacement traces. On the base glasses, median (in the SLS) and cone (in the ALS) cracking was observed during the loading cycle. “Modified” median, radial, and lateral cracking was observed in both glasses during unloading. The introduction of the residual compressive surface stress was found to completely suppress all cracking during the loading cycle (up to 100 N) in both the SLS and ALS. In addition, the initiation of the cracks formed during the unloading cycle was shifted to further down in the cycle, i.e., to lower values of the initiation load. A pronounced tendency for a shift in the cracking from median to radial was also observed on the residually stressed surfaces. A similar shift was observed on stress‐free surfaces during unloading as the value of the initiation load decreased for a given peak load.
The robust covariation-based MUSIC (ROC-MUSIC) algorithm for bearing estimation in impulsive noise environments (1996)

This paper presents a new subspace-based method for bearing estimation in the presence of impulsive noise which can be modeled as a complex symmetric alpha-stable (S/spl alpha/S) process. We define the covariation matrix of the array sensor outputs and show that eigendecomposition-based methods, such as the MUSIC algorithm, can be applied to the sample covariation matrix to extract the bearing information from the measurements. A consistent estimator for the marginals of the covariation matrix is presented and its asymptotic performance is studied. The improved performance of the proposed source localization method in the presence of a wide range of impulsive noise environments is demonstrated via Monte Carlo experiments.
Lecture Notes on Requirements Elicitation (1994)

Requirements elicitation is the first of the four steps in software requirements engineering (the others being analysis, specification, and validation). Software engineers use several elicitation techniques. To facilitate teaching these techniques, materials are provided to support an introductory lecture and four lectures on specific techniques: joint application design, brainstorming, interviewing, and the PIECES framework. A role-playing exercise is provided that allows students to experience each of the techniques. Information for instructors includes educational objectives, pedagogical considerations, additional exercises, and a bibliography.
Mutations and Deletions of the TP53 Gene Predict Nonresponse to Treatment and Poor Outcome in First Relapse of Childhood Acute Lymphoblastic Leukemia (2011)

Alterations of the TP53 gene are of particular importance in the relapse stage of childhood ALL, in which they independently predict high risk of treatment failure in a significant number of patients. Therefore, they will aid in future risk assessment of children with ALL relapse.
Integrated microfluidic oxygenator bundles for blood gas exchange in premature infants (2012)

This paper reports the development of a low volume pumpless lung assist device (LAD) composed of a stack of microfluidic single oxygenators units (SOUs) connected in parallel. SOUs are comprised of a microfluidic vascular network (polydimethylsiloxane) and a gas-permeable polycarbonate (PC) membrane to enhance gas exchange between blood and ambient air. We report results from an in vitro test and the first performance test of the LAD in hypoxic newborn piglet in which we show an increase of up to 40% in peripheral oxygen saturation.
HIV-1 RNA Dysregulates the Natural TLR Response to Subclinical Endotoxemia in Kenyan Female Sex-Workers (2009)

Thus, dysregulation of endotoxin tolerance by HIV-1 RNA may exacerbate HIV chronic immune activation and pathogenesis.
So You Want to Teach an iPhone Programming Course? (2020)

Abstract So You Want To Teach an iPhone ProgrammingCourse?AbstractAccording to a Pew Research survey conducted in April and May 2010, an estimated 82 percentof adult Americans now own a mobile phone and nearly 25% of United States adults use mobileapps on their phones. The Apple iPhone was introduced in 2007 and to date has been a culturalphenomonom in addition to being a commercial success. According to Apple's quarterlyearnings, close to 60 million iPhone’s have been sold through the end of June 2010. The successof the iPhone can at least partially be attributed to the iPhone ecosystem consisting of mobiledevice hardware, the iOS operating system, software developer tools, and the App Store – allcreated and controlled by Apple. To date, over 250,000 applications are available in the AppStore, and Apple has reported that over 1 billion dollars in profit has been paid to iPhonedevelopers.Our department strives to keep its curriculum current and to teach courses using best-of-breedtechnologies. For this reason, an undergraduate, upper-level course on iPhone applicationdevelopment is being offered for the first time during the Fall 2010 semester. Our departmenthas been teaching software development for mobile devices since 2002, but this semester will bethe first using Apple development tools for Apple devices.The driving force for creating a course based on the iPhone platform is two-fold: student interestand market demand. When polled about which smartphone platform they were most interestedin, our students overwhelming chose the Apple iPhone over RIM BlackBerry, Google Android,and Micorosoft Windows Mobile. iPhone’s are considered to be at the forefront of changingtechnology and a portion of the draw is the ability of any programmer to develop applications tobe sold through the iPhone App Store. This is particularly appealing as there is a very lowinvestment threshold and shortened time line in developing relevant and available applicationsfor these devices.In this paper we will discuss our experiences teaching the course. Topics will include obtainingfunding, selection and purchasing Macintosh computers for our mobile computing lab, selectionand purchasing of mobile devices, course pedegodgy, textbook selection, student assessment,and unexpected problems will be presented. A discussion about our choices and the reasoningbehind each decision will be added. A section on student feedback conducted at the end of thesemester will be included. Finally, conclusions and lessons learned (or how to avoid commonpitfalls) will be addressed.