gebhart/patrepeval huggingface dataset:
GPR87 Is an Overexpressed G‐Protein Coupled Receptor in Squamous Cell Carcinoma of the Lung (2007)

Lung cancer is the leading cause of cancer death worldwide. The overall 5-year survival after therapy is about 16% and there is a clear need for better treatment options, such as therapies targeting specific molecular structures. G-protein coupled receptors (GPCRs), as the largest family of cell surface receptors, represent an important group of potential targets for diagnostics and therapy. We therefore used laser capture microdissection and GPCR-focused Affymetrix microarrays to examine the expression of 929 GPCR transcripts in tissue samples of 10 patients with squamous cell carcinoma and 7 with adenocarcinoma in order to identify novel targets in non-small cell lung carcinoma (NSCLC). The relative gene expression levels were calculated in tumour samples compared to samples of the neighbouring alveolar tissue in every patient. Based on this unique study design, we identified 5 significantly overexpressed GPCRs in squamous cell carcinoma, in the following decreasing order of expression: GPR87 > CMKOR1 > FZD10 > LGR4 > P2RY11. All are non-olfactory and GRAFS (glutamate, rhodopsin, adhesion, frizzled/taste2, secretin family) classified. GPR87, LGR4 and CMKOR1 are orphan receptors. GPR87 stands out as a candidate for further target validation due to its marked overexpression and correlation on a mutation-based level to squamous cell carcinoma.
Direct Measurements of Heating by Electromagnetically Trapped Gold Nanoparticles on Supported Lipid Bilayers (2010)

Absorption of electromagnetic irradiation results in significant heating of metallic nanoparticles, an effect which can be advantageously used in biomedical contexts. Also, metallic nanoparticles are presently finding widespread use as handles, contacts, or markers in nanometer scale systems, and for these purposes it is essential that the temperature increase associated with electromagnetic irradiation is not harmful to the environment. Regardless of whether the heating of metallic nanoparticles is desired or not, it is crucial for nanobio assays to know the exact temperature increase associated with electromagnetic irradiation of metallic nanoparticles. We performed direct measurements of the temperature surrounding single gold nanoparticles optically trapped on a lipid bilayer, a biologically relevant matrix. The lipid bilayer had incorporated fluorescent molecules which have a preference for either fluid or gel phases. The heating associated with electromagnetic radiation was measured by visualizing the melted footprint around the irradiated particle. The effect was measured for individual gold nanoparticles of a variety of sizes and for a variety of laser powers. The temperatures were highly dependent on particle size and laser power, with surface temperature increments ranging from a few to hundreds of degrees Celsius. Our results show that by a careful choice of gold nanoparticle size and strength of irradiating electromagnetic field, one can control the exact particle temperature. The method is easily applicable to any type of nanoparticle for which the photothermal effect is sought to be quantified.
Electromagnetic Heating for In-Situ Production of Heavy Oil and Bitumen Reservoirs (2011)

Abstract The Electro-Magnetic (EM) method is a newly developed technology aiming at heavy oil and in-situ bitumen production in an environmentally friendly way with smallest possible surface footprint. This paper outlines the process of the development of the new EM technology for heavy oil and in-situ bitumen production. It documents the step-by-step approach following the roadmap from the white-paper technology analysis to the commissioning and performing of field tests. A reservoir simulation example is provided for in-situ production with EM-heating. The current status of the technology is R&amp;D; pilot operation is expected from 2012/13 on.
Record Atmospheric Fresh Water Capture and Heat Transfer with a Material Operating at the Water Uptake Reversibility Limit (2017)

The capture of water vapor at low relative humidity is desirable for producing potable water in desert regions and for heat transfer and storage. Here, we report a mesoporous metal-organic framework that captures 82% water by weight below 30% relative humidity. Under simulated desert conditions, the sorbent would deliver 0.82 g<sub>H2O</sub> g<sub>MOF</sub><sup>-1</sup>, nearly double the quantity of fresh water compared to the previous best material. The material further demonstrates a cooling capacity of 400 kWh m<sup>-3</sup> per cycle, also a record value for a sorbent capable of creating a 20 °C difference between ambient and output temperature. The water uptake in this sorbent is optimized: the pore diameter of our material is above the critical diameter for water capillary action, enabling water uptake at the limit of reversibility.
A Physically-Modified Saline Suppresses Neuronal Apoptosis, Attenuates Tau Phosphorylation and Protects Memory in an Animal Model of Alzheimer's Disease (2014)

Alzheimer's disease (AD), the leading cause of dementia in the aging population, is characterized by the presence of neuritic plaques, neurofibrillary tangles and extensive neuronal apoptosis. Neuritic plaques are mainly composed of aggregates of amyloid-β (Aβ) protein while neurofibrillary tangles are composed of the hyperphosphorylated tau protein. Despite intense investigations, no effective therapy is currently available to halt the progression of this disease. Here, we have undertaken a novel approach to attenuate apoptosis and tau phosphorylation in cultured neuronal cells and in a transgenic animal model of AD. RNS60 is a 0.9% saline solution containing oxygenated nanobubbles that is generated by subjecting normal saline to Taylor-Couette-Poiseuille (TCP) flow under elevated oxygen pressure. In our experiments, fibrillar Aβ1-42, but not the reverse peptide Aβ42-1, induced apoptosis and cell death in human SHSY5Y neuronal cells. RNS60, but not NS (normal saline), RNS10.3 (TCP-modified saline without excess oxygen) or PNS60 (saline containing excess oxygen without TCP modification), attenuated Aβ(1-42)-induced cell death. RNS60 inhibited neuronal cell death via activation of the type 1A phosphatidylinositol-3 (PI-3) kinase-Akt-BAD pathway. Furthermore, RNS60 also decreased Aβ(1-42)-induced tau phosphorylation via (PI-3 kinase-Akt)-mediated inhibition of GSK-3β. Similarly, RNS60 treatment suppressed neuronal apoptosis, attenuated Tau phosphorylation, inhibited glial activation, and reduced the burden of Aβ in the hippocampus and protected memory and learning in 5XFAD transgenic mouse model of AD. Therefore, RNS60 may be a promising pharmaceutical candidate in halting or delaying the progression of AD.
A classical approach to constructing a power flow controller (2003)

A new approach is described for realizing continuous control of power flow in AC power lines. The approach is based on "classical" electrical engineering concepts using rotary transformers in place of a tap changer in a conventional phase-shifting transformer design. This approach has several apparent benefits compared to the recently-introduced power flow controller based entirely on power electronics.
Genetics and the Specificity of the Aging Process (2003)

The identification and study of long-lived mutant animals has provided valuable insights into the mechanisms that limit the life-span of organisms. Findings with the gene SIR2 suggest that the rate of aging can be regulated under certain conditions. Indeed, increased expression of SIR2 lengthens life-span by acting on biological processes that promote survival under conditions of scarcity. In addition, studies of mutant strains of Caenorhabditis elegans, in particular daf-2, clk-1, and isp-1 mutants, suggest that the biology of reactive oxygen species in the mitochondria and elsewhere might be the main determinant of life-span in this organism. Thus, the aging process may be more specific than previously anticipated on evolutionary grounds.
Crystal Structure of an Active Form of Human MMP-1 (2006)

The extracellular matrix is a dynamic environment that constantly undergoes remodelling and degradation during vital physiological processes such as angiogenesis, wound healing, and development. Unbalanced extracellular matrix breakdown is associated with many diseases such as arthritis, cancer and fibrosis. Interstitial collagen is degraded by matrix metalloproteinases with collagenolytic activity by MMP-1, MMP-8 and MMP-13, collectively known as the collagenases. Matrix metalloproteinase 1 (MMP-1) plays a pivotal role in degradation of interstitial collagen types I, II, and III. Here, we report the crystal structure of the active form of human MMP-1 at 2.67 A resolution. This is the first MMP-1 structure that is free of inhibitor and a water molecule essential for peptide hydrolysis is observed coordinated with the active site zinc. Comparing this structure with the human proMMP-1 shows significant structural differences, mainly in the relative orientation of the hemopexin domain, between the pro form and active form of the human enzyme.
The Design of Innovation: Lessons from and for Competent Genetic Algorithms (2002)

7 69 6 A DESIGN APPROACH TO PROBLEM DIFFICULTY 71 1 Design and Problem Difficulty 71 2 Three Misconceptions 72 3 Hard Problems Exist 76 4 The 3-Way Decomposition and Its Core 77 The Core of Intra-BB Difficulty: Deception 5 77 6 The Core of Inter-BB Difficulty: Scaling 83 7 The Core of Extra-BB Difficulty: Noise 88 Crosstalk: All Roads Lead to the Core 8 89 9 From Multimodality to Hierarchy 93 10 Summary 100 7 ENSURING BUILDING BLOCK SUPPLY 101 1 Past Work 101 2 Facetwise Supply Model I: One BB 102 Facetwise Supply Model II: Partition Success 103 3 4 Population Size for BB Supply 104 Summary 5 106 8 ENSURING BUILDING BLOCK GROWTH 109 1 The Schema Theorem: BB Growth Bound 109 2 Schema Growth Somewhat More Generally 111 3 Designing for BB Market Share Growth 112 4 Selection Press ure for Early Success 114 5 Designing for Late in the Day 116 The Schema Theorem Works 6 118 A Demonstration of Selection Stall 7 119 Summary 122 8 9 MAKING TIME FOR BUILDING BLOCKS 125 1 Analysis of Selection Alone: Takeover Time 126 2 Drift: When Selection Chooses for No Reason 129 3 Convergence Times with Multiple BBs 132 4 A Time-Scales Derivation of Critical Locus 142 5 A Little Model of Noise-Induced Run Elongation 143 6 From Alleles to Building Blocks 147 7 Summary 148 10 DECIDING WELL 151 1 Why is Decision Making a Problem? 151
Novel Poly (glycerol-adipate) Polymers Used for Nanoparticle Making: A Study of Surface Free Energy (2008)

Nanoparticles made of biodegradable polymers has become the best approach for nanoparticle making due to their compatibility with the human body. New glycerol adipate polymers with hydroxyl group substituted with different percent of acyl group, sited as figures within the abbreviated name in the text, and triptophan were synthesized and proposed to be used in the preparction of dexamethason phosphate loaded nanoparticles, using the evaporation-deposition technique. The particle forming ability, size and distribution of the nanoparticles might be related to more important physicochemical characteristics, such as the surface properties of the polymers. In this study surface free energies of five derivatives (0%, 20%, 40%, 100% and triptophan 5%) were determined by means of contact angle measurement carried out on films formed on the glass slides KSC Cam 100 instrument. The results were then incorporated into the Fowkes equation, toobtion the surface energy of the polymers. Also, different concentrations of methanol were used to obtion contact angles, which in turn were used to give the critical surface tension (γ c ) of the polymers, using the Zizman’s method. The results of surface characteristics indicated that the 40% C 8 polymer was probably the most consistent, compared to the others during the preparation stage, in order to form smaller sized particles with a narrower distribution, correlating with the other works carried out on the loaded particles. In conclusion, it seems that this method could be used to predict characteristics of polymers used for the selection of the best polymer in this series and probably other polymers for nanoparticle making, particularly for the loading of ionized drugs.
Catastrophic vs Gradual Collapse of Thin-Walled Nanocrystalline Ni Hollow Cylinders As Building Blocks of Microlattice Structures (2011)

Lightweight yet stiff and strong lattice structures are attractive for various engineering applications, such as cores of sandwich shells and components designed for impact mitigation. Recent breakthroughs in manufacturing enable efficient fabrication of hierarchically architected microlattices, with dimensional control spanning seven orders of magnitude in length scale. These materials have the potential to exploit desirable nanoscale-size effects in a macroscopic structure, as long as their mechanical behavior at each appropriate scale - nano, micro, and macro levels - is properly understood. In this letter, we report the nanomechanical response of individual microlattice members. We show that hollow nanocrystalline Ni cylinders differing only in wall thicknesses, 500 and 150 nm, exhibit strikingly different collapse modes: the 500 nm sample collapses in a brittle manner, via a single strain burst, while the 150 nm sample shows a gradual collapse, via a series of small and discrete strain bursts. Further, compressive strength in 150 nm sample is 99.2% lower than predicted by shell buckling theory, likely due to localized buckling and fracture events observed during in situ compression experiments. We attribute this difference to the size-induced transition in deformation behavior, unique to nanoscale, and discuss it in the framework of "size effects" in crystalline strength.
Protein kinase D activation by deletion of its cysteine‐rich motifs (1999)

Protein kinase D is a serine/threonine kinase that binds phorbol esters in a phospholipid-dependent manner via a tandemly repeated cysteine-rich, zinc finger-like motif (the cysteine-rich domain). Here, we examined whether the cysteine-rich domain plays an additional role in the control of the catalytic kinase activity independently of the binding of allosteric effectors. We found that deletion of cys1, cys2 or the entire cysteine-rich domain increases the basal activity of protein kinase D leading to a constitutively active form of this enzyme. Our results demonstrate, for the first time, that the cysteine-rich domain of Protein kinase D plays a negative role in the regulation of protein kinase D kinase activity.
Lack of Dramatic Enrichment of Fetal DNA in Maternal Plasma by Formaldehyde Treatment (2005)

The discovery of fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis (1)(2)(3)(4)(5)(6). A recent report(7) indicated that the proportion of fetal DNA in maternal plasma can be dramatically enriched through the adoption of a blood-processing protocol involving the addition of formaldehyde to maternal blood samples. Dhallan et al. (7) suggested that these observations might be the result of several factors, including a reduction in background maternal DNA by minimization of maternal cell lysis through formaldehyde-mediated cell membrane stabilization and the use of a gentle centrifugation protocol, as well as the preservation of fetal DNA through nuclease inhibition by formaldehyde.

In view of the profound implications of the study (7), we aimed to validate and investigate the underlying mechanisms of the reported phenomenon. To assess the effects of several contributory factors, our study was conducted in three successive stages. In the first part of the study, we aimed to verify the effects of the previously published protocol (7) on total DNA concentrations in plasma from nonpregnant individuals. In the second part of the study, we evaluated the effects of formaldehyde addition on total and fetal DNA concentrations in maternal plasma in relation to the time of blood processing (0, 6, and 24 h after blood collection). In the last part of the study, we investigated whether the reported enrichment in circulating fetal DNA concentrations (7) might be a consequence of the imprecision of the analytical method chosen by the authors.

All participants were recruited with informed consent from the Prince of Wales Hospital, Hong Kong, with institutional ethics approval. In the first part of the study, blood (24 mL) was collected into 3-mL EDTA tubes from each of eight nonpregnant volunteers and divided into …
Determinants of Effective SMS Advertising: An Experimental Study (2007)

Mobile advertising has become one of the most popular applications in mobile commerce, particularly in the form of text advertising through SMS (Short Messaging Service). However, in the study of mobile advertising little is known regarding the effectiveness of SMS advertising and the factors contributing to its success. This research investigates the significance of a number of factors associated with SMS advertising effectiveness through an experimental study. The findings indicate that incentive, interactivity, appeal, product involvement, and attitude toward SMS advertising in general directly influence attitude toward the advertisement, attitude toward the brand, and purchase intention. The results of the study suggest that a stronger focus on these factors is necessary to improve the effectiveness of SMS advertising campaigns.
<b>CT Evaluation of the Response of Gastrointestinal Stromal Tumors After Imatinib Mesylate Treatment:</b> A Quantitative Analysis Correlated with FDG PET Findings (2004)

FDG PET is sensitive and specific for evaluating tumor response but cannot be used in patients whose baseline FDG PET results are negative for tumors. Although subjective evaluation was a better indicator of treatment response than was tumor density alone, the tumor density measurement is a good indicator and provides a reliable quantitative means of monitoring the tumor. RECIST, using only tumor size, was unreliable for monitoring GISTs during the early stage of imatinib mesylate treatment.
Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology (2014)

In this paper, it is demonstrated how Raman spectroscopy can be used to detect different carotenoids as possible biomarkers in various groups of microorganisms. The question which arose from previous studies concerns the level of unambiguity of discriminating carotenoids using common Raman microspectrometers. A series of laboratory-grown microorganisms of different taxonomic affiliation was investigated, such as halophilic heterotrophic bacteria, cyanobacteria, the anoxygenic phototrophs, the non-halophilic heterotrophs as well as eukaryotes (Ochrophyta, Rhodophyta and Chlorophyta). The data presented show that Raman spectroscopy is a suitable tool to assess the presence of carotenoids of these organisms in cultures. Comparison is made with the high-performance liquid chromatography approach of analysing pigments in extracts. Direct measurements on cultures provide fast and reliable identification of the pigments. Some of the carotenoids studied are proposed as tracers for halophiles, in contrast with others which can be considered as biomarkers of other genera. The limits of application of Raman spectroscopy are discussed for a few cases where the current Raman spectroscopic approach does not allow discriminating structurally very similar carotenoids. The database reported can be used for applications in geobiology and exobiology for the detection of pigment signals in natural settings.
Evolution of North American Dent Corn from Public to Proprietary Germplasm (2006)

ABSTRACT Current corn ( Zea mays L.) hybrids are produced using proprietary inbred lines as parents. These proprietary lines are protected by U.S. Patent and/or the U.S. Plant Variety Protection Act (PVPA) and their use is restricted, but as protection expires these lines become available to the entire corn breeding industry. Our objectives were to gain understanding of this protected germplasm by utilizing pedigree information available in the U.S. Patent and PVPA records to enhance the use of this germplasm in new line development as the lines become publicly available. Ownership, derivation, and lineage of corn inbred lines protected by U.S. Patent or PVPA from 1980 to 2004 were surveyed. Thirty‐three companies have protected 908 corn inbred lines and four of these companies: Dekalb Genetics (DK), Holden's Foundation Seeds (LH), Pioneer Hi‐Bred (PH), and Syngenta (SG) originated 685 of them. We identified the most significant lines by their cumulative use as parents in the development of new lines. Much of today's germplasm originates from seven progenitor lines: B73, LH82, LH123, PH207, PH595, PHG39, and Mo17. The germplasm surveyed is grouped by pedigree lineage into Oh43, Lancaster, Oh07‐Midland, Iodent, Stiff Stalk, Commercial hybrid derived, and Argentine Maiz Amargo backgrounds, with new diversity emerging from the two latter groups. Recycling elite inbred lines using two‐parent crosses followed by pedigree breeding was the most prevalent method of new line development.
On community outliers and their efficient detection in information networks (2010)

Linked or networked data are ubiquitous in many applications. Examples include web data or hypertext documents connected via hyperlinks, social networks or user profiles connected via friend links, co-authorship and citation information, blog data, movie reviews and so on. In these datasets (called "information networks"), closely related objects that share the same properties or interests form a community. For example, a community in blogsphere could be users mostly interested in cell phone reviews and news. Outlier detection in information networks can reveal important anomalous and interesting behaviors that are not obvious if community information is ignored. An example could be a low-income person being friends with many rich people even though his income is not anomalously low when considered over the entire population. This paper first introduces the concept of community outliers (interesting points or rising stars for a more positive sense), and then shows that well-known baseline approaches without considering links or community information cannot find these community outliers. We propose an efficient solution by modeling networked data as a mixture model composed of multiple normal communities and a set of randomly generated outliers. The probabilistic model characterizes both data and links simultaneously by defining their joint distribution based on hidden Markov random fields (HMRF). Maximizing the data likelihood and the posterior of the model gives the solution to the outlier inference problem. We apply the model on both synthetic data and DBLP data sets, and the results demonstrate importance of this concept, as well as the effectiveness and efficiency of the proposed approach.