gebhart/patrepeval huggingface dataset:
Single-Particle Characterization of Aβ Oligomers in Solution (2012)

Determining the pathological role of amyloids in amyloid-associated diseases will require a method for characterizing the dynamic distributions in size and shape of amyloid oligomers with high resolution. Here, we explored the potential of resistive-pulse sensing through lipid bilayer-coated nanopores to measure the size of individual amyloid-β oligomers directly in solution and without chemical modification. This method classified individual amyloid-β aggregates as spherical oligomers, protofibrils, or mature fibers and made it possible to account for the large heterogeneity of amyloid-β aggregate sizes. The approach revealed the distribution of protofibrillar lengths (12- to 155 -mer) as well as the average cross-sectional area of protofibrils and fibers.
A Treatment Planning Comparison of Passive-Scattering and Intensity-Modulated Proton Therapy for Typical Tumor Sites (2011)

Intensity-modulated proton therapy (IMPT) is expected to improve treatment results with fewer side effects than other proton therapies. The purpose of this study was to evaluate the tumor sites for which IMPT was effective under the same beam calculation conditions by planning IMPT for typical cases treated with passive scattering proton therapy (PSPT). We selected 16 cases of nasal cavity, lung, liver or prostate cancers as typical tumor sites receiving PSPT. The dose distributions and dose volume histograms optimized by the IMPT were compared with those optimized by the PSPT. We took particular note of the doses to the skin and organs at risk (OAR) when PSPT was replaced by IMPT. Furthermore, an improvement of the beam angles was also performed to obtain better dose distributions in the IMPT. The IMPT with the same beam angles resulted in near-maximum doses to the skin of average 78%, 64%, 84% and 99% of the PSPT doses for nasal cavity, lung, liver, and prostate cancers, respectively. However, it was difficult to improve the dose homogeneity of the target volume. The change of the IMPT beam angles could reduce the doses to OARs and skin in the case of the nasal cavity, while it had limited effect in the other cases. We concluded that IMPT was effective for reducing the doses to some OARs when treating nasal cavity, lung, liver and prostate cancers. The selection of beam angles was important in the IMPT optimization, especially for nasal cavity cancers.
2015 개정 실과 교육과정에 따른 ‘창의적인 제품 만들기’ 활동 과제 개발과 적합도 분석 (2017)

이 연구는 2015 개정 실과 교육과정에 따른 ‘창의적인 제품 만들기’ 활동 과제를 개발하고 그 적합도를 분석하기 위해 수행되었다. 연구의 목적을 달성하기 위해서 ‘창의적인 제품 만들기’ 활동 과제의 개발 기준을 설정하여 15개의 창의적인 제품 만들기 활동 과제를 개발한 후, 내용 타당도 비율을 구하여 타당도를 검증하였다. 타당도를 검증받은 12개의 활동...
The Energetics of Supported Metal Nanoparticles: Relationships to Sintering Rates and Catalytic Activity (2013)

Transition metal nanoparticles on the surfaces of oxide and carbon support materials form the basis for most solid catalysts and electrocatalysts, and have important industrial applications such as fuel production, fuels, and pollution prevention. In this Account, I review my laboratory group's research toward the basic understanding of the effects of particle size and support material on catalytic properties. I focus on studies of well-defined model metal nanoparticle catalysts supported on single-crystalline oxide surfaces. My group structurally characterized such catalysts using a variety of ultrahigh vacuum surface science techniques. We then measured the energies of metal atoms in these supported nanoparticles, using adsorption calorimetry tools that we developed. These metal adsorption energies increase with increasing size of the nanoparticles, until their diameter exceeds about 6 nm. Below 6 nm, the nature of the oxide support surface reaches also greatly affects the metal adsorption energies. Using both adsorption calorimetry and temperature programmed desorption (TPD), we measured the energy of adsorbed catalytic intermediates on metal nanoparticles supported on single crystal oxide surfaces, as a function of particle size. The studies reveal correlations between a number of characteristics. These include the size- and support-dependent energies of metal surface atoms in supported metal nanoparticles, their rates of sintering, how strongly they bind small adsorbates, and their catalytic activity. The data are consistent with the following model: the more weakly the surface metal atom is attached to the nanomaterial, the more strongly it binds small adsorbates. Its strength of attachment to the nanomaterial is dominated by the number of metal-metal bonds which bind it there, but also by the strength of metal/oxide interfacial bonding. This same combination of bond strengths controls sintering rates as well: the less stable a surface metal atom is in the nanomaterial, the greater is the thermodynamic driving force for it to sinter, and the faster is its sintering rate. These correlations provide key insights into how and why specific structural properties of catalyst nanomaterials dictate their catalytic properties. For example, they explain why supported Au catalysts must contain Au nanoparticles smaller than about 6 nm to have high activity for combustion and selective oxidation reactions. Only below about 6 nm are the Au atoms so weakly attached to the catalyst that they bind oxygen sufficiently strongly to enable the activation of O₂. By characterizing this interplay between industrially important rates (of net catalytic reactions, of elementary steps in the catalytic mechanism, and of sintering) and their thermodynamic driving forces, we can achieve a deeper fundamental understanding of supported metal nanoparticle catalysts. This understanding may facilitate development of better catalytic nanomaterials for clean, sustainable energy technologies.
Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hürthle cell) tumours of the thyroid (2005)

Oxyphil or Hurthle cell tumours of the thyroid are characterised by their consistent excessive number of mitochondria. A recently discovered gene, GRIM-19 has been found to fulfil two roles within the cell: as a member of the interferon-beta and retinoic acid-induced pathway of cell death, and as part of the mitochondrial Complex I assembly. In addition, a gene predisposing to thyroid tumours with cell oxyphilia (TCO) has been mapped to chromosome 19p13.2 in one family. A cluster of genes involved in mitochondrial metabolism occurs in this region; one of these is GRIM-19. We have searched for GRIM-19 mutations in a series of 52 thyroid tumours. Somatic missense mutations in GRIM-19 were detected in three of 20 sporadic Hurthle cell carcinomas. A germline mutation was detected in a Hurthle cell papillary carcinoma arising in a thyroid with multiple Hurthle cell nodules. No mutations were detected in any of the 20 non-Hurthle cell carcinomas tested, nor in any of 96 blood donor samples. In one of the sporadic Hurthle cell papillary carcinomas positive for GRIM-19 mutation, we have also detected a ret/PTC-1 rearrangement. No GRIM-19 mutations were detected in any of the six cases of known familial Hurthle cell tumour tested, so that our results do not support the identification of GRIM-19 as the TCO gene. The GRIM-19 mutations we have detected are the first nuclear gene mutations specific to Hurthle cell tumours to be reported to date; we propose that such mutations can be involved in the genesis of sporadic or familial Hurthle cell tumours through the dual function of GRIM-19 in mitochondrial metabolism and cell death.
Color-capable sub-pixel resolving optofluidic microscope for on-chip cell imaging (2011)

We report on the implementation of a color-capable sub-pixel resolving optofluidic microscope based on the pixel super-resolution algorithm and sequential RGB illumination, for low-cost on-chip color imaging of biological samples with sub-cellular resolution.
Repair of Osteochondral Defect with Tissue-Engineered Two-Phase Composite Material of Injectable Calcium Phosphate and Hyaluronan Sponge (2002)

Articular cartilage has limited capacity for repair. In the present study, tissue-engineered two-phase composite material was used for the repair of osteochondral defects in young adult rabbit knee. This composite material is composed of an injectable calcium phosphate (ICP) and a hyaluronan (HA) derivate of either ACP or HYAFF 11 sponge. The osteochondral defect, 3 mm in diameter and 3 mm deep, was created in the weight-bearing region of the medial femoral condyle. The bone portion of the defect was first filled with ICP to a level approximately 1 mm below the articular surface. HA sponge (3 mm in diameter and 1-1.2 mm thick), with or without loading of autologous bone marrow-derived progenitor cells (MPCs), was then inserted into the defect on top of the ICP as it hardened. Animals were allowed free cage activity postoperatively, and killed 4 or 12 weeks (for the HYAFF 11 sponge group) after the surgery. At 4 weeks, histological examination showed that the defect was filled up to 90-100% of its depth. Whitish repair tissue on the top appeared to be integrated with the surrounding articular cartilage. Four distinct zones of repair tissue were identified: a superficial layer, a chondroid tissue layer, an interface between HA sponge and ICP, and the ICP material. Evidence of extensive osteoclastic and osteoblastic activities was observed in the bone tissue surrounding the defect edge and in ICP material. By 12 weeks, the zonal features of the repair tissue became more distinct; chondrocytes were arranged in a columnar array, and a calcified layer of cartilage was formed beneath the chondroid tissue in some specimens. The healing tissue of the HA sponge material loaded with MPCs had higher cellular density and better integration with the surrounding cartilage than HA sponge material not loaded with MPCs. This study suggests that using a two-phase composite graft may hold potential for the repair of osteochondral defects by providing mechanical support that mimicks subchondral bone, while also providing a chondrogenic scaffold for the top cartilage repair.
Controlled Shrinkage and Re-expansion of a Single Aqueous Droplet inside an Optical Vortex Trap (2007)

This paper describes the shrinkage and re-expansion of individual femtoliter-volume aqueous droplets that were suspended in an organic medium and held in an optical vortex trap. To elucidate the mechanism behind this phenomenon, we constructed a heat- and mass-transfer model and carried out experimental verifications of our model. From these studies, we conclude that an evaporation mechanism sufficiently describes the shrinkage of aqueous droplets held in a vortex trap, whereas a mechanism based on the supersaturation of the organic phase by water that surrounds the droplet adequately explains the re-expansion of the shrunk droplet. The proposed mechanisms correlated well with experimental observations using different organic media, when H2O was replaced with D2O and when an optical tweezer was used to induce droplet shrinkage rather than an optical vortex trap. For H2O droplets, the temperature rise within the droplet during shrinkage was on the order of 1 K or less, owing to the rapid thermal conduction of heat away from the droplet at the microscale and the sharp increase in solubility for water by the organic phase with slight elevations in temperature. Because most chemical species confined to droplets can be made impenetrable to the aqueous/organic interface, a change in the volume of aqueous droplets translates into a change in concentration of the dissolved species within the droplets. Therefore, this phenomenon should find use in the study of fundamental chemical processes that are sensitive to concentration, such as macromolecular crowding and protein nucleation and crystallization.
CRITICA: coding region identification tool invoking comparative analysis (1999)

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).
Biomarkers: Mining the Biofluid Proteome (2005)

Proteomics has brought with it the hope of identifying novel biomarkers for diseases such as cancer. This hope is built on the ability of proteomic technologies, such as mass spectrometry (MS), to identify hundreds of proteins in complex biofluids such as plasma and serum. There are many factors that make this research very challenging beginning with the lack of standardization of sample collection and continuing through the entire analytical process. Fortunately the advances made in the characterization of biofluids using proteomic techniques have been rapid and suggest that these mainly discovery driven approaches will lead to the development of highly specific platforms for diagnosing diseases and monitoring responses to different treatments in the near future.
New, computer-controlled microwave discharge emission spectrometer employing microarc sample atomization for trace and micro elemental analysis (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew, computer-controlled microwave discharge emission spectrometer employing microarc sample atomization for trace and micro elemental analysisL. R. Layman and G. M. HieftjeCite this: Anal. Chem. 1975, 47, 2, 194–202Publication Date (Print):February 1, 1975Publication History Published online1 May 2002Published inissue 1 February 1975https://pubs.acs.org/doi/10.1021/ac60352a027https://doi.org/10.1021/ac60352a027research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A tunable microflow focusing device utilizing controllable moving walls and its applications for formation of micro-droplets in liquids (2007)

This study reports a new microfluidic device capable of fine-tuned sample-flow focusing and generation of micro-droplets in liquids by controlling moving wall structures. Two microfluidic components including an 'active microchannel width controller' and a 'micro chopper' can be used to fine-tune the width of the hydrodynamically pre-focused stream and subsequently generate micro-droplets. In this study, a basic concept of a 'controllable moving wall' structure was addressed and applied as the active microchannel width controller and the micro chopper to generate the proposed function. Pneumatic side chambers were placed next to a main flow channel to construct the controllable moving wall structures. The deformation of the controllable moving wall structure can be generated by the pressurized air injected into the pneumatic side chambers. The proposed chip device was fabricated utilizing polymer material such as PDMS (polydimethylsiloxane) to provide the flexibility of the controllable moving wall deformation. The microfluidic chip device with dimensions of 2.5 cm in width and 3.0 cm in length can be fabricated using a simple fabrication process. Experimental data showed that the deformation of the controllable moving wall structure can be adjusted by applying different air pressures, so that the width of the main flow channel can be controlled accordingly. By utilizing the proposed mechanism, the pre-focused dispersed phase stream could be actively focused into a narrower stream, and well-controlled micro-droplets with smaller diameters could be generated. The stream width can be reduced from 30 µm to 9 µm and micro-droplets with a diameter of 76 µm could be generated by utilizing the proposed device. In addition, to generate micro-droplets within smaller diameters, uniform size distribution of the micro-droplets can be obtained. According to the experimental results, development of the microfluidic device could be promising for a variety of applications such as emulsification, nano-medicine and droplet-based microfluidics.
Changes in myosin heavy‐chain isoform synthesis of chronically stimulated rat fast‐twitch muscle (1992)

Chronic low-frequency stimulation was used for studying the adaptive potential of rat fast-twitch muscle to increased neuromuscular activity. The sequential exchange of myosin heavy chain isoforms HCIIb with HCIId and HCIIa was studied at the translational level using an in-vivo-labeling technique with [35S]methionine. Alterations in heavy chain isoform synthesis, i.e. a decrease in the labeling of HCIIb concomitant with an enhanced labeling of HCIId/IIa, were detectable already two days after the onset of stimulation. This time course corresponds to the previously observed alterations in the amounts of HCIIb and HCIIa mRNAs. However, significant changes in the relative protein amounts of HCIIb and HCIId/IIa were recorded only after an 8-day stimulation period. This delay at the protein level was interpreted to relate to the slow turnover of HCIIb which was estimated from its decay in long-term stimulated muscles with an approximate value of 14.7 days. Therefore, protein degradation seems to be an important post-translational regulatory step in the remodeling process of the thick filament.
Preparation of Recombinant RNase Single-Chain Antibody Fusion Proteins (2003)

Selective cytotoxicity is an important goal of specific drug targeting. Toward this end, toxins isolated primarily from higher plants and bacteria have been coupled to monoclonal antibodies (MAbs) and evaluated for their clinical efficacy in cancer, AIDS, and immunological diseases (1,2). Immune responses against murine monoclonal antibodies MAbs (3,4) and antitoxin antibodies have been detected in both animals and humans treated with immunotoxins (ITs) (5-7) and present a major obstacle to the successful application of this technology. Although development of humanized antibodies have alleviated some of these effects (8, and references therein), the toxins themselves remain a problem. Consequently, the identification of human proteins to be used as components of immunoconjugates is highly desirable.
Successful Treatment with Colestimide for a Bout of Cholestasis in a Japanese Patient with Benign Recurrent Intrahepatic Cholestasis Caused by ATP8B1 Mutation (2008)

Benign recurrent intrahepatic cholestasis (BRIC) is an autosomal recessive disorder characterized by bouts of cholestasis that resolve spontaneously without leaving considerable liver damage. Most of BRIC patients have mutations in ATP8B1 gene coding FIC1 protein. It has been suggested that an imbalance between the gut absorption of bile acids and the liver excretion possibly causes the development of cholestasis. We encountered a Japanese woman patient with familial intrahepatic cholestasis type 1 (FIC1) deficiency manifesting BRIC, in whom a rapid and gross elevation of serum total bile acid (TBA) level preceded that of serum total bilirubin level. Interestingly, the early administration of colestimide prevented the development of hyperbilirubinemia along with the additional elevation of serum TBA level. This case suggests that FIC1 deficiency causes an imbalance between the gut absorption of bile acids and the liver excretion leading to cholestasis, and raised the possibility that colestimide may be used as an optional treatment for BRIC.
Induced Systemic Resistance to Cucumber Diseases and Increased Plant Growth by Plant Growth-Promoting Rhizobacteria Under Field Conditions (1996)

Three field trials were conducted over a 2-year period to determine the capacity of plant growth-promoting rhizobacteria (PGPR) to induce systemic resistance against cucumber diseases, which was previously observed in the greenhouse. PGPR were applied as seed treatments alone or as seed treatments plus a soil drench at transplanting. Induced systemic resistance (ISR) activity, measured by significant reductions in the severity of angular leaf spot challenge-inoculated with Pseudomonas syringae pv. lachrymans on cucumber, occurred with three of three PGPR strains in 1992, with three of four strains in the first trial in 1993, and with four of four strains in the second trial in 1993. Most PGPR treatments also resulted in significant protection from naturally occurring anthracnose (Colletotrichum orbiculare), while ISR controls (plants previously inoculated with C. orbiculare) had a significantly greater incidence of anthracnose compared with nontreated controls. In all three trials, most PGPR strains (with the exception of one strain) significantly promoted early-season plant growth, as measured by length of the main runner and number of leaves per plant. Yield (cumulative fruit weight) was significantly increased by two of three PGPR strains in 1992, two of four strains in the first 1993 trial, and three of four strains in the second 1993 trial compared with nontreated controls. In contrast, the ISR control had no significant effect on promotion of early-season plant growth or yield compared with nontreated controls. These results demonstrated that PGPR-mediated ISR was operative under field conditions with consistent effects against challenge-inoculated angular leaf spot and naturally occurring anthracnose, along with significant effects on early-season plant growth promotion and yield enhancement.