gebhart/patrepeval huggingface dataset:
Fabrication of three-dimensional porous cell-laden hydrogel for tissue engineering (2010)

For tissue engineering applications, scaffolds should be porous to enable rapid nutrient and oxygen transfer while providing a three-dimensional (3D) microenvironment for the encapsulated cells. This dual characteristic can be achieved by fabrication of porous hydrogels that contain encapsulated cells. In this work, we developed a simple method that allows cell encapsulation and pore generation inside alginate hydrogels simultaneously. Gelatin beads of 150-300 microm diameter were used as a sacrificial porogen for generating pores within cell-laden hydrogels. Gelation of gelatin at low temperature (4 degrees C) was used to form beads without chemical crosslinking and their subsequent dissolution after cell encapsulation led to generation of pores within cell-laden hydrogels. The pore size and porosity of the scaffolds were controlled by the gelatin bead size and their volume ratio, respectively. Fabricated hydrogels were characterized for their internal microarchitecture, mechanical properties and permeability. Hydrogels exhibited a high degree of porosity with increasing gelatin bead content in contrast to nonporous alginate hydrogel. Furthermore, permeability increased by two to three orders while compressive modulus decreased with increasing porosity of the scaffolds. Application of these scaffolds for tissue engineering was tested by encapsulation of hepatocarcinoma cell line (HepG2). All the scaffolds showed similar cell viability; however, cell proliferation was enhanced under porous conditions. Furthermore, porous alginate hydrogels resulted in formation of larger spheroids and higher albumin secretion compared to nonporous conditions. These data suggest that porous alginate hydrogels may have provided a better environment for cell proliferation and albumin production. This may be due to the enhanced mass transfer of nutrients, oxygen and waste removal, which is potentially beneficial for tissue engineering and regenerative medicine applications.
오대산 국립공원 계방산 일대 삼림식생의 군락분포에 관한 연구 (2014)

The mountain forest vegetation of Gyebangsan (1,577 m) in Odaesan National Park is classified into deciduous broad-leaved forest, mountain valley forest, coniferous forest, subalpine coniferous forest, subalpine deciduous forest, plantation forest, and other vegetation which includes Actinidia argute community and agricultural land. As for the number of communities distributed in the each forest vegetation which were categorized by the physiognomy classification, deciduous broad-leaved forest had 33 communities, mountain valley forest 41 communities, coniferous forest 8 communities, subalpine coniferous forest 4 communities, subalpine deciduous forest 2 communities, plantation forest 6 communities and other vegetation 4 communities. Regarding the distribution rate of communities in the vegetation, in the deciduous broad-leaved forest. Quercus mongolica community accounted for 80.226% with 30,909,942.967m2, followed by Quercus variabilis community of 2.771% with 1,067,479.335m2. 55.463% of deciduous broad-leaved forest in the Gyebangsan had Quercus mongolica as a dominant or second dominant species. In the mountain valley forest, Fraxinus rhynchophylla - Juglans mandshurica community accounted for 10.955%. And there were ten mixed communities having Fraxinus rhynchophylla and upper layer at a similar level of coverage, taking up 32.776%. In the coniferous forest, Pinus densiflora and the community living with Pinus densiflora accounted for 100%, showing that the coniferous forest has the community with Pinus densiflora as a dominant species at upper layer. For other vegetation, subalpine coniferous forest had a total of four communities including Abies holophylla - Quercus mongolica community, and accounted for 4.980% of vegetation area of Odaesan National Park. Two communities including Betula ermani - Cornus controversa community were found in the subalpine deciduous forest, taking up 0.006% of total vegetation area of Odaesan National Park. Regarding plantation forest, Larix leptolepis was planted the most with 51.652%, followed by Betula platyphylla var. japonica with 38.975%, and Pinus koraiensis with 7.969%. These three species combined accounted for 98.565%. In conclusion, the forest vegetation found in the Gyebangsan of Odaesan National Park has Quercus mongolica as a dominant species at the top layer. A lot of other communities related with this species are expected to be quickly replaced due to vegetation succession and climatic causes. Therefore, Quercus mongolica is expected to become the main species in the deciduous broad-leaved forest, Fraxinus rhynchophylla, Juglans mandshurica and Fraxinus mandshurica in the mountain valley forest. Around the border line between deciduous broad-leaved forest and mountain valley forest, highly humid valley area is expected to be quickly taken up by Cornus controversa and Fraxinus mandshurica, and the slope area by Quercus mongolica. However, in the subalpine coniferous forest, the distribution rate of deciduous broad-leaved trees is expected to increase due to climate warming.
Distribution of soluble impurities in cold glacial ice (2004)

Abstract Understanding the microstructure of ice underpins the interpretation of ice-core measurements and many ice-sheet properties. A detailed study of polar snow and ice using scanning electron microscope (SEM) and X-ray analysis revealed the micro-structural distribution of soluble impurities. Sublimation under vacuum (etching) concentrated impurity from both the bulk and grain boundaries on to the specimen surfaces in detectable quantities. Sublimation in the cold room before examination (pre-etching) collected previously unobservable quantities of impurity at triple junctions. A heterogeneous distribution of impurities was observed. Chloride was frequently found to originate from the lattice, but not usually at triple junctions. Other impurities, particularly sodium chloride, were detected at grain boundaries and bubble surfaces. Sulphate was often found at triple junctions in specimens containing a high bulk concentration of the acid, frequently in conjunction with cations. This suggests the possibility that veins were only filled with significant amounts of impurity when the surrounding grain boundaries were saturated. The model of impurity arrangement inferred from the results reconciles differences between previous SEM studies; additionally it is consistent with and explains recent electrical conduction observations. The disconnected arrangement of impurity-filled grain boundaries and veins limits opportunities for significant post-depositional solute movement.
Comparison of Combination and First Overtone Spectral Regions for Near-Infrared Calibration Models for Glucose and Other Biomolecules in Aqueous Solutions (2004)

Partial least squares calibration models are compared for the measurement of glucose, lactate, urea, ascorbate, triacetin, and alanine in aqueous solutions from single-beam spectra collected over the first overtone (6500−5500 cm-1) and the combination (5000−4000 cm-1) regions of the near-infrared spectrum. Spectra are collected under two sets of conditions with one designed for combination spectra and the other designed for first overtone spectra. As part of the optimization of conditions, an exponential function is presented that accurately characterizes the strong dependency between spectral quality and sample thickness. Sample thickness set for the first overtone and combination spectra are 7.5 and 1.5 mm, respectively. Independent calibration models are established for each solute from both combination and first overtone spectra. Direct comparison reveals superior performance by models generated from combination spectra, particularly for glucose and urea. Standard error of prediction (SEP) values are 1.12 and 0.45 mM for glucose models generated from first overtone and combination spectra, respectively. SEP values for urea are 7.33 and 0.10 mM for first overtone and combination spectra, respectively. Such high SEP values for urea with first overtone spectra correspond to an inability to quantify urea from these spectra because of a lack urea-specific molecular absorption features in this spectral region. Net analyte signal (NAS) is used to quantify the degree of selectivity provided within the first overtone and combination spectral regions. The superior selectivity of combination spectra is confirmed by comparing the length of the NAS vectors for each matrix component.
Electromechanical Unzipping of Individual DNA Molecules Using Synthetic Sub-2 nm Pores (2008)

Nanopores have recently emerged as high-throughput tools for probing and manipulating nucleic acid secondary structure at the single-molecule level. While most studies to date have utilized protein pores embedded in lipid bilayers, solid-state nanopores offer many practical advantages which greatly expand the range of applications in life sciences and biotechnology. Using sub-2 nm solid-state nanopores, we show for the first time that the unzipping kinetics of individual DNA duplexes can be probed by analyzing the dwell-time distributions. We performed high-bandwidth electrical measurements of DNA duplex unzipping as a function of their length, sequence, and temperature. We find that our longer duplexes (>10 bp) follow Arrhenius dependence on temperature, suggesting that unzipping can be approximated as a single-barrier crossing, but the unzipping kinetics of shorter duplexes do not involve a barrier, due to the strong biasing electrical force. Finally, we show that mismatches in the duplex affect unzipping times in a position-sensitive manner. Our results are a crucial step toward sequence variability detection and our single-molecule nanopore sequencing technology, which rely on parallel detection from nanopore arrays.
Prognostic significance of tumor necrosis factors and their receptors in nonsmall cell lung carcinoma (1998)

Although NSCLC exhibits strong coexpression of TNF-alpha, TNF-beta, TNF-R1, and TNF-R2, there is a loss/down-regulation of TNF receptors in high stage tumors. TNF-R1 and TNF-R2 positivity independently predicts favorable outcome in NSCLC, particularly in tumors with no clinically distant metastasis. The current study supports a role for TNFs and their receptors in the evolution and progression of NSCLC.
Characterization of the adenosine deaminase-adenosine deaminase complexing protein binding reaction. (1990)

Glutaraldehyde-fixed membranes from rabbit kidney cortex were used to characterize binding of monomeric adenosine deaminase to the adenosine deaminase complexing protein. With the use of bovine adenosine deaminase it was shown that enzyme binding is a saturable, high affinity process. The K value for binding of the bovine enzyme was 11 nM. Maximum enzyme binding and rate of binding to a constant amount of membrane did not vary significantly from pH 5.0 to 9.5. Metal ions, with the exception of Hg2+, sulfhydryl reagents, and other proteins had little or a slightly stimulatory effect on maximum binding. Mercuric ion inhibited binding. Using biotinylated bovine adenosine deaminase it was shown that purified rabbit, human, and monkey enzymes compete for binding sites on fixed membranes. The K values for the rabbit and human enzymes were 9 and 6 nM, respectively. Mouse or guinea pig adenosine deaminase did not bind to the membranes or compete with the biotinylated bovine enzyme for binding sites. The retention of characteristics required for binding by enzymes from rabbit, human, monkey, and calf tissues argues for biologic significance of the adenosine deaminase-complexing protein interaction. The basis for the apparent failure of rodent adenosine deaminase to bind to complexing protein remains to be determined.
[The anti-arrhythmia activity of quinazopyrine]. (1990)

The antiarrhythmic activity of quinasopirine was studied in the experiments on rats with the use of models of calcium chloride- and aconitine-induced arrhythmias, disorders of cardiac rhythm in myocardial infarction produced by isadrine and pituitrin and also in the experiments on cats in arrhythmias caused by electric stimulation of the myocardium, postinfarction and reperfusion arrhythmias. Quinasopirine exhibits the antiarrhythmic effect being superior to that of anapriline and novocainamide in arrhythmias induced by calcium chloride and aconitine. In other types of the cardiac rhythm disorder its activity is comparable with that of ethmosine, obsidane and cordarone. Quinasopirine reduces automatism and contractile function of the myocardium.
Catalytic Production of Liquid Fuels from Biomass‐Derived Oxygenated Hydrocarbons: Catalytic Coupling at Multiple Length Scales (2009)

The catalytic processing of biomass‐derived feedstocks to liquid fuels and chemical intermediates is complex and expensive. Therefore, conversion processes involving a limited number of reaction, separation, and purification steps are necessary. Coupling of catalytic processes has the potential to lead to the development of new processes, thereby improving the overall economics of biomass conversion. Functional coupling at the molecular scale has the potential to produce novel catalytic materials to replace homogeneous catalysts. Active site coupling of different sites within the same reactor can help reduce operating costs by combining sequential reactions in a single reactor. Chemical reaction coupling of heterogeneous and homogeneous reactions may lead to improvements in overall catalytic performance for liquid phase processes by enhancing surface reactions with liquid phase reactions. Finally, phase coupling leads to improvements in overall yield by improving the equilibrium conversion or by suppressing undesired side reactions.
Lithium perturbation and goosecoid expression identify a dorsal specification pathway in the pregastrula zebrafish (1993)

The zebrafish dorsoventral axis can first be distinguished at gastrulation, upon formation of the embryonic shield, the site of the organizer. We have asked whether the shield is specified before gastrulation. First, we show that brief exposure of premidblastula embryos to lithium, which is known to shut down the phospho-inositol signaling pathway, produces excessive shield formation and extreme hyper-dorsal development. Second, we show that the zebrafish goosecoid homeobox gene is activated at or just after the midblastula in a localized domain of cells that subsequently populate the most anterior region of the incipient shield and axial hypoblast, goosecoid expression is elevated and radialized by early lithium treatment, suggesting that goosecoid plays a role in establishing the organizer and shield. Our results demonstrate that the zebrafish dorsal axis is signaled by a pathway initiated in the cleavage-stage embryo. Furthermore, they provide novel insights into anterior morphogenesis.
Chemical-enzymic synthesis and conformational analysis of sialyl Lewis X and derivatives (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical-enzymic synthesis and conformational analysis of sialyl Lewis X and derivativesYoshitaka Ichikawa, Ying Chih Lin, David P. Dumas, Gwo Jenn Shen, Eduardo Garcia-Junceda, Mark A. Williams, Robert Bayer, Catherine Ketcham, Leslie E. Walker, and Cite this: J. Am. Chem. Soc. 1992, 114, 24, 9283–9298Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://pubs.acs.org/doi/10.1021/ja00050a007https://doi.org/10.1021/ja00050a007research-articleACS PublicationsRequest reuse permissionsArticle Views1221Altmetric-Citations357LEARN 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
Promise and Challenge: Markers of Prostate Cancer Detection, Diagnosis and Prognosis (2004)

Approximately 1 man in 6 will be diagnosed with prostate cancer during his life lifetime, and over 200,000 men in the U.S. are diagnosed with prostate cancer annually. Since the widespread adoption of PSA testing, about 60-70% of men at risk in the U.S. have had a blood test for prostate cancer. With this, prostate cancer death rates have decreased, yet only slightly. Thirty thousand men still die each year from this disease. PSA testing fails to identify a small but significant proportion of aggressive cancers, and only about 30% of men with a "positive" PSA have a positive biopsy. Additionally, of men who are treated for prostate cancer, about 25% require additional treatment, presumably due to disease recurrence. Also of concern is the growing evidence that there are some prostate cancers for which treatment may not be necessary. Very long-term studies from the U.S. and Europe, following men with prostate cancer have found that some tumors do not progress over time. In these individuals, prostate cancer treatment is unnecessary and harmful as these men do not benefit from treatment but will be at risk of treatment-related side effects and complications. They suggest a fundamental problem with prostate cancer: it is not possible, at this time, to predict the natural history of the disease. It is for these reasons that the most important challenge in prostate cancer today is the inability to predict the behavior of an individual tumor in an individual patient. Here we review issues related to performance and validation of biomarkers with a focus on "doing no harm", and bearing in mind that it is the ultimate goal of early detection to save lives. Improved diagnostic and prognostic biomarkers are needed for prostate cancer, and the use of these markers should ultimately translate into increased life span and quality of life. The ultimate goal would be to not only have accurate biomarkers suitable for early diagnosis, but also biomarkers that identify men at greatest risk of developing aggressive disease. Technology has been brought to bear on this problem, and the major approaches are genomics, expression analysis, and proteomics. Proteomics and DNA methylation assays may soon be used in sensitive and specific diagnostic testing of serum and tissues for cancer. Expression arrays may be used to establish both a more specific diagnosis and prognosis for a particular tumor. The proteome is only beginning to be understood, and alternative splicing and post-translational modifications of proteins such as glycosylation and phosphorylation are challenging areas of study. Finally, risk assessment and prognosis are being pursued through analysis of genomic polymorphisms (single nucleotide polymorphisms, SNPs). This huge task is only beginning, and requires the combined expertise of molecular epidemiologists, oncologists, surgeons, pathologists, and basic scientists.
Recombination-dependent Repair of DNA Double-strand Breaks with Purified Proteins from Escherichia coli (1997)

We have developed an in vitro system in which repair of DNA double-strand breaks is performed by purified proteins of Escherichia coli. A segment was deleted from a circular duplex DNA molecule by restriction at two sites. 3' single-stranded overhangs were introduced at both ends of the remaining linear fragment. In a first step, RecA protein catalyzed the formation of a D-loop between one single-stranded tail and a homologous undeleted supercoiled DNA molecule. In a second step, E. coli DNA polymerase II or III used the 3' end in the D-loop as a primer to copy the missing sequences of the linear substrate on one strand of the supercoiled template. Under proper conditions, the integrity of the deleted substrate was restored, as shown by analysis of the products by electrophoresis, restriction, and transformation. In this reaction, DNA synthesis is strictly dependent on recombination, and repair is achieved without formation of a Holliday junction.
Noncontact 3-D Speckle Contrast Diffuse Correlation Tomography of Tissue Blood Flow Distribution (2017)

Recent advancements in near-infrared diffuse correlation techniques and instrumentation have opened the path for versatile deep tissue microvasculature blood flow imaging systems. Despite this progress there remains a need for a completely noncontact, noninvasive device with high translatability from small/testing (animal) to large/target (human) subjects with trivial application on both. Accordingly, we discuss our newly developed setup which meets this demand, termed noncontact speckle contrast diffuse correlation tomography (nc_scDCT). The nc_scDCT provides fast, continuous, portable, noninvasive, and inexpensive acquisition of 3-D tomographic deep (up to 10 mm) tissue blood flow distributions with straightforward design and customization. The features presented include a finite-element-method implementation for incorporating complex tissue boundaries, fully noncontact hardware for avoiding tissue compression and interactions, rapid data collection with a diffuse speckle contrast method, reflectance-based design promoting experimental translation, extensibility to related techniques, and robust adjustable source and detector patterns and density for high resolution measurement with flexible regions of interest enabling unique application-specific setups. Validation is shown in the detection and characterization of both high and low contrasts in flow relative to the background using tissue phantoms with a pump-connected tube (high) and phantom spheres (low). Furthermore, in vivo validation of extracting spatiotemporal 3-D blood flow distributions and hyperemic response during forearm cuff occlusion is demonstrated. Finally, the success of instrument feasibility in clinical use is examined through the intraoperative imaging of mastectomy skin flap.