gebhart/patrepeval huggingface dataset:
Preparation and Application of Fluorescent Carbon Dots (2015)

Fluorescent carbon dots (CDs) are a novel type of fluorescent nanomaterials, which not only possess the specific quantum confinement effects of nanomaterials due to the small size of nanomaterials, but also have good biocompatibility and high fluorescence. Meanwhile, fluorescence CDs overcome the shortcomings of high toxicity of traditional nanomaterials. Moreover, the preparation procedure of fluorescent CDs is simple and easy. Therefore, fluorescent CDs have great potential applied in photocatalysis, biochemical sensing, bioimaging, drug delivery, and other related areas. In this paper, recent hot researches on fluorescent CDs are reviewed and some problems in the progress of fluorescent CDs are also summarized. At last, a future outlook in this direction is presented.
A Bead Aggregation Assay for Detection of Low-Affinity Protein-Protein Interactions Reveals Interactions between N-Terminal Domains of Inositol 1,4,5-Trisphosphate Receptors (2013)

Interactions between proteins are a hallmark of all cellular activities. Such interactions often occur with low affinity, a feature that allows them to be rapidly reversible, but it makes them difficult to detect using conventional methods such as yeast 2-hybrid analyses, co-immunoprecipitation or analytical ultracentrifugation. We developed a simple and economical bead aggregation assay to study low-affinity interactions between proteins. By coating beads with interacting proteins, the weak interactions between many proteins are sufficient to allow stable aggregation of beads, an avidity effect. The aggregation is easily measured to allow quantification of protein-protein interactions under a variety of controlled conditions. We use this assay to demonstrate low-affinity interactions between the N-terminal domains of an intracellular Ca(2+) channel, the type 1 inositol 1,4,5-trisphosphate receptor. This simple bead aggregation assay may have widespread application in the study of low-affinity interactions between macromolecules.
Abstract 9595: Generation of Transgene-Free Induced Pluripotent Stem Cells from Fibroblasts by Small Molecule Chemicals (2011)

Backgrounds: Reprogramming of somatic cells using viral- and non-viral vectors encoding defined transcription factors to generate induced pluripotent stem (iPS) cells has successfully been achieved over the past few years. However, the current established methods to create iPS cells require viral vectors or plasmids to deliver transgenes into the cells. Methods and Results: To obviate the putative problems of genetic contamination in the cells for future clinical application, it is highly demanded to develop new methods to create “safer” iPS cells without any genetic modifications. Here, we for the first time demonstrate successful generation of iPS cell line from mouse fibroblasts with only combinations of small-molecule chemicals such as GSK-3 beta inhibitor, histone deacetylase inhibitor, and G9a histone methyltransferase inhibitor, which act as epigenetic modulators and self-renewal activators. These chemical induced pluripotent stem (ChemiPS) cells have almost the same properties of embryonic stem cells in the expression patterns of pluripotency-related markers, epigenetic status in promoter regions of Oct4 and Nanog, spontaneous differentiation into three germ layers by in vitro embryoid body formation, and formation of teratoma in vivo after injection into mice. Conclusion: This study provides the first evidence that sole chemical combinations can reprogram somatic cells, resulting in transgene-free iPS cells. This method will advance the use of iPS cells in clinical application and disease investigation.
Assessment and learning (2010)

Assesment and Learning: Introduction - John Gardner PART ONE: PURPOSES AND PRACTICE Assessment for Learning in the Classroom - Paul Black and Dylan Wiliam Professional Learning as a Condition for Assessment for Learning - Dave Pedder and Mary James From Teachers to Schools: Scaling up Professional Development for Formative Assessment - Siobhan Leahy & Dylan Wiliam Alternative Perspectives on Learning Outcomes: Challenges for Assessment - Richard Daugherty, Paul Black, Kathryn Ecclestone, Mary James & Paul Newton On the Relationship between Assessment for Formative and Summative Purposes - Wynne Harlen Quality Assessment Practice - John Gardner PART TWO: IMPACT Assessment and Learning: the Learner's Perspective - Louise Hayward Instrumentalism and Achievement: A Sociocultural Understanding of Tensions in Vocational Education - Kathryn Ecclestone Policy and Practice in Assessment for Learning: The Experience of Selected OECD Countries - Judy Sebba The Role of Assessment in Developing Motivation for Learning - Wynne Harlen PART THREE: THEORY Assessment in Harmony with Our Understanding of Learning: Problems and Possibilities - Mary James, with Jenny Lewis Developing a Theory of Formative Assessment - Paul Black and Dylan Wiliam PART FOUR: VALIDITY AND RELIABILITY Validity in Formative Assessment - Gordon Stobart The Reliability of Assessments - Paul Black & Dylan Wiliam Validity, Purpose and the Recycling of Results from Educational Assessments - Paul Newton Concluding Remarks Assessment for Learning: A Compelling Conceptualization - John Gardner
Advantages and limitations of quantitative measures to assess rheumatoid arthritis: joint counts, radiographs, laboratory tests, and patient questionnaires. (2006)

Medical care is advanced by quantitative measures, all of which have advantages and limitations. No single "gold standard" measure, analogous to blood pressure, is available for diagnosis, prognosis, and management of rheumatoid arthritis (RA). Four types of measures have been used, including joint counts, radiographs, laboratory tests, and patient questionnaires. Joint counts are the most specific measure for RA but are poorly reproducible and not performed in most standard care. Radiographs provide an objective record of joint damage, but are scored quantitatively only in clinical research and have little prognostic value for long-term outcomes such as work disability and mortality. Laboratory tests are helpful when positive but frequently are "false negative"--for example, rheumatoid factor (RF), erythrocyte sedimentation rate, or C-reactive protein are normal in 30% to 45% of patients. "False positive" results are also seen; most people with RF or antinuclear antibody do not have a disease. Patient questionnaires are useful to assess and monitor patient status and provide the most significant predictive measures for long-term work disability and mortality. A multidimensional health assessment questionnaire is useful in all rheumatic diseases, with scoring templates and medical history information to save time for the rheumatologist and patient in standard care.
Disodium Ascorbyl Phytostanyl Phosphates (FM-VP4) reduces plasma cholesterol concentration, body weight and abdominal fat gain within a dietary-induced obese mouse model. (2005)

These findings suggest that FM-VP4 may have potential weight-loss and cholesterol lowering activity in both High Fat and Low Fat Diets treated groups.
Copper(II)-catalyzed molecular rearrangements: the behaviour of arylhydrazones of some 3-benzoylazoles in the presence of copper(II) acetate (1993)

The reactivity of arylhydrazones of some 3-benzoylazoles (1,2,4-oxadiazole, isoxazole and 1,2,5-oxadiazole) induced by copper(II) catalysis has been investigated. In the 1,2,4-oxadiazole and isoxazole systems, copper(II) acetate monohydrate in methanol effectively induces molecular rearrangements of the arylhydrazones into the corresponding 1,2,3-triazoles, that is, without competitive oxidation processes. In the 1,2,5-oxadiazole series, no ring transformation occurs by the action of the same salt, the expected rearrangement into triazole oximes being achieved rather with sodium ethoxide in ethanol.
E-DEMOCRACY WRIT SMALL (2010)

This article examines how elected officials' interactions with neighborhood groups, business interests, issue groups, and other stakeholders are shaped by their use of the Internet and by characteristics of local e-government infrastructure. The study utilizes data from a nationwide survey of local elected officials and from an analysis of corresponding local government websites. Results show that Internet use is associated with a significant increase in contact with stakeholders and with increasingly diverse types of communication partners, even after controlling for officials' general propensity to communicate. Both time spent on official duties and city size moderate the influence of Internet use. However, local government web sites do not appear to have a substantive influence on citizen's participation in policy making.
Bacteraemia due to dental flossing (2009)

Dental flossing can produce bacteraemia in periodontally healthy and periodontally diseased individuals at a rate comparable with that caused by some dental treatments for which antibiotic prophylaxis is given to prevent IE.
The surgical management of congenital coronary artery fistula (1994)

Surgical closure of CAF can be recommended because it is a low-risk procedure and leads to good long-term results. The problems with myocardial protection, residual fistula prevention and surgical techniques must be emphasized. For these purposes, special surgical techniques that have been introduced are described.
Flight path planning simulation for VTUAV (2014)

This paper develops a path planning simulation method in AGI software platform for multirotor UAVs in a 3D environment with avoiding the obstacles is presented. A multi-RRT (rapidly exploring random tree, RRT) algorithm is applied to compute the preliminary flight paths.
Preservation Solutions for Kidney Transplantation: History, Advances and Mechanisms (2019)

Solid organ transplantation was one of the greatest medical advances during the past few decades. Organ preservation solutions have been applied to diminish ischemic/hypoxic injury during cold storage and improve graft survival. In this article, we provide a general review of the history and advances of preservation solutions for kidney transplantation. Key components of commonly used solutions are listed, and effective supplementations for current available preservation solutions are discussed. At cellular and molecular levels, further insights were provided into the pathophysiological mechanisms of effective ingredients against ischemic/hypoxic renal injury during cold storage. We pay special attention to the cellular and molecular events during transplantation, including ATP depletion, acidosis, mitochondrial dysfunction, oxidative stress, inflammation, and other intracellular mechanisms.
A Simple and Rapid Solvent ExtractionMethod for Determining Total Lipids in Fish Tissue (1996)

Solvent systems that have been developed for lipid extraction include chloroform-methanol, n-hexane-isopropyl alcohol, and methylene chloride-methanol. The extraction methods are labor intensive, lack precision, or require a large volume of solvent. Correct computation of lipid content calls for full recovery of solvent after extraction, but recovery always is incomplete because of unaccounted solvent residue that remains in jar, filter paper, and homogenized tissue. A rapid and simple extraction method coupled with correct computation was developed for determining total lipids in fish tissue. The method uses chloroform-methanol and an Eberbach blending jar. Variables examined were chloroform-methanol ratio, solvent-to-sample ratio, and phase separation time. Precision was within 0.5%. Conventional computation of lipid content depends on the volume of chloroform measured after filtration. This volume does not include unaccounted solvent residue. Thus, a time-consuming second extraction is required for complete recovery. The mass balance of each extraction and filtration step confirmed that the correct volume of chloroform (measured plus unaccounted) was close to the theoretical volume. The procedure eliminates problems associated with laborious filtration and variation in chloroform volume readings and does not require an exact reading of chloroform volume. Instead it allows use of a theoretical volume, which depends on solvent volume and ratio used.
Human Tdp1 Cleaves a Broad Spectrum of Substrates, Including Phosphoamide Linkages (2005)

Human tyrosyl-DNA phosphodiesterase (Tdp1) hydrolyzes the phosphodiester bond between a DNA 3' end and a tyrosyl moiety. In eukaryotic cells, this type of linkage is found in stalled topoisomerase I-DNA covalent complexes, and Tdp1 has been implicated in the repair of such complexes in vivo. We confirm here that the Tdp1 catalytic cycle involves a covalent reaction intermediate in which a histidine residue is connected to a DNA 3'-phosphate through a phosphoamide linkage. Most surprisingly, this linkage can be hydrolyzed by Tdp1, and unlike a topoisomerase I-DNA complex, which requires modification to be an efficient substrate for Tdp1, the native form of Tdp1 can be removed from the DNA. The spinocerebellar ataxia with axonal neuropathy neurodegenerative disease is caused by the H493R mutant form of Tdp1, which shows reduced enzymatic activity and accumulates the Tdp1-DNA covalent intermediate. The ability of wild type Tdp1 to remove the stalled mutant protein from the DNA likely explains the recessive nature of spinocerebellar ataxia with axonal neuropathy. In addition to its activity on phosphotyrosine and phosphohistidine substrates, Tdp1 also possesses a limited DNA and RNA 3'-exonuclease activity in which a single nucleoside is removed from the 3'-hydroxyl end of the substrate. Furthermore, Tdp1 also removes a 3' abasic site and an artificial 3'-biotin adduct from the DNA. In combination with earlier data showing that Tdp1 can use 3'-phosphoglycolate as a substrate, these data suggest that Tdp1 may function to remove a variety of 3' adducts from DNA during DNA repair.
Phenotypic modulation of nasal septal chondrocytes by cytoskeleton modification (2000)

The reversion to the initial round shape of chondrocytes in monolayer cultures is one of the initial events required for the expression of cartilage-specific macromolecules. Thus, considerable research efforts have focused on developing reliable procedures to maintain a round morphology of cultured chondrocytes. Our study focuses on evaluating the response of dedifferentiated fetal rat chondrocytes to cytochalasin D, an actin-disrupting agent, with special emphasis on the morphological events. Immediately after exposure to the drug, cells round up but flatten again after removing the agent. However, immunocytochemical procedures revealed a disorganization of microfilaments and intermediate filaments. Phase-contrast and scanning electron microscopic observations revealed that on day 6 of culture, cells located at the top of the cell layer adopted a spherical morphology. Prominent differences were noted in control cultures where cells had to aggregate prior to overt chondrogenesis. These morphological changes occurred parallel to the expression of type II collagen, marker of the chondrocytes phenotype, strongly expressed in experimental cultures, but relatively weak in control cultures, and only restricted on areas of polygonal cellular aggregates. Furthermore, [35S]-sulphate incorporation into sulphated glycosaminoglycans increased rapidly with the period of culture to a maximum after 7 days and was then two-fold in treated cultures. Taken together, these findings indicated that cytochalasin-D stimulates chondrogenesis in response to modification of cytoskeleton architecture and the subsequent rounding up of the cells.
Automated removal and replacement of through-hole components in robotic rework (1997)

The need for computer controlled, fully automated rework stations has increased recently due to potential difficulties involved in manual rework of printed circuit board assemblies (PCBAs). An autonomous fully-automated robotic rework cell has been developed for the rework of TH and SM components. This paper concentrates on TH component removal and replacement issues. After a brief introduction to TH rework technology and overall cell structure, it draws attention to the main issues of component removal with regard to gripping and heating. Two multifunctional grippers that are unique in their design are presented as a solution for clinched TH component removals. Since heat is the major issue in the process, dwell times for component removal and replacement are given based on a full scale experimental study. Results of automated TH rework evaluations include the success of leg cutting, spray fluxing, removal and replacement of components.
[Experimental study on bacteriostasis of chitosan and sodium hyaluronate]. (2002)

The above results show that sodium hyaluronate has no bacteriostasis, while chitosan has bacteriostasis on broad spectrum and high relative molecular weigh: chitosan has stronger effect.
Identifying fusion transcripts using next generation sequencing (2016)

Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions have been used successfully for cancer diagnosis, prognosis, and therapeutic applications. In addition, many fusion transcripts are found in normal human cell lines and tissues, with some data supporting their role in normal physiology. Besides chromosomal rearrangement, intergenic splicing can generate them. Global identification of fusion transcripts becomes possible with the help of next generation sequencing technology like RNA-Seq. In the past decade, major advancements have been made for chimeric RNA discovery due to the development of advanced sequencing platform and software packages. However, current software tools behave differently in terms of specificity, sensitivity, time, and computational memory usage. Recent benchmarking studies showed that none of the tools are inclusive. The development of high performance (accurate and fast), and user-friendly fusion detection tool/pipeline is still an open quest. In this article, we review the existing software packages for fusion detection. We explain the methods of the tools, and discuss various factors that affect fusion detection. We summarize conclusions drawn from several comparative studies, and then discuss some of the pitfalls of these studies. We also describe the limitations of current tools, and suggest directions for future development. WIREs RNA 2016, 7:811-823. doi: 10.1002/wrna.1382 For further resources related to this article, please visit the WIREs website.
Seamless texture stitching on a 3D mesh by poisson blending in patches (2014)

In this paper, we propose a novel approach to seamless texture stitching on a 3D mesh. The main idea is to blend the sampled images by least-angle selection of gradients in overlapping patches. This is in contrast to previous works which focus on vertex- or face-based strategies with additional heuristics for robustness. Patches are obtained by growing a uniform mesh segmentation via geodesic projections. Blending is achieved by formulating a screened Poisson equation using discrete differential operators. The processing pipeline further includes an optional step of color transformation for calibration and correction. This is applied to a zippered mesh based on range scans and a morphable model fitted to face photographs.
Immunoregulation of Granuloma Formation in Murine Schistosomiasis Mansoni<sup>a</sup> (1986)

Schistosomiasis mansoni is a chronic, T lymphocyte-mediated granulomatous disease that affects mainly the liver and intestines of the infected host. The chronic inflammatory process and subsequent fibrous repair are the major factors in the pathology of the disease. In the murine model of schistosomiasis at the onset of the chronic stage of the infection, the granulomatous response undergoes spontaneous modulation with concomitant alleviation of the pathologic disturbance. Analysis of the process of modulation revealed that it results from the interaction between inflammatory and regulatory subpopulations of T lymphocytes. At the acute phase of the infection, the granulomatous response is initiated and maintained by inflammatory TDH cells that release lymphokines which mobilize and recruit the macrophages, eosinophils, etc. for the generation of the lesion. Already at this stage, while the inflammatory influence prevails, a low number of suppressor T lymphocytes are present. With the progress of the infection, the overheated inflammatory response is curbed by regulatory processes. At least two, but perhaps more, T suppressor lymphocytes are involved in the maintenance of the modulation of the granulomatous response. Modulation is an active process that needs constant maintenance, probably by recruitment of fresh suppressor cells. Removal of the suppressor population causes an immediate elevation of the granulomatous response. During modulation, T suppressor lymphocytes either abrogate or greatly diminish inflammatory lymphokine production. This in turn may be the cause for decreased cell recruitment and diminution in newly formed granuloma size. Apparently a total abrogation of the granulomatous response is not desirable because released egg antigens can be harmful to liver parenchyma cells. This has been demonstrated both in thymus-deprived and in nude, infected mice. Thus, a smaller inflammatory response has the double advantage of not only being less destructive, but also shielding the underlying tissue from damage by parasite products. The various subpopulations of T lymphocytes communicate with one another by means of soluble suppressor factors that arise from the suppressor T cells. The factors may have different functions. One factor may regulate lymphokine production whereas another may recruit fresh suppressor cells from a pool of precursors. The factors act in an antigen-specific manner. Tentatively, one may assume that these factors are composed of two units: one is the I subregion membrane marker and the other is the specific recognition receptor. The nature of this receptor is still unclear, but it may be an anti-idiotypic determinant.(ABSTRACT TRUNCATED AT 400 WORDS)
Uncertainty Assessment of SAGD Performance Using a Proxy Model Based on Butler's Theory (2008)

Abstract Steam Assisted Gravity Drainage (SAGD) is an efficient method for thermal recovery of bitumen from the vast reserves available worldwide and particularly from the oil sands in western Canada. Flow simulators are available for predicting SAGD performance and are used to support reservoir management decisions; however, the high computational time associated with the use of such complex flow simulation makes it impractical for all locations especially when reservoir uncertainty and variable operational parameters are included in the making decision process. The use of a simpler analytical model as a proxy for the reservoir simulator is shown to be a feasible alternative to flow simulation. A proxy model based on the Butler's SAGD theory is developed to predict the oil flow rate, cumulative oil production and cumulative steam injection profiles during both: the rising and spreading steam chamber periods for a confined SAGD well pair. Modifying factors are used to fit the proxy to flow simulation results to account for conformance and reservoir heterogeneity among other factors. A critical aspect of the proxy model is a realistic parameterization of geological heterogeneity. Monte Carlo Simulation (MCS) and the proxy model permit an efficient transfer of the uncertainty in reservoir and operational parameters through to performance variables such as oil production and steam oil ratio. An example application for a single well pair showed the efficiency of the methodology in terms of computation time. The results permit improved reservoir management of complex SAGD projects.