gebhart/patrepeval huggingface dataset:
Controlling collagen fiber microstructure in three-dimensional hydrogels using ultrasound (2013)

Type I collagen is the primary fibrillar component of the extracellular matrix, and functional properties of collagen arise from variations in fiber structure. This study investigated the ability of ultrasound to control collagen microstructure during hydrogel fabrication. Under appropriate conditions, ultrasound exposure of type I collagen during polymerization altered fiber microstructure. Scanning electron microscopy and second-harmonic generation microscopy revealed decreased collagen fiber diameters in response to ultrasound compared to sham-exposed samples. Results of mechanistic investigations were consistent with a thermal mechanism for the effects of ultrasound on collagen fiber structure. To control collagen microstructure site-specifically, a high frequency, 8.3-MHz, ultrasound beam was directed within the center of a large collagen sample producing dense networks of short, thin collagen fibrils within the central core of the gel and longer, thicker fibers outside the beam area. Fibroblasts seeded onto these gels migrated rapidly into small, circularly arranged aggregates only within the beam area, and clustered fibroblasts remodeled the central, ultrasound-exposed collagen fibrils into dense sheets. These investigations demonstrate the capability of ultrasound to spatially pattern various collagen microstructures within an engineered tissue noninvasively, thus enhancing the level of complexity of extracellular matrix microenvironments and cellular functions achievable within three-dimensional engineered tissues.
Breaking of Water-in-Crude Oil Emulsions. 1. Physicochemical Phenomenology of Demulsifier Action (2006)

Water-in-oil emulsions formed during oil slicks or petroleum production are known to be stabilized by surfactant molecules that naturally occur in the crude oil, e.g., asphaltenes, which are quite lipophilic in nature. Demulsifier substances combine with naturally occurring surfactants to attain a so-called optimum formulation at which the stability of the emulsion is minimum. The attainment of this formulation is related to the hydrophilicity and concentration of the added demulsifier, and a general phenomenology of the demulsification process is outlined.
Reconstruction of mechanically recorded sound by image processing (2004)

Audio information stored in the undulations of grooves in a medium such as a phonograph record or cylinder may be reconstructed, without contact, by measuring the groove shape using precision optical metrology methods and digital image processing. In this approach, audio signal processing is accomplished by two- or three-dimensional image analysis and processing. The viability of these methods was recently demonstrated on a 78 rpm shellac disc using two-dimensional image acquisition and analysis methods [V. Fadeyev and C. Haber, J. Audio Eng. Soc. 51(12), 1172–1185 (2003)]. The present work expands on these results. A three-dimensional reconstruction of mechanically recorded sound is reported. The source material, an Edison cylinder, was scanned using confocal microscopy and resulted in a faithful playback of the recorded information. Methods to accelerate the scan rates and make these techniques practical for use in working archives are reported as well. [Work supported by the Laboratory Technology Research Program (SC-32), within the Office of Science, U.S. Department of Energy under Contract No. DE-AC03-76SF00098.]
Scalable Multiplex Network Embedding (2018)

Network embedding has been proven to be helpful for many real-world problems. In this paper, we present a scalable multiplex network embedding model to represent information of multi-type relations into a unified embedding space. To combine information of different types of relations while maintaining their distinctive properties, for each node, we propose one high-dimensional common embedding and a lower-dimensional additional embedding for each type of relation. Then multiple relations can be learned jointly based on a unified network embedding model. We conduct experiments on two tasks: link prediction and node classification using six different multiplex networks. On both tasks, our model achieved better or comparable performance compared to current state-of-the-art models with less memory use.
Sensitive detection of antigen-specific T-cells using bead-bound antigen for in vitro re-stimulation (2019)

Reliable and sensitive detection of antigen specific cells is essential in several fields of research, whether it concerns monitoring responses to infectious agents or exploring the auto-antigen repertoire in autoimmune diseases. Identification of these cells is however difficult, especially when the cells often are rare and methods not sensitive, specific or practical enough. We propose a novel method of processing antigens before stimulation of cells which consists of covalently binding protein antigen to superparamagnetic micro-beads and using denaturing washes to remove contaminants. Peripheral blood mononuclear cells (PBMCs) from healthy donors were stimulated using both cytomegalovirus and tetanus-diphtheria antigen-beads as well as non-antigenic protein-beads as negative control in an IFNγ FluoroSpot assay in order to detect Th1 and CD8<sup>+</sup> responses. The responses toward the antigen beads were both antigen specific and sensitive, with a detection threshold of 1 IFNγ producing T-cell per 18,000 PBMCs. •Covalently binding antigen to paramagnetic beads allows for harsh denaturing washes without loss of antigen.•Microbeads are phagocytosed by antigen presenting cells, resulting in efficient uptake, processing and presentation of the antigens.•The method allows the usage of relatively impure starting antigen material and whole PBMC samples without high background levels in follow up cellular assays.
Comparative studies between monomeric and polymeric sodium 10-undecenoate micelles (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparative studies between monomeric and polymeric sodium 10-undecenoate micellesC. M. Paleos, C. I. Stassinopoulou, and Angelos MalliarisCite this: J. Phys. Chem. 1983, 87, 2, 251–254Publication Date (Print):January 1, 1983Publication History Published online1 May 2002Published inissue 1 January 1983https://pubs.acs.org/doi/10.1021/j100225a016https://doi.org/10.1021/j100225a016research-articleACS PublicationsRequest reuse permissionsArticle Views159Altmetric-Citations70LEARN 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 options Get e-Alerts
Stabilities and Hydrolysis of Some Iron(III) and Manganese(III) Complexes with Chelating Ligands (1990)

Abstract The stability constants of some iron(III) chelate complexes with commercially available phenolic ligands have been determined by means of spectrophotometric measurements. The ligands studied, ethylenediimino-bis(2-hydroxyphenyl)acetic acid (EHPG), ethylene-diiminobis(2-hydroxy-4-methyl-phenyl)-acetic acid (EDDHMA) and N,N'-bis-(2-hydroxybenzyl-trimethylenedinitrilo-N,N'-diacetic acid (BHTDA), are hexadentate with two phenolic, two carboxylic and two amine groups. The stabilities (log K) of the iron(III) complexes with these phenolic ligands are in the range 37.8–39.3. The protonation constants of the ligands, as well as of their iron(III) and manganese(III) complexes have been determined. The hydrolysis of the iron(III) and manganese(III) complexes has also been studied. The tendency to hydrolysis is a function of the stability, i.e. the more stable the complex, the less prone it is to hydrolyze. On the other hand, the protonation constants of the iron(III) and manganese(III) chelates do not follow any regular pattern. The implications of these results for the action of the complexes as plant fertilizers are discussed.
Electroconcentration by using countercurrent due to pressurized flow and electrophoretic mobility (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectroconcentration by using countercurrent due to pressurized flow and electrophoretic mobilityAkihiro. Hori, Takatoshi. Matsumoto, Yuji. Nimura, Masakazu. Ikedo, Hideki. Okada, and Takao. TsudaCite this: Anal. Chem. 1993, 65, 20, 2882–2886Publication Date (Print):October 15, 1993Publication History Published online1 May 2002Published inissue 15 October 1993https://pubs.acs.org/doi/10.1021/ac00068a027https://doi.org/10.1021/ac00068a027research-articleACS PublicationsRequest reuse permissionsArticle Views78Altmetric-Citations19LEARN 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
ATOM: Commit Message Generation Based on Abstract Syntax Tree and Hybrid Ranking (2019)

Commit messages record code changes (e.g., feature modifications and bug repairs) in natural language, and are useful for program comprehension. Due to the frequent updates of software and time cost, developers are generally unmotivated to write commit messages for code changes. Therefore, automating the message writing process is necessitated. Previous studies on commit message generation have been benefited from generation models or retrieval models, but the code structure of changed code, i.e., AST, which can be important for capturing code semantics, has not been explicitly involved. Moreover, although generation models have the advantages of synthesizing commit messages for new code changes, they are not easy to bridge the semantic gap between code and natural languages which could be mitigated by retrieval models. In this paper, we propose a novel commit message generation model, named ATOM, which explicitly incorporates the abstract syntax tree for representing code changes and integrates both retrieved and generated messages through hybrid ranking. Specifically, the hybrid ranking module can prioritize the most accurate message from both retrieved and generated messages regarding one code change. We evaluate the proposed model ATOM on our dataset crawled from 56 popular Java repositories. Experimental results demonstrate that ATOM increases the state-of-the-art models by 30.72% in terms of BLEU-4 (an accuracy measure that is widely used to evaluate text generation systems). Qualitative analysis also demonstrates the effectiveness of ATOM in generating accurate code commit messages.
Structure of a Murine Leukemia Virus Receptor-Binding Glycoprotein at 2.0 Angstrom Resolution (1997)

An essential step in retrovirus infection is the binding of the virus to its receptor on a target cell. The structure of the receptor-binding domain of the envelope glycoprotein from Friend murine leukemia virus was determined to 2.0 angstrom resolution by x-ray crystallography. The core of the domain is an antiparallel β sandwich, with two interstrand loops forming a helical subdomain atop the sandwich. The residues in the helical region, but not in the β sandwich, are highly variable among mammalian C-type retroviruses with distinct tropisms, indicating that the helical subdomain determines the receptor specificity of the virus.
Learning programs from noisy data (2016)

We present a new approach for learning programs from noisy datasets. Our approach is based on two new concepts: a regularized program generator which produces a candidate program based on a small sample of the entire dataset while avoiding overfitting, and a dataset sampler which carefully samples the dataset by leveraging the candidate program's score on that dataset. The two components are connected in a continuous feedback-directed loop. We show how to apply this approach to two settings: one where the dataset has a bound on the noise, and another without a noise bound. The second setting leads to a new way of performing approximate empirical risk minimization on hypotheses classes formed by a discrete search space. We then present two new kinds of program synthesizers which target the two noise settings. First, we introduce a novel regularized bitstream synthesizer that successfully generates programs even in the presence of incorrect examples. We show that the synthesizer can detect errors in the examples while combating overfitting -- a major problem in existing synthesis techniques. We also show how the approach can be used in a setting where the dataset grows dynamically via new examples (e.g., provided by a human). Second, we present a novel technique for constructing statistical code completion systems. These are systems trained on massive datasets of open source programs, also known as ``Big Code''. The key idea is to introduce a domain specific language (DSL) over trees and to learn functions in that DSL directly from the dataset. These learned functions then condition the predictions made by the system. This is a flexible and powerful technique which generalizes several existing works as we no longer need to decide a priori on what the prediction should be conditioned (another benefit is that the learned functions are a natural mechanism for explaining the prediction). As a result, our code completion system surpasses the prediction capabilities of existing, hard-wired systems.
Improved In Vitro Angiogenesis Model by Collagen Density Reduction and the Use of Type III Collagen (1993)

Angiogenesis was examined by a three-dimensional model in vitro, using human umbilical vein endothelial cells (HUVECs) cultured in a collagen gel. An abundant capillary-like network with a lumen structure was identified histologically and shown to have formed at a collagen density of 0.05% or 0.10% instead of 0.15%, for either type I or type III collagen. At the same density, type III collagen induced a capillary-like network with HUVECs at an earlier stage of culture than type I collagen. In a two-dimensional culture, HUVECs were viable and proliferated to a great extent on the culture dish coated with collagen. This was particularly so in the case of type III collagen at lower density (5 ng/cm2). Type III collagen at a sufficiently low density is thus shown useful for studying angiogenesis in vitro. The capillary-like network that formed in the three-dimensional culture appeared somewhat labile, but became stable with the continuous addition of endothelial cell growth supplement and increase in the plating number of HUVECs.
Direct manipulation of temporal structures in a multimedia application framework (1994)

The design of complex multimedia documents presents new challenges to authoring systems, because spatial and temporal features should be visualized and made accessible in an intuitive and direct-manipulative way. In this study, multimedia presentations are considered as hierarchical compositions of time objects that define serial or parallel synchronization of the inserted media objects. Media composition hierarchies support automatic temporal layout mechanisms. They are integrated into an object-oriented application framework called MET++. It provides direct manipulation interaction on temporal structures in a composition view that displays temporal and compositional relations, allows time transformations on composites, supports the definition of time-dynamic behavior of media objects through time functions, and has a flexible graphical layout in order to visualize context information.
Five Degrees of Happiness (2016)

This paper focuses on achieving optimal responses through supporting children’s judgements, using Smiley Face Likert scales as a rating scale for quantitative questions in evaluations. It highlights the need to provide appropriate methods for children to communicate judgements, highlighting that the traditional Smiley Face Likert scale does not provide an appropriate method. The paper outlines a range of studies, identifying that to achieve differentiated data and full use of rating scales by children that faces with positive emotions should be used within Smiley Face Likert scales. The proposed rating method, the Five Degrees of Happiness Smiley Face Likert scale, was used in a large-scale summative evaluation of a Serious Game resulting in variance within and between children, with all points of the scale used.
Metal bonding with ultra-thin layer for optical applications (2007)

Adhesive bonding is a well-known technics to assembly dies or wafer on a host substrate through polymer or solder bumps. To combine electronic and photonic systems on a single chip, we propose hereby to use AuSn alloy as bonding medium combined to waferscale technology and post-bonding III-V processing alleviating so the need of alignment accuracy between wafers. For instance, high density LED’s array could be realized on driving CMOS wafer taking benefits from the nice electrical, thermal and mechanical properties of this alloy. We present our first technological results using patterned thin bonding layer made of a multilayer Au-Sn composite.
Array technology (1992)

A review of advances in devices and components applicable to modern phased arrays is given. Phase shifters as well as solid-state transmit/receive modules are discussed. Approaches to cost reduction using higher levels of integration (different packaging approaches) and new materials are also covered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Sonification as a possible stroke rehabilitation strategy (2014)

Despite cerebral stroke being one of the main causes of acquired impairments of motor skills worldwide, well-established therapies to improve motor functions are sparse. Recently, attempts have been made to improve gross motor rehabilitation by mapping patient movements to sound, termed sonification. Sonification provides additional sensory input, supplementing impaired proprioception. However, to date no established sonification-supported rehabilitation protocol strategy exists. In order to examine and validate the effectiveness of sonification in stroke rehabilitation, we developed a computer program, termed "SonicPointer": Participants' computer mouse movements were sonified in real-time with complex tones. Tone characteristics were derived from an invisible parameter mapping, overlaid on the computer screen. The parameters were: tone pitch and tone brightness. One parameter varied along the x, the other along the y axis. The order of parameter assignment to axes was balanced in two blocks between subjects so that each participant performed under both conditions. Subjects were naive to the overlaid parameter mappings and its change between blocks. In each trial a target tone was presented and subjects were instructed to indicate its origin with respect to the overlaid parameter mappings on the screen as quickly and accurately as possible with a mouse click. Twenty-six elderly healthy participants were tested. Required time and two-dimensional accuracy were recorded. Trial duration times and learning curves were derived. We hypothesized that subjects performed in one of the two parameter-to-axis-mappings better, indicating the most natural sonification. Generally, subjects' localizing performance was better on the pitch axis as compared to the brightness axis. Furthermore, the learning curves were steepest when pitch was mapped onto the vertical and brightness onto the horizontal axis. This seems to be the optimal constellation for this two-dimensional sonification.
Diastereoselective One-Pot Knoevenagel Condensation/Corey–Chaykovsky Cyclopropanation (2012)

Efforts to substitute the cyclopropane ring in a series of aryl cyclopropylnitriles led to the discovery of an operationally simple one-pot method for Knoevenagel condensation and subsequent Corey-Chaykovsky cyclopropanation giving diastereomerically pure products as a racemic mixture of enantiomers. Method development and results for variably substituted aryl acetonitriles and aldehydes in the reaction are reported. A concise synthesis of (±)-bicifadine in two steps is provided to demonstrate the utility of the method.
Plasma tocopherol and prevalence of colorectal adenomas in a multiethnic population. (1998)

Although vitamin E can block mutagenesis and cell transformation in vitro and can reduce the number of chemically induced colonic adenomas in mice, previous clinical trials have found no protective effect of vitamin E supplements against colorectal adenomas, and epidemiological studies have found only weak protective effects of dietary or plasma alpha-tocopherol against colorectal cancer. We previously examined first diagnosis of colorectal adenomas in a sigmoidoscopy screening population and failed to find a protective effect of dietary vitamin E. Because measurements of dietary intake may not be a good proxy of vitamin E status, we assayed plasma alpha- and gamma-tocopherol concentration for 332 subjects with colorectal adenomas and 363 control subjects from this previous sigmoidoscopy-based study. Increasing alpha-tocopherol and decreasing gamma-tocopherol levels were associated with decreased occurrence of large (> or = 1 cm) but not of small (<1 cm) adenomas; however, after adjustment for potential confounding variables, these trends were not statistically significant. A strong trend (P = 0.02) was observed by using the alpha-tocopherol:gamma-tocopherol ratio, which may be a more sensitive indicator of alpha-tocopherol intake. Subjects in the highest versus lowest quintile of alpha-tocopherol: gamma-tocopherol ratio had an odds ratio of 0.36 (95% confidence interval, 0.14-0.95) for large adenomas. The finding that a high alpha-tocopherol:gamma-tocopherol ratio is associated with decreased occurrence of large, but not of small, colorectal adenomas is consistent with previous findings that alpha-tocopherol may be protective against colon cancer. A high plasma alpha-tocopherol:gamma-tocopherol ratio may be a better predictor of decreased cancer risk than high plasma alpha-tocopherol alone.