gebhart/patrepeval huggingface dataset:
Use of Conditioned Extracellular Matrix as a Tissue-engineered Tumor Matrisome for Prostate Cancer and Melanoma Immunotherapy (2022)

Antigens within the tissue-engineered matrisome stimulated an inhibitory response to tumor growth; this strategy should be explored further as a means of cancer immunotherapy.
Test algorithm for memory cell disturb failures (2002)

The increasing use of two parted register files (one read port and one write port) has introduced complications in complete, accurate testing. This is especially true when the memories appear as embedded cores in Systems On Chips. In this paper, we describe a new fault effect that has been observed, a basic algorithm for detecting this fault, and enhance a well known classic algorithm for memory testing to detect these faults.
Influence of the HDL Receptor SR-BI on Lipoprotein Metabolism and Atherosclerosis (2003)

The scavenger receptor class B type I (SR-BI) was the first molecularly well-defined cell-surface HDL receptor to be described. SR-BI mediates selective HDL cholesterol uptake by formation of a productive lipoprotein/receptor complex, which requires specific structural domains and conformation states of apolipoprotein A-I present in HDL particles. SR-BI is abundantly expressed in several tissues, including the liver, where its expression is regulated by various mechanisms, including the transcriptional activity of nuclear receptors. The importance of SR-BI in overall HDL cholesterol metabolism and its antiatherogenic activity in vivo has been definitively established by SR-BI gene manipulation in mice. Remarkably, SR-BI/apolipoprotein E double-knockout mice develop complex coronary artery disease, myocardial infarction, and heart failure. Additional studies should help to define the importance of SR-BI in human health and disease.
Benchmarking Streaming Computation Engines: Storm, Flink and Spark Streaming (2016)

Streaming data processing has been gaining attention due to its application into a wide range of scenarios. To serve the booming demands of streaming data processing, many computation engines have been developed. However, there is still a lack of real-world benchmarks that would be helpful when choosing the most appropriate platform for serving real-time streaming needs. In order to address this problem, we developed a streaming benchmark for three representative computation engines: Flink, Storm and Spark Streaming. Instead of testing speed-of-light event processing, we construct a full data pipeline using Kafka and Redis in order to more closely mimic the real-world production scenarios. Based on our experiments, we provide a performance comparison of the three data engines in terms of 99th percentile latency and throughput for various configurations.
Characterization of brain network supporting episodic memory in the absence of one medial temporal lobe (2019)

How the brain supports normal episodic memory function without medial temporal lobe (MTL) structures has not been well characterized, which could provide clues for new therapeutic targets for people with MTL dysfunction-related memory impairment. To characterize brain network supporting effective episodic memory function in the absence of unilateral MTL, we investigated the whole-brain cortical interactions during functional magnetic resonance imaging memory encoding paradigms of words and figures in patients who showed a normal range of memory capacity following unilateral MTL resection and healthy controls (HC). Compared to the HC, the patients showed less activation in the left inferior frontal areas and right thalamus together with greater activation in the many cortical areas including the medial prefrontal cortex (mPFC). Task-based functional connectivity (FC) analysis revealed that the mPFC showed stronger interactions with widespread brain areas in both patient groups, including the hippocampus contralateral to the resection. Moreover, the strength of the mPFC FC predicts the individual memory capacity of the patients. Our data suggest that hyperconnectivity of distributed brain areas, especially the mPFC, is a neural mechanism for memory function in the absence of one MTL.
Analysis of the Effects of Five Factors Relevant to In Vitro Chondrogenesis of Human Mesenchymal Stem Cells Using Factorial Design and High Throughput mRNA-Profiling (2014)

The in vitro process of chondrogenic differentiation of mesenchymal stem cells for tissue engineering has been shown to require three-dimensional culture along with the addition of differentiation factors to the culture medium. In general, this leads to a phenotype lacking some of the cardinal features of native articular chondrocytes and their extracellular matrix. The factors used vary, but regularly include members of the transforming growth factor β superfamily and dexamethasone, sometimes in conjunction with fibroblast growth factor 2 and insulin-like growth factor 1, however the use of soluble factors to induce chondrogenesis has largely been studied on a single factor basis. In the present study we combined a factorial quality-by-design experiment with high-throughput mRNA profiling of a customized chondrogenesis related gene set as a tool to study in vitro chondrogenesis of human bone marrow derived mesenchymal stem cells in alginate. 48 different conditions of transforming growth factor β 1, 2 and 3, bone morphogenetic protein 2, 4 and 6, dexamethasone, insulin-like growth factor 1, fibroblast growth factor 2 and cell seeding density were included in the experiment. The analysis revealed that the best of the tested differentiation cocktails included transforming growth factor β 1 and dexamethasone. Dexamethasone acted in synergy with transforming growth factor β 1 by increasing many chondrogenic markers while directly downregulating expression of the pro-osteogenic gene osteocalcin. However, all factors beneficial to the expression of desirable hyaline cartilage markers also induced undesirable molecules, indicating that perfect chondrogenic differentiation is not achievable with the current differentiation protocols.
Estimating contamination between batches in products lines (1984)

Liquid pipelines are frequently used to transport different products or different grades of the same product. This is achieved through batching the products in a particular sequence within a repeated cycle called the ''batching cycle.'' Factors that affect the overall scheme of batching include pipeline parameters such as flow rate, pipeline length, diameter, equipment, etc.; number of receiving stations along the line and products packages; batch duration and total cycle duration; batching sequence and arrangement; and operating procedure and shutdown periods. The factors also include interface contamination spread handling facilities at terminal points; and storage capacity, the availability of each product at the source end, and its demand at the receiving ends. The feasibility and economics of such operations depend upon the extent of the mixing that takes place between different batches in the pipeline. In this article, a rather general method is described to estimate the extent of the contamination (or mixing) spread, particularly in zones between batches that vary significantly in their physical properties.
Cross-Entropy Randomized Motion Planning (2011)

This paper is concerned with motion planning for nonlinear robotic systems operating in constrained environments. Motivated by recent developments in sampling-based motion planning and Monte Carlo optimization we propose a general randomized path planning method based on sampling in the space of trajectories. The idea is to construct a probability distribution over the set of feasible paths and to perform the search for an optimal trajectory through importance sampling. At the core of the approach lies the cross-entropy method for estimation of rare-event probabilities. The algorithm recursively approximates the optimal sampling distribution which guides the set of sampled trajectories towards regions of progressively lower cost until converging to a delta distribution at the optimum. Our main goal is to provide a framework for consistent adaptive sampling correlating the spatial structure of trajectories and their computed costs. The approach is illustrated with two simple examples-a point mass vehicle and the Dubins car, and is then applied to a simulated helicopter flying optimally in a 3-D terrain.
On the Hydrogen-Bonded Status of 2-Azacyclononanone and 2-Azacyclotridecanone in the Solid State (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the Hydrogen-Bonded Status of 2-Azacyclononanone and 2-Azacyclotridecanone in the Solid StateRaymond D. Skwierczynski and Samuel H. GellmanCite this: J. Phys. Chem. 1994, 98, 14, 3694–3696Publication Date (Print):April 1, 1994Publication History Published online1 May 2002Published inissue 1 April 1994https://pubs.acs.org/doi/10.1021/j100065a025https://doi.org/10.1021/j100065a025research-articleACS PublicationsRequest reuse permissionsArticle Views56Altmetric-Citations5LEARN 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
Beyond the Polysulfide Shuttle and Lithium Dendrite Formation: Addressing the Sluggish Sulfur Redox Kinetics for Practical High‐Energy Li‐S Batteries (2020)

Electrolyte modulation simultaneously suppresses polysulfide the shuttle effect and lithium dendrite formation of lithium-sulfur (Li-S) batteries. However, the sluggish S redox kinetics, especially under high S loading and lean electrolyte operation, has been ignored, which dramatically limits the cycle life and energy density of practical Li-S pouch cells. Herein, we demonstrate that a rational combination of selenium doping, core-shell hollow host structure, and fluorinated ether electrolytes enables ultrastable Li stripping/plating and essentially no polysulfide shuttle as well as fast redox kinetics. Thus, high areal capacity (>4 mAh cm<sup>-2</sup> ) with excellent cycle stability and Coulombic efficiency were both demonstrated in Li metal anode and thick S cathode (4.5 mg cm<sup>-2</sup> ) with a low electrolyte/sulfur ratio (10 μL mg<sup>-1</sup> ). This research further demonstrates a durable Li-Se/S pouch cell with high specific capacity, validating the potential practical applications.
Microphotonic Thermal Detectors and Imagers. (2016)

Abstract not provided.
Branched Oligo(ether) Side Chains: A Path to Enhanced Processability and Elevated Conductivity for Polymeric Semiconductors (2021)

Abstract Commercialization of stable conjugated polymers (CPs) with tunable electronic properties will remain a challenge without adequate solution processability due to the importance of techniques such as roll‐to‐roll manufacturing. Consequently, modifying CP backbones with polar side chains has recently resurged as an attractive structural design approach to improve polymer solubility and to provide CPs with the capability of transporting both electrons and ions, which is crucial for applications such as organic electrochemical transistors (OECTs). Here, a new dioxythiophene copolymer comprised of 2,​2'‐bis‐(3,4‐ethylenedioxy)thiophene (biEDOT) and 3,4‐propylenedioxythiophene (ProDOT) substituted with branched oligo(ether) side chains (PE 2 ‐biOE2OE3) is synthesized using two direct hereto(arylation) polymerization (DHAP) techniques. The typical DHAP technique results in a lower molecular weight polymer (PE 2 ‐biOE2OE3(L)), which is soluble in acetone and demonstrated a solid‐state conductivity after oxidative doping of 55 ± 3 S cm −1 . Alternatively, a unique temperature ramp DHAP methodology results in a higher molecular weight polymer (PE 2 ‐biOE2OE3(H)) with an especially high solid‐state conductivity of 430 ± 60 S cm −1 . Notably, the first OECT fabricated from an acetone‐processed polymer is reported, which is stable up to 500 cycles and can provide a pathway for future material design aimed at eliminating the use of toxic chlorinated solvents in OECT active layer processing.
Registration-based initialization during radiation therapy planning (2007)

An established challenge in the field of image analysis has been the registration of images having a large initial misalignment. For example in chemo and Radiation Therapy Planning (RTP), there is often a need to register an image delineating a specific anatomy (usually in the surgery position) with that of a whole body image (obtained preoperatively). In such a scenario, there is room for a large misalignment between the two images that are required to be aligned. Large misalignments are traditionally handled in two ways: 1) Semi-automatically with a user initialization or 2) With the help of the origin fields in the image header. The first approach is user dependant and the second method can be used only if the two images are obtained from the same scanner with consistent origins. Our methodology extends a typical registration framework by selecting components that are capable of searching a large parameter space without settling on local optima. We have used an optimizer that is based on an Evolutionary Scheme along with an information theory based similarity metric that can address these needs. The attempt in this study is to convert a large misalignment problem to a small misalignment problem that can then be handled using application specific registration algorithms. Further improvements along local areas can be obtained by subjecting the image to a non-rigid transformation. We have successfully registered the following pairs of images without any user initialization: CTAC - simCT (neuro, lungs); MRPET/ CT (neuro, liver); T2-SPGR (neuro).
Modulation depth threshold in the Compensation Comparison approach (2007)

Recently, the "Compensation Comparison" method was introduced for measuring retinal straylight. In this article, basic aspects are described, in particular a generalization of the approach using the concept of "precompensation," and including flicker threshold as parameter in the psychophysical model. The model was experimentally verified in lab measurements with and without artificially increased straylight and was tested on the data from the multi-center GLARE study. The resulting flicker threshold estimates were analyzed to better understand their origin. An effect of flicker adaptation over distance was found. The new approach proved suitable to describe Compensation Comparison measurements including precompensation, and also for subjects with poor psychometric behavior.
Artificial intelligence and metagenomics in intestinal diseases (2021)

Gut microbiota has been shown to associate with the development of gastrointestinal diseases. In the last decade, development in whole metagenome sequencing and 16S rRNA sequencing technology has dramatically accelerated the gut microbiome's research and revealed its association with gastrointestinal disorders. Because of high dimensionality and complexity's intrinsic data characteristics, traditional bioinformatical methods could only explain the most significant changes with limited prediction accuracy. In contrast, machine learning is the application of artificial intelligence that provides the computational systems to automatically learn and improve from experience (training cohort) without being explicitly programmed. It is thus capable of unwiring high dimensionality and complicated correlational hitches. With modern computation power, machine learning is widely utilized to analyze microorganisms related to disease onset and other clinical features. It could help explore and identify novel biomarkers or improve the accuracy rate of disease diagnostic. This review summarized the most recent research that utilized machine learning to reveal the role of gut microbiota in intestinal disorders.
Neural activation imaged by MEMRI in mouse models of PTSD: Early Life Stress and Role of the Serotonergic System in Prolonged Response to Fear. (2018)

Posttraumatic stress disorder (PTSD) occurs in some people after exposure to life-threatening fear, and impacts up to 8% of the general population, including veterans and victims of domestic violence. One of the central questions involved in PTSD research is how a traumatic event fundamentally alters neural circuits. Early life stress (ELS) and serotonergic dis-regulation are associated with PTSD, and fear activates serotonergic and noradrenergic systems, and the HPA axis. Mouse lines knocked-out for the serotonin transporter gene (SERT-KO) have increased fear responses to predator stress (PS), with prolongation of the fear response1. Using manganese-enhanced MRI (MEMRI) tract-tracing, we reported that SERT-KO mice have abnormal circuitry in the prelimbic system2. To determine if this circuit is affected by fear, SERT-KO and WT mice were exposed to PS and the effects on neural activity and circuitry assayed by MEMRI before and after stress. Predator stress is a known naturalistic provocateur of PTSD in rodents. Mn2+ is a metabolic contrast agent that reports on neural activity by entering active neurons through voltage-activated Ca2+ channels when delivered systemically3, and is transported along axons tracing multi-synaptic circuitry when injected locally4,5. Mn2+ increases the relaxation rate of protons in water in T1-weighted pulse sequences, and thus produces a hyper-intense signal in T1-weighted MRI.
Simple Calls for Flexible Constructs Using the Traditional File API (1996)

We present the design for a remote qos control interface to the transport protocol based on existing work for similar applications. This puts together the read/write calls from the traditional file system API and an additional primitive. The addition amounts to programming an operating system data- streaming service which may be provided as a system call or otherwise using the standard techniques. Put together these allow much more than the traditional call based control interface. The resulting interface simplifies the mechanisms for distributed control. Parts of this interface have also been implemented in our ongoing experiments with file transfer.
Music-evoked nostalgia: Affect, memory, and personality. (2010)

Participants listened to randomly selected excerpts of popular music and rated how nostalgic each song made them feel. Nostalgia was stronger to the extent that a song was autobiographically salient, arousing, familiar, and elicited a greater number of positive, negative, and mixed emotions. These effects were moderated by individual differences (nostalgia proneness, mood state, dimensions of the Affective Neurosciences Personality Scale, and factors of the Big Five Inventory). Nostalgia proneness predicted stronger nostalgic experiences, even after controlling for other individual difference measures. Nostalgia proneness was predicted by the Sadness dimension of the Affective Neurosciences Personality Scale and Neuroticism of the Big Five Inventory. Nostalgia was associated with both joy and sadness, whereas nonnostalgic and nonautobiographical experiences were associated with irritation.
Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication (2008)

The development of small molecules to control gene expression could be the spearhead of future-targeted therapeutic approaches in multiple pathologies. Among heterocyclic dications developed with this aim, a phenyl-furan-benzimidazole dication DB293 binds AT-rich sites as a monomer and 5'-ATGA sequence as a stacked dimer, both in the minor groove. Here, we used a protein/DNA array approach to evaluate the ability of DB293 to specifically inhibit transcription factors DNA-binding in a single-step, competitive mode. DB293 inhibits two POU-domain transcription factors Pit-1 and Brn-3 but not IRF-1, despite the presence of an ATGA and AT-rich sites within all three consensus sequences. EMSA, DNase I footprinting and surface-plasmon-resonance experiments determined the precise binding site, affinity and stoichiometry of DB293 interaction to the consensus targets. Binding of DB293 occurred as a cooperative dimer on the ATGA part of Brn-3 site but as two monomers on AT-rich sites of IRF-1 sequence. For Pit-1 site, ATGA or AT-rich mutated sequences identified the contribution of both sites for DB293 recognition. In conclusion, DB293 is a strong inhibitor of two POU-domain transcription factors through a cooperative binding to ATGA. These findings are the first to show that heterocyclic dications can inhibit major groove transcription factors and they open the door to the control of transcription factors activity by those compounds.
A new trifluoromethylating agent: synthesis of polychlorinated (trifluoromethyl)benzenes and 1,3-bis(trifluoromethyl)benzenes and conversion into their trichloromethyl counterparts and molecular structure of highly strained polychloro-m-xylenes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new trifluoromethylating agent: synthesis of polychlorinated (trifluoromethyl)benzenes and 1,3-bis(trifluoromethyl)benzenes and conversion into their trichloromethyl counterparts and molecular structure of highly strained polychloro-m-xylenesJ. Castaner, J. Riera, J. Carilla, A. Robert, E. Molins, and C. MiravitllesCite this: J. Org. Chem. 1991, 56, 1, 103–110Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/jo00001a022https://doi.org/10.1021/jo00001a022research-articleACS PublicationsRequest reuse permissionsArticle Views627Altmetric-Citations27LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts