gebhart/patrepeval huggingface dataset:
TagRec: Automated Tagging of Questions with Hierarchical Learning Taxonomy (2021)

Online educational platforms organize academic questions based on a hierarchical learning taxonomy (subject-chapter-topic). Automatically tagging new questions with existing taxonomy will help organize these questions into different classes of hierarchical taxonomy so that they can be searched based on the facets like chapter. This task can be formulated as a flat multi-class classification problem. Usually, flat classification based methods ignore the semantic relatedness between the terms in the hierarchical taxonomy and the questions. Some traditional methods also suffer from the class imbalance issues as they consider only the leaf nodes ignoring the hierarchy. Hence, we formulate the problem as a similarity-based retrieval task where we optimize the semantic relatedness between the taxonomy and the questions. We demonstrate that our method helps to handle the unseen labels and hence can be used for taxonomy tagging in the wild. In this method, we augment the question with its corresponding answer to capture more semantic information and then align the question-answer pair's contextualized embedding with the corresponding label (taxonomy) vector representations. The representations are aligned by fine-tuning a transformer based model with a loss function that is a combination of the cosine similarity and hinge rank loss. The loss function maximizes the similarity between the question-answer pair and the correct label representations and minimizes the similarity to unrelated labels. Finally, we perform experiments on two real-world datasets. We show that the proposed learning method outperforms representations learned using the multi-class classification method and other state of the art methods by 6% as measured by Recall@k. We also demonstrate the performance of the proposed method on unseen but related learning content like the learning objectives without re-training the network.
Combining keyword search and forms for ad hoc querying of databases (2009)

A common criticism of database systems is that they are hard to query for users uncomfortable with a formal query language. To address this problem, form-based interfaces and keyword search have been proposed; while both have benefits, both also have limitations. In this paper, we investigate combining the two with the hopes of creating an approach that provides the best of both. Specifically, we propose to take as input a target database and then generate and index a set of query forms offline. At query time, a user with a question to be answered issues standard keyword search queries; but instead of returning tuples, the system returns forms relevant to the question. The user may then build a structured query with one of these forms and submit it back to the system for evaluation. In this paper, we address challenges that arise in form generation, keyword search over forms, and ranking and displaying these forms. We explore techniques to tackle these challenges, and present experimental results suggesting that the approach of combining keyword search and form-based interfaces is promising.
Dynamics of the reaction atomic oxygen(3P) + hydrogen bromide: experimental investigation and theoretical modeling (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDynamics of the reaction atomic oxygen(3P) + hydrogen bromide: experimental investigation and theoretical modelingKenneth G. McKendrick, David J. Rakestraw, Richard N. Zare, and Rong ZhangCite this: J. Phys. Chem. 1988, 92, 19, 5530–5540Publication Date (Print):September 1, 1988Publication History Published online1 May 2002Published inissue 1 September 1988https://pubs.acs.org/doi/10.1021/j100330a039https://doi.org/10.1021/j100330a039research-articleACS PublicationsRequest reuse permissionsArticle Views115Altmetric-Citations57LEARN 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
Acute Stent-Induced Endothelial Denudation: Biomechanical Predictors of Vascular Injury (2021)

Recent concern for local drug delivery and withdrawal of the first Food and Drug Administration-approved bioresorbable scaffold emphasizes the need to optimize the relationships between stent design and drug release with imposed arterial injury and observed pharmacodynamics. In this study, we examine the hypothesis that vascular injury is predictable from stent design and that the expanding force of stent deployment results in increased circumferential stress in the arterial tissue, which may explain acute injury poststent deployment. Using both numerical simulations and <i>ex vivo</i> experiments on three different stent designs (slotted tube, corrugated ring, and delta wing), arterial injury due to device deployment was examined. Furthermore, using numerical simulations, the consequence of changing stent strut radial thickness on arterial wall shear stress and arterial circumferential stress distributions was examined. Regions with predicted arterial circumferential stress exceeding a threshold of 49.5 kPa compared favorably with observed <i>ex vivo</i> endothelial denudation for the three considered stent designs. In addition, increasing strut thickness was predicted to result in more areas of denudation and larger areas exposed to low wall shear stress. We conclude that the acute arterial injury, observed immediately following stent expansion, is caused by high circumferential hoop stresses in the interstrut region, and denuded area profiles are dependent on unit cell geometric features. Such findings when coupled with where drugs move might explain the drug-device interactions.
Radiative Heat Transfer Computations as a Free Molecular Flow Modeling Tool (2005)

The use of an analogy between radiative heat transfer and free molecular flow is one that is straightforward, but apparently not often used in practice, nor is it often cited in the literature. The purpose of this article is to make this concept more familiar to technical audiences who might find the idea useful. Performing calculations using a direct simulation Monte Carlo model and general‐purpose computational fluid dynamics software solving the analogous radiative heat transfer problem will show validation of the technique for a simple two‐dimensional geometry. Discussion will highlight the significant advantages of the radiative heat transfer analogy in industrial practice. The work also proposes a technical correction to a detailed journal article on the topic.
Exploring Viral Genomics at Lawrence Livermore National Laboratory (2007)

This summer I had the privilege of working at Lawrence Livermore National Laboratory under the Nonproliferation, Homeland and International Security Directorate in the Chemical and Biological Countermeasures Division. I worked exclusively on the Viral Identification and Characterization Initiative (VICI) project focusing on the development of multiplexed polymerase chain reaction (PCR) assays. The goal of VICI is to combine several disciplines such as molecular biology, microfluidics, and bioinformatics in order to detect viruses and identify them in order to effectively and quickly counter infectious disease, natural or engineered. The difficulty in such a countermeasure is that little is known about viral diversity due to the ever changing nature of these organisms. In response, VICI is developing a new microfluidic bioanalytical platform to detect known and unknown viruses by analyzing every virus in a sample by isolating them into picoliter sized droplets on a microchip and individually analyzing them. The sample will be injected into a channel of oil to form droplets that will contain viral nucleic acids that will be amplified using PCR. The multiplexed PCR assay will produce a series of amplicons for a particular virus genome that provides an identifying signature. A device will then detect whether or not DNA is present in the droplet and will sort the empty droplets from the rest. From this point, the amplified DNA is released from the droplets and analyzed using capillary gel electrophoresis in order to read out the series of amplicons and thereby determine the identity of each virus. The following figure depicts the microfluidic process. For the abovementioned microfluidic process to work, a method for detecting amplification of target viral nucleic acids that does not interfere with the multiplexed biochemical reaction is required for downstream sorting and analysis. In this report, the successful development of a multiplexed PCR assay using SYBR Green I as a fluorescent dye to detect amplification of viral DNA that can later be integrated into microfluidic PCR system for sorting and analysis is shown.
Feasibility of Direct Sputum Molecular Testing for Drug Resistance as Part of Tuberculosis Clinical Trials Eligibility Screening (2019)

A rapid diagnosis of drug-resistant tuberculosis (TB) is critical for early initiation of effective therapy. Molecular testing with line probe assays (MTBDR<i>plus</i> and MTBDR<i>sl</i>) on culture isolates has been available for some time and significantly reduces the time to diagnosis of drug resistance. However, routine use of this test directly on sputum is less common. As part of enrollment screening procedures for tuberculosis clinical trials conducted in Hanoi, Vietnam, we evaluated the feasibility and performance of line probe assay (LPA) testing directly on sputum samples from 315 participants with no prior history of TB treatment. Test performance characteristics for the detection of rifampin (RIF) and isoniazid (INH) drug resistance as compared to culture-based drug susceptibility testing (DST) reference standard were calculated. LPA demonstrated high sensitivity and specificity for the diagnosis of drug resistance. Scaling up molecular testing on sputum as part of time-sensitive clinical trial screening procedures in high TB burden settings is feasible and will reduce both time to initiation of appropriate therapy and the risk of late exclusions due to microbiologic ineligibility.
Some observations of acoustic cavitation in water at 1 MHz (1988)

The results are summarized: (1) Nuclei distrubution in fresh tap water changes rapidly with time within the first hour after water has been poured into the tank. It is difficult to reproduce the experimental results at relatively low powers within this period. (2) The most violent action (cavitation and streaming) was observed in tests with fresh tap water. The presence of a reflector enhanced the cavitation activity significantly. Stable bubble pattern with stationary bubbles were observed for most of the tests conducted with a long waiting time and without the presence of a reflector. (3) Sometimes four distinctive types of bubble behavior can be observed in one experiment. For example, at relatively high powers in tests with long waiting time and with the presence of a reflector, it was observed that there were stationary bubbles, rising bubbles, dancing bubbles, and streaming bubbles. (4) For tests conducted with long waiting time, no bubbles were observed even when input power was increased to a very high values (100 volts). However, bubbles can be made to appear suddenly by pertubing the frequency away from 1 MHz. Once the bubbles appear, they remain even when the frequency is returned to 1 MHz. This triggeringmore » phenomenon may be partly related to hysteresis. (5) The bubbles are gas (not vapor) since most of them gradually rise to the surface when the power is turned off. (6) At relatively high powers (/approximately 100 volts/, strong streaming and pulsing were observed. A group of bubbles was observed to move suddenly in the direction away form the transducer. This pulsing action does not occur at a fixed interval. 9 refs., 8 figs.« less
Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia (2012)

Diamond-Blackfan anemia (DBA) is a hypoplastic anemia characterized by impaired production of red blood cells, with approximately half of all cases attributed to ribosomal protein gene mutations. We performed exome sequencing on two siblings who had no known pathogenic mutations for DBA and identified a mutation in the gene encoding the hematopoietic transcription factor GATA1. This mutation, which occurred at a splice site of the GATA1 gene, impaired production of the full-length form of the protein. We further identified an additional patient carrying a distinct mutation at the same splice site of the GATA1 gene. These findings provide insight into the pathogenesis of DBA, showing that the reduction in erythropoiesis associated with the disease can arise from causes other than defects in ribosomal protein genes. These results also illustrate the multifactorial role of GATA1 in human hematopoiesis.
A Cognitive Reserve Network That Moderates the Relationship Between Alzheimer’s Disease Pathology and Cognition (2022)

Abstract Background The new consensus definition of cognitive reserve (CR) provides a framework to study individual differences in cognitive functioning relative to aging and disease. CR denotes a property of the brain that allows for better than expected cognitive performance given the degree of age‐related brain changes or disease. More specifically, individual differences in patterns of brain activity during fMRI tasks might explain the differential susceptibility to pathological burden. Method According to the consensus definitions, we sought to identify and quantify CR from fMRI novelty‐contrast maps in a large multi‐centric sample (DELCODE) consisting of 215 participants with SCD, 79 with MCI, 30 with AD dementia, 56 AD relatives and 156 cognitively normal controls (CN). CSF amyloid‐42/40 ratio, CSF p‐tau and hippocampal volume (ATN) were reduced to a single number, representing a (Alzheimer’s) disease progression (DP) score. To identify a CR network, voxel‐wise linear regression models determined where functional task‐activation moderates the relationship between DP and cognition. Finally, task‐related activity within the CR network was extracted to obtain individual fMRI‐based CR scores. Result The DP score showed a strong negative quadratic association with baseline memory scores. CR voxels, in which higher or lower activation were associated with better cognition, weakening the effect of DP, were mainly located within the novelty network. They included lateral‐occipital and superior‐parietal regions, lingual and fusiform gyrus, cuneus and small parts of cingulate. While there was no association between the CR score and cognition in CNs, higher CR scores in MCI and AD patients were related to higher PACC5 scores. Conclusion We established a DP score that collapses the ATN measures into a single number, while retaining its deleterious effect on an individual’s memory score. Furthermore, a newly identified task‐dependent CR network could be used to establish a CR score, which was related to higher PACC5 scores in MCI and AD patients, suggesting a functional compensation mechanism at later stages of AD that is not yet present in CN. Thus, targeted alteration of brain activity might be a promising route to modify cognitive trajectories in MCI and AD patients. Further, detailed examination of individuals with high CR might reveal additional disease‐modifying factors.
Transvaginal fast-scanning optical-resolution photoacoustic endoscopy (2018)

Photoacoustic endoscopy offers in vivo examination of the visceral tissue using endogenous contrast, but its typical B-scan rate is ∼10 Hz, restricted by the speed of the scanning unit and the laser pulse repetition rate. Here, we present a transvaginal fast-scanning optical-resolution photoacoustic endoscope with a 250-Hz B-scan rate over a 3-mm scanning range. Using this modality, we not only illustrated the morphological differences of vasculatures among the human ectocervix, uterine body, and sublingual mucosa but also showed the longitudinal and cross-sectional differences of cervical vasculatures in pregnant women. This technology is promising for screening the visceral pathological changes associated with angiogenesis.
Plasticity of Porites astreoides Early Life History Stages Suggests Mesophotic Coral Ecosystems Act as Refugia in Bermuda (2021)

As the devastating impacts of global climate change and local anthropogenic stressors on shallow-water coral reefs are expected to rise, mesophotic coral ecosystems have increasingly been regarded as potential lifeboats for coral survival, providing a source of propagules to replenish shallower reefs. Yet, there is still limited knowledge of the capacity for coral larvae to adjust to light intensities that change with depth. This study elucidates the mechanisms underlying plasticity during early life stages of the coral Porites astreoides that enable survival across broad depth gradients. We examined physiological and morphological variations in larvae from shallow (8–10 m) and mesophotic (45 m) reefs in Bermuda, and evaluated differences in survival, settlement patterns and size among recruits depending on light conditions using a reciprocal ex situ transplantation experiment. Larvae released from mesophotic adults were found to have significantly lower respiration rates and were significantly larger than those derived from shallow adults, indicating higher content of energetic resources and suggesting a greater dispersal potential for mesophotic larvae compared to their shallow counterparts. Additionally, larvae released from mesophotic adults experienced higher settlement success and larger initial spat size compared to larvae from shallow adults, demonstrating a potential connection between parental origin, offspring quality, and recruitment success. Although both shallow and mesophotic larvae exhibited the capacity to survive and settle under reciprocal light conditions, all larvae had higher survival under mesophotic light conditions regardless of parental origin, suggesting that conditions experienced under low light may enable longer larval life, further extending the dispersal period. These results indicate that larvae from mesophotic Porites astreoides colonies are likely capable of reseeding shallow reefs in Bermuda, thereby supporting the Deep Reef Refugia Hypothesis.
1-kHz 5-W ArF excimer laser for microlithography with highly narrow 0.7-pm bandwidth and issues on durability related to optical damage (1999)

We present the result of billion level durability test in the newest model of ArF excimer laser, KLES-G5A, for microlithography and durability issues relate to optical damage. The developed ArF laser achieves 5 W of output power with integrated energy stability less than +/- 0.3 percent at 1 kHz repetition rate. The spectral characteristic by FWHM of the deconvolved spectrum is less than 0.7 pm and the 95 percent energy of the total energy is within 2.0 pm band, which is designed to be suitable for partially achromatized refractive projection optics. Durability test of 1 billion pulses has already finished, and we have observed very slight changes in the performance. Prior to the durability test, irradiation examinations have been done. It demonstrates that CaF<SUB>2</SUB> material has superior stability to SiO<SUB>2</SUB> even as the high fluence DUV optical parts of line-narrowed ArF laser.
An Analysis of Tissue-Engineered Pulmonary Valves Implanted in the Elderly Ovine Model (2012)

Abstract Bioprosthetic heart valve replacement, recommended for patients older than 65 years of age, increases the quality of life, however grafts exhibit limited functionality due to degradation and calcification. Decellularized and tissue-engineered pulmonary valves (PV) get repopulated by autologous interstitial cells when implanted into juvenile sheep. Thus, in vivo matrix guided regeneration results in restored valve function. In this study, we investigated the regeneration capacity in elderly sheep. Sheep (Ø 7 yrs old, Ø weight of 88.5 kg) received pulmonary valve replacement. Decellularized PV (n=6), decellularized PV coated with proangiogenic CCN1 (n=6), and decellularized, CCN1 coated and reendothelized PV (n=6) were implanted in orthotopic position. For endothelialization PV were seeded with autologous endothelial cells (EC) differentiated from EPC from peripheral blood. Cells were flow adapted in a pulsatile bioreactor system prior implantation. PV functional analysis in vivo was realized by echocardiography, directly after implantation and prior explantation. Allografts were explanted after six and twelve months in vivo and investigated in respect to endothelium coverage, to the integrity of the extracellular matrix, and to the degree and cellular identity of invaded cells by histological and immunochemical stains. All allografts showed good to adequate function, no stenosis, low gradients and only occasional insufficiency without clinical symptoms. No signs of degradation of the extracellular matrix and minimal calcification restricted at the anastomosis of the grafts were found. All grafts were repopulated with cells but to various degree. Only one, explanted after one year, showed complete repopulation including the leaflets. In general, cell-density in the pulmonary artery was higher on the adventitial than on the luminal side and leaflets were better repopulated at the ventricular than at the arterial side. The majority of cells expressed sm-alpha-actin. Endothelial cells located on the luminal side appeared in some grafts as intact complete monolayer. Beside a slight tendency of better repopulation observed in the reendothelialized PV group, no significant difference of cell densities was found among the groups. Autologous repopulation of decellularized heart valve matrices implanted in the orthotopic position in the elderly sheep demonstrates retained regenerative capacity even in the older organism. This observation combined with the fact that no functional loss must have taken into account, implantation of decellularized heart valves matrices in patients over age 65 remains a therapy option to overcome the drawbacks of current used bioprosthesis.