gebhart/patrepeval huggingface dataset:
Characterization of nanoscale electronic structure in nonpolar GaN using scanning capacitance microscopy (2008)

Scanning capacitance microscopy is used to characterize nanoscale, local electronic structure in nonpolar n-type GaN grown in the a-plane orientation using lateral epitaxial overgrowth (LEO). Analysis of the bias dependence of the scanning capacitance image contrast observed reveals the presence of a linear, positively charged feature aligned along the [1¯100] direction, extending from an LEO window region into the adjacent wing region and terminating a few microns into the wing region. Comparison of the scanning capacitance images with cathodoluminescence and transmission electron microscopy data, revealing the presence of line defects aligned along the [1¯100] direction that emerge from the window regions, indicates that this positively charged feature likely corresponds to a partial dislocation at the edge of a stacking fault. The observation of positive dislocation charge is striking in that studies of GaN grown in the polar c-plane orientation have predominantly revealed the presence only of negatively charged or electrically neutral dislocations.
Flavonol Glycosides from the Leaves ofEmbelia Keniensis (2005)

Five new flavonol glycosides characterized as syringetin 3-O-α-rhamnoside-7-O-β-glucoside, syringetin 3-O-α-rhamnoside-7,4′-di-O-β-glucoside, quercetin-7-O-β-galactosyl (1→3)-β-galactoside, myricetin 3-O-α-rhamnosyl (1→4)-β-galactoside and myricetin 3-O-β-glucosyl (1→2)-β-glucoside-7-O-β-glucosyl-(1→4)-α-rhamnoside have been isolated from a methanolic extract of Embelia keniensis leaves. Known flavonols isolated from the same extract included myricetin, quercetin, kaempferol, myricetin 3-O-α-rhamnoside, myricetin 3-O-β-glucoside, quercetin 3-O-α-rhamnoside, quercetin 3-O-β-glucoside, quercetin 3-O-β-xyloside, isorhamnetin 3-O-α-rhamnoside and myricetin 3-O-rutinoside. Their structures were established from extensive spectroscopic and chemical studies and by comparison with authentic samples.
Systematic naming system for Actaea triterpenes and the demand for dreiding models (2012)

The genus Actaea, recently expanded to include the now obsolete genera Cimicifuga and Souliea, has been the source of ˜200 structurally defined triterpenes (TTs). Except for a few ubiquitous TTs, all are endemic to Actaea and derivatives of the simple cycloartanol, 1. Despite this one common denominator, the TTs comprise chemically diverse substructures, formed by oxidation, ring closure and ring cleavage. Extracts of many Actaea species are ethno-medicinal and CAM products. During their discovery, the TTs were given a wide variety of names, derived haphazardly from names of the species, the traditional medicine, or occasionally from a previously described structure. Often, there is little or no chemical logic to these names. We have developed a systematic naming system based on “actanol” for 1, with all modifications following standard chemical nomenclature. The standard α and β TT stereo designation breaks down in several substructural types with spiro ring systems, and the Cahn-Ingold-Prelog system is used exclusively for defining the skeleton. In the more complex structures, this created a demand for stereo models, and the inability to purchase our favored Dreiding models, led us to establish the Dreiding Model Exchange (http://tigger.uic.edu/˜gfp/dreiding/dreidingexchange.htm), which currently has over 3,000 pieces and is currently actively buying and selling these models.
The architecture and implementation of an extensible web crawler (2010)

Many Web services operate their own Web crawlers to discover data of interest, despite the fact that large-scale, timely crawling is complex, operationally intensive, and expensive. In this paper, we introduce the extensible crawler, a service that crawls the Web on behalf of its many client applications. Clients inject filters into the extensible crawler; the crawler evaluates all received filters against each Web page, notifying clients of matches. As a result, the act of crawling the Web is decoupled from determining whether a page is of interest, shielding client applications from the burden of crawling the Web themselves.This paper describes the architecture, implementation, and evaluation of our prototype extensible crawler, and also relates early experience from several crawler applications we have built. We focus on the challenges and trade-offs in the system, such as the design of a filter language that is simultaneously expressive and efficient to execute, the use of filter indexing to cheaply match a page against millions of filters, and the use of document and filter partitioning to scale our prototype implementation to high document throughput and large numbers of filters. We argue that the low-latency, high selectivity, and scalable nature of our system makes it a promising platform for taking advantage of emerging real-time streams of data, such as Facebook or Twitter feeds.
Assessing the implementation of machine learning models for thermal treatments design (2021)

The latest progress in machine learning (ML) algorithms enabled to predict some steel physical properties previously modelled by linear regression (LR), such as the Ms temperature. Authors claimed that the performance given by ML models could improve the one of previous LR models, although they did not include fair comparisons. In this work, a large database was used to train different ML algorithms, whose Ms temperature predictions were compared to the ones of previous literature empirical models. ML methods were proved to require longer computational times and wider knowledge, while leading to similar results. Therefore, we recommend that ML methods are not always considered as the first option when trying to solve easy problems that can be modelled by LR techniques.
Peptide and protein quantification using iTRAQ with electron transfer dissociation (2008)

Electron transfer dissociation (ETD) has become increasingly used in proteomic analyses due to its complementarity to collision-activated dissociation (CAD) and its ability to sequence peptides with post-translation modifications (PTMs). It was previously unknown, however, whether ETD would be compatible with a commonly employed quantification technique, isobaric tags for relative and absolute quantification (iTRAQ), since the fragmentation mechanisms and pathways of ETD differ significantly from CAD. We demonstrate here that ETD of iTRAQ labeled peptides produces c- and z-type fragment ions as well as reporter ions that are unique from those produced by CAD. Exact molecular formulas of product ions were determined by ETD fragmentation of iTRAQ-labeled synthetic peptides followed by high mass accuracy orbitrap mass analysis. These experiments revealed that ETD cleavage of the N-C(alpha) bond of the iTRAQ tag results in fragment ions that could be used for quantification. Synthetic peptide work demonstrates that these fragment ions provide up to three channels of quantification and that the quality is similar to that provided by beam-type CAD. Protein standards were used to evaluate peptide and protein quantification of iTRAQ labeling in conjunction with ETD, beam-type CAD, and pulsed Q dissociation (PQD) on a hybrid ion trap-orbitrap mass spectrometer. For reporter ion intensities above a certain threshold all three strategies provided reliable peptide quantification (average error <10%). Approximately 36%, 8%, and 16% of scans identified fall below this threshold for ETD, HCD, and PQD, respectively. At the protein level, average errors were 2.3%, 1.7%, and 3.6% for ETD, HCD, and PQD, respectively.
Usefulness of basal and pilocarpine-stimulated salivary flow in primary Sjogren's syndrome. Correlation with clinical, immunological and histological features (2002)

The study of xerostomia using basal and pilocarpine SSF is simple to perform, acceptable to patients and needs no special equipment. We describe a significant increase in SSF using a solution of 5% pilocarpine in comparison with salivary flow obtained after stimulation with ANTT. Twenty-two of the 46 patients with low BSF had stimulated flows over 1.5 ml. These 'responder' patients showed a shorter duration of sicca symptoms, a lower frequency of positive immunological markers and milder grades of scintigraphic patterns and lymphocytic infiltrates in salivary gland biopsies. This subset of patients probably maintain a residual capacity of their salivary glands, as opposed to the 'non-responder' patients, who had a longer duration of sicca syndrome evolution with more severe involvement of the salivary glands.
Innate Lymphoid Cells are Present at Healthy Patients Spinal Enthesis, Providing a Potential Mechanism for Spondyloarthropathy Pathogenesis (2016)

Background The pathogenesis of murine spondyloarthropathy (SpA) has been intimately linked to the presence of Interleukin(IL)-23 responsive, innate like lymphocytes at different anatomical regions including spinal enthesis. Human SpAs are associated with Single nucleotide polymorphisms (SNPs) in genes related to the IL-23 pathway and drugs that block IL-12/23 have shown efficacy. We hypothesized that the normal human enthesis has a population of resident innate lymphoid cells (ILCs) that could be involved in governing entheseal immune homeostasis. In particularly entheseal resident type 3 ILCs (ILC3s) may be critical, since ILC3s in other tissues have been shown to produce inflammatory cytokines in response to IL-23. Methods Normal spinal enthesis were harvested from healthy patients undergoing spinal surgery and enzymatically digested prior to fluorescence activated cell sorting (FACS). Cellular immunophenotyping and cell sorting was performed on enthesis samples harvested from 6 patients; ILC3s, were identified as lineage (CD3- TCRγδ- TCRαβ- CD19- CD14- CD11c- CD1a- CD303- FcεRI- CD34- CD123-) and cellular surface marker CRTH2 negative with positive expression of CD45, CD127, CD117. ILC2s, which have been linked to fibrotic reactions, were identified as lineage negative with positive expression of CD45, CD127 and CRTH2. The expression of RORγt transcript was tested in sorted populations by RTqPCR. Anterior cruciate ligament (femoral enthesis) was obtained from subjects with knee OA and injured enthesis undergoing repair were also collected and analyzed by immunohistochemistry (IHC). Results All sorted samples contained ILC3s, median proportion 0.09% (range 0.015–0.63). Transcript analysis confirmed the expression of RORγt, transcript, an ILC3 related transcription factor, in sorted ILC3 populations, with ILC3s expressing 51-fold greater relative expression in comparison to unsorted digests. 5 of 6 sorted samples contained ILC2s, median proportion 0.20% (range 0–0.49). RORγt expression was detected in knee OA and there was widespread expression of RORγt in inflammatory infiltrates in injured enthesis as shown by IHC. Conclusions Our findings show that ILCs are present in the normal human spinal enthesis and may be greatly increased in frequency following injury. These findings provide strong evidence of ILC presence in normal human enthesis and suggest a potential link between cellular dysregulation of the IL-23/17 axis and SpA pathology at sites of micro damage.
O1‐06‐03: Proteomic Analysis of Extracellular Vesicles in Alzheimer’s Disease Cerebrospinal FLUID (2016)

Cerebrospinal fluid (CSF) contains different types of extracellular vesicles (EVs) with undisclosed biomarker potential for neurodegenerative diseases1. Here we isolated EVs from pooled CSF samples coming from control subjects (CTRL) and patients diagnosed with probable Alzheimer’s disease (AD). We then characterized the EV proteome using high resolution tandem mass spectrometry (LC-MS/MS) and bioinformatic analysis. Our aim was to compare the EVs proteome in AD patients and controls, to highlight candidate biomarkers to be further validated. CSF samples were obtained from the biobank of the University Hospital of Perugia. Two CSF pools were constructed, the AD pool was composed of patients diagnosed with probable AD and with a CSF profile indicative of AD (n=30). The CTRL CSF pool was built from 30 subjects who underwent CSF tapping for diagnostic reasons and, after evaluation, they were found free of any cognitive impairment or any neurodegenerative disease. All the control subjects had a negative AD biomarker profile. EV isolation and proteomic analysis were carried out as previously described1, two replicates were run for each sample. About 800 proteins were consistently identified in all the CSF EV samples. CSF EVs proteome was enriched in heat shock proteins, tetraspanins and endosomal trafficking proteins. Furthermore, CSF EVs were highly enriched in brain-derived proteins including several Intraflagellar Transport Proteins expressed in the choroid plexus, possibly showing that CSF EVs are in part derived from the tissue responsible for CSF production. Statistical analysis found 49 protein up-regulated in AD EVs while 39 were down regulated with respect to the CTRL EVs. Up-regulated proteins in AD EVs were related to cell adhesion and motility, extracellular matrix remodeling and stress response, while down-regulated protein were associated with immune response and proteolysis. Overlap analysis with brain tissue proteomic data from pathologically-confirmed AD patients showed 8 protein candidates to be selected for validation. Proteomic analysis of CSF EVs may give an opportunity to sample pathologically linked brain-derived proteins in CSF. The establishment of EV isolation methods using clinically available CSF volumes is mandatory to perform biomarker validation.
Multivariate analysis applied to complex biological medicines (2019)

A biological medicine (or biologicals) is a term for a medicinal compound that is derived from a living organism. By their very nature, they are complex and often heterogeneous in structure, composition and biological activity. Some of the oldest pharmaceutical products are biologicals, for example insulin and heparin. The former is now produced recombinantly, with technology being at a point where this can be considered a defined chemical entity. This is not the case for the latter, however. Heparin is a heterogeneous polysaccharide that is extracted from the intestinal mucosa of animals, primarily porcine, although there is also a significant market for non-porcine heparin due to social and economical reasons. In 2008 heparin was adulterated with another sulfated polysaccharide. Unfortunately this event was disastrous and resulted in a global public health emergency. This was the impetuous to apply modern analytical techniques, principally NMR spectroscopy, and multivariate analyses to monitor heparin. Initially, traditional unsupervised multivariate analysis (principal component analysis (PCA)) was applied to the problem. This was able to distinguish animal heparins from each other, and could also separate adulterated heparin from what was considered bona fide heparin. Taught multivariate analysis functions by training the analysis to look for specific patterns within the dataset of interest. If this approach was to be applied to heparin, or any other biological medicine, it would have to be taught to find every possible alien signal. The opposite approach would be more efficient; defining the complex heterogeneous material by a library of bona fide spectra and then filtering test samples with these spectra to reveal alien features that are not consistent with the reference library. This is the basis of an approach termed spectral filtering, which has been applied to 1D and 2D-NMR spectra, and has been very successful in extracting the spectral features of adulterants in heparin, as well as being able to differentiate supposedly biosimilar products. In essence, the filtered spectrum is determined by subtracting the covariance matrix of the library spectra from the covariance matrix of the library spectra plus the test spectrum. These approaches are universal and could be applied to biological medicines such as vaccine polysaccharides and monoclonal antibodies.
Selective adenosine release from human B but not T lymphoid cell line. (1990)

Intracellular adenosine formation and release to extracellular space was studied in WI-L2-B and SupT1-T lymphoblasts under conditions which induce or do not induce ATP catabolism. Under induced conditions, B lymphoblasts but not T lymphoblasts, release significant amounts of adenosine, which are markedly elevated by adenosine deaminase inhibitors. In T lymphoblasts, under induced conditions, only simultaneous inhibition of both adenosine deaminase activity and adenosine kinase activities resulted in small amounts of adenosine release. Under noninduced conditions, neither B nor T lymphoblasts release adenosine, even in the presence of both adenosine deaminase or adenosine kinase inhibitors. Comparison of B and T cell's enzyme activities involved in adenosine metabolism showed similar activity of AMP deaminase, but the activities of AMP-5'-nucleotidase, adenosine kinase and adenosine deaminase differ significantly. B lymphoblasts release adenosine because of their combination of enzyme activities which produce or utilize adenosine (high AMP-5'-nucleotidase and relatively low adenosine kinase and adenosine deaminase activities). Accelerated ATP degradation in B lymphoblasts proceeds not only via AMP deamination, but also via AMP dephosphorylation into adenosine but its less efficient intracellular utilization results in the release of adenosine from these cells. In contrast, T lymphoblasts release far less adenosine, because they contain relatively low AMP-5'-nucleotidase and high adenosine kinase and adenosine deaminase activities. In T lymphoblasts, AMP formed during ATP degradation is not readily dephosphorylated to adenosine but mainly deaminated to IMP by AMP deaminase. Any adenosine formed intracellularly in T lymphoblasts is likely to be efficiently salvaged back to AMP by an active adenosine kinase. In general, these results may suggest that adenosine can be produced only by selective cells (adenosine producers) whereas other cells with enzyme combination similar to SupT1-T lymphoblasts can not produce significant amounts of adenosine even in stress conditions.
Shuttling of HDAC5 in H9C2 cells regulates YY1 function through CaMKIV/PKD and PP2A (2006)

YY1 is a transcription factor that can activate or repress transcription of a variety of genes and is involved in several developmental processes. YY1 is a repressor of transcription in differentiated H9C2 cells and in neonatal cardiac myocytes but an activator of transcription in undifferentiated H9C2 cells. We now present a detailed analysis of the functional domains of YY1 when it is acting as a repressor or an activator and identify the mechanism whereby its function is regulated in the differentiation of H9C2 cells. We show that histone deacetylase 5 (HDAC5) is localized to the cytoplasm in undifferentiated H9C2 cells and that this localization is dependent on Ca(2+)/calmodulin-dependent kinase IV (CaMKIV) and/or protein kinase D (PKD). In differentiated cells, HDAC5 is nuclear and interacts with YY1. Finally, we show that HDAC5 localization in differentiated cells is dependent on phosphatase 2A (PP2A). Our results suggest that a signaling mechanism that involves CaMKIV/PKD and PP2A controls YY1 function through regulation of HDAC5 and is important in the maintenance of muscle differentiation.
Temporal Variation in Activity of Bats and the Design of Echolocation-Monitoring Studies (1997)

I used Anabat II bat detectors to monitor echolocation calls of bats over two streams in the Oregon Coast Range for a total of 195 detector-nights. Activity of bats was positively correlated with biomass of insects and minimum nightly temperature, and was negatively correlated with length of night; activity levels at the two streams were positively correlated. Activity of bats was not significantly correlated with either hours of moonlight or with phase of moon. Level of activity within a night generally peaked shortly after sunset with a second, smaller peak in activity shortly before sunrise, but patterns varied substantially among nights. Total nightly activity at a site also varied substantially among nights, sometimes varying several-fold on consecutive nights. To assess the implications of temporal variation in activity of bats on sampling, I randomly sampled subsets of the data using from 2- to 12-night sample periods and calculated mean levels of activity for each subset. For subsets with seven or more nights, >60% of the subsets had means that were within 20% of the mean of the entire dataset. Less than 50% of the subsets had means within 10% of the mean of the entire dataset for any number of nights subsampled. When comparing activity between sites, use of blocked or paired designs improved sampling efficiency by 20%. Failure to account for temporal variation in activity of bats when designing research projects and monitoring programs could result in biased estimates of activity of bats.
Laser peening systems for preventive maintenance against stress corrosion cracking in nuclear power reactors (2006)

Laser peening is a surface enhancement process that introduces compressive residual stress on materials by irradiating laser pulses under aqueous environment. The process utilizes the impulsive effect of high-pressure plasma generated by ablative interaction of each laser pulse. Around a decade ago, the authors invented a new process of laser peening without any surface preparation, while the conventional types required coating that prevented the surface from melting. Taking advantage of the new process without surface preparation, we have applied laser peening without coating (LPwC) to nuclear power plants (NPPs) as a preventive maintenance against stress corrosion cracking (SCC). Toshiba released the first LPwC system in 1999, which delivered laser pulses through waterproof pipes with mirrors. In 2002, fiber-delivery was attained and significantly extended the applicability. Now, the development of the third generation system has been just accomplished, which is extremely simple, reliable and easy-handled.
Ground‐State Chemical Reactivity under Vibrational Coupling to the Vacuum Electromagnetic Field (2016)

The ground-state deprotection of a simple alkynylsilane is studied under vibrational strong coupling to the zero-point fluctuations, or vacuum electromagnetic field, of a resonant IR microfluidic cavity. The reaction rate decreased by a factor of up to 5.5 when the Si-C vibrational stretching modes of the reactant were strongly coupled. The relative change in the reaction rate under strong coupling depends on the Rabi splitting energy. Product analysis by GC-MS confirmed the kinetic results. Temperature dependence shows that the activation enthalpy and entropy change significantly, suggesting that the transition state is modified from an associative to a dissociative type. These findings show that vibrational strong coupling provides a powerful approach for modifying and controlling chemical landscapes and for understanding reaction mechanisms.
Prescriptive provenance for streaming analysis of workflows at scale (2018)

We extend our approach capturing and relating the provenance and performance metrics of computational workflows as a diagnostic tool for runtime optimization and placement. One important challenge is the volume of extracted data, both for performance metrics and provenance, even when specifying filters and focusing on quantities of interest in a simulation. We reduce this data by performing anomaly detection on streaming data and store provenance for the detected anomalies, an approach we call prescriptive provenance. This paper discusses the Chimbuko architecture enabling the approach. We present the use of a protein structure propagation workflow based on NWChemEx. We are testing algorithms for anomaly detection and present preliminary results here obtained with Local Outlier Factor. While scaling remains a challenge, these results show that our robust Chimbuko architecture for streaming analysis with prescriptive provenance is a promising approach.