gebhart/patrepeval huggingface dataset:
Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins (2015)

Here we report the first implementation of activated ion electron transfer dissociation (AI-ETD) for top down protein characterization, showing that AI-ETD definitively extends the m/z range over which ETD can be effective for fragmentation of intact proteins. AI-ETD, which leverages infrared photon bombardment concurrent to the ETD reaction to mitigate nondissociative electron transfer, was performed using a novel multipurpose dissociation cell that can perform both beam-type collisional dissociation and ion-ion reactions on an ion trap-Orbitrap hybrid mass spectrometer. AI-ETD increased the number of c- and z-type product ions for all charge states over ETD alone, boosting product ion yield by nearly 4-fold for low charge density precursors. AI-ETD also outperformed HCD, generating more matching fragments for all proteins at all charge states investigated. In addition to generating more unique fragment ions, AI-ETD provided greater protein sequence coverage compared to both HCD and ETD. In all, the effectiveness of AI-ETD across the entirety of the m/z spectrum demonstrates its efficacy for robust fragmentation of intact proteins.
Influence of temperature on in-plane and out-of-plane mechanical behaviour of GFRP composite (2018)

In this work, the challenges in forming of glass-fibre reinforced PA6, from experimental material characterization and parameter identification to numerical modelling using Finite Element Analyses (FEA) is reviewed and results are presented. Mechanical in-plane behaviour is characterized by tensile and bias extension tests. Out-of-plane characteristics are determined using the cantilever test. The constitutive model is set-up using LS-DYNA, in which the fibre and matrix properties are considered separately. Therefore seperate tensile experiments with unreinforced PA6 are performed. FEA is used to model the tensile and cantilever tests in which the strain-stress curves, influence of displacement on shearing angle and different approaches in modelling the bending stiffness are compared. The advantages and drawbacks of the model are shown and discussed. It is shown that the conducted experiments can be reproduced by using the implemented material model and reasonably good results are achieved.
The Development and Validation of the Psychological Needs of Cancer Patients Scale (2021)

In the present research, the Psychological Needs of Cancer Patients Scale (PNCPS) was developed and validated. Based on Group 1 (400 cancer patients), the exploratory factor analysis identified a 23-item scale with six factors: value and esteem (five items, i.e., reconsider the meaning and purpose of life), independence and control (six items, i.e., private space), mental car (three items, i.e., vent negative emotions), disease care (three items, i.e., acquire knowledge about disease), belonging and companionship (three items, i.e., spend more time at home), and security (three items, i.e., living conditions be better). The structure identified with Group 1 was further tested, based on Group 2 (199 cancer patients), for reliability and validity. The results showed that PNCPS has a clear factor structure and good psychometric characteristics. By taking into account the cultural background of Chinese patients, this scale will advance the study of the psychological needs of those with malignant tumors and thus has a certain reference value for other countries.
EGF‐R and PDGF‐R, but not bcl‐2, overexpression predict overall survival in patients with low‐grade astrocytomas (2004)

PDGF-R and EGF-R expression could be relevant in determining the prognosis of low-grade astrocytomas (LGAs) and in providing a more objective mechanism for their classification.
&lt;title&gt;Motion and structure from combined optical flow: correspondences approach&lt;/title&gt; (1999)

This paper presents the cooperation of optical flow and contour correspondence modules for motion and structure estimation. It enables us to overcome a certain number of problems associated to the separate use of each of the modules, by integrating complementary information. In this hybrid scheme our novelty consists of: (1) simultaneous use of several regions; for each of them the whole region and its boundary are considered as well and (2) introduction of a new iterative scheme induced by the cooperative concept.
Cloud-based platform for personalization in a wellness management ecosystem: Why, what, and how (2010)

Offering personalized services through dynamically formed ecosystems is essential to personal wellness management. In this paper, we present the design of a cloud-enabled platform to facilitate the collection and delivery of evidence for personalization in a multi-provider ecosystem environment. In
Three‐dimensional accelerated acquisition for hyperpolarized <sup>13</sup>C MR  with blipped stack‐of‐spirals and conjugate‐gradient  SENSE (2020)

The proposed method demonstrated effective mapping of metabolism in both kidneys and the heart of healthy pigs. Limitations seen in phantom experiments, may be irrelevant for most clinical applications, but should be kept in mind as well as reconstruction challenges related to residual aliasing. All in all, we show that the blipped stack-of-spirals is a relevant parallel imaging method for hyperpolarized human imaging, facilitating better insights into metabolism compared with nonaccelerated acquisition.
Arylamine-Substituted Oligo(ladder-type pentaphenylene)s:  Electronic Communication between Bridged Redox Centers (2007)

Novel bis(arylamine-substituted) oligo(ladder-type pentaphenylene)s 1-3, with bridge lengths estimated to be 2.2, 4.2, and 6.3 nm, respectively, have been developed, and the model compound 4 with a mono-arylamine substituent was also synthesized. Their absorption spectra in different solvents are almost identical, while distinct bathochromic shifts of the photoluminescence (PL) spectra were observed with increasing solvent polarity due to the polarized excited states. The cyclic voltammetry (CV) and differential pulse voltammetry (DPV) spectra display a two-step oxidation of the bridged diamines in compound 1, which suggests that the electron and charge delocalize in mixed-valence (MV) cation 1+* and that both redox centers can communicate through the pentaphenylene bridge. Only unresolved curves in CV and DPV spectra were observed in the first two oxidation processes of diamines 2 and 3, indicating that the bridges are too long for efficient delocalization over the entire molecules and the radical cations localize at each arylamine center. This finding was further supported by chemical oxidation with SbCl5 and studies of the corresponding UV-vis-NIR absorption spectra of compounds 1-4. A significant intervalence charge-transfer (IVCT) band around 5283 cm-1 (1893 nm) was observed in 1+*. This is the first report of such a highly intense IVCT band in the NIR region with intensity similar to that of the visible band of the radicals, enabling further analysis of the CT process and the coupling matrix element V, classifying 1+* as a class II derivative (V = 1.6 kcal/mol). This study may offer an effective way to improve the understanding of charge transfer and charge-carrier transport in various conjugated oligomers or polymers and facilitate their ongoing exploration in optoelectronic applications.
Cyperus diandrus Torr. (1999)

https://thekeep.eiu.edu/herbarium_specimens_byname/6203/thumbnail.jpg
Bruton's Tyrosine Kinase (Btk) (2012)

Bruton's tyrosine kinase (Btk) is a non-receptor tyrosine kinase belonging to the Tec family of kinases. Btk is critical for B-cell development, differentiation and signalling through the B-cell antigen receptor (BCR) as is evident by its genetic association to a human primary immunodeficiency disease known as X-linked Agammaglobulinemia (XLA). Btk is also present in specific cells of the myeloid lineage and contributes to the activation of the FcγR and FcεR signalling pathways in macrophages, neutrophils and mast cells. Because of its key role in these pathways, Btk is considered a promising target for therapeutic intervention in autoimmune and inflammatory disease. Numerous research groups are actively working to identify Btk inhibitors through the targeting of inactive kinase conformations or covalent active site inhibition. Both strategies have benefited from the rapid growth in structural biology insight for the target. Recently discovered potent and orally bioavailable Btk inhibitors have shown promising efficacy in several pre-clinical animal models of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). These results, coupled with promising initial findings from the study of Btk inhibitors in human clinical trials for oncology, strongly suggest Btk intervention offers significant potential as a treatment strategy in inflammatory disease.
Theory of polarization spreading techniques. I (1994)

Presents an analysis of a series of techniques grouped under the denomination "polarization spreading", the intent of which is that of making the performance of a coherent optical receiver insensitive to the polarization transformations occurring along the optical fiber, without resorting to polarization compensation or control. The principle on which Polarization spreading operates is that of spreading the signal power over different states of polarization, so that heterodyning of at least half of the optical incident bit energy is always ensured. The main results obtained concern a condition that guarantees the maximum heterodyned signal energy, some classes of spreading waveforms satisfying the above condition, the derivation of the structure and the performance of optimum receivers in Gaussian noise. The results encompass most of the binary optical coherent modulation schemes proposed and experimented, such as ASK, FSK and DPSK.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A BLOCH MODEL DESCRIPTION OF THE OVERALL ROTATIONAL LINESHAPE OF A HIGHLY VIBRATIONALLY EXCITED MOLECULE WITH A METHYL GROUP INTERNAL ROTOR (2003)

Author Institution: Department of Chemistry, University of Virginia
Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration (2016)

For efficient polarity and migration, cells need to regulate the magnitude and spatial distribution of actin assembly. This process is coordinated by reciprocal interactions between the actin cytoskeleton and mechanical forces. Actin polymerization-based protrusion increases tension in the plasma membrane, which in turn acts as a long-range inhibitor of actin assembly. These interactions form a negative feedback circuit that limits the magnitude of membrane tension in neutrophils and prevents expansion of the existing front and the formation of secondary fronts. It has been suggested that the plasma membrane directly inhibits actin assembly by serving as a physical barrier that opposes protrusion. Here we show that efficient control of actin polymerization-based protrusion requires an additional mechanosensory feedback cascade that indirectly links membrane tension with actin assembly. Specifically, elevated membrane tension acts through phospholipase D2 (PLD2) and the mammalian target of rapamycin complex 2 (mTORC2) to limit actin nucleation. In the absence of this pathway, neutrophils exhibit larger leading edges, higher membrane tension, and profoundly defective chemotaxis. Mathematical modeling suggests roles for both the direct (mechanical) and indirect (biochemical via PLD2 and mTORC2) feedback loops in organizing cell polarity and motility-the indirect loop is better suited to enable competition between fronts, whereas the direct loop helps spatially organize actin nucleation for efficient leading edge formation and cell movement. This circuit is essential for polarity, motility, and the control of membrane tension.
Fetal sex-specific epigenetic associations with prenatal maternal depressive symptoms (2022)

Prenatal maternal mental health is a global health challenge with poorly defined biological mechanisms. We used maternal blood samples collected during the second trimester from a Singaporean longitudinal birth cohort study to examine the association between inter-individual genome-wide DNA methylation and prenatal maternal depressive symptoms. We found that (1) the maternal methylome was significantly associated with prenatal maternal depressive symptoms <i>only</i> in mothers with a female fetus; and (2) this sex-dependent association was observed in a comparable, UK-based birth cohort study. Qualitative analyses showed fetal sex-specific differences in genomic features of depression-related CpGs and genes mapped from these CpGs in mothers with female fetuses implicated in a depression-associated WNT/β-catenin signaling pathway. These same genes also showed enriched expression in brain regions linked to major depressive disorder. We also found similar female-specific associations with fetal-facing placenta methylome. Our fetal sex-specific findings provide evidence for maternal-fetal interactions as a mechanism for intergenerational transmission.
High Firing Temperature GT36 H-Class Low NOx Combustor Engine Validation and Performance (2020)

Abstract In order to minimize the footprint of human activities on the environment, technologies to reduce greenhouse gases while meeting constantly growing electricity demands are critical. Amongst the various sources of energy production, Gas Turbines (GT) are an efficient way to stabilize the grid with regards to renewable sources like wind and solar energies. The demand for higher efficiency, higher power output while reducing emission levels (especially NO and NO2) at high loads, and for higher flexibility within the H-class Gas Turbine market is thereby a natural consequence. The development and validation of a two-stage sequential combustor, so-called Constant Pressure Sequential Combustion (CPSC) system, to achieve these goals has been accomplished by Ansaldo Energia. The CPSC consists of a premix burner system (First Stage) and of a sequential burner (SB) in series within a can combustor. At the 2017 and 2019 ASME conferences, high pressure test rig validation results of the CPSC were introduced. The advantages with regards to fuel flexibility, hydrogen combustion and low emissions at high firing temperature were presented [1,2,3,4,5]. This article focuses on the validation of the combustor performance in Ansaldo Energia’s Validation Power Plant located in Birr, Switzerland, which includes detailed validation from ignition to full speed no load, part load operation and full load over various ambient and engine thermal state conditions. To allow for detailed validation, dedicated fully instrumented combustor cans were installed in the GT. Detailed validated air distribution and emission models support the results obtained on the engine. Ignition and ramps up to full speed no load have been validated with large variations of the first combustor stage firing temperature to minimize power consumption and start-up time. The potential of the CPSC with regards to turndown capability, with minimum environmental load (MEL) below 25% GT load while keeping CO levels low has been confirmed. The MEL can be kept low over a wide range of ambient temperature and fuel compositions by adjusting the inlet temperature of the sequential burner. Low NOx values were achieved at baseload and peak firing temperature. The operational flexibility and stability of the premixed first stage combustor over the load range and over a large variation of combustor inlet plenum pressures was as well validated along with the operation concept of the gas turbine.
All‐Carbon Quaternary Stereogenic Centers by Enantioselective Cu‐Catalyzed Conjugate Additions Promoted by a Chiral N‐Heterocyclic Carbene (2007)

Necessity is the mother of invention: When the available catalysts do not cut it, a new one has to be developed. A chiral N-heterocyclic carbene (NHC) is used in the first catalytic asymmetric conjugate addition of alkyl- and arylzinc reagents to γ-keto esters (see scheme). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z604511_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Isolation and LC-QToF Characterization of Secondary Metabolites from an Endemic Plant Artemisia heptapotamica Poljak (2023)

Phytochemical investigation of the aerial parts of <i>Artemisia heptapotamica</i> Poljak led to the isolation of ten known compounds, including four alkyl <i>p</i>-coumarates: octadecyl <i>trans</i>-<i>p</i>-coumarate (<b>1</b>), icosy <i>trans</i>-<i>p</i>-coumarate (<b>2</b>), docosyl <i>trans</i>-<i>p</i>-coumarate (<b>3</b>), and tetracosyl <i>trans</i>-<i>p</i>-coumarate (<b>4</b>), one sesquiterpene lactone: santonin (<b>5</b>), four flavonoids; axillarin (<b>6</b>), quercetin 3-<i>O</i>-methyl ether (<b>7</b>), luteolin (<b>8</b>), and quercetin (<b>9</b>), and one phenolic acid derivative: <i>p</i>-coumaric acid (<b>10</b>). The structures of the isolated compounds were identified by various spectroscopic analyses. Additionally, the antimicrobial activity of the total extract and different fractions was screened, and they exhibited no inhibition of the growth of <i>Candida albicans</i>, <i>C. neoformans</i>, <i>Aspergillus fumigatus</i>, methicillin-resistant <i>Staphylococcus aureus</i> (MRS), <i>E. coli</i>, <i>Pseudomonas aeruginosa</i>, <i>Klebsiella pneumonia</i>, and Vancomycin-resistant <i>Enterococci</i> (VRE) at the tested concentrations ranging from 8 to 200 μg/mL. The identification and tentative characterization of the secondary metabolites were conducted using LC-QToF analysis. This method helps in the putative characterization of sesquiterpene lactones, flavonoids, coumarate derivatives, and aliphatic compounds. The developed method identified 43 compounds, of which the majority were sesquiterpene lactones, such as eudesmanolides, germacranolides, and guaianolide derivatives, followed by flavonoids. The proposed LC-QToF method helps develop dereplication strategies and understand the major class of chemicals before proceeding with the isolation of compounds.
Effect of annealing history on free volume in thermoplastics (1986)

The clinical diagnosis of trichinellosis is difficult because its clinical manifestations are nonspecific. Detection of anti-Trichinella IgG by ELISA using T. spiralis muscle larval excretory-secretory (ES) antigens is the most commonly used serological method for diagnosis of trichinellosis, but the main disadvantage is false negativity during the early stage of infection. There is an obvious window period between Trichinella infection and antibody positivity.During the intestinal stage of Trichinella infection, the ES antigens of intestinal worms (intestinal infective larvae and adults) are exposed to host's immune system at the earliest time and elicit the production of specific anti-Trichinella antibodies. Anti-Trichinella IgG antibodies in infected mice were detectable by ELISA with ES antigens of intestinal worms as soon as 8-10 days post infection (dpi), but ELISA with muscle larval ES antigens did not permit detection of infected mice before 12 dpi. Therefore, the new early antigens from T. spiralis intestinal worms should be screened, identified and characterized for early serodiagnosis of trichinellosis.
Cognitive Learning (2019)

Writing is a fundamental task in our daily life. Existing writing improvement tools mostly focus on low-level grammar error correction, rather than enhancing users' writing styles at the cognitive level. In this work, we present a computational approach that allows learners to have fast but effective learning experience with the help of automatic style transfer, visual stylometry analytics, machine teaching and practice. Our system provides a perfect fusion of vividly visualized style features and principles along with informative examples, which together can shape and drive personalized cognitive learning experience. We demonstrate the effectiveness of our system in a scenario of learning from William Shakespeare.
Analysis and Optimization of Loss Functions for Multiclass, Top-k, and Multilabel Classification (2016)

Top-k error is currently a popular performance measure on large scale image classification benchmarks such as ImageNet and Places. Despite its wide acceptance, our understanding of this metric is limited as most of the previous research is focused on its special case, the top-1 error. In this work, we explore two directions that shed more light on the top-k error. First, we provide an in-depth analysis of established and recently proposed single-label multiclass methods along with a detailed account of efficient optimization algorithms for them. Our results indicate that the softmax loss and the smooth multiclass SVM are surprisingly competitive in top-k error uniformly across all k, which can be explained by our analysis of multiclass top-k calibration. Further improvements for a specific k are possible with a number of proposed top-k loss functions. Second, we use the top-k methods to explore the transition from multiclass to multilabel learning. In particular, we find that it is possible to obtain effective multilabel classifiers on Pascal VOC using a single label per image for training, while the gap between multiclass and multilabel methods on MS COCO is more significant. Finally, our contribution of efficient algorithms for training with the considered top-k and multilabel loss functions is of independent interest.
Synthesis and Properties of Long-Chain Aromatic Telechelic Monodispersed Diols Radical-Initiated, Addition of 2-Mercaptoethanol onto α, ω Nonconjugated Dienes (2012)

Abstract The synthesis of aromatic telechelic mono dispersed diols produced from the radical-initiated addition reaction of a twofold excess of 2-mercaptoethanol onto original α,ω nonconjugated dienes reaction is presented. These novel α,ω nonconjugated dienes were prepared by addition reaction of m-isopropyl α,α′dimethyl benzylisocyanate with mono dispersed telechelic diols obtained by fractionation of oligo(ethylene terephthalate)s. In these cases, the long chain α,ω diols were produced selectively and quantitatively. The products are soluble in most organic solvents in contrast to classical oligo (ethylene terephthlate)s and posses a lower glass transition and melting temperatures. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements for the following free supplemental resource: Figures S1-S3.
Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009–2013 in Vietnam (2019)

Routine surveillance and surveillance in response to influenza outbreaks in avian species in Vietnam in 2009-2013 resulted in the isolation of numerous H5N1 influenza viruses of clades 1.1.2, 2.3.2.1a, 2.3.2.1b, 2.3.2.1c, and 2.3.4.1. Consistent with other studies, we found that viruses of clade 2.3.2.1c were dominant in Vietnam in 2013 and circulated in the northern, central, and southern parts of the country. Phylogenetic analysis revealed reassortment among viruses of clades 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c; in contrast, no reassortment was detected between clade 2.3.2.1 viruses and viruses of clades 1.1.2 or 2.3.4.1, respectively. Deep-sequencing of 42 of the 53 isolated H5N1 viruses revealed viral subpopulations encoding variants that may affect virulence, host range, or sensitivity to antiviral compounds; virus isolates containing these subpopulations may have a higher potential to transmit and adapt to mammals. Among the viruses sequenced, a relatively high number of non-synonymous nucleotide polymorphisms was detected in a virus isolated from a barn swallow, possibly suggesting influenza virus adaption to this host.