gebhart/patrepeval huggingface dataset:
Automatic Extraction of Figures from Scientific Publications in High-Energy Physics (2013)

Plots and figures play an important role in the process of understanding a scientificpublication, providing overviews of large amounts of data or ideas that are difficult to in-tuitively present using only the text. State of art in digital libraries, serving as gatewaysto knowledge encoded in scholarly writings, does not take full advantage of the graphicalcontent of documents. Enabling machines to automatically unlock the meaning of scien-tific illustrations would allow immense improvements in the way scientists work and theknowledge is being processed. In this paper we present a novel solution for the initial problem of processing graphicalcontent, obtaining figures from scholarly publications stored in PDF format. Our methodrelies on vector properties of documents and as such, does not introduce additional errors,characteristic for methods based on raster image processing. Emphasis has been placed oncorrectly processing documents in High Energy Physics. The described approach makesdistinction between different classes of objects appearing in PDF documents and usesspatial clustering techniques to group objects into larger logical entities. A number ofheuristics allow the rejection of incorrect figure candidates and the extraction of differenttypes of metadata.
In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. (1994)

It was recently shown that a new class of small nuclear RNAs is encoded in introns of protein-coding genes and that they originate by processing of the pre-mRNA in which they are contained. Little is known about the mechanism and the factors involved in this new type of processing. The L1 ribosomal protein gene of Xenopus laevis is a well-suited system for studying this phenomenon: several different introns encode for two small nucleolar RNAs (snoRNAs; U16 and U18). In this paper, we analyzed the in vitro processing of these snoRNAs and showed that both are released from the pre-mRNA by a common mechanism: endonucleolytic cleavages convert the pre-mRNA into a precursor snoRNA with 5' and 3' trailer sequences. Subsequently, trimming converts the pre-snoRNAs into mature molecules. Oocyte and HeLa nuclear extracts are able to process X. laevis and human substrates in a similar manner, indicating that the processing of this class of snoRNAs relies on a common and evolutionarily conserved mechanism. In addition, we found that the cleavage activity is strongly enhanced in the presence of Mn2+ ions.
Design of novel analogues of short antimicrobial peptide anoplin with improved antimicrobial activity (2014)

Currently, novel antibiotics are urgently required to combat the emergence of drug-resistant bacteria. Antimicrobial peptides with membrane-lytic mechanism of action have attracted considerable interest. Anoplin, a natural α-helical amphiphilic antimicrobial peptide, is an ideal research template because of its short sequence. In this study, we designed and synthesized a group of analogues of anoplin. Among these analogues, anoplin-4 composed of D-amino acids displayed the highest antimicrobial activity due to increased charge, hydrophobicity and amphiphilicity. Gratifyingly, anoplin-4 showed low toxicity to host cells, indicating high bacterial selectivity. Furthermore, the mortality rate of mice infected with Escherichia coli was significantly reduced by anoplin-4 treatment relative to anoplin. In conclusion, anoplin-4 is a novel anoplin analogue with high antimicrobial activity and enzymatic stability, which may represent a potent agent for the treatment of infection.
Disparate Effect of Tamoxifen in Rats with Experimentally Induced Endometriosis* (1990)

The effect of tamoxifen on the growth of endometrial implants was examined in rats with experimentally induced endometriosis. Administration of tamoxifen (1 mg/kg x day) for 60 days completely regressed the endometrial implants. When tamoxifen treatment was withdrawn, recurrence of endometrial implants was observed. Ectopic endometrial implants regressed completely 2 months after ovariectomy in rats with experimentally induced endometriosis. Tamoxifen administration (1 mg/kg x day) for 60 days to ovariectomized rats with regressed implants led to complete recurrence of ectopic endometrial implants. In ovariectomized rats administration of tamoxifen antagonized estradiol-enhanced thymidine incorporation into uterine DNA, but tamoxifen per se stimulated thymidine incorporation. This indicates the agonist/antagonist nature of tamoxifen. Treatment of rats with tamoxifen blocked the normal estrous cycle. However, serum progesterone levels were higher during tamoxifen treatment in rats with intact ovaries than in ovariectomized rats. When ovariectomized rats with regressed implants were administered tamoxifen (1 mg/kg x day) and progesterone (10 mg/kg x day) for 60 days, recurrence of ectopic endometrial implants was not observed. These findings suggest that tamoxifen is effective in regressing endometrial implants in rats with experimentally induced endometriosis, and ovarian progesterone may have a facilitatory effect.
Gamma ray-induced loss of expression of HLA and glyoxalase I alleles in lymphoblastoid cells. (1980)

Gamma rays from a cesium source were used to generate human lymphoblastoid cell line variants that had lost expression of all major histocompatibility complex antigens coded for by a single haplotype. The cell line was heterozygous at the glyoxalase I locus and had the HLA haplotypes HLA-A1, B8, DRw3, and HLA-A2, B5, DRw1. We selected with anti-HLA-B8 antiserum in a population of cells that had been irradiated with 300 R. The incidence of B8-loss variants was 4.1 X 10(-5) on day 5 after irradiation. Analysis of variants showed that expressions of HLA and GLO alleles trans to B8 were retained. However, expression of additional cis-linked HLA and GLO gene products was lost in 12 of 17 variants. Variants that had lost expression of (i) HLA-B8, (ii) HLA-B8, A1, (iii) HLA-B8, A1, DRw3, or (iv) HLA-B8, A1, DRw3 and the cis-linked glyoxalase I allele were obtained. Karyotype analysis was performed on eight variants that had lost expression of two or more cis-linked alleles. Three variants had two normal appearing no. 6 chromosomes, four variants had a deletion that included the region coding for HLA genes on the short arm of one no. 6 chromosome, and one variant had an inversion or translocation involving the short arm of one no. 6.
Phase-jitter dynamics in second-order DPLLs with irrational and integer input frequencies (2003)

As a result of frequency quantization in a digital phase-locked loop (DPLL), the device cannot in general track the input signal exactly but instead exhibits in its limit behaviour small unwanted oscillations called "phase jitter". In recent studies we investigated this phase jitter in a second-order DPLL with sinusoidal input from the viewpoint of the theory of nonlinear dynamics, paying attention mainly to the case of non-integer rational input frequency and small values of gains in the loop. In this paper we shall extend that work to encompass the cases of irrational and integer input signals, and increased gains.
A novel synthesis of chiral cyclopentyl- and cyclohexyl-amines (1999)

A new route to multifunctionalised chiral cyclopentyl- and cyclohexyl-amines was developed by means of a new reaction involving the ring opening of a 2-azabicyclo-[2.2.1] or -[2.2.2] structure in high yields.
Photocatalytic inactivation of viruses using titanium dioxide nanoparticles and low-pressure UV light (2008)

The carcinogenic potential of chlorine disinfection by-products and recent changes in water quality regulations have led to a greater emphasis on alternative disinfection mechanisms. In this study, the efficacy of bench-scale and pilot-scale titanium dioxide (TiO2) photocatalytic disinfection was explored using four bacteriophages (MS2, PRD1, phi-X174, and fr). The optimized bench-scale experiments indicated that 1 mg/L of Degussa P25 TiO2 irradiated by low-pressure ultraviolet (UV) light reduced the dose requirements for viral inactivation in comparison to UV light alone. The highest UV dose reductions for 4-log inactivation of PRD1, MS2, phi-X174, and fr were 19%, 15%, 6%, and 0%, respectively. Bench-scale photocatalysis was inhibited by limited adsorption of the viruses onto the TiO2 nanoparticles, as indicated by the poor results for high TiO2 concentrations. Subsequently, pilot-scale experiments were completed using the Photo-Cat Lab from Purifics. The annular reactor configuration and increased viral adsorption dramatically improved photocatalytic inactivation for samples with high TiO2 concentrations. Using the Photo-Cat Lab, 2-log inactivation of the bacteriophages was achieved with 400 mg/L of Degussa P25 TiO2 and a UV dose of approximately 34 mJ/cm2 (energy consumption of 0.33 kWh/m3)—a 700-fold decrease in energy use compared to bench-scale photocatalysis.
Next‐Generation <i>D</i><sub>2</sub>‐Symmetric Chiral Porphyrins for Cobalt(II)‐Based Metalloradical Catalysis: Catalyst Engineering by Distal Bridging (2019)

Novel D<sub>2</sub> -symmetric chiral amidoporphyrins with alkyl bridges across two chiral amide units on both sides of the porphyrin plane (designated "HuPhyrin") have been effectively constructed in a modular fashion to permit variation of the bridge length. The Co<sup>II</sup> complexes of HuPhyrin, [Co(HuPhyrin)], represent new-generation metalloradical catalysts where the metal-centered d-radical is situated inside a cavity-like ligand with a more rigid chiral environment and enhanced hydrogen-bonding capability. As demonstrated with cyclopropanation and aziridination as model reactions, the bridged [Co(HuPhyrin)] functions notably different from the open catalysts, exhibiting significant enhancement in both reactivity and stereoselectivity. Furthermore, the length of the distal alkyl bridge can have a remarkable influence on the catalytic properties.
The effects of <i>Arctotheca calendula</i> (capeweed) on digestive function of sheep (1991)

The effects of Arctotheca calendula (capeweed) on digestive function in the rumen, caecum and colon of sheep were studied. Three groups of 2-year-old Merino wethers were compared: 13 grazing capeweed-free pasture for 23 days; 8 fed 700 g of lucerne hay daily for 18 days, and 13 fed 6 kg of freshly cut capeweed (dry matter 11.3%) daily for 7 days. Capeweed did not cause diarrhoea and based on measurements of products of fermentation in the rumen, the plants were as nutritious as pasture containing grasses and clovers. The main disadvantage of capeweed in this single feeding trial was that sheep eating it lost body weight due to their inability, or lack of incentive, to consume enough dry matter.
Sugammadex 50 mg/5 ml allows clinicians rationalize its use for residual neuromuscular blockade reversal (2017)

Introduction: Sugammadex reverses very effciently residual rocuronium-induced neuromuscular block at doses range 0.5-1 mg/kg. The current cost of a 200 mg-vial sugammadex (the smallest marketed unit dose) is €71. No previous studies have been performed with lower total milligram unit doses with a proportionally reduced
price.
The objectives of this study were to evaluate the cost of 50 mg unit dose and to demonstrate the stability of 50 mg/5 ml pre-filled syringes.

Method: Retrospective, observational study was performed in a 117-bed primary hospital. Since 2014, the Pharmacy Department provides surgical areas with sugammadex 200 mg vials and 50 mg unit doses. We compared a cohort of patients scheduled for elective surgery under general anesthesia who received sugammadex for neuromuscular reversion before (2013) and after sugammadex 50 mg/5 ml syringes implementation (2014). Clinical Laboratory studied its time stability by Ultra Performance Liquid Chromatography.

Results: No differences between the number and type of surgical procedures were found in 2013 and 2014. In 2014, sugammadex consumption decreased from 880 vials to 140 vials and 700 pre-filled syringes, which represented a cost saving of €33,866. The proportion of syringes versus vials increased progressively in 2015 and 2016.
Fifty mg/5 ml sugammadex syringes maintained its stability at least for 60 days. Conclusions: Sugammadex 50 mg/5 ml syringes are stable for at least 60 days and allows clinicians to rationalize its use, which represents a significant saving
Salt Rejection and Water Transport Through Boron Nitride Nanotubes (2009)

Nanotube-based water-purification devices have the potential to transform the field of desalination and demineralization through their ability to remove salts and heavy metals without significantly affecting the fast flow of water molecules. Boron nitride nanotubes have shown superior water flow properties compared to carbon nanotubes, and are thus expected to provide a more efficient water purification device. Using molecular dynamics simulations it is shown that a (5, 5) boron nitride nanotube embedded in a silicon nitride membrane can, in principle, obtain 100% salt rejection at concentrations as high as 1 M owing to a high energy barrier while still allowing water molecules to flow at a rate as high as 10.7 water molecules per nanosecond (or 0.9268 L m(-2) h(-1)). Furthermore, ions continue to be rejected under the influence of high hydrostatic pressures up to 612 MPa. When the nanotube radius is increased to 4.14 A the tube becomes cation-selective, and at 5.52 A the tube becomes anion-selective.
Astrogliosis (2014)

In addition to their many functions in the healthy central nervous system (CNS), astrocytes respond to CNS damage and disease through a process called astrogliosis. For many decades, astrogliosis was sparsely studied and enigmatic. This article examines recent evidence supporting a definition of astrogliosis as a spectrum of heterogeneous potential changes in astrocytes that occur in a context-specific manner as determined by diverse signaling events that vary with the nature and severity of different CNS insults. Astrogliosis is associated with essential beneficial functions, but under specific circumstances can lead to harmful effects. Potential dysfunctions of astrocytes and astrogliosis are being identified that can contribute to, or be primary causes of, CNS disorders, leading to the notion of astrocytopathies. A conceptual framework is presented that allows consideration of normally occurring and dysfunctional astrogliosis and their different roles in CNS disorders.
Recent Progress in Terahertz Quantum Cascade Lasers (2010)

Terahertz quantum cascade lasers (QCLs) emit radiation due to intersubband optical transitions in semiconductor superlattices that could be engineered by design. Among a variety of possible design schemes, we have pursued designs that utilize strong electron-phonon interaction in the semiconductor as a means to establish population inversion for optical gain. This report describes the recent progress in phonon-depopulated terahertz QCLs. Operation above 160 K has been realized in GaAs/AlGaAsbased QCLs with metal-metal waveguides for frequencies ranging from 1.8-4.4 THz (λ ~ 170-70 μm). A record highest operating temperature of 186 K has been demonstrated for a 3.9-THz QCL based on a diagonal design scheme. Also, operation down to a frequency of 1.45 THz (λ ~ 205 μm) has been achieved. Whereas metal-metal waveguides provide strong mode confinement and low loss at terahertz frequencies, obtaining single-mode operation in a narrow beam-pattern-posed unconventional challenges due to the subwavelength dimensions of the emitting aperture. New techniques in waveguide engineering have been developed to overcome those challenges. Finally, a unique method to tune the resonant-cavity mode of metal-metal terahertz "wire lasers" has been demonstrated to realize continuous tuning over a range of 137 GHz for a 3.8-THz QCL.
Amoebae-resisting Bacteria Isolated from Human Nasal Swabs by Amoebal Coculture (2004)

Amoebae feed on bacteria, and few bacteria can resist their microbicidal ability. Amoebal coculture could therefore be used to selectively grow these amoebae-resisting bacteria (ARB), which may be human pathogens. To isolate new ARB, we performed amoebal coculture from 444 nasal samples. We recovered 7 (1.6%) ARB from 444 nasal swabs, including 4 new species provisionally named Candidatus Roseomonas massiliae, C. Rhizobium massiliae, C. Chryseobacterium massiliae, and C. Amoebinatus massiliae. The remaining isolates were closely related to Methylobacterium extorquens, Bosea vestrii, and Achromobacter xylosoxidans. Thus, amoebal coculture allows the recovery of new bacterial species from heavily contaminated samples and might be a valuable approach for the recovery of as-yet unrecognized emerging pathogens from clinical specimens.
Effects of Forward Model Errors on EEG Source Localization (2013)

Subject-specific four-layer boundary element method (BEM) electrical forward head models for four participants, generated from magnetic resonance (MR) head images using NFT ( www.sccn.ucsd.edu/wiki/NFT ), were used to simulate electroencephalographic (EEG) scalp potentials at 256 recorded electrode positions produced by single current dipoles of a 3-D grid in brain space. Locations of these dipoles were then estimated using gradient descent within five template head models fit to the electrode positions. These were: a spherical model, three-layer and four-layer BEM head models based on the Montreal Neurological Institute (MNI) template head image, and these BEM models warped to the recorded electrode positions. Smallest localization errors (4.1-6.2 mm, medians) were obtained using the electrode-position warped four-layer BEM models, with largest localization errors (~20 mm) for most basal brain locations. When we increased the brain-to-skull conductivity ratio assumed in the template model scalp projections from the simulated value (25:1) to a higher value (80:1) used in earlier studies, the estimated dipole locations moved outwards (12.4 mm, median). We also investigated the effects of errors in co-registering the electrode positions, of reducing electrode counts, and of adding a fifth, isotropic white matter layer to one individual head model. Results show that when individual subject MR head images are not available to construct subject-specific head models, accurate EEG source localization should employ a four- or five-layer BEM template head model incorporating an accurate skull conductivity estimate and warped to 64 or more accurately 3-D measured and co-registered electrode positions.
Stabilization of an associated folding intermediate of bovine growth hormone by site-directed mutagenesis. (1988)

By using oligonucleotide-directed mutagenesis, Lys-112 of bovine growth hormone (bGH) was changed to leucine, and its resulting effect on folding was studied. Equilibrium denaturation curves for the mutant protein exhibit biphasic or nonsymmetrical transitions by a variety of spectroscopic and hydrodynamic techniques, whereas the wild-type protein at the same concentration exhibits symmetrical transitions. The mutant protein refolds slower (by a factor of 30) and more readily precipitates upon refolding than the wild-type protein. These folding characteristics of the mutant protein are demonstrated to be a result of stabilization of an associated folding intermediate. A 38-amino acid fragment (96-133) derived from the mutant protein is helical, likely amphipathic, and more stabilized by increasing peptide concentration than is the corresponding helical peptide from the wild-type protein. The increased stability of the associated intermediate and the increased helicity of the peptide from the mutant protein are explained by preferential intermolecular interactions between helices due to enhanced hydrophobic attraction by their amphipathic surfaces.
Genomic Profiles Associated with Early Micrometastasis in Lung Cancer: Relevance of 4q Deletion (2009)

Thus, our data indicate, for the first time, that early hematogenous dissemination of tumor cells might be driven by a specific pattern of genomic changes.
Elongational and shear flow behavior of calcium carbonate filled low density polyethylene: Effect of filler particle size, content, and surface treatment (2011)

Abstract In this article, calcium carbonate filled low density polyethylene (LDPE) was prepared and the influence of filler content, particle size, and surface treatment with stearic acid on the strain hardening and viscoelastic properties of the composites were investigated. Both elongational and shear rheological measurements were conducted on the different formulations and completed by microscopical observations and by differential scanning thermal analysis. The obtained results indicate that the effect of filler content and particle size are negligible on strain hardening behavior. Also the filler surface treatment has a less important effect on the nonlinear elongational tests in comparison with low frequency range measurements. However in shear rheology, we noted the absence of yield stress and network structure at different filler contents, and the presence of shear thinning behavior. Scanning electron microscopy (SEM) observations showed the enhancement of dispersion for surface treated samples, while differential scanning calorimetry (DSC) experiments have shown that the content of crystallinity of LDPE matrix is slightly affected by the presence of filler. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
A GaAs RF transceiver IC for 1.9 GHz digital mobile communication systems (2002)

A 3.4 V single power supply GaAs single-chip RF transceiver IC for 1.9 GHz digital mobile communication systems such as the Japanese Personal Handy Phone System (PHS) consists of both analog and digital circuits. The analog circuits contain a power amplifier (PA), an SPDT switch (SW), two attenuators (ATTs) for transmitting and receiving modes, and a low-noise amplifier (LNA). The digital circuits contain a negative voltage generator (NVG) for single voltage operation and a logic circuit to control the analog circuits and the NVG.
Tasty Burgers, Soggy Fries: Probing Aspect Robustness in Aspect-Based Sentiment Analysis (2020)

Aspect-based sentiment analysis (ABSA) aims to predict the sentiment towards a specific aspect in the text. However, existing ABSA test sets cannot be used to probe whether a model can distinguish the sentiment of the target aspect from the non-target aspects. To solve this problem, we develop a simple but effective approach to enrich ABSA test sets. Specifically, we generate new examples to disentangle the confounding sentiments of the non-target aspects from the target aspect's sentiment. Based on the SemEval 2014 dataset, we construct the Aspect Robustness Test Set (ARTS) as a comprehensive probe of the aspect robustness of ABSA models. Over 92% data of ARTS show high fluency and desired sentiment on all aspects by human evaluation. Using ARTS, we analyze the robustness of nine ABSA models, and observe, surprisingly, that their accuracy drops by up to 69.73%. We explore several ways to improve aspect robustness, and find that adversarial training can improve models' performance on ARTS by up to 32.85%. Our code and new test set are available at https://github.com/zhijing-jin/ARTS_TestSet