gebhart/patrepeval huggingface dataset:
Diag2graph: Representing Deep Learning Diagrams In Research Papers As Knowledge Graphs (2020)

Which are the segmentation algorithms proposed during 2018-2019 in CVPR that have CNN architecture?’ Answering this question involves identifying and analyzing the deep learning architecture diagrams from several research papers. Retrieving such information poses significant challenge as most of the existing academic search engines are primarily based on only the text content. In this paper, we introduce Diag2Graph, an end-to-end framework for parsing deep learning diagram-figures, that enables powerful search and retrieval of architectural details in research papers. Our proposed approach automatically localizes figures from research papers, classifies them, and analyses the content of the diagram-figures. The key steps in analyzing the Figure content is the extraction of the different components data and finding their structural relation. Finally, the extracted components and their relations are represented in the form of a deep knowledge graph. A thorough evaluation on a real-word annotated dataset has been done to demonstrate the efficacy of our approach.
A multi-cytokine inhibitory peptide (BNZ 132-1) that is a potential therapeutic agent for HAMTSP and other necrotizing diseases. (2015)

We previously showed that the pathogenic mechanism of HAM-TSP involves the by-stander inflammatory damages of CNS cells by the hyper T-cell immunity caused by the HTLV-1. Thus we propose that suppressing this T-cell hyper-activation would be a key to prevent the progress of myelopathy in HAM-TSP. So far, three gc-family cytokines, IL-2, IL-15, and most likely IL-9 have been implicated in this process. Because these 3 cytokine share gc-subunit for signal transduction, they show functional redundancy. Because cellular responses to cytokines are sigmoid in shape with respect to cytokine doses, neutralizing one factor in a combination of 3 cytokines would not linearly lead to 33% inhibition even though the 3 factors were equally present in the mixture. This suggests that the use of a single monoclonal antibody (mAb) against one factor in a mixture of redundant cytokines often results in non-satisfactory effect, implying that a combinatorial blocking of all involved factors is needed to effectively treat clinical cases. A combined use of antibodies for each factor may solve the problem, but is infeasible in the clinic due to the costly nature of the Ab therapy. We therefore designed a peptide based on the conserved and divergent nature of the 6 gc-cytokines at their D-helix that is involved in their interaction with the gc-subunit. After computer simulated docking and high-throughput biological screening, we synthesized three peptides with different target specificities. The lead peptide (named BNZ 132-1) blocks IL-2, IL-9, and IL-15 in vitro. PEG-conjugation of this peptide enabled stability in vivo (T1/2 over 80 h in primates and in rodents) and efficiently blocked the in vivo propagation of an IL-15 dependent CD8 T cell leukemia in mice that we have generated in the past. In addition, BNZ 132-1 efficiently and specifically blocked the ex vivo activation and proliferation of CD8 T cells isolated freshly from HAM-TSP patients. We have already completed in vitro proof-of-concept, in vivo efficacy, toxicology/pharmacokinetics/pharmacodynamics studies and have obtained a patent on this compound. We will soon apply for the IND approval of this peptide for treating HAM-TSP. The structural nature, various unique biological characteristics and the drug potential of this peptide will be discussed.
Tissue ablation using an acoustic waveguide for high‐intensity focused ultrasound (1997)

High-intensity focused ultrasound (HIFU) has been shown capable of selective tissue destruction in humans, with promise as a tool for ablation of tumors, although one practical problem is reflection of sound at gas or bony interfaces within the body. We evaluated a water-filled cylindrical metal tube as a waveguide for HIFU, since such a general technique might be useful for ablation of otherwise inaccessible tumors in the body. Our studies indicate that such a waveguide is capable of propagating HIFU from a piezoelectric source, with resultant heating of tissue specimens to greater than 80 degrees C, causing focal tissue destruction.
Electron microscopic autoradiographic localization of prolactin mRNA in rat pituitary. (1989)

Recent immunoelectron microscopic studies have shown that immunoreactive prolactin (PRL) in rat pituitary can be detected not only in typical PRL cells, characterized by large secretory granules, but also in another type of cell, which contains small secretory granules. To determine whether or not these two cell types are involved in PRL biosynthesis, we developed a procedure to investigate PRL gene expression by using in situ hybridization at the ultrastructural level. Rat pituitary was fixed and vibratome sections were incubated with a PRL [35S]-cDNA probe and subsequently flat-embedded in Araldite. Semi-thin and ultra-thin sections were processed for autoradiography. The results indicate that only the two PRL cell types were labeled. When immunolabeling for PRL was applied to ultra-thin sections, only immunopositive cells were seen to contain silver grains. In these cells the silver grains were associated with the rough endoplasmic reticulum and nucleus. When a growth hormone (GH) [35S]-cDNA probe was used as a control, only GH-secreting cells were labeled. This study confirms that the two PRL cell types are involved in biosynthesis of PRL. Moreover, this simple in situ hybridization technique provides a new approach to accurately localize mRNA in complex tissue and to investigate the subcellular distribution of mRNA under differing experimental conditions.
The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies (2010)

International audience
Supplementary Figure S2 from Milatuzumab–SN-38 Conjugates for the Treatment of CD74<sup>+</sup> Cancers (2023)

&lt;p&gt;PDF file - 1.5 MB, Reversed-phase HPLC analyses for cleavage of ME-capped CL2E-SN-38 by cathepsin-B&lt;/p&gt;
Towards generic FutureGrid image management (2011)

In this paper, we briefly outline the current design of a generic image management service for FutureGrid. The service is intended to generate, store, and verify images while interfacing with different localized cloud IaaS image. Additionally, we will also use the service to generate images for traditional bare-metal deployments.
Quantitative Detection of Low-Copy-Number mRNAs Differing at Single Nucleotide Positions (2003)

Accurate analysis of mRNA expression levels of SNPs, highly homologous genes, and splicing variants requires techniques capable of quantifying low-copy-number mRNAs differing at single nucleotide positions. We have used an RT-PCR-based technique based on co-amplification of closely related target mRNA transcripts and assessed the effect of the stochastic distribution of low-copy-number templates on sampling variation when quantifying rare mRNA transcripts. The technique was optimized for maximal sensitivity to enable the analysis of samples containing a subpopulation of target cells and small microdissected samples. We demonstrate that the input level of template molecules is a critical determinant of the achievable assay precision. A minimum of approximately 50 molecules of template is required to discriminate between 2-fold differences in the expression levels of two transcripts. At levels above 1000 molecules of input template, the stochastic effects on sampling variation become negligible.
Measuring and Maximizing the Effectiveness of Honor Codes in Online Courses (2015)

We measure the effectiveness of a traditional honor code at deterring cheating in an online examination, and we compare it to that of a stern warning. Through experimental evaluation in a 409-student online course, we find that a pre-task warning leads to a significant decrease in the rate of cheating while an honor code has a smaller (non-significant) effect. Unlike much prior work, we measure the rate of cheating directly and we do not rely on potentially inaccurate post-examination surveys. Our findings demonstrate that replacing traditional honor codes with warnings could be a simple and effective way to deter cheating in online courses.
(1+1)-Dimensional modulation instability of spatially incoherent light (2002)

We present a comprehensive study of the one-dimensional modulation instability of partially spatially incoherent light in noninstantaneous self-focusing media. For this instability to occur, the nonlinearity has to exceed a specific threshold that depends on the coherence properties of the beam. Above this threshold a uniform-intensity partially spatially coherent wave front becomes unstable and breaks up into periodic trains of one-dimensional stripes.
ChemInform Abstract: DIRECT OXIDATION OF BENZIMIDAZOLE‐2‐THIOL TO THE BENZIMIDAZOLE‐2‐SULFONIC ACID WITH SUPEROXIDE ION (1982)

Abstract Benzimidazol‐2‐thiol (I) wird durch das Superoxidion ‐ erzeugt in situ aus K02 in aprotischen Lösungsmitteln (DMSO, THF oder MeCN) ‐ zu der Sulfonsäure (II) oxidiert.
Gain spectra analysis of bilayer quantum dot lasers beyond 1.3&#x03BC;m (2010)

In this paper we report on the analysis of molecular beam epitaxy (MBE) grown GaAs and InGaAs capping bilayer QD laser material via a number of characterization techniques. The InGaAs capped bilayer QD lasers extends the room temperature lasing wavelength to 1.45μm. The further analysis of the materials using the multi-section technique allows the gain and absorption spectrum to be obtained under various CW and pulsed bias conditions and at a range of currents and temperatures. The spectral measurement of gain demonstrates that net modal gain is achieved beyond 1.5μm at room temperature. Analysis of the temperature and current density dependence of gain allows insight into the increase in threshold current around room temperature for a GaAs capped bilayer laser.
A situation and threat assessment algorithm for a rear-end collision avoidance system (2008)

Rear-end collisions are common accident scenarios and a frequent cause of these accidents is driver distraction. This paper presents a situation assessment (SA) algorithm that estimates driver distraction by continuously assessing the steering actions of the driver. A collision avoidance (CA) system is proposed, which combines the SA with a threat assessment (TA) algorithm that estimates the effort needed to avoid a collision. It is shown that the SA algorithm proposed enables the CA system to initiate earlier brake interventions when the driver is assessed as being distracted, without significantly increasing the risk of false interventions in real traffic. The CA system has been evaluated in both collision situations on a test track and during 200 driving hours in real traffic conditions.
Front Cover: Upregulation of the Glutaminase II Pathway Contributes to Glutamate Production upon Glutaminase 1 Inhibition in Pancreatic Cancer (2019)

DOI: 10.1002/pmic.201800451 Much like the classic arcade game “Whack-a-Mole”, cancer cells are able to upregulate a different metabolic pathway when one pathway is inhibited. Specifically, using metabolomics technologies with isotopic labelling, Sunag Udupa et al. demonstrate in article number 1800451 the production of glutamate from glutamine via the glutaminase II pathway when the glutaminase 1 pathway is inhibited. This metabolic adaptability of tumors justifies the need for targeting multiple metabolic pathways, aiming at both main and adaptive metabolic networks.
Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T (2019)

The ventro-intermediate nucleus (Vim), as part of the motor thalamic nuclei, is a commonly used target in functional stereotactic neurosurgery for treatment of drug-resistant tremor. As it cannot be directly visualized on routinely used magnetic resonance imaging (MRI), its clinical targeting is performed using indirect methods. Recent literature suggests that the Vim can be directly visualized on susceptibility-weighted imaging (SWI) acquired at 7 T. Our work aims to assess the distinguishable Vim on 7 T SWI in both healthy-population and patients and, using it as a reference, to compare it with: (1) The clinical targeting, (2) The automated parcellation of thalamic subparts based on 3 T diffusion MRI (dMRI), and (3) The multi-atlas segmentation techniques. In 95.2% of the data, the manual outline was adjacent to the inferior lateral border of the dMRI-based motor-nuclei group, while in 77.8% of the involved cases, its ventral part enclosed the Guiot points. Moreover, the late MRI signature in the patients was always observed in the anterior part of the manual delineation and it overlapped with the multi-atlas outline. Overall, our study provides new insight on Vim discrimination through MRI and imply novel strategies for its automated segmentation, thereby opening new perspectives for standardizing the clinical targeting.
A CMOS silicon spin qubit (2016)

Silicon, the main constituent of microprocessor chips, is emerging as a promising material for the realization of future quantum processors. Leveraging its well-established complementary metal-oxide-semiconductor (CMOS) technology would be a clear asset to the development of scalable quantum computing architectures and to their co-integration with classical control hardware. Here we report a silicon quantum bit (qubit) device made with an industry-standard fabrication process. The device consists of a two-gate, p-type transistor with an undoped channel. At low temperature, the first gate defines a quantum dot encoding a hole spin qubit, the second one a quantum dot used for the qubit read-out. All electrical, two-axis control of the spin qubit is achieved by applying a phase-tunable microwave modulation to the first gate. The demonstrated qubit functionality in a basic transistor-like device constitutes a promising step towards the elaboration of scalable spin qubit geometries in a readily exploitable CMOS platform.
Quantitative PET in the 2020s: a roadmap (2020)

Positron emission tomography (PET) plays an increasingly important role in research and clinical applications, catalysed by remarkable technical advances and a growing appreciation of the need for reliable, sensitive biomarkers of human function in health and disease. Over the last 30 years, a large amount of the physics and engineering effort in PET has been motivated by the dominant clinical application during that period, oncology. This has led to important developments such as PET/CT, whole-body PET, 3D PET, accelerated statistical image reconstruction, and time-of-flight PET. Despite impressive improvements in image quality as a result of these advances, the emphasis on static, semi-quantitative 'hot spot' imaging for oncologic applications has meant that the capability of PET to quantify biologically relevant parameters based on tracer kinetics has not been fully exploited. More recent advances, such as PET/MR and total-body PET, have opened up the ability to address a vast range of new research questions, from which a future expansion of applications and radiotracers appears highly likely. Many of these new applications and tracers will, at least initially, require quantitative analyses that more fully exploit the exquisite sensitivity of PET and the tracer principle on which it is based. It is also expected that they will require more sophisticated quantitative analysis methods than those that are currently available. At the same time, artificial intelligence is revolutionizing data analysis and impacting the relationship between the statistical quality of the acquired data and the information we can extract from the data. In this roadmap, leaders of the key sub-disciplines of the field identify the challenges and opportunities to be addressed over the next ten years that will enable PET to realise its full quantitative potential, initially in research laboratories and, ultimately, in clinical practice.
Poly(methyl methacrylate)-block-polyethylene-block-poly(methyl methacrylate) Triblock Copolymers as Compatibilizers for Polyethylene/Poly(methyl methacrylate) Blends (2014)

Poly(methyl methacrylate)-block-polyethylene-block-poly(methyl methacrylate) (PMMA–PE–PMMA) triblock copolymers were prepared by a combination of ring-opening metathesis polymerization (ROMP), hydrogenation, and reversible addition–fragmentation chain-transfer (RAFT) polymerization. The number-average molar masses of the PMMA end blocks were varied (Mn = 1, 4, 12, and 31 kg mol–1), whereas that of the PE middle block was kept constant at Mn = 13 kg mol–1. The copolymers were evaluated as compatibilizers in PE/PMMA homopolymer blends containing PE in a 4:1 excess by weight. The compatibilized blends displayed significant improvements in elastic modulus, hardness, and scratch resistance as compared to uncompatibilized binary blends. The effects of the PMMA end-block molar mass and compatibilizer concentration on the blend morphology and mechanical properties were investigated. The triblock copolymer with the highest-molar-mass PMMA end blocks was most effective, presumably because of enhanced stress transfer between phases by virtue of a higher degree of entanglement of the end blocks with the PMMA dispersed phase.
A Time-Frequency Analysis for the Online Detection of the N2pc Event-Related Potential (ERP) Component in Individual EEG Datasets (2020)

The N2pc event-related potential component measures direction and time course of selective visual attention and represents an important biomarker in cognitive neuroscience. While its subtractive origin strongly influences the amplitude, thus hindering its detection, other external factors, such as subject's inefficiency to allocate attention to the cued target, or the heterogeneity of the visual context, may strongly affect the elicitation of the component itself. It would therefore be extremely important to create a tool that, using as few sweeps as possible, could reliably establish whether an N2pc is present in an individual subject. In the present work, we propose an approach by resorting to a time-frequency analysis of N2pc individual signals; in particular, power at each frequency band (α/β/δ/θ) was computed in the N2 time range and correlated to the estimated amplitude of the N2pc. Preliminary results on fourteen human volunteers of a visual search design showed a very high correlation coefficient (over 0.9) between the low frequency bands power and the mean absolute amplitude of the component, using only 40 sweeps. Results also seemed to suggest that N2pc amplitude values higher than 0.5 μV could be accurately classified according to time-frequency indices.Clinical Relevance - The online detection of the N2pc presence in individual EEG datasets would allow not only to study the factors responsible of N2pc variability across subjects and conditions, but also to investigate novel search variants on participants with a predisposition to show an N2pc, reducing time and costs and the possibility to obtain biased results.
Stereochemistry of [M(bidentate ligand)2(unidentate ligand)]. Crystal structure of iodobis(pyrrolidinyldithiocarbamato)iron(III)–iodine (2/1) (1980)

The crystal structure of a complex analysing as FeL2I2, L = pyrrolidinyldithiocarbamate, has been determined at 295(1) K by X-ray diffraction and refined to a residual of 0.046 for 1 422 ‘observed’ reflections. Crystals are monoclinic, P21/c, a= 6.735(4), b= 18.28(2), c= 15.11(1)Å, β= 96.71(5)°, and Z= 4. The substance has been shown to be a molecular complex, [Fel{S2CN(CH2)4}2]·0.5 I2, the iodine molecule being located on a crystal-lographic centre of symmetry. The bond lengths are as expected [Fe–I 2.652(3), Fe–S 2.271(4)–2.305(5)Å]; for the iodine molecule, I–I is 2.779(3)Å. The latter has a contact at 3.516(3)Å to the complexed iodine atom. The stereochemistry of the five-co-ordinate complex is a square pyramid with the iodine atom in the apical site, distorted towards a square pyramid with the iodine atom in a basal site. This distortion is discussed in terms of repulsion theory.
Papain gel containing methylene blue for simultaneous caries removal and antimicrobial photoinactivation against Streptococcus mutans biofilms (2016)

This study intended to evaluate the effects of a papain-gel with a red-light absorbing pigment (methylene blue – MB) to mediate photodynamic therapy (PDT) against Streptococcus mutans biofilms. The PapaMBlue was compared with free MB to generate reactive oxygen species using fluorescence probes (SOSG and HPF). PDT (660-nm light) was carried out against S. mutans biofilms grown on either plastic dishes or on collagen membrane and assayed by CFU, live-dead staining using confocal microscopy, transmission electron microscopy and H&E staining for collagen films. Cytotoxicity and subcellular localization was studied in human fibroblasts. Sponges of bioabsorbable type I collagen membrane were exposed to papain based gel, irradiated with laser and analyzed about their integrity by ATR-FTIR. The PapaMBlue produced higher amounts of singlet oxygen and hydroxyl radicals than free MB, possibly due to better disaggregation of the dye in solution. The PapaMBlue antimicrobial effects on biofilms proved to be capable of reducing the S. mutans. Both MTT and PrestoBlue assays showed higher cell viability and metabolism scores in fibroblasts treated with PapaMBlue and MB, possibly due to stimulation of mitochondrial activity and that collagen triple helix is unaffected. The PapaMBlue is equally effective as MB in destroying S. mutans biofilms growing on plastic or collagen without affecting fibroblasts.
Influence of in vitro oxygen concentrations on preimplantation embryo development, gene expression and production of hanwoo calves following embryo transfer (2006)

This study evaluated the effects of two different oxygen (O2) concentrations on in vitro embryo development, embryo quality, and gene expression and the in vivo development following embryos transfer to recipients of natural and synchronized estrus in bovines. Cumulus oocyte complexes were in vitro matured in TCM199 supplemented with FSH (10 microg/ml), LH (10 microg/ml), and 10% (v/v) FBS. Presumptive zygotes were cultured in SOF medium either under 5% (low) or 20% (high) O2 in air. Cleavage rates did not differ between groups. Blastocyst and hatched blastocyst development in 5% O2 were significantly (P < 0.05) higher than in 20% O2. Total cell number of in vivo blastocyst was significantly (P < 0.05) higher than that of in vitro blastocyst. ICM ratio and apoptosis of in vivo blastocyst were significantly (P < 0.05) lower than that of in vitro blastocyst. Using real time PCR, we have found that for the set of genes (GLUT-1, MnSOD, VEGF, Bax, and Bcl-2) analyzed, there were differences in mRNA expression between in vitro produced (IVP) and in vivo produced embryos. Interestingly, the abundance of transcript for IFN-tau in IVP embryos produced under 5% O2 concentration was similar to in vivo counterparts. The pregnancy and twin rates of natural recipients were significantly (P < 0.05) higher than those of synchronized counterparts. No significant difference in the offspring sex was observed. In conclusion, low (5%) O2 concentration during IVC was beneficial for enhancing the embryo quality and recipients of natural estrus were more suitable than synchronized estrus for stable production of Hanwoo calves.