gebhart/patrepeval huggingface dataset:
Development of PET-Hat: Wearable PET system for brain research (2009)

1532 Objectives Brain functional studies using PET have advantages over fMRI in some areas such as auditory research, in which acoustic noise from MRI during acquisition interferes with delicate stimulation. However commercially available PET systems are expensive and designed for whole body studies, are not optimized for brain functional studies. Thus we are developing a low cost, small size, wearable brain PET system named PET-Hat. Methods The PET-Hat employed double counter-balanced systems for the mechanical supports. The detector ring can freely move with the counter balanced systems. The PET can also freely swivel. These motions enable subject to move relatively freely with the PET during acquisition. The detector consists of a GSO block, a tapered light guide, and a flat panel photomultiplier tube (FP-PMT). Two types of GSOs are used to form depth-of-interaction (DOI) detector to minimize the ring diameter. The tapered light guide is used to increase the size of the GSO blocks and reduce the number of FP-PMTs. Sixteen detector blocks are arranged in a 280mm diameter ring. Transaxial and axial field-of-view (FOV) are 22cm and 5cm, respectively. Results The PET-Hat could move freely with the subject with the counter-balanced systems. Energy resolution of the block detectors was ~15% FWHM and timing resolution was ~4.6nsFWHM. Transaxial resolution and axial resolution at the center of the FOV were 4.9mmFWHM and 3.5mmFWHM, respectively. Sensitivity was ~1% at the center of the axial FOV. Conclusions We conclude that the PET-Hat is a promising, low cost, small size, wearable brain PET system for brain functional studies. Research Support This work was supported by the Japan Science and Technology Agency
PERCUTANEOUS ETHANOL INJECTION THERAPY FOR HEPATOCELLULAR-CARCINOMA (REVIEW) (1993)

Recently, ultrasound-guided percutaneous ethanol injection therapy (PEIT) has been widely performed in the treatment of hepatocellular carcinoma. Histopathologic examinations after the therapy have revealed that PEIT can destroy the tumor completely in most cases. Findings in imaging modalities and serum tumor marker levels have also shown a remarkable anticancer effect of this procedure. In addition, PEIT has achieved considerably high long-term survival rates. PEIT is a generally safe procedure and serious complications are rare. PEIT seems to be a valuable therapy and could even be an alternative to surgery in the treatment of hepatocellular carcinoma. This paper reviews the pertinent literature on this new therapy.
CLASSIFYING VISUAL FIELD DATA (1996)

We develop a prediction model for classifying an eye according to glaucoma status based on its visual field. We develop measures of both diffuse and localized defects in the visual field as potential predictors of glaucoma. To identify predictors of abnormal fields, we must describe the variability in the fields of normal eyes, hence we first model the mean, variance and correlation structures of normal fields with use of generalized estimating equations. The best measures of diffuse loss include a field's mean level, contrasts of the upper and lower halves, and contrasts of the nasal and temporal halves. Local loss is measured by the depth, area, volume and location of the field's largest defect. We develop logistic regression models to classify eyes as having glaucoma or not. We present ROC curves of the results that are highly competitive with current clinical methods of classification.
Biomanycores, open-source parallel code for many-core bioinformatics (2011)

International audience
Hydrodynamic Cavitation – A Promising Technology for Biomass Pretreatment (2019)

Biofuels can be produced from biomass feedstocks via thermochemical or biochemical biomass conversion technologies. Among the liquid biofuels, bioethanol is recommended for blending with petrol to run the spark ignition engines. First generation bioethanol production technology is successfully implemented at commercial scale in different countries. Because of simple and efficient technology, the fermentable sugars from sugar/starch crops is quickly recovered and used for bioethanol production via a fermentation process. As compared to these crops, the lignocellulosic biomass (LCB) feedstocks have a complex cell wall structure to protect the fermentable sugars. Generally, the LCB feedstocks comprise 75% of carbohydrates (40-50% of
Insight into the GTPase Activity of Tubulin from Complexes with Stathmin-like Domains (2007)

Microtubules are dynamically unstable tubulin polymers that interconvert stochastically between growing and shrinking states, a property central to their cellular functions. Following its incorporation in microtubules, tubulin hydrolyzes one GTP molecule. Microtubule dynamic instability depends on GTP hydrolysis so that this activity is crucial to the regulation of microtubule assembly. Tubulin also has a much lower GTPase activity in solution. We have used ternary complexes made of two tubulin molecules and one stathmin-like domain to investigate the mechanism of the tubulin GTPase activity in solution. We show that whereas stathmin-like domains and colchicine enhance this activity, it is inhibited by vinblastine and by the N-terminal part of stathmin-like domains. Taken together with the structures of the tubulin-colchicine-stathmin-like domain-vinblastine complex and of microtubules, our results lead to the conclusions that the tubulin-colchicine GTPase activity in solution is caused by tubulin-tubulin associations and that the residues involved in catalysis comprise the beta tubulin GTP binding site and alpha tubulin residues that participate in intermolecular interactions in protofilaments. This site resembles the one that has been proposed to give rise to GTP hydrolysis in microtubules. The widely different hydrolysis rates in these two sites result at least in part from the curved and straight tubulin assemblies in solution and in microtubules, respectively.
Wind Turbine Design Cost and Scaling Model (2006)

This model intends to provide projections of the impact on cost from changes in economic indicators such as the Gross Domestic Product and Producer Price Index.
ChemInform Abstract: Synthesis of a Novel Class of Non‐Peptide NK‐2 Receptor Ligand, Derived from 1‐Phenyl‐3‐pyrrol‐1‐ylindan‐2‐carboxamides. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Experimental evidence of carrier leakage in InGaAsN quantum-well lasers (2003)

Carrier leakage processes are shown experimentally as one of the factors contributing to the temperature sensitivity of InGaAsN quantum well lasers. The utilization of the direct barriers of GaAs0.85P0.15 instead of GaAs, surrounding the InGaAsN quantum-well (QW)-active region, leads to significant suppression of carrier leakage at elevated temperatures of 90–100 °C. Threshold current densities of only 390 and 440 A/cm2 was achieved for InGaAsN QW lasers (Lcav=2000 μm) with GaAs0.85P0.15-direct barriers at temperature of 80 and 90 °C, respectively.
Ab initiocalculation of band-gap renormalization in highly excited GaAs (2004)

We present ab initio quasiparticle self-energy calculations in crystalline GaAs for cases of intense electronic excitation $(\ensuremath{\sim}10%$ of valence electrons excited into conduction band), relevant for high-intensity ultrashort pulsed laser experiments. Calculations are performed using an out-of-equilibrium generalization of the $\mathrm{GW}$ approximation based on the Keldysh Green's function approach. Our results indicate that while the quasiparticle band gap is a sensitive function of the amount of excitation, it is not possible to induce complete band-gap closure in this system by purely electronic means.
Antibody response to the rubella virus structural proteins in infants with the congenital rubella syndrome (1986)

Forty-five serum samples from 31 newborns and infants with the congenital rubella syndrome (CRS) were tested by immunoprecipitation to determine their antibody spectra to each of the structural proteins of rubella virus. Most sera (37/45) contained little or no E2 protein-specific antibody, but some (6/45) precipitated a greater amount of the E2 glycoprotein than the E1 glycoprotein. The relative E1/E2 ratio was found to decrease with time when serial serum samples from the same patient were tested. No correlation between the IgG class hemagglutination inhibition antibody titers and the E1/E2 ratio could be demonstrated. However, in some serum specimens relatively high neutralizing antibody titers were correlated with immunoprecipitation of the E2 glycopolypeptide. None of the CRS sera reacted well with the C protein. The immunoprecipitation patterns found in CRS sera were qualitatively different from those observed in a series of 25 sera from young adults with conventional serologic evidence of rubella immunity following natural infection. All of the natural immune sera recognized each of the three structural polypeptides of rubella virus.
Transcriptomic Approaches to Toxicity Assessment# (2013)

College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, South Korea. *Corresponding author: Sgk@snu.ac.kr#Grant Support: This research was supported by a grant (10182KFDA992-2201) from Korea Food & Drug Administration in 2011.
Co‐translational modification of nascent immunoglobulin heavy and light chains (1979)

We have investigated the in vivo co-translational covalent modification of nascent immunoglobulin heavy and light chains. Nascent polypeptides were separated from completed polypeptides by ion-exchange chromatography of solubilized ribosomes on QAE-Sephadex. First, we have demonstrated that MPC 11 nascent heavy chains are quantitatively glycosylated very soon after the asparaginyl acceptor site passes through the membrane into the cisterna of the rough endoplasmic reticulum. Nonglycosylated completed heavy chains of various classes cannot be glycosylated after release from the ribosome, due either to rapid intramolecular folding and/or intermolecular assembly, which cause the acceptor site to become unavailable for the glycosylation enzyme. Second, we have shown that the formation of the correct intrachain disulfide loop within the first light chain domain occurs rapidly and quantitatively as soon as the appropriate cysteine residues of the nascent light chain pass through the membrane into the cisterna of the endoplasmic reticulum. The intrachain disulfide loop in the second or constant region domain of the light chain is not formed on nascent chains, because one of the cysteine residues involved in this disulfide bond does not pass through the endoplasmic reticulum membrane prior to chain completion and release from the ribosome. Third, we have demonstrated that some of the initial covalent assembly (formation of interchain disulfide bonds) occurs on nascent heavy chains prior to their release from the ribosome. The results are consistent with the pathway of covalent assembly of the cell line, in that completed light chains are assembled onto nascent heavy chains in MPC 11 cells (IgG2b), where a heavy-light half molecule is the major initial covalent intermediate; and completed heavy chains are assembled onto nascent heavy chains in MOPC 21 cells (IgG1), where a heavy chain dimer is the major initial disulfide linked intermediate.
Tribological evaluation of selected biodegradable oils with long chain fatty acids (2010)

Purpose The purpose of this paper is to evaluate local biodegradable oils with long chain fatty acids namely: castor ( Ricinus communis L.), jojoba ( Simmondsia chinensis L.), olive ( Oleo europaea L.), and sunflower ( Helianthus annuus L.) oils for lubrication candidacy as a substitute to petroleum mineral oils. Design/methodology/approach Evaluation criteria includes antiwear, lubricity, and extreme pressure (load carrying capacity) using the four‐ball configuration, oxidation induction by pressure differential scanning calorimetry, thermal stability by thermo‐gravimetric analyses, and viscometry using relevant American Society of Testing and Materials (ASTM) standards. Findings The results show that the lubrication films at the interface failed by the decomposition of the metallic soaps formed by the chemical reaction of the constituent fatty acid molecules and the rubbing surfaces. The biodegradable oils show superior lubricant performance compared to the paraffin‐based mineral oil, despite their poor oxidation stability. Oxidation induction and thermo‐gravimetric characteristics of the biodegradable oils are closely related to their polyunsaturated and monounsaturated fatty acid composition. Originality/value The paper shows how these biodegradable oils could be used as good substitute for petroleum mineral oils in as‐received state or little antioxidant additives.
Effect of Model Variables on in vitro Erosion (2015)

The aim of this study was to investigate the effects of tooth type (molar/premolar), tooth surface (buccal/lingual), smear layer or no smear layer, storage of specimens in deionised water, mode and speed of agitation, and rinsing method between cycles on mean step height loss and Knoop microhardness (KHN) change. Polished human enamel specimens embedded in acrylic resin were prepared from sound permanent molar and premolar tooth surfaces. A 0.3% (pH 3.2) solution of citric acid was used to erode the specimens, in a cycling procedure, consisting of 10 min immersion followed by rinsing in deionised water for 30 s with a spray bottle, for 5 cycles. The specimens were analysed with a non-contact white light profilometer and KHN. Molar teeth (148.99±24.49 KHN) and buccal surfaces (155.62±30.35 KHN) produced significantly less microhardness change compared to premolar (186.40±20.74 KHN) and lingual surfaces (179.76±23.21 KHN; p<0001). The effect of storage and rinsing showed little difference in mean step height loss (<1 µm) and microhardness change. With no smear layer a significantly lower mean step height loss and microhardness change (p<0.001) was observed. Agitation was performed with Orbital, Gyro and See-Saw rockers at 30, 40, 60, and 70 rpm. The mean step height loss was largest for See-Saw at 70 rpm (11.73±0.91 μm) and lowest for Orbital at 30 rpm (2.76±1.12 μm). A statistical difference was found between all types of agitation and speeds (p<0.001). In conclusion, this study has shown that the variables investigated here have a significant impact on the measurable outcome, highlighting the importance of accurate and detailed method sections.
How Subtle Can It Get? (2020)

Flying drones have become common objects in our daily lives, serving a multitude of purposes. Many of these purposes involve outdoor scenarios where the user combines drone control with another activity. Traditional interaction methods rely on physical or virtual joysticks that occupy both hands, thus restricting drone usability. In this paper, we investigate one-handed human-to-drone-interaction by leveraging three modalities: force, touch, and IMU. After prototyping three different combinations of these modalities on a smartphone, we evaluate them against the current commercial standard through two user experiments. These experiments help us to find the combination of modalities that strikes a compromise between user performance, perceived task load, wrist rotation, and interaction area size. Accordingly, we select a method that achieves faster task completion times than the two-handed commercial baseline by 16.54% with the merits of subtle user behaviours inside a small-size ring-form device and implements this method within the ring-form device. The last experiment involving 12 participants shows that thanks to its small size and weight, the ring device displays better performance than the same method implemented on a mobile phone. Furthermore, users unanimously found the device useful for controlling a drone in mobile scenarios (AVG = 3.92/5), easy to use (AVG = 3.58/5) and easy to learn (AVG = 3.58/5). Our findings give significant design clues in search of subtle and effective interaction through finger augmentation devices with drone control. The users with our prototypical system and a multi-modal on-finger device can control a drone with subtle wrist rotation (pitch gestures: 43.24° amplitude and roll gestures: 46.35° amplitude) and unnoticeable thumb presses within a miniature-sized area of (1.08 * 0.61 cm2).
Overcoming Data Scarcity in Speaker Identification: Dataset Augmentation with Synthetic MFCCs via Character-level RNN (2020)

Autonomous speaker identification suffers issues of data scarcity due to it being unrealistic to gather hours of speaker audio to form a dataset, which inevitably leads to class imbalance in comparison to the large data availability from non-speakers since large-scale speech datasets are available online. In this study, we explore the possibility of improving speaker recognition by augmenting the dataset with synthetic data produced by training a Character-level Recurrent Neural Network on a short clip of five spoken sentences. A deep neural network is trained on a selection of the Flickr8k dataset as well as the real and synthetic speaker data (all in the form of MFCCs) as a binary classification problem in order to discern the speaker from the Flickr speakers. Ranging from 2,500 to 10,000 synthetic data objects, the network weights are then transferred to the original dataset of only Flickr8k and the real speaker data, in order to discern whether useful rules can be learnt from the synthetic data. Results for all three subjects show that fine-tune learning from datasets augmented with synthetic speech improve the classification accuracy, F1 score, precision, and the recall when applied to the scarce real data vs non-speaker data. We conclude that even with just five spoken short sentences, data augmentation via synthetic speech data generated by a Char- RNN can improve the speaker classification process. Accuracy and related metrics are shown to improve from around 93% to 99% for three subjects classified from thousands of others when fine-tuning from exposure to 2500-1000 synthetic data points. High F1 scores, precision and recall also show that issues due to class imbalance are also solved.
Pathophysiology of periarticular bone changes in osteoarthritis (2016)

Under physiological conditions, the subchondral bone of diarthrodial joints such as the hip, knee, and phalanges forms an integrated biocomposite with the overlying calcified and hyaline articular cartilage that is optimally organized to transfer mechanical load. During the evolution of the osteoarthritic process both the periarticular bone and cartilage undergo marked changes in their structural and functional properties in response to adverse biomechanical and biological signals. These changes are mediated by bone cells that modify the architecture and properties of the bone through active cellular processes of modelling and remodelling. These same biomechanical and biological factors also affect chondrocytes in the cartilage matrix altering the composition and structure of the cartilage and further disrupting the homeostatic relationship between the cartilage and bone. This chapter reviews the structural alterations and cellular mechanisms involved in the pathogenesis of osteoarthritis bone pathology and discusses potential approaches for targeting bone remodelling to attenuate the progression of the osteoarthritic process.
Five-Year Survival Is Similar in Thyroid Cancer Patients with Distant Metastases Prepared for Radioactive Iodine Therapy with either Thyroid Hormone Withdrawal or Recombinant Human TSH (2011)

Preparation for RAI therapy using either THW or rhTSH stimulation was associated with similar 5-yr overall survival rates in patients with RAI avid thyroid cancer metastases to lung or bone.
On the Interplay between Strong Regularity and Graph Densification (2017)

In this paper we analyze the practical implications of Szemerédi's regularity lemma in the preservation of metric information contained in large graphs. To this end, we present a heuristic algorithm to find regular partitions. Our experiments show that this method is quite robust to the natural sparsification of proximity graphs. In addition, this robustness can be enforced by graph densification.
Characterization of MLKL-mediated Plasma Membrane Rupture in Necroptosis (2018)

Necroptosis is a programmed cell death pathway triggered by activation of receptor interacting protein kinase 3 (RIPK3), which phosphorylates and activates the mixed lineage kinase-like domain pseudokinase, MLKL, to rupture or permeabilize the plasma membrane. Necroptosis is an inflammatory pathway associated with multiple pathologies including autoimmunity, infectious and cardiovascular diseases, stroke, neurodegeneration, and cancer. Here, we describe protocols that can be used to characterize MLKL as the executioner of plasma membrane rupture in necroptosis. We visualize the process of necroptosis in cells using live-cell imaging with conventional and confocal fluorescence microscopy, and in fixed cells using electron microscopy, which together revealed the redistribution of MLKL from the cytosol to the plasma membrane prior to induction of large holes in the plasma membrane. We present in vitro nuclear magnetic resonance (NMR) analysis using lipids to identify putative modulators of MLKL-mediated necroptosis. Based on this method, we identified quantitative lipid-binding preferences and phosphatidyl-inositol phosphates (PIPs) as critical binders of MLKL that are required for plasma membrane targeting and permeabilization in necroptosis.
Purification and characterization of a calmodulin-sensitive adenylate cyclase from Bordetella pertussis (1985)

Bordetella pertussis, the bacterium responsible for whooping cough, releases a soluble, calmodulin-sensitive adenylate cyclase into its culture medium. B. pertussis mutants deficient in this enzyme are avirulent, indicating that the adenylate cyclase contributes to the pathogenesis of the disease. It has been proposed that B. pertussis adenylate cyclase may enter animal cells and increase intracellular adenosine cyclic 3',5'-phosphate (cAMP) levels. We have purified the enzyme extensively from culture medium using anion-exchange chromatography in the presence and absence of calmodulin and gel filtration chromatography. The enzyme was purified 1600-fold to a specific activity of 608 mumol of cAMP min-1 mg-1 and was free of islet activating protein. The molecular weight of the enzyme was 43 400 in the absence of calmodulin and 54 200 in the presence of calmodulin. The Km of the bacterial enzyme for adenosine 5'-triphosphate was 2.0 mM, whereas the Km of the calmodulin-sensitive adenylate cyclase from bovine brain was 0.07 mM. Although the enzyme was not purified to homogeneity, its turnover number of 27 000 min-1 is the highest documented for any adenylate cyclase preparation.
The Mode of Incorporation of Farnesyl Pyrophosphate into Verrucarol. Preliminary communication (1973)

Abstract In the course of the biosynthesis of verrucarol ( 3 ) from farnesyl pyrophosphate in Myrothecium roridum , strain S 1135, a hydride shift occurs from the central double bond of the precursor to C(2) of the product.