gebhart/patrepeval huggingface dataset:
Intrachromosomal amplification of chromosome 21 (iAMP21) may arise from a breakage–fusion–bridge cycle (2007)

Intrachromosomal amplification of chromosome 21 (iAMP21), involving amplification of the RUNX1 gene and duplication of chromosome 21, dup(21q), defines a new cytogenetic subgroup in B-lineage acute lymphoblastic leukemia (ALL) with a poor prognosis. Characterization of this abnormality has become vital to ensure that the most accurate detection method is used. We have previously defined common regions of amplification and deletion of chromosome 21 in these patients, although the level and extent of amplification within the amplicon was highly variable. This study, using interphase fluorescence in situ hybridization (FISH) with chromosome 21 locus specific probes, substantiated these findings in a large series of patients and confirmed that the amplicon always included RUNX1. Thus, FISH with probes directed to the RUNX1 gene remains the most reliable detection method. Metaphase FISH, supported by G- and multiple color chromosomal banding (mBAND) revealed the patient specific morphology and genetic profile of the dup(21q) chromosomes, as well as the complexity of the intrachromosomal changes giving rise to them. These findings suggested that iAMP21 had arisen from a breakage-fusion-bridge cycle: a mechanism previously described in tumors, which we report for the first time in ALL.
Print Media (1972)

Oscar Ogg, The 26 Letters (New York: Crowell, 1971—$7.50) Douglass McMurtrie with the assistance of John Adamson (eds) The Invention of Printing: A Bibliography (New York: Burt Franklin, 1970—price not known) Jim Allee Hart, Views on the News: The Developing Editorial Syndrome 1500-1800 (Carbondale: Southern Illinois University Press, 1970—$7.95) Louis M. Lyons, Newspaper Story: One Hundred Years of the Boston Globe (Cambridge: Harvard University Press, 1971—$9.95) Michael L. Johnson, The New Journalism: The Underground Press, the Artists of Nonfiction, and Changes in the Established Media (Lawrence: University Press of Kansas, 1971—$6.95/2.95)
ChemInform Abstract: Alkylation and Acylation of Phenylthio‐2,3‐dideoxyhex‐2‐enopyranosides at the Anomeric Centre by Polarity Inversion. (1987)

Abstract Substitution of the tri‐O‐acetyl‐D‐glucal (I) with thiophenol (II) produces the dideoxyenopyranosides (III).
Development of Novel Sugar Isomerases by Optimization of Active Sites in Phosphosugar Isomerases for Monosaccharides (2012)

Phosphosugar isomerases can catalyze the isomerization of not only phosphosugar but also of monosaccharides, suggesting that the phosphosugar isomerases can be used as sugar isomerases that do not exist in nature. Determination of active-site residues of phosphosugar isomerases, including ribose-5-phosphate isomerase from Clostridium difficile (CDRPI), mannose-6-phosphate isomerase from Bacillus subtilis (BSMPI), and glucose-6-phosphate isomerase from Pyrococcus furiosus (PFGPI), was accomplished by docking of monosaccharides onto the structure models of the isomerases. The determinant residues, including Arg133 of CDRPI, Arg192 of BSMPI, and Thr85 of PFGPI, were subjected to alanine substitutions and found to act as phosphate-binding sites. R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI displayed the highest catalytic efficiencies for monosaccharides at each position. These residues exhibited 1.8-, 3.5-, and 4.9-fold higher catalytic efficiencies, respectively, for the monosaccharides than the wild-type enzyme. However, the activities of these 3 variant enzymes for phosphosugars as the original substrates disappeared. Thus, R133D of CDRPI, R192 of BSMPI, and T85Q of PFGPI are no longer phosphosugar isomerases; instead, they are changed to a d-ribose isomerase, an l-ribose isomerase, and an l-talose isomerase, respectively. In this study, we used substrate-tailored optimization to develop novel sugar isomerases which are not found in nature based on phosphosugar isomerases.
Early Weight Gain Predicts Retinopathy in Preterm Infants: New, Simple, Efficient Approach to Screening (2009)

The weight, insulin-like growth factor, neonatal retinopathy of prematurity algorithm detected early 100% of infants who developed retinopathy of prematurity requiring treatment and correctly predicted the majority who did not require treatment. With this simple postnatal evaluation, costly stressful eye examinations can be markedly reduced (approximately 75% of infants). In addition, early identification of children at risk may lead to the initiation of interventions and possibly prevent sight-threatening retinopathy of prematurity.
Preparation of Biodiesel by Transesterification of Rapeseed Oil with Methanol Using Solid Base Catalyst Calcined K2CO3/γ‐Al2O3 (2010)

Abstract We report here the preparation of biodiesel by transesterification of rapeseed oil with methanol using calcined K 2 CO 3 /γ‐Al 2 O 3 as a solid base catalyst. The prepared catalysts were characterized using SEM, IR and BET, and their catalytic activities were evaluated. The reaction conditions were optimized, and in particular, the conversion can be as high as 98.62% under the optimal reaction conditions. In addition, the effect of the presence of water in the reaction system on the catalytic activity was also studied.
Analysis of balanced active doubler for broad-band operation - the frequency-tuning concept (2002)

A comprehensive analysis of an active balanced frequency doubler is described and proposed as a new concept: tuning the center frequency at which the doubler exhibits its highest performance to extend the usable bandwidth of the device. The concept is validated using a fabricated V-band pseudomorphic high electron-mobility transistor frequency doubler. For this device, a substantial improvement in the usable bandwidth (more than double) is achieved, demonstrating that the proposed concept is particularly suitable for the realization of high spectral purity and widely tunable V-band frequency sources.
Early Versus Late Allogeneic Hematopoietic Cell Transplantation in Patients with AML - Results From the Randomized AML 2003 Trial (2013)

The optimal timing of hematopoietic cell transplantation (HCT) in AML is still under debate. We addressed this question in the AML 2003 study, a large, multicenter, open-label, randomized study of the German SAL group. All patients received one cycle of induction therapy (IT). Upfront molecular characterization, HLA typing and donor search were performed. The transplant strategy was tailored to AML risk and to donor availability. Patients aged 18-60 years were randomly assigned upfront 1:1 to either one of two transplant strategies: In the control arm HLA-identical sibling HCT was scheduled in first complete remission for patients with intermediate cytogenetic risk AML and related or unrelated compatible HCT for patients with a complex karyotype (CK). In the experimental arm the indication for allogeneic HCT was extended to patients with an FLT3-ITD allelic ratio >0.8 (mutant/wild type), >10% marrow blasts on day 15 after IT1 and patients with adverse karyotypes, including: -7, -5, del(5q), inv(3q), t(3;3), t(6;9), t(6;11), t(11;19) (q23;p13.1). Furthermore, HCT was scheduled earlier, i.e. in aplasia after the first or the second cycle of IT. Between December 1st, 2003 and November 26th, 2009 1179 patients were assigned randomly either to the experimental (N=598) or the control intervention (N=581). The median age was 48 years (range, 18 to 60 years) and the median observation time now is 52 months. In the intent-to-treat analysis the hazard ratio of the treatment effect (experimental versus control) was 0.92 (95% CI, 0.75 to 1.14; P = .45) for the primary endpoint overall survival (OS) and 0.85 (95% CI, 0.71 to 1.02; P = .08) for the secondary endpoint event-free survival (EFS). However, the rate of patients who received allogeneic HCT as first post-remission therapy was only 39% in the experimental arm and 20% in the control arm. Thus, the analysis according to the intent-to-treat could not discriminate appropriately between the two treatment strategies. In an exploratory analysis, we therefore analyzed the effect of allogeneic HCT as a time-dependent covariate in a Cox-regression model. We adjusted for the cytogenetic risk, age, ECOG performance status, white blood cell count, and LDH at diagnosis. In this as-treated analysis the adjusted hazard ratio for the treatment (allogeneic HCT versus chemotherapy) was 0.73 (95% CI, 0.59 - 0.89; P = .002) for OS and 0.67 (95% CI, 0.55 - 0.82; P < .001) for EFS. This analysis corrects appropriately for a classical time-selections bias. However, a patient selection based on comorbidity or fitness cannot be ruled out. In conclusion, a survival benefit from early compared to late allogeneic HCT could not be shown in the intent-to-treat analysis of this large randomized trial using a risk-adapted transplant strategy. However, the results of the as-treated analysis suggest a substantial benefit from allogeneic HCT in first remission versus chemotherapy.
Determinants of Price Differentials in Oklahoma Value-Added Feeder Cattle Auctions (2012)

Many value-added practices cannot be observed by feeder cattle buyers. Third-party verification can decrease market inefficiency associated with this asymmetric information. We evaluate the effectiveness of a verification program, the Oklahoma Quality Beef Network, in increasing received prices. We estimate the value of verification, weaning, vaccinating, certification and phenotypic traits of feeder cattle at Oklahoma auctions. Results indicate that the OQBN program adds $2.39 to $5.74/cwt. Vaccinating calves adds $1.44/cwt, and weaning calves adds $2.05/cwt. Differential values for lot size, average weight, hide color, frame size, conditioning, Brahman influence, gender and other characteristics are also reported.
Temperature-Induced Activation of Graphite Co-intercalation Reactions for Glymes and Crown Ethers in Sodium-Ion Batteries (2018)

The intercalation of solvated ions into graphite leads to ternary graphite intercalation compounds (t-GICs). Here, we study the impact of temperature on the electrochemical activity of graphite electrodes for co-intercalation reactions between 20 and 80 °C in sodium cells. For this, a range of linear ethers (mono-, di-, tri-, and tetraglyme) are studied. For the first time, pentaglyme and several crown ethers are also investigated. We find that several solvents that appear as unsuitable for the co-intercalation reaction at room temperature provide higher capacities at elevated temperatures. The most evident example is pentaglyme. While poor performance is found at room temperature for this solvent (20 mAhg−1 and large polarization), almost complete utilization (∼110 mAh g−1) and excellent rate capability are obtained at 45 °C. We find that the reactions involving mono-, di-, tetra-, and (at elevated temperatures also) pentaglyme are thermodynamically controlled, whereas the reaction with triglyme is kinetically limited. We also find that the crown ether 18c6 can be used as an electrolyte solvent above its melting point, which, for the first time, demonstrates the synthesis of t-GICs with crown ethers by electrochemical methods. Additionally, parasitic reactions are found to appear at elevated temperatures. Overall, we demonstrate that new co-intercalation reactions can be activated by temperature. The chemistry of these compounds might therefore be much richer than previously thought.
Congestion avoidance in large supra-high-speed packet switching networks using neural arbiters (2002)

The authors propose artificial neural network (ANN) based arbitration for fast and intelligent processing of transit packets and assigning network access to the local packets in large supra-high-speed packet switched telecommunication networks. Use is made of: (i) S. Grossberg's (Ed., Neural Networks and Natural Intelligence, MIT press, Cambridge, MA, USA, 1989) adaptive resonance theory based neural network, a two-layer ANN along with a fuzzy logic based preprocessor to maintain distributed cut-through links between the communicating users; and (ii) a buffer stealer (another ANN based arbiter) to throttle local source access to the network during heavy load conditions. With the incorporation of these additional complexities at the nodal structure, it is possible to most efficiently utilize the available network resources under all possible, i.e., both certain and uncertain, operating conditions. The proposed techniques are applied in a 4*4 Manhattan street network. The main objective is to avoid network layer level congestion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
THE INSULIN/IGF-1 SIGNALING PATHWAY IN HEALTHY AGING (2018)

Since the discovery of the first genes to regulate aging three decades ago, it has been clear that the insulin/IGF-1 (Insulin-like Growth Factor 1) signaling pathway can regulate lifespan. Since then, studies in organisms including C. elegans and mice have found that many dietary, genetic, and pharmaceutical interventions that reduce signaling downstream of insulin/IGF-1 promote longevity and healthspans. However, the molecular and physiological mechanisms which mediate these effects have proven elusive. In this session, we will discuss new findings regarding the sensing of nutrients and the regulation of healthspan and longevity downstream of insulin/IGF-1 signaling, concentrating on the mTOR (mechanistic Target Of Rapamycin) protein kinase and the FOXO (Forkhead box O) family of transcription factors. Topics will include: 1) the molecular mechanisms by which mTOR complex 1 (mTORC1) signaling is regulated by amino acids; 2) how storage of glucose as trehalose can extend longevity via a FOXO-dependent mechanism; 3) the hithero unappreciated role of mTOR complex 2 (mTORC2) in longevity and healthspan; and 4) the role of FOXO transcription factors in maintaining healthy stem cells.
Theoretical and Experimental Studies of Ethanol Decomposition and Electrooxidation over Pt-Modified Tungsten Carbide (2014)

Density functional theory (DFT) calculations, surface science experiments, and electrochemical measurements were performed to investigate tungsten monocarbide (WC) and Pt-modified WC for ethanol electrooxidation. DFT was used to calculate the binding energies of ethanol and potential reaction intermediates on model surfaces. Temperature programmed desorption (TPD) experiments were performed under ultrahigh vacuum (UHV) conditions to determine the decomposition pathways of ethanol on WC and Pt-modified WC surfaces. On WC the major pathway was C-O scission to produce ethylene, while on Pt/WC the preferred pathway was the C-C bond cleavage. High-resolution electron energy-loss spectroscopy (HREELS) was used to further understand the bond-breaking sequence of ethanol on WC and Pt/WC surfaces. Furthermore, electrochemical half-cell measurements were performed for Pt/WC in acidic electrolytes containing ethanol. Pt/WC was shown to be active for the electrooxidation of ethanol using both cyclic voltammetry (CV) and chronoamperometry (CA). In-situ infrared spectroscopy was also employed to demonstrate that Pt/WC was more effective than Pt for the total oxidation of ethanol to CO2.
Immunoglobulin light chain gene rearrangements in precursor-B-acute lymphoblastic leukemia: characteristics and applicability for the detection of minimal residual disease. (2006)

We analyzed the frequency and characteristics of Vk-Jk and Vlambda-Jlambda rearrangements inpatients with precursor-B-acute lymphoblastic leukemia (ALL) and evaluated the applicability of these rearrangements as targets for minimal residual disease (MRD) detection. Using the BIOMED-2 primer sets, Vk-Jk and Vlambda-Jlambda rearrangements were detected in 30% and 17% of patients, respectively. Vk-Jk rearrangements were particularly frequent in common-ALL, children between 5-10 years, and TEL-AML1-positive patients. Vk-Jk and Vlambda-Jlambda rearrangements showed a good stability between diagnosis and relapse and reached good sensitivities in real-time quantitative polymerase chain reaction analysis. Our data show that Vk-Jk and Vlambda-Jlambda rearrangements can be successfully applied for MRD detection in a subset of patients with precursor-B-ALL.
NeST: A Neural Network Synthesis Tool Based on a Grow-and-Prune Paradigm (2019)

Deep neural networks (DNNs) have begun to have a pervasive impact on various applications of machine learning. However, the problem of finding an optimal DNN architecture for large applications is challenging. Common approaches go for deeper and larger DNN architectures but may incur substantial redundancy. To address these problems, we introduce a network growth algorithm that complements network pruning to learn both weights and compact DNN architectures during training. We propose a DNN synthesis tool (NeST) that combines both methods to automate the generation of compact and accurate DNNs. NeST starts with a randomly initialized sparse network called the seed architecture. It iteratively tunes the architecture with gradient-based growth and magnitude-based pruning of neurons and connections. Our experimental results show that NeST yields accurate, yet very compact DNNs, with a wide range of seed architecture selection. For the LeNet-300-100 (LeNet-5) architecture, we reduce network parameters by 70.2× (74.3×) and floating-point operations (FLOPs) by 79.4× (43.7×). For the AlexNet, VGG-16, and ResNet-50 architectures, we reduce network parameters (FLOPs) by 15.7× (4.6×), 33.2× (8.9×), and 4.1× (2.1×) respectively. NeST's grow-and-prune paradigm delivers significant additional parameter and FLOPs reduction relative to pruning-only methods.
figure S2 from Visualization of Breast Cancer Metabolism Using Multimodal Nonlinear Optical Microscopy of Cellular Lipids and Redox State (2023)

&lt;p&gt;Figure S2 contains extra experiments to prove that deuterium labeling can work in tracking lipid biosynthesis.&lt;/p&gt;
Binary information propagation in circular magnetic nanodot arrays using strain induced magnetic anisotropy (2016)

Nanomagnetic logic has emerged as a potential replacement for traditional Complementary Metal Oxide Semiconductor (CMOS) based logic because of superior energy-efficiency (Salahuddin and Datta 2007 Appl. Phys. Lett. 90 093503, Cowburn and Welland 2000 Science 287 1466-68). One implementation of nanomagnetic logic employs shape-anisotropic (e.g. elliptical) ferromagnets (with two stable magnetization orientations) as binary switches that rely on dipole-dipole interaction to communicate binary information (Cowburn and Welland 2000 Science 287 1466-8, Csaba et al 2002 IEEE Trans. Nanotechnol. 1 209-13, Carlton et al 2008 Nano Lett. 8 4173-8, Atulasimha and Bandyopadhyay 2010 Appl. Phys. Lett. 97 173105, Roy et al 2011 Appl. Phys. Lett. 99 063108, Fashami et al 2011 Nanotechnology 22 155201, Tiercelin et al 2011 Appl. Phys. Lett. 99 , Alam et al 2010 IEEE Trans. Nanotechnol. 9 348-51 and Bhowmik et al 2013 Nat. Nanotechnol. 9 59-63). Normally, circular nanomagnets are incompatible with this approach since they lack distinct stable in-plane magnetization orientations to encode bits. However, circular magnetoelastic nanomagnets can be made bi-stable with a voltage induced anisotropic strain, which provides two significant advantages for nanomagnetic logic applications. First, the shape-anisotropy energy barrier is eliminated which reduces the amount of energy required to reorient the magnetization. Second, the in-plane size can be reduced (∼20 nm) which was previously not possible due to thermal stability issues. In circular magnetoelastic nanomagnets, a voltage induced strain stabilizes the magnetization even at this size overcoming the thermal stability issue. In this paper, we analytically demonstrate the feasibility of a binary 'logic wire' implemented with an array of circular nanomagnets that are clocked with voltage-induced strain applied by an underlying piezoelectric substrate. This leads to an energy-efficient logic paradigm orders of magnitude superior to existing CMOS-based logic that is scalable to dimensions substantially smaller than those for existing nanomagnetic logic approaches. The analytical approach is validated with experimental measurements conducted on dipole coupled Nickel (Ni) nanodots fabricated on a PMN-PT (Lead Magnesium Niobate-Lead Titanate) sample.
Synthesis of a Prodrug Designed To Release Multiple Inhibitors of the Epidermal Growth Factor Receptor Tyrosine Kinase and an Alkylating Agent:  A Novel Tumor Targeting Concept (2003)

The synthesis of a novel acetoxymethyltriazene designed to be a prodrug of multiple inhibitors of the epidermal growth factor receptor (EGFR) and a methyldiazonium species is described. Studies with each of the expected metabolites demonstrated significant EGFR tyrosine kinase inhibitory activities and the released methyldiazonium was trapped with p-nitrobenzylpyridine. Their ability to damage genomic DNA in whole cells was demonstrated by using the single cell microelectrophoresis (comet) assay. The results suggest that this approach may well represent a novel drug combination strategy involving single molecules masking multiple bioactive agents.
Structural analysis of online handwritten mathematical symbols based on support vector machines (2013)

Mathematical expression recognition is still a very challenging task for the research community mainly because of the two-dimensional (2d) structure of mathematical expressions (MEs). In this paper, we present a novel approach for the structural analysis between two on-line handwritten mathematical symbols of a ME, based on spatial features of the symbols. We introduce six features to represent the spatial affinity of the symbols and compare two multi-class classification methods that employ support vector machines (SVMs): one based on the “one-against-one” technique and one based on the “one-against-all”, in identifying the relation between a pair of symbols (i.e. subscript, numerator, etc). A dataset containing 1906 spatial relations derived from the Competition on Recognition of Online Handwritten Mathematical Expressions (CROHME) 2012 training dataset is constructed to evaluate the classifiers and compare them with the rule-based classifier of the ILSP-1 system participated in the contest. The experimental results give an overall mean error rate of 2.61% for the “one-against-one” SVM approach, 6.57% for the “one-against-all” SVM technique and 12.31% error rate for the ILSP-1 classifier.
Deep Learning in Medical Ultrasound Analysis: A Review (2019)

Ultrasound (US) has become one of the most commonly performed imaging modalities in clinical practice. It is a rapidly evolving technology with certain advantages and with unique challenges that include low imaging quality and high variability. From the perspective of image analysis, it is essential to develop advanced automatic US image analysis methods to assist in US diagnosis and/or to make such assessment more objective and accurate. Deep learning has recently emerged as the leading machine learning tool in various research fields, and especially in general imaging analysis and computer vision. Deep learning also shows huge potential for various automatic US image analysis tasks. This review first briefly introduces several popular deep learning architectures, and then summarizes and thoroughly discusses their applications in various specific tasks in US image analysis, such as classification, detection, and segmentation. Finally, the open challenges and potential trends of the future application of deep learning in medical US image analysis are discussed. Keywords: Deep learning, Medical ultrasound analysis, Classification, Segmentation, Detection