gebhart/patrepeval huggingface dataset:
DOWN'S Syndrome Acute Lymphoblastic LEUKEMIA: A HIGHLY Heterogeneous DISEASE DRIVEN by an Aberrant CRLF2/JAK2 Cooperation – A REPORT FROM the Ibfm-STUDY GROUP. (2009)

Abstract Abstract 11 Children with Down's Syndrome (DS) have an increased risk for acute lymphoblastic leukemia (ALL). We have previously identified somatic mutations in R683 of JAK2 in 20% of DS-ALLs (Bercovich et al, Lancet 2008;372:1484). However the cooperating cytokine receptor and other molecular features have been obscured. Here we report that gene expression analysis reveals that DS-ALL is a highly heterogeneous disease not definable as unique ALL subtype. However, 62% (33 of 53) of the DS-ALL samples analyzed were characterized by aberrant expression of the type I cytokine receptor CRLF2 caused by two types of genomic aberrations. CRLF2 encodes one chain of the heterodimeric receptor of the TSLP cytokine involved in inflammation and lymphoid development and has been recently reported to be involved in translocations to the IgH locus or micro-deletions in 3% of ALLs in children without DS. We have confirmed its cell surface expression on primary DS-ALL cells by Flow cytometry analysis. Consisting with a possible role of CRLF2 as a cytokine receptor, all specimens with the R683 mutated JAK2 had high CRLF2 expression. We further show that CRLF2 and R683 mutated JAK2 cooperate in conferring cytokine independent growth of pro-B cells. Furthermore in 3 of 23 DS-ALL patients with wt. JAK2 we identified a novel activating somatic mutation in CRLF2 replacing the juxta-membrane F232 with Cystein. Mutated CRLF2 but not wild type CRLF2 conferred cytokine independent growth of BaF3 cells associated with phosphorylation of STAT5. Aberrant expression of CRLF2 was also associated with a younger age at diagnosis and worse prognosis. Intriguingly, bioinformatic analysis revealed that gene expression of DS-ALLs is enriched with DNA damage and BCL6 responsive genes suggesting the possibility that DS is associated with B-cell lymphocytic genomic instability leading to the genomic aberrations activating CRLF2. Thus DS confers increased risk for genetically highly diverse ALLs with frequent somatic anomaly in CRLF2, whose higher expression further selects for the activating mutations in itself or in JAK2 (figure). Our data also suggests that the majority of DS children with ALL may benefit from therapy blocking the CRLF2/JAK2 pathway. Disclosures: No relevant conflicts of interest to declare.
Search for pair production of first-generation scalar leptoquarks at s=13  TeV (2019)

A search for the pair production of first-generation scalar leptoquarks is performed using proton-proton collision data recorded at 13 TeV center-of-mass energy with the CMS detector at the LHC. The data correspond to an integrated luminosity of 35.9 fb -1 . The leptoquarks are assumed to decay promptly to a quark and either an electron or a neutrino, with branching fractions and 1 -, respectively. The search targets the decay final states comprising two electrons, or one electron and large missing transverse momentum, along with two quarks that are detected as hadronic jets. First-generation scalar leptoquarks with masses below 1435 (1270) GeV are excluded for 1.00.5. These are the most stringent limits on the mass of first-generation scalar leptoquarks to date. The data are also interpreted to set exclusion limits in the context of an R-parity violating supersymmetric model, predicting promptly decaying top squarks with a similar dielectron final state.
Transmodulation of Epidermal Growth Factor Receptor Function by Cyclic AMP-dependent Protein Kinase (1999)

Binding of epidermal growth factor (EGF) to its receptor (EGFR) augments the tyrosine kinase activity of the receptor and autophosphorylation. Exposure of some tissues and cells to EGF also stimulates adenylyl cyclase activity and results in an increase in cyclic AMP (cAMP) levels. Because cAMP activates the cAMP-dependent protein kinase A (PKA), we investigated the effect of PKA on the EGFR. The purified catalytic subunit of PKA (PKAc) stoichiometrically phosphorylated the purified full-length wild type (WT) and kinase negative (K721M) forms of the EGFR. PKAc phosphorylated both WT-EGFR as well as a mutant truncated form of EGFR (Delta1022-1186) exclusively on serine residues. Moreover, PKAc also phosphorylated the cytosolic domain of the EGFR (EGFRKD). Phosphorylation of the purified WT as well as EGFRDelta1022-1186 and EGFRKD was accompanied by decreased autophosphorylation and diminished tyrosine kinase activity. Pretreatment of REF-52 cells with the nonhydrolyzable cAMP analog, 8-(4-chlorophenylthio)-cAMP, decreased EGF-induced tyrosine phosphorylation of cellular proteins as well as activation of the WT-EGFR. Similar effects were also observed in B82L cells transfected to express the Delta1022-1186 form of EGFR. Furthermore, activation of PKAc in intact cells resulted in serine phosphorylation of the EGFR. The decreased phosphorylation of cellular proteins and diminished activation of the EGFR in cells treated with the cAMP analog was not the result of altered binding of EGF to its receptors or changes in receptor internalization. Therefore, we conclude that PKA phosphorylates the EGFR on Ser residues and decreases its tyrosine kinase activity and signal transduction both in vitro and in vivo.
Bidirectional converter interface for a battery energy storage test bench (2011)

This paper presents the bidirectional converter interface for a 6 kV battery energy storage test bench. The power electronic interface consists a two stage converter topology having a low voltage dc-ac grid connected converter and a new dual active bridge dc-dc converter with high transformation ratio. The dc-dc converter controls the battery charge/discharge current while the grid converter controls the common dc-link voltage and the grid current. The applied control structures and the hardware implementation of both converters are presented, together with their interaction. Experimental results of the test bench show good performance for the bidirectional power flow with a maximum operating power of 100 kW.
The effect of prolonged ischemia upon regional energy reserves in the experimental glioblastoma. (1967)

Changes in levels of known anaerobic energy reserves [glucose, glycogen, adenosine triphosphate (ATP), and phosphocreatine and lactic acid] have been determined in microgram quantities of three different but homogeneous cytologic zones of the experimental glioblastoma during prolonged ischemic incubation. Normal murine white matter was studied under identical conditions. Lightly anesthetized white matter, once rendered ischemic, rapidly cleaves glucose and glycogen to form lactate in quantities expected from anaerobic hexose degradation, and in addition rapidly exhausts endogeneous ATP and phosphocreatine reserves. Peripherally situated cells of the ischemic experimental glioblastoma produce lactate in significant excess to that expected from measured hexose degradation, and in addition maintain low but readily measurable levels of ATP despite prolonged incubation. The rate of expenditure of energy reserves (metabolic rate) is several fold greater at the tumor periphery in comparison to the tumor core. Observations made at the microchemical level provide experimental confirmation for certain theoretic models which have been formulated to explain the observed growth rates of transplanted experimental tumors.
Structural and functional consequences of the presence of a fourth disulfide bridge in the scorpion short toxins: Solution structure of the potassium channel inhibitor HsTX1 (1999)

We have determined the three-dimensional structure of the potassium channel inhibitor HsTX1, using nuclear magnetic resonance and molecular modeling. This protein belongs to the scorpion short toxin family, which essentially contains potassium channel blockers of 29 to 39 amino acids and three disulfide bridges. It is highly active on voltage-gated Kv1.3 potassium channels. Furthermore, it has the particularity to possess a fourth disulfide bridge. We show that HsTX1 has a fold similar to that of the three-disulfide-bridged toxins and conserves the hydrophobic core found in the scorpion short toxins. Thus, the fourth bridge has no influence on the global conformation of HsTX1. Most residues spatially analogous to those interacting with voltage-gated potassium channels in the three-disulfide-bridged toxins are conserved in HsTX1. Thus, we propose that Tyr21, Lys23, Met25, and Asn26 are involved in the biological activity of HsTX1. As an additional positively charged residue is always spatially close to the aromatic residue in toxins blocking the voltage-gated potassium channels, and as previous mutagenesis experiments have shown the critical role played by the C-terminus in HsTX1, we suggest that Arg33 is also important for the activity of the four disulfide-bridged toxin. Docking calculations confirm that, if Lys23 and Met25 interact with the GYGDMH motif of Kv1.3, Arg33 can contact Asp386 and, thus, play the role of the additional positively charged residue of the toxin functional site. This original configuration of the binding site of HsTX1 for Kv1.3, if confirmed experimentally, offers new structural possibilities for the construction of a molecule blocking the voltage-gated potassium channels.
Effects of thermal processing and pulp filtration on physical, chemical and sensory properties of winter melon juice (2016)

The low sugar/low acid LPNB juice with 'fresh' flavor could be developed to replace water for reconstituting FCOJ with enhanced nutritional value. © 2016 Society of Chemical Industry.
Fast likelihood computation techniques in nearest-neighbor based search for continuous speech recognition (2001)

This paper describes two effective algorithms that reduce the computational complexity of state likelihood computation in mixture-based Gaussian speech recognition systems. We consider a baseline recognition system that uses nearest-neighbor search and partial distance elimination (PDE) to compute state likelihoods. The first algorithm exploits the high dependence exhibited among subsequent feature vectors to predict the best scoring mixture for each state. The method, termed best mixture prediction (BMP), leads to further speed improvement in the PDE technique. The second technique, termed feature component reordering (FCR), takes advantage of the variable contribution levels made to the final distortion score for each dimension of the feature and mean space vectors. The combination of two techniques with PDE reduces the computational time for likelihood computation by 29.8% over baseline likelihood computation. The algorithms are shown to yield the same accuracy level without further memory requirements for the November 1992 ARPA Wall Street Journal (WSJ) task.
Speech recognition in nonstationary noise based on parallel HMMs and spectral subtraction (1996)

Abstract This paper proposes a method of speech recognition in a nonstationary noisy environment, combining the parallel HMMs and the spectral subtraction. In the proposed method, a set of hypothesis is generated with respect to the combination of the speech and the noise that can produce the observed data by a series of subtraction processes. Using HMMs prepared separately for the speech and the noise, the probabilities of occurrence are calculated. The 100‐word recognition in the noisy environment in an ordinary car running in an urban area, is defined as the task in the experiment. Comparative experiments, are made for the proposed method, the ordinary spectral subtraction method and other parallel HMM methods. Then, the effectiveness of the proposed method is verified.
Supplementary Figure 2 from Oncolytic Vaccinia Virus Disrupts Tumor-Associated Vasculature in Humans (2023)

&lt;p&gt;Supplementary Figure 2 PDF file - 144K, Bevacizumab reduces TK1 levels &amp; blocks VEGF-mediated JX-594 sensitization in HUVECs, demonstrated by decreased transgene expression (GFP) and decreased burst size&lt;/p&gt;
Coded excitation ultrasound: Efficient implementation via frequency domain processing (2016)

Modern imaging systems use single-carrier short pulses for transducer excitation. The usage of coded signals allowing for pulse compression is known to improve signal-to-noise ratio (SNR), for example in radar and communication. One of the main challenges in applying coded excitation (CE) to medical imaging is frequency dependent attenuation in biological tissues. Previous work overcame this challenge and verified significant improvement in SNR and imaging depth by using an array of transducer elements and applying pulse compression at each element. However, this approach results in a large computational load. A common way of reducing the cost is to apply pulse compression after beamforming, which reduces image quality. In this work we propose a high-quality low cost method for CE imaging by integrating pulse compression into the recently developed frequency domain beamforming framework. This approach yields a 26-fold reduction in computational complexity without compromising image quality. This reduction enables efficient implementation of CE in array imaging paving the way to enhanced SNR, improved imaging depth and higher frame-rate.
Synthesis and structure of bifunctional N-alkylbenzimidazole phenylboronate derivatives (2006)

N-Methyl and N-n-butyl-2-(2-boronophenyl)benzimidazoles are accessed from the corresponding mono-N-alkyl-ortho-phenylenediamines, either using a polyphosphoric acid-mediated cyclisation with ortho-bromobenzoic acid, or preferably using an Oxone-mediated cyclisation of the corresponding aldehyde, followed by a lithium-exchange and borylation sequence. The resulting boronic acids show unusual physical and chemical properties, as shown by 11B NMR and X-ray crystallography.
Neutrophil-to-lymphocyte Ratio is a Predictive Marker for Invasive Malignancy in Intraductal Papillary Mucinous Neoplasms of the Pancreas (2016)

NLR is an independent predictive marker for the presence of IPMN-associated invasive carcinoma. Further prospective studies are needed to assess the predictive ability of NLR and how it can be applied in the clinical setting.
Surface Activated Bonding between Au layer and vertically aligned Multi-Wall Carbon Nanotubes (2010)

In this research, vertically aligned Muti-Walled Carbon Nanotubes (CNTs) and Au-layer were bonded by Surface Activated Bonding method. Vertically aligned CNTs were grown by acetylene-CVD with Fe catalyst and were formed bump shape with 200 μm diameter and around 200 μm height. These CNT bumps and Au layer were cleaned and activated by Argon Fast Atom Beam (Ar-FAB) process and bonded with some load. As a result, MWNTs-Au bonding was succeeded on condition that CNT bumps and Au layer were Ar-FAB processed longer than 300 sec, and bonding pressure was larger than 0.17 MPa, and the average resistance of CNT was 130 kΩ. Furthermore, when the bonding pressure was 0.7 MPa, the average resistance of one was 16 Ω.
Detection of hypovolemia using short-time Fourier transform analysis of S1 heart sounds (2002)

We present preliminary findings from applying the short-time spectral analysis to intra-operatively recorded heart sound signals. The goal is to detect hypovolemia as revealed by changes in the S1 and S4 heart sound. We present a statistic based on the temporal distribution of energy bursts as a candidate classification feature.
Site-Specific Incorporation of Fluorotyrosines into Proteins in Escherichia coli by Photochemical Disguise (2010)

Fluorinated analogues of tyrosine can be used to manipulate the electronic environments of protein active sites. The ability to selectively mutate tyrosine residues to fluorotyrosines is limited, however, and can currently only be achieved through the total synthesis of proteins. As a general solution to this problem, we genetically encoded the unnatural amino acids o-nitrobenzyl-2-fluorotyrosine, -3-fluorotyrosine, and -2,6-difluorotyrosine in Escherichia coli. These amino acids are disguised from recognition by the endogenous protein biosynthetic machinery, effectively preventing global incorporation of fluorotyrosine into proteins.
A global perspective on acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF): results from an international survey (2018)

<b>Background:</b> AE-IPF is a deadly complication of IPF, for which no international guidelines exist, resulting in global variability in prevention, diagnosis and treatment strategies. <b>Methods:</b> Pulmonologists with ILD expertise were invited to participate in a survey designed by an international expert panel. <b>Results:</b> 469 pulmonologists responded (66 countries, 64% experts). Significant geographical variability in approach to managing AE-IPF was found (figure). Common preventive measures include antifibrotics and antacids. Diagnostic differences are most pronounced regarding use of KL-6 and viral testing, while HRCT, BNP and d-dimer are broadly used. High dose steroids are widely administered (92%), but use of immunosuppressant and other strategies is highly variable (fig). Very few (4%) responders never use immunosuppression. Antifibrotics are initiated during AE-IPF by 66%. Invasive ventilation or ECMO are mainly used as a bridge to transplantation. Most physicians educate patients comprehensively on the severity of AE-IPF (82%) and consider palliative care (63%). <b>Conclusion:</b> International approaches to the prevention, diagnosis and treatment of AE-IPF are diverse. Global international guidelines and trials to evaluate these approaches are needed.
Electron Collection in Host–Guest Nanostructured Hematite Photoanodes for Water Splitting: The Influence of Scaffold Doping Density (2015)

Nanostructuring has proven to be a successful strategy in overcoming the trade-off between light absorption and hole transport to the solid/electrolyte interface in hematite photoanodes for water splitting. The suggestion that poor electron (majority carrier) collection hinders the performance of nanostructured hematite electrodes has led to the emergence of host-guest architectures in which the absorber layer is deposited onto a transparent high-surface-area electron collector. To date, however, state of the art nanostructured hematite electrodes still outperform their host-guest counterparts, and a quantitative evaluation of the benefits of the host-guest architecture is still lacking. In this paper, we examine the impact of host-guest architectures by comparing nanostructured tin-doped hematite electrodes with hematite nanoparticle layers coated onto two types of conducting macroporous SnO2 scaffolds. Analysis of the external quantum efficiency spectra for substrate (SI) and electrolyte side (EI) illumination reveals that the electron diffusion length in the host-guest electrodes based on an undoped SnO2 scaffold is increased substantially relative to the nanostructured hematite electrode without a supporting scaffold. Nevertheless, electron collection is still incomplete for EI illumination. By contrast, an electron collection efficiency of 100% is achieved by fabricating the scaffold using antimony-doped SnO2, showing that the scaffold conductivity is crucial for the device performance.
Supplementary Figure 3 from Skin-Test Infiltrating Lymphocytes Early Predict Clinical Outcome of Dendritic Cell–Based Vaccination in Metastatic Melanoma (2023)

&lt;p&gt;PDF file - 71K, KLH-specific T cell responses according to SKIL classification: Regardless of the number of epitopes or the increasingly stringent criteria for TAA-specific immune responses; the levels of KLH-specific T cell responses were similar and highly variable between individuals. One-way ANOVA was used for comparison of KLH-specific T cell responses in groups of patients with increasing breadth of TAA-specific CD8+ T cell responses. Student t-test was used for comparison of KLH-specific T cell responses in groups of patients as defined by different SKIL criteria&lt;/p&gt;
Abstract 11295: Sonoreperfusion Therapy for Microvascular Obstruction Using Microbubbles and Low Dose tPa (2014)

Background: Despite successful epicardial recanalization in acute myocardial infarction, adequate microvascular perfusion often fails due to embolization of thrombotic debris causing microvascular obstruction (MVO). We previously reported that long tone burst high mechanical index ultrasound (US) + microbubbles (MB) restored microvascular perfusion (sonoreperfusion, SRP) in an in vitro flow model using PBS perfusate. We sought to demonstrate SRP efficacy in whole blood perfusate with and without low dose tPa. Methods: The model comprised a 4 mm diameter phantom vessel with a 40 μm pore mesh to simulate a microvascular cross section and upstream pressure reflecting thrombus burden. Bovine whole blood and 2x10 6 /ml lipid MB (~3 μm) infused at 0.75 ml/min simulated microvascular flow. Bovine blood microthrombi were injected onto the mesh until upstream pressure was 30 mmHg. US was delivered for 20 min (1 MHz, 1.5 MPa peak negative pressure, 3 sec pulse interval, 1000-5000 cycles) with and without low dose tPa (2.5 μg/ml) during measurement of upstream pressure to assess SRP efficacy (n = 3-7). Lytic rate (rate of pressure drop in the first 4 min) and lytic index (1/area under pressure-time curve) quantified SRP efficacy. Results: In whole blood, lytic rate was 2.6 ± 1.5 mmHg/min at 1000 cycles US+MB increasing to 7.3 ± 3.2 mmHg/min at 5000 cycles US+MB (p&lt;0.01) without tPa. The lytic index was similar for tPa only (2.0 ± 0.5) x 10 -3 mmHg -1 .min -1 and 5000 cycles US + MB without tPa (2.3 ± 0.5) x 10 -3 mmHg -1 .min -1 (p=0.5) but increased to (3.6 ± 0.8) x 10 -3 mmHg -1 .min -1 (p&lt;0.01) for 5000 cycles US+MB+tPa, indicating an additive effect of tPa with US + MB therapy (Fig 1). Conclusions: In whole blood, US + MB therapy restored microvascular perfusion. Similarly to our previous findings with PBS perfusate, SRP efficacy varied with cycle length in the presence of MB. The addition of tPa increased SRP efficacy in blood, suggesting a potential additive effect of low dose tPa and US + MB therapy in vivo .
Key roles of carbon solubility in single-walled carbon nanotube nucleation and growth (2015)

Elucidating the roles played by carbon solubility in catalyst nanoparticles is required to better understand the growth mechanisms of single-walled carbon nanotubes (SWNTs). Here, we highlight that controlling the level of dissolved carbon is of key importance to enable nucleation and growth. We first performed tight binding based atomistic computer simulations to study carbon incorporation in metal nanoparticles with low solubilities. For such metals, carbon incorporation strongly depends on their structures (face centered cubic or icosahedral), leading to different amounts of carbon close to the nanoparticle surface. Following this idea, we then show experimentally that Au nanoparticles effectively catalyze SWNT growth when in a face centered cubic structure, and fail to do so when icosahedral. Both approaches emphasize that the presence of subsurface carbon in the nanoparticles is necessary to enable the cap lift-off, making the nucleation of SWNTs possible.
Retinal Vascular Caliber and Brachial Flow-Mediated Dilation (2010)

Persons with wider retinal venules have reduced brachial FMD, independent of other vascular risk factors. This suggests that retinal venular caliber, previously shown to predict stroke, may be a marker of underlying systemic endothelial dysfunction.
Spin-polarized tunneling between Fe thin films and an optically pumped GaAs probe (1999)

It is well known that two electrodes separated by a potential barrier, of which electron densities of states are spin-polarized. yield spin-polarized electron tunneling[1]. Since scanning tunneling microscopy (STM) is based on the electron tunneling, if a sample and a probe have spin-polarized electron states, tunneling electrons detected by STM should be spin-polarized. To evaluate spin-polarization of the electrons allows the investigation of surface magnetism on nanometer scale.
Helicity dynamics in reconnection events of topologically complex vortex flows (2021)

Abstract