gebhart/patrepeval huggingface dataset:
Supplementary Figures 1 through 6 and Supplementary Tables 1 through 3 from Highly Active Combination of BRD4 Antagonist and Histone Deacetylase Inhibitor against Human Acute Myelogenous Leukemia Cells (2023)

&lt;p&gt;PDF - 352K, Supplemental Figure 1: Chemical structures of the molecules used in the studies. Supplemental Figure 2: Effects of (R)-JQ1 in AML cells. Supplemental Figure 3: ChIP of BRD4 and POLII in JQ1 treated AML cells. Supplemental Figure 4: JQ1 effects on CDK6 mRNA expression in AML cells. Supplemental Figure 5: JQ1 effects on mRNA and protein expression in FLT3-ITD expressing AML cells. Supplemental Figure 6: Isobologram analyses of BET protein antagonist and PS in AML cells. Supplemental Table 1: Clinical presentation and mutation status of primary AML samples. Supplemental Table 2: Top gene expression changes in AML cells following JQ1 treatment. Supplemental Table 3: Ingenuity Pathway analysis of AML cells following JQ1 treatment.&lt;/p&gt;
Lung cancer models reveal SARS-CoV-2-induced EMT contributes to COVID-19 pathophysiology (2020)

COVID-19 is an infectious disease caused by SARS-CoV-2, which enters host cells via the cell surface proteins ACE2 and TMPRSS2. Using a variety of normal and malignant models and tissues from the aerodigestive and respiratory tracts, we investigated the expression and regulation of <i>ACE2</i> and <i>TMPRSS2</i>. We find that <i>ACE2</i> expression is restricted to a select population of highly epithelial cells. Notably, infection with SARS-CoV-2 in cancer cell lines, bronchial organoids, and patient nasal epithelium, induces metabolic and transcriptional changes consistent with epithelial to mesenchymal transition (EMT), including upregulation of <i>ZEB1</i> and <i>AXL</i>, resulting in an increased EMT score. Additionally, a transcriptional loss of genes associated with tight junction function occurs with SARS-CoV-2 infection. The SARS-CoV-2 receptor, ACE2, is repressed by EMT via TGFbeta, ZEB1 overexpression and onset of EGFR TKI inhibitor resistance. This suggests a novel model of SARS-CoV-2 pathogenesis in which infected cells shift toward an increasingly mesenchymal state, associated with a loss of tight junction components with acute respiratory distress syndrome-protective effects. AXL-inhibition and ZEB1-reduction, as with bemcentinib, offers a potential strategy to reverse this effect. These observations highlight the utility of aerodigestive and, especially, lung cancer model systems in exploring the pathogenesis of SARS-CoV-2 and other respiratory viruses, and offer important insights into the potential mechanisms underlying the morbidity and mortality of COVID-19 in healthy patients and cancer patients alike.
Development and evaluation of a method for segmentation of cardiac, subcutaneous, and visceral adipose tissue from Dixon magnetic resonance images (2019)

Magnetic resonance imaging (MRI) has evolved into the gold standard for quantifying excess adiposity, but reliable, efficient use in longitudinal studies requires analysis of large numbers of images. The objective of this study is to develop and evaluate a segmentation method designed to identify cardiac, subcutaneous, and visceral adipose tissue (VAT) in Dixon MRI scans. The proposed method is evaluated using 10 scans from volunteer females 18- to 35-years old, with body mass indexes between 30 and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>39.99</mml:mn> <mml:mtext> </mml:mtext> <mml:mi>kg</mml:mi> <mml:mo>/</mml:mo> <mml:msup><mml:mrow><mml:mi>m</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:mrow> </mml:math> . Cross-sectional area (CSA) for cardiac adipose tissue (CAT), subcutaneous adipose tissue (SAT), and VAT, is compared to manually-traced results from three observers. Comparisons of CSA are made in 191 images for CAT, 394 images for SAT, and 50 images for VAT. The segmentation correlated well with respect to average observer CSA with Pearson correlation coefficient ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:mrow> </mml:math> ) values of 0.80 for CAT, 0.99 for SAT, and 0.99 for VAT. The proposed method provides accurate segmentation of CAT, SAT, and VAT and provides an option to support longitudinal studies of obesity intervention.
Regulated enzymes (2012)

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Regulation of autoimmune diabetes by non‐islet‐specific T cells — a role for the glucocorticoid‐induced TNF receptor (2004)

Diabetogenic BDC2.5 CD4 T cells induce diabetes when injected into NOD.scid mice. However, when co-transferred with the OVA-specific DO11.10 CD4 T cells, BDC2.5 T cells failed to cause diabetes. This inhibition depended upon the stimulation of DO11.10 T cells only with soluble OVA, which skewed their differentiation to a Th2-type pattern of cytokine secretion in vivo. However, in vivo neutralization of IL-4, IL-10 or TGF-beta using monoclonal antibodies did not prevent the inhibition whereas treatment with an antibody against the glucocorticoid-induced TNF receptor abrogated the protection from disease. In the protected mice, the diabetogenic T cells could be isolated from their spleens and shown to transfer diabetes when injected into new NOD.scid recipients. Thus, the inhibition took place without the physical or functional elimination of the diabetogenic T cells.
Time evolution of magnetization in the FeRh system near antiferromagnetic-ferromagnetic transition temperature (abstract) (1994)

The body-centered cubic FeRh is known to exhibit a first-order phase transition from antiferromagnetic to ferromagnetic at about 400 K, accompanied by a volume expansion of about 1%. The time evolution of the magnetization M of ordered Fe0.5Rh0.5 and FeRh0.958Pt0.042 just below and above the transition temperature (T0) was measured as functions of temperature and magnetic field. Around T0, the magnetization increased logarithmically with time up to M*(=41 emu/g), the value of which indicates that the ferromagnetic grains occupy one third of the antiferromagnetic matrix. When M=M*, there appeared a jump in M. After that, M varies as M(t) =M∞[1−exp(−t/τ)], where τ is a relaxation time. It should be noted that the value of M* is independent of both temperatures and external magnetic fields. Microscopic observation and x-ray diffraction measurement showed that the ferromagnetic grains nucleated in the antiferromagnetic matrix began to grow with time just below T0. In this work, the time evolution of the phase transition was analyzed by considering the magnetic free energy, the elastic energy, and the strain energy at the surface of the grains. The above mentioned magnetic relaxation process is deeply related to the time evolution of the grain size.
Oncologic resection of pancreatic cancer with isolated liver metastasis: Favorable outcomes in select patients (2023)

In select patients with PDAC and isolated liver metastasis, curative-intent surgery can result in meaningful survival. This aggressive approach seems most beneficial in patients following induction chemotherapy.
Opportunistic Temporal Fair Mode Selection and User Scheduling for\n Full-duplex Systems (2019)

In-band full-duplex (FD) communications - enabled by recent advances in\nantenna and RF circuit design - has emerged as one of the promising techniques\nto improve data rates in wireless systems. One of the major roadblocks in\nenabling high data rates in FD systems is the inter-user interference (IUI) due\nto activating pairs of uplink and downlink users at the same time-frequency\nresource block. Opportunistic user scheduling has been proposed as a means to\nmanage IUI and fully exploit the multiplexing gains in FD systems. In this\npaper, scheduling under long-term and short-term temporal fairness for\nsingle-cell FD wireless networks is considered. Temporal fair scheduling is of\ninterest in delay-sensitive applications, and leads to predictable latency and\npower consumption. The feasible region of user temporal demand vectors is\nderived, and a scheduling strategy maximizing the system utility while\nsatisfying long-term temporal fairness is proposed. Furthermore, a short-term\ntemporal fair scheduling strategy is devised which satisfies user temporal\ndemands over a finite window-length. It is shown that the strategy achieves\noptimal average system utility as the window-length is increased\nasymptotically. Subsequently, practical construction algorithms for long-term\nand short-term temporal fair scheduling are introduced. Simulations are\nprovided to verify the derivations and investigate the multiplexing gains. It\nis observed that using successive interference cancellation at downlink users\nimproves FD gains significantly in the presence of strong IUI.\n
Direct Organocatalytic Asymmetric Mannich‐Type Reactions in Aqueous Media: One‐Pot Mannich‐Allylation Reactions. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Hypoglycemia: A tale of three causes (2016)

A 52-year old male with a history of insulin treated T2DM complicated by end stage renal disease (ESRD requiring hemodialysis and prior gastric bypass surgery presented with severe recurrent hypoglycemia with seizures. A 72 hour fast demonstrated hyperinsulinemic hypoglycemia. Abdominal CT scan and endoscopic ultrasound guided biopsy demonstrated a pancreatic neuroendocrine tumor (pNET). Symptoms persisted despite pNET resection and on further testing he was found to have a highly specific insulin antibody resulting in insulin autoimmune syndrome. He responded well to prednisone therapy with resolution of hypoglycemia and decline in the insulin autoantibody titers. This study concludes that autoimmune forms of hypoglycemia are uncommon and interpretation of tests can be challenging. However, insulin autoimmune syndrome (IAS) should be considered in a patient with both fasting and postprandial hypoglycemia in setting of very high insulin levels with associated anti-insulin antibodies and elevated insulin to C peptide molar ratio.
Decoupling of Mass Transport Mechanisms in the Stagewise Swelling of Multiple Emulsions (2015)

This contribution reports on the mass transport kinetics of osmotically imbalanced water-in-oil-in-water (W1/O/W2) emulsions. Although frequently studied, the control of mass transport in W1/O/W2 emulsions is still challenging. We describe a microfluidics-based method to systematically investigate the impact of various parameters, such as osmotic pressure gradient, oil phase viscosity, and temperature, on the mass transport. Combined with optical microscopy analyses, we are able to identify and decouple the various mechanisms, which control the dynamic droplet size of osmotically imbalanced W1/O/W2 emulsions. So, swelling kinetics curves with a very high accuracy are generated, giving a basis for quantifying the kinetic aspects of transport. Two sequential swelling stages, i.e., a lag stage and an osmotically dominated stage, with different mass transport mechanisms are identified. The determination and interpretation of the different stages are the prerequisite to control and trigger the swelling process. We show evidence that both mass transport mechanisms can be decoupled from each other. Rapid osmotically driven mass transport only takes place in a second stage induced by structural changes of the oil phase in a lag stage, which allow an osmotic exchange between both water phases. Such structural changes are strongly facilitated by spontaneous water-in-oil emulsification. The duration of the lag stage is pressure-independent but significantly influenced by the oil phase viscosity and temperature.
Characterization of molecular and cellular phenotypes associated with a heterozygous CNTNAP2 deletion using patient-derived hiPSC neural cells (2015)

Neurodevelopmental disorders, such as autism spectrum disorders (ASD) and schizophrenia (SZ), are complex disorders with a high degree of heritability. Genetic studies have identified several candidate genes associated with these disorders, including contactin-associated protein-like 2 (<i>CNTNAP2</i>). Traditionally, in animal models or <i>in vitro</i>, the function of <i>CNTNAP2</i> has been studied by genetic deletion or transcriptional knockdown, which reduce the expression of the entire gene; however, it remains unclear whether the mutations identified in clinical settings are sufficient to alter <i>CNTNAP2</i> expression in human neurons. Here, using human induced pluripotent stem cells (hiPSCs) derived from two individuals with a large (289kb) and heterozygous deletion in <i>CNTNAP2</i> (affecting exons 14-15) and discordant clinical outcomes, we have characterized <i>CNTNAP2</i> expression patterns in hiPSC neural progenitor cells (NPCs), two independent populations of hiPSC-derived neurons and hiPSC-derived oligodendrocyte precursor cells (OPCs). First, we observed exon-specific changes in <i>CNTNAP2</i> expression in both carriers; although the expression of exons 14-15 is significantly decreased, the expression of other exons is upregulated. Second, we observed significant differences in patterns of allele-specific expression in <i>CNTNAP2</i> carriers that were consistent with clinical outcome. Third, we observed a robust neural migration phenotype that correlated with diagnosis and exon- and allele-specific <i>CNTNAP2</i> expression patterns, but not with genotype. In all, our data highlight the importance of considering the nature, location and regulation of mutated alleles when attempting to connect GWAS studies to gene function.
Unveiling the strong interaction among hadrons at the LHC (2020)

One of the key challenges for nuclear physics today is to understand from first principles the effective interaction between hadrons with different quark content. First successes have been achieved using techniques that solve the dynamics of quarks and gluons on discrete space-time lattices . Experimentally, the dynamics of the strong interaction have been studied by scattering hadrons off each other. Such scattering experiments are difficult or impossible for unstable hadrons and so high-quality measurements exist only for hadrons containing up and down quarks. Here we demonstrate that measuring correlations in the momentum space between hadron pairs produced in ultrarelativistic proton–proton collisions at the CERN Large Hadron Collider (LHC) provides a precise method with which to obtain the missing information on the interaction dynamics between any pair of unstable hadrons. Specifically, we discuss the case of the interaction of baryons containing strange quarks (hyperons). We demonstrate how, using precision measurements of proton–omega baryon correlations, the effect of the strong interaction for this hadron–hadron pair can be studied with precision similar to, and compared with, predictions from lattice calculations . The large number of hyperons identified in proton–proton collisions at the LHC, together with accurate modelling of the small (approximately one femtometre) inter-particle distance and exact predictions for the correlation functions, enables a detailed determination of the short-range part of the nucleon-hyperon interaction.
Differentially expressed genes identified in human melanoma cell lines with different metastatic behaviour using high density oligonucleotide arrays (2002)

The increasing incidence of melanoma and the lack of effective treatment, with the exception of tumour excision before the onset of the metastatic phase, make it important to identify genes that may function as new molecular markers for diagnosis and/or prognosis or as new targets for therapy. Recently, a new technique using high density oligonucleotide arrays has been developed to simultaneously screen for the expression of thousands of genes. We used this technique to compare the mRNA expression patterns of two human melanoma cell lines with different metastatic behaviour. Eight differentially expressed genes, namely apolipoprotein CII, tyrosinase-related protein 1, transforming growth factor-beta superfamily, subtilisin-like protein, elongation factor 1 alpha2, alpha2-macroglobulin, human cell division cycle 10 and serine/threonine protein kinase (DYRK1A), were selected to validate the array results by Northern blotting and reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, a reliable correlation between differential expression of these genes in the melanoma cell lines and in fresh lesions of melanocytic tumour progression was demonstrated by RT-PCR analysis. Altogether, our data indicate that high density oligonucleotide arrays are a valuable and reliable tool to screen for differentially expressed genes, and that our study may be considered a basic step in the characterization of genes that are involved in the (malignant) progression of melanoma.
χc1 and χc2 Resonance Parameters with the Decays χc1,c2→J/ψμ+μ− (2017)

The decays χ_{c1}→J/ψμ^{+}μ^{-} and χ_{c2}→J/ψμ^{+}μ^{-} are observed and used to study the resonance parameters of the χ_{c1} and χ_{c2} mesons. The masses of these states are measured to be m(χ_{c1})=3510.71±0.04(stat)±0.09(syst) MeV and m(χ_{c2})=3556.10±0.06(stat)±0.11(syst) MeV, where the knowledge of the momentum scale for charged particles dominates the systematic uncertainty. The momentum-scale uncertainties largely cancel in the mass difference m(χ_{c2})-m(χ_{c1})=45.39±0.07(stat)±0.03(syst) MeV. The natural width of the χ_{c2} meson is measured to be Γ(χ_{c2})=2.10±0.20(stat)±0.02(syst) MeV. These results are in good agreement with and have comparable precision to the current world averages.
Removal Efficiency of Water-Based Drill-In Fluid Filter Cake Using Polylactic Acid (2012)

Abstract Water-based drilling fluids consisting of xanthan gum, starch, sized calcium carbonate and salt particles have been used to drill horizontal wells. Available chemical methods of removing filter cake like mineral acids, esters, oxidizers, and chelating agents are limited at certain conditions. Drilling fluid was designed based on calcium carbonate particles and an ester of lactic acid. The objective of the latter is to remove calcium carbonate once the drilling operation is complete and there is a need to remove the filter cake. Extensive lab work was done to: 1) determine thermal stability of the drilling fluid (70-72 pcf) for 24 hrs, 2) characterize the filter cake using computer tomography, 3) assess potential formation damage for different rock types (limestone and sandstone) using a modified HPHT filter press, and 4) determine the removal efficiency of the filter cake and the return permeability. The results obtained showed that the drill-in fluid has stable rheological properties up to 250°F over 24 hrs. A CT scan showed that the filter cake contained two layers, one layer close to the rock surface, which contained a mixture of calcium carbonate and acid-precursor, and one layer close to the drilling fluid that contained a mixture of XC-polymer and starch. The polymer layer was removed by using 10% solution of alpha amylase. The rest of the filter cake was removed by lactic acid that was produced from the hydrolysis of the ester. The removal efficiency of the filter cake was nearly 100% and the return permeability was about 100%, when using a ratio of polylactic acid to calcium carbonate 3 to 1. The decrease in the CT number of the core after the removal process indicated that the filter cake was completely removed and no formation damage occurred. This paper will discuss the development of this new drilling fluid and will give recommendations for field applications.
Multilayer ferromagnetic composites enabling on-chip magnetic-core inductors beyond 1 GHZ (2015)

This paper reports of fabricated unpatterned ferromagnetic NiFe/AlN multilayer composites and an established process flow for magnetic core material suitable for integration with Silex 3D RF TSV technology. The fabricated single-loop test inductors achieved an inductance enhancement of 4.8 and a quality factor enhancement of 4.5 at 400 MHz. Simulations show that magnetic material in connection with 3D TSV inductors result in an inductance enhancement up to a factor of 5 at GHz frequencies for the same inductor area or the same inductance can be achieved at 9 times smaller area and cost.
Compact Fiber-Optic Current Sensor With a Polarization Splitter and a 22.5$^\circ$ Faraday Rotator (2022)

In this letter, a novel implementation of a polarimetric fiber-optic current sensor scheme based on polarizing beam splitter and a <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$22.5^{\circ }$</tex-math></inline-formula> Faraday rotator will be presented. The developed sensor employs a compact and pigtailed component realized by joining a polarizing beam splitter and a Faraday rotator, it does not require any external adjustment to work and shows very high immunity to external electromagnetic and mechanical interference. The experimental results prove good sensitivity of the sensor allowing for the measurement of small value of current down to 100 mA.
Monitoring Network Traffic with Radial Traffic Analyzer (2006)

Extensive spread of malicious code on the Internet and also within intranets has risen the user's concern about what kind of data is transferred between her or his computer and other hosts on the network. Visual analysis of this kind of information is a challenging task, due to the complexity and volume of the data type considered, and requires special design of appropriate visualization techniques. In this paper, we present a scalable visualization toolkit for analyzing network activity of computer hosts on a network. The visualization combines network packet volume and type distribution information with geographic information, enabling the analyst to use geographic distortion techniques such as the HistoMap technique to become aware of the traffic components in the course of the analysis. The presented analysis tool is especially useful to compare important network load characteristics in a geographically aware display, to relate communication partners, and to identify the type of network traffic occurring. The results of the analysis are helpful in understanding typical network communication activities, and in anticipating potential performance bottlenecks or problems. It is suited for both off-line analysis of historic data, and via animation for on-line monitoring of packet-based network traffic in real time
The Directional Attack on Wireless Localization -or- How to Spoof Your Location with a Tin Can (2009)

802.11 localization algorithms provide the ability to accurately position and track wireless clients thereby enabling location-based services and applications. However, we show that these localization techniques are vulnerable to non-cryptographic attacks where an adversary uses a low-cost directional antenna to appear from the localization algorithm's perspective to be in another arbitrary location of their choosing. The attacker's ability to actively influence where they are positioned is a key distinguishing feature of the directional attack relative to prior localization attacks that use transmit power control to introduce localization errors. We implement a representative set of received signal strength-based localization algorithms and evaluate the attack in a real office building environment. To mitigate the attack's effectiveness, we develop and evaluate an attack detection scheme that offers a high detection rate with few false positives.