gebhart/patrepeval huggingface dataset:
Myxoid liposarcoma with t(12;16) (q13;p11) contains site-specific differences in methylation patterns surrounding a zinc-finger gene mapped to the breakpoint region on chromosome 12. (1990)

The q13 to q15 region of human chromosome 12 is frequently and consistently rearranged in malignant and benign adipose tissue tumors as well as benign tumors of smooth muscle and salivary glands. A reciprocal translocation, (12;16) (q13;p11), is characteristic of the myxoid subtype of liposarcoma, whereas translocations within 12q13-14 are frequently observed in benign lipomas. We are using pulsed-field gel electrophoresis to study the 12q13-q14 region in order to detect and clone the respective translocation breakpoints in these tumors. The locus GLI, which encodes a zinc-finger protein, has been mapped to the same region as the myxoid liposarcoma breakpoint. Pulsed-field analysis of myxoid liposarcoma and lipoma DNA has allowed us to construct a 600-kilobase physical map surrounding the GLI locus, which shows that breakpoints in both types of tumor are outside this region. However, myxoid liposarcoma DNA samples contained altered restriction fragments detectable with GLI probes that were highly specific and reproducible from case to case. These altered fragments are due to highly specific and reproducible methylation differences that are unique to myxoid liposarcoma DNA. These methylation changes may prove to be useful clinically as a diagnostic tool to differentiate subtypes of liposarcoma.
Electromechanical Test Rig for Characterisation of Viscoelastic Material (2015)

Viscoelastic materials are widely used for passive damping of undesired vibrations. The characteristics of this kind of materials cannot be obtained theoretically; however, experimental modeling should be performed. In this paper, a test rig is developed in order to characterize the viscoelastic material experimentally. Moreover, a particular kind of material is used to test the validity of the new device. Unlike the devices in the previous works, the torque here is not measured directly using a torque transducer which is quite expensive. However, in this test rig a current sensor is used for measuring the current, thereafter the torque is calculated indirectly. Furthermore, the operating frequency of this device is relatively higher than the other devices used for the same purpose. The results showed the validity of the device at characterizing the viscoelastic material
The Impact of Macrophage Nucleotide Pools on HIV-1 Reverse Transcription, Viral Replication, and the Development of Novel Antiviral Agents (2012)

Macrophages are ubiquitous and represent a significant viral reservoir for HIV-1. Macrophages are nondividing, terminally differentiated cells, which have a unique cellular microenvironment relative to actively dividing T lymphocytes, all of which can impact HIV-1 infection/replication, design of inhibitors targeting viral replication in these cells, emergence of mutations within the HIV-1 genome, and disease progression. Scarce dNTPs drive rNTP incorporation into the proviral DNA in macrophages but not lymphocytes. Furthermore, the efficacy of a ribose-based inhibitor that potently inhibits HIV-1 replication in macrophages, has prompted a reconsideration of the previously accepted dogma that 2'-deoxy-based inhibitors demonstrate effective inhibition of HIV-1 replication. Additionally, higher levels of dUTP and rNTP incorporation in macrophages, and lack of repair mechanisms relative to lymphocytes, provide a further mechanistic understanding required to develop targeted inhibition of viral replication in macrophages. Together, the concentrations of dNTPs and rNTPs within macrophages comprise a distinctive cellular environment that directly impacts HIV-1 replication in macrophages and provides unique insight into novel therapeutic mechanisms that could be exploited to eliminate virus from these cells.
What does phenotype have to do with it? (2017)

A recurring theme in this column and in articles published in Neurology ® Genetics is the problem of interpreting DNA variants, ever more present as next-generation sequencing invariably leads to the identification of multiple rare variants in a given individual. This is discussed in this issue in 2 articles and an accompanying editorial.1–3
Integrated Feedback Scheduling and Control Codesign for Motion Coordination of Networked Induction Motor Systems (2014)

This paper investigates the codesign of remote speed control and network scheduling for motion coordination of multiple induction motors through a shared communication network. An integrated feedback scheduling algorithm is designed to allocate the optimal sampling period and priority to each control loop to optimize the global performance of a networked control system (NCS), while satisfying the constraints of stability and schedulability. A speed synchronization method is incorporated into the scheduling algorithm to improve the speed synchronization performance of multiple induction motors. The rational gain of the network speed controllers is calculated using the Lyapunov theorem and tuned online by fuzzy logic to guarantee the robustness against complicated variations on the communication network. Furthermore, a state predictor is designed to compensate the time delay which occurred in data transmission from the sensor to the controller, as a part of the networked controller. Simulation results support the effectiveness of the proposed control‐and‐scheduling codesign approach.
Chemical Recycling of Mixed Plastic Waste for the Production of Aromatics and Olefins as Monomers for Circular Polyolefins and Polycarbonate.SABIC TRUCIRCLE™ (Case Study) (2023)

Pyrolysis oil from used plastics and bio-based feedstocks are alternative feeds to traditional fossil feedstock. The pyrolysis oils and bio-based feeds are converted into olefins and other valuable chemical products that are used for the production of circular products. Circular and renewable polymers have identical properties to virgin-based polymers and allows plastics to be recycled repeatedly, without loss of quality. Certification via audited systems ensures that each ton of recycled or renewable feedstock is counted once only. The produced virgin polymers (PE, PP, and PC) are part of the SABIC's TRUCIRCLE™ portfolio and represent a considerable milestone on the journey toward closing the loop and creating a circular economy for plastics. This chapter describes some of the technical challenges encountered by SABIC during the implementation of the production of chemically recycled circular polymers.
p22phox in the macula densa regulates single nephron GFR during angiotensin II infusion in rats (2007)

Angiotensin II (ANG II) infusion increases renal superoxide (O(2)(-)) and enhances renal vasoconstriction via macula densa (MD) regulation of tubuloglomerular feedback, but the mechanism is unclear. We targeted the p22(phox) subunit of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) with small-interfering RNA (siRNA) to reduce NADPH oxidase activity and blood pressure response to ANG II in rats. We compared single nephron glomerular filtration rate (SNGFR) in samples collected from the proximal tubule (PT), which interrupts delivery to the MD, and from the distal tubule (DT), which maintains delivery to the MD, to assess MD regulation of GFR. SNGFR was measured in control and ANG II-infused rats (200 ng.kg(-1).min(-1) for 7 days) 2 days after intravenous injection of vehicle or siRNA directed to p22(phox) to test the hypothesis that p22(phox) mediates MD regulation of SNGFR during ANG II. The regulation of SNGFR by MD, determined by PT SNGFR-DT SNGFR, was not altered by siRNA in control rats (control + vehicle, 13 +/- 1, n = 8; control + siRNA, 12 +/- 2 nl/min, n = 8; not significant) but was reduced by siRNA in ANG II-treated rats (ANG II + vehicle, 13 +/- 2, n = 7; ANG II + siRNA, 7 +/- 1 nl/min, n = 8; P < 0.05). We conclude that p22(phox) and NADPH oxidase regulate the SNGFR during ANG II infusion via MD-dependent mechanisms.
Using tropical maize germplasm for temperate breeding (2000)

Despite many efforts, little truly exotic germplasm is represented in U.S. maize hybrids. A wide array of tropical materials is available and use of elite tropical materials that have been through the inbreeding process is the quickest way to use tropical maize germplasm for temperate breeding programs, but how does one choose which material to use? Because of reaction to photoperiod, evaluating tropical germplasm sources is virtually impossible in the U.S. Corn Belt. N. C. State is involved in the development of inbred lines with high percentages of exotic germplasm via a process called incorporation by Simmonds, rather than the backcross introgression procedures adopted by most breeders. The advanced, largely-tropical lines at N.C. State all trace back to intercrosses among elite tropical hybrids. Results of second generation lines derived by phenotypic selection while selfing are reported here, including the results of testing under temperate and tropical conditions using both a temperate and a tropical tester. The results suggest that selection in either a very different location or with a very different tester can result in definite improvement in breeding value. Rarely would more extreme comparisons be made, yet all the rank correlations between testers and between environments were consistently positive and significant. Six lines have been released from these studies: NC298 and NC300 in 1991. NC304 in 1994, NC340 in 1997, and NC348 and NC350 in 1998. A joint public-private program called GEM (Germplasm Enhancement of Maize) also has been developed to move tropical germplasm more rapidly into breeding programs. The first widespread testing of family topcrosses from 50%-tropical materials has now been completed, and those results are summarized here.
Cryogenic Carbon Capture (2012)

Advanced Research Projects Agency-Energy project sheet summarizing general information about the Innovative Materials and Processes for Advanced Carbon Capture Technologies (IMPACCT) program including critical needs, innovation and advantages, impacts, and contact information. This sheet discusses a process for carbon capture through desublimation as part of the "Cryogenic Carbon Capture" project.
Piezoelectrically transduced single-crystal-silicon plate resonators (2008)

We report on the design, fabrication and characterization of piezoelectrically actuated single-crystal silicon plate resonators vibrating mainly in their bulk acoustic wave modes. Two resonator types are presented: one operates in the square extensional mode at 26 MHz with Q~18000 and motional resistance R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ~0.240 kOmega, while the other resonator features a resonance at 22 MHz with Q~51000 and R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ~1.5 kOmega. The resonators are characterized electrically and by scanning laser interferometry. Measured vibration fields are compared to simulated eigenmodes.
Solution Structures of Ca2+-CIB1 and Mg2+-CIB1 and Their Interactions with the Platelet Integrin αIIb Cytoplasmic Domain (2011)

The calcium- and integrin-binding protein 1 (CIB1) is a ubiquitous Ca(2+)-binding protein and a specific binding partner for the platelet integrin αIIb cytoplasmic domain, which confers the key role of CIB1 in hemostasis. CIB1 is also known to be involved in apoptosis, embryogenesis, and the DNA damage response. In this study, the solution structures of both Ca(2+)-CIB1 and Mg(2+)-CIB1 were determined using solution-state NMR spectroscopy. The methyl groups of Ile, Leu, and Val were selectively protonated to compensate for the loss of protons due to deuteration. The solution structure of Ca(2+)-CIB1 possesses smaller opened EF-hands in its C-domain compared with available crystal structures. Ca(2+)-CIB1 and Mg(2+)-CIB1 have similar structures, but the N-lobe of Mg(2+)-CIB1 is slightly more opened than that of Ca(2+)-CIB1. Additional NMR experiments, such as chemical shift perturbation and methyl group solvent accessibility as measured by a nitroxide surface probe, were carried out to further characterize the structures of Ca(2+)-CIB1 and Mg(2+)-CIB1 as well as their interactions with the integrin αIIb cytoplasmic domain. NMR measurements of backbone amide proton slow motion (microsecond to millisecond) dynamics confirmed that the C-terminal helix of Ca(2+)-CIB1 is displaced upon αIIb binding. The EF-hand III of both Ca(2+)-CIB1 and Mg(2+)-CIB1 was identified to be directly involved in the interaction of CIB1 with αIIb. Together, these data illustrate that CIB1 behaves quite differently from related EF-hand regulatory calcium-binding proteins, such as calmodulin or neuronal calcium sensor proteins.
Smart polymers for responsive drug-delivery systems (2008)

The rapid advancement of biomedical research has led to many creative applications for biocompatible polymers. As modern medicine discerns more mechanisms, both of physiology and of pathophysiology, the approach to healing is to mimic, or if possible, to recreate the physiology of healthy functioning. Thus, the area of smart polymers for responsive drug delivery has evolved. The developments fall under two categories: externally regulated or pulsatile systems (also known as 'open-loop' systems) and self-regulated systems (also known as 'closed-loop'). The externally controlled devices apply external triggers for pulsatile delivery such as: ultrasonic, magnetic, electric, light and chemical or biochemical agents. The self-regulated systems, on the other hand, are defined as systems where the controlled variable is detected, and as a result, the system output is adjusted accordingly. The release rate is controlled by feedback information, without any external intervention. The self-regulated systems utilize several approaches for the rate control mechanisms such as thermal, pH-sensitive polymers, enzyme-substrate reactions, pH-sensitive drug solubility, competitive binding, antibody interactions and metal-concentration-dependent hydrolysis.
Comprehensive Analysis of Input Waveform Shaping for Efficiency Enhancement in Class B Power Amplifiers (2019)

Over the years, different high efficiency power amplifier (PA) design techniques have been proposed and implemented which eliminate input non-linearity considering its negative impact on PA output power and efficiency. This work rather exploits input non-linearity to improve PA efficiency. A generic analysis of a Class B PA under input non-linearity is presented opening the scope of input second harmonic manipulation to improve PA performances. This renders extended and new design space of second harmonic source termination to high efficiency PA design. Theoretical analyses are well supported with load-pull measurement results of a 0.7 mm and a 24 mm GaN devices where about 4.5% drain efficiency improvement compared to conventional Class B PA is observed.
Resolving subcellular plant metabolism (2019)

Plant cells are characterized by a high degree of compartmentalization and a diverse proteome and metabolome. Only a very limited number of studies has addressed combined subcellular proteomics and metabolomics which strongly limits biochemical and physiological interpretation of large-scale 'omics data. Our study presents a methodological combination of nonaqueous fractionation, shotgun proteomics, enzyme activities and metabolomics to reveal subcellular diurnal dynamics of plant metabolism. Subcellular marker protein sets were identified and enzymatically validated to resolve metabolism in a four-compartment model comprising chloroplasts, cytosol, vacuole and mitochondria. These marker sets are now available for future studies that aim to monitor subcellular metabolome and proteome dynamics. Comparing subcellular dynamics in wild type plants and HXK1-deficient gin2-1 mutants revealed a strong impact of HXK1 activity on metabolome dynamics in multiple compartments. Glucose accumulation in the cytosol of gin2-1 was accompanied by diminished vacuolar glucose levels. Subcellular dynamics of pyruvate, succinate and fumarate amounts were significantly affected in gin2-1 and coincided with differential mitochondrial proteome dynamics. Lowered mitochondrial glycine and serine amounts in gin2-1 together with reduced abundance of photorespiratory proteins indicated an effect of the gin2-1 mutation on photorespiratory capacity. Our findings highlight the necessity to resolve plant metabolism to a subcellular level to provide a causal relationship between metabolites, proteins and metabolic pathway regulation.
Fractionation of Blue Wheat Anthocyanin Compounds and Their Contribution to Antioxidant Properties (2008)

Demands for anthocyanin-rich foods and supplements are steadily increasing due to their significant roles in human health and food coloration. In the development of blue wheat as a functional food ingredient, dry milling was employed to separate the bran fraction where anthocyanins are concentrated 2.3-fold as compared to whole grain (13.9 mg/100 g). Anthocyanins were then extracted with aqueous ethanol and partially purified into a highly concentrated powder. The total anthocyanin content in the isolated powder as analyzed by high-performance liquid chromatography (HPLC) averaged 3378 mg/100 g and afforded a 243-fold increase in concentration relative to the whole grain product. Four main anthocyanins, delphinidin-3-glucoside (45%), cyanidin-3-glucoside (28%), delphinidin-3-rutinoside (22%), and cyanidin-3-rutinoside (2%), were isolated from the powder using preparative HPLC. Anthocyanin products and compounds were assessed against scavenging of 2,2-diphenyl-1-picryl-hydrazyl and 2,2'-azino-di-(3-ethylbenzthiazoline sulfonate) radicals and inhibition of human low-density lipoprotein cholesterol oxidation. Significant differences in antioxidant capacity were observed with anthocyanin powder and compounds exceeding that of butylated hydroxytoluene, indicating a potential for the development of blue wheat-based natural antioxidants and colorants.
Modeling Alpha-Synuclein Pathology in a Human Brain-Chip to Assess Blood-Brain Barrier Disruption in Parkinson’s Disease (2020)

Abstract Parkinson’s disease and related synucleinopathies are characterized by the abnormal accumulation of alpha-synuclein aggregates, loss of dopaminergic neurons, and gliosis in the substantia nigra. Although clinical evidence and in vitro studies indicate disruption of the Blood-Brain Barrier in Parkinson’s disease, the mechanisms mediating the endothelial dysfunction remain elusive. Lack of relevant models able to recapitulate the order of events driving the development of the disease in humans has been a significant bottleneck in the identification of specific successful druggable targets. Here we leveraged the Organs-on-Chips technology to engineer a human Brain-Chip representative of the substantia nigra area of the brain containing dopaminergic neurons, astrocytes, microglia, pericytes, and microvascular brain endothelial cells, cultured under fluid flow. Our αSyn fibril-induced model was capable of reproducing several key aspects of Parkinson’s disease, including accumulation of phosphorylated αSyn (pSer129-αSyn), mitochondrial impairment, neuroinflammation, and compromised barrier function. This model is poised to enable research into the dynamics of cell-cell interactions in human synucleinopathies and to serve as testing platform for novel therapeutic interventions, including target identification and target validation.
The effects of refined barley β‐glucan on the physico‐structural properties of low‐fat dairy products: curd yield, microstructure, texture and rheology (2004)

Abstract The beneficial role of dietary fibre in human nutrition has lead to a growing demand for incorporation of novel fibres, particularly barley β‐glucans, into foods. Barley β‐glucans are regarded as dietary fibre ingredients that are partially soluble in water. The aim of the present work was to investigate the possibility of using barley β‐glucan in milk systems in relation to the coagulation properties of milk containing β‐glucan, and to the rheology, texture and microstructure of fresh curds. The rate of coagulation and optimum coagulum cutting time were evaluated using rheological measurements. Results show that coagulation/gelation time of the milk can be reduced significantly with the incorporation of β‐glucan; curd yield increased and the viscoelastic properties of the curd were altered with β‐glucan additions. The relationships between curd rheological behaviour and its microstructure are discussed in relation to use of novel hydrocolloids in dairy processing. The results suggest that barley β‐glucan has the potential to be used as a fat replacer in low‐fat dairy systems. Copyright © 2004 Society of Chemical Industry
Dynamic power analysis under laser stimulation: a new Dynamic Laser Simulation approach (2010)

International audience
Figure S6 from Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy (2023)

&lt;p&gt;DMR methylation in MBL and CLL sampl&lt;/p&gt;
Table S5 from EMP2 Is a Novel Regulator of Stemness in Breast Cancer Cells (2023)

&lt;p&gt;Secondary tumor formation following anti-EMP2 therapy.&lt;/p&gt;
Electrical impedance tomography for non-invasive identification of fatty liver infiltrate in overweight individuals (2021)

Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of cardiometabolic diseases in overweight individuals. While liver biopsy is the current gold standard to diagnose NAFLD and magnetic resonance imaging (MRI) is a non-invasive alternative still under clinical trials, the former is invasive and the latter costly. We demonstrate electrical impedance tomography (EIT) as a portable method for detecting fatty infiltrate. We enrolled 19 overweight subjects to undergo liver MRI scans, followed by EIT measurements. The MRI images provided the a priori knowledge of the liver boundary conditions for EIT reconstruction, and the multi-echo MRI data quantified liver proton-density fat fraction (PDFF%) to validate fat infiltrate. Using the EIT electrode belts, we circumferentially injected pairwise current to the upper abdomen, followed by acquiring the resulting surface-voltage to reconstruct the liver conductivity. Pearson's correlation analyses compared EIT conductivity or MRI PDFF with body mass index, age, waist circumference, height, and weight variables. We reveal that the correlation between liver EIT conductivity or MRI PDFF with demographics is statistically insignificant, whereas liver EIT conductivity is inversely correlated with MRI PDFF (R = -0.69, p = 0.003, n = 16). As a pilot study, EIT conductivity provides a portable method for operator-independent and cost-effective detection of hepatic steatosis.