gebhart/patrepeval huggingface dataset:
The Alternative RelB NF-kB Subunit Exerts a Critical Survival Function upon Metabolic Stress in Diffuse Large B-Cell Lymphoma-Derived Cells (2022)

Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma in adults and reveals distinct genetic and metabolic signatures. NF-κB transcription factor family is involved in diverse biological processes enabling tumor development and resistance to anticancer-therapy through activation of its two main pathways, the canonical and the alternative NF-κB pathways, the main actor of the latter being the RelB NF-kB subunit. RelB DNA binding activity is frequently activated in DLBCL patients and cell lines. RelB activation defines a new DLBCL subgroup with dismal outcome upon immunochemotherapy, and RelB confers DLBCL cell resistance to DNA damage. However, whether RelB can impact on DLBCL cell metabolism and survival upon metabolic stress is unknown. Here, we reveal that RelB controls DLBCL oxidative energetic metabolism. Accordingly, RelB inhibition reduce DLBCL mitochondrial ATP production, and sensitizes DLBCL cells to apoptosis induced by Metformin and L-asparaginase (<sup>®</sup>Kidrolase), two FDA approved antimetabolic drugs targeting mitochondrial metabolism. RelB also confers DLBCL cell resistance to glutamine deprivation, an essential amino acid that feeds the TCA cycle. Taken together, our findings uncover a new role for RelB in the regulation of DLBCL cell metabolism and DLBCL cell survival upon metabolic stress.
Superconductivity in the Endohedral Ga Cluster Compound PdGa<sub>5</sub> (2021)

Superconductivity is observed below T<sub>c</sub> = 1.6 K in an endohedral Ga cluster compound PdGa<sub>5</sub> using magnetization and heat capacity measurements. Electronic structure calculations show that the density of states (DOS) at the Fermi level is dominated by Ga s and p states and that the overall shape of DOS is similar to what was found in other endohedral Ga cluster superconductors, such as Mo<sub>x</sub>Ga<sub>5x+1</sub>, ReGa<sub>5</sub>, and T<sub>2</sub>Ga<sub>9</sub> (T = Rh and Ir). Our results provide a more complete picture of the relationship between the valence electron count and superconductivity in the family of endohedral Ga cluster superconductors.
Making the Smallest Medical Devices (2014)

This article presents an overview of various alternative methods of nanoscale fabrication to bring revolution in the medical device development. Carbon nanotubes are considered to have great potential in biology and medicine, thanks to their desirable properties. These nanotubes are a macromolecular form of carbon; although their diameters are suitably nanoscale, ranging from 0.4 nm to 100 nm, they can be as much as several thousand nanometers long. Nanoscale fabrication can create devices that can work on individual cells and provide treatments that would be impossible if we were trying to issue them in bulk throughout the body. Nanoparticles can be fabricated using both top-down and bottom-up fabrication methods. In the top-down method, nanoparticles are carved from the bulk materials using techniques such as electron-beam lithography, reactive ion etching, and wet etching. Hybrid methods promise to integrate bottom-up and top-down nanofabrication in new and innovative ways by leveraging the strengths and unique features of both approaches.
Multiple wavelength operation of distributed feedback fiber lasers (2002)

Summary form only given. Multiple wavelength distributed feedback (DFB) fiber lasers are attractive for a range of applications in optical communications, including soliton and microwave generation. Although such lasers have been demonstrated experimentally, it is not obvious how several laser modes can coexist in a homogeneously broadened gain medium. We propose that the coexistence of two or more fundamental modes of the same polarization can be attributed to the effect of dynamic gain gratings set up by the standing waves of different laser modes. A gain grating is in anti-phase with the standing wave pattern that created it, and therefore its presence is destructive for the corresponding laser mode. On the other hand, its interaction with other laser modes is small because of the frequency mismatch. Thus, the effect of the gain gratings is a reduction of the power of the dominant mode and an increase of the available gain for the other modes, resulting in a stable multiple wavelength operation of the laser.
A real-time ultrasound calibration system with automatic accuracy control and incorporation of ultrasound section thickness (2008)

This paper presents a real-time, freehand ultrasound (US) calibration system, with automatic accuracy control and incorporation of US section thickness. Intended for operating-room usage, the system featured a fully automated calibration method that requires minimal human interaction, and an automatic accuracy control mechanism based on a set of ground-truth data. We have also developed a technique to quantitatively evaluate and incorporate US section thickness to improve the calibration precision. The experimental results demonstrated that the calibration system was able to consistently and robustly achieve high calibration accuracy with real-time performance and efficiency. Further, our preliminary results to incorporate elevation beam profile have demonstrated a promising reduction of uncertainties to estimate elevation-related parameters.
An Automated T-maze Based Apparatus and Protocol for Analyzing Delay- and Effort-based Decision Making in Free Moving Rodents (2018)

Many neurological and psychiatric patients demonstrate difficulties and/or deficits in decision making. Rodent models are helpful to produce a deeper understanding of the neurobiological causes underlying the decision-making problems. A cost-benefit based T-maze task is used for measuring decision making in which rodents choose between a high reward arm (HRA) and a low reward arm (LRA). There are two paradigms of the T-maze decision-making task, one in which the cost is a time delay and the other in which it is physical effort. Both paradigms require a tedious and labor-intensive management of experimental animals, multiple doors, pellet reward, and arm choice recordings. In the current work, we invented an apparatus based on traditional T-maze with full automation for pellet delivery, door management and choice recordings. This automated setup can be used for the evaluation of both delay- and effort-based decision making in rodents. With the protocol described here, our lab investigated the decision-making phenotypes of multiple genetically modified mice. In the representative data, we showed that the mice with ablated medial habenular showed aversions of both delay and effort and tended to choose the immediate and effortless reward. This protocol helps to decrease the variability caused by experimenter intervention and to enhance experiment efficiency. In addition, chronic silicon probe or microelectrode recording, fiber-optic imaging and/or manipulation of neural activity can be easily applied during the decision-making task using the setup described here.
Strategies for Removal of Formate Brine-Based Drill in Fluid (DIF) Filtercake in Gravel-Packed Completions: A Laboratory Evaluation (2010)

Abstract Formate brines and drilling fluids were primarily developed for high pressure drilling and completion applications. This completion fluid system is now being employed in more benign pressure environments and also to drill and complete formations with specific properties. This was the case where a potassium formate brine with 1.25 specific gravity (S.G.) was specified as the base fluid for the drill-in fluid (DIF) as well as completion brine for several openhole completions requiring gravel packing in offshore Brunei. The DIF used to drill the open hole deposits a protective filtercake on the borehole wall that is typically removed by means of a suitable removal system, enabling undamaged production. Openhole filtercake breaker systems that are typically employed range from mineral and organic acids, which aggressively attack the filtercake and result in an incomplete cake removal, to ortho-esters, which hydrolyze in the brine and lead to the formation of a delayed acid, which has proven more efficient. The ortho-esters are mixed in the base brine and placed inside the open hole or gravel pack and allowed to react over time. Formate brines, however, have proven to be poor base fluids for the ortho-esters because of their inherently high pH. A laboratory evaluation was conducted to address this problem. The tests showed that these ortho-ester-based systems, when mixed in a potassium chloride or sodium-bromide brine system, can be employed to break the formate-based DIF filtercake. A chelant-based breaker system, however, provides the most efficient cleanup with the necessary delay. This paper addresses the challenges and details of the laboratory testing performed to arrive at an optimized chelant-based delayed-breaker system in formate brine for removal of formate-based filtercakes. The paper also presents results of the performance of the ortho-ester system.
Serum Concentrations of Oocyte-Secreted Factors BMP15 and GDF9 During IVF and in Women With Reproductive Pathologies (2019)

Oocyte-secreted factors bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) are critical for folliculogenesis and fertility. This study developed ELISAs for the measurement of BMP15 and GDF9 in serum and investigated their usefulness as biomarkers of female reproductive function. Serum samples were obtained from women undergoing infertility treatments (n = 154) and from perimenopausal and postmenopausal women (n = 28). Serum concentrations of BMP15 and GDF9 were analyzed in women relative to age, anti-Müllerian hormone, number of oocytes retrieved, and polycystic ovary syndrome (PCOS) after superovulation for in vitro fertilization. BMP15 and GDF9 immunoassays were validated for specificity, sensitivity (24 and 26 pg/mL, respectively), and reproducibility. BMP15 and GDF9 were detectable in 61% and 29% of women, respectively. BMP15 and GDF9 varied 64-fold and 15-fold, respectively, between women, but they did not change within subjects following ovarian stimulation with gonadotropins. Serum GDF9 concentration, but not BMP15 concentration, was associated with oocyte number retrieved in patients without PCOS (P = 0.018). GDF9 and BMP15 associations with oocyte number differed significantly (P < 0.05) with PCOS status. GDF9 concentrations were lower in poor responders (women with fewer than four oocytes retrieved or with cancelled cycles; P = 0.020). Serum BMP15, but not GDF9, was lower in women >55 years of age, compared with women of reproductive age (P < 0.01). This study develops and validates immunoassays to quantitate BMP15 and GDF9 in human serum and to correlate concentrations with female reproductive potential. Although assay sensitivities require improvement, this study demonstrates the diagnostic potential of oocyte-secreted BMP15 and GDF9 as serum biomarkers in reproductive medicine.
Quantum angular-momentum selection rules for absorption of twisted light by bound electrons (Conference Presentation) (2018)

We analyze the novel features of high-multipole excitation of quantum systems with twisted light, i.e, by the photons that carry extra orbital angular momentum (OAM) along the propagation direction. It was previously demonstrated experimentally [1] that OAM of the twisted light is passed to the internal degrees of freedom of an atom for electric quadrupole transitions. We extended these results to the analysis of individual S->D transition amplitudes by measuring Rabi frequencies for Ca40+ ions placed in a Paul trap. It is shown that relative strengths transitions into different Zeeman-split levels - most of them forbidden for plane-wave photons - depends on the target atom’s position with respect to the optical vortex center. The data compare favorably with the theoretical predictions. The selection rules also point to circular dichroism and birefringence of the twisted light interacting with non-chiral atomic matter. Collaboration with Carl E. Carlson, Christian T. Schmiegelow, Ferdinand Schmidt-Kaler, and Maria Solyanik is gratefully acknowledged. [1] C. T. Schmiegelow, J. Schulz, H. Kaufmann, T. Ruster, U. G. Poschinger, and F. Schmidt-Kaler, Nature communications, 7 (October 2016), DOI: 10.1038/ncomms12998.
A low&#8211;cost high&#8211;accuracy CMOS smart temperature sensor (1999)

A high-accuracy CMOS temperature sensor with ADC and bus interface has been integrated in a 0.7µm CMOS process. Accuracy has been improved by applying a chopper technique and dynamic element matching. The circuit consumes 300µW@3.0V. Uncalibrated accuracy is typically better than 1°C for a temperature range of -20 to +100°C, measured on 112 samples from two different batches.
Switchable Neutral Bistable Rotaxanes (2004)

Two switchable neutral bistable [2]rotaxanes have been synthesized, and their chemically induced mechanical switching has been studied in solution by 1H NMR spectroscopy. One of the rotaxanes was prepared by a thermodynamically controlled slippage mechanism, while the other rotaxane was obtained by a dynamic covalent chemistry protocol involving the assembly of its dumbbell component by olefin metathesis. The recognition sites present in the rod section of the dumbbell component, namely, naphthodiimide (NpI) and pyromellitic diimide (PmI) residues, were chosen in the knowledge that the ring component, 1,5-dinaphtho[38]crown-10 (1/5DNP38C10), will bind preferentially to the NpI site. However, upon introduction of Li+ ions into the solution, a 1:2 complex is formed between the PmI site, encircled by the 1/5DNP38C10 ring and two Li+ ions. Since this complex is more stable overall than the binding between the 1/5DNP38C10 ring and the NpI site, the ring component moves from the NpI site to the PmI one. This mechanical movement can be reversed by adding an excess of [12]crown-4 to the solution to act as a sequestering agent for the Li+ ions.
Anti-Angiogenic and Anti-Tumor Properties of Proteasome Inhibitors (2005)

Tumor growth and metastasis depend on the formation of blood vessels, angiogenesis, to supply the developing mass with nutrients, oxygen, and waste removal. The proteasome, a massive multisubunit catabolic body, exerts a regulatory influence on angiogenesis. Inhibition of the proteasome activity has been found to inhibit angiogenesis and induce apoptosis in human cancer cells with limited toxicity to normal cells. Therefore, the dual action of angiogenesis inhibition and cell death induction makes proteasome inhibition an attractive modality for chemotherapy. A variety of proteasome inhibitors have been studied including: antibiotics such as lactacystin, the green tea polyphenols, and the boronic acid Velcade (MLN-341). Most recently, certain classes of copper compounds have been found to act as potent proteasome inhibitors. The potential of particular organic compounds, such as 8-hydroxyquinoline, to spontaneously bind with tumor cellular copper and form proteasome inhibitors provides a new modality of anti-proteasome and anti-angiogenesis chemotherapy. This review examines angiogenesis, the proteasome, representative proteasome inhibitors, and the emerging role of copper. The formation of new blood vessels, or angiogenesis, is an important and necessary function in both embryonic development and wound repair. Therefore, the ability to regenerate or form new vessels for blood flow is essential. The control of angiogenic pathways is tightly regulated in normal differentiated adult cells, which generally do not stimulate blood vessel growth unless injury occurs. However, cancerous tissues stimulate angiogenesis that in turn leads to increased tumor formation and possible metastases. Many of the factors involved in angiogenesis are regulated by the proteasome, which recently has become a focus in anti-cancer therapies due to its involvement in cell cycle and apoptosis control. Here we discuss angiogenesis and its relation to the proteasome. Additionally, current modalities of anti-angiogenic treatment, mainly proteasome inhibitory strategies, are reviewed. Furthermore, proteasome inhibitors, both natural and synthetic, and their anti-angiogenic effects as well as future approaches to anti-angiogenic chemotherapies are also discussed.
Resolution enhancement of 2-photon microscopy using high-refractive index microspheres (2018)

Intravital microscopy using multiphoton processes is the standard tool for deep tissue imaging inside of biological specimens. Usually, near-infrared and infrared light is used to excite the sample, which enables imaging several mean free path inside a scattering tissues. Using longer wavelengths, however, increases the width of the effective multiphoton Point Spread Function (PSF). Many features inside of cells and tissues are smaller than the diffraction limit, and therefore not possible to distinguish using a large PSF. Microscopy using high refractive index microspheres has shown promise to increase the numerical aperture of an imaging system and enhance the resolution. It has been shown that microspheres can image features ~λ/7 using single photon process fluorescence. In this work, we investigate resolution enhancement for Second Harmonic Generation (SHG) and 2-photon fluorescence microscopy. We used Barium Titanate glass microspheres with diameters ∼20–30 μm and refractive index ∼1.9–2.1. We show microsphere-assisted SHG imaging in bone collagen fibers. Since bone is a very dense tissue constructed of bundles of collagen fibers, it is nontrivial to image individual fibers. We placed microspheres on a dense area of the mouse cranial bone, and achieved imaging of individual fibers. We found that microsphere assisted SHG imaging resolves features of the bone fibers that are not readily visible in conventional SHG imaging. We extended this work to 2-photon microscopy of mitochondria in mouse soleus muscle, and with the help of microsphere resolving power, we were able to trace individual mitochondrion from their ensemble.
Tralokinumab for moderate-to-severe UC: a randomised, double-blind, placebo-controlled, phase IIa study (2014)

ClinicalTrials.gov number: NCT01482884.
Validation of dynamic three-dimensional whole heart magnetic resonance myocardial perfusion imaging at 3.0 Tesla against fractional flow reserve for the detection of flow-limiting coronary heart disease (2012)

We demonstrate the feasibility of 3D myocardial perfusion CMR at 3 Tesla against fractional flow reserve (FFR) in 53 patients for the detection of flow-limiting coronary artery disease and show good agreement between the techniques. This technique shows excellent diagnostic sensitivity and specificity and may offer an alternative method of detecting ischaemia for the purpose of guiding revascularisation and risk stratification.
Node density independent localization (2006)

This paper presents an enhanced version of a novel radio interferometric positioning technique for node localization in wireless sensor networks that provides both high accuracy and long range simultaneously. The ranging method utilizes two transmitters emitting radio signals at almost the same frequencies. The relative location is estimated by measuring the relative phase offset of the generated interference signal at two receivers. Here, we analyze how the selection of carrier frequencies affects the precision and maximum range. Furthermore, we describe how the interplay of RF multipath and ground reflections degrades the ranging accuracy. To address these problems, we introduce a technique that continuously refines the range estimates as it converges to the localization solution. Finally, we present the results of a field experiment where our prototype achieved 4~cm average localization accuracy for a quasi-random deployment of 16 COTS motes covering the area of two football fields. The maximum range measured was 170~m, four times the observed communication range. Consequently, node deployment density is no longer constrained by the localization technique, but rather by the communication range.
Machine Translated Text Detection Through Text Similarity with Round-Trip Translation (2021)

Hoang-Quoc Nguyen-Son, Tran Thao, Seira Hidano, Ishita Gupta, Shinsaku Kiyomoto. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Implementation Issues of a List Sphere Decoder (2006)

Since finding the nearest point in a lattice for multi-input multi-output (MIMO) channels is NP-hard, simplified algorithms such as sphere decoder (SD) have been proposed. List sphere decoder (LSD), which is a modified version of SD, allows soft information to be extracted for channel decoding and iterative detection/decoding. In this paper, recently proposed efficient methods for reducing the computational complexity of SD and LSD with depth-first tree searching are summarized. Numerous simulations have been carried out and comparison has been made based on the average number of processing cycles. We also present two efficient schemes which can decrease hardware complexity without significant performance degradation, restricted list updating in LSD and restricted node storing at each tree level.
Effect of rIFN‐γ on Antibody‐Mediated Cytotoxicity via Human Monocyte IgG Fc Receptor II (CD32) (1992)

Human monocytes and macrophages express an isoform of IgG Fc receptor II (Fc gamma RII), Fc gamma RIIa. Two allotypic variants of this receptor could be distinguished with respect to their ability to bind murine (m)IgG1 complexes either strongly or weakly, defined as high-responder (HR) and low-responder (LR), respectively. We investigated the effect of recombinant (r)IFN-gamma on the ability of freshly isolated monocytes, and those cultured for 40 h and 9 days, to mediate antibody-dependent cell-mediated cytotoxicity (ADCC). Using human erythrocytes (E) sensitized with mIgG1 as target cells, Fc gamma RII was studied selectively. Cells which had been cultured for 40 h exhibit a significantly decreased Fc gamma RII expression, and Fc gamma RII-mediated ADCC activity as compared with freshly isolated monocytes. Co-culture with rIFN-gamma (40 h) reversed this decrease. Short-term rIFN-gamma-cultured cells, and fresh cells express similar numbers of Fc gamma RII, and exhibit comparable Fc gamma RII-mediated ADCC activity. Phagocytic activity was not affected. Prolonged culture of monocytes for 9 days, co-cultured with rIFN-gamma either from day 0 or from day 7, did not affect expression or functional activity of Fc gamma RII. Furthermore, the effects were observed in both HR and LR individuals. Our results show that rIFN-gamma has strong effects on Fc gamma RII-mediated responses specifically during the early stages of monocyte maturation, most likely by affecting receptor expression levels.