gebhart/patrepeval huggingface dataset:
Plug and play methods for magnetic resonance imaging. (2019)

Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic tool that provides excellent soft-tissue contrast without the use of ionizing radiation. But, compared to other clinical imaging modalities (e.g., CT or ultrasound), the data acquisition process for MRI is inherently slow. Furthermore, dynamic applications demand collecting a series of images in quick succession. As a result, reducing acquisition time and improving imaging quality for undersampled datasets have been active areas of research for the last two decades. The combination of parallel imaging and compressive sensing (CS) has been shown to benefit a wide range of MRI applications. More recently, deep learning techniques have been shown to outperform CS methods. Some of these techniques pose the MRI reconstruction as a direct inversion problem and tackle it by training a deep neural network (DNN) to map from the measured Fourier samples and the final image. Considering that the forward model in MRI changes from one dataset to the next, such methods have to be either trained over a large and diverse corpus of data or limited to a specific application, and even then they cannot ensure data consistency. An alternative is to use (PnP) algorithms, which iterate image denoising with forward-model based signal recovery. PnP algorithms are an excellent fit for compressive MRI because they decouple image modeling from the forward model, which can change significantly among different scans due to variations in the coil sensitivity maps, sampling patterns, and image resolution. Consequently, with PnP, state-of-the-art image-denoising techniques, such as those based on DNNs, can be directly exploited for compressive MRI image reconstruction. The objective of this article is two-fold: i) to review recent advances in plug-and-play methods, and ii) to discuss their application to compressive MRI image reconstruction.
Performance Analysis of Protection Schemes Compatible with Smooth Migration from TDM-PON to Hybrid WDM/TDM-PON (2007)

We propose a novel protection scheme compatible with smooth migration from TDM-PON to WDM/TDM-PON. We show that our scheme is very cost-effective while keeping connection availability, recovery time and power budget at the acceptable level.
Microwave circuit model of the three-port transistor laser (2010)

Based on an earlier charge control analysis, we have constructed a microwave circuit model of a three-port quantum-well (QW) transistor laser (TL) by extending Kirchhoff’s law to include electron-photon interaction, to yield an electrical-optical form of Kirchhoff’s law. The TL circuit model includes both intrinsic device elements and extrinsic parasitic elements, and fits accurately measured microwave S-parameters upto 20 GHz and matches also measured eye-diagram data up to 13 Gb/s (equipment-limited). The TL model yields both electrical and optical device parameters as well as physical quantities such as QW charge density, nQW∼1016 cm−3, which is useful in the analysis of the device physics of TL operation. The low density indicates that the base QW charge level is not as important as the current driving the QW and supplying electron-hole recombination, and implies that the quasi-Fermi level is discontinuous in the TL base. The model is used to simulate a directly modulated TL up to 40 Gb/s, for example, a TL employed in an optical communication link.
Formation of Multicellular Epithelial Structures (2005)

The kidney is primarily comprised of highly polarized epithelial cells. Much has been learned recently about the mechanisms of epithelial polarization. However, in most experimental systems the orientation of this polarity is determined by external cues, such as growth of epithelial cells on a filter support. When Madin-Darby canine kidney (MDCK) cells are grown instead in a three-dimensional (3D) collagen gel, the cells form hollow cysts lined by a monolayer of epithelial cells, with their apical surfaces all facing the central lumen. We have found that expression of a dominant-negative (DN) form of the small GTPase Rac1 causes an inversion of epithelial polarity, such that the apical surface of the cells instead faces the periphery of the cyst. This indicates that the establishment of polarity and the orientation of polarity can be experimentally separated by growing cells in a 3D collagen gel, where there is no filter support to provide an external cue for orientation. DN Rac1 causes a defect in the assembly of laminin into its normal basement membrane network, and addition of a high concentration of exogenous laminin rescues the inversion of polarity caused by DN Rac1.
Implications of Surface Charge and Curvature for the Binding Orientation of<i>Thermomyces lanuginosus</i>Lipase on Negatively Charged or Zwitterionic Phospholipid Vesicles As Studied by ESR Spectroscopy (2005)

The triglyceride lipase (EC 3.1.1.3) Thermomyces lanuginosus lipase (TLL) binds with high affinity to unilamellar phospholipid vesicles that serve as a diluent interface for both lipase and substrate, but it displays interfacial activation on only small and negatively charged such vesicles [Cajal, Y., et al. (2000) Biochemistry 39, 413-423]. The productive-mode binding orientation of TLL at the lipid-water interface of small unilamellar vesicles (SUV) consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) was previously determined using electron spin resonance (ESR) spectroscopy in combination with site-directed spin-labeling [Hedin, E. M. K., et al. (2002) Biochemistry 41, 14185-14196]. In our investigation, we have studied the interfacial orientation of TLL when bound to large unilamellar vesicles (LUV) consisting of POPG, and bound to SUV consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC). Eleven single-cysteine TLL mutants were spin-labeled as previously described, and studied upon membrane binding using the water soluble spin-relaxation agent chromium(III) oxalate (Crox). Furthermore, dansyl-labeled vesicles revealed the intermolecular fluorescence quenching efficiency between each spin-label positioned on TLL, and the lipid membrane. ESR exposure and fluorescence quenching data show that TLL associates closer to the negatively charged PG surface than the zwitterionic PC surface, and binds to both POPG LUV and POPC SUV predominantly through the concave backside of TLL opposite the active site, as revealed by the contact residues K74C-SL, R209C-SL, and T192C-SL. This orientation is significantly different compared to that on the POPG SUV, and might explain the differences in activation of the lipase. Evidently, both the charge and accessibility (curvature) of the vesicle surface determine the TLL orientation at the phospholipid interface.
Laser welding assembling of an implantable bio-medical device: investigation of temperature field (2011)

Laser welding is a commonly used process to assemble medical devices. The heat produced during the laser welding process may have an adverse effect on the mechanical integrity of the case assembly and the functionality of heat sensitive electronic components. In order to maintain the mechanical integrity of the case assembly and to protect the subcomponents, it is important to control the temperature in the assembling process, the investigation of the temperature distribution in the assembly during laser welding is thus necessary. In this paper, we report an experimental method and a numerical simulation for the investigation of the temperature field in the process of laser welding the eyelet to the case subassembly of the Functional Electrical Battery Powered Microstimulator (FEBPM). A pulsed 1064nm Nd:YAG laser is used as an example in this paper.
[Electrophysiological effects of the new antiarrhythmic drug flecainide (R 818) in man (author's transl)]. (1981)

The electrophysiological effects of the new antiarrhythmic drug Flecainide (R 818) was tested in altogether 27 patients with and without disturbances of sinus node function and intraventricular conduction. Flecainide was given intravenously in a dose of 1 mg/kg and 2 mg/kg. Constant "therapeutic" plasma levels were reached by application of 1 mg/kg as a bolus and an additional infusion of 1 mg/kg during the test period of 20 min. The drug had no significant effects on sinus node function even in patients with sinus node dysfunction tested so far. Intracardiac conduction time was prolonged within all compartments of the heart in a dose-dependent manner. After bolus injection of 1 mg/kg, the HRA-A interval lengthened by 10.4%, the A-H interval by 13.5%, the H-V time by 15.7% and the V-RVA interval by 29.1% of the control value. In addition, the QRS complex widened by 8.1%. After 2 mg/kg Flecainide the HRA-A interval was prolonged by 9.0%, the A-H interval by 24.4%, the H-V time by 40.2%, and the V-RVA interval by 16.5% of the control value. The QRS complex widened by 24.2%. In contrast, there was only a small and often insignificant increase in the refractoriness of the different compartments of the heart (5-15% increase of the control value). In two patients with bundle branch block, a higher degree A-V block distal the H potential occurred after 2 mg/kg Flecainide. These electrophysiological effects may explain some antiarrhythmic actions of Flecainide. In addition, possible side effects of the drug can be assessed. In patients with intraventricular conduction defects the drug should be used with caution especially when given iv in higher doses.
Noise characteristics of transistors fabricated in an advanced silicon bipolar technology (1996)

The RF noise of transistors fabricated in an advanced silicon bipolar technology is investigated. The influence of the lateral scaling on the noise figure is studied experimentally and compared with the predictions of conventional noise modeling. Reasonable agreement is found without any fitting of model parameters to the measured noise characteristics. The potential of the investigated technology for low-noise applications is demonstrated by noise figures below 1 dB for frequencies up to 2 GHz and below 2 dB up to 7 GHz.
<i>Eimeria</i> species which infect the chicken contain virus-like RNA molecules (1990)

There is increasing support for the presence of viruses and virus-like particles inside protozoan cells. This study describes viral-like RNA molecules that have been detected in two species of Eimeria that infect the chicken. The RNA molecule identified in E. maxima has been characterized: subcellular fractionation studies have shown that the RNA is present in the cytoplasm, probably as an abundant ribonucleoprotein that is insensitive to RNAse A treatment. Electron microscopy has demonstrated that this RNA molecule is double stranded. In addition, all E. maxima strains examined so far contain this RNA molecule.
Magnetic force microscopy study of shape engineered <scp>FEBID</scp> iron nanostructures (2013)

The capability to control matter down to the nanoscale level in combination with the novel magnetic properties of nanomaterials have attracted increasing attention in the last few decades due to their applications in magnetic sensing, hard disc data storage and logic devices. Therefore, many efforts have been devoted to the implementation of both nanofabrication methods as well as characterization of magnetic nanoelements. In this study, Fe‐based nanostructures have been synthesized on Si(100) by focused electron beam induced deposition (FEBID) utilizing iron pentacarbonyl as precursor. The so obtained nanostructures exhibit a remarkably high iron content (Fe &gt; 80 at.%), expected to give rise to a ferromagnetic behaviour. For that reason, magnetic force microscopy (MFM) analyses were performed on the obtained FEBID Fe nanostructures. Moreover, object oriented micromagnetic framework (OOMMF) magnetic simulations have been executed to study the influence of the geometry on the magnetic properties of iron single‐domain nanowires. FEBID is a mask‐less nanofabrication method based on the injection of precursor gas molecules in proximity of the deposition area where their decomposition is locally induced by a focused electron beam.
LDPC-coded MIMO systems with unknown block fading channels: soft MIMO detector design, channel estimation, and code optimization (2006)

This paper considers the design of a practical low-density parity check (LDPC)-coded multiple-input multiple-output (MIMO) system composed of M transmit and N receive antennas operating in a flat-fading environment where channel state information (CSI) is assumed to be unavailable both to the transmitter and the receiver. A soft iterative receiver structure is developed, which consists of three main blocks: a soft MIMO detector and two LDPC component soft decoders. We first propose at the component level several soft-input soft-output MIMO detectors whose performances are much better than the conventional minimal mean square error (MMSE)-based detectors. In particular, one optimal soft MIMO detector and two simplified suboptimal detectors are developed that do not require an explicit channel estimate and offer an effective tradeoff between complexity and performance. In addition, a modified expectation maximization (EM)-based MIMO detector is developed that completely removes positive feedback between input and output extrinsic information and provides much better performance compared with the direct EM-based detector that has strong correlations especially in fast-fading channels. At the structural level, the LDPC-coded MIMO receiver is constructed in an unconventional manner where the soft MIMO detector and LDPC variable node decoder form one super soft-decoding unit, and the LDPC check node decoder forms the other component of the iterative decoding scheme. By exploiting the proposed receiver structure, tractable extrinsic information transfer functions of the component soft decoders are obtained, which further lead to a simple and efficient LDPC code degree profile optimization algorithm with proven global optimality and guaranteed convergence from any initialization. Finally, numerical and simulation results are provided to confirm the advantages of the proposed design approach for the coded MIMO system.
Population parameter estimates for performance and reproductive traits in Polish Large White nucleus herds. (1991)

Performance test records from on-farm tests of young Polish Large White boars and reproductive records of Polish Large White sows from 94 nucleus farms during 1978 to 1987 were used to estimate population parameters for the measured traits. The number of boar performance records after editing was 114,347 from 3,932 sires, 21,543 dams, 44,493 litters and 1,075 herd-year-seasons. Reproductive performance records of sows involved 41,080 litters from 2,348 sires, 18,683 dams and 1,520 herd-year-seasons. Both data sets were analyzed by using restricted maximum-likelihood programs. The model used for the performance records included fixed herd-year-seasons, random sires, dams and error effects, and covariances for the year of birth of sire and year of birth of dam. The model used for the reproduction data set was the same as the performance data with parity as an additional fixed effect. Estimated heritabilities were .27, .29, .26, .07, .06, .06 for average daily gain standardized to 180 d (ADG), backfat thickness standardized to 110 kg BW (BF), days to 110 kg (DAYS), litter size at birth born alive (NBA), litter size at 21 d (N21) and litter weight at 21 d (W21), respectively. Estimated common environmental effects for the same traits were .09, .10, .09, .06, .07 and .08, respectively. Genetic correlations were .25 (ADG and BF), -.99 (ADG and DAYS), -.21 (BF and DAYS), .91 (NBA and N21), .68 (NBA and W21) and .80 (N21 and W21). The respective phenotypic correlations were .23, -.99, -.20, .88, .75, .86. These population parameters for Polish Large White pigs are similar to those for breeds in other countries.
Fully automated, sequential focused ion beam milling for cryo-electron tomography (2019)

Abstract Cryo-electron tomography (cryoET) has become a powerful technique at the interface of structural biology and cell biology, with the unique ability to determine structures of macromolecular complexes in their cellular context. A major limitation of cryoET is its restriction to relatively thin samples. Sample thinning by cryo-focused ion beam (cryoFIB) milling has significantly expanded the range of samples that can be analyzed by cryoET. Unfortunately, cryoFIB milling is low-throughput, time-consuming and manual. Here we report a method for fully automated sequential cryoFIB preparation of high-quality lamellae, including rough milling and polishing. We reproducibly applied this method to eukaryotic and bacterial model organisms, and show that the resulting lamellae are suitable for cryoET imaging and subtomogram averaging. Since our method reduces the time required for lamella preparation and minimizes the need for user input, we envision the technique will render previously inaccessible projects feasible.
The development of heparan sulfate sugars as therapeutics: Versatility that couples stem cells, tissue engineering, and wound repair (2004)

Abstract The extracellular matrix (ECM) is a dynamically complex component of all tissues, especially during phases of growth and development. Although historically thought of as “ground substance” or “glycocalyx,” it actually functions as a scaffold for tissue morphogenesis, provides cues for cell proliferation and differentiation, promotes the maintenance of differentiated tissues, and both triggers and enhances the repair response after injury. Although various types of collagens, adhesion glycoproteins, growth factors, and chemokines are present in the extracellular matrices in tissue‐ and temporal‐specific manners, a large fraction of the bioactivity is carried by its sugar component, and especially the heparan sulfate glycosaminoglycans. Because tissue morphogenesis is mediated by multiple ECM influences and by multiple active sites on these components, it is now becoming clear that heparan sulfates play major roles in orchestrating these complex arrangements, particularly during growth and repair processes. Because of their extractability, robustness, and resistance to chemical treatment, biologically active, ECM‐derived sugars seem to be well placed for use in tissue repair, regeneration, and engineering. They also seem to have a promising future in “programming” stem cells for tissue replacement. Drug Dev. Res. 62:303–316, 2004. © 2004 Wiley‐Liss, Inc.
Data from The Wnt Pathway Inhibitor RXC004 Blocks Tumor Growth and Reverses Immune Evasion in Wnt Ligand–dependent Cancer Models (2023)

&lt;div&gt;&lt;p&gt;Wnt signaling is implicated in the etiology of gastrointestinal tract cancers. Targeting Wnt signaling is challenging due to on-target toxicity concerns and lack of druggable pathway components. We describe the discovery and characterization of RXC004, a potent and selective inhibitor of the membrane-bound &lt;i&gt;o&lt;/i&gt;-acyl transferase Porcupine, essential for Wnt ligand secretion. Absorption, distribution, metabolism, and excretion and safety pharmacology studies were conducted with RXC004 &lt;i&gt;in vitro&lt;/i&gt;, and pharmacokinetic exposure assessed &lt;i&gt;in vivo&lt;/i&gt;. RXC004 effects on proliferation and tumor metabolism were explored in genetically defined colorectal and pancreatic cancer models &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. RXC004 effects on immune evasion were assessed in B16F10 immune “cold” and CT26 immune “hot” murine syngeneic models, and in human cell cocultures. RXC004 showed a promising pharmacokinetic profile, inhibited Wnt ligand palmitoylation, secretion, and pathway activation, and demonstrated potent antiproliferative effects in Wnt ligand–dependent (&lt;i&gt;RNF43&lt;/i&gt;-mutant or &lt;i&gt;RSPO3&lt;/i&gt;-fusion) colorectal and pancreatic cell lines. Reduced tumor growth and increased cancer cell differentiation were observed in SNU-1411 (&lt;i&gt;RSPO3&lt;/i&gt;-fusion), AsPC1 and HPAF-II (both &lt;i&gt;RNF43&lt;/i&gt;-mutant) xenograft models, with a therapeutic window versus Wnt homeostatic functions. Additional effects of RXC004 on tumor cell metabolism were confirmed &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; by glucose uptake and &lt;sup&gt;18&lt;/sup&gt;fluorodeoxyglucose-PET, respectively. RXC004 stimulated host tumor immunity; reducing resident myeloid-derived suppressor cells within B16F10 tumors and synergizing with anti-programmed cell death protein-1 (PD-1) to increase CD8&lt;sup&gt;+&lt;/sup&gt;/regulatory T cell ratios within CT26 tumors. Moreover, RXC004 reversed the immunosuppressive effects of HPAF-II cells cocultured with human peripheral blood mononuclear cells, confirming the multiple anticancer mechanisms of this compound, which has progressed into phase II clinical trials.&lt;/p&gt;Significance:&lt;p&gt;Wnt pathway dysregulation drives many gastrointestinal cancers; however, there are no approved therapies that target the pathway. RXC004 has demonstrated the potential to block both tumor growth and tumor immune evasion in a genetically defined, clinically actionable subpopulation of Wnt ligand–dependent gastrointestinal cancers. The clinical utility of RXC004, and other Porcupine inhibitors, in such Wnt ligand–dependent cancers is currently being assessed in patient trials.&lt;/p&gt;&lt;/div&gt;
Abstract A02: MEK-CDK4/6 inhibition induces plasma cell tumor infiltration and sensitizes de novo MPNSTs to immune checkpoint blockade (2022)

Abstract Malignant peripheral nerve sheath tumors (MPNSTs) are deadly, Ras-driven sarcomas that lack effective therapies. Many tumors are unresectable and toxic chemotherapies are ineffectual. The sensitivity of MPNSTs to immune checkpoint blockade (ICB) therapies is not known, although sarcomas are generally unresponsive. Patient tumor analyses comparing MPNSTs to benign precursors identified Ras effectors, MEK and CDK4/6 kinases, as rational targets for therapy. We tested the efficacy of dual MEK-CDK4/6 inhibition versus single drug therapy using preclinical MPNST models. In MPNST cells, low-dose drug combinations synergistically reactivated the retinoblastoma (RB1) tumor suppressor, induced cell death and decreased clonogenic survival. In de novo MPNSTs in immune competent mice, combination therapy caused tumors to shrink, substantially delayed resistant tumor outgrowth and improved survival relative to monotherapies. Tumor regression was associated with an immune activation gene expression profile featuring plasma cell infiltration, an event not previously observed with MEK-CDK4/6 inhibitor therapy. In other human tumor types, intratumoral plasma cells prognose better overall survival and improved response to ICB therapies. Excitingly, MEK-CDK4/6 therapy sensitized de novo MPNSTs to anti-programmed death ligand 1 (PD-L1) therapy with the combination achieving complete tumor ablation and apparent cure in 10% of mice. These findings implicate a critical role for plasma cells in mediating MPNST regression in response to kinase inhibitor therapy and sensitizing tumors to PD-L1 targeting. This novel therapeutic combination is a promising option for MPNST therapy that could improve ICB efficacy in other solid tumors. Citation Format: Joshua Lingo, Jordan Kohlmeyer, Courtney Kaemmer, Amanda Scherer, Ellen Voigt, Michael Chimenti, Munir Tanas, Varun Monga, Ben Darbro, David Meyerholz, Rebecca Dodd, Dawn Quelle. MEK-CDK4/6 inhibition induces plasma cell tumor infiltration and sensitizes de novo MPNSTs to immune checkpoint blockade [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A02.