gebhart/patrepeval huggingface dataset:
MicroRNAs as potential drug targets for therapeutic intervention in colorectal cancer (2015)

Targeting miRNAs provides an emerging opportunity to develop effective miRNA-based replacement therapy or antagonists to alter expression in colon cancer patient tumors. However, the biggest challenge is to overcome obstacles associated with pharmacokinetics, delivery and toxicity in order to translate the potential of miRNAs into efficacious anticancer drugs.
Robust Topology Optimization of Foundry-Manufacturable Photonic Devices: An Open-Source FDTD Toolbox (2020)

Integrated photonic foundries require development kits composed of compact, robust, broadband, 3D devices. We report on a novel, open-source density-based topology optimization framework that reliably designs devices to meet these stringent criteria.
A layered naming architecture for the internet (2004)

Currently the Internet has only one level of name resolution, DNS, which converts user-level domain names into IP addresses. In this paper we borrow liberally from the literature to argue that there should be three levels of name resolution: from user-level descriptors to service identifiers; from service identifiers to endpoint identifiers; and from endpoint identifiers to IP addresses. These additional levels of naming and resolution (1) allow services and data to be first class Internet objects (in that they can be directly and persistently named), (2) seamlessly accommodate mobility and multi-homing and (3) integrate middleboxes (such as NATs and firewalls) into the Internet architecture. We further argue that flat names are a natural choice for the service and endpoint identifiers. Hence, this architecture requires scalable resolution of flat names, a capability that distributed hash tables (DHTs) can provide.
A randomised, double‐blind, placebo‐controlled study of the LAG‐3‐depleting monoclonal antibody GSK2831781 in patients with active ulcerative colitis (2023)

Despite evidence of target cell depletion in blood, GSK2831781 failed to reduce inflammation in the colonic mucosa suggesting no pharmacological effect. The study was terminated early (NCT03893565).
Detection of Trace Proteins in Multicomponent Mixtures Using Displacement Chromatography (2011)

Model protein feed mixtures containing three abundant and seven trace proteins at various concentrations were identified and employed in a series of displacement experiments. Reversed-phase liquid chromatography (RPLC) and matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry were used to evaluate the compositions of both the feed mixtures and effluent fractions from the displacement experiments. The results demonstrated that trace proteins were focused at the boundaries between the abundant solutes where they were enriched and concentrated. For many of the multicomponent feed mixtures, mass spectrometry analyses of the displacement column effluent fractions resulted in the identification of trace proteins that were not detectable in the feed. In addition, the use of minimal or no salt in the carrier solutions enabled the analysis of displacement fractions by direct infusion mass spectrometry. These results are significant in that they indicate that while the presence of abundant proteins can often be problematic for the detection of trace components, displacement chromatography may be able to employ these abundant proteins to focus trace proteins in the displacement train, thus facilitating detection.
Low-cost single-phase powered induction machine drive for residential applications (2004)

In conjunction with the 2003 future energy challenge (FEC), a low-cost integrated machine end drive system is considered for residential applications between 50 and 500 W. The objective is to remain cost competitive with traditional single phase induction machine solutions while improving system performance. The basic architecture includes a power factor correction boost rectifier, a hex-bridge inverter, control circuitry implementing selective harmonic elimination, auxiliary power supplies, and a three phase induction machine designed for inverter operation. This paper discusses system design, performance, cost, and lifetime.
Reducing Write Amplification of Flash Storage through Cooperative Data Management with NVM (2017)

Write amplification is a critical factor that limits the stable performance of flash-based storage systems. To reduce write amplification, this article presents a new technique that cooperatively manages data in flash storage and nonvolatile memory (NVM). Our scheme basically considers NVM as the cache of flash storage, but allows the original data in flash storage to be invalidated if there is a cached copy in NVM, which can temporarily serve as the original data. This scheme eliminates the copy-out operation for a substantial number of cached data, thereby enhancing garbage collection efficiency. Simulated results show that the proposed scheme reduces the copy-out overhead of garbage collection by 51.4% and decreases the standard deviation of response time by 35.4% on average. Measurement results obtained by implementing the proposed scheme in BlueDBM, 1 an open-source flash development platform developed by MIT, show that the proposed scheme reduces the execution time and increases IOPS by 2--21% and 3--18%, respectively, for the workloads that we considered. This article is an extended version of Lee et al. [2016], which was presented at the 32nd International Conference on Massive Data Storage Systems and Technology in 2016.
A Numerical Technique for the Approximation of Thermal Zones (2011)

The concept of thermal zones has been proposed in recent years as a means for providing operational information regarding which physical areas (or zones) in a data center are being supplied by the different air conditioning units, in order to gain insights as to optimal use of cooling equipment [1, 2]. One methodology for computing such thermal zones consists of explicit tracing of streamlines of an air velocity field [2]. In the present work, we propose an alternative technique which does not require explicit tracing of streamlines. Specifically, the problem of identifying thermal zones is being formulated as a boundary value problem for convective transport. Using a numerical method capable of solving convection-dominated problems accurately leads to identification of the zones by a simple postprocessing of the numerical solution of the boundary value problem, making the procedure convenient to apply, especially in three-dimensional domains.
Generative Model for Layers of Appearance and Deformation. (2005)

The dimensional alterations of denture bases were verified in function of the acrylic resin post-pressing time. Twenty stone cast/wax base sets were confected for routine flasking procedure. Thermosetting acrylic resin (Clássico) was prepared according to the instructions of the manufacturer. After final pressing, the acrylic resin was submitted to polymerization in water at 74 degrees C during 9 hours, following the immediate, 6-, 12-, and 24-hour post-pressing times. The resin bases were fixed on the casts with instantaneous adhesive and the sets were laterally sectioned in the regions corresponding to the distal aspect of canines (A), mesial aspect of first molars (B), and posterior palatal zone (C). The gap between the stone cast and the resin base was measured with a comparative microscope at five referential positions for each kind of sectioning. Data submitted to ANOVA and Tukey's test showed that there was no statistically significant difference between the immediate and the 6-hour post-pressing times as well as between the 12- and the 24-hour post-pressing times. However, there was statistically significant difference between the immediate/6-hour groups and the 12-/24-hour groups.
A pretargeting system for tumor PET imaging and radioimmunotherapy (2015)

Labeled antibodies, as well as their fragments and antibody-derived recombinant constructs, have long been proposed as general vectors to target radionuclides to tumor lesions for imaging and therapy. They have indeed shown promise in both imaging and therapeutic applications, but they have not fulfilled the original expectations of achieving sufficient image contrast for tumor detection or sufficient radiation dose delivered to tumors for therapy. Pretargeting was originally developed for tumor immunoscintigraphy. It was assumed that directly-radiolabled antibodies could be replaced by an unlabeled immunoconjugate capable of binding both a tumor-specific antigen and a small molecular weight molecule. The small molecular weight molecule would carry the radioactive payload and would be injected after the bispecific immunoconjugate. It has been demonstrated that this approach does allow for both antibody-specific recognition and fast clearance of the radioactive molecule, thus resulting in improved tumor-to-normal tissue contrast ratios. It was subsequently shown that pretargeting also held promise for tumor therapy, translating improved tumor-to-normal tissue contrast ratios into more specific delivery of absorbed radiation doses. Many technical approaches have been proposed to implement pretargeting, and two have been extensively documented. One is based on the avidin-biotin system, and the other on bispecific antibodies binding a tumor-specific antigen and a hapten. Both have been studied in preclinical models, as well as in several clinical studies, and have shown improved targeting efficiency. This article reviews the historical and recent preclinical and clinical advances in the use of bispecific-antibody-based pretargeting for radioimmunodetection and radioimmunotherapy of cancer. The results of recent evaluation of pretargeting in PET imaging also are discussed.
ULTRAFAST SPECTROSCOPY OF METHYL VIOLOGEN: EFFECTS OF ZEOLITE ENTRAPMENT (2008)

Author Institution: Department of Chemistry, The Ohio State University, Columbus, OH 43210
Effects of Delta1 and Jagged1 on Early Human Hematopoiesis: Correlation with Expression of Notch Signaling‐Related Genes in CD34 + Cells (2006)

It has been shown that Notch signaling mediated by ligands of both Jagged and Delta families expands the hematopoietic stem cell compartment while blocking or delaying terminal myeloid differentiation. Here we show that Delta1- and Jagged1-expressing stromal cells have distinct effects on the clonogenic and differentiation capacities of human CD34(+) CD38(+) cells. Jagged1 increases the number of bipotent colony-forming unit-granulocyte macrophage (CFU-GM) and unipotent progenitors (CFU-granulocytes and CFU-macrophages), without quantitatively affecting terminal cell differentiation, whereas Delta1 reduces the number of CFU-GM and differentiated monocytic cells. Expression analysis of genes coding for Notch receptors, Notch targets, and Notch signaling modulators in supernatant CD34(+) cells arising upon contact with Jagged1 and Delta1 shows dynamic and differential gene expression profiles over time. At early time points, modest upregulation of Notch1, Notch3, and Hes1 was observed in Jagged1-CD34(+) cells, whereas those in contact with Delta1 strikingly upregulated Notch3 and Hes1. Later, myeloid progenitors with strong clonogenic potential emerging upon contact with Jagged1 upregulated Notch1 and Deltex and downregulated Notch signaling modulators, whereas T/NK progenitors originated by Delta1 strikingly upregulated Notch3 and Deltex and, to a lesser extent, Hes1, Lunatic Fringe, and Numb. Together, the data unravel previously unrecognized expression patterns of Notch signaling-related genes in CD34(+) CD38(+) cells as they develop in Jagged1- or Delta1-stromal cell environments, which appear to reflect sequential maturational stages of CD34(+) cells into distinct cell lineages.
Selective interaction of megalin with postsynaptic density-95 (PSD-95)-like membrane-associated guanylate kinase (MAGUK) proteins (2003)

Megalin is an integral membrane receptor belonging to the low-density lipoprotein receptor family. In addition to its role as an endocytotic receptor, megalin has also been proposed to have signalling functions. Using interaction cloning in yeast, we identified the membrane-associated guanylate kinase family member postsynaptic density-95 (PSD-95) as an interaction partner for megalin. PSD-95 and a truncated version of megalin were co-immunoprecipitated from HEK-293 cell lysates overexpressing the two proteins, which confirmed the interaction. The two proteins were found to be co-localized in these cells by confocal microscopy. Immunocytochemical studies showed that cells in the parathyroid, proximal tubuli of the kidney and placenta express both megalin and PSD-95. We found that the interaction between the two proteins is mediated by the binding of the C-terminus of megalin, which has a type I PSD-95/ Drosophila discs-large/zona occludens 1 (PDZ)-binding motif, to the PDZ2 domain of PSD-95. The PSD-95-like membrane-associated guanylate kinase ('MAGUK') family contains three additional members: PSD-93, synapse-associated protein 97 (SAP97) and SAP102. We detected these proteins, apart from SAP102, in parathyroid chief cells, a cell type having a marked expression of megalin. The PDZ2 domains of PSD-93 and SAP102 were also shown to interact with megalin, whereas no interaction was detected for SAP97. The SAP97 PDZ2 domain differed at four positions from the other members of the PSD-95 subfamily. One of these residues was Thr(389), located in the alphaB-helix and part of the hydrophobic pocket of the PDZ2 domain. Surface plasmon resonance experiments revealed that mutation of SAP97 Thr(389) to alanine, as with the other PSD-95-like membrane-associated guanylate kinases, induced binding to megalin.
The Role of Proteasomes in the Thymus (2021)

The thymus provides a microenvironment that supports the generation and selection of T cells. Cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells (mTECs) are essential components of the thymic microenvironment and present MHC-associated self-antigens to developing thymocytes for the generation of immunocompetent and self-tolerant T cells. Proteasomes are multicomponent protease complexes that degrade ubiquitinated proteins and produce peptides that are destined to be associated with MHC class I molecules. cTECs specifically express thymoproteasomes that are essential for optimal positive selection of CD8 + T cells, whereas mTECs, which contribute to the establishment of self-tolerance in T cells, express immunoproteasomes. Immunoproteasomes are also detectable in dendritic cells and developing thymocytes, additionally contributing to T cell development in the thymus. In this review, we summarize the functions of proteasomes expressed in the thymus, focusing on recent findings pertaining to the functions of the thymoproteasomes and the immunoproteasomes.
Rotational–Vibrational Spectroscopy of NH2D Using High-Resolution Laser Techniques (1970)

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Secure Software Development by Example (2005)

When trying to incorporate security into a program, software developers face either too much theoretical information that they cannot apply or exhaustive and discouraging recommendation lists. This article gives an overview of security concerns at each step of a project's life cycle.
Blowout Fracture after Descemet's Stripping Automated Endothelial Keratoplasty (2014)

We present the case of an 86-year-old woman who developed a blowout fracture after Descemet's stripping automated endothelial keratoplasty (DSAEK). Sixteen months after DSAEK, she suffered a blow to her left eye caused by a fall. Computed tomography confirmed the presence of a blowout fracture of the inferior wall of the left orbit with soft tissue prolapsing into the orbit. The patient complained of no abnormal symptoms, and her operated cornea was intact and clear. There was no abnormal finding in both the anterior and posterior segments. This case highlights that the DSAEK technique provides adequate tectonic stability of the globe throughout the traumatic event in contrast to penetrating keratoplasty, which can lead to devastating vision damage after trauma.
Supermolecular structure of the enteropathogenic Escherichia coli type III secretion system and its direct interaction with the EspA-sheath-like structure (2001)

Enteropathogenic Escherichia coli (EPEC) secretes several Esp proteins via the type III secretion system (secreton). EspA, EspB, and EspD are required for translocation of the effector proteins into host cells, in which EspB and EspD are thought to form a pore in the host membrane. Recent study has shown that EspA forms a filamentous structure that assembles as a physical bridge between bacteria and host cell surfaces, which then functions as a conduit for the translocation of bacterial effectors into host cells. To investigate the supermolecular structure of the type III secreton in EPEC, we partially purified it from the bacteria membrane and observed it via transmission electron microscopy. The EPEC type III secreton was composed of a basal body and a needle part and was similar to those of Salmonella and Shigella, except for a sheath-like structure at the tip of the needle. The length of sheath-like structures varied; it extended more than 600 nm and was 10 times longer than the Shigella needle part. The putative major needle component, EscF, was required for both secretion of Esp proteins and needle complex formation. Interestingly, elongation of the sheath-like structure was observed under constitutive expression of EspA but not of EscF. Furthermore, the transmission electron microscopy view with immunogold labeled anti-EspA antibodies clearly showed that EspA is a component of the sheath-like structure. This study revealed, to our knowledge for the first time, the supermolecular structure of the EPEC type III secreton and its direct association with the EspA-sheath-like structure.
Orientation‐Dependent Intercalation Channels for Lithium and Sodium in Black Phosphorus (2019)

Black phosphorus (BP) with unique 2D structure enables the intercalation of foreign elements or molecules, which makes BP directly relevant to high-capacity rechargeable batteries and also opens a promising strategy for tunable electronic transport and superconductivity. However, the underlying intercalation mechanism is not fully understood. Here, a comparative investigation on the electrochemically driven intercalation of lithium and sodium using in situ transmission electron microscopy is presented. Despite the same preferable intercalation channels along [100] (zigzag) direction, distinct anisotropic intercalation behaviors are observed, i.e., Li ions activate lateral intercalation along [010] (armchair) direction to form an overall uniform propagation, whereas Na diffusion is limited in the zigzag channels to cause the columnar intercalation. First-principles calculations indicate that the diffusion of both Li and Na ions along the zigzag direction is energetically favorable, while Li/Na diffusion long the armchair direction encounters an increased energy barrier, but that of Na is significantly larger and insurmountable, which accounts for the orientation-dependent intercalation channels. The evolution of chemical states during phase transformations (from Li<sub>x</sub> P/Na<sub>x</sub> P to Li<sub>3</sub> P/Na<sub>3</sub> P) is identified by analytical electron diffraction and energy-loss spectroscopy. The findings elucidate atomistic Li/Na intercalation mechanisms in BP and show potential implications for other similar 2D materials.
Synchronization and timing in CMS HCAL (2007)

The synchronization and timing of the hadron calorimeter (HCAL) for the Compact Muon Solenoid has been extensively studied with test beams at CERN during the period 2003-4, including runs with 40 MHz structured beam. The relative phases of the signals from different calorimeter segments are timed to 1 ns accuracy using a laser and equalized using programmable delay settings in the front-end electronics. The beam was used to verify the timing and to map out the entire range of pulse shapes over the 25 ns interval between beam crossings. These data were used to make detailed measurements of energy-dependent time slewing effects and to tune the electronics for optimal performance.
Somatostatinergic ligands in dopamine-sensitive and -resistant prolactinomas (2008)

Although the SSTRs are expressed in prolactinomas, the somatostatinergic ligands analyzed do not appear to be highly effective in suppressing PRL. D2DR remains the primary target for effective treatment of prolactinomas.
Asymptotic Analysis of Complex LASSO via Complex Approximate Message\n Passing (CAMP) (2011)

Recovering a sparse signal from an undersampled set of random linear\nmeasurements is the main problem of interest in compressed sensing. In this\npaper, we consider the case where both the signal and the measurements are\ncomplex. We study the popular reconstruction method of $\\ell_1$-regularized\nleast squares or LASSO. While several studies have shown that the LASSO\nalgorithm offers desirable solutions under certain conditions, the precise\nasymptotic performance of this algorithm in the complex setting is not yet\nknown. In this paper, we extend the approximate message passing (AMP) algorithm\nto the complex signals and measurements and obtain the complex approximate\nmessage passing algorithm (CAMP). We then generalize the state evolution\nframework recently introduced for the analysis of AMP, to the complex setting.\nUsing the state evolution, we derive accurate formulas for the phase transition\nand noise sensitivity of both LASSO and CAMP.\n
The Hip in Adults with Classic Bladder Exstrophy: A Biomechanical Analysis (2000)

We studied the untreated pelvic deformity in 14 adult patients with bladder exstrophy to determine the relative hip-joint force and stress and their effects on the clinical status of the hip. Pelvic radiographs were used for biomechanical analysis to calculate joint force and joint stress (force/area) relative to partial body weight, which allowed comparison between patients and age-matched controls. IOWA hip ratings were used for clinical evaluation, and hips were scored radiographically for degenerative joint disease. The mean relative joint force and joint stress was significantly higher for exstrophy patients (p < 0.001). In addition, the mean distance from the body center to the center of the femoral head was significantly increased (p < 0.001) in bladder exstrophy patients. An increase in diastasis correlated with an approximate 30% increase in the distance from the center of the femoral head to the body midline. The mean distance from the greater trochanter to the femoral head center was significantly less (p < 0.02) and the center–edge angle was significantly decreased in exstrophy patients (p < 0.05). Two patients' hips showed significant subluxation, and one of these showed degenerative hip disease in association with poor IOWA and radiographic scores.The force and stress on the hip joint are increased in untreated adult bladder exstrophy patients. Further longitudinal study is indicated to validate these findings and to determine whether clinically important degenerative changes are occurring. This could affect treatment recommendations in childhood.
A Real Time Simulator of a PEV's On Board Battery Charger (2019)

This paper presents an FPGA based real time (RT) simulator for a Plug in Electrical Vehicle”s (PEV) on board battery charger. Common values for the switching frequencies of the AC-DC and DC-DC stages range between tens of kilohertz to hundreds of kilohertz, so the design effort aimed obtaining a very small time step in order to account for the switching effects. By taking advantage of the parallel structure of the FPGA and using Xilinx's Vivado High Level Synthesis tool, a time step of 40ns was obtained. The RT simulator was validated through simulation means and experimentally on a custom ZYNQ based board. The purpose of the developed intellectual property (IP) is to reduce the development cost and time of the charger's control system with the aid of hardware in the loop (HIL) simulations.