gebhart/patrepeval huggingface dataset:
A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated Cys-His domain and functions as a transcriptional repressor. (1994)

The class II major histocompatibility complex (MHC) molecules function in the presentation of processed peptides to helper T cells. As most mammalian cells can endocytose and process foreign antigen, the critical determinant of an antigen-presenting cell is its ability to express class II MHC molecules. Expression of these molecules is usually restricted to cells of the immune system and dysregulated expression is hypothesized to contribute to the pathogenesis of a severe combined immunodeficiency syndrome and certain autoimmune diseases. Human complementary DNA clones encoding a newly identified, cysteine-rich transcription factor, NF-X1, which binds to the conserved X-box motif of class II MHC genes, were obtained, and the primary amino acid sequence deduced. The major open reading frame encodes a polypeptide of 1,104 amino acids with a symmetrical organization. A central cysteine-rich portion encodes the DNA-binding domain, and is subdivided into seven repeated motifs. This motif is similar to but distinct from the LIM domain and the RING finger family, and is reminiscent of known metal-binding regions. The unique arrangement of cysteines indicates that the consensus sequence CX3CXL-XCGX1-5HXCX3CHXGXC represents a novel cysteine-rich motif. Two lines of evidence indicate that the polypeptide encodes a potent and biologically relevant repressor of HLA-DRA transcription: (a) overexpression of NF-X1 from a retroviral construct strongly decreases transcription from the HLA-DRA promoter; and (b) the NF-X1 transcript is markedly induced late after induction with interferon gamma (IFN-gamma), coinciding with postinduction attenuation of HLA-DRA transcription. The NF-X1 protein may therefore play an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by IFN-gamma.
Viral-Mediated Temporally Controlled Dopamine Production in a Rat Model of Parkinson Disease (2005)

Regulation of gene expression is necessary to avoid possible adverse effects of gene therapy due to excess synthesis of transgene products. To reduce transgene expression, we developed a viral vector-mediated somatic regulation system using inducible Cre recombinase. A recombinant adeno-associated virus (AAV) vector expressing Cre recombinase fused to a mutated ligand-binding domain of the estrogen receptor alpha (CreER(T2)) was delivered along with AAV vectors expressing dopamine-synthesizing enzymes to rats of a Parkinson disease model. Treatment with 4-hydroxytamoxifen, a synthetic estrogen receptor modulator, activated Cre recombinase within the transduced neurons and induced selective excision of the tyrosine hydroxylase (TH) coding sequence flanked by loxP sites, leading to a reduction in transgene-mediated dopamine synthesis. Using this strategy, aromatic L-amino acid decarboxylase (AADC) activity was retained so that l-3,4-dihydroxyphenylalanine (L-dopa), a substrate for AADC, could be converted to dopamine in the striatum and the therapeutic effects of L-dopa preserved, even after reduction of TH expression in the case of dopamine overproduction. Our data demonstrate that viral vector-mediated inducible Cre recombinase can serve as an in vivo molecular switch, allowing spatial and temporal control of transgene expression, thereby potentially increasing the safety of gene therapy.
Mimicking cell–cell interactions at the biomaterial–cell interface for control of stem cell differentiation (2006)

The ability to regulate stem cell proliferation and differentiation has relevance in numerous medical applications, including medical devices, tissue engineering, and regenerative medicine. To control cellular behavior at the biomaterial or scaffold interface, many studies have employed surface modifications that mimic the extracellular matrix. Strikingly absent is the immobilization of cell-surface ligands to the biomaterial surface. One cell-to-cell signaling pathway that has been shown to regulate tissue development and stem cell fate is the Notch pathway. Recently, the Notch signaling pathway was identified as a key regulator of epithelial differentiation. Utilizing this knowledge, we applied an affinity immobilization scheme designed to attach and orient the Notch ligand, Jagged-1, in an active conformation on a biomaterial surface. When epithelial stem cells were plated on the bound ligand, the Notch/CBF-1 signaling pathway was stimulated and the cells upregulated both intermediate- and late-stage differentiation markers. In addition, the ligand promoted tight clustering and extensive stratification. Soluble Jagged-1 showed no Notch/CBF-1 signaling and very little, if any, cell differentiating activity. The high potency of bound Jagged-1 suggests that modification of a surface with a Notch ligand presents a powerful method to control stem cell differentiation at the cell-biomaterial interface.
Rapid thermal chemical vapor deposition of <i>in situ</i> boron-doped polycrystalline silicon-germanium films on silicon dioxide for complimentary-metal-oxide-semiconductor applications (1997)

In situ boron-doped polycrystalline Si1−xGex (x&gt;0.4) films have been formed on the thermally grown oxides in a rapid thermal chemical vapor deposition processor using SiH4-GeH4-B2H6-H2 gas system. Our results showed that in situ boron-doped Si1−xGex films can be directly deposited on the oxide surface, in contrast to the rapid thermal deposition of undoped silicon-germanium (Si1−xGex) films on oxides which is a partially selective process and requires a thin silicon film pre-deposition to form a continuous film. For the in situ boron-doped Si1−xGex films, we observed that with the increase of the germane percentage in the gas source, the Ge content and the deposition rate of the film are increased, while its resistivity is decreased down to 0.66 mΩ cm for a Ge content of 73%. Capacitance-voltage characteristics of p-type metal-oxide-semiconductor capacitors with p+-Si1−xGex gates showed negligible polydepletion effect for a 75 Å gate oxide, indicating that a high doping level of boron at the poly-Si1−xGex/oxide interface was achieved.
P‐15: An Efficient Liquid Crystal Display Driving Scheme Using Orthogonal Block‐Circulant Matrix (2000)

Abstract In this paper, orthogonal block‐circulant (OBC) matrices are identified, which result in efficient implementation of the Multi‐Line Addressing (MLA) and the Active Addressing schemes. The row driving waveforms are time‐shifted versions of each other, thus reducing the hardware complexity.
Microfluidic generation of transient cell volume exchange for convectively driven intracellular delivery of large macromolecules (2018)

Efficient intracellular delivery of target macromolecules remains a major obstacle in cell engineering and other biomedical applications. We discovered a unique cell biophysical phenomenon of transient cell volume exchange by using microfluidics to rapidly and repeatedly compress cells. This behavior consists of brief, mechanically induced cell volume loss followed by rapid volume recovery. We harness this behavior for high-throughput, convective intracellular delivery of large polysaccharides (2000 kDa), particles (100 nm), and plasmids while maintaining high cell viability. Successful proof of concept experiments in transfection and intracellular labeling demonstrated potential to overcome the most prohibitive challenges in intracellular delivery for cell engineering.
Solution-Processed Squaraine Bulk Heterojunction Photovoltaic Cells (2010)

The donor, 2,4-bis[4-(N,N-diisobutylamino)-2,6-dihydroxyphenyl] squaraine (SQ) is used with the acceptor, [6,6]-phenyl C70 butyric acid methyl ester (PC70BM) to result in efficient, solution-processed, small-molecule bulk heterojunction photovoltaic cells. The distribution of the donor nanoparticles in the acceptor matrix as a function of relative concentrations results in a trade-off between exciton dissociation and hole mobility (and hence, cell series resistance). A bulk heterojunction solar cell consisting of an active region with a component ratio of SQ to PC70BM of 1:6 has a power conversion efficiency of 2.7 +/- 0.1% with a 8.85 +/- 0.22 mA/cm(2) short-circuit current density and an open-circuit voltage of 0.89 +/- 0.01 V obtained under simulated 1 sun (100 mW/cm(2)) air mass 1.5 global (AM1.5 G) solar illumination. This is a decrease from 3.3 +/- 0.3% at 0.2 sun intensity, and is less than that of a control planar heterojunction SQ/C60 cell with 4.1 +/- 0.2% at 1 sun, suggesting that the nanoparticle morphology introduces internal resistance into the solution-based thin film. The nanomorphology and hole mobility in the films is strongly dependent on the SQ-to-PC70BM ratio, increasing by greater than 2 orders of magnitude as the ratio increases from 28% to 100% SQ.
Digital Optoelectrical Pulse Method for Vernier-Type Rotary Encoders (2015)

This paper proposes the digital optoelectrical pulse (DOP) method for vernier-type rotary encoders in highresolution applications. A 25-b encoder using the DOP method is demonstrated. In rotary encoders, the low-bit data of an angle measurement are easily generated using a periodic signal. The high-bit data of an absolute angle measurement can be obtained using various methods such as binary code, gray code, pseudorandom code, M code, or the vernier method. The vernier method has a significant advantage over the above methods for small-sized rotary encoders because it requires fewer grating tracks than do other methods. The vernier method uses grating tracks to generate periodic signals rather than digitally coded signals. In the vernier method, periodic signals with slightly different frequencies are used. The high-bit data of an absolute angle measurement can be obtained using the difference of two periodic signals. Complete absolute angle data are obtained by concatenating the high-bit data and the low-bit data. However, the high-bit data and the low-bit data are, in general, not synchronized. As a result, significant intermediate-bit errors occur at the concatenation point. The DOP method is developed in this paper to mitigate these intermediate-bit error problems. A system on a chip (SoC) that uses the proposed method is designed and fabricated using a 0.18-μm CMOS image sensor process. A 25-b absolute encoder is constructed using an SoC that provides absolute angle data without intermediate-bit errors.
Market-based coordination of thermostatically controlled loads-Part I: A mechanism design formulation (2016)

This paper focuses on the coordination of a population of thermostatically controlled loads (TCLs) with unknown parameters to achieve group objectives. The problem involves designing the device bidding and market clearing strategies to motivate self-interested users to realize efficient energy allocation subject to a peak energy constraint. This coordination problem is formulated as a mechanism design problem, and we propose a mechanism to implement the social choice function in dominant strategy equilibrium. The proposed mechanism consists of a novel bidding and clearing strategy that incorporates the internal dynamics of TCLs in the market mechanism design, and we show it can realize the team optimal solution. This paper is divided into two parts. Part I presents a mathematical formulation of the problem and develops a coordination framework using the mechanism design approach. Part II presents a learning scheme to account for the unknown load model parameters, and evaluates the proposed framework through realistic simulations.
Results of flight tests of a two-channel radar system with real-time MTI processing (2003)

In synthetic aperture radar (SAR), only fixed targets are mapped on their correct positions. Moving targets are displaced in azimuthal direction due to the Doppler frequency shift caused by target velocities. The detection and correct positioning of moving targets within SAR images is a problem that can be solved by using multiple antennas and multi-channel receivers. For the detection of slow moving targets or moving targets that are backfolded into the clutter spectrum, a good suppression of fixed target echoes is necessary to gain subclutter visibility. Space-time adaptive processing (STAP) shows good performance in clutter suppression and is state of the art. However, the main disadvantage of conventional STAP techniques is the very high computational load. Therefore, performing STAP in real-time for the purpose of on-board subclutter moving target indication (MTI) requires special techniques. To estimate the true azimuthal positions of moving targets, phase differences between receiver channels can be evaluated e.g. by using the well-known monopulse method. Alternatively, STAP can be applied to solve this problem as well. STAP in real-time is discussed for two applications. First, STAP can be used for suppressing clutter and jammers. Moreover, clutter filter coefficients gained by STAP can be used for the purpose of correct positioning of moving targets within SAR images. Results of this real-time STAP technique as well as results of the moving target repositioning technique are presented: the clutter suppression quality and the moving target repositioning accuracy are demonstrated with real SAR data and moving targets recorded during a measurement campaign.
Immunosequencing reveals diagnostic signatures of chronic viral infection in T cell memory (2015)

ABSTRACT B and T cells expand clonally in response to pathogenic infection, and their descendants, which share the same receptor sequence, can persist for years, forming the basis of immunological memory. While most T cell receptor (TCR) sequences are seen very rarely, ‘public’ TCRs are present in many individuals. Using a combination of high throughput immunosequencing, statistical association of particular TCRs with disease status, and machine learning, we identified of a set of public TCRs that discriminates cytomegalovirus (CMV) infection status with high accuracy. This pathogen-specific diagnostic tool uses a very general assay that relies only on a training cohort coupled with immunosequencing and sophisticated data analysis. Since all memory T cell responses are encoded in the common format of somatic TCR rearrangements, a key advantage of reading T cell memory to predict disease status is that this approach should apply to a wide variety of diseases. The underlying dataset is the largest collection of TCRs ever published, including ∼300 gigabases of sequencing data and ∼85 million unique TCRs across 640 HLA-typed individuals, which constitutes by far the largest such collection ever published. We expect these data to be a valuable public resource for researchers studying the TCR repertoire.
Characterization of a mitogen-activated protein kinase from<i>Pneumocystis carinii</i> (1998)

The pathogenic fungus Pneumocystis carinii causes severe pneumonia in patients with impaired immunity, particularly patients with acquired immunodeficiency syndrome. The life cycle of P. carinii is poorly understood, and the inability to continuously culture P. carinii is a major limitation in understanding its cell biology. In fungi homologous to P. carinii, pheromone mating factors signal through a mitogen-activated protein kinase (MAPK) signal transduction cascade, resulting in mitotic cell cycle arrest and entry into a pathway of conjugation, cellular differentiation, and proliferation. Using degenerate PCR and library screening, we have identified a MAPK cDNA in P. carinii that is highly homologous to fungal MAPKs involved in the pheromone mating signal transduction cascade, and we demonstrate MAPK activity in P. carinii lysates with a specific antiserum derived from the translated P. carinii MAPK cDNA sequence.
Lysine-functionalized nanodiamonds: synthesis, physiochemical characterization, and nucleic acid binding studies (2012)

The lysine-substituted ND particles generated in this study exhibit stable aqueous formulations and show potential for use as carriers for genetic materials.
A Crosstalk-Friendly Signaling Method (2018)

As computer performance continues to increase at an exponential rate, the system bus bandwidth must scale in proportion. Increased bandwidth demands and smaller chassis sizes lead to a scenario where crosstalk noise becomes a primary limiter of bus performance. The goal of this paper is to remove the crosstalk bottleneck to allow very dense routing on printed circuit boards and packages, so the maximum computational capability can be designed into the smallest possible volume. This paper presents a new nonbinary signaling scheme called “crosstalk-harnessed signaling” (CHS) that encodes the data so that each bit is spread across multiple conductors in a way whereby crosstalk becomes part of the signal and can be removed during the decoding process. CHS can be implemented with relatively simple low-power circuits and can realize bus bandwidth gains over binary signaling as high as 2–3 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${\times}$ </tex-math></inline-formula> while allowing <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2{\times}$ </tex-math></inline-formula> increase in routing density and increased pin efficiency compared to differential signaling. Finally, passive test board measurements corroborate simulations in demonstrating the benefits of CHS in crosstalk compensation over binary signaling to maximize the channel bandwidth density.
An improved photonic bandgap fiber based on an array of rings (2006)

We describe the modeling, fabrication and characterization of a silica-core photonic bandgap fiber based on a 2-d array of raised-index cladding rings. The use of rings to form the cladding is shown to re-order the cladding modes in such a way as to broaden the photonic band gaps and reduce bend sensitivity. We compare the performance of the ring fiber with that of a similar fiber made using solid rods.
Experimental simulation of solids distribution in coal liquefaction dissolvers (1981)

A major element of the coal dissolution section of any liquefaction plant is the dissolver. The design of the SRC-I Demonstration Plant Dissolver planned for Western Kentucky based on data generated from the Wilsonville and Ft. Lewis dissolvers is discussed. Two different columns of 127 mm (5 inch) and 305 mm (12 inch) diameters were used to investigate the effect of gas and liquid velocities on solids distribution and accumulation using an air/water/sand system. 6 refs.
Antimicrobial and Antioxidative Probiotic Lactobacillus Fermentum Me-3 (2009)

Aging of population, new emerging infections, allergies as well as atherosclerosis and cardio- vascular diseases have become serious problems for world community. There is a clear need for healthy nutrition and development of functional food (FF), including probiotics. Probiotics are beneficial microbes that consumed as FF normalize the composition of the intestinal microbiota, improve the immune and metabolic functions of host. This book presents the strain Lactobacillus fermentum ME-3 as a novel antimicrobial and a unique antioxidative probiotic. The functional properties of the ME-3 include both high antimicrobial activity against food-borne pathogens and high antioxidative activity which makes the strain a perfect natural protector against oxidative stress. The probiotic ME-3 was elaborated according to the regulations of WHO/FAO (2002). The special industrial technology has been developed for incorporation of the probiotic into cheese and milk products in Estonia. The book should help to shed some light on the aspects of elaboration of probiotic FF and could be useful to students of (bio)medicine or to anybody who is interested in “good bugs”.
Approximating MRI-Based Anatomically Guided PET Reconstruction with a Convolutional Neural Network (2018)

In this work, we investigate whether MRI-Based anatomically guided PET reconstruction can be mimicked by a purely image-based convolutional neural network (CNN). The performance of the CNN is evaluated on 49 [ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">18</sup> F]FDG data sets acquired on a Siemens mMR.
Evasin‐4, a tick‐derived chemokine‐binding protein with broad selectivity can be modified for use in preclinical disease models (2013)

Rhipicephalus sanguineus, the common brown dog tick, produces several chemokine-binding proteins which are secreted into the host in its saliva to modulate the host response during feeding. Two of these demonstrate very restricted selectivity profiles. Here, we describe the characterization of the third, which we named Evasin-4. Evasin-4 was difficult to produce recombinantly using its native signal peptide in HEK cells, but expressed very well using the urokinase-type plasminogen activator signal peptide. Using SPR, Evasin-4 was shown to bind most CC chemokines. Investigation of the neutralization properties by inhibition of chemokine-induced chemotaxis showed that binding and neutralization did not correlate in all cases. Two major anomalies were observed: no binding was observed to CCL2 and CCL13, yet Evasin-4 was able to inhibit chemotaxis induced by these chemokines. Conversely, binding to CCL25 was observed, but Evasin-4 did not inhibit CCL25-induced chemotaxis. Size-exclusion chromatography confirmed that Evasin-4 forms a complex with CCL2 and CCL18. In accordance with the standard properties of unmodified small proteins, Evasin-4 was rapidly cleared following in vivo administration. To enhance the in vivo half-life and optimize its potential as a therapeutic agent, Fc fusions of Evasin-4 were created. Both the N- and C-terminal fusions were shown to retain binding activity, with the C-terminal fusion showing a modest reduction in potency.
19.5L: <i>Late‐News Paper</i> : High Efficiency and Long Lifetime Quantum‐Dot Light‐Emitting Diodes for Flat Panel Display Applications (2013)

Abstract Colloidal quantum‐dot based hybrid light‐emitting diodes (QD‐LEDs) that exhibit high efficiency, long lifetime, solution processability, color tunability and narrow emission bandwidth are reported. The devices possess maximum current and power efficiency of 3.2 cd/A and 2.1 lm/W for blue, 60 cd/A and 54 lm/W for green, and 15 cd/A and 18 lm/W for red emission. With exceptional good lifetime, the current QD‐LEDs are promising for flat panel display applications.