gebhart/patrepeval huggingface dataset:
Compartmentalized Glucose Metabolism in Pseudomonas putida Is Controlled by the PtxS Repressor (2010)

Metabolic flux analysis revealed that in Pseudomonas putida KT2440 about 50% of glucose taken up by the cells is channeled through the 2-ketogluconate peripheral pathway. This pathway is characterized by being compartmentalized in the cells. In fact, initial metabolism of glucose to 2-ketogluconate takes place in the periplasm through a set of reactions catalyzed by glucose dehydrogenase and gluconate dehydrogenase to yield 2-ketogluconate. This metabolite is subsequently transported to the cytoplasm, where two reactions are carried out, giving rise to 6-phosphogluconate, which enters the Entner-Doudoroff pathway. The genes for the periplasmic and cytoplasmic set of reactions are clustered in the host chromosome and grouped within two independent operons that are under the control of the PtxS regulator, which also modulates its own synthesis. Here, we show that although the two catabolic operons are induced in vivo by glucose, ketogluconate, and 2-ketogluconate, in vitro we found that only 2-ketogluconate binds to the regulator with an apparent K(D) (equilibrium dissociation constant) of 15 muM, as determined using isothermal titration calorimetry assays. PtxS is made of two domains, a helix-turn-helix DNA-binding domain located at the N terminus and a C-terminal domain that binds the effector. Differential scanning calorimetry assays revealed that PtxS unfolds via two events characterized by melting points of 48.1 degrees C and 57.6 degrees C and that, in the presence of 2-ketogluconate, the unfolding of the effector binding domain occurs at a higher temperature, providing further evidence for 2-ketogluconate-PtxS interactions. Purified PtxS is a dimer that binds to the target promoters with affinities in the range of 1 to 3 muM. Footprint analysis revealed that PtxS binds to an almost perfect palindrome that is present within the three promoters and whose consensus sequence is 5'-TGAAACCGGTTTCA-3'. This palindrome overlaps with the RNA polymerase binding site.
Quantitative Tagged Magnetic Resonance Imaging of the Normal Human Left Ventricle (2000)

Magnetic resonance imaging with tissue tagging is a noninvasive technique for measuring three-dimensional motion and deformation in the human heart. Tags are regions of tissue whose longitudinal magnetization has been altered before imaging so that they appear dark in subsequent magnetic resonance images. They then move with the underlying tissue and serve as easily identifiable landmarks within the heart for the detailed detection of motion. Many different motion and strain parameters can be determined from tagged magnetic resonance imaging. Strain components that are based on a high density of tag data, such as circumferential and longitudinal shortening, or parameters that are combinations of multiple strain components, have highest measurement precision and tightest normal ranges. The pattern of three-dimensional motion and strain in the heart is important clinically, because it reflects the basic mechanical function of the myocardium at both local and global levels. Localized abnormalities can be detected and quantified if the pattern of deformation in a given heart is compared to the normal range for that region, because normal motion and strain in the left ventricle is spatially heterogeneous. Contraction strains typically are greatest in the anterior and lateral walls and increase toward the apex. The direction of greatest contraction lies along a counter clockwise helix from base to apex (viewed from the base) and approximates the epicardial muscle fiber direction. This fiber geometry also results in long-axis torsion during systole. Ejection is accomplished primarily by radially inward motion of the endocardium and by descent of the base toward the apex during systole.
Decreased Notch Pathway Signaling in the Endometrium of Women With Endometriosis Impairs Decidualization (2014)

Decreased Notch signaling is associated with endometriosis and contributes to impaired decidualization through the down-regulation of FOXO1.
A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data (2018)

A common goal in data-analysis is to sift through a large data-matrix and detect any significant submatrices (i.e., biclusters) that have a low numerical rank. We present a simple algorithm for tackling this biclustering problem. Our algorithm accumulates information about 2-by-2 submatrices (i.e., 'loops') within the data-matrix, and focuses on rows and columns of the data-matrix that participate in an abundance of low-rank loops. We demonstrate, through analysis and numerical-experiments, that this loop-counting method performs well in a variety of scenarios, outperforming simple spectral methods in many situations of interest. Another important feature of our method is that it can easily be modified to account for aspects of experimental design which commonly arise in practice. For example, our algorithm can be modified to correct for controls, categorical- and continuous-covariates, as well as sparsity within the data. We demonstrate these practical features with two examples; the first drawn from gene-expression analysis and the second drawn from a much larger genome-wide-association-study (GWAS).
2K+ Graph Construction Framework: Targeting Joint Degree Matrix and Beyond (2019)

In this paper, we study the problem of generating synthetic graphs that resemble real-world graphs in terms of their degree correlations and potentially additional properties. We present an algorithmic framework that generates simple undirected graphs with the exact target joint degree matrix, which we refer to as 2K graphs, in linear time in the number of edges. Our framework imposes minimal constraints on the graph structure, which allows us to target additional graph properties during construction, namely, node attributes (2K+A), clustering (both average clustering, 2.25K, and degree-dependent clustering, 2.5K), and number of connected components (2K+CC). We also define, for the first time, the problem of directed 2K graph construction, provide necessary and sufficient conditions for realizability, and develop efficient construction algorithms. We evaluate our approach by creating synthetic graphs that target real-world graphs both undirected (such as Facebook) and directed (such as Twitter), and we show that it brings significant benefits, in terms of accuracy and running time, compared to the state-of-the-art approaches.
A New MATV system with integrated UHD and HD broadcasting: Implementation and Test Results (2023)

This paper discusses the implementation of a novel Master Antenna Television (MATV) system that can receive Advanced Television Systems Committee (ATSC) 3.0-based terrestrial Ultra High Definition (UHD) broadcasting signal and convert them into both ATSC 3.0-based UHD and ATSC 1.0-based High Definition (HD) signal simultaneously. The new MATV system includes ATSC 3.0 demodulator, ATSC 3.0 re-constructor, and ATSC 3.0 modulator compliant with ATSC 3.0 standards, as well as ATSC 1.0 media signal processor and ATSC 1.0 modulator conforming to ATSC 1.0 standards. Additionally, this system includes a feature that transcodes MMT/ROUTE streams to MPEG2-TS streams to generate ATSC 1.0 signal. This paper highlights the need for such a system due to the transition from HD to UHD broadcasting services in South Korea and the fact that many households still do not possess ATSC 3.0-based UHDTVs. Laboratory tests were conducted to evaluate the performance of the Radio Frequency (RF) signal and service quality. The test results showed that the new MATV system is capable of providing both UHD and HD services. Therefore, the developed MATV system has been proven to be a solution for households that do not possess ATSC 3.0-based UHDTVs.
Experimental and numerical investigation of ultrasonic transmission through the skull bone and associated temperature rise (2008)

The feasibility of transcranial high-intensity focused-ultrasound (HIFU) therapy within the brain relies on the ability to transmit ultrasound through the skull bone at relatively high ultrasound power. Absorption of ultrasound through the skull bone may cause important temperature rises, and is therefore an important parameter to control. Ultrasonic measurements have shown that the ultrasound beam undergoes a significant attenuation when propagating through the skull, with values on the order of 10 to 20 dB/cm/MHz. To predict temperature rise from such values, it is fundamental to weigh the relative role of absorption to the total ultrasonic attenuation (scattering + absorption + specular reflection). In this work, two types of numerical simulations and experiments are performed to investigate this relative role. Through-transmission of 1 MHz ultrasound was performed numerically using a 3D Finite-Difference Time-Domain (FDTD) algorithm coupled to a 3D bone model obtained from high-resolution synchrotron microtomography, and compared to experimental measurements obtained with the same bone sample. Temperature rises were numerically simulated using the 3D bone model coupled to the heat equation, and compared to infrared thermography obtained experimentally while high-intensity ultrasound was propagating through the sample.
Novel Treatment of Cryptococcal Meningitis via Neurapheresis Therapy (2018)

Cryptococcal meningitis (CM) has emerged as the most common life-threatening fungal meningitis worldwide. Current management involves a sequential, longitudinal regimen of antifungals; despite a significant improvement in survival compared with uniform mortality without treatment, this drug paradigm has not led to a consistent cure. Neurapheresis therapy, extracorporeal filtration of yeasts from cerebrospinal fluid (CSF) in infected hosts, is presented here as a novel, one-time therapy for CM. In vitro filtration of CSF through this platform yielded a 5-log reduction in concentration of the yeast and a 1-log reduction in its polysaccharide antigen over 24 hours. Additionally, an analogous closed-loop system achieved 97% clearance of yeasts from the subarachnoid space in a rabbit model over 4-6 hours. This is the first publication demonstrating the direct ability to rapidly clear, both in vitro and in vivo, the otherwise slowly removed fungal pathogen that directly contributes to the morbidity and mortality seen in CM.
Mass Defect (in Mass Spectrometry) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy's Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Mechanism of the Tissue-Specific Action of the Selective Androgen Receptor Modulator S-101479 (2013)

Selective androgen receptor modulators (SARMs) comprise a new class of molecules that induce anabolic effects with fewer side effects than those of other anabolic agents. We previously reported that the novel SARM S-101479 had a tissue-selective bone anabolic effect with diminished side effects in female animals. However, the mechanism of its tissue selectivity is not well known. In this report, we show that S-101479 increased alkaline phosphatase activity and androgen receptor (AR) transcriptional activity in osteoblastic cell lines in the same manner as the natural androgen ligand dihydrotestosterone (DHT); conversely, stimulation of AR dimerization was very low compared with that of DHT (34.4%). S-101479 increased bone mineral content in ovariectomized rats without promoting endometrial proliferation. Yeast two-hybrid interaction assays revealed that DHT promoted recruitment of numerous cofactors to AR such as TIF2, SRC1, β-catenin, NCoA3, gelsolin and PROX1 in a dose-dependent manner. SARMs induced recruitment of fewer cofactors than DHT; in particular, S-101479 failed to induce recruitment of canonical p160 coactivators such as SRC1, TIF2 and notably NCoA3 but only stimulated binding of AR to gelsolin and PROX1. The results suggest that a full capability of the AR to dimerize and to effectively and unselectively recruit all canonical cofactors is not a prerequisite for transcriptional activity in osteoblastic cells and resulting anabolic effects in bone tissues. Instead, few relevant cofactors might be sufficient to promote AR activity in these tissues.
Design of single-mode photonic crystal optical waveguldes (2001)

Summary form only given. Photonic crystals have inspired a lot of interest recently due to their potential for controlling the propagation of light. Photonic crystals with line defects can be used for guiding light. A conventional method for making a two-dimensional (2D) dielectric-core photonic crystal (or PBG) waveguide is to remove one row of air columns. This usually results in a multimode waveguide. We present a more systematic way of making single-mode dielectric-core 2D PBG waveguides. It was recently shown that the main guiding mechanisms in dielectric-core PBG waveguides are total internal reflection and distributed Bragg reflection (DBR). The confinement of the guided mode in the center slab of the waveguide suggests that the properties of such modes can be modified by modifying the guiding structure in the vicinity of the center slab.
Inhibition of dog renin activity by pepstatin A. (1979)

The inhibitory effect of pepstatin A, an isovaleryl pentapeptide isolated from streptmyces, was studied. Pepstatin A inhibited the action of dog renin on homologus substrate. The Ki value was 7.7 X 10(-7) M and the mode of the inhibition was non-competitive. Pestatin A suppressed angiotensin I generation in dog plasma. Dose-dependent hypotensive effect of pepstatin A was observed in rats with sustained increase in blood pressure during continuous infusion of dog renin. It is concluded that pepstatin A inhibits the dog renin activity in vitro and in vivo.
Automatic Generation of Sound Zero-Knowledge Protocols (2008)

Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that essentially rely on ZK-POKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic chip Trusted Platform Module (TPM).&#13;\n&#13;\nImplementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills.&#13;\n&#13;\nTo overcome these challenges, we have designed and implemented a compiler with corresponding languages that given a high-level ZK-PoK protocol specification automatically generates a sound implementation of this. The output is given in form of -protocols, which are the most efficient protocols for ZK-PoK currently known. Our compiler translates ZK-PoK protocol specifications, written in a high-level protocol description language, into Java code or \\LaTeX\\ documentation of the protocol.&#13;\nThe compiler is based on a unified theoretical framework that encompasses a large number of existing ZK-PoK techniques. Within this framework we present a new efficient ZK-PoK protocol for exponentiation homomorphisms in hidden order groups. Our protocol overcomes several limitations of the existing proof techniques.
Extraction of the hepatic vasculature in rats using 3-D micro-CT images (2000)

High-resolution micro-computed tomography (CT) scanners now exist for imaging small animals. In particular, such a scanner can generate very large three-dimensional (3-D) digital images of the rat's hepatic vasculature. These images provide data on the overall structure and function of such complex vascular trees. Unfortunately, human operators have extreme difficulty in extracting the extensive vasculature contained in the images. Also, no suitable tree representation exists that permits straight-forward structural analysis and information retrieval. This work proposes an automatic procedure for extracting and representing such a vascular tree. The procedure is both computation and memory efficient and runs on current PCs. As the results demonstrate, the procedure faithfully follows human-defined measurements and provides far more information than can be defined interactively.
Skeletal muscle overexpression of nuclear respiratory factor 1 increases glucose transport capacity (2003)

Nuclear respiratory factor 1 (NRF-1) is a transcriptional activator of nuclear genes that encode a range of mitochondrial proteins including cytochrome c, various other respiratory chain subunits, and delta-aminolevulinate synthase. Activation of NRF-1 in fibroblasts has been shown to induce increases in cytochrome c expression and mitochondrial respiratory capacity. To further evaluate the role of NRF-1 in the regulation of mitochondrial biogenesis and respiratory capacity, we generated transgenic mice overexpressing NRF-1 in skeletal muscle. Cytochrome c expression was increased approximately twofold and delta-aminolevulinate synthase was increased approximately 50% in NRF-1 transgenic muscle. The levels of some mitochondrial proteins were increased 50-60%, while others were unchanged. Muscle respiratory capacity was not increased in the NRF-1 transgenic mice. A finding that provides new insight regarding the role of NRF-1 was that expression of MEF2A and GLUT4 was increased in NRF-1 transgenic muscle. The increase in GLUT4 was associated with a proportional increase in insulin-stimulated glucose transport. These results show that an isolated increase in NRF-1 is not sufficient to bring about a coordinated increase in expression of all of the proteins necessary for assembly of functional mitochondria. They also provide the new information that NRF-1 overexpression results in increased expression of GLUT4.
Beta vulgaris rubra L. (Beetroot) Peel Methanol Extract Reduces Oxidative Stress and Stimulates Cell Proliferation via Increasing VEGF Expression in H2O2 Induced Oxidative Stressed Human Umbilical Vein Endothelial Cells (2021)

The antioxidant capacity of polyphenols and flavonoids present in dietary agents aids in arresting the development of reactive oxygen species (ROS) and protecting endothelial smooth muscle cells from oxidative stress/induced necrosis. Beetroot (<i>Beta vulgaris</i>&nbsp;var. rubra L.; BVr) is a commonly consumed vegetable representing a rich source of antioxidants. Beetroot peel's bioactive compounds and their role in human umbilical vein endothelial cells (HUVECs) are still under-researched. In the present study, beetroot peel methanol extract (BPME) was prepared, and its effect on the bio-efficacy, nuclear integrity, mitochondrial membrane potential and vascular cell growth, and immunoregulation-related gene expression levels in HUVECs with induced oxidative stress were analysed. Gas chromatography-mass spectroscopy (GC-MS) results confirmed that BPME contains 5-hydroxymethylfurfural (32.6%), methyl pyruvate (15.13%), furfural (9.98%), and 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-Pyran-4-one (12.4%). BPME extract effectively enhanced cell proliferation and was confirmed by MTT assay; the nuclear integrity was confirmed by propidium iodide (PI) staining assay; the mitochondrial membrane potential (Δψ<sub>m</sub>) was confirmed by JC-1 staining assay. Annexin V assay confirmed that BPME-treated HUVECs showed 99% viable cells, but only 39.8% viability was shown in HUVECs treated with H<sub>2</sub>O<sub>2</sub> alone. In addition, BPME treatment of HUVECs for 48 h reduced mRNA expression of lipid peroxide (LPO) and increased NOS-3, Nrf-2, GSK-3β, GPX, endothelial nitric oxide synthase (eNOS) and vascular cell growth factor (VEGF) mRNA expression levels. We found that BPME treatment decreased proinflammatory (nuclear factor-κβ (F-κβ), tissue necrosis factor-α (TNF-α), toll-like receptor-4 (TLR-4), interleukin-1β (IL-1β)) and vascular inflammation (intracellular adhesion molecule (ICAM), vascular cell adhesion molecule (VCAM), EDN<sub>1</sub>, IL-1β)-related mRNA expressions. In conclusion, beetroot peel treatment effectively increased vascular smooth cell growth factors and microtubule development, whereas it decreased vascular inflammatory regulators. BPME may be beneficial for vascular smooth cell regeneration, tissue repair and anti-ageing potential.
Flexible Technologies to Increase Optical Network Capacity (2022)

Increased global traffic puts tough requirements not just on fiber communications links but on the entire network. This manifests itself in multiple ways, including how to optimize wavelength routing around the network, how to maximize the benefits arising from fine-control DSP with increasingly accurate real-time monitoring, and how to best deploy multiband or multiple fiber connectivity. This article will summarize research into all these areas to present a full picture of how future optical networks will play their role in supporting the continuing traffic demands of broadband, 5G, and associated applications.
LP‐2: High Performance LCD Backlighting using High Intensity Red, Green and Blue Light Emitting Diodes (2001)

Abstract By using red, green, and blue (RGB) light emitting diodes (LEDs) instead of cold cathode fluorescent lamps in edge lit LCD backlights brightness and color performance (gamut) of LCD displays can be improved considerably. However: the design of an RGB‐LED backlight and electronic control need special attention: the colors of the separate LEDs need to be mixed well to obtain a good spatial color uniformity while a good balance between the red, green and blue levels has to be maintained to stabilize the white point. Additional features of an RGB‐LED backlight solution are: dynamic white point control (tune color point of backlight to LCD and/or displayed material), large dimming range, long lifetime, ruggedness, and the absence of mercury.