Miracle-dz/UniFAR-FTUs huggingface dataset:
Transient Response of Multiconductor Transmission Lines Excited by a Nonuniform Electromagnetic Field

The time-domain transmission-line equations for uniform multiconductor transmission lines in a conductive, homogeneous medium excited by a transient, nonuniform electromagnetic (EM) field, are derived from Maxwell's equations. Depending on how the line voltage is defined, two formulations are possible. One of these formulations is considerably more convenient to apply than the other. The assumptions made in the derivation of the transmission-line equations and the boundary conditions at the terminations are discussed. For numerical calculations, the transmission -line equations are represented by finite-difference techniques, and numerical examples are included.
Natural Flavonoids Interact with Dinitrobenzene System in Aprotic Media: An Electrochemical Probing

Three structurally related natural flavonoids (FlOH), quercetin (Q), rutin (R) and morin (M), were investigated by cyclic voltammetry to probe their interactions with hazardous 1,4-dinitrobenzene (1,4-DNB) using a glassy carbon electrode. Scavenging of 1,4-DNB by FlOH was inferred from a positive shift in reduction potential, decrease in anodic peak current, and irreversible electrochemical behavior of 1,4-DNB on increasing the flavonoid concentration. The homogeneous bi-molecular rate constant (k2) was determined using the Nicholson-Shain equation and found to be higher for the dianion. Morin posed a comparatively higher k2 value for its interaction with the 1,4-DNB electrochemical system owing to its more acidic nature and least intramolecular hydrogen bonding. The cyclic voltammetric (CV) results were further supported by HyperchemPM3 quantum mechanical semi-empirical calculations, which point towards ErCi interactions between flavonoids and 1,4-DNB. The present investigation is biologically significant in terms of natural flavonoidal scavenging activity toward toxins such as dinitroaromatics.
The 10,400- and 14,500-dalton proteins encoded by region E3 of adenovirus function together to protect many but not all mouse cell lines against lysis by tumor necrosis factor

We have reported that the E3 14,700-dalton protein (E3 14.7K protein) protects adenovirus-infected mouse C3HA fibroblasts against lysis by tumor necrosis factor (TNF) (L. R. Gooding, L. W. Elmore, A. E. Tollefson, H. A. Brady, and W. S. M. Wold, Cell 53:341-346, 1988). We have also observed that the E1B 19K protein protects adenovirus-infected human but not mouse cells against TNF lysis (L. R. Gooding, L. Aquino, P. J. Duerksen-Hughes, D. Day, T. M. Horton, S. Yei, and W. S. M. Wold, J. Virol. 65:3083-3094, 1991). We now report that, in the absence of E3 14.7K, the E3 10.4K and E3 14.5K proteins are both required to protect C127 as well as several other mouse cell lines against TNF lysis. The 14.7K protein can also protect these cells from TNF in the absence of the 10.4K and 14.5K proteins. This protection by the 10.4K and 14.5K proteins was not observed in the C3HA cell line. These conclusions are based on 51Cr release assays of cells infected with virus E3 mutants that express the 14.7K protein alone, that express both the 10.4K and 14.5K proteins, and that delete the 14.7K in combination with either the 10.4K or 14.5K protein. The 10.4K protein was efficiently coimmunoprecipitated together with the 14.5K protein by using an antiserum to the 14.5K protein, suggesting that the 10.4K and 14.5K proteins exist as a complex in the infected mouse cells and consistent with the notion that they function in concert. Considering that three sets of proteins (E3 14.7K, E1B 19K, and E3 10.4K/14.5K proteins) exist in adenovirus to prevent TNF cytolysis of different cell types, it would appear that TNF is a major antiadenovirus defense of the host.
Structure-Function Studies of the Adipocyte-secreted Hormone Acrp30/Adiponectin

Acrp30/adiponectin is an adipocyte-specific secretory protein that has recently been implicated as a mediator of systemic insulin sensitivity with liver and muscle as target organs. Acrp30 is found as two forms in serum, as a lower molecular weight trimer-dimer and a high molecular weight complex. Little is know about the regulation and significance of these Acrp30 complexes in serum and about the events that lead to the generation of the bioactive ligand. Here, we show that there is a profound sexual dimorphism of Acrp30 levels and complex distribution in serum. Female mice display significantly higher levels of the high molecular weight complex in serum than males. In both females and males, levels of the high molecular weight complex are significantly reduced in response to a systemic increase of insulin. The ratio of the two complexes is restored upon normalization of glucose levels. Structurally, we show that oligomer formation of Acrp30 critically depends on disulfide bond formation mediated by Cys-39. Mutation of Cys-39 results in trimers that are subject to proteolytic cleavage in the collagenous domain. Surprisingly, Acrp30(C39S) or wild-type Acrp30 treated with dithiothreitol are significantly more bioactive than the higher order oligomeric forms of the protein with respect to reduction of serum glucose levels. Furthermore, treatment of primary hepatocytes with trimeric and higher order forms of Acrp30 confirms that the increased bioactivity seen in vivo is reflected in an augmented potency to reduce glucose output in the presence of gluconeogenic stimuli. Combined, these results shed new light on the regulation of this complex protein and suggest a new model for in vivo activation of the protein, implicating a serum reductase activity.
Efficient Harmonic Balance Simulation of Nonlinear Microwave Circuits with Dynamic Neural Models

This paper presents a novel approach aimed at enhancing the speed and accuracy of harmonic balance (HB) simulation of nonlinear circuits represented by dynamic neural network (DNN) models. A set of constraint functions are proposed using the boundary information extracted from the time-domain training data for developing DNN models. Using these constraints, an expanded HB formulation of DNN is presented ensuring the DNN HB solutions to be within its training region. To further enhance the simulation efficiency, we propose a systematic method for setting the initial values of the DNN HB variables taking advantage of the knowledge of frequency-domain training data. The proposed methods are demonstrated through the HB simulations of a power amplifier circuit and DBS subsystem. It is shown that for simulation of DNN-based circuits, the proposed HB method gives more accurate solutions in shorter time than that using conventional HB method
Color in Perspective

Simple constraints on the sets of possible surface reflectance and illuminants are exploited in a new color constancy algorithm that builds upon Forsyth's (1990) theory of color constancy. Forsyth's method invokes the constraint that the surface colors under a canonical illuminant all fall within an established maximal convex gamut of possible colors. However, the method works only when restrictive conditions are imposed on the world: the illumination must be uniform, the surfaces must be planar, and there can be no specularities. To overcome these restrictions, we modify Forsyth's algorithm so that it works with the colors under a perspective projection (in a chromaticity space). The new algorithm working in perspective is simpler than Forsyth's method and more importantly the restrictions on the illuminant, surface shape and specularities can be relaxed. The algorithm is then extended to include a maximal gamut constraint on a set of illuminants that is analogous to the gamut constraint on surface colors. Tests on real images show that the algorithm provides good color constancy.
Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.

Type I restriction endonucleases such as EcoR124I cleave DNA at undefined loci, distant from their recognition sequences, by a mechanism that involves the enzyme tracking along the DNA between recognition and cleavage sites. This mechanism was examined on plasmids that carried recognition sites for EcoR124I and recombination sites for resolvase, the latter to create DNA catenanes. Supercoiled substrates with either one or two restriction sites were linearized by EcoR124I at similar rates, although the two‐site molecule underwent further cleavage more readily than the one‐site DNA. The catenane from the plasmid with one EcoR124I site, carrying the site on the smaller of the two rings, was cleaved by EcoR124I exclusively in the small ring, and this underwent multiple cleavage akin to the two‐site plasmid. Linear substrates derived from the plasmids were cleaved by EcoR124I at very slow rates. The communication between recognition and cleavage sites therefore cannot stem from random looping. Instead, it must follow the DNA contour between the sites. On a circular DNA, the translocation of non‐specific DNA past the specifically bound protein should increase negative supercoiling in one domain and decrease it in the other. The ensuing topological barrier may be the trigger for DNA cleavage.
Calcium Signaling in Cardiac Ventricular Myocytes

Abstract: Calcium (Ca) is a multifunctional regulator of diverse cellular functions. In cardiac muscle Ca is a direct central mediator of electrical activation, ion channel gating, and excitation‐contraction (E‐C) coupling that all occur on the millisecond time scale. The key amplification step in E‐C coupling is under tight control of very local [Ca]. Ca also directly activates signaling via kinases and phosphatases (e.g., Ca‐calmodulin‐dependent protein kinase [CaMKII] and calcineurin) that occur over a longer time scale (seconds to minutes), and the co‐localization of these Ca‐dependent modulators to their targets and to Ca is also critical in distinct signaling pathways. Finally, Ca‐dependent signaling is also involved in long‐term (minutes to hours/days) alterations in gene expression (or excitation‐transcription coupling). These pathways are involved in hypertrophy and heart failure, and they can alter the expression of some of the key Ca regulatory proteins involved in E‐C coupling and their regulation by kinases and phosphatases. There may again be physical microenvironments involved in this nuclear transcription, such that they sense a discrete Ca signal that is distinct from that involved in E‐C coupling. In this way cells can use Ca signaling in multiple ways that function in spatially and temporally distinct manners.
Spatial Information Divergence: Using Global and Local Indices to Compare Geographical Masks Applied to Crime Data

Advances in Geographic Information Science (GISc) and the increasing availability of location data have facilitated the dissemination of crime data and the abundance of crime mapping websites. However, data holders acknowledge that when releasing sensitive crime data there is a risk of compromising the victims' privacy. Hence, protection methodologies are primarily applied to the data to ensure that individual privacy is not violated. This article addresses one group of location protection methodologies, namely geographical masks that are applicable for crime data representations. The purpose is to identify which mask is the most appropriate for crime incident visualizations. A global divergence index (GDi) and a local divergence index (LDi) are developed to compare the effects that these masks have on the original crime point pattern. The indices calculate how dissimilar the spatial information of the masked data is from the spatial information of the original data in regards to the information obtained via spatial crime analysis. The results of the analysis show that the variable radius mask and the donut geomask should be primarily used for crime representations as they produce less spatial information divergence of the original crime point pattern than the alternative local random rotation mask and circular mask.
Closing the loop between neural network simulators and the OpenAI Gym

Since the enormous breakthroughs in machine learning over the last decade, functional neural network models are of growing interest for many researchers in the field of computational neuroscience. One major branch of research is concerned with biologically plausible implementations of reinforcement learning, with a variety of different models developed over the recent years. However, most studies in this area are conducted with custom simulation scripts and manually implemented tasks. This makes it hard for other researchers to reproduce and build upon previous work and nearly impossible to compare the performance of different learning architectures. In this work, we present a novel approach to solve this problem, connecting benchmark tools from the field of machine learning and state-of-the-art neural network simulators from computational neuroscience. This toolchain enables researchers in both fields to make use of well-tested high-performance simulation software supporting biologically plausible neuron, synapse and network models and allows them to evaluate and compare their approach on the basis of standardized environments of varying complexity. We demonstrate the functionality of the toolchain by implementing a neuronal actor-critic architecture for reinforcement learning in the NEST simulator and successfully training it on two different environments from the OpenAI Gym.
Vascular graft infections

Purpose of review This review provides a focus on infections of prosthetic vascular grafts used to treat peripheral arterial diseases. Recent findings The incidence of infections varies between 1 and 6%. Risk factors of infection are not well identified. Main causative pathogens are Gram-negative bacilli, Staphylococcus aureus, and coagulase-negative staphylococci, without clear differences according to location of graft and time of onset of infection. There is no consensual diagnostic criterion. The basic principles for management of graft infections have been known for many years. A surgical approach combining graft excision, complete debridement, and maintaining distal vascular flow is required. Antimicrobial therapy is always instituted to reduce sepsis and prevent secondary graft infection, but there are no evidence-based data to recommend any regimen. However, antibiotics should have bactericidal activity whatever the bacteria growth phase, reduce the microbial burden, penetrate within the biofilm, and prevent further biofilm formation. Mortality and morbidity from these infections remain significant. Summary A multidisciplinary approach with a limited number of reference centres, recruiting sufficient numbers of patients to perform controlled trials, and to provide expert recommendations, could be the best way to answer unresolved questions and improve the prognosis.
Isolation and characterization of the human UGT2B15 gene, localized within a cluster of UGT2B genes and pseudogenes on chromosome 4.

Glucuronidation is a major pathway of androgen metabolism and is catalyzed by UDP-glucuronosyltransferase (UGT) enzymes. UGT2B15 and UGT2B17 are 95% identical in primary structure, and are expressed in steroid target tissues where they conjugate C19 steroids. Despite the similarities, their regulation of expression are different; however, the promoter region and genomic structure of only the UGT2B17 gene have been characterizedX to date. To isolate the UGT2B15 gene and other novel steroid-conjugating UGT2B genes, eight P-1-derived artificial chromosomes (PAC) clones varying in length from 30 kb to 165 kb were isolated. The entire UGT2B15 gene was isolated and characterized from the PAC clone 21598 of 165 kb. The UGT2B15 and UGT2B17 genes are highly conserved, are both composed of six exons spanning approximately 25 kb, have identical exon sizes and have identical exon-intron boundaries. The homology between the two genes extend into the 5'-flanking region, and contain several conserved putative cis-acting elements including Pbx-1, C/EBP, AP-1, Oct-1 and NF/kappaB. However, transfection studies revealed differences in basal promoter activity between the two genes, which correspond to regions containing non-conserved potential elements. The high degree of homology in the 5'-flanking region between the two genes is lost upstream of -1662 in UGT2B15, and suggests a site of genetic recombination involved in duplication of UGT2B genes. Fluorescence in situ hybridization mapped the UGT2B15 gene to chromosome 4q13.3-21.1. The other PAC clones isolated contain exons from the UGT2B4, UGT2B11 and UGT2B17 genes. Five novel exons, which are highly homologous to the exon 1 of known UGT2B genes, were also identified; however, these exons contain premature stop codons and represent the first recognized pseudogenes of the UGT2B family. The localization of highly homologous UGT2B genes and pseudogenes as a cluster on chromosome 4q13 reveals the complex nature of this gene locus, and other novel homologous UGT2B genes encoding steroid conjugating enzymes are likely to be found in this region of the genome.
Active compliance control for a hydraulically-actuated articulated robotic leg

This paper focus on the modelling and control of a hydraulically-actuated biologically-inspired articulated robotic leg. The leg has two hydraulically-actuated degrees of freedom (DoF), the hip and knee joints, and a passive spring DoF, the ankle joint. After a brief description of the prototype leg, the paper developed a nonlinear model of the leg, including its kinematics and dynamics. Subsequently, an actively compliant control architecture based on outer virtual compliant leg model and inner torque controller was designed to achieve a spring-damper like touchdown dynamics behavior. Lastly, both a Pushdown experiment and a Dropdown experiment were carried to verify the designed controller. The result confirmed that a hydraulically-actuated robot articulated leg can successfully emulate virtual passive components through proper mechanical design and actively compliant control under dynamic situations.
Genetic analysis of temperature-sensitive mutants which define the genes for the major herpes simplex virus type 2 DNA-binding protein and a new late function

Eleven temperature-sensitive mutants of herpes simplex virus type 2 (HSV-2) exhibit overlapping patterns of complementation that define four functional groups. Recombination tests confirmed the assignment of mutants to complementation groups 1 through 4 and permitted the four groups to be ordered in an unambiguous linear array. Combined recombination and marker rescue tests (A. E. Spang, P. J. Godowski, and D. M. Knipe, J. Virol. 45:332-342, 1983) indicate that the mutations lie in a tight cluster near the center of UL to the left of the gene for DNA polymerase in the order 4-3-2-1-polymerase. The seven mutants that make up groups 1 and 2 fail to complement each other and mutants in HSV-1 complementation group 1-1, the group thought to define the structural gene for the major HSV-1 DNA-binding protein with a molecular weight of 130,000. At 38 degrees C, mutants in groups 1 and 2 synthesize little or no viral DNA, and unlike cells infected with the wild-type virus, mutant-infected cells exhibit no detectable nuclear antigen reactive with monoclonal or polypeptide-specific antibody to the major HSV-2 DNA-binding protein. The four mutants that make up groups 3 and 4 do not complement each other, nor do they complement mutants in group 2. They do, however, complement mutants in group 1 as well as representative mutants of HSV-1 complementation group 1-1. At 38 degrees C, mutants in groups 3 and 4 are phenotypically DNA+, and nuclei of mutant-infected cells contain the HSV-2 DNA-binding protein. Thus, the four functional groups appear to define two closely linked genes, one encoding an early viral function affecting both viral DNA synthesis and expression of the DNA-binding protein with a molecular weight of 130,000 (groups 1 and 2), and the other encoding a previously unidentified late viral function (groups 3 and 4). The former gene presumably represents the structural gene for the major HSV-2 DNA-binding protein.
A Trypanosome Structure Involved in Transmitting Cytoplasmic Information During Cell Division

African trypanosomes are protozoan parasites that cause sleeping sickness in humans through a tsetse fly vector. The procyclic form ofTrypanosoma brucei has a single, attached flagellum that describes a helical path along the cell from posterior to anterior. During division, a specific flagellum-flagellum connection is elaborated between the new and old flagellum. This connector was present only during cell duplication and was found to be involved in the replication of the helical cell pattern and polarity. This finding implicates the concept of cytotaxis in cell morphogenesis in trypanosomes.
Pseudomonas aeruginosa variants isolated from patients with cystic fibrosis are killed by a bactericidal protein from human polymorphonuclear leukocytes

The susceptibility of paired mucoid and nonmucoid variants of Pseudomonas aeruginosa isolated from 13 patients with cystic fibrosis (CF) to killing by a 55,000-Da bactericidal protein (BP55) from human polymorphonuclear leukocytes was studied. Mucoid and nonmucoid variants were equally sensitive to killing by BP55 at both pH 5.6 and pH 7.2. Eleven of the isolates were resistant to the bactericidal activity of 10% normal human serum but were as sensitive as the serum-sensitive isolates to BP55. Similarly, the 15 isolates with lipopolysaccharides (LPS) containing O-polysaccharide side chains (smooth LPS) were as sensitive to BP55 as those isolates with rough LPS.P. aeruginosa isolates from patients in poor clinical condition were more likely to have LPS of the smooth type and to be resistant to killing by 10% human serum than the isolates from patients in good clinical condition. We have concluded that the susceptibility of the P. aeruginosa isolates from patients with CF to killing by BP55 does not correlate with mucoid or nonmucoid variations, with the presence or absence of smooth LPS, or with the sensitivity or resistance to killing by normal human serum.
Criteria for evaluation of therapeutic response to antifungal drugs.

A therapeutic trial of antifungal therapy in humans requires not only well-defined objectives and a sufficient number of patients, but also standardized criteria for the diagnosis and evaluation of response, including the efficacy, failure, and toxicity of any new agent or treatment modality. Generally, the retention of a patient in a study should require, as a minimum, confirmation of the etiologic diagnosis by culture of the organism from the infected site. Two different systems for evaluation of therapy are proposed. The first is a set of definitions of response to therapy; these are adaptable for use in any type of prospective clinical trial and emphasize cure as the best possible outcome. The second system of evaluation employs scored criteria and thereby enables quantitative comparison of the status of a patient before therapy with his or her status at intervals during therapy, at the end of therapy, and at intervals after therapy. This system provides an objective means of measuring improvement in a given patient; thus it is most useful in those diseases in which significant improvement rather than cure is a more realistic goal of therapy, e.g., coccidioidomycosis.