gebhart/patrepeval huggingface dataset:
Reconfigurable miniature three dimensional fractal tree antennas (2004)

When used as antenna elements, fractal tree structures can be designed to produce multiband characteristics or to achieve miniaturization. Dipole antennas that use fractal tree structures as end loads can achieve a resonant frequency lower than a standard dipole of comparable length. In addition, increasing the density of fractal tree end loads can significantly improve the miniaturization of such antennas. Two design examples are considered where these miniature fractal tree antennas are made reconfigurable by the introduction of strategically placed reactive loads or RF switches. The first design is a fractal dipole antenna that operates at several frequency bands by adding reactive loads in the tree structure. The second design considered is a reconfigurable miniature dipole antenna that achieves a 43% size reduction with respect to its conventional counterpart (i.e., a half-wave dipole for the lowest operating band) and has a tunable bandwidth of nearly 70%.
The interaction of monomeric actin with two binding sites on Acanthamoeba actobindin (1991)

Actobindin was previously shown to be an 88-residue polypeptide (Mr 9761) with an internal tandem repeat of 33-34 amino acids. Sedimentation equilibrium experiments have confirmed this Mr for native actobindin. Pyreneglyoxal-labeled actobindin had a similar Mr by sedimentation equilibrium analysis and bound to actin in a manner qualitatively similar to unmodified actobindin as determined by gel electrophoretic analysis of covalently cross-linked products. The stoichiometry of the actin-actobindin interaction was determined from the change in apparent Mr of pyrene-glyoxal-labeled actobindin in the presence of actin, as determined by scanning the ultracentrifuge cell at a wavelength that detected only the labeled protein. These data were consistent with the formation of a complex containing two actin and one actobindin molecules. The overall KD describing the binding of the first actin to either of the two sites on actobindin was 3.3 microM. The binding constant for the second actin suggested either negative cooperativity or inequality of the two actin-binding sites. Similar binding constants were obtained by analysis of the fluorescence enhancement that occurred when actobindin bound to actin labeled with either pyrene iodoacetamide or 4-(N-iodoacetoxyethyl-N-methyl)-7-nitrobenz-2-oxa-1,3-diazole. Cross-linking experiments with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide and N-hydroxy-sulfosuccinimide qualitatively agreed with predictions made from a two-binding site model. Additionally, both the fluorescence and cross-linking experiments suggested that the interaction of the two actin molecules may contribute to the stability of the heterotrimeric complex.
Hypermethylation of <i>ASC/TMS1</i> Is a Sputum Marker for Late-Stage Lung Cancer (2006)

DNA hypermethylated gene promoter sequences are extremely promising cancer markers. Their use for risk assessment, early diagnosis, or prognosis depends on the timing of this gene change during tumor progression. We studied this for the proapoptotic gene ASC/TMS1 in lung cancer and used the findings to develop a sputum marker. ASC/TMS1 protein levels are reduced in all lung cancer types (30 of 40; 75%) but not in 10 preinvasive lesions. Hypermethylation of ASC/TMS1 is also associated with invasive cancers (41 of 152 or 27.0% of all lung cancer types) with variation in incidence between histopathologic types including 32.1% (26 of 81) of adenocarcinomas, 13.2% (7 of 53) of squamous cell carcinomas, 38.5% (5 of 13) of large-cell carcinomas, and 60% (3 of 5) of small-cell lung cancers. The hypermethylation is particularly correlated with late tumor stages being present in only 14% of stage I but 60% of later-stage tumors. The incidence of ASC/TMS1 hypermethylation in sputum DNA fully mimics the tissue findings being present in only 2% (2 of 85) of high-risk, cancer-free smokers, 15% (3 of 18) of patients with stage I non-small-cell lung cancer (NSCLC), but 41% of patients with stage III NSCLC (18 of 44), including 56% (10 of 18) of those with adenocarcinoma. Importantly, sputum is positive for this marker in 24% (10 of 42) of very high risk, clinically cancer-free individuals previously resected for stage I NSCLC. Thus, hypermethylation of ASC/TMS1 is a marker for late-stage lung cancer and, in sputum, could predict prognosis in patients resected for early-stage disease.
Electron and phonon energy spectra in a three-dimensional regimented quantum dot superlattice (2002)

We report on theoretical investigation of the electron and phonon energy spectra in a three-dimensional regimented quantum dot superlattice. Our results are obtained by numerical solution of the Schr\"odinger and elasticity equations using the finite-difference method. The calculations are performed for a Ge/Si material system taking into account characteristic band-gap offsets, elastic stiffness constants, and other relevant parameters. Coupling among quantum dots in such a regimented structure results in formation of extended electron states and minibands, provided that the disorder in the system is small. Electron and phonon densities of states of these artificial quantum dot crystals are also calculated. We demonstrate that the acoustic-phonon dispersion in the quantum dot superlattice undergoes strong modification, which leads to emergence of quasioptical branches. These branches are much lower in energy than optical phonons in bulk semiconductors and thus may strongly affect energy relaxation processes. Other phenomena that originate from the specific electron and phonon spectra in quantum dot superlattices, such as negative differential conductivity and carrier scattering anisotropy, are also discussed.
Vane Shear Strength Testing in Soils: Field and Laboratory Studies (1988)

Description Twenty-two papers discuss: reviews of the vane test on land and offshore; field and laboratory vane theory and interpretation; new laboratory test methods; and comparisons of field vane testing to laboratory testing and other methods of in situ testing.
Microfluidics for Gametes, Embryos, and Embryonic Stem Cells (2011)

Microfluidics is a young but established field that holds significant potential for scientific discovery. The utility of microfluidics can improve our knowledge of basic biology as well as expand our understanding in specialized areas such as assisted reproduction and stem cell developmental biology. This review describes the technology of microfluidics and discusses applications within assisted reproduction technology and embryonic stem cell growth and directed differentiation. Development of an integrated microfluidic platform for assisted reproduction, which can manipulate gametes, embryos, embryonic stem cells, their culture environment, and incorporate biomarker analysis, could have a dramatic impact on the basic understanding of embryo/embryonic stem cell development, as well as provide significant improvements in current technologies used to treat infertility, preserve fertility, and derive therapeutic cells from stem cells.
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles (2021)

JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.
Complement and microglia mediate early synapse loss in Alzheimer mouse models (2016)

Synapse loss in Alzheimer's disease (AD) correlates with cognitive decline. Involvement of microglia and complement in AD has been attributed to neuroinflammation, prominent late in disease. Here we show in mouse models that complement and microglia mediate synaptic loss early in AD. C1q, the initiating protein of the classical complement cascade, is increased and associated with synapses before overt plaque deposition. Inhibition of C1q, C3, or the microglial complement receptor CR3 reduces the number of phagocytic microglia, as well as the extent of early synapse loss. C1q is necessary for the toxic effects of soluble β-amyloid (Aβ) oligomers on synapses and hippocampal long-term potentiation. Finally, microglia in adult brains engulf synaptic material in a CR3-dependent process when exposed to soluble Aβ oligomers. Together, these findings suggest that the complement-dependent pathway and microglia that prune excess synapses in development are inappropriately activated and mediate synapse loss in AD.
Repeatability of the Glaucoma Hemifield Test in automated perimetry. (1995)

Although there is concordance of Glaucoma hemifield Test results on consecutive testing, there is enough disagreement to result in improved specificity from the use of a second test in a clinical trial setting.
Cimetidine as adjunctive treatment for acetaminophen overdose (1995)

The aim of this study was to determine if cimetidine in addition to N-acetylcysteine and standard supportive care provide additional hepatoprotection following acute acetaminophen poisoning. It was designed as a prospective study with alternate month treatment protocol, and the work was carried out at a regional certified poison information centre. For a 2-year period, consultations received by the Rocky Mountain Poison Center involving acute acetaminophen overdose patients with a serum level above the nomogram line, but who would not receive N-acetylcystine therapy until at least 8 h postingestion, were prospectively evaluated for adjunctive treatment with cimetidine. All patients received standard supportive therapy and N-acetylcysteine treatment. During odd numbered months, cimetidine 300 mg was administered intravenously every 6 h for the duration of N-acetylcysteine therapy. Forty-one cimetidine treated patients were compared to 66 patients in the control group. The peak measured AST levels (+/- s.e.) were 1259+/-330 and 1301+/-451 for the control and cimetidine treatment groups, respectively (P = 0.94). Fourteen of 64 patients (21%) in the control group and 8/41 patients (20%) in the cimetidine group developed an AST > 1000 IUL-1. There were no statistical differences between the cimetidine-treated and control groups when classified by AST < 100 IUL-1, 100-1000 IUL-1, or > 1000 IUL-1. The addition of cimetidine therapy to standard N-acetylcysteine treatment did not provide additional hepatoprotection in acutely acetaminophen poisoned patients when treatment was started later than 8 h post overdose.(ABSTRACT TRUNCATED AT 250 WORDS)
Continuous Real-Time Visualizationof the Human Cerebral Microcirculation During Avm Surgery Using Orthogonal Polarization Spectral Imaging (2006)

With intraoperative orthogonal polarization spectral imaging, microcirculatory hemodynamic changes in the human brain can be readily observed and quantified. In AVM surgery, a dramatic increase in microvascular flow was observed in the perinidal brain tissue, which seems consistent with current hypotheses regarding normal perfusion pressure breakthrough.
Development of an InGaAs SPAD 2D array for flash LIDAR (2018)

An InGaAs Single-Photon Avalanche Photodiode (SPAD) array and a hybrid photon-counting image sensor have been developed for time-resolved applications in the near infrared region, especially for Flash LIDAR. The implemented array has a 100 μm pitch 32×32 matrix, and the active area in each pixel has a diameter of 12 μm. A dedicated read-out IC incorporates an active quenching and recharge circuit, and an in-pixel time-to-digital converter with 318 ps resolution for providing stable Geiger-mode operation of the InGaAs SPAD pixels and a simultaneous time-resolving function. The uniformity of the electrical field in the entire two-dimensional area is one of the key characteristics as it affects most performance parameters. The breakdown voltage mapping revealed the SPAD array has an excellent uniformity. Full characterizations of dark count rate, photon detection probability, and timing jitter were performed and will be discussed. Methods of suppressing afterpulses were examined by utilizing an adjustable hold-off function. The results showed that the function worked effectively to reduce the afterpulse probability. Finally we prove that the InGaAs SPAD image sensor has the capability of accurate timing detection for constructing a flash LIDAR in the near future.
Metamorphic virus detection using feature selection techniques (2014)

In this article, a non-signature based statistical scanner for metamorphic malware detection, employing feature ranking methods like Term Frequency-Inverse Document Frequency-Class Frequency (TF-IDF-CF), Galavotti-Sebastiani-Simi Coefficient (GSS), Term Significance (TS) and Odds Ratio (OR) is proposed. Malware and benign models for classification are created by considering top ranked features obtained through each feature selection method. The proposed statistical detector was tested on synthetic and live specimens. Accuracy of 100% is attained with the synthetic malware dataset, whereas, accuracy above 92% is obtained for the live metamorphic samples involving complex obfuscation techniques. Further, relevance of feature ranking methods at varying feature length is evaluated using McNemar test. Thus, the non-signature based scanner designed by us could be used for the detection of sophisticated metamorphic malware.
Solid-state ion sensors. Theoretical and practical issues (1986)

Integrated ion-sensor devices may be constructed using the methods of microcircuit fabrication. The suitabilities of the silicon integrated circuit and thick-film hybrid circuit processes for this purpose are compared and it is argued that the hybrid approach will offer advantages in many cases. Theoretical questions about the operation of both the hybrid and ISFET (ion-sensitive field-effect transistor) types of device are discussed and possible origins are suggested for the output drift that is commonly observed in ISFET. Practical issues which might affect the commercial development of integrated ion-sensor devices are noted.
Immune Response to Salmonella Enteritidis Infection in Broilers Immunized Orally With Chitosan-Based Salmonella Subunit Nanoparticle Vaccine (2020)

<i>Salmonella enterica</i> serovar Enteritidis (<i>S</i>. Enteritidis, SE) infection in broilers causes a huge economic loss and public health risk. We previously demonstrated that orally delivered chitosan based (CS) <i>Salmonella</i> subunit nanoparticle (NP) vaccine containing immunogenic outer membrane proteins (OMP) and flagellin (FLA) of SE [CS-NP(OMP+FLA)] induces immune response in broilers. The objective of this study was to evaluate the dose- and age-dependent response and efficacy of CS-NP(OMP+FLA) vaccine in broilers. Three-day old birds were vaccinated and boosted once or twice. Additional groups were vaccinated at three weeks with no booster or boosted once a week later. Each dose of CS-NP vaccine had either 10 or 50 μg of OMP+FLA antigens. Our data revealed that two doses of vaccine were required to induce substantial immune response. Birds received 2 doses of CS-NP(OMP+FLA) vaccine at 3 days and 3 weeks of age with 10 μg antigens, and birds inoculated twice at 3 and 4 weeks of age with 50 μg antigens had lowest challenged bacterial load in the cecal contents with over 0.5 log<sub>10</sub> reduction. In CS-NP(OMP+FLA) vaccinated birds, antigen-specific splenocyte proliferation, mucosal and systemic antibody response and the frequency of IFNγ-producing T cells were increased compared to control groups. At the molecular level, in the cecal tonsils of CS-NP(OMP+FLA) immunized birds, mRNA levels of toll-like receptor (TLR) 2 and TLR 4, and cytokines IL-4 and IL-10 were upregulated. The CS-NP(OMP+FLA) vaccine given orally has the potential to induce a protective immune response against SE infection in broilers.
Ground bounce in digital VLSI circuits (2003)

This paper is concerned with the analysis and optimization of the ground bounce in digital CMOS circuits. First, an analytical method for calculating the ground bounce is presented. The proposed method relies on accurate models of the short-channel MOS device and the chip-package interface parasitics. Next the effect of ground bounce on the propagation delay and the optimum tapering factor of a multistage buffer is discussed and a mathematical relationship for total propagation delay in the presence of the ground bounce is obtained. Effect of an on-chip decoupling capacitor on the ground bounce waveform and circuit speed is analyzed next and a closed form expression for the peak value of the differential-mode component of the ground bounce in terms of the on-chip decoupling capacitor is provided. Finally, a design methodology for controlling the switching times of the output drivers to minimize the ground bounce is presented.
A Novel Gaze Tracking Method Based on the Generation of Virtual Calibration Points (2013)

Most conventional gaze-tracking systems require that users look at many points during the initial calibration stage, which is inconvenient for them. To avoid this requirement, we propose a new gaze-tracking method with four important characteristics. First, our gaze-tracking system uses a large screen located at a distance from the user, who wears a lightweight device. Second, our system requires that users look at only four calibration points during the initial calibration stage, during which four pupil centers are noted. Third, five additional points (virtual pupil centers) are generated with a multilayer perceptron using the four actual points (detected pupil centers) as inputs. Fourth, when a user gazes at a large screen, the shape defined by the positions of the four pupil centers is a distorted quadrangle because of the nonlinear movement of the human eyeball. The gaze-detection accuracy is reduced if we map the pupil movement area onto the screen area using a single transform function. We overcame this problem by calculating the gaze position based on multi-geometric transforms using the five virtual points and the four actual points. Experiment results show that the accuracy of the proposed method is better than that of other methods.
Guangdong and Florida Populations of ‘<i>Candidatus</i> Liberibacter asiaticus’ Distinguished by a Genomic Locus with Short Tandem Repeats (2010)

Huanglongbing (HLB) (yellow shoot disease) is a highly destructive disease that threatens citrus production worldwide. The disease was first observed in Guangdong, P.R. China, over 100 years ago, and was found in Florida, United States, in 2005. 'Candidatus Liberibacter asiaticus' has been associated with HLB in many citrus-growing regions around the world, including Guangdong and Florida. The global epidemiology of HLB, as well as management of the disease, relies on knowledge of 'Ca. L. asiaticus' populations in different geographical regions around the world. In this study, we identified a genetic marker containing small tandem repeats in the genome of 'Ca. L. asiaticus' and comparatively analyzed the tandem repeat numbers (TRNs) in 'Ca. L. asiaticus' populations from Guangdong and Florida. Analyses of TRNs showed that the bacterial population in Guangdong was different from that in Florida. The Guangdong population consisted predominately of strains with a TRN of 7 (TRN(7)) at a frequency of 47.6%. The Florida population consisted predominately of strains with a TRN of 5 (TRN(5)) at a frequency of 84.4%. TRNs ranged from 3 to 16. The apparent absence of TRNs of 9, 10, 11, and 12 separated the bacterial strains into two groups: TRNs < 10 (TRN(<10)) and TRNs > 10 (TRN(>10)). In Florida, TRN(<10) strains (103/109, or 94.5%) were widely distributed in all HLB-affected counties. TRN(>10) strains (6/109, or 5.5%) were found in central Florida. This is the first report documenting the differentiation of 'Ca. L. asiaticus' populations between Asia and North America and the possible presence of two differentially distributed genotypes of 'Ca. L. asiaticus' in Florida.
Toxin–antitoxin systems and regulatory mechanisms in Mycobacterium tuberculosis (2018)

There has been a significant reduction in annual tuberculosis incidence since the World Health Organization declared tuberculosis a global health threat. However, treatment of M. tuberculosis infections requires lengthy multidrug therapeutic regimens to achieve a durable cure. The development of new drugs that are active against resistant strains and phenotypically diverse organisms continues to present the greatest challenge in the future. Numerous phylogenomic analyses have revealed that the Mtb genome encodes a significantly expanded repertoire of toxin-antitoxin (TA) loci that makes up the Mtb TA system. A TA loci is a two-gene operon encoding a 'toxin' protein that inhibits bacterial growth and an interacting 'antitoxin' partner that neutralizes the inhibitory activity of the toxin. The presence of multiple chromosomally encoded TA loci in Mtb raises important questions in regard to expansion, regulation and function. Thus, the functional roles of TA loci in Mtb pathogenesis have received considerable attention over the last decade. The cumulative results indicate that they are involved in regulating adaptive responses to stresses associated with the host environment and drug treatment. Here we review the TA families encoded in Mtb, discuss the duplication of TA loci in Mtb, regulatory mechanism of TA loci, and phenotypic heterogeneity and pathogenesis.
Alcohol-acetaminophen syndrome (2000)

In long-term alcohol users, the syndrome of hepatotoxicity from acetaminophen taken in therapeutic or modestly excessive doses is distinctive. It is characterized by striking elevation of transaminase levels and the potential for acute liver failure with high morbidity and mortality rates. A high index of suspicion should be maintained; in any patient with evidence of acute hepatic injury, a complete history of over-the-counter drug use should be obtained and acetaminophen levels checked. If there is doubt about the dose or time of ingestion, one should err on the side of treatment with acetylcysteine, because it is both effective and safe. Therapy should be initiated as early as possible, but even late administration may be of benefit. Timely contact with a medical center that has liver transplantation capabilities should be made before encephalopathy becomes advanced. Heightened awareness of this preventable and treatable condition is needed by healthcare providers and acetaminophen users alike. Because the minimum safe dose of acetaminophen is not known in the setting of chronic alcohol use, it seems prudent in such situations to avoid acetaminophen altogether, especially during brief periods of abstinence.
The First Reusable Multiple-Band Ligator for Endoscopic Hemostasis of Variceal Bleeding, Nonvariceal Bleeding and Mucosal Resection (1999)

A new multiband ligator is presented which is fully reusable. Experience in 67 patients (22 with varices and 45 with early cancers undergoing mucosal resection) showed good technical function and no significant complications. Use of this device may significantly reduce the costs of endoscopic ligation.