gebhart/patrepeval huggingface dataset:
Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family (2012)

Codon usage patterns of 23 Poaceae chloroplast genomes were analysed in this study. Neutrality analysis indicated that the codon usage patterns have significant correlations with GC12 and GC3 and also showed strong bias towards a high representation of NNA and NNT codons. The Nc-plot showed that although a large proportion of points follow the parabolic line of trajectory, several genes with low ENc values lie below the expected curve, suggesting that mutational bias played a major role in the codon biology of the Poaceae chloroplast genome. Parity Rule 2 plot analysis showed that T was used more frequently than A in all the genomes. Correspondence analysis of relative synonymous codon usage indicated that the first axis explained only a partial amount of variation of codon usage. Furthermore, the gene length and expression level were also found to drive codon usage variation. These findings revealed that besides natural selection, other factors might also exert some influences in shaping the codon usage bias in Poaceae chloroplast genomes. The optimal codons of these 23 genomes were also identified in this study.
Leslie matrix models (1989)

A review of the Leslie matrix model theory and its literature 1941-1987 is presented. The point of view is that of a mathematician who focuses on the parts of the theory which are relevant to demography. Works of a decidedly applied nature are not dealt with.
Scene Compliant Trajectory Forecast With Agent-Centric Spatio-Temporal Grids (2020)

Forecasting long-term human motion is a challenging task due to the non-linearity, multi-modality and inherent uncertainty in future trajectories. The underlying scene and past motion of agents can provide useful cues to predict their future motion. However, the heterogeneity of the two inputs poses a challenge for learning a joint representation of the scene and past trajectories. To address this challenge, we propose a model based on grid representations to forecast agent trajectories. We represent the past trajectories of agents using binary 2-D grids, and the underlying scene as a RGB birds-eye view (BEV) image, with an agent-centric frame of reference. We encode the scene and past trajectories using convolutional layers and generate trajectory forecasts using a Convolutional LSTM (ConvLSTM) decoder. Results on the publicly available Stanford Drone Dataset (SDD) show that our model outperforms prior approaches and outputs realistic future trajectories that comply with scene structure and past motion.
Curing behavior and thermal properties of trifunctional epoxy resin cured by 4, 4’-diaminodiphenyl sulfone (2009)

A novel trifunctional epoxy resin 4-(3, 3-dihydro-7-hydroxy-2, 4, 4-trimethyl-2H-1-benzopyran-2-yl)-1, 3-benzenediol glycidyl (shorted as TMBPBTH-EPOXY) was synthesized in our lab to improve thermal performance. Its curing behavior and performance were studied by using 4, 4-diaminodiphenyl sulfone (DDS) as hardener with the mass ratio of 100:41 of TMBPBTH-EPOXY and DDS. The curing activation energy was investigated by differential scanning calorimetry (DSC) to be 64.0 kJ/mol estimated by Kissinger's method and 68.7 kJ/mol estimated by Flynn-Wall-Ozawa method respectively. Thermogravimetric analyzer (TGA) was used to investigate the thermal decomposition of cured compounds. It was found that when curing temperature was lower than 180C, the thermal decomposition temperature increased with the rise of curing temperature and curing time. On the other hand, when the curing temperature was higher than 180C, the thermal decomposition temperature went down instead with the increase of curing time that might be the over-crosslinking of TMBPBTH-EPOXY and DDS hardener. The glass transition temperature (Tg) of cured TMBPBTH-EPOXY/DDS compound determined by dynamic mechanical thermal analysis (DMTA) is 290.1C.
MECHANICAL PROPERTIES OF SINTER/FORGED LOW-ALLOY STEELS (1970)

The paper describes preliminary work on sinter/forged low-alloy steels. The mechanical properties and structures of both atomized and blended alloys were investigated. By using a good-quality atomized powder of the SAE 4600 type, tensile and fatigue properties equivalent to those of wrought steels could be obtained. Atomized alloy powders with higher oxygen contents had poor ductility and impact values because of surface oxides on the powder particles.Blended iron alloys gave tensile strengths up to 72 tonf/in2 (1112 MN/m2) with much higher ductility and impact-resistance than would be obtained with conventionally pressed and sintered alloys.
Upstream box/TATA box order is the major determinant of the direction of transcription (1991)

Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of transcription. We have constructed promoters with an 'octamer' upstream sequence ATTTGCAT (or its complement ATGCAAAT) in combination with several different TATA boxes and initiation (cap) sites, and tested these promoters in transfection experiments with cultured cells. TATA boxes derived from the adenovirus major late promoter (TATAAAA), immunoglobulin kappa light chain (TTATATA) and heavy chain (TAAATATA) promoter functioned equally well or even better when inverted. Only the beta-globin TATA box (CATAAAA) was poorly active when inverted. In addition, a symmetrical TATA box (TATATATA) derived from a casein gene was very active. Our results suggest that the asymmetry of most TATA boxes (consensus TATAAAA) is not a primary determinant of the polarity of transcription. We also found that the initiation (cap) site, which usually consists of an adenine embedded in a pyrimidine-rich region (PyPyCAPyPyPyPyPy), was permissive towards sequence alterations; even a randomly composed sequence worked well. However, an inverted, hence purine-rich, cap site reduced transcript levels to 1/7th, as did an oligo G sequence. Irrespective of the presence of a cap site, the configuration: 'TATA box/octamer' yielded a strong leftward, rather than rightward transcription. From this, we conclude that the polarity of transcription is primarily determined by the linear order of an upstream sequence relative to a TATA box, rather than by the individual orientations of either of these two elements.
Recycling Perovskite Solar Cells To Avoid Lead Waste (2016)

Methylammonium lead iodide (MAPbI3) perovskite based solar cells have recently emerged as a serious competitor for large scale and low-cost photovoltaic technologies. However, since these solar cells contain toxic lead, a sustainable procedure for handling the cells after their operational lifetime is required to prevent exposure of the environment to lead and to comply with international electronic waste disposal regulations. Herein, we report a procedure to remove every layer of the solar cells separately, which gives the possibility to selectively isolate the different materials. Besides isolating the toxic lead iodide in high yield, we show that the PbI2 can be reused for the preparation of new solar cells with comparable performance and in this way avoid lead waste. Furthermore, we show that the most expensive part of the solar cell, the conductive glass (FTO), can be reused several times without any reduction in the performance of the devices. With our simple recycling procedure, we address both the risk of contamination and the waste disposal of perovskite based solar cells while further reducing the cost of the system. This brings perovskite solar cells one step closer to their introduction into commercial systems.
Power supply with arc handling for high peak power magnetron sputtering (2004)

High power pulsed magnetron sputtering (HPPMS) can generate a dense plasma with high target material ion content, using essentially conventional magnetron sputtering equipment. However, process arcs, which generate macroparticles and target damage, are not avoidable due especially to imperfections in vacuum system hardware and target materials. Arc handling is required for practical application of HPPMS. An experimental power supply capable of peak powers up to 3 MW, peak currents to 3000 A, at discharge voltages reaching 2 kV has been designed and built. It has voltage ring-up capability for pulse by pulse plasma ignition. This power supply technology enables the practical application of a whole range of sputtering processes, based on pulsing magnetrons operating at high peak powers. Power supply performance for typical pulses and for arc handling at peak currents into the kiloamp range is shown with temporal current and voltage characteristics of the discharge for typical pulses and for arcing operation.
Control of a Single-Phase Grid-Connected Voltage Source Inverter with LCL Filter (2013)

Thesis (Ph.D, Electrical & Computer Engineering) -- Queen's University, 2013-09-30 13:47:56.337
Platelet-Rich Plasma: A Comprehensive Review of Emerging Applications in Medical and Aesthetic Dermatology. (2021)

Platelet-rich plasma (PRP) has been integrated into numerous treatment regimens for medical and aesthetic dermatology. While some of these approaches are well-established, many uses are underreported in the literature. We sought to identify and summarize the emerging dermatologic applications for PRP by conducting a comprehensive PubMed search of studies published between 2000 and 2020. These studies were reviewed to synthesize collection methods, treatment schedule, adverse effects, and the impact of therapy for new and emerging uses for PRP. In general, we identified positive treatment outcomes for skin rejuvenation, scar revision, alopecia, pigmentary disorders, lichen sclerosus, leprosy-induced peripheral neuropathy, plaque psoriasis, and nail disorders. Widely, therapy was well-tolerated and suitable for all reported phototypes. The variations in collection and application sequences make concrete recommendations difficult to discern, underscoring the need for a standardized approach to preparation and treatment methods. We hope this review serves as an outline for new and interesting uses for PRP and will help readers familiarize themselves with this exciting technology for comfortable integration into their practices.
Representations Systems, Perceptual Position, and Presence in Immersive Virtual Environments (1993)

This paper discusses factors that may contribute to the participant's sense of presence in immersive virtual environments. We distinguish between external factors, that is those wholly determined by the hardware and software technology employed to generate the environment, and subjective factors, that is how sensory inputs to the human participant are processed internally. The therapeutic technique known as neurolinguistic programming (NLP) is used as a basis for measuring such internal factors. NLP uses the idea of representation systems (visual, auditory, and kinesthetic) and perceptual position (egocentric or exocentric) to code subjective experience. The paper also considers one external factor, that is how the virtual environment represents a participant—either as a complete body, or just an arrow cursor that responds to hand movements. A case-control pilot experiment is described, where the controls have self-representation as an arrow cursor, and the experimental group subjects as a simple virtual body. Measurements of subjects' preferred representation systems and perceptual positions are obtained based on counts of types of predicates and references used in essays written after the experiment. These, together with the control variable (possession/absence of a virtual body), are used as explanatory variables in a regression analysis, with reported sense of presence as the dependent variable. Although tentative and exploratory in nature, the data analysis does suggest a relationship between reported sense of presence, preferred representation system, perceptual position, and an interaction effect between these and the virtual body factor.
Oncogenic activity of separase (2008)

AbstractSeparase, an endopeptidase, plays a pivotal role in chromosomal segregation by separating sister chromatids during the metaphase to anaphase transition. Using a mouse mammary tumor model we have recently demonstrated that overexpression of Separase induces aneuploidy and tumorigenesis (Zhang et al., 2008, PNAS doi:10.1073). Here we have described our views on the oncogenic activity of Seprase and its possible mechanism of action in the development of aneuploidy and tumorigenesis.
Synthesis and Spectroscopic and NLO Properties of “Push-Pull” Structures Incorporating the Inductive Electron-Withdrawing Pentafluorophenyl Group (2002)

A series of “push-pull” molecules, each incorporating a pentafluorophenyl ring as an inductive accepting group, has been synthesised. The NLO properties of these compounds were measured in solution by EFISH (operating at 1907 nm) and in the solid state by the Kurtz powder technique (at 1907 nm). Values of μβ, the product of the molecule dipole moment and its first-order hyperpolarizability, of up to 200 × 10−48 esu were obtained. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Syphilis: a pediatric perspective. (1998)

1. Lillian Sung, MD*
2. Noni E. MacDonald, MD, FRCP(C)†


 

1. 

2. *Fellow, Pediatric Infectious Diseases.

3. 

4. †Chief, Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

1. The chancre of primary syphilis typically is painless.

2. The only approved therapy for congenital syphilis, neurosyphilis, and syphilis in pregnancy is penicillin.

Treponema pallidum , the causative agent of syphilis, belongs to the family Spirochaetaceae and is a unicellular, spiral organism that cannot be cultivated in vitro.

In contrast with gonorrhea, the number of cases of syphilis reported to the Centers for Disease Control and Prevention (CDC) rose from 30.5 per 100,000 population in 1980 to 54.5 in 1990. Fortunately, the number of reported cases since 1990 has declined steadily, with only 26.2 cases per 100,000 having been reported in 1995. The number of cases of congenital syphilis mirrors this pattern, with 277 cases reported to the CDC in 1980, increasing to 3,865 cases in 1990, and decreasing to 1,548 cases in 1995.

The increased incidence of syphilis in the 1980s may have been associated with the increase in prevalence of human immunodeficiency virus (HIV) infection in the United States. Up to 15% of adolescents and adults who have syphilis are coinfected with HIV.

As with gonorrhea, transmission of syphilis is primarily by sexual contact and only rarely by other forms of close contact. An infected woman may pass the organism to her fetus during pregnancy, resulting in congenital syphilis.

Syphilis traditionally is divided into stages: primary, secondary, latent, and tertiary. Other manifestations of the disease that will be considered individually are central nervous system (CNS) syphilis and congenital syphilis.

Primary syphilis is classically manifested by a single, painless papule that appears following a 3-week incubation period. This papule then develops into a painless, spirochete-filled chancre with a smooth base and raised borders. Because the primary chancre appears at the site of inoculation, the chancre is located most commonly on the external genitalia, but it also may be found on …
Single variable domains from the T cell receptor β chain function as mono- and bifunctional CARs and TCRs (2019)

Cell therapy using T cell receptors (TCRs) and chimeric antigen receptors (CARs) represents a new wave of immunotherapies garnering considerable attention and investment. Further progress in this area of medicine depends in part on improving the functional capabilities of the engineered components, while maintaining the overall size of recombinant constructs to ensure their compatibility with existing gene delivery vehicles. We describe a single-variable-domain TCR (svd TCR) that utilizes only the variable domain of the β chain (Vβ). This Vβ module not only works in TCR and CAR formats, but also can be used to create single-chain bispecific CARs and TCRs. Comparison of individual ligand-binding Vβ domains in different formats suggests that the lone Vβ sequence controls the sensitivity and a major part of the specificity of the CAR or TCR construct, regardless of signaling format, in Jurkat and primary T cells.
CMOS compatible MIM decoupling capacitor with reliable sub-nm EOT high-k stacks for the 7 nm node and beyond (2016)

We demonstrate a record-low EOT (equivalent oxide thickness) of 0.8 nm for a metal-insulator-metal (MIM) decoupling capacitor, which is compatible with back-end-of-line (BEOL) processing. This results in 2-plate MIM capacitance density of 43 fF/um <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and leakage current density (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) of 5 fA/um <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 1V, 125 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sup> C. Moreover, we identify that symmetry of CV/IV/TDDB characteristics for both positive and negative bias polarities is a key consideration for stacking more than one MIM capacitor for further capacitance density increase. We develop a novel tri-layer high-k stack with buffer layers between HfO2 and metal electrodes, which substantially improves the electrical bias symmetry, and achieve V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">use</sub> = 1.32 V (10 yr/1 ppm/1 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /125 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sup> C) at EOT = 0.8 nm. These results should support record stacked-MIM (> 2-plate) capacitance densities, with sub-nm EOT, for the 7 nm node and beyond.
Differential A*: an adaptive search method illustrated with robot path planning for moving obstacles and goals, and an uncertain environment (2003)

Differential A* is presented. It is a method that builds on the A*/configuration-space approach to adapt quickly to changes in the space by determining and updating the localized regions affected by those changes rather than regenerating the entire space. This is particularly effective with moving obstacles or goals and in an uncertain environment because only small parts of the space are affected at a time. This technique can provide significant speed improvements over, with the same desired results, as complete space regeneration. The A* search algorithm and its relationship to the configuration space method of path planning are presented. The connection of A* to wave propagation in configuration space for path planning is described. The differential A* method is outlined, with the focus on path planning. Examples of moving obstacles and goals and planning in an uncertain environment are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Static Detection of Deadlock for Java Libraries (2005)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
Platelet-activating factor (PAF) enhances tumor necrosis factor production by alveolar macrophages. Prevention by PAF receptor antagonists and lipoxygenase inhibitors. (1989)

The effect of platelet-activating factor (PAF) on TNF production by rat alveolar macrophages (AM) and the role of endogenous leukotriene B4 (LTB4) in this regulation were examined. When AM were cultured with PAF alone, no change in TNF production was observed. However, the concomitant addition of PAF and muramyl dipeptide to AM cultures markedly enhanced (2- to 3-fold) TNF production in a concentration-dependent fashion with peak effect at 10(-10)M PAF. This enhancement occurred when muramyl dipeptide and PAF were present together at the initiation of the 24-h culture. Stimulation of TNF production by PAF was blocked by specific, but structurally different PAF receptor antagonists, BN 52021, CV3988 and WEB 2086. Additionally, the stereoisomer of PAF, [S]PAF, and the biologically inactive precursor/metabolite of PAF, lyso-PAF failed to induce significant enhancement in TNF production. In parallel, addition of PAF to AM triggered LTB4 release in a concentration-dependent manner. Inhibition of 5-lipoxygenase by nordihydro-guaiaretic acid or AA-861 blocked the PAF-induced augmentation of both TNF and LTB4 production. This was partially reversed by addition of exogenous LTB4. Collectively, these data suggest that PAF enhances TNF production by interaction with a specific putative receptor and by subsequent induction of endogenous 5-lipoxygenase activity in AM.
Adrenocortical Carcinoma (2014)

Adrenocortical carcinoma is a rare endocrine tumor with a poor prognosis. These tumors can be diagnostically challenging, and diagnostic algorithms and criteria continue to be suggested. Myxoid and oncocytic variants are important to recognize to not confuse with other tumors. In addition, the diagnostic criteria are different for oncocytic adrenal carcinomas than conventional carcinomas. Adrenocortical carcinomas usually occur in adults, but can also occur in children. In children these tumors are diagnostically challenging as the histologic features of malignancy seen in an adult tumor may not be associated with aggressive disease in a child. Adrenocortical carcinomas occur with increased frequency in Beckwith-Wiedemann and Li-Fraumeni syndromes, but most occur sporadically. Gene expression profiling by transcriptome analysis can discriminate adrenocortical carcinomas from adenomas and divide carcinomas into prognostic groups. The increasing understanding of the pathogenesis of these tumors may provide increasing treatment targets for this aggressive tumor.
Quinolone Antimicrobial Agents (1992)

This chapter reviews the chemistry, microbiology, pharmacology, and clinical use of the fluoroquinolone antimicrobial agents. The molecular and clinical problems of bacterial resistance are reviewed. The clinical areas in which fluoroquinolones have been investigated are detailed, with particular attention to areas of appropriate and inappropriate use.
(Re) opening lines. (2005)

How will acquiring new medical device technologies affect your managed care contracts? In anticipation of changes, consider including provisions in these agreements that: Clarify how coverage for new technology will be managed. Establish a process should payment disputes occur over new technology coverage.
SEROLOGICAL STUDIES ON AZOPROTEINS (1934)

A study was made of the specificity of artificial compound-antigens containing aliphatic chains. Striking specificity was exhibited in the reactions of compounds with short chains containing a carboxyl group; for instance succinic acid could be differentiated from malonic or glutaric acid which contain one fewer and one more carbon atom respectively. With the substances containing longer chains, reactions were observed which, although specific to a certain extent, appear to depend mainly on the general physicochemical properties of long aliphatic chains. With a limited number of substances the influence of substituents -halogen, OH, NH(2)-on the serological specificity was investigated. By means of inhibition reactions it was possible to demonstrate the serological specificity of cis-trans isomers such as maleic and fumaric acid.