gebhart/patrepeval huggingface dataset:
Analysis of eight out genes in a cluster required for pectic enzyme secretion by Erwinia chrysanthemi: sequence comparison with secretion genes from other gram-negative bacteria (1992)

Many extracellular proteins produced by Erwinia chrysanthemi require the out gene products for transport across the outer membrane. In a previous report (S. Y. He, M. Lindeberg, A. K. Chatterjee, and A. Collmer, Proc. Natl. Acad. Sci. USA 88:1079-1083, 1991) cosmid pCPP2006, sufficient for secretion of Erwinia chrysanthemi extracellular proteins by Escherichia coli, was partially sequenced, revealing four out genes sharing high homology with pulH through pulK from Klebsiella oxytoca. The nucleotide sequence of eight additional out genes reveals homology with pulC through pulG, pulL, pulM, pulO, and other genes involved in secretion by various gram-negative bacteria. Although signal sequences and hydrophobic regions are generally conserved between Pul and Out proteins, four out genes contain unique inserts, a pulN homolog is not present, and outO appears to be transcribed separately from outC through outM. The sequenced region was subcloned, and an additional 7.6-kb region upstream was identified as being required for secretion in E. coli. out gene homologs were found on Erwinia carotovora cosmid clone pAKC651 but were not detected in E. coli. The outC-through-outM operon is weakly induced by polygalacturonic acid and strongly expressed in the early stationary phase. The out and pul genes are highly similar in sequence, hydropathic properties, and overall arrangement but differ in both transcriptional organization and the nature of their induction.
A Generic Framework for Modeling MAC Protocols in Wireless Broadband Access Networks (2007)

In this article we present a simple yet accurate generic analytical model for a family of slotted CSMA/CA-based MAC protocols widely used in various wireless broadband access networks. The proposed model is based on a hierarchical three-level renewal process concept, which leads directly to some important MAC protocol performance metrics, such as throughput and average frame service time. The applicability of the model is demonstrated by extensive simulation results.
Cutaneous onchocerciasis in an American traveler (2005)

A case report of cutaneous onchocercias acquired during travels to Africa is presented. The salient epidemiologic, clinical, diagnostic, and therapeutic aspects are reviewed. Clinical and laboratory differences between onchocerciasis patients who are inhabitants of endemic areas and those who are occasional visitors to such areas are discussed. Parasitic infections, including onchocerciasis, should be considered in the differential diagnosis of pruritic eruptions in patients with a history of foreign travel to Africa, Central and South America.
Drive modelling and performance estimation of IPM motor using SVPWM and Six-step Control Strategy (2021)

This paper presents a comprehensive evaluation of the performance of an interior permanent magnet (IPM) traction motor drive, and analyses the impact of different modulation techniques. The most widely used modulation methods in traction motor drives are Space vector modulation (SVPWM), over-modulation, and six-step modulation have been implemented. A two-dimensional electromagnetic finite element model of the motor is co-simulated with a dynamic model of a field-oriented control (FOC) circuit. For accurate tuning of the current controllers, extended complex vector synchronous frame current regulators are employed. The DC-link voltage utilization, harmonics in the output waveforms, torque ripple, iron losses, and AC copper losses are calculated and compared with sinusoidal excitation. Overall, it is concluded that the selection of modulation technique is related to the operating condition and motor speed, and a smooth transition between different modulation techniques is essential to achieve a better performance.
Prognostic significance of microinvasion with ductal carcinoma in situ of the breast: a meta-analysis (2022)

Our meta-analysis suggests that DCIS/microinvasion may display more aggressive biological and clinical behavior than pure DCIS, highlighting the potential need for closer follow-up and consideration of adjuvant treatment strategies in DCIS patients with microinvasive disease.
Bayesian assessment of modeling uncertainties application to fire risk assessment (2002)

Uncertainties in the prediction of models can be important contributors to the uncertainties in probabilistic risk assessment results, yet are usually not treated. This paper discusses the assessment of uncertainties associated with a simple model when large amounts of benchmarking data are not available, and applies a Bayesian approach for quantification. The application is to a problem of interest in fire risk assessment: estimation of the velocity of flame spread over a horizontal cable tray. The uncertainties in the available predictive model are formally assessed and possible reasons for the deviation between predictions and observations are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Phase I Study of Ultra Low Dose Interleukin-2 and Stem Cell Factor in Patients with HIV Infection or HIV and Cancer (2006)

Administration of IL-2 with SCF is safe and well tolerated and leads to expansion of lymphocyte subsets in patients with HIV or HIV and cancer; however, the changes in NK cell and Treg expansion seen with this cytokine combination were no different than those seen with a similar dose of IL-2 alone.
Variable Transmittance Coatings Using Electrochromic Lithium Chromate and Amorphous  WO 3 Thin Films (1997)

A thin film, counterion, variable transmittance electrochromic device is described with the structure: . The structure is prepared by sequential deposition of the layers using a combination of sputtering and evaporation processes. The "counterelectrode" has a Li capacity of ∼0.5 mC/cm2 nm and exhibits weak anodic coloration with a luminous efficiency of 3 to 4 cm2/C. Variable transmittance devices, with an area of 20 cm2, have been fabricated using 40 to 80 nm thick films and cathodically coloring a‐. The luminous transmittance range and switching speed of as‐fabricated devices are typically 10 to 70% and 30 s, respectively. Multicycle switching reveals a decrease in switching speed over the first 5000 cycles while the luminous transmittance range is unchanged.
Model of aircraft noise adaptation (1977)

Development of an aircraft noise adaptation model, which would account for much of the variability in the responses of subjects participating in human response to noise experiments, was studied. A description of the model development is presented. The principal concept of the model, was the determination of an aircraft adaptation level which represents an annoyance calibration for each individual. Results showed a direct correlation between noise level of the stimuli and annoyance reactions. Attitude-personality variables were found to account for varying annoyance judgements.
Coronary Angiography and Angioplasty after Acute Myocardial Infarction (1997)

Although many patients benefit from angiography and angioplasty after myocardial infarction, others probably do not. Substantial resources are at stake.
Education in stroke prevention: efficacy of an educational counselling intervention to increase knowledge in stroke survivors. (2007)

Although contact with patients in ambulatory clinical settings is limited due to time constraints, it is still possible to improve knowledge and initiate lifestyle changes utilizing motivational interviewing and a stage of change model. Stroke nurses may wish to consider these techniques in their practice setting.
Effects of Intracavernosal Trazodone Hydrochloride: Animal and Human Studies (1990)

Trazodone hydrochloride is an oral antidepressant agent which has been associated with the improvement of erections in impotent men and the development of prolonged erections or priapism in potent men. An in vivo study in animal and human subjects was performed to gain experience with the effect of intracavernosal trazodone. In the anesthetized New Zealand White rabbit, intracavernosal trazodone or its major metabolite m-chlorophenylpiperazine (m-CPP) produced full penile erection in 76% and 84% of animals studied respectively with doses ranging from one to 15 mg. On the other hand, intracavernosal administration of five mg. papaverine resulted in a prolonged erection in 90% of animals studied. In 13 selected volunteer patients, intracavernosal trazodone caused tumescence but not full penile erection with corporal body pressures of 28.2 +/- 5.8 mm. Hg. Intracavernosal papaverine or papaverine and phentolamine in these subjects resulted in significantly higher corporal body pressures of 58 +/- 18 mm. Hg (p less than .05). Intracavernosal administration of alpha adrenoceptor agonists but not normal saline resulted in complete detumescence of trazodone- or m-CPP-induced prolonged erection in the animal studies. Intracavernosal trazodone results in erectile activity that appears in part based on its local alpha blocking activity but like other intracavernosal alpha-blocking agents is not as effective in initiating penile erections as are intracavernosal agents that directly induce smooth muscle relaxation.
Zonation of Parenchymal and Nonparenchymal Metabolism in Liver (1996)

The enormous number of different liver functions are carried out by parenchymal and four main types of nonparenchymal cells, either alone or in cooperation. Although the liver tissue is uniform on the level of histology, it is heterogenous on the level of morphometry and histochemistry. This heterogeneity is related to the blood supply; cells located in the upstream or periportal zone differ from those in the downstream or perivenous zone in their equipment with key enzymes, translocators, receptors, and subcellular structures and therefore have different functional capacities. This is the basis of the model of metabolic zonation, according to which glucose release from glycogen and via gluconeogenesis, amino acid utilization and ammonia detoxification, protective metabolism, bile formation, and the synthesis of certain plasma proteins such as albumin and fibrinogen occur mainly in the periportal area, whereas glucose utilization, xenobiotic metabolism, and the formation of other plasma proteins such as alpha 1-antitrypsin or alpha-fetoprotein occur predominantly in the perivenous zone. The mor- phologic and functional heterogeneity is the result of zonal differences in the activation of the cellular genome caused by gradients in oxygen, substrate, hormone, and mediator levels, in innervation, as well as in cell-to-cell and cell-to-biomatrix interactions.
Interval Type-2 FNN-Based Quantized Tracking Control for Hypersonic Flight Vehicles With Prescribed Performance (2019)

This paper presents a tracking control scheme with quantization mechanism for hypersonic flight vehicles (HFVs) with prescribed performance using an interval type-2 fuzzy neural network (IT2FNN). A parameterized tracking error model of the HFV is derived with some considered uncertainties, which are approximated by an IT2FNN. The tracking control of the velocity and altitude of the HFV is designed by using a prescribed performance control technique. It allows that transient characteristics of the tracking errors can be improved and adjusted by some prescribed performance functions. According to an adaptive backstepping control design procedure, novel continuous control laws of the fuel equivalency ratio, canard deflection, and elevator deflection are designed with logarithmic quantization mechanism, for the sake of avoiding inadvertently increasing the effective gains of continuous controllers as well as reducing loads of the communication from controller unit to actuator unit. Besides, the limited tracking errors of the flight path angle and angle-of-attack can be achieved by applying the designed controllers. Finally, the presented tracking controllers with quantization mechanism are validated by comparative simulations.
324 PRODUCTION OF GENETICALLY MODIFIED PIGS BY ARTIFICIAL REPRODUCTIVE TECHNOLOGIES USING FROZEN EPIDIDYMAL SPERM (2012)

Genetically modified (GM) pigs are useful tools for many types of biomedical research. The objective of this study was to develop a reliable protocol for the reproduction of GM pigs using frozen epididymal sperm. Epididymal sperm were collected from 3 GM boars: (1) humanized Kusabira-Orange (huKO) transgenic, (2) mutant human hepatocyte nuclear factor 1a (HNF-1a) transgenic, and (3) a1,3-galactosyltransferase gene knockout (GalT-KO). Additionally, a wild type (WT) boar was also used for sperm collection. After collection, the sperm were frozen in Niwa and Sasaki freezing medium (Niwa et al. 1989 Manual for Cryopreservation of Pig Spermatozoa 19–23; 1.0 × 109 sperm mL–1) using 0.5-mL straws. The sperm were cooled utilising the 2-step method, from 25 to 15°C at a rate of 0.17°C min–1, and then from 15 to 5°C at 0.08°C min–1. After cooling to 5°C, the straws were frozen in liquid nitrogen with 3% glycerol for storage. After storage for 0.5 to 21 months, the straws were thawed by immersion into a 37°C water bath. The recovered sperm were washed by centrifugation in PBS + 1 mg mL–1 BSA and were resuspended in either Beltsville thawing solution (Pursel and Johnson. 1975 J. Anim. Sci. 40, 99–102) for intra-fallopian AI or in porcine fertilization medium (PFM, Research Institute for the Functional Peptides, Yamagata, Japan) for IVF. Prepubertal gilts (6.5 months), in which oestrus was induced by 1000 IU eCG and 1500 IU hCG given 66 or 72 h apart, were surgically inseminated with 0.9–7.9 × 106 progressive motile sperm 41 to 51 h after receiving an hCG injection. Oocytes, which matured in vitro either in modified porcine oocyte medium (IFP) or modified NCSU23 medium, were inseminated in PFM for 8 h with either 0.5 (huKO, GalT-KO) or 1.6 (HNF-1a) × 106 progressive motile sperm mL–1. The in vitro fertilized oocytes were cultured in porcine zygote medium-5 (Research Institute for the Functional Peptides) for 5 to 6 days until they were transferred. Some of these oocytes were examined for their fertilization rates. Blastocysts were transferred into the uterus of the recipient 150 h after hCG treatment. The fertilization rates for huKO, HNF-1a and GalT-KO sperm were 63.5% (61/96), 62.5% (70/112) and 92.4% (61/66), respectively; 50.8% (31/61), 82.9% (58/70) and 60.7% (37/61) of these were monospermic. The rate at which the IVF embryos developed into blastocysts was 47.8–52.4%. This study demonstrates that IVF using frozen epididymal sperm is more efficient method for reproducing genetically modified pigs than AI (87.5 v. 33.3%). Table 1. Pig production efficiencies of frozen epididymal sperm from genetically modified pigs utilising AI and IVF This study was supported by JST, ERATO, NAKAUCHI Stem Cell and Organ Regeneration Project, Tokyo.
Accuracy and precision analysis of 3-D cancer atlas registration for targeted prostate biopsy via predictive deformation modeling (2008)

Electroencephalographic examinations were conducted on 250 emotionally disturbed children and adolescents (175 boys and 75 girls) between the ages of 6 and 18. ll8 (47.2%) of the children and adolescents had an EEG which corresponded with their age group. 88 (35.2%) of the patients showed a HV alteration without any pathological graphologic elements. The electroencephalography in 44 cases (17.6%) clearly showed abnormal and/or pathological alterations. Frequently conspicuous findings were present in children with aggressive behavior, learning problems, anxiety syndromes as well as enuresis and encopresis. The alterations were less pronounced in those children who stuttered and the obsessive neurotics. No statistical significance, however, could be established. A correlation could not be established between a particular psychological symptom and a specific EEG alteration. Our results correspond in this regard with those presented in the literature. The majority of the authors, however, recorded conspicuous EEG findings much more frequently than we did. Basically, an electroencephalographic examination for emotionally disturbed children seems to be necessary for the recognition of somatic factors. For the evaluation, however, the range of variation of the normal encephalogram in children and its special characteristics at various age levels should be taken into consideration.
Atomic force microscopy of structures produced by electrospraying polymer solutions (1998)

Solutions of synthetic [poly(ethylene oxides), polyvinylpyrrolidone, polyacrylamide, and poly(vinylalcohol)] and natural linear polymers (single- and double-strand DNA) have been electrosprayed onto mica surface and imaged with an atomic force microscope. Depending on the electrospray ionization (ESI) conditions (concentration, solvent, sign of ion charge) each polymer studied could be imaged as globular or fibrillar forms. Globules were observed after electrospray (ES) of dilute solutions such as are routinely used in mass spectroscopy studies of polymers. An increase in the polymer concentration resulted in formation of larger multimolecular globular clusters, then extended fibers, presumably consisting of single (0.2–0.5 nm high) and multiple (>0.6 nm high) polymer strands. Further increase in the polymer concentration produced complex structures including branched fibers, “pins,” and “beads-on-a-string.” Formation of these structures is discussed in terms of known mechanisms of ESI.
Label Smoothing and Logit Squeezing: A Replacement for Adversarial Training? (2019)

Adversarial training is one of the strongest defenses against adversarial attacks, but it requires adversarial examples to be generated for every mini-batch during optimization. The expense of producing these examples during training often precludes adversarial training from use on complex image datasets. In this study, we explore the mechanisms by which adversarial training improves classifier robustness, and show that these mechanisms can be effectively mimicked using simple regularization methods, including label smoothing and logit squeezing. Remarkably, using these simple regularization methods in combination with Gaussian noise injection, we are able to achieve strong adversarial robustness -- often exceeding that of adversarial training -- using no adversarial examples.
DirAc: An Integrated Circuit for Direct Acquisition of the M-Code Signal (2004)

Abstract : This paper describes the first integrated circuit (IC) designed, fabricated, and tested to perform direct acquisition of the M code signal. This DirAc IC prototype provides direct acquisition capability for test receivers and also demonstrates the feasibility of performing direct acquisition over extended regions of time and frequency uncertainty. The IC is designed and fabricated using 180 nm technology, and has been tested to demonstrate complete functionality and full performance. It uses parallel code matched filters, with FFT-based backend processing to search over 800 Hz of frequency uncertainty and 10 msec of time uncertainty in parallel, using off-chip memory for noncoherent integration. Multiple such timefrequency tiles are searched serially. Inputs are sampled at 2 bits each inphase and quadraphase. The DirAc IC supports a maximum integration time (combined coherent and noncoherent integration) of 1.28 seconds, and includes compensation for code Doppler. Coherent integration time up to 10 msec can be used. The DirAc IC's architecture takes advantage of the M-code signal's binary offset carrier (BOC) modulation to reduce acquisition processing complexity. DirAc supports different modes and features of the M-code signal. Hardware is time-shared between inphase and quadraphase processing and also between upper and lower sidebands of the BOC modulation. The architecture uses a pipelined design to provide the equivalent processing capability of 3.2 million parallel correlators, performing 2 tera operations per second. Average power consumption in a typical application is less than 1 mW. The IC design and layout process are also described, identifying techniques used to efficiently design and layout the IC. Theoretical predictions are provided for search speed and for the ability to work at different levels of carrier-to-noise density ratio.
Characterization of Unique Signature Sequences in the Divergent Maternal Protein Bcl2l10 (2011)

Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. Bcl2l10 is an antiapoptotic member of the Bcl-2 family that has evolved rapidly throughout the vertebrate lineage and which shows conserved abundant expression in eggs and oocytes. In this paper, we have unraveled two major sites of divergence between human Bcl2l10 and its vertebrate homologs. The first one provides length variation at the N-terminus (before the BH4 domain) and the second one is located between the predicted α5-α6 pore-forming helices, providing an unprecedented case in the superfamily of helix-bundled pore-forming proteins. These two particular indels were studied phylogenetically and through biochemical and cell biological techniques, including truncation and site-directed mutagenesis. While deletion of the N-terminal extension had no significant functional impact in HeLa cells, our results suggest that the human Bcl2l10 protein evolved a calcium-binding motif in its α5-α6 interhelical region by acquiring critical negatively charged residues. Considering the reliance of female eggs on calcium-dependent proteins and calcium-regulated processes and the exceptional longevity of oocytes in the primate lineage, we propose that this microstructural variation may be an adaptive feature associated with high maternal expression of this Bcl-2 family member.
Improved Electrical Performance for Multilayer MoS2 Transistors by Using a Fully Encapsulated Al2O3 Dielectric Layer (2018)

A fully encapsulated Al2O3 dielectric is developed to improve device performance in multilayer MoS2 transistors. Compared with bottom gated MoS2 field effect transistors, top gated transistor with top Al2O3 dielectric layer and bottom Al2O3 passivation layer shows great electrical property improvement with an on-off current ratio of 210 5 , a threshold voltage of 0.5 V, a subthreshold swing of 120 mV/dec and a high field effect mobility of 79 cm 2 V -1 s -1 , which are ascribed to optimized device structure as top gate/Al2O3/MoS2/Al2O3/SiO2/Si. Low threshold voltage and high field effect mobility are propitious to low power consumption solid-state electrons.
Prebiotic RNA polymerisation: energetics of nucleotide adsorption and polymerisation on clay mineral surfaces (2017)

We measured the binding energy and bonding parameters between model nucleotide functional groups and model clay mineral surfaces in solutions of acidic pH. We demonstrate that basal surfaces of clay minerals interact most strongly with nucleobases and show that the adsorption of the phosphate group to clay edges could facilitate polymerisation. Our results suggest that Al- and Fe-rich edge sites behave similarly in nucleotide polymerisation through change of the phosphodiester bond strength. We present an internally consistent set of thermodynamic parameters that represent the nucleotide-clay mineral system.
Model Selection in Time Series Studies of Influenza-Associated Mortality (2012)

GCV criterion is recommended for selection of Poisson models to estimate influenza-associated mortality and morbidity burden with proper adjustment for confounding. These findings shall help standardize the Poisson modeling approach for influenza disease burden studies.