gebhart/patrepeval huggingface dataset:
Origin of transfer of IncF plasmids and nucleotide sequences of the type II oriT, traM, and traY alleles from ColB4-K98 and the type IV traY allele from R100-1 (1986)

The complete nucleotide sequences of the ColB4-K98 (ColB4) plasmid transfer genes oriT, traM, and traY as well as the traY gene of R100-1 are presented and compared with the corresponding regions from the conjugative plasmids F, R1, and R100. The sequence encoding the oriT nick sites and surrounding inverted repeats identified in F was conserved in ColB4. The adenine-thymine-rich sequence following these nick sites was conserved in R1 and ColB4 but differed in F and R100, indicating that this region may serve as the recognition site for the traY protein. A series of direct repeats unique to the ColB4 plasmid was found in the region of dyad symmetry following this AT-rich region. This area also encodes 21-base-pair direct repeats which are homologous to those in F and R100. The traM gene product may bind in this region. Overlapping and following these repeats is the promoter(s) for the traM protein. The traM protein from ColB4 is similar to the equivalent products from F, R1, and R100. The traY protein from ColB4 is highly homologous to the R1 traY gene product, while the predicted R100-1 traY product differs at several positions. These differences presumably define the different alleles of traM and traY previously identified for IncF plasmids by genetic criteria. The translational start codons of the ColB4 and R100-1 traY genes are GUG and UUG, respectively, two examples of rare initiator codon usage.
Design and Control of a Shape Memory Alloy Actuated Robotic Catheter (2008)

This paper details the development of a Neural Network (NN) controller for a Shape Memory Alloy (SMA) actuated catheter, with potential application to tele-operated cardiac ablation procedures. The robotic catheter prototype consists of a central tubular structure actuated by four SMA tendons. A dual-camera imaging system provides position feedback of the catheter tip. Open loop bending responses are obtained and associated nonlinearities are identified. A NN controller is designed using time-shifted input-output maps generated from randomized open loop measurements. The tracking performance of this NN controller is compared with PI/PID controllers for various reference trajectories.
Permanent skin replacement using engineered epidermis containing fewer than 5% syngeneic keratinocytes. (1998)

This study was conducted to investigate permanent skin replacement using heterologous (syngeneic-allogeneic) epidermal substitutes containing fewer than 5% syngeneic keratinocytes. Keratinocytes were isolated from the skin of new-born Balb/c (B) and C3H/HeN (C) mice and cocultured in different ratios: 20%B-80%C, 10%B-90%C, 5%B-95%C, and 2%B-98%C (and vice versa). After 4 to 5 days, graftable epidermal substitutes were obtained and transplanted onto adult Balb/c or C3H/HeN male mice. Recipients always received the heterografts containing the lower percentage of their own keratinocytes. On Days 15 and 30 postgrafting, all heterografts showed significant graft take (> 75%) and skin replacement compared with allografts. Regenerated tissues were well structured and well vascularized. These tissues contained only syngeneic keratinocytes. These results led us to question whether this was an active immune situation. Structural analyses revealed the presence of leukocyte infiltration that was dependent on the percentage of allogeneic keratinocytes present in the heterologous implant. However, even with the 2% syngeneic-98% allogeneic implant, infiltration was lower than with the allograft. Leukocyte phenotyping confirmed the presence of immune cells infiltrating the heterologous implants and revealed the involvement of CD8+ and CD4+ lymphocytes in this immune activation. The percentages of these two cell populations were lower than those obtained with the allografts, suggesting moderate cellular activation after each heterograft compared with the allografts. In conclusion, it is possible to generate functional skin even after 2% syngeneic-98% allogeneic heterografts; there was moderate cellular immune activation compared with the allografts.
Tarp regulates early<i>Chlamydia</i>-induced host cell survival through interactions with the human adaptor protein SHC1 (2010)

Many bacterial pathogens translocate effector proteins into host cells to manipulate host cell functions. Here, we used a protein microarray comprising virtually all human SRC homology 2 (SH2) and phosphotyrosine binding domains to comprehensively and quantitatively assess interactions between host cell proteins and the early phase Chlamydia trachomatis effector protein translocated actin-recruiting phosphoprotein (Tarp), which is rapidly tyrosine phosphorylated upon host cell entry. We discovered numerous novel interactions between human SH2 domains and phosphopeptides derived from Tarp. The adaptor protein SHC1 was among Tarp's strongest interaction partners. Transcriptome analysis of SHC1-dependent gene regulation during infection indicated that SHC1 regulates apoptosis- and growth-related genes. SHC1 knockdown sensitized infected host cells to tumor necrosis factor-induced apoptosis. Collectively, our findings reveal a critical role for SHC1 in early C. trachomatis-induced cell survival and suggest that Tarp functions as a multivalent phosphorylation-dependent signaling hub that is important during the early phase of chlamydial infection.
Automated Probabilistic Analysis of Air Traffic Control Communications (2013)

Abstract : Initiatives to integrate autonomous Unmanned Aerial Vehicles (UAVs) with regular airport operations require automated onboard situational awareness to maintain safety at all times. More specifically, this requires the capability to sense, interpret, and predict what other aircraft are doing, based on the same incoming data that are available to a human pilot. This includes not only baseline knowledge of the airport layout, operational practices and landmarks, but also an ability to interpret radio communications with Air Traffic Control (ATC) and correlate them with observable movements and positions of other aircraft. This analysis informs an autonomous UAV's control mechanisms which ultimately regulate its kinetic behavior at the airport. As with any operational domain governed by human actions and control, there are many inherent challenges in interpreting ATC communications -- a noisy data stream not only in terms of signal quality, but more significantly in the range of human deviations from the strictest procedures. This makes the analysis a natural application for Artificial Intelligence techniques, where the goal is to support automated reasoning that mimics a human pilot's decision processes. This paper provides a detailed discussion of a probabilistic reasoning approach using Bayesian Networks to classify ATC communications and synthesize them with baseline knowledge of an airport and produce real-time hypotheses about the states and trajectories of other aircraft. This provides a key component for automated situational awareness, which also requires correlation with sensor data, and ultimately a functional set of behaviors to act accordingly, although these latter capabilities are beyond the scope of this paper. The probabilistic communications analysis methodology is described, along with testing results using a real-world sample data set annotated for ground truth, to evaluate performance.
Role of Transepidermal and Transfollicular Routes in Percutaneous Absorption of Steroids: In vitro Studies on Human Skin (1994)

Percutaneous absorption theoretically comprises two components: the transepidermal and the transfollicular routes. The aim of the present work was to confirm this hypothesis in the human skin by comparing the in vitro percutaneous absorption of four steroids through scar skin without hair follicles and sebaceous glands and through normal adjacent skin from abdominal or mammary plasties. In all cases, the absorption of the four steroids was significantly higher in normal skin than in scar skin. The cumulative percentages of progesterone and testosterone after 8 h of application were, respectively, 3.1- and 2.4-fold higher in normal skin than in scar skin. After 24 h of application, the cumulative percentages of estradiol and hydrocortisone were 1.7- and 2.4-fold higher in normal skin than in scar skin. At the end of the experiments, the quantities of drugs remaining in the skin after 8 or 24 h of application were the same in normal skin and in scar skin except for progesterone for which they were 2-fold greater in normal than in scar skin. In each case, a histological characterization of the scar skin was made in comparison with the normal adjacent skin. The main modifications observed on scar skin were the following: absence of hair follicles and sebaceous glands, thinning of the collagenous fibers with parallel orientation to the dermoepidermal junction and decrease in the number or disappearance of the elastic fibers. These experiments confirmed that human skin appendages, hair follicles and sebaceous glands, constitute a route of penetration for steroids and thus probably for other chemicals of similar molecular weight and properties.
On the Properties of Non-Media Digital Watermarking: A Review of State of the Art Techniques (2016)

Over the last 25 years, there has been much work on multimedia digital watermarking. In this domain, the primary limitation to watermark strength has been in its visibility. For multimedia watermarks, invisibility is defined in human terms (that is, in terms of human sensory limitations). In this paper, we review recent developments in the non-media applications of data watermarking, which have emerged over the last decade as an exciting new sub-domain. Since by definition, the intended receiver should be able to detect the watermark, we have to redefine invisibility in an acceptable way that is often application-specific and thus cannot be easily generalized. In particular, this is true when the data is not intended to be directly consumed by humans. For example, a loose definition of robustness might be in terms of the resilience of a watermark against normal host data operations, and of invisibility as resilience of the data interpretation against change introduced by the watermark. In this paper, we classify the data in terms of data mining rules on complex types of data such as time-series, symbolic sequences, data streams, and so forth. We emphasize the challenges involved in non-media watermarking in terms of common watermarking properties, including invisibility, capacity, robustness, and security. With the aid of a few examples of watermarking applications, we demonstrate these distinctions and we look at the latest research in this regard to make our argument clear and more meaningful. As the last aim, we look at the new challenges of digital watermarking that have arisen with the evolution of big data.
An approach to the design of sparse array systems (1994)

Sparse arrays have been proposed for two-dimensional arrays for three-dimensional ultrasound imaging in order to reduce the number of channels in the system. Such arrays have been designed by picking array elements in a random fashion, either according to a uniform or a Gaussian distribution. A random array can have large variations in the level of the maximum sidelobe. A method for optimization of the sidelobe level of 1-D sparse arrays has been demonstrated. This shows that weighting can give responses that resemble filled Dolph-Chebyshev arrays. The initial thinning pattern is of less importance for the final result, but the less ideal the unweighted pattern is, the more dynamic range is required from the weight function
Mapping of the Primary Mannose Binding Site of Pradimicin A (2011)

Pradimicin A (PRM-A) is an actinomycete-derived antibiotic with the lectin-like property of being able to recognize D-mannopyranoside (Man) in the presence of Ca(2+) ion. PRM-A and its derivatives have been attracting a great deal of attention as the only family of natural carbohydrate receptors with nonpeptidic skeleton and, more recently, as conceptually novel drug candidates for human immunodeficiency virus (HIV). Despite its scientific interest and potential therapeutic importance, understanding how PRM-A recognizes Man has been severely limited. Conventional interaction analysis of PRM-A with Man in solution has been frustrated by aggregation of PRM-A and the three-component equilibrium consisting of the [PRM-A(2)/Ca(2+)], [PRM-A(2)/Ca(2+)/Man(2)], [PRM-A(2)/Ca(2+)/Man(4)] complexes, and their mixed oligomers. In this Article, we demonstrate the interaction analysis of PRM-A with methyl α-D-mannopyranoside (Man-OMe) in the solid state, which benefits from aggregate-forming propensity of PRM-A and eliminates the problem associated with the complicated equilibrium in solution. Isothermal titration calorimetry (ITC) analysis and coprecipitation experiments revealed that the primary Man binding of PRM-A is markedly tighter than the secondary one, leading to preparation of the solid aggregate solely composed of the [PRM-A(2)/Ca(2+)/Man-OMe(2)] complex. The simple 1:1 complexes of biosynthetically (13)C-enriched PRM-As and [(13)C(6)]Man-OMe facilitated the analysis of the primary Man binding of PRM-A by two-dimensional dipolar-assisted rotational resonance (2D-DARR), which clearly identified that the cavity consisted of D-alanine moiety and ABC rings of PRM-A is the Man binding site. Interestingly, the proposed Man binding site of PRM-A seems to resemble the typical architecture of artificial carbohydrate receptors.
Outcomes for children with lesbian or gay parents. A review of studies from 1978 to 2000 (2002)

Twenty-three empirical studies published between 1978 and 2000 on nonclinical children raised by lesbian mothers or gay fathers were reviewed (one Belgian/Dutch, one Danish, three British, and 18 North American). Twenty reported on offspring of lesbian mothers, and three on offspring of gay fathers. The studies encompassed a total of 615 offspring (age range 1.5-44 years) of lesbian mothers or gay fathers and 387 controls, who were assessed by psychological tests, questionnaires or interviews. Seven types of outcomes were found to be typical: emotional functioning, sexual preference, stigmatization, gender role behavior, behavioral adjustment, gender identity, and cognitive functioning. Children raised by lesbian mothers or gay fathers did not systematically differ from other children on any of the outcomes. The studies indicate that children raised by lesbian women do not experience adverse outcomes compared with other children. The same holds for children raised by gay men, but more studies should be done.
Thromboxane A2 (TXA2) receptor blockade suppresses monocyte chemoattractant protein-1 (MCP-1) expression by stimulated vascular endothelial cells (2000)

In a previous study, it was reported that stimulation with a TXA2 receptor agonist, U46619, augments the expression of adhesion molecules by human umbilical vein endothelial cells (HUVEC). In the present study we showed that U46619 augments the expression of MCP-1 in HUVEC, both at the protein and mRNA levels. Pretreatment with TXA2 receptor antagonists greatly diminishes the extent of tumour necrosis factor-alpha (TNF-alpha)-, platelet-activating factor (PAF)-, or U46619-induced mRNA accumulation and production of MCP-1. Protein kinase C (PKC) inhibitors diminish U46619-induced mRNA accumulation and production of MCP-1. NAC, which inhibits nuclear factor kappaB (NF-kappaB) activation and activating protein 1 (AP-1) binding activity, inhibits the expression of MCP-1 at the protein and mRNA levels. These results indicate that in HUVEC stimulation via the TXA2 receptors augments MCP-1 production by induction of the NF-kappaB and AP-1 binding activity through the PKC system.
Bacterial and Fungal Infection in Acute Liver Failure (1996)

Patients with acute liver failure (ALF) have increased susceptibility to infections, principally as a result of impaired phagocytic function, reduced complement levels, and the need for invasive procedures. Bacteriologically proven infection is recorded in up to 80% of these patients and fungal infection (predominantly candidiasis) in 32%. Clinical signs such as high temperature and high WBC are absent in 30% of the cases. Pneumonia accounts for 50% of infective episodes, and bacteremia and urinary tract infection a further 20 to 25% each, at a median 5, 3, and 2 days, respectively, after the onset of ALF. Selective parenteral and enteral antisepsis regimens (SPEAR) were evaluated in prospective controlled studies, but early systemic antibiotics alone are as effective as SPEAR. With early antibiotics, the incidence of infective episodes is reduced to 20% and the overall mortality to 44%, with a reduction in progression to encephalopathy and an increased opportunity for transplantation.
A NEW CLASS OF PHOSPHORUS-NITROGEN COMPOUNDS<sup>1</sup> (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA NEW CLASS OF PHOSPHORUS-NITROGEN COMPOUNDS1Robert R. Holmes and James A. ForstnerCite this: J. Am. Chem. Soc. 1960, 82, 20, 5509–5510Publication Date (Print):October 1, 1960Publication History Published online1 May 2002Published inissue 1 October 1960https://pubs.acs.org/doi/10.1021/ja01505a055https://doi.org/10.1021/ja01505a055research-articleACS PublicationsRequest reuse permissionsArticle Views113Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Affordable Naval Surveillance Radar Concept (2007)

Current planned large surveillance radars for shipboard applications employing active aperture technologies are projected to be very expensive. The current planned radars for smaller ships, although less expensive, are limited in performance. This paper provides a new innovative naval surveillance radar architecture that promises to provide naval surveillance radars with high performance at lower cost. The radar uses a fairly inexpensive line array antenna for transmitting a broad beam and fairly inexpensive planar phased array antenna having digital beamforming in one dimension to form many narrow receive beams. The innovation is to rotate the antennas about 45 degrees on the ship relative to the local horizon so that the multipath and antenna sidelobes for most clutter and targets are minimized. For a mechanically rotating array, a transmitter can be located below deck and the transmission signal can be transferred through a passive rotary joint and passive line array antenna thus providing a simple low cost transmission system. On receive, the receive only phased array antenna can be fairly low cost and digital beamforming of multiple beams along the fan transmit beam can easily be accomplished. For non rotating radars, high power phase shifters would need to be employed in the transmit line array antenna to scan the beam.
Quasi-phasematching (2006)

The use of microstructured crystals in quasi-phasematched (QPM) nonlinear interactions has enabled operation of nonlinear devices in regimes inaccessible to conventional birefringently phasematched media. This review addresses basic aspects of the theory of QPM interactions, microstructured ferroelectrics and semiconductors for QPM, devices based on QPM media, and a series of techniques based on engineering of QPM gratings to tailor spatial and spectral response of QPM interactions. Because it is not possible in a brief review to do justice to the large body of results that have been obtained with QPM media over the past twenty years, the emphasis in this review will be on aspects of QPM interactions beyond their use simply as highly nonlinear alternatives to conventional birefringent media.
Hydrolysis and photolysis of flumioxazin in aqueous buffer solutions (2004)

To determine the degradation rates and degradation products of the herbicide flumioxazin in aqueous buffer solutions (pH 5, 7 and 9), its hydrolysis and photolysis were investigated at 30 degrees C in the dark, and in a growth chamber fitted with fluorescent lamps simulating the UV output of sunlight. The rate of hydrolysis of flumioxazin was accelerated by increasing pH. The t(1/2) values at pH 5, 7 and 9 were 16.4, 9.1 and 0.25 h, respectively. Two degradation products were detected and their structural assignments were made on the basis of LC-MS data. Degradation product I was detected in all buffer solutions while degradation product II was detected in acidic buffer only. Both degradation products appeared to be stable to further hydrolysis. After correcting for the effects of hydrolysis, the photolytic degradation rate also increased as a function of pH and was approximately 10 times higher at pH 7 than that at pH 5, showing t(1/2) values of 4.9 and 41.5 h, respectively. Degradation products formed by photolysis were the same as those formed by hydrolysis. Flumioxazin was degraded more extensively at high pH and should degrade in surface water.
Quantized zero-bias conductance plateau in semiconductor-superconductor heterostructures without topological Majorana zero modes (2018)

Recent observations of robust zero-bias quantized conductance plateaus of height $2{e}^{2}/h$ in quantum dot-semiconductor-superconductor nanowire heterostructures have been interpreted as clear evidence for the presence of non-Abelian topologically protected Majorana zero modes (MZMs), since other sources of low-energy conductance are believed to be unable to produce such quantized plateaus. Based on extensive numerical calculations, we show that, in fact, quantized conductance plateaus of height $2{e}^{2}/h$ can also arise as a result of partially separated Andreev bound states (ps-ABSs), in which the component Majorana bound states are somewhat shifted in space without being topological MZMs. As ps-ABSs can form rather generically in the topologically trivial phase, even in the absence of disorder, our results conclusively establish that the observation of quantized conductance plateaus of height $2{e}^{2}/h$ does not represent sufficient evidence for the existence of topologically protected MZMs localized at the opposite ends of a wire.
Single photon emission from a site-controlled quantum dot-micropillar cavity system (2009)

We demonstrate the deterministic integration of single site-controlled quantum dots (SCQDs) into micropillar cavities. Spatial resonance between single positioned QDs and GaAs/AlAs micropillar cavities was achieved using cross markers for precise SCQD-cavity alignment. Cavity effects are clearly reflected in an enhanced photoluminescence intensity when tuning SCQD emission lines through the fundamental cavity resonance. Single photon emission from a spatially and spectrally coupled SCQD-resonator system is confirmed by photon autocorrelation measurements yielding a g(2)(0) value of 0.12.