gebhart/patrepeval huggingface dataset:
Analytic Equations for Photonic Frequency Converter Design (2021)

Photonic frequency converters are optical systems used to translate data at RF or microwave frequencies to new carrier frequencies for processing or retransmission. The conventional architecture includes RF to optical conversion using Mach-Zehnder modulators, inherently nonlinear devices. The mixing process occurs in photodiodes acting as optical to electrical square law detectors. Therefore, the frequency converter performance metrics are governed by complex nonlinear functions that vary widely with power levels, bias points and specific configurations that require lengthy simulations to assess; this makes understanding the performance impacts of various architectures and components difficult. This work provides analytic expressions for the primary metrics of photonic frequency converters, validated thru comparison with simulations and experiment. The derived equations are useful for the design of photonic frequency converting links, whether integrated or non-integrated. The nominal architecture comprises two Mach-Zehnder modulators in parallel within a larger interferometer. Equations are presented that describe the performance of single drive, dual drive, single detection, and balanced detection implementations. Lastly, this work provides a means of assessing the component metrics necessary for high performance photonic frequency converters as well as the upper limits on system performance.
Anterior pituitary proopiomelanocortin expression is decreased in hypertensive rat strains. (1994)

Studies comparing neuroendocrine differences between the spontaneously hypertensive rat (SHR) and the normotensive Wistar-Kyoto (WKY) strains have suggested altered anterior pituitary corticotrope expression of POMC associated with the development of hypertension in SHR animals. One major difficulty in comparing the SHR and WKY strains is that the two strains exhibit genetic differences unrelated to blood pressure status, because inbred in the SHR genome is a profile of behavioral characteristics different from those in the WKY, including hyperactivity in a novel environment and hyperreactivity in responding to stress. The present studies examine two new inbred rat strains, the WKHT and WKHA, which independently express the hypertension and behavioral traits, respectively. Together with the SHR and WKY, these genetically related, homozygous strains permit a more definitive means of examining the neuroendocrine correlates of either hypertension or behavior. The adult (5-month-old) male anterior pituitary gland content of the POMC peptides beta-endorphin and ACTH was decreased approximately 50% in the SHR and WKHT strains compared to that in the WKY strain, whereas hormone levels in the WKHA strain were not significantly different from those in the WKY strain. Reduced POMC peptide levels were, therefore, specifically associated with the hypertensive trait. Hormone content in prehypertensive weanling (5- to 7-week-old) SHR and WKHT animals was also reduced approximately 35% compared to that in WKY animals. Northern blot analysis identified a 45% decrease in POMC mRNA expression in the hypertensive SHR and WKHT strains, which paralleled the changes in tissue hormone content. Using both immunocytochemistry and in situ hybridization histochemistry, the number of labeled cells per unit area of tissues section was reduced approximately 45% in anterior pituitary tissues from SHR and WKHT rats compared to that in WKY tissues. The levels of POMC mRNA per cell, determined by quantitative densitometry, were not statistically different in the anterior pituitaries of WKHT, SHR, and WKY rats. The decrease in hormone content and POMC mRNA levels may, thus, reflect decreased anterior pituitary gland corticotrope populations. Although POMC peptide levels in the anterior pituitaries of adult WKHA animals were not significantly different from those in WKY animals, the morphological studies demonstrated a 30% increase in the corticotrope population in the WKHA strain. In contrast, POMC mRNA levels in WKHA animals were decreased 30%, and the amount of POMC mRNA per corticotrope was decreased approximately 35% compared to that in WKY, SHR, and WKHT tissues.(ABSTRACT TRUNCATED AT 400 WORDS)
Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament (2016)

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
Oropharyngeal Tularemia (1980)

A case of oropharyngeal tularemia mimicking a peritonsillar abscess is presented. This diagnosis should be entertained in patients who are seen initially with ulcerative-exudative pharyngitis with or without tonsillitis and whose routine cultures are negative and/or are unresponsive to penicillin. Institution of appropriate therapy depends largely on the clinical diagnosis because cultures on ordinary media are routinely negative, and it takes several days for antibody titers to reach diagnostic significance.
In Vivo Corneal Confocal Microscopy in Marfan Syndrome (2007)

Highly reflective extracellular matrix of the stroma and brightly reflective particles among the endothelial cells were the 2 main corneal findings observed by using in vivo corneal confocal microscopy in patients with Marfan syndrome compared with a control group. Further studies need to be made to confirm these findings and eventually find new criteria for Marfan syndrome from the examination of in vivo corneal confocal microscopy.
The new policy architecture for Closing the Gap: Innovation and regression (2021)

This paper describes the core elements of the new policy architecture for Closing the Gap set out in the National Partnership on Closing the Gap finalised in mid-2020. These issues are significant as Closing the Gap is the central pillar in government policy relating to Indigenous affairs. It outlines the genesis of the new arrangements and considers the ramifications of the adoption of shared decision making and codesign processes in its development and implementation. The paper explicitly identifies and considers a series of risks to the successful implementation of the new policy architecture, and suggests a series of further reforms that would minimise the likelihood of failure.
Ultrasonic atomization of pMDI wood resin. (2009)

A novel, patent-pending approach to the application of wood resins based on an ultrasonic principle was developed in this study.Liquid polymeric methane diphenyl-diisocyanate (pMDI) resin was successfully atomized using a bench-scale 25 kHz ultrasonic atomizer.The optimal average sizes of the resin droplets generated at a flow rate of 0.7 mL/min and power input of 5.0 J/s were about 90 mm.In addition to fewer fine droplets than that produced by conventional spinning-disk atomizers, the droplets of pMDI resin produced by the ultrasonic atomizer had a more uniform droplet size distribution.These results indicate the potential advantages of implementing ultrasonic atomization in oriented strandboard production, including elimination of the hazardous fraction of fine resin droplets and potential production cost savings from improved resin efficiency.The ultrasonic atomization of wood resins appears to be a promising alternative to the spinning-disk atomizer.
Integrated Phytochemical Analysis Based on UPLC-Q-TOF-MS/MS, Network Pharmacology, and Experiment Verification to Explore the Potential Mechanism of Platycodon grandiflorum for Chronic Bronchitis (2020)

In this study, ingredient analysis, network pharmacology analysis, and experiment verification were combined, and revealed that PG can be used to treat CB by reducing inflammation. Our findings provide novel insight into the mechanism of action of Chinese medicine. Furthermore, our data are of value for the research and development of novel drugs and the application thereof.
Porphyromonas canoris sp. nov., an Asaccharolytic, Black-Pigmented Species from the Gingival Sulcus of Dogs (1994)

A new species, Porphyromonas canoris, is proposed for black-pigmented asaccharolytic strains isolated from subgingival plaque samples from dogs with naturally occurring periodontal disease. This bacterium is an obligately anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organism. On laked rabbit blood or sheep blood agar plates, colonies are light brown to greenish brown after 2 to 4 days of incubation and dark brown after 14 days of incubation. Colonies on egg yolk agar and on nonhemolyzed sheep blood agar are orange. The cells do not grow in the presence of 20% bile and have a guanine-plus-cytosine content of 49 to 51 mol%. The type strain is VPB 4878 (= NCTC 12835). The average levels of DNA-DNA hybridization between P. canoris strains and other members of the genus Porphyromonas are as follows: Porphyromonas gingivalis ATCC 33277T (T = type strain), 6.5%; Porphyromonas gingivalis cat strain VPB 3492, 5%; Porphyromonas endodontalis ATCC 35406T, 1%; Porphyromonas salivosa NCTC 11362T, 5%; and Porphyromonas circumdentaria NCTC 12469T, 6%. The level of hybridization between P. canoris NCTC 12835T DNA and Porphyromonas asaccharolytica ATCC 25260T DNA is 3%. P. canoris cells produce major amounts of acetic, propionic, isovaleric, and succinic acids and minor amounts of isobutyric and butyric acids as end products of metabolism in cooked meat medium. The major cellular fatty acid is 13-methyltetradecanoic acid (iso-C15:0). Glutamate and malate dehydrogenases are present, as are glucose-6-phosphate dehydrogenase activity (65.7 nmol mg of protein-1 min-1) and 6-phosphogluconate dehydrogenase activity (63.0 nmol mg of protein-1 min-1).(ABSTRACT TRUNCATED AT 250 WORDS)
Armadillogorgia cyathella and Ophidiogorgia paradoxa, two new genera and species of primnoid octocorals (Coelenterata: Anthozoa) from South Georgia and South Orkney Islands (1980)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Platform-Agnostic Steal-Time Measurement in a Guest Operating System (2018)

Steal time is a key performance metric for applications executed in a virtualized environment. Steal time measures the amount of time the processor is preempted by code outside the virtualized environment. This, in turn, allows to compute accurately the execution time of an application inside a virtual machine (i.e. it eliminates the time the virtual machine is suspended). Unfortunately, this metric is only available in particular scenarios in which the host and the guest OS are tightly coupled. Typical examples are the Xen hypervisor and Linux-based guest OSes. In contrast, in scenarios where the steal time is not available inside the virtualized environment, performance measurements are, most often, incorrect. In this paper, we introduce a novel and platform agnostic approach to calculate this steal time within the virtualized environment and without the cooperation of the host OS. The theoretical execution time of a deterministic microbenchmark is compared to its execution time in a virtualized environment. When factoring in the virtual machine load, this solution -as simple as it is- can compute the steal time. The preliminary results show that we are able to compute the load of the physical processor within the virtual machine with high accuracy.
Combined Effect of Reduced Band Number and Increased Bandwidth on Shallow Water Remote Sensing: The Case of WorldView 2 (2012)

WorldView 2 (WV2), launched in September 2009, is a satellite with hyperspatial resolution ( <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim$</tex></formula> 0.5–2 m) capability for Earth surface observation. It has eight spectral bands with enhanced signal-to-noise ratio to cover the visible-to-near-infrared (V–NIR) domain, thus providing a great potential for remote sensing of coastal ecosystem, in particular, the aquatic environments with shallow bottoms (e.g., coral reefs and seagrass beds). Traditionally, it requires <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim$</tex></formula> 15 spectral bands in the V–NIR domain for reliable analytical retrieval of bottom properties (e.g., bathymetry) from remotely observed radiance spectrum. Data from WV2, however, have eight bands, and the width of each band is quite wide ( <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim$ </tex></formula> 50 nm or more). Thus, the spectral configuration of WV2 is far from optimal for spectral remote sensing of various complex shallow environments, and it is important and necessary to know how such a band setting affects the reliability of remote-sensing retrievals. Here, we applied a hyperspectral optimization scheme [hyperspectral optimization processing exemplar (HOPE)] to a simulated shallow-bottom data set (sandy bottom) and compared retrievals from both hyperspectral and WV2 spectral settings. Retrieved results suggest that, for bottom contribution making up 40% or more of the measured signal, the depths derived from both hyperspectral and WV2 settings are generally consistent for waters shallower than 5 m. However, depths derived with WV2 setting have greater uncertainty and, in general, are shallower than those derived from the hyperspectral setting, particularly for waters deeper than 10 m. Options to produce higher confident properties from such band settings are discussed.
A complexity effective communication model for behavioral modeling of signal processing applications (2004)

In this paper, we argue that the address space of memory regions that participate in inter task communication is over-specified by the traditional communication models used in behavioral modeling, resulting in sub-optimal implementations. We propose shared messaging communication model and the associated channels for efficient inter task communication of high bandwidth data streams in behavioral models of signal processing applications. In shared messaging model, tasks communicate data through special memory regions whose address space is unspecified by the model without introducing non determinism. Address space to these regions can be assigned during mapping of application to specific architecture, by exploring feasible alternatives. We present experimental results to show that this flexibility reduces the complexity (e.g., communication latency, memory usage) of implementations significantly (up to an order of magnitude).
New Nanotechnology Applications in Single Cell Analysis: Why and How? (2011)

Cell heterogeneity is intrinsic to both genetically programmed differentiation and stochastic/epigenetic variation. The scientific and technological challenge is to quantitatively study the nature and extent of the heterogeneity of populations of cells. In order to reach this goal, scientists need to measure the complete molecular content “omes” of single cells. This is not achievable by the classical approach implementing chromatography/electrophoresis microsystem separation and analysis by mass spectroscopy and nuclear magnetic resonance, due to their lack of high throughput technology and their lack of sufficiently high detection sensitivity. Here we propose that single cell “omic” measurements can be realized with the new interdisciplinary nanotechnology combining physics and chemistry with biology. Our nanoscience approach is based on the implementation of novel Nano in Micro Array (NiMA) biosensor chip platform that can analyze the complete proteome and glycome by means of accommodating up to 2,500 different cell samplings (positioned in microwells) and 250,000 probe markers (positioned in nanowells) per chip. Using a combination of chemical, mechanical, optical, and electrical detection with Secondary Ion Mass Spectrometry (SIMS) and by Scanning Probe Microscopy (SPM), we can quantify all biomolecules approaching detection of a single protein molecule. The gained knowledge about molecular heterogeneity quantified at the single molecular level within each individual cell in the form of “omes” (proteome, glycome, transcriptome, and metabolome) is fundamental to our understanding of causative relationships and formulations of natural laws. This will be a large step toward comprehension and prediction of processes associated with complex living systems like the evolution of life, embryogenesis and morphogenesis, immunity, adaptivity, self–nonself recognition, neural plasticity, and learning, as well as driving forces leading to diseased states of living organisms such as cancer, bacterial, and viral disease, neurodegenerative disorders, and autoimmunity.
Relationship between Retroviral Replication and RNA Interference Machineries (2006)

Small interfering RNAs (siRNAs) associated with gene silencing are cellular defense mechanisms against invading viruses. The viruses fight back by suppressors or escape mechanisms. The retroviruses developed a unique escape mechanism by disguising as DNA proviruses. An evolutionary relationship between the siRNA machinery and the replication machinery of retroviruses is likely. The RNA cleavage enzymes PIWI and RNase H proteins are structurally related. This relationship can be extended from structure to function, since the retroviral reverse transcriptase (RT)/RNase H can also cause silencing of viral RNA by siRNA. Thus, both enzymes can cleave RNA-DNA hybrids and double-stranded RNA (dsRNA) with various efficiencies shown previously and here, demonstrating that their specificities are not absolute. Other similarities may exist, for example between PAZ and the RT and between RNA-binding proteins and the viral nucleocapsid protein. Dicer has some similarities with the viral integrase, since both specifically generate dinucleotide 3'-overhanging ends. We described previously the destruction of the human immunodeficiency virus (HIV) RNA by a DNA oligonucleotide ODN (oligodeoxynucleotide). Variants of the ODN indicated high length and sequence specificities, which is reminiscent of siRNA and designated here as "siDNA." Cleavage of the viral RNA in the presence of the ODN is caused by the retroviral RT/RNase H and cellular RNase H activities. Several siRNA-mediated antiviral defense mechanisms resemble the interferon system.
Supplementary Figure 5 from Hedgehog Signaling Regulates Metabolism and Polarization of Mammary Tumor-Associated Macrophages (2023)

&lt;p&gt;Supplementary Figure 5&lt;/p&gt;
Data-Driven Risk-Sensitive Control for Personalized Lane Change Maneuvers (2022)

Most current research in the field of autonomous vehicle control assumes that all vehicles will follow the same patterns of automated driving behavior, resulting in systems with “conservative” or “average” driving styles. These systems may not be acceptable to drivers who prefer a more aggressive style of driving, however, while extremely cautious drivers may consider the standard outputs to be too aggressive. To address this problem, in this paper, we introduce Risk Sensitive Control (RSC), an inverse optimal control algorithm that estimates risk-sensitive driving features and incorporates them into a receding-horizon controller. RSC uses a meta-learning algorithm to update the parameters of the cost function, continuously improving the controller online as more and more driving data is gathered from the user and subjective risk feedback. An estimator takes into account individual differences in subjective risk analysis, in terms of driving features and surrounding vehicle locations, by adjusting the cost function and its constraints. We test this approach using five lane change scenarios, some safe and some risky, with thirty real drivers in a CARLA simulation environment. Our quantitative and qualitative evaluations demonstrate that the proposed framework is able to generate a user’s preferred driving maneuvers during lane changes, i.e., control commands the user associates with lower subjective risk, outperforming conventional, model-based predictive control methods in terms of replicating the user’s own driving behavior.
Liver x receptor alpha drives chemoresistance in response to side-chain hydroxycholesterols in triple negative breast cancer (2020)

Abstract Triple negative breast cancer (TNBC) is challenging to treat successfully because targeted therapies do not exist. Instead, systemic therapy is typically restricted to cytotoxic chemotherapy, which fails more often in patients with elevated circulating cholesterol. Liver x receptors are ligand-dependent transcription factors that are homeostatic regulators of cholesterol, and are linked to regulation of broad-affinity xenobiotic transporter activity in non-tumor tissues. We show that LXR ligands confer chemotherapy resistance in TNBC cell lines and xenografts, and that LXRalpha is necessary and sufficient to mediate this resistance. Furthermore, in TNBC patients who had cancer recurrences, LXRalpha and ligands were independent markers of poor prognosis and correlated with P-glycoprotein expression. However, in patients who survived their disease, LXRalpha signaling and P-glycoprotein were decoupled. These data reveal a novel chemotherapy resistance mechanism in this poor prognosis subtype of breast cancer. We conclude that systemic chemotherapy failure in some TNBC patients is caused by co-opting the LXRalpha:P-glycoprotein axis, a pathway highly targetable by therapies that are already used for prevention and treatment of other diseases.
Additional file 8: of De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii (2017)

Annotation file of the strain JS10 with the cumulative results of bioinformatics analyses. (XLSX 315Â kb)