gebhart/patrepeval huggingface dataset:
Thermal Intermolecular Hetero Diels–Alder Cycloadditions of Aldehydes and Imines viao-Quinone Dimethides (2000)

Hervorragende Regio- und Stereoselektivität wird bei der Cycloaddition von Benzocyclobutenen mit Aldehyden oder Iminen erreicht (siehe Schema). Die Reaktionen verlaufen in hoher Ausbeute und zudem unkatalysiert – sogar bei Raumtemperatur. Y=H, OMe; X=NR′, O; TBS=tert-Butyldimethylsilyl.
A note on lower bounds (Corresp.) (1986)

A new lower bound for the parameters of (nonlinear) <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</tex> -ary codes is introduced. For some q this bound improves on the Varshamov-Gilbert bound, the "modular" algebraic-geometric bound, and the very recent Vl\breve{a}duts bound.
Surgical Treatment of Single-Level Lumbar Stenosis Is Associated with Lower 2-Year Mortality and Total Cost Compared with Nonsurgical Treatment (2023)

Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
An RNA-seq primer for pulmonologists (2019)

<b>RNA sequencing is a powerful tool for high-resolution transcriptomic analysis and can be leveraged to better understand the molecular underpinnings of diverse lung diseases</b>http://bit.ly/2mqBnl4
The Discrete Cosine Maximum Ignorance Assumption (2021)

The performance of colour correction algorithms are dependent on the reflectance sets used. Sometimes, when the testing reflectance set is changed the ranking of colour correction algorithms also changes. To remove dependence on dataset we can make assumptions about the set of all possible reflectances. In the Maximum Ignorance with Positivity (MIP) assumption we assume that all reflectances with per wavelength values between 0 and 1 are equally likely. A weakness in the MIP is that it fails to take into account the correlation of reflectance functions between wavelengths (many of the assumed reflectances are, in reality, not possible). In this paper, we take the view that the maximum ignorance assumption has merit but, hitherto it has been calculated with respect to the wrong coordinate basis. Here, we propose the Discrete Cosine Maximum Ignorance assumption (DCMI), where all reflectances that have coordinates between max and min bounds in the Discrete Cosine Basis coordinate system are equally likely. Here, the correlation between wavelengths is encoded and this results in the set of all plausible reflectances 'looking like' typical reflectances that occur in nature. This said the DCMI model is also a superset of all measured reflectance sets. Experiments show that, in colour correction, adopting the DCMI results in similar colour correction performance as using a particular reflectance set.
Advancing neuromodulation using a dynamic control framework (2011)

The current state of neuromodulation can be cast in a classical dynamic control framework such that the nervous system is the classical "plant", the neural stimulator is the controller, tools to collect clinical data are the sensors, and the physician's judgment is the state estimator. This framework characterizes the types of opportunities available to advance neuromodulation. In particular, technology can potentially address two dominant factors limiting the performance of the control system: "observability," the ability to observe the state of the system from output measurements, and "controllability," the ability to drive the system to a desired state using control actuation. Improving sensors and actuation methods are necessary to address these factors. Equally important is improving state estimation by understanding the neural processes underlying diseases. Development of enabling technology to utilize control theory principles facilitates investigations into improving intervention as well as research into the dynamic properties of the nervous system and mechanisms of action of therapies. In this paper, we provide an overview of the control system framework for neuromodulation, its practical challenges, and investigational devices applying this framework for limited applications. To help motivate future efforts, we describe our chronically implantable, low-power neural stimulation system, which integrates sensing, actuation, and state estimation. This research system has been implanted and used in an ovine to address novel research questions.
Reductive catalytic fractionation of pine wood: elucidating and quantifying the molecular structures in the lignin oil (2020)

In-depth structural analysis of biorefined lignin is imperative to understand its physicochemical properties, essential for its efficient valorization to renewable materials and chemicals. Up to now, research on Reductive Catalytic Fractionation (RCF) of lignocellulose biomass, an emerging biorefinery technology, has strongly focused on the formation, separation and quantitative analysis of the abundant lignin-derived phenolic monomers. However, detailed structural information on the linkages in RCF lignin oligomers, constituting up to 50 wt% of RCF lignin, and their quantification, is currently lacking. This study discloses new detailed insights into the pine wood RCF lignin oil's molecular structure through the combination of fractionation and systematic analysis, resulting in the first assignment of the major RCF-derived structural units in the <sup>1</sup>H-<sup>13</sup>C HSQC NMR spectrum of the RCF oligomers. Specifically, β-5 γ-OH, β-5 ethyl, β-1 γ-OH, β-1 ethyl, β-β 2x γ-OH, β-β THF, and 5-5 inter-unit linkages were assigned unambiguously, resulting in the quantification of over 80% of the lignin inter-unit linkages and end-units. Detailed inspection of the native lignin inter-unit linkages and their conversion reveals the occurring hydrogenolysis chemistry and the unambiguous proof of absence of lignin fragment condensation during proper RCF processing. Overall, the study offers an advanced analytical toolbox for future RCF lignin conversion and lignin structural analysis research, and valuable insights for lignin oil valorization purposes.
Faculty Opinions recommendation of The patterns and dynamics of genomic instability in metastatic pancreatic cancer. (2010)

Pancreatic cancer is an aggressive malignancy with 5-year mortality of 97-98%, usually due to widespread metastatic disease. Previous studies indicate that this disease has a complex genomic landscape, with frequent copy number changes and point mutations Despite the clinical importance of metastasis, there remain fundamental questions about the clonal structures of metastatic tumours 6,7 , including phylogenetic relationships among metastases, the scale of on-going parallel evolution in metastatic and primary sites 7 , and how the tumour disseminates. Here, we harness advances in DNA sequencing We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.
Architecture-Driven Development Approach for WSAN Applications (2015)

Wireless Sensor and Actuator Networks (WSANs) are highly heterogeneous regarding hardware, software, and application requirements. Developing WSAN applications is a hard task, as it requires domain and network knowledge and there is a lack of methodologies, architectures, and patterns to help software developers with such task. Moreover, non-functional requirements play an essential role to ensure the application and network performance, and must be taken into account from the early stages of application development. We propose a ModelDriven Architecture framework to develop WSAN applications that enables developers to express functional and non-functional requirements. The framework encompasses a generic middleware meta-model including: (i) features shared among different WSAN middleware, (ii) meta-model of a target middleware including features of a specific WSAN middleware, and (iii) model transformations. We evaluate our approach by verifying the support to specify non-functional requirements and the automatic code generation of a middleware tailored to the requirements ofa target application.
Design and analysis of interoperating components (2007)

Components are modular units (e.g., objects, modules, or programs) that interact by exchanging data. Two or more components interoperate when they exchange information [16]. It is conservatively estimated that the cost of programming errors in component interoperability just in the capital facilities industry in the U.S. alone is $15.8 billion per year. A primary driver for this high cost is fixing flaws in incorrect data exchanges between interoperating components [17]. Interoperating components are difficult to design, build, and evolve. 
We propose an approach for the design and analysis of interoperating components. The core of our approach is an abstraction in which foreign objects (i.e., objects that are not defined in a host programming language) are abstracted as graphs and abstract operations access and manipulate them. These operations navigate to data elements, read and write data, add and delete data elements, and load and save data. 
We offer different uses for the proposed abstraction. We build a framework called Reification Object-Oriented Framework (ROOF) which uses our abstraction to reduce the multiplicity of platform API calls to a small set of operations on foreign objects that are common to all platforms [48]. With ROOF, we hide the tremendously ugly, hard-to-learn, hard-to-maintain, and hard-to-evolve code that programmers must write or generate today, i.e., we simplified code of interoperating components, making it scalable and easier to write, maintain, and evolve. 
Our abstraction makes the task of static checking of interoperating components tractable by reducing the multiplicity of platform APIs to a small set of operations on foreign objects that are common to all platforms. By introducing a simple extension to grammars of object-oriented languages, we enable the collection of information about foreign objects at compile time. Static type checking uses this information to find possible errors that could otherwise be detected only at the runtime. We designed Foreign Object REification Language (FOREL), an extension for object-oriented languages that provides a general abstraction for foreign component access and manipulation based on ROOF. FOREL type checking coupled with a conservative static analysis mechanism reports potential errors when referencing foreign components. 
While ROOF and FOREL offer new approaches for developing interoperating components, many components are still written using low-level platform API calls. We use our abstraction to design and build a tool called a Verifier for Interoperating c Omponents for finding Logic f Aults (Viola) that finds errors in components exchanging XML data. Viola creates models of the source code of components by extracting abstract operations and computing approximate specifications of the data (i.e., schemas) that these components exchange. With these extracted models, Viola's static analysis mechanism reports potential errors for a system of interoperating components.
Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage-Dependent Anion Channel Gating in Two-Dimensional Lipid Crystalline Bilayers (2014)

The N-terminus of the voltage-dependent anion channel (VDAC) has been proposed to contain the mechanistically important gating helices that modulate channel opening and closing. In this study, we utilize magic angle spinning nuclear magnetic resonance (MAS NMR) to determine the location and structure of the N-terminus for functional channels in lipid bilayers by measuring long-range (13)C-(13)C distances between residues in the N-terminus and other domains of VDAC reconstituted into DMPC lipid bilayers. Our structural studies show that the distance between A14 Cβ in the N-terminal helix and S193 Cβ is ∼4-6 Å. Furthermore, VDAC phosphorylation by a mitochondrial kinase at residue S193 has been claimed to delay mitochondrial cell death by causing a conformational change that closes the channel, and a VDAC-Ser193Glu mutant has been reported to show properties very similar to those of phosphorylated VDAC in a cellular context. We expressed VDAC-S193E and reconstituted it into DMPC lipid bilayers. Two-dimensional (13)C-(13)C correlation experiments showed chemical shift perturbations for residues located in the N-terminus, indicating possible structural perturbations to that region. However, electrophysiological data recorded on VDAC-S193E showed that channel characteristics were identical to those of wild type samples, indicating that phosphorylation of S193 does not directly affect channel gating. The combination of NMR and electrophysiological results allows us to discuss the validity of proposed gating models.
Enhancing a model of auditory information processing to exhibit accommodation (1992)

A speculative model of the ‘‘internal representation’’ of a sound in the auditory system stores only the peak energy trajectories from a cochlear filterbank [P. W. Ellis and B. L. Vercoe, J. Acoust. Soc. Am. 91, 2334(A) (1992)]. This representation appears to code relevant features, as verified by resynthesis, and can be used for signal separation. One marked shortcoming is the absence of accommodation: a loud but steady stimulus has equal prominence throughout its duration; the subjective experience is that such sounds are rapidly relegated to ‘‘background.’’ A related problem with the model is that high-energy components distort and mask nearby low-energy features, even when the former are static and the latter varying; on listening to such a sound, the quieter details are far better resolved by our ears than is apparent in the representation. A simple subtractive feedback scheme can remove the influence of stable components, regardless of energy. Differentiation in time achieves this, but more interesting results are obtained by feeding back a higher-level analysis. Examples of sonic details separated by such methods will be shown and played.
10. Adeno-Associated Virus Type-1 Vectors Transduce Human Polarized Airway Epithelia without Polarity Preference (2006)

The choice of appropriate adeno-associated virus serotypes for gene therapy to the human lung can differ depending on the animal model and model system in which such serotypes are evaluated. In the present study, we sought to compare the efficiency of rAAV2/1, rAAV2/2, and rAAV2/5 vector transduction in polarized human airway epithelia. Since similar vector purity is paramount to such a comparison, we developed a uniform procedure for purification of these serotype vectors using an adenovirus-free packaging system and HPLC. Results from these experiments demonstrated that apical transduction of human polarized airway epithelia with rAAV2/1 was 100-fold more efficient than rAAV2/2 and rAAV2/5. Additionally, the profile of apical transduction in human airway epithelia (rAAV2/1>>rAAV2/2=rAAV2/5) was significantly different than that seen following nasal administration of these vectors to mouse lung (rAAV2/5>rAAV2/1>>rAAV2/2), emphasizing differences in transduction of these serotypes between these two species. In stark contrast to rAAV2/2 and rAAV2/5 vectors, which demonstrated much greater transduction efficiencies from the basolateral membranes, rAAV2/1 transduced both apical and basolateral membrane of human airway epithelia with similar efficiency. Such serotype-specific difference in apical and basolateral transduction mirrored differences in internalization of vector genomes at short time points post-infection for a given serotype. However, the overall level of transduction across serotypes did not correlate with vector internalization. These results suggested that enhanced receptor-mediated endocytosis was not likely responsible for the greater rAAV2/1 transduction of human airway epithelia. With the hypothesis that differences in post-entry barriers influenced the efficiency of apical transduction with these three serotypes in the human airway, we tested the effectiveness of proteasome inhibitors (LLnL and doxorubicin, known to augment intracellular processing of rAAV2 and rAAV5 to the nucleus) to augment transduction with these three serotypes. Augmentation of rAAV2/1 apical transduction of human polarized airway epithelia was 10-fold lower than that for rAAV2/2 and rAAV2/5. Cellular fractionation assays demonstrated that proteasome inhibitors significantly increased virion nuclear uptake for rAAV2/2 and rAAV2/5, but not for rAAV2/1. Cumulatively, these findings suggest that the ubiquitin/proteasome pathway is less of a barrier for rAAV2/1 as compared to the other AAV serotypes. They also demonstrate that AAV1 serotype transduction biology is quite different from AAV2 and AAV5 in human airway epithelia and is potentially a more efficient vector for gene therapy to the airway.
Structure of Electrochemically Deposited Copper on Gold (III) Alloy (1991)

Abstract : We measured the X-ray apsorption spectrum from a half monolayer (as determined from the deposition charge) of Cu deposited on Au(III) in a sulfuric acid solution. The measurements were performed in situ, with the gold electrode immersed in solution, and at controlled potential. The exciting X-rays were incident at grazing angle and the spectrum was detected by measuring the fluorescence from the monolayer with an energy dispersive IIPGe detector. Spectra were obtained with the electric vector of the X-rays both perpendicular and parallel to the sample surface.
The apiosyltransferase celery UGT94AX1 catalyzes the biosynthesis of the flavone glycoside apiin (2023)

Apiose is a unique branched-chain pentose found in plant glycosides and a key component of the cell wall polysaccharide pectin and other specialized metabolites. More than 1,200 plant-specialized metabolites contain apiose residues, represented by apiin, a distinctive flavone glycoside found in celery (Apium graveolens) and parsley (Petroselinum crispum) in the family Apiaceae. The physiological functions of apiin remain obscure, partly due to our lack of knowledge on apiosyltransferase during apiin biosynthesis. Here, we identified UGT94AX1 as an A. graveolens apiosyltransferase (AgApiT) responsible for catalyzing the last sugar modification step in apiin biosynthesis. AgApiT showed strict substrate specificity for the sugar donor, UDP-apiose, and moderate specificity for acceptor substrates, thereby producing various apiose-containing flavone glycosides in celery. Homology modeling of AgApiT with UDP-apiose, followed by site-directed mutagenesis experiments, identified unique Ile139, Phe140, and Leu356 residues in AgApiT, which are seemingly crucial for the recognition of UDP-apiose in the sugar donor pocket. Sequence comparison and molecular phylogenetic analysis of celery glycosyltransferases suggested that AgApiT is the sole apiosyltransferase-encoding gene in the celery genome. Identification of this plant apiosyltransferase gene will enhance our understanding of the physioecological functions of apiose and apiose-containing compounds.
EMI Filter Volume Minimization of a Three-Phase, Three-Level T-Type PWM Converter System (2016)

In this study, the power density of a two-stage, i.e., LCLCL, electromagnetic interference (EMI) filter for a 10 kW three-phase, T-type three-level, boost-type PWM rectifier system is optimized concerning construction volume. It is found that reasonable boundary conditions limit or define most component values and only few degrees of freedom are remaining. In this context, the ratio of the first filter stage's common to differential mode inductance, k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> = L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cm,1</sub> /L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dm,1</sub> , is identified to particularly affect the total filter volume. For given switching frequency and DC-link voltage of f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> = 48 kHz and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dc</sub> = 700 V, a flat minimum of the overall filter volume results for 10 <; k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> <; 40. The boxed volume of the filter realized for k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> = 18 is 763 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> (46.6 in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ), which corresponds to a filter power density of 13.1 kW / dm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> (215 W / in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ). Measurements of conducted EMI confirm that the rectifier system complies with the considered limits of conducted EMI (CISPR 11, class A).
Class- and Splice Variant-specific Association of CD98 with Integrin β Cytoplasmic Domains (2000)

CD98 is a type II transmembrane protein involved in neutral and basic amino acid transport and in cell fusion events. CD98 was implicated in the function of integrin adhesion receptors by its capacity to reverse suppression of integrin activation by isolated integrin beta(1A) domains. Here we report that CD98 associates with integrin beta cytoplasmic domains with a unique integrin class and splice variant specificity. In particular, CD98 interacted with the ubiquitous beta(1A) but not the muscle-specific splice variant, beta(1D), or leukocyte-specific beta(7) cytoplasmic domains. The ability of CD98 to associate with integrin cytoplasmic domains correlated with its capacity to reverse suppression of integrin activation. The association of CD98 with integrin beta(1A) cytoplasmic domains may regulate the function and localization of these membrane proteins.
Anti-inflammatory activity of the bradykinin B1R antagonist in a model of LPS-induced lung inflammation in cynomolgus monkey (2016)

A model of LPS-induced lung inflammation in cynomolgus monkeys was developed to compare the anti-inflammatory activity of bradykinin B<sub>1</sub>R antagonist to those of a PDE4 inhibitor and dexamethasone. 6 naive cynomolgus monkeys (6 kg) were challenged once a week. In the first week, bronchoalveolar lavage (BAL) was collected from the left lung (flushed with 10 mL PBS solution), using a pediatric bronchoscope under anaesthesia (zoletil, xylazine). In the second week, BAL was performed 12 h after intratracheal LPS nebulization for 5 min (20 µg/kg). In addition, the monkeys received the vehicle (0.5% CMC) orally 1 h before and 6 h after LPS. In weeks 3, 4 and 5, the animals were challenged with LPS and they received at random the test compound orally bid: B<sub>1</sub>R antagonist (30 mg/kg), PDE4 inhibitor (0.5 mg/kg) or dexamethasone (1 mg/kg). BAL was performed 12 h after LPS challenge. BALF total cell count, differential cell count, BALF protein, and BALF IL-8 were measured. At 12 h post LPS, BAL cells were elevated (p &lt; 0.05) over baseline (LPS: 20.10<sup>6</sup> vs naive: 2.10<sup>6</sup>, neutrophils LPS: 77 % vs naive: 1.8 %), BALF protein was increased (p &lt; 0.05) (LPS: 3 mg/ml vs naive: 0.8 mg/ml) and BALF IL-8 was increased (p &lt; 0.05) (LPS: 1.1 ng/ml vs naive: 0.2 ng/ml). All inflammatory parameters returned to baseline level one week after LPS challenge. All treatments, B<sub>1</sub>R antagonist, PDE4 inhibitor and dexamethasone, reduced (p &lt; 0.05) LPS-induced BAL neutrophilia (80 % inhibition), BALF protein (90 % inhibition) and BALF IL-8 (80 % inhibition). These data show that the anti-inflammatory activity of the B<sub>1</sub>R antagonist was similar to the activity of dexamethasone and the PDE4 inhibitor.