gebhart/patrepeval huggingface dataset:
Adenovirus IL-13–Induced Airway Disease in Mice (2008)

Interleukin 13 (IL-13) is considered to be a key driver of the development of airway allergic inflammation and remodeling leading to airway hyperresponsiveness (AHR). How precisely IL-13 leads to the development of airway inflammation, AHR, and mucus production is not fully understood. In order to identify key mediators downstream of IL-13, we administered adenovirus IL-13 to specifically induce IL-13-dependent inflammation in the lungs of mice. This approach was shown to induce cardinal features of lung disease, specifically airway inflammation, elevated cytokines, AHR, and mucus secretion. Notably, the model is resistant to corticosteroid treatment and is characterized by marked neutrophilia, two hallmarks of more severe forms of asthma. To identify IL-13-dependent mediators, we performed a limited-scale two-dimensional SDS-PAGE proteomic analysis and identified proteins significantly modulated in this model. Intriguingly, several identified proteins were unique to this model, whereas others correlated with those modulated in a mouse ovalbumin-induced pulmonary inflammation model. We corroborated this approach by illustrating that proteomic analysis can identify known pathways/mediators downstream of IL-13. Thus, we have characterized a murine adenovirus IL-13 lung model that recapitulates specific disease traits observed in human asthma, and have exploited this model to identify effectors downstream of IL-13. Collectively, these findings will enable a broader appreciation of IL-13 and its impact on disease pathways in the lung.
Cyanobacterial carboxysomes contain an unique rubisco‐activase‐like protein (2019)

Summary In plants, rubisco activase (Rca) regulates rubisco by removing inhibitory molecules such as ribulose‐1,5‐bisphosphate (Ru BP ). In cyanobacteria, a homologous protein (activase‐like cyanobacterial protein, ALC ), contains a distinctive C‐terminal fusion resembling the small‐subunit of rubisco. Although cyanobacterial rubisco is believed to be less sensitive to Ru BP inhibition, the ALC is widely distributed among diverse cyanobacteria. Using microscopy, biochemistry and molecular biology, the cellular localization of the ALC , its effect on carboxysome/cell ultrastructure in Fremyella diplosiphon , and its function in vitro were studied. Bioinformatic analysis uncovered evolutionary relationships between the ALC and rubisco. ALC localizes to carboxysomes and exhibits ATP ase activity. Furthermore, the ALC induces rubisco aggregation in a manner similar to that of another carboxysomal protein, M35, and this activity is affected by ATP . An alc deletion mutant showed modified cell morphology when grown under enriched CO 2 and impaired regulation of carboxysome biogenesis, without affecting growth rate. Carbamylation of Fremyella recombinant rubisco was inhibited by Ru BP , but this inhibition was not relieved by the ALC . The ALC does not appear to function like a canonical Rca; instead, it exerts an effect on the response to CO 2 availability at the level of a metabolic module, the carboxysome, through rubisco network formation, and carboxysome organization.
Appearance of the Na+‐motive terminal oxidase in Bacillus FTU grown under three different conditions lowering the Δ\gmH+ level (1992)

The terminal oxidases and coupled Na+ transport have been studied in intact cells and inside-out subcellucar vesicles of alkalo- and halotolerant Bacillus FTU grown under different conditions. Cells grown at pH 7.5 are shown to possess a system of respiration-dependent Na+ transport which is (i) inhibited by protonophorous uncoupler and (ii) activated by the delta psi-discharging agent valinomycin, suggesting that the Na+ transport is due to cooperation of the H(+)-motive oxidase and Na+/H+ antiporter. On the other hand, growth under conditions lowering the delta mu H+ level, namely (i) pH 8.6, (ii) pH 7.5 in the presence of protonophore, and (iii) pH 7.5 in the presence of low cyanide concentrations results in appearance of terminal oxidase-supported Na+ transport which is stimulated by protonophores (the Na(+)-motive oxidase). In all three cases, the appearance of ascorbate (+ TMPD) oxidation resistant to low and sensitive to high cyanide concentrations was found to occur. It is concluded that not only alkaline pH but also other conditions which lower delta mu H+ can cause substitution of Na+ for H+ as a coupling ion.
Miniaturization of free space optical systems (2010)

Coherent illumination enables not only integrated optics, but also miniaturized free-space optics that takes advantage of the amplitude and phase control afforded by optical microelectromechanical systems (MEMS) and photonic crystals. These technologies also provide a practical and cost-effective means for integration and packaging of optical systems. The properties of miniaturized optical systems based on optical MEMS and photonic crystals are described, and efficient analysis and design approaches to miniaturized optical scanners and tunable diffractive optical elements are demonstrated. The impact of photonic crystals on free-space micro-optics is discussed.
Liquefied Natural Gas Development: Overview and the Growth of Future Gas Supply for the North American Market (2005)

The business of liquefied natural gas (LNG) has very quickly become a topical and important energy concern. While the liquefication process has been developed and refined for a number of decades and importation of LNG is an accepted practice in the Middle East, Japan, Korea and parts of Europe, it is a relatively new source of supply in North America. However, increased North American demand for natural gas, coupled with diminishing production from accessible basins in Western Canada and the reduced costs and efficiencies of ships, liquefaction plants and storage terminals, have rendered LNG a viable and price competitive supply alternative. The LNG industry provides unique challenges to producers, regulators, consumers and stakeholders. Producers must not only negotiate development, joint venture and sale and purchase agreements, but also arrange for shipping and transportation and terminal services agreements. In North America, while regulators have divided jurisdiction over LNG terminal facilities on the basis of the location of the facility, the stage of production and the degree of integration with related infrastructure, they also appear to be encouraging further development by facilitating regulatory approval. As the Fairwinds and Qatar Petroleum projects demonstrate, the evolution of the LNG industry is dependent upon a delicate collaboration of governments, regulators, producers, financiers, consumers and stakeholders.
Free Radicals in Irradiated Single Crystals of 5-halo-uracil Derivatives: 5-bromouracil, 5-bromodeoxyuridine and 5-iododeoxyuridine (1969)

SummaryElectron-spin-resonance spectra of x- or γ-irradiated single crystals of 5-bromouracil (BU), 5-bromodeoxyuridine (BUDR) and 5-iododeoxyuridine (IUDR) were recorded at room temperature as a function of crystal orientation in the magnetic field at 35 GHz (Q-band) and, less extensively, at 10 GHz (X-band). The observed positions of hyperfine lines were fitted to theoretical curves by a computer programme. The results clearly show the existence of two distinct groups of lines, A and B. While the g-factor of group A is close to the free electron value, group B is shifted to lower magnetic fields and is further subject to large variations with changing orientation, both in position and intensity of hyperfine lines.Both groups are correlated to radicals at the pyrimidine group. It is proposed that one of these radicals is formed by hydrogen addition at the oxygen atom bound to C4. Two resonance structures are possible, differing in localization of the unpaired spin density at either C4 or C6. The observed hyperfine splittings of group A fit completely into this scheme for all three substances investigated, if the unpaired spin is assumed to reside mainly at C6 in IUDR and at C4 in BU and BUDR.Two different radicals are proposed to account for group B having in common the main unpaired spin density at C5. The radical structure assigned to BU may be formed by abstraction of hydrogen from N1. It is characterized by two resonance structures with unpaired spin densities at N1 and C5 linked by a conjugated double bond. In BUDR and IUBR, the radical representing group B is produced by addition of a hydrogen atom at C6 resulting in two β-protons at this position.
Retinoid X Receptor-Antagonistic Diazepinylbenzoic Acids. (1999)

Several dibenzodiazepine derivatives were identified as novel retinoid X receptor (RXR) antagonists on the basis of inhibitory activity on retinoid-induced cell differentiation of human promyelocytic leukemia cells HL-60 and transactivation assay using retinoic acid receptors (RARs) and RXRs in COS-1 cells. 4-(5H-2,3-(2,5-Dimethyl-2,5-hexano)-5-n- propyldibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX603, 6c) is an N-n-propyl derivative of an RXR pan-agonist HX600 (6a), and exhibited RXR-selective antagonistic activity. Similar RXR-antagonistic activities were observed with 4-(5H-2,3-(2,5-dimethyl-2,5-hexano)-5-methyl- 8-nitrodibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX531, 7a) and 4-(5H-10,11-dihydro-5,10-dimethyl-2,3-(2,5-dimethyl- 2,5-hexano)-dibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX711, 8b), which also inhibited transactivation of RARs induced by an RAR agonist, Am80. These compounds inhibited HL-60 cell differentiation induced by the combination of a low concentration of the retinoid agonist Am80 with an RXR agonist (a retinoid synergist, HX600). These results indicated that HX603 (6c), and the related RXR antagonists inhibit the activation of RAR-RXR heterodimers as well as RXR homodimers, which is a distinct characteristic different from that of the known RXR antagonist, LG100754 (9).
Light-emitting devices with one- and two-dimensional air/semiconductor gratings embedded by wafer fusion technique (2002)

We report on DFB MQW light-emitting devices with one- and two-dimensional air/semiconductor gratings inside a semiconductor. After demonstrating a CW oscillation of a 1D device, we show a very unique properties of 2D device which reflects the photonic band characteristic.
Crystal coherence length effects on the infrared optical response of MgO thin films (2010)

The role of crystal coherence length on the infrared optical response of MgO thin films was investigated with regard to Reststrahlen band photon-phonon coupling. Preferentially (001)-oriented sputtered and evaporated ion-beam assisted deposited thin films were prepared on silicon and annealed to vary film microstructure. Film crystalline coherence was characterized by x-ray diffraction line broadening and transmission electron microscopy. The infrared dielectric response revealed a strong dependence of dielectric resonance magnitude on crystalline coherence. Shifts to lower transverse optical phonon frequencies were observed with increased crystalline coherence. Increased optical phonon damping is attributed to increasing granularity and intergrain misorientation.
Ultrafast Laser Applications in Manufacturing Processes: A State-of-the-Art Review (2020)

Abstract With the invention of chirped pulse amplification for lasers in the mid-1980s, high power ultrafast lasers entered into the world as a disruptive tool, with potential impact on a broad range of application areas. Since then, ultrafast lasers have revolutionized laser–matter interaction and unleashed their potential applications in manufacturing processes. With unprecedented short pulse duration and high laser intensity, focused optical energy can be delivered to precisely define material locations on a time scale much faster than thermal diffusion to the surrounding area. This unique characteristic has fundamentally changed the way laser interacts with matter and enabled numerous manufacturing innovations over the past few decades. In this paper, an overview of ultrafast laser technology with an emphasis on femtosecond laser is provided first, including its development, type, working principle, and characteristics. Then, ultrafast laser applications in manufacturing processes are reviewed, with a focus on micro/nanomachining, surface structuring, thin film scribing, machining in bulk of materials, additive manufacturing, bio manufacturing, super high resolution machining, and numerical simulation. Both fundamental studies and process development are covered in this review. Insights gained on ultrafast laser interaction with matter through both theoretical and numerical researches are summarized. Manufacturing process innovations targeting various application areas are described. Industrial applications of ultrafast laser-based manufacturing processes are illustrated. Finally, future research directions in ultrafast laser-based manufacturing processes are discussed.
Fully Substituted Carbon Centers by Diastereoselective Spirocyclization: Stereoselective Synthesis of (+)-Lepadiformine C (2010)

Reductive lithiation of N-Boc alpha-amino nitriles generated alpha-amino alkyllithium reagents with unexpected selectivity. The intermediate radical prefers to align with the nitrogen lone pair, and this interaction leads to an A(1,3)-strain effect that biases the conformation of the radical. In cyclohexane rings with alpha-substituents the net effect is an inversion of configuration on reductive lithiation. In the presence of a tethered electrophile the alkyllithium cyclizes to produce a spiro compound, again with inversion of configuration. The overall result is retention of configuration in the cyclization reaction. The same overall selectivity is found with alpha-oxygen alkyllithium cyclizations, but in this case both steps proceed with retention. The difference can be explained by careful consideration of the intermediate geometries. The alpha-amino spirocyclization was utilized in a concise and stereoselective synthesis of lepadiformine C.
Cellular evolution into wideband services (2002)

An evolution of cellular is presented-an evolutionary time-division multiple access scheme, that combines GSM compatibility with high performance and wideband service capabilities. Several evolutionary steps are considered, including linear, higher level modulation. It enables higher bit rate services to be mixed with low bit rates in a combined scheme. The performance of the evolutionary scheme in terms of spectral efficiency is improved through the new modulation and diversity techniques. A high flexibility is achieved in the implementation and deployment of the scheme, since services ranging from low to high bit rates can co-exist on the same carrier. This evolutionary path allows for successive introduction of new services and new features into an existing GSM system.
High-yield purification of platelet-derived endothelial cell growth factor: structural characterization and establishment of a specific antiserum (1989)

Platelet-derived endothelial cell growth factor (PD-ECGF) is a 45-kDa protein that stimulates the growth of endothelial cells [Miyazono, K., et al. (1987) J. Biol. Chem. 262, 4098-4103]. Here, we describe a method to purify large quantities of PD-ECGF from human platelet lysate at a high yield (14% overall recovery). The purification method involves five steps, using high-performance liquid chromatography grade hydroxylapatite and hydrophobic chromatographies as the two final steps. The purified material contained two major components of apparent molecular weight values of 46,000 and 44,000. These components coeluted in a high-resolving reversed-phase chromatography and were found to give similar peptide maps after treatments with staphylococcal V8 protease, suggesting that the 44-kDa form is related to the 46-kDa molecule. Partial tryptic digestion of native PD-ECGF revealed that the molecule contains a trypsin-resistant domain of 37-39 kDa. A rabbit antiserum was produced against the purified material and was found to specifically recognize PD-ECGF in immunoblotting. When added to the cell culture medium, an immunoglobulin fraction of the antiserum neutralized the activity of purified PD-ECGF. Furthermore, it completely neutralized the endothelial cell mitogenic activity of platelet lysate, indicating that PD-ECGF is the only mitogen in platelet lysate for this cell type.
Self‐centering seismic‐resistant structures: Historical overview and state‐of‐the‐art (2021)

This state‐of‐the‐art review provides an overview of the evolution of self‐centering structures from early historical structures that inherently exhibited a recentering response to modern systems engineered for enhanced seismic resilience. From the early research investigations that were conducted since the 1960s, to the sharp increase of interest in this topic over the last two decades, self‐centering seismic‐resistant structures that can mitigate both damage and residual drifts following major earthquakes have seen significant advances. These systems achieve the intended self‐centering response by either allowing for the rocking of primary structural elements in a controlled manner, commonly coupled with mechanical restraints and energy dissipation devices, or by including self‐centering devices as main structural or supplemental structural members. To better explain the concepts and the underlying mechanics governing their seismic response, detailed schematic illustrations were developed in this article, highlighting the fundamentals behind each of these systems. This article covers a historical overview, presents the state of the research and of the art, discusses general design challenges and practical considerations, and concludes with future research needs to advance the development and broader application of self‐centering systems in real structures.
Reversible Chemical Reactions for Single‐Color Multiplexing Microscopy (2014)

Recent developments in biology demand an increasing number of simultaneously imaged structures with standard fluorescence microscopy. However, the number of multiplexed channels is limited for most multiplexing modalities, such as spectral multiplexing or fluorescence-lifetime imaging. We propose extending the number of imaging channels by using chemical reactions, controlling the emissive state of fluorescent dyes. As proof of concept, we reversibly switch a fluorescent copper sensor to enable successive imaging of two different structures in the same spectral channel. We also show that this chemical multiplexing is orthogonal to existing methods. By using two different dyes, we combine chemical with spectral multiplexing for the simultaneous imaging of four different structures with only two spectrally different channels. We characterize and discuss the approach and provide perspectives for extending imaging modalities in stimulated emission depletion microscopy, for which spectral multiplexing is technically demanding.
Molecular and functional phenotypes of melanoma cells with abnormalities in HLA Class I antigen expression (1996)

Analysis of melanoma cell lines with abnormalities in HLA Class I antigen expression has identified two serological phenotypes caused by distinct molecular defects. One is characterized by lack of HLA Class I antigen expression which is not induced by IFN-gamma or by incubation at 25 degrees C for 24 hrs. This phenotype reflects structural changes in the beta(2)m gene which interfere with its transcription and/or translation or result in the synthesis of a defective beta(2)-mu polypeptide unable to associate with HLA Class I heavy chains. The other phenotype manifests very low HLA Class I antigen expression which is enhanced by IFN-gamma or by incubation at 25 degrees C for 24 hrs. This phenotype reflects abnormalities in TAP heterodimer expression, which cause defects in stable assembly and intracellular transport of the HLA Class I antigen trimolecular complex. Loss of HLA Class I antigens renders melanoma cells resistant to lysis by HLA Class I antigen-restricted cytotoxic T cells which specifically recognize melanoma associated antigens. Therefore, abnormalities in HLA Class I antigen expression may have a negative impact on the outcome of T cell based immunotherapy. Characterization of the molecular defects underlying loss of HLA Class I antigens may suggest approaches to restore their expression. Inclusion of these approaches in the protocols of T cell based immunotherapy may improve its efficacy.
Application of the C3 inhibitor compstatin in a human whole blood model designed for complement research – 20 years of experience and future perspectives (2022)

The complex molecular and cellular biological systems that maintain host homeostasis undergo continuous crosstalk. Complement, a component of innate immunity, is one such system. Initially regarded as a system to protect the host from infection, complement has more recently been shown to have numerous other functions, including involvement in embryonic development, tissue modeling, and repair. Furthermore, the complement system plays a major role in the pathophysiology of many diseases. Through interactions with other plasma cascades, including hemostasis, complement activation leads to the broad host-protective response known as thromboinflammation. Most complement research has been limited to reductionistic models of purified components and cells and their interactions in vitro. However, to study the pathophysiology of complement-driven diseases, including the interaction between the complement system and other inflammatory systems, holistic models demonstrating only minimal interference with complement activity are needed. Here we describe two such models; whole blood anticoagulated with either the thrombin inhibitor lepirudin or the fibrin polymerization peptide blocker GPRP, both of which retain complement activity and preserve the ability of complement to be mutually reactive with other inflammatory systems. For instance, to examine the relative roles of C3 and C5 in complement activation, it is possible to compare the effects of the C3 inhibitor compstatin effects to those of inhibitors of C5 and C5aR1. We also discuss how complement is activated by both pathogen-associated molecular patterns, inducing infectious inflammation caused by organisms such as Gram-negative and Gram-positive bacteria, and by sterile damage-associated molecular patterns, including cholesterol crystals and artificial materials used in clinical medicine. When C3 is inhibited, it is important to determine the mechanism by which inflammation is attenuated, i.e., whether the attenuation derives directly from C3 activation products or via downstream activation of C5, since the mechanism involved may determine the appropriate choice of inhibitor under various conditions. With some exceptions, most inflammatory responses are dependent on C5 and C5aR1; one exception is venous air embolism, in which air bubbles enter the blood circulation and trigger a mainly C3-dependent thromboembolism, with the formation of an active C3 convertase, without a corresponding C5 activation. Under such conditions, an inhibitor of C3 is needed to attenuate the inflammation. Our holistic blood models will be useful for further studies of the inhibition of any complement target, not just C3 or C5. The focus here will be on targeting the critical complement component, activation product, or receptor that is important for the pathophysiology in a variety of disease conditions.
Integrated high speed hybrid silicon transmitter (2013)

We review recent progress made on the hybrid silicon platform towards realizing an integrated high speed WDM transmitter on silicon. Using ion implantation enhanced quantum well intermixing, four band gaps are integrated on a single chip and used to demonstrate a DFB laser array operating over 200 nm from 1250 to 1450 nm. Results from an independent effort to improve on hybrid silicon EA modulator performance are also described. Together these demonstrations pave the way to realize a terabit transmitter on silicon.