gebhart/patrepeval huggingface dataset:
Energy Expenditures by Caribou while Cratering in Snow (1985)

The rate of energy expenditure by caribou (Rangifer tarandus granti) digging in snow for lichens was determined by heart rate telemetry and an analysis of cratering mechanics. Based on a significant linear relationship between energy expenditure and heart rate, the mean cost per digging stroke in light, uncrusted snow was 118 J, whereas in denser (0.36 g/cm3) snow with a thin, hard crust the mean cost was 219 J/stroke. The cost of cratering through snow compacted by a snowmobile was 481 J/stroke. A comparison of metabolic and mechanical energy required for cratering suggested that caribou have evolved an energetically-efficient mechanism for obtaining food from beneath the snow layer. J. WILDL. MANAGE. 49(4):987-993 The ability of caribou to obtain lichens and other forages from beneath the snow by digging is well known. The amount of time caribou and reindeer (R. t. tarandus) reportedly spend digging for food in winter varies from only a few minutes per day in areas of shallow or patchy snow (Boertje 1981, Duquette 1984) to approximately 2 hours/day where snow is deep and continuous (Segal 1962, Thing 1977). During the winter months, caribou often obtain energy by catabolizing body fat and protein (McEwan and Whitehead 1970, Dauphine 1976), and thus it is important to the body condition and survival of the animal that the energy cost of obtaining food be low or be compensated for by the energy derived from the forage. Previous estimates of the energy expenditure associated with digging in snow by caribou and reindeer (Makarova and Segal 1958, Thing 1977) did not include the energy costs of digging in different snow types and at different rates. The most frequently used field method for measuring energy expenditure, using a gastight muzzle mask to measure oxygen consumption (White and Yousef 1978), cannot easily be used to measure digging costs because the mask restricts the animal's ability to smell and/or eat the forage. In addition, the valves in the mask may freeze or become clogged with snow, thereby affecting energy cost determinations. Heart rate telemetry has been used successfully with several domestic and wild ungulate species to predict energy expenditure (e.g., Webster 1967, Yamamoto et al. 1979, Renecker and Hudson 1983, Nilssen et al. 1984, Richards and Lawrence 1984) and appeared to be suitable for measuring cratering costs under various conditions. This study was supported by State of Alaska funds for organized research through the Inst. of Arct. Biol. and by a Graduate Fellowship in Resource Problems from the Univ. of Alaska to the senior author. The heart rate transmitters were implanted by R. A. Dieterich. We thank B. C. Anderson, S. L. Zeylmaker, N. J. Ferron, and D. R. Ashby for assisting with data collection and training and handling of captive caribou. R. D. Cameron and D. R. Klein provided helpful comments on the manuscript. We also thank E. A. Sturm and D. A. Borchert for pre-
Synthesis of <i>cis‐Hedione</i><sup>®</sup> and Methyl Jasmonate <i>via</i> Cascade <i>Baylis–Hillman</i> Reaction and <i>Claisen</i> Ortho Ester Rearrangement (2005)

Abstract The exocyclically unsaturated conjugated keto esters 10 , obtained via a Claisen ortho ester rearrangement of the allylic hydroxy ketones 9 , were either directly hydrogenated or partially isomerized into the endocyclically unsaturated tetrasubstituted didehydrojasmonoid intermediates 14 , prior to a more selective hydrogenation with Pd/C in cyclohexane to the disubstituted oxocyclopentaneacetates 15 ( Scheme 2 ). The key intermediates 9 were obtained either by a four‐step sequence, including acetal protection/deprotection from enone 1 , in the specific case of hydroxy ketone 9a ( Scheme 1 ), or more directly and generally by a Baylis–Hillman reaction from cyclopent‐2‐en‐1‐one ( 16 ) and the appropriate aldehydes 17 ( Scheme 2 ). The judicious choice of these aldehydes opens versatile modifications for the stereoselective introduction of the partially cis ‐ or epimerized trans ‐C(2) jasmonoid side chain, while the Baylis–Hillman reaction, catalyzed by chiral [1,1′‐binaphthalene]‐2,2′‐diols (BINOLs) 19 ( Scheme 3 ), may be efficiently conducted in a one‐pot cascade fashion including the ortho ester Claisen rearrangement.
Spurring Radical Reactions of Organic Halides with Tin Hydride and TTMSS Using Microreactors (2008)

Tributyltin hydride-mediated radical reactions of organic halides were successfully carried out in a continuous flow system using a microreactor. The reactions proceeded within a very short period of time, coupled with quickly decomposing radical initiators such as V-65 and V-70. The continuous flow reaction system was applied to gram scale synthesis of a key intermediate for furofuran lignans.
Multi-stacked quantum dot resonant-cavity photodetectoroperating at 1.06 µm (1998)

A resonant-cavity pin photodiode with two quantum dot absorbing regions is described. Each absorbing region consists of a stack of five self-assembled, quantum-dot layers, that are formed by the deposition of six monolayers of In0.5Ga0.5As, with GaAs spacer layers. To optimise the responsivity, the quantum dot stacks are placed at the antinodes of the cavity. The peak efficiency is 65% at 1.06 µm with a spectral bandwidth of 1.3 nm.
Essential oil composition, phenolic content, antioxidant, and antimicrobial activity of cultivated<i>Satureja rechingeri</i>Jamzad at different phenological stages (2015)

Satureja rechingeri is a rare endemic and endangered species found in Iran. Its propagation, variations in essential oil and phenolic content, as well as antioxidant and antimicrobial activities at different phenological stages are reported in this study. The chemical composition of essential oils obtained by hydro-distillation from the aerial parts were determined by GC and GC-MS. A total of 47 compounds were identified in the essential oils of S. rechingeri at different phenological stages. The major components of all oils were carvacrol (83.6%-90.4%), p-cymene (0.8%-2.9%) and γ-terpinene (0.6%-2.4%). The total phenolic content and the antioxidant activity of methanolic extracts were determined with the Folin-Ciocalteau reagent and by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing antioxidant power (FRAP) assay, respectively. Total phenols varied from 35.5 to 37.5 mg gallic acid equivalents/g dry weight (dw), and IC50 values in the radical scavenging assay ranged from 46.2 to 50.2 mg/mL, while those in the FRAP assay were between 49.6 and 52.5 μM quercetin equivalents/g dw. By the disc diffusion method and by determination of the minimum inhibitory concentrations (MIC), the essentials oils of the various phenological stages were found to have high activities against four medically important pathogens.
Retinal release from opsin in molecular dynamics simulations (2010)

The crystal structures of opsin in the ligand-free and the G-protein-interacting states showed two inter-helical openings between transmembrane (TM) helices TM1 and TM7 and between TM5 and TM6 near the extracellular side that were thought to serve as the retinal uptake and release gates. However, it is unclear which opening is for 11-cis-retinal uptake or all-trans-retinal release although speculations have been proposed based on the structural features of opsin and retinal. In this work, we simulated the exit process of all-trans-retinal from the ligand-free opsin structure by the classical molecular dynamics (MD) and random acceleration molecular dynamics (RAMD). In the 64 ns classical MD simulation, retinal remained in the receptor but moved significantly toward the TM5-TM6 opening and almost inserted into the opening after 50 ns. Complete exit was observed in 114 out of 160 RAMD trajectories with the TM5-TM6 opening being the predominant egress gate while egress from the TM1-TM7 opening was observed in only a few trajectories when relatively large acceleration was applied and large structural alteration of the protein resulted. These results suggest that photolyzed all-trans-retinal is likely released through the TM5-TM6 opening. Based on the unidirectional mechanism of retinal exchange suggested by experiment, we speculate that the TM1-TM7 opening serves as the 11-cis-retinal uptake gate. The spatial occupancy maps of retinal computed from the 160 RAMD trajectories further indicated that retinal experienced significant interactions with the receptor during the exit process. The implications of these findings for disease mechanisms of rhodopsin mutants are discussed.
Immunogenic Properties of Lipid A (1984)

Lipid A, the endotoxic principle of gram-negative bacterial lipopolysaccharides, when suitably exposed on the surface of bacterial cells, becomes immunogenic, eliciting the formation of antibodies specific to lipid A. Antibodies to lipid A occur naturally in the serum of normal humans and many animal species; the two exceptions found so far are mice (all strains tested) and guinea pigs. Antibodies to lipid A occur more frequently in patients with infections caused by gram-negative bacteria, such as urinary tract infections. Antibodies to lipid A interacted with free lipid A but not with lipid A as present in the intact lipopolysaccharide molecule. Antibodies to lipid A were induced in rabbits, but not in mice, following a single injection of immunogenic lipid A. Because of similarities between the lipid A of many gram-negative bacteria, antibodies to lipid A showed wide cross-reactions. With regard to biologic activity, antibodies to lipid A have been variously shown to be protective, damaging, or without effect.
Mutations in the GTP-binding site of GSα alter stimulation of adenylyl cyclase (1989)

Mutational replacements of specific residues in the GTP-binding pocket of the 21-kDa ras proteins (p21ras) reduce their GTPase activity. To test the possibility that the cognate regions of G protein alpha chains participate in GTP binding and hydrolysis, we compared signaling functions of normal and mutated alpha chains (termed alpha s) of Gs, the stimulatory regulator of adenylyl cyclase. alpha s chains were expressed in an alpha s-deficient S49 mouse lymphoma cell line, cyc-. alpha s in which leucine replaces glutamine 227 (corresponding to glutamine 61 of p21ras) constitutively activates adenylyl cyclase and reduces the kcat for GTP hydrolysis more than 100-fold. There is a smaller reduction in GTPase activity in another mutant in which valine replaces glycine 49 (corresponding to glycine 12 of p21ras). This mutant alpha s is a poor activator of adenylyl cyclase. Moreover, the glycine 49 protein, unlike normal alpha s, is not protected against tryptic cleavage by hydrolysis resistant GTP analogs; this finding suggests impairment of the mutant protein's ability to attain the active (GTP-bound) conformation. We conclude that alpha s residues near glutamine 227 and glycine 49 participate in binding and hydrolysis of GTP, although the GTP binding regions of alpha s and p21ras are not identical.
Encapsulins: molecular biology of the shell (2017)

Compartmentalization is both a fundamental principle of cellular organization and an emerging theme in prokaryotic biology. Work in the past few decades has shown that protein-based organelles called microcompartments enhance the function of encapsulated cargo proteins. More recently, the repertoire of known prokaryotic organelles has expanded beyond microcompartments to include a new class of smaller proteinaceous compartments, termed nanocompartments (also known as encapsulins). Nanocompartments are icosahedral capsids that are smaller and less complex than microcompartments. Encapsulins are formed by a single species of shell protein that self-assembles and typically encapsulates only one type of cargo protein. Significant progress has been made in understanding the structure of nanocompartment shells and the loading of cargo to the interior. Recent analysis has also demonstrated the prevalence of encapsulin genes throughout prokaryotic genomes and documented a large diversity of cargo proteins with a variety of novel functions, suggesting that nanocompartments play an important role in many microbes. Here we review the current understanding of encapsulin structure and function and highlight exciting open questions of physiological significance.
Dynamic train unit coupling and decoupling at cruising speed: Systematic classification, operational potentials, and research agenda (2021)

The possibility to couple train units into consists, which can be vehicles or platoons, has been proposed to improve, among other, average passenger speed, energy efficiency, and railway infrastructure capacity utilization. We systematically review and categorize the technologies and application of coupling train units into vehicles or platoons, identifying different generations of train coupling, which are used for railway operations. The requirements, compatibility in terms of infrastructure and vehicle equipment as well as backward compatibility are analyzed. The potential of a dynamic train unit coupling and decoupling at cruising speed is proposed, and identified as the 4th generation of train coupling. The possibility of current technology to implement a mechanical dynamic coupling and decoupling at cruising speed is reviewed, with functional requirements and steps of such a process. Based on dynamic coupling at cruising speed, various operating concepts are presented, with focus on commuter-networks between polycentric agglomerations. The potential of dynamic coupling and decoupling at cruising speed might reach travel time reductions in the order of 1/3 and no transfers, for a typical test case in Switzerland between Bern and Zurich.
Temperature-Dependent Optical Properties of Flexible Donor–Acceptor Polymers (2015)

Optical properties of five donor–acceptor polymers of interest for light-harvesting in organic photovoltaic devices have been studied experimentally and computationally. Experimentally recorded absorption spectra in solution of the five polymers are shown to be significantly temperature-dependent. The polymers were subjected to a first-principles computational treatment using density functional theory optimizations and excitation calculations. For two of the polymers, APFO-3 and PTI-1, a methodology that accounts for a thermally induced distribution of conformations based on Boltzmann statistics is applied to produce size- and temperature-converged optical results. This provides a deeper understanding of the temperature dependence of optical properties and improves the computational predictions of absorption wavelength and intensity at experimentally accessible temperatures, as compared to results from traditional quantum chemical calculations based on optimized polymers. Together, the combined experimental and computational temperature studies elucidate and quantify the significant influence of structural flexibility on the optical absorption properties of typical donor–acceptor polymers.
The ΔF508-CFTR mutation results in increased biofilm formation by<i>Pseudomonas aeruginosa</i>by increasing iron availability (2008)

Enhanced antibiotic resistance of Pseudomonas aeruginosa in the cystic fibrosis (CF) lung is thought to be due to the formation of biofilms. However, there is no information on the antibiotic resistance of P. aeruginosa biofilms grown on human airway epithelial cells or on the effects of airway cells on biofilm formation by P. aeruginosa. Thus we developed a coculture model and report that airway cells increase the resistance of P. aeruginosa to tobramycin (Tb) by >25-fold compared with P. aeruginosa grown on abiotic surfaces. Therefore, the concentration of Tb required to kill P. aeruginosa biofilms on airway cells is 10-fold higher than the concentration achievable in the lungs of CF patients. In addition, CF airway cells expressing DeltaF508-CFTR significantly enhanced P. aeruginosa biofilm formation, and DeltaF508 rescue with wild-type CFTR reduced biofilm formation. Iron (Fe) content of the airway in CF is elevated, and Fe is known to enhance P. aeruginosa growth. Thus we investigated whether enhanced biofilm formation on DeltaF508-CFTR cells was due to increased Fe release by airway cells. We found that airway cells expressing DeltaF508-CFTR released more Fe than cells rescued with WT-CFTR. Moreover, Fe chelation reduced biofilm formation on airway cells, whereas Fe supplementation enhanced biofilm formation on airway cells expressing WT-CFTR. These data demonstrate that human airway epithelial cells promote the formation of P. aeruginosa biofilms with a dramatically increased antibiotic resistance. The DeltaF508-CFTR mutation enhances biofilm formation, in part, by increasing Fe release into the apical medium.
Perceived quality of channel zapping (2006)

The end user experience of service quality is critical to the success of a service provider's IPTV deployment program. A key element involved in validating IPTV quality of experience (QoE) is how quickly and reliably users can change TV channels, often referred to as channel zapping. Currently there is no knowledge about the explicit relation between zapping time and the user perceived quality as expressed as a Mean Opinion Score (MOS). We have proposed a model where the MOS depends on the zapping time on a logarithmic scale. In order to validate our model we have conducted a number of subjective tests in order to get insight in this relation. The tests were performed by 21 test subjects at TNO and at Acreo. It turns out that the correlation between the subjective data and the perceptive model is very high (0.99). Therefore we conclude that our perceptive model is very useful for assessing the perceived quality of zapping. The result is not limited to IPTV but applies to any type of TV service with channel switching times that are not instantaneous, regardless whether it is terrestrial or satellite based.
Fast diffusion‐weighted steady state free precession imaging of in vivo knee cartilage (2011)

Quantification of molecular diffusion with steady state free precession (SSFP) is complicated by the fact that diffusion effects accumulate over several repetition times (TR) leading to complex signal dependencies on transverse and longitudinal magnetization paths. This issue is commonly addressed by setting TR > T(2), yielding strong attenuation of all higher modes, except of the shortest ones. As a result, signal attenuation from diffusion becomes T(2) independent but signal-to-noise ratio (SNR) and sequence efficiency are remarkably poor. In this work, we present a new approach for fast in vivo steady state free precession diffusion-weighted imaging of cartilage with TR << T(2) offering a considerable increase in signal-to-noise ratio and sequence efficiency. At a first glance, prominent coupling between magnetization paths seems to complicate quantification issues in this limit, however, it is observed that diffusion effects become rather T(2) (ΔD ≈ 1/10 ΔT(2)) but not T(1) independent (ΔD ≈ 1/2 ΔT(1)) for low flip angles α ≈ 10 - 15°. As a result, fast high-resolution (0.35 × 0.35 - 0.50 × 0.50 mm(2) in-plane resolution) quantitative diffusion-weighted imaging of human articular cartilage is demonstrated at 3.0 T in a clinical setup using estimated T(1) and T(2) or a combination of measured T(1) and estimated T(2) values.
Towards &#x201C;real-time&#x201D; tool-tissue interaction detection in robotically assisted laparoscopy (2008)

The real-time detection of surgeonpsilas action could be very useful for intelligent intraoperative assistance. Robotic assisted surgery provides quantified information that can be used to detect these actions. In this paper we present our attempt at spotting tool-tissue interactions from real surgery data, in the context of robotic assisted laparoscopy with the daVincitrade system, using both kinematic information and visual information. Our early results are encouraging in this very challenging context.
Proteome Analysis of Human Sebaceous Follicle Infundibula Extracted from Healthy and Acne-Affected Skin (2014)

Acne vulgaris is a very common disease of the pilosebaceous unit of the human skin. The pathological processes of acne are not fully understood. To gain further insight sebaceous follicular casts were extracted from 18 healthy and 20 acne-affected individuals by cyanoacrylate-gel biopsies and further processed for mass spectrometry analysis, aiming at a proteomic analysis of the sebaceous follicular casts. Human as well as bacterial proteins were identified. Human proteins enriched in acne and normal samples were detected, respectively. Normal follicular casts are enriched in proteins such as prohibitins and peroxiredoxins which are involved in the protection from various stresses, including reactive oxygen species. By contrast, follicular casts extracted from acne-affected skin contained proteins involved in inflammation, wound healing and tissue remodeling. Among the most distinguishing proteins were myeloperoxidase, lactotransferrin, neutrophil elastase inhibitor and surprisingly, vimentin. The most significant biological process among all acne-enriched proteins was 'response to a bacterium'. Identified bacterial proteins were exclusively from Propionibacterium acnes. The most abundant P. acnes proteins were surface-exposed dermatan sulphate adhesins, CAMP factors, and a so far uncharacterized lipase in follicular casts extracted from normal as well as acne-affected skin. This is a first proteomic study that identified human proteins together with proteins of the skin microbiota in sebaceous follicular casts.