gebhart/patrepeval huggingface dataset:
Improved method for measuring the apparent CO2 photocompensation point resolves the impact of multiple internal conductances to CO2 to net gas exchange (2015)

There is a growing interest in accurate and comparable measurements of the CO2 photocompensation point (Γ*), a vital parameter to model leaf photosynthesis. The Γ* is measured as the common intersection of several CO2 response curves, but this method may incorrectly estimate Γ* by using linear fits to extrapolate curvilinear responses and single conductances to convert intercellular photocompensation points (Ci *) to chloroplastic Γ*. To determine the magnitude and minimize the impact of these artefacts on Γ* determinations, we used a combination of meta-analysis, modelling and original measurements to develop a framework to accurately determine Ci *. Our modelling indicated that the impact of using linear fits could be minimized based on the measurement CO2 range. We also propose a novel method of analysing common intersection measurements using slope-intercept regression. Our modelling indicated that slope-intercept regression is a robust analytical tool that can help determine if a measurement is biased because of multiple internal conductances to CO2 . Application of slope-intercept regression to Nicotiana tabacum and Glycine max revealed that multiple conductances likely have little impact to Ci * measurements in these species. These findings present a robust and easy to apply protocol to help resolve key questions concerning CO2 conductance through leaves.
Regulation of glycosaminoglycan biogenesis is critical for sensitive‐period‐dependent vocal ontogeny (2017)

In the brain, the extracellular matrix (ECM) plays a central role during neural development and thus modulates critical-period regulated behavioral ontogeny. The major components of the ECM are glycosaminoglycans (GAGs) including chondroitin sulfate (CS). However, the specific roles of GAGs in behavioral development are largely unknown. It has been shown that xylosides affect the biological functions of GAGs through modulating GAG biosynthesis. Particularly, xylosides affect GAG biosynthesis through priming of GAG chains (priming activity), competing with endogenous core proteins that carry GAG initiation sites (decoy activity), or both. Using birdsong as our model, we investigated, for the first time, how xyloside-mediated modulation of GAG biogenesis affects song development. Xylosides infused into motor cortex of juvenile birds alter song development by specifically affecting ontogeny of the stereotyped sequence rather than the acoustic structure of syllables. Further analyses reveal that observed changes can be attributed to the priming activity rather than the decoy activity of xylosides. Collectively, these results suggest that regulation of GAG biogenesis through chemical biology approaches may allow promising therapeutic interventions of critical-period-dependent central nervous system plasticity. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1401-1412, 2017.
Formation of extended plasma channels in a condensed medium upon axicon focusing of a femtosecond laser pulse (2005)

The formation of plasma channels of a femtosecond laser pulse in the bulk of fused silica is studied by numerical simulation, and the advantages of using a conical lens (axicon) over conventional parabolic lenses are shown. It is found that the length of the plasma channel formed with the help of an axicon exceeds the length of the channel formed upon lens focusing.
Viscosity of cohesive granular flows (2020)

Cohesive granular materials such as wet sand, snow, and powders can flow like a viscous liquid. However, the elementary mechanisms of momentum transport in such athermal particulate fluids are elusive. As a result, existing models for cohesive granular viscosity remain phenomenological and debated. Here we use discrete element simulations of plane shear flows to measure the viscosity of cohesive granular materials, while tuning the intensity of inter-particle adhesion. We establish that two adhesion-related, dimensionless numbers control their viscosity. These numbers compare the force and energy required to break a bond to the characteristic stress and kinetic energy in the flow. This progresses the commonly accepted view that only one dimensionless number could control the effect of adhesion. The resulting scaling law captures strong, non-Newtonian variations in viscosity, unifying several existing viscosity models. We then directly link these variations in viscosity to adhesion-induced modifications in the flow micro-structure and contact network. This analysis reveals the existence of two modes of momentum transport, involving either grain micro-acceleration or balanced contact forces, and shows that adhesion only affects the latter. This advances our understanding of rheological models for granular materials and other soft materials such as emulsions and suspensions, which may also involve inter-particle adhesive forces.
Cholesterol-enriched diet disrupts the blood-testis barrier in rabbits (2014)

About 15% of heterosexual couples in the USA suffer from infertility issues; male infertility accounts for ∼50% of all infertility cases and roughly 50% of male infertility is idiopathic. Increased levels of plasma cholesterol affect spermatogenesis and male fertility negatively, but by unclear mechanisms. Clearly, spermatogenesis occurs in immune-privileged seminiferous tubules that are protected by the blood-testis barrier (BTB), and BTB disruption results in sperm damage and male infertility. Accordingly, using rabbits fed a 2% cholesterol-enriched diet for 2, 4, and 6 wk to raise levels of plasma cholesterol, we tested the hypothesis that elevated levels of plasma cholesterol disrupt the BTB functionally and biochemically. The cholesterol-enriched diet increased lipid deposition dramatically and time-dependently in the seminiferous tubules and disrupted the BTB as evidenced by increased IgG staining within the seminiferous tubules. Total protein levels of the tight-junction proteins ZO-1 and occludin were increased in the seminiferous tubules of rabbits fed the cholesterol-enriched diet, and the distribution patterns of tight-junction proteins were markedly affected, including an increased accumulation of tight-junction proteins in endosomes. Disruption of the integrity of the BTB due to increased plasma levels of cholesterol might play a role in male infertility.
Mapping damage during the Bam (Iran) earthquake using interferometric coherence (2007)

We use changes in the interferometric coherence to map earthquake damage that occurred in the city of Bam during the Bam earthquake on 26 December 2003. The approach presented here defines a coherence change index that can be interpreted quantitatively in terms of damage during a catastrophic event like a major earthquake. Using five differential interferometric synthetic aperture radar images, we compute maps of interferometric coherence. Three coherence change images are computed from these based on different interferograms. These three damage assessments yield very similar results despite the range of times and interferometric baselines spanned. This coherence‐based damage assessment also agrees closely with independent damage maps derived from other types of imagery. Using existing or planned synthetic aperture radar (SAR) satellites, coherence‐based damage assessments can be obtained within days after a catastrophic event, provided the necessary reference images are prepared ahead of time. As SAR sensors can operate independently of weather conditions and daylight, this may present a reliable and robust means of damage assessment.
Fas-induced Apoptosis Is Mediated by Activation of a Ras and Rac Protein-regulated Signaling Pathway (1996)

Fas induces apoptosis in lymphocytes via a poorly defined intracellular signaling mechanism. We and others have previously demonstrated the involvement and significance of a signaling cascade from the Fas receptor via sphingomyelinases and ceramide to Ras in apoptosis (Gulbins, E., Bissonette, R., Mahboubi, A., Nishioka, W., Brunner, T., Baier G., Baier-Bitterlich, G., Byrd, C., Lang, F., Kolesnick, R., Altman, A., and Green, D. (1995) Immunity 2, 341; Cifone, M. G., DeMaria, R., Roncali, P., Rippo, M. R., Azuma, M., Lanier, L. L., Santoni, A., and Testi, R. (1994) J. Exp. Med. 180, 1547-1552; Gill, B. M., Nishikata, H., Chan, G., Delovitch, T. L., and Ochi, A. (1994) Immunol. Rev. 142, 113-126). Here, we demonstrate an activation of the small G-proteins Rac 1 and Rac 2 after Fas receptor triggering. Expression of a transdominant inhibitory Ras mutant (N17Ras) prevents Rac 1 and Rac 2 stimulation, suggesting a signaling cascade from the Fas receptor via Ras to Rac 1 and Rac 2. Genetic and pharmacological inhibition of Ras or Rac 1 and Rac 2 stimulation blocks Fas-induced apoptosis, pointing to an important function of a Ras and Rac protein-regulated signaling pathway in Fas-mediated programmed cell death.
Coextruded Microlayer Film and Sheet (1988)

Multilayer coextrusion can be used to produce microlayer films which can be designed to provide unique characteristics. Based on the optical theory for the wave length of reflected light from the normal incidence, 400 alternating layers of poly carbonate (PC) and polypropylene were coextruded with the expected result that the 25 μm film blocked over 80% of the UV light while transmitting 80% of the visible light. Ultrathin PC films (2 μm thick), made by delaminating multilayer extrusions, had DC breakdown voltages similar to solution cast films of the same thickness. Increase of the number of microlayers of PC/styrene-acrylonitrile composites resulted in improved tensile and impact strength—with a notable reduction in notch sensitivity for the latter property.
Dermacentor variabilisandBoophilus microplus(Acari: Ixodidae): Experimental Vectors ofBabesia equito Equids : Table 1 (2002)

The experimental vector competence of five laboratory-reared ixodid tick species representing three genera [Amblyomma americanum (L.), Boophilus microplus (Canestrini), D. andersoni Stiles, D. occidentalis Marx, and D. variabilis (Say)] for Babesia equi (Laveran 1901) was evaluated by delayed transfer of male ticks from infected to susceptible equids or by infesting the latter animals with adult ticks previously fed as nymphs on infected equids. After feeding for 5, 6, or 13 d on acquisition hosts, ticks were forcibly removed and held off the host at 26 degrees C, approximately 93% RH, and a photoperiod of 14:10 (L:D) h for 6, 12, or 27 d. Intrastadial transmission to susceptible ponies by D. variabilis males, and transstadial transmission to susceptible burros by B. microplus adults, was demonstrated by blood smear and indirect immunofluorescence serology. The data indicated that male D. variabilis and adult B. microplus, tick species that occur on equids in North America and, in the case of the latter tick, also extensively in tropical and subtropical regions of the world, may be competent natural vectors of B. equi
The Application of MicrocelTMColumn Flotation to Fine Coal Cleaning (1992)

Column flotation is widely recognized as providing an improved separation efficiency, primarily as a result of incorporating a froth washing mechansim to remove the entrained mineral matter. However, the use of columns has several shortcomings, including low throughput and plugging problems associated with bubble generators. To overcome some of these problems, a new column known as Microcel TM has been developed. It is based on using microbubbles in the range of 0.1–0.4 mm by employing static, in‐line mixers for bubble generation. The use of smaller air bubbles improves the probability of bubble‐particle collision and, hence, the flotation rate, allowing shorter columns to be used and reducing both air and energy consumption. In addition, the bubble generators are non-plugging, require no fresh water and are externally mounted for easy maintenance. In this communication, the underlying principles of this technology are presented with the test results obtained using laboratory, pilot‐scale, and full‐size columns on a variety of coal samples. The results are compared with those obtained using a bank of mechanically agitated flolation cells.
Sodium tanshinone IIA sulfonate ameliorates cerebral ischemic injury through regulation of angiogenesis (2021)

Vascular remodeling and neuroprotection are two major adaptable methods for treating ischemic stroke. Edaravone is a protective agent for the treatment of stroke and was used as a positive control in the present study. Sodium tanshinone IIA sulfonate (STS) has demonstrated therapeutic clinical effects in cerebral infarction in China, while its mechanisms of action in ischemic stroke have remained elusive. The angiogenesis and neuroprotective effects of STS were evaluated in a rat model induced by middle cerebral artery occlusion and 3 days of reperfusion. When used at the same dose, the magnitude of the therapeutic effect of STS was similar to that of edaravone in terms of decreased blood-brain barrier damage as indicated by reduced Evans blue leakage, improved neurological deficits, alleviated cerebral edema and inhibition of histopathological changes caused by ischemia/reperfusion. The TUNEL assay demonstrated that the ability of STS to inhibit neuronal apoptosis was equivalent to that of edaravone. Immunofluorescence detection of CD31 and α-smooth muscle actin indicated that the vascular density was significantly reduced in the vehicle group compared with that in the sham operation group, STS increased the microvessel density in the ischemic area. Furthermore, in the vehicle group the protein expression of vascular endothelial growth factor (VEGF) and VEGF receptor 2 (VEGFR) as determined by fluorescence microscopy and immunohistochemistry was significantly reduced compared with that in the sham group. However, STS promoted their expression compared to the vehicle group respectively, and increaed the mRNA expression of VEGF, VEGFR, CD31 and angiopoietin-1 as determined by reverse transcription-quantitative PCR, but these changes were not significant or not present for edaravone apart from Ang-1. In conclusion, STS protected against ischemic brain injury by promoting angiogenesis in ischemic areas and inhibiting neuronal apoptosis. These results provide a potential treatment for stroke recovery.
Catalytic Mechanism of S-Ribosylhomocysteinase (LuxS):  Direct Observation of Ketone Intermediates by 13C NMR Spectroscopy (2003)

S-Ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether linkage of S-ribosylhomocysteine (SRH) to produce l-homocysteine and 4,5-dihydroxy-2,3-pentanedione (DHPD). This is a key step in the biosynthetic pathway of the type II autoinducer (AI-2) in both Gram-positive and Gram-negative bacteria. Previous studies demonstrated that LuxS contains a catalytically essential Fe2+ ion. The catalytic mechanism of LuxS was investigated using 2- and 3-13C-labeled SRH as substrate and 13C NMR spectroscopy. These studies revealed the presence of 2- and 3-keto intermediates in the catalytic pathway. The 2-keto intermediate was chemically synthesized, and its chemical and kinetic competence was demonstrated. The results support a catalytic mechanism in which the metal ion catalyzes an internal redox reaction, shifting the carbonyl group from the C-1 position to the C-3 position. Subsequent beta-elimination at the C-4 and C-5 positions releases homocysteine as a free thiol. The results also suggest that Cys-84 and Glu-57 are the possible general acids/bases for proton transfer during catalysis and that the keto intermediates are released from the enzyme active site before rebinding and completion of the reaction.
Large field-of-view KD*P modulator for solar polarization measurements (2005)

This paper will describe the evolution of the Marshall Space Flight Center's (MSFC) electro-optical polarimeter with emphasis on the field-of-view characteristics of the KD*P modulator. Understanding those characteristics was essential to the success of the MSFC solar vector magnetograph. The paper will show how the field-of-view errors of KD*P look similar to the linear polarization patterns seen in simple sunspots and why the placement of the KD*P in a collimated beam was essential in separating the instrumental polarization from the solar signal. Finally, this paper will describe a modulator design which minimizes those field-of-view errors.
Overexpression of the Rabies Virus Glycoprotein Results in Enhancement of Apoptosis and Antiviral Immune Response (2002)

A recombinant rabies virus (RV) carrying two identical glycoprotein (G) genes (SPBNGA-GA) was constructed and used to determine the effect of RV G overexpression on cell viability and immunity. Immunoprecipitation analysis and flow cytometry showed that tissue culture cells infected with SPBNGA-GA produced, on average, twice as much RV G as cells infected with RV carrying only a single RV G gene (SPBNGA). The overexpression of RV G in SPBNGA-GA-infected NA cells was paralleled by a significant increase in caspase 3 activity followed by a marked decrease in mitochondrial respiration, neither of which was observed in SPBNGA-infected cells. Furthermore, fluorescence staining and confocal microscopy revealed an increased extent of apoptosis and markedly reduced neurofilament and F actin in SPBNGA-GA-infected primary neuron cultures compared with neuronal cells infected with SPBNGA, supporting the concept that RV G or motifs of the RV G gene trigger the apoptosis cascade. Mice immunized with SPBNGA-GA showed substantially higher antibody titers against the RV G and against the nucleoprotein than SPBNGA-immunized mice, suggesting that the speed or extent of apoptosis directly determines the magnitude of the antibody response.
Nanoscale Heterogeneities and Composition–Reactivity Relationships in Copper Vanadate Photoanodes (2021)

The photoelectrochemical performance of thin film photoelectrodes can be impacted by deviations from the stoichiometric composition, both at the macroscale and at the nanoscale. This issue is especially pronounced for the class of ternary compounds that are currently investigated for simultaneously achieving the optoelectronic characteristics and chemical stability required for solar fuel generation. Here, we combine macroscopic photoelectrochemical testing with atomic force microscopy (AFM) and scanning transmission X-ray microscopy (STXM) to reveal relationships between photoelectrochemical activity, nanoscale morphology, and local chemical composition in copper vanadate (CVO) thin films as a model system. For films with varying Cu/(Cu + V) ratios around the ideal stoichiometry of stoiberite Cu<sub>5</sub>V<sub>2</sub>O<sub>10</sub>, AFM resolves submicrometer morphology variations, which correlate with variations of the Cu content resolved by STXM. Both stoichiometric and Cu-deficient films exhibit a clear photoresponse, which indicates electronic tolerance to reduced Cu content. While both films exhibit homogeneous O and V content, they are also characterized by local regions of Cu enrichment and depletion that extend beyond individual grains. By contrast, Cu-rich photoelectrodes exhibit a tendency toward CuO secondary phase formation and a significantly reduced photoelectrochemical activity, indicating a significantly poor electronic tolerance to Cu-enrichment. These findings highlight that the average film composition at the macroscale is insufficient for defining structure-function relationships in complex ternary compounds. Rather, correlating microscopic variations in chemical composition to macroscopic photoelectrochemical performance provides insights into photocatalytic activity and stability that are otherwise not apparent from pure macroscopic characterization.
Adipokines at the crossroad between obesity and cardiovascular disease (2014)

Obesity, and especially excessive visceral adipose tissue accumulation, is considered as a low-grade inflammatory state that is responsible for adipocyte dysfunction and associated metabolic disorders. Adipose tissue displays endocrine functions by releasing pro- or anti-inflammatory bioactive molecules named adipokines. An altered expression of these molecules, provoked by obesity or adipocyte dysregulation, contributes to major metabolic diseases such as insulin resistance and type 2 diabetes mellitus that are important risk factors for cardiovascular disease. However, obesity is also characterised by the expansion of perivascular adipose tissue that acts locally via diffusion of adipokines into the vascular wall. Local inflammation within blood vessels induced by adipokines contributes to the onset of endothelial dysfunction, atherosclerosis and thrombosis, but also to vascular remodelling and hypertension. A fast expansion of obesity is expected in the near future, which will rapidly increase the incidence of these cardiovascular diseases. The focus of this review is to summarise the link between metabolic and cardiovascular disease and discuss current treatment approaches, limitations and future perspectives for more targeted therapies.
Purification and Properties of Seryl Transfer Ribonucleic Acid Synthetase from Escherichia coli (1970)

Abstract Seryl-tRNA synthetase (EC 6.1.1.11, l-serine:tRNA ligase (AMP)) has been purified to apparent homogeneity from Escherichia coli K12. The protein has a molecular weight of 95,000 to 100,000 and appears to be a dimer of identical subunits. It is suggested that there is a single seryl-tRNA synthetase in E. coli.
Shaping mitochondria: The complex posttranslational regulation of the mitochondrial fission protein DRP1 (2008)

Mitochondria are essential and dynamic cellular organelles differing in size, subcellular distribution, and internal structure. These aspects of mitochondrial morphology are intimately controlled by a growing number of mitochondrial morphology shaping proteins. The past decade has revealed remarkable and often unexpected new insights into the molecular regulation and physiological impact of mitochondrial morphology maintenance. Obviously, proper mitochondrial dynamics, resulting from a tightly regulated equilibrium between opposing mitochondrial fusion and fission activities, is a prerequisite for normal organelle function. Consequently, a disturbance of these activities results in mitochondrial dysfunction and, thus, can lay the foundation for human disorders. Here we specifically focus on recent advances in our understanding of the regulation, activity, and function of dynamin-related protein 1, the main factor for controlled mitochondrial fission.
Capacitor Properties and Pore Structure of Single- and Double-Walled Carbon Nanotubes (2009)

The correlation between capacitance and the structure of carbon nanotubes (CNTs) was revealed. The electrochemical behaviors of single- and double-walled CNTs were characteristic due to the electrochemical doping mechanism of semiconducting nanotubes, which are amphoteric and can be doped by both donors and acceptors. The capacitance and the sheet conductance of CNTs, as capacitor electrodes were dependent on their porous and electronic structure. High specific capacitance was obtained for uncapped single-walled CNTs having inner micropores with a diameter of .
Lignin Formation and the Effects of Gravity (1997)

Table of Content Summary Progress Report 1. Whether compression wood formation occurs in microgravity or not.2. To develop methodology to determine the basic processes involved in lignification: Definition of rate-limiting step(s)involved in formation of the monomeric lignin precursorsfrom phenylalanine; how the corresponding monolignolsare transported to the plasma membrane and how the variousmetabolites and corresponding enzymes are organized at thesubcellular level2.1 Phenylpropanoid-nitrogen recycling during lignification 2.2 Metabolic flux studies and selective monolignol formation 2.3. Lignin and suberin forming processes Future Work Published manuscripts, manuscripts in preparation and work currently underway Figures iii