Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the role of LHCII-LHCII, PSII-LHCII and PSI-LHCII interactions in state transitions

The light-dependent reactions of photosynthesis take place in the plant chloroplast thylakoid membrane, a complex three-dimensional structure divided into the stacked grana and unstacked stromal lamellae domains. Plants regulate the macro-organization of photosynthetic complexes within the thylakoid membrane to adapt to changing environmental conditions and avoid oxidative stress. One such mechanism is the state transition which regulates photosynthetic light harvesting and electron transfer. State transitions are driven by changes in the phosphorylation of light harvesting antenna complex II (LHCII), which cause a decrease in grana diameter and stacking, a decreased energetic connectivity between photosystem II (PSII) reaction centres and an increase in the relative LHCII antenna size of photosystem I (PSI) compared to PSII. Phosphorylation is believed to drive these changes by weakening the intra-membrane lateral PSII-LHCII and LHCII-LHCII interactions and the inter-membrane stacking interactions between these complexes, while simultaneously increasing the affinity of LHCII for PSI. We investigated the relative roles and contributions of these three types of interaction to state transitions using a lattice-based model of the thylakoid membrane based on existing structural data, developing a novel algorithm to simulate protein complex dynamics. Monte Carlo simulations revealed that state transitions are unlikely to lead to a large-scale migration of LHCII from the grana to the stromal lamellae. Instead, the increased light harvesting capacity of PSI is largely due to the more efficient recruitment of LHCII already residing in the stromal lamellae into PSI-LHCII supercomplexes upon its phosphorylation. Likewise, the increased light harvesting capacity of PSII upon dephosphorylation was found to be driven by a more efficient recruitment of LHCII already residing in the grana into functional PSII-LHCII clusters, primarily driven by lateral interactions. Statement of significance For photosynthesis to operate at maximum efficiency the activity of the light-driven chlorophyll-protein complexes, photosystems I and II (PSI and PSII) must be fine-tuned to environmental conditions. Plants achieve this balance through a regulatory mechanism known as the state transition, which modulates the relative light-harvesting antenna size and therefore excitation rate of each photosystem. State transitions are driven by changes in the extent of the phosphorylation of light harvesting complex II (LHCII), which modulate the interactions between PSI, PSII and LHCII. Here we developed a novel algorithm to simulate protein complex dynamics and then ran Monte Carlo simulations to understand how these interactions cooperate to affect the organization of the photosynthetic membrane and bring about state transitions.
Bayesian inference for gene expression and proteomics

1. An introduction to high-throughput bioinformatics data Keith Baggerly, Kevin Coombes and Jeffrey S. Morris 2. Hierarchical mixture models for expression profiles Michael Newton, Ping Wang and Christina Kendziorski 3. Bayesian hierarchical models for inference in microarray data Anne-Mette K. Hein, Alex Lewin and Sylvia Richardson 4. Bayesian process-based modeling of two-channel microarray experiments estimating absolute mRNA concentrations Mark A. van de Wiel, Marit Holden, Ingrid K. Glad, Heidi Lyng and Arnoldo Frigessi 5. Identification of biomarkers in classification and clustering of high-throughput data Mahlet Tadesse, Marina Vannucci, Naijun Sha and Sinae Kim 6. Modeling nonlinear gene interactions using Bayesian MARS Veerabhadran Baladandayuthapani, Chris C. Holmes, Bani K. Mallick and Raymond J. Carroll 7. Models for probability of under- and over-expression: the POE scale Elizabeth Garrett-Mayer and Robert Scharpf 8. Sparse statistical modelling in gene expression genomics Joseph Lucas, Carlos Carvalho, Quanli Wang, Andrea Bild, Joseph Nevins and Mike West 9. Bayesian analysis of cell-cycle gene expression Chuan Zhou, Jon Wakefield and Linda L. Breeden 10. Model-based clustering for expression data via a Dirichlet process mixture model David Dahl 11. Interval mapping for Expression Quantitative Trait Loci mapping Meng Chen and Christina Kendziorski 12. Bayesian mixture model for gene expression and protein profiles Michele Guindani, Kim-Anh Do, Peter Muller and Jeffrey S. Morris 13. Shrinkage estimation for SAGE data using a mixture Dirichlet prior Jeffrey S. Morris, Kevin Coombes and Keith Baggerly 14. Analysis of mass spectrometry data using Bayesian wavelet-based functional mixed models Jeffrey S. Morris, Philip J. Brown, Keith Baggerly and Kevin Coombes 15. Nonparametric models for proteomic peak identification and quantification Merlise Clyde, Leanna House and Robert Wolpert 16. Bayesian modeling and inference for sequence motif discovery Mayetri Gupta and Jun S. Liu 17. Identifying of DNA regulatory motifs and regulators by integrating gene expression and sequence data Deuk Woo Kwon, Sinae Kim, David Dahl, Michael Swartz, Mahlet Tadesse and Marina Vannucci 18. A misclassification model for inferring transcriptional regulatory networks Ning Sun and Hongyu Zhao 19. Estimating cellular signaling from transcription data Andrew V. Kossenkov, Ghislain Bidaut and Michael Ochs 20. Computational methods for learning Bayesian networks from high-throughput biological data Bradley Broom and Devika Subramanian 21. Modeling transcriptional regulation: Bayesian networks and informative priors Alexander J. Hartemink 22. Sample size choice for microarray experiments Peter Muller, Christian Robert and Judith Rousseau.
Neural network and crop residue index multiband models for estimating crop residue cover from Landsat TM and ETM+ images

Crop residues on the soil surface provide not only a barrier against water and wind erosion, but they also contribute to improving soil organic matter content, infiltration, evaporation, temperature, and soil structure, among others. In Argentina, soybean (Glycine max (L.) Merill) and corn (Zea mays L.) are the most important crops. The objective of this work was to develop and evaluate two different types of model for estimating soybean and corn residue cover: neural networks (NN) and crop residue index multiband (CRIM) index, from Landsat images. Data of crop residue were acquired throughout the summer growing season in the central plains of Córdoba (Argentina) and used for training and validating the models. The CRIM, a linear mixing model of composite soil and residue, and the NN design, included reflectance and digital numbers from a combination of different TM bands to estimate the fractional residue cover. The results show that both methodologies are appropriate for estimating the residue cover from Landsat data. The best developed NN model yielded R2 = 0.95 when estimating soybean and corn residue cover fraction, whereas the best fit using CRIM yielded R2 = 0.87; in addition, this index is dependent on the soil and residue lines considered.
Field thermal monitoring during the August 2003 eruption at Piton de la Fournaise (La Réunion)

[1] A detailed set of thermal images collected during the last day of the August 2003 eruption of Piton de la Fournaise (La Reunion), clearly revealed several dynamic processes associated with a spatter cone containing a lava pond and feeding a channelized lava flow. Periods of steady effusion were interrupted by brief pulses of lava effusion that closely coincide with peaks in seismic tremor amplitude. The thermal measurements show that roofing of a lava channel during steady effusion and cooling of surface flows decrease thermal radiance in two different ways. Here we show that the decrease in thermal radiance because of channel roofing is not related to a decrease in volcanic activity, as might be interpreted from satellite data. In addition, we introduce a new method of representing thermal data (hereby named “Radiative Thermogramme”) that successfully describes thermal patterns produced by distinct eruptive processes within the same span of time. This graphic solution can be directly correlated with volcanic field processes and provides a useful tool for interpreting a high number of thermal data in a wide range of volcanic activities.
CLIMATOLOGICAL WAVE DATA FOR COLOMBO, CEYLON

Abstract : Deep-water wave statistics for Colombo on the west coast of Ceylon have been compiled using the Sverdrup-Munk-Bretschneider wave-hindcast method applied to 12-hourly weather maps of the West Indian and South Atlantic Oceans for the one-year period from June 1968 through May 1969. Results of the wave- hindcast analysis are presented in the form of monthly and annual height-period- direction frequency distributions. The predominant waves are in the one to three foot height range, have periods centered about 13-14 seconds, and arrive from westerly to south-southwesterly directions. Wave action is most frequent in May through September and least in December. The wind waves and local swell on the west coast of Ceylon strongly reflect the seasonal Monsoons. The principal source of distant swell for this coast is the prevailing westerly wind belt of the Southern Hemisphere between Argentina and the longitude of Ceylon (80 degrees E). The subtropical anticyclone in the central Indian Ocean is a relatively quiet source region for swell compared to the Moonsoon belt and the prevailing westerlies.
Bipolar affective disorder: A review of novel forms of therapy

Abstract Normothymic, antidepressant and antipsychotic pharmaceutics are, in accordance with international guidelines, employed both in the therapy and the prevention of bipolar disorder (BD). Long-term studies on the mechanisms of action of such medications, as well as on the pathogenetic background of BD, have led to the discovery of effective, albeit unconventional pharmacotherapeutic approaches. These methods have the potential to successfully treat mania and depression, as well as to counter affective episode relapse. Allopurinol - commonly used to treat gout, secondary hyperuricemia and Lesch-Nyhan syndrome, acts by inhibiting the synthesis of uric acid, levels of which are often increased in manic patients. Due to this, an evaluation of the potential effect of allopurinol on the reduction of mania symptoms seems to be reasonable. Additionally, the numerable research papers coming out of research regarding the role of purine neurotransmitters in mood alterations, indicate that adenosine agonists act analogously to dopamine antagonists. N-acetylcysteine (NAC), a supporting agent in the pharmacotherapy of depressive episodes in bipolar disorder, substantially accelerates mood stabilization in patients. In turn, memantine, known for its procognitive effect, not only has antimanic and normothymic properties, but also boosts the neuroprotective action of traditional lithium therapy. In view of the latest opinions, the subtle pro-inflammatory process is typical for the pathophysiology of bipolar disease. Acetylsalicylic acid (ASA) (a popular analgesic, antipyretic and antiphlogistic agent) may be useful in BD therapy. This is because that, via its effect upon cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), ASA modulates leukocyte recruitment in neuro-inflammation. Apart from the above-mentioned medications, this article introduces the results of recent investigations of ketamine, modafinil and tamoxifen, including their receptor mechanisms, as well as certain genetic aspects or elements of their pharmacodynamics, for use in BD therapy. We put forward that, possibly, more insightful cognition of these drugs will allow significant enrichment in the range of pharmacotherapy for BD in the near future.
Market Interactions between Aquaculture and Common-Property Fisheries: Examining the Empirical Evidence from the Bristol Bay Sockeye Salmon Fishery in Alaska

The impressive growth of world aquaculture has led to profound transformations in the economic structure of several capture fisheries. Evidence from the Alaska salmon fisheries supports this argument as a connection has been suggested between the recent trends of declining ex-vessel prices and the rapid development of salmon farming elsewhere in the world. In Bristol Bay, home of the largest sockeye salmon runs in the globe, participation in the limited-entry fishery has declined by approximately 20% since 2001. Likewise, permit market values have plummeted to historic low levels, with economic conditions not likely to improve significantly in the mid-term future. To examine this problem, we develop a formal analytical framework for the study of market interactions between a limited-entry fishery and an aquaculture sector. We adapt the model of regulated open-access developed by Homans and Wilen to examine the implications of aquaculture development on the actions of fishermen and the regulatory sector in a restricted-access setting. Results indicate that the emergence of a low-cost aquaculture sector brings about important structural changes in the restricted-access fishery, rendering limited-entry regulations irrelevant as participation rates decline due to the falling prices. An important implication is that, despite the limited-entry constraint, the fishery moves to an institutional arrangement closer to regulated open access, with resource rents drastically reduced. Model predictions are compared with the empirical evidence available from the Bristol Bay sockeye fishery. The advantages of cooperative management relative to the current competitive structure of the fishery are highlighted.
First three‐dimensional simulation of the Perkins instability in the nighttime midlatitude ionosphere

A three‐dimensional numerical simulation in the nighttime midlatitude ionosphere is developed for the first time and applied to the Perkins instability in the midlatitude F region. Growth of the Perkins instability is successfully reproduced under nighttime condition, and the numerical results basically agree with a linear theory and previous two‐dimensional numerical studies. Northwest‐southeast (NW‐SE) alignment of density perturbations is generated from random seeding by applying a southeastward neutral wind. The perturbations are dominant at altitudes of 200–300 km where a steep density gradient exists, which is consistent with the altitude of 630‐nm airglow emission that often shows NW‐SE alignment. Further simulation in terms of the E‐F coupling can be done in the near future.
Designer Receptors Exclusively Activated by Designer Drugs Approach to Treatment of Sleep-disordered Breathing

Rationale: Obstructive sleep apnea is recurrent upper airway obstruction caused by a loss of upper airway muscle tone during sleep. The main goal of our study was to determine if designer receptors exclusively activated by designer drugs (DREADD) could be used to activatethegenioglossusmuscleasapotentialnoveltreatmentstrategyforsleepapnea.WehavepreviouslyshownthattheprototypicalDREADDligandclozapine-N-oxideincreasedpharyngealdiameterinmiceexpressingDREADDinthehypoglossalnucleus.However,theneedfordirectbrainstemviralinjectionsandclozapine-N-oxidetoxicitydiminishedtranslationalpotentialofthisapproach,andbreathingduringsleepwasnotexamined. Objectives: Here, we took advantage of our model of sleep-disordered breathing in diet-induced obese mice, retrograde properties of the adeno-associated virus serotype 9 (AAV9) viral vector, and the novel DREADD ligand J60. Methods: We administered AAV9-hSyn-hM3(Gq)-mCherry or control AAV9 into the genioglossus muscle of diet-induced obese mice and examined the effect of J60 on genioglossus activity, pharyngeal patency, and breathing during sleep. Measurements and Main Results: Compared with control, J60 increased genioglossus tonic activity by greater than sixfold and tongue uptake of 2-deoxy-2-[ 18 F] ﬂ uoro- D -glucose by 1.5-fold. J60 increased pharyngeal patency and relieved upper airway obstruction during non-REM sleep. Conclusions: We conclude that following intralingual administration of AAV9-DREADD, J60 can activate the genioglossus muscle and improve pharyngeal patency and breathing during sleep. M.M. , and V.Y. P. designed the experiments. T.F. C. , H.P., C.F. , M.R. A. , J.B. , L.J.K. , R.L. , M.E. C. , K.F. , and M.J.B. performed the experiments. T.F. C. , H.P., C.F. , J.B. , R.L. , S.R. S. , K.F. , M.J.B. , M.M. , and V.Y. P. analyzed the data. T.F. C. , H.P., and M.J.B. did the statistical analysis. J.B. , M.M. , and D.D. F. provided reagents. T.F. C. , M.R. A. , J.B. , L.G. B. , L.U.S., K.F. , R.G. S. , A.R. S. , M.J.B. , M.M. , D.D. F. , and V.Y. P. wrote the manuscript.
Development of an optical polarimeter for in-vivo glucose monitoring

In our investigation, we present both multi-spectral in vitro and preliminary single wavelength in vivo results supporting the use of optical polarimetry as a potential non-invasive method for glucose sensing. The site utilized for our in vivo measurements is the anterior chamber of the eye in a rabbit model. The anterior chamber of the eye contains a relatively clear and minimal scattering fluid known as the aqueous humor. The glucose levels of the aqueous humor are correlated to those of blood, therefore providing a mechanism to indirectly estimate blood glucose levels. A device to effectively couple light through the anterior chamber is also presented. As for the in vitro experiments, a multi-spectral approach is demonstrated as a method to minimize prediction error when glucose is not the only optically active component that varies in concentration.
Bryozoans from the Rönnklint section, Gotland

Abstract The Ronnklint section is a sea cliff in the Silurian strata of Gotland north of Visby, where the upper part of the Lower Visby Marl and the Upper Visby Marl are excellently exposed. The rich bryozoan fauna from the section comprises twenty six species. There is no faunal shift at the boundary between the Lower and Upper Visby Marl. One new species (Fistulipora pusilla) is described.
The Aguacaliente Fault, source of the Cartago 1910 destructive earthquake (Costa Rica)

On 4 May 1910, the most destructive earthquake in the history of Costa Rica (Ms 6.4) destroyed the city of Cartago, a major city located in the Valle Central of Costa Rica. Using both palaeo‐seismological and morphotectonic analyses, we have found evidence that points to the Aguacaliente Fault (AF) as the source of this earthquake. This structure is a N100° E trending, strike‐slip fault situated to the south of Cartago and within a wide band of deformation. We excavated two trenches near Bermejo, south of Cartago. We found evidence of three surface ruptures within the last 1000 years on this fault. The age of the most recent rupture is consistent with the Cartago 1910 earthquake. The AF is a seismogenic source capable of producing large earthquakes (Mw 6.5–6.9) with an estimated recurrence interval of about 500 years.
Development of GIS techniques for automated topographic and hydrologic analysis

This paper describes the development of a GIS interface which can be used to construct lumped hydrologic models for flood estimation on natural and urban catchments. The interface is currently being implemented with the runoff routing model WBNM, but is a general procedure and could be used with a range of flood hydrograph and daily flow models. The GIS interface utilises digital contour and watercourse data to automatically delineate subcatchments, to measure generalised subcatchment attributes, and to allocate lag times to the subcatchments. The key algorithms in the GIS interface are compared with traditional manual map interpretation techniques, and to some currently available GIS procedures. The GIS interface dramatically reduces the time required to delineate subcatchments and measure their topographic and hydrologic attributes. It also has significant potential to increase the reproducibility and accuracy of streamflow prediction, while reducing the inherent user subjectivity involved in more traditional methods.
Minimum 10Be exposure ages of early Pliocene for the Table Mountain plateau and the Sirius Group at Mount Fleming, Dry Valleys, Antarctica

Using accelerator mass spectrometry (AMS), we have measured 10Be and 26Al in quartz from granites and sandstones from Table Mountain and Mount Fleming, Antarctica. Our data show that the plateau surface at Table Mountain had formed by early Pliocene time at the latest. Granites fringing but within the Sirius Group at Table Mountain give a minimum exposure age of 2.6 Ma for this deposit. A sandstone clast on the Ferrar dolerite surface just outside and below, and thus postdating, the Sirius Group has a minimum age of 2.9 Ma. Two samples from the Sirius Group at Mount Fleming have 10Be concentrations that have reached secular equilibrium. This deposit is at least 4.8 m.y. old. The Sirius Group at Mount Fleming cannot have been deposited after 3.0–2.5 Ma, as implied by biostratigraphic data. Our dates contradict the hypothesis that in the Pliocene East Antarctica was deglaciated and the climate was significantly warmer and wetter. The preservation of these surfaces indicates a continuous cold desert in the dry valleys since the beginning of the Pliocene. The high 10Be concentrations we have measured cannot be reconciled with uplift of the Transantarctic Mountains at a rate of 1 km/m.y. during the past 3 m.y.
What are the situationa l and behavioral factors associated with condomless anal sex without pre-exposure prophylaxis in MSM?

Results: In the OLE, 19% of anal intercourses were unprotected (i.e. no PrEP or condom). Of these, 85% were attributable to sexual intercourse with main partners and 47% with HIV-negative partners. The following factors were positively associated with condomless anal sex without PrEP: a depressive episode in the previous 12 months [aR (95% CI), P-value: 1.49 (1.02–2.17), 0.039], a higher number of sexual intercourses during the previous 4 weeks [1.01 [1.002–1.02], 0.014], and sexual intercourses under the influence of alcohol [1.45 (1.10–1.92), 0.008]. By contrast, condomless anal sex without PrEP was less frequent during sexual intercourses with known casual, unknown casual and multiple partners [0.20 (0.14–0.30),<0.001; 0.10 (0.05–0.20),<0.001; 0.11 (0.05–0.29),<0.001, respectively], as well as with HIVþ partners with an undetectable viral load and HIVþ partners with a detectable/unknown viral load or unknown serology status [0.57 (0.38–0.86), 0.007; 0.52 (0.32–0.87), 0.012, respectively].
SURVEY OF PHENANTHERENE BIODEGRADATION'S MODEL IN CONTAMINATED SOILS BY ACINETOBACTER SP

Backgrounds and Objectives: Polycyclic aromatic hydrocarbons (PAHs) are a group of hazardous pollutants which have carcinogenic and mutagenic properties and accumulated in environment by different actions, therefore treatment of them is important. Biological treatments are simple and cheep technologies. This technology was recommended as a costeffective method for treatment of these pollutants. In order to investigate the trend of pollution reduction of petroleum hydrocarbons in bioremediation, the phenanthrene biodegradation’s model in contaminated soils was studied. Materials and Methods: Firstly, PAHs capable degrading bacteria was isolated from petroleum contaminated soils and then their ability for biodegradation of phenanthrene was assessed in slurry phase. After that by using Acinetobacter which have the most potential of removing phenanthrene from soil, the biodegradation model was investigated in bench scale. Results: Phenantherene removal efficiency was obtained 99.4% for 100 mg/kg and 96 % for 500 mg/kg concentrations in 33 and 60 days biodegradation period respectively. Phenantherene reduction rate varied from 2.99 to 8.86 and 1.4 to 11.09 mg/kg/day for 100 and 500 mg/kg concentrations, respectively. Conclusion: Rate of phenantherene removal is depended on primary concentration of contamination and by increasing of primary concentration, phenantherene removal rate was increased. Also removal efficiency followed zero and first order kinetic model with good correlation.