Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodiversity, ecosystem functioning and food webs in fresh waters: assembling the jigsaw puzzle

SUMMARY 1. Dramatic advances have been made recently in the study of biodiversity–ecosystem functioning (B-EF) relations and food web ecology. These fields are now starting to converge, and this fusion has the potential to improve our understanding of how environmental stressors modulate ecosystem processes and the supply of ‘goods and services’. 2. Food web structure and dynamics can exert particularly strong influences on B-EF relations in fresh waters, as consumer–resource interactions (e.g. trophic cascades) are often more important than horizontal interactions within trophic levels. For instance, many freshwater food webs are size structured, with large organisms tending to occupy the higher trophic levels and often exerting powerful effects on ecosystem processes. However, because they are also vulnerable to perturbations, non-random losses of these large taxa can alter both food web structure and ecosystem functioning profoundly. 3. Recently, the focus of food web research has shifted away from exploring patterns, towards developing an understanding of processes (e.g. quantifying fluxes of individuals, biomass, energy, nutrients) and how the two interact. Many of the bestcharacterized food webs are from fresh waters, and these ecosystems are now being used to address some of the shortcomings of earlier B-EF studies. I have identified several key gaps in our current knowledge and highlighted potentially fruitful avenues of future B-EF and food web research. 4. A major challenge for this newly emerging research is to place it within a unified theoretical framework. The application of metabolic theory and ecological stoichiometry may help to achieve this goal by considering biological systems within the constraints imposed upon them by physical and chemical laws.
Single cell in vivo brain optogenetic stimulation by two-photon excitation fluorescence transfer

Optogenetic manipulation with single-cell resolution can be achieved by two-photon excitation; however, this frequently requires relatively high laser powers or holographic illumination. Here we developed a practical strategy to improve the efficiency of two-photon stimulation by positioning fluorescent proteins or small fluorescent molecules with high two-photon cross-sections in the vicinity of opsins. This generates a highly localized source of endogenous single-photon illumination that can be tailored to match the optimal opsin absorbance. Through neuronal and vascular stimulation in the live mouse brain, we demonstrate the utility of this technique to achieve more efficient opsin stimulation, without loss of cellular resolution. We also provide a theoretical framework for understanding the potential advantages and constrains of this methodology, with suggestions for future improvements. Altogether, this fluorescence transfer illumination method allows experiments difficult to implement in the live brain such as all-optical neural interrogation and control of regional cerebral blood flow.
Anatomia dos órgãos vegetativos de Dieffenbachia picta Schott (Araceae) com ênfase na distribuição de cristais, laticíferos e grãos de amido

We studied the distribution of crystals, laticifers and starch grains of the vegetative organs from dumb cane, Dieffenbachia picta Schott (Araceae), known in Brazil as "comigo-ninguem-pode" for such structures are meant to be responsible for mechanical and chemical irritation events carried out by the plant. We described the anatomy of leaves, aerial stems, rhizomes and roots with histological sections dyed in toluidine blue. We checked the chemical nature of crystals and the presence of lipids, alkaloids, starch grains and proteins with various reagents. Druses and calcium oxalate raphides - associated with lipids, alkaloids and proteins - were found in idioblasts spread in the parenchyma of all organs, in the collenchyma of the shoot and in the root meristems. Regarding the dissolution time, it was analogous for crystals in both young and old leaves; it was higher in stems than in leaves and higher in rhizomes than in roots. Starch grains associated with proteins were found in the chlorenchyma of the aerial stem (rod-shaped) and in rhizomes (spherical and rod-shaped). Laticifers were found interspersing parenchyma and collenchyma; raphides, alkaloids and lipids were found in latex. We found a higher number of crystals and laticifers in the aerial stem, and therefore such structure is the most dangerous organ if eaten or swallowed.
Shaping Durum Wheat for the Future: Gene Expression Analyses and Metabolites Profiling Support the Contribution of BCAT Genes to Drought Stress Response

Global climate change, its implications for agriculture, and the complex scenario presented by the scientific community are of worldwide concern. Drought is a major abiotic stress that can restrict plants growth and yields, thus the identification of genotypes with higher adaptability to drought stress represents one of the primary goals in breeding programs. During abiotic stress, metabolic adaptation is crucial for stress tolerance, and accumulation of specific amino acids and/or as secondary metabolites deriving from amino acid metabolism may correlate with the increased tolerance to adverse environmental conditions. This work, focused on the metabolism of branched chain-amino acids (BCAAs) in durum wheat and the role of branched-chain amino acid aminotransferases (BCATs) in stress response. The role of BCATs in plant response to drought was previously proposed for Arabidopsis, where the levels of BCAAs were altered at the transcriptional level under drought conditions, triggering the onset of defense response metabolism. However, in wheat the role of BCAAs as a trigger of the onset of the drought defense response has not been elucidated. A comparative genomic approach elucidated the composition of the BCAT gene family in durum wheat. Here we demonstrate a tissue and developmental stage specificity of BCATs regulation in the drought response. Moreover, a metabolites profiling was performed on two contrasting durum wheat cultivars Colosseo and Cappelli resulting in the detection of a specific pattern of metabolites accumulated among genotypes and, in particular, in an enhanced BCAAs accumulation in the tolerant cv Cappelli further supporting a role of BCAAs in the drought defense response. The results support the use of gene expression and target metabolomic in modern breeding to shape new cultivars more resilient to a changing climate.
Modeling egg development of the pest Clavipalpus ursinus (Coleoptera: Melolonthidae) using a temperature‐dependent approach

Abstract Predicting the population dynamics of insects in natural conditions is essential for their management or preservation, and temperature‐dependent development models contribute to achieving this. In this research the effects of temperature and soil moisture content on egg development and hatching of Clavipalpus ursinus (Blanchard) were evaluated. The eggs were exposed to seven temperature treatments with averages of 7.2, 13.0, 15.5, 19.7, 20.6, 22.0 and 25.3°C, in combination with three soil moisture contents of 40%, 60% and 80%. A linear and two non‐linear (Lactin and Briere) models were evaluated in order to determine the thermal requirements of this developmental stage. Temperature affected significantly the time of development and egg hatching, while no significant effect was observed for moisture content. Thermal requirements were set as: 7.2°C for lower developmental threshold, 20.6°C for optimum developmental threshold, 25.3°C for maximum temperature and 344.83 degree‐days for the thermal constant. The linear model described satisfactorily egg development at intermediate temperatures; nevertheless, a slightly better fit of the observed data was obtained with the Lactin model. Egg development took place inside a narrow range of temperatures. Consequently, an increment of soil temperature could generate a negative impact on the population size of this species or changes in its biological parameters.
The Genome of Microthlaspi erraticum (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils

Microthlaspi erraticum is widely distributed in temperate Eurasia, but restricted to Ca2+-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring Microthlaspi erraticum individuals are confronted with a high concentration of Ca2+ ions while Mg2+ ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of Microthlaspi erraticum. Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg2+ transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg2+ ions efficiently in the presence of an overwhelming amount of Ca2+ ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca2+-rich and Mg2+ -poor soils.
Factors regulating phytoplankton production and standing crop in the world's freshwaters

A regression analysis of global data for freshwater phytoplankton production, chlorophyll, and various nutrient parameters revealed the following: A high proportion of the variance in both annual phytoplankton production and mean annual chlorophyll could be explained by annual phosphorus input (loading), once a simple correction for water renewal time was applied. Good relationships were also found between phosphorus loading and mean total phosphorus concentration, and between total phosphorus concentration and chlorophyll. The slope of the regression of total phosphorus on phosphorus loading for stratified lakes was not significantly different from that for unstratified lakes, suggesting that the effect of stratification on phosphorus concentration is insignificant compared to external sources of the element. Nutrient input, which was unavailable in previous analyses, appears to be an important factor in controlling freshwater production. There is some evidence for a correlation between latitude and nutrient input, and it is possible that this may explain the good correlation between latitude and production observed by earlier investigators. In an earlier synthesis of IBP freshwater primary production results, Brylinsky and Mann (1973) and Brylinsky (in press) concluded that variables related to energy availability had a greater influence on phytoplankton production than those related to nutrient availability. They found that 57% of the variability in global primary production could be explained by latitude alone. Brylinsky and Mann, however, recognized the scarcity of good data for nutrient input to lakes in the IBP data set. They suggested (p. 12) that some of the influence attributed to energy might be due to its driving of circulation systems, so that nutrient availability might be affected directly. Recently, more data on nutrients, including input and output dynamics, have accumulated, chiefly as the result of investigations of the eutrophication of lakes. These data, plus our own experimental studies in lakes, suggested that nutrients played a preeminent role in controlling phytoplankton production and standing crop. Of all the variables which may control aquatic production and standing crop. only nutrients are amenable to control by humans. It therefore seemed worthwhile to repeat Brylinsky and Mann’s analysis, including this new information (Schindler and Fee 1974). The following analysis is highly biased toward glacial lakes in north temperate and subarctic regions, where most limnological activity has been concentrated. More complete data are sorely needed for water bodies in tropical and arctic regions, in the southern hemisphere, and in unglaciated areas before a definitive global analysis of production and factors affecting it can be made. Increases in the annual input of nu
Threshold Life Tables and Their Applications

Abstract The rapid emergence of centenarians has highlighted the importance of survival probabilities at extreme ages and has motivated actuaries to look for alternative ways to close of life tables in place of assigning a death probability of 1 at an arbitrarily chosen age. Using the asymptotic results of modern extreme value theory, we propose a model, which we call the threshold life table, to extrapolate survival distributions to extreme ages and to determine the appropriate end point of a life table. By combining the threshold life table with the Lee-Carter model for stochastic mortality forecasting, we consider applications to the valuation of a life annuity portfolio and to the prediction of the highest attained age. We illustrate the theoretical results using U.S., Canadian, and Japanese mortality data.
An evaluation of a mitigation strategy for deer-vehicle collisions

High mule deer Odocoileus hemionus mortality in southwestern Utah led to the establishment of a mitigation strategy with two major objectives: 1) reduction of wildlife-vehicle collisions and 2) restoration of landscape connectivity to facilitate wildlife movement across the roaded landscape. During our study, we assessed the effectiveness of the mitigation measures in reducing mule deer mortality in the following ways: 1) we compared the number of deer-vehicle collisions in the newly fenced area with a control area without fencing; 2) we analyzed the ‘end-of-the-fence’ problem, defined here as increased mortality of mule deer at the ends of the 2.4-m high exclusion fences; and 3) we evaluated the frequency of animal crossings of the new underpasses using remotely-sensed cameras and compared them with crossing frequency rates for a 20-year-old control underpass. We compared six years of pre-construction mortality (during 1998-2003) with two years of post-construction data on mortality (during 2005-2006) and found a 98.5% decline in deer mortalities in the treatment (i.e. fenced, jump-outs and underpasses) vs a 2.9% decline in the control (i.e. no fences, no jump-outs and no underpasses). We detected no end-of-the-fence problems related to deer mortality. Migratory movements during fall and spring were clearly reflected in the use of underpass. Overall results demonstrated that the mitigation strategy was effective and reduced the number of deer-vehicle accidents, while allowing wildlife movement across the landscape.
A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. III. Quantifying the Energy Costs of Ion Transport in Salt-Stressed Roots of Arabidopsis

Salt stress defense mechanisms in plant roots, such as active Na+ efflux and storage, require energy in the form of ATP. Understanding the energy required for these transport mechanisms is an important step toward achieving an understanding of salt tolerance. However, accurate measurements of the fluxes required to estimate these energy costs are difficult to achieve by experimental means. As a result, the magnitude of the energy costs of ion transport in salt-stressed roots relative to the available energy is unclear, as are the relative contributions of different defense mechanisms to the total cost. We used mathematical modeling to address three key questions about the energy costs of ion transport in salt-stressed Arabidopsis roots: are the energy requirements calculated on the basis of flux data feasible; which transport steps are the main contributors to the total energy costs; and which transport processes could be altered to minimize the total energy costs? Using our biophysical model of ion and water transport we calculated the energy expended in the trans-plasma membrane and trans-tonoplast transport of Na+, K+, Cl−, and H+ in different regions of a salt-stressed model Arabidopsis root. Our calculated energy costs exceeded experimental estimates of the energy supplied by root respiration for high external NaCl concentrations. We found that Na+ exclusion from, and Cl− uptake into, the outer root were the major contributors to the total energy expended. Reducing the leakage of Na+ and the active uptake of Cl− across outer root plasma membranes would lower energy costs while enhancing exclusion of these ions. The high energy cost of ion transport in roots demonstrates that the energetic consequences of altering ion transport processes should be considered when attempting to improve salt tolerance.
Thinning Jeffrey pine stands to reduce susceptibility to bark beetle infestations in California, U.S.A.

1 Bark beetles (Coleoptera: Curculionidae, Scolytinae) are commonly recognized as important tree mortality agents in coniferous forests of the western U.S.A. 2 High stand density is consistently associated with bark beetle infestations in western coniferous forests, and therefore thinning has long been advocated as a preventive measure to alleviate or reduce the amount of bark beetle‐caused tree mortality. 3 The present study aimed to determine the effectiveness of thinning to reduce stand susceptibility to bark beetle infestations over a 10‐year period in Pinus jeffreyi forests on the Tahoe National Forest, California, U.S.A. Four treatments were replicated three times within 1‐ha square experimental plots. Treatments included thinning from below (i.e. initiating in the smallest diameter classes) to a residual target basal area (cross‐sectional area of trees at 1.37 m in height) of: (i) 18.4 m2/ha (low density thin); (ii) 27.6 m2/ha (medium density thin); (iii) 41.3 m2/ha (high density thin); and (iv) no stand manipulation (untreated control). 4 Throughout the present study, 107 trees died as a result of bark beetle attacks. Of these, 71% (75 trees) were Abies concolor killed by Scolytus ventralis; 20.6% (22 trees) were Pinus ponderosa killed by Dendroctonus ponderosae; 4.7% (five trees) were P. jeffreyi killed by Dendroctonus jeffreyi; 1.8% (two trees) were P. jeffreyi killed by Ips pini; 0.9% (one tree) were P. jeffreyi killed by Orthotomicus (= Ips) latidens; 0.9% (one tree) were P. ponderosa killed by both Dendroctonus brevicomis and D. ponderosae; and 0.9% (one tree) were P. jeffreyi killed by unknown causes. 5 In the low density thin, no pines were killed by bark beetles during the 10‐year period. Significantly fewer trees (per ha/year) were killed in the low density thin than the high density thin or untreated control. No significant treatment effect was observed for the percentage of trees (per year) killed by bark beetles.
BLAST analysis of Phaseolin gene from common bean (Phaseolus vulgaris)

The common bean (Phaseolus vulgaris) contains major seed storage protein which is known as the phaseolin. The phaseolin is the salt-soluble glycoprotein that accounts of some 50 per cent of the total protein in mature bean seeds. The computational packages and online servers are the current tools used in the nucleotide or protein sequence analysis and characterization. The query full length nucleotide sequence of phaseolin gene was subjected to BLAST analysis with the homologous nucleotide sequences. The sequences homologues to the phaseolin gene query sequence were retrieved on the bases of query coverage, maximum identity and e-value.
The Effect of Long-Term Aerial Exposure on Heart Rate, Ventilation, Respiratory Gas Exchange and Acid-Base Status in the Crayfish Austropotamobius Pallipes

1. 1. When first removed into air, crayfish showed transient increases in heart rate ( f H) and scaphognathite rate ( f R) which rapidly recovered to submerged levels and were unchanged for 24 h. The rate of O2 consumption(Moo2) increased from an initially low level and was then maintained for 24 h in air at the same level as in settled submerged animals. 2. 2. There was an initial acidosis in the haemolymph which was both respiratory and metabolic due to the accumulation of CO2 and lactate. Progressive compensation by elevation of the levels of bicarbonate buffer in the haemolymph and reduction of circulating lactate levels returned pH towards submerged levels after 24 h in air. 3. 3. Exposure to air resulted in a marked internal hypoxia with haemolymph O2, tensions, both postbranchial P a , oo2 and prebranchial P v , oo2, remaining low throughout the period of exposure. The oxygen content or the haemolymph was initially reduced, with a - v OO2 content difference close to zero. Within 24 h both C a , oo2 and C v , OO2 had returned towards their levels in submerged animals. These changes are explained by the Bohr shift on the haemocyanin consequent upon the measured pH changes. 4. 4. After 48 h in air, MO2 and fH were significantly reduced and ventilation became intermittent. There was a slight secondary acidosis, increase in lactic acid levels and reduction in a - v O2 content difference in the haemolymph. 5. 5. When crayfish were returned to water after 24 h in air, MOO2, fH fR were initially elevated by disturbance and there was a period of hyperventilation. In the haemolymph there was an initial slight alkalosis, and an increase in C a , OO2 lactic acid. All variables returned to their settled submerged levels within 8 h.
Levetiracetam vs. Fosphenytoin for Second-Line Treatment of Status Epilepticus: Propensity Score Matching Analysis Using a Nationwide Inpatient Database

Objective: Status epilepticus is a major emergency condition. The choice of antiepileptic drugs for second-line treatment after benzodiazepine remains controversial, including levetiracetam vs. fosphenytoin. We compare the safety of intravenous levetiracetam and fosphenytoin as a second-line treatment in patients with status epilepticus using a nationwide database. Methods: An observational study conducted with the Japanese Diagnosis Procedure Combination inpatient database identified adult patients who had been admitted for status epilepticus and who had received intravenous diazepam on the day of admission from March 1, 2011 to March 31, 2018. Patients who received intravenous levetiracetam on the day of admission were defined as the levetiracetam group and those who received intravenous fosphenytoin on the day of admission were defined as the fosphenytoin group. Propensity score matching was performed to compare outcomes obtained for the levetiracetam and fosphenytoin groups. Results: The analysis examined data of 5,667 patients. Overall, 1,403 (25%) patients received levetiracetam; 4,264 (75%) received fosphenytoin. One-to-one propensity score matching created 1,363 matched pairs. No significant difference was found in in-hospital mortality (5.2 vs. 5.1%; odds ratio, 1.03; 95% confidence interval, 0.73–1.46). The proportion of vasopressor use on the day of admission was significantly lower for the levetiracetam group than for the fosphenytoin group (3.2 vs. 4.9%; odds ratio, 0.63; 95% confidence interval, 0.43–0.92). No significant difference was found in other secondary outcomes including total hospitalization cost. Conclusion: Levetiracetam was related to significantly reduced vasopressor use on the day of admission than that found for fosphenytoin, in adult status epilepticus.