Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoacclimation in microphytobenthos and the role of xanthophyll pigments

Estuarine microphytobenthos are frequently exposed to excessively high irradiances. Photoinhibition in microalgae is prevented by various photophysiological responses. We describe here the role of the xanthophyll pigments in photoacclimation. The pigment composition of the microphytobenthos was studied in three European estuaries (Barrow, Ireland; Eden, UK; Tagus, Portugal). Using HPLC-analyses, microscale changes in biomass and pigment composition were monitored over short (hourly) and long (seasonal) time scales. In the Barrow estuary, the biomass of microphytobenthos (measured as chlorophyll a) increased significantly in the top 400–500 µm of the sediment surface within 1 h of emersion; simultaneously, the xanthophyll pool size (diadinoxanthin plus diatoxanthin, dd + dt) almost doubled. A more gradual conversion of dd into dt was observed, with the dt:dd ratio increasing from <0.1 at the start of emersion to >0.3 after 3 h emersion. Similar trends in the dt:dd ratio were observed in the surface sediments of the Eden and the Tagus estuaries. Higher ratios were recorded in the Tagus estuary, which may be explained by higher incident irradiance. In addition, seasonal studies carried out in the Eden and Tagus estuaries showed that the xanthophyll pool size increased by 10% in the summer months. The pool size was highest in the Tagus estuary. Concurrently, high values for the de-epoxidation state were recorded, with values for dt/(dt + dd) > 0.35 recorded in the summer. At the Eden, the ratio never exceeded 0.3. The de-epoxidation state was higher in winter than in summer, which was ascribed to the low winter temperatures. During a vertical migration study, a negative relationship between chlorophyll a and the de-epoxidation state was observed. It is suggested that this relationship originates from ‘micro-migration’ within the biofilm. Migration within the euphotic zone may provide an alternative means for cells to escape photodamage. In this paper, we propose that both xanthophyll cycling and ‘micro’-migration play an important role in photoacclimation and it appears that these processes operate in parallel to regulate the photosynthetic response.
A Comparison of Richness Hotspots, Rarity Hotspots, and Complementary Areas for Conserving Diversity of British Birds

Biodiversity conservation requires efficient methods for choosing priority areas for in situ conservation management. We compared three quantitative methods for choosing 5% (an arbitrary figure) of all the 10 × 10 km grid cells in Britain to represent the diversity of breeding birds: (1) hotspots of richness, which selects the areas richest in species; (2) hotspots of range-size rarity (narrow endemism), which selects areas richest in those species with the most restricted ranges; and (3) sets of complementary areas, which selects areas with the greatest combined species richness. Our results show that richness hotspots contained the highest number of species-in-grid-cell records (with many representations of the more widespread species), whereas the method of complementary areas obtained the lowest number. However, whereas richness hotspots included representation of 89% of British species of breeding birds, and rarity hotspots included 98%, the areas chosen using complementarity represented all the species, where possible, at least six times over. The method of complementary areas was also well suited to supplementing the existing conservation network. For example, starting with grid cells with over 50% area cover by existing “Sites of Special Scientific Interest,” we searched for a set of areas that could complete the representation of all the most threatened birds in Britain, the Red Data species. The method of complementary areas distinguishes between irreplaceable and flexible areas, which helps planners by providing alternatives for negotiation. This method can also show which particular species justify the choice of each area. Yet the complementary areas method will not be fully able to select the best areas for conservation management until we achieve integration of some of the more important factors affecting viability, threat, and cost.
Meiotic analysis of the interspecific and intergeneric hybrids between Hystrix patula Moench and H. duthiei ssp. longearistata, Pseudoroegneria, Elymus, Roegneria, and Psathyrostachys species (Poaceae, Triticeae)

Interspecific and intergeneric hybridizations were carried out in an investigation of genome homology between Hystrix patula and other species of Hystrix, as well as the generic relationships between H. patula and its related species. Meiotic pairing in the hybrids H. patula × H. duthiei ssp. longearistata (Ns–), H. patula × Pseudoroegneria spicata (St), H. patula × Pse. libanotica (St), Elymus sibiricus (StH) × H. patula, H. patula × E. wawawaiensis (StH), Roegneria ciliaris (StY) × H. patula, H. patula × R. grandis (StY), and H. patula × Psathyrostachys huashanica (Nsh) averaged 1.32, 6.53, 5.62, 10.08, 12.83, 3.57, 3.98, and 0.29 bivalents per cell, respectively. The results indicate that: (1) H. patula has no genome homology with H. duthiei ssp. longearistata or the Ns genome from Psathyrostachys; (2) H. patula contains the same StH genomes as the Elymus species, and the St genome is homologous to the genome of Pse. spicata and Pse. libanotica; and (3) H. patula has a low genome affinity with the StY genomes of Roegneria. Therefore, it is reasonable to treat H. patula Moench as E. hystrix L. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 153, 213–219.
Net ecosystem productivity of boreal jack pine stands regenerating from clearcutting under current and future climates

Life cycle analysis of climate and disturbance effects on forest net ecosystem productivity (NEP) is necessary to assess changes in forest carbon (C) stocks under current or future climates. Ecosystem models used in such assessments need to undergo well‐constrained tests of their hypotheses for climate and disturbance effects on the processes that determine CO2 exchange between forests and the atmosphere. We tested the ability of the model ecosys to simulate diurnal changes in CO2 fluxes under changing air temperatures (Ta) and soil water contents during forest regeneration with eddy covariance measurements over boreal jack pine (Pinus banksiana) stands along a postclearcut chronosequence. Model hypotheses for hydraulic and nutrient constraints on CO2 fixation allowed ecosys to simulate the recovery of C cycling during the transition of boreal jack pine stands from C sources following clearcutting (NEP from −150 to −200 g C m−2 yr−1) to C sinks at maturity (NEP from 20 to 80 g C m−2 yr−1) with large interannual variability. Over a 126‐year logging cycle, annualized NEP, C harvest, and net biome productivity (NBP=NEP–harvest removals) of boreal jack pine averaged 47, 33 and 14 g C m−2 yr−1. Under an IPCC SRES climate change scenario, rising Ta exacerbated hydraulic constraints that adversely affected NEP of boreal jack pine after 75 years. These adverse effects were avoided in the model by replacing the boreal jack pine ecotype with one adapted to warmer Ta. This replacement raised annualized NEP, C harvest, and NBP to 81, 56 and 25 g C m−2 yr−1 during a 126‐year logging cycle under the same climate change scenario.
Toward a Phylogenetic-based Generic Classification of Neotropical Lecythidaceae—II. Status of Allantoma , Cariniana , Couratari , Couroupita , Grias and Gustavia

The morphological features of all clades of neotropical Lecythidaceae subfam. Lecythidoideae (Brazil nut family) with actinomorphic androecia ( Allantoma , Grias , Gustavia ) as well as three clades with zygomorphic androecia ( Cariniana , Couroupita , and Couratari ) are described. These clades are those that were recovered by a phylogeny based on molecular data, and all, except Allantoma and Cariniana , have been recognized as genera without changes for over a hundred years. The latter two genera have recently been circumscribed such that they now also represent monophyletic clades; thus, the authors conclude that the clades discussed in this paper represent well-defined genera based on both morphological and molecular data. Morphological descriptions of these six clades of the non- Bertholletia clade are included and a key to the 16 clades of New World Lecythidaceae is presented.
Nesting habitat selection of Mediterranean raptors in managed pinewoods: searching for common patterns to derive conservation recommendations

Summary Investigating habitat selection is a key step in improving the population conservation of forest species in areas managed for different purposes, from timber harvesting to hunting or recreation. Because economic resources allocated to conservation are limited, studies that assess cost-effective strategies are necessary, especially when concerning non-threatened species. We studied nest-site habitat selection of two raptor communities (totalling 245 nests from the five most common species: Short-Toed Eagle Circaetus gallicus, Goshawk Accipiter gentilis, Sparrowhawk A. nisus, Common Buzzard Buteo buteo and Booted Eagle Aquila pennata) in two pinewoods in central Spain separated by 200 km. Using a Generalised Linear Mixed Model for each species and with locality as a random factor, we obtained five models of habitat selection. We highlighted the common nesting patterns in order to facilitate an integrated management of forestry in relation to raptor nesting habitat selection. The most important variable for all species, with the exception of the Sparrowhawk was the nest-tree diameter at breast height, with raptors preferentially selecting nesting trees of large width. Tall trees and a high amount of tree cover around the nesting tree were also important habitat features for several species. Our results suggest that pinewoods should retain unharvested patches with moderate tree coverage (30–70%) containing not only several large trees (diameter at breast height > 40 cm) but also small ones. At the landscape level, open forests and heterogeneous habitats are preferred. These forest patches should be dispersed throughout the landscape.
Orange-Brown Precipitate: A Threat to the Success of Endodontic Treatment â€“ An In Vitro Study

AIM: The aim of the present study was to evaluate the effect of various intermediate irrigating solutions in the removal of orange-brown precipitate formed due to alternative use of sodium hypochlorite (NaOCl) and chlorhexidine (CHX) root canal irrigants. METHODS: The root canals of 50 mandibular premolars were prepared using ProTaper Universal Rotary instruments (Dentsply Maillefer, Ballaigues, Switzerland) up to size F3. The roots were randomly divided into five experimental groups specified by the intermediate irrigant used; Group 1: No intermediate irrigant used (control), Group 2: Saline, Group 3: 7% maleic acid (MA), Group 4: 4% sodium thiosulfate, and Group 5: 70% isopropyl alcohol (n = 10). After final irrigation with CHX, the specimens were evaluated for the presence/absence of orange-brown precipitate under stereomicroscope. RESULTS: Mean precipitate for all experimental groups was calculated using ANOVA F test which showed orange-brown precipitate (parachloroanaline) in all groups except Group 4 and Group 5 which were highly significant (p < 0.001) at all the levels of root canal. Intergroup pairwise comparison was done using Tukeyâ€™s post hoc test. CONCLUSION: About 7% MA is effective in minimizing the formation of orange-brown precipitate when used as intermediate irrigant between NaOCl and CHX. However, the precipitate was not observed with 4% sodium thiosulfate and 70% isopropyl alcohol.
Neural Network Repair of Lossy Compression Artifacts in the September 2015 to March 2016 Duration of the MMS/FPI Data Set

During the September 2015 to March 2016 duration (sometimes referred to as Phase 1A) of the Magnetospheric Multiscale Mission, the Dual Electron Spectrometers (DES) were configured to generously utilize lossy compression. While this maximized the number of velocity distribution functions downlinked, it came at the expense of lost information content for a fraction of the frames. Following this period of lossy compression, the DES was reconfigured in a way that allowed for 95% of the frames to arrive to the ground without loss. Using this high‐quality set of frames from on‐orbit observations, we compressed and decompressed the frames on the ground to create a side‐by‐side record of the compression effect. This record was used to drive an optimization method that (a) derived basis functions capable of approximating the lossless sample space and with nonnegative coefficients and (b) fitted a function which maps the lossy frames to basis weights that recreate the frame without compression artifacts. This method is introduced and evaluated in this paper. Data users should expect a higher level of confidence in the absolute scale of density/temperature measurements and notice less sinusoidal bias in the velocity X and Y components (GSE)
The Impact of Low Carb-KETO Diets on CAD-Why more Research is needed

Coronary Artery Disease (CAD) is the result of multiple factors – many of which are now routinely tested for - which interact with each other and the patient to produce an inflammatory effect within the walls of the coronary arteries, impairing the ability of these arteries to increase coronary blood flow when needed. Fundamental to changes in these multiple factors as measured by blood tests, are the effect various diets have when consumed by people for an extended period of time. However, changes in these blood tests are poorly correlated with changes in CAD – limiting our current knowledge about the true effect these diets have on CAD. This paper takes a look at the only studies, which have looked at the impact of LowCarb-Ketogenic diets (LCKD) on these blood tests and corresponding changes in CAD.
DNA fingerprinting of water yam (Dioscorea alata) cultivars in Brazil based on microsatellite markers

This study aimed to fingerprint 36 water yam (Dioscorea alata) accessions using microsatellite markers. Ten accessions were collected in local markets from several municipalities in Brazil, eight were obtained from the 'Instituto Agronomico de Campinas' (IAC) germplasm collection and eighteen were collected directly from growers from Sao Paulo state. A total of nine microsatellite loci were used in the analysis. Loci revealed high polymorphism verified by elevated PIC values (0.57-0.77), and by high gene diversity and Shannon-Wiener indices (0.69 and 1.29 on average, respectively). The accessions were classified into two groups based on clustering analysis. One group contained mostly accessions from the IAC collection, including a commercial cultivar acquired in a market in the city of Cuiaba, Mato Grosso state. The second group was composed of most accessions, including those collected directly from growers and markets in Sao Paulo, a few accessions from the IAC collection, and an accession from Puerto Rico, named 'Florida', which is the most cultivated in Brazil. Several duplicates were identified in this study, including accessions obtained from two farmers in Mogi Guacu and Mogi Mirim, Sao Paulo state. However, some of these accessions were allocated in different sub-groups, within this second group. Results suggested the hypothesis of different origins for accessions currently cultivated in Brazil. Similar accessions obtained from different municipalities revealed the commercialization of the same accessions at different locations.
Cyclic Changes in Transpiration of Sunflower Leaves in a Steady Environment

Concurrent cyclic changes of leaf temperature, transpiration rate, and stomatal aperture were found to occur in plants of sunflower (Helianthus annuus L.) exposed to a steady aerial environment and with their roots in water. These cyclic changes were less regular with plants in drying soils and did not occur at all with plants in soils with a water potential less than —120 J kg-1. A sequence of possible events which lead to the repeated cycling is suggested; these involve relative changes in the turgor of epidermal and guard cells. The possibility that repeated cycling may be caused by a changing concentration of carbon dioxide in the sub-stomatal cavities is also discussed. The irregularity and eventual cessation of these cyclic changes are considered to be due to the reduction in turgor of the epidermal and guard cells as the availability of water to these cells is reduced.
Students’ Responses toward Scientific Argumentation with ADI Learning Model to Physics Literacy: A Case of Indonesian Senior High School Students

The aim of this study is to explore Indonesian students' responses towards scientific argumentation with ADI learning model to physics literacy by using survey study. The sample included 100 Indonesian senior high school students (47% male and 53% female) who were studying at public school in East Java province. The Responses towards Scientific Argumentation ADI Learning Model to Physics Literacy (RT-SAPL) questionnaire was developed with Indonesian language and validated through an exploratory factor analysis of participants' responses. For measuring the correlation among three dimensions of scale, the Pearson Correlation product moment was used. The findings indicated: the instrument used in this study had satisfactory validity and reliability. Meanwhile, the construct validities of the RT-SAPL were varying from . 617 and . 832 and extracting 70.655% of the variance with overall Cronbach's alpha constant was . 854. Moreover, the dimension of ADI learning model came in the first rank and followed by Scientific argumentation as well as the degree of responses towards scientific argumentation with ADI learning model to physics literacy. Finally, the findings have also indicated a significant relationship among factors of RT-SAPL.
Effects of self-pollination and cross-pollination of Vaccinium darrowii (Ericaceae) and other low-chill blueberries.

Partial to complete self-incompatibility is normal in most Vaccinium L. (Ericaceae) species. Wild blueberry plants of several Florida provenances and species were self- and cross-pollinated in a greenhouse free of pollinators. Fruit set of V. darrowii Camp (2x), V. corymbosum L. (4x), V. arboreum Marsh (2x), and F1 (V. darrowii · V. corymbosum) hybrids was higher after cross-pollination than after self-pollination. Partial to complete self-incompatibility was present in V. darrowii, V. corymbosum, and their tetraploid F1 hybrids. The three V. arboreum clones tested were fully self- incompatible. Intra- and interpopulation crosses in V. corymbosum, V. darrowii, and V. darrowii ·V. corymbosumhybrids were highly successful, and self-pollination reduced all fertility parameters. Advanced selections of V. corymbosum were the most self- compatible clones tested, possibly because self-compatibility has been increased by breeders selecting for reliable fruit set in large fields planted with one or a few clones. One southern highbush selection and two F1 hybrids had fruit set of more than 70% after self-pollination. These plants could be potentially used to breed plants that could be planted in single blocks providing reliable yield.
Salvage harvest planning for spruce budworm outbreak using multistage stochastic programming

Forest supply chain planning must deal with many natural disturbance uncertainties such as fires, insects, and windthrow. One important consideration is wood infestation by invasive insects, as it causes environmental and economic harm. An example of invasive insects in Eastern Canada is the spruce budworm (Choristoneura fumiferana (Clemens)), which is the most destructive insect in North America’s conifer stands. In 2017, more than 5 million ha of forest were defoliated by spruce budworm in Quebec. Repeated defoliation causes tree mortality, reduction of growth rates, and reduced lumber quality. Consequently, different wood qualities with greatly varied values are found in the forest. Changes in the outbreak intensity impact wood values throughout the forest. One of the common actions to mitigate the economic and environmental damages is salvage harvesting. However, because of the large uncertainties and lack of detailed information, it is a difficult problem to model. We propose a multistage stochastic mixed-integer programming model for harvest scheduling under various outbreak intensities. The objective is to maximize revenues of wood value minus logistic costs while satisfying demand for wood in the industry. The results show that when there is an outbreak throughout the forest, the priority for salvage harvesting is to focus on forest areas with the lowest level of infestation.
Food webs in tropical Australian streams: shredders are not scarce

1. Macroinvertebrates were collected in dry and wet seasons from riffles and pools in two streams in tropical north Queensland. Total biomass, abundance and species richness were higher in riffles than in pools but did not differ between streams or seasons. 2. Gut contents of all species were identified. Cluster analysis based on gut contents identified five dietary groups: I, generalist collectors; II, generalist shredders and generalist predators; III, generalist scrapers; IV, specialist shredders; and V, specialist predators. Species were allocated to functional feeding groups (FFGs) based on these dietary groups. 3. Many species were generalist in their diets, but specialist predators and shredders were particularly prominent components of the invertebrate assemblages in terms of biomass and species richness. 4. Community composition (proportions of biomass, abundance and species richness of the different FFGs) varied between habitat types, but not between streams or seasons, although differences between riffles and pools varied with season. 5. Comparison of the fauna of 20 streams showed that our study sites were similar to, or not atypical of, low-order streams in the Queensland wet tropics.
Neurodegeneration in Multiple Sclerosis: Relationship to Neurological Disability

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the CNS. Most MS patients follow a relapsing-remitting course (RR-MS) for 8 to 15 years that transforms into a secondary progressive disease course (SP-MS). In this review, we discuss current data that describe MS as a neurodegenerative disease in which axonal loss is the major cause of irreversible neurological disability in MS patients. Neurological deficits in MS patients have two pathogeneses: acute inflammatory demyelination and axonal degeneration. Disability caused by inflammatory demyelination clinically dominates the early stages of RR-MS and is reversible. Axonal transection occurs at sites of inflammation and begins at disease onset but is clinically silent in RR-MS because the CNS compensates for neuronal loss. Once a threshold of axon loss is ex ceeded, MS patients enter an irreversible secondary progressive stage. In SP-MS, axonal degeneration is caused by chronic demyelination and may be irreversibly progressive. This view of MS provides a concep tional framework that explains conversion of RR-MS to SP-MS and provides a rationale for early aggressive anti-inflammatory and neuroprotective therapies. NEUROSCIENTIST 5:48-57, 1999