Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating on relationship between effective quantum efficiency and irradiance

Abstract Models describing the relationship between effective quantum efficiency of PS II (ΦPSII) and irradiance (I) are routinely used to determine how irradiance influences effective quantum efficiency and photosynthetic electron transport rate (ETR). However, with no single model one can accurately describe the relationship between ΦPSII and I, and explain the interdependence between ΦPSII and biophysical properties of photosynthetic pigments, especially in plants growing under low level irradiances. Basing on the mechanistic model of photosynthetic electron transport rate we have developed the model of the relationship between ΦPSII and I. The new model reveals that ΦPSII increases with photochemistry (kP) and heat dissipation (kD). Furthermore, the values of key parameters calculated using the new model were compared with the values calculated with two other empirical models. The new model was perfectly fitted to the light-response curves of ΦPSII. The key calculated photosynthetic parameters: maximum ΦPSII, maximum ETR and their corresponding saturation irradiance were close to the measured values. In addition, our model associates ΦPSII with intrinsic features of photosynthetic pigments. We concluded that ΦPSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules. Highlight A model of the relationship between effective quantum efficiency of PS II (ΦPSII) and irradiance (I) has been developed. Using this new model it was found that ΦPSII decreased with increasing I due to the decrease in the effective absorption cross-section of photosynthetic pigments molecules. Abbreviations ETR Electron transport rate ETRmax Maximum electron transport rate F Steady-state fluorescence Fm′ Maximum fluorescence in the light Fv Variable fluorescence yield of the dark-adapted leaf gi Degeneration of energy level of photosynthetic pigment molecules in the ground state i gk Degeneration of energy level of photosynthetic pigment molecules in the excited state k I Irradiance NPQ Non-photochemical quenching N0 Total light-harvesting pigment molecules PARsat Saturation irradiance corresponding to ETRmax kP Rate of photochemical reaction kD Rate of non-radiative heat dissipation PS II Photosystem II ae Initial slope of light-response curve of electron transport rate α′ Fraction of light absorbed by PS II β′ Leaf absorptance ξ1 Probability of photochemistry ξ2 Probability of non-radiative heat dissipation ξ3 Probability of fluorescence σik Eigen-absorption cross-section of photosynthetic pigment from ground state i to excited state k due to light illumination Effective optical absorption cross-section of photosynthetic pigment molecule from ground state i to excited state k due to light illumination φ Exciton-use efficiency in PS II τ Average lifetime of the photosynthetic pigment molecules in the lowest excited state ΣPSII Effective quantum efficiency of PS II
Directional orientation of pheasant chicks at the drinking dish and its potential for research on avian magnetoreception

Abstract. Magnetoreception has been widely studied in birds mainly through the paradigm of homing or seasonally appropriate migratory direction. It was found that in total darkness or under selected light regimes (differing in colour and/or intensities), migratory birds display orientation towards certain “fixed” directions which do not correspond to the migratory or homing direction. This “fixed orientation” might correspond to the so-called magnetic alignment recorded in animals of different non-avian taxa. Here we demonstrate that also “common”, non-migratory birds, pheasants, adopt a preferred position and body orientation when drinking at a circular dish. We recorded these parameters by means of camera traps in a pheasantry under control conditions and under experimental exposure to bright blue light. We identified three types of orientation at the edge of drinking dish: standing radially or tangentially with left or right eye to the dish. The position of tangentially drinking chicks was significantly non-random. While the position of radially drinking chicks was random under control conditions, it became significantly non-random, concentrated at about the north and south pole of the dish, under bright blue light. Our results show that this alignment has some similarities with the “fixed orientation”. We suggest that the preference towards a “fixed” direction serves to calibration, organization and reading of the mental (cognitive) map of the space and as a direction indicator. We discuss heuristic potential of the presented research (experimental and evaluation) design for further study on magnetoreception.
The antioxidant activity of date seed: preliminary results of a preclinical in vivo study

Chronic diseases (diabetes, cardiovascular diseases and cancer), are by far the leading causes of mortality and morbidity worldwide. Oxidative stress is one of the underlying mechanism in the development and enhancement of chronic diseases. Polyphenols are particularly abundant in date seeds and can contribute in the progress of chronic diseases due to antioxidant properties. The present work studies the effects of date seeds and examines the oxidative stress status on serum and organs of Male Wistar rats after feeding them with basal diet comprising 0, 2, 4 or 8 g/kg date seed powder (DSP) for a period of 13 weeks. Isonitrogenous and isocaloric diets were subjected to all the four groups. Antioxidant status, protein and lipid oxidative biomarkers were measured in the serum and organs and histopathology was done. The results showed that DSP suggestively (P < 0.05) elevated the antioxidant defense system of the serum and organs. DSP decreased protein and lipid oxidative damages in the liver, muscle and brain. In addition, DSP did not alter the organs’ function based on the analysis of biochemical markers. The results indicate that oxidative stress-related diseases could be possibly prevented by the DSP bioactive antioxidants.
Rhythmic neural spiking and attentional sampling arising from cortical receptive field interactions

Growing evidence suggests that distributed spatial attention may invoke theta (3-9 Hz) rhythmic sampling processes. The neuronal basis of such attentional sampling is however not fully understood. Here we show using array recordings in visual cortical area V4 of two awake macaques that presenting separate visual stimuli to the excitatory center and suppressive surround of neuronal receptive fields elicits rhythmic multi-unit activity (MUA) at 3-6 Hz. This neuronal rhythm did not depend on small fixational eye movements. In the context of a distributed spatial attention task, during which the monkeys detected a spatially and temporally uncertain target, reaction times (RT) exhibited similar rhythmic fluctuations. RTs were fast or slow depending on the target occurrence during high or low MUA, resulting in rhythmic MUA-RT cross-correlations at at theta frequencies. These findings suggest that theta-rhythmic neuronal activity arises from competitive receptive field interactions and that this rhythm may subserve attentional sampling. Highlights Center-surround interactions induce theta-rhythmic MUA of visual cortex neurons The MUA rhythm does not depend on small fixational eye movements Reaction time fluctuations lock to the neuronal rhythm under distributed attention
Choise of Explant Material and Media for in vitro Callus Regeneration in Sultana Grape Cultivar (Vitis vinifera L.)

The study was carried out to choise of explant material and culture media for callus regeneration in ‘Sultana’ (Vitis vinifera L.). Leaf disc and node explants were the main explant materials which were taken from in vitro shoots which were obtained from macroshoot tip explants. The initial macroshoot tip were cultured on MS (Murashige and Skoog) medium including BAP (6-benzylaminopurine) (1 mg L-1) and in vitro shoots were subcultured on shoot multiplication medium with BAP (1 mg L-1) + IBA (Indole-3-butyric acid) (0.1 mg L-1) In order to investigate callus regeneration potential of Sultana grape cultivar, leaf disc explants were cultured on two different MS medium including BAP in combination with 2,4-D (2,4-dichlorophenoxyacetic acid) whereas node explants cultured on four different MS medium including BAP in combination with 2,4-D and NAA (naphthalene acetic acid). The intensity of callus proliferation was greater in leaf disc culture than in node culture. In all media combinations, MS medium including BAP (1 mg L-1) + 2,4-D (0.1 mg L-1) were found to be the most effective on callus regeneration. In this medium, callus regeneration rate was found to be 100% and the average diameter of callus was found to be 6.3 mm.
Susceptibility of Fraxinus angustifolia clones to Hymenoscyphus fraxineus in lowland Croatia

Nutrition status of the ash host could play an important role in resistance to the Hymenoscyphus fraxineus according to obtained preliminary results on three types of agar medium with leaf extracts from native Fraxinus species. Experiment revealed the fastest growth of the pathogen isolates on agar enriched with F. excelsior leaf extract, followed by the agar with F. ornus leaf extract, and the slowest growth was obtained on the agar with F. angustifolia leaf extracts. Study on narrow- leaved ash resistance to the pathogen revealed significant differences between nine tested clones, among which the clones BJ25, BJ38, NG03 and NG31 turned out to be the less susceptible to the H. fraxineus. Significant differences were obtained also between genotypes in clonal seed orchards for leaf unfolding parameter. Earlier leaf unfolding was obtained in clone NG03 which revealed smaller necrosis in inoculation experiment, while the clone NG55 revealed later leaf unfolding and longer necrosis lengths, leading to conclusion that phenology could play an important role in narrow-leaved ash clones' resistance to H. fraxineus.
Biochar as a growing media component for containerized production of Douglas-fir

In the inland northwestern United States (US), Douglas-fir artificial regeneration commonly includes growing seedlings in media containing sphagnum peat. Concerns over the sustainability of peat and rising plant production costs are initiating investigation of growing media alternatives. Biochar is a potential media amendment that has positive physical and chemical properties for seedling production, including high water and nutrient retention due to large surface area, which may reduce leaching losses and improve fertilizer use efficiency. We used different amounts of biochar to amend peat-based growing media to determine if seedling growth response to various fertilizer rates differed with biochar amendments. Every 13 weeks for 39 weeks, replicate seedlings were measured for photosynthetic activity, destructively harvested, and analyzed for leaf nitrogen concentration. Biochar did not reduce fertilizer rates required to grow equal-sized seedlings or improve seedling growth. When mixed with peat at rates.
Pollen Ontogeny in Ruppia (Alismatidae)

Premise of research. Plants of Ruppia exhibit hydrophily (water pollination). Transitions to hydrophily have been repeatedly accompanied by modifications to pollen characters. However, comprehensive investigations of pollen development in hydrophilous plants are limited, and most center on taxa that, unlike Ruppia, exhibit significant exine reduction. Investigating the consequences of the transition to water pollination for the pattern of pollen development in a comparative context will yield information about the lability of the pollen developmental pathway as well as the functional pollen traits required for successful water pollination. Methodology. Inflorescences of Ruppia maritima were field collected and anthers prepared for microscopy. Anthers and developing pollen grains at the sporogenous, microspore mother cell, tetrad, free microspore, and mature grain stages were studied using combined LM, SEM, and TEM. Pivotal results. A thin but distinct callose special wall surrounds Ruppia tetrads, and portions are often shared by adjacent tetrads. Divergence in exine development between the proximal and distal walls occurs during the free microspore stage, resulting in heteropolar pollen grains with a reduced exine on much of the distal surface. There are no major ultrastructure differences in the endexine or intine between the proximal and distal surfaces. On the proximal surface, muri that comprise the reticulum consist of a solid ridge of sporopollenin, with no infratectal columellae. We show, unequivocally, that a distinct foot layer surrounds the entire microspore. Tapetal cells invade the anther locule before meiosis, and this timing supports the close relationship of Ruppiaceae and Cymodoceaea. Ruppia is confirmed to have tricellular pollen at the time of dispersal. Conclusions. Modifications to the pollen developmental program involving both timing and location of developmental events have given rise to traits that are hypothesized to be adaptive for water pollination.
Risk factors associated with Parkinson’s disease: An 11-year population-based South Korean study

Objective To validate various known risk factors of Parkinsonism and to establish basic information to formulate public health policy by using a 10-year follow-up cohort model. Methods This population based nation-wide study was performed using the National Health Insurance Database of reimbursement claims of the Health Insurance Review and Assessment Service of South Korea data on regular health check-ups in 2003 and 2004, with 10 years’ follow-up. Results We identified 7,746 patients with Parkinsonism. Old age, hypertension, diabetes, depression, anxiety, taking statin medication, high body mass index, non-smoking, non-alcohol drinking, and low socioeconomic status were each associated with an increase in the risk of Parkinsonism (fully adjusted Cox proportional hazards model: hazard ratio (HR) 1.259, 95% confidence interval (CI) 1.194–1.328 for hypertension, HR 1.255, 95% CI 1.186–1.329 for diabetes, HR 1.554, 95% CI 1.664–1.965 for depression, HR 1.808, 95% CI 1.462–1.652 for anxiety, and HR 1.157, 95% CI 1.072–1.250 for taking statin medication). Conclusions In our study, old age, depression, anxiety, and a non-smoker status were found to be risk factors of Parkinsonism, in agreement with previous studies. However, sex, hypertension, diabetes, taking statin medication, non-drinking of Alcohol, and lower socioeconomic status have not been described as risk factors in previous studies and need further verification in future studies.
Nutrient Composition of Whole Green Frogs, Rana clamitans and Southern Toads, Bufo terrestris

ABSTRACT Whole prey samples of green frogs, Rana clamitans, and southern toads, Bufo terrestris, were analyzed for proximate composition (moisture, lipid, protein, ash), fat-soluble vitamins A and E, and selected minerals. The green frogs (n=7) were obtained from a pond in Cold Springs Harbor, NY in August 1996. The southern toads (n=5) were collected in July 1996 on St. Catherine's Island, GA. Water (77.5 ± 1.3 vs. 71.8 ± 2.9, %) and crude protein (71.2 ± 3.3 vs. 61.0 ± 1.2, % DM) percentages were significantly higher in frogs than in toads; all other proximate constituents were similar. Vitamin A was extremely variable, but averaged approximately 29,000 IU/kg DM (both species), while vitamin E in frogs was significantly lower (82.2 ± 1 5 .6 IU/kg DM) than in toads (369.3 ± 169.0 IU/kg DM). Frogs contained extremely high magnesium levels (2.5 ± 0.1 %DM) that may be considered excessive and affect mineral nutrition. Frogs also contained significantly higher values of calcium and sodium than toads. Copper,.
Expression of Xyloglucanase (AaXEG2) in Open-field-grown Poplars

The transgenic expression of Aspergillus aculeatus xyloglucanase with 35S promoter, which has been maintained in greenhouse-grown transgenic poplars for 10 years, was assessed to determine their expression level in open-field-grown poplars. This level was slightly decreased in the poplars grown in fertile soil for four years, and there were proportionatel y decreased levels of xyloglucanase activity among their tissues, in which the shoots exhibited slightly lower specific activities than was observed in the leaves and roots. Xyloglucan content was greatly decreased in the walls of the tissues in the transgenic lines, although the degradation levels of xyloglucan were slightly lower for the poplars grown in fertile soil than for those grown in non-fertile soil. The results showed that the level of expression, together with xyloglucan degradation in their walls, was decreased for the poplars grown in fertile soil.
Molecular phylogenetics and new (infra)generic classification to alleviate polyphyly in tribe Hydrangeeae (Cornales: Hydrangeaceae)

Tribe Hydrangeeae of Hydrangeaceae currently contains nine morphologically diverse genera, many of which are well-known garden ornamentals. Previous studies have shown eight of these genera to be phylogenetically nested within Hydrangea, rendering the latter polyphyletic. To clarify the phylogeny of tribe Hydrangeeae, the present study sequenced four chloroplast regions and ITS for an extensive set of taxa, including the type for all nine genera involved. The resulting phylogenetic hypotheses corroborate the polyphyly of Hydrangea. Since polyphyletic taxa are deemed unacceptable by both sides in the ongoing debate concerning the adherence to strict monophyly in biological classifications, a new (infra)generic classification for tribe Hydrangeeae is proposed. In order to create a stable, evolutionary informative classification a broader circumscription of the genus Hydrangea is proposed, to include all eight satellite genera of the tribe. Such treatment is considered highly preferable to an alternative where Hydrangea is to be split into several morphologically potentially unidentifiable genera. To facilitate the acceptance of the new classification proposed here, and in order to create a classification with high information content, the familiar generic names were maintained as section names where possible.
Chemical compositions and antioxidant capacity of by-products generated during the apricot kernels processing

ABSTRACT The compositions and antioxidant capacity were investigated about the by-products (blanching water concentrate (BWC) and debitterizing water concentrate DWC) produced during the industrial processing of apricot kernels, to evaluate the by-products’ potential utilization. The results indicate that the by-products contain a great number of compounds like amygdalin, protein, phenolics, and flavonoids. Among them, the amygdalin has the highest content both in BWC and DWC, which is 33.48 ± 0.04 and 23.89 ± 0.03 (g/100 g dry base weight), respectively. Furthermore, the by-products exert good antioxidant functions including the higher reducing power and radical-scavenging capacity on the 2,2-Diphenyl-1-Picrylhydrazyl (DPPH) and hydroxyl radicals, which is mainly attributed to the phenolic compounds, not the highest content of amygdalin by the principal component analysis and verification test of DPPH radical-scavenging capacity. In conclusion, the by-products definitely have great potential for utilization and should be recycled from the wastewater in the apricot kernels processing industry, especially for amygdalin.
Upscaling biodiversity: Estimating the species-area relationship from small samples

The challenge of biodiversity upscaling, estimating the species richness of a large area from scattered local surveys within it, has attracted increasing interest in recent years, producing a wide range of competing approaches. Such methods, if successful, could have important applications to multi‐scale biodiversity estimation and monitoring. Here we test 19 techniques using a high quality plant data set: the GB Countryside Survey 1999, detailed surveys of a stratified random sample of British landscapes. In addition to the full data set, a set of geographical and statistical subsets was created, allowing each method to be tested on multiple data sets with different characteristics. The predictions of the models were tested against the “true” species–area relationship for British plants, derived from contemporaneously surveyed national atlas data. This represents a far more ambitious test than is usually employed, requiring 5–10 orders of magnitude in upscaling. The methods differed greatly in their performance; while there are 2,326 focal plant taxa recorded in the focal region, up‐scaled species richness estimates ranged from 62 to 11,593. Several models provided reasonably reliable results across the 16 test data sets: the Shen and He and the Ulrich and Ollik models provided the most robust estimates of total species richness, with the former generally providing estimates within 10% of the true value. The methods tested proved less accurate at estimating the shape of the species–area relationship (SAR) as a whole; the best single method was Hui's Occupancy Rank Curve approach, which erred on average by <20%. A hybrid method combining a total species richness estimate (from the Shen and He model) with a downscaling approach (the Sizling model) proved more accurate in predicting the SAR (mean relative error 15.5%) than any of the pure upscaling approaches tested. There remains substantial room for improvement in upscaling methods, but our results suggest that several existing methods have a high potential for practical application to estimating species richness at coarse spatial scales. The methods should greatly facilitate biodiversity estimation in poorly studied taxa and regions, and the monitoring of biodiversity change at multiple spatial scales.
Madagopsina gen. n. and Gracilopsina gen. n. (Diptera: Diopsidae) from Madagascar with description of four new species

Madagopsina gen. n. and Gracilopsina gen. n. are described as endemic Diopsidae taxa for Madagascar. Three Madagascan Diopsidae, earlier alternately placed in Diopsis , Eurydiopsis or Cyrtodiopsis (also as Teleopsis ), are now referred to Madagopsina gen. n. , while two of these three species proved to be conspecific. This gives rise to Madagopsina apollo (Brunetti) comb. n. and Madagopsina apographica (Seguy) comb. n. = anjahanaribei (Vanschuytbroeck) syn. n. The two species are redescribed. Madagopsina apographica proved to have a mixed type series. Three new species are allocated to the genus as Madagopsina freidbergi sp. n. , Madagopsina parvapollina sp. n. and Madagopsina tschirnhausi sp. n. For Eurydiopsis vadoni Vanschuytbroeck (later also placed in Cyrtodiopsis and Teleopsis ) the genus Gracilopsina gen. n. is erected, leading to Gracilopsina vadoni (Vanschuytbroeck) comb. n. Gracilopsina vadoni is redescribed and is shown to have a mixed type series. One new species is allocated to the genus as Gracilopsina sinespina sp. n. A key is presented to the two genera and seven species. Madagascar now counts five Diopsidae genera and 12 species, of which two genera and 11 species are endemic. The genus Cladodiopsis is no longer an endemic Madagascar genus as it also occurs in the Comoros. The phylogenetic position of Madagopsina gen. n. is discussed based on molecular data. The intra- and intergeneric phylogeny of both new genera is discussed based on morphology and geometric morphometrics analyses of wing shape. Data are presented on sexual dimorphism with respect to eye span in the genera. The resulting allometric lines (eye span/body length) are also included in the phylogenetic analysis. The allometric lines for the closely related M. parvapollina sp. n. , and the much larger M. apollo are compared and discussed. Allometric slopes and intercepts are identical for females of both species, while in males allometric slopes are identical, but intercepts differ considerably. An identical phenomenon was found in two closely related East African Diopsis species with a small and a large species. Various morphological characters, including eggs, are discussed. The importance of intersternite 1–2 and synsternum 7+8 as differential characters is indicated.