Miracle-dz/UniFAR-FTUs huggingface dataset:
Photoperiodism and rhythmic response to light

Abstract. Seedlings of Pharhitis nil show a circadian rhythm in the capacity to flower in response to the timing of a second red light pulse given at various times after a first saturating exposure to red when this is given together with a benzyladeninc spray. There are also changes in the photon irradiance required for half maximum response to the second red pulse. The photochemical properties of phytochrome in the photoperiodically sensitive cotyledons were also shown to change rhythmically. Oscillations in both pr→ Pfr and Pfr→ Pr photoconversion characteristics persisted over at least two circadian cycles with a periodicity of about 12 h. There were, however, no significant oscillations in either Pfr peak absorbance or in Δ(ΔA). The changes in sensitivity for the photoconversion of Pr→ Pfr did not parallel the much larger changes in sensitivity of the flowering response to red light. The amplitude of the Pr→ Pfr rhythm was at least as great as that for Pr→ Pfr, but the flowering response to far-red light was not rhythmic, nor was there any large change in sensitivity. The changes in photoconversion properties may reflect a basic biochemical oscillation which affects both photoreceptor properties and sensitivity to photoreceptor input. There was also a marked rhythm in the Pfr/P ratio that would be established by a saturating pulse of red light and this too may have affected the flowering response to such a pulse. Far-red light inhibited flowering when given at any time during the inductive night. After 14 h in darkness, Pfr could still be measured in the cotyledons and it was concluded that far-red light inhibited flowering by removing Pfr As red light also inhibited flowering at this time, there may be two pools of phytochrome with different kinetic properties.
Spring diet of ringed seals (Phoca hispida) from northwestern Spitsbergen, Norway

Complete gastro-intestinal tracts (GITs) from 267 ringed seals from five different locations in Spitsbergen were collected during spring of the years 2002 –2004. Diet was assessed based on hard part remains from prey. Invertebrates constituted ,2% of all prey (relative frequency, Ni). Fish otoliths were found in all seals; 1.7, 34.3, and 64.0% of the recovered otoliths were found in the stomach, small and large intestines, respectively, emphasizing the importance of analysing the whole GIT, not only the stomach. Otoliths from stomachs and small intestines with minimal signs of erosion were measured to back-calculate pre-ingested prey size and biomass. Based on measured polar cod (Boreogadus saida) otoliths (n ¼ 7007), the ringed seals fed on fish in the length range 44.4 – 229.2 mm, primarily consuming the youngest year classes. Adult females ate smaller polar cod more often than adult males or juveniles. Polar cod dominated the diet, with a frequency of occurrence (FO) of 100%, Ni of 71.9%, and a biomass contribution of 77.2%. The taxon Stichaeidae was the second most frequent prey type (FO ¼ 55.6%) followed by Cottidae (FO ¼ 35.6%). The diet of ringed seals from one locality markedly differed from the others, with a greater species diversity, low Ni of polar cod (15%), and a dominance of Stichaeidae (Ni ¼ 67%). Location of sampling, as well as sex and age of the seals, had significant influences on ringed seal diet in spring.
Tensor-to-scalar ratio forecasts for extended LiteBIRD frequency configurations

LiteBIRD is a planned JAXA-led CMB B-mode satellite experiment aiming for launch in the late 2020s, with a primary goal of detecting the imprint of primordial inflationary gravitational waves. Its current baseline focal-plane configuration includes 15 frequency bands between 40 and 402 GHz, fulfilling the mission requirements to detect the amplitude of gravitational waves with the total uncertainty on the tensor-to-scalar ratio, $\delta r$, down to $\delta r<0.001$. A key aspect of this performance is accurate astrophysical component separation, and the ability to remove polarized thermal dust emission is particularly important. In this paper we note that the CMB frequency spectrum falls off nearly exponentially above 300 GHz relative to the thermal dust SED, and a relatively minor high frequency extension can therefore result in even lower uncertainties and better model reconstructions. Specifically, we compare the baseline design with five extended configurations, while varying the underlying dust modeling, in each of which the HFT (High-Frequency Telescope) frequency range is shifted logarithmically towards higher frequencies, with an upper cutoff ranging between 400 and 600 GHz. In each case, we measure the tensor-to-scalar ratio $r$ uncertainty and bias using both parametric and minimum-variance component-separation algorithms. When the thermal dust sky model includes a spatially varying spectral index and temperature, we find that the statistical uncertainty on $r$ after foreground cleaning may be reduced by as much as 30--50 % by extending the upper limit of the frequency range from 400 to 600 GHz, with most of the improvement already gained at 500 GHz. We also note that a broader frequency range leads to better ability to discriminate between models through higher $\chi^2$ sensitivity. (abridged)
Studying the effective brain connectivity using multiregression dynamic models

Bartlett M. , Cussens J. (2013). Advances in Bayesian network learning using integer programming. In Proceedings of the 29th Conference on Uncertainty in Artificial Intelligence (UAI 2013). AUAI Press. To appear. vector of time-varying intercept and connectivity parameters; Ft(r) are the “regressors” at time t, a vector comprised of the value 1 (for the intercept) and values of data for the parent nodes of region r at the current time t. Note that state space models do not assume nonstationarity, though when state covariance Wt(r) = 0 for all t and r, the usual static regression model is obtained. When Wt(r) is unknown, it can be defined via a scalar discount factor (DF), such that a DF=1 produces a static model. The conditional forecast distribution of Yt(r) given the past up to time t-1 at its parents is a Student t distribution, and thus the joint log predictive likelihood (LPL) can be calculated as the sum of this distribution over nodes. Figure 2 (bottom) illustrates a 3-node DAG MDM, considering region 1 as the parent of region 2 and region 3; and region 2 as the parent of region 3. The orange ovals represent the (time-varying) effective connectivity strength between two regions, the purple ovals the intercepts, and the blue circles the observation noise.
The buffering constituents of herbage and of silage

The buffering capacity values of several herbage species and of silage made from this herbage, and the contributions of plant constituents to this buffering, between pH 4 and 6, were determined, and found to vary with the herbage species; values in the silages were normally two to three times greater than those in the plant materials. The anion fraction of the plant materials accounted for 68–80% of the total buffering capacity, and for 73–88% in the silages. Buffering caused by plant proteins was estimated to be 10–20% of the total buffering capacity. The buffering capacity of wilted red clover (Trifolium pratense) was 18% lower than that of fresh red clover, and the total organic acid content of wilted clover was also lower than that in fresh clover. The organic acids were responsible for most of the buffering effect in herbages and silages. In Italian ryegrass (Lolium multiflorum), the main buffers were malate and citrate, but, in red clover, glycerate and malate were the main buffers. The clovers studied contained a high level of glycerate (4% of dry matter). During ensilage, malate, citrate and glycerate were extensively broken down. The increased buffering capacity during ensilage was caused mainly by the formation of lactates and acetates.
An Early Weaning Calf Program: Summarization and Review

Abstract Experimental data over 3 yr encompassing 277 calves raised under an early weaning program at the Purina Research Farm were summarized. Thirty other recently published experiments also were reviewed briefly for comparison. Calves in this report averaged 49.2 kg body weight during a 28-day preweaning period following 3 days on colostrum. Daily averages were . 42 kg intake of dry milk replacer, . 47 kg intake of calf starter, . 32 kg gain in body weight, 136 g estimated intake of digestible protein, and 3.17 Mcal estimated intake of digestible energy. Intake of calf starter accounted for 65% of variation in total gain of body weight. Estimates of digestible nutrient intake accounted for 88% of variation in final metabolic body weight. Calves on milk replacers containing poorer quality protein consumed less calf starter and gained less. Estimates of intake of digestible protein and digestible energy and their average ratio of 43.0 are reviewed relative to studies in which requirements were investigated.
GENETIC TRANSFORMATION OF Bar GENE AND ITS INHERITANCE AND SEGREGATION BEHAVIOR IN THE RESULTANT TRANSGENIC COTTON GERMPLASM (BR001)

The Agrobacterium-mediated genetic transformation technique in cotton using two genotype independent approaches were exploited. The segregation and inheritance of the Bar gene as well as various agronomic and fiber quality traits of the resultant transgenic cotton germplasm (BR001) and its background germplasm (Coker 312) were also studied. PCR and Southern blot analyses showed successful integration of the foreign gene in case of both approaches. Although the transformation efficiency of shoot apex culture method was higher than Pollen Tube Pathway via ovarian injection method, the number of plants developed in the soils was almost the same. Moreover, the Mendelian inheritance and segregation studies confirmed that a single nuclear dominant gene governed the herbicide resistance characters in BR001. The present study suggests that both genotype independent approaches can be utilized in order to save time as well as to avoid chimeras.
Tannin content in acorns (Quercus spp.) from Poland

Oak acorns used to be an important human food, up until recent times. The major factor inhibiting their use in modern nutrition is their high tannin content. Polish oak trees were screened in order to find out whether there are any major geographical or interspecific differences in tannin and total phenolic contents in acorns, which might help us to establish further directions in the search for low-tannin individuals. We studied the level of phenolic compounds using the standard Polish and European Pharmacopoeia method, with Folin-Ciocalteu reagent and hide powder. Altogether 49 acorn samples of Quercus robur, 13 of Q. petraea, 1 of Q. pubescens (all native) and 12 of Q. rubra (introduced) were collected in different regions of Poland. The amount of investigated phenolics in Q. robur and Q. petraea acorns was similar, and tannins constituted the main component. The Q. pubescens sample was distinguished by the lowest tannin and total phenolic content and a relatively high amount of non-tannin phenolics. Q. rubra had a slightly lower tannin content than Q. robur and Q. petraea acorns, but the level of other phenolics was much higher. The results for Q. robur suggest geographical variability of phenolic content as well as a relationship between the phytochemical and biometric parameters of oak acorns. Additional key words: polyphenols, oak acorns, phytochemistry, food security Addresses: Ł. Łuczaj, University of Rzeszów, Institute of Applied Biotechnology and Basic Sciences, Department of Botany, Werynia 502, 36-100 Kolbuszowa, Poland, e-mail: lukasz.luczaj@interia.pl A. Adamczak, Institute of Natural Fibres and Medicinal Plants, Department of Botany, Breeding and Agricultural Technology, Kolejowa 2, 62-064 Plewiska near Poznań, Poland M. Duda, University of Rzeszów, Institute of Applied Biotechnology and Basic Sciences, Department of Botany, Werynia 502, 36-100 Kolbuszowa, Poland
Investigating the amino acid digestibility of alternative protein sources and determining the impact of dietary fiber on energy, nitrogen, and amino acid digestibility in growing pigs

Cotten, Bradley M. M.S., Purdue University, May 2015. Investigating the amino acid digestibility of alternative protein sources and determining the impact of dietary fiber on energy, nitrogen, and amino acid digestibility in growing pigs. Major Professor: Olayiwola Adeola. Three experiments were designed to quantify the nitrogen (N) and amino acid (AA) digestibility of various protein sources fed to growing pigs. The protein ingredients were sunflower meal, cottonseed meal, canola meal, camelina meal, egg albumen, casein, blood meal, plasma meal, potato protein concentrate, soy protein concentrate, soy protein isolate, and linseed meal, which were fed as the sole source of amino acids for the animals and were included in semi-purified, corn starch-based diets. A semipurified, nitrogen-free diet (NFD) was used to estimate endogenous losses of AA. In each experiment, pigs were surgically fitted with a simple T-cannula at the distal ileum and fed four experimental diets and the NFD based on a 5 X 2 crossover arrangement in a randomized crossover design, with 5 diets and 2 periods. For experiment 1 (Exp. 1), sunflower meal, cottonseed meal, canola meal, and camelina meal were fed to 19, 42-kg barrows to determine the apparent (AID) and standardized (AID) digestibility of AA at the terminal ileum. The AID and SID of N and all AA were greatest for sunflower meal (P < 0.05), and canola meal had similar AID and SID of N, Met, Thr, Leu, and Val. The AID and SID of all essential AA, except for Met and Trp, was lower in camelina meal
Seedling recruitment in semi-natural pastures: the effects of disturbance, seed size, phenology and seed bank

We examined recruitment patterns in semi-natural pastures and their relationships to disturbance and species composition at different spatial scales (0.01 m2 up to 4 m2) of both the vegetation and the seed bank. Possible associations between seedling recruitment and phenology were also studied. The study was performed in four pastures with different management history. Seedling recruitment was generally enhanced by disturbance, with the greatest effect for small-seeded species that germinate in the autumn. The local species-pool contributed to a large extent to seedling recruitment; 83 % of the recruited species were found in the vegetation, whereas 44 % of the recruited species were found in the seed bank. There were a total of 88 species found in the vegetation at different spatial scales; 61 % were recorded at the smallest spatial scale (0.01 m2). The area sampled at this scale comprised 1.25% of the area examined, indicating a small scale structuring of diversity in the pastures. The species number in the vegetation varied between 7 and 14 for the smallest scale (0.01 m2), and between 23 and 42 for the largest scale (4 m2), in the four pastures. The species number in the seed bank was less variable. Like most studies of perennial grasslands, we found no close correspondence between species distribution in the vegetation and in the seed bank. Two of the pastures had a joint management history and exhibited a close similarity of species in the seed bank, despite that one of the pastures was abandoned already in the beginning of this century.
Plasmid and chromosomally encoded luminescence marker systems for detection of Pseudomonas fluorescens in soil

Luminescent strains of Pseudomonas fluorescens 10586 were constructed in which luciferase production was constitutive by introduction of Vibrio fischeri luxABE genes on the chromosome and on a multicopy plasmid. Light production in liquid batch culture was directly proportional to biomass concentration during exponential growth and enabled detection by luminometry of 1.7 × 103 and 8.9 × 104 cells/ml for the plasmid and chromosomally marked strains, respectively. Luminescent colonies of both strains were detectable by eye, enabling viable cell enumeration on solid media against a background of non‐luminescent strains. Following inoculation into sterile and non‐sterile soil lower levels of detection were increased but detection of 8.1–59 × 103and 2.2–30 × 103 cells per g of soil was possible for plasmid and chromosomally marked strains. Maximum specific growth rate in liquid culture was unaffected by introduction of lux marker genes on the chromosome, but was reduced in the plasmid marked strain. The chromosomally encoded marker was stable in both liquid culture and in soil, but the plasmid was unstable during continuous subculturing in liquid medium and during growth in soil. The chromosomally encoded luminescence‐marker system therefore provides a convenient, non‐extractive technique for quantification of genetically modified soil microbial inocula.
Three decades of vegetation changes in peatlands isolated in an agricultural landscape

Questions What vegetation changes occurred over three decades on two large temperate peatlands (1115 ha) isolated in an agricultural landscape and affected by a human-ignited fire? Location Southwest Quebec, Canada. Methods In 2012, we revisited 103 plots first sampled in 1984–85. Changes in species composition were evaluated using the Sorensen dissimilarity index, in species frequency with Chi-square goodness-of-fit tests, and in species cover using one-sample t-tests. Tree encroachment was evaluated using aerial photographs and satellite imagery. We used linear discriminant analyses (LDA) and ANOVA to evaluate the impact of tree encroachment on species composition. Results We found a floristic dissimilarity of 35% between 1984 and 1985 and 2012. Most species whose frequency and mean cover increased were peatland species, while most species with lower frequency and mean cover in 2012 were non-peatland species. The total area occupied by forest increased from 26% to 51%, an overall gain of 280 ha of forest. The species composition of old and new forests as well as of open sectors was highly distinct, as shown by the LDA that correctly assigned 97% of the sampling plots to these groups. Non-peatland species were 15 and five times more abundant than peatland species in old and new forests than open habitats, respectively. Conclusions Gradual drying of the peatland margins due to drainage of the surrounding catchment, as well as post-fire succession are likely the main drivers of the changes observed. Overall, our study showed that peatlands isolated in an anthropogenic landscape are dynamic ecosystems where vegetation communities can experience substantial changes in a short time frame. The broader implication is that peatland conservation in highly modified landscapes must be linked to restoration.
Ultrastructural Study of the Development of Pleistophora schubergi Zwölfer, 1927 (Protozoa, Microsporida) in Larvae of the Spruce Budworm, Choristoneura fumiferana and Its Subsequent Taxonomic Change to the Genus Endoreticulatus

This study demonstrates that Pleistophora schubergi Zwolfer, 1927, a microsporidium originally isolated from the midgut epithelium of Nygmia phaeorrhoea Don (Euproctis chrysorrhoea L.) and Porthetria dispar L. , and subsequently reported in several other insects including the spruce budworm, Choristoneura fumiferana (the host used in this investigation), does not belong in the genus Pleistophora Gurley, 1893. Pleistophora schubergi lacks the major features that are characteristic of Pleistophora typicalis, the type species of this genus. A comparison of ultrastructural observations reported for the type species of the genus Pleistophora, P. typicalis, and our observations of P. schubergi revealed significant differences. A thick (0.5 μm) amorphous coat, derived from parasite secretions and deposited external to the parasite plasmalemma, surrounds all developmental stages in P. typicalis. Double membranes, derived from host rough endoplasmic reticulum cisternae encircle the parasite plasmalemma of all developmental stages in P. schubergi. The sporophorous vesicle encases the spores in P. typicalis, and originates from the parasite-secreted coat that is present around meronts. In P. schubergi, the host endoplasmic reticulum cisternae form the envelope that surrounds the meronts. Moreover, the sporophorous vesicle envelope in P. typicalis persists around groups of spores, while in P. schubergi this envelope breaks easily to release the spores in the host cytoplasm. By comparing the characteristics of the microsporidium found in the spruce budworm with those of the recently created polysporous genera that sporulate within a vesicle, we found that P. schubergi does belong in the new genus Endoreticulatus Brooks et al. 1988, and consequently rename it Endoreticulatus schubergi (Zwolfer, 1927) n. comb.
MINI‐REVIEW: Habitat analogues for reconciliation ecology in urban and industrial environments

Summary 1. Current views of anthropogenic environments emphasize the extreme novelty of urban and industrial ecosystems. Proponents of reconciliation ecology argue that we need to use such habitats to conserve biodiversity, given the inadequacy of natural reserve systems. 2. Some of the harshest anthropogenic ecosystems may be able to support indigenous biodiversity due to their structural or functional resemblance to natural ecosystems, habitats, or microsites that may be present in the region but not part of the historic ecosystem on a particular site. Here we review recent work that evaluates similarities between urban and industrial ecosystems and natural analogues, and explore the potential for these in reconciliation ecology. 3. We find that artificial habitats represent a gradient of ecological novelty which may be independent of the degree of human influence. While hard-surfaced habitats such as walls and quarries are the most investigated artificial analogues (of natural rock pavements and cliffs), there are many other examples spanning a range of habitats in both terrestrial and marine settings. Analogous ecosystems may be present in the region but limits to dispersal can prevent appropriate species from reaching urban or industrial sites, and small differences in abiotic conditions can sometimes prevent colonization by native biota in otherwise similar artificial habitats. We suggest that a search for habitat analogues represents an important principle to guide reconciliation ecology in urban and industrial lands. In constrast, analogous ecosystems may also support pest species that exploit the similarities between anthropogenic habitats and their ancestral habitats. 4. Synthesis and applications. Identifying analogous habitats and ecosystems could enhance biodiversity conservation and ecosystem services in anthropogenic environments. Abiotic and biotic differences between artificial analogues and natural systems can be frequently overcome by ecological engineering to make the environment more suitable for native biodiversity, and ⁄ or assisted dispersal to allow suitable native organisms to reach appropriate sites within artificial ecosystems. Altering some habitats to become less analogous may help reduce impacts of pest species in urban and industrial areas.