Miracle-dz/UniFAR-FTUs huggingface dataset:
Diurnal variation in thigmotropic inhibition of stem elongation

Wind, touching, and/or mechanical stress can restrict stem elongation. Removal of the registration of the growth retardant daminozide for use on edible crops increased interest in thigmotropic inhibition of stem elongation to control plant height in greenhouse crops, as well as a general desire by growers to decrease chemical inputs for fl oriculture crops. Since stem elongation varies diurnally, the question arises as to whether wind inhibition of stem elongation varies over a 24-hour period. Tomato (Lycopersicon esculentum) ‘MoneyMaker’ and cosmos (Cosmos bipinnatus) ‘Imperial Pink’ seedlings were placed under each of 10 wind perturbation treatments [applied for different durations and at different times during a 24-hour period; wind speed (perpendicular to the media) at seedling level was 30 km·h–1 (18.6 mph)] for 30 days. Data were collected on plant height and leaf number on days 1 and 30. The effect of wind on stem elongation differed with species; wind treatments restricted stem elongation more on cosmos than tomato (53% and 20%, respectively, across treatments). Tomato elongation was most restricted when seedlings received wind all day, all night, or all day and night. Within short-term treatments, internode length was least when tomato seedlings received a mid-day wind treatment. Cosmos elongation was most restricted when seedlings received a wind treatment all day or all night. Within shortterm treatments, cosmos internode elongation was most restricted with earlyand mid-day wind treatments. Data here suggest wind effects on elongation vary diurnally. In addition, the magnitude of wind effects on
Persistence of southern flying squirrel winter aggregations: roles of kinship, familiarity, and intruder squirrels

Abstract Southern flying squirrels (Glaucomys volans) are seasonally gregarious and rely on the thermoregulatory benefits of well-constructed nests and presence of nest mates to survive harsh winter conditions. Prior work has shown that kinship components are important to how winter aggregations form in captivity and that relatedness between individuals is higher than expected in undisturbed populations examined in the field. Over the course of 2 falls, 2006 and 2007, we created related and unrelated groups in a laboratory colony at Wake Forest University. We presented each group type with related and unrelated individuals as intruders. Once formed, aggregations persisted when presented with an intruder squirrel. Squirrels from existing aggregations were found in the same nest box 98% of the time. Factors of relatedness and familiarity were crucial in determining whether the intruder was accepted into an existing aggregation or nested alone. We found that related groups were more tolerant of truly novel (unrelated unfamiliar) intruders and more likely to incorporate them into the aggregation than were unrelated groups. Unrelated groups never accepted unrelated unfamiliar intruders in 2006, whereas some were accepted in 2007 due to increased colony-wide familiarity. Acceptance of intruders was dependent on relatedness. Intruders were more likely to be found in an aggregation when either the existing group was composed of kin or the intruder was related to at least one group member. We also found effects of familiarity of individuals on the choice of nest mates.
The Staphylococci: A Postgenomic View

Staphylococci that can cause disease in humans are Staphylococcus aureus, S. epidermidis, S. haemolyticus, S. saprophyticus, S. hominis, S. warneri, S. lugdunensis, S. schleiferi subsp. schleiferi, S. capitis subsp. ureolyticus, and S. simulans. This chapter briefly discusses the often complex biology of the organism before the genomic insights determined from the sequence. One of the most valuable tools that can arise from whole genome sequences are whole-genome microarrays. A study on core variable genes revealed new information about the S. aureus genome and its evolution. S. haemolyticus are generally more resistant to antiobiotics than other staphylococci, and it could be that they accumulate more of these genes than other species. As the methods for classifying strains into dominant types become more widespread, further epidemiological patterns and associations between certain lineages, toxins, and the infections they cause are being considered. Unlike the genomic islands in other staphylococci that are often associated with virulence, the arginine catabolism mobile element (ACME) island is associated with drug resistance. Each of the sequenced staphylococcal genomes carries genes common to all other sequenced staphylococci, genes specific to particular species, genes specific to particular lineages, and mobile genetic elements (MGEs).
The potential for increasing the concentrations of micro-nutrients relevant to human nutrition in meat, milk and eggs

SUMMARY A possible outcome of policies designed to reduce obesity in the human population and to mitigate greenhouse gas (GHG) emissions may be a decrease in human consumption of livestock products. However, livestock products currently make substantial contributions to intakes of specific micro-nutrients. Therefore, the present review examines the potential for increasing micro-nutrient concentrations of milk, muscle meats and eggs by nutritional and genetic means. Of the trace elements, copper (Cu), iron (Fe) and zinc (Zn) concentrations were largely resistant to manipulation by dietary means, but iodine (I) and selenium (Se) could be readily manipulated. Similarly, while α-tocopherol concentrations were readily manipulated, responses to dietary supplementation with retinol, folate and cobalamin were lower and riboflavin was resistant to dietary manipulation. There were differences between products in the ease with which composition could be manipulated: egg concentrations were most responsive followed by milk and muscle meats. However, livestock products with increased micro-nutrients concentrations can supply a substantial proportion of the daily reference nutrient intake.
NF-κB elements associated with the Stat6 site in the germline γ1 immunoglobulin promoter are not necessary for the transcriptional response to CD40 ligand

Both germline transcription and switch recombination of heavy chain genes are likely to be regulated by cis elements binding transcription factors in the promoter regions of germline immunoglobulin genes. To identify cis-acting elements important in germline transcription of the murine c1 heavy chain gene, we have used a transgenic approach. Seventeen kb c1 immunoglobulin transgenes with mutations in three NF-jB sites in the c1 proximal promoter, a putative CD40 response element, are expressed well. Compared to wild-type transgenes, there is no deficiency in the expression of the transgenes with mutations of the three NF-jB sites after induction of splenic B cells with IL-4 alone, CD40L, or CD40L 1 IL-4. There may be a small reduction in the response of these mutant transgenes after induction with LPS 1 IL-4. We also prepared transgenes that were truncated at 2150 (rather than 22100) and therefore included the wild-type Stat6 binding site at 2123 and the three wild-type NF-jB sites. Nevertheless, c1 germline transcripts were not expressed from these transgenes. We conclude that the three proximal NF-jB sites are dispensable for expression of c1 germline transcripts under most conditions. However, cis-acting elements distal to 2150 must be critical to this transcription.
Simulating Aggregation Algorithms for Empirical Verification of Resilient and Adaptive Federated Learning

Federated learning (FL) environments are dynamic: Users are recruited to participate, may drop out of participation, may vary in their availability and speed, and may suffer bandwidth variations. As such, production environments demand a resilient and adaptive design. Insisting on synchronous FL, with potentially millions or hundreds of thousands of clients, will lead to various issues—bursts in processing and communication loads, complicated procedures to handle laggards, and special protocols to manage client failures.In this paper, we focus on asynchronous, adaptive, and resilient operating environments for FL. We develop a simulation scheme and a set of associated aggregation algorithms as a method for investigating the soundness of asynchronous and adaptive system designs and operational principles. Our simulation model can capture the statistical impact of FL clients’ intermittent operations. We also propose an aggregation algorithm usable when clients’ participation and refresh rates vary. We suggest an approach for identifying valid and adaptive operating configurations including those that can be used to trade-off computational load and convergence speeds in FL programs.
Photobiosynthetic Opportunity and Ability for UV-B Generated Vitamin D Synthesis in Free-Living House Geckos (Hemidactylus turcicus) and Texas Spiny Lizards (Sceloporus olivaceous)

Abstract The opportunity and ability to photobiosynthesize vitamin D3 by exposing skin to ultraviolet-B (UVB) irradiation from the sun was compared using the nocturnal/crepuscular Mediterranean House Gecko Hemidactylus turcicus and the diurnal Texas Spiny Lizard Sceloporus olivaceous. Texas spiny lizards had a greater opportunity for photobiosynthetic production of vitamin D3 than geckos. This was revealed by vitamin D3 photoproduct production in models (ampoules containing an alcohol solution of vitamin D3 precursor) placed at locations inhabited by free-living lizards at similar times of occupancy. Alternatively, geckos seemed able to maximize their limited photobiosynthetic opportunity with a higher rate of conversion of provitamin D3 to photoproducts. This was revealed by photoproduct conversion in patches of lizard skin exposed to ultraviolet lamps in the laboratory. Stomach-content analysis showed the spiny lizards to have dietary sources of vitamin D3, the geckos may or may not. This is the first documentation that mostly nocturnal geckos may rely on photobiosynthesis of vitamin D3 and that they might have a more sensitive mechanism than diurnal lizards to compensate for their limited exposure to natural UVB radiation. Future studies should investigate sexual, seasonal, age, and species differences in photobiosynthetic opportunity and ability.
Antibacterial activity of leaf extracts of Tridax procumbens against Xanthomonas campestris pv. mangiferaeindicae

Mango bacterial canker disease (MBCD) caused by Xanthomonas campestris pv. mangiferaeindicae (Xcmi) is one of the important diseases of mango affecting a number of commercial cultivars. The pathogen affects different plant parts like leaf, stem and fruit. Favorable environmental conditions cause severe loss to the crop. Leaf extract of various plants were tested against Xcmi; out of them, antibacterial activity of leaf extract of Tridax procumbens was studied against 25 strains of Xcmi collected from different parts of Marathwada region of Maharashtra. The in vitro studies have been performed by using cup-plate method to examine the activity. Fresh leaf extracts of T. procumbens plants was used for the antibacterial assay. The maximum activity was recorded against Xcmi.15 (Mean activity zone – 22.09 mm) followed by Xcmi.16 (Mean activity zone – 21.68 mm) and minimum against Xcmi.07 (Mean activity zone – 18.04 mm) strain under investigation. The ultimate aim of the research work was to develop economically and technically viable field formulations for the farmers, which will be Bio-ecologically compatible for management of plant bacterial diseases.
Aquatic fulvic acids in algal‐rich antarctic ponds

We isolated fulvic acids from two antarctic coastal ponds by means of preparative scale column chromatography with XAD-8 resin. Both ponds are on Ross Island. Pony Lake at Cape Royds has abundant phytoplankton populations, and Feather Pond at Cape Bird has a luxuriant benthic algal mat. Neither site has higher plants in the watershed. The dissolved organic carbon (DOC) concentration in Pony Lake was very high, but the percentage of DOC accounted for by fulvic acid was low, as has been observed for other lakes with algal-derived DOC sources. Fulvic acid from Pony Lake was more enriched in nitrogen than fulvic acid from Feather Pond, with a C: N atomic ratio of 13 in Pony Lake and a C: N ratio of 24 in Feather Pond. The [ 13 C] NMR spectra for the coastal pond samples showed that the content of sp 2 -hybridized carbon atoms (aromatic or olefinic) was only 16.5% of the total spectral area for Pony Lake and only 20.1% for Feather Pond
Ecology, nutrition, and timing of reproductive events in an Asian primate, the Hanuman langur (Presbytis entellus)

Ecological conditions, feeding and ranging behaviour as well as physical condition of female Hanuman langurs (Presbytis entellus) were studied in order to analyse the major influences on the timing of reproductive events. The langurs inhabited a semi-evergreen forest dominated by Sal trees (Skorea robusta). The climate was dominated by the summer monsoon lasting from May to September. Availability of plant phytophases was markedly seasonal, with fruiting as well as flushing of the six main food plants during the monsoon. Feeding and ranging behaviour of the females varied with food availability and its distribution. High dietary quality was only obtained during a short period from May to July. Physical condition of the females varied in accordance with dietary quality and energy expenditure, with a good physical condition during the second half of the year. Births occurred from January until June, with most births around the energetically worst period of the year. The results indicate that, in contrast to several other non-human primates, most females of this population gave birth too early to meet the optimum lactation requirements. Complete weaning mainly took place during an energetically bad time of the year (October to December). However, it can be inferred that the reduction of suckling bouts prior to the next conception took place when high quality food was available. Conceptions were confined to the months of July to November, coinciding with the time of best physical condition. Moreover, females who conceived were in a better physical condition than those who failed to conceive, suggesting a primary influence of nutrition on the probability of conception. Seasonality and timing of births may be the result of a regular seasonal shortfall of resources influencing the ability of the females to ovulate and to conceive.
Nematode assemblages in banana (Musa acuminata) monocultures and banana plantations with Juçara palms (Euterpe edulis) in the southern Mata Atlântica, Brazil

Summary – The composition of the nematode fauna at two different agrosystems (banana monocultures and mixed banana-palmito plantations) was investigated at six study sites on the coastal plain of southern Brazil. Nematode abundance was higher and the number of families was lower (25 compared to 33) in the soil of banana monocultures. The assemblages in the soil of the banana monocultures were dominated by bacterial feeders and plant parasites, whereas in the soil of the mixed plantations the proportion of the other trophic groups was higher. In the monocultures, the percentage of families categorised as colonisers (c-p 1 families) was higher and the persisters lower. The difference in the assemblage of c-p groups was significant between sites of the two different systems. Principal component analysis (PCA) ordination of the samples by nematode family composition showed site-specific assemblages, similarity between two sites of each system and significant dissimilarities between the two systems. The MI 1-5 and the MI 2-5 were lower in the banana monocultures. Additionally, the MI 2-5 of banana site B2 was significantly higher than that of the two other banana sites. The ratio F/B was higher and the ratio (F + B)/plant feeders was lower in the banana-palmito plantations. The differences between the systems in nearly all measured parameters indicate a higher degree of disturbance and nutrient enrichment of the soil under monocultures. However, a low number of plant parasites and dominance of c-p 3 taxa at both agroecosystems show that the soil of both agroecosystems seems to be of an advanced successional stage. This may be a result of a less intensive ‘organic’ cultivation without the use of plant protection products and fertilisers and with additional non-host plants. Despite many non-controlled variables in the smallholder systems, according to the results the nematodes can be regarded as suitable indicators of soil disturbance in banana and banana-palmito agro-ecosystems.
Resistance of cereals to aphids: Interaction between hydroxamic acids and the aphid Sitobion avenae (Homoptera: Aphididae)

SUMMARY The hydroxamic acids in the seedlings of four varieties of winter wheat were extracted initially in boiling methanol in order to avoid enzymatic hydrolysis. The increase in numbers of aphids on these varieties of wheat were recorded. HPLC analysis of hydroxamic acids in the extracts showed the presence of DIMBOA-glucoside, DIMBOA-aglucone and its benzoxazolinone (MBOA). There was a highly significant negative correlation between the concentration of DIMBOA-aglucone in the seedlings and aphid performance. However, the association between aphid performance and DIMBOA-aglucone in the tips of the seedlings was weaker. In general aphid infestation of wheat seedlings slightly increased the concentration of all the hydroxamic acid derivatives. Moreover, aphids ingested hydroxamic acids and were able to detoxify some of the DIMBOA-aglucone they ingested.
DNA Mechanics and Transcriptional Regulation in the E. coli lac operon

Many gene regulatory motifs in both prokaryotes and eukaryotes involve physical manipulations of the genetic material, often on length scales short enough that the mechanical properties of the DNA significantly impact gene expression. One class of such manipulations, called “action at a distance”, includes transcription factor-mediated DNA looping, in which a binding site some distance away on the DNA is brought into close proximity with the transcription machinery at the promoter. DNA looping is a key component of several important regulatory systems in bacteria, and is crucial to the combinatorial control that is common at eukaryotic promoters regulated by more transcription factors than can physically bind adjacent to the promoter. Here we use a prototypical DNA looping protein, the Lac repressor from E. coli, to explore questions regarding the role of DNA mechanics in DNA looping and combinatorial control, particularly concerning the role of sequence flexibility in short-length-scale looping. We combine a statistical mechanical model of looping by the Lac repressor with a single-molecule technique called tethered particle motion that allows us to quantify this looping, and the systematic tuning of four biologically relevant and experimentally tractable parameters: loop length, loop sequence, repressor-DNA affinity, and repressor concentration. We show that this combination is a powerful approach to measuring repressor-DNA binding affinities and sequence-dependent DNA flexibilities in a way that is orthogonal, and therefore complementary, to conventional ensemble assays. Our results show that the sequence dependence to looping is more complicated than has been observed in other contexts, suggesting that “sequence flexibility” as a general term is misleading, and, we argue, that the measurement of sequence flexibilities depend more strongly than previously appreciated on the shape of the deformation used to make the measurement. Finally, we present preliminary results with a more complicated system that is a case study for broader issues in combinatorial control, and a new hidden Markov model approach, based on variational Bayesian inference, to analyze these more complicated systems, which we hope will allow more precise dissections of, and more robust extraction of kinetic parameters from, tethered particle motion assays.
Emerging issues of HT-2 and T-2 toxins in European cereal production

HT-2 and T-2 toxins are two of the most potent trichothecenes; they have a combined (HT-2+T-2) temporary Tolerable Daily Intake (TDI) of 0.06 µg/kg body weight/day. The distribution of HT-2 and T-2 appears to be largely restricted to Europe. Of the cereal species, HT-2 and T-2 usually have higher incidences and concentrations on oats followed by barley and then wheat, however, this can vary between countries. Survey data from Nordic countries have indicated that these mycotoxins have increased in recent years, reaching concentrations of >1000 µg/kg HT-2+T-2 in some samples. HT-2 and T-2 have also been detected in malting barley in France, and in particular in spring sown varieties. A newly identified species, Fusarium langsethiae, has been implicated as a producer of HT-2 and T-2 in European cereals. There is limited data available regarding this species' pathogenicity and mycotoxin production. The impact of agronomy on the concentration of HT-2 and T-2 in cereals has not been clearly identified, but it i.
Transgenic technologies for enhanced molecular breeding of white clover (Trifolium repens L.)

Abstract. White clover is an important pasture legume of temperate regions, generally through co-cultivation with a pasture grass in a mixed-sward setting. White clover provides herbage with high nutritional quality to grazing animals, along with the environmental benefit of biological nitrogen fixation. Several key agronomic traits are amenable to modification in white clover through use of transgenic technology. Efficient methods for Agrobacterium-mediated transformation of white clover have been developed. The current status of transgenic research is reviewed for the following traits: resistance to viruses and insect pests; aluminium tolerance and phosphorus acquisition efficiency; control of leaf senescence and seed yield; biosynthesis of flavonoids and rumen bypass proteins for bloat safety and enhanced ruminant nutrition; cyanogenesis; and drought tolerance. Future prospects for transgenic technology in molecular breeding in white clover are also discussed.
The involvement of the transpirational bypass flow in sodium uptake by high‐ and low‐sodium‐transporting lines of rice developed through intravarietal selection

We report the characterization of high- and low-sodium-transporting lines developed by intravarietal selection within a cultivar, IR36, of rice (Oryza sativa L.). The purpose was to investigate the mechanistic basis of sodium uptake in material in which differences in salt uptake could be isolated from the many other morphological and physiological characteristics that affect the phenotypic expression of salt tolerance. The lines differed in mean sodium transport by a factor of 2. They differed in vigour and water use efficiency, which are characters that modify the effects of salt transport, by only 12% or 13%. The lines did not differ significantly in other physiological traits that are components of salt resistance: compartmentalization at the leaf and cellular levels. There was a strong correlation between the transport of sodium and a tracer for apoplastic pathways (trisodium, 3-hydroxy-5,8,10-pyrene trisulphonic acid, PTS) in both lines. The regression coefficient for sodium transport on PTS transport was the same in both lines. The individual variation in PTS transport was similar to that in sodium transport, and the variation in the transport of both was very much greater than the variation in any other character studied. The high-sodium-transporting line took up proportionately more PTS than the low-sodium-transporting line. It is concluded that the transpirational bypass flow is of major importance in sodium uptake by rice and that selection for differences in sodium transport has been brought about by selection for heritable differences in the bypass flow.