Miracle-dz/UniFAR-FTUs huggingface dataset:
Promoter Decoding of Transcription Factor Translocation Dynamics

Many cellular signaling pathways exhibit a bowtie topology: multiple distinct signal inputs converge on a single master transcription factor, which controls the expression of downstream genes. Recent evidence suggests that information about signal inputs can be encoded by regulating the activation dynamics of the master transcription factor. However, it was unclear whether this is sufficient to obtain specificity in gene expression, such that each input induces a specific set of output genes. Using the budding yeast transcription factor Msn2 as a model system, we address this question. We systematically dissect how different promoters decode transcription factor translocation dynamics in single cells (Chapter 2). We find that promoters fall into four main classes depending on the threshold of signal required for activation and on the timescale of activation. Furthermore, we provide insight into the mechanistic basis for promoter class. We show that it is possible to differentially control expression of the different promoter classes by control of Msn2 dynamics. We find that slow promoters exhibit dramatically higher noise in gene expression, but are able to filter out Msn2 oscillations. This highlights a general trade-off: for promoters, implementing a high-pass temporal filter comes at the cost of much higher noise in gene expression. Applying tools from information theory and focusing on gene expression, we rigorously quantify the limits on information transduction through regulation of Msn2 dynamics (Chapter 3). Although we find that the amount of information transduced by Msn2 to target genes is only sufficient for reliable binary decisions, information transduction can be improved by
Observations on the effect of environmental temperature and environment at moult on the heat production and energy requirements of hens and cockerels of a White Leghorn strain

SUMMARY The heat production of hens and cockerels of a White Leghorn strain (‘H & N’) was measured after acclimation to environmental temperatures of 16, 23, 27 and 33 °C. No difference in fasting heat production was found between 16 and 23 °C for well-feathered hens in the first few months after moult though there were substantial reductions at 27 °C and above. Both hens and cockerels showed a trend of increasing net availability of metabolizable energy with increasing environmental temperature though this was non-significant. There were significant reductions between 16 and 27 °C in the metabolizable energy requirements for maintenance for both sexes. Results are also given for the heat production of laying hens exposed to short daylight periods and high or low environmental temperatures. Although the mean fasting heat production of the high-temperature group was greater, the difference was not statistically significant.
Symbiotic characteristics of Rhizobium meliloti: and appraisal of the systematic treatment of nodulation and nitrogen fixation interactions between hosts and Rhizobia of diverse origins

The symbiotic properties of 42 isolates of Rhizobium meliloti collected from widely separated sites in the upper basin of the Darling River were tested in bacteriologically controlled culture with 18 species and varieties of Medicago, three species of Melilotus, and one species of Trigonella. Seven strains of Rh. Meliloti of commercial interest were included in the experiments for comparative purposes. Nodule formation occurred on all plants in 889 out of 974 symbiotic combinations examined. Only Medicago laciniata (L.) Mill, among the hosts and the isolate from M. laciniata among the rhizobia exhibited distinctive nodule formation behaviour. Nitrogen fixation occurred in 637 combinations. On the basis of nitrogen fixation, eight groups of Rh. Meliloti were recognized; there were nine host groups. The groups could be arranged in an interlocking pattern of increasing host and bacterial specificity. These results, which modified to a small degree the bacterial and host groupings previously reported, strongly suggested that the pattern will be widely applicable to Rh. meliloti of diverse origin. In general, the isolates examined were promiscuous and 24 were capable of effective symbioses in association with 10 or more of the hosts. M. laciniata, Trigonella suavissima Lindl. , and Medicago rugosa Desr. were the hosts most highly strain-specific in their requirements for nitrogen fixation, and Medicago sativa L. was the most promiscuous. A system for classifying host species into compatibility groups is proposed.
Caffeine content variation in single green Arabica coffee seeds

Abstract Coffea arabica L. is highly homozygotic and caffeine content in most cultivars is reported to be similar (approximately 1%). The caffeine content was analysed using individual seeds of cultivars Catuaí Vermelho, Mundo Novo and Bourbon Vermelho, and varieties Mokka and Laurina of C. arabica. Seeds were cut transversely in half, a thin slice from each was extracted in a mixture of chloroform and methanol, and caffeine was measured by high performance liquid chromatography. The extraction procedure was validated by comparison with two conventional methods less suited for analysing large numbers of seeds. The results revealed an unexpectedly large variation [Catuaí Vermelho: 3.72–25.9 mg g− 1 (seeds); Mundo Novo: 5.06–18.59 mg g− 1; Bourbon Vermelho: 6.76–16.59 mg g− 1] even in types naturally low in caffeine such as Laurina (1.17–9.97 mg g− 1) and Mokka (2.01–9.64 mg g− 1). The mean values for all cultivars were always in the range of the caffeine content found in the literature. Several studies showed that C. arabica has approximately 10% cross-pollination, but the variation observed in caffeine content in individual seeds was too large to be explained by cross-pollination.
FAKTOR PENENTU SIKAP KONSUMEN UNTUK BERBELANJA DARING MELALUI MARKETPLACE

The purpose of this study is to examine the effect of perceived benefit, perceived website quality and online trust to attitude toward online shopping. This study used a purposive sampling technique that was only consumers who have made purchases online through a marketplace that can be a respondent. The number of respondents who filled out the research questionnaire and which can be processed were 130 respondents. From testing multiple linear regression shows that perceived benefit, perceived website quality and online trust have a significant positive effect on attitude toward online shopping, where attitude is one determinant ofn person's behavior.
Genetic approaches in plant physiology

summary The use of genetics in plant biology aims at the physiological and molecular genetical characterization of the phenotypic variation for the trait under study. Efficient mutant and gene isolation procedures have been developed for a number of plant models such as Arabidopsis thaliana. For this, the map position of the genes and insertion mutagenesis are used. The latter also allows the characterization of genes that are not easily recognized in mutant approaches, by using enhancer or gene-trapping procedures and reverse genetics. In addition to mutants, natural variation present among wild and cultivated varieties of a species provides an important source of genetic variation. The use of molecular markers, advanced mapping populations and specific cytogenetic stocks in case of polyploids, enables a detailed characterization of such natural variation even when it is of a quantitative and polygenic nature. Examples of the various genetic approaches are given.
Development and Fecundity of Deraeocoris nebulosus (Heteroptera: Miridae) on Bemisia argentifolii (Homoptera: Aleyrodidae)

The developmental and reproductive biology of the native predaceous mirid Deraeocoris nebulosus was studied in the laboratory using immatures of the whitefly Bemisia argentifolii as prey. Nymphs were kept individually in ventilated Petri dishes and provided with a constant supply of prey colonized on excised sweet potato leaves rooted in hydroponic solution and kept at 27C. Females were kept similarly and daily egg production was recorded. There were five nymphal instars. Mean development from first instar to adult was 13.3 d; there were no significant differences in development rate between the sexes. After a 3-d preoviposition period, females produced about 10-14 eggs per day for nearly 20 days before oviposition rate declined with age. Females lived an average of 32.8 d (range 3-58 d), and mean fecundity was 242.3 eggs per female (range 0-392).
Phenotypic plasticity in a maternal trait in red deer

Summary 1. Phenotypic plasticity and microevolution represent the two processes by which phenotypic traits in a population can track environmental change. While there is a growing literature documenting microevolution in reproductive traits in naturally occurring animal populations, few studies to date have examined either between-individual variation in levels of plasticity or how selection acts on plasticity. 2. We present here mixed-effect linear models analysing changes in calving date in relation to autumn rainfall observed over a 30-year study of 2147 red deer on the Isle of Rum, Scotland. The study period is characterized by a phase of low and rising population density (up to and including 1980), followed by a phase of high and fluctuating population density (1981 to present). 3. Variation within individual females explained a population-level trend of delayed calving dates following years of high autumn rainfall. There was significant variation between females both in their average calving dates and in their individual plastic responses of calving date to autumn rainfall. 4. Females born in the low population density phase were, on average, phenotypically plastic for the calving date‐autumn rainfall relationship, and showed significant variation in plasticity. Selection favoured individuals with early average calving dates among these females. 5. Among females born at high population density, there was on average no significant plasticity for calving date, but variation in plastic responses was still present. Selection favoured females with increasingly positive plastic responses of calving date to autumn rainfall. 6. We argue that early experience of high population density affects the physiological condition of females, making an environmental response (calving early following dry autumns) in later life physiologically untenable for all but a few high quality individuals. These same few individuals also tend to be fitter and have higher reproductive success.
Efeitos diretos e indiretos e correlações canônicas para caracteres relacionados com a produção de pimentão

O trabalho foi realizado com os seguintes objetivos: (a) estudar os efeitos diretos e indiretos de oito caracteres de planta e fruto sobre a producao de pimentao (Capsicum annuum L.), utilizando-se de analise de trilha, e (b) obter as correlacoes canonicas entre o grupo dos principais fatores de producao (peso(5) e numero total de frutos) e os grupos: (1) producao precoce-numero de frutos e producao precoce-peso de frutos; (2) comprimento, largura e numero de loculos do fruto, e (3) comprimento e largura do fruto. Empregaram-se seis genotipos de pimentao e os hibridos possiveis entre eles, obtidos mediante esquema dialelico, excluindo-se os reciprocos. Os resultados mostraram que as avaliacoes da producao de pimentao podem ser feitas nas primeiras colheitas, em vista do efeito pronunciado do carater producao precoce-peso de frutos sobre o peso total de frutos, e da significância das correlacoes canonicas entre producao precoce-numero e peso de frutos e peso total de frutos. O numero total de frutos foi o carater que apresentou maior efeito positivo sobre o peso total de frutos. Menor largura e maior numero de loculos por fruto determinaram maior peso total de frutos.
Time‐Place Learning by Garden Warblers (Sylvia borin): Route or Map?

1 Garden warblers are able to learn to go to four different feeding places at different times of day (time-place learning). We investigated whether or not the birds rely on a fixed route by preventing them from entering one of the places at the normal time (blocking experiments). At the end of the blocking period the birds were allowed to visit any of the four feeding places. 2 In two such blocking experiments, one in which the blocking period was first thing in the morning (from 06.00–10.00 h), the other in which it was later in the day (from 12.00–16.00 h), there was no subsequent shift in the phase of visiting the places during the rest of the day, apart from a tendency to go to the first place of the day after the morning block. These results suggest that the birds do not rely on following a fixed route, but instead use a time-place map.
A high mountain population of the ring-tailed lemur Lemur catta on the Andringitra Massif, Madagascar

The ring-tailed lemur Lemur catta is generally considered to be a species of dry deciduous forest, gallery forest and spiny thorn scrub at relatively low altitudes. During a survey of the summit zone of the Andringitra Massif, one of the most climatically extreme areas on Madagascar, we recorded this species above the tree-line at 2520 m in an area composed mostly of exposed rock, low ericoid bush and subalpine vegetation. Information was collected on food plants consumed by this species. This pelage coloration of the local population of L. catta differed from museum specimens and photographs taken from other areas of this species's range. The taxonomic status of the Andringitra population is in need of further study.
N availability and mechanisms of N conservation in deciduous and semideciduous tropical forest legume trees

Prior to abscission, nutrients are redeployed from leaves and redistributed to other parts of the plant. Data comparing nutrient resorption to soil fertility and leaf life span remains controversial in the literature. We compared nitrogen (N) conservation mechanisms among four legume trees with different leaf life spans (Hymenaea courbaril L. var. stilbocarpa (Hayne) Lee et Lang. , Lonchocarpus guilleminianus (Tul.) Malme, Enterolobium contortisiliquum (Vell.) Morong and Peltophorum dubium (Spreng.) Taub. ), from a semideciduous tropical forest, remnant of the Atlantic Forest. We hypothesized that these mechanisms differ among the four species and are affected by their leaf life span and by the availability of N, both as a mineral in the soil and, in the case of L. guilleminianus and E. contortisiliquum, from symbiotic nitrogen fixation (SNF), as these species form associations with rhizobia. The plants were grown in a greenhouse using pots filled with forest soil, enriched (50 or 100 mg of NH4NO3 plant-1week-1) or not with nitrogen. H. courbaril, a semideciduous tree, without SNF, and with the highest leaf life span, presented the greatest N-resorption efficiency (NRE), N-resorption proficiency (NRP) and N-use efficiency (NUE). Increase in soil N and the presence of symbiotic N fixation led to a decrease in NRE, NRP and NUE.
Analysis of Tester Lines for Rice (Oryza sativa L.) Heading-time Genes Using Reciprocal Photoperiodic Transfer Treatments

Abstract Sixteen heading-time tester lines of rice ( Oryza sativa L.) for the E1 , E2 , E3 , Se1 , Ef1 and U loci were subjected to transfer treatments from short (10 h) to long photoperiods (24 h) and vice versa at various times after sowing. Based on heading response, the 16 lines were classified into four groups, which corresponded well to the genotype at the Se1 , Ef1 and E1 loci. Using an analytical model, we estimated seven parameters for the three pre-flowering developmental phases of each line, the basic vegetative phase (BVP), the subsequent photoperiod-sensitive phase (PSP), and the post photoperiod-sensitive phase until heading (PPP). The Se1 locus had an extremely large effect on PSP and large effects on BVP and PPP; Ef1 had a large effect on BVP and a considerable effect on PPP; and E1 had a considerable effect on PSP, although effects were modified by non-allelic interactions at these three loci. The effects of three other loci were almost negligible. Thus the Se1 , Ef1 and E1 loci play principal roles in determining the heading time of rice, which is further diversified not only by the action of genes of other heading-time loci but also by non-allelic interactions. Based on these results, causal genetic pathways to flowering (heading) in rice are proposed.
Audio Surveillance System(ASS): Merging of Acoustic Events Recognition and Classification through Deep Learning

Despite the widespread use of Closed-Circuit TV for security purposes, CCTVs still include several weak points that can affect the quality of the provided surveillance services. Scientists and engineers are taking advantage of the continuous advancements in computer science by utilizing technology to improve acoustic recognition & classification approaches with the most efficient manners but at the cost of higher complexities. In this research, we focused on overcoming missing data paired with the use of existent surveillance approaches by adding acoustic surveillance features. We propose a low-complexity fully optimized algorithm that combines acoustic’s recognition and classification algorithms. The proposed Audio Surveillance System (ASS) algorithm uses acoustic input which is then processed through the algorithm using the employed deep learning approaches to extract irregular patterns and classify them into appropriate categories to be used as a surveillance input.
Interrelationships between plant growth regulators and fruit tree mineral nutrition.

Information is presented for fruit trees to show the effect of applied growth substances on mineral uptake and tissue mineral levels. The effects of nutrient supply to the roots on hormone synthesis and levels in the plant are also considered. The data are discussed in terms of a direct effect of applied growth substances on the actual nutrient absorption occurring in the roots, and of an indirect influence occurring via growth effects induced by growth substances which weaken or strengthen sink demand and consequently affect mineral nutrition. In a few cases, the evidence for a direct effect on mineral uptake by the root is quite sound, but most experiments are inconclusive with respect to the explanation of the observed phenomena.
Sources of shared variability in meat weight distribution and conformation in Pekin ducklings

A factor analysis with a varimax rotation was applied to ten highly intercorrelated carcass meatiness and conformation traits on 96 Pekin ducks to disclose the main sources of shared variability, deduce the factors that describe meat distribution and conformation and predict total carcass meat from orthogonal meatiness and conformation traits. Meat weight distribution and conformation appeared to be controlled by common and unique factors. The communalties for meati- ness traits ranged from 0.542 for neck meat to 0.870 for breast meat and those for conformation traits ranged from 0.555 for breast width to 0.717 for shank length and the uniqueness (special size factors) made the balance. Findings indicated that most of the common variability (68.4 %) in meat weight distribution and conformation could be accounted for by factors representing breast, length and wing meat factors. The first and third independent meatiness and conformation traits derived from factor analysis accounted for 73.8 % of the variation in total carcass meat. (© Elsevier / Inra)
Responses of soil respiration to elevated CO2, air warming, and changing soil water availability in a model old‐field grassland

Responses of soil respiration to atmospheric and climatic change will have profound impacts on ecosystem and global carbon (C) cycling in the future. This study was conducted to examine effects on soil respiration of the concurrent driving factors of elevated atmospheric CO2 concentration, air warming, and changing precipitation in a constructed old‐field grassland in eastern Tennessee, USA. Model ecosystems of seven old‐field species were established in open‐top chambers and treated with factorial combinations of ambient or elevated (+300 ppm) CO2 concentration, ambient or elevated (+3 °C) air temperature, and high or low soil moisture content. During the 19‐month experimental period from June 2003 to December 2004, higher CO2 concentration and soil water availability significantly increased mean soil respiration by 35.8% and 15.7%, respectively. The effects of air warming on soil respiration varied seasonally from small reductions to significant increases to no response, and there was no significant main effect. In the wet side of elevated CO2 chambers, air warming consistently caused increases in soil respiration, whereas in the other three combinations of CO2 and water treatments, warming tended to decrease soil respiration over the growing season but increase it over the winter. There were no interactive effects on soil respiration among any two or three treatment factors irrespective of time period. Treatment‐induced changes in soil temperature and moisture together explained 49%, 44%, and 56% of the seasonal variations of soil respiration responses to elevated CO2, air warming, and changing precipitation, respectively. Additional indirect effects of seasonal dynamics and responses of plant growth on C substrate supply were indicated. Given the importance of indirect effects of the forcing factors and plant community dynamics on soil temperature, moisture, and C substrate, soil respiration response to climatic warming should not be represented in models as a simple temperature response function, and a more mechanistic representation including vegetation dynamics and substrate supply is needed.