Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular determination of sex-ratio in Yellowhammer Emberiza citrinella offspring

Theory predicts skewed offspring sex-ratios in a range of situations in which the economics of producing the two sexes differ. Offspring sex-ratio skews in birds are relatively scarcely observed compared to other taxa. This could be because avian molecular sexing techniques, which allow young birds to be sexed, have only recently become available. Alternatively, birds may be largely constrained from adaptively manipulating the sex-ratio of their offspring. We used a recently-developed molecular sexing technique for birds to sex 420 Yellowhammer Emberiza citrinella offspring from 168 clutches found in Oxfordshire. Clutch sex-ratio of the population did not depart from the expected binomial distribution, and there was no variation in clutch sex-ratio with laying date, breeding attempt, or a variety of habitat variables which were predicted to differentially affect the survival and future reproductive success of offspring of the two sexes. There was no difference in size or growth rate of the sexes and nestling mortality was not sex-biased. Hence, although we can identify possible advantages of manipulating the sex-ratio in this species, it seems not to be used as a breeding strategy. Given the lack of consistent evidence for skewed avian offspring sex-ratios, more experimental work is required to determine whether, and how, birds may adaptively manipulate their offspring sex-ratio.
Ultrastructure of the frontal gland in Prorhinotermes simplex (Isoptera: Rhinotermitidae) and quantity of the defensive substance

The frontal gland as a sac-like organ in Prorhinotermes simplex is present only in presoldiers, soldiers, and imagoes, but exists also in nymph-soldier intercastes. The secretory epithelium consists of a single type of secretory cells adhering directly to the cuticular intima. Secretory vacuoles originate in electron dense vesicles, which are transformed into large electron lucent vacuoles. Intermediate vacuoles frequently contain lipid droplets. The frontal gland cells in presoldiers reveal modifications connected with the production of a new cuticle; the new cuticle is thin and compact, whereas the old one is thick, porous, and wrinkled. None of these cuticles is present in soldiers (sic! ). In soldiers, the cuticular intima is of endocuticular origin and is formed by dispersed dense material; the apical parts of secretory cells are formed by numerous irregular finger-like projections, true microvilli are completely lacking. In imagoes, the cuticle is composed of an epicuticle, a layer of epicuticular filaments, and one more basal layer; sexual differences were not observed. In nymph-soldier intercastes, the structure of the gland differs in the head and in the metathorax; the head part of the gland resembles the imaginal gland whereas the thoracic part resembles more that of the soldier; the development of secretory vacuoles stops at the stage of presence of lipid droplets. E-1-nitropentadecene was found in the highest amount in soldiers (comparable to P. inopinatus soldiers), in moderate amount in imagoes, and it is missing in both presoldiers and intercastes.
Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments

We used two large-scale metabarcoding datasets to evaluate phylogenetic signals at global marine and regional terrestrial scales using co-occurrence and co-exclusion networks. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance and the significance of observed patterns relating networks and phylogenies were evaluated against two null models. In all datasets, we found that phylogenetically close OTUs significantly co-occurred more often, and OTUs with intermediate phylogenetic relatedness co-occurred less often, than expected by chance. Phylogenetically close OTUs co-excluded less often than expected by chance in the marine datasets only. Simultaneous excess of co-occurrences and co-exclusions were observed in the inversion zone between close and intermediate phylogenetic distance classes in marine surface. Similar patterns were observed by using either pairwise sequence or phylogenetic distances, and by using both null models. These results suggest that environmental filtering and dispersal limitation are the preponderant forces driving co-occurrence of protists in both environments, while signal of competitive exclusion was only detected in the marine surface environment. The discrepancy in the co-exclusion pattern is potentially linked to the individual environments: water bodies are more homogeneous while tropical forest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.
Heritability jointly Explained by Host Genotype and Microbiome:Will Improve Traits Prediction?

As we observe the 70th anniversary of the publication by Robertson that formalized the notion of ‘heritability’, geneticists remain puzzled by the problem of missing/hidden heritability, where heritability estimates from genome-wide association studies (GWAS) fall short of that from twin-based studies. Many possible explanations have been offered for this discrepancy, including existence of genetic variants poorly captured by existing arrays, dominance, epistasis, and unaccounted-for environmental factors; albeit these remain controversial. We believe a substantial part of this problem could be solved or better understood by incorporating the host’s microbiota information in the GWAS model for heritability estimation; ultimately also increasing human traits prediction for clinical utility. This is because, despite empirical observations such as (i) the intimate role of the microbiome in many complex human phenotypes, (ii) the overlap between genetic variants associated with both microbiome attributes and complex diseases, and (iii) the existence of heritable bacterial taxa, current GWAS models for heritability estimate do not take into account the contributory role of the microbiome. Furthermore, heritability estimate from twin-based studies does not discern microbiome component of the observed total phenotypic variance. Here, we summarize the concept of heritability in GWAS and microbiome-wide association studies (MWAS), focusing on its estimation, from a statistical genetics perspective. We then discuss a possible method to incorporate the microbiome in the estimation of heritability in host GWAS.
Associations of yield and yield components among selected durum wheats (Triticum turgidum L.)

Associations of seed yield (SY) and important agronomic traits were studied among selected durum wheats (Triticum turgidum L.) to establish the relationship and pinpoint the best selection criteria. Controlled glasshouse studies were conducted over two years (2002–2003) using 14 diverse lines. The result from simple correlation analysis indicated that SY had a significant (P<0.01) negative correlation with heading date as well as positive associations with plant height (PH), number of spikelets per spike (SP), kernel numbers per spike (KS) and 1000-kernel weight (KW). A further path analysis on the association of seed yield on five selected traits allocated high values for KW and SP. The direct path value of the analysis showed that there was no association between SY and PH. The indirect path values further suggested that selection for KW would bring about simultaneous and favorable changes to KS, SP, and PH than selecting the traits per se. Improved seed yield among durum lines may be achieved by directly selecting for KW and SP.
Episodic Memories: How do the Hippocampus and the Entorhinal Ring Attractors Cooperate to Create Them?

The brain is capable of registering a constellation of events, encountered only once, as an episodic memory that can last for a lifetime. As evidenced by the clinical case of the patient HM, memories preserving their episodic nature still depend on the hippocampal formation, several years after being created, while semantic memories are thought to reside in neocortical areas. The neurobiological substrate of one-time learning and life-long storing in the brain, that must exist at the cellular and circuit level, is still undiscovered. The breakthrough is delayed by the fact that studies jointly investigating the rodent hippocampus and entorhinal cortex are mostly targeted at understanding the spatial aspect of learning. Here we present the concept of an entorhinal cortical module, termed EPISODE module, that could explain how the representations of different elements constituting episodic memories can be linked together. The new model that we propose here reconciles the structural and functional observations made in the entorhinal cortex and explains how the downstream hippocampal processing organizes the representations into meaningful sequences.
COMBINING ABILITY ANALYSIS FOR DIFFERENT YIELD COMPONENTS IN MAIZE (Zea mays L.) INBRED LINES

The present study was carried out to determine the combining ability of yield and yield components by crossing six diverse maize inbred lines in a half diallel mating design. Fifteen F 1 progenies along with their six parents were planted in randomized complete block design with three replications. GCA to SCA ratios were less than one for plant height, cob diameter, cob length and number of kernels row/cob indicating a preponderance of additive over non additive gene action. The crosses P 1 ×P 2 , P 3 ×P 5 and P 5 ×P 6 were exhibited significant and positive SCA effects for yield and cob diameter, number of row/cob and number of grains/cob of yield contributing characters. The parents P 1 (IL 4 ), P 3 (IL 18 )and P 5 (IL 23 were good general combiner for grain yield and yield attributing characters. It can be concluded that these parental lines can be desirable parents for hybrids as well as for inclusion in breeding program, since they may contribute favorable alleles in the synthesis of new varieties.
Popularity Distributions with Social Influence Comparing YouTube with Hollywood

This thesis considers a model for popularity based on a ‘rich-get-richer’ effect. Basically, popular items tend to become increasingly popular. However, quality of items also plays a role in popularity. The model thus incorporates both a ‘rich-get-richer’ as well as a ‘good-get-richer’ effect. The balance between these two effects is interpreted as the amount of social influence. Formal analysis of the model suggests that the distribution of popularity becomes more unequal and more uncertain with rising social influence. Higher quality has a dual role: it results in a higher average popularity, but increases the uncertainty as well. The model is tested against data from the YouTube market and the Hollywood movie industry. Comparing the results for these two markets suggests that social influence is higher for on-line markets than for traditional markets. When markets go on-line, producers should be prepared to take the increase in risk into account. Some books might break all records, while others remain on the shelf, and it becomes harder to predict which books that will be.
Utilization of Alcohols by Rhodopseudomonas sp. No. 7 Isolated from n-Propanol–Enrichment Cultures

A purple non-sulfur bacterium, Rhodopseudomonas sp. No. 7, was isolated from n-propanol–enrichment cultures under anaerobic-light conditions. Strain No. 7 can produce hydrogen from alcohols. The rate of hydrogen production from n-propanol was 34 μl/hr/mg dry cells. Strain No. 7 showed multiplication by budding and the best growth on n-propanol among other organic compounds tested. But its growth on n-propanol was poor under aerobic-dark conditions. NAD-linked alcohol dehydrogenase, NAD-linked aldehyde dehydrogenase, acyl-CoA synthetase and malate synthetase were found in strain No. 7. These enzymes were constitutive. On the other hand, isocitrate lyase was induced in cells grown on ethanol but not on n-propanol. No activity of phenazine methosulfate-linked alcohol dehydrogenase was detected in strain No. 7.
Attractiveness of bait matrices and matrix/toxicant combinations to the citrus pests Iridomyrmex purpureus (F.Smith) and Iridomyrmex rufoniger gp sp. (Hym., Formicidae)

Abstract: Six bait matrices were tested for palatability to the ants Iridomyrmex purpureus and I. rufoniger gp sp. , which are important pests of citrus in south‐eastern Australia. Granulated citrus pulp and rice bran impregnated with brown sugar were not accepted by either species, but ground dry dog food and ground insects (with or without added sugar) were highly attractive to both ant species. The ground dog food was impregnated with various toxicants at concentrations of up to 1% (w/w) and tested for palatability to both ant species. Technical grade pyriproxyfen, fipronil, and fenoxycarb were incorporated using organic solvents, whereas formulated fenoxycarb (Insegar®) was incorporated as an aqueous suspension prior to drying and granulation. Relative to the blank samples (carrier solvents only), bait acceptance by I. purpureus was not significantly reduced (P > 0.05) by any of the treatments except 1% technical fenoxycarb. Bait acceptance by I. rufoniger gp sp. was significantly suppressed by 0.2% fipronil, but not by higher concentrations. When water was used as the carrier solvent the blank sample was significantly (P < 0.05) less attractive to I. purpureus than the untreated control, suggesting that wetting of dog food‐based baits in field situations may irreversibly reduce their attractiveness. Laboratory colonies were used in choice and no‐choice tests to assess the efficacy of dog food baits containing fipronil (0.05–0.2% w/w). The corrected mortality for I. purpureus ranged from 88 to 100% and from 90 to 97% in the no‐choice and choice tests, respectively. In no‐choice tests I. rufoniger gp sp. corrected mortality varied from 52 to 60%, but in choice tests the corrected mortality did not exceed 26%. Ground dog food containing fipronil (0.05–0.2% w/w) has the potential to provide effective control of I. purpureus in citrus orchards, but alternative toxicants or lower fipronil concentrations may be required for control of I. rufoniger gp sp.
Effects of Concrete-Bamboo Cages on Coral Fragments: Evaluation of a Low-Tech Method Used in Artisanal Ocean-Based Coral Farming

To evaluate the effect of inexpensive cages made from concrete and bamboo on the skeletal extension rates of the scleractinian corals Acropora gomezi and Pavona cactus, fragments were cultured without cages, inside partial cages, and inside full cages with bamboo covers of two mesh sizes at different depths around Sambangan Island, Indonesia. An additional experiment was designed to assess the impact of shading by cages on skeletal extension. Linear extension rates of all fragments were measured over a period of four months. Culture inside cages led to significantly reduced extension rates of A. gomezi at both depths, while P. cactus only showed significantly reduced extension rates when cultured in full cages at greater depth. Caging lead to a significant increase in skeletal damage at both depths in A. gomezi, and at shallow depth in P. cactus. Shaded fragments of A. gomezi had much smaller extension rates (5 ± 1 mm/132 days, mean ± SE) than unshaded fragments (24 ± 1 mm/132 days) and sustained significantly more damage, while shaded fragments of P. cactus grew significantly better (15 ± 0 mm/132 days) than unshaded fragments (12 ± 0 mm/132 days) and sustained less damage, although the difference was not significant. The culture of coral fragments without cages may yield the best results. However, the choice of the optimal culture method will depend on the species to be cultured and the conditions encountered in the reef.
The benefits of stealing from a predator: foraging rates, predation risk, and intraspecific aggression in the kleptoparasitic spider Argyrodes antipodiana

In the trade-off between food and safety, the role of aggressive intraspecific interactions has not been extensively examined. Here I present information on this system using a kleptoparasitic spider, Argyrodts antipodiana, and its host spider and potential predator, Eriophora pustulosa. A. antipodiana can feed either at a potentially dangerous site (the hub of its host's web with the host), or at a relatively safe site (on food bundles around the edge of the host's web). I found that A. antipodiana can gain food very quickly when feeding with the host, apparently by exploiting the host's ability to digest the prey. Thus A, antipodiana follows predictions based on foraging models in that it accepts a higher predation risk at the hub because of the higher food payoff. A. antipodiana also aggressively competes for access to more food. However, aggressive competition increases the pre- dation risk from the host, especially at the hub where the host is very close. Consequently, A. antipodiana modifies its level of intraspecific aggressiveness in accordance with its position on the web: at the hub,where the cost of aggression is high (due to predation risk), A. antipodiana reduces its aggressiveness, but it is aggressive away from the hub when competing for food bundles. The ability of A, antipodiana to change interaction intensity as a function of its position on the web enables it to exploit a rich, but risky, food source and provides a new angle for examining food and safety trade offs in light of intraspecific competition for food. Kty words: Argyrodes antipodiana, foraging, intraspecific aggression, kleptoparasite, predation spider, trade-offs. [Behav Ecol 8:663-667 (1997)] ecent work has highlighted the importance of predation . in the
Increasing importance of small phytoplankton in a warmer ocean

The macroecological relationships among marine phytoplankton total cell density, community size structure and temperature have lacked a theoretical explanation. The tiniest members of this planktonic group comprise cyanobacteria and eukaryotic algae smaller than 2 μm in diameter, collectively known as picophytoplankton. We combine here two ecological rules, the temperature–size relationship with the allometric size‐scaling of population abundance to explain a remarkably consistent pattern of increasing picophytoplankton biomass with temperature over the −0.6 to 22 °C range in a merged dataset obtained in the eastern and western temperate North Atlantic Ocean across a diverse range of environmental conditions. Our results show that temperature alone was able to explain 73% of the variance in the relative contribution of small cells to total phytoplankton biomass regardless of differences in trophic status or inorganic nutrient loading. Our analysis predicts a gradual shift toward smaller primary producers in a warmer ocean. Because the fate of photosynthesized organic carbon largely depends on phytoplankton size, we anticipate future alterations in the functioning of oceanic ecosystems.
Use of polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis to detect a point mutation in the catalase-peroxidase gene (katG) ofMycobacterium tuberculosis

Abstract We have previously reported that a significant percentage (44%) of isoniazid-resistant Mycobacterium tuberculosis strains carry an arginine to leucine mutation in codon 463 (R463L) in the catalase-peroxidase gene ( katG ). For the current study, we compared the utility of one mutation screening method, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis, with a reference method, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), to detect this mutation. The PCR-SSCP method detects mutations by electrophoretic mobility shifts of single-stranded DNA in nondenaturing polyacrylamide gels. The RFLP method detects a loss in an Msp I restriction site which occurs when the R463L is present. Eighty one M. tuberculosis strains, including the wild type strain H37Rv, with isoniazid susceptibility in the range 32 μg ml −1 were evaluated. The results for the PCR-SSCP method were in complete agreement with the PCR- Msp I RFLP reference method. Of 81 M. tuberculosis strains analysed, 13 showed mobility shifts by the PCR-SSCP method and all of those strains carried the R463L as detected by the PCR- Msp I RFLP method. All of the remaining 54 strains had PCR-SSCP and PCR- Msp I RFLP results identical to the wild type (R463) M. tuberculosis strain, H37Rv. It is concluded that the described PCR-SSCP is a reliable method for screening M. tuberculosis strains for the katG R463L mutation.
Climate‐related trends in Australian vegetation cover as inferred from satellite observations, 1981–2006

Using Advanced Very High Resolution Radiometer data spanning 1981–2006 and calibrated for long‐term analyses of vegetation dynamics, we examine whether vegetation cover has increased across Australia and whether there has been a differential response of vegetation functional types in response to changes in climatic growing conditions. Trends in vegetation cover are interpreted within Budyko's energy – water limitation framework. Results from an Australia‐wide analysis indicate that vegetation cover (as described by the fraction of Photosynthetically Active Radiation absorbed by vegetation; fPAR) has increased, on average, by 0.0007 per year – an increase of ∼8% over the 26 years. The majority of this change is due to a 0.0010 per year increase in persistent fPAR (representing nondeciduous perennial vegetation types; up 21%). In contrast, recurrent fPAR (representing deciduous, annual and ephemeral vegetation types) decreased, on average, by 0.0003 per year (down 7%), the trends of which are highly seasonal. Over the same period, Australian average annual precipitation increased by 1.3 mm yr−2 (up 7%). A site‐based analysis using 90 long‐term meteorological stations with minimal localized land‐cover changes showed that energy‐limited sites where total fPAR increased generally experienced decreases in precipitation, and water‐limited sites that experienced decreases in cover were almost always associated with decreases in precipitation. Interestingly, where vegetation cover increased at water‐limited sites, precipitation trends were variable indicating that this is not the only factor driving vegetation response. As Australia is a generally highly water‐limited environment, these findings indicate that the effective availability of water to plants has increased on average over the study period. Results also show that persistent vegetation types have benefited more than recurrent types from recent changes in growing conditions. Regardless of what has been driving these changes, the overall response of vegetation over the past 2–3 decades has resulted in an observable greening of the driest inhabited continent on Earth.