Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of additive genetic variance of reproduction traits in Austrian Simmental

Heritabilities and genetic correlations were estimated in first, second and all parities for dystocia and stillbirth for the Austrian Simmental population. Method R was applied to estimate the (co)variance components with a linear animal model. In total, 1,399,990 calving records were analyzed. There were 363,097 firstand 274,486 second-parity records. The largest pedigree file consisted of 1,842,324 animals. Both traits were recorded categorically, 4 and 2 classes for calving ease and stillbirth, respectively. The model contained direct and maternal genetic effects. For calving ease, estimates of heritability for direct genetic effects were (in %), 9.26, 2.52 and 4.22 for first, second and all parities, respectively. For maternal effects, the estimated heritabilities were smaller, 4.49, 2.40 and 1.99, respectively. Genetic correlations between direct and maternal effects were negative as expected, -0.26, -0.52 and -0.35, respectively. Estimated heritabilities of both direct and maternal effects were much lower for stillbirth. For direct effects, heritabilities were, in %, 1.73, 0.47 and 0.57, respectively; for maternal effects, estimations were 1.54, 0.37 and 0.56, respectively. Finally, genetic correlations were -0.04, -0.30 and -0.06, respectively. In consequence, heritabilities were clearly heterogeneous over parities and this should be taken into account in the evaluation model.
Release and Establishment in the Southeastern United States of Neohydronomus affinis (Coleoptera: Curculionidae), an Herbivore of Waterlettuce

The South American weevil Neohydronomus affinis Hustache was first released in North America as a biological control for waterlettuce, Pistia stratiotes L. , at Kreamer Island, Lake Okeechobee, Fla. , on 29 April 1987. Releases were made at six additional sites in southern Florida. Periodic observations at several of these sites indicate the weevils have become established and are dispersing. At some sites, weevil-infested plants are exhibiting symptomology typical of plants in other countries where N. affinis has been used successfully to control this aquatic weed.
Sets in homotopy type theory †

Homotopy type theory may be seen as an internal language for the ∞-category of weak ∞-groupoids. Moreover, weak ∞-groupoids model the univalence axiom. Voevodsky proposes this (language for) weak ∞-groupoids as a new foundation for Mathematics called the univalent foundations. It includes the sets as weak ∞-groupoids with contractible connected components, and thereby it includes (much of) the traditional set theoretical foundations as a special case. We thus wonder whether those ‘discrete’ groupoids do in fact form a (predicative) topos. More generally, homotopy type theory is conjectured to be the internal language of ‘elementary’ of ∞-toposes. We prove that sets in homotopy type theory form a ΠW-pretopos. This is similar to the fact that the 0-truncation of an ∞-topos is a topos. We show that both a subobject classifier and a 0-object classifier are available for the type theoretical universe of sets. However, both of these are large and moreover the 0-object classifier for sets is a function between 1-types (i.e. groupoids) rather than between sets. Assuming an impredicative propositional resizing rule we may render the subobject classifier small and then we actually obtain a topos of sets.
Interaction with Protocadherin-γ Regulates the Cell Surface Expression of Protocadherin-α*

The protocadherin-α (CNR/Pcdhα) and protocadherin-γ (Pcdhγ) proteins, members of the cadherin superfamily, are putative cell recognition/adhesion molecules in the brain. Overexpressed cadherins are generally expressed on the cell surface and elicit cell adhesion activity in several cell lines, although hardly any overexpressed CNR/Pcdhα proteins are expressed on the cell surface, except on HEK293T cells, which show low expression. We analyzed the expression of CNR/Pcdhα and Pcdhγ in HEK293T cells and found that they formed a protein complex and that Pcdhγ enhanced the surface expression of CNR/Pcdhα. This enhanced surface expression was confirmed by flow cytometry analysis and by marking cell surface proteins with biotin. The enhancement was observed using different combinations of CNR/Pcdhα and Pcdhγ proteins. The surface expression activity was enhanced by the extracellular domains of the proteins, which could bind each other. Their cytoplasmic domains also had binding activity and influenced their localization. Their protein-protein interaction was also detected in extracts of mouse brain and two neuroblastoma cell lines. Thus, interactions between CNR/Pcdhα and Pcdhγ regulate their surface expression and contribute to the combinatorial diversity of cell recognition proteins in the brain.
Investigation of rumen methanogens in New Zealand livestock : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand.

Methane emitted by farmed ruminants contributes 30.3% to New Zealand’s anthropogenic greenhouse gas inventory. Methanogens living in the rumen produce methane from H2 and CO2 as a byproduct of feed fermentation. The use of vaccines and small molecule inhibitors against the methanogens are promising methods to reduce methane emissions from extensively-grazed ruminants in New Zealand. Knowledge of the methanogens present in New Zealand ruminants is an important first step for successful vaccine and inhibitor development to target all methanogens. In this study, the methanogen diversity of farmed ruminants (sheep [Ovis aries], cattle [Bos taurus] and red deer [Cervus elaphus]) was investigated using molecular ecological techniques. Ruminants fed different diets had largely similar rumen methanogen communities. The major methanogen groups identified were from the Methanobrevibacter ruminantium clade (Mbb. ruminantium and closely-related species), Methanobrevibacter gottschalkii clade (Mbb. gottschalkii and closely-related species), Methanosphaera spp. , and the putative methanogens belonging to the group designated Rumen Cluster C. A total of 37.5 - 57% of 16S rRNA genes in the rumen of a group of cows originated from members of Rumen Cluster C. Chloroform treatment of cows increased the abundance of Rumen Cluster C to 82% - 93% of archaeal 16S rRNA genes. In parallel, a total of 22% of mcrA genes belonged to an unassigned group of archaea, and chloroform treatment increased the unassigned group of archaea to 92% of all mcrA genes. This suggested that Rumen Cluster C archaea contain the gene mcrA. No members of the Rumen Cluster C group have previously been cultured, and currently there is no reported rumen isolate of Methanosphaera spp. A strain of Methanosphaera sp. was isolated from a sheep rumen and initial characterization suggests that this may be a new species. Three enrichment cultures were obtained containing members of Rumen Cluster C as the only archaea. Initial studies of these enrichment cultures showed that these three isolates were from three different sub-groups of Rumen Cluster C and that they produced methane. The investigation of methanogen diversity in New Zealand farmed ruminants and isolation of previously uncultured rumen methanogens reported here in this thesis will significantly aid the development of methane reduction strategies for farmed ruminants in New Zealand.
Biomarkers to Distinguish Bacterial From Viral Pediatric Clinical Pneumonia in a Malaria-Endemic Setting

BACKGROUND Differentiating the etiology of acute febrile respiratory illness in children is a challenge in low-income, malaria-endemic settings because the main pathogens responsible (viruses, bacteria, and malaria parasites) overlap in clinical presentation and frequently occur together as mixed infections. The critical task is to rapidly identify bacterial pneumonia to enable appropriate antibiotic treatment, ideally at point of care. Current diagnostic tests are insufficient and there is a need for the discovery and development of new tools. Here we report the identification of a unique biomarker signature that can be identified in blood samples. METHODS Blood samples from 195 pediatric Mozambican patients with clinical pneumonia were analyzed with an aptamer-based high dynamic range assay to quantify ∼1200 proteins. For discovery of new biomarkers, we identified a training set of patient samples in which the underlying etiology of the pneumonia was established as bacterial, viral or malaria. Proteins whose abundances varied significantly between patients with verified etiologies (FDR<0.01) formed the basis for predictive diagnostic models that were created using machine learning techniques (Random Forest, Elastic Net). These models were validated on a dedicated test set of samples. RESULTS 219 proteins had significantly different abundances between bacterial and viral infections, and 151 differed between bacterial infections and a mixed pool of viral and malaria infections. Predictive diagnostic models achieved >90% sensitivity and >80% specificity, regardless of whether one or two pathogen classes were present. Bacterial pneumonia was strongly associated with markers of neutrophil activity, in particular neutrophil degranulation. Degranulation markers included HP, LCN2, LTF, MPO, MMP8, PGLYRP1, RETN, SERPINA1, S100A9, and SLPI. CONCLUSION Blood protein signatures highly associated with neutrophil biology reliably differentiated bacterial pneumonia from other causes. With appropriate technology, these markers could provide the basis for a rapid diagnostic for field-based triage for antibiotic treatment of pediatric pneumonia.
Temporal and Spatial Variation in Fecundity of Yellowtail Rockfish

Abstract Fecundities of the commercially important yellowtail rockfish Sebastes flavidus were compared to determine interannual variability and geographic variation, which will assist in stock assessment, characterization, and management. Gravimetrically estimated fecundities were compared in 1985–1991 between California, the southern extent of the species' distribution, and coastal waters of Washington, near the center of the species' abundance, where yellowtail rockfish are most heavily fished. California yellowtail rockfish were older, smaller in weight and length, and had smaller mesenteric fat deposits and more extensive disease and parasite pathologies than Washington fish. Egg production of this comparatively fecund viviparous fish increased linearly and sigmoidally with body weight and length, and asymptotically with age. Significant interannual differences were found in fecundities of young fish ( age 14) or in .
Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic microbiota. Targeting these diazotrophs, we selected nearly 600 microbes from a collection isolated from these plants and confirmed their ability to incorporate heavy nitrogen (15N2) metabolites in vitro. Sequencing their genomes and conducting comparative bioinformatic analyses showed that these genomes had substantial phylogenetic diversity. We examined each diazotroph genome for the presence of nif genes essential to nitrogen fixation (nifHDKENB) and carbohydrate utilization genes relevant to the mucilage polysaccharide digestion. These analyses identified diazotrophs that possessed canonical nif gene operons, as well as many other operon configurations with concomitant fixation and release of >700 different 15N labeled metabolites. We further demonstrated that many diazotrophs possessed alternative nif gene operons and confirmed their genomic potential to derive chemical energy from mucilage polysaccharide to fuel nitrogen fixation. These results confirm that some diazotrophic bacteria associated with Sierra Mixe maize were capable of incorporating atmospheric nitrogen into their small molecule extracellular metabolites through multiple nif gene configurations while others were able to fix nitrogen without the canonical (nifHDKENB) genes. Data Summary Genetic resources, including biological materials and nucleic acid sequences, were accessed under an Access and Benefit Sharing (ABS) Agreement between the Sierra Mixe community and the Mars Corporation, and with authorization from the Mexican government. An internationally recognized certificate of compliance has been issued by the Mexican government under the Nagoya Protocol for such activities (ABSCH-IRCC-MX-207343-3). Any party seeking access to the nucleic acid sequences underlying the analysis reported here is subject to the full terms and obligations of the ABS agreement and the authorization from the government of Mexico. Individuals wishing to access nucleic acid sequence data for scientific research activities should contact Mars Incorporated Chief Science Officer at CSO@effem.com.
Comparison between the sponge fauna living outside and inside the coralligenous bioconstruction. A quantitative approach

Coralligenous habitat results from a multi-stratified accumulation of crustose coralline algae and animal builders in a dynamic equilibrium with disruptive agents. The result is a complex architecture crossed by crevices and holes. Due to this three-dimensional structure, coralligenous may host a rich and diversified fauna, more abundant than any other Mediterranean habitat. Unfortunately, very few data are available about the cryptic fauna that lives inside the conglomerate. As already reported for coral reefs, the cryptic fauna plays an important role in the exchange of material and energy between water column and benthic assemblages. Here we compare the sponge community present inside and outside the coralligenous framework of Portofino Promontory (Ligurian Sea) at different depths (15 and 30 meters) not only in terms of taxonomic diversity but for the first time also in term of biomass. Sponges present on the surface of each block were collected, weighed and identified; after blocks dissolution in HCl, target cryptic sponges were separated from other organisms, weighed, and identified. We recorded a total of 62 sponge species. The average number of sponge taxa occurring outside the coralligenous accretions is lower than the number of taxa identified inside. This pattern is confirmed also regarding sponge biomass. These results underlines that studies focused on coralligenous functioning should take in account the important contribution of cryptic fauna, as recently evidenced also for tropical reef habitats.
Parallel evolution in courtship songs of North American and European green lacewings (Neuroptera: Chrysopidae)

Green lacewings of the Chrysoperla carnea species group use substrate-borne vibrational duetting songs rather than morphology or pheromones for species recognition. Because each of the many cryptic, reproductively isolated song species typically has an extensive geographic range, potentially interfertile biological species are broadly sympatric, and therefore must use distinct regions of acoustic song space if they are to remain reproductively isolated. However, this constraint does not apply to species restricted to different continents, giving rise to the possibility of parallel evolution of song phenotypes between continents. Here we describe a striking example of parallel song evolution, between a known European species, Chrysoperla pallida, and a newly discovered vivid-green North American species, Chrysoperla calocedrii sp. nov. To verify this parallelism, we show that: (1) the songs of the two species have measurably similar multi-volley temporal and frequency structure; (ii) the songs share the same basic genetic pathway; (iii) each species is unable to discriminate between its own and the other's song in playback trials, confirming the acoustic niche overlap; (iv) the two species readily establish normal duets with each other in the lab, leading to copulation and the production of vigorous hybrid progeny bearing an intermediate song phenotype; (v) they have distinct morphologies in both adults and larvae, suggesting different adaptive responses and therefore independent evolutionary histories; and (vi) they occupy relatively distant positions in a Bayesian phylogenetic analysis of 4630 bp of protein-coding mitochondrial DNA, rejecting the alternative hypothesis of similarity through recent common ancestry. We include a formal description of C. calocedrii sp. nov. as a new species, and provide additional observations of its behaviour, ecology, and life history. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 776–796.
The microscopical anatomy of metamorphosis in a haploid salamander, triton taeniatus laur

The microscopical examination of the first haploid salamander to live through metamorphosis shows that the transformation to a terrestrial vertebrate was normal and practically completed at the time of its death. All the organs and structures that develop shortly before and during metamorphosis and are typical for the adult salamander, e.g., the integument, the pharyngeal derivatives, and various glands of special function, are present.
Effects of Different Skin Contact Times on Treixadura Wine Composition

Wines produced from the same Treixadura must were subjected to different skin contact times (0, 5, and 22 hours), and inoculated with Saccharomyces cerevisiae. The carboxylic acids, sugars, glycerol, and ethanol were analyzed by HPLC. The higher alcohol, ester, acetate, volatile phenol, and fatty acid content was studied by GC. Statistical analysis of results confirm the influence of skin contact time on subsequent wine composition.
An oscillation underlying feeding and a number of other behaviours in fifth‐instar Locusta migratoria nymphs

ABSTRACT. Behavioural evidence is presented for the presence of an oscillation underlying feeding and a number of other activities in fifth‐instar Locusta migratoria nymphs raised and observed under LD 12:12 with constant access to food. With the oscillation represented for convenience as a sine wave, these behaviours occurred significantly more often in the peak half of the cycle than in the trough half. The period of the oscillation differed between insects, the range being from 12.0 to 16.5 min, but was constant for each insect. Feeding did not occur on every cycle but when it did occur it usually began near the peak of an oscillation. Off‐peak feeding was generally associated with defecation. Other more frequently exhibited behaviours, such as the initiation of locomotion and a variety on non‐locomotory behaviours, occurred on peaks when there was no feeding. Once feeding or locomotion had commenced and during the short period of settling afterwards, rhythmicity in the non‐locomotory behaviour was lost. The nature of the oscillator is not known, other than it is apparently endogenous and is not reset during a 12‐h light phase. The presence of such an intermediate length oscillator may have important implications in the organization of complex behaviour
Can postural control performance be an indicator of truck drivers’ sleep deprivation?

Long-haul drivers work in irregular schedules due to load delivery demands. In general, driving and sleeping occur at irregular times and, consequently, partial sleep deprivation and/or circadian misalignment may emerge and result in sleepiness at the wheel. In this way, the aim of this study was to verify changes in the postural control parameters of professional drivers after one-night working. Eight male truck drivers working at night – night drivers (ND) and nine day drivers (DD) volunteered to participate in this study. The night drivers’ postural stability was assessed immediately before and after an approximately 430 km journey by two identical force platforms at departure and arrival sites. The DD group was measured before and after a day's work. An interaction effect of time of day and type of shift in both conditions: eyes open (p < 0.01) and eyes closed (p < 0.001) for amplitude of mediolateral movements was observed. Postural stability, measured by force platform, is affected by a night of work, suggesting that it could be an effect of circadian and homeostatic influences over postural control.
Heterogeneity of inflammation and host metabolism in a typhoid fever model

Systemic infections can lead to severe inflammation and altered host metabolism. These host responses are being extensively studied, but their spatial relationships in infected tissues remain largely unknown. The goal of this thesis was to investigate the spatial organization of metabolic and inflammatory patterns in Salmonella-infected tissues and to elucidate the impact of host heterogeneity on host-Salmonella interactions in a murine typhoid fever model. We showed that antimicrobial effector mechanisms such as generation of ROS and RNS occurred predominantly in granulomatous lesions. However, a substantial fraction of Salmonella resided outside of these lesions and was therefore not covered by these antimicrobial regions. Heterogeneous exposure to RNS induced distinct, locally adapting Salmonella subpopulations (see chapter 2.1). We also investigated host metabolic enzyme activities in various tissue regions. Using a novel combination of immunostaining with enzyme histochemistry, we showed that granulomas had a distinct metabolic profile with a high capacity for generation of NADPH, an essential substrate for local generation of bacteriostatic/bactericidal ROS and RNS. Indeed, adaptation of GFP-based live/dead discrimination revealed extensive Salmonella killing that predominantly occurred in granulomas (see chapter 2.2). The spatial segregation of live Salmonella from regions with massive killing also offered a potential explanation why surface-associated Salmonella antigens, but not internal antigens that are inaccessible in live Salmonella, were required for protective immunity (see chapter 2.3). In conclusion, this thesis revealed markedly heterogeneous conditions in Salmonella-infected host tissues that had profound impact on disease mechanisms, infection control, and immunity.
The possibility of using crustacean waste products (CWP) on rainbow trout (Oncorhynchus mykiss) feeding.

Crustacean waste product (CWP) generated from the fishing industry could be used in diets for rainbow trout as an alternative animal protein. Some experiments have been undertaken with penaid species, showing that it is possible to partially replace fish meal with CWP in penaid feeds. This study has been designed to assess whether CWP could be used to partially replace fish meal in diets for rainbow trout. The results show that CWP improved the digestibility of the diet, yielding the highest performance, and also that the addition of large amounts of CWP to a low-protein diet did not depress appetite. Fish fed on a diet containing 47% protein and CWP had a feed conversion ratio of 0.79 and a percentage weight gain of 123.87 for marked fish and 147.57 for the whole stock. These results indicate that CWP may be recommended for use as an alternative to fish meal sparing in rainbow trout diets, but that partial replacement requires amino acid supplementation.