Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Growth and Milk-Composition in Southern Elephant Seals (Mirounga-Leonina)

Growth rates and changes in body composition of pups were monitored during the 3-week lactation period of southern elephant seals at Macquarie Island. Despite a slight decrease in weight in the first days post-partum, pups attained a mass of 114+/-16.6 kg (mean+/-s.d.) at weaning, representing an average growth rate of 3.53+/-0.80 kg day-1 over the entire lactation period. The proportion of body mass represented by fat was less than 3% at birth, increasing to 40.8+/-12.7% at weaning. Lean tissue mass altered little for most of the lactation period, but did show an increase in the last four days. The fat content of the milk reflected these changes, starting at 16.1+/-6.98% on Day 1 of lactation and increasing to 39.5+/-15.2% about the time of weaning. Fat content of the milk was, however, highly variable and at weaning ranged from 7% to 55%. Although the growth rate of the pup was correlated with mass lost by its mother during lactation, there was no relationship between maternal mass and weaning weight of pups. It is suggested that growth rates may be related to maternal condition and not simply mass, and, further, that differences in growth rates between populations of southern elephant seals are related to maternal energy reserves.
Microbiological monitoring of raw milk from selected farm in the Trentingrana region

Abstract A study was conducted to monitor raw milk hygiene, and to understand the relationship between different bacterial groups found in raw milk collected from stables in the Trentingrana area. Twenty stables in Trento province were sampled. Each farmer provided one milk sample every 2 months for 8 months. The milk samples were examined for total bacterial count, coliforms, enterococci, psycrotrophic, acidificant and proteolytic microflora. The bacterial counts of four milk samples for each stable, examined over an 8-months period were averaged and expressed as mean bacterial count per milliliter. In most samples, coliforms and enterococci were below 2Log cfu/ml; this suggests that herds and milking hygiene were well controlled by all farmers. The milk refrigeration practice seems to have no influence on the growth of its microflora but to affect that of acidifying and proteolytic bacteria.
The Mcm2-7 Replicative Helicase is Essential to Coordinate DNA replication, Checkpoint Regulation and Sister Chromatid Cohesion

DNA replication is a complex and highly regulated cellular process that ensures faithful duplication of the entire genome. To prevent genomic instability, several additional processes are coordinated with DNA replication. Eukaryotic cells employ a conserved surveillance mechanism called the S-phase checkpoint to activate a phosphorylation cascade while encountering DNA damage during DNA replication. In addition, DNA replication must also coordinate with sister chromatid cohesion, so that sister DNAs emerged from the forks are physically connected until chromosomal segregation takes place. Mcm2-7, the eukaryotic replicative helicase that unwinds dsDNA and positions at the vanguard of the replication fork, is likely the commonality among these cellular processes. In my thesis work, I find that ATP hydrolysis in one specific active site (Mcm6/2) is required to mediate DNA replication checkpoint response, sister chromatid cohesion and DNA replication initiation. Further examination reveals that a subcircuit of the checkpoint pathway including MEC1 and MRC1 and ends with Mcm2-7 is required to mediate sister chromatid cohesion. Finally, misregulation of these processes causes genomic instability and likely missegregation of chromosomes. My findings lead to a model that the regulation of ATP hydrolysis at the Mcm6/2 active site by Mrc1 modulates Mcm2/5 gate open and gate closure during initiation, DNA damage and sister chromatid cohesion.
α2β1 Integrin Mediates Dermal Fibroblast Attachment to Type VII Collagen via a 158-Amino-Acid Segment of the NC1 Domain

Abstract Dermal fibroblasts are in apposition to type VII (anchoring fibril) collagen in both unwounded and wounded skin. The NC1 domain of type VII collagen contains multiple submodules with homology to known adhesive molecules, including fibronectin type III-like repeats and a potential RGD cell attachment site. We previously reported the structure and matrix binding properties of authentic and recombinant NC1. In this study, we examined the interaction between dermal fibroblasts and the NC1 domain of type VII collagen. We found that both recombinant and authentic NC1 vigorously promoted human fibroblast attachment. Adhesion of fibroblasts to NC1 was dose dependent, saturable, and abolished by both polyclonal and monoclonal antibodies to NC1. Cell adhesion to NC1 was divalent cation dependent and specifically inhibited by a monoclonal antibody directed against the α2 or β1 integrin subunits, but not by the presence of RGD peptides. Furthermore, the cell-binding activity of NC1 was not conformation dependent, since heat-denatured NC1 still promoted cell adhesion. Using a series of recombinant NC1 deletion mutant proteins, the cell binding site of NC1 was mapped to a 158-aa (residues 202–360) subdomain. We conclude that human dermal fibroblasts interact with the NC1 domain of type VII collagen and this cell–matrix interaction is mediated by the α2β1 integrin and is RGD independent.
Approach to climatophilous vegetation series of Serra da Estrela (Portugal)

Abstract This work contains the study results of climatophilous vegetation series from Serra da Estrela, the highest mountain on the Portuguese mainland. Located in central-northern Portugal in the Estrelensean Sector (Carpetan-Leonese Subprovince), the Serra da Estrela has several bioclimatic stages, mainly resulting from slope and altitude ranges: mesomediterranean, submediterranean mesotemperate, supramediterranean, submediterranean supratemperate, and submediterranean orotemperate. In each of these belts are observed changes in plant communities that determine variations in terms of the vegetation series. The methodology was based on Dynamic-Catenal Phytosociology. The results show the presence of five climatophilous series; their structural characteristics and dynamics are described in this paper: 1. Lycopodio clavati–Junipereto nani S. ; 2. Saxifrago spathularis–Betuleto celtibericae S. ; 3. Holco mollis–Querco pyrenaicae S. ; 4. Arbuto–Querco pyrenaicae cytisetoso grandiflori S. ; e 5. Viburno tini–Querco roboris S.
THE FORAGING SPECIALIZATIONS OF INDIVIDUAL BUMBLEBEES

Bumblebees of any one species in Maine forage for pollen and/or nectar from a large variety of morphologically diverse flowers, but individuals have limited foraging repertoires at any one time. Unspecialized individuals were sometimes unsuccessful in ex- tracting nectar and/or pollen from highly rewarding flowers. In any one area with a variety of concurrently blooming plants, the bumblebees had ap- parent species preferences. Superimposed on the species preferences were individual prefer- ences. Individuals had primary foraging specialties (their majors) and secondary specialities (their minors). Minors were often bridges to new majors. Queens in Maine necessarily have several successive majors during their lifetime since the blooming time of the plants they utilize are brief relative to their life-span as foragers. However, the blooming time of most plants available to Bombus fervidus workers are long relative to their lifetime. Switching was rarely observed in these bees, even in some individuals observed daily for up to 1 mo at the same foraging area containing other plant species in bloom that were highly attractive to other individuals of the same bumblebee species. On a per flower basis, those flowers producing the most food rewards generally had the largest number of bees majoring from them, and the food rewards available were roughly comparable between different kinds of flowers, regardless of their differences in rates of nectar production. Specializing was usually preceded by sampling a variety of rewarding as well as non- rewarding flowers. When the flowers from which bees were majoring in an area were experi- mentally removed many of the bees sampled flowers of other concurrently blooming plants, but they generally did not switch to flowers from which the food rewards were being depleted by specialists, unless these were experimentally fortified with syrup. Upon finding superior food rewards in enriched blossoms, they switched immediately. Flower-specificity is related to site-specificity. Many bees shared the same foraging area, but different individual bees at the same site utilized the flowers of different plant species. When the foraging area contained landmarks, the bees visited clumps of flowers in a sequence (foraging path) that was generally repeated several times on the same foraging trip when the foraging site was small. The foraging behavior of bumblebees is discussed from a comparative standpoint with other bees and in relation to food distribution and availability in the environment.
Cats are Rare Where Coyotes Roam

Domestic cats (Felis catus) have caused the extinction of many island species and are thought to kill many billions of birds and mammals in the continental United States each year. However, the spatial distribution and abundance of cats and their risk to our protected areas remains unknown. We worked with citizen scientists to survey the mammals at 2,117 sites in 32 protected areas and one urban area across 6 states in the eastern United States using camera traps. We found that most protected areas had high levels of coyote (Canis latrans) activity, but few or no domestic cats. The relative abundance of domestic cats in residential yards, where coyotes were rare, was 300 times higher than in the protected areas. Our spatial models of cat distribution show the amount of coyote activity and housing density are the best predictors of cat activity, and that coyotes and cats overlap the most in small urban forests. Coyotes were nocturnal at all sites, while cats were nocturnal in protected areas, but significantly more diurnal in urban sites. We suggest that the ecological impact of free-ranging cats in the region is concentrated in urban areas or other sites, such as islands, with few coyotes. Our study also shows the value of citizen science for conducting broadscale mammal surveys using photo-vouchered locations that ensure high data quality.
Effect of Phytase on the Growth Performances of Growth of Laying Hens (Warren)

This study consists of supplementing the feeding of laying hens with phytase at various proportions and evaluating its influence on the average weight and the index of consumption. The experiment was led during 6 weeks on 4 batches of 50 laying hens. These batches respectively received a supplementation of 0 G/kg food (pilot batch), 1.36 g/kg (batch 1), 2.72 g/kg (batch 2), 4.05 g/kg (batch 3). Each week the laying hens are weighed and the feeding efficiency index calculated. The results revealed that the best batch was batch one in terms of profit of weight gained the feeding efficiency index.
Order Testudines: 2013 update. In : Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013)

The present paper presents an update of a list of chelonian taxa published in 2011 (Fritz 2011), which generally has followed the “Checklist of chelonians of the world” by Fritz & Havas (2007). Although chelonians (terrapins, turtles and tortoises) do not constitute a species-rich group, there exists considerable interest in their taxonomy and systematics, a fact being related with the unique morphology, the debated phylogenetic relationships and the delicate conservations status of these reptiles. Consequently, quite a number of taxonomic changes has been proposed in the past two years.
Are invasive ants better plant-defense mutualists? A comparison of foliage patrolling and herbivory in sites with invasive yellow crazy ants and native weaver ants

Benefits arising from facultative mutualisms between ants and plants vary with the identity of the ant partner. Invasive and native ants are both attracted to plants that offer extrafloral nectar, but few studies have compared their abilities to displace herbivores and benefit plants. Yellow crazy ants Anoplolepis gracilipes have invaded eucalypt woodlands of Arnhem Land, northern Australia, where they displace the native dominant weaver ant Oecophylla smaragdina. We compared the plant defense services provided by A. gracilipes and O. smaragdina ants on trees with (Acacia lamprocarpa) and without (Eucalyptus tetrodonta) extrafloral nectar rewards through surrogate herbivore (termite) addition experiments and surveys of herbivore damage. Anoplolepis gracilipes were more likely than O. smaragdina to discover termites on A. lamprocarpa, but the likelihood of termite discovery on E. tetrodonta did not vary with ant species. Anoplolepis gracilipes were also more thorough in their attacks of termites, recruited 3.4–4 times more workers to termites, and were 3.4 times quicker at discovering termites on A. lamprocarpa than were O. smaragdina. Discovery of termites by other predators did not vary significantly between trees in A. gracilipes and O. smaragdina sites. Herbivory scores did not reflect the foliage patrolling pattern by the ants. Old A. lamprocarpa leaves and both new and old leaves and branches on E. tetrodonta in A. gracilipes sites had higher chewing herbivory scores than their counterparts in O. smaragdina sites. Our results reveal that the more aggressive and efficient foliar patrolling by A. gracilipes does not translate to increased plant protection. Ant invasions can disrupt native ant–plant mutualisms despite invasive ants possessing many traits associated with effective plant guarding.
Integrated assessment models for ecologists: the present and the future

Aim Human impacts on the biosphere are a matter of urgent and growing concern, with ecologists increasingly being asked to project biodiversity futures. The Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is likely to comprehensively assess such projections, yet despite being widely used and potentially critical tools for analysing socio-environmental futures, integrated assessment models (IAMs) have received little attention from ecological modellers. We aim to raise awareness and understanding of IAMs among ecologists by describing the structure and composition of IAMs, assessing their utility for biodiversity projections and identifying limitations that hamper greater interaction between scientists using IAMs and those using ecological models. We also hope to inspire more accessible and applicable models by suggesting development needs for IAMs. Methods We conduct a systematic review of four state-of-the-art IAMs, which describes and contrasts key model features and analyses six aspects of IAMs that are of fundamental interest to ecologists. Conclusions IAMs could be valuable for modelling biodiversity futures; however, current IAMs were not developed for this application and challenges remain for ecologists looking to use their outputs. Separating and understanding the differences resulting from IAM formulation and those resulting from specific scenario assumptions is currently problematic, and current IAMs may be unable to accurately represent environmental conditions for both Earth-system projections and for building robust models of biodiversity because key ecological processes are absent. We suggest that model intercomparisons would identify differences in model dynamics, and detailed studies of how dynamical interactions between components influence behaviour would address why such differences arise. Bio-economic fisheries models and agriculture pollination models provide starting points for integrating key ecological feedbacks within IAMs. Ultimately, making IAMs more accessible within the multidisciplinary study of global change, drawing on user-centred research, would enable more resolved, reliable and accurate assessment of how Earth's socio-ecological system is approaching planetary boundaries.
286 THE EFFECT OF IN VITRO MATURATION MEDIUM ON CRYOSURVIVAL, CELL NUMBERS AND APOPTOTIC INDEXES OF BOVINE EMBRYOS

The success of in vitro maturation (IVM) has a significant impact on the oocytes ability to develop to blastocyst stage. The quality of the produced blastocysts can be evaluated using staining techniques. The aims of this study were (a) to compare the effect of different IVM media on embryo production rates, and (b) to utilize differential (DF) and TUNEL staining to evaluate the quality and cryosurvival of the produced blastocysts. Abattoir-derived oocytes were randomly divided into the IVM groups: (1) M199 IVM (n = 2305): TCM-199 with glutamax-I (GIBCO, Paisley, UK), 0.25 mM Na-pyruvate, 100 IU mL−1 penicillin, and 100 μg mL−1 streptomycin; (2) FBS IVM (n = 2484): M199 IVM medium with hormones (10 μg mL−1 LH, 2 μg mL−1 FSH, and 100 μg mL−1 β-estradiol), and 10% FBS (GIBCO, New Zealand); and (3) FAFBSA IVM (n = 2411): as group (2), but FBS was replaced with 4 mg mL−1 fatty acid free albumin. Fertilized oocytes were denuded and cultured in modified SOFaaci + 4 mg mL−1 FAFBSA in 5% O2 (Holm P et al. 1999 Theriogenology 52, 683–700). Fresh, Grade I Day 7 blastocysts were stained with TUNEL (n = 114) or with DF (n = 149). In addition, 184 Grade I Day 7 blastocysts were frozen in AG Freeze (AB Technology, Pullman, WA, USA), thawed, and cultured for 24 h. The re-expanded embryos were stained with TUNEL (n = 96) or with DF (n = 88). Modified TUNEL protocol (Upstate, Lake Placid, NY, USA; Makarevich A and Markkula M 2002 Biol. Reprod. 66, 386–392) and DF staining protocol (Thouas G.A. et al. 2001 Reprod Biomed Online 3, 25–29) were used. The results of embryo cleavage and D7 embryo development are based on logistic regression models, and the results of proportion of ICM and apoptotic index on general linear mixed models. After FBS IVM, 83.6% of the fertilized oocytes were estimated to cleave and 25.5% to develop to the blastocyst stage by Day 7. The estimations for embryo cleavage and Day 7 development rates were significantly lower in FAFBSA IVM and M199 IVM groups (P < 0.0001): 74.0% and 15.0% for the FAFBSA, and 76.1% and 8.8% for the M199, respectively. The re-expansion rates (%) after thawing were 86.5, 90.6, and 73.3 for the FBS, FAFBSA, and M199 IVM groups, respectively. Freezing reduced the ICM proportions and elevated the apoptotic indexes (P < 0.001). The rate of ICM reduction after freezing was not influenced by the IVM medium. There was a significant interaction between the apoptotic index and the IVM group (P = 0.04). The increase of the apoptotic index was smallest in FAFBSA IVM and greatest in M199 IVM. The results indicate that exclusion of serum from IVM medium results in lower embryo cleavage and development rates. Freezing reduced ICM and increased apoptotic index of Day 7 embryos in every IVM group studied. FAFBSA IVM seemed to produce embryos of better quality as evidenced by the smallest increase in the apoptotic index after freezing.
TheDPL1Gene Is Involved in Mediating the Response to Nutrient Deprivation inSaccharomyces cerevisiae

Abstract Sphingosine-1-phosphate is a sphingolipid metabolite involved in the regulation of cell proliferation in mammalian cells. The major route of sphingosine-1-phosphate degradation is through cleavage at the C2–3bond by sphingosine phosphate lyase. The recent identification of the first dihydrosphingosine/sphingosine phosphate lyase gene inSaccharomyces cerevisiaeestablishes that phosphorylated sphingoid base metabolism is conserved throughout evolution. Thedpl1Δ deletion mutant, which accumulates endogenous phosphorylated sphingoid bases, exhibits unregulated proliferation upon approach to stationary phase. The increased proliferation rate during respiratory growth was associated with failure to appropriately recruit cells into the G1phase of the cell cycle. Several genes were found to be overexpressed or prematurely expressed during nutrient deprivation in thedpl1Δ strain, including glucose-repressible genes and G1cyclins. These studies implicate a role forDPL1and phosphorylated sphingoid bases in the regulation of global responses to nutrient deprivation in yeast.
Tumor-specific Immunity to Transplanted Dibenz[a,h]-anthracene-induced Sarcomas

Summary Subcutaneous fibrosarcomas were induced in inbred mice by the implantation of glycerol-moistened crystals of dibenz[ a,h ]anthracene. Eleven dibenz[ a,h ]anthracene-induced sarcomas were investigated. The data demonstrate that the temporary growth of these tumors in other mice of the same inbred strain often produced a tumorspecific immunity to subsequent challenge inoculations of the same tumor. Normal tissues from the very mouse in which an antigenic tumor arose failed either to induce the immunity or to respond to it. The results are similar to previous findings with 3-methylcholanthrene-induced fibrosarcomas and therefore suggest that tumor-specific antigenicity may be a general property of fibrosarcomas induced by the aromatic hydrocarbons in mice.
Comparison between APSIM and NZ-DNDC models when describing N-dynamics under urine patches

Nitrous oxide (N2O) emissions from soil are the result of complex interactions between physical, chemical and biological processes. We compared two process-based models (APSIM and NZ-DNDC) with measurements of N2O emissions, soil and content (0–75 mm) and water-filled pore space from a series of field campaigns where known amounts of animal urine-N were applied to four soil types under permanent pastures, in two regions within New Zealand, at different times of the year. We also compared cumulative N2O emissions with an N2O inventory emission factor approach (EF3 method). Overall, the two process-based models performed less well than the EF3 method for simulating cumulative N2O emissions over the complete data set. However, in winter, the APSIM model correlated well with measurements (r = 0.97), while NZ-DNDC performed well on the Otago soils (r = 0.83 and 0.92 for Wingatui and Otokia, respectively). The process-based models have the potential to account for the effect of weather conditions and soil type on N2O emissions that are not accounted for by the EF3 method. However, further improvements are currently needed. The fractions of N lost to different processes within the complex soil–plant atmosphere system differed between the two models. The size of the predicted plant uptake, leaching and NH3 volatilisation fluxes are large compared with N2O emissions and could affect the simulated soil N pools and thus the predicted N2O fluxes. To simulate N2O fluxes accurately, it is therefore important to ensure these processes are well modelled and further validation studies are needed.
Seasonal Use of Estuaries by Winter Flounder in the Southern Gulf of St. Lawrence

Abstract The seasonal distribution of winter flounder Pleuronectes americanus in the southern Gulf of St. Lawrence was examined by analyzing data from research surveys conducted from 1986 to 1994 in the southern Gulf and from beach seining, trawling, and sampling of commercial fisheries in the Miramichi Estuary. During June–August, most winter flounder were found in coastal waters (<40 m deep) and within a temperature range of 3–16°C. Abundance in coastal waters declined sharply between September and late November–early December. Winter flounder were not captured in deep offshore waters during winter; rather, large numbers moved into the Miramichi Estuary during October and November and remained until spring. The brackish water under the ice of the Miramichi Estuary was warmer (–1 to 0°C) than the full salt water under the ice of the southern Gulf (below –1.5°C) and could provide a thermal refuge for winter flounder as well as protection from ice contact during winter storms. Adult winter flounder left th.