Miracle-dz/UniFAR-FTUs huggingface dataset:
An assessment of the potential impact of climate change on grass yield in Ireland over the next 100 years

The impact of climate change on grassland agriculture may affect yield, livestock numbers, winter housing, slurry storage and land spreading, and the production system. The potential change in grass yield in Ireland due to climate change was estimated using simulation modelling. The estimation took account of the spatial variation of soil and climate. The approach adopted was to: (i) use statistically downscaled climate data derived from the Hadley HADCM3 climate model; (ii) simulate daily weather for 30 separate years from monthly climate data (baseline, 2055 and 2075) using a stochastic weather generator; (iii) simulate 30 years of grass yields for each climate period using the Johnstown Castle Grass Model; (iv) summarize the 30 yield predictions for each climate period as a mean response to climate; and (v) quantify the change in yield as a result of climate change. Grass yield was predicted to decrease in the east of the country due to summer drought stress. In the west grass yield was predicted to increase. The major impacts of yield change were considered to be: (i) grass may cease to be a viable crop in the southeast and east if it requires irrigation to compensate for drought; (ii) theoretical turnout date may become earlier in the season; (iii) stock may have to remain housed at times when currently grazed outside, thus extending storage requirements; and (iv) alternative forage crops may become more suitable for winter feed conservation. No catastrophic impacts are foreseen, but the exact implications will also depend on regional agricultural policy.
Grazing behaviour and species selection of heifer calves fed different forages.

The aim of this experiment was to determine whether there was a difference in the behaviour of calves grazing different forages. Weaned dairy heifer calves (n = 64) were assigned to two different forage feeding treatments: ryegrass pasture and a clover-herb mix. Behavioural observations were recorded every 10 minutes over a 72 h period. Behaviours recorded were standing, walking, lying or sitting, grazing, ruminating, drinking/grooming, playing and various combinations of these. Calves grazing pasture spent more time lying and ruminating compared to calves grazing the clover-herb mix (34.6% vs 16.7%), and less time standing and grazing (17.2% vs 32.2%). Calves were less active from late evening and early morning and more likely to be ruminating earlier in the day and grazing later in the day. Plant selection (measured as plant disappearance rate) was determined in calves grazing the clover-herb mix. Red clover had the highest disappearance rate on all days compared to other species (P<0.05). Plantain, chicory and white clover eaten on day one did not differ in proportions eaten, but by day three less red clover and chicory remained compared to plantain and white clover (P<0.05).
Market Access Approach to Urban Growth

This paper studies urban growth in Korean cities. First, I document that population growth patterns change over time and that the current population distribution supports random urban growth. I confirm two empirical laws—Zipf’s law and Gibrat’s law—both of which hold in the period of 1995-2015, but do not hold in the earlier period of 1975-1995. Second, I find a systematic employment growth pattern of Korean cities in spite of the random population growth. I examine market access effects on employment growth. Market access, a geographical advantage, has a significant influence on urban employment growth. The market access effect is higher in the Seoul metropolitan area than in the rest of the country. This effect is stronger on employment growth in the manufacturing industry compared to employment growth in the service industry. These results are robust with various checks (e.g., different definitions of urban areas). The results here suggest that policymakers should consider geographical characteristics when they make policy decisions with respect to regional development.
La nutrition protéique modifie l'ingestion des vaches laitières : analyse bibliographique

L'alimentation azotee des vaches laitieres peut modifier l'ingestion mais cet effet n'a jamais ete quantifie pour le prendre en compte dans le rationnement. Le protocole d'etude a conduit a retenir 155 reponses a des variations de complementation azotee issues de 58 publications pour etudier les reponses d'ingestion provoquees par l'incorporation de complements riches en azote dans la ration de vaches laitieres. L'apport d'azote degradable augmente l'ingestion mais uniquement lorsque le regime en est deficitaire. L'apport de proteines digestibles accroit globalement l'ingestion, mais la reponse est tres variable, comprise entre -0,6 et 2 kg de MS/j. L'utilisation de matieres premieres comme le gluten de mais a un effet specifique defavorable a l'ingestion (-0,7 kg MS/j). De meme, si l'amelioration de la nutrition proteique de la vache s'effectue au detriment de la disponibilite en azote degradable dans le rumen pour les microbes, les effets positifs en moyenne de 1 kg de MS/j tendent a disparaitre. Enfin, la reponse aux proteines est accrue par differents facteurs additifs lies aux caracteristiques du regime: +0,5 kg de MS/j lorsque le regime est une ration complete, +0,8 kg MS/j s'il n'y a pas de substances tampons, +0,4 kg de MS/j en moyenne s'il est utilise pendant une longue periode et +0,4 kg de MS/j si la vache est en deficit proteique. Ces resultats montrent que la complementation en proteines interfere de facon importante avec la nutrition energetique.
Reconstitution of the extrinsic 23 and 17 kDa proteins with spinach PSII which had been exchanged for the 33 kDa protein from different plant species

The 33 kDa protein of photosystem II (PSII) plays an important role in maintaining the function of the Mn cluster, and is common to all of the organisms and totally exchangeable in binding to PSII from various different organisms (Enami et al., 2000, Plant Cell Physiol. 41, 1354-1364). The amino acid sequence of the 33 kDa protein showed a relatively high homology above 40% from cyanobacteria to higher plants. Thus, the structure of the 33 kDa protein has been considered to be conserved during evolution from cyanobacteria to higher plants. In this study, reconstitution experiments were performed for the extrinsic 23 and 17 kDa proteins from spinach with spinach PSII which had been exchanged for the 33 kDa protein from different sources. Spinach PSII was treated with 2.6 M urea/0.2 M NaCl to remove all of the extrinsic proteins, and then reconstituted with the 33 kDa protein from a cyanobacterium (Synechococcus vulcanus), a red alga (Cyanidium caldarium) or a higher plant (Spinach). The results showed that, while spinach PSII bearing the higher plant 33kDa protein retained the full ability of binidng the 23 kDa and 17 kDa proteins, PSII of which the 33 kDa protein had been replaced with the red algal or cyanobacterial 33kDa protein partially rebound the 23kDa protein but totally failed to bind the 17kDa protein. This suggests that the structure of the 33kDa protein interacting with other extrinsic proteins is different between higher plants and red algae or cyanobacteria.
Interactive effects of ocean warming and acidification on sperm motility and fertilization in the mussel Mytilus galloprovincialis

As we did not measure total alkalinity [AT] during our experiment, we calculated an estimated range of values based on data sourced from IMOS Ocean Portal (https://imos.aodn.org.au/imos123/), Takahashi et al. (2014), and Foster et al. (2014); each directly comparable to the region and time our seawater was collected. Corresponding AT ranges from across these sources were used to calculate possible ranges for the reported levels of pCO2 (* partial pressure of CO2) using CO2SYS software (Pierrot et al. 2006) with the constants of Mehrbach et al (1973) as refitted by Dickson and Millero (1987). We accept that there will be some level of error in these estimations, however, the differences in pCO2 between each treatment are much greater than the calculated ranges.
The complete mitochondrial genome of the Songpu mirror carp, Cyprinus carpio

Abstract In this study, the complete mitochondrial genome sequences of Cyprinus carpio (strain Songpu) were reported for the first time. The genome is found to be 16 582 bp in length accurately using the next-generation sequencing technology and bioinformatics tools, and it has a base composition of A (31.9%), G (15.7%), C (27.5%) and T (24.9%), indicating that the percentage of A + T (56.8%) was higher than G + C (43.2%). The whole genome contains a typically conserved structure, which includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region (D-loop). To obtain the phylogenetic relationship between Songpu mirror carp and other species, 11 mitochondrial genomes were used for phylogenetic analysis. The result shows the Songpu mirror carp is closely related to Cyprinu carpio carpio that is also a member of the genus Cyprinu.
Prevalence and Persistence of Select Foodborne Pathogens in a mid-Atlantic Turkey Processing Facility

Stam, Christina Nicole. Prevalence and Persistence of Select Foodborne Pathogens in a mid-Atlantic Turkey Processing Facility. (Under the direction of Dr. Lee-Ann Jaykus). Listeria monocytogenes, Salmonella and Campylobacter combined are responsible for the majority of foodborne disease hospitalizations and over 1200 deaths annually in the U.S. alone. Although raw poultry has been identified as a source of these pathogens, most microbiological studies have focused on broilers with little attention given to turkey processing. The purpose of this research was to investigate the prevalence of select pathogens (L. monocytogenes, Salmonella spp., and Campylobacter spp.) and microbiological indicators (Enterococcus spp.) in the turkey processing environment. Environmental samples were collected in one Southeastern processing facility using swab methods at two month intervals over a period of 14 months. Samples were taken from conveyors, drains, walls and various food contact surfaces. Isolation and identification of bacteria was done using the USDA-FSIS Microbiology Laboratory Guidebook protocols. The prevalence of contamination was 11.5%, 7.4%, and 0.4% for L. monocytogenes, Salmonella, and Campylobacter, respectively. Enterococcus spp. , an environmental indicator of fecal contamination, were isolated from over >75% of the samples screened. Salmonella isolates were typed using pulsed-field gel electrophoresis (PFGE) and Enterococcus isolates were speciated by PCR with antibiotic resistance profiles characterized using the SensiTitre system. A diverse set of relatively nonpersistent Salmonella strains were obtained from the processing environment, as evaluated by PFGE. Thirty-nine percent of the Enterococcus isolates were speciated as E. faecium and 55% were E. faecalis. Both E. faecalis as E. faecium strains were susceptible to most antibiotics of human clinical relevance. Thirty-three L. monocytogenes strains were screened for their biofilm formation capabilities using a microtiter well assay. None of the strains formed a biofilm in monoculture; however, sixteen of the strains were able to form a biofilm in the presence of another organism. Data collected in prevalence studies such as this one can help processors identify contamination frequency and sites in an effort to control resident pathogenic bacteria in the processing environment. PREVALENCE AND PERSISTENCE OF SELECT FOODBORNE PATHOGENS IN A MID-ATLANTIC TURKEY PROCESSING FACILITY
Grower Acceptance of Economic Thresholds for Weed Management in Illinois

Although economic thresholds are often used to make insect control decisions, the use of thresholds for weed management has been limited. Surveys of growers, agricultural chemical dealers, and farm managers/rural appraisers helped identify limitations to grower acceptance of economic thresholds for weed management. Most growers were concerned about harvest problems due to weeds, with 64% identifying this factor as a major limitation. Landlord perception and weed seed production were identified by 38% of the growers as major limitations, while 36% of the growers listed general appearance of the field as reasons. In contrast, 75% of the agricultural chemical dealers and 63% of the farm managers surveyed listed field appearance as a major reason limiting grower acceptance of economic thresholds for weed management. Since grower concerns involve risk management and future profitability, economic weed thresholds that address long-term costs and benefits of weed control decisions may be more fully accepted.
Identification and characterization of neuroendocrine pathways involved in the regulation of seasonal body weight cycles

16 Introduction 17 Materials and methods 19 Results 22 Discussion 31 References 36 III. Orexin-B interacts with Neuropeptide Y neurons in the Intergeniculate Leaflet and in peripheral part of the Suprachiasmatic Nucleus of Djungarian hamsters (Phodopus sungorus) 41 Abstract 4
Exploring the spatial distribution patterns of South African Cape hakes using generalised additive models

We developed delta generalised additive models (GAMs) to predict the spatial distribution of different size classes of South African hakes, Merluccius capensis and M. paradoxus, using demersal trawl survey data and geographical (latitude and longitude) and environmental features (depth, temperature, bottom dissolved oxygen and sediment type). Our approach consists of fitting, for each hake size class, two independent models, a binomial GAM and a quasi-Poisson GAM, whose predictions are then combined using the delta method. Delta GAMs were validated using an iterative cross-validation procedure, and their predictions were then employed to produce distribution maps for the southern Benguela. Delta GAM predictions confirmed existing knowledge about the spatial distribution patterns of South African hakes, and brought new insights into the factors influencing the presence/absence and abundance of these species. Our GAM approach can be used to produce distribution maps for spatially explicit ecosystem models of the southern Benguela in a rigorous and objective way. Ecosystem models are critical features of the ecosystem approach to fisheries, and distribution maps constructed using our GAM approach will enable a reliable allocation of species biomasses in spatially explicit ecosystem models, which will increase trust in the spatial overlaps and, therefore, the trophic interactions predicted by these models.
Anti-depressant-like effect of curculigoside isolated from Curculigo orchioides Gaertn root

Purpose: To investigate the anti-depressant-like activity of curculigoside from Curculigo orchioides Gaertn and its underlying mechanism(s). Methods: Antidepressant-like activity was determined in mice through forced swimming test (FST), tail suspending test (TST), and open field test (OFT). Mechanism of action was investigated by measuring levels of dopamine (DA), norepinephrine (NE), and 5-hydroxytryptamine (5-HT) in chronic mild stress (CMS) rats using high-performance liquid chromatography-electron capture detector (HPLC-ECD). Western blotting was used to investigate the effect of curculigoside on the expression of brain-derived neurotrophic factor (BDNF) protein in rats. Results: In FST and TST, treatment of mice with curculigoside (10, 20, 40 mg/kg, p.o.) significantly reduced immobility time, which was, however, unaffected by locomotor activity when assessed in the OFT. The treatment led to significant increases in DA, NE and 5-HT, and up-regulation of BDNF protein expression in the hippocampus of the CMS rats. Conclusion: These results demonstrate that curculigoside exerts significant anti-depressant-like activity on mice, the mechanism of which involves increase in the levels of DA, NE, 5-HT, and up-regulation of BDNF expression. Thus, curculigoside can be considered a potential drug candidate for the treatment of depressive disorders. Keywords: Curculigo orchioides Gaertn, Curculigoside, Antidepressant-like activity, Behavioral studies
Tansley review No. 102 plant hybridization

Most studies of plant hybridization are concerned with documenting its occurrence in different plant groups. Although these descriptive, historical studies are important, the majority of recent advances in our understanding of the process of hybridization are derived from a growing body of experimental microevolutionary studies. Analyses of artificially synthesized hybrids in the laboratory or glasshouse have demonstrated the importance of gametic selection as a prezygotic isolating barrier; the complex genetic basis of hybrid sterility, inviability and breakdown; and the critical role of fertility selection in hybrid speciation. Experimental manipulations of natural hybrid zones have provided critical information that cannot be obtained in the glasshouse, such as the evolutionary conditions under which hybrid zones are formed and the effects of habitat and pollinator-mediated selection on hybrid-zone structure and dynamics. Experimental studies also have contributed to a better understanding of the biology of different classes of hybrids. Analyses of morphological character expression, for example, have revealed transgressive segregation in the majority of later-generation hybrids. Other studies have documented a high degree of variability in fitness among different hybrid genotypes and the rapid response of such fitness to selection - evidence that hybridization need not be an evolutionary dead end. However, a full accounting of the role of hybridization in adaptive evolution and speciation will probably require the integration of experimental and historical approaches.
ENVIRONMENTAL UNPREDICTABILITY AND LEATHERBACK SEA TURTLE (DERMOCHELYS CORIACEA) NEST LOSS

This study evaluates the nesting pattern of individual leatherback turtles, the fate of individual nests, and the seemingly maladaptive nesting strategy involved in high nest loss. Sandy Point, St. Croix, U.S. Virgin Islands, is a high-energy beach characterized by deep, unobstructed access. Gravid leatherbacks deposit as many as 10 clutches (x = 4.9) annually and exhibit a high degree of nest dispersal along the length and width of the beach. Short-term erosion and accretion cycles result in the annual loss of 45-60% of the nests laid. The zones of greatest instability vary from year to year. Wide nest dispersal may reduce the prospect that a high proportion of repro- ductive effort will be lost with the destruction of any particular zone of habitat. I suggest that nest dispersal should occur whenever nest survival is not strongly correlated with available environmental information. The predictability of perturbation (i.e., stable vs. unstable nesting habitats) may serve as a control determining the nesting strategies of sea turtles.
Variation in egg composition in semi-captive Barnacle Geese

Egg composition was examined in a semi-captive flock of Barnacle Geese Branta leucopsis in relation to egg size, laying sequence and to the age, size and aggressiveness of the male and female. The proportion of yolk in the eggs was within the normal range for precocial species, but the proportion of lipid (14%) was high even in comparison with other geese. The last egg was the smallest of the clutch, but the proportions of yolk and lipid were independent of egg size and laying sequence. Egg composition did not vary with the date of clutch initiation. There were no significant correlations between body weight and size, aggressiveness or breeding experience of either male or female and egg composition. Although there were no significant differences in weight and dimensions of egg from different sized clutches, there was a significant negative correlation between clutch size and the amount of yolk and of lipid. Eggs in repeat clutches were similar in size to those of the first clutch, but had lower proportions of both yolk and lipid. This indicated some compromising of the energetic commitment to individual eggs in relation to an environmental factor (in captivity need for re-laying to be rapid if it is to be successful, or change in food quality).
Effects of Three Fusarium Species on the Quality of Barley and Malt

In this study, field-grown barley was artificially infected during the heading stage with three Fusarium species, F. culmorum, F. graminearum, and F. poae. The objective was to investigate possible differences among Fusarium species in terms of how severely they affect the quality of barley under Finnish field conditions. Moreover, we studied the effects of heavy infection on corresponding malt quality. Field trials were carried out with two different barley cultivars at two experimental farms. Spike samples collected during the growing period were analyzed for Fusarium infection and moisture content. Total precipitation and temperature data were collected daily. In addition, the harvested barley samples were analyzed for overall microbial flora and for mycotoxins. The infection rate and the amount of mycotoxins produced in the barley samples differed among species. F. graminearum was found to have the most negative effects on barley quality in terms of the studied parameters. Samples were malted in laboratory scale. All three Fusarium species increased the gushing potential of malt. Heavy fungal infection increased the enzyme activities in malt resulting in darker wort color and increased soluble nitrogen and free amino nitrogen content. However, high Fusarium contamination reduced lautering performance.
Molecular Characterization of Microbial Communities Associated with Accelerated Low-water Corrosion (ALWC) on European Harbour Structures

The microbial communities associated with different corrosion deposit layers retrieved from a harbour steel structure affected by ALWC (Accelerated Low Water Corrosion) were determined by 16S rDNA PCR-DGGE analysis. Comparative analysis of populations associated with ALWC layers and NLWC (Normal Low Water Corrosion) layers evidenced clear differences in the structure and composition of the communities. Dominant phylotypes related to sulphate-reducing bacteria pertaining to Desulfobacteraceae, Desulfobulbaceae and Desulfovibrionaceae were identified in both type of deposits (fraction of 52% and 44% of the total NLWC and ALWC communities, respectively). Phylotypes related to sulphur-oxidizing bacteria belonging to Alpha-, Gamma- and Epsilonproteobacteria were unique to ALWC deposits, while phylotypes related to oxygenic photosynthetic microorganisms (cyanobacteria, diatoms) were only retrieved in NLWC deposits. This suggested that biologically-mediated sulphur cycle was the dominant process within ALWC deposits vs. chemically-mediated sulphur cycle within NLWC deposits. Since most of the members identified are heterotrophs, it is speculated that organic carbon may be available through water pollution and/or proliferation of photosynthetic biomass. Differences in oxygen concentration between ALWC and NLWC areas due to photosynthetic activities in NLWC may be an important factor contributing to the acceleration of corrosion by the mechanism of differential aeration.