Miracle-dz/UniFAR-FTUs huggingface dataset:
Reducing CH 4 Emissions from Grazing Ruminants in New Zealand: Challenges and Opportunities

Almost half of New Zealand's greenhouse gas emissions arise from agriculture and enteric methane () emissions arising from ruminant animals constitute 30% of total -e emissions. Enteric emissions have increased by 9% since 1990. Extensive research has been undertaken to develop reliable methods for measuring enteric emissions. New Zealand studies using the SF6 tracer technique suggest that on average this technique yields similar values to the 'gold' standard of calorimetry, but with a larger variance. National inventory estimates based on results obtained using the technique will therefore overestimate the uncertainty. Mitigating emissions can be achieved by changing feed type but there are practical and cost barriers to the use of alternative feeds. Forages containing condensed tannins do reduce emissions but are agronomically inferior to the forages currently used. Rumen additives have shown some success in-vitro but results from in-vivo trials with both monensin and fumaric acid have been disappointing. The development of methods for directly manipulating rumen microorganisms are at an early stage and work to develop vaccines that can inhibit methanogenesis has yielded mixed results. The successful identification of sheep with contrasting yields raises the possibility that, in the long term, a breeding approach to mitigation is feasible.
Monocyclic Psaronius from the lower Pennsylvanian of the Illinois Basin

A new species of Psaronius is described from permineralized monocyclic stems with distichous leaf scars. Diameters for the steles are 3.5–4.4 cm, up to 6.5 cm for the stem, and 8 cm for the trunk which includes inner and outer roots; the longest of 11 specimens is 32 cm. These specimens from the lower Pennsylvanian of western Illinois are the oldest known histologically preserved stems and roots for the genus. Psaronius simplicicaulis sp.nov., with its distichous leaf arrangement, is very similar to Mississippian – early Pennsylvanian Megaphyton specimens, indicating that the earliest known marattialean tree ferns were smaller in diameter than their late Pennsylvanian relatives and probably monocyclic with distichous fronds. The middle Pennsylvanian increase in the distribution and abundance of Psaronius generally coincides with increased size, polycyclic stelar anatomy, and polystichy.
THE PHENOLOGY OF SEXUAL REPRODUCTION BY GREEN ALGAE (BRYOPSIDALES) ON CARIBBEAN CORAL REEFS

Recent field observations of highly organized, species‐ and sex‐specific patterns of synchronous gamete release by tropical green algae (Bryopsidales) invite a variety of future studies into the ecology and life histories of an important component of tropical reef communities. This paper details sexual reproduction by 22 algal species within five common genera (Caulerpa, Halimeda, Penicillus, Rhipocephalus, and Udotea), including field observations on the spatial occurrence, timing, and color changes associated with fertility, data on gamete size and behavior, and descriptions of coincident changes in local species abundances. Ecologically ephemeral episodes of sexual reproduction involved macroscopic changes that reliably indicated developmental state and sexual identity. The time from onset of fertility to gamete release was 36 h (Halimeda), 48 h (Caulerpa, Penicillus, and Rhipocephalus), or 96 h (Udotea). All species produced flagellated, negatively buoyant, anisogamous gametes. Microgametes of all species were similar in size; however, considerable species‐specific differences were seen in the size of macrogametes. In Caulerpa, Halimeda, and Udotea flabellum (Ellis and Solander) Lamouroux, the volumetric ratio of macrogametes to microgametes ranged from 2:1 to 45: 1, whereas more extreme levels of anisogamy (104: 1) were observed for Penicillus spp. , Rhipocephalus phoenix (Ellis and Solander) Kuetzing, and other Udotea spp. The macrogametes of Caulerpa and Halimeda showed strong positive phototaxis. Although only a subset (generally about 5%) of the thalli representing each species released gametes on a given morning, most species underwent bouts of sexual reproduction on numerous occasions during the seasonal peak of reproductive activity (March–May). As might be expected for holocarpic species, dramatic declines in local algal abundance coincided with these periods. The density of sand‐dwelling genera such as Penicillus fell by 80– 90% during this 3‐month period in 1997. Similar declines in the cover of sprawling species such as Caulerpa racemosa ((Forsskal) J. Agardh) exposed large (35–50 m2) sections of previously overgrown reef substrate.
Protected areas and the conservation of grouse, partridges and pheasants in east Asia

Grouse, partridges and pheasants belong to the highly threatened avian order Galliformes. We collected together existing data on the distribution of these species in east Asia (China and Pakistan south and east to the Lesser Sundas in Indonesia and Palawan in the Philippines) from published and unpublished sources. From this we extracted 1068 records of 101 east Asian endemics (plus three other species that have been found in east Asian protected areas) in 369 protected areas. One species was found in 108 protected areas and a further two in 39 and 38 protected areas: six species were not known from any. Of the threatened endemics, 84% were recorded in 10 or fewer protected areas compared with 50% of endemic species that are non‐threatened. A near‐minimum network designed to include each species in three protected areas wherever possible comprised 49 irreplaceable sites and 33 others. Comparison with other studies should indicate which of these protected areas are also important for other groups of organisms, such as plants and swallowtail butterflies. There is a need for improvement in knowledge of occurrence in protected areas. This should be provided from further collation of existing information and from undertaking targeted surveys. There is also a need to consider which protected areas are suitable for inclusion in a network and how many such areas are required to ensure that each species is adequately represented.
Condition Varies with Habitat Choice in Postbreeding Forest Birds

ABSTRACT. Many birds that are experiencing population declines require extensive tracts of mature forest habitat for breeding. Recent work suggests that at least some may shift their habitat use to early-successional areas after nesting but before migration. I used constant-effort mist netting in regenerating clearcuts (4–8 years postcut) and dense mature-forest understories to assess (1) whether most bird species of mature forests show habitat shifts after breeding; and (2), on the basis of several measures of condition, whether birds using early-successional habitats garnered any benefits or penalties, compared with those that remained in forests. I captured 3,845 individual birds of 46 species at four pairs of sites in mature Allegheny hardwood forests in northwestern Pennsylvania during the postbreeding periods of 2005–2008. Most, but not all, forest birds were captured at higher rates in cuts than in forests, and that pattern persisted through the postbreeding season. Using an information-theoretic approach, I found strong support for a species-habitat interactive effect on both molt progression and body condition as measured by residuals from speciesspecific regression of mass on wing chord. Some, but not all, forest birds appeared to be in better condition when captured in cuts than when in forests. I found no support for a habitat effect on presence of fat or ectoparasites. My result s reveal that habitat choice in the postbreeding season is correlated with physiological condition for a subset of forest birds, which suggests that the maintenance of such early-successional habitats in mature forest may benefit these species.
WATER STRESS TOLERANCE OF WHEAT (TRITICUM AESTIVUM L.): VARIATIONS IN HYDROGEN PEROXIDE ACCUMULATION AND ANTIOXIDANT ACTIVITY IN TOLERANT AND SUSCEPTIBLE GENOTYPES

An experiment was conducted on five wheat (Triticum aestivum L.) cultivars, C 306, PBW 175 (tolerant to water stress), DL 153-2 (moderately tolerant to water stress), HD 2428 and HD 2329 (recommended for irrigated conditions, susceptible to water stress), under pot culture conditions to study the effect of water stress on oxidative injury and antioxidant activity. Water stress significantly decreased relative water content (RWC), ascorbic acid content and membrane stability, and increased hydrogen peroxide and malondialdehyde content, a measure of lipid peroxidation, and activities of antioxidant enzymes in all the genotypes at 7, 17 and 27 days after anthesis (DAA). Water stress tolerant genotypes C 306 and PBW 175, closely followed by DL 153-2, were superior to HD 2428 and HD 2329 in maintaining high RWC, ascorbic acid content and membrane stability and lower hydrogen peroxide content and lipid peroxidation (malondialdehyde content) under water stress at the three stages. The highest activities of glutathione reductase and catalase under water stress were observed in C 306, PBW 175 and DL 153-2 and the lowest activities in HD 2428 and HD 2329 at all the stages. Superoxide dismutase activity at all stages under irrigated conditions and at the first and second stages under water stress conditions did not show significant variation among the different genotypes, but at the last stage under water stress the enzyme activity was highest in C 306, closely followed by PBW 175 and DL 153-2, and lowest in HD 2428 and HD 2329. It is apparent that water stress induces an increase in hydrogen peroxide content and consequently lipid peroxidation and membrane injury (reduced membrane stability). The degree of oxidative stress and antioxidant activity seems to be closely associated with the tolerance/susceptibility of a genotype to water stress.
Effects of kiore (Rattus exulans Peale) on recruitment of indigenous coastal trees on northern offshore islands of New Zealand

Possible effects of kiore (Rattus exulans) on selected indigenous tree species in coastal forests ot northern New Zealand are surveyed from recent field sampling and a literature review Recruitment rates are compared on islands with and without kiore (i) on the same island before or at the time of rat eradication compared with recruitment some years later, and (II) on geographically separated islands with and without kiore In addition kiore‐proof exclosurcs enabled some comparisons to be made of seed germination and survival in the presence and absence of kiore There is evidence that kiore have substantially reduced recruitment of Pittosporum crassifohum, Poutena costata Streblus banksu, and Nestegis apetala by eating the seed Seed consumption and/or depressed recruitment is demonstrated for Rhopalostyhs sapida, Vitex lucens and Pisoma brunoniana, but the extent ot recruitment reduction is not yet clear No depressive effect by kiore on the recruitment ot some species, including Dysoxylum spectabde Beilchm.
Identification and expression characterization of pepsinogen A in orange‐spotted grouper, Epinephelus coioides

To understand the molecular mechanisms associated with digestive physiology of the stomach of orange-spotted grouper Epinephelus coioides, a cDNA library was constructed and 331 expressed sequence tags (EST) were generated and annotated. About 37·17% of 226 identified ESTs were possibly related to digestive enzymes. Two type-A pepsinogens differing in putative isoelectric point were identified and characterized for the first time in E. coioides. The complete cDNAs were 1312 and 1314 bp in length, and the deduced polypeptide sequences comprised 376 and 377 amino acids, respectively. Both genes consisted of eight introns of various lengths. Alignment and a phylogenetic tree based on the amino acid sequences of pepsins indicated that pepsin A1 and A2 could be classified into two different subtypes. Northern blot hybridization showed that there were two forms of transcripts for pepsinogen A1 and three for pepsinogen A2. Reverse transcription-PCR (RT-PCR) followed by Southern blot analysis revealed that two type-A pepsinogen mRNAs were present in the adult stomach tissue, and pepsinogen A2 was also detectable in the mid-intestine. Furthermore, pepsinogen A1 transcript was first detected at 29 days post-hatching, while pepsinogen A2 was continuously expressed through hatching to adult fish. These results imply that transcriptional regulation and physiological function of the two type-A pepsinogens may be different.
Polyphenoloxidase and Its Thermal Deactivation in Western Rock Lobster (Panulirus cygnus) Processing

ABSTRACT Polyphenoloxidase (PPO) activity results in blackening or melanosis of tissues in western rock lobster (WRL). The aim of this study is to establish the thermal deactivation constants for WRL PPO and compare them to the thermal lethality of commercial cooking. Decimal reduction values were determined for a range of temperatures, and the theoretical process lethality at 90°C (F90) was calculated. F90 was equal to 36.11 minutes. Process lethality values for standardized commercial cooking of WRL were determined. Comparison of these results to the theoretical F90 value clearly showed that current commercial cooking is inadequate to achieve deactivation of WRL PPO
The use of genomics in the management of livestock

Variation among animals exists at all stages of our livestock supply chains. In contrast, most manufacturing supply chains possess little, if any, unintended variation within each segment. This variation is generally an unwanted nuisance. However, when properly managed, it can provide opportunities to target multiple product end-points and turn-off dates in a dynamic manner. Moreover, optimal management can lead to high degrees of compliance with the needs of the processing segment of the supply chain and/or end-users. Management decisions can be divided into initial group formation (e.g. mating groups, feedlot entry groups) and ongoing changes to the management plan in the light of new information (including market forces, weather and genetic status of animals). In both cases, the best pattern of decision making depends, explicitly or implicitly, on the predicted effect of these decisions on future animal and processing performance. The present paper provides an overview of key factors that affect these predictions, and hence optimal management, and emphasises the potential role of genetic and genomic information for increasing focus and improving profitability in the beef supply chain.
Incomplete Latin squares

A description is given of the statistical procedure appropriate for the analysis of a Latin square having missing the whole of one row, one column or one treatment, or one row and one column, or either and a treatment. These are the only types of incomplete Latin squares (except those which can be dealt with by the missing plot technique) for which a neat statistical analysis is possible. It is shown that incomplete Latin squares of these types give unbiased estimates of error and are therefore valid experimental arrangements. They are consequently likely to be of use when the experimental material is such as to preclude the use of a complete Latin square owing to the fact that the number in one or both of the natural groups is one less than the number of treatments to be tested.
Lung dysfunction causes systemic hypoxia in estrogen receptor β knockout (ERβ−/−) mice

Estrogen receptor β (ERβ) is highly expressed in both type I and II pneumocytes as well as bronchiolar epithelial cells. ERα is not detectable in the adult lung. Lungs of adult female ERβ knockout (ERβ−/−) mice have already been reported to have fewer alveoli and reduced elastic recoil. In this article, we report that, by 5 months of age, there are large areas of unexpanded alveoli in lungs of both male and female ERβ−/− mice. There is increased staining for collagen and, by EM, abnormal clusters of collagen fibers are seen in the alveolar septa of ERβ−/− mice. Immunohistochemical analysis and Western blotting with lung membrane fractions of ERβ−/− mice revealed down-regulation of caveolin-1, increased expression of membrane type-1 metalloproteinase, matrix metalloproteinase 2 (active form), and tissue inhibitors of metalloproteinases 2. Hypoxia, measured by immunohistochemical analysis for hypoxia-inducible factor 1α and chemical adducts (with Hypoxyprobe), was evident in the heart, ventral prostate, periovarian sac, kidney, liver, and brain of ERβ−/− mice under resting conditions. Furthermore, both male and female adult ERβ−/− mice were reluctant to run on a treadmill and tissue hypoxia became very pronounced after exercise. We conclude that ERβ is necessary for the maintenance of the extracellular matrix composition in the lung and loss of ERβ leads to abnormal lung structure and systemic hypoxia. Systemic hypoxia may be responsible for the reported left and right heart ventricular hypertrophy and systemic hypertension in ERβ−/− mice.
Hydroids (Cnidaria, Hydrozoa) of Coral Reefs: Preliminary Results on Community Structure, Species Distribution and Reproductive Biology in Juan de Nova Island (Southwest Indian Ocean)

The first field investigation of the marine life at Juan de Nova gave an opportunity to study hydroid diversity in April-May 2004. Species richness was high, with 95 species belonging to 26 families and 44 genera. Thecates dominated (72%), with three families particularly diverse: Haleciidae, Sertulariidae and Aglaopheniidae . There were four different sub-communities with a few species in common: two intertidal and two subtidal. One was located on reef flats subject to strong hydrodynamic conditions, and included rheophilic and photophilic species such as Millepora exaesa, Nemalecium sp. , Dynamena crisoides, Thyroscyphus fruticosus, Thyroscyphus sp. and Aglaophenia cupressina . The second was found where the reef flat experienced calmer conditions, and comprised mainly Plumularioidea and Haleciidae species with small sized colonies (1-3cm) and large populations, densely covering the hard substrata of coral patches. The third sub-community colonized the reef platform (5-20m), with hydroids widespread and diverse. The fourth was on the outer slope, deeper (30m), and was characterized by the presence of four Solanderia species, several Aglaophenids and Thyroscyphus aequalis . Most of the species were brooders (84%). Present data are discussed regarding environmental parameters, and compared with data from the Iles Glorieuses, other islands of the Mozambique Channel. Keywords :Hydrozoa, coral reefs, species richness, distribution, reproductive biology, Indian Ocean West Indian Ocean Journal of Marine Science Vol. 5 (2) 2006: pp. 123-132
Platforms and networks in triterpenoid pharmacology

Using the pentacyclic, naturally occurring triterpenoids, oleanolic, ursolic, and betulinic acids, as starting materials, we have developed a new series of multifunctional drugs for potential clinical use. These agents have anti‐inflammatory, anti‐oxidative, anti‐proliferative, pro‐apoptotic, and differentiating activities. Two synthetic oleanane triterpenoids, 2‐cyano‐3,12‐dioxooleana‐1,9(11)‐dien‐28‐oic acid (CDDO) and its C‐28 methyl ester (CDDO‐Me), are presently in Phase I clinical trials in cancer patients. Three themes are emphasized in this review: (1) The importance of the unique structures of the triterpenoid platforms that have been used as a start for new synthesis; (2) The concept that these new drugs interact with entire physiological networks, rather than solely with single molecular targets; and (3) The coupling in real time between the triterpenoid platforms and the physiological networks with which they interact, as seen in the reversibility of the Michael reactions, which mediate their activity. We suggest that further development of such new, multifunctional drugs will most likely occur in the more flexible environment of small biotech or pharmaceutical companies. Drug Dev Res 68:174–182, 2007. © 2007 Wiley‐Liss, Inc.
The Kinetics of Functional Response

Holling's Type II functional-response relationship is presented, and the formulations expressing the underlying organismal interactions which might generate such a relation arc generalized into the Type III response typical of predators showing learning behavior. An equation derived through an analogy with allosteric enzyme kinetics is given which will account for both Type II and Type III responses. The response behavior can be explained by three parameters: maximal feeding rate (F); an affinity constant (G) related to handling times, capture efficiencies, etc.; and the number of encounters (n) a predator must have with a prey item before becoming maximally efficient at utilizing the prey item as a resource. A discussion follows on the biological processes which result in shifts from Type II to Type III functional responses. Most of the learning processes involve changes in predator behavior associated with increasing encounters with prey, thus supporting parameter n as a major determinant in shifting thc functional response. Three hypotheses concerning the values parameters F, G, and n will assume under different ecological situations are posited: (l) food preferences will be reflected in an increase in resource-utilization efficiency (F) and affinity (G) and a decrease in values of n encounters; (2) a size ordering of the predators will result in shifts up in the resource-utilization efficiency (F) and affinity (G); while (3) increasing habitat complexity will generate decreases in n and F.
Long time series of soil moisture obtained using neural networks: application to AMSR-E and SMOS

(1) CESBIO (CNES, CNRS, UPS, IRD), Toulouse, France (nemesio.rodriguez@cesbio.cnes.fr), (2) Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, Netherlands. , (3) Institut National de Recherche Agronomique (INRA), Bordeaux, France. , (4) European Space Research and Technology Centre (ESTEC), ESA, Noordwijk, Netherlands. , (5) European Space Research Institute (ESRIN), ESA, Frascati, Italy.
Early biotic interactions among introduced and native benthic species reveal cryptic predation and shifts in larval behaviour

Recurrent introductions of non-indigenous species generate novel interactions that vary with local conditions and the composition of the receiving community. Most studies examine relationships of newcomers with native species, but interactions among introduced species could also affect community shifts. As early ontogenetic stages are particularly vulnerable to biotic interactions, we explored direct and indirect interactions across early life-history stages in space-dominating marine invertebrates. We used introduced ascidians and both native and introduced mussels. To increase generality, we ran our experiments in two distant locations, one in the northern and one in the southern hemisphere (Mediterranean and South Africa). We found no sperm interference between the ascidians, nor were there interspecific effects on settlement or metamorphosis success. However, larvae of the ascidian species reacted to each other by shifting from aggregated to random settlement. Juvenile mussels consumed large numbers of ascidian larvae, though larvae that avoided mussel predation showed higher settlement success. Mussel species in the southern hemisphere locality (native Perna perna and introduced Mytilus galloprovincialis) consumed more ascidian larvae than mussels in the northern locality (native M. galloprovincialis) with a tendency for ascidian larvae to avoid settling close to mussels in the latter locality. We conclude that larval consumption by mussels affects the establishment of ascidians, but that the magnitude of this effect is context dependant. These results emphasize the importance of the composition of the receiving community in determining its susceptibility to invasion. Whether the species comprising this community are native or introduced is, however, less important than what manner of species they are.