Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating the performance of otolith morphometrics in deriving age compositions and mortality rates for assessment of data-poor tropical fisheries

Deepwater snappers (Family Lutjanidae) are important to artisanal and subsistence fisheries in Pacific Island countries. Most species of deepwater snapper are considered vulnerable to exploitation due to their extended longevity and low natural mortality rates. However, the sustainability of deepwater snapper fisheries in Pacific Island countries remains uncertain because there are limited resources available to collect the required data for comprehensive stock assessments. Reliable estimates of the age composition for exploited deepwater snapper populations are limited primarily because of the lack of skills and resources required for routine age estimation from sectioned otoliths. The development of alternative low-cost approaches to derive estimates of age for deepwater snappers is required. We evaluated the performance of using otolith morphometrics (weight, length, width, and thickness) to obtain estimates of age for the most important target species in these fisheries: Etelis carbunculus, E. marshi, E. coruscans, and Pristipomoides filamentosus. We compared age compositions and fishing mortality rates (F) derived from otolith morphometrics with those derived from counts of annual increments in otoliths. We then used the ratio of F to natural mortality (M) as a biological indicator to evaluate the potential effects on management responses by comparing estimates of F/M derived from otolith morphometrics with those derived from annual increment counts. Age compositions and estimates of F and F/M did not differ significantly between those derived from otolith morphometrics and those derived from annual increment counts for all species. These results demonstrate that management responses would likely be similar whether based on age estimates derived from sectioned otoliths, or predicted from otolith morphometrics. In the absence of sufficient resources to section otoliths for age estimation, we recommend that otolith morphometrics be used as a proxy for age in assessments of deepwater snapper fisheries in Pacific Island countries, and potentially for other similar data-limited fisheries.
End-of-Season Carcass and Reproductive Traits in Original and Replacement Male Broiler Breeders

Abstract Reproductive efficiency of male broiler breeders declines toward the end of a production cycle. It is common to add young, replacement males (spiking) to a breeder flock to maintain or increase fertility. To date, no study has reported if there are differences in the carcass and reproductive morphology between original and spiked males at the end of the breeding period. In this study, the weight, fleshing traits, footpad condition, and testes size of 327 Hubbard males (237 original and 90 replacement) from a commercial operation were examined. The original birds (63 wk of age) had significantly higher BW, breast weight, girth measurement, keel length, and spur length than the spiked males (48 wk of age). While external indicators of size and fleshing differed betweenreplacement and original roosters, testis weight was not affected by the age of the bird. It was found that average testis weight correlated well with BW in birds in which testicular regression had not taken place but only weakly with spur length. Because original males had a higher BW and were more heavily fleshed than replacement males, their ability to successfully complete matings may have been impeded. Further research is needed to link growth profiles with semen quality, sexual behavioral, and longevity of a male breeder in a commercial flock.
Correlating small mammal community characteristics and habitat integrity in the Caledon Nature Reserve, South Africa

Abstract This study quantifies habitat-specific small mammal patterns in the Caledon Nature Reserve, Free State province, South Africa. Small mammal community variables were correlated with an Ecological Index, the current method used to interpret habitat integrity in Free State nature reserves. It also reports on the seasonal abundance, species richness and diversity of small mammals present in specific habitats and addresses the most successful methods to sample these taxa, such as the duration of trapping to ensure unbiased sampling, and in which season should effort be concentrated to obtain optimal results. Our results support expectations that small mammal species richness increase with Ecological Index value, the number of specialist species in Free State grasslands increases with succession up to the climax phase, and that Mastomys coucha dominance acts as an indicator of habitat disturbance. It also supports previous studies that have shown a minimum trapping period of 3 days and nights, and best trap success and species richness at the end of autumn–early winter.
Endemicity analysis, parsimony and biotic elements: a formal comparison using hypothetical distributions

There is as yet no general agreement regarding the most appropriate solution to the problem of identifying areas of endemism, not even in particular cases. In this study, we compared Endemicity Analysis (EA), Parsimony Analysis of Endemicity (PAE), and Biotic Elements Analysis (BE) based on their ability to identify hypothetical predefined patterns that represent nested, overlapping, and disjoint areas of endemism supported by species with different degrees of sympatry. We found that PAE performs poorly when applied to patterns that either overlap with each other or are supported by species with imperfect sympatry. BE exhibits a counterintuitive sensitivity to the degree of congruence among the distributions of endemic species, being unable to recognize areas of endemism supported by perfectly sympatric species. In contrast, in all cases examined we found that EA results in a high proportion of correctly identified distributional patterns. In addition to highlighting the strengths and limitations of these approaches, our results show how different methods can lead to seemingly conflicting conclusions and caution about the possibility of identifying distributional patterns that are merely methodological artefacts.
Distribution, body size, and brood characteristics of four species of mysids (Crustacea: Peracarida) in the Avon-Heathcote Estuary, New Zealand

Four species of mysids are resident in the Avon-Heathcote Estuary, Christchurch. Tenagomysis macropsis is by far the most abundant daytime species and has a wide distribution, not linearly correlated with salinity. Tenagomysis novae-zealandiae and T. chiltoni are much less abundant, increase in numbertoward the upper estuarineregion, and (especially T. chiltoni) have distributions significantly correlated with salinity (P < 0.05–0.001). T. chiltoni has a spring/summer population maximum. Gastrosaccus australis appears to be an obligate nocturnal plankter and its; distribution in the system is unresolved. The largest mysid was T. chiltoni and the smallest T. novae-zealandiae, although there was considerable intraspecific size variation. For all 3 Tenagomysis species, males were mature at a smaller size than females, whereas the opposite was true for G. australis. For each species, ovigerous females generally achieved the maximum size recorded. Embryo numbers carried in the marsupium ranged from 4 to 25 for T. macropsis, from 6 to 19 for T. novae-zealandiae, and from 22 to 39 for T. chiltoni. Embryo sizes for the New Zealand species are in accord with the range found generally for coastal mysids.
Sugarcane leaf area index modeling under different soil water conditions

The knowledge of the Leaf Area Index (LAI) variation during the whole crop cycle is essential to the modeling of the plant growth and development and, consequently, of the crop yield. Sugarcane LAI evolution models were developed for different crop cycles, by adjusting observed LAI values and growing degree-days summation data on a power-exponential function. The resultant equations simulate adequately the LAI behavior during the entire crop cycle. The effect of different water stress levels was calculated in different growth periods, upon the LAI growth The LAI growth deficit was correlated with the ratio between actual evapotranspiration and maximum evapotranspiration, and a constant named kuu was obtained hi each situation. It was noticed that the kLAI must be estimated not Just for different growth periods, but also for different water stress levels in each growth period.
Chemical control of ufra disease of rice.

Abstract Ufra disease, caused by the rice stem nematode, Ditylenchus angustus, is the most important disease of deep-water rice. Rice plants showing symptoms of ufra disease 15 days after artificial inoculation with the nematode, were treated three times with 0.2% diazinon (60 e.c.), 0.1% benomyl (50 w.p.) and carbofuran granules (3%) at the rate of 22.4 kg product/ha at 15 day intervals. Forty-five days after the first application, 82% of each of benomyl treated and carbofuran treated plants, 17% of the diazinon treated plants and 18% of the untreated control plants recovered and flowered normally. Preliminary attempts to evaluate these findings in deep-water rice under field conditions, showed that 58% of benomyl treated, 61% of carbofuran treated and 10% each of diazinon treated and untreated control plants recovered and flowered normally. The results indicate that there is a possibility of using benomyl, a systemic fungicide and carbofuran, a systemic insecticide, for the control of ufra disease.
ALLEVIATION OF WATERLOGGING DAMAGE TO YOUNG BARLEY PLANTS BY APPLICATION OF NITRATE AND A SYNTHETIC CYTOKININ, AND COMPARISON BETWEEN THE EFFECTS OF WATERLOGGING, NITROGEN DEFICIENCY AND ROOT EXCISION

Summary A study was made of the effects of either 6-benzylaminopuiine (BAP), a synthetic cytokinin, or calcium nitrate on the response of the shoots of 13-day-old barley plants to soil waterlogging. Spraying leaves daily with BAP resulted in small improvements in leaf extension and retarded the premature loss of chlorophyll in the older leaves after 7 days waterlogging, but the rates of accumulation of dry matter and inorganic nutrients in shoots were reduced to the same extent as in unsprayed plants. After a further 7 days waterlogging, during which spraying was discontinued, plants treated with BAP were no longer appreciably different from untreated ones. When calcium nitrate was added daily to the surface of the waterlogged soil, no symptoms of waterlogging damage appeared. Leaf extension, shoot weight, emergence of tillers, chlorophyll concentrations and the accumulation of inorganic nutrients in shoots were similar to those in plants in non-waterlogged soil after 7 and 14 days. The effect was dependent on the presence of a narrow zone of aerated soil close to the surface, in which root growth and function could continue. When plants were grown for 13 days in aerated nutrient solution, and then transferred to solutions lacking nitrate, the development of leaf chlorosis, the decrease in the concentration of nitrogen in the shoots and their retarded accumulation of dry matter were all similar to that caused by waterlogging. The premature loss of chlorophyll in the older leaves was retarded by spraying with BAP. Chlorosis of the older leaves could also be promoted in plants in aerated nutrient solution by excising part of the root system. Mechanisms by which BAP and calcium nitrate alleviate symptoms of waterlogging damage, and the significance of nitrogen deficiency and root excision in relation to waterlogging damage, are discussed.
Dendrochronologiczna analiza przyrostów rocznych świerka pospolitego (Picea abies (L.) Karsten) poza naturalnym zasięgiem a cechy biometryczne szyszek

ABSTRACT Dendrochronologiczna analiza przyrostow rocznych świerka pospolitego ( Picea abies (L.) Karsten) poza naturalnym zasiegiem a cechy biometryczne szyszek Addresses Marcin Koprowski – Pracownia Dendrochronologiczna; Instytut Ekologii i Ochrony Środowiska UMK;ul. Gagarina 9; 87−100 Torun; e−mail: koper@umk.pl Praca naukowa finansowana ze środkow na nauke w latach 2005−2007 jako projekt badawczy Wstep Areal naturalnego wystepowania świerka pospolitego podzielony jest w Polsce na dwie cześci. W polnocno−wschodniej cześci kraju rosną drzewa z zasiegu borealno−baltyckiego, natomiastwyzynna i gorska cześc poludniowa znajduje sie w zasiegu hercynsko−karpackiem [Boratynski1998]. Udzial czlowieka w ksztaltowaniu środowiska leśnego sprawil, ze gatunek ten zostalwprowadzony w rejony, ktore znajdują sie poza jego naturalnym zasiegiem. Powszechne wyste−powanie świerka z dala od granicy jego arealu, np. w Polsce w polnocno−zachodniej, umozliwiaprześledzenie dynamiki przyrostowej tego gatunku na obszarze gdzie przewazają odmienne nizw zakresie naturalnego zasiegu cechy klimatu. Pod wzgledem dendrochronologicznym świerk pospolity jest gatunkiem stosunkowodobrze poznanym [Makinen i in. 2001; Wilson, Hopfmuller 2001; Makinen i in. 2003; Dittmar,Elling 2004; Vitas 2004]. W Polsce, do tej pory, przedmiotem zainteresowania byly glowniedrzewa rosnące w obrebie naturalnego zasiegu [Feliksik, Wilczynski 2000; Zielski, Koprowski2001; Koprowski, Zielski 2002; Koprowski, Zielski 2006]. Badania nad wplywem czynnikowśrodowiskowych u świerkow z roznych proweniencji prowadzili Burczyk i Giertych [1988].
Non‐anemic homozygous βo thalassemia in an African‐American family: Association of high fetal hemoglobin levels with β thalassemia alleles

We have studied a four‐generation (23 subjects) African‐American family with βo thalassemia and high fetal hemoglobin (HbF) levels. The βo thalassemia in this family is due to the splicing site mutation, β IVS2+1G→A, that leads to aberrant mRNA processing and the absence of β globin. Two members of this family are homozygous for βo thalassemia and are non‐anemic. All family members who are heterozygous for the β IVS2+1G→A mutation have elevated HbF, with the exception of two individuals who also have severe α‐globin chain deficiency. We excluded linkage with the hereditary persistence of fetal hemoglobin loci on chromosomes 6 and X. We also excluded the presence of all previously described determinants in the β globin gene cluster associated with elevated HbF production. One thalassemia allele is in the Cameroon‐like (HS2)/Benin‐like β globin gene cluster haplotype, and the other is in the Senegal‐like (HS2)/Benin‐like β globin gene cluster haplotype. We speculate that in the homozygotes, those erythroid cells that express low to absent levels of γ globin are selectively destroyed. In contrast, in the heterozygotes, the presence of the normal β globin allele would ameliorate the globin chain imbalance and thus allow survival of erythroid cells that express the abnormal transcript, leading to a typical βo thalassemia phenotype. Thus, the heterocellular γ globin expression together with in vivo preferential survival of HbF‐containing erythroid cells ameliorates Cooley's anemia in the βo thalassemia homozygotes. It remains to be determined what sequences linked to each thalassemia allele and what trans‐acting factors contribute to high HbF levels. Am. J. Hematol. 68:43–50, 2001. © 2001 Wiley‐Liss, Inc.
The salicylic acid‐dependent defence pathway is effective against different pathogens in tomato and tobacco

The role of salicylic acid (SA) was investigated in basal defence and induced resistance to powdery mildew (Oidium neolycopersici) and grey mould (Botrytis cinerea) in tomato (Lycopersicon esculentum) and tobacco (Nicotiana tabacum). A comparison of NahG transgenic tomato and tobacco (unable to accumulate SA) to their respective wild types revealed that in tomato, SA was not involved in basal defence against O. neolycopersici but NahG tobacco showed an enhanced susceptibility to O. neolycopersici infection, the effect becoming more obvious as the plants grew older. In contrast, SA played no role in the basal defence of tobacco against B. cinerea, but seemed to contribute to basal defence of tomato against B. cinerea. Activation of the SA-dependent defence pathway via benzothiadiazole (BTH) resulted in induced resistance against O. neolycopersici in tobacco but not in tomato. Microscopic analysis revealed that BTH treatment could prevent penetration of the Oidium germ tube through tobacco leaves, whereas penetration was successful on tomato leaves irrespective of BTH treatment. In contrast, soil or leaf treatment with BTH induced resistance against B. cinerea in tomato but not in tobacco. It is concluded that the SA-dependent defence pathway is effective against different pathogens in tomato and tobacco.
Pollen Dispersal in a Mountain Area

Abstract Atmospheric pollen, phenologic and meteorologic data collected during 12 intervals throughout one year in Tauber traps at different elevations allowed conclusions on vertical pollen dispersal in a mountain/valley system in the Niederhorn, Switzerland. Thus, pollen spectra at higher elevations near the timberline cannot be explained by dispersal through upslope winds but through gradient winds, i.e., winds from the general prevailing direction. The gradient wind direction lying perpendicular to the slope in consideration resulted in high elevation pollen spectra representing a regional aspect whereas the lower elevation spectra more or less faithfully recorded the local vegetation. High pollen numbers occur only during the respective local pollen production period. Secondary high pollen numbers related to precipitation maxima amount to about 10%, exceptionally 20% of the total annual pollen of the respective taxon. Thus, the washout of the pollen filtered in the vegetation seems to be of minor imp.
Rhodocytin Induces Platelet Aggregation by Interacting with Glycoprotein Ia/IIa (GPIa/IIa, Integrin α2β1)

Although glycoprotein Ia/IIa (GPIa/IIa, integrin α2β1) has established its role as a collagen receptor, it remains unclear whether GPIa/IIa mediates activation signals. In this study, we show that rhodocytin, purified from the Calloselasma rhodostoma venom, induces platelet aggregation, which can be blocked by anti-GPIa monoclonal antibodies. Studies with rhodocytin-coupled beads and liposomes loaded with recombinant GPIa/IIa demonstrated that rhodocytin directly binds to GPIa/IIa independently of divalent cations. In vitro kinase assays and Western blotting of GPIa immunoprecipitates revealed that Src and Lyn constitutively associate with GPIa/IIa and that Src activity increases transiently after rhodocytin stimulation. Src specifically associates with p130 Crk-associated substrate (Cas) in a manner dependent upon Cas phosphorylation, suggesting that Src is responsible for Cas tyrosine phosphorylation. While all these phenomena occur early after rhodocytin stimulation in a cAMP-resistant manner, tyrosine phosphorylation of Syk and phospholipase Cγ2, intracellular Ca2+ mobilization, and platelet aggregation occur later in a cAMP-sensitive manner. Cytochalasin D, which interferes with actin polymerization and blocks receptor clustering, inhibits all the rhodocytin-mediated signals we examined in this study. We suggest that rhodocytin, by clustering GPIa/IIa, activates GPIa/IIa-associated Src, which then mediates downstream activation signals.
Prevalence of gastrointestinal protozoa and association with risk factors in free-range pigs in Kenya

The current study investigated the occurrence of gastrointestinal tract (GIT) protozoa and associated risk factors in free range pigs in Busia District, Kenya. A total of 306 pigs from 135 farms in 6 Divisions were sampled for feces, which were analysed for parasites using direct smear and McMaster floatation methods. Associations between the occurrence of the parasites and explanatory variables (sex, age, division of origin and rainfall) were undertaken using ANOVA, chi-square and Pearson’s correlation statistics. The following gastrointestinal protozoan parasites were identified: Entamoeba spp. (87%), Balantidium coli (64%), Tritrichomonas suis (42%) and Coccidia spp (33%). The mean coccidial oocysts per gram (OPG) of all the sampled pigs was 1,276 (range = 0-28,000 OPG) and the proportions of the species included: Eimeria debliecki (40%), E. suis (26%), E. porci (16%), E. scabra (13%) and E. polita (5%). There was negative correlation between the amount of rainfall in the division of pig origin and prevalence of Eimeria spp, Tt. suis, and Entamoeba spp, but a positive correlation with prevalence of B. coli. The prevalences of Eimeria spp. , Entamoeba spp. and Tt. suis were higher in males than females; but it was only the sex-differences for Tt. suis which were statistically significant (p < 0.05). The prevalences of Tt. suis in sows were significantly (p < 0.05) lower than that of growers and piglets. It was concluded that GIT protozoan parasites of economic and zoonotic significance occur in pigs in the study area and effective control strategies should be implemented.
Secular Trends in Incidence of Childhood IDDM in 10 Countries

Standardized childhood insulin-dependent diabetes mellitus (IDDM) incidence data were collected from 21 ethnic groups in 10 countries to evaluate temporal trends in the disease between 1966 and 1986. Population-based registries contributed information concerning periods from 6 to 21 yr. The incidence rates were modeled with Poisson regression. For the past 2 decades, a linear increase in IDDM risk for people <15 yr of age has been observed in most of Europe and the Western Pacific but not in North America. The temporal variation did not appear to differ significantly by age or sex in most locations. The observed pattern of temporal variation suggests that a proportion of diabetes in childhood may be caused by a potentially preventable environmental factor.
Survivorship, Growth, and Detection of a Knob-scaled Lizard in Queretaro, Mexico

Abstract A deep understanding of the processes affecting the population dynamics of living organisms requires fine-scale analyses of basic demographic parameters such as stage-specific survival and growth rates. In this study we estimated survival, detection, and transition rates (growth) for different stages of the life cycle of a Knob-scaled Lizard of the genus Xenosaurus. We also examined potential sources of variation for these parameters by means of a multiple-model inference framework. Our capture–mark–recapture data revealed that survival rates were homogeneous among stage classes but markedly different between the rainy and dry seasons. Contrary to our expectation, survival probability was higher during dry months. Detection probability varied considerably among stage classes and through time. Consistent with theoretical predictions, the rate at which lizards moved from a particular stage class to the following (transition rates) varied among stage classes, with the fastest rates observed in yearlings and the slowest in adults. Also consistent with our predictions, we found a tendency toward faster transition rates during rainy months. We discuss the potential causes and implications of the patterns of variation observed in these key demographic parameters.