Miracle-dz/UniFAR-FTUs huggingface dataset:
ASSESSING BYCATCH REDUCTION POTENTIAL OF VARIABLE STRENGTH HOOKS FOR PILOT WHALES IN A WESTERN NORTH ATLANTIC PELAGIC LONGLINE FISHERY

The pelagic longline fishery off Cape Hattaras in the western North Atlantic Ocean, which targets swordfish (Xiphias gladius, Linnaeus 1758) and tunas (Thunnus spp.), has a high frequency of interactions with marine mammals, particularly pilot whales (Globicephala spp.). The typical hooks used in the this fishery are size 16/0 ''strong'' hooks that straighten at 250 lb of pull (113 kg); some fishermen use alternative ''weak'' hooks that straighten at 150 lb of pull (68 kg). Other commonly used hooks in this fishery are size 18/0 strong hooks that straighten at 350 lb (159 kg) of pull, and the weak equivalent hooks that straighten at 225 lb (102 kg). Taking advantage of the size difference between large bycatch animals and relatively smaller target species, weak hooks could be implemented to reduce bycatch. Twenty-one pelagic longline sets were made targeting yellowfin tuna (T. albacares, Bonnaterre 1788) and bigeye tuna (T. obesus, Lowe 1839) using alternating 16/0 strong and weak hooks. Nine additional sets targeted swordfish with size 18/0 hooks and the same alternating hook methodology. No significant reduction in total tuna catch (a , 0.05) or of any target species, although weak hooks exhibited higher catch per unit effort (CPUE) for tuna and swordfish. The only species with a significant difference in total catch between strong and weak 16/0 hooks was the pelagic stingray (Pteroplatytrygon violacea, Bonaparte, 1832), with more individuals caught by the strong hook. The sets with 18/0 hooks had similar catches for all species, except the target species swordfish. Swordfish CPUE was higher with the strong hooks, and had significantly higher total catches. Seven weak hooks were retrieved straightened, and one of these hooks was observed being straightened by a pilot whale. While not conclusive, such results suggest further research into weak hooks for the reduction of large animal bycatch in the pelagic longline fishery.
Natural history, population dynamics, and habitat use of humpback whales over 30 years on an Alaska feeding ground

The rigorous program of monitoring humpback whales (Megaptera novaeangliae), implemented by Glacier Bay National Park and Preserve in 1985, augmented by additional data collected in southeastern Alaska since 1968, constitutes one of the longest studies of living whales in the world. This monitoring program, now a National Park Service (NPS) Inventory and Monitoring Program Vital Sign, employed consistent methods for summer surveys from 1985 to 2014 to document the number of whales and gather longitudinal records on individuals in Glacier Bay and Icy Strait. Survey effort averaged 355.4 h/yr (SD = 45.8), resulting in 9485 encounters with 662 individual whales, including 276 calves. The population increased at a rate of 5.1%/yr, from 41 individuals in 1985 to 239 individuals in 2013, primarily due to long-term site fidelity and local recruitment. We documented sighting histories of >30 yr in southeastern Alaska, for 54 whales, including one 45-yr sighting history. Almost half of the whales first identified as calves returned in subsequent years, at a mean age of 3.2 yr (SE = 0.28, range = 1–17 yr). Over 75% of females had their first calf by age 13. The maximum female reproductive span was 32 yr, and the maximum number of calves was 11. We estimated mean effective calving rate with a simple ratio and used logistic regression to estimate calving probability. Both methods resulted in similar maximal estimates that were somewhat lower than previously published values for this species: 0.324 (95% CL: 0.28–0.36) calves·female−1·yr−1 vs. calving probability of 0.319 (95% CL: 0.29–0.35). Minimal estimates, in which the first calf of each known-aged female was omitted, were 0.302 (95% CL: 0.27–0.34) calves·mature female−1·yr−1 vs. calving probability of 0.305 (95% CL: 0.27–0.34) calves·mature female−1·yr−1. This monitoring program has guided Park management actions and documented this once critically endangered population's trajectory toward recovery, often through collaboration with other agencies and organizations, fostering the continued protection and understanding of this distinctive species. Our findings highlight the value of marine protected areas for migratory species with strong seasonal site fidelity and the role of long-term monitoring in interpreting population-level responses to changing marine ecosystems.
Dissipation of fluroxypyr in a Malaysian agricultural soil with simulation using the PERSIST and VARLEACH model.

The study was carried out to compare the dissipation of fluroxypyr in a Malaysian agricultural soil based on field experimentation and simulation using the PERSIST and VARLEACH model. A plot situated in an oil palm plantation near Sepang, Selangor, Malaysia was selected for the field experiment. The plot was treated with fluroxypyr at the recommended dosage (72.5 g ha-1). The soil samples from the field trial were collected and analyses conducted in the laboratory according to the sampling schedule. Simulation of fluroxypyr persistence and leaching was also conducted using computer-run software, PERSIST and VARLEACH. The predicted data obtained using PERSIST for fluroxypyr was found to be higher than the observed data from field measurements. However, the predicted data for fluroxypyr using VARLEACH matched well with the observed data from the field trial.
Phylogeographical studies of Glycine soja: implicating the refugium during the Quaternary glacial period and large-scale expansion after the Last Glacial Maximum

Wild soybean (Glycine soja Sieb. & Zucc.), the progenitor of cultivated soybean (Glycine max (L.) Merr. ), is widely distributed in the Sino-Japanese Floristic Region (SJFR). Therefore, it is an excellent model organism to study the effect of Quaternary climatic changes on the distribution and migration of plant taxa in the SJFR. To investigate the phylogeography of G. soja, a total of 632 individuals representing 52 populations throughout the species distribution range were genotyped by using the sequencing data of a nuclear locus, AF105221, and a chloroplast locus, trnQ-rps16. We detected a total of 23 haplotypes from two loci, including five common and 18 rare haplotypes. Among them, 17 rare haplotypes were limited to Northeast Asia (Northeast China (NEC) and Korea) and the Yangzi River basin (middle and downstream of the Yangzi River (MDYR) and the eastern end of Southwest China (SWC)). Moreover, two common haplotypes were detected throughout the species distribution wide range. All the haplotypes from Japan and the Korean peninsula were also found in China. The haplotype distribution patterns of the two loci suggested that Northeast Asia (NEC and Korea) and the Yangzi River basin (MDYR and the eastern end of SWC) might have been the refugia for G. soja during the Quaternary glacial period, and G. soja expanded rapidly after the end of the Last Glacial Maximum. There was a land bridge between East China, the Korean peninsula, and Japan that permitted gene flow among populations of these regions in the ice age during the Quaternary.
Mechanisms Regulating Early Mesendodermal Differentiation of Human Embryonic Stem Cells: A Dissertation

Key regulatory events take place at very early stages of human embryonic stem cell (hESC) differentiation to accommodate their ability to differentiate into different lineages; this work examines two separate regulatory events. To investigate precise mechanisms that link alterations in the cell cycle and early differentiation, we examined the initial stages of mesendodermal lineage commitment and observed a cell cycle pause that occurred concurrently with an increase in genes that regulate the G2/M transition, including WEE1. Inhibition of WEE1 prevented the G2 pause. Directed differentiation of hESCs revealed that cells paused during commitment to the endo- and mesodermal, but not ectodermal, lineages. Functionally, WEE1 inhibition during meso- and endodermal differentiation selectively decreased expression of definitive endodermal markers SOX17 and FOXA2. These findings reveal a novel G2 cell cycle pause required for endodermal differentiation. A role for phenotypic transcription factors in very early differentiation is unknown. From a screen of candidate factors during early mesendodermal differentiation, we found that RUNX1 is selectively and transiently up-regulated. Transcriptome and functional analyses upon RUNX1 depletion established a role for RUNX1 in promoting cell motility. In parallel, we discovered a loss of repression for several epithelial genes, indicating that RUNX1 knockdown impaired an epithelial to mesenchymal transition during differentiation. Cell biological and biochemical approaches revealed that RUNX1 depletion compromised TGFβ2 signaling. Both the decrease in motility and deregulated epithelial marker expression upon RUNX1 depletion were rescued by reintroduction of TGFβ2, but not TGFβ1. These findings identify novel roles for RUNX1-TGFβ2 signaling in mesendodermal lineage commitment.
Use of genetic markers in pig breeding programs

The objective of this thesis was to investigate the use of genetic markers in commercial pig breeding, with a special emphasis on genomically imprinted genes. For the latter purpose, an association study was undertaken to identify genomically imprinted QTL related to sow fertility traits in two commercial pig populations. Furthermore, several simulation studies were performed to evaluate methods to estimate breeding values with marker data. Finally, a new method was designed to estimate the parental origin of marker alleles in crossed populations when the pedigree is unknown. The association study involved approximately sows from two commercial pig populations. The sows were genotyped for SNP markers, of which were finally used. The results revealed one SNP with a significant imprinting effect on the trait litter size in one population. The imprinting effect of this SNP was not significant in the other population but its effect was similar. The SNP was located close to the gene DIO3, which has a known imprinting status. Furthermore, several SNP with significant additive and dominance effects were found in both populations. The simulation studies were designed to evaluate the effect of the number of genes and the relative importance of these genes on the trait on performance of distinct methods to estimate breeding values with markers. Results of the first study showed that the performance of these methods is affected by gene number and size. Results of the second study continued on these results and showed that genetic gain achievable by selecting on breeding values estimated by these methods strongly depends on the number of genes and their relative size. Knowledge of parental origin of marker or gene alleles is of crucial importance to study genomically imprinted genes. A method based on the Dirichlet Process was designed to estimate the parental origin of SNP alleles in crossed populations. The method performed better than methods that did not account crossbreeding, and the performance of the method was strongly improved when some genotypes of some parental individuals were available in the data. The last chapter evaluated the influence of genomic imprinting on genetic parameters of genes. An important conclusion of this chapter is that genomically imprinted genes have less variance compared to similar, non-imprinted genes. This lower variance leads to lower power of statistical methods to detect these genes and lower genetic gain achievable in breeding programs. On the other hand, however, genomically imprinted genes could be effectively used in crossbreeding programs.
Effect of starter culture addition on fatty acid profile, oxidative and sensory stability of traditional fermented sausage (Petrovská klobása)

This work is concerned with the oxidative stability and sensory characteristics of traditional fermented sausage Petrovská klobása, produced with the addition of commercial starter culture (SC). Fatty acids profile, thiobarbituric acid-reactive substance (TBARS) values and sensory properties of odor and taste have been determined at the end of drying and after 2 and 5 months of storage. The sum of saturated, unsaturated and polyunsaturated fatty acids was not significantly different (P>0.05) in SC and control sausage at the end of storage. After 5 months of storage TBARS value of SC sausage amounted to 0.57 mg MDA/kg, and it was significantly lower (P<0.05) compared to control (0.84 mg MDA/kg). Also, sensory properties of odor and taste of SC sausage (3.66) were better in comparison to control (3.55). This study demonstrated that the addition of starter culture can hinder lipid oxidation and contribute to the preservation of desirable sensory characteristics of fermented sausages during a long storage period.
Evaluation of ant baits for control of Pheidole megacephala (Hymenoptera: Formicidae) on Lord Howe Island, Australia.

Lord Howe Island is a small sub-tropical island off the east coast of Australia. African bigheaded ant Pheidole megacephala (F.) was discovered on the island in 2003 and been subject to ongoing attempts at eradication resulting from concerns over its impact on native biota. In 2006-2007 a trial was conducted to evaluate various commercial and experimental ant baits, including AmdroTM Granular Ant bait (hydramethylnon) and Distance® Plus Ant Bait (pyriproxyfen), for the control of P. megacephala on Lord Howe Island. Pyriproxyfen eliminated P. megacephala within 33 weeks, as did a combined pyriproxyfen/ hydramethylnon experimental bait, whereas formulations containing hydramethylnon alone reduced numbers to low levels but did not entirely eliminate P. megacephala from those blocks. Abundance of P. megacephala in blocks treated with Hydramethylnon-based baits returned to normal by 91 weeks after treatment whereas abundance remained low in the block treated with pyriproxyfen.
Effects of Plant Age on Nitrogen Uptake and Distribution by Greenhouse Plants

Water-soluble nitrogen (N) fertilizer is used intensively in greenhouse crop production. Any N not used by a crop is subject to leaching as nitrate (NO3-N), which may pollute groundwater. A close correlation between N supply and N uptake by plants would increase the efficiency of N fertilization and minimize the possibility of NO3-N pollution. The objectives of this study were to measure N uptake by American marigold (Tagetes erecta L. `First Lady') and New Guinea impatiens (NGI) (Impatiens hawkeri Bull. `Selenia') during growth to determine the effect of plant age on N uptake, determine if the two species have a preference for NO3-N or ammonium (NH4-N), and determine the total N required for 70 days of growth. The plants were grown in solution culture using solutions supplying 120 mg each of NO3-N and NH4-N. At 10-day intervals, six cultures were chosen at random for nutrient solution analysis and plant sampling for dry weight and tissue analysis. Nitrate-N uptake was greater than NH4-N uptake throughout the experiment for both marigold and NGI. Total N uptake by marigold was greater during the first 50 days after transplanting with maximum N uptake during the period 30 to 50 days. In contrast, N uptake by NGI was greater during the period 40 to 70 days after transplanting. Maximum N uptake for NGI occurred during the period 60 to 70 days. Results of this study suggest that early N fertilization of marigold could be more important for their growth and quality than N applied later. For NGI, N fertilization later in the crop's development appears to be more important than early on. The total N absorbed by marigold during the experiment was 1.1 g N/plant; for NGI the quantity was 0.5 g N/plant. E-mail teljaoual@pssci.umass. edu; phone (413) 545-3083.
Ameliorating Role of Nitric Oxide in Germinating Mung Bean Seeds ( Vigna Radiata ) Under Lead Stress

Protective role of nitric oxide (NO) on seed germination and growth was studied in mung bean seeds (Vigna radiata) subjected to lead (Pb) stress. Germination percentage was increased up to 50 μM sodium nitroprusside (SNP) and then steady declined. Under lead stress, and absence of SNP, percentage of germination, fresh biomass, succulent value and the activity of α-amylase and protease as well as HATPase were significantly decreased. This was accompanied with a significant increase of hydrogen peroxide and malondialdhyde accumulation, catalase and guiacol peroxidase activities. Furthermore, total phenolic compounds as well as some individual phenolic acids were increased in a dose-dependent manner of lead. The protein pattern showed appearance of stress protein with M. M. of 110, 97 and 21 KDa at various lead stresses. Moreover, supplementation of SNP, as source of NO, increased fresh biomass, succulent values and enhanced the activities of H-ATPase, αamylase, protease, catalase and guiacol peroxidase in lead stressed germinating bean seeds, whereas reduced the lead-induced increase in lead, hydrogen peroxide, malondialdhyde and phenolics accumulation. A new stress protein with M.M. 65 KDa was appeared in all lead stressed seedlings in presence of SNP. Taken together these results suggest that SNP could increase antioxidant capability in mung bean seeds leading to an improvement in the plasma membrane integrity and enhancement of the activities of hydrolytic enzymes and hence, an ameliorating role against the inhibitory impact of this toxicant on the germination and growth of mung bean seeds under lead stress.
The reptiles of Anatolia: a checklist and zoogeographical analysis

Biogeographia - vol. XXI — 2000 (Pubb/icato il 30 giugno 2000) Biogeografia de|l’AnatoIia The reptiles of Anatolia: a checklist and zoogeographical analysis 1 ROBERTO SINDACO *, ALBERTO VENCH1”, GIUSEPPE M. CARPANETO **, MARCO A. BOLOGNA** ”‘c/0 Museo Ciz/ico di Storizz Naturzzle, CI’. 89 - I-10022 Czzmulgnolzz (TO) (Italy) **Dz'pzzrtiment0 Ali Biologia, Universitiz degli Studi “Roma Tre”, Vizzle G. Marconi, 446 — ]—00146R0mzz (Italy) Key words: reptiles, Anatolia, Near East, zoogeography, faunas. SUMMARY The geographical distribution 0F Reptiles in the Anatolian region is examined and discussed, in comparison with the reptile faunas of other Near East areas. The study area was confined to the Asiatic territories included within the political borders of the Turkish Republic, and the Greek islands along the Turkish coasts; the Turkish Thrace was excluded because on the European continental shelf. An updated checklist of the 109 species of indigenous reptiles (8 Turtles, 1 Amphisbaenian, 55 Lizards, 45 Snakes), belonging to 48 genera and 19 families, is presented. For each species are given: (1) the general distribution, (2) the distribution in Anatolia, (3) the main chorotype and the detailed one, (4) a short notice on affinities when available, (5) an outline of subspecies occurring in Anatolia, (6) a map with both bibliographic and unpublished records (for indigenous species only). The term “endemicq was used For species found solely in Anatolia or living within Anatolia and extending to some restricted adjacent areas. The highest number (10) of endemic taxa is referable to an “Armenianq pattern of distribution, which usually includes species inhabiting mountains or plateaux. These are usually adapted to steppe or rocky habitats in the north—eastern Anatolia and, more or less marginally, also in Transcaucasia. Excluding the endemic species, representing the 26% of the reptile fauna, three chorotypes are dominant: the SW—Asiatic (23%), the E—Mediterranean (18%), and the Turano—Mediterranean (9%). Other chorotypes are represented by low percentages, except for the Mediterranean (5%). From the similarity dendrogram, six larger divisions corresponding to main geographic regions of Anatolia were selected and then compared with 13 selected geographic areas outside Anatolia, in order to check their faunistic affinities. INTRODUCTION The herpetofauna of the Near East is very rich and diverse. In terms of species richness and taxonomic diversity of reptiles, this area harbours the most remarkable reptile fauna within the Western Palaearctic region, owing to the high habitat diversity and historical zoogeographical factors. Present knowledge is based on some major works dealing with national or regional areas (e.g., Baran, 1976, Basoglu and Baran, 1977, 1980; Baran and Atatiir, 1998: Turkey; Disi, 1 Zoological researches in the Near East by the Universities of Rome: 197. This study was supported by grants from MURST 1999 (University of “Roma Tre”) “Variazione geograﬁm e diversita a livello di specie, faune e zoocenosi: cause storiche ed ecologicheq. ,
Sweet GLUTs: Quantitative Analysis of Glucose Transporter and Fructolytic Enzyme Transcript Densities in Ruby-throated Hummingbirds (Archilochus colubris)

Hummingbirds are able to fuel energetically expensive hovering flight entirely with recently ingested glucose or fructose. In other animals, several steps in the pathway of flux of sugars from the gut to muscle are rate-limiting, such as transport into muscle and subsequent phosphorylation. I examined relative expression of facilitative sugar transporters and enzymes of fructolysis in various ruby-throated hummingbird (Archilochus colubris) tissues via quantitative polymerase chain reaction. I hypothesized that the expression of these proteins would be upregulated in hummingbird flight muscle compared to other vertebrates. I found that hummingbird pectoralis displays the highest expression of certain sugar transporter transcripts among vertebrates. I also demonstrated that relative transcript densities of fructolytic enzymes are minimal in hummingbird muscle, suggesting that fructolysis is not a pathway used to rapidly metabolize fructose in these muscles.
The biogeography of Mediterranean cephalopods

Biogeographia vol. XXIV - 2003 (Printed October, 31 st 2003) Marine biogeography of the Mediterranean Sea: patterns and dynamics of biodiversity The biogeography of Mediterranean cephalopods* GIAMBATTISTA BELLO Servizia Ittico Am/7z'e7zz‘zz[e, Proz/incizz zli Bzlri, Viz; Amenclolzz 189/B, £70126 Bari (Italy) *To the memory of Dr. Kit Nesis, who suddenly passed away in a cold winter day. He was a great cephalopod systematist and biogeographer, and a kind Man. Key words: Cephalopoda, Mediterranean Sea, distribution, alien species. evolution. SUMMARY This paper presents an updated picture of the Mediterranean teuthobiogeography. Sixty-five cephalopod species have been recorded in the Mediterranean, i.e., about 9% of the world teuthofauna, belonging to the following orders: Spirulida (1 species), Sepiida (4), Sepiolida (15). Teuthida (30), and Octopoda (15). Only 53 ofthem are represented by well established populations in this basin: all the others either have been very rarely collected or are recent occurrences, including cephalopods recently entered from the Atlantic Ocean and from the Red Sea through the Suez Canal. The width of the cephalopod horizontal distribution is discussed in relation to their modes of life and reproduction. In particular the in Jim speciation ofa flock of endemic or quasi-endemic sepioline species is attributed to certain body Features (small size, “locl;—and—l(eyq copulatory organs), reproductive strategies, short life span, and habitat. A concise history of the knowledge of the Mediterranean teuthoFauna is also illustrated. A list of the Mediterranean cephalopods is reported in Appendix I. INTRODUCTION Mangold and Boletzky (1988) published an essay on “Mediterranean Cephalopod Fauna”, which represents the first modern piece of literature dedicated to the biogeography of the Mediterranean cephalopods. In that paper the Mediterranean was dealt with in geological and paleogeographic contexts. In more recent years, new data have been accumulated on the distribution and, more important, on the taxonomy, ecology and reproductive biology of cephalopods living in the Mediterranean and the eastern Atlantic Ocean, producing a positive impact on the field of cephalopod biogeography (Boletzky, 1999).