Miracle-dz/UniFAR-FTUs huggingface dataset:
Polycyclic aromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment

Yetti E, Thontowi A, Yopi. 2016. Polyaromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment.Biodiversitas 17: 857-864. Oil spills are one of the main causes of pollution in marine environments. Oil degrading bacteria play an important role for bioremediation of oil spill in environment. We collected 132 isolates of marine bacteria isolated from several Indonesia marine areas, i.e. Pari Island, Jakarta, Kamal Port, East Java and Cilacap Bay, Central Java. These isolates were screened for capability to degrade polyaromatic hydrocarbons (PAHs). Selection test were carried out qualitatively using sublimation method and growth assay of the isolates on several PAHs i.e. phenanthrene, dibenzothiophene, fluorene, naphtalene, phenotiazine, and pyrene. The fifty-eight isolates indicated in having capability to degrade PAHs, consisted of 25 isolates were positive on naphthalene (nap) and 20 isolates showed ability to grow in phenanthrene (phen) containing media. Further, 38 isolates were selected for dibenzothiophene (dbt) degradation and 25 isolates were positive on fluorene (flr). On the other hand, 23 isolates presented capability to degrade in phenothiazine (ptz) and 15 isolates could grow in media with pyrene (pyr). Based on homology analysis of partial 16S rDNA gene, we obtained six taxonomy classes of PAH degrading bacteria, namely I±-Proteobacteria (31%), I³-Proteobacteria (43%), Firmicutes Bacilli (12%), Actinobacteria; Micrococcales (9%), Actinobacteria; Propionibacteriales (2%), and Bacteroidetes; Flavobacteriia (3%). In this research, we obtained diverse PAH degrading bacteria from marine areas.Keywords: Bacteria, degradation, marine environment, polyaromatic hydrocarbon
Is an Efficacious and Minimally Toxic Amonafide Derivative in Murine Models of Human Cancer 1

Amonafide is a DNA intercalator in clinical development for the treatment of cancer. The drug has a 5-position amine that is variably acetylated to form a toxic metabolite in humans, increasing adverse effects and complicating the dosing of amonafide. Numonafides, 6-amino derivatives of amonafide that avoid the toxic acetylation, also show in vitro anticancer activity, as we have previously described. Here, we report the in vitro and in vivo activities of two numonafides, 6-methoxyethylamino-numonafide (MEAN) and 6-amino-numonafide (AN) with comparisons to amonafide. The in vitro potencies and cellular anticancer mechanisms are similar for the two numonafides and amonafide. Results from several mouse models of human cancer demonstrate that AN and MEAN require slightly higher doses than amonafide for equal efficacy in short-term dosing models, but the same dose of all three compounds in long-term dosing models are equally efficacious. MEAN is tolerated much better than amonafide and AN at equally efficacious doses based on weight change, activity, stool consistency, and dose tolerance with survival as the end point. The studies presented here demonstrate that MEAN is much less toxic than amonafide or AN in mouse models of human liver and gastric cancers while being equally efficacious in vivo and inhibiting cancer cells through similar mechanisms. These findings demonstrate that numonafides can be less toxic than amonafide and support further preclinical development and novel anticancer agents or as replacements or amonafide.
Tempo et mode de l'évolution des populations cavernicoles de l'espèce Astyanax mexicanus

Le poisson Astyanax mexicanus est un modele particulierement interessant pour l'etude de l'evolution. En effet, dans cette espece de poissons d'eau douce, il existe des populations vivant de facon perenne dans des grottes. Dans cet environnement, l'obscurite est totale et permanente et les ressources en nourriture souvent faibles. Les poissons cavernicoles se sont adaptes a la vie souterraine et ils presentent de nombreuses modifications phenotypiques comme la depigmentation, la perte des yeux, l’augmentation du nombre et de la taille d’organes sensoriels non-visuels et plusieurs changements du comportement. Un des problemes majeurs est de savoir si ces modifications phenotypiques sont dues a des mutations preexistantes a la colonisation de l'environnement cavernicole ou si elles sont apparues apres. Pour repondre a cette question, connaitre l'âge des populations est un facteur important car dans une population recente, il n'y aura probablement pas eu suffisamment de temps pour l'apparition de beaucoup de mutations et leur fixation. L'objet de cette these est donc l'estimation de l'âge d'une population, celle de la grotte Pachon qui est souvent consideree comme etant une des plus anciennes et une des plus isolees. Au cours de ces travaux de these, nous avons developpe une nouvelle methode de datation qui repose d’une part sur la caracterisation du polymorphisme nucleotidique a l’interieur de chaque population et entre populations, et d’autre part la comparaison de ces donnees avec des simulations de l’evolution du polymorphisme. Les resultats obtenus, ainsi que la reanalyse de donnees sur le polymorphisme d’haplotypes mitochondriaux et de loci microsatellites precedemment publiees, suggerent que les populations cavernicoles seraient bien plus recentes qu’habituellement indique dans la litterature (quelques milliers d’annees, et non plusieurs centaines de milliers d’annees). Les consequences d’un tempo rapide d’evolution sur le mode d’evolution de ces poissons cavernicoles ont aussi ete presentees.
TWO-STAGE NORMALIZATION OF OUTPUT SIGNALS OF ARTIFICIAL NEURAL NETWORKS

In the article the problem of interpretation output signals of artificial neural networks was considered in cases when softmax regression is used in them which calculated with heuristics often applied in practice. To use alternative multi-fold activation function in artificial neural network for objects categorizing is proposed. It is shown that output signals, that can be get in case of using the function, possible to be interpreted as probability of full group of events. Additionally, the form of distribution allows to estimate how precise the proposition is. With aim of developed artificial neural net that recognizes hand-written characters from 0 through 9 experiments were made that checks proposed approach.
ITS sequence analysis of Artemisia halodendron in different habitat gradients

The aim of the present study is to investigate the difference between ITS sequences of Artemisia halodendron Turcz. from different habitat gradients in Horqin Sandy Land, with Artemisia depauperata Krasch. selected as the outgroup. Results indicate that the total length of A. halodendron ITS is 696 bp, the lengths of unaligned ITS-1 and ITS-2 sequences varied from 253 to 256 bp and 264 to 269 bp, respectively, and GC content of ITS-1 and ITS-2 sequences ranged from 54.02% to 54.77% and 56.75% to 58.64%, respectively. This indicates a high difference of length and composition of sequences in ITS-1 than ITS-2. The genetic identity between ITS sequences of A. halodendron from nine populations ranged from 85.7% to 99.7% which indicates some genetic differentiation between sequences. In the maximum parsimony (MP) tree, most ITS sequences from A. halodendron show two major clades: Clade I and Clade II, with Clade II older than Clade I. The order is subp4 → subp1 → subp2 → subp3 → subp8 → subp6 → subp7 → subp9 → subp5, and corresponding habitat order is: inter-dune lowlands → semi-mobile dune → mobile dune → semi-fixed dune → fixed dune. This indicates a close relation between the evolutionary processes of A. halodendron and desertification forming processes and ecological restoration processes of Horqin Sandy Land.
Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in the Peromyscus mexicanus species group (Mammalia: Rodentia: Cricetidae)

Mountain-associated species, which exhibit allopatric distributions associated with elevation, endemisms and complex evolutionary histories, pose challenging evolutionary scenarios in which to discern the diversification of species. The Peromyscus mexicanus mice group, distributed along mountains in southern Mexico and Central America, is morphometrically variable, a key rationale for the ongoing controversy regarding its species delimitation. Based on the recognized 15 mitochondrial lineages for the group, we analysed external and craniodental morphometric variables to test whether lineages can be differentiated morphometrically and allow for the delimitation of species. We also aimed to test the prediction that the phylogenetic structure of the morphometric data is concordant with that of the molecular information. Based on 19 craniodental measurements from 521 specimens, multivariate and discriminant analyses showed that lineages are morphometrically discernible, representing distinct phenotypes, and that overall size and mandible measurements are significant features that discriminate lineages, supporting hypotheses about differences in feeding habits between species. Also, a pattern of increasing size with elevation was observed, further supported by specific morphological differences exhibited between highland and lowland lineages inhabiting the same mountain. Our results demonstrate that P. mexicanus is both genetically and morphometrically variable, where most highland montane species are differentiated from lowland species; also, a significant correlation between mitochondrial and morphometric information is indicative of phenetic concordance, altogether in agreement with a recent taxonomic proposal for the group. We suggest that the group's intricate diversification responds to ecological diversification and adaptation to a variety of mountain habitats and Pleistocene biogeographic climatic dynamics.
Genetic diversity of the floury race of maize Avati Moroti from the Guarani tribe in Paraguay

Avati Moroti is a race of floury maize widely used by the Guarani people in South America, whose variability and potential value for breeding has been neglected so far. The objective of this research was to explore the genetic variability within the main Paraguayan race Avati Moroti. We studied the genetic variability available in the 20 accessions of Paraguayan Avati Moroti included in the South American core collection made by CIMMYT. Thirty individuals per accession were genotyped with 30 SSR (simple sequence repeat); we determined genetic diversity and made a cluster analysis in order to define genetic relationships among accessions. Mean of polymorphic loci (0.96), alleles per locus (3.57), alleles per polymorphic locus (3.65), expected (0.48) and observed (0.43) heterozygosity, and coefficient of consanguinity (0.12) revealed that Avati Moroti contains a genetic diversity comparable to the most variable maize races of maize. The cluster analysis classified the 20 populations in eight groups, five of them with a single accession, and a large group representing a central pool of germplasm. These results indicate that there is a large variability available in this race, and encourage the collection of more samples of Avati Moroti, particularly in marginal areas that were scarcely sampled.
Phenolic compounds and the biological effects of Pu-erh teas with long-term storage

ABSTRACT Pu-erh tea has gained more and more popularity and attracted much attention for its various biological effects. The objective of this study was to determine the active phenolic compounds and the biological effects of 15 differently aged Pu-erh teas. The results showed that 43 active phenolics, containing 7 flavan-3-ols, 11 organic acids, and esters, 3 proanthocyanidin dimers, 2 benzotropolones, and 20 flavonoid glycosides were identified based on high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight tandem mass spectrometry (HPLC-ESI-QTOF-MS/MS). In particular, 2’-O-galloylhyperin and quercetin-3-O-p-coumaroyl-rhamnosyl-arabinosyl-hexoside were identified from constituents of tea for the first time. The 15 Pu-erh teas exhibited strong DPPH and ABTS scavenging activity in a concentration-dependent manner with IC50 0.99–2.12 and 0.97–2.67 mmol Trolox equivalent antioxidant capacity/g, respectively. All of the Pu-erh teas tested significantly inhibited the proliferation of SMMC-7721 cells, in a dosage-dependent manner. Of the 15 Pu-erh teas examined, the cake tea P6 had the strongest effect on SMMC-7721 cells with IC50 = 65.88 ± 3.53 µg/mL. The others Pu-erh teas had an IC50 = 96 – 509 µg/mL. Our results also indicated that not all the older Pu-erh teas display stronger anti-activities and anti-cancer than the younger ones and the youngest Pu-erh tea did not possess the highest level of active components. This study provides useful information for consumers to deeply understand the chemical constituents and bioactivity of Pu-erh tea preserved for a long time.
Comparison of three different indirect methods to evaluate ungulate population densities

Reliable species population estimates are important for population conservation and management. Information about population sizes is needed to introduce certain preservation and regulation approaches. Several different methods, both performed in the field and analytical, can be used to estimate species densities. The aim of this thesis was to evaluate densities of moose (Alces alces), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and fallow deer (Dama dama) in a confined area in Vasterbotten, Sweden, via three different non-invasive wildlife census methods: camera trapping, traditional dung pellet group counts, and DNA-based ID-ing of dung samples. Due to analytical problems in the lab, the latter method was excluded from any further analysis. Species densities were estimated via the Random Encounter Model (REM) from recorded pictures of camera traps. Further investigations from camera trap data were made to compare sex-ratio, day- and night-capture events, the influence of snow depth and the use of habitat type among the ungulate species. Density estimates of dung counts considered the defecation rate of each species and the accumulation period of dung. For moose, camera traps yielded a population estimate similar to dung counts. However, estimated densities from the dung count approach were much lower for all other three ungulate species than densities from the camera trapping. Even though the use of camera traps is more time consuming and costly, this method is evaluated as a trustworthy estimator of population sizes. In addition, further information about habitat associations, activity patterns, behaviour, or community structure can be successfully accomplished.
Declining breeding populations of White-naped Cranes in Eastern Mongolia, a ten-year update

Summary Eastern Mongolia supports one of the most important breeding populations of the White-naped Crane Antigone vipio (WNC), which is classified as ‘Vulnerable’ by the IUCN. Large numbers of WNCs were found to be breeding at high densities within the Ulz River basin during surveys conducted in 2000 and 2001, along a 270 km section of the river. Following these surveys, an extended drought continuing for at least a decade has threatened wetland ecosystems throughout Eastern Mongolia. This study reports the findings of surveys conducted in 2010 and 2011 along the same section of the Ulz River surveyed a decade earlier, as well as a generalised survey of other sites where breeding WNCs had previously been recorded. Along the Ulz River, populations declined from 42 territorial pairs in 2001 to 17 in 2011. Estimates of detection probability using distance sampling and occupancy methods at two locations gave consistent results of 23%–27% detectability. With a minimum population of 234 WNCs observed across all sites in 2011, these detection probabilities suggest that the areas surveyed support the majority of breeding WNCs in the western population. Although we cannot exclude the movement of WNCs beyond the survey area, these findings also suggest that the population has declined between 2001 and 2011. Exploration of key habitat variables using occupancy models and generalized linear mixed models found that WNCs favoured areas of high wet vegetation (estimated as ‘wet meadow’ coverage and using normalized difference vegetation index), and low grazing pressure. Given the importance of water resources to WNCs and nomadic herding communities, use of wetland habitat must be carefully managed to balance the needs of cranes and people, particularly during periods of drought.
Herbicide selectivity in the early development of Alexander palm and peach palm

O uso de herbicidas destaca-se como metodo eficiente no controle de plantas daninhas e a seletividade destes as especies de palmeira e um aspecto importante a ser avaliado. Devido a escassez de trabalhos na literatura com relacao ao uso de herbicidas em palmeiras, principalmente para os estagios iniciais de crescimento, este estudo teve como objetivo avaliar a seletividade de alguns herbicidas no desenvolvimento inicial de mudas de palmeira-real australiana (Archentophoenix alexandrae) e de palmeira pupunha (Bactris gasipaes). O estudo foi conduzido em duas epocas, em delineamento experimental inteiramente casualizado, com oito tratamentos e quatro repeticoes. Os tratamentos foram herbicidas e doses, em g i.a. ha-1: fluazifop-p-butyl (93,8), sethoxydim (184,0), quizalofop-p-ethyl (75,0), clethodim + fenoxaprop-p-ethyl (50,0 + 50,0), fomesafen (225,0), lactofen (168,0), nicosulfuron (50,0) e testemunha sem aplicacao de herbicida. As mudas de ambas as palmeiras foram transplantadas para vasos plasticos de 3,1L. A aplicacao foi realizada sobre mudas de palmeira-real australiana com 25 a 30 cm de estatura no primeiro estudo e 30 a 40 cm no segundo estudo e em mudas da palmeira pupunha com 40 a 55 cm nos dois estudos. Os herbicidas causaram leves injurias visuais durante o desenvolvimento inicial apenas nas plantas de palmeira pupunha. Todos os herbicidas utilizados foram seletivos e podem ser utilizados para a palmeira pupunha nos estadios de desenvolvimento de 1 a 4 folhas. Para a palmeira-real australiana apenas fluazifop-p-butyl, quizalofop-p-ethyl e lactofen nao afetaram o desenvolvimento inicial nos estadios de desenvolvimento de 1 a 4 folhas.
Phytotoxic grass residues reduce germination and initial root growth of ponderosa pine

1975. Phytotoxic grass residues reduce germination and initial root growth of ponderosa pine. Extracts of green foliage of Arizona and mountain muhly significantly reduced germination of ponderosa pine seeds, and retarded speed of elongation and mean radicle length. Three possible routes of release of the inhibitor were investigated: (1) leaching from live foliage, (2) root exudation, and (3) overwinter leaching from dead residues. The principal route remains uncertain. The ecological implications of the inhibitory substance are discussed. for allelopathy ponderosa
Review of Ecological and Conservation Perspectives on Future Options for Arthropod Management in Cape Floristic Region Pome Fruit Orchards

Intensification of agriculture can have spin-offs on surrounding areas and ecosystems. There is a necessity to pursue sustainable agricultural practices to meet the increasing demand for food production while aligning with international conservation targets. Arthropod pest control techniques in Cape Floristic Region pome orchards, South Africa, that preserve biodiversity while simultaneously controlling pests, are reviewed here. Emphasis is placed on the chronic pests: Mediteranean fruit fly (Ceratitis capitata) (Wiedemann), Natal fruit fly (Ceratitis rosa) (Karsch) and codling moth (Cydia pomonella) (L.), while other sporadic and perennial pests are also considered. Biological control (biocontrol) is an important, sustainable pest control measure. However, certain risks associated with releasing living organisms into the environment must not be ignored. Monitoring of release programmes is essential. The sterile insect technique (SIT) offers a species-specific approach for controlling pests. However, the technique is research and management intensive. Globally SIT has shown great success, but lack of financial support has limited SIT uptake in SouthAfricanpomefruit orchards. SIT has shown increased effectiveness as an integrated technique, particularly with parasitoid release and pheromone-based mating disruption. Habitat management, the preservation of natural vegetation and use of beneficial plant species increases crop resilience, encourages conservation biological control and maintains crop health. Area-wide control is stressed as a favourable strategy which deals with entire pest populations rather than isolated farm-by-farm approaches. Other techniques covered include pheromonebased mating disruption, attract-and-kill and physical barriers such as sticky tree-bands, which all show integration potential with biologically-based techniques, while minimising insecticide application. The usefulness of insecticides as a curative approach is recognised, and ways of preserving insecticide life-spans by limiting insect resistance are discussed.
HABITAT PREFERENCES, DISTRIBUTION, AND ABUNDANCE OF GOBIUS VITTATUS (GOBIIDAE) IN THE KVARNER AREA (NORTHERN ADRIATIC SEA)

Habitat data for many Mediterranean gobies are absent or scarce and mostly restricted to very limited qualitative descriptions. The striped goby, Gobius vittatus was considered to be rare or very rare, and many aspects of its ecology are still unknown. In the present work we aimed at collecting data on distribution, abundance and microhabitat preferences of G. vittatus in the Kvarner area (northern Adriatic Sea). G. vittatus was one of the most common epibenthic fish in the investigated area, being recorded at 66 % of SCUBA dives. G. vittatus was most frequently found at a mixed rock and sand bottom, characterised by steep or medium slope from 5 to 34 m depth. The most frequently co-occurring epibenthic fish species with G. vittatus was Parablennius rouxi. The abundance of G. vittatus varied significantly across months and was positively correlated with temperature.