Miracle-dz/UniFAR-FTUs huggingface dataset:
A new framework for analysing automated acoustic species detection data: Occupancy estimation and optimization of recordings post‐processing

The development and use of automated species detection technologies, such as acoustic recorders, for monitoring wildlife are rapidly expanding. Automated classification algorithms provide cost‐ and time‐effective means to process information‐rich data, but often at the cost of additional detection errors. Appropriate methods are necessary to analyse such data while dealing with the different types of detection errors. We developed a hierarchical modelling framework for estimating species occupancy from automated species detection data. We explore design and optimization of data post‐processing procedures to account for detection errors and generate accurate estimates. Our proposed method accounts for both imperfect detection and false‐positive errors and utilizes information about both occurrence and abundance of detections to improve estimation. Using simulations, we show that our method provides much more accurate estimates than models ignoring the abundance of detections. The same findings are reached when we apply the methods to two real datasets on North American frogs surveyed with acoustic recorders. When false positives occur, estimator accuracy can be improved when a subset of detections produced by the classification algorithm is post‐validated by a human observer. We use simulations to investigate the relationship between accuracy and effort spent on post‐validation, and found that very accurate occupancy estimates can be obtained with as little as 1% of data being validated. Automated monitoring of wildlife provides opportunity and challenges. Our methods for analysing automated species detection data help to meet key challenges unique to these data and will prove useful for many wildlife monitoring programmes.
Description of subadult Pallisentis (Pallisentis) rexus (Acanthocephala: Quadrigyridae) from the vertebrate intermediate host in Thailand with an examination of the species identity

Subadults (considerably developed immatures) of the quadrigyrid acanthocephalan Pallisentis rexus Wongkham & Whitfield, 1999 are described from the swamp eel, Monopterus albus (Zieuw, 1793) in Thailand. The species is placed in the subgenus Pallisentis. Our specimens are compared with adults of the same species collected from the freshwater snakehead Ophicephalus striata Bloch also from Thailand. Discrepancies from the original description are noted, certain structures, e.g., proboscis hook roots and brain (cepahalic ganglion), are re-interpreted, and additional information provided.
The exploitation of limpets in a Mediterranean Marine Protected Area: assessing the effectiveness of protection in the intertidal zone

Limpets are intertidal keystone grazers and their overexploitation could have significant consequences for intertidal communities. Limpets are harvested around the Sinis Peninsula (Sardinia, Italy) but harvesting is prohibited within the “Penisola del Sinis - Isola di Mal di Ventre” Marine Protected Area (MPA). This work assesses the effects of human harvesting on the population dynamics of three common Mediterranean species of Patella , namely, P. rustica , P. caerulea and P. ulyssiponensis , testing the effectiveness of the MPA and the role of site accessibility in limiting the intensity of such harvesting pressure. In the period between June 2015 and August 2016, limpet abundance and size were recorded on a monthly basis by means of photographic frames within linear transects at ten sites spread out along the coastline of the Sinis Peninsula to assess growth and temporal patterns. Limpets older than two years are extremely rare in the study area. Limpets are more abundant within the MPA in comparison with non-protected areas and within less accessible sites in comparison with areas where the intertidal zone is easily accessible from land. Despite this, overall human-induced mortality in the area is high, indeed the pool of limpets observed with a mean density of 104.3 ± 9.7 limpets/m 2 during the first survey was reduced by 99.2%in less than one year. This work demonstrates that human harvesting strongly affects the population dynamics of Patella species in the area and that within the MPA this stressor is not efficiently reduced.
Regulation of E2F-1 gene expression in human breast cancer cells

Regulation of E2F-1 Gene Expression in Human Breast Cancer Cells. (May 2005) Sharon Khethiwe Ngwenya, B.S., Oakwood College Chair of Advisory Committee: Dr. Stephen Safe 17β-Estradiol induces E2F-1 gene expression in ZR-75 and MCF-7 human breast cancer cells. Analysis of the E2F-1 gene promoter in MCF-7 cells previously showed that hormone-induced transactivation required interactions between estrogen receptor α (ERα)/Sp1 bound to upstream GC-rich sites and NFYA bound to downstream CCAAT sites within the -169 to -54 promoter region. This promoter region was also E2-responsive in ERα-positive ZR-75 cells; however, further analysis of the promoter showed that cooperative ERα/Sp1/NFY interactions were not necessary for hormone-induced transactivation in ZR-75 cells. The upstream GC-rich motifs are activated independently by ERα/Sp1 in ZR-75 but not MCF-7 cells, and the downstream CCAAT sites were also E2-responsive. E2 also induced reporter gene activity in ZR-75 cells transfected with an expression plasmid containing the yeast GAL4 DNA binding domain fused to pM-NFYA and a construct containing five tandem GAL4 response elements. Subsequent studies showed that hormonal activation of pE2F-1jm1 and pM-NFYA are dependent on non-genomic pathways in which E2 activates cAMP/protein kinase A. Hormone-dependent regulation of E2F-1
Caracterização citogenética em espécies do gênero Zephyranthes herb. (Amaryllidaceae)

No presente trabalho foram estudados a caracterizacao citogenetica e os padroes de banda CMA/DAPI em sete especies de Zephyranthes e uma de Habranthus com o objetivo de avaliar as diferencas cariotipicas entre essas especies. Todos os individuos apresentaram nucleo interfasico reticulado ou semi-reticulado e cariotipo formado por um conjunto de cromossomos metacentricos, alem de cromossomos submetacentricos e acrocentricos. Zephyranthes robusta, com 2n=12 e formula cariotipica 4M+2SM, apresentou cariotipo mais simetrico. Z. sylvatica apresentou complemento cromossomico formado por 2n=12 sendo 1M+5SM, 2n=13 sendo 1M+5SM+(B)SM e 2n=18 formadas por trincas, uma com metacentricos e cinco apenas com submetacentricos (1M+5SM). Para as especies cultivadas, Zephyranthes rosea Lindl. Apresentou cariotipo com 2n=24 e formula cariotipica 4M+7SM+1A. Zephyranthes grandiflora Lindl. apresentou a mesma contagem cromossomica da especie anterior, sendo que foram observados 2M+5SM+5A. Zephyranthes aff. rosea Lindl. , apresentou 2n=25, sendo 3M+(1M“trinca”) +7SM+1A. Alem disso, pode-se observar a presenca de trissomia no par quatro metacentrico. Zephyranthes brachyandra Herb. apresentou cariotipo com 2n=24+1B e formula 4M+3SM+5A+1B. Para Zephyranthes candida Herb. observou-se 2n=38, sendo 9M+5SM+5A. Em H. itaobinus Ravena observou-se variacao numerica nas contagens onde na maioria das populacoes os complementos cromossomicos foram formados por 2n=45 ou 5M+12SM+5A+(B)M e em uma unica populacao a especie apresentou cariotipo com 2n=44, 6M+12SM+5A+3(B)M. Foram observadas bandas DAPI subterminais e intersticiais apenas em Z. robusta e em Z. brachyandra. As demais especies nao apresentaram heterocromatina rica em AT. Nas especies com 2n=12 foi observado um bloco CMA+ em um par cromossomico de Z. robusta e Zephyranthes sp. , enquanto em Z. sylvatica foi observado um pequeno bloco terminal adicional. Z. rosea e Z. grandiflora, tiveram quatro bandas CMA+, enquanto em Z. brachyandra, ocorreram oito bandas intersticiais puntiformes, alem da RON heterocromatica e de um bloco maior no terminal do braco curto do cromossomo B. Em Z. candida, observouse 14 bandas CMA subterminais e em H. itaobinus, sete bandas, com forte amplificacao diferenciada na RON heterocromatica. Sao discutidas as implicacoes taxonomicas e a evolucao cariotipica para as especies estudadas.
Caractérisation d’ Escherichia coli résistant aux antibiotiques dans différents systèmes avicoles de la province de l’Est et de la ville de Kigali au Rwanda

Antibiotic resistance has become a global public health concern as a wide num­ber of resistant bacteria are continuously emerging. Animals have been pointed out as one of the sources of antibiotic-resistant bacteria that can be transferred to humans. To enrich the data on antibiotic resistance in animals in Rwanda, a cross-sectional study was carried out in the Eastern Province and in Kigali City to isolate Escherichia coli from free-range and commercial poultry farms. Fecal samples were collected from 294 poultry farms and E. coli strains were isolated and identified. In total 241 E. coli isolates were subjected to an antibi­otic sensitivity test using five antibiotics (gentamicin, streptomycin, rifampicin, doxycycline and erythromycin). Antibiotic use in poultry was low in free-range poultry farms (30.9%) compared to layer and broiler production farms (100%). Among 151 farmers who reported using antibiotics in poultry, almost half (49.7%) always used antibiotics with a veterinarian prescription. Out of 241 E. coli isolates, 43.2% had a multiple resistance to four of the five antibiotics tested. Almost all the isolates (98.8%) were resistant to erythromycin, 78.8% were resistant to streptomycin, 77.6% were resistant to doxycycline, 69.3% were resistant to rifampicin and only a few were resistant to gentamicin (3.7%). No statistically significant difference was observed regarding isolate resistance against antibiotics according to the farming system type. However, resistance of isolates to doxycycline was significantly higher in farms where antibiotic use was reported (84%) than in farms where antibiotic use was not reported (70%). The observed antibiotic resistance of E. coli shows the existence of a potential source of resistance that can be transferred to pathogenic bacteria and impact humans as well as animals.
Linking management practices with range health in northern temperate pastures

Abstract: Little information exists on the management and range health (RH) of northern temperate pastures, where health is defined as the ability to sustain ecosystem function. We surveyed 102 pastures for RH and their associated managers during 2012–2013 across central Alberta, Canada. Pastures were generally diverse mixes of introduced grasses and contained few legumes, despite most (55%) being seeded to legumes. The majority of pastures were healthy (mean RH score = 78.8% ± 1.3%), with 2.9% having scores <50%. Criteria reducing scores were noxious weeds, bare soil, and evidence of erosion. Most pastures had a reported history of cultivation (75.5%), with those previously cultivated and seeded to introduced forage having greater stocking rates [6.18 ± 0.91 animal-unit-months (AUM) ha-1] compared with those lacking cultivation (2.14 ± 2.91 AUM ha-1). Farms with horses or mixed livestock tended to practice year-round continuous grazing and supplemental hay feeding. Stocking rates on continuous and rotationally grazed pastures were similar regardless of grazing season, with the highest stocking on pastures used year-round (19.54 ± 2.03 AUM ha-1) or throughout the dormant season (20.29 ± 3.10 AUM ha-1). Use of management inputs was variable, with manuring and harrowing common and fertilizing, over-seeding, and aerating infrequent. Herbicide use was reported on 15.7% of pastures, despite 83.3% containing noxious weeds. Use of prescribed fire was rare, although 36.3% of pastures had evidence of fire. Industrial disturbances were reported on 48.3% of pastures. Overall, these results indicate that these pastures experience complex management and the limited decline in RH is due to high stocking under year-long grazing.
The Effects of Cultivation Area and Altitude Variation on the Composition of Essential Oil of Laurus nobilis l. Grown in Eastern, Western and Central Karadeniz Region

Laurus nobilis L. is one of the most valuable non-wood forest products on world export market and Turkey. Turkey is the biggest provider country for Laurus nobilis in the world. Therefore, laurel is an important commercial product for our country. In this study, the effects of cultivation area and altitude variation on essential oil content and quantity of laurel leaves were examined which grown in Trabzon, Bartin and Samsun. It was aimed to determine chemical composition of laurel’s leaves grown in Karadeniz region. Laurus nobilis L. leaves were collected in three different height ranges. These were 0-100 m, 100-300 m, 300-600 m. Leaves were shade-dried and crushed. A device called ‘’Clevenger’’ was used for getting volatile oil and their yields were calculated according to dry weight. The yields of essential oils ranged between 0.91% to 1.66 %. These essential oils were obtained from Bartin (B 2 ) (100-300 m) and Artvin (A 1 ) (0-100 m) respectively. The major components of these essential oils were 1,8- cineole (19.71%-35.63%), α-terpinyl acetate (12.86%-21.24%), sabinene (5.98%-9.40%), α- pinene (3.67%-8.45%) and β- pinene (2.91%-5.87%) were the most abundant volatile compounds in the leaves of bay.
The whole-genome panorama of cancer drivers

The advance of personalized cancer medicine requires the accurate identification of the mutations driving each patient’s tumor. However, to date, we have only been able to obtain partial insights into the contribution of genomic events to tumor development. Here, we design a comprehensive approach to identify the driver mutations in each patient’s tumor and obtain a whole-genome panorama of driver events across more than 2,500 tumors from 37 types of cancer. This panorama includes coding and non-coding point mutations, copy number alterations and other genomic rearrangements of somatic origin, and potentially predisposing germline variants. We demonstrate that genomic events are at the root of virtually all tumors, with each carrying on average 4.6 driver events. Most individual tumors harbor a unique combination of drivers, and we uncover the most frequent co-occurring driver events. Half of all cancer genes are affected by several types of driver mutations. In summary, the panorama described here provides answers to fundamental questions in cancer genomics and bridges the gap between cancer genomics and personalized cancer medicine.
Five years of coral recovery following a freighter grounding in the Florida Keys.

Coral community recovery has been followed forfive years since the destruction of aportion of Molasses Reef, Kzy Largo National Mm'ne Sanctuary, by a 122 meter freighteq which ran aground in August 1984. Unclewater repetitive and random photographic methods, visual counts, and art@ial substrates were used between 1984 and 1989 to assm coralpopulatwns, cover, recruitment, and the fate of coral colonies damaged by the grounding. We report here on &a Md results from random photographic methods and underwater visual censuses. Coral abundances had redeveloped in 1989from virtually 0% in an area of major impact to a level approximating 6578% of supposedpre-impactpopulations though colonies were very s d Cover of hard corals in 1989 was 22% of pre-impact cover, and gorgonian cover approximately 40% of pre-impact cover and tend to have high rates of recruitment. Coralrecruiiment has been domnated by species which brood larvae. These species are also numerical domiin mature surrounding communities. Though recovery would occur naturally over an extencledperiod of time, transplantahbn could be used as a way to increase the relative abundance of species which only rarely have been found as coral recruit$. k e include primarily the large massive corals conspicuous in typical mature reefcommunities. Most of these species are broadcast spawners, which have longplanktonic stages, low recruitment rates, and low relative abundances in mature communities. Transplantation also restores the habitat complexrexrty essential to the development of the associated invertebrate and f ih assemblages charactektic of these diveme ecosystems.
Effects of water stress on Lupinus albus III. Response of seed yield and vegetative growth to water stress imposed during two or three growth stages

Lup;nus albus cv. 'Ultra' plants were grown in a controlled environment under restricted watering regimes imposed during two or three growth stages from floral initiation to the end of the second order lateral flowering. Water stress reduced seed weight by between 43 % and 72 % compared with non-stressed plants. Plar:ts stressed during the preflowering stage or during the full flowering period had lowest seed yields. Flower and pod numbers of a particular stem order were reduced by water deficit imposed during flowering of that order and also when water stress occurred during previous growth stages. Water stress stimulated se~d and pod growth rates which then declined when adequate water was re-applied. Vegetative growth rates from early-stressed plants recovered fully. The potential for recovery of seed yield from stress was not realised. It was concluded that L. albus seed yield is unlikely to recover from the effects of drought during a normal season. During the main seed-filling stage, nitrogen fixation supplied directly an estimated 33% of the seed nitrogen requirement in non-stre~sed ;Jlants. Leaves of these plants supplied an estimated 47% and pods contributed 15% of seed nitrogen requirement. For two late-stressed treatments, leaves supplied approximately 21 % and 32% of the seed nitrogen and pods supplied 440,0 and 32%. Some of this pod nitrogen may have been translocated from lea, es which had senesced earlier. Thus most of the reserve nitrogen supplied to the seed arose directly or indirectly from the leaves.
Molecular, morphological and acoustic identification of Eumops maurus and Eumops hansae (Chiroptera: Molossidae) with new reports from Central Amazonia

Eumops maurus and Eumops hansae are rarely captured Neotropical molossid bats for which information on taxonomy, natural history, and spatial distribution are scarce. This translates into a poor understanding of their ecology and limits the delimitation of useful characters for their identification. Here, we describe records of these two molossids from the Central Brazilian Amazon, providing data on their external and craniodental morphology, DNA barcode (COI) sequences complemented by acoustic data for the species. Morphological characters, DNA sequence data and phylogenetic relationships within the genus Eumops were consistent with those previously described for both species. Echolocation call characteristics did not differ significantly so as to be useful for separating E. maurus and E. hansae from other congeners. Our records are, respectively the first and the second for Central Amazonia as one individual previously attributed to Eumops amazonicus from Manaus may be considered a junior synonym for E. hansae. These new records increase the extent of the species’ known ranges, partially filling in previous existing gaps in their distribution in central South America. Our data further suggest that these molossid bats forage in a wider range of habitats than previously thought.
Effects of the Deepwater Horizon oil spill on protected marine species

The Deepwater Horizon (DWH) incident was the largest offshore oil spill in the history of the United States, contaminating surface waters, the water column, deep-sea corals and benthos, nearshore and coastal ecosystems, and natural resources across 5 states and an ocean area of more than 112 000 km2 in the Gulf of Mexico (GoM). Protected marine species — sea turtles and marine mammals, in particular — were a main focus of the DWH Natural Resource Damage Assessment (NRDA). The DWH spill overlapped in time and space with sea turtle and marine mammal habitats and life stages throughout the northern GoM. Thus, the DWH NRDA Trustees (2016; www.gulfspillrestoration.noaa.gov/restoration-planning/gulf-plan/) performed several activi ties to assess adverse effects of oil exposure on sea turtles and marine mammals to quantify the full extent and nature of the impacts to these taxa across the region. A synopsis of the Trustees’ assessment activities and conclusions is presented in the DWH NRDA Programmatic Damage Assessment and Restoration Plan (DWH NRDA Trustees 2016). This Theme Section presents several of these specific sea turtle and marine mammal assessment activities and associated findings. This Overview provides a context for the Theme Section papers, introduces basic NRDA concepts and discusses generally why and how protected marine species were assessed in the DWH NRDA.
Cytotoxicity and biocompatibility of high mol% yttria containing zirconia

Objectives Yttria-stabilized tetragonal phase zirconia has been used as a dental restorative material for over a decade. While it is still the strongest and toughest ceramic, its translucency remains as a significant drawback. To overcome this, stabilizing the translucency zirconia to a significant cubic crystalline phase by increasing the yttria content to more than 8 mol% (8YTZP). However, the biocompatibility of a high amount of yttria is still an important topic that needs to be investigated. Materials and Methods Commercially available 8YTZP plates were used. To enhance cell adhesion, proliferation, and differentiation, the surface of the 8YTZP is sequentially polished with a SiC-coated abrasive paper and surface coating with type I collagen. Fibroblast-like cells L929 used for cell adherence and cell proliferation analysis, and mouse bone marrow-derived mesenchymal stem cells (BMSC) used for cell differentiation analysis. Results The results revealed that all samples, regardless of the surface treatment, are hydrophilic and showed a strong affinity for water. Even the cell culture results indicate that simple surface polishing and coating can affect cellular behavior by enhancing cell adhesion and proliferation. Both L929 cells and BMSC were nicely adhered to and proliferated in all conditions. Conclusions The results demonstrate the biocompatibility of the cubic phase zirconia with 8 mol% yttria and suggest that yttria with a higher zirconia content are not toxic to the cells, support a strong adhesion of cells on their surfaces, and promote cell proliferation and differentiation. All these confirm its potential use in tissue engineering.
Suitability of major agricultural land uses around Kibale National Park

The current agriculture land uses around Kibale National Park forest have been expanding towards the forest area threatening its conservation efforts and this has contributed to crop raiding and destruction to the neighbouring agricultural communities. This study was conducted to identify and assess the suitability of major agricultural land uses around Kibale National Park. The major agricultural land uses included; Banana (Musa spp), Maize (Zea mays) and Tea production (Camellia sinensis) and these were identified using three randomly selected transects of 5 km per transect, and obtaining information using a structured questionnaire administered to 30 key farming households near Kibale National Park. Soil samples were also taken within the identified major agricultural land uses at the depths of 0-15 and 15-30 cm. Physical suitability of the major agricultural land-uses was assessed by matching their requirements with existing land qualities extracted from the Uganda soil memoires. Results showed that, western part of Kabarole District is highly suitable for tea production, the southern part is highly suitable for maize and the northern part is highly suitable for banana. The central part of Kabarole was found to be highly suitable for both banana and maize. The study finally recommended a buffer zone of 3.5 km from the national park planted with tea and eucalyptus around the national park boundary for crop defense separating agricultural communities and Kibale National Park since there not affected by animal raids and destruction. Key words: Major agricultural land use, land qualities, land suitability.