Miracle-dz/UniFAR-FTUs huggingface dataset:
Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

Abstract. There is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, while no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated to assess the suggestion that a poor fossil record is largely responsible for the difference in estimates of placental origins. The completeness of fossil specimens was measured using the character completeness metric, which quantifies the completeness of fossil taxa as the percentage of phylogenetic characters available to be scored for any given taxon. Our data set comprised 33 published cladistic matrices representing 445 genera, of which 333 were coded at the species level. Therewas no significant difference in eutherian completeness across the Cretaceous/Paleogene (K/Pg) boundary. This suggests that the lack of placental mammal fossils in the Cretaceous is not due to a poor fossil record but more likely represents a genuine absence of placental mammals in the Cretaceous. This result supports the “explosivemodel” of early placental evolution, whereby placentalmammals originated around the time of the K/Pg boundary and diversified soon after. No correlation was found between the completeness pattern observed in this study and those of previous completeness studies on birds and sauropodomorph dinosaurs, suggesting that different factors affect the preservation of these groups. No correlations were found with various isotope proxy measures, but Akaike information criterion analysis found that eutherian character completeness metric scores were best explained by models involving the marine-carbonate strontium-isotope ratios (87Sr/86Sr), suggesting that tectonic activity might play a role in controlling the completeness of the eutherian fossil record.
Antifungal Activity of Geraniol on Candida albicans Isolates of Pediatric Clinical Importance

Geraniol is a plant-derived monoterpene alcohol that has antifungal effect. The aim of this study was to evaluate the geraniol for antifungal activity against Candida albicans isolates of pediatric clinical importance. The minimum inhibitory concentration (MIC) and the minimum fungicidal concentration (MFC) were determined by the broth microdilution techniques. We also investigated possible geraniol action on cell walls (0.8M sorbitol) and cell membranes (Geraniol to ergosterol binding). For 90% of isolates, the MIC and MFC of the phytochemical was 64
Spatio-Temporal Distribution of the Cryptic Flies of the Drosophila willistoni (Diptera: Drosophilidae) Subgroup in a Neotropical Forest

Abstract Identifying cryptic species is a challenging but critical task for conservation biology because such identifications improve the resolution of taxonomic inventories and increase our ability to precisely assess the biodiversity of environments as well as the conservation status of rare species. To understand the temporal and spatial distribution of the cryptic species contained in the Drosophila willistoni subgroup, we re-examined all of the individuals of this subgroup identified in a previous work that analyzed drosophilids associated with a forest patch in the Brazilian Cerrado from December 2007 to November 2008. Each collection consisted of banana-baited traps distributed in three vertical strata of the forest (0-, 4-, and 8-m heights) at three horizontal positions (edge, transition between edge and river, and river area). Our results revealed that the specimens originally identified as D. willistoni consisted of three cryptic species: D. willistoni (n = 1,344), D. paulistorum (n = 1,001), and D. tropicalis (one male). Most D. willistoni and D. paulistorum specimens were collected during the rainy season on the ground of the edge forest patch. However, D. paulistorum was more temporally and spatially restricted than D. willistoni. Our findings confirm that these three cryptic species of the subgroup D. willistoni differ not only in abundance but also in ecological tolerance. This study contributes to the improved understanding of the Brazilian savanna communities, whose high levels of species richness and endemism are well documented for plants but poorly known for insects.
Productivity and morphological characteristics of buffel grass intercropped with butterfly pea under shade conditions

: Forage production in the Brazilian semiarid region can be enhanced by irrigation and shading to maximize water use. We evaluated the productivity and morphological characteristics of buffel grass ( Cenchrus ciliaris ) intercropped with butterfly pea ( Clitoria ternatea ) under shade conditions using an irrigated area with an artificial shading system (26, 39, 55%, or full sunlight). Butterfly pea was implemented in half of the land parcels in a randomized block using a split plot design with three replications. One hundred twenty days after planting was designated as the uniformity cut and the cutting was performed every 45 days for four consecutive cycles. The morphological analysis was performed during the first and fourth cycle, and the herbage mass was determined. The shadow had a quadratic effect on the leaf appearance rate in the first cycle, while shading had a quadratic deviation effect on the leaf elongation rate in the second cycle and an increased linear effect on the length of the sheet in the first cycle. Shading had a quadratic effect on the herbage mass in the third cycle and decreased linearity in the fourth cycle. The highest percentage of buffel grass was found in the single system in the first and second cycles. In addition, we observed a decreased linear effect of shade in the first cycle and the quadratic deviation effect of shade in the second cycle. A quadratic effect of shade was observed in the third and fourth cycles. The survival of the butterfly pea had a quadratic effect with a minimum rate level of 21% shading. The crude protein content showed a system effect in four cycles with higher crude protein in the intercropping system in the first and second cycles. There was also a quadratic effect of shade in the third cycle and linear increase in the fourth cycle. In conclusion, shading increased the leaf appearance rates and elongation at intermediate levels. In addition, a high level of shading increased the leaf length and survival of butterfly pea while it decreased the mass of the forage produced.
Incidence of diseases in Japanese quail (Coturnix coturnix japonica) with special reference to bacterial and viral diseases in some selected areas of Bangladesh

Quail industry has become a promising sector in livestock of Bangladesh in last decade. This study was aimed to find out the incidence of bacterial and viral diseases in Japanese quail (Coturnix coturnix japonica) in Bangladesh. This is the first report about the incidences of diseases in Japanese quail in Bangladesh. The incidences of diseases were investigated by the clinical signs, gross lesions in different organs and histopathological changes of different tissues in bacterial and viral diseases. A total number of 476 birds, either diseased or dead, from 40 quail farms were included in this study. The result showed that the occurrence of viral and bacterial diseases in Japanese quail were 25.21% and 34.45%, respectively where as 15.13% cases were mixed infection. Newcastle disease was found as most prevalent (11.35%) among the viral diseases. On the other hand, colibacillosis was the highest prevalent disease accounting for 15.34% among all bacterial diseases. Moreover, 22.48% cases were other types of infections (mycoplasmosis, coccidiosis, aspergillosis, deficiency disorder and internal parasitic problem) and 2.73% cases were unidentified. The highest numbers of diseases were found in the age group 21 to 30 days (23.53%) whilst the quails aged between 11 to 40 days (59.67) were most vulnerable to various diseases. The highest occurrences of diseases were found in rainy season (39.29%). It can be concluded that Newcastle disease and colibacillosis are the most frequent challenge for the quail farming in Bangladesh. Strict bio-security and proper management system might effectively reduce the incidences of the reported diseases. Asian Australas. J. Biosci. Biotechnol. 2016, 1 (3), 410-418
Effects of Phytogenic Additives and Organic Acids, alone or in combination, on the Performance, Intestinal Quality and Immune Responses of Broiler Chickens

ABSTRACT The present study was conducted to evaluate the effects of phytogenic additives (PA) and organic acids (OA), alone or in combination, on the performance, intestinal histomorphometry and lipid oxidation, and immune responses of broiler chickens. In this experiment, 820 one-day-old chicks were distributed according to a completely randomized design in a 2 × 2 + 1 factorial arrangement, with four replicates of 41 broilers each. The dietary treatments consisted of a control diet with no PA or OA (CD); CD with OA and no PA (CD+OA-PA); CD with PA and no OA (CD+PA-CD); CDwith both PA and OA (CD+PA+CD); and CD + avilamycin + monesin sodium. Broiler performance was not affected by the alternative feed additives, except from 1 to 21 days, when broilers fed the CD or CD+PA+OA diets showed higher body weight gain than those fed the CD with only OA. The broilers fed the diet containing avilamycin and monensin presented better performance. The supplementation of PA and OA increased bursalcortical area on21 and 42 days post-hatch. On 21 days post-hatch, broilers fed the AGP diet presented higher ileal villus height than those fed the control diet. The pH values of the jejunum content were reduced on the OA-fed chickens. Higher villus height and crypt depth were found in the alternative additive-fed chickens on 7 days post-hatch. On 42 days post-hatch, the percentage of the bursal cortex increased in PA-fed broilers; however, there was no increase in antibody production. The PA-fed chickens presented lower thiobarbituric acid reactive substances (TBARS) values in the small intestine. The dietary supplementation of phytogenic additives, individually or in combination associated with organic acids, does not affect broiler live performance or intestinal histomorphometry; however, it enhances immune responses and intestinal quality.
Design matters : an evaluation of the impact of small man­made forest clearings on tropical bats using a before­after­ control­impact design

Design matters : an evaluation of the impact of small man­made forest clearings on tropical bats using a before­after­control­impact ABSTRACT 21 In recent years, large clearings (> 1,000 ha) accounted for gradually smaller amounts of total annual deforestation in the Brazilian Amazon, whereas the proportion of small clearings (< 50 ha) nowadays more than 80% of annual deforestation. Despite the ubiquity of small clearings in fragmented Amazonian landscapes, most 25 fragmentation research has focused on the effects of large-scale deforestation, leading to 26 a poor understanding of the impacts of smaller barriers on Amazonian vertebrates. We 27 capitalized on the periodical re-isolation of experimental forest fragments at the 28 Biological Dynamics of Forest Fragments Project in the Central Amazon as a before- 29 after-control-impact experiment to investigate the short-term effects of small clearings 30 on bat assemblages. Over the course of three years we sampled six control sites in 31 continuous forest, the interiors and edges of eight forest fragments as well as eight sites 32 in the surrounding matrix. Sampling took place both before and after the experimental 33 manipulation (clearing of a 100 m wide strip of regrowth around each fragment), 34 resulting in ~4,000 bat captures. Species were classified as old-growth specialists and 35 habitat generalists according to their habitat affinities and a joint species distribution 36 modeling framework was used to investigate the effect of fragment re-isolation on 37 species occupancy. Following fragment re-isolation, species richness declined in all 38 habitats other than fragment edges and, although responses were idiosyncratic, this 39 decline was more pronounced for forest specialist than for generalist species. 40 Additionally, fragment re-isolation led to a reduction in the similarity between 41 assemblages in modified habitats (fragment interiors, edges and matrix) and continuous 42 forest. Sampling of controls in continuous forest both prior to and after re-isolation 43 revealed that much of the variation in bat species occupancy between sampling periods 44 did not arise from fragment re-isolation but rather reflected natural spatiotemporal variability. This emphasizes the need to sample experimental controls both before and 46 after experimental manipulation and suggests caution in the interpretation of results 47 from studies in which the effects of habitat transformations are assessed based solely on 48 data collected using space-for-time substitution approaches.
Assessing consumer preferences and willingness to pay for organic tomatoes in Albania: a conjoint choice experiment study

Albania has potential for developing the organic agriculture sector; however, it is a new industry and constraints abound including lack of consumer preferences information for organic food. Knowledge on consumer preferences and behaviour toward organic (bio) products is crucial for market development benefiting potential entrepreneurs and government policies. They need to know the preference for preferred product attributes and willingness to pay. Tomato, which is the most important vegetable in terms of consumption and production in Albania, is the subject of this study. A conjoint choice experiment with the most important product attributes: production type (bio vs . conventional), production system (open field vs . greenhouse), origin and price were used to design the choice surveys. Four distinct classes have been identified as significant using latent class analysis. The classes are summarized as: bio-ready consumers, price sensitive consumers, variety seeking consumers and quality seeking consumers. Origin played a small influence on preference. Education and income did show some influence on preference for organic tomatoes. Although the organic food market in Albania is in its infancy stage, organic tomatoes are clearly preferred and many consumers are willing to pay a premium price.
Studies of factors involved in cold stress responses of plants

Cold stress is one of the most important environmental factors that limits geographical distribution and agricultural productivity of plants. The aim of this study was to gain knowledge about the roles of the plant hormones brassinosteroids in cold stress responses of plants. The results demonstrate that brassinosteroids function as positive regulators of cold-responsive gene expression and freezing tolerance in Arabidopsis thaliana and elucidates underlying molecular modes.
Study of genetic diversity in lemon balm (Melissa officinalis l.) populations based on morphological traits and essential oils content

Lemon balm (Melissa officinalis L.) is one of the most important medicinal plants in the world trade that has many applications in drug and flavoring industrials. In order to evaluate the genetic diversity of different lemon balm populations based on morphological, agronomic and essential oils characters, nine populations from different areas of Iran were collected. In addition, two populations from Germany and Japan were examined. The experiment was carried out based randomized complete block design with three replications. Analysis of variance showed that these populations were significantly different for majority of characters such as plant height, number of tiller, chlorophyll index, leaf width, leaf length, leaf area index, fresh weight, dry weight and dry weight to fresh weight ratio except for number of node and stem diameter. Populations were classified in four groups using cluster analysis based on Ward’s algorithm. High levels of phenotypic variation using Shannon-Weaver diversity index (DI) were found among the countries of origin (DI= 0.95-1.00). Qazvin2 population was more diverse than others (DI = 0.99) whereas populations from Germany and Kurdistan displayed lower diversity indices (DI = 0.96). No clear association was detected between phenotypic diversity and origin of Iranian populations. The results of the character distribution and phenotypic diversity analysis permitted some broad generalization about collection and conservation of lemon balm landraces. This also indicated the presence of important genes for future lemon balm breeding purposes. Despite the limitation in estimating the total genetic variation, the present study indicated that morphological traits were useful for preliminary evaluation and can be used as a general approach for assessing genetic diversity among morphologically distinguishable lemon balm populations.
Charlock mustard (Sinapis arvensis): a weed reservoir for begomoviruses and associated betasatellite in Jordan

Abstract Four crop-infecting begomoviruses were found naturally affecting Charlock mustard (Sinapis arvensis L.) plants in Jordan and characterized at the molecular level. Symptoms included leaf curling and stunting. PCR analysis showed the presence of Tomato yellow leaf curl virus (TYLCV), Tomato yellow leaf curl Sardinia virus (TYLCSV), Squash leaf curl virus (SLCV) and Watermelon chlorotic stunt virus (WmCSV). These viruses were associated with Cotton leaf curl Gezira betasatellite (CLCuGβ). Sequence analysis revealed that TYLCV and TYLCSV had 98.5% and 99.3% nucleotide (nt) sequence identities with a previously described TYLCV strain from Florida and TYLCSV from Sardinia, respectively. The other two viruses, SLCV and WmCSV, shared 99.7% and 99.5% nt identities with previously described strains from Jordan. Sequence analysis also showed that CLCuGβ had 98.8% nt identity with a strain from Israel. To our knowledge, this is the first report of S. arvensis as a natural host of SLCV, WmCSV, TYLCSV and CLCuGβ.
Characterization of Cytoplasmic α-Synuclein Aggregates

The α-synuclein fibrillation process has been associated with the pathogenesis of several neurodegenerative diseases. Here, we have characterized the cytoplasmic α-synuclein aggregates using a fractionation procedure with which different aggregate species can be separated. Overexpression of α-synuclein in cells produce two distinct types of aggregates: large juxtanuclear inclusion bodies and small punctate aggregates scattered throughout the cytoplasm. Biochemical fractionation results in an inclusion-enriched fraction and two small aggregate fractions. Electron microscopy and thioflavin S reactivity of the fractions show that the juxtanuclear inclusion bodies are filled with amyloid-like α-synuclein fibrils, whereas both the small aggregate fractions contain non-fibrillar spherical aggregates with distinct size distributions. These aggregates appear sequentially, with the smallest population appearing the earliest and the fibrillar inclusions the latest. Based on the structural and kinetic properties, we suggest that the small spherical aggregates are the cellular equivalents of the protofibrils. The proteins that co-exist in the Lewy bodies, such as proteasome subunit, ubiquitin, and hsp70 chaperone, are present in the fibrillar inclusions but absent in the protofibrils, suggesting that these proteins may not be directly involved in the early aggregation stage. As predicted in the aggresome model, disruption of microtubules with nocodazole reduced the number of inclusions and increased the size of the protofibrils. Despite the increased size, the protofibrils remained non-fibrillar, suggesting that the deposition of the protofibrils in the juxtanuclear region is important in fibril formation. This study provides evidence that the cellular fibrillation also involves non-fibrillar intermediate species, and the microtubule-dependent inclusion-forming process is required for the protofibril-to-fibril conversion in cells.
A comparative Study of Adiponectin and Oxidative Stress (malondialdehyde and peroxynitrite) levels in Iraqi Patients with Acromegaly

The aim of this study is to find a relationship between oxidative stress and adiponectin in Iraqi patients with acromegaly. The present study included 30 patients with acromegaly disease attending at Al-Yarmuk teaching hospital , and 30 healthy individuals as a control group.The two groups with ages ranging (30-55) years. The results revealed a highly significant elevation in all parameters (GH,IGF-1 , adiponectin , malondialdehyde , and peroxynitrite ) levels in sera of patients when compared with healthy control . It can be concluded that oxidative stress (malondialdehyde and peroxynitrite ) may be valuable in detecting of endocrine diseases like acromegaly .
Short Communication - Effect of Alfalfa Hay on Rumen Fermentation Patterns and Serum Biochemical Profile of Growing Naemi Lambs with ad libitum Access to Total Mixed Rations

Total mixed rations (TMR) based diet is a high energy diet, which negatively deteriorates the rumen health through pH reduction . This study investigated the effect of different protocols of alfalfa hay supplementary on ruminal characteristics and performance of growing Naemi lambs fed TMR. Four groups, each of 3 months old growing Naemi male lambs (28.85±1.09 kg), were fed on TMR (NDF=41. 95%) (T1). TMR plus 100 g alfalfa hay (NDF= 43.3%) daily (T2), TMR plus 200 g alfalfa hay (NDF= 43.3%) every two days (T3) and TMR plus 300 g alfalfa hay (NDF= 43.3%) every three days (T4). Rumen fluid samples were analyzed for volatile fatty acids and ammonia nitrogen levels. Acetic acid improved significantly in exper- imental groups, while propionic acid decreased significantly in T1. Valeric acid and butyric acid decreased significantly in T1 and T2 while isovolaric acid and the ratio of acetic acid and propionic acid and glucose increased significantly in T1. In conclusion, feeding TMR with alfalfa hay, regardless of the supplementary protocol, causes a significant change in rumen fermentation patterns as a result of increasing the intake level of NDF from the alfalfa hay. This shift in the fermentation pattern may positively affect the rumen environment and consequently growing lambs’ health and productivity.
Studies on seasonal incidence of plume moth, Sphenarchus caffer Zeller in Dolichos Bean, Lablab purpureus L. and its relation with abiotic factors

The present study was carried out to find the correlation between the seasonal incidence of plume moth, Sphenarches caffer with weather variables during kharif 2015-16 and kharif 2016-17 respectively. The results revealed that the standard week wise data pertaining to plume moth S. caffer population during kharif 2015-16 revealed that the highest population incidence was recorded with two peaks i.e., once at 47th standard week and second one at 49th standard week with 3.0 and 3.3 larvae per plant, respectively, while during kharif 2016-17 the highest population incidence of S. caffer was observed with two peaks i.e. once at 49th standard week and second one at 50th standard week with 2.8 and 3.7 larvae per plant, respectively. The observations on the relationship between plume moth, S. caffer larval population with preceding one week (one week lag) weather parameters during kharif 2015-16 revealed that there was a significant negative correlation with maximum temperature (-0.427*) and evaporation (-0.517*) at 5 % level of significance whereas significant positive correlation with evening relative humidity (0.074*) at 5 % level of significance. During kharif 2016-17 minimum temperature (-0.293*) and evaporation (0.676**) were negatively significant with S. caffer larval population at 5% level and 1% level of significance, respectively while evening relative humidity (0.186*) was positively significant at 5 % level of significance.