Miracle-dz/UniFAR-FTUs huggingface dataset:
Yersinia enterocolitica: Prevalence, virulence, and antimicrobial resistance from retail and processed meat in Egypt

Background and Aim: The objectives of this study were to investigate the prevalence of Yersinia enterocolitica in retail chicken meat, ground and processed beef meat, determine their virulence-associated genes, antimicrobial susceptibility pattern, molecular detection of extended-spectrum β-lactamases, and their capability of biofilm formation in vitro. Materials and Methods: A total of 210 samples (120 retail chicken meat, 30 ground beef, 30 beef burger, and 30 sausage samples) were collected from different retail chicken outlets and markets located at Mansoura city between December 2016 and April 2017. Meat samples were examined bacteriologically for the existence of Y. enterocolitica; bacterial colonies that displayed positive biochemical properties were subjected to polymerase chain reaction targeting 16 rRNA gene. Y. enterocolitica isolates were tested for their susceptibility to six antimicrobial agents using disk diffusion method. Uniplex PCR was used for screening Y. enterocolitica isolates for the presence of two virulence chromosome-associated genes (ail and yst), and β-lactamases (blaTEM and blaSHV). The capability of Y. enterocolitica to form biofilms was detected by tube method. Results: Thirty Y. enterocolitica isolates (14.29%) were recovered including 19 (15.83%) isolates from chicken meat, 3 (10%) from ground beef, 5 (16.67%) from beef burger, and 3 (10%) from sausage samples. Regarding ail gene, it was detected in 6.67% (2/30), while yst gene detected in 20% (6/30) Y. enterocolitica isolates. About 80%, 70%, 63.33%, and 50% of Y. enterocolitica isolates were sensitive to ciprofloxacin, gentamicin, cefotaxime, and streptomycin, respectively, while 83.33% of Y. enterocolitica isolates were resistant to both ampicillin and cephalothin. Interestingly, 21 (70%) isolates had the capability of biofilms formation in vitro. Among the multidrug-resistant (MDR) strains, a significant difference (p<0.05) was found between MDR and biofilm formation. However, biofilm formation was correlated with the resistance of the isolates to β-lactam antimicrobials and the presence of β-lactam-resistant genes. Conclusion: The presence of Y. enterocolitica in chicken meat, ground and processed beef meat represents a significant health risk for meat consumers, which reflects the contamination of slaughterhouses and processing operations, therefore, strict hygienic measures should be applied to minimize carcasses contamination.
Diatoms associated with two South African kelp species: Ecklonia maxima and Laminaria pallida

Kelp forests are believed to host a large biomass of epiphytic fauna and flora, including diatoms, which constitute the base of aquatic food webs and play an important role in the transfer of energy to higher trophic levels. Epiphytic diatom assemblages associated with two common species of South African kelps, Ecklonia maxima and Laminaria pallida, were investigated in this study. Primary blades of adult and juvenile thalli of both kelp species were sampled at False Bay in July 2017 and analysed using scanning electron microscopy. Our findings showed that both kelp species hosted relatively low densities of diatoms (ranging from 7 [SD 5] cells mm−2 on adult specimens of L. pallida to 43 [SD 66] cells mm−2 on blades of juvenile E. maxima), with Amphora and Gomphoseptatum reaching the highest absolute abundances. Although non-metric multidimensional scaling showed overlapping and largely scattered sample sets, a significant relationship between the diatom communities and the species and age of the host macroalga was detected by two-way PERMANOVA. In general, more abundant and diverse diatom communities were observed on juvenile thalli than on adult thalli, with species belonging to Navicula and Rhoicosphenia contributing significantly to the observed dissimilarity. Due to a significant interaction between species and age effects, however, the overall ability of kelp species, their age, and their interaction to explain the variation in diatom community structure was limited. We suggest that the low densities of epiphytic diatoms were directly related to the sloughing of epithelial cells observed in both kelp species. We further speculate that on such unstable substrata some diatom taxa might adapt to an endophytic life to avoid the antifouling mechanisms developed by their hosts.
Rethinking Phylogeny and Ontogeny in Hominin Brain Evolution

Theories of hominin and human cognitive evolution have traditionally focused on the phylogeny of the human brain, and on comparisons of human and primate brains in relation to social or ecological variables. Far less attention has been paid to ontogenetic processes, despite the recognition that experience has a profound influence on adult cognition. In this paper we discuss the interplay between phylogeny and ontogeny by examining relationships between human brain size, developmental scheduling and cognition. The correlates of large brains include not only altered subsistence and life-history strategies to meet associated energetic costs, but also on macro- and micro-scale structural adaptations required to meet increased processing costs. This means that larger brains are of necessity more highly interconnected brains, with higher degrees of folding of the neocortex (gyrification) and higher ratios of myelinated connections between neurons (white matter) to neurons themselves (grey matter). Here we argue that the combination of these evolutionary trends underpins the complexity of human behaviour, as the neural circuits involved in cognitive mechanisms such as the mirror neuron system (the system governing motor emulation and imitation) and theory of mind (fundamental in social cognition) mature only slowly, and require considerable socially-scaffolded experience to develop to their full potential. These abilities are likely to be fundamental in characteristically human behaviours such as the cultural transmission of complex forms of tool manufacture and use, attested to in the archaeological record. Their elaborated modern human forms, we argue, are possible only in the context of the evolution of relatively slower trajectories of brain growth and hence longer periods during which the growing brain can be influenced by experience among modern humans relative to other primates. Here we review some of the differences in ontogenetic brain development between humans and other primates, and compare the rates and trajectories of neural development between ourselves and our closest living relatives the chimpanzees to suggest that the human pattern of expanded periods of growth coupled with slower trajectories of neural development is likely to have been of huge significance during hominin evolution. In addition, we discuss fossil and archaeological proxies which might allow the reconstruction of evolutionary patterns of development, suggesting that it is only post-Homo erectus and specifically among Homo heidelbergensis and Homo neanderthalensis populations that developmental patterns approximate those of modern humans, arguing for a similar – but not identical – role for socially-scaffolded learning of complex technical skills as among modern groups in these species.
Ethical Challenges of Germline Genetic Enhancement

The new reproductive technologies have opened the door to different processes of germline genetic enhancement by which the characteristics of an individual according to the interests of the agents involved could be selected during its gestation. Although the initiative is apparently oriented towards developing individuals that would excel in society, critical voices raise the concerns about that this approach would generate and need for a reflection on the ethical, social and legal implications of these techniques and their implementation in society. We reviewed the literature about these issues throughout their historical records to date, focusing on the moral arguments and non-clinical aspects that affect the legal and social environment. We have observed various trends of thought with divergent positions (proactive, preventive, and regulatory) as well as a large number of articles that try to reconcile the different approaches. This review illustrates a series of concepts from the ethics and philosophy fields which are frequently used in studies that evaluate the ethical implications of germline genetic enhancement, such as dignity, benefit, autonomy, and identity. In addition, amongst the many unresolved controversies surrounding genetic enhancement, we identify procreative beneficence, genetic disassociation, gender selection, the value of disability, embryo chimerization, and the psychosocial inequality of potentially enhanced individuals as crucial. We also develop possible scenarios for future debate. We consider especially important the definition and specification of three aspects which are essential for the deployment of new reproductive technologies: the moral status of the embryo undergoing enhancement, the legal status of the enhanced individual, and the responsibility of the agents executing the enhancement. Finally, we propose the precautionary principle as a means to navigate ethical uncertainties.
Review of Alzheimer’s Disease Classification Techniques

Alzheimer’s disease is a brain degeneration illness. It requires earlier detection in order to improve the quality of life of the patient. Many researchers have studied different computed aided approaches in order to help in the diagnosis of the disease. However, there are few well-known techniques that were used in most of the studies. It is challenging in mild cognitive impairment classification too. Therefore, this paper will review the common used methods and the state-of-art methods in Alzheimer’s disease classification. This helps researchers to identify the suitable methodologies in different stages of classification.
Life‐history traits of the Whiting polyploid line of the parasitoid Nasonia vitripennis

In hymenopterans, males are normally haploid (1n) and females diploid (2n), but individuals with divergent ploidy levels are frequently found. In species with ‘complementary sex determination’ (CSD), increasing numbers of diploid males that are often infertile or unviable arise from inbreeding, presenting a major impediment to biocontrol breeding. Non‐CSD species, which are common in some parasitoid wasp taxa, do not produce polyploids through inbreeding. Nevertheless, polyploidy also occurs in non‐CSD Hymenoptera. As a first survey on the impacts of inbreeding and polyploidy of non‐CSD species, we investigate life‐history traits of a long‐term laboratory line of the parasitoid Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae) (‘Whiting polyploid line’) in which polyploids of both sexes (diploid males, triploid females) are viable and fertile. Diploid males produce diploid sperm and virgin triploid females produce haploid and diploid eggs. We found that diploid males did not differ from haploid males with respect to body size, progeny size, mate competition, or lifespan. When diploid males were mated to many females (without accounting for mating order), the females produced a relatively high proportion of male offspring, possibly indicating that these males produce less sperm and/or have reduced sperm functionality. In triploid females, parasitization rate and fecundity were reduced and body size was slightly increased, but there was no effect on lifespan. After one generation of outbreeding, lifespan as well as parasitization rate were increased, and a body size difference was no longer apparent. This suggests that outbreeding has an effect on traits observed in an inbred polyploidy background. Overall, these results indicate some phenotypic detriments of non‐CSD polyploids that must be taken into account in breeding.
Seed mix design and first year management influence multifunctionality and cost‐effectiveness in prairie reconstruction

Agricultural intensification continues to diminish many ecosystem services in the North American Corn Belt. Conservation programs may be able to combat these losses more efficiently by developing initiatives that attempt to balance multiple ecological benefits. In this study, we examine how seed mix design and first year management influence three ecosystem services commonly provided by tallgrass prairie reconstructions (erosion control, weed resistance, and pollinator resources). We established research plots with three seed mixes, with and without first year mowing. The grass‐dominated “Economy” mix had 21 species and a 3:1 grass‐to‐forb seeding ratio. The forb‐dominated “Pollinator” mix had 38 species and a 1:3 grass‐to‐forb seeding ratio. The grass:forb balanced “Diversity” mix, which was designed to resemble regional prairie remnants, had 71 species and a 1:1 grass‐to‐forb ratio. To assess ecosystem services, we measured native stem density, cover, inflorescence production, and floral richness from 2015 to 2018. The Economy mix had high native cover and stem density, but produced few inflorescences and had low floral richness. The Pollinator mix had high inflorescence production and floral richness, but also had high bare ground and weed cover. The Diversity mix had high inflorescence production and floral richness (comparable to the Pollinator mix) and high native cover and stem density (comparable to the Economy mix). First year mowing accelerated native plant establishment and inflorescence production, enhancing the provisioning of ecosystem services during the early stages of a reconstruction. Our results indicate that prairie reconstructions with thoughtfully designed seed mixes can effectively address multiple conservation challenges.
Methane yield and species diversity dynamics of perennial wild plant mixtures established alone, under cover crop maize (Zea mays L.), and after spring barley (Hordeum vulgare L.)

The cultivation of perennial wild plant mixtures (WPMs) in biogas cropping systems dominated by maize (Zea mays L.) restores numerous ecosystem functions and improves both spatial and temporal agrobiodiversity. In addition, the colorful appearance of WPM can help enhance landscape beauty. However, their methane yield per hectare (MYH) varies greatly and amounts to only about 50% that of maize. This study aimed at decreasing MYH variability and increasing accumulated MYH of WPM by optimizing the establishment method. A field trial was established in southwest Germany in 2014, and is still running. It tested the effects of three WPM establishment procedures (E1: alone [without maize, in May], E2: undersown in cover crop maize [in May], E3: WPM sown after whole‐crop harvest of spring barley [Hordeum vulgare L.] in June) on both MYH and species diversity of two WPMs [S1, S2]). Mono‐cropped maize and cup plant (Silphium perfoliatum L.) were used as reference crops. Of the WPM treatments tested, S2E2 achieved the highest (19,296 mN3/ha , 60.5% of maize) and S1E1 the lowest accumulated MYH (8,156 mN3/ha , 25.6% of maize) in the years 2014–2018. Cup plant yielded slightly higher than S2E2 (19,968 mN3/ha , 62.6% of maize). In 2014, the WPM sown under maize did not significantly affect the cover crop performance. From 2015 onward, E1 and E2 had comparable average annual MYH and average annual number of WPM species. With a similar accumulated MYH but significantly higher number of species (3.5–10.2), WPM S2E2 outperformed cup plant. Overall, the long‐term MYH performance of WPM cultivation for biogas production can be significantly improved by undersowing with maize as cover crop. This improved establishment method could help facilitate the implementation of WPM cultivation for biogas production and thus reduce the trade‐off between bioenergy and biodiversity.
Prediction of Osyris lanceolata (Hochst. Steud.) site suitability using indicator plant species and edaphic factors in humid highland and dry lowland forests in Kenya

Osyris lanceolata (African Sandalwood) belongs to the family Santalaceae that hosts some of the most valuable species for perfumery oil extraction. In India and Australia, Santalum album and Santalum spicatum are well developed for perfumery oil extraction through establishment of commercial plantations. In Africa, O. lanceolata has attracted significant attention as potential perfumery oils extraction species. However, African Sandalwood exploitation is through unsustainable smuggling from natural forests and woodlands. Since sustainable production of O. lanceolata oils is only feasible through establishment of commercial plantations, there is need to understand ecological requirements of the species before the remaining natural stands disappear. The aim of this study was to determine plant species and edaphic factors that can predict African Sandalwood site suitability for domestication programs. Sample plots with and without O. lanceolata were selected from natural stands in a humid highland forest and a dry lowland forest, vegetation sampled using nested-intensity plots and soils sampled in the plots simultaneously. Vegetation data was recorded according to species abundance. Soil samples were analyzed for nutrients, texture and moisture retention. Canonical Correspondence Analysis using CANOCO software was used to determine species association and relationship between species to soil variables. In the highland forest, O. lanceolata clustered with Rhus natalensis and six other species, and was correlated to soil nitrogen, moisture and clay. In lowland forest, O. lanceolata clustered with R. natalensis and Hypoestes forskahlii but did not correlate with any of the soil variables. The clustering of African Sandalwood with R. natalensis in both forest types suggests strong predictive capacity of R. natalensis for O. lanceolata site suitability in humid and dry areas. Inconsistence of O. lanceolata relationship with soil variables in the two study sites provides opportunity for further studies in different soil types. Key words: CANOCO, domestication, edaphic, hemi-parasites, species association, African Sandalwood.
New records of Digitaria filiformis var. laeviglumis (Paniceae, Panicoideae, Poaceae) for the Flora del Bajío and Durango, Mexico

Background and Aims: Since its publication in 1920, Digitaria filiformis var. laeviglumis had been considered as an endangered taxon endemic to New Hampshire, USA. However, a recent inventory of the grasses of Mexico showed that it also occurs outside its type locality. New findings for the ongoing project Flora del Bajío have yielded additional new records. The objective of this work is to report this taxon from the Mexican states of Michoacán and Durango, increasing the number of known localities of Digitaria filiformis var. laeviglumis.Methods: Online databases and herbaria were reviewed. Botanical herbarium specimens were collected in the state of Michoacán. Key results: Digitaria filiformis var. laeviglumis is reported as new for the Flora del Bajío in the state of Michoacán, as well as from a herbarium specimen from Durango which has both var. laeviglumis and var. filiformis mounted on the same sheet and that was misplaced among other specimens.Conclusions: With the addition of this variety, the number of taxa in the subfamily Panicoideae increases for the Flora del Bajío and the state Durango. With these findings there are more intermediate localities between the northern and southern range for this variety.
A brief history and technical review of the expert system research

The expert system is a computer system that emulates the decision-making ability of a human expert, which aims to solve complex problems by reasoning knowledge. It is an important branch of artificial intelligence. In this paper, firstly, we briefly introduce the development and basic structure of the expert system. Then, from the perspective of the enabling technology, we classify the current expert systems and elaborate four expert systems: The Rule-Based Expert System, the Framework-Based Expert System, the Fuzzy Logic-Based Expert System and the Expert System Based on Neural Network.
Histopathological variations in gills, liver and kidney of nile tilapia - Oreochromis niloticus exposed to benzalkoniumbhloride mixture with treated produced water

The microscopic examination of tissue in order to study the manifestations of disease is very important. This paper investigated the histopathological variation in some organs of juveniles of Nile tilapia- Oreohromis niloticus exposed to benzalkonium chloride (BAC)-treated produced water (TPW) mixture in a 96hour acute toxicity test. Fish specimens of average body length and weight 7.80 cm and 25.05g, respectively were used. At the end of exposure 2 survivor fish in each concentration across triplicates were randomly harvested for the histological examination. Histological preparations of gills, kidney and liver were analysed for histopathological alterations. Results of histological examination revealed various degrees of legions ( gills- cellular necrosis and epithelial rupture (CN), kidney - glomerular expansion (GE) and dilation of Bowman’s space (BC) and liver - expanded central vein (CV) and melanomacrophages aggregate (M)) depending on concentrations of the toxicant as against untreated (control) that recorded no abnormality. The results showed that the severity of tissue alterations recorded was a function of toxicity ofbenzalkonium chloride (BAC) mixture with treated produced water (TPW). It is strongly recommended its disposal followed a thorough treatment. Keywords: Benzalkonium-chloride, treated-produced-water, histopathology, cellular necrosis, O. niloticus
Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites

P2 is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C-H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C-H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups breaking planarity rules. For example, in SH3 domains, a conserved bent aromatic residue is observed near the ligand binding site. FABP3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, deuteration of protein and/or solvent are promising variables in protein crystal optimization.
Purified glycerin in balanced diets of broiler chickens treated from 1 to 42 days of age

ABSTRACT We evaluated the technical feasibility of purified glycerin inclusion in balanced diets of broiler chickens treated from 1 to 42 days of age. A total of 240 broiler chickens were distributed in a completely randomized design into four treatments (0, 2, 4, and 6% purified glycerin inclusion), with six replicates of 10 broilers each. We evaluated productive performance (at 7, 21, and 42 days), edible viscera (heart, liver, and gizzard), carcass yield and cuts, color, chemical and physical composition, [. ]