Miracle-dz/UniFAR-FTUs huggingface dataset:
Stressed by Maternity: Changes of Cortisol Level in Lactating Domestic Cats

Simple Summary Milk feeding is the most important part of maternal care in the first weeks of the offspring’s life as it contributes to growth and development of the young, but at considerable energetic expense to the mother. One of the indicators that can be used to assess the physiological state of the female is the cortisol level relating to the stress of animals. Presumably, the more offspring there are in the litter, the higher the level of stress on the mother and, accordingly, the higher the cortisol concentrations. This study presents our data obtained in domestic cats whose litter size varied from 1 to 7 kittens. We found that the highest cortisol concentrations were observed at the peak of lactation, i.e., in 4 weeks of kittens’ life, when the offspring’s milk needs were at maximum. Moreover, during the period of offspring’s growth, the hormone level was higher in females with 1–3 kittens. In addition, cortisol concentrations in less productive cats were very high, even before mating. Abstract Lactation is the most energetically expensive component of maternal care in mammals. Increased reproductive investment can lead to physiological stress for the mothers, based on the exhaustion of energy resources and increase in glucocorticoids level. This study aimed to estimate the changes in cortisol concentrations during lactation in domestic cats and compared the differences among litter sizes. Eleven females gave birth to 27 litters, which were divided in two groups—small (1–3 kittens) and large (4–7 kittens) litters. Blood samples were collected from each female before mating, after parturition, at 4 and 8 weeks of lactation. We showed that the cortisol level in females changed significantly during lactation—the highest concentrations were observed at the peak of lactation at 4 weeks. Cortisol levels varied significantly among females but did not depend on their maternal experience. We also revealed that there were no differences in cortisol levels between females with small and large litters, but at 4 weeks of lactation, the hormone concentrations were higher in females with small litters. It is likely that these females initially invested less in reproduction, giving birth to fewer offspring.
Prevalence and Genetic Diversity of Staphylococcal Enterotoxin (-Like) Genes sey, selw, selx, selz, sel26 and sel27 in Community-Acquired Methicillin-Resistant Staphylococcus aureus

Staphylococcal enterotoxins (SEs) are virulence factors of Staphylococcus aureus associated with various toxic diseases due to their emetic and superantigenic activities. Although at least 27 SE(-like) genes have been identified in S. aureus to date, the newly identified SE(-like) genes have not yet been well characterized by their epidemiological features. In this study, the prevalence and genetic diversity of SE gene sey and SE-like genes selw, selx, selz, sel26, and sel27 were investigated for 624 clinical isolates of community-acquired methicillin-resistant S. aureus (CA-MRSA). The most prevalent SE(-like) gene was selw (92.9%), followed by selx (85.6%), sey (35.4%) and selz (5.6%), while sel26 and sel27 were not detected. Phylogenetically, sey, selw, selx, and selz were discriminated into 7, 10, 16, and 9 subtypes (groups), respectively. Among these subtypes, sey was the most conserved and showed the highest sequence identity (>98.8%), followed by selz and selx. The SE-like gene selw was the most divergent, and four out of ten genetic groups contained pseudogenes that may encode truncated product. Individual subtypes of SE(-like) genes were generally found in isolates with specific genotypes/lineages of S. aureus. This study revealed the putative ubiquity of selw and selx and the prevalence of sey and selz in some specific lineages (e.g., ST121) in CA-MRSA, suggesting a potential role of these newly described SEs(-like) in pathogenicity.
THE EVOLUTION OF THE VERTEBRATE β‐GLOBIN GENE PROMOTER

Abstract Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed “promoter shuffling”) that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous β‐globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the β‐globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human β‐like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the β‐globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base‐pair substitutions, it is clear that some redefinition of the term “promoter shuffling” is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the β‐globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate β‐globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression.
Screening of Anticancer and Immunomodulatory Activities of Panamanian Plants

Fifty-one extracts, from six Panamanian plants species selected on the basis of their toxicities against Artemia salina, belonging to five families and five genera, were screened for their in vitro anticancer (TK-10, UACC-62, MCF-7) and immunomodulatory activities [inhibition of complement, classical (CP) and alternative (AP) complement pathway and lymphoproliferation]. The results showed that 9 (17.6%) of 51 extracts presented anticancer activity against cancer cell lines, while 28 (54.9%) of 51 extracts stimulated normal spleen cells proliferation, and 25 (49.0%) inhibited in vitro lymphoid tumor cell growth. Finally, 7 (19.4%) and 10 (27.8%) out of 36 extracts showed high and moderate anticomplementary activity on CP, respectively. Moreover, out of 36 extracts, 1 (2.8%) produced higher inhibition while 4 (11.1%) showed moderate inhibition in the alternate pathway. The dichloromethane, methanolic and aqueous extracts from the leaf (3.0, 3.2, 4.2) and branch (3.5, 5.7, 5.8) of Trichospermum galeottii and from the leaf (2.4, 2.5, 5.6) and stem (2.3, 2.3, 4.7) of Sauraria yasicae were the most active immunomodulatory plants. The dichloromethane extract from the root of Morinda panamensis (8.7, 4.4, 6.3) was active against the three cancer cell lines, while the dichloromethane extract from the bark of Trichospermum galeottii(TK-10 = 3.4,UACC-62 = 9.4) and the bark of Morinda panamensis (UACC-62 = 5.5, MCF-7 = 5.9) as well as the methanolic extract from the root of Morinda rojoc (UACC-62 = 9.2, MCF-7 = 9.4) exhibited selectivity against two cancer cell lines.
Species diversity and genetic differentiation of stygofauna (Syncarida : Bathynellacea) across an alluvial aquifer in north-eastern Australia

Abstract. Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.
Abatement of acidification in mining lakes in Germany

Open-cast lignite mining has exposed formerly anaerobic layers to the air. Pyrite and marcasite are oxidized to sulfuric acid and iron sulfate, which later hydrolyses to iron hydroxide. When the pit is refilled with groundwater, its pH is 2–3. These geogenically acidified mining lakes are brown, with high iron content. Biological conditions differ greatly from those in most natural lakes and resemble those in sulfur-acidic lakes impaired by acid rain. The usability of these fish-free lakes is also restricted for recreational purposes. Neutralization with lime is expensive. The iron-buffered water has a high base buffering capacity stabilizing at pH 2–4. The complex of potential measures for neutralization comprises: the revegetation of the waste heaps, the hydrological regime and coupled transport processes, the selection of suitable filling water and in-lake technologies. Desulfurication takes place with sulfidic binding of iron and natural neutralization under locally anaerobic conditions in the reclaimed overburden heaps, in the deep water of mining lakes, in macrophyte stands and in the sediments. Anaerobic conditions should be established within the lakes during stratification periods: in the hypolimnion of eutrophic or the monimolimnion of meromictic lakes. Acidic lakes often are not sufficiently productive to achieve deep-water oxygen depletion. Measures to increase the stability of stratification may be necessary, for example by installation of barriers to establish an environment suitable for biological neutralization. Carbon sources for microbial desulfurication may be added artificially or autochthonically produced by primary producers. Therefore, a controlled eutrophication may be useful in the initial filling stages of acidic mining lakes.
Gold Nanoparticles Induce Oxidative Stress and Apoptosis in Human Kidney Cells

Gold nanoparticles (AuNPs) are highly attractive for biomedical applications. Therefore, several in vitro and in vivo studies have addressed their safety evaluation. Nevertheless, there is a lack of knowledge regarding their potential detrimental effect on human kidney. To evaluate this effect, AuNPs with different sizes (13 nm and 60 nm), shapes (spheres and stars), and coated with 11-mercaptoundecanoic acid (MUA) or with sodium citrate, were synthesized, characterized, and their toxicological effects evaluated 24 h after incubation with a proximal tubular cell line derived from normal human kidney (HK-2). After exposure, viability was assessed by the MTT assay. Changes in lysosomal integrity, mitochondrial membrane potential (ΔΨm), reactive species (ROS/RNS), intracellular glutathione (total GSH), and ATP were also evaluated. Apoptosis was investigated through the evaluation of the activity of caspases 3, 8 and 9. Overall, the tested AuNPs targeted mainly the mitochondria in a concentration-dependent manner. The lysosomal integrity was also affected but to a lower extent. The smaller 13 nm nanospheres (both citrate- and MUA-coated) proved to be the most toxic among all types of AuNPs, increasing ROS production and decreasing mitochondrial membrane potential (p ≤ 0.01). For the MUA-coated 13 nm nanospheres, these effects were associated also to increased levels of total glutathione (p ≤ 0.01) and enhanced ATP production (p ≤ 0.05). Programmed cell death was detected through the activation of both extrinsic and intrinsic pathways (caspase 8 and 9) (p ≤ 0.05). We found that the larger 60 nm AuNPs, both nanospheres and nanostars, are apparently less toxic than their smaller counter parts. Considering the results herein presented, it should be taken into consideration that even if renal clearance of the AuNPs is desirable, since it would prevent accumulation and detrimental effects in other organs, a possible intracellular accumulation of AuNPs in kidneys can induce cell damage and later compromise kidney function.
A Highly Accurate 3d Reconstruction method for Small Object Scanning

In this paper, we propose a 3d reconstruction scheme for micrometer-level scanning of decimeter-scale objects, with both real-time efficiency and high accuracy, by improving classical point cloud registration methods and graph-based optimization methods. We find several major factors which significantly influence the accuracy of point cloud registration in such scanning contexts and discard other less relevant factors with the concern of efficiency. We utilize a group of keyframe selecting strategies to make the initial estimation of camera poses attainable in real-time. To eliminate the accumulated modeling error of localization, we perform online local pose-graph optimization and offline global bundle adjustment as a postprocessing step, by incorporating the metric structure of the graph of the real-time registration results. The numerical experiments indicate that the proposed method can achieve the accuracy required by many industrial applications such as dental restoration and mechanical measurements.
Intercropping winter cereals with Caucasian clover for forage in northern Europe

Intercropping cereal crops with perennial legumes for forage has been demonstrated as a means to improve nutritive value compared to cereal crops alone. Our objective was to determine whether sowing winter rye (Secale cereale L.) or winter triticale (x Triticosecale Wittmack) into living Caucasian clover (Trifolium ambiguum M. Bieb.) improves yield or nutritive value compared to monoculture cereal crop forage in northern Europe. The experiments were conducted near Mochełek and Falęcin, Poland. In autumn 2010 and 2011, winter rye was sown into existing Caucasian clover or in monoculture at Mochełek, and winter triticale was sown into Caucasian clover or in monoculture at Falęcin, with monoculture clover as a third crop treatment at both locations. The following spring, first harvest of forage from the three crop treatments was taken at two maturities: when monoculture cereals reached heading (BBCH 51) or grain milk stage (BBCH 71), and two additional harvests were taken from mixture plots and monoculture clover before autumn. First harvest forage yields of mixtures were similar to monoculture cereal at Falęcin, less than monoculture cereal at Mochełek, and greater than monoculture clover at both locations. Full season forage yields of mixtures were greater than both monoculture cereal and clover crops at both locations. The proportion of clover in mixtures was 20–31% in the first harvest, resulting in slightly lower neutral detergent fiber concentrations than in monoculture cereal crop at Falęcin, but no improvement in nutritive value at Mochełek. By spring 2012, most Caucasian clover had died from Sclerotinia trifoliorum infection at both locations, so forage was not harvested in the second year of the experiment. Although total season forage yields were greater for mixtures than for either monoculture cereal or Caucasian clover, this system cannot be recommended for northern Europe because of failure for Caucasian clover to persist.
Investigation of the Impacts of Antibiotic Exposure on the Diversity of the Gut Microbiota in Chicks

Simple Summary Broad-spectrum antibiotics have been a cornerstone in the treatment of bacterial diseases. However, growing evidence suggests that antibiotics have effects on host-associated gut microbiota communities. In this study, we report persistent significant changes in the abundance of gut microbiota and their functional metabolite pathways in chickens due to enrofloxacin and diclazuril exposure. These changes may affect the taxonomic, genomic, and functional capacity of the chicken gut microbiota, reducing bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Understanding the biology of competitive exclusion of adaptive functions during antibiotic exposure in the gut may inform the design of new strategies to treat infections, while preserving the ecology of chicken-beneficial constituents. Abstract The dynamic microbiota in chickens can be affected by exposure to antibiotics, which may alter the composition and substrate availability of functional pathways. Here, 120 Jing Hong chicks at 30 days of age were randomly divided into four treatments totaling seven experimental groups: control chicks not exposed to antibiotics; and chicks exposed to enrofloxacin, diclazuril, and their mixture at 1:1 for 14 days and then not exposed for a withdrawal period of 15 days. Fecal samples were collected from the 7 groups at 8 time-points (exposure to 4 antibiotics and 4 withdrawal periods) to perform in-depth 16S rRNA sequencing of the gut microbiota. Taxon-independent analysis showed that the groups had significantly distinct microbial compositions (p < 0.01). Based on the microbial composition, as compared with the control group, the abundances of the phyla Firmicutes, Actinobacteria, Thermi, and Verrucomicrobia, as well as the families Lactobacillus, Lactococcus, S24-7, and Corynebacterium, were decreased in the antibiotic-exposed chicks (p < 0.01). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analyses revealed significant differences in microbiota metabolite pathways due to the genera of the antibiotic-responsive microbes (p < 0.01), especially the pathways relating to cell growth and death, immune system diseases, carbohydrate metabolism, and nucleotide metabolism. Oral treatment with enrofloxacin, diclazuril, and their mixture modified the gut microbiota composition and the microbial metabolic profiles in chickens, with persistent effects (during the withdrawal period) that prevented the return to the original community and led to the formation of a new community.
MC-Explorer: Analyzing and Visualizing Motif-Cliques on Large Networks

Large networks with labeled nodes are prevalent in various applications, such as biological graphs, social networks, and e-commerce graphs. To extract insight from this rich information source, we propose MC-Explorer, which is an advanced analysis and visualization system. A highlight of MC-Explorer is its ability to discover motif-cliques from a graph with labeled nodes. A motif, such as a 3-node triangle, is a fundamental building block of a graph. A motif-clique is a "complete" subgraph in a network with respect to a desired higher-order connection pattern. For example, on a large biological graph, we found out some motif-cliques, which disclose new side effects of a drug, and potential drugs for healing diseases. MC-Explorer includes online and interactive facilities for exploring a large labeled network through the use of motif-cliques. We will demonstrate how MC-Explorer can facilitate the analysis and visualization of a labeled biological network.An online demo video of MC-Explorer can be accessed from https://www.dropbox. com/s/vkalumc28wqp8yl/demo.mov
Simultaneous Nasal Carriage by Methicillin-Resistant and Methicillin Susceptible Staphylococcus aureus of Lineage ST398 in a Live Pig Transporter

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)398 is a livestock associated (LA) lineage with zoonotic potential, especially in humans with live pig contact. The objective of this study was to characterize two S. aureus strains of lineage ST398 (one methicillin-resistant (MRSA), one methicillin-susceptible (MSSA)) isolated from the same nasal sample of a patient admitted in the Intensive-Care Unit of a Spanish Hospital, and with previous occupational exposure to live pigs, by whole-genome-sequencing (WGS). The sample was obtained during routine surveillance for MRSA colonization. Purified genomic DNA was sequenced using Illumina HiSeq 2000 and processed using conventional bioinformatics software. The two isolates recovered were both S. aureus t011/ST398 and showed similar resistance-phenotypes, other than methicillin susceptibility. The possession of antibiotic resistance genes was the same, except for the mecA-gene located in SCCmecV in the MRSA isolate. The MSSA isolate harbored remnants of a SCCmec following the deletion of 17342bp from a recombination between two putative primases. Both isolates belonged to the livestock-associated clade as defined by three canonical single-nucleotide-polymorphisms, and neither possessed the human immune evasion cluster genes, chp, scn, or sak. The core genome alignment showed a similarity of 99.6%, and both isolates harbored the same mobile genetic elements. The two nasal ST398 isolates recovered from the patient with previous occupational exposure to pigs appeared to have a livestock origin and could represent different evolutionary steps of animal-human interface lineage. The MSSA strain was formed as a result of the loss of the mecA gene from the livestock-associated-MRSA lineage.
The Effects of Car Traffic on Breeding Bird Populations in Woodland. II. Breeding Dispersal of Male Willow Warblers (Phylloscopus trochilus) in Relation to the Proximity of a Highway

1. In this study the dispersal activity of male willow warblers Phylloscopus trochilus breeding next to a highway carrying heavy traffic was investigated. 2. Breeding dispersal distances of yearling males along the road were larger than at further distances and were in the same order of magnitude as natal dispersal distances (medians being 303 and 515 m, respectively). 3. A simulation of dispersal directions, adjusted for actual landscape features, indicated that breeding dispersal was actively directed away from the road. 4. There appeared to be a relation between dispersal and breeding performance for yearling males, unsuccessful males moving more frequently and further (median 294 m) than successful males (median 120 m)