Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteome, Bioinformatic, and Functional Analyses Reveal a Distinct and Conserved Metabolic Pathway for Bile Salt Degradation in the Sphingomonadaceae

This study highlights the biochemical diversity of bacterial degradation of steroid compounds in particular bile salts. Furthermore, it substantiates and advances knowledge of a variant pathway for degradation of steroids by sphingomonads, a group of environmental bacteria that are well known for their broad metabolic capabilities. ABSTRACT Bile salts are amphiphilic steroids with digestive functions in vertebrates. Upon excretion, bile salts are degraded by environmental bacteria. Degradation of the bile salt steroid skeleton resembles the well-studied pathway for other steroids, like testosterone, while specific differences occur during side chain degradation and the initiating transformations of the steroid skeleton. Of the latter, two variants via either Δ1,4- or Δ4,6-3-ketostructures of the steroid skeleton exist for 7-hydroxy bile salts. While the Δ1,4 variant is well known from many model organisms, the Δ4,6 variant involving a 7-hydroxysteroid dehydratase as a key enzyme has not been systematically studied. Here, combined proteomic, bioinformatic, and functional analyses of the Δ4,6 variant in Sphingobium sp. strain Chol11 were performed. They revealed a degradation of the steroid rings similar to that of the Δ1,4 variant except for the elimination of the 7-OH as a key difference. In contrast, differential production of the respective proteins revealed a putative gene cluster for the degradation of the C5 carboxylic side chain encoding a CoA ligase, an acyl-CoA dehydrogenase, a Rieske monooxygenase, and an amidase but lacking most canonical genes known from other steroid-degrading bacteria. Bioinformatic analyses predicted the Δ4,6 variant to be widespread among the Sphingomonadaceae, which was verified for three type strains which also have the predicted side chain degradation cluster. A second amidase in the side chain degradation gene cluster of strain Chol11 was shown to cleave conjugated bile salts while having low similarity to known bile salt hydrolases. This study identifies members of the Sphingomonadaceae that are remarkably well adapted to the utilization of bile salts via a partially distinct metabolic pathway. IMPORTANCE This study highlights the biochemical diversity of bacterial degradation of steroid compounds, in particular bile salts. Furthermore, it substantiates and advances knowledge of a variant pathway for degradation of steroids by sphingomonads, a group of environmental bacteria that are well known for their broad metabolic capabilities. Biodegradation of bile salts is a critical process due to the high input of these compounds from manure into agricultural soils and wastewater treatment plants. In addition, these results may also be relevant for the biotechnological production of bile salts or other steroid compounds with pharmaceutical functions.
Use of an enclosed elk population to assess two non-invasive methods for estimating population size

Non-invasive genetic sampling and spatially explicit capture-recapture (SCR) models are used increasingly to estimate abundance of wildlife populations, but have not been adequately tested on gregarious animals such as elk (Cervus canadensis), for which correlated space use and movements violate model assumptions of independence. To evaluate the robustness and accuracy of SCR, and to assess the utility of an alternative non-invasive method for estimating density of gregarious ungulates, we utilized a tule elk (Cervus canadensis nannodes) population of known size within a fenced enclosure on the San Luis National Wildlife Refuge in central California. We evaluated fecal genetic SCR to camera trap-based random encounter model (REM) approaches to density estimation based on comparison to the true abundance. We also subsampled the dataset to explore the effects of varying search effort and elk density on the precision and accuracy of results. We found that SCR outperformed REM methods in the full datasets, and reliably provided accurate (relative bias <10%) and reasonably precise (relative standard error ≤20%) estimates of density at moderately low to high densities (6–17 elk/km2), when the subsampling scenarios yielded a minimum average of 20 recaptures. We also found that the number of samples used to construct detection histories was a reliable predictor of precision, and could be used to establish minimum sampling requirements in future population surveys of elk. Although field-testing in free-ranging populations is needed, our results suggest that non-invasive genetic SCR is a promising tool for future population studies and monitoring of elk and potentially other gregarious ungulates. In contrast, the REM estimate of density was highly inaccurate, imprecise, and highly sensitive to camera parameters.
Glycerol Monolaurate Ameliorated Intestinal Barrier and Immunity in Broilers by Regulating Intestinal Inflammation, Antioxidant Balance, and Intestinal Microbiota

Extensive interactions occur between a poultry host and its gut microbiome. Glycerol monolaurate (GML) possesses a large range of antimicrobial and immunoregulatory properties. This study was conducted to investigate the impact of different doses of GML (basal diets complemented with 0, 300, 600, 900, or 1200 mg/kg GML) on growth performance, intestinal barrier, and cecal microbiota in broiler chicks. Results revealed that feed intake increased after 900 and 1200 mg/kg GML were administered during the entire 14-day experiment period. Dietary GML decreased crypt depth and increased the villus height-to-crypt depth ratio of the jejunum. In the serum and jejunum, supplementation with more than 600 mg/kg GML reduced interleukin-1β, tumor necrosis factor-α, and malondialdehyde levels and increased the levels of immunoglobulin G, jejunal mucin 2, total antioxidant capacity, and total superoxide dismutase. GML down-regulated jejunal interleukin-1β and interferon-γ expression and increased the mRNA level of zonula occludens 1 and occludin. A reduced expression of toll-like receptor 4 and a tendency of down-regulated nuclear factor kappa-B was shown in GML-treated groups. In addition, GML modulated the composition of the cecal microbiota of the broilers, improved microbial diversity, and increased the abundance of butyrate-producing bacteria. Spearman’s correlation analysis revealed that the genera Barnesiella, Coprobacter, Lachnospiraceae, Faecalibacterium, Bacteroides, Odoriacter, and Parabacteroides were related to inflammation and intestinal integrity. In conclusion, GML ameliorated intestinal morphology and barrier function in broiler chicks probably by regulating intestinal immune and antioxidant balance, as well as intestinal microbiota. IMPORTANCE Antibiotic residues and resistance issues led to the ban of antibiotic growth promoters. GML is considered an efficacious antibiotic growth promoter alternative for animal health and has the potential to become a unique fungicide owing to its established safety, antibacterial properties, and immunomodulatory capacity. Despite the potential of GML as an additive in poultry feed, little is known about the influence of GML on cecal microbiota in broilers. The significance of our research was to determine the microbial mechanism by which GML worked.
Neutrophil extracellular traps arm DC vaccination against NPM-mutant myeloproliferation

Neutrophil extracellular traps (NET) are web-like chromatin structures composed by dsDNA and histones, decorated with anti-microbial proteins. Their interaction with dendritic cells (DC) allows DC activation and maturation toward presentation of NET-associated antigens. Differently from other types of cell death that imply protein denaturation, NETosis preserves the proteins localized onto the DNA threads for proper enzymatic activity and conformational status, including immunogenic epitopes. Besides neutrophils, leukemic cells can release extracellular traps displaying leukemia-associated antigens, prototypically mutant nucleophosmin (NPMc+) that upon mutation translocates from nucleolus to the cytoplasm localizing onto NET threads. We tested NPMc+ immunogenicity through a NET/DC vaccine to treat NPMc-driven myeloproliferation in transgenic and transplantable models. Vaccination with DC loaded with NPMc+ NET (NPMc+ NET/DC) reduced myeloproliferation in transgenic mice, favoring the development of antibodies to mutant NPMc and and the induction of a CD8+ T cell response. The efficacy of this vaccine was also tested in mixed NPMc/WT bone marrow chimeras in a competitive bone marrow transplantation setting, where the NPMc+ NET/DC vaccination impaired the expansion of NPMc+ in favor of WT myeloid compartment. NPMc+ NET/DC vaccination also achieved control of an aggressive leukemia transduced with mutant NPMc, effectively inducing an anti-leukemia CD8 T cell memory response. eTOC Summary NPMc is an AML-triggering mutation inducing translocation of NPM into the cytoplasm, allowing its association to NET threads. On NET, NPMc becomes immunogenic acting as an alarmin and exposing immunogenic peptides. We demonstrate that NET can be exploited as anti-tumor weapons in DC-based vaccination strategies.
A new species of the Hydroporus planus-group from northern Morocco with close affinities to H. analis Aubé, 1838 and H. decipiens Sharp, 1878 (Coleoptera: Dytiscidae: Hydroporinae)

Summary Hydroporus bertrandi n. sp. is described from the Rif Mountains of northern Morocco. It is a member of the Hydroporus planus-group with close affinities to H. analis Aubé, 1838 and H. decipiens Sharp, 1878, as evidenced by the strongly rugose ventral abdominal surface. The new species differs from these close relatives mainly by larger size, finer punctation on the elytra and metacoxal plates, different sculpture on the lateral parts of the metaventrite, and the different shape of the median lobe of aedeagus. Illustrations of dorsal habitus, parts of the ventral surface and male genitalia are provided for the three species. Environmental characteristics of the habitats where H. bertrandi n. sp. was sampled in the Rif are described and illustrated and a distribution map of the species is provided. Analysis of a partial CO1 alignment shows that H. bertrandi n. sp. is more closely related to H. analis than to H. decipiens; furthermore, a publicly available CO1 barcode points to the presence of H. bertrandi n. sp. or a closely related species in Tunisia. Additional notes are provided concerning the variability of H. analis and H. decipiens and external morphological features helpful to distinguish these two species.
No rest for the weary: restricted resting behaviour of green turtles (Chelonia mydas) at a deep-neritic foraging area influences expression of life history traits

ABSTRACT For breath-holding marine animals, tradeoffs between ‘active’ and resting behaviours during periods of submergence can have consequences for acquisition and allocation of energy to vital life history requirements. In this study, we fitted 18 green turtles (Chelonia mydas) with detachable time-depth recorder (TDR) systems to obtain and analyse fine-scale dive behaviour and daily activity – with a focus on resting dive bouts – at Bahía de los Angeles (BLA), a warm-temperate foraging area in the Gulf of California, México. Our results showed that resting bout durations increased with water depths among all turtles, but patterns of resting bout durations and depths varied widely among individuals. To evaluate potential consequences to green turtles of tradeoffs between time spent ‘active’ versus resting, we also compared behavioural parameters (e.g. time spent resting, home range sizes) and life history traits (e.g. growth rates, body size at maturity) of green turtle populations from around the world, including BLA. We found that BLA green turtles spend less time resting, spend more time actively swimming and diving, occupy larger home ranges, and exhibit slower growth rates and smaller adult body sizes compared to their counterparts in other parts of the world. Unique characteristics of the BLA foraging habitat (e.g. patchy resources and temperature extremes) appear to require increased diel movements and foraging activity and decreased resting opportunities. These interactions between habitat and turtle behaviour not only influence expression of life history traits, but can also increase turtles’ exposure to human activities (e.g. vessel traffic and fisheries bycatch) as they move throughout the area.
Jurors’ emotional state, attentional focus, and judicial judgment in a criminal court

ABSTRACT In order to consider the relevant relationships between emotion, information processing and judicial judgment, this study evaluated the impact of positive (amusement), negative (sadness) or neutral mood induction on 128 mock jurors’ visual attentional focus, as measured by their eye fixations on the face of a witness filmed while giving testimony in a criminal court. Participants then rated their perceptions of the witness's and their own emotions on the Differential Emotional Scale, before indicating their final judicial judgment. As expected, results showed that sadness can favour information processing in a in more effortful mode, with more steady visual attention, while a positive emotional state such as amusement can favour information processing based more on the witness's emotions, a source of useful clues for establishing the judicial judgment. These results are discussed in relation to how the cognitive approach can shed light on the processes underlying judicial judgment.
Differences in the bird community between a regenerating area and a native forest in Southeastern Brazil

ABSTRACT Restoration of degraded areas might be assessed via faunal communities of a particular region, and birds are one of the taxa most suitable in such assessments. This study evaluated the dynamics of a bird community in an area of Cerrado under natural regeneration, comparing it with one in the forest remnants. Birds were censused by a total of 24 point counts in both areas comprising 96 h of total sampling. Richness, abundance and diversity were greater at the regeneration area, possibly due to the heterogeneity of habitats, the consequent niche diversity, and the connectivity between patches of vegetation. Functional groups were also distinct between both sites, including species composition, feeding guilds and foraging strata. The regeneration site presented a higher abundance of omnivorous, granivorous and nectarivorous species, which might be related to the presence of sparser canopy, multiple opportunities for the development of grasses and forest-edge plants blooms in open areas. In contrast, higher abundance of invertebrate predators and frugivorous was found in the forested area, further confirming the relationship between those guilds and dense vegetation cover with closed canopies.
A new species of Caipirasuchus (Notosuchia, Sphagesauridae) from the Late Cretaceous of Brazil and the evolutionary history of Sphagesauria

Sphagesauridae is a group of notosuchian crocodyliforms from the Late Cretaceous of South America characterized by highly specialized jaws and dentition. Here, we describe a new sphagesaurid from the Santo Anastácio Formation (Caiuá Group, Bauru Basin), south-east Brazil. The specimen is composed of a partial palate, neurocranium, mandible and fragmentary teeth. It represents a new species that can be assigned to Caipirasuchus due to the presence of a lateromedially narrow and anteroposteriorly long mandibular symphyseal region, apicobasal ridges on the posterior teeth, a diastema between D5 and D6, and a linear row of large neurovascular foramina on the lateral surface of the dentary. It differs from previously described Caipirasuchus species based on a ventrolaterally inclined surface of the dentaries posterior to the tooth row, a connection between the anteroventral margin of the external mandibular fenestra and the floor of the Meckelian canal, and the anterior process of the angular forming a ‘V’-shaped suture in its contact with the splenial. The results of a phylogenetic analysis of notosuchians recovered the so-called ‘advanced notosuchians’ in a clade, for which we propose a phylogenetic definition and erect the name Sphagesauria. We also recovered two more inclusive clades encompassing an array of Mesozoic notosuchians, here named Xenodontosuchia, which includes Sphagesauria + Baurusuchia, and Eunotosuchia, including Xenodontosuchia, Uruguaysuchidae and other Cretaceous forms. http://zoobank.org/urn:lsid:zoobank.org:pub:FD8D706F-9E01-4C09-BE4E-DC3BEDE151DC
A strengths model and violence risk assessment with individuals not criminally responsible on account of mental disorder (NCRMD) in Canada

ABSTRACT A Strengths Model of violence risk assessment, integrating a strengths-based psychosocial history in mental health recovery and protective factors of violent risk reduction, is proposed to address the concern about overprediction of violence in assessment with forensic mental health patients based on risk factors of violence. A case illustration is presented to demonstrate the Model’s capability to promote a more balanced violence risk assessment and formulate individualized risk management and recovery plan predicated on the person’s strengths and resources. Implications for clinical practice and the potential in research to enhance predictive validity and accuracy in violence risk assessment are discussed.
Response of Mangrove Development to Air Temperature Variation Over the Past 3000 Years in Qinzhou Bay, Tropical China

Mangroves, a blue carbon ecosystem between land and ocean in the (sub)tropics, are sensitive to changes in climate and the sea level. It is imperative to reconstruct the historical dynamics of their development to predict the fate of mangrove ecosystems in the backdrop of rapid global changes. This study analyzes records of the sources of organic matter from sediment core Q43 of Qinzhou Bay in tropical China by using the endmember mixing model based on stable organic carbon isotopes and C/N ratio. Mangrove-derived organic matter (MOM) is regarded as a reliable indicator for reconstructing the historical development of mangroves. The variations in MOM in Qinzhou Bay over the past ∼3,000 cal yr BP indicate that mangrove forests underwent two periods of flourishment: ∼2,200–1,750 cal yr BP and ∼1,370–600 cal yr BP, as well as three periods of deterioration: ∼3,000–2,200 cal yr BP, ∼1,750–1,370 cal yr BP, and ∼600–0 cal yr BP. Of factors that might have been influential, changes in the relative sea level and the regional hydrological environment (e.g., seawater temperature, salinity, and hydrodynamic conditions) did not appear to have notable effects on mangrove flourishing/degradation. However, climate change, especially the variation in air temperature, formed the primary factor controlling mangrove development. The stages of mangrove flourishing/deterioration corresponded to the warm/cold periods of the climate, respectively. Noteworthy is that the rapid rise in air temperature during the Anthropocene warm period should have promoted mangrove development, but the increasing intensity of human activity has reversed this tendency leading to the degradation of mangroves.
Characterization of a Novel Bacteriophage swi2 Harboring Two Lysins Can Naturally Lyse Escherichia coli

The novel virulent Siphoviridae bacteriophage swi2 was isolated from a pig farm, and its biological characteristics, genome architecture, and infection-related properties were characterized. Phage swi2 has a high titer of 1.01 × 1012 PFU/mL with good tolerance to UV rays and remains stable in the pH range of 6–10 and at temperatures less than 50°C. One-step growth analysis revealed that phage swi2 had a 25 min latent period with a large burst size (1,000 PFU/cell). The biological characteristics indicated that swi2 had good host infectivity and effective lytic activities. The genome of phage swi2 is composed of 47,611 bp with a G + C content of 46.50%. Eighty-nine orfs were predicted, and only 18 of them have known functions. No virulence genes or drug resistance genes were found in the genome. Genome sequence comparison of phage swi2 showed that there were a total of 10 homologous phages in the database with low similarity (less than 92.51% nucleotide identity and 66% query coverage). The predicted host lysis-related genes of phage swi2 consist of one holin, two endolysins, and Rz/Rz1 equivalents. Antibacterial activity assays showed that both endolysins could naturally reduce the host Escherichia coli 51 titers by -1 log unit both in vitro and in vivo, EDTA showed no obvious synergistic action, and holin had no lytic effects on the host cell. These results provide necessary information for the development of antibiotic alternatives for the treatment of multidrug-resistant Escherichia coli infection.
First Isolation and Molecular Characterization of blaCTX-M-121-Producing Escherichia coli O157:H7 From Cattle in Xinjiang, China

The bovine Escherichia coli O157:H7 is a major foodborne pathogen causing severe bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome in humans. Cattle are recognized major reservoir and source of E. coli O157:H7. We investigated the antibiotic resistance, molecular profiles, and intrinsic relationship between 21 isolates of E. coli O157:H7 from cattle farms and slaughtering houses in Xinjiang. Using pulsed-field gel electrophoresis (PFGE) molecular typing, two types of PFGE were revealed through cluster analysis, including clusters I and II, with 66 and 100% similarity of PFGE spectra between 21 isolates. We also detected that 18 isolates (86%) carried at least one virulence gene, 16 isolates (76%) carried the eae gene, and 7 (33%) carried the stx1 + stx2 + eae + hly + tccp genes. Eighteen isolates were susceptible to antibiotics. Three isolates were resistant to antibiotics, and two were multidrug resistant. One of the two multidrug-resistant isolates detectably carried the blaCTX−M−121 gene. This is the first finding of the blaCTX−M−121 gene detected in E. coli O157:H7 isolated from cattle in Xinjiang. The blaCTX−M−121 gene is transferable between the bacterial strains via plasmid transmission. The results indicated that E. coli O157:H7 may have undergone clonal propagation in cattle population and cross-regional transmission in Xinjiang, China.
Using Technology to Identify Children With Autism Through Motor Abnormalities

Autism is a neurodevelopmental disorder typically assessed and diagnosed through observational analysis of behavior. Assessment exclusively based on behavioral observation sessions requires a lot of time for the diagnosis. In recent years, there is a growing need to make assessment processes more motivating and capable to provide objective measures of the disorder. New evidence showed that motor abnormalities may underpin the disorder and provide a computational marker to enhance assessment and diagnostic processes. Thus, a measure of motor patterns could provide a means to assess young children with autism and a new starting point for rehabilitation treatments. In this study, we propose to use a software tool that through a smart tablet device and touch screen sensor technologies could be able to capture detailed information about children’s motor patterns. We compared movement trajectories of autistic children and typically developing children, with the aim to identify autism motor signatures analyzing their coordinates of movements. We used a smart tablet device to record coordinates of dragging movements carried out by 60 children (30 autistic children and 30 typically developing children) during a cognitive task. Machine learning analysis of children’s motor patterns identified autism with 93% accuracy, demonstrating that autism can be computationally identified. The analysis of the features that most affect the prediction reveals and describes the differences between the groups, confirming that motor abnormalities are a core feature of autism.