Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosomal Integration of Huge and Complex bla NDM-Carrying Genetic Elements in Enterobacteriaceae

In this study, a detailed genetic dissection of the huge and complex bla NDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six bla NDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core bla NDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex bla NDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.
Protein Secondary Structure Prediction With a Reductive Deep Learning Method

Protein secondary structures have been identified as the links in the physical processes of primary sequences, typically random coils, folding into functional tertiary structures that enable proteins to involve a variety of biological events in life science. Therefore, an efficient protein secondary structure predictor is of importance especially when the structure of an amino acid sequence fragment is not solved by high-resolution experiments, such as X-ray crystallography, cryo-electron microscopy, and nuclear magnetic resonance spectroscopy, which are usually time consuming and expensive. In this paper, a reductive deep learning model MLPRNN has been proposed to predict either 3-state or 8-state protein secondary structures. The prediction accuracy by the MLPRNN on the publicly available benchmark CB513 data set is comparable with those by other state-of-the-art models. More importantly, taking into account the reductive architecture, MLPRNN could be a baseline for future developments.
Natural Biostimulants Elicit Plant Immune System in an Integrated Management Strategy of the Postharvest Green Mold of Orange Fruits Incited by Penicillium digitatum

This study was aimed at testing the integrated use of a natural biostimulant based on seaweed (Ascophyllum nodosum) and plant (alfalfa and sugarcane) extracts and reduced dosages of the conventional synthetic fungicide Imazalil (IMZ) to manage postharvest rots of orange fruits. The following aspects were investigated: (i) the effectiveness of postharvest treatment with natural biostimulant alone or in mixture with IMZ at a reduced dose against green mold caused by Penicillium digitatum; (ii) the differential expression of defense genes in orange fruits treated with the natural biostimulant both alone and in combination with a reduced dose of IMZ; (iii) the persistence of the inhibitory activity of both biostimulant and the mixture biostimulant/IMZ against green mold; and (iv) the residue level of fungicide in citrus peel when applied alone or in combination with the biostimulant. Treatments with the chemical plant resistance-inducer potassium phosphite, alone or with a reduced dose of IMZ, were included for comparison. The mixture of natural biostimulant and IMZ at a low dose consistently reduced the incidence and severity of fruit green mold and induced a significant increase of the expression level of β-1,3-glucanase-, peroxidase (PEROX)-, and phenylalanine ammonia-lyase (PAL)-encoding genes in fruit peel, suggesting that the natural biostimulant elicits a long-lasting resistance of citrus fruits to infections by P. digitatum. Interestingly, the residual concentration of IMZ in fruits treated with the biostimulant/fungicide mixture was significantly lower than that of IMZ in fruits treated only with the fungicide at the same dose and by far below the threshold values set by the European Union. This study laid the foundations for (i) conceiving a practical and more eco-friendly alternative to the conventional postharvest management of green mold of citrus fruits, based almost exclusively on the use of synthetic fungicide IMZ, alone or mixed with potassium phosphite and (ii) providing a better insight into the mechanisms of disease resistance induction by biostimulants.
Strength Lies in Diversity: How Community Diversity Limits Salmonella Abundance in the Chicken Intestine

The transfer of the intestinal microbiota from adult to juvenile animals reduces Salmonella prevalence and abundance. The mechanism behind this exclusion is unknown, however, certain member species may exclude or promote pathogen colonization and Salmonella abundance in chickens correlates with intestinal community composition. In this study, newly hatched chicks were colonized with Salmonella Typhimurium and 16S rRNA libraries were generated from the cecal bacterial community at 21, 28, 35, and 42 days of age. Salmonella was quantified by real-time PCR. Operational taxonomic units (OTUs) were assigned, and taxonomic assignments were made, using the Ribosomal Database Project. Bacterial diversity was inversely proportional to the Salmonella abundance in the chicken cecum (p < 0.01). In addition, cecal communities with no detectable Salmonella (exclusive community) displayed an increase in the abundance of OTUs related to specific clostridial families (Ruminococcaceae, Eubacteriaceae, and Oscillospiraceae), genera (Faecalibacterium and Turicibacter) and member species (Ethanoligenens harbinense, Oscillibacter ruminantium, and Faecalibacterium prausnitzii). For cecal communities with high Salmonella abundance (permissive community), there was a positive correlation with the presence of unclassified Lachnospiraceae, clostridial genera Blautia and clostridial species Roseburia hominis, Eubacterium biforme, and Robinsoniella peoriensis. These findings strongly support the link between the intestinal bacterial species diversity and the presence of specific member species with Salmonella abundance in the chicken ceca. Exclusive bacterial species could prove effective as direct-fed microbials for reducing Salmonella in poultry while permissive species could be used to predict which birds will be super-shedders.
Centriolar Protein C2cd3 Is Required for Craniofacial Development

The primary cilium is a ubiquitous, microtubule-based cellular organelle. Primary cilia dysfunction results in a group of disorders termed ciliopathies. C2 domain containing 3 centriole elongation regulator (C2cd3), encodes a centriolar protein essential for ciliogenesis. Mutations in human C2CD3 are associated with the human ciliopathy Oral-Facial-Digital syndrome type 14 (OFD14). In order to better understand the etiology of ciliopathies including OFD14, we generated numerous murine models targeting C2cd3. Initial analysis revealed several tissue-specific isoforms of C2cd3, and while the loss of C2cd3 has previously been reported to result in exencephaly, tight mesencephalic flexure, pericardial edema, abnormal heart looping and a twisted body axis, further analysis revealed that genetic background may also contribute to phenotypic variation. Additional analyses of a conditional allelic series targeting C-terminal PKC-C2 domains or the N-terminal C2CD3N-C2 domain of C2cd3 revealed a variable degree of phenotypic severity, suggesting that while the N-terminal C2CD3N-C2 domain was critical for early embryonic development as a whole, there was also a craniofacial specific role for the C2CD3N-C2 domains. Together, through generation of novel models and evaluation of C2cd3 expression, these data provide valuable insight into mechanisms of pathology for craniofacial ciliopathies that can be further explored in the future.
Metabolomic Profiling of Pregnancies With Polycystic Ovary Syndrome Identifies a Unique Metabolic Signature and Potential Predictive Biomarkers of Low Birth Weight

Background Polycystic ovary syndrome (PCOS) is a complex syndrome with clinical features of an endocrine/metabolic disorder. Various metabolites show significant association with PCOS; however, studies comparing the metabolic profile of pregnant women with and without PCOS are lacking. In this study, metabolomics analysis of blood samples collected from PCOS women and age and BMI matched controls in the second trimester of pregnancy was performed to identify metabolic differences between the two groups and determine their association with pregnancy outcome. Methods Sixteen PCOS and fifty-two healthy women in their second trimester underwent targeted metabolomics of plasma samples using tandem mass spectrometry with the Biocrates MxP® Quant 500 Kit. Linear regression models were used to identify the metabolic alterations associated with PCOS, followed by enrichment and Receiver Operating Characteristic (ROC) analyses to determine the best indicators of pregnancy outcomes. Results PCOS women had lower birth weight babies compared to healthy controls. As a group, systolic blood pressure (SBP) at both second trimester and at delivery negatively correlated with birth weight. Regression models indicated significant increases in the triglycerides C20:4_C34:3 and C18:2_C38:6 in the PCOS group [false discovery rate (FDR) <0.05]. Enrichment analysis revealed significant elevations in triglycerides containing arachidonic acid, linoleic acid and palmitic acid in the PCOS group. A number of indicators of baby birth weight were identified including SBP at delivery, hexosylceramide (d18:2/24:0), ceramide (d18.0/24.1) and serine, with an AUC for all predictors combined for low birth weight (≤2500grams) of 0.88 (95%CI: 0.75-1.005, p<0.001). Conclusions PCOS pregnancies resulted in babies with a lower birth weight, marked by a unique metabolic signature that was enriched with specific triglycerides and unsaturated fatty acids. The functional significance of these associations needs further investigation.
The Time Course of Event-Related Brain Potentials in Athletes’ Mental Rotation With Different Spatial Transformations

Studies have found that athletes outperformed non-athletes in mental rotation tasks with both object-based and egocentric transformations (ET), but the effect of sport expertise on the processing stages (i.e., perceptual stage, rotation stage, and decision stage) remains conflicted. Bearing the view that the stages occur sequentially and the high temporal resolution of event-related brain potentials, this study focused on brain processing during mental rotation and was designed to determine the time course of electrophysiological changes in athletes and non-athletes. A total of 42 divers and non-athletes were recruited for the study. A mental body rotation task with object-based and egocentric transformation conditions was conducted, and the reaction time (RT), accuracy, performance stages, N2 latency, amplitude, and the amplitude of rotation-related negativity (RRN) were recorded. Behavioral results demonstrated higher accuracy for athletes at 120° and 180°. Moreover, as compared to non-athletes, the enlarged amplitude of N2 and RRN were confirmed in both transformations for athletes and were correlated with the performance stages and athletes’ professional training years. The present study provided a deeper insight into the relationship between sports training, behavior performance, and brain activity.
Cardiovascular Magnetic Resonance as Pathophysiologic Tool in Diabetes Mellitus

Diabetes mellitus can independently contribute to cardiovascular disease and represents a severe risk factor for premature development of cardiovascular disease. A three-fold higher mortality than the general population has been observed in type 1 diabetes mellitus whereas a two- to four-fold increased probability to develop cardiovascular disease has been observed in type 2 diabetes mellitus. Cardiovascular magnetic resonance, a non-radiative modality, is superior to all other modalities in detecting myocardial infarction. The main cardiovascular magnetic resonance sequences used include a) balanced steady-state free precession (bSSFP) for function evaluation; b) T2-W for oedema detection; c) T1 W for ischemia detection during adenosine stress; and d) late gadolinium enhanced T1-W images (LGE), evaluated 15 min after injection of paramagnetic contrast agent gadolinium, which permit the diagnosis of replacement fibrosis, which appears white in the middle of suppressed, nulled myocardium. Although LGE is the technique of choice for diagnosis of replacement fibrosis, it cannot assess diffuse myocardial fibrosis. The application of T1 mapping (native or pre contrast and post contrast) allows identification of diffuse myocardial fibrosis, which is not detectable my other means. Native T1 and Contrast-enhanced T1 mapping are involved in the extracellular volume fraction (ECV) calculation. Recently, 1H-cardiovascular magnetic resonance spectroscopy has been applied to calculate the amount of myocardial triglycerides, but at the moment it is not part of the routine assessment of diabetes mellitus. The multifaceted nature of cardiovascular magnetic resonance has the great potential of concurrent evaluation of function and myocardial ischemia/fibrosis in the same examination and represents an indispensable tool for accurate diagnosis of cardiovascular disease in diabetes mellitus.
Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns

Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized functions. According to current evidence, mRNAs are mostly transported in rather small packages of one to three copies, rarely containing different transcripts. This opens up fascinating logistic problems: how are hundreds of different mRNA cargoes sorted into distinct packages and how are they coupled to and released from motor proteins to produce the observed mRNA distributions? Are all mRNAs transported by the same transport machinery, or are there different adaptors or motors for different transcripts or classes of mRNAs? A variety of often indirect evidence exists for the involvement of proteins in mRNA localization, but relatively little is known about the essential activities required for the actual transport process. Here, we summarize the different types of available evidence for interactions that connect mammalian mRNAs to motor proteins to highlight at which point further research is needed to uncover critical missing links. We further argue that a combination of discovery approaches reporting direct interactions, in vitro reconstitution, and fast perturbations in cells is an ideal future strategy to unravel essential interactions and specific functions of proteins in mRNA transport processes.
Problematic Internet Use Was Associated With Psychological Problems Among University Students During COVID-19 Outbreak in China

Background: As the coronavirus disease 2019 (COVID-19) pandemic progressed globally, school closures and home quarantine may cause an increase in problematic Internet use among students in universities. Such a traumatic stress event may also contribute to the development of posttraumatic stress disorder (PTSD), depressive, and anxiety symptoms. This study aimed to evaluate the prevalence of PTSD, depressive, and anxiety symptoms as well as the predictive role of problematic Internet use in the above-mentioned psychological problems in university students. Methods: A cross-sectional study was conducted through an online survey of 8,879 students in China between April 20 and April 26, 2020. The presence of PTSD, depressive, and anxiety symptoms and problematic Internet use were evaluated using PTSD Checklist for DSM-5, the Center for Epidemiologic Studies Depression 9-item scale, the generalized anxiety disorder 7-item scale, and the Young diagnostic questionnaire, respectively. Sociodemographic information and the knowledge, attitude, and practice (KAP) toward COVID-19 data were also collected. Results: A total of 4,834 (54.4%) participants were female, and 7,564 (85.2%) were undergraduate students. A total of 615 students (6.9%) reported PTSD symptoms; 5.2% (465) and 10.1% (896) reported moderate to severe depressive and anxiety symptoms, respectively. The problematic Internet use was significantly associated with higher risk of PTSD, depressive, and anxiety symptoms (odds ratio 2.662 [95% CI, 2.239–3.165], odds ratio 4.582 [95% CI, 3.753–5.611], odds ratio 3.251 [95% CI, 2.814–3.757], respectively; all P < 0.001). Lower attitude and practice scores also contributed to the risk of depressive, anxiety, and PTSD symptoms (P < 0.05). Conclusions: Psychological problems should be paid more attention, and problematic Internet use may be a predictor when screening high-risk students for psychological problems. Our results will aid in timely psychological screening, which is meaningful in the prevention and intervention of psychological problems.
Savanna Rodents’ Selective Removal of an Encroaching Plant’s Seeds Increased With Grass Biomass

In savannas across the planet, encroaching woody plants are altering ecosystem functions and reshaping communities. Seed predation by rodents may serve to slow the encroachment of woody plants in grasslands and savannas. Our goals for this study were to determine if rodents in an African savanna selectively removed seeds of an encroaching plant and if foraging activity was influenced by the local vegetation structure or by the landscape context. From trials with two species of seeds (encroacher = Dichrostachys cinerea, non-encroaching overstory tree = Senegalia nigrescens) at 64 seed stations, we recorded 1,065 foraging events by seven species of granivorous rodents. We found a strong positive relationship between rodent activity and the number of seeds removed during trials. Foraging events were dominated by rodent seed predators, with <10.6% of events involving a rodent with the potential for secondary dispersal. Rodents selectively removed the seeds of the encroaching species, removing 32.6% more D. cinerea seeds compared to S. nigrescens. Additionally, rodent activity and the number of seeds removed increased at sites with more grass biomass. Our results suggest a potential mechanistic role for rodents in mitigating the spread of woody plants in grass dominated savannas.
A Homozygous Deep Intronic Mutation Alters the Splicing of Nebulin Gene in a Patient With Nemaline Myopathy

Nemaline myopathy is a rare disorder affecting the muscle sarcomere. Mutations in nebulin gene (NEB) are known to be responsible for about 50% of nemaline myopathy cases. Nebulin is a giant protein which is formed integrally with the sarcomeric thin filament. This complex gene is under extensive alternative splicing giving rise to multiple isoforms. In this study, we report a 6-year-old boy presenting with general muscular weaknesses. Identification of rod-shaped structures in the patient' biopsy raised doubt about the presence of a nemaline myopathy. Next-generation sequencing was used to identify a causative mutation for the patient syndrome. A homozygous deep intronic substitution was found in the intron 144 of the NEB. The variant was predicted by in silico tools to create a new donor splice site. Molecular analysis has shown that the mutation could alter splicing events of the nebulin gene leading to a significant decrease of isoforms level. This change in the expression level of nebulin could give rise to functional consequences in the sarcomere. These results are consistent with the phenotypes observed in the patient. Such a discovery of variants in this gene will allow a better understanding of the involvement of nebulin in neuromuscular diseases and help find new treatments for the nemaline myopathy.
Detecting Climate Signals in Southern Ocean Krill Growth Habitat

Climate change is rapidly altering the habitat of Antarctic krill (Euphausia superba), a key species of the Southern Ocean food web. Krill are a critical element of Southern Ocean ecosystems as well as biogeochemical cycles, while also supporting an international commercial fishery. In addition to trends forced by global-scale, human-driven warming, the Southern Ocean is highly dynamic, displaying large fluctuations in surface climate on interannual to decadal timescales. The dual roles of forced climate change and natural variability affecting Antarctic krill habitat, and therefore productivity, complicate interplay of observed trends and contribute to uncertainty in future projections. We use the Community Earth System Model Large Ensemble (CESM-LE) coupled with an empirically derived model of krill growth to detect and attribute trends associated with “forced,” human-driven climate change, distinguishing these from variability arising naturally. The forced trend in krill growth is characterized by a poleward contraction of optimal conditions and an overall reduction in Southern Ocean krill habitat. However, the amplitude of natural climate variability is relatively large, such that the forced trend cannot be formally distinguished from natural variability at local scales over much of the Southern Ocean by 2100. Our results illustrate how natural variability is an important driver of regional krill growth trends and can mask the forced trend until late in the 21st century. Given the ecological and commercial global importance of krill, this research helps inform current and future Southern Ocean krill management in the context of climate variability and change.