Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of oxygen and carbon dioxide on the growth of prevalent Enterobacteriaceae andPseudomonasspecies isolated from fresh and controlled-atmosphere-stored vegetables

Abstract To obtain more insight into the specific impact of modified gas conditions on the composition of microflora of minimally processed vegetables, the prevalent bacteria on mungbean sprouts and cut chicory endive were determined during storage under controlled atmospheric (CA) conditions at 8°C. Enumeration of the total mesophilic counts, Enterobacteriaceae,Pseudomonasspecies, and lactic acid bacteria indicated that Enterobacteriaceae andPseudomonasspecies constituted the major populations found on these products before and after CA storage. Identification of the predominant species within these populations revealed that on fresh and CA-stored mungbean sprouts,Enterobacter cloacae, Pantoea agglomerans, Pseudomonas fluorescens, Ps. viridilividaandPs. corrugatawere the prevalent species. On chicory endive,Rahnella aquatilisand severalPseudomonasspecies were found on the fresh product, while after CA storage,Escherichia vulnerisandPs. fluorescenswere the main species. Growth of the predominant epiphytes was subsequently quantified in pure culture, using an agar model system at 8°C under 1.5 or 21% O2with 0, 5, 20, or 50% CO2. In general, these CA conditions did not strongly influence maximum population densities and lag times were not detected. For each of the strains, however, maximum specific growth rates were reduced at increased CO2concentrations, independent of the 02concentration applied. This effect was more pronounced forPseudomonasspecies than forEnterobacteriaceae. Notably, the agar model study showed that individual species ofEnterobacteriaceaeorPseudomonasresponded similarly to the specific CA conditions applied. This did not correlate with the shift in predominant species observed on chicory endive. Our data underline the complexity of the ecological conditions to which micro-organisms on vegetables are subjected during storage under modified gas conditions.
Optimal Position of Attachment for Removable Thermoplastic Aligner on the Lower Canine Using Finite Element Analysis

Malocclusion is considered as a developmental disorder rather than a disease, and it may be affected by the composition and proportions of masseter muscle fibers. Orthodontics is a specialty of dentistry that deals with diagnosis and care of various irregular bite and/or malocclusion. Recent developments of 3D scanner and 3D printing technology has led to the use of a removable thermoplastic aligner (RTA), which is widely used due to its aesthetic excellence, comfortableness, and time efficiency. However, orthodontics using only an RTA has lower treatment efficacy and accuracy due to the differing movement of teeth from the plan. In order to improve these disadvantages, attachments were used, and biomechanical analyses were performed with and without them. However, there is insufficient research on the movement of teeth and the transfer of load according to the attachment position and shape. Therefore, in our study, we aimed to identify the optimal shape and position of attachments by analyzing various shapes and positions of attachments. Through 3D finite element analysis (FEA), simple tooth shape and mandibular canine shape were extracted in order to construct the orthodontics model which took into account the various shapes and positions of attachments. The optimal shape of a cylinder was derived through the FEA of simple tooth shape and analyzing various positions of attachments on teeth revealed that fixing the attachments at the lingual side of the tooth rather than the buccal side allowed for torque control and an effective movement of the teeth. Therefore, we suggest fixing the attachments at the lingual side rather than the buccal side of the tooth to induce effective movement of teeth in orthodontic treatment with the RTA in case of canine teeth.
Maternal Psychosocial Risk Profiles in Pregnancy: Associations With Postpartum Maternal Health and Child Outcomes

Previous research on prenatal stress and social support has primarily involved variable-centered approaches, with limited knowledge on whether profiles exist, how early childhood adversity experiences predict these profiles, and whether these profiles are differentially associated with maternal and child outcomes postnatally. Using a pregnancy cohort (N = 1,994), we identify three distinct profiles of maternal stress and maternal social support: low stress–high support (69.4%), moderate stress–moderate support (25.7%), and high stress–low support (4.9%). Mothers in the high stress–low support group experienced more physical/emotional abuse in childhood, whereas mothers in the moderate stress–moderate support group experienced more family dysfunction. The moderate and the high stress groups had poorer reproductive and physical health, and mothers reported their children had poorer developmental outcomes compared with the low stress–high support mothers. Identifying levels of stress and social support in pregnancy and implementing interventions for mothers at risk is crucial in the pursuit to mitigate family-wide deleterious outcomes.
Genetic Variation in Bovine Neutrophil Sensitivity to Glucocorticoid Challenge

Blood neutrophils use CD62L and CD18 adhesion molecules to contact and migrate rapidly through blood vessels in defense against infections in underlying tissues. Previous work showed that glucocorticoid hormones repress expression of CD62L and CD18, causing neutrophilia and increased mastitis susceptibility in dairy cows. The aim of this study was to determine whether bovine neutrophil sensitivity to glucocorticoids exhibits genetic variability. Test animals included 60 pedigreed Holstein bulls treated on 3 consecutive days with a synthetic glucocorticoid (dexamethasone) and five untreated control bulls. Five indicator traits of neutrophil glucocorticoid sensitivity were monitored, including circulating neutrophil counts and two measures on each of CD62L and CD18 expression. Random regression models with treatment-specific serial correlation were used to estimate genetic and non-genetic sources of variation before, during and after glucocorticoid administration. Significant genetic variation was observed for neutrophil CD18 expression, with longitudinal heritability estimates ranging from 0.10 to 0.54 and influenced by dexamethasone. Significant genetic variation was also observed for blood neutrophil counts (heritability estimates ranging from 0.11 to 0.24) but was not influenced by dexamethasone administration. Estimated genetic correlations between circulating neutrophil counts and various indicators of CD62L and CD18 expression were large and negative (-0.44 to - 0.78). These results imply significant genetic variability and pleiotropic effects for neutrophil traits that are important for stress-induced disease susceptibility in dairy cattle and might be exploited by genetic selection.
Co-consumption of Vegetables and Fruit, Whole Grains, and Fiber Reduces the Cancer Risk of Red and Processed Meat in a Large Prospective Cohort of Adults from Alberta’s Tomorrow Project

We examined whether co-consumption of red and processed meat with key foods items and food constituents recommended for cancer prevention (vegetables and fruit, whole grains, and fiber) mitigates cancer incidence. In a prospective cohort of 26,218 adults aged 35–69 years at baseline, dietary intake was collected through 124-item past-year food frequency questionnaire. Incidence of all-cause and 15 cancers previously linked to red and processed meat intake was obtained through data linkage with a cancer registry (average follow-up 13.5 years). Competing risk Cox Proportional Hazard models estimated cancer risk and Accelerated Failure Time models estimated time-to-cancer occurrence for different combinations of intake levels while considering mortality from vital statistics and established confounders. Co-consumption of low vegetables and fruit intake with high processed meat was associated with higher incidence of all-cause and 15 cancers (men: HR = 1.85, 1.91; women: HR = 1.44, 1.49) and accelerated time-to-cancer occurrence (men: 6.5 and 7.1 years and women: 5.6 and 6.3 years, respectively), compared to high vegetables and fruit with low processed meat intake. Less pronounced and less consistent associations were observed for whole grains and fiber and for red meat. The findings provide initial evidence toward refining existing cancer prevention recommendations to optimize the intake and combination of foods in the general adult population.
Clinical Impact of the Epithelial-Mesenchymal Transition in Lung Cancer as a Biomarker Assisting in Therapeutic Decisions

Lung cancer is one of the most common solid cancers and represents the leading cause of cancer death worldwide. Over the last decade, research on the epithelial-mesenchymal transition (EMT) in lung cancer has gained increasing attention. Here, we review clinical and histological features of non-small-cell lung cancer associated with EMT. We then aimed to establish potential clinical implications of EMT in current therapeutic options, including surgery, radiation, targeted therapy against oncogenic drivers, and immunotherapy.
Genetic Transformation in Peach (Prunus persica L.): Challenges and Ways Forward

Almost 30 years have passed since the first publication reporting regeneration of transformed peach plants. Nevertheless, the general applicability of genetic transformation of this species has not yet been established. Many strategies have been tested in order to obtain an efficient peach transformation system. Despite the amount of time and the efforts invested, the lack of success has significantly limited the utility of peach as a model genetic system for trees, despite its relatively short generation time; small, high-quality genome; and well-studied genetic resources. Additionally, the absence of efficient genetic transformation protocols precludes the application of many biotechnological tools in peach breeding programs. In this review, we provide an overview of research on regeneration and genetic transformation in this species and summarize novel strategies and procedures aimed at producing transgenic peaches. Promising future approaches to develop a robust peach transformation system are discussed, focusing on the main bottlenecks to success including the low efficiency of A. tumefaciens-mediated transformation, the low level of correspondence between cells competent for transformation and those that have regenerative competence, and the high rate of chimerism in the few shoots that are produced following transformation.
Mechanistic Insights into the Release of Doxorubicin from Graphene Oxide in Cancer Cells

Liposomal doxorubicin (L-DOX) is a popular drug formulation for the treatment of several cancer types (e.g., recurrent ovarian cancer, metastatic breast cancer, multiple myeloma, etc.), but poor nuclear internalization has hampered its clinical applicability so far. Therefore, novel drug-delivery nanosystems are actively researched in cancer chemotherapy. Here we demonstrate that DOX-loaded graphene oxide (GO), GO-DOX, exhibits much higher anticancer efficacy as compared to its L-DOX counterpart if administered to cellular models of breast cancer. Then, by a combination of live-cell confocal imaging and fluorescence lifetime imaging microscopy (FLIM), we suggest that GO-DOX may realize its superior performances by inducing massive intracellular DOX release (and its subsequent nuclear accumulation) upon binding to the cell plasma membrane. Reported results lay the foundation for future exploitation of these new adducts as high-performance nanochemotherapeutic agents.
Non‐local genotypes of a resident grass species reduce invertebrate species richness

1. Effects of the genotypic identity of a plant can extend beyond the individual phenotype to the community. Because plant material is moved around at an increasing rate, introductions of non‐local plant genotypes that are difficult to distinguish from local ones are probably common. Even though such introductions can cause cryptic invasions, their effects on local communities remain largely unexplored.
An Integrated Metabolomics Study of Glucosinolate Metabolism in Different Brassicaceae Genera

Glucosinolates are a group of plant secondary metabolites that can be hydrolyzed into a variety of breakdown products such as isothiocyanates, thiocyanates, and nitriles. These breakdown products can facilitate plant defense and function as attractants to natural enemies of insect pests. As part of the diet, some of these compounds have shown cancer-preventing activities, and the levels of these metabolites in the edible parts of the plants are of interest. In this study, we systematically examined variations in glucosinolates, their precursors, and their breakdown products in 12 commonly consumed vegetables of the Brassicaceae family with gas chromatography—quadrupole time-of-flight mass spectrometer (GC-Q-TOF/MS), liquid chromatography–quadrupole time-of-flight mass spectrometer (LC-Q-TOF/MS), and liquid chromatography—triple quadrupole mass spectrometer (LC-QQQ/MS), using both untargeted and targeted approaches. The findings were integrated with data from literature to provide a comprehensive map of pathways for biosynthesis of glucosinolates and isothiocyanates. The levels of precursor glucosinolates are found to correlate well with their downstream breakdown products. Further, the types and abundances of glucosinolates among different genera are significantly different, and these data allow the classification of plants based on morphological taxonomy. Further validation on three genera, which are grown underground, in damp soil, and above ground, suggests that each genus has its specific biosynthetic pathways and that there are variations in some common glucosinolate biosynthesis pathways. Our methods and results provide a good starting point for further investigations into specific aspects of glucosinolate metabolism in the Brassica vegetables.
Antimicrobial Mechanism of pBD2 against Staphylococcus aureus

Antimicrobial peptides (AMPs) show high antibacterial activity against pathogens, which makes them potential new therapeutics to prevent and cure diseases. Porcine beta defensin 2 (pBD2) is a newly discovered AMP and has shown antibacterial activity against different bacterial species including multi-resistant bacteria. In this study, the functional mechanism of pBD2 antibacterial activity against Staphylococcus aureus was investigated. After S. aureus cells were incubated with different concentrations of pBD2, the morphological changes in S. aureus and locations of pBD2 were detected by electron microscopy. The differentially expressed genes (DEGs) were also analyzed. The results showed that the bacterial membranes were broken, bulging, and perforated after treatment with pBD2; pBD2 was mainly located on the membranes, and some entered the cytoplasm. Furthermore, 31 DEGs were detected and confirmed by quantitative real-time PCR (qRT-PCR). The known functional DEGs were associated with transmembrane transport, transport of inheritable information, and other metabolic processes. Our data suggest that pBD2 might have multiple modes of action, and the main mechanism by which pBD2 kills S. aureus is the destruction of the membrane and interaction with DNA. The results imply that pBD2 is an effective bactericide for S. aureus, and deserves further study as a new therapeutic substance against S. aureus.
Serum Iron, Total Iron-Binding Capacity, Unbound Iron-Binding Capacity, Transferrin Saturation, Serum Copper, and Hematological Parameters in Pregnant Akkaraman Ewes Infected with Gastro-Intestinal Parasites

The aim of this study was to investigate serum iron parameters, and copper and iron deficiency anemia in ewes infected with gastro-intestinal parasites. This study was conducted with 60 pregnant Akkaraman ewes. In the statistical analyses, values obtained from both parasite infected and uninfected ewes were compared. Significant decreases were observed in PCV (P < 0.05), Hb (P < 0.05), RBC (P < 0.05), total protein (P < 0.05), albumin (P < 0.05), globulin (P < 0.05), and MCHC (P < 0.01), and a significant increase was seen in the WBC value (P < 0.05) in the parasite infected group. Furthermore, the parasite infected group had lower serum Fe (P < 0.001), TS % (P < 0.001), and serum Cu (P < 0.01) levels, and had higher UIBC values (P < 0.05) compared to the values obtain from the uninfected group. Therefore, in addition to antiparasite drug treatment in parasite infected pregnant ewes, iron preparations should also be administered in order to treat iron deficiency. Ozet: Bu araflt›rman›n amac›; mide-ba¤›rsak parazitleriyle enfekte gebe akkaraman ›rk› koyunlarda serum demir parametreleri, bak›r ve demir eksiklii anemisini araflt›rmakt›r. Araflt›rma 60 gebe akkaraman ›rk› koyun uzerinde yurutuldu. ‹statistiksel analizde, parazitli koyunlarda elde edilen deerler parazitle enfekte olmayan koyunlar›n deerleriyle karfl›laflt›r›ld›¤›nda PCV (P < 0,05), Hb (P < 0,05), RBC (P < 0,05), total protein (P < 0,05), albumin (P < 0,05), globulin (P < 0,05), MCHC (P < 0,01) deerlerinde azal›fl ve WBC deerinde (P < 0,05) art›fl gozlendi. Ayr›ca parazitli grubun parazitsiz gruba gore daha dufluk serum Fe (P < 0,001), % TS (P < 0,001), serum Cu (P < 0,01) deerlere ve daha yuksek UIBC (P < 0,05) sahip olduu saptand›. Sonuc olarak; parazitli gebe koyunlarda antiparaziter ilac uygulamalar›n ek olarak ayn› zamanda demir eksikliini tedavi etmek icin demir preparatlar›
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks

The identification of a protein fold type from its amino acid sequence provides important insights about the protein 3D structure. In this paper, we propose a deep learning architecture that can process protein residue-level features to address the protein fold recognition task. Our neural network model combines 1D-convolutional layers with gated recurrent unit (GRU) layers. The GRU cells, as recurrent layers, cope with the processing issues associated to the highly variable protein sequence lengths and so extract a fold-related embedding of fixed size for each protein domain. These embeddings are then used to perform the pairwise fold recognition task, which is based on transferring the fold type of the most similar template structure. We compare our model with several template-based and deep learning-based methods from the state-of-the-art. The evaluation results over the well-known LINDAHL and SCOP_TEST sets, along with a proposed LINDAHL test set updated to SCOP 1.75, show that our embeddings perform significantly better than these methods, specially at the fold level. Supplementary material, which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety. org/10.1109/TCBB.2020. 3012732, source code and trained models are available at http://sigmat.ugr. es/~amelia/CNN-GRU-RF+/.
Danon Disease-Associated LAMP-2 Deficiency Drives Metabolic Signature Indicative of Mitochondrial Aging and Fibrosis in Cardiac Tissue and hiPSC-Derived Cardiomyocytes

Danon disease is a severe X-linked disorder caused by deficiency of the lysosome-associated membrane protein-2 (LAMP-2). Clinical manifestations are phenotypically diverse and consist of hypertrophic and dilated cardiomyopathies, skeletal myopathy, retinopathy, and intellectual dysfunction. Here, we investigated the metabolic landscape of Danon disease by applying a multi-omics approach and combined structural and functional readouts provided by Raman and atomic force microscopy. Using these tools, Danon patient-derived cardiac tissue, primary fibroblasts, and human induced pluripotent stem cells differentiated into cardiomyocytes (hiPSC-CMs) were analyzed. Metabolic profiling indicated LAMP-2 deficiency promoted a switch toward glycolysis accompanied by rerouting of tryptophan metabolism. Cardiomyocytes’ energetic balance and NAD+/NADH ratio appeared to be maintained despite mitochondrial aging. In turn, metabolic adaption was accompanied by a senescence-associated signature. Similarly, Danon fibroblasts appeared more stress prone and less biomechanically compliant. Overall, shaping of both morphology and metabolism contributed to the loss of cardiac biomechanical competence that characterizes the clinical progression of Danon disease.
miR-101b Regulates Lipid Deposition and Metabolism of Primary Hepatocytes in Teleost Yellow Catfish Pelteobagrus fulvidraco

Excessive fat deposition in the hepatocytes, associated with excess dietary fat intake, was related to the occurrence of fatty livers in fish. miR-101b plays the important roles in controlling lipid metabolism, but the underlying mechanism at the post-transcriptional level remains unclear. The purpose of this study is to explore the roles and mechanism of miR-101b-mediating lipid deposition and metabolism in yellow catfish Pelteobagrus fulvidraco. We found that miR-101b directly targeted fatty acid translocase (cd36), caspase9 (casp9) and autophagy-related gene 4A (atg4a). Furthermore, using palmitic acid (PA) or oleic acid (OA) to incubate the primary hepatocytes of yellow catfish, we demonstrated that miR-101b inversely regulated cd36, casp9, and atg4a expression at the transcriptional level; the inhibition of miR-101b aggravated fatty acids (FAs, PA or OA)-induced lipid accumulation, indicating that miR-101b mediated FAs-induced variations of lipid metabolism in yellow catfish. Taken together, our study gave novel insight into the regulatory mechanism of lipid deposition and metabolism and might provide potential targets for the prevention and treatment of fatty livers in fish.
Significance of Habitat and Stock Re‐Testing for Enhancement of Natural Fisheries: Experimental Analyses with Queen Conch Strombus gigas

The queen conch Strombus gigas is a large, commercially important gastropod mollusc native to the Caribbean region that has become severely depleted because of overfishing and habitat destruction. Over the last 10 yr attempts have been made to rehabilitate conch stocks through releases of hatchery-reared stocks, but successes have been few. Some of the reasons for high mortality in hatchery-reared conch are elucidated by recent experiments conducted at Lee Stocking Island in the central Bahamas. Field experiments with juvenile queen conch indicate that sites with similar depths, sediments, and macrophyte cover do not provide equivalent food and shelter for conch. Transplants of conch were successful only in sites known to be historically significant as nursery grounds. While small-scale transplants can be used to screen potential outplant sites, only comprehensive understanding of the habitat requirements, behavior, feeding ecology, and predator-prey relationships will lead to long-term enhancement of fishery stocks. Differences in morphology, behavior, and habitat utilization between wild and hatchery-reared stocks also had significant effects on the survivorship and growth of outplanted stock. Therefore, hatcheries must develop culture methods that do not reduce the natural fitness of wild stock. Successful enhancement of natural fisheries through outplanting of hatchery-reared stocks depends upon: 1) development of hatchery animals sufficiently well adapted to survive in the field; and 2) release of the stock in suitable habitats at the optimal time. Close linkage between laboratory and field research, and hatchery operators will he necessary for the ultimate success of stock enhancement efforts.