Miracle-dz/UniFAR-FTUs huggingface dataset:
A Synthesis of Deepwater Horizon Impacts on Coastal and Nearshore Living Marine Resources

The 2010 Deepwater Horizon (DWH) oil blowout in the Gulf of Mexico began on April 20, originating in the deep sea 66 km off the Louisiana coast. By early June, DWH oil had spread to coastal Louisiana, Mississippi, Alabama and western Florida. An estimated 2,113 km of shoreline were oiled, making DWH the largest marine oil spill in global history by length of affected shoreline. Additionally, a series of oil spill response measures were deployed, including diversions of Mississippi River discharge to forestall oil coming ashore, and the establishment of large-scale fishery closures, with both affecting coastal resources to varying degrees. Here, we review published studies and describe additional analyses evaluating long-term impacts of DWH on coastal/nearshore biological resources. We assembled time-series data collected by state, federal and academic partners on population abundance and environmental conditions to evaluate species and community change. Our study focused on plankton, invertebrates, fishes and dolphins, and 13 “key species” were selected to conduct semi-quantitative vulnerability-resilience (V-R) analyses. At one extreme, early life stages of Gulf Menhaden (Brevoortia patronus) were not affected due to seasonal spawning and larval development preceding the spill. In contrast, demographically independent populations of the common Bottlenose Dolphin, (Tursiops truncatus) suffered a variety of severe and ongoing health effects owing to oil exposure. Virtually all of the heavily oiled salt marsh habitat was in Louisiana, with the majority occurring in Barataria Bay. Multispecies trawl survey abundances declined post-DWH throughout eastern coastal Louisiana but remained stable elsewhere. A regime shift in composition of Barataria Bay trawl survey catches occurred during and following the spill, the persistence of which was associated with long-term reductions in average salinity and increases in water clarity. In some cases, fishery closures were associated with measurable but ephemeral increases in abundance of some targeted and bycatch species. Freshwater flooding of marshes was ineffective in preventing coastal oiling and severely affected benthic euryhaline resources including Eastern Oyster (Crassostrea virginica) and Marsh Periwinkle (Littoraria irrorata). The flooding response measure experiment also indicates the directionality of impacts that further planned water diversions may have on ecological communities of lower Mississippi River basins.
New Mechanistic Insights, Novel Treatment Paradigms, and Clinical Progress in Cerebrovascular Diseases

The past decade has brought tremendous progress in diagnostic and therapeutic options for cerebrovascular diseases as exemplified by the advent of thrombectomy in ischemic stroke, benefitting a steeply increasing number of stroke patients and potentially paving the way for a renaissance of neuroprotectants. Progress in basic science has been equally impressive. Based on a deeper understanding of pathomechanisms underlying cerebrovascular diseases, new therapeutic targets have been identified and novel treatment strategies such as pre- and post-conditioning methods were developed. Moreover, translationally relevant aspects are increasingly recognized in basic science studies, which is believed to increase their predictive value and the relevance of obtained findings for clinical application.This review reports key results from some of the most remarkable and encouraging achievements in neurovascular research that have been reported at the 10th International Symposium on Neuroprotection and Neurorepair. Basic science topics discussed herein focus on aspects such as neuroinflammation, extracellular vesicles, and the role of sex and age on stroke recovery. Translational reports highlighted endovascular techniques and targeted delivery methods, neurorehabilitation, advanced functional testing approaches for experimental studies, pre-and post-conditioning approaches as well as novel imaging and treatment strategies. Beyond ischemic stroke, particular emphasis was given on activities in the fields of traumatic brain injury and cerebral hemorrhage in which promising preclinical and clinical results have been reported. Although the number of neutral outcomes in clinical trials is still remarkably high when targeting cerebrovascular diseases, we begin to evidence stepwise but continuous progress towards novel treatment options. Advances in preclinical and translational research as reported herein are believed to have formed a solid foundation for this progress.
Geographic Mosaics of Fly Pollinators With Divergent Color Preferences Drive Landscape-Scale Structuring of Flower Color in Daisy Communities

The striking variation in flower color across and within Angiosperm species is often attributed to divergent selection resulting from geographic mosaics of pollinators with different color preferences. Despite the importance of pollinator mosaics in driving floral divergence, the distributions of pollinators and their color preferences are seldom quantified. The extensive mass-flowering displays of annual daisy species in Namaqualand, South Africa, are characterized by striking color convergence within communities, but also color turnover within species and genera across large geographic scales. We aimed to determine whether shifts between orange and white-flowered daisy communities are driven by the innate color preferences of different pollinators or by soil color, which can potentially affect the detectability of different colored flowers. Different bee-fly pollinators dominated in both community types so that largely non-overlapping pollinator distributions were strongly associated with different flower colors. Visual modeling demonstrated that orange and white-flowered species are distinguishable in fly vision, and choice experiments demonstrated strongly divergent color preferences. We found that the dominant pollinator in orange communities has a strong spontaneous preference for orange flowers, which was not altered by conditioning. Similarly, the dominant pollinator in white communities exhibited an innate preference for white flowers. Although detectability of white flowers varied across soil types, background contrast did not alter color preferences. These findings demonstrate that landscape-level flower color turnover across Namaqua daisy communities is likely shaped by a strong qualitative geographic mosaic of bee-fly pollinators with divergent color preferences. This is an unexpected result given the classically generalist pollination phenotype of daisies. However, because of the dominance of single fly pollinator species within communities, and the virtual absence of bees as pollinators, we suggest that Namaqua daisies function as pollination specialists despite their generalist phenotypes, thus facilitating differentiation of flower color by pollinator shifts across the fly pollinator mosaic.
Living at the Edge: Increasing Stress for Plants 2–13 Years After the Retreat of a Tropical Glacier

Rapid warming is a major threat for the alpine biodiversity but, at the same time, accelerated glacial retreat constitutes an opportunity for taxa and communities to escape range contraction or extinction. We explored the first steps of plant primary succession after accelerated glacial retreat under the assumption that the first few years are critical for the success of plant establishment. To this end, we examined plant succession along a very short post-glacial chronosequence in the tropical Andes of Ecuador (2–13 years after glacial retreat). We recorded the location of all plant individuals within an area of 4,200 m2 divided into plots of 1 m2. This sampling made it possible to measure the responses of the microenvironment, plant diversity and plants traits to time since the glacial retreat. It also made it possible to produce species-area curves and to estimate positive interactions between species. Decreases in soil temperature, soil moisture, and soil macronutrients revealed increasing abiotic stress for plants between two and 13 years after glacial retreat. This increasing stress seemingly explained the lack of positive correlation between plant diversity and time since the glacial retreat. It might explain the decreasing performance of plants at both the population (lower plant height) and the community levels (lower species richness and lower accumulation of species per area). Meanwhile, infrequent spatial associations among plants indicated a facilitation deficit and animal-dispersed plants were almost absent. Although the presence of 21 species on such a small sampled area seven years after glacial retreat could look like a colonization success in the first place, the increasing abiotic stress may partly erase this success, reducing species richness to 13 species after 13 years and increasing the frequency of patches without vegetation. This fine-grain distribution study sheds new light on nature's responses to the effects of climate change in cold biomes, suggesting that faster glacial retreat would not necessarily result in accelerated plant colonization. Results are exploratory and require site replications for generalization.
Gamma/Delta T Cells in the Course of Healthy Human Pregnancy: Cytotoxic Potential and the Tendency of CD8 Expression Make CD56+ γδT Cells a Unique Lymphocyte Subset

To date, pregnancy is an immunological paradox. The semi-allogenic fetus must be accepted by the maternal immune system, while defense against pathogens and immune surveillance cannot be compromised. Gamma/delta T cells are believed to play an important role in this immunological puzzle. In this study, we analyzed peripheral blood CD56+ γδT cells from pregnant women (1st, 2nd, and 3rd trimester) and non-pregnant women by multicolor flow cytometry. Interestingly, γδT cells represent almost half of CD3+/CD56+ cells. Among γδT cells, the CD56+ population expands in the 2nd and 3rd trimester. CD56+ γδT cells maintained a predominantly CD4–/CD8– or CD8+ phenotype, while CD56– γδT cells were in similar rates CD4–/CD8– or CD4+ during pregnancy. Investigation of the lysosomal degranulation marker CD107a revealed a preserved elevated rate of potentially cytotoxic CD56+ γδT cells in pregnancy, while their cytotoxic strength was reduced. Furthermore, CD56+ γδT cells continuously showed a higher prevalence of PD-1 expression. CD56+ γδT cells’ rate of PD-1 increased in the 1st trimester and decreased hereafter back to normal level. We correlated the cytotoxic potential and the expression of the inhibitory immune checkpoint PD-1 and were able to demonstrate that highly cytotoxic cells within this CD56+ γδT population tend to express PD-1, which might allow the inhibition of these cells after binding its ligand in the placenta. These findings should support the understanding of the complex processes, which ensure the maintenance of pregnancy.
Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review

Background and Aim: Accumulating evidence have implicated gut microbiota alterations in pediatric and adult patients with inflammatory bowel disease (IBD); however, the results of different studies are often inconsistent and even contradictory. It is believed that early changes in new-onset and treatment-naïve pediatric patients are more informative. We performed a systematic review to investigate the gut microbiota profiles in pediatric IBD and identify specific microbiota biomarkers associated with this disorder. Methods: Electronic databases were searched from inception to 31 July 2020 for studies that observed gut microbiota alterations in pediatric patients with IBD. Study quality was assessed using the Newcastle–Ottawa scale. Results: A total of 41 original studies investigating gut microbiota profiles in pediatric patients with IBD were included in this review. Several studies have reported a decrease in α-diversity and an overall difference in β-diversity. Although no specific gut microbiota alterations were consistently reported, a gain in Enterococcus and a significant decrease in Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Roseburia, Ruminococcus, and Lachnospira were found in the majority of the included articles. Moreover, there is insufficient data to show specific microbiota bacteria associated with disease activity, location, and behavior in pediatric IBD. Conclusions: This systematic review identified evidence for differences in the abundance of some bacteria in pediatric patients with IBD when compared to patients without IBD; however, no clear overall conclusion could be drawn from the included studies due to inconsistent results and heterogeneous methodologies. Further studies with large samples that follow more rigorous and standardized methodologies are needed.
Cerebrospinal Fluid Inflammatory Cytokine Levels in Patients With Major Psychiatric Disorders: A Multiplex Immunoassay Study

Aim: Accumulating evidence suggests that neural inflammation plays an important role in psychiatric disorders. We aimed to identify inflammatory cytokines involved in the pathophysiology of such disorders by quantifying them in cerebrospinal fluid (CSF) samples from a large sample of patients with major psychiatric disorders and healthy controls. Methods: The subjects included 94 patients with schizophrenia, 68 with bipolar disorder, 104 with major depressive disorder, and 118 healthy controls, matched for age, sex, and ethnicity (Japanese). Lumbar puncture was performed to collect these CSF samples. A multiplex immunoassay was then performed to measure CSF cytokine levels using magnetic on-bead antibody conjugation for 19 inflammatory cytokines. Results: CSF interferon-β level was significantly higher in total psychiatric patients than in healthy controls (corrected p = 0.000029). In diagnostic group comparisons, CSF interferon-β level was significantly higher in patients with schizophrenia, or bipolar disorder (corrected p = 0.000047 or 0.0034) than in healthy controls. Conclusion: We present novel evidence that CSF IFN-β level showed prominent statistical differences between psychiatric groups and healthy controls. This suggests IFN-β as the most important player among the 19 cytokines tested here in the inflammation-related pathophysiology of major psychiatric disorders.
Green Tea Polyphenol-Sensitive Calcium Signaling in Immune T Cell Function

Polyphenol compounds found in green tea have a great therapeutic potential to influence multiple human diseases including malignancy and inflammation. In this mini review, we describe effects of green tea and the most important component EGCG in malignancy and inflammation. We focus on cellular mechanisms involved in the modification of T cell function by green tea polyphenol EGCG. The case is made that EGCG downregulates calcium channel activity by influencing miRNAs regulating expression of the channel at the post-transcriptional level.
The Use of Fluorescence Spectra for the Detection of Scab and Rot in Fruit and Vegetable Crops

Using Fluorescence Spectrometer Lumina, fluorescence spectra of surface slices of apples and potatoes were measured. Some of the samples were healthy, some were infected: apples had scabs, potatoes had rot and mechanical damage. For apples, two zones were found where the emission spectra of healthy and scab-affected samples differed significantly from each other. This is the region of 400–450 nm with excitation of 300–350 nm, as well as the region of 680–750 nm with excitation of 400–450 nm. For potatoes, the differences between a healthy and rot-affected sample were found only in the region of 400–450 nm with excitation at 300–350 nm. The found differences are clearly manifested in the correlation coefficients between the spectra - the minimum correlation coefficient for healthy apples and scab at 450 nm excitation r = 0.51. Also, healthy and diseased samples are well separated using principal component analysis (PCA). The revealed differences in the fluorescence spectra can be used for the detection and separation of diseased and healthy fruits and vegetables.
Comparative Transcriptome Analysis of Streptomyces nodosus Mutant With a High-Yield Amphotericin B

Antibiotics play an important role in human health. Most antibiotics are derived from microbial secondary metabolites. Amphotericin is a polyene macrolide antibiotic synthesized by Streptomyces nodosus. S. nodosus ZJB2016050 with high-yield amphotericin B (AmB) was obtained by traditional mutagenesis using S. nodosus ATCC14899 as the original strain. The differences in the characterization of the two strains were found in color, mycelium morphology, and AmB yield. Subsequent comparative transcriptome explained the yield differences between the two strains. Pathways including the carbohydrate metabolic pathway and the secondary product synthesis pathway were targeted. The upregulation of glucokinase, phosphoglycerate mutase, and pyruvate dehydrogenase accelerates the consumption of glucose and has great effects on the accumulation of precursors. One of the competitive secondary metabolites of the polyketone synthetase (PKS) II type sapromomycin analog synthesis gene cluster was downregulated, which competes for malonyl-CoA. Five PKS modules (except for the first module amphA) of the amphotericin synthetic gene cluster in the high-yielding strain were downregulated, which resulted in the total amphotericin A (AmA) and AmB of S. nodosus ZJB2016050 being less than that of the wild-type S. nodosus ATCC14899. Combined with gene differential expression in the pentose phosphate pathway and the reaction mechanism of the ER5 domain, the reason that S. nodosus ZJB2016050 preferred to synthesize AmB was probably related to intracellular reduction.
Identification and Immunocorrelation of Prognosis-Related Genes Associated With Development of Muscle-Invasive Bladder Cancer

Improved understanding of the molecular mechanisms and immunoregulation of muscle-invasive bladder cancer (MIBC) is essential to predict prognosis and develop new targets for therapies. In this study, we used the cancer genome atlas (TCGA) MIBC and GSE13507 datasets to explore the differential co-expression genes in MIBC comparing with adjacent non-carcinoma tissues. We firstly screened 106 signature genes by Weighted Gene Co-expression Network Analysis (WGCNA) and further identified 15 prognosis-related genes of MIBC using the univariate Cox progression analysis. Then we systematically analyzed the genetic alteration, molecular mechanism, and clinical relevance of these 15 genes. We found a different expression alteration of 15 genes in MIBC comparing with adjacent non-carcinoma tissues and normal tissues. Meanwhile, the biological functions and molecular mechanisms of them were also discrepant. Among these, we observed the ANLN was highly correlated with multiple cancer pathways, molecular function, and cell components, revealing ANLN may play a pivotal role in MIBC development. Next, we performed a consensus clustering of 15 prognosis-related genes; the results showed that the prognosis, immune infiltration status, stage, and grade of MIBC patients were significantly different in cluster1/2. We further identified eight-genes risk signatures using the least absolute shrinkage and selection operator (LASSO) regression analysis based on the expression values of 15 prognosis-related genes, and also found a significant difference in the prognosis, immune infiltration status, stage, grade, and age in high/low-risk cohort. Moreover, the expression of PD-1, PD-L1, and CTLA4 was significantly up-regulated in cluster1/high-risk-cohort than that in cluster2/low-risk-cohort. High normalized enrichment score of the Mitotic spindle, mTORC1, Complement, and Apical junction pathway suggested that they might be involved in the distinct tumor immune microenvironment (TIME) of cluster1/2 and high-/low-risk-cohort. Our study identified 15 prognosis-related genes of MIBC, provided a feasible stratification method to help for the future immunotherapy strategies of MIBC patients.
Socioeconomic Drought in a Mexican Semi-arid City: Monterrey Metropolitan Area, a Case Study

The Monterrey Metropolitan Area (MMA) is located in northeastern Mexico in a semi-arid region. As in other areas of the world, prolonged and severe meteorological droughts are recurrent. Meteorological droughts affect the level of dam reservoirs, rivers, and groundwater (aquifers) in the region to the extent they become hydrological droughts which in turn may contribute to socioeconomic droughts. The recent dry event (2011–2013) in northern Mexico severely affected various socioeconomic sectors and may serve as an example of future climatic and hydrologic conditions in this region. Meteorological droughts in northeastern Mexico, mostly induced by anomalously intense subsidence, frequently result in hydrological droughts and intense pressure in the water resources services of the Monterrey Metropolitan Area (MMA), one of the largest cities in Mexico. Landfalling tropical cyclones entering northeastern Mexico historically have alleviated water crises during prolonged droughts. In 2013, the rains from tropical cyclone Ingrid helped to recover water levels in the system of dam reservoirs that provides water to the MMA. However, water management is only one part of a complex socioeconomic system that must respond to the growing demands for water in a region where aquifers are already overexploited. Trends in the atmospheric circulation indicate that droughts in the region may become more severe in the coming decades. Improved water management programs and protocols should be considered in addition to closer reviews of the hydraulic infrastructure. Water transfers from one region to another should be carefully planned because solving a problem in one place may adversely affect another. The use of climate information may be critical to avoidance of water conflicts in the future.
DeepRTCP: Predicting ATP-Binding Cassette Transporters Based on 1-Dimensional Convolutional Network

ATP-binding cassette (ABC) transporters can promote cells to absorb nutrients and excrete harmful substances. It plays a vital role in the transmembrane transport of macromolecules. Therefore, the identification of ABC transporters is of great significance for the biological research. This paper will introduce a novel method called DeepRTCP. DeepRTCP uses the deep convolutional neural network and a feature combined of reduced amino acid alphabet based tripeptide composition and PSSM to recognize ABC transporters. We constructed a dataset named ABC_2020. It contains the latest ABC transporters downloaded from Uniprot. We performed 10-fold cross-validation on DeepRTCP, and the average accuracy of DeepRTCP was 95.96%. Compared with the start-of-the-art method for predicting ABC transporters, DeepRTCP improved the accuracy by 9.29%. It is anticipated that DeepRTCP can be used as an effective ABC transporter classifier which provides a reliable guidance for the research of ABC transporters.
Rotten to the Cortex: Ceramide-Mediated Lipotoxicity in Diabetic Kidney Disease

Diabetic kidney disease (DKD) is a prevalent and progressive comorbidity of diabetes mellitus that increases one’s risk of developing renal failure. Progress toward development of better DKD therapeutics is limited by an incomplete understanding of forces driving and connecting the various features of DKD, which include renal steatosis, fibrosis, and microvascular dysfunction. Herein we review the literature supporting roles for bioactive ceramides as inducers of local and systemic DKD pathology. In rodent models of DKD, renal ceramides are elevated, and genetic and pharmacological ceramide-lowering interventions improve kidney function and ameliorate DKD histopathology. In humans, circulating sphingolipid profiles distinguish human DKD patients from diabetic controls. These studies highlight the potential for ceramide to serve as a central and therapeutically tractable lipid mediator of DKD.