Miracle-dz/UniFAR-FTUs huggingface dataset:
Implication of Surface Properties, Bacterial Motility, and Hydrodynamic Conditions on Bacterial Surface Sensing and Their Initial Adhesion

Biofilms are structured microbial communities attached to surfaces, which play a significant role in the persistence of biofoulings in both medical and industrial settings. Bacteria in biofilms are mostly embedded in a complex matrix comprised of extracellular polymeric substances that provide mechanical stability and protection against environmental adversities. Once the biofilm is matured, it becomes extremely difficult to kill bacteria or mechanically remove biofilms from solid surfaces. Therefore, interrupting the bacterial surface sensing mechanism and subsequent initial binding process of bacteria to surfaces is essential to effectively prevent biofilm-associated problems. Noting that the process of bacterial adhesion is influenced by many factors, including material surface properties, this review summarizes recent works dedicated to understanding the influences of surface charge, surface wettability, roughness, topography, stiffness, and combination of properties on bacterial adhesion. This review also highlights other factors that are often neglected in bacterial adhesion studies such as bacterial motility and the effect of hydrodynamic flow. Lastly, the present review features recent innovations in nanotechnology-based antifouling systems to engineer new concepts of antibiofilm surfaces.
iNOS Associates With Poor Survival in Melanoma: A Role for Nitric Oxide in the PI3K-AKT Pathway Stimulation and PTEN S-Nitrosylation

We previously showed that inducible nitric oxide synthase (iNOS) protein expression in melanoma tumor cells is associated with poor patient prognosis. Here, we analyzed the association between iNOS and the oncogenic PI3K-AKT pathway. TCGA data show that iNOS and phospho-Akt Ser473 expression were associated significantly only in the subset of tumors with genetically intact PTEN. Employing a stage III melanoma TMA, we showed that iNOS protein presence is significantly associated with shorter survival only in tumors with PTEN protein expression. These findings led to our hypothesis that the iNOS product, nitric oxide (NO), suppresses the function of PTEN and stimulates PI3K-Akt activation. Melanoma cells in response to NO exposure in vitro exhibited enhanced AKT kinase activity and substrate phosphorylation, as well as attenuated PTEN phosphatase activity. Biochemical analysis showed that NO exposure resulted in a post-translationally modified S-Nitrosylation (SNO) PTEN, which was also found in cells expressing iNOS. Our findings provide evidence that NO-rich cancers may exhibit AKT activation due to post-translational inactivation of PTEN. This unique activation of oncogenic pathway under nitrosative stress may contribute to the pathogenesis of iNOS in melanoma. Significance: Our study shows that iNOS expression is associated with increased PI3K-AKT signaling and worse clinical outcomes in melanoma patients with wt (intact) PTEN. Mutated PTEN is already inactivated. We also demonstrate that NO activates the PI3K-AKT pathway by suppressing PTEN suppressor function concurrent with the formation of PTEN-SNO. This discovery provides insight into the consequences of inflammatory NO produced in human melanoma and microenvironmental cells. It suggests that NO–driven modification provides a marker of PTEN inactivation, and represents a plausible mechanism of tumor suppressor inactivation in iNOS expressing subset of cancers.
Nutrition as Metabolic Treatment for Anxiety

Despite the overwhelming prevalence of anxiety disorders in modern society, medications and psychotherapy often fail to achieve complete symptom resolution. A complementary approach to medicating symptoms is to address the underlying metabolic pathologies associated with mental illnesses and anxiety. This may be achieved through nutritional interventions. In this perspectives piece, we highlight the roles of the microbiome and inflammation as influencers of anxiety. We further discuss the evidence base for six specific nutritional interventions: avoiding artificial sweeteners and gluten, including omega-3 fatty acids and turmeric in the diet, supplementation with vitamin D, and ketogenic diets. We attempt to integrate insights from the nutrition science-literature in order to highlight some practices that practitioners may consider when treating individual patients. Notably, this piece is not meant to serve as a comprehensive review of the literature, but rather argue our perspective that nutritional interventions should be more widely considered among clinical psychiatrists. Nutritional psychiatry is in its infancy and more research is needed in this burgeoning low-risk and potentially high-yield field.
Cognitive Impairments and Risk Factors After Ruptured Anterior Communicating Artery Aneurysm Treatment in Low-Grade Patients Without Severe Complications: A Multicenter Retrospective Study

Background: Cognitive impairment is the main factor affecting quality of life in patients with low-grade aneurysmal subarachnoid hemorrhage. Objective: We explored cognitive impairments and risk factors after treatment for ruptured anterior communicating artery (AComA) aneurysms in low-grade (Hunt-Hess grade of 1–3) patients without severe complications. Methods: One-hundred-twenty-six patients with a Hunt-Hess grade of 1–3 who underwent microsurgical clipping or endovascular embolization for ruptured AComA aneurysm treatment at three academic institutions in China from January 2015 to December 2017 were assessed with the modified Telephone Interview for Cognitive Status (TICS-m), the modified Rankin Scale (mRS), and the instrumental activities of daily living (IADL) scale 2 or more years after microsurgical clipping or endovascular coiling. Multiple cox-regression analysis was used to identify variables independently associated with cognitive impairment. Results: Of the total of 126 patients, 115 (91.3%) achieved good clinical outcomes (mRS score 0–2) and 109 (86.5%) had excellent quality of life (IADL score 8). Twenty-eight (22.2%) patients showed cognitive impairments (TICS-m≤27). The multivariate COX regression analysis showed that the female patients and longer duration of loss of consciousness at onset of subarachnoid hemorrhage (SAH) were independently associated with cognitive impairment. Cognitive outcome at the latest follow-up was not significantly different between patients treated after surgical clipping and coiling. Conclusion: About one in five patients showed cognitive impairments after treatment for ruptured AComA aneurysms. Patients who are of the female sex, and who have a longer duration of a loss of consciousness at the onset of SAH may be at risk of cognitive impairment.
Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples of Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either “early” (6–46 days post-partum, n = 33) or “late” (109–184 days post-partum, n = 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p < 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift from Staphylococcus and Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such as Janthinobacterium agaricidamnosum, Novosphingobium clariflavum, Ottowia beijingensis, and Flavobacterium cucumis. These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).
Distal Bias of Meiotic Crossovers in Hexaploid Bread Wheat Reflects Spatio-Temporal Asymmetry of the Meiotic Program

Meiotic recombination generates genetic variation and provides physical links between homologous chromosomes (crossovers) essential for accurate segregation. In cereals the distribution of crossovers, cytologically evident as chiasmata, is biased toward the distal regions of chromosomes. This creates a bottleneck for plant breeders in the development of varieties with improved agronomic traits, as genes situated in the interstitial and centromere proximal regions of chromosomes rarely recombine. Recent advances in wheat genomics and genome engineering combined with well-developed wheat cytogenetics offer new opportunities to manipulate recombination and unlock genetic variation. As a basis for these investigations we have carried out a detailed analysis of meiotic progression in hexaploid wheat (Triticum aestivum) using immunolocalization of chromosome axis, synaptonemal complex and recombination proteins. 5-Bromo-2′-deoxyuridine (BrdU) labeling was used to determine the chronology of key events in relation to DNA replication. Axis morphogenesis, synapsis and recombination initiation were found to be spatio-temporally coordinated, beginning in the gene-dense distal chromosomal regions and later occurring in the interstitial/proximal regions. Moreover, meiotic progression in the distal regions was coordinated with the conserved chromatin cycles that are a feature of meiosis. This mirroring of the chiasma bias was also evident in the distribution of the gene-associated histone marks, H3K4me3 and H3K27me3; the repeat-associated mark, H3K27me1; and H3K9me3. We believe that this study provides a cytogenetic framework for functional studies and ongoing initiatives to manipulate recombination in the wheat genome.
Identification of a Novel Pattern Recognition Receptor DM9 Domain Containing Protein 4 as a Marker for Pro-Hemocyte of Pacific Oyster Crassostrea gigas

DM9 refers to an uncharacterized protein domain that is originally discovered in Drosophila melanogaster. Two proteins with DM9 repeats have been recently identified from Pacific oyster Crassostrea gigas as mannose-specific binding pattern-recognition receptors (PRRs). In the present study, a novel member of DM9 domain containing protein (designated as CgDM9CP-4) was identified from C. gigas. CgDM9CP-4, about 16 kDa with only two tandem DM9 domains, was highly enriched in hemocytes and gill. The transcripts level of CgDM9CP-4 in circulating hemocytes were decreased after LPS, PGN and Vibrio splendidus stimulations. The recombinant protein of CgDM9CP-4 (rCgDM9CP-4) displayed a broad binding spectrum towards various pathogen-associated molecular patterns (PAMPs) (LPS, PGN, β-glucan and Mannose) and microorganisms (Staphylococcus aureus, Micrococcus luteus, V. splendidus, V. anguillarum, Escherichia coli, Pichia pastoris and Yarrowia lipolytica). CgDM9CP-4 was mostly expressed in gill and some of the hemocytes. Flow cytometry analysis demonstrated that the CgDM9CP-4-positive hemocytes accounted for 7.3% of the total hemocytes, and they were small in size and less in granularity. CgDM9CP-4 was highly expressed in non-phagocytes (~82% of total hemocytes). The reactive oxygen species (ROS) and the expression levels of cytokines in CgDM9CP-4-positive hemocytes were much lower than that in CgDM9CP-4-negative hemocytes. The mRNA expression level of CgDM9CP-4 in hemocytes was decreased after RNAi of hematopoietic-related factors (CgGATA, CgRunt, CgSCL, and CgNotch). In addition, CgDM9CP-4-positive cells were found to be much more abundant in hemocytes from gill than that from hemolymph, with most of them located in the gill filament. All these results suggested that CgDM9CP-4 was a novel member of PRR that expressed in undifferentiated pro-hemocytes to mediate immune recognition of pathogens.
Toluene Dioxygenase-Catalyzed cis-Dihydroxylation of Quinolines: A Molecular Docking Study and Chemoenzymatic Synthesis of Quinoline Arene Oxides

Molecular docking studies of quinoline and 2-chloroquinoline substrates at the active site of toluene dioxygenase (TDO), were conducted using Autodock Vina, to identify novel edge-to-face interactions and to rationalize the observed stereoselective cis-dihydroxylation of carbocyclic rings and formation of isolable cis-dihydrodiol metabolites. These in silico docking results of quinoline and pyridine substrates, with TDO, also provided support for the postulated cis-dihydroxylation of electron-deficient pyridyl rings, to give transient cis-dihydrodiol intermediates and the derived hydroxyquinolines. 2-Chloroquinoline cis-dihydrodiol metabolites were used as precursors in the chemoenzymatic synthesis of enantiopure arene oxide and arene dioxide derivatives of quinoline, in the context of its possible mammalian metabolism and carcinogenicity.
Viral Infections, the Microbiome, and Probiotics

Viral infections continue to cause considerable morbidity and mortality around the world. Recent rises in these infections are likely due to complex and multifactorial external drivers, including climate change, the increased mobility of people and goods and rapid demographic change to name but a few. In parallel with these external factors, we are gaining a better understanding of the internal factors associated with viral immunity. Increasingly the gastrointestinal (GI) microbiome has been shown to be a significant player in the host immune system, acting as a key regulator of immunity and host defense mechanisms. An increasing body of evidence indicates that disruption of the homeostasis between the GI microbiome and the host immune system can adversely impact viral immunity. This review aims to shed light on our understanding of how host-microbiota interactions shape the immune system, including early life factors, antibiotic exposure, immunosenescence, diet and inflammatory diseases. We also discuss the evidence base for how host commensal organisms and microbiome therapeutics can impact the prevention and/or treatment of viral infections, such as viral gastroenteritis, viral hepatitis, human immunodeficiency virus (HIV), human papilloma virus (HPV), viral upper respiratory tract infections (URTI), influenza and SARS CoV-2. The interplay between the gastrointestinal microbiome, invasive viruses and host physiology is complex and yet to be fully characterized, but increasingly the evidence shows that the microbiome can have an impact on viral disease outcomes. While the current evidence base is informative, further well designed human clinical trials will be needed to fully understand the array of immunological mechanisms underlying this intricate relationship.
Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic Material

Researchers in phylogenetic systematics typically choose a few individual representatives of every species for sequencing based on convenience (neighboring populations, herbarium specimens, samples provided by experts, garden plants). However, few studies are based on original material, type material or topotypic material (living specimens from the locality where the type material was collected). The use of type or topotypic material in phylogenetic studies is paramount particularly when taxonomy is complex, such as that of Antirrhinum (Plantaginaceae). In this paper, we used topotypic materials of Antirrhinum at the species level (34 species proposed by previous authors), 87 specimens representing the species distributions and >50,000 informative nucleotide characters (from ∼4,000 loci) generated by the genotyping-by-sequencing (GBS) technique: (i) to test two explicit taxonomic hypotheses widely followed by local taxonomic treatments; (ii) to robustly estimate phylogenetic relationships; (iii) to investigate the evolution of key morphological characters and biogeographic centers of differentiation. Two GBS phylogenies based on two datasets (87 localities and 34 topotypic specimens) revealed that: (1) Sutton’s (1988) taxonomic account is the most congruent with phylogenetic results, whereas division of Antirrhinum into three major clades disagrees with Rothmaler’s (1956) infrageneric classification; (2) monophyly of populations currently included in the same species is primarily supported; (3) the historically recognized Antirrhinum majus group is not monophyletic; (4) sister-group relationships are robust for eight species pairs; (5) the evolutionary radiation of 26 species since the Pliocene is underpinned given a high rate of diversification (0.54 spp. Myr–1); (6) a geographic pattern of speciation is reconstructed, with northern Iberia as the center of early diversification followed by more recent speciation in southeastern Iberia; and (7) multiple acquisitions of key taxonomic characters in the course of Antirrhinum diversification are strongly supported, with no evidence of hybridization between major clades. Our results also suggest incipient speciation in some geographic areas and point to future avenues of research in evolution and systematics of Antirrhinum.
The Role of Creative Publicity in Different Periods of the COVID-19 Outbreak in China: Taking the Creative Publicity of Chinese Poetry as an Example

When humans are confronted with an epidemic situation or a continuous natural disaster, success depends largely on how critical information is conveyed to as many people as possible, how individuals' emotional experiences of the crisis are elicited, and how their behaviors are directed going forward. Efficient publicity is key to successful epidemic prevention and control. This study explores the role of creative publicity by comparing the influence of creative publicity and general publicity in different periods of the COVID-19 outbreak in China. The effects of creative and general publicity differed across varying periods of the COVID-19 outbreak. Specifically, compared to general publicity, creative publicity had a significant impact on individuals' emotional arousal in the early period of the COVID-19 outbreak while it significantly promoted individuals' emotional arousal, behavioral regulation, and willingness to actively disseminate information in the middle period. In the stable period of the COVID-19 outbreak, creative publicity performed better than general publicity in regulating individuals' behavior. On the other hand, general publicity was more effective than creative publicity in regulating individuals' behavior and actively disseminating information about the epidemic in the early period of the COVID-19 outbreak. In conclusion, creative and general publicity had differing effects in different periods of the COVID-19 outbreak, which may relate to the characteristics of the publicity format and people's psychological conditions in different periods of the COVID-19 outbreak.
Preparing Graduates for Interprofessional Practice in South Africa: The Dissonance Between Learning and Practice

With South Africa's tumultuous history and resulting burden of disease and disability persisting post-democracy in 1994, a proposed decentralization of heath care with an urgent focus on disease prevention strategies ensued in 2010. Subsequently a nationwide call by students to adapt teaching and learning to an African context spoke to the need for responsive health professions training. Institutions of higher education are therefore encouraged to commit to person-centered comprehensive primary health care (PHC) education which equates to distributed training along the continuum of care. To cope with the complexity of patient care and health care systems, interprofessional education and collaborative practice has been recommended in undergraduate clinical training. Stellenbosch University, South Africa, introduced interprofessional home visits as part of the students' contextual PHC exposure in a rural community in 2012. This interprofessional approach to patient assessment and management in an under-resourced setting challenges students to collaboratively find local solutions to the complex problems identified. This paper reports on an explorative pilot study investigating students' and graduates' perceived value of their interprofessional home visit exposure in preparing them for working in South Africa. Qualitative semi-structured individual and focus group interviews with students and graduates from five different health sciences programmes were conducted. Primary and secondary data sources were analyzed using an inductive approach. Thematic analysis was conducted independently by two researchers and revealed insights into effective patient management requiring an interprofessional team approach. Understanding social determinants of health, other professions' roles, as well as scope and limitations of practice in a resource constrained environment can act as a precursor for collaborative patient care. The continuity of an interprofessional approach to patient care after graduation was perceived to be largely dependent on relationships and professional hierarchy in the workplace. Issues of hierarchy, which are often systemic, affect a sense of professional value, efficacy in patient management and job satisfaction. Limitations to using secondary data for analysis are discussed, noting the need for a larger more comprehensive study. Recommendations for rural training pathways include interprofessional teamwork and health care worker advocacy to facilitate collaborative care in practice.
Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin

Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.