Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment

In increasingly urban landscapes, the loss of native pollen and nectar floral resources is impacting ecologically important pollinators. Increased urbanization has also brought about the rise of urban gardens which introduce new floral resources that may help replace those the pollinators have lost. Recently, studies have shown that the microbial communities of nectar may play an important role in plant-pollinator interactions, but these microbial communities and the floral visitors in urban environments are poorly studied. In this study we characterized the floral visitors and nectar microbial communities of Ascelpias curassavica, a non-native tropical milkweed commonly, in an urban environment. We found that the majority of the floral visitors to A. curassavica were honey bees followed closely by monarch butterflies. We also found that there were several unique visitors to each site, such as ants, wasps, solitary bees, several species of butterflies and moths, Anna’s hummingbird, and the tarantula hawk wasp. Significant differences in the nectar bacterial alpha and beta diversity were found across the urban sites, although we found no significant differences among the fungal communities. We found that the differences in the bacterial communities were more likely due to the environment and floral visitors rather than physiological differences in the plants growing at the gardens. Greater understanding of the impact of urbanization on the nectar microbiome of urban floral resources and consequently their effect on plant-pollinator relationships will help to predict how these relationships will change with urbanization, and how negative impacts can be mitigated through better management of the floral composition in urban gardens.
Response of wild Trumpeter Swan ( Cygnus buccinator ) broods to wetland drawdown and changes in food abundance

A brief period of drawdown can stimulate wetland productivity and enhance the attractiveness of a site for breeding Trumpeter Swans ( Cygnus buccinator ) by providing a nutrient pulse. Drawdown of a pond in Aurora, Ontario, lasting about 8 weeks in late summer and fall 2009 followed by re-flooding increased the abundance of invertebrates, especially snails, in the following year. This response was ephemeral, lasting 1 year. Wild Trumpeter Swans and their cygnets responded by selective feeding the year after drawdown, despite the risk of predation by Snapping Turtles ( Chelydra serpentina ). There was a strong correlation between the feeding activity of two cygnets and the local abundance of snails in the pond in 2010. The nutritional content, especially protein, calcium, phosphorus, and magnesium, of a variety of abundant foods satisfied the requirements for skeletal growth and development and was higher than that of available commercial duck grower rations. The responsive feeding behaviours of the cygnets are typical of specific appetitive behaviour and suggest that swans rapidly exploit unpredictable nutrient fluxes in their local environment.
Proteome-scale analysis of phase-separated proteins in immunofluorescence images

Phase separation is an important mechanism that mediates the spatial distribution of proteins in different cellular compartments. While phase-separated proteins share certain sequence characteristics, including intrinsically disordered regions (IDRs) and prion-like domains, such characteristics are insufficient for making accurate predictions; thus, a proteome-wide understanding of phase separation is currently lacking. Here, we define phase-separated proteomes based on the systematic analysis of immunofluorescence images of 12 073 proteins in the Human Protein Atlas. The analysis of these proteins reveals that phase-separated candidate proteins exhibit higher IDR contents, higher mean net charge and lower hydropathy and prefer to bind to RNA. Kinases and transcription factors are also enriched among these candidate proteins. Strikingly, both phase-separated kinases and phase-separated transcription factors display significantly reduced substrate specificity. Our work provides the first global view of the phase-separated proteome and suggests that the spatial proximity resulting from phase separation reduces the requirement for motif specificity and expands the repertoire of substrates. The source code and data are available at https://github.com/cheneyyu/deepphase.
Post-traumatic stress disorder risk and witnessing team members in acute psychological stress during combat

Background Occupational groups operating in dangerous environments may witness the development of acute stress reaction (ASR) in team members. Witnessing ASR in team members may increase the risk of developing subsequent post-traumatic stress disorder (PTSD) symptoms. Aims To describe ASR symptoms that individuals witness, assess the relationship between witnessing a team member exhibiting ASR symptoms and an individual's own PTSD symptoms, and describe common intervention responses by peers. Method Cross-sectional, anonymous surveys were conducted with US soldiers who were previously deployed (sample 1; n = 176) and currently deployed sample 2; n = 497). Surveys assessed combat experiences, PTSD (PTSD Checklist-5), ASR exposure and intervention responses. Analyses included frequencies and binary logistic regression. Results Witnessing at least one ASR symptom during a combat-related event was reported by 51.7% in sample 1 and 42.4% in sample 2; the most commonly observed symptoms were being unable to function or being detached. Controlling for combat experiences, high levels of witnessing a team member exhibit ASR symptoms was associated with increased risk of subthreshold PTSD or PTSD in sample 1 (odds ratio (OR) = 8.69, 95% CI 2.29–42.60) and approached significance in sample 2 (OR = 1.67, 95% CI 0.98–2.81). Common intervention responses included providing a directive or yelling; many also reported being unsure how to respond. Conclusions Witnessing team members who exhibit ASR symptoms appears to be associated with screening positive for subthreshold PTSD or PTSD. Results suggest the need for further research into how to prepare individuals to manage ASR in team members and to examine ASR in other high-risk occupations.
Elucidation of the Molecular Mechanism of Wet Granulation for Pharmaceutical Standard Formulations in a High-Speed Shear Mixer Using Near-Infrared Spectroscopy

The granulation process of pharmaceutical standard formulation in a high-speed shear wet granulation (HSWG) was measured by in-line near-infrared spectroscopy (NIRS) and agitation power consumption (APC) methods. The F-1, F-2, and F-3 formulations (500 g) contained 96% w/w α-lactose monohydrate (LA), potato starch (PS), and a LA:PS = 7:3 mixture, respectively, and all the formulations contained 4% w/w hydroxypropyl cellulose. While adding purified water at 10 mL/min, the sample powder was mixed. The calibration models to measure the amount of binding water (Wa) and APC of the HSWG formulations were established based on NIRS of the samples measured for 60 min by partial least-squares regression analysis (PLS). Molecular interaction related to APC between the particle surface and binding liquor was analyzed based on NIRS. The predicted values of Wa and APC for all formulations were superimposed with the measured values on a straight line, respectively. The regression vector (RV) of the calibration model for Wa indicated the chemical information of all the water in the samples. In contrast, the RV for APC suggested that APC changes in the processes are related to powder aggregation because of surface tension of binding water between particles.
Insights into the Role of microRNAs in Colorectal Cancer (CRC) Metabolism

Simple Summary Tumour cells have been shown to demonstrate changes in metabolic pathways as compared to normal cells. Colorectal cancer (CRC) is one of the most frequently diagnosed cancers globally. Some studies suggest that microRNAs (miRNAs) could play potential role in cancer cell metabolism. Our review aims to identify the role of different miRNAs in regulating the metabolism of CRC cells. Certain miRNAs could become potential biomarkers and even therapeutic targets based on their importance in CRC cell metabolism. Abstract Colorectal cancer (CRC) is one of the most frequently diagnosed cancers, with a high mortality rate globally. The pathophysiology of CRC is mainly initiated by alteration in gene expression, leading to dysregulation in multiple signalling pathways and cellular processes. Metabolic reprogramming is one of the important cancer hallmarks in CRC, which involves the adaptive changes in tumour cell metabolism to sustain the high energy requirements for rapid cell proliferation. There are several mechanisms in the metabolic reprogramming of cancer cells, such as aerobic glycolysis, oxidative phosphorylation, lactate and fatty acids metabolism. MicroRNAs (miRNAs) are a class of non-coding RNAs that are responsible for post-transcriptional regulation of gene expression. Differential expression of miRNAs has been shown to play an important role in different aspects of tumorigenesis, such as proliferation, apoptosis, and drug resistance, as well as metabolic reprogramming. Increasing evidence also reports that miRNAs could function as potential regulators of metabolic reprogramming in CRC cells. This review provides an insight into the role of different miRNAs in regulating the metabolism of CRC cells as well as to discuss the potential role of miRNAs as biomarkers or therapeutic targets in CRC tumour metabolism.
Fermentation Production Technology of Lipase with Candida sp. 99-125

Lipase catalyses many ester synthesis and transesterification reaction. The lipase from Candida sp. has good esterification ability without positional specificity for triglycerides and has potential application in the synthesis of short chain esters as flavor compounds or biofuels such as biodiesel. The fermentation of lipase with Candida sp.99-125 has been studied. The effects of different carbon resources and nitrogen resources on the lipase production were investigated. It was found that soybean oil and soy powder can enhance the lipase production. The optimal medium composition is 4% soybean oil, 4% soy powder, 0.1% K 2HPO 4 and 0.1% KH 2PO 4. The suitable shake flask fermentation conditions was identified and the lipase activity in shake flask reached 5000 IU/mL. The process was scaled up from a laboratory bioreactor (30L) to a pilot fermentor (1m 3). The amount of lipase reached 8100 IU/mL in 30L fermentor and 8000 IU/mL in 1m 3 fermentor.
Carex muskingumensis and Osmotic Stress: Identification of Reference Genes for Transcriptional Profiling by RT-qPCR

Carex muskingumensis is a highly valued perennial ornamental grass cultivated worldwide. However, there is limited genetic data regarding this species. Selection of proper reference genes (RGs) for reverse transcription quantitative PCR (RT-qPCR) data normalization has become an essential step in gene expression analysis. In this study, we aimed to examine expression stability of nine candidate RGs in C. muskingumensis plants, subjected to osmotic stress, generated either by salinity or PEG treatment. The identification of genes exhibiting high expression stability was performed by four algorithms (geNorm, NormFinder, BestKeeper and deltaCt method). The results showed that the combination of two genes would be sufficient for reliable expression data normalization. ADP (ADP-ribosylation factor) and TBP (TATA-box-binding protein) were identified as the most stably expressed under salinity treatment, while eIF4A (eukaryotic initiation factor 4A) and TBP were found to show the highest stability under PEG-induced drought. A set of three genes (ADP, eIF4A and TBP) displayed the highest expression stability across all experimental samples tested in this study. To our best knowledge, this is the first report regarding RGs selection in C. muskingumensis. It will provide valuable starting point information for conducting further analyses in this and related species concerning their responses to water shortage and salinity stress.
Sleep as a Novel Biomarker and a Promising Therapeutic Target for Cerebral Small Vessel Disease: A Review Focusing on Alzheimer’s Disease and the Blood-Brain Barrier

Cerebral small vessel disease (CSVD) is a leading cause of cognitive decline in elderly people and development of Alzheimer’s disease (AD). Blood–brain barrier (BBB) leakage is a key pathophysiological mechanism of amyloidal CSVD. Sleep plays a crucial role in keeping health of the central nervous system and in resistance to CSVD. The deficit of sleep contributes to accumulation of metabolites and toxins such as beta-amyloid in the brain and can lead to BBB disruption. Currently, sleep is considered as an important informative platform for diagnosis and therapy of AD. However, there are no effective methods for extracting of diagnostic information from sleep characteristics. In this review, we show strong evidence that slow wave activity (SWA) (0–0.5 Hz) during deep sleep reflects glymphatic pathology, the BBB leakage and memory deficit in AD. We also discuss that diagnostic and therapeutic targeting of SWA in AD might lead to be a novel era in effective therapy of AD. Moreover, we demonstrate that SWA can be pioneering non-invasive and bed–side technology for express diagnosis of the BBB permeability. Finally, we review the novel data about the methods of detection and enhancement of SWA that can be biomarker and a promising therapy of amyloidal CSVD and CSVD associated with the BBB disorders.
Shifting into high gear: how Interstitial Cells of Cajal change the motility pattern of the developing intestine.

The first contractile waves in the developing embryonic gut are purely myogenic, they only involve smooth muscle. Here, we provide evidence for a transition from smooth-muscle to Interstitial Cell of Cajal (ICC) driven contractile waves in the developing chicken gut. In-situ hybridization staining for ANO1, a known ICC marker, shows that ICCs are already present throughout the gut as from embryonic day 7 (E7). We devised a protocol to reveal ICC oscillatory and propagative calcium activity in embryonic gut whole-mount and find that the first steady calcium oscillations in ICCs occur at E14. We show that the activation of ICCs leads to an increase in contractile wave frequency, regularity, directionality and velocity between E12 and E14. We finally demonstrate that application of the c-KIT antagonist imatinib mesylate in organ culture specifically depletes the ICC network and inhibits the transition to a regular, rhythmic wave pattern. We compare our findings to existing results in the mouse and predict that a similar transition should take place in the human fetus between 12 and 14 weeks of development. Together, our results point to an abrupt physiological transition from smooth-muscle mesenchyme self-initiating waves to ICC-driven motility in the fetus, and clarify the contribution of ICCs to the contractile wave pattern.
Cell-Type-Specific Metabolic Profiling Achieved by Combining Desorption Electrospray Ionization Mass Spectrometry Imaging and Immunofluorescence Staining.

Cell-type-specific metabolic profiling in tissue with heterogeneous composition has been of great interest across all mass spectrometry imaging (MSI) technologies. We report here a powerful new chemical imaging capability in desorption electrospray ionization (DESI) MSI, which enables cell-type-specific and in situ metabolic profiling in complex tissue samples. We accomplish this by combining DESI-MSI with immunofluorescence staining using specific cell-type markers. We take advantage of the variable frequency of each distinct cell-type in the lateral septal nucleus (LSN) region of mouse forebrain. This allows computational deconvolution of the cell-type-specific metabolic profile in neurons and astrocytes by convex optimization - a machine learning method. Based on our approach, we observed 107 metabolites that show different distributions and intensities between astrocytes and neurons. We subsequently identified 23 metabolites using high resolution mass spectrometry (MS) and tandem MS, which include small metabolites such as adenosine and N-acetylaspartate previously associated with astrocytes and neurons, respectively, as well as accumulation of several phospholipid species in neurons which have not been studied before. Overall, this method overcomes the relatively low spatial resolution of DESI-MSI and provides a new platform for in situ metabolic investigation at the cell-type level in complex tissue samples with heterogeneous cell-type composition.
Ligand and pH-induced Structure Transition of Gypsy Moth Lymantria dispar Pheromone-binding Protein 1 (LdisPBP1).

Pheromone-binding proteins (PBPs) are small, water-soluble proteins found in the lymph of pheromone-sensing hairs. PBPs are essential in modulating pheromone partitioning in the lymph and at pheromone receptors of olfactory sensory neurons. The function of a PBP is associated with its ability to structurally convert between two conformations. Although mechanistic details remain unclear, it has been proposed that the structural transition between these forms is affected by two factors: pH and presence/absence of ligand. To better understand the PBP conformation transition, the structure of the gypsy moth (Lymantria dispar) LdisPBP1 was elucidated at pH 4.5 and 35 °C using NMR spectroscopy. In addition, the effects of sample pH and binding of the species' pheromone, (+)-disparlure, (7R, 8S)-epoxy-2-methyloctadecane, and its enantiomer were monitored via [15N]-HSQC spectroscopy. LdisPBP1 in acidic conditions has seven helices, with its C-terminal residues forming the seventh helix within the pheromone binding pocket, and its N-terminal residues disordered. In conditions where this conformation is made favorable, free LdisPBP1 would have limited ligand binding capacity due to the seventh helix occupancy in the internal binding pocket. Our findings suggest that even in the presence of 4-fold ligand at acidic pH, LdisPBP1 is only ~ 60% in its pheromone-bound form. Furthermore, evidence of a different LdisPBP1 form is seen at higher pH, with transition pH between 5.6 and 6.0. This suggests that LdisPBP1 at neutral pH exists as a mixture of at least two conformations. These findings have implications concerning PBP ligand binding and release mechanism.
Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector

Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli.
Loss of MAGEL2 in Prader-Willi syndrome leads to decreased secretory granule and neuropeptide production

Prader-Willi syndrome (PWS) is a developmental disorder caused by loss of maternally imprinted genes on 15q11-q13, including melanoma antigen gene family member L2 (MAGEL2). The clinical phenotypes of PWS suggest impaired hypothalamic neuroendocrine function; however, the exact cellular defects are unknown. Here, we report deficits in secretory granule (SG) abundance and bioactive neuropeptide production upon loss of MAGEL2 in humans and mice. Unbiased proteomic analysis of Magel2pΔ/m+ mice revealed a reduction in components of SG in the hypothalamus that was confirmed in 2 PWS patient–derived neuronal cell models. Mechanistically, we show that proper endosomal trafficking by the MAGEL2-regulated WASH complex is required to prevent aberrant lysosomal degradation of SG proteins and reduction of mature SG abundance. Importantly, loss of MAGEL2 in mice, NGN2-induced neurons, and human patients led to reduced neuropeptide production. Thus, MAGEL2 plays an important role in hypothalamic neuroendocrine function, and cellular defects in this pathway may contribute to PWS disease etiology. Moreover, these findings suggest unanticipated approaches for therapeutic intervention.
COVID-19 restrictions and mental distress among American adults: evidence from Corona Impact Survey (W1 and W2)

Abstract Background The present study examines the impact of coronavirus-related restrictions on mental health among American adults, and how this relationship varies as a function of time and two measures of vulnerability (preexisting physical symptoms and job insecurity). Methods We draw on data from two waves of Corona Impact Survey, which were fielded in late April and early of May 2020. Multilevel models were used to analyze the hierarchically nested data. Results Experiencing coronavirus disease-2019 restrictions significantly raise mental distress. This association is stronger for individuals with preexisting health conditions and those who worry about job prospects. These findings hold with the inclusion of region-wave covariates (number of deaths, wave dummy and aggregate measure of restrictions). Finally, there is a cross-level interaction: the restriction-distress connection is more pronounced in the second wave of data. Conclusions Our research indicates that people who are more physically and/or financially vulnerable suffer more from the imposed restrictions, i.e. ‘social isolation’. The mental health impact of coronavirus pandemic is not constant but conditional on the level of vulnerability.
Validation of an adapted instrument to measure female genital fistula-related stigma

ABSTRACT Female genital fistula results in severe physical, psychological, and social sequelae. Qualitative research confirms stigma pervasiveness; however, no quantitative instrument exists to measure fistula-related stigma. We adapted an existing HIV-related stigma instrument to fistula-related stigma and assessed its reliability and validity. We recruited 60 Ugandan women seeking genital fistula surgery (December 2014–June 2015). We used exploratory factor analysis to explore the scale’s latent structure and evaluated internal consistency reliability with Raykov’s ρ statistic. We assessed construct validity through linear regression of stigma with quality of life, depressive symptoms and self-esteem. We retained 15 items across factors ‘enacted stigma’ and ‘internalised stigma’ (ρ = 0.960 and ρ = 0.748, respectively). Stigma was inversely associated with all quality of life domains; effect sizes were largest for environmental (enacted stigma, 0.69-point reduction) and psychological (internalised stigma, 0.67-point reduction) domains. Both stigma domains were associated positively with depressive symptoms and inversely with self-esteem, with 0.75 and 1.05-point increases in depressive symptoms and 0.45 and 0.77-point decreases in self-esteem for enacted and internalised stigma, respectively. Results suggest the reliability and validity of the adapted fistula stigma instrument. This instrument may help us understand stigma levels, compare stigma across individuals and communities, prioritise stigma-reduction strategies, and assess intervention impact.