Miracle-dz/UniFAR-FTUs huggingface dataset:
Disruption of Folate Metabolism Causes Poor Alignment and Spacing of Mouse Conceptuses for Multiple Generations

Abnormal uptake or metabolism of folate increases risk of human pregnancy complications, though the mechanism is unclear. Here, we explore how defective folate metabolism influences early development by analysing mice with an Mtrrgt hypomorphic mutation. MTRR is necessary for methyl group utilisation from the folate cycle, and the Mtrrgt allele disrupts this process. We show that the spectrum of phenotypes previously observed in Mtrrgt/gt conceptuses at embryonic day (E) 10.5 is apparent from E8.5 including developmental delay, congenital malformations, and placental phenotypes (e.g., eccentric chorioallantoic attachment). Notably, we report misalignment of some Mtrrgt conceptuses within their implantation sites from E6.5. The degree of skewed growth occurs across a continuum, with eccentric chorioallantoic attachment now re-characterised as a severe form of conceptus misalignment. Additionally, some Mtrrgt/gt conceptuses display twinning. Therefore, we implicate folate metabolism in blastocyst orientation and spacing at implantation. Embryo development is influenced by skewed growth since developmental delay and heart malformations (but not neural tube defects) associate with severe misalignment of Mtrrgt/gt conceptuses. Patterning of trophoblast lineage markers is largely unaffected in skewed Mtrrgt/gt conceptuses at E8.5 indicating trophoblast differentiation was normal when misaligned. Typically, the uterus guides conceptus orientation. Accordingly, we manipulate the maternal Mtrr genotype and assess conceptus alignment. Mtrr+/gt, and Mtrrgt/gt mothers, plus Mtrr+/+ mothers, exhibit misaligned conceptuses at E6.5. While progesterone and/or BMP2 signalling required for decidualisation might be disrupted, normal gross decidual morphology, patterning, and blood perfusion is evident regardless of conceptus alignment, arguing against a uterine defect. Given the important finding that Mtrr+/+ mothers also display conceptus misalignment, a grandparental effect is explored. Multigenerational phenotype inheritance is characteristic of the Mtrrgt model, though the mechanism remains unclear. Genetic pedigree analysis reveals that severe skewing associates with the Mtrr genotype of either maternal grandparent. Moreover, misalignment is independent of the uterus and instead is attributed to an embryonic mechanism based on blastocyst transfer experiments. Overall, our data indicates that abnormal folate metabolism influences conceptus orientation over multiple generations with implications for subsequent development. Our study casts light on the complex role of folate metabolism during development beyond a direct maternal effect.
Integration of Biobanks in National eHealth Ecosystems Facilitating Long-Term Longitudinal Clinical-Omics Studies and Citizens' Engagement in Research Through eHealthBioR

Biobanks have long existed to support research activities with BBMRI-ERIC formed as a European research infrastructure supporting the coordination for biobanking with 20 country members and one international organization. Although the benefits of biobanks to the research community are well-established, the direct benefit to citizens is limited to the generic benefit of promoting future research. Furthermore, the advent of General Data Protection Regulation (GDPR) legislation raised a series of challenges for scientific research especially related to biobanking associate activities and longitudinal research studies. Electronic health record (EHR) registries have long existed in healthcare providers. In some countries, even at the national level, these record the state of the health of citizens through time for the purposes of healthcare and data portability between different providers. The potential of EHRs in research is great and has been demonstrated in many projects that have transformed EHR data into retrospective medical history information on participating subjects directly from their physician's collected records; many key challenges, however, remain. In this paper, we present a citizen-centric framework called eHealthBioR, which would enable biobanks to link to EHR systems, thus enabling not just retrospective but also lifelong prospective longitudinal studies of participating citizens. It will also ensure strict adherence to legal and ethical requirements, enabling greater control that encourages participation. Citizens would benefit from the real and direct control of their data and samples, utilizing technology, to empower them to make informed decisions about providing consent and practicing their rights related to the use of their data, as well as by having access to knowledge and data generated from samples they provided to biobanks. This is expected to motivate patient engagement in future research and even leads to participatory design methodologies with citizen/patient-centric designed studies. The development of platforms based on the eHealthBioR framework would need to overcome significant challenges. However, it would shift the burden of addressing these to experts in the field while providing solutions enabling in the long term the lower monetary and time cost of longitudinal studies coupled with the option of lifelong monitoring through EHRs.
Directions of Deep Brain Stimulation for Epilepsy and Parkinson’s Disease

Background Deep brain stimulation (DBS) is an effective treatment for movement disorders and neurological/psychiatric disorders. DBS has been approved for the control of Parkinson disease (PD) and epilepsy. Objectives A systematic review and possible future direction of DBS system studies is performed in the open loop and closed-loop configuration on PD and epilepsy. Methods We searched Google Scholar database for DBS system and development. DBS search results were categorized into clinical device and research system from the open-loop and closed-loop perspectives. Results We performed literature review for DBS on PD and epilepsy in terms of system development by the open loop and closed-loop configuration. This study described development and trends for DBS in terms of electrode, recording, stimulation, and signal processing. The closed-loop DBS system raised a more attention in recent researches. Conclusion We overviewed development and progress of DBS. Our results suggest that the closed-loop DBS is important for PD and epilepsy.
Pioglitazone Inhibits Diabetes-Induced Atrial Mitochondrial Oxidative Stress and Improves Mitochondrial Biogenesis, Dynamics, and Function Through the PPAR-γ/PGC-1α Signaling Pathway

Background: Oxidative stress contributes to adverse atrial remodeling in diabetes mellitus. This remodeling can be prevented by the PPAR-γ agonist pioglitazone via its antioxidant and anti-inflammatory effects. In this study, we examined the molecular mechanisms underlying the protective effects of pioglitazone on atrial remodeling in a rabbit model of diabetes. Methods: Rabbits were randomly divided into control, diabetic, and pioglitazone-treated diabetic groups. Echocardiographic, hemodynamic, and electrophysiological parameters were measured. Serum PPAR-γ levels, serum and tissue oxidative stress and inflammatory markers, mitochondrial morphology, reactive oxygen species (ROS) production rate, respiratory function, and mitochondrial membrane potential (MMP) levels were measured. Protein expression of the pro-fibrotic marker TGF-β1, the PPAR-γ coactivator-1α (PGC-1α), and the mitochondrial proteins (biogenesis-, fusion-, and fission-related proteins) was measured. HL-1 cells were transfected with PGC-1α small interfering RNA (siRNA) to determine the underlying mechanisms of pioglitazone improvement of mitochondrial function under oxidative stress. Results: The diabetic group demonstrated a larger left atrial diameter and fibrosis area than the controls, which were associated with a higher incidence of inducible atrial fibrillation (AF). The lower serum PPAR-γ level was associated with lower PGC-1α and higher NF-κB and TGF-β1 expression. Lower mitochondrial biogenesis (PGC-1α, NRF1, and TFAM)-, fusion (Opa1 and Mfn1)-, and fission (Drp1)-related proteins were detected. Mitochondrial swelling, higher mitochondrial ROS, lower respiratory control rate, and lower MMP were observed. The pioglitazone group showed a reversal of structural remodeling and a lower incidence of inducible AF, which were associated with higher PPAR-γ and PGC-1α. The pioglitazone group had lower NF-κB and TGF-β1 expression levels, whereas biogenesis-, fusion-, and fission-related protein expression was higher. Further, mitochondrial structure and function were improved. In HL-1 cells, PGC-1α siRNA transfection blunted the effect of pioglitazone on Mn-SOD protein expression and MMP collapse in H2O2-treated cells. Conclusion: Diabetes mellitus induces adverse atrial structural, electrophysiological remodeling, and mitochondrial damage and dysfunction. Pioglitazone prevented these abnormalities through the PPAR-γ/PGC-1α pathway.
Muscle Strength and Power: Primary Outcome Measures to Assess Cold Water Immersion Efficacy After Exercise With a Strong Strength or Power Component

Citation: Lindsay A and Peake JM (2021) Muscle Strength and Power: Primary Outcome Measures to Assess Cold Water Immersion Efficacy After Exercise With a Strong Strength or Power Component. Front. Sports Act. Living 3:655975. doi: 10.3389/fspor.2021. 655975 Muscle Strength and Power: Primary Outcome Measures to Assess Cold Water Immersion Efficacy After Exercise With a Strong Strength or Power Component
The Representation of Roma in the Romanian Media During COVID-19: Performing Control Through Discursive-Performative Repertoires

This article investigates the narratives employed by the Romanian media in covering the development of COVID-19 in Roma communities in Romania. This paper aims to contribute to academic literature on Romani studies, particularly in Central and Eastern Europe, by adopting as its case study the town of Ţăndărei, a small town in the south of Romania, which in early 2020 was widely reported by Romanian media during both the pre- and post-quarantine period. The contributions rest on anchoring the study in post-foundational theory and media studies to understand the performativity of Roma identity and the discursive-performative practices of control employed by the Romania media in the first half of 2020. Aroused by the influx of ethnic Romani returning from Western Europe, the Romanian mainstream media expanded its coverage through sensationalist narratives and depictions of lawlessness and criminality. These branded the ethnic minority as a scapegoat for the spreading of the virus. Relying on critical social theory, this study attempts to understand how Roma have been portrayed during the Coronavirus crisis. Simultaneously, this paper resonates with current Roma theories about media discourses maintaining and reinforcing a sense of marginality for Roma communities. To understand the dynamics of Romanian media discourses, this study employs NVivo software tools and language-in-use discourse analysis to examine the headlines and sub headlines of approximately 300 articles that have covered COVID-19 developments in Roma communities between February and July 2020. The findings from the study indicate that the media first focused on exploiting the sensationalism of the episodes involving Roma. Second, the media employed a logic of polarization to assist the authorities in retaking control of the pandemic and health crisis from Romania. The impact of the current study underlines the need to pay close attention to the dynamics of crises when activating historical patterns of stigma vis-à-vis Roma communities in Eastern Europe.
Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies

In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.
Construction of Two Alternative Polyadenylation Signatures to Predict the Prognosis of Sarcoma Patients

Background Increasing evidence indicates that alternative polyadenylation (APA) is associated with the prognosis of cancers. Methods We obtained gene expression and APA profiles of 259 sarcoma patients from the TCGA dataportal and TC3A database, respectively. The prognostic signatures, clinical nomograms, and regulatory networks were studied by integrated bioinformatics analyses. Then, the immune cell infiltration profile was obtained from the ImmuCellAI. The association between APA-based signature and immune cells was studied. Results A total of 61 and 38 APA events were identified as overall survival (OS)- and progress free-survival (PFS)-related biomarkers, respectively. Two signatures were generated. The area under the curves (AUC) values of OS signature were 0.900, 0.928, and 0.963 over 2-, 4-, and 6-years, respectively. And the AUC values of PFS signature at 2-, 4-, and 6-years were 0.826, 0.840, and 0.847, respectively. Overall and subgroup analyses indicated that high-risk patients had a worse prognosis than low-risk patients (all p-values < 0.05). In addition, immunomics analyses indicated that there are different patterns of immune cell infiltration between low- and high-risk patients. Furthermore, two clinical-APA nomograms were established and the C-indexes were 0.813 and 0.809 for OS nomogram and PFS nomogram, respectively. Finally, two APA regulatory networks were constructed. FIP1L1-VPS26B was identified as a key regulating relationship and validated in the pan-cancer analyses. Conclusion In this study, we identified prognostic predictors based on APA events with high accuracy for risk stratification in sarcoma patients and uncovered interesting regulatory networks in sarcoma that could be underlying mechanisms. This study not only provides novel potential prognostic biomarkers but promote precision medicine and provide potential novel research interests for immunotherapy.
Intra-Population Variability in Group Size of Indo-Pacific Humpback Dolphins (Sousa chinensis)

Group size is a key social trait influencing population dynamics of group-living animals. The Indo-Pacific humpback dolphins (IPHDs), Sousa chinensis, a shallow water delphinid species, display a fission-fusion social system. Yet little is known about how social organization of this species vary with temporal scales and behavioral state. In this study, we sampled group size estimates from the world’s second largest population of humpback dolphins (Sousa spp.), which inhabit the eastern waters of Zhanjiang, China. IPHD group sizes changed seasonally and inter-annually, but not with tidal phases. Group sizes also changed with behavioral state of IPHD groups and with number of mother-calf pairs present. IPHDs formed larger groups in the autumn than in other seasons, which might be related to seasonal changes in food availability and reproductive cycle. Of the groups observed, we recorded the presence of mother-calf pair in 85 groups (i.e., nursery groups: 47 ones with one pair, 25 ones with two pairs, and others with three pairs). Notably, nursery groups were about 2–4 times larger than non-nursery groups. In addition, group sizes greatly increased with the number of mother-calf pairs. Living in relatively large groups, more protection, food, and resources might be available for IPHD mothers and calves, and such social strategy provide higher reproduction efficiency and survival success for this species. During our observations, feeding (45.5%) and traveling (25.2%) represented the majority of IPHD’s behavioral budget, while socializing (8.4%) and resting/milling (6.8%) were not frequently observed. Resting/milling groups were approximately 50% smaller than feeding, traveling, or socializing groups, while the latter three types had a similar mean group size. Large groups when IPHDs foraged, traveled, or socialized, might provide more added group benefits. For the first time, our findings clearly revealed intra-population variability in IPHD group sizes across different behavioral and temporal variables, and provided a better understanding of IPHDs’ adaptations to various biological processes and ecological constraints.
NADH Fluorescence Lifetime Imaging Microscopy Reveals Selective Mitochondrial Dysfunction in Neurons Overexpressing Alzheimer’s Disease–Related Proteins

Alzheimer’s disease (AD), the most prevalent form of dementia, affects globally more than 30 million people suffering from cognitive deficits and neuropsychiatric symptoms. Substantial evidence for the involvement of mitochondrial dysfunction in the development and/or progression of AD has been shown in addition to the pathological hallmarks amyloid beta (Aβ) and tau. Still, the selective vulnerability and associated selective mitochondrial dysfunction cannot even be resolved to date. We aimed at optically quantifying mitochondrial function on a single-cell level in primary hippocampal neuron models of AD, unraveling differential involvement of cell and mitochondrial populations in amyloid precursor protein (APP)-associated mitochondrial dysfunction. NADH lifetime imaging is a highly sensitive marker-free method with high spatial resolution. However, deciphering cellular bioenergetics of complex cells like primary neurons has still not succeeded yet. To achieve this, we combined highly sensitive NADH lifetime imaging with respiratory inhibitor treatment, allowing characterization of mitochondrial function down to even the subcellular level in primary neurons. Measuring NADH lifetime of the same neuron before and after respiratory treatment reveals the metabolic delta, which can be taken as a surrogate for cellular redox capacity. Correlating NADH lifetime delta with overexpression strength of Aβ-related proteins on the single-cell level, we could verify the important role of intracellular Aβ-mediated mitochondrial toxicity. Subcellularly, we could demonstrate a higher respiration in neuronal somata in general than dendrites, but a similar impairment of somatic and dendritic mitochondria in our AD models. This illustrates the power of NADH lifetime imaging in revealing mitochondrial function on a single and even subcellular level and its potential to shed light into bioenergetic alterations in neuropsychiatric diseases and beyond.
Relationships Between Perivascular Adipose Tissue and Abdominal Aortic Aneurysms

Abdominal aortic aneurysms (AAAs) are typically asymptomatic, and there is a high mortality rate associated with aneurysm rupture. AAA pathogenesis involves extracellular matrix degradation, vascular smooth muscle cell phenotype switching, inflammation, and oxidative stress. There is increasing evidence of excessive adipocyte accumulation in ruptured AAA walls. These excessive numbers of adipocytes in the vascular wall have been closely linked with AAA progression. Perivascular adipose tissue (PVAT), a unique type of adipose tissue, can be involved in adipocyte accumulation in the AAA wall. PVAT produces various chemokines and adipocytokines around vessels to maintain vascular homeostasis through paracrine and autocrine mechanisms in normal physiological conditions. Nevertheless, PVAT loses its normal function and promotes the progression of vascular diseases in pathological conditions. There is evidence of significantly reduced AAA diameter in vessel walls of removed PVAT. There is a need to highlight the critical roles of cytokines, cells, and microRNA derived from PVAT in the regulation of AAA development. PVAT may constitute an important therapeutic target for the prevention and treatment of AAAs. In this review, we discuss the relationship between PVAT and AAA development; we also highlight the potential for PVAT-derived factors to serve as a therapeutic target in the treatment of AAAs.
A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments

Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3–V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to “Candidatus Actinomarinales,” “Candidatus Microtrichales,” and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.