Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally-mixed coastal temperate habitat

Coastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonization by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae-degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga-associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well-known alga-degrading marine flavobacterial genus in a tidally-mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low-abundance component of healthy macroalgal microbiota and can also colonize particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga-degrading bacteria that influence coastal carbon cycling. Originality-significance statement Glycan-degrading bacteria play a crucial role in marine habitats to remineralize organic carbon sequestered in algal biomass. Yet, resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we investigate the seasonal dynamics of abundance and activity of an environmentally relevant glycan-degrading bacterial genus in two constrasted compartments of the same coastal habitat, i.e. the surface of diverse macroalgae and the water column. These results provide insights into the recurring temporal patterns and environmental constraints driving natural populations of alga-degrading bacteria that influence ocean carbon cycling.
TNF-NFkB-p53 axis restricts in vivo survival of hPSC-derived dopamine neuron

Ongoing, first-in-human clinical trials illustrate the feasibility and translational potential of human pluripotent stem cell (hPSC)-based cell therapies in Parkinson’s disease (PD). However, a major unresolved challenge in the field is the extensive cell death following transplantation with <10% of grafted dopamine neurons surviving. Here, we performed a pooled CRISPR/Cas9 screen to enhance survival of postmitotic dopamine neurons in vivo. We identified p53-mediated apoptotic cell death as major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival. As a translationally applicable strategy to purify postmitotic dopamine neurons, we performed a cell surface marker screen that enabled purification without the need for genetic reporters. Combining cell sorting with adalimumab pretreatment, a clinically approved and widely used TNFa inhibitor, enabled efficient engraftment of postmitotic dopamine neurons leading to extensive re-innervation and functional recovery in a preclinical PD mouse model. Thus, transient TNFa inhibition presents a clinically relevant strategy to enhance survival and enable engraftment of postmitotic human PSC-derived dopamine neurons in PD. Highlights In vivo CRISPR-Cas9 screen identifies p53 limiting survival of grafted human dopamine neurons. TNFα-NFκB pathway mediates p53-dependent human dopamine neuron death Cell surface marker screen to enrich human dopamine neurons for translational use. FDA approved TNF-alpha inhibitor rescues in vivo dopamine neuron survival with in vivo function.
Applying Skeletons to Speed Up the Arc-Flags Routing Algorithm

The Single-Source Shortest Path problem is classically solved by applying Dijkstra’s algorithm. However, the plain version of this algorithm is far too slow for real-world applications such as routing in large road networks. To amend this, many speed-up techniques have been developed that build on the idea of computing auxiliary data in a preprocessing phase, that is used to speed up the queries. One well-known example is the Arc-Flags algorithm that is based on the idea of precomputing edge flags to make the search more goal-directed. To explain the strong practical performance of such speed-up techniques, several graph parameters have been introduced. The skeleton dimension is one such parameter that has already been used to derive runtime bounds for some speed-up techniques. Moreover, it was experimentally shown to be low in real-world road networks. We introduce a method to incorporate skeletons , the underlying structure behind the skeleton dimension, to improve routing speed-up techniques even further. As a proof of concept, we develop new algorithms called SKARF and SKARF + that combine skeletons with Arc-Flags , and demonstrate via extensive experiments on large real-world road networks that SKARF + yields a significant reduction of the search space and the query time of about 30% to 40% over Arc-Flags . We also prove theoretical bounds on the query time of SKARF , which is the first time an Arc-Flags variant has been analyzed in terms of skeleton dimension.
Gallium nitride-based light-emitting diodes with embedded air voids grown on Ar-implanted AlN/sapphire substrate

GaN-based light-emitting diodes (LEDs) grown on sapphire with ex situ AlN nucleation layer prepared by radio-frequency sputtering were investigated. GaN-based epitaxial layers grown on the Ar-implanted AlN/sapphire (AIAS) substrates exhibited selective growth and subsequent lateral growth due to the difference of lattice constants between the implanted and implantation-free regions. Consequently, air voids over the implanted regions were formed around the GaN/AlN/sapphire interfaces. We proposed the growth mechanisms of the GaN layer on the AIAS substrates and characterized the LEDs with embedded air voids. With a 20 mA current injection, experimental results indicate that the light output power of LEDs grown on the AIAS substrates was enhanced by 25% compared with those of conventional LEDs. This enhancement can be attributed to the light scattering at the GaN/air void interfaces to increase the light extraction efficiency of the LEDs.
Epileptic prediction using spatiotemporal information combined with optimal features strategy on EEG

Objective Epilepsy is the second most common brain neurological disease after stroke, which has the characteristics of sudden and recurrence. Seizure prediction is seriously important for improving the quality of patients’ lives. Methods From the perspective of multiple dimensions including time-frequency, entropy and brain network, this paper proposed a novel approach by constructing the optimal spatiotemporal feature set to predict seizures. Based on strong independence and large information capabilities, the two-dimensional feature screening algorithm is performed to eliminate unnecessary redundant features. In order to verify the effectiveness of the optimal feature set, support vector machine (SVM) was used to classify the preictal and interictal states on both the Kaggle intracranial EEG and CHB-MIT scalp EEG dataset. Results This model achieved an average accuracy of 98.01%, AUC of 0.96, F-Score of 98.3% and FPR of 0.0383/h on the Kaggle dataset; On the CHB-MIT dataset, the average accuracy, AUC, F-score and FPR were 95.93%, 0.92, 94.97% and 0.0473/h, respectively. Further ablation experiments have confirmed that the temporal and spatial features fusion has better performance than the individual temporal or spatial features. Conclusion Compared to the state-of-the-art methods, our approach outperforms most of these existing techniques. The results show that our approach can effectively extract the spatiotemporal information of epileptic EEG signals to predict epileptic seizures with high performance.
miRNA deregulation and relationship with metabolic parameters after Mediterranean dietary intervention in BRCA-mutated women

Background Breast cancer onset is determined by a genetics-environment interaction. BRCA1/2 gene alterations are often genetically shared in familial context, but also food intake and hormonal assessment seem to influence the lifetime risk of developing this neoplasia. We previously showed the relationship between a six-months Mediterranean dietary intervention and insulin, glucose and estradiol levels in BRCA1/2 carrier subjects. The aim of the present study was to evidence the eventual influence of this dietary intervention on the relationship between circulating miRNA expression and metabolic parameters in presence of BRCA1/2 loss of function variants. Methods Plasma samples of BRCA-women have been collected at the baseline and at the end of the dietary intervention. Moreover, subjects have been randomized in two groups: dietary intervention and placebo. miRNA profiling and subsequent ddPCR validation have been performed in all the subjects at both time points. Results ddPCR analysis confirmed that five (miR-185-5p, miR-498, miR-3910, miR-4423 and miR-4445) of seven miRNAs, deregulated in the training cohort, were significantly up-regulated in subjects after dietary intervention compared with the baseline measurement. Interestingly, when we focused on variation of miRNA levels in the two timepoints, it could be observed that miR-4423, miR-4445 and miR-3910 expressions are positively correlated with variation in vitaminD level; whilst miR-185-5p difference in expression is related to HDL cholesterol variation. Conclusions We highlighted the synergistic effect of a healthy lifestyle and epigenetic regulation in BC through the modulation of specific miRNAs. Different miRNAs have been reported involved in the tumor onset acting as tumor suppressors by targeting tumor-associated genes that are often downregulated.
Long-term organoid culture of a small intestinal neuroendocrine tumor

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are rare and highly heterogeneous neoplasms whose incidence has markedly increased over the last decades. A grading system based on the tumor cells’ proliferation index predicts high-risk for G3 NETs. However, low-to-intermediate grade (G1/G2) NETs have an unpredictable clinical course that varies from indolent to highly malignant. Cultures of human cancer cells enable to perform functional perturbation analyses that are instrumental to enhance our understanding of cancer biology. To date, no tractable and reliable long-term culture of G1/G2 NET has been reported to permit disease modeling and pharmacological screens. Here, we report of the first long-term culture of a G2 metastatic small intestinal NET that preserves the main genetic drivers of the tumor and retains expression patterns of the endocrine cell lineage. Replicating the tissue, this long-term culture showed a low proliferation index, and yet it could be propagated continuously without dramatic changes in the karyotype. The model was readily available for pharmacological screens using targeted agents and as expected, showed low tumorigenic capacity in vivo. Overall, this is the first long-term culture of NETs to faithfully recapitulate many aspects of the original neuroendocrine tumor.
The bioenergetic “CK Clamp” technique detects substrate-specific changes in mitochondrial respiration and membrane potential during early VML injury pathology

Volumetric muscle loss (VML) injuries are characterized by non-recoverable loss of tissue resulting in contractile and metabolic dysfunction. The characterization of metabolic dysfunction in volumetric muscle loss-injured muscle has been interpreted from permeabilized myofiber respiration experiments involving saturating ADP levels and non-physiologic ATP:ADP concentration ratios. The extent to which this testing condition obscures the analysis of mitochondrial (dys) function after volumetric muscle loss injury is unclear. An alternative approach is described that leverages the enzymatic reaction of creatine kinase and phosphocreatine to assess mitochondrial respiration and membrane potential at clamped physiologic ATP:ADP ratios, “CK Clamp. ” The objective of this study was to validate the CK Clamp in volumetric muscle loss-injured muscle and to detect differences that may exist between volumetric muscle loss-injured and uninjured muscles at 1, 3, 5, 7, 10, and 14 days post-injury. Volumetric muscle loss-injured muscle maintains bioenergetic features of the CK Clamp approach, i.e., mitochondrial respiration rate (JO2) titters down and mitochondrial membrane potential is more polarized with increasing ATP:ADP ratios. Pyruvate/malate/succinate-supported JO2 was significantly less in volumetric muscle loss-injured muscle at all timepoints compared to uninjured controls (−26% to −84%, p < 0.001) and electron conductance was less at day 1 (−60%), 5 (−52%), 7 (−35%), 10 (−59%), and 14 (−41%) (p < 0.001). Palmitoyl-carnitine/malate-supported JO2 and electron conductance were less affected following volumetric muscle loss injury. volumetric muscle loss-injury also corresponded with a more polarized mitochondrial membrane potential across the clamped ATP:ADP ratios at day 1 and 10 (pyruvate and palmitoyl-carnitine, respectively) (+5%, p < 0.001). This study supports previous characterizations of metabolic dysfunction and validates the CK Clamp as a tool to investigate bioenergetics in traumatically-injured muscle.
Education for the translation of Advanced Therapy Medicinal Products

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Differential activation of spinal and parabrachial glial cells in a neuropathic pain model

The clinical burden faced by chronic pain patients is compounded by affective comorbidities, such as depression and anxiety disorders. Emerging evidence suggests that reactive glial cells in the spinal cord dorsal horn play a key role in the chronification of pain, while supraspinal glia are important for psychological aspects of chronic pain. The lateral parabrachial nucleus (LPBN) in the brainstem is a key node in the ascending pain system, and is crucial for the emotional dimension of pain. Yet, whether astrocytes and microglia in the LPBN are activated during chronic pain is unknown. Here, we evaluated the occurrence of glial activation in the LPBN of male Sprague–Dawley rats 1, 4, and 7 weeks after inducing a chronic constriction injury (CCI) of the sciatic nerve, a prevalent neuropathic pain model. CCI animals developed mechanical and thermal hypersensitivity that persisted for at least 4 weeks, and was mostly reversed after 7 weeks. Using immunohistochemical staining and confocal imaging, we found that CCI caused a strong increase in the expression of the astrocytic marker GFAP and the microglial marker Iba1 in the ipsilateral spinal dorsal horn, with peak expression observed 1 week post-injury. Moreover, morphology analysis revealed changes in microglial phenotype, indicative of microglia activation. In contrast, CCI did not induce any detectable changes in either astrocytes or microglia in the LPBN, at any time point. Thus, our results indicate that while neuropathic pain induces a robust glial reaction in the spinal dorsal horn, it fails to activate glial cells in the LPBN.
NDRG2 regulates the formation of reactive astrocyte-derived progenitor cells via Notch signaling pathway after brain traumatic injury in rats

In response to traumatic brain injury, a subpopulation of cortical astrocytes is activated, resulting in acquisition of stem cell properties, known as reactive astrocytes-derived progenitor cells (Rad-PCs). However, the underlying mechanisms remain largely unknown during this process. In this study, we examined the role of N-myc downstream-regulated gene 2 (NDRG2), a differentiation- and stress-associated molecule, in Rad-PCs after cortical stab injury in adult rats. Immunohistochemical analysis showed that in the cerebral cortex of normal adult rats, NDRG2 was exclusively expressed in astrocytes. After liu cortical injury, the expression of NDRG2 was significantly elevated around the wound and most cells expressing NDRG2 also expressed GFAP, a reactive astrocyte marker. Importantly, NDRG2-expressing cells were co-labeled with Nestin, a marker for neural stem cells, some of which also expressed cell proliferation marker Ki67. Overexpression of NDRG2 further increased the number of NDRG2/Nestin double-labeling cells around the lesion. In contrast, shRNA knockdown of NDRG2 decreased the number of NDRG2+/Nestin+ cells. Intracerebroventricular administration of stab-injured rats with a Notch antagonist, DAPT, led to a significant decrease in Nestin+/NDRG2+ cells around the injured boundary, but did not affect NDRG2+ cells. Moreover, overexpression or knockdown of NDRG2 led to up- and down-regulation of the expression of Notch intracellular domain NICD and Notch target gene Hes1, respectively. Taken together, these results suggest that NDRG2 may play a role in controlling the formation of Rad-PCs in the cerebral cortex of adult rats following traumatic injury, and that Notch signaling pathway plays a key role in this process.
Spatial integration of dendrites in fast-spiking basket cells

Dendrites of fast-spiking basket cells (FS BCs) impact neural circuit functions in brain with both supralinear and sublinear integration strategies. Diverse spatial synaptic inputs and active properties of dendrites lead to distinct neuronal firing patterns. How the FS BCs with this bi-modal dendritic integration respond to different spatial dispersion of synaptic inputs remains unclear. In this study, we construct a multi-compartmental model of FS BC and analyze neuronal firings following simulated synaptic protocols from fully clustered to fully dispersed. Under these stimulation protocols, we find that supralinear dendrites dominate somatic firing of FS BC, while the preference for dispersing is due to sublinear dendrites. Moreover, we find that dendritic diameter and Ca2+-permeable AMPA conductance play an important role in it, while A-type K+ channel and NMDA conductance have little effect. The obtained results may give some implications for understanding dendritic computation.
Integrated ecosystem assessment around islands of the tropical South Mid-Atlantic Ridge

The South Mid Atlantic Ridge comprises three main oceanic islands in the equatorial and tropical portions of the Atlantic Ocean. These islands are isolated from each other and equidistant from both the continental margins of South America and Africa, sharing common patterns but with different types of human use and pressures. Moreover, the areas beyond national jurisdiction between those islands are visited and exploited by distant fishing fleets and include large areas of shipping activity for commodities. Here, a pioneering integrated ecosystem assessment (IEA) process is constructed for the region among Saint Peter and Saint Paul’s Archipelago (Brazil), Saint Helena Island and Ascension Island (UK overseas territories). For that, we used a qualitative assessment of risks arising from anthropogenic activities, representing a novel contribution to the field. The Options for Delivering Ecosystem-Based Marine Management (ODEMM) approach was applied to trace sector–pressure–component pathways. A ‘linkage framework’ was outlined including pressures affecting each ecosystem component, and supported a process of knowledge attributions that scored the impact risks. All results were validated with regional stakeholders through workshops, including local and international management bodies, non-governmental organizations (NGOs) and scientists. The approach focused on a significant area among encompassing the open ocean, shallow and deep-sea biomes, analyzing the main sectors and pressures affecting the ecological components. Our results identified 14 sectors and 16 key pressures associated with 23 ecosystem components, totaling 780 impact chains. Fishing, shipping, wastewater, and tourism/recreation appeared as the top impacting sectors. Fishing and shipping were the most connected with ecosystem components links. Litter, species extraction, contaminants, and bycatch were the pressures that had the highest risk of impact values. Lastly, demersal and pelagic fish and pelagic and demersal elasmobranchs were the groups with the highest risk related to overall impacts, which were supported by local and regional evidence from long term monitoring programs and local studies. Our study demonstrated that these seemingly pristine islands and oceanic waters are already experiencing human impacts that should be addressed by local both conservation measures and international agreements. We also highlight the pressures that should be prioritized for better monitoring and policy, as well as those linkage components that have been less investigated.
Impact of the treatment crossover design on comparative efficacy in EMPOWER-Lung 1: Cemiplimab monotherapy as first-line treatment of advanced non-small cell lung cancer

Objectives In randomized-controlled crossover design trials, overall survival (OS) treatment effect estimates are often confounded by the control group benefiting from treatment received post-progression. We estimated the adjusted OS treatment effect in EMPOWER-Lung 1 (NCT03088540) by accounting for the potential impact of crossover to cemiplimab among controls and continued cemiplimab treatment post-progression. Methods Patients were randomly assigned 1:1 to cemiplimab 350 mg every 3 weeks (Q3W) or platinum-doublet chemotherapy. Patients with disease progression while on or after chemotherapy could receive cemiplimab 350 mg Q3W for ≤108 weeks. Those who experienced progression on cemiplimab could continue cemiplimab at 350 mg Q3W for ≤108 additional weeks with four chemotherapy cycles added. Three adjustment methods accounted for crossover and/or continued treatment: simplified two-stage correction (with or without recensoring), inverse probability of censoring weighting (IPCW), and rank-preserving structural failure time model (RPSFT; with or without recensoring). Results In the programmed cell death-ligand 1 ≥50% population (N=563; median 10.8-month follow-up), 38.2% (n=107/280) crossed over from chemotherapy to cemiplimab (71.3%, n=107/150, among those with confirmed progression) and 16.3% (n=46/283) received cemiplimab treatment after progression with the addition of histology-specific chemotherapy (38.7%, n=46/119, among those with confirmed progression). The unadjusted OS hazard ratio (HR) with cemiplimab versus chemotherapy was 0.566 (95% confidence interval [CI]: 0.418, 0.767). Simplified two-stage correction—the most suitable method based on published guidelines and trial characteristics—produced an OS HR of 0.490 (95% CI: 0.365, 0.654) without recensoring and 0.493 (95% CI: 0.361, 0.674) with recensoring. The IPCW and RPSFT methods produced estimates generally consistent with simplified two-stage correction. Conclusions After adjusting for treatment crossover and continued cemiplimab treatment after progression with the addition of histology-specific chemotherapy observed in EMPOWER-Lung 1, cemiplimab continued to demonstrate a clinically important and statistically significant OS benefit versus chemotherapy, consistent with the primary analysis.