Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the variability of pairwise coexistence within multispecies systems

The persistence of virtually every single species depends on both the presence of other species and the heterogeneous environmental conditions. Because in natural settings many of these conditions are unknown, research has been centered on finding the fraction of possible conditions (probability) leading to species coexistence. The focus has been on the coexistence probability of two species in isolation or that of an entire multispecies system. However, it is unclear how a system can affect differently the coexistence expectation of each of its constituent pairs. Here, we derive long-term (using analytical calculations) and short-term (using simulations and experimental data) system-level indicators of the effect of multispecies systems on pairwise coexistence under unknown environmental conditions. We demonstrate that the fraction of conditions incompatible with the possible coexistence of a pair of species in isolation tends to become vanishingly small within systems of increasing numbers of species. Yet, the fraction of conditions allowing pairwise coexistence in isolation remains approximately the center of the probability distribution of pairwise coexistence across all possible systems. While the likelihood of short-term survival is always greater than or equal to that of long-term survival, we found in general stronger (resp. weaker) short-term buffering effects within systems than in isolation under negative (resp. positive) long-term effects. We show that both long-term and short-term effects of a system are not equally distributed across all of its possible pairs, but these differences can be mapped and anticipated under environmental uncertainty. Author Summary It is debated whether the frequency at which two species coexist in isolation or within a single environmental context is representative of their coexistence expectation within larger systems and across different environmental conditions. Here, using analytical calculations, simulations, and experimental data, we show how multispecies systems can provide the opportunity of pairwise coexistence regardless of whether a pair of species cannot coexist in isolation across different environmental conditions. However, we show that this opportunity is not homogeneously granted across all pairs within the same system. We provide a framework to understand and map the long-term and short-term effects that a system has on the coexistence of each of its constituent pairs. Our work can have useful applications in bio-restoration and bio-medicine subject to unknown environmental conditions.
A ripening-associated ethylene response factor ERF.D7 activates ARF2 orthologs to regulate tomato fruit ripening

Despite the obligatory nature of ethylene to climacteric fruit ripening and the identification of 77 Ethylene Response Factors (ERFs) in the tomato genome, the role of only limited ERFs has been validated in the ripening process. Here, using a comprehensive morpho-physiological, molecular and biochemical approach, we demonstrate the regulatory role of SlERF.D7 in tomato fruit ripening. The expression of SlERF.D7 positively responds to exogenous ethylene and auxin treatments, most likely in a RIN-independent manner. Overexpression of SlERF.D7 promotes ripening and its silencing has the opposite effects. Alterations in its expression modulated ethylene production, pigment accumulation, and fruit firmness. Consistently, genes involved in ethylene biosynthesis and signalling, lycopene biosynthesis, and cell wall loosening were upregulated in the overexpression lines and downregulated in RNAi lines. These transgenic lines also accumulated altered levels of IAA at late-breaker stages. A positive correlation between ARF2 orthologs transcripts and SlERF.D7 mRNA levels and the fact that ARF2A and ARF2B are direct targets of SlERF.D7 underpinned the perturbed auxin-ethylene crosstalk for the altered ripening program observed in the transgenic fruits. Overall, this study uncovers that SlERF.D7 positively regulates SlARF2A/B abundance to amalgamate auxin and ethylene signalling pathways for controlling tomato fruit ripening. Highlight The present study identifies a new ripening regulator, SlERF.D7, that controls tomato fruit ripening by activating other known-ripening regulators, SlARF2A and SlARF2B.
Aging decreases the lateralization of gravity-related effort minimization during vertical arm movements

Motor lateralization refers to differences in the neural organization of cerebral hemispheres, resulting in different control specializations between the dominant and the non-dominant motor systems. Multiple studies proposed that the dominant hemisphere is specialized for open-loop optimization-like processes. Recently, comparing arm kinematics between upward and downward movements, we found that the dominant arm outperformed the non-dominant one regarding gravity-related motor optimization in healthy young participants. The literature about aging effects on motor control presents several neurophysiological and behavioral evidences for an age-related reduction of motor lateralization. Here, we compare the lateralization of a well-known gravity-related optimal motor control process between young and older adults. Forty-one healthy young (mean age = 24.3 ± 3 years) and forty-two healthy older adults (mean age = 72.0 ± 6 years) performed single degree-of-freedom vertical arm movements between two targets (upward and downward). Participants alternatively reached with their dominant and non-dominant arms. We recorded arm kinematics and electromyographic activities of the prime movers (Anterior and Posterior Deltoids) and we analyzed parameters thought to represent the hallmark of the gravity-related optimization process (i.e directional asymmetries and negative epochs on the phasic EMG activity). We found strong age x arm interaction effects on all parameters; i.e., relative durations to peak acceleration and peak velocity and the negativity of antigravity muscles’ phasic signals. Although all three parameters showed a lateralization effect where the dominant arm was superior to the non-dominant arm in young adults (as in Poirier et al. 2022), we found no such effect in older adults. With both arms, the results of older adults lied between those of the dominant and non-dominant arm of young adults. These results add to those of recent literature showing that feedforward motor control remains functional in older adults. More, the results obtained with the non-dominant arm may support a previously hypothesized increased reliance on predictive mechanisms in older adults.
Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics

Functional magnetic resonance imaging (fMRI) with optogenetic neural manipulation is a powerful tool that enables brain-wide mapping of effective functional networks. To achieve flexible manipulation of neural excitation throughout the mouse cortex, we incorporated spatiotemporal programmable optogenetic stimuli generated by a digital micromirror device into an MR scanner via an optical fiber bundle for the first time. This approach offered versatility in space and time in planning the photostimulation pattern, combined with in situ optical imaging and cell-type or circuit-specific genetic targeting in individual mice. Brain-wide effective connectivity obtained by fMRI with optogenetic stimulation of atlas-based cortical regions is generally congruent with anatomically defined axonal tracing data but is affected by the types of anesthetics that act selectively on specific connections. fMRI combined with flexible optogenetics opens a new path to investigate dynamic changes in functional brain states in the same animal through high-throughput brain-wide effective connectivity mapping.
Networks of Phenological Synchrony Reveal a Highly Interconnected Ecosystem and Potential Vulnerability to Climate-Driven Mismatches

As anthropogenic climate change alters species’ phenology, phenological shifts may cascade to disrupt species interactions to impact ecosystem functioning. We present a 108-year phenology dataset of 8,840 event dates for 251 phenophases for seven amphibian species, 58 birds, 14 insects, and 163 plant species, including 52 species introduced to New York. The dataset was collected at a single location in the Northeastern United States, providing continuity in monitoring since the early 1900s. We show that linear phenology analyses can underestimate the magnitude of phenological shift relative to circular methods, particularly for species experiencing extreme advancements. However, species phenologies are generally advancing, with faster advancements of insects and amphibians compared to birds and plants. Additionally, in our dataset, species with event dates later in the year are advancing more rapidly than species earlier in the year, and this relationship is stronger for animals than for plants. We present a novel, network-based approach for visualizing community and ecosystem-scale phenological synchrony. Using this approach, we find a high degree of synchrony between the monitored species, and this approach reveals that plants are more central in the phenological network, as well as species with phenological events earlier in the year. While many synchronous species are shifting at relatively similar rates and display similar temperature sensitivities, we highlight two species interactions potentially vulnerable to changing climate: Eastern Tent Caterpillars and Monarchs. Our results illustrate the utility of long-term ecological monitoring for investigating ecosystem responses to climate change and identifying potentially vulnerable phenological networks. Significance Statement The purpose of this study is to understand how climate change has affected the phenology of an ecological community for over 100+ years. We present a novel approach to analyzing and visualizing community-level phenological data. We find that plants are central to phenological networks, as are species that flower, fruit, or undergo other phenological events earlier in the year. This is important because understanding which species are most central to an ecosystem, as well as which species are vulnerable to climate-driven mismatches (e.g., a butterfly emerges before the flowers that it feeds on bloom) that could cascade through an ecosystem.
Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine.
Hydrokinetic turbines for power generation in Nigerian river basins

This work presents a design for Hydrokinetic Renewable Energy (HRE), for off grid power generation for remote riverine regions in developing nations. The uniqueness of this technique for power generation using streams and other marine currents to generate electric energy is detailed. The problem of the impact of greenhouse gas emissions on the environment, rapid increase in human population, industries, modernization and our lifestyle put immense pressure on most power generation plants and infrastructures. Thus, global warming and carbon footprints of using fossil fuels to generate energy has driven the interest for energy generation from renewable sources. The Upper River Benue and Lower River Niger coastal basins, as well as the River Niger Basin on the Lower Niger sub-basin area of southeastern Nigeria was selected as a case study for the design of the hydrokinetic power generation technology. The results show that for a hydrokinetic turbine the level of power output is directly proportional to the flow velocity. Therefore the cost of its installation is reduced drastically from about $7,900 per installed kW to about $2,500 per kW, is easily assessable, less technical and a familiar motor technology for most of these communities. It is also a predictable form of energy in comparison to other emerging renewable energy fields like wind, solar and wave. Also this form of renewable energy is less harmful to the environment, has a lower noise emission and produces no greenhouse gases or any solid waste. HRE will bring energy security that is essential for the riverine dweller and curb rural urban migration and both improves the rural communities' standard of living and enhances their productivity.
Power and precision: Evaluation and recommendations of quantitative trait analysis methods for RNA expression levels in the Hybrid Rat Diversity Panel

The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of various plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power.
Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling

Abscission is the programmed separation of plant organs. It is widespread in the plant kingdom with important functions in development and environmental response. In Arabidopsis, abscission of floral organs (sepals, petals, and stamens) is controlled by two receptor-like protein kinases HAESA (HAE) and HAESA LIKE-2 (HSL2), which orchestrate the programmed dissolution of the abscission zone connecting floral organs to the developing fruit. In this work, we use single-cell RNA-Sequencing to characterize the core HAE/HSL2 abscission gene expression program. We identify the MAP KINASE PHOSPHATASE-1/MKP1 gene as a negative regulator of this pathway. MKP1 acts prior to activation of HAE/HSL2 signaling to establish a signaling threshold required for the initiation of abscission. By analogy to electrical circuit control, we liken MKP1 to a molecular grounding mechanism that dissipates errant pathway activation absent HAE/HSL2 signaling. Furthermore, we use single-cell data to identify genes expressed in two sub-populations of abscission zone cells: those proximal and those distal to the plane of separation. We identify INFLORESCENCE DEFICIENT IN ABSCISSION/IDA, encoding the activating ligand of HAE/HSL2, as one of the mRNAs most highly enriched in distal abscission zone cells at the base of the abscising organs. We show how this expression pattern forms a biophysical circuit breaker whereby, when the organ is shed, the source of the IDA peptide is removed, leading to cessation of HAE/HSL2 signaling. Overall, this work provides insight into the multiple control mechanisms acting on the abscission-signaling pathway.
Myeloid mechano-metabolic programming restricts anti-tumor immunity

Tumor progression is accompanied by fibrosis, which is associated with diminished anti-tumor immune infiltrate. Here, we demonstrate that tumor infiltrating myeloid cells respond to the stiffened fibrotic tumor microenvironment (TME) by initiating a TGF-beta (TGFβ)-directed, collagen biosynthesis program. A collateral effect of this programming is an untenable metabolic milieu for productive CD8 T cell anti-tumor responses, as collagen-synthesizing macrophages consume environmental arginine, synthesize proline, and secrete ornithine that compromises CD8+ T cell function. Thus, a stiff and fibrotic TME may impede anti-tumor immunity not only by direct physical exclusion of CD8+ T cells, but also via secondary effects of a myeloid mechano-metabolic programming we identified that creates an inhospitable metabolic milieu for CD8+ T cells.
Antibiotic-tolerant persisters are pervasive among clinical Streptococcus pneumoniae isolates and show strong condition-dependence

Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet, in S. pneumoniae nothing is known about antibiotic-tolerant persisters. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. Here, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. In optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which shows that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof-of-concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections which will set stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research. IMPORTANCE S. pneumoniae is considered a serious threat by the Centers of Disease Control and Prevention through arising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance and more specifically by antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting persistence is a general trait in S. pneumoniae cultures and that a broad range of genetic elements are controlling the phenotype. Together, our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
Autism excitation-inhibition imbalance linked to brain hyperconnectivity: An analysis based on 657 autistic subjects

The large heterogeneity in autism spectrum disorder (ASD) is a major drawback for the development of therapies. Here, we apply consensus-subtyping strategies based on functional connectivity patterns to a population of N=657 quality-assured autistic subjects. We found two major subtypes (each divided hierarchically into several minor subtypes): Subtype 1 exhibited hypoconnectivity (less average connectivity than typically developing controls) and subtype 2, hyperconnectivity. The two subtypes did not differ in structural imaging metrics in any of the regions analyzed (64 cortical and 14 subcortical), nor in any of the behavioral scores (including Intelligence Quotient, ADI and ADOS). Finally, we used the Allen Human Brain Atlas of gene transcription to show that subtype 2, corresponding with about 42% of all patients, had significant enrichment (after multiple comparisons correction) to excitation-inhibition (E/I) imbalance, a leading reported mechanism in the developmental pathophysiology of ASD. Altogether, our results support a link between E/I imbalance and brain hyperconnectivity in ASD, an association that does not exist in hypoconnected autistic subjects.
Differences in HIV, STI and Other Risk Factors Among Younger and Older Male Sex Workers Who Have Sex With Men in Nairobi, Kenya

Introduction Previous surveys of male sex workers (MSW) in sub-Saharan Africa have not fully documented the HIV and sexually transmitted infections (STIs) rates and vulnerabilities by age category. Methods The bio-behavioral survey of MSW in Nairobi, Kenya, utilized respondent-driven sampling to recruit MSW. Structured interviews captured MSW's behavioral aspects, and biological tests for HIV and other STIs. Results Analysis of the two age categories, 18–24 years (younger MSW) and 25 years and above (older MSW), shows that of all participants, a significantly higher proportion of younger MSW (59.6% crude, 69.6% RDS-adjusted) were recruited compared to older MSW (40.4% crude, 30.4% RDS-adjusted, P < 0.001). Young male sex workers were more likely to report multiple sexual partnerships in the last 12 months and had multiple receptive anal intercourses (RAI) acts in the last 30 days than older MSW: 0–2 RAI acts (20.6 vs. 8.6%, P = 0.0300), 3–5 RAI acts (26.3 vs. 11.5, P < 0.001), and >5 RAI acts (26.3 vs. 11.5%, P < 0.01). Furthermore, younger MSW were significantly more likely to have 3–5 insertive anal intercourse (IAI) with a regular male sex partner in the last 30 days than older MSW (24.3 vs. 8.0%, P < 0.01). Younger MSW were also more likely to report other STIs [28.5% (95% CI: 19.1–40.4%)] than older MSW [19.0% (95% CI: 7.7–29.2%)]. However, older MSWs were more likely to be infected with HIV than younger MSW (32.3 vs. 9.9 %, P < 0.01). Conclusions Owing to the high risk sexual behaviors, HIV and STIs risks among younger and older MSW, intensified and targeted efforts are needed on risk reduction campaigns and expanded access to services.