Miracle-dz/UniFAR-FTUs huggingface dataset:
Vulnerability, Trustworthiness, and Motivation as Emergent Themes in Cooperation With Community-Based Water Management in Southwestern Uganda

Discipline and context specific inquiries into the nature and dynamics of trust are beginning to give way to cross-boundary understandings which seek to outline its more consistent elements. Of particular note within these is an argument that trust is premised on vulnerability; that it has an important nexus with assessments of the ability, benevolence, and integrity of the trust target; and that it can also be motivated. The current work seeks to shed preliminary light on the applicability of this argument to a context in which it has not previously been examined: community-based water management in southwestern Uganda. Using a deductive, theory-driven analysis of focus group discussions with residents, we show that when our participants were simply asked to discuss their relationships with local management committees, vulnerability, ability, benevolence, and integrity consistently emerged as salient themes. Motivation, however, emerged as most salient for women. Further analysis suggests that this may have been because women are more directly involved in water provision, thereby increasing their perceived need for the resource. Our results, therefore, lend credence to the cross-boundary nature of this increasingly nuanced theoretical understanding of trust but also suggest some general guidance for improving community-based resource management efforts by providing preliminary evidence regarding the relative roles of trustworthiness and motivation.
Performance of a Superior Bradyrhizobium japonicum and a Selected Sinorhizobium fredii Strain with Soybean Cultivars

Strain 532C of Bradyrhizobium japonicum has outperformed other soybean [Glycine max (L.) Merr. ] rhizobial strains in Ontario trials conducted with cv. Evans. Strain HH303 of Sinorhizobium fredii has proven effective with some Ontario cultivars. The objective of this research was to compare the performance of 532C with that of USDA 110, CB 1809, a three-strain mixture, and HH303, by 16 commonly-grown, early-maturing soybean cultivars. Trials were conducted from 1988 to 1990 (only five cultivars were used in 1990) on soils that had low available N and had not grown soybeans previously []
Functional Relevance of Citrulline in the Vegetative Tissues of Watermelon During Abiotic Stresses

A non-protein amino acid, citrulline, is a compatible solute involved in the maintenance of cellular osmolarity during abiotic stresses. Despite its significance, a coherent model indicating the role of citrulline during stress conditions has not yet emerged. We have used watermelon, naturally rich in citrulline, as a model to understand its accumulation during drought stress and nitrogen perturbation using transcriptomic and metabolomic analysis. Experiments were performed in the semi-controlled environment, and open field to study the accumulation of drought-induced citrulline in the vegetative tissues of watermelon by monitoring the stress treatments using physiological measurements. The amino acid profiling of leaves and stems in response to drought stress showed up to a 38 and 16-fold increase in citrulline content, respectively. Correlation between amino acids indicated a concomitant activation of a metabolic pathway that included citrulline, its precursor (ornithine), and catabolic product (arginine). Consistent with its accumulation, the gene expression analysis and RNA-Sequencing confirmed activation of citrulline biosynthesis-related genes – Ornithine carbamoyl-transferase (OTC), N-acetylornithine deacetylase (AOD) and Carbamoyl phosphate synthases (CPS), and down-regulation of catabolic genes; Arginosuccinate lyase (ASL) and Arginosuccinate synthases (ASS) in drought-stressed leaf tissues. Based on the relative abundance in the nitrogen-depleted vegetative tissues and down-regulation of genes involved in citrulline biosynthesis, we also demonstrated that the nitrogen status of the plant regulates citrulline. Taken together, these data provide further insights into the metabolic and molecular mechanisms underlying the amino acid metabolism under environmental stress and the significance of non-protein amino acid citrulline in plants.
Benefits of early arrival at breeding grounds vary between males

Summary 1. It is often assumed that, in migratory birds, males of highest phenotypic quality are the first to arrive at breeding grounds, as only males in good body condition can afford the costs of early arrival. Here it is argued that variation in how much an individual can gain from being early may sometimes override these patterns of condition dependence. Benefits from early arrival will depend on how good the chances of an individual are of successfully occupying and defending a high-quality territory. Other studies have shown that these chances depend on male resource-holding power (RHP) and on value asymmetries (VA), as resulting from prior ownership. 2. Patterns of spring arrival were studied in a polygynous population of the dusky warbler Phylloscopus fuscatus Blyth, a species with high breeding-site tenacity. During the period of postnuptial moult, just before departure to winter quarters, about half of the males preoccupied and vigorously defended high-quality territories. Apparently these males enhanced their success in competition over these territories in the following breeding season by taking advantage of having prior ownership. 3. Males with good chances of obtaining a high-quality territory (i.e. males that had occupied such territories before) were the first to arrive in spring, suggesting that high motivation drives early arrival. In contrast, there was no indication for male quality or body condition to affect arrival patterns. 4. Interestingly, males of small body size, possibly reflecting low RHP, invested more in gaining prior ownership than did large males. 5. The present study suggests that, in some species, individual variation in benefits rather than in costs resulting from early arrival determine which males are the first to arrive.
Population genomic evidence of a Southeast Asian origin of Plasmodium vivax

Plasmodium vivax is the most prevalent and widespread human malaria parasite, with almost three billion people living at risk of infection. With the discovery of its closest genetic relatives in African great apes (Plasmodium vivax-like), the origin of P. vivax has been proposed to be located in the sub-Saharan African area. However, the limited number of genetic markers and samples investigated questioned the robustness of this result. Here, we examined the population genomic variation of 447 human P. vivax strains and 19 ape P. vivax-like strains originating from 24 different countries across the world. We identified 2,005,455 high quality single-nucleotide polymorphism loci allowing us to conduct an extensive characterization to date of P. vivax worldwide genetic variation. Phylogenetic relationships between human and ape Plasmodium revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like. By investigating a variety of aspects of P. vivax variation, we identified several striking geographical patterns in summary statistics as function of increasing geographic distance from Southeast Asia, suggesting that P. vivax may derived from serial founder effects from a single origin located in Asia.
On-farm selection for quality and resistance to pest/diseases of cocoa in Sulawesi: (ii) quality and performance of selections against Phytophthora pod rot and vascular-streak dieback

The cocoa industry in Sulawesi, the main region of cocoa production in Indonesia, is threatened by destructive diseases, including vascular-streak dieback (VSD) caused by the basidiomycete Oncobasidium theobromae and stem canker and Phytophthora pod rot (PPR) or black pod, caused by Phytophthora palmivora. Using the considerable genetic diversity of cocoa on farms, host resistance was identified and tested with the participation of farmers. Forty-nine local and international cocoa selections with promising resistance characteristics (as well as susceptible controls) were side-grafted onto mature cocoa in a replicated trial with single-tree plots. Developing grafts were assessed in the dry season for severity of VSD infection, scored from 0 (no infection) to 4 (graft death). All of the 49 clones in the trial became infected with VSD in at least some replicates. Average severity varied from 0.2 to 1.6. Potential VSD-resistance was found in eight clones, including DRC 15, KA2 106 and a local Sulawesi selection, VSD2Ldg. Some of the most susceptible clones were local Sulawesi selections from areas with a history of little or no VSD. Thirty-four pod-bearing clones were evaluated over a 2-year period for yield, quality and resistance to natural infections of PPR. Cumulative PPR incidence for all clones was 22% but varied from 8.6 to 43% among clones. Clones with less than 15% PPR incidence were designated as resistant, including DRC 16 and local Sulawesi selections, Aryadi 1, Aryadi 3 and VSD1Ldg. Scavina 12 was moderately resistant in the trial with a PPR incidence of 23%. Cumulative incidences of the mirid, Helopeltis spp. , determined in the same evaluation period, indicated that DRC16 was the most susceptible clone with an incidence of 52% in ripe pods and 23% in immature pods. In comparison, KKM4 showed evidence of resistance to Helopeltis spp. , with incidences of 34 and 0.8% in ripe and immature pods, respectively. The impact of diseases and pests (including cocoa pod borer) on bean losses and bean quality varied between clones but generally the bean size (or bean count) was affected more than the fat content or shell content.
Antibody repertoire and gene expression dynamics of diverse human B cell states during affinity maturation

In response to antigen challenge, B cells clonally expand, undergo selection and differentiate to produce mature B cell subsets and high affinity antibodies. However, the interplay between dynamic B cell states and their antibody-based selection is challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells undergoing affinity maturation. We define unique gene expression and antibody repertoires of known and novel B cell states, including a pre-germinal centre state primed to undergo class switch recombination. We dissect antibody class-dependent gene expression of germinal centre and memory B cells to find that class switching prior to germinal centre entry dictates the capacity of B cells to undergo antibody-based selection and differentiate. Together, our analyses provide unprecedented resolution into the gene expression and selection dynamics that shape B cell-mediated immunity.
Serum levels and tumour expression of leptin and leptin receptor as promising clinical biomarkers of specific feline mammary carcinoma subtypes

Obesity is a risk factor for human breast cancer, being associated with increased serum levels of leptin. In cat, although obesity is a common nutritional disorder, the role of leptin and its receptor in mammary carcinoma is unknown. In this study, serum levels of leptin and leptin receptor (ObR) were evaluated in 58 cats with mammary carcinoma and compared with healthy controls by ELISA, as tumour expression by immunohistochemistry. Results showed that the free leptin index is decreased in cats with mammary carcinoma (p=0.0006), particularly for those with luminal B and HER2-positive disease that showed significantly lower serum leptin levels (p<0.0001 and p<0.005, respectively). Serum leptin levels above 4.17 pg/mL were associated with ulcerating tumours (p=0.0005) and shorter DFS (p=0.0217). Elevated serum ObR levels were found in all cats with mammary carcinoma (p<0.0001), with levels above 16.89 ng/mL being associated with smaller tumours (p=0.0118), ER-negative status in HER2-positive tumours (p=0.0291) and increased serum levels of CTLA-4 (p=0.0056), TNF-α (p=0.0025), PD-1 (p=0.0023) and PD-L1 (p=0.0002). In tumour samples, leptin was overexpressed in luminal B and triple-negative carcinomas (p=0.0046), whereas ObR was found overexpressed in luminal B samples (p=0.0425). Altogether, our results reinforce the importance of feline mammary carcinoma in comparative oncology.
Drosophila suzukii oxidative stress response involves Jheh gene cluster but not transposable elements

The study of the mechanisms involved in adaptation remains a timely issue, particularly in the context of global changes. To better understand these mechanisms of rapid adaptation, invasive species are a good model because they are subjected to new and/or different environmental factors. Using different lines of different geographical origin of the invasive pest Drosophila suzukii, we characterized the phenotypic response to oxidative stress. Subsequently, we tested the involvement of the Jheh gene cluster in this response and the possible role of transposable elements. We show that the resistance to oxidative stress of the lines appears to be related to their invasive status and we confirm the role of the Jheh gene cluster in this response. We have not identified any transposable elements in this gene region that could influence the expression of the gene. Summary statement The responses to oxidative stress of the invasive species, Drosophila suzukii, show variability between genotypes related to their invasion status. The genes of the juvenile hormone epoxide hydrolase cluster are involved in this response.
Robust gene expression-based classification of cancers without normalization

Binary classification using gene expression data is commonly used to stratify cancers into molecular subgroups that may have distinct prognoses and therapeutic options. A limitation of many such methods is the requirement for comparable training and testing data sets. Here, we describe and demonstrate a self-training implementation of probability ratio-based classification prediction score (PRPS-ST) that facilitates the porting of existing classification models to other gene expression data sets. We demonstrate its robustness through application to two binary classification problems in diffuse large B-cell lymphoma using a diverse variety of gene expression data types and normalization methods.
Spectrin-based Membrane Mechanics Is Asymmetric and Remodels during Neural Development

Perturbation of spectrin-based membrane mechanics causes hereditary elliptocytosis and spinocerebellar ataxia, but the underlying cellular basis of pathogenesis remains unclear. Here, we introduced the conserved disease-associated spectrin mutations into the C. elegans genome and studied the contribution of spectrin to neuronal migration and dendrite formation in developing larvae. The loss of spectrin generates an ectopic actin polymerization outside of the existing front and secondary membrane protrusions, leading to defective neuronal positioning and dendrite morphology in adult animals. Spectrin accumulates in the lateral and the rear of migrating neuroblasts and redistributes from the soma into the newly formed dendrites, indicating that the spectrin-based membrane skeleton is asymmetric and remodels to regulate actin assembly and cell shape during development. We affinity-purified spectrin from C. elegans and showed that its binding partner ankyrin functions with spectrin. Asymmetry and remodeling of membrane skeleton may enable spatiotemporal modulation of membrane mechanics for distinct developmental events. Significance Statement The biomechanical regulation of neural development is largely unknown. The spectrin-based membrane skeleton is essential for the structural integrity of the plasma membrane. This study addresses the function and behavior of spectrin in neuroblast migration and dendrite formation. The loss of spectrin generates an ectopic actin polymerization outside of the existing front, leading to defective neuronal positioning and dendrite morphology. Spectrin is absent from the leading edge but accumulates in the posterior of migrating neuroblasts and redistributes from the soma into the nascent dendrites, indicating that the membrane skeleton is asymmetric and remodels. Asymmetry and remodeling of the membrane skeleton may enable spatiotemporal modulation of membrane mechanics for distinct developmental events.
Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence

Significance Turbulence has long been known to drive phytoplankton fitness and species succession: motile species dominate in calmer environments and non-motile species in turbulent conditions. Yet a mechanistic understanding of the effect of turbulence on phytoplankton migratory behavior and physiology is lacking. By combining a method to generate turbulent cues, quantification of stress accumulation and physiology, and a mathematical model of stress dynamics, we show that motile phytoplankton use their mechanical stability to sense the intensity of turbulent cues and integrate these cues in time via stress signaling to trigger switches in migratory behavior. The stress-mediated warning strategy we discovered provides a paradigm for how phytoplankton cope with turbulence, thereby potentially governing which species will be successful in a changing ocean. Turbulence is an important determinant of phytoplankton physiology, often leading to cell stress and damage. Turbulence affects phytoplankton migration both by transporting cells and by triggering switches in migratory behavior, whereby vertically migrating cells can actively invert their direction of migration upon exposure to turbulent cues. However, a mechanistic link between single-cell physiology and vertical migration of phytoplankton in turbulence is currently missing. Here, by combining physiological and behavioral experiments with a mathematical model of stress accumulation and dissipation, we show that the mechanism responsible for the switch in the direction of migration in the marine raphidophyte Heterosigma akashiwo is the integration of reactive oxygen species (ROS) signaling generated by turbulent cues. Within timescales as short as tens of seconds, the emergent downward-migrating subpopulation exhibited a twofold increase in ROS, an indicator of stress, 15% lower photosynthetic efficiency, and 35% lower growth rate over multiple generations compared to the upward-migrating subpopulation. The origin of the behavioral split as a result of a bistable oxidative stress response is corroborated by the observation that exposure of cells to exogenous stressors (H2O2, UV-A radiation, or high irradiance), in lieu of turbulence, caused comparable ROS accumulation and an equivalent split into the two subpopulations. By providing a mechanistic link between the single-cell mechanics of swimming and physiology on the one side and the emergent population-scale migratory response and impact on fitness on the other, the ROS-mediated early warning response we discovered contributes to our understanding of phytoplankton community composition in future ocean conditions.
LRRK2-phosphorylated Rab10 sequesters Myosin Va with RILPL2 during ciliogenesis blockade

Pathogenic LRRK2 phosphorylation of Rab10 GTPase dramatically redistributes Myosin Va and RILPL2 proteins to the mother centriole and sequesters Myosin Va at that location in a manner that likely interferes with its role in ciliogenesis. Activating mutations in LRRK2 kinase causes Parkinson’s disease. Pathogenic LRRK2 phosphorylates a subset of Rab GTPases and blocks ciliogenesis. Thus, defining novel phospho-Rab interacting partners is critical to our understanding of the molecular basis of LRRK2 pathogenesis. RILPL2 binds with strong preference to LRRK2-phosphorylated Rab8A and Rab10. RILPL2 is a binding partner of the motor protein and Rab effector, Myosin Va. We show here that the globular tail domain of Myosin Va also contains a high affinity binding site for LRRK2-phosphorylated Rab10. In the presence of pathogenic LRRK2, RILPL2 and MyoVa relocalize to the peri-centriolar region in a phosphoRab10-dependent manner. PhosphoRab10 retains Myosin Va over pericentriolar membranes as determined by fluorescence loss in photobleaching microscopy. Without pathogenic LRRK2, RILPL2 is not essential for ciliogenesis but RILPL2 over-expression blocks ciliogenesis in RPE cells independent of tau tubulin kinase recruitment to the mother centriole. These experiments show that LRRK2 generated-phosphoRab10 dramatically redistributes a significant fraction of Myosin Va and RILPL2 to the mother centriole in a manner that likely interferes with Myosin Va’s role in ciliogenesis.
Colonisation bactérienne de différents types d'aliments incubés in sacco dans le rumen ; conséquences pour l'estimation de la dégradabilité de l'azote

La population bactérienne du rumen est constituée en majorité de bactéries fixées aux particules alimentaires. Nous avons voulu déterminer in sacco les différences entre aliments, fourrages et concentrés, dans la cinétique et l’importance de cette colonisation bactérienne après différents temps d’incubation dans le rumen, et ses conséquences sur l’estimation de la dégradabilité de l’azote alimentaire.
Testosterone induces a female ornament followed by enhanced territoriality in a tropical songbird

We know little of the proximate mechanisms underlying expression of signaling traits in female vertebrates. Across males the expression of sexual and competitive traits, including ornamentation and aggressive behavior, is often mediated by testosterone. In the White-shouldered Fairywren (Malurus alboscapulatus) of New Guinea, females of different subspecies differ in presence or absence of white shoulder patches and melanic plumage, while males are uniformly ornamented. Previous work has shown that ornamented females circulate more testosterone and exhibit more territorial aggression than do unornamented females. We investigated the degree to which testosterone regulates expression of ornamental plumage and territorial behavior by implanting free-living unornamented females with testosterone. Every testosterone-treated female produced a male-like cloacal protuberance, and 15 of 20 replaced plucked brown feathers with white shoulder patch feathers, but did not produce melanic plumage characteristic of ornamented females. Testosterone treatment did not elevate territorial behavior prior to production of the plumage ornament and exhaustion of the implant. However, females with experimentally induced ornamentation, but exhausted implants, increased the vocal components of territory defense relative to fully unornamented control and also to testosterone-implanted females. Our results suggest that testosterone induces partial acquisition of the ornamental plumage phenotype, and that ornament expression, rather than testosterone alone, results in elevated territorial behavior. Lay Summary Testosterone regulates expression of a suite of competitive traits in male organisms and could have similar function in females. Empirical tests are needed to determine the extent to which testosterone promotes production of ornamentation and competitive behaviors in female animals. We supplemented testosterone in unornamented females of a species where naturally occurring ornamented females circulate higher testosterone and are more territorially aggressive. Implanted females produced partial ornamentation, which was followed by increased territoriality that was apparently unrelated to testosterone circulation itself.
Fatty acid composition of developing soybeans

La composition en acides gras et la teneur totale en acides gras libres de 7 cultivars de soja au cours du developpement des graines a partir du 45e jour apres floraison jusqu'au 75e jour et a intervalles de 10 jours, ont ete determinees. Dans presque tous les cultivars, les teneurs en acides palmitique, stearique et oleique et la teneur totale en acides gras libres diminuent au cours de la maturation des graines alors que les teneurs en acides linoleique et linolenique augmentent