Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary morphology of two island-endemic murid rodent clades is consistent with persistent, incumbent-imposed competitive interactions

A lineage colonizing a geographic region with no competitors may exhibit rapid diversification due to greater ecological opportunity. The resultant species diversity of this primary-colonizing (incumbent) clade may limit subsequent lineages' ability to persist unless these non-incumbent lineages are ecologically distinct. We compare the diversity in diet-related mandibular morphology of two sympatric murid rodent clades endemic to Luzon Island, Philippines—incumbent Phloeomyini and secondary-colonizing Chrotomyini—to the mandibular morphological diversity of Sahul Hydromyini, the sister clade of Chrotomyini and the incumbent murid lineage on the supercontinent of Sahul. This three-clade comparison allows us to test the hypothesis that incumbent lineages can force persistent ecological distinction of subsequent colonists at the time of colonization and throughout the subsequent history of the two sympatric clades. We find that Chrotomyini forms a subset of the diversity of their clade plus Sahul Hydromyini that minimizes overlap with Phloeomyini. We also infer that this differentiation extends to the stem ancestor of Chrotomyini and Sahul Hydromyini, consistent with a biotic filter imposed by Phloeomyini. Our work illustrates that incumbency has the potential to have a profound influence on the ecomorphological diversity of colonizing lineages at the island scale even when the traits in question are evolving at similar rates among independently colonizing clades.
Population variability under stressors is dependent on body mass growth and asymptotic body size

The recruitment and biomass of a fish stock are influenced by their environmental conditions and anthropogenic pressures such as fishing. The variability in the environment often translates into fluctuations in recruitment, which then propagate throughout the stock biomass. In order to manage fish stocks sustainably, it is necessary to understand their dynamics. Here, we systematically explore the dynamics and sensitivity of fish stock recruitment and biomass to environmental noise. Using an age-structured and trait-based model, we explore random noise (white noise) and autocorrelated noise (red noise) in combination with low to high levels of harvesting. We determine the vital rates of stocks covering a wide range of possible body mass (size) growth rates and asymptotic size parameter combinations. Our study indicates that the variability of stock recruitment and biomass are probably correlated with the stock's asymptotic size and growth rate. We find that fast-growing and large-sized fish stocks are likely to be less vulnerable to disturbances than slow-growing and small-sized fish stocks. We show how the natural variability in fish stocks is amplified by fishing, not just for one stock but for a broad range of fish life histories.
Poultry Coccidiosis: Design and Interpretation of Vaccine Studies

Eimeria infection impacts upon chicken welfare and economic productivity of the poultry sector. Live coccidiosis vaccines for chickens have been available for almost 70 years, but the requirement to formulate blends of oocysts from multiple Eimeria species makes vaccine production costly and logistically demanding. A multivalent vaccine that does not require chickens for its production and can induce protection against multiple Eimeria species is highly desirable. However, despite the identification and testing of many vaccine candidate antigens, no recombinant coccidiosis vaccine has been developed commercially. Currently, assessment of vaccine efficacy against Eimeria, and the disease coccidiosis, can be done only through in vivo vaccination and challenge experiments but the design of such studies has been highly variable. Lack of a “standard” protocol for assessing vaccine efficacy makes comparative evaluations very difficult, complicating vaccine development, and validation. The formulation and schedule of vaccination, the breed of chicken and choice of husbandry system, the species, strain, magnitude, and timing of delivery of the parasite challenge, and the parameters used to assess vaccine efficacy all influence the outcomes of experimental trials. In natural Eimeria infections, the induction of strong cell mediated immune responses are central to the development of protective immunity against coccidiosis. Antibodies are generally regarded to be of lesser importance. Unfortunately, there are no specific immunological assays that can accurately predict how well a vaccine will protect against coccidiosis (i.e., no “correlates of protection”). Thus, experimental vaccine studies rely on assessing a variety of post-challenge parameters, including assessment of pathognomonic lesions, measurements of parasite replication such as oocyst output or quantification of Eimeria genomes, and/or measurements of productivity such as body weight gain and feed conversion rates. Understanding immune responses to primary and secondary infection can inform on the most appropriate immunological assays. The discovery of new antigens for different Eimeria species and the development of new methods of vaccine antigen delivery necessitates a more considered approach to assessment of novel vaccines with robust, repeatable study design. Careful consideration of performance and welfare factors that are genuinely relevant to chicken producers and vaccine manufacturers is essential.
The Role of Gut Microbiota and Environmental Factors in Type 1 Diabetes Pathogenesis

Type 1 Diabetes (T1D) is regarded as an autoimmune disease characterized by insulin deficiency resulting from destruction of pancreatic β-cells. The incidence rates of T1D have increased worldwide. Over the past decades, progress has been made in understanding the complexity of the immune response and its role in T1D pathogenesis, however, the trigger of T1D autoimmunity remains unclear. The increasing incidence rates, immigrant studies, and twin studies suggest that environmental factors play an important role and the trigger cannot simply be explained by genetic predisposition. Several research initiatives have identified environmental factors that potentially contribute to the onset of T1D autoimmunity and the progression of disease in children/young adults. More recently, the interplay between gut microbiota and the immune system has been implicated as an important factor in T1D pathogenesis. Although results often vary between studies, broad compositional and diversity patterns have emerged from both longitudinal and cross-sectional human studies. T1D patients have a less diverse gut microbiota, an increased prevalence of Bacteriodetes taxa and an aberrant metabolomic profile compared to healthy controls. In this comprehensive review, we present the data obtained from both animal and human studies focusing on the large longitudinal human studies. These studies are particularly valuable in elucidating the environmental factors that lead to aberrant gut microbiota composition and potentially contribute to T1D. We also discuss how environmental factors, such as birth mode, diet, and antibiotic use modulate gut microbiota and how this potentially contributes to T1D. In the final section, we focus on existing recent literature on microbiota-produced metabolites, proteins, and gut virome function as potential protectants or triggers of T1D onset. Overall, current results indicate that higher levels of diversity along with the presence of beneficial microbes and the resulting microbial-produced metabolites can act as protectors against T1D onset. However, the specifics of the interplay between host and microbes are yet to be discovered.
Characterization of the bZIP Transcription Factor Family in Pepper (Capsicum annuum L.): CabZIP25 Positively Modulates the Salt Tolerance

The basic leucine zipper (bZIP) proteins compose a family of transcription factors (TFs), which play a crucial role in plant growth, development, and abiotic and biotic stress responses. However, no comprehensive analysis of bZIP family has been reported in pepper (Capsicum annuum L.). In this study, we identified and characterized 60 bZIP TF-encoding genes from two pepper genomes. These genes were divided into 10 groups based on their phylogenetic relationships with bZIP genes from Arabidopsis. Six introns/exons structural patterns within the basic and hinge regions and the conserved motifs were identified among all the pepper bZIP proteins, on the basis of which, we classify them into different subfamilies. Based on the transcriptomic data of Zunla-1 genome, expression analyses of 59 pepper bZIP genes (not including CabZIP25 of CM334 genome), indicated that the pepper bZIP genes were differentially expressed in the pepper tissues and developmental stages, and many of the pepper bZIP genes might be involved in responses to various abiotic stresses and phytohormones. Further, gene expression analysis, using quantitative real-time PCR (qRT-PCR), showed that the CabZIP25 gene was expressed at relatively higher levels in vegetative tissues, and was strongly induced by abiotic stresses and phytohormones. In comparing with wild type Arabidopsis, germination rate, fresh weight, chlorophyll content, and root lengths increased in the CabZIP25-overexpressing Arabidopsis under salt stress. Additionally, CabZIP25-silenced pepper showed lower chlorophyll content than the control plants under salt stress. These results suggested that CabZIP25 improved salt tolerance in plants. Taken together, our results provide new opportunities for the functional characterization of bZIP TFs in pepper.
Predisposition to Alzheimer’s and Age-Related Brain Pathologies by PM2.5 Exposure: Perspective on the Roles of Oxidative Stress and TRPM2 Channel

Accumulating epidemiological evidence supports that chronic exposure to ambient fine particular matters of <2.5 μm (PM2.5) predisposes both children and adults to Alzheimer’s disease (AD) and age-related brain damage leading to dementia. There is also experimental evidence to show that PM2.5 exposure results in early onset of AD-related pathologies in transgenic AD mice and development of AD-related and age-related brain pathologies in healthy rodents. Studies have also documented that PM2.5 exposure causes AD-linked molecular and cellular alterations, such as mitochondrial dysfunction, synaptic deficits, impaired neurite growth, neuronal cell death, glial cell activation, neuroinflammation, and neurovascular dysfunction, in addition to elevated levels of amyloid β (Aβ) and tau phosphorylation. Oxidative stress and the oxidative stress-sensitive TRPM2 channel play important roles in mediating multiple molecular and cellular alterations that underpin AD-related cognitive dysfunction. Documented evidence suggests critical engagement of oxidative stress and TRPM2 channel activation in various PM2.5-induced cellular effects. Here we discuss recent studies that favor causative relationships of PM2.5 exposure to increased AD prevalence and AD- and age-related pathologies, and raise the perspective on the roles of oxidative stress and the TRPM2 channel in mediating PM2.5-induced predisposition to AD and age-related brain damage.
Current Progress in Particle-Based Systems for Transdermal Vaccine Delivery

Transcutaneous immunization (TCI) via needle-free and non-invasive drug delivery systems is a promising approach for overcoming the current limitations of conventional parenteral vaccination methods. The targeted access to professional antigen-presenting cell (APC) populations within the skin, such as Langerhans cells (LCs), various dermal dendritic cells (dDCs), macrophages, and others makes the skin an ideal vaccination site to specifically shape immune responses as required. The stratum corneum (SC) of the skin is the main penetration barrier that needs to be overcome by the vaccine components in a coordinated way to achieve optimal access to dermal APC populations that induce priming of T-cell or B-cell responses for protective immunity. While there are numerous approaches to penetrating the SC, such as electroporation, sono- or iontophoresis, barrier and ablative methods, jet and powder injectors, and microneedle-mediated transport, we will focus this review on the recent progress made in particle-based systems for TCI. This particular approach delivers vaccine antigens together with adjuvants to perifollicular APCs by diffusion and deposition in hair follicles. Different delivery systems including nanoparticles and lipid-based systems, for example, solid nano-emulsions, and their impact on immune cells and generation of a memory effect are discussed. Moreover, challenges for TCI are addressed, including timely and targeted delivery of antigens and adjuvants to APCs within the skin as well as a deeper understanding of the ill-defined mechanisms leading to the induction of effective memory responses.
On the Nature of the Mother-Infant Tie and Its Interaction With Freudian Drives

The affective bond between an infant and its caregiver, the so-called mother-infant tie, was analyzed by various reputable psychologists (e.g., Ainsworth, Clark, Erikson, Anna Freud, Harlow, Klein, Spitz, and Winnicott) but both the basic tenets of the bond and the importance of the trauma of maternal deprivation for personality disorders in adults were introduced by Bowlby. Although Bowlby was a trained psychoanalyst, he rejected central cornerstones of Freudian theory (esp. drive theory) and used concepts promulgated by renowned ethologists (Tinbergen and Lorenz) to establish his framework of “instinctive behavior” that has been developed further into the concept of “attachment theory” under the influence of Mary Ainsworth. However, since any precise experimental facts were lacking when Bowlby formulated his ideas on the concept of instinctive behavior, the whole framework is a descriptive, category-driven approach (like the ones of Freudian drives). In order to connect the mother-infant tie – as propounded by Bowlby – with experimental data, this manuscript undertakes a biochemical analysis of it because this strategy proved somewhat successful in relation to Freudian drives. The analysis unfolded that the neurochemical oxytocin, released by the action of sensory nerves, is of utmost importance for the operation of the mother-infant tie. Furthermore, multiple evidences have been presented to the fact that there is strong interaction between unconsciously operating Freudian drives and the consciously acting mother-infant tie (that is now classified as a drive). The outlined interaction in conjunction with the classification of attachment urges as drives gave a very detailed insight into how a SEEKING-derived reward can be evoked during operation of the mother-infant tie. In summary, there is no need to marginalize either the mother-infant tie or Freudian drives but rather there is need to respect both (principally different) impulses in moving toward a more extensive description.
Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content

Secondary metabolites of the flavonoid pathway participate in plant defense, and bHLH and MYB transcription factors regulate the synthesis of these metabolites. Here, we define the regulatory mechanisms in response to pathogens. Two transcription factors from Populus alba var. pyramidalis, PalbHLH1 and PalMYB90, were overexpressed together in poplar, and transcriptome analysis revealed differences in response to pathogen infection. The transgenic plants showed elevated levels of several key flavonoid pathway components: total phenols, proanthocyanidins (PAs), and anthocyanins and intermediates quercetin and kaempferol. Furthermore, PalbHLH1 and PalMYB90 overexpression in poplar enhanced antioxidase activities and H2O2 release and also increased resistance to Botrytis cinerea and Dothiorella gregaria infection. Gene expression profile analysis showed most genes involved in the flavonoid biosynthesis pathway or antioxidant response to be upregulated in MYB90/bHLH1-OE poplar, but significant differential expression occurred in response to pathogen infection. Specifically, expression of PalF3H (flavanone 3-hydroxylase), PalDFR (dihydroflavonol 4-seductase), PalANS (anthocyanin synthase), and PalANR (anthocyanin reductase), which function in initial, middle, and final steps of anthocyanin and PA biosynthesis, respectively, was significantly upregulated in D. gregaria-infected MYB90/bHLH1-OE poplar. Our results highlight that PalbHLH1 and PalMYB90 function as transcriptional activators of flavonoid pathway secondary-metabolite synthesis genes, with differential mechanisms in response to bacterial or fungal infection.
Efficiency in Magnocellular Processing: A Common Deficit in Neurodevelopmental Disorders

Several neurodevelopmental disorders (NDDs) including Developmental Dyslexia (DD), Autism Spectrum Disorder (ASD), but not Attention Deficit Hyperactive Disorder (ADHD), are reported to show deficits in global motion processing. Such behavioral deficits have been linked to a temporal processing deficiency. However, to date, there have been few studies assessing the temporal processing efficiency of the Magnocellular M pathways through temporal modulation. Hence, we measured achromatic flicker fusion thresholds at high and low contrast in nonselective samples of NDDs and neurotypicals (mean age 10, range 7–12 years, n = 71) individually, and group matched, for both chronological age and nonverbal intelligence. Autistic tendencies were also measured using the Autism-Spectrum Quotient questionnaire as high AQ scores have previously been associated with the greater physiological amplitude of M-generated nonlinearities. The NDD participants presented with singular or comorbid combinations of DD, ASD, and ADHD. The results showed that ASD and DD, including those with comorbid ADHD, demonstrated significantly lower flicker fusion thresholds (FFTs) than their matched controls. Participants with a singular diagnosis of ADHD did not differ from controls in the FFTs. Overall, the entire NDD plus control populations showed a significant negative correlation between FFT and AQ scores (r = −0.269, p < 0.02 n = 71). In conclusion, this study presents evidence showing that a temporally inefficient M pathway could be the unifying network at fault across the NDDs and particularly in ASD and DD diagnoses, but not in singular diagnosis of ADHD.
School Violence Among a Nationally Representative Sample of Adolescents in Chile

Background: School violence is widely acknowledged as a public health problem with considerable consequences on student learning and social development. There are also a wide range of health consequences. A large share of previous research on school violence has focused on populations in the global north, with significant gaps in the state of knowledge in the world's emerging economies. To this end, the present study provides an examination of correlates for school-based violence in Chile using a nationally representative cohort. Methods: Six independent variables were considered (age, sex, physical activity, sedentary life style, bullying victimization, food insecurity) within a logistic regression model to ascertain the strength and direction of associations with physical fighting. Results: Among the surveyed students, ~13.08% reported being involved in two or more physical fights during the twelve month recall period. Males were significantly over represented among those reporting being involved in a fight OR 2.91 (CI = 1.98–4.27). Those who reported experiencing food insecurity were 5.29 (CI = 1.43–19.50) times more likely to have been involved in a physical fight. Students who reported being bullied were 2.41 (CI = 1.67–3.47) times more likely to have been involved in physical fights. While age provided protection from involvement in physical fights with an adjusted odds ratio of 0.91 (CI = 0.84–0.98). Conclusion: Consistent with previous research, our results suggest that the use of school-based interventions that target multiple risk behaviors may be helpful in reducing rates of physical fighting.
Needle Fasciotomy or Collagenase Injection in the Treatment of Dupuytren’s Contracture: A Retrospective Study

Background: Dupuytren’s contracture is common among older people in Sweden. Previous studies comparing the treatment with an injection of collagenase with percutaneous needle fasciotomy found no differences. Methods: We retrospectively compared the degree of improvement in the deficit in extension of the joints in 2 groups of patients who had been treated with collagenase (71 fingers) or needle fasciotomy (109 fingers) before and 1 year after treatment. We compared the improvement of the extension deficit among the metacarpophalangeal (MCP) and proximal interphalangeal joints before and after the intervention; additionally, the level of improvement was classified into 3 levels (mild = 0° to 29°; moderate = 30° to 60°; considerable = 61° and more). Results: The degree of improvement of extension in the MCP joints was 11° greater in the collagenase group (P = 0.001). The number of patients who had an improvement of >60° (considerable) in extension was greater in the collagenase group (P = 0.02). Conclusion: Collagenase was more effective than needle fasciotomy in treating extension deficits of the MCP joints in Dupuytren’s contracture in this retrospective analysis. Further prospective studies are required to confirm the finding.
Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype

Editing the fetal γ-globin promoters in hematopoietic stem cells from sickle cell disease patients induces therapeutic γ-globin levels. Sickle cell disease (SCD) is caused by a single amino acid change in the adult hemoglobin (Hb) β chain that causes Hb polymerization and red blood cell (RBC) sickling. The co-inheritance of mutations causing fetal γ-globin production in adult life hereditary persistence of fetal Hb (HPFH) reduces the clinical severity of SCD. HPFH mutations in the HBG γ-globin promoters disrupt binding sites for the repressors BCL11A and LRF. We used CRISPR-Cas9 to mimic HPFH mutations in the HBG promoters by generating insertions and deletions, leading to disruption of known and putative repressor binding sites. Editing of the LRF-binding site in patient-derived hematopoietic stem/progenitor cells (HSPCs) resulted in γ-globin derepression and correction of the sickling phenotype. Xenotransplantation of HSPCs treated with gRNAs targeting the LRF-binding site showed a high editing efficiency in repopulating HSPCs. This study identifies the LRF-binding site as a potent target for genome-editing treatment of SCD.
Life history stage explains behavior in a social network before and during the early breeding season in a cooperatively breeding bird

In species with stage-structured populations selection pressures may vary between different life history stages and result in stage-specific behaviors. We use life history stage to explain variation in the pre and early breeding season social behavior of a cooperatively breeding bird, the Florida scrub-jay (Aphelocoma coerulescens) using social network analysis. Life history stage explains much of the variation we observed in social network position. These differences are consistent with nearly 50 years of natural history observations and generally conform to a priori predictions about how individuals in different stages should behave to maximize their individual fitness. Where the results from the social network analysis differ from the a priori predictions suggest that social interactions between members of different groups are more important for breeders than previously thought. Our results emphasize the importance of accounting for life history stage in studies of individual social behavior.