Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecology, Evidence, and Objectivity: In Search of a Bias-Free Methodology

For at least the past 25 years or so, there has been a twofold sense of “crisis” in ecology. One indication of this is the spate of articles and books calling for a reformation of the discipline and bearing such titles as “The New Ecology. ” On the part of practitioners, the unease concerns its theories, concepts, and methods. On the part of the general public, the unease concerns the perceived “bias” of its results. This paper is an attempt by two philosophers of science to clarify one critical methodological issue – hypothesis/model testing – and in the process to identify ways to gird the objectivity of ecological claims. What is significant about our approach is a distinction between the tasks appropriate to Bayesian Inference and Evidential Statistics – confirming hypotheses on the one hand and measuring evidence for models on the other. These two inferential paradigms are contrasted with the testing methods long-dominant in the discipline – Fisher-Neyman-Pearson Significance Testing and Popper Falsificationism – and a case made for a much greater use of Bayesian and Evidentialist Methods. In particular, it is argued that Evidential Statistics, here in the form of the likelihood ratios of competing predictive and explanatory multiple models avoids the main forms of otherwise unsettling cognitive bias. It also provides a Darwinian alternative to the “convergence” accounts of objectivity associated with the development of physics which is more appropriate to ecology. Keywords: Scientific method, Bayesian inference, evidential statistics, confirmation, evidence, significance testing, falsificationism, hypothetico-deductivism, convergence, objectivity
An Overview of VPAC Receptors in Rheumatoid Arthritis: Biological Role and Clinical Significance

The axis comprised by the Vasoactive Intestinal Peptide (VIP) and its G protein-coupled receptors (GPCRs), VPAC1, and VPAC2, belong to the B1 family and signal through Gs or Gq proteins. VPAC receptors seem to preferentially interact with Gs in inflammatory cells, rather than Gq, thereby stimulating adenylate cyclase activity. cAMP is able to trigger various downstream pathways, mainly the canonical PKA pathway and the non-canonical cAMP-activated guanine nucleotide exchange factor (EPAC) pathway. Classically, the presence of VPACs has been confined to the plasma membrane; however, VPAC1 location has been described in the nuclear membrane in several cell types such as activated Th cells, where they are also functional. VPAC receptor signaling modulates a number of biological processes by tipping the balance of inflammatory mediators in macrophages and other innate immune cells, modifying the expression of TLRs, and inhibiting MMPs and the expression of adhesion molecules. Receptor signaling also downregulates coagulation factors and acute-phase proteins, promotes Th2 over Th1, stimulates Treg abundance, and finally inhibits a pathogenic Th17 profile. Thus, the VIP axis signaling regulates both the innate and adaptive immune responses in several inflammatory/autoimmune diseases. Rheumatoid arthritis (RA) is a complex autoimmune disease that develops on a substrate of genetically susceptible individuals and under the influence of environmental factors, as well as epigenetic mechanisms. It is a heterogeneous disease with different pathogenic mechanisms and variable clinical forms between patients with the same diagnosis. The knowledge of VIP signaling generated in both animal models and human ex vivo studies can potentially be translated to clinical reality. Most recently, the beneficial effects of nanoparticles of VIP self-associated with sterically stabilized micelles have been reported in a murine model of RA. Another novel research area is beginning to define the receptors as biomarkers in RA, with their expression levels shown to be associated with the activity of the disease and patients-reported impairment. Therefore, VPAC expression together VIP genetic variants could allow patients to be stratified at the beginning of the disease with the purpose of guiding personalized treatment decisions.
Archeological Tourist Destination Image Formation: Influence of Information Sources on the Cognitive, Affective and Unique Image

A destination’s image is a critical factor in tourists’ perceptions and evaluations of said destination. This paper analyzes the formation of the tourist destination image of Segóbriga Archeological Park, a cultural destination located in the province of Cuenca (Spain) that holds great heritage value. To this end, the paper adopted a multidimensional approach and used PLS-SEM to analyze the destination image, taking into account not only its cognitive and affective components, but also the unique image component. The latter has received less attention in the literature and is a novel factor among cultural destinations. The results show that this component is essential to the overall image of an archeological destination, but is not influenced by information sources.
Human Milk Microbiome and Maternal Postnatal Psychosocial Distress

Human milk contains many bioactive components, including bacteria, which are transferred to the developing infant through breastfeeding. Milk bacteria appear to, amongst others, originate from the maternal gut. A mother’s postnatal psychosocial distress may alter maternal gut microbiota, which in turn may affect the bacteria present in milk. The aim of this study was to explore whether maternal postnatal psychosocial distress was related to alterations in the relative abundances of specific bacteria and to milk microbial diversity. Healthy mothers (N = 77; N = 51 with complete data) collected breast milk samples at 2, 6, and 12 weeks postpartum and filled in mood questionnaires on experienced stress, anxiety, and depressive symptoms at 6 weeks postpartum. A metataxonomic approach (16S rRNA gene sequencing (region V3 and V4) using Illumina MiSeq technology) was used to assess bacterial abundances and diversity. For the group as a whole, an increase in diversity of the milk bacterial community was observed during the first 3 months of breastfeeding (Shannon index). This general increase in diversity appears to be explained by an increase of Lactobacillus and other minor genera, together with a decrease in Staphylococcus. With respect to psychological distress and milk microbial composition, no significant differences in the relative abundance of major bacterial genera were detected between women with high (N = 13) and low (N = 13) psychosocial distress. However, progressive and distinct changes in the content of Firmicutes, Proteobacteria, and Bacteroidetes at the phylum level and Acinetobacter, Flavobacterium, and Lactobacillus at the genera level were observed in milk samples of women with low psychosocial distress. With respect to milk microbial diversity, high maternal psychosocial distress, compared to low maternal psychosocial distress, was related to significantly lower bacterial diversity in milk at 3 months post-delivery. Anxiety, stress, and depressive symptoms separately were unrelated to specific bacterial profiles. The current study suggests a potential relation between maternal psychosocial distress and milk microbiota, providing first evidence of a possible mechanism through which post-partum psychological symptoms may affect infant development and health.
Editorial: Machine Learning Methods for High-Level Cognitive Capabilities in Robotics

Department of Information Science and Engineering, Ritsumeikan University, Kyoto, Japan, Department of Computer Engineering, Boǧaziçi University, Istanbul, Turkey, Department of Intermedia Art and Science, School of Fundamental Science and Engineering, Waseda University, Tokyo, Japan, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Osaka, Japan, Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
The True Self. Critique, Nature, and Method

The history of philosophy gives us many different accounts of a true self, connecting it to the essence of what a person is, the notion of conscience, and the ideal human being. Some proponents of the true self can also be found within psychology, but its existence is mostly rejected. Many psychological studies, however, have shown that people commonly believe in the existence of a true self. Although folk psychology often includes a belief in a true self, its existence is disputed by psychological science. Here, we consider the critique raised by Strohminger et al., stating that the true self is (1) radically subjective and (2) not observable, hence cannot be studied scientifically (Strohminger et al., 2017). Upon closer investigation, the argument that the self is radically subjective is not convincing. Furthermore, rather than accepting that the true self cannot be studied scientifically, we ask: What would a science have to look like to be able to study the true self? In order to answer this question, we outline the conceptual nature of the true self, which involves phenomenological and narrative aspects in addition to psychological dimensions. These aspects together suggest a method through which this concept can be investigated from the first-person perspective. On a whole, we propose an integrative approach to understanding and investigating the true self.
Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon

RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.
Escape From X-Chromosome Inactivation: An Evolutionary Perspective

Sex chromosomes originate as a pair of homologus autosomes that then follow a general pattern of divergence. This is evident in mammalian sex chromosomes, which have undergone stepwise recombination suppression events that left footprints of evolutionary strata on the X chromosome. The loss of genes on the Y chromosome led to Ohno’s hypothesis of dosage equivalence between XY males and XX females, which is achieved through X-chromosome inactivation (XCI). This process transcriptionally silences all but one X chromosome in each female cell, although 15–30% of human X-linked genes still escape inactivation. There are multiple evolutionary pathways that may lead to a gene escaping XCI, including remaining Y chromosome homology, or female advantage to escape. The conservation of some escape genes across multiple species and the ability of the mouse inactive X to recapitulate human escape status both suggest that escape from XCI is controlled by conserved processes. Evolutionary pressures to minimize dosage imbalances have led to the accumulation of genetic elements that favor either silencing or escape; lack of dosage sensitivity might also allow for the escape of flanking genes near another escapee, if a boundary element is not present between them. Delineation of the elements involved in escape is progressing, but mechanistic understanding of how they interact to allow escape from XCI is still lacking. Although increasingly well-studied in humans and mice, non-trivial challenges to studying escape have impeded progress in other species. Mouse models that can dissect the role of the sex chromosomes distinct from sex of the organism reveal an important contribution for escape genes to multiple diseases. In humans, with their elevated number of escape genes, the phenotypic consequences of sex chromosome aneuplodies and sexual dimorphism in disease both highlight the importance of escape genes.
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States

As an economically important crop, apple is one of the most cultivated fruit trees in temperate regions worldwide. Recently, a large number of high-quality transcriptomic and epigenomic datasets for apple were made available to the public, which could be helpful in inferring gene regulatory relationships and thus predicting gene function at the genome level. Through integration of the available apple genomic, transcriptomic, and epigenomic datasets, we constructed co-expression networks, identified functional modules, and predicted chromatin states. A total of 112 RNA-seq datasets were integrated to construct a global network and a conditional network (tissue-preferential network). Furthermore, a total of 1,076 functional modules with closely related gene sets were identified to assess the modularity of biological networks and further subjected to functional enrichment analysis. The results showed that the function of many modules was related to development, secondary metabolism, hormone response, and transcriptional regulation. Transcriptional regulation is closely related to epigenetic marks on chromatin. A total of 20 epigenomic datasets, which included ChIP-seq, DNase-seq, and DNA methylation analysis datasets, were integrated and used to classify chromatin states. Based on the ChromHMM algorithm, the genome was divided into 620,122 fragments, which were classified into 24 states according to the combination of epigenetic marks and enriched-feature regions. Finally, through the collaborative analysis of different omics datasets, the online database AppleMDO (http://bioinformatics.cau.edu.cn/AppleMDO/) was established for cross-referencing and the exploration of possible novel functions of apple genes. In addition, gene annotation information and functional support toolkits were also provided. Our database might be convenient for researchers to develop insights into the function of genes related to important agronomic traits and might serve as a reference for other fruit trees.
Can Baseline Electromyography Predict Response to Biofeedback for Anorectal Disorder? A Long-Term Follow-Up Study

Background Biofeedback has been recommended for the treatment of anorectal disorders, especially constipation and fecal incontinence (FI). The objective of this study was to assess the long-term efficacy of biofeedback and evaluate baseline electromyography (EMG) as a predictor for maintenance of long-term improvement. Methods A retrospective chart review was performed on randomly selected patients who underwent biofeedback between the years 1990 and 2000. Clinical characteristics, including EMG values at baseline (resting and contraction) as well as EMG after exercises, were collected. Patients were contacted and were classified as “improved” if they had self-reported symptomatic improvement and “not-improved” if their symptoms were unchanged or worsened. Results A total of 41 subjects were included. Majority (85.4%) were female, the mean age was 48.95 ± 15.46 (range 22 - 77 years) and the median follow-up was 4 years (range 4 - 5 years). Constipation was the primary indication for biofeedback in 27/41 (65.9%), FI in 9/41 (22%) and “other” in 5/41 (12.1%). Within constipation, 55.6% reported long-term improvement as compared to 66.7% of FI and 80% of the other patients. There was borderline difference in the baseline EMG (3.11 ± 1.85 µV, improved, and 7.41 ± 11.01 µV, not improved, P = 0.06) but no significant difference in post-exercise resting (3.13 ± 3.21 µV, improved, and 4.28 ± 3.63 µV, not improved, P = 0.33) and contraction EMG between the two groups. Conclusions Biofeedback is an important treatment tool in anorectal disorders. Over 50% of our subjects maintained their improvement 4 - 5 years after completing biofeedback therapy. A lower resting baseline EMG showed a trend of association with improvement in the long term.
Plant and insect herbivore community variation across the Paleocene–Eocene boundary in the Hanna Basin, southeastern Wyoming

Ecosystem function and stability are highly affected by internal and external stressors. Utilizing paleobotanical data gives insight into the evolutionary processes an ecosystem undergoes across long periods of time, allowing for a more complete understanding of how plant and insect herbivore communities are affected by ecosystem imbalance. To study how plant and insect herbivore communities change during times of disturbance, we quantified community turnover across the Paleocene–Eocene boundary in the Hanna Basin, southeastern Wyoming. This particular location is unlike other nearby Laramide basins because it has an abundance of late Paleocene and Eocene coal and carbonaceous shales and paucity of well-developed paleosols, suggesting perpetually high water availability. We sampled approximately 800 semi-intact dicot leaves from five stratigraphic levels, one of which occurs late in the Paleocene–Eocene thermal maximum (PETM). Field collections were supplemented with specimens at the Denver Museum of Nature & Science. Fossil leaves were classified into morphospecies and herbivore damage was documented for each leaf. We tested for changes in plant and insect herbivore damage diversity using rarefaction and community composition using non-metric multidimensional scaling ordinations. We also documented changes in depositional environment at each stratigraphic level to better contextualize the environment of the basin. Plant diversity was highest during the mid-late Paleocene and decreased into the Eocene, whereas damage diversity was highest at the sites with low plant diversity. Plant communities significantly changed during the late PETM and do not return to pre-PETM composition. Insect herbivore communities also changed during the PETM, but, unlike plant communities, rebound to their pre-PETM structure. These results suggest that insect herbivore communities responded more strongly to plant community composition than to the diversity of species present.
Intracutaneous Delivery of Gelatins Reduces Fat Accumulation in Subcutaneous Adipose Tissue

Subcutaneous adipose tissue (SAT) accumulation is a constitutional disorder resulting from metabolic syndrome. Although surgical and non-surgical methods for reducing SAT exist, patients remain non-compliant because of potential adverse effects and cost. In this study, we developed a new minimally-invasive approach to achieve SAT reduction, using a microneedle (MN) patch prepared from gelatin, which is capable of regulating fat metabolism. Four gelatin types were used: three derived from fish (SA-FG, GT-FG 220, and GT-FG 250), and one from swine (SM-PG 280). We applied gelatin-based MN patches five times over 4 weeks to rats with high-fat diet (HD)-induced obesity, and determined the resulting amount of SAT. We also investigated the histological features and determined the expression levels of fat metabolism-associated genes in SAT using hematoxylin and eosin staining and western blotting, respectively. SAT decreased following treatment with all four gelatin MN patches. Smaller adipocytes were observed in the regions treated with SA-FG, GT-FG 250, and SM-PG 280 MNs, demonstrating a decline in fat accumulation. The expression levels of fat metabolism-associated genes in the MN-treated SAT revealed that GT-FG 220 regulates fatty acid synthase (FASN) protein levels. These findings suggest that gelatin MN patches aid in decreasing the quantity of unwanted SAT by altering lipid metabolism and fat deposition.
Traumatic vertebral artery injury: a review of the screening criteria, imaging spectrum, mimics, and pitfalls

Purpose Traumatic vertebral artery injury (TVAI) can have a varied clinical presentation and appearance on imaging. In this review, we present the screening criteria, spectrum of imaging features, grading, and imaging pitfalls of TVAI. Our review focuses on the imaging of TVAI on computed tomography angiography (CTA), magnetic resonance angiography (MRA), and cases of TVAI mimics. Imaging The imaging spectrum on CTA can range from either focal or long segment luminal stenosis (the most common findings), smooth or tapered narrowing of lumen, string of pearls appearance, concentric intramural haematoma, intimal flap (the most definite sign), and double lumen of the artery. On time-of-flight MRA, the most common findings include loss of flow void within the vessel due to slow flow, thrombosis or occlusion, and hyperintense signal within the vessel wall due to intramural haematoma on T1 fat-saturated images. Conclusion The reader should be aware of the screening criteria, common and uncommon findings, variant anatomy, artifacts, and mimics of TVAI when evaluating cases of craniocervical trauma, to be competent in calling in or ruling out injury.