Miracle-dz/UniFAR-FTUs huggingface dataset:
Bettongs, Potoroos and the Musky Rat-kangaroo

Rat-kangaroos have not coped well with the impact of European settlement in Australia. Of the 11 species present in 1788, two are extinct, two are either mostly or totally restricted to offshore islands and the range of all other species has been much reduced. Habitat alienation, altered fire regimes, grazing, predation by introduced carnivores, competition from rabbits and timber harvesting have variously taken their toll on these little-seen animals. The rat-kangaroo was one of the first Australian marsupials to be seen alive in Europe. Collected close to the settlement at Sydney Cove, a pair of them were exhibited in London in 1789. These animals were called by the local Aboriginal people 'Pot-o-roo', and by the European settlers, 'Kangooroo rat'. They were the Long-nosed Potoroo, Potorous tridactylus, the first of what we now call 'Rat-kangaroos' to be discovered. Bettongs, Potoroos and the Musky Rat-kangaroo provides an extraordinary glimpse into the secretive lives of these unusual marsupials. It also reveals little-known facts about the critical functional role these creatures play in maintaining the forest and woodland habitats in which they live.
Genetic variability and trait association studies in Indian mustard (Brassica juncea)

Thirty released varieties of Indian mustard [Brassica juncea (L.) Czern and Coss. ] were evaluated during winter (rabi) 2006–07 and 2007–08 under irrigated and rainfed environments. Analysis of variance on 14 quantitative traits was carried out and pooled analysis over the environments was conducted. The mean, range, phenotypic, genotypic and environmental variance, genotypic and phenotypic coefficient of variation, heritability in broad sense and genetic advance were calculated. Path coefficient analysis was carried out using correlation coefficients to know the yield- contributing traits having true associations with seed yield. Improvement in seed yield can be achieved by selection using the correlation and path analysis data generated in this study. 1 000-seed weight was positively correlated with siliqua length. 1 000-seed weight and total siliquae/plant also had higher phenotypic and genotypic direct effects on seed yield/ plant, revealing that indirect selection for these traits would be effective in improving seed yield. The high heritability coupled with high genetic advance for 1 000-seed weight would also be of great use for indirect selection for improvement in seed yield. The material used in the study is of diverse nature and can be used in the breeding programme for development of improved genotypes in mustard.
Continuous Delivery Practices in a Large Financial Organization

Continuous Delivery is an agile software development practice in which developers frequently integrate changes into the main development line and produce releases of their software. An automated Continuous Integration infrastructure builds and tests these changes. Claimed advantages of CD include early discovery of (integration) errors, reduced cycle time, and better adoption of coding standards and guidelines. This paper reports on a study in which we surveyed 152 developers of a large financial organization (ING Nederland), and investigated how they adopt a Continuous Integration and delivery pipeline during their development activities. In our study, we focus on topics related to managing technical debt, as well as test automation practices. The survey results shed light on the adoption of some agile methods in practice, and sometimes confirm, while in other cases, confute common wisdom and results obtained in other studies. For example, we found that refactoring tends to be performed together with other development activities, technical debt is almost always "self-admitted", developers timely document source code, and assure the quality of their product through extensive automated testing, with a third of respondents dedicating more than 50% of their time to do testing activities.
The Immune Response to the fVIII Gene Therapy in Preclinical Models

Neutralizing antibodies to factor VIII (fVIII), referred to as “inhibitors,” remain the most challenging complication post-fVIII replacement therapy. Preclinical development of novel fVIII products involves studies incorporating hemophilia A (HA) and wild-type animal models. Though immunogenicity is a critical aspect of preclinical pharmacology studies, gene therapy studies tend to focus on fVIII expression levels without major consideration for immunogenicity. Therefore, little clarity exists on whether preclinical testing can be predictive of clinical immunogenicity risk. Despite this, but perhaps due to the potential for transformative benefits, clinical gene therapy trials have progressed rapidly. In more than two decades, no inhibitors have been observed. However, all trials are conducted in previously treated patients without a history of inhibitors. The current review thus focuses on our understanding of preclinical immunogenicity for HA gene therapy candidates and the potential indication for inhibitor treatment, with a focus on product- and platform-specific determinants, including fVIII transgene sequence composition and tissue/vector biodistribution. Currently, the two leading clinical gene therapy vectors are adeno-associated viral (AAV) and lentiviral (LV) vectors. For HA applications, AAV vectors are liver-tropic and employ synthetic, high-expressing, liver-specific promoters. Factors including vector serotype and biodistribution, transcriptional regulatory elements, transgene sequence, dosing, liver immunoprivilege, and host immune status may contribute to tipping the scale between immunogenicity and tolerance. Many of these factors can also be important in delivery of LV-fVIII gene therapy, especially when delivered intravenously for liver-directed fVIII expression. However, ex vivo LV-fVIII targeting and transplantation of hematopoietic stem and progenitor cells (HSPC) has been demonstrated to achieve durable and curative fVIII production without inhibitor development in preclinical models. A critical variable appears to be pre-transplantation conditioning regimens that suppress and/or ablate T cells. Additionally, we and others have demonstrated the potential of LV-fVIII HSPC and liver-directed AAV-fVIII gene therapy to eradicate pre-existing inhibitors in murine and canine models of HA, respectively. Future preclinical studies will be essential to elucidate immune mechanism(s) at play in the context of gene therapy for HA, as well as strategies for preventing adverse immune responses and promoting immune tolerance even in the setting of pre-existing inhibitors.
Late-Onset Epilepsy With Unknown Etiology: A Pilot Study on Neuropsychological Profile, Cerebrospinal Fluid Biomarkers, and Quantitative EEG Characteristics

Introduction: Despite the fact that epilepsy has been associated with cognitive decline, neuropsychological, neurobiological, and neurophysiological features in patients with late-onset epilepsy of unknown etiology (LOEU) are still unknown. This cross-sectional study aims to investigate the neuropsychological profile, cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD), and resting-state quantitative electroencephalographic (qEEG) cortical rhythms in LOEU patients with mild cognitive impairment (LOEU-MCI) and with normal cognition (LOEU-CN), compared to non-epileptic MCI (NE-MCI) and cognitively normal (CN) controls. Methods: Consecutive patients in two clinical Units diagnosed with LOEU-CN (19), LOEU-MCI (27), and NE-MCI (21) were enrolled, and compared to age and sex-matched cognitively normal subjects CN (11). Patients underwent standardized comprehensive neuropsychological evaluation and CSF core AD biomarkers assessment (i.e., CSF Aβ42, phospho-tau and total tau, classified through A/T/(N) system). Recordings of resting-state eyes-closed electroencephalographic (EEG) rhythms were collected and cortical source estimation of delta (<4 Hz) to gamma (>30 Hz) bands with exact Low Resolution Electromagnetic Tomography (eLORETA) was performed. Results: Most LOEU patients had an MCI status at seizure onset (59%). Patients with LOEU-MCI performed significantly worse on measures of global cognition, visuo-spatial abilities, and executive functions compared to NE-MCI patients (p < 0.05). Regarding MCI subtypes, multiple-domain MCI was 3-fold more frequent in LOEU-MCI than in NE-MCI patients (OR 3.14, 95%CI 0.93–10.58, p = 0.06). CSF Aβ42 levels were lower in the LOEU-MCI compared with the LOEU-CN group. Finally, parietal and occipital sources of alpha (8–12 Hz) rhythms were less active in the LOEU-MCI than in the NE-MCI and CN groups, while the opposite was true for frontal and temporal cortical delta sources. Discussion: MCI status was relatively frequent in LOEU patients, involved multiple cognitive domains, and might have been driven by amyloidosis according to CSF biomarkers. LOEU-MCI status was associated with abnormalities in cortical sources of EEG rhythms related to quiet vigilance. Future longitudinal studies should cross-validate our findings and test the predictive value of CSF and EEG variables.
Microscopic Anatomy of the Gill and Lung of the Apple Snail Pomacea maculata, with Notes on the Volume of the Lung

ABSTRACT The anatomy of the gills of aquatic gastropods has not been extensively studied, and in particular, there are few recent studies that contain ultramicroscopic images. Similarly, the literature on the anatomy of the lungs of air-breathing terrestrial snails is not voluminous. Apple snails of the genus Pomacea possess both a gill and a fully functional lung. The lung is used to breathe air and as a flotation device. This study reports on the anatomy of the gill, lung, and pneumostome of the invasive species Pomacea maculata. The gill has a structure similar to that reported in other gastropods. The gill is monopectinate and consists of numerous triangular filaments. Ciliary tracts populate the distal portions of the filaments. The filaments are primarily connective tissue, interspersed with abundant muscle bands and hemolymph sinuses. The lung is a large ovoid sac; the floor is attached to the foot of the snail and the roof of the lung underlies the mantle epithelium. The lung tissue layers consist of connective tissue and smooth muscle bundles, and hemolymph spaces are present in both the floor and roof. Cells that contain calcium granules are very abundant in the lung tissue. Patches of cilia adorn the epithelium adjacent to the central airspace. The pneumostome is a muscular structure and is heavily ciliated. The lung volume of a 50-g animal is about 6 mL. The results of this study add to the knowledge of the anatomy of respiratory organs in molluscs and show that the lung is a major site of storage of calcium.
A novel test of flexible planning in relation to executive function and language in young children

In adult humans, decisions involving the choice and use of tools for future events typically require episodic foresight. Previous studies suggest some non-human species are capable of future planning; however, these experiments often cannot fully exclude alternative learning explanations. Here, we used a novel tool-use paradigm aiming to address these critiques to test flexible planning in 3- to 5-year-old children, in relation to executive function and language abilities. In the flexible planning task, children were not verbally cued during testing, single trials avoided consistent exposure to stimulus–reward relationships, and training trials provided experience of a predictable return of reward. Furthermore, unlike most standard developmental studies, we incorporated short delays before and after tool choice. The critical test choice included two tools with equal prior reward experience—each only functional in one apparatus. We tested executive function and language abilities using several standardized tasks. Our results echoed standard developmental research: 4- and 5-year-olds outperformed 3-year-olds on the flexible planning task, and 5-year-old children outperformed younger children in most executive function and language tasks. Flexible planning performance did not correlate with executive function and language performance. This paradigm could be used to investigate flexible planning in a tool-use context in non-human species.
Studying Complex Adaptive Systems With Internal States: A Recurrence Network Approach to the Analysis of Multivariate Time-Series Data Representing Self-Reports of Human Experience

We discuss formal, theoretical, and practical issues with the statistical analysis of multivariate time-series data that represent self-reports of human experience, often referred to as Ecological Momentary Assessment (EMA) data or Experience Sampling Method (ESM) data. We argue that such time series likely violate the assumptions required for valid statistical inference, such as the memoryless-ness property (due to the presence of long-range temporal correlations) and ergodicity (due to non-stationarity and non-homogeneity of central moments). Moreover, we consider the common practice of interpreting outcomes of self-reports as if they were outcomes of classical physical measurements as extremely problematic and suggest to consider them as records of the temporal evolution of observables of a complex adaptive system with internal state dynamics. We propose to address some of these issues by analyzing the change profile instead of the observed time series, using recurrence-based analyses, specifically (multiplex) recurrence networks. We analyze a publicly available dataset in which four participants rated six questions about their self-esteem and physical self, twice a day over a period of 512 days and introduce the concept of recurrence networks weighted by recurrence time. The edge weights represent either recurrence times or recurrence time frequencies and results show that the scaling relation between vertex degree and vertex strength (the weighted variant of vertex degree) is associated to the scaling relation between frequency and spectral power based on the “raw” time series. We present a new spiral layout for recurrence networks that might be more appropriate when the detection of critical periods, regime shifts, and tipping points requires insight into the temporal order in which those events occur. We conclude that a complex systems approach to analyzing multivariate time series of self-reports of human experience is preferred over and above fitting statistical models like the Gaussian Graphical Model or its derivatives.
Covid-19: Nine in 10 pregnant women with infection when admitted for delivery are asymptomatic, small study finds

Nearly 90% of pregnant women admitted to hospital for delivery who test positive for SARS-CoV-2 have no symptoms of the infection, a small study has found.1 Researchers led by Dena Goffman at Columbia University Irving Medical Center in New York, USA, screened all 215 pregnant women admitted to two New York City hospitals from 22 March to 4 April 2020 for symptoms of covid-19 and for infection with SARS-CoV-2. The results, reported in a letter to the New England Journal of Medicine ,1 showed that four women (1.9%) had fever or other symptoms of covid-19 on admission and tested positive for SARS-CoV-2. Swabs from 210 of the 211 …
Demographics of the Ribbed Mussel Geukensia demissa (Dillwyn, 1817) and the Effects of Its Simulated Manual Harvest on Salt Marsh Health in South Carolina, Usa

ABSTRACT The ribbed mussel Geukensia demissa is a mytilid bivalve that inhabits salt marshes along the east coast of North America. It is an important ecosystem engineer, contributing to salt marsh species diversity and landscape-scale ecosystem processes. Furthermore, local interest in the human consumption of G. demissa in South Carolina has created demand for this species from both restaurant and retail outlets. In response, commercial harvest of G. demissa increased markedly between 2014 and 2016. There are, however, currently no species-specific commercial or recreational harvesting regulations for G. demissa in this state, either in terms of minimum size or maximum quantity, raising concerns about the sustainability of commercial harvest, especially considering that harvesting practices can be destructive to the salt marsh ecosystem. The goal of the current study was to characterize the demographics of G. demissa at a harvested site and at two unharvested reference sites over the course of 1 y. Furthermore, the current study investigated the effects of simulated harvest on parameters of salt marsh health. Quarterly and monthly demographic sampling at commercially harvested and unharvested sites in South Carolina revealed that patches of G. demissa primarily consist of large individuals with low rates of recruitment. A similar relationship between size and age was observed at each of the sites. A year-long manipulation experiment revealed that selective harvesting practices mitigated the effect of harvest on metrics of smooth cordgrass, Spartina alterniflora health, but not on recruitment of G. demissa. The current study offers important demographic information on G. demissa in South Carolina that can be used to support future management decisions associated with its commercial and recreational fisheries.
Small Carnivoran Fauna of the Mascall Formation, Crooked River Basin, Central Oregon

ABSTRACT The Hemingfordian North American Land Mammal Age is a poorly known time period, although recently discovered sites in central Oregon have begun to cast light on a diverse mammalian fauna. Here, we describe four small carnivorans new to this region, one of which is a new species. Cryptailurus tinaynakti, sp. nov., is a hypercarnivorous feliform. UOMNH F-70218 is the dp4 of a diminutive mustelid similar in morphology to that of extant martens, but likely of a new species based upon discussed patterns in mustelid deciduous dentition. The occurrence of two additional species, Leptocyon leidyi and Bassariscus antiquus, increases both their geographic and temporal ranges. The early to middle Miocene was a time of transition from sparse woodland to grassland ecosystems in much of North America. The Hemingfordian fauna of the Pacific Northwest inhabited a diverse wet woodland ecosystem, surprisingly rich in carnivorans. With the description of these additional small taxa, we can now get a clearer picture of what must have been a diverse assemblage of mammals with a variety of ecological roles in an undersampled period of time.
Over-Expression of a 14-3-3 Protein From Foxtail Millet Improves Plant Tolerance to Salinity Stress in Arabidopsis thaliana

In plants, 14-3-3 proteins are recognized as mediators of signal transduction and function in both development and stress response. However, there are only a few preliminary functional researches in the C4 crop foxtail millet. Here, phylogenetic analysis categorized foxtail millet 14-3-3s (SiGRFs) into 10 discrete groups (Clusters I to X). Transcriptome and qPCR analyses showed that all the SiGRFs responded to at least one abiotic stress. All but one SiGRF-overexpressing (OE) Arabidopsis thaliana line (SiGRF1) exhibited insensitivity to abiotic stresses during seed germination and seedling growth. Compared with the Col-0 wild-type, SiGRF1-OEs had slightly lower germination rates and smaller leaves. However, flowering time of SiGRF1-OEs occurred earlier than that of Col-0 under high-salt stress. Interaction of SiGRF1 with a foxtail millet E3 ubiquitin-protein ligase (SiRNF1/2) indicates that the proteinase system might hydrolyze SiGRF1. Further investigation showed that SiGRF1 localized in the cytoplasm, and its gene was ubiquitously expressed in various tissues throughout various developmental stages. Additionally, flowering-related genes, WRKY71, FLOWERING LOCUS T, LEAFY, and FRUITFULL, in SiGRF1-OEs exhibited considerably higher expression levels than those in Col-0 under salinity-stressed conditions. Results suggest that SiGRF1 hastens flowering, thereby providing a means for foxtail millet to complete its life cycle and avoid further salt stress.
Combinatorial Low Dose Arsenic Trioxide and Cisplatin Exacerbates Autophagy via AMPK/STAT3 Signaling on Targeting Head and Neck Cancer Initiating Cells

Head and neck squamous cell carcinoma (HNSCC) is a highly lethal disease with high-level of epidemic both in the world and Taiwan. Previous studies support that head and neck cancer-initiating cells (HN-CICs), a subpopulation of cancer cells with enhanced stemness properties, contribute to therapy resistance and tumor recurrence. Arsenic trioxide (As2O3; ATO) has shown to be an effective anti-cancer drug targeting acute promyelocytic leukemia (APL). Combinatorial treatment with high dose of ATO and cisplatin (CDDP) exert synergistic apoptotic effects in cancer cell lines of various solid tumors, however, it may cause of significant side effect to the patients. Nevertheless, none has reported the anti-cancerous effect of ATO/CDDP targeting HN-CICs. In this study, we aim to evaluate the low dose combination of ATO with conventional chemo-drugs CDDP treatment on targeting HN-CICs. We first analyzed the inhibitory tumorigenicity of co-treatment with ATO and chemo-drugs on HN-CICs which are enriched from HNSCC cells. We observed that ATO/CDDP therapeutic regimen successfully synergized the cell death on HN-CICs with a Combination Index (CI) <1 by Chou-Talalay's analysis in vitro. Interestingly, the ATO/CDDP regimen also induced exaggerated autophagy on HN-CICs. Additionally, this drug combination strategy also empowered both preventive and therapeutic effect by in vivo xenograft assays. Finally, we provide the underlying molecular mechanisms of ATO-based therapeutic regimen on HN-CICs. Together, low dose of combinatorial ATO/CDDP regimen induced cell death as well as exacerbated autophagy via AMPK-STAT3 mediated pathway in HN-CICs.
Tryptophan Metabolic Pathways Are Altered in Obesity and Are Associated With Systemic Inflammation

Background: Obesity is a condition with a complex pathophysiology characterized by both chronic low-grade inflammation and changes in the gut microbial ecosystem. These alterations can affect the metabolism of tryptophan (TRP), an essential amino acid and precursor of serotonin (5-HT), kynurenine (KYN), and indoles. This study aimed to investigate alterations in KYN and microbiota-mediated indole routes of TRP metabolism in obese subjects relatively to non-obese controls and to determine their relationship with systemic inflammation. Methods: Eighty-five obese adults (avg. BMI = 40.48) and 42 non-obese control individuals (avg. BMI = 24.03) were recruited. Plasma levels of TRP catabolites were assessed using Ultra High Performance Liquid Chromatography-ElectroSpray-Ionization-Tandem Mass Spectrometry. High-sensitive C-reactive protein (hsCRP) and high-sensitive interleukin 6 (hsIL-6) were measured in the serum as markers of systemic inflammation using enzyme-linked immunosorbent assay. Results: Both KYN and microbiota-mediated indole routes of TRP metabolism were altered in obese subjects, as reflected in higher KYN/TRP ratio and lower 5-HT and indoles levels, relatively to non-obese controls. HsIL-6 and hsCRP were increased in obesity and were overall associated with TRP metabolic pathways alterations. Conclusion: These results indicate for the first time that KYN and indole TRP metabolic pathways are concomitantly altered in obese subjects and highlight their respective associations with obesity-related systemic inflammation.