Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic and plumage variation in Vermivora hybrids

ABSTRACT Hybrids with different combinations of traits can be used to identify genomic regions that underlie phenotypic characters important to species identity and recognition. Here, we explore links between genomic and plumage variation in Blue-winged Warbler x Golden-winged Warbler (Vermivora cyanoptera x V. chrysoptera) hybrids, which have traditionally been categorized into 2 discrete types. “Lawrence's” hybrids are yellow overall, similar to Blue-winged Warblers, but exhibit the black throat patch and face mask of Golden-winged Warblers. “Brewster's” hybrids are similar to Golden-winged Warblers, but lack the black throat patch and face mask, and sometimes have yellow on their underparts. Previous studies hypothesized that (1) first generation hybrids are of the Brewster's type and can be distinguished by the amount of yellow on their underparts, and that (2) the throat patch/mask phenotype is consistent with Mendelian inheritance and controlled by variation in a locus near the Agouti-signaling protein (ASIP) gene. We addressed these hypotheses using whole genome re-sequencing of parental and hybrid individuals. We found that Brewster's hybrids had genomic hybrid index scores indicating this phenotype can arise by majority ancestry from either parental species, that their plumage varied in levels of carotenoid pigmentation, and individuals captured in multiple years grew consistently less yellow over time. Variation in carotenoid pigmentation showed little relationship with genomic hybrid index score and is thus inconsistent with previous hypotheses that first generation hybrids can be distinguished by the amount of yellow in their plumage. Our results also confirm that variation near ASIP underlies the throat patch phenotype, which we refined to an ∼10–15 Kb region upstream of the coding sequence. Overall, our results support the notion that traditional categorization of hybrids as either Lawrence's or Brewster's oversimplifies continuous variation in carotenoid pigmentation, and its inferred underlying genetic basis, and is based primarily on one discrete trait, which is the throat patch/mask phenotype. LAY SUMMARY We used whole genome sequences of hybrid Vermivora warblers to examine the genetic basis and inheritance of plumage pigmentation. Yellow carotenoid pigmentation varied among hybrids, decreased between years, and showed no clear relationship with degree of admixture, suggesting a complex genetic basis. The ASIP gene was previously linked to melanic (black) throat pigmentation and we refined the causal region to ∼10–15 Kb upstream of the coding sequence. We conclude that first generation hybrids in this system may not be readily distinguished by their degree of carotenoid pigmentation.
Carbon dynamics in a forested peatland in north-eastern Ontario, Canada

The long-term carbon accumulation rate in a forested peatland in north-east Ontario was examined in relation to gas production and factors which control carbon transport. Plots of cumulative total mass and cumulative carbon mass against calibrated radiocarbon age estimates when applied to an existing model of peat accumulation, suggest that only very slow decay is occurring within the catotelm. Gas samples collected from depth show that both carbon dioxide and methane are present. Accelerator mass spectrometry (AMS) radiocarbon analysis yields age estimates of both gases which are between 500 and 2000 years younger than conventional age estimates on adjacent peat (.)
ANTIOXIDANT, ANTHELMINTIC AND ENZYME INHIBITORY POTENTIAL OF STREPTOMYCES VARIABILIS STRAIN PO-178 ISOLATED FROM WESTERN GHAT SOIL OF AGUMBE, KARNATAKA, INDIA

INTRODUCTION Among various ecological habitats, soil is one of the richest reservoirs supporting a variety of organisms including microorganisms. Rhizosphere is the region of soil present in vicinity to plant roots and is influenced by secretions of plant roots called root exudates. This region is thought to be of great importance to plant health and soil fertility. The exudates from plant roots stimulate the growth of microbial populations in soil and thus, the microbial activity is greatest in rhizosphere region. Actinomycetes forms a key part of soil microorganisms. The species of the genus Streptomyces are saprophytic and are commonly associated with soils. It has been found that about 90 % of soil actinomycetes are reported to be Streptomyces species. In soil, Streptomyces species significantly contribute to the turnover of complex biopolymers such as cellulose, pectin, lignin etc. They are noteworthy as they are the prolific producers to a range of bioactive metabolites including antibiotics. Western Ghats of India covers an area of 1, 80, 000 km and represent just under 6 % of the land area of India. The area represents > 30 % of all plant, fish, herpeto-fauna, birds and mammal species found in India which include some of the globally threatened species. Agumbe, a region of Western Ghats of Shivamogga district, Karnataka, India is shown to be a rich reservoir for Streptomyces species having potent industrial and agricultural significance in terms of production of bioactive metabolites. Streptomyces species from Agumbe region of Western Ghats have shown to antimicrobial, antioxidant, enzyme inhibitory, insecticidal, cytotoxic, anthelmintic, analgesic, antiinflammatory, CNS depressant and antipyretic activities. Streptomyces variabilis strain PO-178 (Figure 1) of this study was isolated from a rhizosphere soil of Agumbe, Karnataka, India. The extract from this strain was shown to possess antimicrobial, insecticidal, cytotoxic, analgesic, antiinflammatory, antipyretic and CNS depressant activity. In continuation part of our previous study, the present study was conducted with an aim of determining antioxidant, anthelmintic and enzyme inhibitory activity of butanol extract of S.variabilis PO-178 isolated from rhizosphere soil of Agumbe, Karnataka, India.
Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin

Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.
Similarity of brain activity patterns during learning and subsequent resting state predicts memory consolidation

Long-term memory depends on memory consolidation that seems to rely on learning-induced changes in the brain activity. Here, we introduced a novel approach analyzing continuous EEG data to study learning-induced changes as well as trait-like characteristics in brain activity underlying consolidation. Thirty-one healthy young adults performed a learning task and their performance was retested after a short (~1h) delay, that enabled us to investigate the consolidation of serial-order and probability information simultaneously. EEG was recorded during a pre- and post-learning rest period and during learning. To investigate the brain activity associated with consolidation performance, we quantified similarities in EEG functional connectivity of learning and pre-learning rest (baseline similarity) as well as learning and post-learning rest (post-learning similarity). While comparable patterns of these two could indicate trait-like similarities, changes in similarity from baseline to post-learning could indicate learning-induced changes, possibly spontaneous reactivation. Individuals with higher learning-induced changes in alpha frequency connectivity (8.5–9.5 Hz) showed better consolidation of serial-order information. This effect was stronger for more distant channels, highlighting the role of long-range centro-parietal networks underlying the consolidation of serial-order information. The consolidation of probability information was associated with learning-induced changes in delta frequency connectivity (2.5–3 Hz) and seemed to be dependent on more local, short-range connections. Beyond these associations with learning-induced changes, we also found substantial overlap between the baseline and post-learning similarity and their associations with consolidation performance, indicating that stable (trait-like) differences in functional connectivity networks may also be crucial for memory consolidation. Significance statement We studied memory consolidation in humans by characterizing how similarity in neural oscillatory patterns during learning and rest periods supports consolidation. Previous studies on similarity focused on learning-induced changes (including reactivation) and neglected the stable individual characteristics that are present over resting periods and learning. Moreover, learning-induced changes are predominantly studied invasively in rodents or with neuroimaging or event-related electrophysiology techniques in humans. Here, we introduced a novel approach that enabled us 1) to reveal both learning-induced changes and trait-like individual differences in brain activity and 2) to study learning-induced changes in humans by analyzing continuous EEG. We investigated the consolidation of two types of information and revealed distinct learning-induced changes and trait-like characteristics underlying the different memory processes.
Cap and Gap: The Fiscal Effects of Property Tax Levy Limits in New York

Abstract This is the first study to examine the fiscal effects of the New York property tax levy limit, using variation from the degree of fiscal stringency across school districts and over time in its first five years of implementation. Based on a difference-in-differences estimator, coupled with an event study specification, we find that the tax limit has imposed a real cap on many school districts; that is, at-limit districts’ total current expenditures per pupil are significantly lower than what they would have spent absent the limit. For those affected school districts, this expenditure gap does not come from spending on teacher salaries or fringe benefits but rather from other instructional salaries/expenses, central administration, transportation, interfund transfers, and undistributed spending. We also find heterogeneity in the constraining effects of the tax limit across different need-based groups of school districts.
GUN1-independent retrograde signaling targets the ethylene pathway to repress photomorphogenesis

When germinating in the light, Arabidopsis seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrograde signals are not yet fully known. Here, we show that lincomycin-treated seedlings (which lack developed chloroplasts) show strong phenotypic similarities to seedlings treated with ethylene (ET) precursor 1-aminocyclopropane-1-carboxylic acid (ACC), as both signals inhibit cotyledon separation in the light. We show that the lincomycin-induced phenotype partly requires a functioning ET signaling pathway, but could not detect increased ET emissions in response to lincomycin treatment. The two treatments show overlap in up-regulated gene transcripts, downstream of transcription factors ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1). The induction of the ethylene signaling pathway is triggered by an unknown retrograde signal acting independently of GENOMES UNCOUPLED1 (GUN1). Our data show how two apparently different stress responses converge to optimize photomorphogenesis. One Sentence Summary Chloroplast retrograde signaling targets the ethylene-regulated gene network to repress photomorphogenesis in Arabidopsis
Altered blood cell traits underlie a major genetic locus of severe COVID-19

Purpose: The genetic locus 3p21.31 has been associated with severe coronavirus disease 2019 (COVID-19), but the underlying pathophysiological mechanism is unknown. Methods: To identify intermediate traits of the COVID-19 risk variant, we performed a phenome-wide association study (PheWAS) with 923 phenotypes in 310,999 European individuals from UK Biobank. For candidate target genes, we examined associations between their expression and the polygenic score (PGS) of 1,263 complex traits in a meta-analysis of 31,684 blood samples. Results: Our PheWAS identified and replicated multiple blood cell traits to be associated with the COVID-19 risk variant, including monocyte count and percentage (p = 1.07e-8, 4.09e-13), eosinophil count and percentage (p = 5.73e-3, 2.20e-3), and neutrophil percentage (p = 3.23e-3). The PGS analysis revealed positive associations between the expression of candidate genes and genetically predicted counts of specific blood cells: CCR3 with eosinophil and basophil (p = 5.73e-21, 5.08e-19); CCR2 with monocytes (p = 2.40e-10); and CCR1 with monocytes and neutrophil (p = 1.78e-6, 7.17e-5). Conclusions: Multiple blood cell traits, especially monocyte, eosinophil, and neutrophil numbers, are associated with the COVID-19 risk variant and the expression of its candidate target genes, representing probable mechanistic links between the genetic locus 3p21.31 and severe COVID-19.
School Counselor Perspectives on Implementing a Modular Treatment for Youth

ABSTRACT Despite great advancements in the development of evidence-based treatments (EBTs) for youth mental health problems, few EBTs have been adopted by or successfully implemented in schools. This is of concern, as schools are the most common entry point for youth mental health services. Modular psychotherapies may be a particularly good fit for the school context given their flexible nature. This study examined the experiences of school counselors implementing of a modular therapy. School counselors (n = 20) were recruited from a larger randomized controlled effectiveness trial in five school districts. Counselors participated in semi-structured interviews, and content analysis was used to elucidate barriers and facilitators to successful implementation of the protocol. Barriers and facilitators fell into four broad categories, consistent with the Consolidated Framework for Implementation Research: (1) intervention components, (2) school setting, (3) school counselors, and (4) study-specific processes. School counselors generally found the flexible nature of the protocol to be a good fit for their students and emphasized the benefits of training and ongoing consultation. Counselors highlighted many logistical barriers specific to the school counseling setting (e.g., lack of time, space, and competing job demands). Findings underscore the need for the development, testing, and implementation of brief and flexible mental health treatments that are tailored through school stakeholder engagement.
PROSPECTS OF ONION (ALLIUM CEPA L.) FERTILIZATION BY SELENIUM. MINI-REVIEW

Allium cepa is widely used all over the world both in culinary and medicine. High antioxidant activity of biologically active compounds present in onion bulbs and the ability to transfer inorganic forms of selenium to methylated derivatives of selenium-containing aminoacids known to protect the organism against different forms of cancer may be considered as a background for the development of functional product with high antioxidant activity. The review discusses the results of the main investigations devoted to problems of A.cepa biofortification with Se, interaction of the element with other antioxidants and trace elements of the plant, intervarietal variability and beneficial effect on human health.
Variation in the Branchial Formula of Semiterrestrial Crabs (Decapoda: Brachyura: Grapsidae and Ocypodidae) in Relation to Physiological Adaptations to the Environment

ABSTRACT Variation of the branchial formula of 18 species of crabs collected from littoral and supralittoral regions on Phuket Island, Thailand, was examined in relation to the semiterrestrial environment. All species inhabiting water-logged substrata (3 species of Macrophthalmus, 3 species of Metaplax, and Chiromantes dussumieri) had an identical branchial formula consisting of 8 pairs of well-developed branchiae. In contrast, crabs inhabiting well-drained substrata had respiratory organs other than branchiae (6 species of Uca with well-developed inner linings of the branchiostegites, forming lungs, and Ilyoplax delsmani, I. gangetica, Dotillopsis brevitarsis, and Dotilla myctiroides with "tympana" on the meral segments of the thoracic pereiopods). The branchiae were more reduced and/or absent in the species occupying higher ground. In general, the major branchiae except the podobranchiae were divided into 3 types by histological observation: the highly osmoregulatory branchiae, the weakly osmoregulatory branchiae, and the respiratory branchiae. The species inhabiting well-drained substrata, especially species of the genus Uca with fewer branchiae, had more highly osmoregulatory branchiae than the species inhabiting water-logged substrata, even when they lived at almost the same tidal level. The reduction and/or disappearance of branchiae in the species inhabiting well-drained substrata is discussed in relation to the morphology of branchiae, the development of respiratory organs (lungs and tympana), and semiterrestrial environments.
NINETY-NINTH ANNUAL MEETING AMERICAN SOCIETY OF MAMMALOGISTS HYATT REGENCY WASHINGTON ON CAPITOL HILL, WASHINGTON, D.C.

Program Committee: Kayce C. Bell, Brad R. Blood, Patrice K. Connors, Elmer J. Finck, Daniel Greene, John D. Hanson, Andrew G. Hope, Sharon A. Jansa, Douglas A. Kelt, Eileen A. Lacey, Enrique P. Lessa, Jessica E. Light, Ryan A. Long, Jesus Maldonado (2019 Co-Host), Verity L. Mathis, Christy McCain, Michael McGowan, Link E. Olson, R. Neal Platt, Janet L. Rachlow, Andrew Ricketts, Luis A. Ruedas, James M. Ryan, Steven R. Sheffield, Robert S. Sikes, Winston P. Smith, Kelly A. Speer, Cody W. Thompson (Chair), Don Wilson (2019 Co-Host), Neal Woodman (2019 Co-Host) Members were notified by e-mail of online access to the program before the meeting and the meeting program was provided to members attending the meeting. Full program and abstracts are available at http://www.mammalsociety. org/meetings. Abridged minutes of the directors’ and members’ meetings follow.
Is there a correlation between pulmonary inflammation index with COVID-19 disease severity and outcome?

Rational: the radiologic pulmonary inflammatory index (PII) may be used as early predictor of inflammation as laboratory assessments in COVID-19. The purpose of this study was to compare the clinical and radiological features between the cases of COVID-19 necessitating ICU and those who did not, and to correlate the PII with other inflammatory markers and outcome. Patients and methods: This study included 72 patients with confirmed COVID-19. Their electronic records of were retrospectively revised and the demographic, clinical, laboratory, HRCT data, PII and the outcomes of the patients were analyzed. Results: They were 50/50% males/females, mean age was 47.1 (16.8). During their stay, 15.3% necessitated ICU admittance, 68% cured, 9 cases referred and five cases (6.9%) died. The baseline lesions identified were ground glass opacification in (93%), higher PII and >3 lobes affection were considerably recorded in those who required ICU (P= 0.041 and 0.013). There were correlations between PII with age (r=0.264, P=0.031), ferritin (r=0.225, P=0.048) and D Dimer (r=0.271, P=0.043). Conclusions: The use of PII together with clinical and laboratory data may be valuable in defining the inflammatory state of COVID-19. It was correlated with other inflammatory indices as D dimer, ferritin even before clinical deterioration.
Frequency and Management of Drug and Chemical Poisoning among Children Attending an Emergency Department in a Single Hospital in Saudi Arabia

Background: Accidental poisoning is one of the common medical emergencies in children that leads to morbidity and mortality. Medications and chemical agents play a major role in these adverse events resulting in social, economic, and health consequences. Aims of the study: The study aimed to evaluate the frequency and management of poisoning among children attending the emergency room at East Jeddah Hospital, Jeddah city, Saudi Arabia. Methods: This study was a retrospective chart review of all acute pediatric poisoning incidences in children (0-16 years of age) from October-21-2016 to March-03-2020 who were admitted to the emergency department of East Jeddah Hospital, Jeddah city, Saudi Arabia. Data was analyzed via SPSS software. Results: A total of 69 incidences of acute poisoning were admitted to the emergency room at East Jeddah Hospital; males were 55.1 %. Most children were under 5 years of age (59.4%). Unintentional poisoning occurred among 56.5% of observed cases of which 52.2% occurred in children younger than 5 years; 7.20% (5) patients were 12 to 16 years of age and had deliberate self-poisoning. The association between type of poisoning and age groups was statistically significant (Chi-square=28.5057, p=0.0001). Most incidences occurred at home (92.8%). Medicines were the most common cause of poisoning (73.9%). An excessive dose of prescribed medicine poisoning accidents was reported in 10.1% cases. Analgesics such as paracetamol were the most documented medication associated with poisoning (39.1%) followed by anticonvulsants and other central nervous system active medicines (18.8 %). The most common route of poisoning was oral administration (81.2%). One mortality case was documented due to poisoning. Conclusion: A total of 69 incidences of acute poisoning in children occurred in a single hospital over 3 years. Most incidents were accidental and occurred in children younger than 5 years of age. Medicines were the most common cause of poisoning. Analgesics such as paracetamol were the most common documented medicine associated with poisoning.