Miracle-dz/UniFAR-FTUs huggingface dataset:
Creeping Bellflower Response to Glyphosate and Synthetic Auxin Herbicides

S UMMARY . Creeping bellﬂower ( Campanula rapunculoides ) is a difﬁcult to manage weed commonly found in turfgrass and residential areas. We evaluated the efﬁcacy of selected postemergence herbicides (glyphosate, dicamba, clopyralid, quinclorac, and triclopyr) on greenhouse-grown creeping bellﬂower. The experiment was conducted in Jan. 2016 and repeated in Sept. 2016. Each herbicide was applied at ﬁve rates plus a nontreated control. Clopyralid caused greater creeping bellﬂower biomass reduction and mortality than the other herbicides investigated. The herbicide dose required to cause 50% mortality was lowest for clopyralid [86–138 g (cid:1) ha L 1 acid equivalent (a.e.)] compared with dicamba (221–536 g (cid:1) ha L 1 a.e. ), glyphosate (196–678 g (cid:1) ha L 1 a.e. ), triclopyr (236–782 g (cid:1) ha L 1 a.e. ), and quinclorac ( > 3000 g (cid:1) ha L 1 a.e. ). Clopyralid could be an effective herbicide for managing creeping bellﬂower, although it is currently not registered for use in many habitats where this plant is a problematic weed.
Mass Amphibian Mortality during Overwintering Related To Fungal Pathogen But Not Larval Environment: An Explanation for Declines?

Development of infectious diseases within hosts may be shaped by environmental conditions that cause tradeoffs in energetic demands for immune responses against demands for host growth and survival. Environmental conditions may influence these tradeoffs by affecting size of hosts, or tradeoffs may change across seasons, thereby altering the impacts of diseases on hosts. In the present study, we exposed northern leopard frog (Lithobates pipiens) tadpoles to varying larval environments (low leaf litter, high density of conspecifics, 40 µg/L atrazine, caged fish, or control) that influenced size at metamorphosis, a measure of host quality. Subsequently, we exposed these metamorphs of to Batrachochytrium dendrobatidis (Bd), a fungal pathogen linked to worldwide host population declines, at metamorphosis and/or 12 weeks later, prior to overwintering. Bd exposure dramatically reduced survival during overwintering and the effect was strongest when frogs were exposed both at metamorphosis and before overwintering. Larval environments, which determined host size, did not influence effects of Bd. Stage-structured models built to assess the impacts of Bd exposure on host populations suggest that Bd exposure at metamorphosis or before overwintering would reduce annual population growth rates by an average of 19% and 41%, respectively. Our study indicates that northern leopard frog hosts suffered little effects of Bd exposures following metamorphosis and that lower host quality did not hamper a frog’s ability to respond to Bd. Instead, we provide evidence that Bd exposure can reduce survival and result in population size reductions via reduced recruitment from overwintering mortality, providing a plausible mechanism for enigmatic declines of amphibians in temperate regions.
Occurrence of Glaucus atlanticus in the Midriff Islands Region, Gulf of California, Mexico

Abstract: A recent molecular study on pelagic nudibranchs showed that Glaucus marginatus (Reinhardt and Bergh, 1864) is a complex of three cryptic species, whereas the congener G. atlanticus (Forster, 1777) remain as one species. The objective of the present study was to determine the identity of pelagic nudibranchs collected in the Gulf of California using both molecular and traditional taxonomy. New DNA sequences (COI) and GenBank data were used to confirm the specimens' identity as G. atlanticus. Records from G. atlanticus were obtained from databases to determine the species geographic range. Present results increase that range northwards by approximately 150 km in the Gulf of California. Molecular data indicate that G. atlanticus from the Gulf has a wide infl uence from populations from the North and South Pacific and Indian Oceans. There is no current evidence of other cryptic species.
Middle Triassic conodont assemblages from the Germanic Basin: implications for multi-element taxonomy and biogeography

Conodonts have been a key tool for biostratigraphical, evolutionary and palaeobiogeographical studies, and the Germanic Basin has been one of the most important regions for these studies. However, few modern studies provide systematic data on the mainly endemic conodonts of the Middle Triassic Germanic Basin. Here we document conodonts from two sections in Germany, one Bithynian in age and the other late Anisian to early Ladinian in age. The two sections captured two episodes of marine fauna invasion in the Germanic epicontinental basin during the Middle Triassic. The conodont Neogondolella mombergensis, elsewhere reported as appearing globally, is reviewed and revised, confirming previous suggestions that this species only occurs in the Germanic Basin. Apparatuses of Neogondolella haslachensis and Nicoraella germanica from the Germanic Basin are proposed. It was generally expected that S and M elements within clades have a very high morphological stability compared to P elements. However, the apparatus of Nicoraella germanica differs significantly from that of south China, indicating that the morphology of S elements within a genus can be unstable, and thus promotes our understanding of conodont evolution. The rarely documented genus Gondolatus, which was suggested as representing pathological specimens, is confirmed as a valid genus in the Germanic Basin. Our data suggest that endemic conodonts evolved twice, not only in the Upper Muschelkalk Subgroup, but also in the Lower Muschelkalk Subgroup.
Expression of NOD1 and NOD2 transcripts in the healthy and diseased equine endometrium

Summary : In mares, endometrial diseases are the main cause of reduced fertility and have a high financial impact on equine breeding. Of particular importance are subclinical diseases, since they can only be diagnosed by the histological examination of an endometrial biopsy. Moreover, the precise pathogenesis of some frequent subclinical diseases, i.e. nonsuppurative endometritis and endometrosis (peri- glandular fibrosis), is unknown. The reason for the increased susceptibility of some mares to develop a persistent postbreeding endometritis (PPBE) is also still unsolved. The nucleotide-binding oligomerization domain proteins 1 and 2 (NOD1 and NOD2) are innate immunity receptors of epithelial and antigen presenting cells. On the one hand, they defend against intracellular bacteria and thus help to prevent and clear tissue infections. On the other hand, their altered expression can contribute to tissue inflammation and fibrosis. It has been shown that NOD1 and NOD2 are also involved in the pathogenesis of uterine diseases in women and other species. To the best of the authors’ knowledge, no data are published in regard to the expression of NOD1 and NOD2 in the equine endometrium. The aim of this study was to examine if NOD1 and NOD2 transcripts are expressed in the healthy and diseased equine endometrium. Endometrial samples of 31 adult mares were investigated by PCR and histology. The former was performed in comparison on native and formalin-fixed paraffin- embedded (FFPE) samples. By PCR, transcripts of NOD1 and NOD2 were detected in native and FFPE endometrial samples of all 31 mares. The morphology of endometrial glands was secretory (n=19), proliferative (n=6) or in transition between both stages (n=6). Five tissue samples had no pathological alterations; two of these were from a gravid mare. The remaining showed one or several endometrial diseases including different forms of endometritis (n=12), endometrosis (n=20), angiosclerosis (n=20), perivasculitis and vasculitis (n=1), infiltration with neoplastic lymphocytes (n=1) and placental retention (n=1). Results of this study are consistent with a constitutive expression of NOD1 and NOD2 transcripts during all stages of the endometrial cycle within the healthy and diseased equine endometrium. They imply a functional importance of NOD1 and NOD2 in the equine endometrium for the regulation of physiological processes as well as the pathogenesis of endometrial diseases. In human beings, certain polymorphisms and mutations of NOD genes have been identified as predisposing factors for chronic inflammation. Thus, it appears possible that NOD gene polymorphisms may also contribute to the resistance or susceptibility of mares to develop PPBE. This study provides the basis for future investigation into the contribution of NOD1 and NOD2 to the pathogenesis of equine endometrial diseases. The results of those future studies may reveal information that is beneficial for the prevention and treatment of equine endometrial diseases.
Assessment of the Diversity of Lactic Acid Bacteria Involved in Cocoa Fermentation of Six Main Cocoa Producing Regions of Côte d’ivoire

Aims: The variability of lactic acid bacteria (LAB) species involved in cocoa bean fermentation would cause inconsistency in the quality of cocoa. The aims of this study is to investigate the physicochemical parameters of cocoa bean fermentation in order to assess the activity and the molecular diversity of LAB involved in cocoa fermentation from six other of d’Ivoire. Spontaneous heap fermentations conducted in six cocoa producing regions Physicochemical analysis of cocoa as titratable acidity sugars out. In LAB isolation was performed using plate culture on MRS medium and their fermentative type as well as their profile were determined. In addition, LAB species were determined by restriction profile analysis of the 16S gene. Results: a total of 568 LAB were isolated from cocoa fermentation. Biochemical and morphological identification of these germs revealed the clear dominance of the bacilli form (81.16%) and the heterofermentative type (over 80%) with facultative heterofermentative type recording more than half (54.4%) of the isolated population. Their molecular identification by sequencing the hypervariable zone of the 16S rDNA gene of a few representatives from each restriction group revealed 08 species with a predominance of Lactobacillus plantarum (76.76%) and Leuconostoc mesenteroides (15.31%) associated with minority species. This species diversity could be exploited for selecting appropriate starter cultures. Conclusion: This diversity of LAB species could be responsible for the variability of cocoa quality in Côte d’Ivoire.
Reconstructing geographic range-size dynamics from fossil data

Abstract. Ecologists and paleontologists alike are increasingly using the fossil record as a spatial data set, in particular to study the dynamics and distribution of geographic range sizes among fossil taxa. However, no attempts have been made to establish how accurately range sizes and range-size dynamics can be preserved. Two fundamental questions are: Can common paleo range-size reconstruction methods accurately reproduce known species' ranges from locality (i.e., point) data? And, are some reconstruction methods more reliable than others? Here, we develop a methodological framework for testing the accuracy of commonly used paleo range-size reconstruction methods (maximum latitudinal range, maximum great-circle distance, convex hull, and alpha convex hull) in different extinction-related biogeographic scenarios. We use the current distribution of surface water bodies as a proxy for “preservable area,” in which to test the performance of the four methods. We find that maximum greatcircle distance and convex-hull methods most reliably capture changes in range size at low numbers of fossil sites, whereas convex hull performs best at predicting the distribution of “victims” and “survivors” in hypothetical extinction scenarios. Our results suggest that macroevolutionary and macroecological patterns in the relatively recent past can be studied reliably using only a few fossil occurrence sites. The accuracy of range-size reconstruction undoubtedly changes through time with the distribution and area of fossiliferous sediments; however, our approach provides the opportunity to systematically calibrate the quality of the spatial fossil record in specific environments and time intervals, and to delineate the conditions under which paleobiologists can reconstruct paleobiogeographical, macroecological, and macroevolutionary patterns over critical intervals in Earth history.
Microtubule-associated protein IQ67 DOMAIN5 regulates interdigitation of leaf pavement cells in Arabidopsis thaliana

Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation and cell morphology. Its organization and dynamics are coordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis, as indicated by reduced interdigitation of neighboring cells in the leaf epidermis of iqd5 mutants. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced asymmetric expansion. Lastly, we provide evidence for IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays. Our work thus identifies IQD5 as a novel player in PC shape regulation, and, for the first time, links calcium signaling to developmental processes that regulate multi-polar growth in PCs. Highlight Microtubule-localized Arabidopsis IQ67 DOMAIN5 regulates pavement cell morphogenesis in the leaf epidermis and links calcium-calmodulin signaling to lobe initiation and asymmetric expansion during early phases of interdigitated cell growth.
Assessing household livelihood vulnerability to climate change: The case of Northwest Vietnam

ABSTRACT This study applied livelihood vulnerability index (LVI) and livelihood effect index (LEI) to assess vulnerability from climate variability and change of three agricultural and natural resources dependent commune in northwest Vietnam, a country that is expected to bear some of the most severe impacts of climate change. Based on a survey of 335 farm household data, complemented with secondary data on climate factors, a composite index was calculated and differential vulnerabilities were compared. The results of the analysis suggest that one of the communities, “Pa Vay Su,” was more vulnerable than the others, particularly in relation to housing, knowledge and skills, socio-demographics, health and water security, social networks, and livelihood strategy. “Hien Luong” commune, on the other hand, was more vulnerable in relation to other LVI indicators with the exception of food security, climate variability, and natural disasters. “Moc Chau” community was more vulnerable in relation to water security, social demographic than Hien Luong commune. Overall, the article shows that three different vulnerability assessment indices can be broadly applied in comparable setting in other areas of country and they could usefully establish the basis for a nationally applicable index to identify and prioritize adaptation and mitigation needs.
Phytochemical screening and In-vitro antioxidant activities of aqueous extract of Enicostemma littorale Blume

The present study was carried out to evaluate the potential of aqueous extract of Enicostemma littorale Blume, through phytochemical analysis and antioxidant activities. The phytochemical analysis indicated the presence of alkaloids, flavonoids, saponins, phenols, glycosides, tannins,carbohydrates, proteins, carotenoids and lycopenes. In the antioxidant studies, the DPPH assay of the plant extract showed potent antioxidant capacity with an IC50 value of 31.09 I¼g/mg to that of standard (ascorbic acid) as 20.89 I¼g/mg. The extract showed potent scavenging of ABTS with IC50 value of 27.81 I¼g/mg on comparison with the standard (ascorbic acid) as 18.08 I¼g/mg. The extract also exhibited efficient Ferric Reducing Antioxidant Potential (FRAP) activity with an IC50 value of 18 I¼g of ascorbic acid/mg extract. These results indicated the antioxidant potential of aqueous extract of Enicostemma littorale.
Infectious bronchitis virus attaches to lipid rafts and enters cells via clathrin mediated endocytosis

Due to its economic importance to in poultry industry, the biology and pathogenesis of infectious bronchitis virus (IBV) have been investigated extensively. However, the molecular mechanisms involved in IBV entry are not well characterized. In this study, systematic approaches were used to dissect IBV entry process in various susceptible cells. First, we observed that lipid rafts were involved in IBV attachment. Second, low pH in intracyplasmic vesicles was required for virus entry. By using the specific clathrin mediated endocytosis (CME) inhibitor or knock down of clathrin heavy chain (CHC), we demonstrated that IBV mainly utilized the CME for its entry. Furthermore, GTPase dynamin1 was involved in virus containing vesicle scission and internalization. Surprisingly, CME adaptor Eps15 had no effect on IBV internalization. Third, the penetration of IBV into cells led to active cytoskeleton rearrangement. After internalization, virus particles moved along with the classical endosome/lysosome track, as evidenced by co-localization of R18 labeled IBV with vehicle markers Rab5/Rab7/LAMP1 along with the infection time course. Functional inactivation of Rab5 and Rab7 significantly inhibited IBV infection. VCP, a protein helps early endosome maturation, was involved virus trafficking. Finally, by using the dual R18/DiOC labeled IBV, we observed that membrane fusion with late endosome/lysosome membranes was induced between 2-3 h.p.i. Taken together, our findings demonstrate that IBV virions attach to lipid rafts and are internalized into cells via CME, move along with early/late endosomes-lysosomes, finally fuse with late endosome-lysosome membranes, release virus genome into cytoplasm. This study provides comprehensive images of IBV attachment-internalization-trafficking-fusion steps. IMPORTANCE IBV, the avian coronavirus isolated in 1937, infects chicken and causes economic loss in poultry industry. It has been reported that the entry of IBV requires low pH. However, the molecular mechanisms underlying IBV internalization and trafficking remain to be clarified. Therefore, we employed multiple chemical and molecular approaches to dissect the entry mechanisms of IBV in susceptible cells. Our results showed IBV entry was significantly inhibited when clathrin-mediated endocytosis (CME) was blocked by chemical inhibitor or depletion of clathrin protein. Moreover, by using R18-labeled IBV, we found that IBV particles attached to lipid rafts, led to actin rearrangement, and moved along with the entire endosomal system. R18/DiOC labeling method showed that IBV fused with late endosomes or lysosomes. This is the first report to describe the entire entry process of IBV, allowing for a better understanding of the infection process of group III avian coronavirus.
Life history traits, but not body size, vary systematically along latitudinal gradients on three continents in the widespread yellow dung fly

Large‐scale clinal variation in body size and other life‐history traits is common enough to have stimulated the postulation of several eco‐geographical rules. Whereas some clinal patterns are clearly adaptive, the causes of others remain unclear. We present a comprehensive intraspecific population comparison for the cosmopolitan yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae) to check for consistent world‐wide patterns. Common garden assessment of various life history traits permitted continental comparison of (clinal) quantitative genetic differentiation (Qst) with putatively neutral genetic differentiation (Fst) derived from field‐caught flies. Latitudinal clines in fly development time, growth rate, and overwintering propensity were consistent among North American, European and Japanese populations. Increased winter dormancy incidence and duration at higher latitude, combined with a faster growth rate and shorter development time, suggest that flies are adaptated to season length more than to temperature. The resulting body size clines, in contrast, were not very consistent; importantly, they were not negative, as expected under seasonal constraints, but flat or even positive clines. Quantitative genetic differentiation QST exceeded neutral molecular variation FST for most traits, suggesting that natural selection plays a consistent role in mediating global dung fly life histories. We conclude that faster growth and development in response to shorter growing seasons at higher latitudes may indirectly counteract expected direct effects of temperature on body‐size, potentially resulting in flat or inconsistent body size clines in nature.
scVAE: Variational auto-encoders for single-cell gene expression data

Motivation Models for analysing and making relevant biological inferences from massive amounts of complex single-cell transcriptomic data typically require several individual data-processing steps, each with their own set of hyperparameter choices. With deep generative models one can work directly with count data, make likelihood-based model comparison, learn a latent representation of the cells and capture more of the variability in different cell populations. Results We propose a novel method based on variational auto-encoders (VAEs) for analysis of single-cell RNA sequencing (scRNA-seq) data. It avoids data preprocessing by using raw count data as input and can robustly estimate the expected gene expression levels and a latent representation for each cell. We tested several count likelihood functions and a variant of the VAE that has a priori clustering in the latent space. We show for several scRNA-seq data sets that our method outperforms recently proposed scRNA-seq methods in clustering cells and that the resulting clusters reflect cell types. Availability and implementation Our method, called scVAE, is implemented in Python using the TensorFlow machine-learning library, and it is freely available at https://github.com/scvae/scvae.
Reducing retrospective patterns in stock assessment and impacts on management performance

Reducing retrospective patterns in stock assessment and impacts on management performance Cody S. Szuwalski,* James N. Ianelli, and André E. Punt Bren School of Environmental Science and Management, Marine Science Institute, University of California, Santa Barbara, CA 93106, USA National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Centre, 7600 Sand point Way NE, Seattle, WA 98115, USA School of Aquatic and Fishery Sciences, University of Washington, 1122 Boat Street, Seattle, WA 98195, USA