Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing

Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa. ABSTRACT Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism. IMPORTANCE Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa. Here, we transcriptionally profiled the response of N. crassa to characterize the global response to sulfur starvation. We also used DNA affinity purification sequencing to identify the direct downstream targets of the transcription factor responsible for regulating genes involved in sulfur uptake and assimilation. Along with genes involved in sulfur metabolism, this transcription factor regulated a number of uncharacterized transporter genes and genes involved in mitochondrial electron transfer. Our data also suggest a connection between sulfur, nitrogen, and carbon metabolism, indicating that the regulation of a number of metabolic pathways is intertwined.
Onset and progression of puberty in Klinefelter syndrome

Klinefelter syndrome (KS) (47,XXY and variants, KS) is the most common sex chromosome disorder in humans. However, little is known about the onset and progression of puberty in patients with KS. In this study, we describe the onset and progression of puberty in a large series of boys with KS in a single tertiary centre.
Functional coordination of non‐myocytes plays a key role in adult zebrafish heart regeneration

Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes, but also involves complex interactions between distinct cardiac cell types including non‐cardiomyocytes (non‐CMs). However, the subpopulations, distinguishing molecular features, cellular functions, and intercellular interactions of non‐CMs in heart regeneration remain largely unexplored. Using the LIGER algorithm, we assemble an atlas of cell states from 61,977 individual non‐CM scRNA‐seq profiles isolated at multiple time points during regeneration. This analysis reveals extensive non‐CM cell diversity, including multiple macrophage (MC), fibroblast (FB), and endothelial cell (EC) subpopulations with unique spatiotemporal distributions, and suggests an important role for MC in inducing the activated FB and EC subpopulations. Indeed, pharmacological perturbation of MC function compromises the induction of the unique FB and EC subpopulations. Furthermore, we developed computational algorithm Topologizer to map the topological relationships and dynamic transitions between functional states. We uncover dynamic transitions between MC functional states and identify factors involved in mRNA processing and transcriptional regulation associated with the transition. Together, our single‐cell transcriptomic analysis of non‐CMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of this process.
MsTGANet: Automatic Drusen Segmentation From Retinal OCT Images

Drusen is considered as the landmark for diagnosis of AMD and important risk factor for the development of AMD. Therefore, accurate segmentation of drusen in retinal OCT images is crucial for early diagnosis of AMD. However, drusen segmentation in retinal OCT images is still very challenging due to the large variations in size and shape of drusen, blurred boundaries, and speckle noise interference. Moreover, the lack of OCT dataset with pixel-level annotation is also a vital factor hindering the improvement of drusen segmentation accuracy. To solve these problems, a novel multi-scale transformer global attention network (MsTGANet) is proposed for drusen segmentation in retinal OCT images. In MsTGANet, which is based on U-Shape architecture, a novel multi-scale transformer non-local (MsTNL) module is designed and inserted into the top of encoder path, aiming at capturing multi-scale non-local features with long-range dependencies from different layers of encoder. Meanwhile, a novel multi-semantic global channel and spatial joint attention module (MsGCS) between encoder and decoder is proposed to guide the model to fuse different semantic features, thereby improving the model’s ability to learn multi-semantic global contextual information. Furthermore, to alleviate the shortage of labeled data, we propose a novel semi-supervised version of MsTGANet (Semi-MsTGANet) based on pseudo-labeled data augmentation strategy, which can leverage a large amount of unlabeled data to further improve the segmentation performance. Finally, comprehensive experiments are conducted to evaluate the performance of the proposed MsTGANet and Semi-MsTGANet. The experimental results show that our proposed methods achieve better segmentation accuracy than other state-of-the-art CNN-based methods.
Double‐stranded RNA targeting fungal ergosterol biosynthesis pathway controls Botrytis cinerea and postharvest grey mould

Summary Pathogenic fungi cause major postharvest losses. During storage and ripening, fruit becomes highly susceptible to fungi that cause postharvest disease. Fungicides are effective treatments to limit disease. However, due to increased public concern for their possible side effects, there is a need to develop new strategies to control postharvest fungal pathogens. Botrytis cinerea, a common postharvest pathogen, was shown to uptake small double‐stranded RNA (dsRNA) molecules from the host plant. Such dsRNA can regulate gene expression through the RNA interference system. This work aimed to develop a synthetic dsRNA simultaneously targeting three essential transcripts active in the fungal ergosterol biosynthesis pathway (dsRNA‐ERG). Our results show initial uptake of dsRNA in the emergence zone of the germination tube that spreads throughout the fungus and results in down‐regulation of all three targeted transcripts. Application of dsRNA‐ERG decreased B. cinerea germination and growth in in vitro conditions and various fruits, leading to reduce grey‐mould decay. The inhibition of growth or decay was reversed by the addition of ergosterol. While dual treatment with dsRNA‐ERG and ergosterol‐inhibitor fungicide reduced by 100‐fold the required amount of fungicide to achieve the same protection rate. The application of dsRNA‐ERG induced systemic protection as shown by decreased decay development at inoculation points distant from the treatment point in tomato and pepper fruits. Overall, this study suggests that dsRNA‐ERG can effectively control B. cinerea growth and grey‐mould development suggesting its efficacy as a future method for postharvest control of fungal pathogens.
Fassettia, a new North American genus of family Ceratophyllaceae: evidence based on cladistic analyses of current molecular data of Ceratophyllum

Abstract. The major goal of this study was to re-analyse a published molecular dataset based on ITS and matK sequences of the genus Ceratophyllum (Ceratophyllaceae) within a cladistic framework, operating only with rooted trees. The problem is lack of an identifiable suitable outgroup to Ceratophyllum. We show different ways to root trees and thus resolve the sister group relationships within this genus. We root the trees using an all zero outgroup or a combination of exemplar taxa from among monocots (Acorus), eudcots (Ranunculus) and Chloranthus. Ceratophyllum echinatum was consistently strongly supported as sister to all of the remaining taxa of the genus. This observation is congruent with the earlier results of Les who noted the uniqueness of C. echinatum in a series of comprehensive morphological and biosystematic studies. We, here, transfer C. echinatum to a new and presumably monotypic genus Fassettia Mavrodiev. The exact taxonomic circumscription of Fassettia requires further investigation.
Survival and Recruitment among Non-Migratory Canada Geese (Branta canadensis): Influence of Gosling Sex, Hatching Date, Mass at Fledging, and Family Type

Abstract. Among some Arctic-nesting geese, mass at fledging impacts first-year survival and recruitment into the breeding population, but this might not be true for temperate-nesting geese. For 25 years, we examined what variables impacted survival and recruitment of 731 Canada Geese (Branta canadensis) fledglings raised in Connecticut, USA by tracking individually marked birds throughout their lives. At fledging, the number of females (391) were similar to males (340), but by the end of the first year of life, females (247) outnumbered males (187). This can be explained due to the apparent survival rates for juvenile females (0.63) being higher than for males (0.55). Dispersal rate from natal areas were similar for males and females during the first year of life and cannot account for why females outnumbered males after one year of life. Apparent survival rates of female fledglings to the end of the second year was 0.48. For the 247 females still alive at the end of their first year of life, 190 were still alive at the end of their second year of life, yielding a 0.77 apparent survival rates during their second year of life. Sex was the only variable that explained the survival of fledglings until the end of their first year of life. The probability of females surviving the second year of life was not influenced by hatching date, fledging age, fledging mass, or family type. Heavier females at fledging were more likely to be recruited into the breeding population than lighter ones. Our results indicate that while an inability to acquire sufficient mass as a gosling does not affect survival, it impacts the ability to be recruited.
Insights into Bruneian students’ transformative mobility experiences from their community outreach activities in Vietnam

This article is concerned with the internationalisation of higher education and student mobility for society and community engagement purposes. Drawing on the specific case study of Universiti Brunei Darussalam’s Community Outreach Programme overseas, it examines the programme’s operation in Vietnam as well as investigates Bruneian students’ experiences during their programme activities in this Asian country. The article also explores the impacts of such experiences on the students’ growth and transformations. The reported growth and transformations, on the one hand, demonstrate the importance of social engagement beyond campus and correspond to the internationalisation in higher education for society agenda recently advocated by international education scholars and practitioners. They also offer rich insights into (inter-Asian) student mobility for non-academic purposes, which remain largely under-researched. On the other hand, underlying the students’ transformative experiences are many issues associated with student safety and wellbeing that require ethical responses and appropriate adaptive pedagogies.
Osteology and Digital Reconstruction of the Skull of the Early Tetrapod Whatcheeria deltae

ABSTRACT The Early Carboniferous stem tetrapod Whatcheeria deltae is among the earliest-branching limbed tetrapods represented by multiple near-complete specimens, making it an important taxon in understanding the vertebrate water-to-land transition. However, all preserved skulls of Whatcheeria suffer from post-mortem crushing and lateral compression, which has made cranial reconstruction problematic. In this study, computed tomography data of three Whatcheeria specimens were segmented using visualization software to digitally separate each individual skull bone from matrix. Digital methods were used to repair and retrodeform the bones and produce the first complete three-dimensional skull reconstruction of Whatcheeria. We provide a revised description of the cranial and lower jaw anatomy of Whatcheeria based on CT data, focusing on sutural morphology and previously unknown anatomical details. Our findings suggest that Whatcheeria had one of the narrowest skulls of any known early tetrapod, a gap between the nasals, and significant overlap of the lacrimal onto the nasal and prefrontal. Sutural morphology is used to infer loading regime in the skull during feeding and suggests the skull of Whatcheeria was well adapted to resist stresses induced by biting large prey with its enlarged anterior fangs.
A New Triodus Shark Species (Xenacanthidae, Xenacanthiformes) from the Lowermost Permian of France and Its Paleobiogeographic Implications

ABSTRACT The Xenacanthiformes from Central and Eastern European deposits have been extensively studied, but the systematics of the species from the French Carboniferous–Permian Autun Basin (Saône-et-Loire) remains debated. Numerous xenacanthiform remains are still identified under the doubtful genus ‘Expleuracanthus’, and many of them consist of isolated dorsal spines which are difficult to identify. Numerous well-preserved specimens are still undescribed and the diversity of the xenacanthiform fauna from the Autun Basin is poorly understood. For example, specimens of the genus Triodus from the Muse oil-shale bed (OSB) of the Autun Basin have no specific attribution, whereas this genus is widely distributed across European Carboniferous–Permian basins. In this study, we describe new specimens of Triodus from the lowermost Permian of the Muse OSB. They allow the erection of a new species, Triodus aeduorum sp. nov., and discussion of the validity of several species from the same locality: ‘Expleuracanthus’ frossardi is considered as a nomen dubium and other Triodus specimens need for the time being to be left in open nomenclature as Triodus sp. These results highlight the endemism of the Triodus species in each European Carboniferous–Permian basin and raise the question of how they migrated from one to another.
Career development and internal migration: a Scottish case study

ABSTRACT A growing body of literature has focused on issues of migration in career development and guidance, however typically this research has focused on international migration rather than migration within a country’s borders. This paper presents a specific case study of internal migration in the UK context, focusing on young people from two island communities as they move through higher education and into the working world. The paper is specifically focused on the importance of cultural differences, including workplace cultures, with regard to students’ career development. The findings demonstrate the relevance of internal migration pathways to career development and indicate that a culturally informed approach to career guidance practice is important when working with internal as well as international migrants.
The First Braincase of the Basal Aetosaur Aetosauroides scagliai (Archosauria: Pseudosuchia) from the Upper Triassic of Brazil

ABSTRACT The phylogenetic relationships of Pseudosuchia, the crocodile-line of Archosauria, are still poorly resolved, in part, due to the lack of crucial braincase information for several key taxa. Recently, erpetosuchids and ornithosuchids have been recovered as close relatives to Aetosauria, sharing several braincase features. Here we provide the description of the first braincase of the basal aetosaur Aetosauroides based on specimens from the Upper Triassic Candelária Sequence of Brazil. Our study revealed the presence of an exoccipital lateral ridge and a medial ridge on the supraoccipital (both shared with all aetosaurs and erpetosuchids, but absent in ornithosuchids) and an anterolateral exit for the internal carotids (shared with all aetosaurs and ornithosuchids, but not with erpetosuchids). Aetosauroides lacks a medial contact between the exoccipitals (shared with the aetosaurs Desmatosuchus smalli and Tecovasuchus) and possesses a single hypoglossal foramen (contrasting with Stagonolepis robertsoni and Desmatosuchus spurensis). It also differs from the putative Argentinian Aetosauroides (PVSJ 326) by the presence of a ridge connecting the basal tubera medially (contrasting also with all stagonolepidoideans) and by a bulbous and ventrolaterally recurved basipterygoid process (contrasting with Paratypothorax). These features show that the braincase of aetosaurs is suitable for providing further phylogenetic information and may contribute to resolving controversies within Pseudosuchia relationships.
Erratum: Phylogeny, Systematics, and Evolution of Hypsodonty in the Aplodontiinae (Mammalia, Rodentia, Aplodontiidae), with the Description of Several New Species

Whereas aplodontiid rodents are represented today by a single living species, their fossil record is diverse in number of species (>100), in morphology, and in ecology. Recent phylogenetic efforts are beginning to make sense of the relationships among diverse members of the clade, but there is still much to learn about the relationships within the morphologically coherent subfamilies of this large group. The subfamily Aplodontiinae, including the extant Aplodontia, ranges from the mid-Miocene through recent, including only eight described species. This is the least diverse clade of aplodontiids, even though it is the only extant group. This study describes three new species, increasing the diversity of described fossil aplodontiids by more than a third. The description herein of Liodontia bathypotamos, n. sp. , from the late Hemingfordian of Montana, Liodontia dailyi, n. sp. , from the late Hemingfordian of Nevada, and Aplodontia minor, n. sp. , from the late Hemphillian of Oregon extends the geographic and temporal range of the subfamily. A phylogenetic analysis of all known aplodontiines finds support for slow diversification and possible anagenetic change within lineages while also suggesting substantial missing time in the aplodontiine fossil record. However, the morphological changes, including rapid increases in hypsodonty, along the aplodontiine lineage yield an extant species, Aplodontia rufa, that, despite its early divergence from the rest of crown group Rodentia, is not at all representative of the ‘primitive’ rodent it is commonly assumed to be. http://zoobank.org/urn:lsid:zoobank.org:pub:BCF8D9FB-E231-459F-A83C-FD98DE568744 Citation for this article: Hopkins, S. S. B. 2019. Phylogeny, systematics, and evolution of hypsodonty in the Aplodontiinae (Mammalia, Rodentia, Aplodontiidae), with the description of several new species. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2019. 1668401.
A New Baenid Turtle, Palatobaena knellerorum sp. nov., from the Lower Paleocene (Danian) Denver Formation of South-Central Colorado, U.S.A.

ABSTRACT Baenidae are the most diverse clade of turtles from the latest Cretaceous and earliest Paleogene of North America. Palatobaena species have a distinctive cranial bauplan within baenid turtles and we herein describe a new species, P. knellerorum, based on a complete cranium from the lower Paleocene Denver Formation in the Denver Basin, Colorado. Palatobaena knellerorum differs from other Palatobaena species in the extreme degree of its dorsally oriented orbits, as well as the presence of a broad pentagonal midline crest formed by the supraoccipital and parietals. It can be further diagnosed from other species of Palatobaena by the following unique combination of characters: having a broadly rounded cranium, presence of upper temporal emargination that extends well anterior to the otic chamber, a broad exposure of the supraoccipital on the dorsal skull roof, a broadly rounded ‘tongue groove’ between the maxillae and premaxillae, and a deeply emarginated nasal region that exposes the underlying premaxillae in dorsal view. Palatobaena knellerorum most closely resembles the Maastrichtian/Danian taxon Palatobaena cohen and the Danian taxon P. bairdi. A phylogenetic analysis places P. knellerorum as sister to P. bairdi, and these taxa are sister to P. cohen. Palatobaena knellerorum overlaps in time with P. cohen, but the two are separated geographically with P. knellerorum restricted to the Denver Basin and P. cohen restricted to the Williston Basin. Cranial anatomical data and sedimentological data suggest Palatobaena spp. were bottom dwelling turtles living in shallow water environments that used a putative proboscis to prey upon freshwater-shelled invertebrates.
Can China promote stability in the Black Sea Region?

ABSTRACT China has become an increasingly important actor in the Black Sea Region (BSR), and this looks set to continue in the future. Beijing has actively engaged with all of the Black Sea states and has looked to invest largely, but not exclusively, in ports and infrastructure projects as part of its Belt and Road Initiative (BRI). This article examines Beijing’s growing influence in the Black Sea and explores the effect this will have on the region. It will be argued that China’s engagement is seen by some of the littoral states as an important way of balancing Russian influence in the region and Beijing’s presence is likely to lead to a recalibration of Russian behaviour in the BSR. Chinese engagement in the Black Sea might therefore serve as a force for stability or at least encourage the continuation of the status quo, by limiting Russian revanchism, as Moscow will be increasingly sensitive to Beijing’s interest and investments.
Screening of natural compounds identifies ferutinin as an antibacterial and anti-biofilm compound

Abstract Antibacterial screenings are most commonly targeted at planktonic bacteria but less effort is dedicated to the exploration of agents acting on biofilms. Here, a natural compounds library was screened against Staphylococcus aureus using a 384-well plate platform to identify compounds preventing biofilm formation. Five structurally diverse hits were selected for follow-up studies: honokiol, tschimganidin, ferutinin, oridonin and deoxyshikonin. The compounds were evaluated against different bacterial species for their capacity to prevent and disrupt biofilms. The development of resistance and cytotoxicity were also investigated. Ferutinin displayed the best antibacterial activity, with a minimum inhibitory, bactericidal and biofilm preventive concentration of 25 µM against S. aureus. It efficiently disrupted pre-formed biofilms (over 5-log reduction of viable cells) and reduced biofilm formation on a catheter in the presence of neutrophils. This work provides new information on the antibacterial activity of five natural compounds and identified ferutinin as a promising candidate against S. aureus biofilms.