bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyto‐morphological and clinical approach to infections presenting with discharging sinuses mimicking malignancy
Authors: Ravi Soundarya , Stephen Norton , Sreerekha Jinkala , Ramassamy Sivaranjini , Behera Biswanath , Gochhait Debasis 
Published: August 2020

AbstractIntroductionDischarging sinuses is a form of chronic unhealed infection that can present at any site due to a variety of infectious organisms. These discharging sinuses may be associated with mass lesions and lymphadenopathy to mimic some neoplastic processes. Identifying these infections with accuracy and promptness is essential, as the treatment regimens are specific. Fine‐needle aspiration (FNA) of these lesions, along with appropriate cytochemical stains, aids in the rapid and precise diagnosis of these infections and excludes neoplasms at these sites. Also, material for culture and other studies can be obtained by FNA.Material and methodsThis retrospective study was conducted in the Department of pathology from 2018 to 2020. A total of 179 patients with similar clinical presentation and confirmed infection on cytology were identified. On the evaluation of the requisition forms, 32 (18%) patients were identified with discharging sinus associated along with swelling.ResultsThe five infections (32 cases) that were identified, included 18 cases of tuberculosis (56.25%) followed by 9 cases of actinomycosis (28.12%), 3 cases of pheohypomycosis (9.37%), and one case each of Nocardia (3.12%) and eumycetoma (3.12%) which presented as swelling with discharging sinus. Special stains were performed in all cases for confirmation. Histopathological/Microbiological correlation was done whenever available.ConclusionInfections presenting as swelling with discharging sinuses mimicking malignancy can be diagnosed on FNAC with good accuracy.
Alveolar rhabdomyosarcomas involving serous cavity fluid specimens exhibit diverse cytomorphologies: A case report and review of the literature
Authors: Jones Robert M. , VandenBussche Christopher J. 
Published: August 2020

AbstractInvolvement of serous cavity specimens by alveolar rhabdomyosarcoma (ARMS) is a rare event and only a few case reports have been reported in the literature, with conflicting cytomorphologic patterns. Herein, we report on a 41‐year‐old man with no significant past medical history who presented with pancytopenia and shortness of breath and was found to have widely metastatic sinonasal alveolar rhabdomyosarcoma, including involvement of the pleura. The pleural fluid specimen was cellular and contained ARMS cells in small‐to‐medium sized three‐dimensional fragments that resembled an adenocarcinoma or mesothelioma, and numerous single cells were seen in the background. The individual tumor cells demonstrated variable morphology; all were large, with varying degree of cytoplasm, and multinucleated cells were commonly seen in the background. The cells were negative for calretinin and claudin‐4 and were positive for myogenin, confirming the diagnosis. Given the cytomorphologic diversity of ARMS seen in serous fluid specimens, patient history and the use of confirmatory immunostains are essential.
PDX1−/NKX6.1+ progenitors derived from human pluripotent stem cells as a novel source of insulin‐secreting cells
Authors: Memon Bushra , Younis Ihab , Abubaker Fadhil , Abdelalim Essam M. 
Published: August 2020

AbstractAimBeta cell replacement strategies are a promising alternative for diabetes treatment. Human pluripotent stem cells (hPSCs) serve as a scalable source for producing insulin‐secreting cells for transplantation therapy. We recently generated novel hPSC‐derived pancreatic progenitors, expressing high levels of the transcription factor NKX6.1, in the absence of PDX1 (PDX1−/NKX6.1+). Herein, our aim was to characterize this novel population and assess its ability to differentiate into insulin‐secreting beta cells in vitro.Materials and MethodsThree different hPSC lines were differentiated into PDX1−/NKX6.1+ progenitors, which were further differentiated into insulin‐secreting cells using two different protocols. The progenitors and beta cells were extensively characterized. Transcriptome analysis was performed at different stages and compared with the profiles of various pancreatic counterparts.ResultsPDX1−/NKX6.1+ progenitors expressed high levels of nestin, a key marker of pancreatic islet‐derived progenitors, in the absence of E‐cadherin, similar to pancreatic mesenchymal stem cells. At progenitor stage, comparison of the two populations showed downregulation of pancreatic epithelial genes and upregulation of neuronal development genes in PDX1−/NKX6.1+ cells in comparison to the PDX1+/NKX6.1+ cells. Interestingly, on further differentiation, PDX1−/NKX6.1+ cells generated mono‐hormonal insulin+ cells and activated pancreatic key genes, such as PDX1. The transcriptome profile of PDX1−/NKX6.1+‐derived beta (3D‐beta) was closely similar to those of human pancreatic islets and purified hPSC‐derived beta cells. Also, the 3D‐beta cells secreted C‐peptide in response to increased glucose concentrations indicating their functionality.ConclusionThese findings provide a novel source of insulin‐secreting cells that can be used for beta cell therapy for diabetes.
How faithfully does intramembranous bone regeneration recapitulate embryonic skeletal development?
Authors: Ko Frank C. , Sumner D. Rick 
Published: August 2020

AbstractPostnatal intramembranous bone regeneration plays an important role during a wide variety of musculoskeletal regeneration processes such as fracture healing, joint replacement and dental implant surgery, distraction osteogenesis, stress fracture healing, and repair of skeletal defects caused by trauma or resection of tumors. The molecular basis of intramembranous bone regeneration has been interrogated using rodent models of most of these conditions. These studies reveal that signaling pathways such as Wnt, TGFβ/BMP, FGF, VEGF, and Notch are invoked, reminiscent of embryonic development of membranous bone. Discoveries of several skeletal stem cell/progenitor populations using mouse genetic models also reveal the potential sources of postnatal intramembranous bone regeneration. The purpose of this review is to compare the underlying molecular signals and progenitor cells that characterize embryonic development of membranous bone and postnatal intramembranous bone regeneration.
A nontoxic fungal natural product modulates fin regeneration in zebrafish larvae upstream of FGF‐WNT developmental signaling
Authors: Cavanah Paul , Itou Junji , Rusman Yudi , Tahara Naoyuki , Williams Jessica M. , Salomon Christine E. , Kawakami Yasuhiko 
Published: August 2020

AbstractBackgroundThe regeneration of larvae zebrafish fin emerged as a new model of regeneration in the last decade. In contrast to genetic tools to study fin regeneration, chemical probes to modulate and interrogate regeneration processes are not well developed.ResultsWe set up a zebrafish larvae fin regeneration assay system and tested activities of natural product compounds and extracts, prepared from various microbes. Colomitide C, a recently isolated product from a fungus obtained from Antarctica, inhibited larvae fin regeneration. Using fluorescent reporter transgenic lines, we show that colomitide C inhibited fibroblast growth factor (FGF) signaling and WNT/β‐catenin signaling, which were activated after larvae fin amputation. By using the endothelial cell reporter line and immunofluorescence, we showed that colomitide C did not affect migration of the blood vessel and nerve into the injured larvae fin. Colomitide C did not show any cytotoxic activities when tested against FGF receptor‐amplified human cancer cell lines.ConclusionColomitide C, a natural product, modulated larvae fin regeneration likely acting upstream of FGF and WNT signaling. Colomitide C may serve as a template for developing new chemical probes to study regeneration and other biological processes.
Foraging by an avian ecosystem engineer extensively modifies the litter and soil layer in forest ecosystems
Authors: Maisey Alex C. , Haslem Angie , Leonard Steven W. J. , Bennett Andrew F. 
Published: August 2020

AbstractEcosystem engineers physically modify their environment, thereby altering habitats for other organisms. Increasingly, “engineers” are recognized as an important focus for conservation and ecological restoration because their actions affect a range of ecosystem processes and thereby influence how ecosystems function. The Superb LyrebirdMenura novaehollandiaeis proposed as an ecosystem engineer in forests of southeastern Australia due to the volume of soil and litter it turns over when foraging. We measured the seasonal and spatial patterns of foraging by Lyrebirds and the amount of soil displaced in forests in the Central Highlands, Victoria. We tested the effects of foraging on litter, soil nutrients and soil physical properties by using an experimental approach with three treatments: Lyrebird exclusion, Lyrebird exclusion with simulated foraging, and non‐exclusion reference plots. Treatments were replicated in three forest types in each of three forest blocks. Lyrebirds foraged extensively in all forest types in all seasons. On average, Lyrebirds displaced 155.7 Mg/ha of litter and soil in a 12‐month period. Greater displacement occurred where vegetation complexity (<50 cm height) was low. After two years of Lyrebird exclusion, soil compaction (top 7.5 cm) increased by 37% in exclusion plots compared with baseline measures, while in unfenced plots it decreased by 22%. Litter depth was almost three times greater in fenced than unfenced plots. Soil moisture, pH, and soil nutrients showed no difference between treatments. The enormous extent of litter and soil turned over by the Superb Lyrebird is unparalleled by any other vertebrate soil engineer in terrestrial ecosystems globally. The profound influence of such foraging activity on forest ecosystems is magnified by its year‐round pattern and widespread distribution. The disturbance regime that Lyrebirds impose has implications for diverse ecosystem processes including decomposition and nutrient cycling, the composition of litter‐ and soil‐dwelling invertebrate communities, the shaping of ground‐layer vegetation patterns, and fire behavior and post‐fire ecosystem recovery. Maintaining Lyrebird populations as a key facilitator of ecosystem function is now timely and critical as unprecedented wildfires in eastern Australia in summer 2019–2020 have severely burned ~12 million ha of forest, including ~30% of the geographic range of the Superb Lyrebird.
Trophic niche similarities of sympatric Turdus thrushes determined by fecal contents, stable isotopes, and bipartite network approaches
Authors: Bosenbecker Camila , Bugoni Leandro 
Published: August 2020

AbstractAn ecological niche has been defined as an n‐dimensional hypervolume formed by conditions and resources that species need to survive, grow, and reproduce. In practice, such niche dimensions are measurable and describe how species share resources, which has been thought to be a crucial mechanism for coexistence and a major driver of broad biodiversity patterns. Here, we investigate resource partitioning and trophic interactions of three sympatric, phylogenetically related and morphologically similar species of thrushes (Turdus spp.). Based on one year of data collected in southern Brazil, we investigated niche partitioning using three approaches: diet and trophic niche assessed by fecal analysis, diet and niche estimated by stable isotopes in blood and mixing models, and bipartite network analysis derived from direct diet and mixing model outputs. Approaches revealed that the three sympatric thrushes are generalists that feed on similar diets, demonstrating high niche overlap. Fruits from C3 plants were one of the most important food items in their networks, with wide links connecting the three thrush species. Turdus amaurochalinus and T. albicollis had the greatest trophic and isotopic niche overlap, with 90% and 20% overlap, respectively. There was partitioning of key resources between these two species, with a shared preference for fig tree fruits—Ficus cestrifolia (T. amaurochalinus PSIRI% = 11.3 and T. albicollis = 11.5), which was not present in the diet of T. rufiventris. Results added a new approach to the network analysis based on values from the stable isotope mixing models, allowing comparisons between traditional dietary analysis and diet inferred by isotopic mixing models, which reflects food items effectively assimilated in consumer tissues. Both are visualized in bipartite networks and show food‐consumers link strengths. This approach could be useful to other studies using stable isotopes coupled to network analysis, particularly useful in sympatric species with similar niches.
Seed bank characteristics in a Pinus densata forest and its relationship with vegetation diversity in Southeast Tibet, China
Authors: Lu Jie , Li Zhaoqing , Gao Tan , Tang Xiaoqin 
Published: August 2020

AbstractObjectiveWe aimed to understand the basic characteristics of the underground seed bank of Pinus densata forest and its relationship with aboveground vegetation, to provide a theoretical basis for vegetation restoration.MethodsThe study sites were Dongjiu Bridge (DJ), Linji Bridge (LZ), and Birishen Mountain Scenic Spot (RB) in Gongbu Nature Reserve, Southeast Tibet, China. Species composition and distribution pattern of the underground seed bank in P. densata forest were analyzed. Germination data and field investigations were used to examine the similarities between aboveground vegetation and underground seed banks, and their responses to the environment.ResultsThere were 47 species belonging to 27 families in the underground seed bank of the P. densata forest. Asteraceae, Rosaceae, Labiatae, and Poaceae were dominant, accounting for 40.4% of the total number of families. Underground seed density was 2,114, 1,952, and 1,141 seeds/m2 in DJ, LZ, and BR, respectively. The percentage of different life‐forms in each sampling location was shown to be perennial herbs > shrubs > annual herbs > trees > subshrubs. The Shannon–Wiener diversity index, Margalef richness index, and Simpson's dominance index of each sample showed that species decreased with higher elevation, while the Pielou evenness index showed the opposite trend. Elevation, slope position, slope aspect, and slope were positively correlated with the Pielou evenness index and negatively correlated with the Shannon–Wiener diversity index, Margalef richness index, and Simpson's dominance index. The Sørensen index, comparing the similarity between the underground seed bank and aboveground vegetation of DJ, LZ, and BR was 0.46, 0.35, and 0.31, respectively.ConclusionThe underground seed bank of P. densata forest has high seed density and high species richness, but there was little similarity between aboveground vegetation and underground seed bank. Elevation and slope position had a great influence on the uniformity of species distribution.
Diversity of medium and large mammals in the Loka Abaya National Park, southern Ethiopia
Authors: Diriba Guta , Tamene Sintaheyu , Mengesha Girma , Asefa Addisu 
Published: August 2020

AbstractWe evaluated the richness, diversity, and composition of the medium and large mammal community in the Loka Abaya National Park (LANP), southern Ethiopia, and how these parameters differ among four habitat types: wooded grassland, riverine forest, hilly scrubland and wetland, and between seasons. We recorded a total of 2,573 individual animals of 28 medium and large mammal species in the park. This included three globally threatened species: the endangered African wild dog (Lycaon pictus), the vulnerable Leopard (Panthera pardus), and Hippopotamus (Hippopothamus amphibius). Season had little effect on species richness, diversity, and composition both across and within habitat types. However, species richness across seasons was significantly different among the four habitat types, in the declining order of the following: wooded grassland > riverine forest > hilly scrubland > wetland. The strongest similarity in species composition, both across and within seasons, was found between wooded grassland and riverine forest. In terms of relative abundance, mammal assemblage of the wooded grassland and wetland habitats had more evenly distributed number of species with different relative abundance categories. Overall, Anubis Baboon (Papio anubis), Grivet Monkey (Chlorocebus aethiops), and Greater Kudu (Tragelephus strepsiceros) were the three most abundant species across habitat types. In conclusion, findings of our study reveal that LANP plays an important role in Ethiopia's mammal conservation. Our findings will serve as baseline information for managers of the park to make effective conservation decisions and as a baseline for researchers wishing to conduct related ecological studies.
A landscape‐scale assessment of the relationship between grassland functioning, community diversity, and functional traits
Authors: van 't Veen Hanneke , Chalmandrier Loïc , Sandau Nadine , Nobis Michael P. , Descombes Patrice , Psomas Achilleas , Hautier Yann , Pellissier Loïc 
Published: August 2020

AbstractLivestock farmers rely on a high and stable grassland productivity for fodder production to sustain their livelihoods. Future drought events related to climate change, however, threaten grassland functionality in many regions across the globe. The introduction of sustainable grassland management could buffer these negative effects. According to the biodiversity–productivity hypothesis, productivity positively associates with local biodiversity. The biodiversity–insurance hypothesis states that higher biodiversity enhances the temporal stability of productivity. To date, these hypotheses have mostly been tested through experimental studies under restricted environmental conditions, hereby neglecting climatic variations at a landscape‐scale. Here, we provide a landscape‐scale assessment of the contribution of species richness, functional composition, temperature, and precipitation on grassland productivity. We found that the variation in grassland productivity during the growing season was best explained by functional trait composition. The community mean of plant preference for nutrients explained 24.8% of the variation in productivity and the community mean of specific leaf area explained 18.6%, while species richness explained only 2.4%. Temperature and precipitation explained an additional 22.1% of the variation in productivity. Our results indicate that functional trait composition is an important predictor of landscape‐scale grassland productivity.
Spatial grain of adaptation is much finer than ecoregional‐scale common gardens reveal
Authors: Davidson Bill E. , Germino Matthew J. 
Published: August 2020

AbstractAdaptive variation among plant populations must be known for effective conservation and restoration of imperiled species and predicting their responses to a changing climate. Common‐garden experiments, in which plants sourced from geographically distant populations are grown together such that genetic differences may be expressed, have provided much insight on adaptive variation. Common‐garden experiments also form the foundation for climate‐based seed‐transfer guidelines. However, the spatial scale at which population differentiation occurs is rarely addressed, leaving a critical information gap for parameterizing seed‐transfer guidelines and assessing species’ climate vulnerability. We asked whether adaptation was evident among populations of a foundational perennial within a single “empirical” seed‐transfer zone (based on previous common‐garden findings evaluating very distant populations) but different “provisional” seed zones (groupings of areas of similar climate and are not parameterized from common‐garden data). Seedlings from three populations originating from similar conditions within an intermediate elevation were planted into gardens nearby at the same elevation, or 250–450 m higher or lower in elevation and 0.4–25 km away. Substantial variation was observed between gardens in survival (ranging 2%–99%), foliar crown volume (7.8–22.6 dm3), and reproductive effort (0%–65%), but not among the three transplanted populations. The between garden variation was inversely related to climatic differences between the gardens and seed‐source populations, specifically the site differences in maximum–minimum annual temperatures. Results suggest that substantial site‐specificity in adaptation can occur at finer scales than is accounted for in empirical seed‐transfer guidance when the guidance is derived from broadscale common‐garden studies. Being within the same empirical seed zone, geographic unit, and even within 10 km distance may not qualify as “local” in the context of seed transfer. Moving forward, designing common‐garden experiments so that they allow for testing the scale of adaptation will help in translating the resulting seed‐transfer guidance to restoration projects.
Trade‐off between fecundity and survival generates stabilizing selection on gall size
Authors: Weaver Amanda K. , Hood Glen Ray , Foster Michael , Egan Scott P. 
Published: August 2020

AbstractComplex interactions within multitrophic communities are fundamental to the evolution of individual species that reside within them. One common outcome of species interactions are fitness trade‐offs, where traits adaptive in some circumstances are maladaptive in others. Here, we identify a fitness trade‐off between fecundity and survival in the cynipid wasp Callirhytis quercusbatatoides that induces multichambered galls on the stem of its host plant Quercus virginiana. We first quantified this trade‐off in natural populations by documenting two relationships: a positive association between the trait gall size and fecundity, as larger galls contain more offspring, and a negative association between gall size and survival, as larger galls are attacked by birds at a higher rate. Next, we performed a field‐based experimental evolution study where birds were excluded from the entire canopy of 11 large host trees for five years. As a result of the five‐year release from avian predators, we observed a significant shift to larger galls per tree. Overall, our study demonstrates how two opposing forces of selection can generate stabilizing selection on a critical phenotypic trait in wild populations, and how traits can evolve rapidly in the predicted direction when conditions change.