bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sahul’s megafauna were vulnerable to plant-community changes due to their position in the trophic network
Authors: Llewelyn John , Strona Giovanni , McDowell Matthew C. , Johnson Christopher N. , Peters Katharina J. , Stouffer Daniel B. , de Visser Sara N. , Saltré Frédérik , Bradshaw Corey J. A. 
Published: January 2021

AbstractExtinctions stemming from environmental change often trigger trophic cascades and coextinctions. However, it remains unclear whether trophic cascades were a large contributor to the megafauna extinctions that swept across several continents in the Late Pleistocene. The pathways to megafauna extinctions are particularly unclear for Sahul (landmass comprising Australia and New Guinea), where extinctions happened earlier than on other continents. We investigated the role of bottom-up trophic cascades in Late Pleistocene Sahul by constructing pre-extinction (~ 80 ka) trophic network models of the vertebrate community of Naracoorte, south-eastern Australia. These models allowed us to predict vertebrate species’ vulnerability to cascading extinctions based on their position in the network. We tested whether the observed extinctions could be explained by bottom-up cascades, or if they should be attributed to other external causes. Species that disappeared from the community were more vulnerable, overall, to bottom-up cascades than were species that survived. The position of extinct species in the network – having few or no predators – also suggests they might have been particularly vulnerable to a new predator. These results provide quantitative evidence that trophic cascades and naivety to predators could have contributed to the megafauna extinction event in Sahul.
Genome streamlining, proteorhodopsin, and organic nitrogen metabolism in freshwater nitrifiers
Authors: Podowski Justin C. , Paver Sara F. , Newton Ryan J. , Coleman Maureen L. 
Published: January 2021

AbstractMicrobial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth’s largest lakes. Surprisingly, ammonia oxidizing Bacteria (AOB) related to Nitrosospira dominated over ammonia oxidizing Archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival in conditions where ammonia oxidation is inhibited or substrate limited. Nitrite oxidizing Bacteria (NOB) Ca. Nitrotoga and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.ImportanceMicroorganisms play critical roles in Earth’s nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth’s largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low nutrient waters, and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.
Neisseria gonorrhoeaesubverts formin-dependent actin polymerization to colonize human macrophages
Authors: Ivanov Stanimir S. , Castore Reneau , Circu Magdalena , Dragoi Ana-Maria 
Published: January 2021

ABSTRACTDynamic reorganization of the actin cytoskeleton dictates plasma membrane morphology and is frequently subverted by bacterial pathogens for entry and colonization of host cells. The human-adapted bacterial pathogenNeisseria gonorrhoeaecan colonize and replicate when cultured with human macrophages, however the basic understanding of how this process occurs is incomplete.N. gonorrhoeaeis the etiological agent of the sexually transmitted disease gonorrhea and tissue resident macrophages are present in the urogenital mucosa which is colonized by the bacteria. We uncovered that when gonococci colonize macrophages they can establish an intracellular or a cell surface-associated niche that support bacterial replication independently. Unlike other intracellular bacterial pathogens, which enter host cells as single bacterium, establish an intracellular niche and then replicate, gonococci invade human macrophages as a colony. Individual diplococci are rapidly phagocytosed by macrophages and transported to lysosomes for degradation. However, we found that surface-associated gonococcal colonies of various sizes can invade macrophages by triggering actin skeleton rearrangement resulting in plasma membrane invaginations that slowly engulf the colony. The resulting intracellular membrane-bound organelle supports robust bacterial replication. The gonococci-occupied vacuoles evaded fusion with the endosomal compartment and were enveloped by a network of actin filaments. We demonstrate that gonococcal colonies invade macrophages via a process mechanistically distinct from phagocytosis that is regulated by the actin nucleating factor FMNL3. Our work provides insights into the gonococci life-cycle in association with human macrophages and defines key host determinants for macrophage colonization.
Inactivated rabies virus vectored SARS-CoV-2 vaccine prevents disease in a Syrian hamster model
Authors: Kurup Drishya , Malherbe Delphine C. , Wirblich Christoph , Lambert Rachael , Ronk Adam J. , Diba Leila Zabihi , Bukreyev Alexander , Schnell Matthias J. 
Published: January 2021

SummarySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent coronavirus that has caused a worldwide pandemic. Although human disease is often asymptomatic, some develop severe illnesses such as pneumonia, respiratory failure, and death. There is an urgent need for a vaccine to prevent its rapid spread as asymptomatic infections accounting for up to 40% of transmission events. Here we further evaluated an inactivated rabies vectored SARS-CoV-2 S1 vaccine CORAVAX in a Syrian hamster model. CORAVAX adjuvanted with MPLA-AddaVax, a TRL4 agonist, induced high levels of neutralizing antibodies and generated a strong Th1-biased immune response. Vaccinated hamsters were protected from weight loss and viral replication in the lungs and nasal turbinates three days after challenge with SARS-CoV-2. CORAVAX also prevented lung disease, as indicated by the significant reduction in lung pathology. This study highlights CORAVAX as a safe, immunogenic, and efficacious vaccine that warrants further assessment in human trials.
Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity
Authors: Grandjean Dominique , Al Marzooqi Dana Humaid , Lecoq-Julien Clothilde , Muzzin Quentin , Al Hammadi Hamad Katir , Alvergnat Guillaume , Al Blooshi Kalthoom Mohammad , Al Mazrouei Salah khalifa , Alhmoudi Mohammed Saeed , Al Ahbabi Faisal Musleh , Mohammed Yasser Saifallah , Alfalasi Nasser Mohammed , Almheiri Noor Majed , Al Blooshi Sumaya Mohamed , Desquilbet Loïc 
Published: January 2021

ABSTRACTThis study aimed to evaluate the sensitivity of 21 dogs belonging to different United Arab Emirates (UAE) Ministry of Interior (MOI), trained for COVID-19 olfactory detection.The study involved 17 explosives detection dogs, two cadaver detection dogs and two dogs with no previous detection training. Training lasted two weeks before starting the validation protocol. Sequential five and seven-cone line-ups were used with axillary sweat samples from symptomatic COVID-19 individuals (SARS-CoV-2 PCR positive) and from asymptomatic COVID-19 negative individuals (SARS-CoV-2 PCR negative). A total of 1368 trials were performed during validation, including 151 positive and 110 negative samples. Each line-up had one positive sample and at least one negative sample. The dog had to mark the positive sample, randomly positioned behind one of the cones. The dog, handler and data recorder were blinded to the positive sample location.The calculated overall sensitivities were between 71% and 79% for three dogs, between83% and 87% for three other dogs, and equal to or higher than 90% for the remaining 15 dogs (more than two thirds of the 21 dogs).After calculating the overall sensitivity for each dog using all line-ups, “matched” sensitivities were calculated only including line-ups containing COVID-19 positive and negative samples strictly comparable on confounding factors such as diabetes, anosmia, asthma, fever, body pain, diarrhoea, sex, hospital, method of sweat collection and sampling duration. Most of the time, the sensitivities increased after matching.Pandemic conditions in the U.A.E., associated with the desire to use dogs as an efficient mass-pretesting tool has already led to the operational deployment of the study dogs.Future studies will focus on comparatives fields-test results including the impact of the main COVID-19 comorbidities and other respiratory tract infections.
‘Candidatus Sarmatiella mevalonica’ endosymbiont of the ciliate Paramecium provides insights on evolutionary plasticity among Rickettsiales
Authors: Castelli Michele , Lanzoni Olivia , Nardi Tiago , Lometto Stefano , Modeo Letizia , Potekhin Alexey , Sassera Davide , Petroni Giulio 
Published: January 2021

SummaryMembers of the bacterial order Rickettsiales are obligatorily associated with a wide range of eukaryotic hosts. Their evolutionary trajectories, in particular concerning the origin of shared or differential traits among distant sub‐lineages, are still poorly understood. Here, we characterized a novel Rickettsiales bacterium associated with the ciliate Paramecium tredecaurelia and phylogenetically related to the Rickettsia genus. Its genome encodes significant lineage‐specific features, chiefly the mevalonate pathway gene repertoire, involved in isoprenoid precursor biosynthesis. Not only this pathway has never been described in Rickettsiales, it also is very rare among bacteria, though typical in eukaryotes, thus likely representing a horizontally acquired trait. The presence of these genes could enable an efficient exploitation of host‐derived intermediates for isoprenoid synthesis. Moreover, we hypothesize the reversed reactions could have replaced canonical pathways for producing acetyl‐CoA, essential for phospholipid biosynthesis. Additionally, we detected phylogenetically unrelated mevalonate pathway genes in metagenome‐derived Rickettsiales sequences, likely indicating evolutionary convergent effects of independent horizontal gene transfer events. Accordingly, convergence, involving both gene acquisitions and losses, is highlighted as a relevant evolutionary phenomenon in Rickettsiales, possibly favoured by plasticity and comparable lifestyles, representing a potentially hidden origin of other more nuanced similarities among sub‐lineages.
The Association of Coloproctology of Great Britain and Ireland consensus guidelines in emergency colorectal surgery
Authors: Miller Andrew S. , Boyce Kathryn , Box Benjamin , Clarke Matthew D. , Duff Sarah E. , Foley Niamh M. , Guy Richard J. , Massey Lisa H. , Ramsay George , Slade Dominic A. J. , Stephenson James A. , Tozer Phil J. , Wright Danette 
Published: January 2021

AbstractAimThere is a requirement for an expansive and up to date review of the management of emergency colorectal conditions seen in adults. The primary objective is to provide detailed evidence‐based guidelines for the target audience of general and colorectal surgeons who are responsible for an adult population and who practise in Great Britain and Ireland.MethodsSurgeons who are elected members of the Association of Coloproctology of Great Britain and Ireland Emergency Surgery Subcommittee were invited to contribute various sections to the guidelines. They were directed to produce a pathology‐based document using literature searches that were systematic, comprehensible, transparent and reproducible. Levels of evidence were graded. Each author was asked to provide a set of recommendations which were evidence‐based and unambiguous. These recommendations were submitted to the whole guideline group and scored. They were then refined and submitted to a second vote. Only those that achieved >80% consensus at level 5 (strongly agree) or level 4 (agree) after two votes were included in the guidelines.ResultsAll aspects of care (excluding abdominal trauma) for emergency colorectal conditions have been included along with 122 recommendations for management.ConclusionThese guidelines provide an up to date and evidence‐based summary of the current surgical knowledge in the management of emergency colorectal conditions and should serve as practical text for clinicians managing colorectal conditions in the emergency setting.
Implications for the colorectal surgeon following the 100 000 Genomes Project
Authors: McDermott Frank D. , Newton Katy , Beggs Andrew D. , Clark Susan K. 
Published: January 2021

AbstractAimThe 100 000 Genomes Project was completed in 2019 with the objective of integrating genomic medicine into routine National Health Service (NHS) clinical pathways. This project and genomic research will revolutionize the way we practice colorectal surgery in the 21st century. This paper aims to provide an overview of genomic medicine and its implications for the colorectal surgeon.ResultsWithin NHS England, consolidation has created seven regional Genomic Laboratory Hubs. DNA from solid tumours, including colorectal cancers, will be assessed using 500‐gene panels, results will be fed back to Genome Tumour Advisory Boards. Identifying variants from biopsies earlier in the clinical pathway may alter surgical and other treatment options for patients. However, there is an important distinction between somatic variants within a tumour biopsy and germline variants that may suggest a heritable condition such as Lynch syndrome. Novel drugs, for example immunotherapy, will increase treatment options including downstaging cancers and changing the surgical approach. The use of circulating tumour DNA (liquid biopsies) will have applications in diagnosis, treatment and surveillance of cancer. There are many exciting potential future applications of this technology for offering personalized medicine that will require multidisciplinary working and the colorectal community.ConclusionThere are many challenges but also exciting opportunities to embed new ‘omic’ technologies and innovation into 21st century colorectal surgery. The next phase for the colorectal community is how we engage with this change, with questions around training, identification of genomic multidisciplinary team (MDT) champions and how we collaborate with the core members of the MDT, clinical geneticists and national genomic testing.
Cutaneous involvement as initial presentation of multicentric plasmacytic Castleman disease
Authors: Chen Hongxiao , Ba Wei , Chen Hao , Yang Hongyu 
Published: January 2021

AbstractCastleman disease (CD) is an unusual lymphoproliferative disorder characterized by multiple lymphadenopathy accompanied by marked systemic inflammatory symptoms. CD can be unicentric (UCD) or multicentric (MCD), and it can be classified into three types based on histopathology: hyaline vascular type, plasma cell type, and mixed hyaline vascular and plasma cell type. CD involving skin is an unusual clinical manifestation. Abnormalities including rash, hyperpigmentation, cherry hemangiomatosis, paraneoplastic pemphigus, and Kaposi sarcoma have been reported to occur in MCD. Here, we reported an unusual case of MCD which presented initially with disseminated dark brown papules, patches, and plaques, and pathologically demonstrated plasma cell type CD, a finding which is rarely reported. The peculiar clinicopathological features will be discussed.
Primary epithelioid angiosarcoma of the thyroid: A case report
Authors: Bravaccini Sara , Caprara Licia , Cortecchia Stefania , De Lillo Margherita , Lega Stefania , Poli Francesca , Tasca Ignazio , Vacirca Anna , Cimatti Maria Chiara , Tumedei Maria Maddalena , Ravaioli Sara , Puccetti Maurizio 
Published: January 2021

AbstractAngiosarcoma of the thyroid is a rare and aggressive primary malignant tumour of the thyroid. We report the case of a 69‐year‐old woman who presented with a red and sore skin area at the right‐anterior region of the neck. Ultrasound examination and computed tomography scan showed a non‐homogeneous mass in the right thyroid lobe. Fine needle aspiration cytology was suggestive of atypical vascular proliferation and so the patient underwent right thyroid lobectomy. The specimen measured 6 × 5 × 2.5 cm, and a reddish nodule was found, including a whitish central area of maximum 4 cm in diameter. Immunohistochemistry showed CD31 and ERG positivity, while thyroglobulin, calcitonin and TTF‐1 expression were negative, indicating a diagnosis of angiosarcoma.
Is relationship evolution good or bad? It depends! A qualitative and quantitative examination of the relational behaviors and the stimulants of supply chain integration
Authors: Verghese Anto John , Koufteros Xenophon , Schoenherr Tobias , Vanpoucke Evelyne 
Published: January 2021

AbstractBuyer–supplier (B–S) relationships are dynamic. Nevertheless, research on external supply chain integration (SCI) has largely adopted a static‐snapshot perspective and has failed to grasp SCI's dynamic reality. The scant research devoted to SCI's dynamic perspectives suggests that the strength and scope of ties between buyers and suppliers differ based on integration levels. However, ambiguity persists regarding the relational behaviors exhibited across integration levels, as well as the stimulants that motivate firms to evolve their relationships. With buyers increasingly relying upon suppliers (and vice‐versa) and compounded by the knowledge that nearly half of SCI initiatives end up as failures, the need for a holistic framework that takes into account the underlying dynamics of relational behaviors and stimulants cannot be overstated. Using a mixed‐methods approach, six relational behaviors that differ in their saliency across SCI levels are identified, and eight stimulants that motivate B–S relationships to evolve are extracted. Specifically, we note that once a stimulant is activated, it remains influential across SCI levels, though its potency may vary. Our research significantly extends the contemporary understanding of SCI by (i) providing a holistic framework to comprehend SCI from a behavioral perspective, and (ii) noting that the highest integration levels do not necessarily typify successful B–S relationships. In doing so, we combine an evolutionary perspective with a relationship portfolio perspective for examining B–S relationship dynamics, thereby offering a comprehensive view to yield finer‐grained insights into B–S relationship dynamics.
Concepts and applications of ultrafast cardiac ultrasound imaging
Authors: Petrescu Aniela , D'hooge Jan , Voigt Jens‐Uwe 
Published: January 2021

AbstractThe concept of ultrafast echocardiographic imaging has been around for decades. However, only recent progress in ultrasound machine hardware and computer technology allowed to apply this concept to echocardiography. High frame rate echocardiography can visualize phenomena that have never been captured before. It enables a wide variety of potential new applications, including shear wave imaging, speckle tracking, ultrafast Doppler imaging, and myocardial perfusion imaging. The principles of these applications and their potential clinical use will be presented in this manuscript.
An exploration of student access to a learning management system—challenges and recommendations for educators and researchers
Authors: Chan Albert K.M. , Botelho Michael G. , Lam Otto L.T. 
Published: January 2021

AbstractIntroductionThis study examined student access to online resources of a faculty's learning management system (LMS). Issues relating to current e‐learning resources usage were identified and formed the basis for recommendations to help assist stakeholders in teaching, learning and research.MethodsLearning analytics from four cohorts of undergraduate dental students were extracted from the database of a LMS spanning between 2012 and 2016. Individual datasets were combined into one master file, re‐categorised, filtered and analysed based on cohort, year of study, course and nature of online resource.ResultsA total of 157,293 access events were documented. The proportion of administrative to learning data varied across cohorts, with oldest cohort having the highest ratio (82:18) in their final year and most recent cohort having a ratio of 33:67 in their 4th year demonstrating a higher proportion to learning. SevenLearningdomains were identified in the access data: access to problem‐based learning resources was the highest and next was fixed prosthodontics videos. The prosthodontics discipline had the highest access across the curriculum while some others had very limited or even no learning access events.ConclusionA number of limitations have been identified with the analytics and learning resources in this LMS and engagement with learning resource provision. More detailed data capture of access use and unique identifiers to resources as well as keyword tagging of the resources are required to allow accurate mapping and support of students learning. Moreover, motivation or nudging of students behaviour to more actively engage with learning content needs exploration.