bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmon louse infestation levels on sea trout can be predicted from a hydrodynamic lice dispersal model
Authors: Bøhn Thomas , Nilsen Rune , Gjelland Karl Øystein , Biuw Martin , Sandvik Anne Dagrun , Primicerio Raul , Karlsen Ørjan , Serra‐Llinares Rosa Maria 
Published: December 2021

AbstractThe abundance of the parasitic salmon louse has increased with the growth in aquaculture of salmonids in open net pens. This represents a threat to wild salmonid populations as well as a key limiting factor for salmon farming. The Norwegian ‘traffic light’ management system for salmon farming aims to increase aquaculture production while securing sustainable wild salmonid populations. However, this system is at present solely focusing on mortality in wild Atlantic salmon, while the responses of sea trout with different ecological characteristics are not included.We analyse lice counts on sea trout from surveillance data and use Bayesian statistical models to relate observed lice infestations to the environmental lice infestation pressure, salinity and current speed. These models can be used in risk assessment to predict when and where lice numbers surpass threshold levels for expected serious health effects in wild sea trout.We find that in production areas with the highest density of salmon farms (West coast), more than 50% of the sea trout experienced lice infestations above the levels of expected serious health effects.We also observed high lice infestations on sea trout in areas with salinities below louse tolerance levels, indicating that fish had been infested elsewhere but were returning to low‐saline waters to delouse. This behavioural response may over time disrupt anadromy in sea trout.The observed infestations on sea trout can be explained by the hydrodynamic lice dispersal model, which provides continuous estimates of lice exposure along the whole Norwegian coast. These estimates, which are used in Atlantic salmon research and management, can also be used for sea trout.Synthesis and applications. Wild sea trout, spending its entire feeding migration in fjords and coastal areas, is at higher risk than wild Atlantic salmon to lice infestations from industrial salmon farming. The high levels of lice infestation we observed on sea trout question the environmental sustainability of the current aquaculture industry in areas with intensive farming. We discuss the complex responses of sea trout to salmon lice and how the Norwegian ‘traffic light’ management system may include data on sea trout.
Assessment of plant diversity and foliar chemistry on the Sri Lankan ultramafics reveals inconsistencies in the metal hyperaccumulator trait
Authors: Fernando Denise R. M. , van der Ent Antony , Weerasinghe Asiri S. , Wijesundara Douglas Siril A. , Fernando Gunawarna W. A. Rohan , Fernando Anthony E. , Iqbal Mohamed C. M. , Miranda Charlotte H. , Gosse Jordan M. , Samithri Sadhana , Rajakaruna Nishanta 
Published: December 2021

AbstractSome of the largest expanses of ultramafic soils occur in South Asia, but knowledge of the plant diversity and biogeochemistry of these systems in Sri Lanka is very limited. This study aimed to assess the plant diversity and bedrock and foliar chemistry of all known Sri Lankan ultramafic outcrops. The field survey yielded a total of 132 plant taxa from 44 families. The enigmatic nickel hyperaccumulator Rinorea bengalensis (Violaceae), first reported in Sri Lanka over four decades ago, was rediscovered at a newly surveyed ultramafic site, however, it did not hyperaccumulate nickel. No new metal hyperaccumulator plants were identified, suggesting that R. bengalensis is a facultative nickel hyperaccumulator. This study is the first to highlight the floristic diversity of all known Sri Lankan ultramafic outcrops while revealing the facultative nature of nickel and copper hyperaccumulation among some of Sri Lanka's ultramafic plants.
Experimental evolution of Pseudomonas putida under silver ion versus nanoparticle stress
Authors: Dong Feng , Quevedo Ana C. , Wang Xiang , Valsami‐Jones Eugenia , Kreft Jan‐Ulrich 
Published: December 2021

SummaryWhether the antibacterial properties of silver nanoparticles (AgNPs) are simply due to the release of silver ions (Ag+) or, additionally, nanoparticle‐specific effects, is not clear. We used experimental evolution of the model environmental bacterium Pseudomonas putida to ask whether bacteria respond differently to Ag+ or AgNP treatment. We pre‐evolved five cultures of strain KT2440 for 70 days without Ag to reduce confounding adaptations before dividing the fittest pre‐evolved culture into five cultures each, evolving in the presence of low concentrations of Ag+, well‐defined AgNPs or Ag‐free controls for a further 75 days. The mutations in the Ag+ or AgNP evolved populations displayed different patterns that were statistically significant. The non‐synonymous mutations in AgNP‐treated populations were mostly associated with cell surface proteins, including cytoskeletal membrane protein (FtsZ), membrane sensor and regulator (EnvZ and GacS) and periplasmic protein (PP_2758). In contrast, Ag+ treatment was selected for mutations linked to cytoplasmic proteins, including metal ion transporter (TauB) and those with metal‐binding domains (ThiL and PP_2397). These results suggest the existence of AgNP‐specific effects, either caused by sustained delivery of Ag+ from AgNP dissolution, more proximate delivery from cell‐surface bound AgNPs, or by direct AgNP action on the cell's outer membrane.
Precambrian Tectonic Affinity of the Southern Langshan Area, Northeastern Margin of the Alxa Block: Evidence from Zircon U‐Pb Dating and Lu‐Hf Isotopes
Authors: NIU Pengfei , QU Junfeng , ZHANG Jin , ZHANG Beihang , ZHAO Heng 
Published: December 2021

AbstractThe Alxa Block is the westernmost part of the North China Craton (NCC), and is regarded as one of the basement components of the NCC. Its geological evolution is of great significance for the understanding of the NCC. However, the Precambrian basement of the Alxa Block is still poorly studied. In this study, we present new in situ LA‐ICP‐MS zircon U‐Pb and Lu‐Hf isotope data from the Diebusige Metamorphic Complex (DMC) which located in the eastern Alxa Block. Field and petrological studies show that the DMC consists mainly of metamorphic supracrustal rocks and minor metamorphic plutonic rocks and has experienced amphibolite‐granulite facies metamorphism. Zircon U‐Pb dating results suggested that the amphibolite sample yields a crystallization age of 2636 ± 14 Ma and metamorphic ages of 2517–2454 Ma and 1988–1952 Ma, proving the existence of exposed Archean rocks in the Langshan area and indicating that late Neoarchean to Paleoproterozoic metamorphic events existed in the Alxa Block. Two paragneiss samples show that the magmatic detrital zircons from the DMC yield 207Pb/206Pb ages ranging from 2.48 Ga to 2.10 Ga with two youngest peaks at 2.13 Ga and 2.16 Ga, respectively, and they were also overprinted by metamorphic events at 1.97–1.90 Ga and 1.89–1.79 Ga. Compilation of U‐Pb ages of magmatic detrital and metamorphic zircons suggested that the main part of the DMC may have been formed at 2.1–2.0 Ga. Zircon Lu‐Hf isotope data show that the source materials of the main part of the DMC were originated from the reworking of ancient Archean crust (3.45–2.78 Ga). The Hf isotope characteristics and the tectonothermal event records exhibit different evolution history with the Khondalite Belt and the Yinshan Block and the other basements of the Alxa Block, indicating that the Langshan was likely an independent terrain before the middle Paleoproterozoic and was subjected to the middle to late Paleoproterozoic tectonothermal events with the Khondalite Belt as a whole.
Treatment with immune checkpoint inhibitors after EGFR‐TKIs in EGFR‐mutated lung cancer
Authors: Ito Takashi , Nagashima Hiromi , Akiyama Masachika , Utsumi Yu , Sato Hideomi , Chiba Shinji , Sugai Mayu , Ube Kenji , Mori Yoshiaki , Watanabe Kana , Fukuhara Tatsuro , Maemondo Makoto 
Published: December 2021

AbstractBackgroundEpidermal growth factor receptor‐tyrosine kinase inhibitors (EGFR‐TKIs) have become the gold standard for EGFR‐mutated non‐small cell lung cancer (NSCLC) treatment. Immune checkpoint inhibitors (ICIs) have been developed for the treatment of several malignancies, including lung cancer. However, it is known that ICIs have poorer efficacy in EGFR‐mutated NSCLC.MethodsWe collected data for patients with EGFR‐mutated NSCLC receiving monotherapy with ICIs after EGFR‐TKIs between December 2015 and March 2020 in three institutions, and retrospectively analyzed the association between patient characteristics and efficacy of ICIs.ResultsA total of 25 patients were included in this study. We defined responders as patients undergoing 90 days or longer of ICI treatment. Comparing characteristics between responders and non‐responders, more tumors with L858R EGFR mutation were observed in responders than in non‐responders (L858R: 66.7% and 25.0%, respectively, p < 0.05). There was no difference in incidence of T790M resistance mutation before ICI treatment. The PD‐L1 positive rate was slightly higher in responders but not statistically significant (22.2% and 12.5%, respectively). Median duration of EGFR‐TKI pretreatment was shorter in ICI responders compared with nonresponders (13.3 and 19.9 months, respectively). The survival of patients with L858R tumors was significantly longer than that of patients with exon 19 deletion (HR: 0.35, 95% CI: 0.13–0.93, p = 0.026).ConclusionsICI treatment tends to have better efficacy in patients with L858R‐mutated tumors. This study suggests that patients with L858R‐mutated NSCLC are candidates for ICI treatment after EGFR‐TKI treatment.
BoomBox: An Automated Behavioural Response (ABR) camera trap module for wildlife playback experiments
Authors: Palmer Meredith S. , Wang Chris , Plucinski Jacinta , Pringle Robert M. 
Published: December 2021

Abstract

Camera traps (CTs) are a valuable tool in ecological research, amassing large quantities of information on the behaviour of diverse wildlife communities. CTs are predominantly used as passive data loggers to gather observational data for correlational analyses. Integrating CTs into experimental studies, however, can enable rigorous testing of key hypotheses in animal behaviour and conservation biology that are otherwise difficult or impossible to evaluate.

We developed the 'BoomBox', an open‐source Arduino‐compatible board that attaches to commercially available CTs to form an Automated Behavioural Response (ABR) system. The modular unit connects directly to the CT’s passive infrared (PIR) motion sensor, playing audio files over external speakers when the sensor is triggered. This creates a remote playback system that captures animal responses to specific cues, combining the benefits of camera trapping (e.g. continuous monitoring in remote locations, lack of human observers, large data volume) with the power of experimental manipulations (e.g. controlled perturbations for strong mechanistic inference).

Our system builds on previous ABR designs to provide a cheap (~100USD) and customizable field tool. We provide a practical guide detailing how to build and operate the BoomBox ABR system with suggestions for potential experimental designs that address a variety of questions in wildlife ecology. As proof‐of‐concept, we successfully field tested the BoomBox in two distinct field settings to study species interactions (predator–prey and predator–predator) and wildlife responses to conservation interventions.

This new tool allows researchers to conduct a unique suite of manipulative experiments on free‐living species in complex environments, enhancing the ability to identify mechanistic drivers of species' behaviours and interactions in natural systems.
Rapid alignment updating with Extensiphy
Authors: Field Jasper Toscani , Abrams A. Jeanine , Cartee John C. , McTavish Emily Jane 
Published: December 2021

Abstract

High‐throughput sequencing has become commonplace in evolutionary studies. Large, rapidly collected genomic datasets are used to capture biodiversity and for monitoring global and national scale disease transmission patterns, among many other applications. Updating homologous sequence datasets with new samples is cumbersome, requiring excessive program runtimes and data processing. We describe Extensiphy, a bioinformatics tool to efficiently update multiple sequence alignments with whole‐genome short‐read data. Extensiphy performs reference based sequence assembly and alignment in one process while maintaining the alignment length of the original alignment. Input data‐types for Extensiphy are any multiple sequence alignment in fasta format and whole‐genome, short‐read fastq sequences.

To validate Extensiphy, we compared its results to those produced by two other methods that construct whole‐genome scale multiple sequence alignments. We measured our comparisons by analysing program runtimes, base‐call accuracy, dataset retention in the presence of missing data and phylogenetic accuracy.

We found that Extensiphy rapidly produces high‐quality updated sequence alignments while preventing alignment shrinkage due to missing data. Phylogenies estimated from alignments produced by Extensiphy show similar accuracy to other commonly used alignment construction methods.

Extensiphy is suitable for updating large sequence alignments and is ideal for studies of biodiversity, ecology and epidemiological monitoring efforts.
Deletion of SA β‐Gal+ cells using senolytics improves muscle regeneration in old mice
Authors: Dungan Cory M. , Murach Kevin A. , Zdunek Christopher J. , Tang Zuo Jian , Nolt Georgia L. , Brightwell Camille R. , Hettinger Zachary , Englund Davis A. , Liu Zheng , Fry Christopher S. , Filareto Antonio , Franti Michael , Peterson Charlotte A. 
Published: December 2021

AbstractSystemic deletion of senescent cells leads to robust improvements in cognitive, cardiovascular, and whole‐body metabolism, but their role in tissue reparative processes is incompletely understood. We hypothesized that senolytic drugs would enhance regeneration in aged skeletal muscle. Young (3 months) and old (20 months) male C57Bl/6J mice were administered the senolytics dasatinib (5 mg/kg) and quercetin (50 mg/kg) or vehicle bi‐weekly for 4 months. Tibialis anterior (TA) was then injected with 1.2% BaCl2 or PBS 7‐ or 28 days prior to euthanization. Senescence‐associated β‐Galactosidase positive (SA β‐Gal+) cell abundance was low in muscle from both young and old mice and increased similarly 7 days following injury in both age groups, with no effect of D+Q. Most SA β‐Gal+ cells were also CD11b+ in young and old mice 7‐ and 14 days following injury, suggesting they are infiltrating immune cells. By 14 days, SA β‐Gal+/CD11b+ cells from old mice expressed senescence genes, whereas those from young mice expressed higher levels of genes characteristic of anti‐inflammatory macrophages. SA β‐Gal+ cells remained elevated in old compared to young mice 28 days following injury, which were reduced by D+Q only in the old mice. In D+Q‐treated old mice, muscle regenerated following injury to a greater extent compared to vehicle‐treated old mice, having larger fiber cross‐sectional area after 28 days. Conversely, D+Q blunted regeneration in young mice. In vitro experiments suggested D+Q directly improve myogenic progenitor cell proliferation. Enhanced physical function and improved muscle regeneration demonstrate that senolytics have beneficial effects only in old mice.
Myoepithelioma‐like tumour of the vulval region: A case report
Authors: Lin Yee Sing , Parasyn Andrew , Paulus Felik , Davidson Trent 
Published: December 2021

AbstractMyoepithelioma‐like tumours of the vulvar region (MELTVR) are a newly described group of spindle cell neoplasm. Morphologically, they consist of epithelioid to spindled cells in a myxoid to collagenous stroma and can resemble epithelioid sarcomas, myoepithelial carcinomas or extraskeletal myxoid chondrosarcomas. However, they have a distinct pattern of immunohistochemical staining characterised by positivity for EMA, ER, PR and negativity for cytokeratin, GFAP and S100. Nuclear staining for INI‐1 is lost. In addition, they lack the characteristic gene arrangements of these other lesions. MELTVR can recur locally when incompletely excised, however, do not appear to metastasize. We report a case of a MELTVR in a 49‐year‐old woman arising in the right mons pubis.
Epidemiological, clinical, pathological and genetic characteristics of epidermolysis bullosa in New Zealand
Authors: Gear Russell , Poke Gemma , Neas Katherine , Finnigan Jacqui , Cassidy Sharon , Forsyth Deanna , Blishen Mo , Purvis Diana 
Published: December 2021

AbstractObjectiveTo establish the epidemiological, clinical, pathological and genetic characteristics of epidermolysis bullosa (EB) in New Zealand (NZ).MethodsParticipants were recruited through the Dystrophic Epidermolysis Bullosa Research Association of New Zealand (DEBRA NZ). Dedicated EB nurse medical records, Genetic Health Service NZ (GHSNZ) records and, where available, public hospital records were manually reviewed for relevant clinical data.ResultsNinety‐two participants took part in the study (56% participation rate). Forty‐nine (53%) participants had EB simplex (EBS), 40 (43%) had dystrophic EB (DEB), and 3 (3%) had junctional EB (JEB). Point prevalence for EB of all types was 19.5 per million, and 10.4, 8.6 and 0.9 per million for EBS, DEB and JEB, respectively. Thirty‐four participants had intermediate or severe EB. There were 29 paediatric cases and almost even numbers of males and females. Compared to NZ European and Māori, prevalence rates were lower for Pacific and Asian people and higher in the Middle Eastern/Latin American/African population. Eight out of 14 skin biopsy results were informative, and 14 of 15 genetic test results were informative.ConclusionNew Zealand has similar prevalence rates of EB compared with other national cohorts. This is likely to be an underestimate due to methodological limitations. Recent advancements in genomic testing have resulted in an improved diagnostic rate in our population. Further research into ethnic differences in prevalence, and exploring the characteristics of lethal forms of EB, is warranted. A dynamic registry may be helpful for the EB community in NZ.
Ram epididymal sperm frozen in an extender containing ethylene glycol have higher post‐thaw longevity and in vitro fertility
Authors: Ahmadi Ebrahim , Shams‐Esfandabadi Naser , Nazari Hassan , Davoodian Najmeh , Kadivar Ali 
Published: December 2021

AbstractBackgroundEstablishing an efficient, simple and inexpensive method for freezing ram epididymal sperm so that the quality and fertility of spermatozoa could be maintained for a longer period after thawing is of great practical value.ObjectivesTo optimize freezing and thawing protocol for ram epididymal sperm using either ethylene glycol (EG) or glycerol (GLY) as cryoprotectants (CPAs). Then, to evaluate the post‐thaw longevity and in vitro fertility of spermatozoa that were frozen and thawed according to the optimized protocol.Materials and methodsAt first, an optimum protocol for freezing and thawing sperm using EG or GLY were investigated, and the next experiments were performed using the spermatozoa that had been frozen and thawed according to the optimized protocol for each CPA. In the next experiments, frozen‐thawed and fresh sperm were diluted in an isotonic culture medium and subsequently incubated at 39°C for 4 h. The motility characteristics and functional membrane integrity (FMI) of spermatozoa were evaluated after thawing, after dilution (t0), and after incubation (t4). The in vitro fertility of the spermatozoa was assessed at t0 and t4.ResultsFor both CPAs, the highest motility parameters and FMI was found for spermatozoa frozen at 3 cm above LN2 and thawed at 50 and 65°C (P < 0.05). In comparison to the spermatozoa of GLY group, the spermatozoa of the EG group had higher total and progressive motility at t0, as well as higher FMI, total and progressive motility, and linearity at t4 (P < 0.05). Fertility of frozen‐thawed sperm was higher than that of fresh sperm at t0 (P < 0.05). Incubation treatment increased the fertility of fresh sperm while decreased the fertility of frozen‐thawed sperm, and this decline was more severe in GLY than in the EG group.ConclusionBased on the findings, EG can be a more suitable CPA for freezing ram epididymal sperm.
Extracorporeal membrane oxygenation seems to induce impairment of primary hemostasis pathology as measured by a Multiplate analyzer: An observational retrospective study
Authors: Garaj Michal , Durila Miroslav , Vajter Jaromir , Solcova Michaela , Marecek Frantisek , Hrachovinová Ingrid 
Published: December 2021

AbstractBackgroundExtracorporeal membrane oxygenation (ECMO) support is often associated with bleeding complications caused by secondary or primary hemostasis pathology. However, there are limited data investigating primary hemostasis using Multiplate aggregometry with specific diagnostics tests for vWF (von Willebrand factor) deficiency.AimsThe aim of this study was to find out whether short‐term ECMO produces the pathology of primary hemostasis that is detected by Multiplate aggregometry and to investigate the pathology of vWF.MethodsIn this study, blood samples of 20 patients undergoing lung transplantations with short‐term perioperative ECMO support were analyzed. The multimeric structure, the levels of von Willebrand factor antigen (vWF), ristocetin cofactor (RCo), collagen‐binding protein (CB), and the results of multiple electrode aggregometry RISTO (ristocetin), ADP (adenosine diphosphate), ASPI (Aspirin®; arachidonic acid), and TRAP (thrombin receptor activating peptide) tests were compared to the samples obtained before and after ECMO support.ResultsThe Multiplate ADP and RISTO tests showed the presence of significant pathology in primary hemostasis after surgery (p < 0.05), suggesting the presence of acquired platelet dysfunction. Although the RISTO tests suggest the presence of acquired vWF deficiency, laboratory tests for vWF antigen and RCo and CB tests showed an increase in this case. The multimeric structure of vWF did not show clinically significant deterioration.ConclusionsMultiple aggregometry ADP, ASPI, and TRAP tests seem to be able to detect primary hemostasis pathology (platelets aggregation and adhesion pathology) that is present during short‐term perioperative ECMO support in lung transplantation procedures. Interestingly, RISTO tests seem to be more suitable for the diagnosis of platelet dysfunction than the diagnosis of acquired vWF deficiency in this situation.