bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new model of forelimb ecomorphology for predicting the ancient habitats of fossil turtles
Authors: Dudgeon Thomas W. , Livius Marissa C. H. , Alfonso Noel , Tessier Stéphanie , Mallon Jordan C. 
Published: November 2021

AbstractVarious morphological proxies have been used to infer habitat preferences among fossil turtles and their early ancestors, but most are tightly linked to phylogeny, thereby minimizing their predictive power. One particularly widely used model incorporates linear measurements of the forelimb (humerus + ulna + manus), but in addition to the issue of phylogenetic correlation, it does not estimate the likelihood of habitat assignment. Here, we introduce a new model that uses intramanual measurements (digit III metacarpal + non‐ungual phalanges + ungual) to statistically estimate habitat likelihood and that has greater predictive strength than prior estimators. Application of the model supports the hypothesis that stem‐turtles were primarily terrestrial in nature and recovers the nanhsiungchelyid Basilemys (a fossil crown‐group turtle) as having lived primarily on land, despite some prior claims to the contrary.
Boreal tree species change as a climate mitigation strategy: impact on ecosystem C and N stocks and soil nutrient levels
Authors: Kjønaas O. Janne , Bárcena Teresa G. , Hylen Gro , Nordbakken Jørn‐Frode , Økland Tonje 
Published: November 2021

AbstractTo increase the annual uptake of CO2 as well as the long‐term storage of carbon (C) in forests, the Norwegian government consider large‐scale replacements of native, deciduous forests with faster‐growing species like Norway spruce. To assess the effects of tree species change on ecosystem C and nitrogen (N) stocks and soil chemistry, we used a paired plot approach including stands of native downy birch and planted 45‐ to 60‐yr‐old Norway spruce. The birch stands were used as reference for the assessment of differences following the tree species change. We found significantly higher C and N stocks in living tree biomass in the spruce stands, whereas no significant differences were found for dead wood. The cover of understory species groups, and the C and N stocks of the aboveground understory vegetation were significantly higher in the birch stands. The tree species change did not affect the soil organic carbon (SOC) stock down to 1 m soil depth; however, the significantly higher stock in the forest floor of the spruce stands suggested a re‐distribution of SOC within the profile. There was a significant positive correlation between the SOC stock down to 30 cm soil depth and the total ecosystem C stock for the birch stands, and a negative correlation for the spruce stands. Significant effects of tree species change were found for C and N concentrations, C/N, exchangeable acidity, base saturation, and exchangeable Ca, K, Mg, Na, S, and Fe in the organic horizon or the upper mineral soil layer. The total ecosystem C stock ranged between 197 and 277 Mg/ha for the birch stands, and 297 and 387 Mg/ha for the spruce stands. The ecosystem C accumulation varied between 32 and 142 Mg/ha over the past 45–60 yr, whereas the net ecosystem C capture was considerably lower and potentially negative. Our results suggest that the potential to meet the governments' targets to increase C sequestration depend on the C debt incurred from the removed birch stands, the rotation length, and potentially also the susceptibility of the different stand types to future risk factors related to climate change.
From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the neonMicrobe R package
Authors: Qin Clara , Bartelme Ryan , Chung Y. Anny , Fairbanks Dawson , Lin Yang , Liptzin Daniel , Muscarella Chance , Naithani Kusum , Peay Kabir , Pellitier Peter , St. Rose Ayanna , Stanish Lee , Werbin Zoey , Zhu Kai 
Published: November 2021

AbstractSoil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON’s newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced by neonMicrobe can be linked to NEON’s other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporating neonMicrobe into reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and the neonMicrobe R package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.
MetaBARFcoding: DNA‐barcoding of regurgitated prey yields insights into Christmas shearwater (Puffinus nativitatis) foraging ecology at Hōlanikū (Kure Atoll), Hawaiʻi
Authors: Nimz Ilana , Renshaw Mark A. , Baczenas John , Vanderlip Cynthia , Hyrenbach K. David , Iacchei Matthew 
Published: November 2021

AbstractMorphological identification of digested prey remains from a generalist predator can be challenging, especially when attempting to match degraded remains to taxonomic keys. DNA techniques, whereby prey is sequenced and matched to large public nucleotide sequence databases, are increasingly being used to augment morphological identification. We used “metaBARFcoding” (DNA metabarcoding) to target a region of the cytochrome c oxidase subunit I (COI) mitochondrial gene to identify prey in highly digested regurgitations from Christmas shearwaters Puffinus nativitatis at Hōlanikū (Kure Atoll). Metabarcoding was used to bulk‐process 92 water samples from regurgitations collected from 2009 to 2017, providing an overview of the seabird's diet. We additionally Sanger‐sequenced 100 prey items from 50 randomly chosen regurgitations to verify that metabarcoding characterized key components of the diet. The metabarcoding technique identified 87 unique taxa from 29 families of fish and squid, spanning diverse taxa, including reef‐associated, pelagic–oceanic, and mesopelagic species. Rare prey (frequency of occurrence ≤5% of samples) constituted 66% of the species richness, demonstrating the highly diverse diet of this generalist predator. Overall, 81% of the families detected in the contemporary diet were previously documented in Christmas shearwater diets from the Northwestern Hawaiian Islands. Our results indicate that metabarcoding the COI region is useful in identifying a wide range of taxa from highly digested regurgitations, thus facilitating this approach to study seabird diets.
An integrative genomics approach identifies KDM4 as a modulator of trained immunity
Authors: Moorlag Simone J.C.F.M. , Matzaraki Vasiliki , van Puffelen Jelmer H. , van der Heijden Charlotte , Keating Sam , Groh Laszlo , Röring Rutger Jan , Bakker Olivier B. , Mourits Vera P. , Koeken Valerie A.C.M. , de Bree L. Charlotte J. , Smeekens Sanne P. , Oosting Marije , Gamboa Raúl Aguirre , Riksen Niels P. , Xavier Ramnik J. , Wijmenga Cisca , Kumar Vinod , van Crevel Reinout , Novakovic Boris , Joosten Leo A.B. , Li Yang , Netea Mihai G. 
Published: November 2021

AbstractInnate immune cells are able to build memory characteristics via a process termed “trained immunity.” Host factors that influence the magnitude of the individual trained immunity response remain largely unknown. Using an integrative genomics approach, our study aimed to prioritize and understand the role of specific genes in trained immunity responses. In vitro‐induced trained immunity responses were assessed in two independent population‐based cohorts of healthy individuals, the 300 Bacillus Calmette‐Guérin (300BCG; n = 267) and 200 Functional Genomics (200FG; n = 110) cohorts from the Human Functional Genomics Project. Genetic loci that influence cytokine responses upon trained immunity were identified by conducting a meta‐analysis of QTLs identified in the 300BCG and 200FG cohorts. From the identified QTL loci, we functionally validated the role of PI3K‐Akt signaling pathway and two genes that belong to the family of Siglec receptors (Siglec‐5 and Siglec‐14). Furthermore, we identified the H3K9 histone demethylases of the KDM4 family as major regulators of trained immunity responses. These data pinpoint an important role of metabolic and epigenetic processes in the regulation of trained immunity responses, and these findings may open new avenues for vaccine design and therapeutic interventions.
Different pathways, same goals: A large‐scale qualitative study of autistic and non‐autistic patient‐generated definitions of recovery from an eating disorder
Authors: Sedgewick Felicity , Leppanen Jenni , Austin Amelia , Tchanturia Kate 
Published: November 2021

AbstractBackgroundDefinitions of recovery from an eating disorder (ED) have generally been formulated around clinical conceptualisations, rather than based on the views of patients. This paper therefore asked those with lived experience of ED for their own definitions of recovery.MethodData were collected as part of an online study looking at EDs, autism and relationships. About 173 participants identified as recovered from ED and gave free‐response definitions of recovery. Responses were subject to thematic analysis.ResultsSeven major themes were identified: Weight restoration, lack of ED behaviours, thoughts and behaviours, cognitions, emotional responses, getting on with life, and ongoing challenges.ConclusionsMany definitions of recovery given by those who have lived experience of ED echoed those used by clinicians and researchers. There were also points of divergence around the ongoing challenges of recovery. Our findings highlight the need for continuing support post‐weight restoration to facilitate the successful long‐term recovery for those with ED.
Biological activity and profiling of Salvia sclarea essential oil obtained by steam and hydrodistillation extraction methods via chemometrics tools
Authors: Aćimović Milica G. , Cvetković Mirjana T. , Stanković Jeremić Jovana M. , Pezo Lato L. , Varga Ana O. , Čabarkapa Ivana S. , Kiprovski Biljana 
Published: November 2021

AbstractSalvia sclarea L. or clary sage is cultivated worldwide in temperate and sub‐tropical climates, as an ornamental and essential oil (EO) bearing plant. EO is obtained from fresh spikes in full flowering stage and is recognized as an important commercial product for food, beverage and cosmetic industries. This study investigated the EO composition of S. sclarea grown in Serbia (Southeast Europe) obtained by two different methods, steam (SD) and hydrodistillation (HD). GC‐MS analysis identified oxygenated monoterpenes as the main class of compounds for all EOs (between 81.8% and 88.2% depending on the distillation process). The most abundant oxygenated monoterpenes were linalyl acetate and linalool. In addition, in vitro antimicrobial (modified resazurin microtitre‐plate assay) and antioxidant activities (DPPH· assay) and total polyphenol content of obtained EOs were also evaluated. According to the assay used for the evaluation of the antibacterial activity, Gram‐negative bacteria were more sensitive to S. sclarea EO in comparison to Gram‐positive bacteria. EOs exhibited low antioxidant capacity, below 3% neutralized DPPH· radicals, reaching up to approximately 400 µg AAE mL‐1. This study also investigated a possibility for predicting retention indices (RIs) of compounds isolated from EOs. In total, 78 experimentally obtained RIs were applied to construct the prediction model. The quantitative structure‐chromatographic retention relationship (QSRR) model was used to anticipate the experimentally obtained RIs. Five molecular descriptors were selected by factor analysis and genetic algorithm to predict RIs. The obtained accuracy of the QSRR model reached r2 = .912, which showed that these models might be applied for predicting retention indices.
The Zygomatic Implant Perforated (ZIP) flap reconstructive technique for the management of low‐level maxillary malignancy – clinical & patient related outcomes on 35 consecutively treated patients
Authors: Butterworth Chris J. , Lowe Derek , Rogers Simon N. 
Published: November 2021

AbstractBackgroundThe zygomatic implant perforated (ZIP) flap technique provides immediate reconstruction and rapid dental rehabilitation for low‐level malignant tumors.MethodsPatients who underwent ZIP flap reconstruction between December 2015 and February 2021 were followed prospectively.ResultsThirty‐five consecutively treated patients were studied with 16 undergoing surgery alone and 19 undergoing surgery followed by radiotherapy. The median time to fit the prosthesis was 29 days with all patients requiring adjuvant radiotherapy receiving their fixed dental prosthesis prior to its commencement. Vascularized flap (100%), zygomatic implant (98.4%), and prosthesis (97%) survival were excellent and the ZIP flap protocol was highly rated by patient‐related outcome measures especially for the chewing domain.ConclusionsThe ZIP flap technique provides an excellent means of providing an autogenous oronasal seal and a foundation for immediate cortically anchored fixed dental rehabilitation.Clinical SignificanceThis technique provides rapid and robust rehabilitation for patients presenting with low‐level maxillary malignancy despite the use of radiotherapy.
Intrinsic functional connectivity in the default mode network predicts mnemonic discrimination: A connectome‐based modeling approach
Authors: Wahlheim Christopher N. , Christensen Alexander P. , Reagh Zachariah M. , Cassidy Brittany S. 
Published: November 2021

AbstractThe ability to distinguish existing memories from similar perceptual experiences is a core feature of episodic memory. This ability is often examined using the mnemonic similarity task in which people discriminate memories of studied objects from perceptually similar lures. Studies of the neural basis of such mnemonic discrimination have mostly focused on hippocampal function and connectivity. However, default mode network (DMN) connectivity may also support such discrimination, given that the DMN includes the hippocampus, and its connectivity supports many aspects of episodic memory. Here, we used connectome‐based predictive modeling to identify associations between intrinsic DMN connectivity and mnemonic discrimination. We leveraged a wide range of abilities across healthy younger and older adults to facilitate this predictive approach. Resting‐state functional connectivity in the DMN predicted mnemonic discrimination outside the MRI scanner, especially among prefrontal and temporal regions and including several hippocampal regions. This predictive relationship was stronger for younger than older adults, primarily for temporal–prefrontal connectivity. The novel associations established here are consistent with mounting evidence that broader cortical networks including the hippocampus support mnemonic discrimination. They also suggest that age‐related network disruptions undermine the extent that the DMN supports this ability. This study provides the first indication of how intrinsic functional properties of the DMN support mnemonic discrimination.
The Covid‐19 pandemic reinforces the need for sustainable health planning
Authors: Garcia Ana Cristina , Beja André , Cupertino de Barros Fernando Passos , Delgado António Pedro , Ferrinho Paulo 
Published: November 2021

AbstractThe 2030 Agenda for Sustainable Development highlighted the growing attention to the adequacy of health planning models to sustainable development. A re‐reading of the results of a round table debate on “sustainable planning”, which took place at the 5th National Congress of Tropical Medicine (Portugal, 2019) under a participant observation strategy, framed by the findings of a “synthesis of better evidence” literature review and cross–referenced with the reflections of different authors and experts about the momentum created by the COVID–19 pandemic, underlined the challenges to sustainable health planning that have emerged and are projected beyond the current pandemic context. Variable perceptions of the term “sustainable health development”, leading to the potential loss of their relevance in guiding the elaboration of policies and strategic plans, and the potential higher effectiveness of the participatory approaches of health planning in achieving sustainable health were highlighted in the debate and literature, in general and in public health emergency contexts. Those results gained new relevance during the current COVID–19 pandemic, bringing back to the forefront a reflection of the inadequate planning framework that has usually been used to understand and respond to global health challenges, despite the already existing experience, evidence and support instruments.
Association of CYBA C242T and superoxide dismutase 2 A16V genetic variants with preeclampsia
Authors: Hu Kaifeng , Liu Xinghui , Bai Huai , Zhou Mi , Jiang Chenyu , Fan Ping 
Published: November 2021

AbstractObjectiveTo investigate the relationship between NADPH oxidase p22phox subunit (CYBA; C242T) and superoxide dismutase 2 (SOD2; A16V) polymorphisms and the risk of preeclampsia (PE) in Chinese women.MethodsThis case‐control study included 325 patients with PE and 1294 controls. The genotypes were determined by polymerase chain reaction‐restriction fragments length polymorphism method. Clinical, metabolic, and oxidative stress parameters were analyzed.ResultsParticipants with T allele of the CYBA C242T polymorphism had a decreased risk of PE (OR = 0.62, 95% CI: 0.42–0.92, P = 0.016) and those with the A allele of the SOD2 A16V polymorphism had increased risk of PE (OR = 1.44, 95% CI: 1.09–1.89, P = 0.010). The coexistence of the SOD2 AA + AV genotypes and the CYBA CC genotype further increased the risk of PE (OR = 2.32, 95% CI: 1.31–4.10, P = 0.003) when the CT + TT/VV combined genotype was the reference category.ConclusionThe T allele of the CYBA C242T polymorphism is related to a decreased risk of PE, while the A allele of the SOD2 A16V polymorphism and its combination with the CYBA CC genotype are associated with an increased risk of PE in Chinese women.
Alone in the disaster? The independent nature of behavioural instructions for evacuation
Authors: Bartolucci Andrea , Lüders Adrian 
Published: November 2021

AbstractIn disaster evacuation, the most reasonable reaction is seen as to evacuate through independence. On the contrary, people often stay and behave socially interdependent, hence stressing the gap between evacuation instructions and actual people's behaviour. The present research analyses the content of a set of behavioural instructions and provides an overview of common framing of evacuation communication. That is informed by psychological models that explain behaviour based distinguish between the independent self (i.e., everyone for themselves) and interdependent self (i.e., all together). Results of this article highlight that, despite the prevalence of interdependent behaviour, most of the instructions focuses on the independent behaviours rather than on interdependent instructions that do not reflect actual people's behaviour in case of evacuation. The objective of this article is to increase authorities' awareness on the relation between existing instructions (independent) and actual behaviour (interdependent); the final aim is to help authorities to design and create better instructional communication campaign for disaster evacuation.
Comparative morphological study of skeletal muscle weight among the red jungle fowl (Gallus gallus) and various fowl breeds (Gallus domesticus)
Authors: Endo Hideki , Tsunekawa Naoki , Kudo Kohei , Oshida Tatsuo , Motokawa Masaharu , Sonoe Mitsuru , Wanghongsa Sawai , Tirawattanawanich Chanin , Phimphachanhvongsod Viengsavanh , Sasaki Takeshi , Yonezawa Takahiro , Akishinonomiya Fumihito 
Published: November 2021

AbstractWe examined the weight distribution of skeletal muscles of the red jungle fowl, then compared these values with those of domesticated populations to determine how muscle distribution has changed by selecting breeding. Sonia, Fayoumi, and Rhode Island Red were selected for comparison from livestock breeds, while Japanese Shamo and Thai fighting cocks were selected from cockfighting groups. Principal component analysis was applied using body size‐free data. The mass distribution of muscles clearly differed between the wild, livestock, and cockfighting groups, demonstrating that muscle distribution has changed after selecting breeding, coupled with functional demands of each group. The red jungle fowl, which has the ability to fly, could be clearly distinguished from the flightless domesticated populations due to differences in flight pectoral muscle size. The cervical muscles in the wild population were smaller than in the domesticated groups; these do not contribute to flight. The gluteal muscles were larger in the fighting cock group, functionally coupled to their traditionally preferred upright posture. Wild bird populations typically exhibit reduced weight of their hind limbs, associated with flight, but as the red jungle fowl displays largely terrestrial behavior, these muscles are similar in arrangement and relative size to those of the livestock groups. We showed that the mass distribution pattern of skeletal muscles expresses selecting breeding strategy and clearly reflects the specific traits for each group.
Overview of approved CAR‐T therapies, ongoing clinical trials, and its impact on clinical practice
Authors: Sengsayadeth Salyka , Savani Bipin N. , Oluwole Olalekan , Dholaria Bhagirathbhai 
Published: November 2021

AbstractIn recent years, we have seen rapid expansion of chimeric antigen receptor T‐cell (CAR‐T) therapies in multiple malignancies. CAR‐T therapy has profoundly altered the treatment landscape of non‐Hodgkin lymphoma, B‐cell acute lymphoblastic leukemia, and multiple myeloma. Currently available CD19 and B‐cell maturation antigen‐directed CAR‐T therapies have shown high overall response rate and durable remissions in patients who have failed standard therapies. Multiple studies are underway exploring the role of CAR‐T‐cell therapy as earlier line of treatment. In high‐grade B‐cell lymphoma, CD19 CAR‐T therapy may replace autologous hematopoietic cell transplantation as second line therapy in near future. CAR‐T‐cell therapy targeting novel tumor‐associated antigens will help expand utility of this treatment modality in other hematological malignancies. It may also help overcome limitations of currently approved CAR‐T‐cell therapies. In this review, we have provided an overview of currently approved CAR‐T therapies and upcoming clinical trials which may potentially impact the clinical practice.