bluuebunny/crossref_metadata_2025_split huggingface dataset:
The association between referral by specialists in oral diagnosis on survival rates of patients with oral cancer: A retrospective cohort study
Authors: Sousa‐Neto Sebastião Silvério , Martins Allisson Filipe Lopes , Moreira Victor Hugo Lopes de Oliveira , Pereira João Gabriel Batista , Freitas Nilceana Maya Aires , Curado Maria Paula , Leles Claudio Rodrigues , Mendonça Elismauro Francisco 
Published: May 2024

AbstractBackgroundTo assess the influence of diagnosis and referral provided by specialists in oral diagnosis on disease‐free survival and overall survival of patients with oral cancer.MethodsA cohort of 282 patients with oral cancer treated at a regional cancer hospital from 1998 to 2016 was analyzed retrospectively. The referral register of the patients was analyzed and assigned to two groups: (1) those referred by oral diagnosis specialists (n = 129), or (2) those referred by nonspecialized professionals (n = 153). The cancer treatment evolution was assessed from the patients' records, and the outcome was registered concerning cancer recurrence and death. Sociodemographic and clinicopathological variables were explored as predictors of disease‐free survival and overall survival.ResultsGroup 1 exhibited lower T stages and a reduced incidence of regional and distant metastases. Surgery was performed in 75.2% of cases in Group 1, while in Group 2, the rate was 60.8%. Advanced T stages and regional metastases reduced the feasibility of surgery. Higher TNM stages and tumor recurrence were associated with decreased disease‐free survival, while surgical intervention was a protective factor. Higher TNM stage had a negative impact on the overall survival.ConclusionSpecialized oral diagnosis did not directly impact disease‐free survival and overall survival and did not influence the indication of surgery in oral cancer; however, it was associated with the diagnosis of early tumors and better prognosis.
A roadmap to carefully select methods for dark‐diversity studies
Authors: Paganeli Bruno , Fujinuma Junichi , Trindade Diego P. F. , Carmona Carlos P. , Pärtel Meelis 
Published: May 2024

AbstractDark diversity includes ecologically suitable species currently absent in a site, albeit theoretically able to arrive from the surrounding region. Various methods can estimate the likelihood that an absent species is in the dark diversity of a site. Recent developments in estimation of dark diversity have advanced the field, yet uncertainty on method selection might lead to confusion and misleading results. Here, we provide methodological guidance by reanalyzing a data set used in a recently published dark‐diversity study (Hostens et al. 2023; Journal of Vegetation Science 34: e13212). Using various approaches to estimate dark diversity, we discuss why their estimations differ, and examine which methods are more appropriate than others for the particular data set. In this study, the hypergeometric method based on species co‐occurrences outperformed the other considered methods (species distribution modelling, Beals index). Further, we show how estimations of dark diversity can be combined with a Bayesian framework to examine which characteristics of sites and species are related to their tendency to have higher dark‐diversity size (sites) than expected or to be more frequently in dark diversity (species). This paper hopefully enhances confidence in dark‐diversity methods, allowing progress in both ecological theory and biodiversity conservation.
Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States
Authors: Barmentlo Niek W. G. , Meirmans Patrick G. , Stiver William H. , Yarkovich Joseph G. , McCann Blake E. , Piaggio Antoinette J. , Wright Dominic , Smyser Timothy J. , Bosse Mirte 
Published: May 2024

AbstractDespite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high‐density single‐nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.
Exploring habitat use and movement patterns of humpback whales in a reoccupation area off Brazil: A comparison with the Abrolhos Bank
Authors: Righi Bianca M. , Baumgarten Julio E. , Morete Maria Emilia , Souza Rafaela C. F. , Marcondes Milton C. C. , Sousa‐Lima Renata S. , Teixeira Niel N. , Tonolli Fernanda A. S. , Gonçalves Maria Isabel C. 
Published: May 2024

AbstractAfter the worldwide moratorium on whaling, humpback whale populations began to recover, reoccupying former areas of use, as also observed on the Brazilian coast. Abrolhos Bank represents the area of greatest humpback whale concentration but the number of individuals to the north has increased, as has happened in the region of Serra Grande. To compare relative abundance, habitat use, and movement patterns between a well‐established breeding and a reoccupation area, visual monitoring from land‐based stations was performed: 160 days in the Abrolhos Archipelago located on the Abrolhos Bank and 133 days in Serra Grande in 2014, 2015, 2018, and 2019. While relative abundance varied annually in the Abrolhos Archipelago, it gradually increased in Serra Grande, surpassing the number registered in Abrolhos in 2019. Group composition frequency was similar between areas except for mother and calf accompanied by one or more escorts, which were more frequent in Abrolhos. Despite similar movement speed and linearity values, whales in Serra Grande had a higher reorientation rate. Monitoring different areas occupied by this population supports decisions about spatial management of the Brazilian coast in relation to the implementation of anthropogenic activities, especially in areas where whales have recently returned to occupy.
Characterization of rice (Oryza sativa L.) landraces from Majuli and surrounding riverine ecologies in Assam: Assessment of morphogenetic variability and submergence tolerance
Authors: Mudhale Abhijeet , Sar Puranjoy , Kumar Jitendra , Bhowmick Prolay Kumar , Banerjee Amrita , Chakraborty Koushik , Basak Nabaneeta , Patra Bhaskar Chandra , Bisht Dipak Singh , Iquebal Mir Asif , Priyamedha  , Vinod K. K. , S Gopala Krishnan , Kumar Gaurav , Mandal Nimai Prasad , Roy Somnath 
Published: May 2024

AbstractRice landraces from the fragile riverine ecosystems surrounding Majuli islands in Assam are pivotal for local livelihoods, as well as for their potential in developing flood tolerant varieties. We characterized 87 landraces from Majuli, Dhemaji, and North Lakhimpur districts in Assam by assessing 36 agro‐morphological traits, submergence tolerance, and microsatellite diversity. Multivariate analyses revealed that grain and leaf characteristics, plant height, and tillering are important traits differentiating the cultivar types. Sixty‐six SSR markers generated 271 alleles with an average of 4.1 alleles per marker with population structuring in two clusters having an allele frequency divergence of 0.124. The Bao or deep‐water landraces displayed the highest phenotypic and genetic diversity, with potential genetic links to the aus and wild species. Sali (winter rice) and bora (sticky rice) landraces were predominantly indica type. Nearly 47% of the germplasm exhibited tolerance to two‐week submergence at seedling stage. Surveying SUB1A and SNORKEL genes revealed the presence of SUB1A‐1 and SNORKEL genes in 64% and 57% of the tolerant accessions, respectively. This study highlights the untapped potential of rice landraces in a fragile ecological region, providing insights into their agronomical traits, submergence tolerance, and genetic diversity. The findings lay the foundation for improved germplasm management and developing flood‐resilient rice varieties, crucial for sustainable agriculture in riverine ecosystems.
Important but ignored: Research progress on crab foraging behaviour and its implications for aquaculture
Authors: Liu Dapeng , Zhu Boshan , Liu Xiaoshou , Wang Fang 
Published: May 2024

AbstractCrab fisheries play a crucial role in global fishery economics, but they heavily rely on wild catches. With the decline and exploratory limits of wild populations, expanding the scale and production of aquaculture becomes vital for the sustainability of crab fisheries. The development of crab aquaculture encounters significant dietary challenges, stemming from suboptimal formulated feeds and inefficient feeding management. Leveraging insights from crab foraging behaviours offers a promising solution to these issues; however, progress is hindered by a lack of comprehensive behavioural data and the underappreciation of these insights in aquaculture. To bridge this gap, we systematically examine the progress in studies of crab foraging behaviour, analysing the influences of predators, prey, and environmental characteristics, and discuss possibilities for future research and development in the field by combining these findings with the demands of aquaculture. This review identifies a discrepancy in research focus, with inadequate emphasis on the major cultured species and their behavioural responses to factors limiting aquaculture productivity, aiming to enhance our comprehension of crab foraging behaviour and facilitate growth in the crab industry.
Intentions to use mental health and suicide prevention resources among individuals with symptoms of the suicide crisis syndrome and/or suicidal ideation
Authors: Rogers Megan L. , Richards Jenelle A. , Peterkin Devon , Park Ji Yoon , Astudillo‐García Claudia I. , Barzilay Shira , Blum Yarden , Chistopolskaya Ksenia , Dudeck Manuela , Enikolopov Sergey , Husain M. Ishrat , Jiménez Alberto , Yilmaz Fatma Kantas , Kuśmirek Oskar , Lee Ming‐Been , Menon Vikas , Peper‐Nascimento Jefté , Pilecka Barbara , Streb Judith , Ünübol Başak , Valvassori Samira S. , Contreras Maria Valeria , Wu Chia‐Yi , You Sungeun , Galynker Igor 
Published: May 2024

AbstractIntroductionThe suicide crisis syndrome (SCS) has demonstrated efficacy in predicting suicide attempts, showing potential utility in detecting at‐risk individuals who may not be willing to disclose suicidal ideation (SI). The present international study examined differences in intentions to utilize mental health and suicide prevention resources among community‐based adults with varying suicide risk (i.e., presence/absence of SCS and/or SI).MethodsA sample of 16,934 community‐based adults from 13 countries completed measures about the SCS and SI. Mental health and suicide prevention resources were provided to all participants, who indicated their intentions to use these resources.ResultsIndividuals with SCS (55.7%) were just as likely as those with SI alone (54.0%), and more likely than those with no suicide‐related symptoms (45.7%), to report willingness to utilize mental health resources. Those with SI (both with and without SCS) were more likely to seek suicide prevention resources (52.6% and 50.5%, respectively) than those without SI (41.7% and 41.8%); however, when examining endorsements for personal use, those with SCS (21.6%) were more likely to use resources than individuals not at risk (15.1%).ConclusionsThese findings provide insight into individuals' willingness to use resources across configurations of explicitly disclosed (SI) and indirect (SCS) suicide risk.
The effect of tire inflation pressure and tillage systems on soil properties, growth and yield of maize and soybean in a silty clay loam soil
Authors: Shaheb Md Rayhan , Misiewicz Paula A. , Godwin Richard J. , Dickin Edward , White David R. , Grift Tony E. 
Published: May 2024

AbstractSoil compaction causes adverse effects on soil structure and the performance of crops. There is significant literature supporting the hypothesis that reducing tire inflation pressure can help to minimize compaction, but there is no data on the potential benefits of high flexion tires operating at reduced tire pressures in Midwestern United States agriculture. Hence, a field‐scale study was established in Illinois to determine the potential benefits of high flexion tires at low tire pressure (LTP) in comparison with those operated at standard tire inflation pressure (STP) on soil condition, crop growth and yield of maize and soybean for three tillage systems; deep tillage (450 mm), shallow tillage (100 mm) and no‐till. Two adjacent experiments were established in typical maize/soybean and soybean/maize rotations, respectively. The experiment used a 2 × 3 factorial design with five completely randomized blocks. The results showed that the use of LTP tires resulted in lower soil penetrometer resistance for three tillage systems in 2017 and 2018 in the maize field and 2018 in the soybean field. This improved plant establishment and the number of plants per hectare of maize in both 2016 (*p ≤ .05) and 2018 (**p ≤ .01) and plant establishment (***p ≤ .001) and the number of plants per hectare (***p ≤ .001) of soybean in 2018. The penetrometer resistance was higher in the no‐till plots compared to deep and shallow tillage plots in maize and was higher in the deep tillage plots compared to the shallow tillage in the soybean field. The use of LTP tires resulted in an increased grain yield of maize by 4.31% (15.02 Mg ha−1) and 2.70% (14.76 Mg ha−1) in 2017 (**p ≤ .01) and 2018 (*p ≤ .05), respectively, and soybean by 3.70% (4.25 Mg ha−1) in 2018 (*p ≤ .05). The depth of tillage had a significant effect on soybean and maize yields in 2017 (***p ≤ .001) and 2018 (***p ≤ .001), respectively, with higher yields of both soybean and maize in the deep and shallow tillage compared to no‐till plots. The study concludes that the use of the LTP systems can be a potential means of addressing soil compaction and maintaining soil porosity while increasing crop productivity in silty clay loam soils in Central Illinois.
Molecular incompatibility between pig CD200 and human CD200 receptor in in vitro xenogeneic immune responses
Authors: Kim Bomin , Yan Ji‐Jing , Kang Tae Kyeom , Lee Wook‐Bin , Jeong Jong Cheol , Yang Jaeseok 
Published: May 2024

AbstractOverexpression of human CD200 (hCD200) in porcine endothelial cells (PECs) has been reported to suppress xenogeneic immune responses of human macrophages against porcine endothelial cells. The current study aimed to address whether the above‐mentioned beneficial effect of hCD200 is mediated by overcoming the molecular incompatibility between porcine CD200 (pCD200) and hCD200 receptor or simply by increasing the expression levels of CD200 without any molecular incompatibility across the two species. We overexpressed hCD200 or pCD200 using lentiviral vectors with V5 marker in porcine endothelial cells and compared their suppressive activity against U937‐derived human macrophage‐like cells (hMCs) and primary macrophages. In xenogeneic coculture of porcine endothelial cells and human macrophage‐like cells or macrophages, hCD200‐porcine endothelial cells suppressed phagocytosis and cytotoxicity of human macrophages to a greater extent than pCD200‐porcine endothelial cells. Secretion of tumor necrosis factor‐α, interleukin‐1β, and monocyte chemoattractant protein‐1 from human macrophages and expression of M1 phenotypes (inducible nitric oxide synthase, dectin‐1, and CD86) were also suppressed by hCD200 to a greater extent than pCD200. Furthermore, in signal transduction downstream of CD200 receptor, hCD200 induced Dok2 phosphorylation and suppressed IκB phosphorylation to a greater extent than pCD200. The above data supported the possibility of a significant molecular incompatibility between pCD200 and human CD200 receptor, suggesting that the beneficial effects of hCD200 overexpression in porcine endothelial cells could be mediated by overcoming the molecular incompatibility across the species barrier rather than by simple overexpression effects of CD200.
Unsteady Aerodynamic Forcing Due to Distortion in a Boundary Layer Ingesting Fan
Authors: Mårtensson Hans , Billson Mattias 
Published: May 2024

Abstract
Boundary Layer Ingestion (BLI) is a concept with the potential to reduce energy consumption needed for aircraft propulsion. For the fan this results in a need to work well in an environment of increased continuous distortion. The objective of this study is to increase the understanding of unsteady aerodynamic forces due to total pressure distortion in a BLI fan. This is done by using computational fluid dynamics to analyze a fan design intended for a BLI installation. Results include low subsonic to transonic operating speeds and distortion in a wide range of wave numbers. The forcing exhibits a significant dependency on the aeroacoustic cut-on/cut-off condition. This is in particular true at part speed where the normalized unsteady force rises sharply before dropping suddenly as the corrected speed or engine order increases. Unsteady pressure in the blade passage is observed to exhibit the same increase in level followed by a sudden drop once the cut-on limit is passed and undamped pressure waves propagating out from the blade row appear. The unsteady forces on the first three modes exhibit different sensitivities to the distortion wavelength but all are affected by the acoustic condition. By comparing results for the reference fan to a similar fan design with a higher blade count the cascade properties of the blade row are found to dominate the interaction. A result of this is that a higher blade count fan may be less affected by the distortion, and be less prone to propagate noise due to low engine order distortion.
The genomic and phylogenetic analysis of
Marseillevirus cajuinensis
raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization
Authors: de Azevedo Bruna Luiza , Queiroz Victória Fulgêncio , de Aquino Isabella Luiza Martins , Machado Talita Bastos , de Assis Felipe Lopes , Reis Erik , Araújo Júnior João Pessoa , Ullmann Leila Sabrina , Colson Philippe , Greub Gilbert , Aylward Frank , Rodrigues Rodrigo Araújo Lima , Abrahão Jônatas Santos 
Published: May 2024

ABSTRACT

Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that
M. cajuinensis
forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the
Marseilleviridae
lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family.

IMPORTANCE

Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first
Marseillevirus
isolated from saltwater samples, which we called
Marseillevirus cajuinensis
. Most of
M. cajuinensis
genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand,
M. cajuinensis
encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity.
Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire
Authors: Barnett Samuel E. , Shade Ashley 
Published: May 2024

ABSTRACT

We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.