bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition
Authors: Wu Chen , Deng Cecilia , Hilario Elena , Albert Nick W. , Lafferty Declan , Grierson Ella R. P. , Plunkett Blue J. , Elborough Caitlin , Saei Ali , Günther Catrin S. , Ireland Hilary , Yocca Alan , Edger Patrick P. , Jaakola Laura , Karppinen Katja , Grande Adrian , Kylli Ritva , Lehtola Veli‐Pekka , Allan Andrew C. , Espley Richard V. , Chagné David 
Published: July 2021

AbstractBilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi‐C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker‐trait association between these two species, as the loci involved in key characters are orthologous.
Organizational social context and psychopathology of youth in residential care: The intervening role of youth–caregiver relationship quality
Authors: Silva Carla Sofia , Calheiros Maria Manuela , Carvalho Helena , Magalhães Eunice 
Published: July 2021

AbstractDrawing on an ecological approach with multiple informants, this study investigated the mediating role of youth–caregiver relationship quality in associations between different features of residential care settings' organizational social context and youth's psychopathology. Participants were 378 youth aged between 12 and 25 years old, and 54 caregivers aged between 24 and 57 years old, from 29 generalist residential youth care settings in Portugal. Given the hierarchical structure of data, analyses were performed using multilevel modeling. Results revealed that organizational social contexts characterized by higher levels of engagement, stress, and centralization, as perceived by the caregivers, were associated with lower levels of youth's externalizing problems (e.g., aggressive behavior and delinquency), reported by the caregivers, via better youth–caregiver relationship quality, perceived by the youth in care. These findings highlight the relevance of creating an organizational social context in residential care settings that supports caregivers in establishing high‐quality relationships with the youth in care, thereby promoting their mental health. This study contributes to the clarification of conflicting findings in previous studies of this field, by offering further empirical investigation of these issues.
Abacavir pharmacokinetics in African children living with HIV: A pooled analysis describing the effects of age, malnutrition and common concomitant medications
Authors: Tikiso Tjokosela , McIlleron Helen , Burger David , Gibb Diana , Rabie Helena , Lee Janice , Lallemant Marc , Cotton Mark F. , Archary Moherndran , Hennig Stefanie , Denti Paolo 
Published: July 2021

AimsAbacavir is part of WHO‐recommended regimens to treat HIV in children under 15 years of age. In a pooled analysis across four studies, we describe abacavir population pharmacokinetics to investigate the influence of age, concomitant medications, malnutrition and formulation.MethodsA total of 230 HIV‐infected African children were included, with median (range) age of 2.1 (0.1–12.8) years and weight of 9.8 (2.5–30.0) kg. The population pharmacokinetics of abacavir was described using nonlinear mixed‐effects modelling.ResultsAbacavir pharmacokinetics was best described by a two‐compartment model with first‐order elimination, and absorption described by transit compartments. Clearance was predicted around 54% of its mature value at birth and 90% at 10 months. The estimated typical clearance at steady state was 10.7 L/h in a child weighing 9.8 kg co‐treated with lopinavir/ritonavir, and was 12% higher in children receiving efavirenz. During coadministration of rifampicin‐based antituberculosis treatment and super‐boosted lopinavir in a 1:1 ratio with ritonavir, abacavir exposure decreased by 29.4%. Malnourished children living with HIV had higher abacavir exposure initially, but this effect waned with nutritional rehabilitation. An additional 18.4% reduction in clearance after the first abacavir dose was described, suggesting induction of clearance with time on lopinavir/ritonavir‐based therapy. Finally, absorption of the fixed dose combination tablet was 24% slower than the abacavir liquid formulation.ConclusionIn this pooled analysis we found that children on lopinavir/ritonavir or efavirenz had similar abacavir exposures, while concomitant TB treatment and super‐boosted lopinavir gave significantly reduced abacavir concentrations.
Future minds and a new challenge to anti‐natalism
Authors: Gould Deke Caiñas 
Published: July 2021

AbstractSome futurists and philosophers have urged that recent developments in biotechnology promise advancements that challenge standard accepted views of human nature, the self, and ethical obligation. Additionally, some have urged that developments in artificial intelligence similarly raise interesting new challenges to our conceptions of the mind, morality, and the future direction for conscious entities generally. Some have even gone so far as to argue in defense of “artificial replacement,” which is the view that humanity should be prepared to “hand over the keys,” so to speak, to a new sort of intelligent collection of entities and that we should go extinct gracefully. These views suggest a new challenge to the anti‐natalist view that people should stop procreating: perhaps humanity is obligated to not allow itself to go extinct quite yet, at least until we have ensured that these next stages of intelligent entity have emerged. When we take into consideration some possibilities for entities with minds relevantly different from our own, we confront a challenge to the asymmetry argument that concerns human‐like minds. Call this the “future minds challenge to anti‐natalism.” I will examine some assumptions that underlie such a challenge, and I will argue that some famous articulations of the anti‐natalist stance should be revised in light of such technological advancements.
Exome sequencing of familial adenomatous polyposis‐like individuals identifies both known and novel causative genes
Authors: Xavier Alexandre , Scott Rodney J. , Talseth‐Palmer Bente 
Published: July 2021

AbstractInherited polyposis syndromes are predominantly caused by pathogenic variants in APC and are linked to familial adenomatous polyposis (FAP). However, after clinical screening, 20%–30% of individuals diagnosed with FAP do not carry a pathogenic variant in APC (often categorised as FAP‐like). Other known inherited adenomatous polyposis syndromes such as MUTYH, POLD1/E, or NTHL1‐associated polyposis only account for, 3 a fraction of the remaining cases. A cohort of 48 individuals clinically diagnosed with a FAP‐like phenotype was selected based on a strong family history of colorectal cancer and no previous pathogenic variant found in APC and/or MUTYH, by genetic screening. Using whole exome sequencing, FAP‐like patients were found to carry pathogenic variants in MUTYH, APC, POLE and TP53, as well as DNA‐repair genes and inflammation related genes. Additionally, a comprehensive assessment of copy number variation revealed two loci of interest that appeared to be associated with polyposis risk. In total, 6 out of 48 polyposis were explained through re‐sequencing. This study highlights the potential role of DNA‐repair as well as inflammation‐related variants towards polyp development.
Reasons for not providing initial support to a colleague, friend, or family member experiencing a mental health problem or crisis
Authors: Morgan Amy J. , Rossetto Alyssia 
Published: July 2021

AbstractAimTo investigate reasons for not helping a person experiencing a mental health problem, and explore factors associated with not offering help.MethodsData were collected as part of a randomized controlled trial evaluating Mental Health First Aid (MHFA) in the workplace conducted with 608 Australian adults. Participants were asked if a colleague, friend, or family member had any mental health problem in the last 12 months, whether they had tried to help them, and reasons for not helping. These reasons were content analysed and predictors of not helping were explored with logistic regression.ResultsA minority of participants did not offer help, with reasons for not helping (n = 107) related to the recipient already being helped, characteristics of the recipient such as perceived illness type, the type of relationship between helper and recipient, distance or time barriers, and a lack of skills or knowledge.ConclusionsSome reasons for not helping cannot be modified but others could be used to inform the curricula of MHFA or other gatekeeper training.
Diarrhoea with the angiotensin receptor neprilysin inhibitor sacubitril + valsartan: A pharmacovigilance study
Authors: Guion‐Firmin Julia , Tessier Samuel , Lepelley Marion , Faillie Jean‐Luc , Montastruc Jean‐Louis 
Published: July 2021

AbstractDiarrhoea is an adverse drug reaction of the angiotensin receptor neprilysin inhibitor (ARNI) sacubitril + valsartan. It was also described with olmesartan and more recently with other angiotensin receptor blockers. The study was performed to compare diarrhoea reports in pharmacovigilance databases with sacubitril + valsartan and valsartan. The study used reports of diarrhoea with the ARNI sacubitril + valsartan registered: first in the French PharmacoVigilance Database (FPVD) and second in Vigibase®, the WHO Global Individual Case Safety Report database. After description of the main characteristics, disproportionality analyses were performed. Results are reported as reporting odds ratios (ROR) with 95% confidence interval. We found 29 reports of diarrhoea with sacubitril + valsartan in the FPVD and 686 in Vigibase®. With sacubitril + valsartan, diarrhoea occurred more frequently in males around 70 years with a median delay of 3 days. With valsartan, diarrhoea occurred more frequently in females around 68 years with a median delay of 0.5 days. In the FPVD, a significant association was found with sacubitril + valsartan in comparison with valsartan alone before (ROR = 8.78 [5.19–14.85]) and after (ROR = 11.19 [5.89–21.25]) exclusion of concomitant drugs known to be associated with diarrhoea. A significant association was also found in Vigibase® after adjustment on age, sex, reporter and its location (ROR = 1.31 [1.14–1.50]). Diarrhoea reported with sacubitril + valsartan has marked differences in gender, delay of occurrence and frequency of reporting in comparison with diarrhoea with valsartan. From a pharmacodynamic point of view, these results suggest a specific role of sacubitril in diarrhoea.
Hot moments drive extreme nitrous oxide and methane emissions from agricultural peatlands
Authors: Anthony Tyler L. , Silver Whendee L. 
Published: July 2021

AbstractAgricultural peatlands are estimated to emit approximately one third of global greenhouse gas (GHG) emissions from croplands, but the temporal dynamics and controls of these emissions are poorly understood, particularly for nitrous oxide (N2O). We used cavity ring‐down spectroscopy and automated chambers in a drained agricultural peatland to measure over 70,000 individual N2O, methane (CH4), and carbon dioxide (CO2) fluxes over 3 years. Our results showed that N2O fluxes were high, contributing 26% (annual range: 16%–35%) of annual CO2e emissions. Total N2O fluxes averaged 26 ± 0.5 kg N2O‐N ha−1y−1and exhibited significant inter‐ and intra‐annual variability with a maximum annual flux of 42 ± 1.8 kg N2O‐N ha−1y−1. Hot moments of N2O and CH4emissions represented 1.1 ± 0.2 and 1.3 ± 0.2% of measurements, respectively, but contributed to 45 ± 1% of mean annual N2O fluxes and to 140 ± 9% of mean annual CH4 fluxes. Soil moisture, soil temperature, and bulk soil oxygen (O2) concentrations were strongly correlated with soil N2O and CH4emissions; soil nitrate () concentrations were also significantly correlated with soil N2O emissions. These results suggest that IPCC benchmarks underestimate N2O emissions from these high emitting agricultural peatlands by up to 70%. Scaling to regional agricultural peatlands with similar management suggests these ecosystems could emit up to 1.86 Tg CO2e y−1(range: 1.58–2.21 Tg CO2e y−1). Data suggest that these agricultural peatlands are large sources of GHGs, and that short‐term hot moments of N2O and CH4are a significant fraction of total greenhouse budgets.
Pathological characteristics of liver sinusoidal thrombosis in COVID‐19 patients: A series of 43 cases
Authors: Kondo Reiichiro , Kawaguchi Nao , McConnell Matthew J. , Sonzogni Aurelio , Licini Lisa , Valle Clarissa , Bonaffini Pietro A. , Sironi Sandro , Alessio Maria Grazia , Previtali Giulia , Seghezzi Michela , Zhang Xuchen , Sun Zhaoli , Utsumi Teruo , Strazzabosco Mario , Iwakiri Yasuko 
Published: July 2021

AbstractAimCoronavirus disease (COVID‐19) is characterized by pneumonia with secondary damage to multiple organs including the liver. Liver injury (elevated alanine aminotransferase [ALT] and aspartate aminotransferase [AST]) often correlates with disease severity in COVID‐19 patients. The aim of this study is to identify pathological microthrombi in COVID‐19 patient livers by correlating their morphology with liver injury, and examine hyperfibrinogenemia and von Willebrand factor (vWF) as mechanisms of their formation.MethodsForty‐three post‐mortem liver biopsy samples from COVID‐19 patients were obtained from Papa Giovanni XXIII Hospital in Bergamo, Italy. Three morphological features of microthrombosis (sinusoidal erythrocyte aggregation [SEA], platelet microthrombi [PMT], and fibrous thrombi) were evaluated.ResultsWe found liver sinusoidal microthrombosis in 23 COVID‐19 patients (53%) was associated with a higher serum ALT and AST level compared to those without (ALT: 10‐fold, p = 0.04; AST: 11‐fold, p = 0.08). Of 43 livers, PMT and SEA were observed in 14 (33%) and 19 (44%) cases, respectively. Fibrous thrombi were not observed. Platelet microthrombi were associated with increased ALT (p < 0.01), whereas SEA was not (p = 0.73). In COVID‐19 livers, strong vWF staining in liver sinusoidal endothelial cells was associated with significantly increased platelet adhesion (1.7‐fold, p = 0.0016), compared to those with weak sinusoidal vWF (2‐fold, p < 0.0001). Sinusoidal erythrocyte aggregation in 19 (83%) liver samples was mainly seen in zone 2. Livers with SEA had significantly higher fibrinogen (1.6‐fold, p = 0.031) compared to those without SEA in COVID‐19 patients.ConclusionsLiver PMT is a pathologically important thrombosis associated with liver injury in COVID‐19, while SEA is a unique morphological feature of COVID‐19 patient livers. Sinusoidal vWF and hyperfibrinogenemia could contribute to PMT and SEA formation.
Distinct dynamics of Vibrio parahaemolyticus populations in two farming models
Authors: Yang Qian , Wang Qingyao , Wu Junmin , Zhang Yixiang , Wei Dawei , Qu Baocheng , Liu Ying , Fu Songzhe 
Published: July 2021

Abstract

Aims
Despite the recent prosperity of shrimp cultivation in China, very little is known about how different shrimp farming models influence the dynamics of Vibrio parahaemolyticus populations and the antibiotic resistance of this bacterium.

Methods and Results
To this end, we conducted continuous surveillance of V. parahaemolyticus on four farms over 3 years: two traditional shrimp farms with daily water exchange and two farms operated in the recirculating aquaculture systems (RAS). No antibiotics were used in these farms to exclude the potential impacts of antibiotics on the emergence of antibacterial resistance. Multilocus sequence typing was utilized to characterize the dynamics of V. parahaemolyticus populations. Whole-genome sequencing (WGS) was conducted to determine the representative sequence types (STs) at each farm. Results revealed that the population structure of V. parahaemolyticus remained stable over time in both RAS farms, with only nine and four STs observed at each. In contrast, annual replacement of V. parahaemolyticus populations was observed in traditional farms with 26 and 28 STs identified in rearing water. WGS of 50 isolates divided them into five clusters, of which ST917a isolates harboured a genomic island that disrupted the gene recA. Pair-wised genomic comparison of isolates from the same STs showed that they were genetically related but belonged to different clones associated with geographical distribution.

Conclusions
These results suggested that RAS presented a specific ecological niche by minimizing the water exchanges with the external environment. In contrast, traditional farming might pose a food safety issue by introducing new V. parahaemolyticus populations with antibiotic resistance genes.

Significance and Impact of the Study
Our results expose the potential food safety issue associated with conventional agriculture and should encourage the development of preventive strategies to reduce the emergence of resistant V. parahaemolyticus populations.
Drying of persimmon fruit (Diospyros kaki L.) pretreated by different osmotic processes
Authors: Corrêa Jefferson Luiz Gomes , Lopes Francemir José , de Mello Júnior Ronaldo Elias , de Jesus Junqueira João Renato , de Mendonça Kamilla Soares , Macedo Leandro Levate , Salvio Luís Gustavo Amaral 
Published: July 2021

AbstractPersimmon is a short shelf life fruit with interesting potential for application in different industrial segments. The immersion of food in a hypertonic (30 and 45 °Brix) or even hypotonic medium can be used as a pretreatment for the drying process. In this study, the convective drying of persimmons was preceded by osmotic dehydration (OD) with fructose in a standard atmosphere, pulsed vacuum osmotic dehydration (PVOD), ultrasound (US)‐assisted OD, and US pretreatment in distilled water. Pretreatment times were 0, 10, and 30 min. The samples were subjected to convective drying at 40 and 60°C, 0.5 m s−1. The effects of the pretreatments on the drying kinetics, volumetric shrinkage, and rehydration capacity were investigated. Fick's model and the Dincer and Dost model were used to fit the drying evolution. In addition to the influence of the osmotic solution concentration, moisture content and solid gain were functions of the treatment type. Convective drying required 260–740 min. The use of PVOD and US pretreatments resulted in the shortest drying times. The dried fruits showed particular characteristics with each different pretreatment. Both tested models presented satisfactory adjustments, but Fick's model was the best approach. In general, the treatments caused structural modifications in the persimmon fruits that modified the drying kinetics and the properties of the dried food.Practical ApplicationsConvective drying is a food processing method used to extend the shelf life of fruits, such as persimmons. The use of pretreatments is an interesting strategy to improve the drying process. However, the combination of these technologies can influence drying kinetics. Therefore, the use of mathematical models is important to represent the behavior of these processes.
Comparison of nonenhanced computed tomography and ultrasonography for detection of ureteral calculi in cats: A prospective study
Authors: Testault Isabelle , Gatel Laure , Vanel Maïa 
Published: July 2021

AbstractBackgroundRadiographs and ultrasound (US) are the primary imaging modalities used to assess ureteral calculi in cats. Reports describing the use of nonenhanced computed tomography (CT) are scarce.Hypothesis/ObjectivesTo compare US and nonenhanced CT for detection, number and localization of ureteral calculi in cats.AnimalsFifty‐one cats with at least 1 ureteral calculus, and 101 ureters.MethodsProspective case series. All cats underwent an US followed by a nonenhanced CT. Cats were included in the study if at least 1 ureteral calculus was diagnosed on either modality. Number of calculi and their localization (proximal, middle, and distal) were recorded on both modalities. Pelvic dilatation and maximal ureteral diameter were recorded with US.ResultsMore calculi were detected by nonenhanced CT (126) compared to US (90), regardless of localization (P < .001). More ureters were affected on nonenhanced CT (70) compared to US (57; P < .001). The number of calculi detected was significantly different between US and nonenhanced CT in the proximal (P = .02) and distal ureteral region (P < .001). Bilateral calculi were more frequent with nonenhanced CT (19 cats) compared to US (9 cats; P < .001). A pelvic size superior to 5 mm and a maximal ureteral diameter value superior to 3 mm were always associated with ureteral calculi.Conclusions and Clinical ImportanceComputed tomography is an emerging imaging modality in cats with a suspected ureteral obstruction. Combination of CT and US can be beneficial for case management.
Syntactic Prediction Adaptation Accounts for Language Processing and Language Learning
Authors: Havron Naomi , Babineau Mireille , Fiévet Anne‐Caroline , de Carvalho Alex , Christophe Anne 
Published: July 2021

AbstractA previous study has shown that children use recent input to adapt their syntactic predictions and use these adapted predictions to infer the meaning of novel words. In the current study, we investigated whether children could use this mechanism to disambiguate words whose interpretation as a noun or a verb is ambiguous. We tested 2‐ to 4‐year‐old French children using the phrase la petite followed by a homophone that could be interpreted as either a noun or a verb. We assigned the children to a noun condition or a verb condition. Before the test, those in the noun condition were exposed to sentences where la petite predicted nouns, and those in the verb condition to sentences where la petite predicted verbs. At testing, 3‐ to 4‐year‐olds, but not 2‐year‐olds, from the verb condition looked at the verb interpretation longer than did the children in the noun condition. This suggests a progression in children's ability to rely on input to adapt their predictions in language comprehension.