bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesocrystalline Architecture in Hyaline Foraminifer Shells Indicates a Non‐Classical Crystallisation Pathway
Authors: Arns A. I. , Evans D. , Schiebel R. , Fink L. , Mezger M. , Alig E. , Linckens J. , Jochum K. P. , Schmidt M. U. , Jantschke A. , Haug G. H. 
Published: June 2022

AbstractCalcareous foraminifer shells (tests) represent one of the most important archives for paleoenvironmental and paleoclimatic reconstruction. To develop a mechanistic understanding of the relationship between environmental parameters and proxy signals, knowledge of the fundamental processes operating during foraminiferal biomineralization is essential. Here, we apply microscopic and diffraction‐based methods to address the crystallographic and hierarchical structure of the test wall of different hyaline foraminifer species. Our results show that the tests are constructed from micrometer‐scale oriented mesocrystals built of nanometer‐scale entities. Based on these observations, we propose a mechanistic extension to the biomineralization model for hyaline foraminifers, centered on the formation and assembly of units of metastable carbonate phases to the final mesocrystal via a non‐classical particle attachment process, possibly facilitated by organic matter. This implies the presence of metastable precursors such as vaterite or amorphous calcium carbonate, along with phase transitions to calcite, which is relevant for the mechanistic understanding of proxy incorporation in the hyaline foraminifers.
Difficult and complicated oral ulceration: an expert consensus guideline for diagnosis
Authors: Zeng Xin , Jin Xin , Zhong Liang , Zhou Gang , Zhong Ming , Wang Wenmei , Fan Yuan , Liu Qing , Qi Xiangmin , Guan Xiaobing , Yan Zhimin , Shen Xuemin , Wu Yingfang , Fan Lijie , Wang Zhi , He Yuan , Dan Hongxia , Yang Jiantang , Wang Hui , Liu Dongjuan , Feng Hui , Jiao Kai , Chen Qianming 
Published: June 2022

AbstractThe complexity of oral ulcerations poses considerable diagnostic and therapeutic challenges to oral specialists. The expert consensus was conducted to summarize the diagnostic work-up for difficult and complicated oral ulcers, based on factors such as detailed clinical medical history inquiry, histopathological examination, and ulceration-related systemic diseases screening. Not only it can provide a standardized procedure of oral ulceration, but also it can improve the diagnostic efficiency, in order to avoid misdiagnosis and missed diagnosis.
Enhancing spatiotemporal focusing of light deep inside scattering media with Time-Gated Reflection Matrix
Authors: Yu Zhipeng , Li Huanhao , Zhong Tianting , Lai Puxiang 
Published: June 2022

AbstractTime-gated reflection matrix (RM) has been successfully used for optical imaging deep inside scattering media. Recently, this method was extended to enhance the spatiotemporal focusing of light ultra-deep inside scattering media. This is achieved by calibrating the decomposition of the RM with the Tikhonov regularization parameter to convert multiply scattered photons that share the same time of flight with the singly scattered photons into singly scattered photons. Such a capability suggests a reshaping to the interaction mechanism between light and scattering media, which may benefit or inspire wide optical applications that desire enhanced spatiotemporal focusing of light at depths inside scattering media.
Childhood maltreatment mediates the effect of the genetic background on psychosis risk in young adults
Authors: Marchi Mattia , Elkrief Laurent , Alkema Anne , van Gastel Willemijn , Schubart Chris D. , van Eijk Kristel R. , Luykx Jurjen J. , Branje Susan , Mastrotheodoros Stefanos , Galeazzi Gian M. , van Os Jim , Cecil Charlotte A. , Conrod Patricia J. , Boks Marco P. 
Published: June 2022

AbstractChildhood maltreatment (CM) and genetic vulnerability are both risk factors for psychosis, but the relations between them are not fully understood. Guided by the recent identification of genetic risk to CM, this study investigates the hypothesis that genetic risk to schizophrenia also increases the risk of CM and thus impacts psychosis risk. The relationship between schizophrenia polygenetic risk, CM, and psychotic-like experiences (PLE) was investigated in participants from the Utrecht Cannabis Cohort (N = 1262) and replicated in the independent IMAGEN cohort (N = 1740). Schizophrenia polygenic risk score (SZ-PRS) were calculated from the most recent GWAS. The relationship between CM, PRS, and PLE was first investigated using multivariate linear regression. Next, mediation of CM in the pathway linking SZ-PRS and PLE was examined by structural equation modeling, while adjusting for a set of potential mediators including cannabis use, smoking, and neuroticism. In agreement with previous studies, PLE were strongly associated with SZ-PRS (B = 0.190,p = 0.009) and CM (B = 0.575,p < 0.001). Novel was that CM was also significantly associated with SZ-PRS (B = 0.171,p = 0.001), and substantially mediated the effects of SZ-PRS on PLE (proportion mediated = 29.9%,p = 0.001). In the replication cohort, the analyses yielded similar results, confirming equally strong mediation by CM (proportion mediated = 34.7%,p = 0.009). Our results suggest that CM acts as a mediator in the causal pathway linking SZ-PRS and psychosis risk. These findings open new perspectives on the relations between genetic and environmental risks and warrant further studies into potential interventions to reduce psychosis risk in vulnerable people.
Exploring pharmacological options for adolescent depression: a preclinical evaluation with a sex perspective
Authors: Ledesma-Corvi Sandra , Hernández-Hernández Elena , García-Fuster M. Julia 
Published: June 2022

AbstractThere is an urgent need for developing novel pharmacological treatment options for adolescent depression, and to ensure an optimal translational outcome to the clinic, sex should be included as a biological variable in preclinical studies. In this context, the present study compared the antidepressant-like potential of ketamine and cannabidiol, with the clinical standard fluoxetine, in adolescent rats exposed to maternal deprivation (as a model of early-life stress), while including a sex perspective. Moreover, changes in drug efficacy over time were evaluated by re-exposing rats to the same dose regimens during adulthood. Antidepressant-like responses were scored through a battery of distinctive tests (forced-swim, novelty-suppressed feeding, and sucrose preference) across time. The main results proved an antidepressant-like potential for ketamine and cannabidiol in adolescent rats, although their efficacy was dependent on sex and prior stress exposure, as well as on treatment length and the behavioral feature analyzed. In general, while all tested antidepressants in male rats improved certain affective-like features, female rats were mainly unresponsive to the treatments performed (except for certain benefits induced by ketamine), demonstrating the need for further characterizing proper treatments for this particular sex. Moreover, when rats were re-exposed in adulthood to the same drug regimens as in adolescence, a drop in efficacy was observed. These findings may have translational ramifications in that ketamine or cannabidiol could be moved forward as antidepressants for the adolescent depressed population, but not before further characterizing their potential long-term safety and/or beneficial vs. harmful effects for both sexes.
Measurable residual disease analysis in paediatric acute lymphoblastic leukaemia patients with ABL-class fusions
Authors: Venn Nicola C. , Huang Libby , Hovorková Lenka , Muskovic Walter , Wong Marie , Law Tamara , Heatley Susan L. , Khaw Seong Lin , Revesz Tom , Dalla Pozza Luciano , Shaw Peter J. , Fraser Chris , Moore Andrew S. , Cross Siobhan , Bendak Katerina , Norris Murray D. , Henderson Michelle J. , White Deborah L. , Cowley Mark J. , Trahair Toby N. , Zuna Jan , Sutton Rosemary 
Published: June 2022

Abstract
Background
ABL-class fusions including NUP214-ABL1 and EBF1-PDGFRB occur in high risk acute lymphoblastic leukaemia (ALL) with gene expression patterns similar to BCR-ABL-positive ALL. Our aim was to evaluate new DNA-based measurable residual disease (MRD) tests detecting these fusions and IKZF1-deletions in comparison with conventional immunoglobulin/T-cell receptor (Ig/TCR) markers.

Methods
Precise genomic breakpoints were defined from targeted or whole genome next generation sequencing for ABL-fusions and BCR-ABL1. Quantitative PCR assays were designed and used to re-measure MRD in remission bone marrow samples previously tested using Ig/TCR markers. All MRD testing complied with EuroMRD guidelines.

Results
ABL-class patients had 46% 5year event-free survival and 79% 5year overall survival. All had sensitive fusion tests giving high concordance between Ig/TCR and ABL-class fusion results (21 patients, n = 257 samples, r2 = 0.9786, P < 0.0001) and Ig/TCR and IKZF1-deletion results (9 patients, n = 143 samples, r2 = 0.9661, P < 0.0001). In contrast, in BCR-ABL1 patients, Ig/TCR and BCR-ABL1 tests were discordant in 32% (40 patients, n = 346 samples, r2 = 0.4703, P < 0.0001) and IKZF1-deletion results were closer to Ig/TCR (25 patients, n = 176, r2 = 0.8631, P < 0.0001).

Conclusions
MRD monitoring based on patient-specific assays detecting gene fusions or recurrent assays for IKZF1-deletions is feasible and provides good alternatives to Ig/TCR tests to monitor MRD in ABL-class ALL.
A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex
Authors: Chindemi Giuseppe , Abdellah Marwan , Amsalem Oren , Benavides-Piccione Ruth , Delattre Vincent , Doron Michael , Ecker András , Jaquier Aurélien T. , King James , Kumbhar Pramod , Monney Caitlin , Perin Rodrigo , Rössert Christian , Tuncel Anil M. , Van Geit Werner , DeFelipe Javier , Graupner Michael , Segev Idan , Markram Henry , Muller Eilif B. 
Published: June 2022

AbstractPyramidal cells (PCs) form the backbone of the layered structure of the neocortex, and plasticity of their synapses is thought to underlie learning in the brain. However, such long-term synaptic changes have been experimentally characterized between only a few types of PCs, posing a significant barrier for studying neocortical learning mechanisms. Here we introduce a model of synaptic plasticity based on data-constrained postsynaptic calcium dynamics, and show in a neocortical microcircuit model that a single parameter set is sufficient to unify the available experimental findings on long-term potentiation (LTP) and long-term depression (LTD) of PC connections. In particular, we find that the diverse plasticity outcomes across the different PC types can be explained by cell-type-specific synaptic physiology, cell morphology and innervation patterns, without requiring type-specific plasticity. Generalizing the model to in vivo extracellular calcium concentrations, we predict qualitatively different plasticity dynamics from those observed in vitro. This work provides a first comprehensive null model for LTP/LTD between neocortical PC types in vivo, and an open framework for further developing models of cortical synaptic plasticity.
POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean
Authors: Goettel Wolfgang , Zhang Hengyou , Li Ying , Qiao Zhenzhen , Jiang He , Hou Dianyun , Song Qijian , Pantalone Vincent R. , Song Bao-Hua , Yu Deyue , An Yong-qiang Charles 
Published: June 2022

AbstractSeed protein, oil content and yield are highly correlated agronomically important traits that essentially account for the economic value of soybean. The underlying molecular mechanisms and selection of these correlated seed traits during soybean domestication are, however, less known. Here, we demonstrate that a CCT gene, POWR1, underlies a large-effect protein/oil QTL. A causative TE insertion truncates its CCT domain and substantially increases seed oil content, weight, and yield while decreasing protein content. POWR1 pleiotropically controls these traits likely through regulating seed nutrient transport and lipid metabolism genes. POWR1 is also a domestication gene. We hypothesize that the TE insertion allele is exclusively fixed in cultivated soybean due to selection for larger seeds during domestication, which significantly contributes to shaping soybean with increased yield/seed weight/oil but reduced protein content. This study provides insights into soybean domestication and is significant in improving seed quality and yield in soybean and other crop species.
Wafer-scale solution-processed 2D material analog resistive memory array for memory-based computing
Authors: Tang Baoshan , Veluri Hasita , Li Yida , Yu Zhi Gen , Waqar Moaz , Leong Jin Feng , Sivan Maheswari , Zamburg Evgeny , Zhang Yong-Wei , Wang John , Thean Aaron V-Y. 
Published: June 2022

AbstractRealization of high-density and reliable resistive random access memories based on two-dimensional semiconductors is crucial toward their development in next-generation information storage and neuromorphic computing. Here, wafer-scale integration of solution-processed two-dimensional MoS2 memristor arrays are reported. The MoS2 memristors achieve excellent endurance, long memory retention, low device variations, and high analog on/off ratio with linear conductance update characteristics. The two-dimensional nanosheets appear to enable a unique way to modulate switching characteristics through the inter-flake sulfur vacancies diffusion, which can be controlled by the flake size distribution. Furthermore, the MNIST handwritten digits recognition shows that the MoS2 memristors can operate with a high accuracy of >98.02%, which demonstrates its feasibility for future analog memory applications. Finally, a monolithic three-dimensional memory cube has been demonstrated by stacking the two-dimensional MoS2 layers, paving the way for the implementation of two memristor into high-density neuromorphic computing system.
Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria
Authors: Vögeli Bastian , Schulz Luca , Garg Shivani , Tarasava Katia , Clomburg James M. , Lee Seung Hwan , Gonnot Aislinn , Moully Elamar Hakim , Kimmel Blaise R. , Tran Loan , Zeleznik Hunter , Brown Steven D. , Simpson Sean D. , Mrksich Milan , Karim Ashty S. , Gonzalez Ramon , Köpke Michael , Jewett Michael C. 
Published: June 2022

AbstractCarbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL−1), as well as hexanoic acid (3.06 ± 0.03 gL−1) and 1-hexanol (1.0 ± 0.1 gL−1) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL−1 in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology.
Structural independence of hydrogen-bond symmetrisation dynamics at extreme pressure conditions
Authors: Meier Thomas , Trybel Florian , Khandarkhaeva Saiana , Laniel Dominique , Ishii Takayuki , Aslandukova Alena , Dubrovinskaia Natalia , Dubrovinsky Leonid 
Published: June 2022

AbstractThe experimental study of hydrogen-bonds and their symmetrization under extreme conditions is predominantly driven by diffraction methods, despite challenges of localising or probing the hydrogen subsystems directly. Until recently, H-bond symmetrization has been addressed in terms of either nuclear quantum effects, spin crossovers or direct structural transitions; often leading to contradictory interpretations when combined. Here, we present high-resolution in-situ 1H-NMR experiments in diamond anvil cells investigating a range of systems containing linear O-H ⋯  O units at pressure ranges of up to 90 GPa covering their respective H-bond symmetrization. We found pronounced minima in the pressure dependence of the NMR resonance line-widths associated with a maximum in hydrogen mobility, precursor to a localisation of hydrogen atoms. These minima, independent of the chemical environment of the O-H ⋯  O unit, can be found in a narrow range of oxygen oxygen distances between 2.44 and 2.45 Å, leading to an average critical oxygen-oxygen distance of $${\bar{r}}_{{{{{{{{\rm{OO}}}}}}}}}^{{{{{{{{\rm{crit}}}}}}}}}=2.443(1)$$

r

¯

OO

crit

=
2.443

(

1

)

Å.
Amplification of downstream flood stage due to damming of fine-grained rivers
Authors: Ma Hongbo , Nittrouer Jeffrey A. , Fu Xudong , Parker Gary , Zhang Yuanfeng , Wang Yuanjian , Wang Yanjun , Lamb Michael P. , Cisneros Julia , Best Jim , Parsons Daniel R. , Wu Baosheng 
Published: June 2022

AbstractRiver dams provide many benefits, including flood control. However, due to constantly evolving channel morphology, downstream conveyance of floodwaters following dam closure is difficult to predict. Here, we test the hypothesis that the incised, enlarged channel downstream of dams provides enhanced water conveyance, using a case study from the lower Yellow River, China. We find that, although flood stage is lowered for small floods, counterintuitively, flood stage downstream of a dam can be amplified for moderate and large floods. This arises because bed incision is accompanied by sediment coarsening, which facilitates development of large dunes that increase flow resistance and reduce velocity relative to pre-dam conditions. Our findings indicate the underlying mechanism for such flood amplification may occur in >80% of fine-grained rivers, and suggest the need to reconsider flood control strategies in such rivers worldwide.
Transient evolution of permeability and friction in a slowly slipping fault activated by fluid pressurization
Authors: Cappa Frédéric , Guglielmi Yves , De Barros Louis 
Published: June 2022

AbstractThe mechanisms of permeability and friction evolution in a natural fault are investigated in situ. During three fluid injection experiments at different places in a fault zone, we measured simultaneously the fluid pressure, fault displacements and seismic activity. Changes in fault permeability and friction are then estimated concurrently. Results show that fault permeability increases up to 1.58 order of magnitude as a result of reducing effective normal stress and cumulative dilatant slip, and 19-to-60.8% of the enhancement occurs without seismic emissions. When modeling the fault displacement, we found that a rate-and-state friction and a permeability dependent on both slip and slip velocity together reasonably fit the fault-parallel and fault-normal displacements. This leads to the conclusion that the transient evolution of fault permeability and friction caused by a pressure perturbation exerts a potentially dominant control on fault stability during fluid flow.
Island-specific evolution of a sex-primed autosome in a sexual planarian
Authors: Guo Longhua , Bloom Joshua S. , Dols-Serrate Daniel , Boocock James , Ben-David Eyal , Schubert Olga T. , Kozuma Kaiya , Ho Katarina , Warda Emily , Chui Clarice , Wei Yubao , Leighton Daniel , Lemus Vergara Tzitziki , Riutort Marta , Sánchez Alvarado Alejandro , Kruglyak Leonid 
Published: June 2022

AbstractThe sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5–13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.
Reticulate evolution in the Pteris fauriei group (Pteridaceae)
Authors: Chao Yi-Shan , Ebihara Atsushi , Chiou Wen-Liang , Tsai Jer-Min , Huang Yu-Wen , Ranker Tom A. 
Published: June 2022

AbstractThePteris faurieigroup (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of theP. faurieigroup and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of theP. faurieigroup generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.
Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks
Authors: Tosi Micaela , Drummelsmith John , Obregón Dasiel , Chahal Inderjot , Van Eerd Laura L. , Dunfield Kari E. 
Published: June 2022

AbstractSustainable agricultural practices such as cover crops (CCs) and residue retention are increasingly applied to counteract detrimental consequences on natural resources. Since agriculture affects soil properties partly via microbial communities, it is critical to understand how these respond to different management practices. Our study analyzed five CC treatments (oat, rye, radish, rye-radish mixture and no-CC) and two crop residue managements (retention/R+ or removal/R−) in an 8-year diverse horticultural crop rotation trial from ON, Canada. CC effects were small but stronger than those of residue management. Radish-based CCs tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. CC species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated CC effects on bacterial abundance and fungal evenness (i.e., more sensitive in R− than R+), as well as microbial taxa. Several microbial structure features (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota), some affected by CCs, were correlated with early biomass production of the following tomato crop. Our study suggests that, whereas mid-term CC effects were small, they need to be better understood as they could be influencing cash crop productivity via plant-soil feedbacks.