bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated extraction of chemical synthesis actions from experimental procedures
Authors: Vaucher Alain C. , Zipoli Federico , Geluykens Joppe , Nair Vishnu H. , Schwaller Philippe , Laino Teodoro 
Published: July 2020

AbstractExperimental procedures for chemical synthesis are commonly reported in prose in patents or in the scientific literature. The extraction of the details necessary to reproduce and validate a synthesis in a chemical laboratory is often a tedious task requiring extensive human intervention. We present a method to convert unstructured experimental procedures written in English to structured synthetic steps (action sequences) reflecting all the operations needed to successfully conduct the corresponding chemical reactions. To achieve this, we design a set of synthesis actions with predefined properties and a deep-learning sequence to sequence model based on the transformer architecture to convert experimental procedures to action sequences. The model is pretrained on vast amounts of data generated automatically with a custom rule-based natural language processing approach and refined on manually annotated samples. Predictions on our test set result in a perfect (100%) match of the action sequence for 60.8% of sentences, a 90% match for 71.3% of sentences, and a 75% match for 82.4% of sentences.
Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids
Authors: Redondo-Salvo Santiago , Fernández-López Raúl , Ruiz Raúl , Vielva Luis , de Toro María , Rocha Eduardo P. C. , Garcillán-Barcia M. Pilar , de la Cruz Fernando 
Published: July 2020

AbstractPlasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I–VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.
An FGF15/19-TFEB regulatory loop controls hepatic cholesterol and bile acid homeostasis
Authors: Wang Yifeng , Gunewardena Sumedha , Li Feng , Matye David J. , Chen Cheng , Chao Xiaojuan , Jung Taeyoon , Zhang Yuxia , Czerwiński Maciej , Ni Hong-Min , Ding Wen-Xing , Li Tiangang 
Published: July 2020

AbstractBile acid synthesis plays a key role in regulating whole body cholesterol homeostasis. Transcriptional factor EB (TFEB) is a nutrient and stress-sensing transcriptional factor that promotes lysosomal biogenesis. Here we report a role of TFEB in regulating hepatic bile acid synthesis. We show that TFEB induces cholesterol 7α-hydroxylase (CYP7A1) in human hepatocytes and mouse livers and prevents hepatic cholesterol accumulation and hypercholesterolemia in Western diet-fed mice. Furthermore, we find that cholesterol-induced lysosomal stress feed-forward activates TFEB via promoting TFEB nuclear translocation, while bile acid-induced fibroblast growth factor 19 (FGF19), acting via mTOR/ERK signaling and TFEB phosphorylation, feedback inhibits TFEB nuclear translocation in hepatocytes. Consistently, blocking intestinal bile acid uptake by an apical sodium-bile acid transporter (ASBT) inhibitor decreases ileal FGF15, enhances hepatic TFEB nuclear localization and improves cholesterol homeostasis in Western diet-fed mice. This study has identified a TFEB-mediated gut-liver signaling axis that regulates hepatic cholesterol and bile acid homeostasis.
Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood
Authors: Li Shantao , Crawford Forrest W. , Gerstein Mark B. 
Published: July 2020

AbstractMultiple mutational processes drive carcinogenesis, leaving characteristic signatures in tumor genomes. Determining the active signatures from a full repertoire of potential ones helps elucidate mechanisms of cancer development. This involves optimally decomposing the counts of cancer mutations, tabulated according to their trinucleotide context, into a linear combination of known signatures. Here, we develop sigLASSO (a software tool at github.com/gersteinlab/siglasso) to carry out this optimization efficiently. sigLASSO has four key aspects: (1) It jointly optimizes the likelihood of sampling and signature fitting, by explicitly factoring multinomial sampling into the objective function. This is particularly important when mutation counts are low and sampling variance is high (e.g., in exome sequencing). (2) sigLASSO uses L1 regularization to parsimoniously assign signatures, leading to sparse and interpretable solutions. (3) It fine-tunes model complexity, informed by data scale and biological priors. (4) Consequently, sigLASSO can assess model uncertainty and abstain from making assignments in low-confidence contexts.
Engineered CRISPR/Cas9 enzymes improve discrimination by slowing DNA cleavage to allow release of off-target DNA
Authors: Liu Mu-Sen , Gong Shanzhong , Yu Helen-Hong , Jung Kyungseok , Johnson Kenneth A. , Taylor David W. 
Published: July 2020

AbstractCRISPR/Cas9 is a programmable genome editing tool widely used for biological applications and engineered Cas9s have increased discrimination against off-target cleavage compared with wild-type Streptococcus pyogenes (SpCas9) in vivo. To understand the basis for improved discrimination against off-target DNA containing important mismatches at the distal end of the guide RNA, we performed kinetic analyses on the high-fidelity (Cas9-HF1) and hyper-accurate (HypaCas9) engineered Cas9 variants. We show that DNA cleavage is impaired by more than 100- fold for the high-fidelity variants. The high-fidelity variants improve discrimination by slowing the observed rate of cleavage without increasing the rate of DNA rewinding and release. The kinetic partitioning favors release rather than cleavage of a bound off-target substrate only because the cleavage rate is so low. Further improvement in discrimination may require engineering increased rates of dissociation of off-target DNA.
Determination of interatomic coupling between two-dimensional crystals using angle-resolved photoemission spectroscopy
Authors: Thompson J. J. P. , Pei D. , Peng H. , Wang H. , Channa N. , Peng H. L. , Barinov A. , Schröter N. B. M. , Chen Y. , Mucha-Kruczyński M. 
Published: July 2020

AbstractLack of directional bonding between two-dimensional crystals like graphene or monolayer transition metal dichalcogenides provides unusual freedom in the selection of components for vertical van der Waals heterostructures. However, even for identical layers, their stacking, in particular the relative angle between their crystallographic directions, modifies properties of the structure. We demonstrate that the interatomic coupling between two two-dimensional crystals can be determined from angle-resolved photoemission spectra of a trilayer structure with one aligned and one twisted interface. Each of the interfaces provides complementary information and together they enable self-consistent determination of the coupling. We parametrise interatomic coupling for carbon atoms by studying twisted trilayer graphene and show that the result can be applied to structures with different twists and number of layers. Our approach demonstrates how to extract fundamental information about interlayer coupling in a stack of two-dimensional crystals and can be applied to many other van der Waals interfaces.
AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network
Authors: Abu-Thuraia Afnan , Goyette Marie-Anne , Boulais Jonathan , Delliaux Carine , Apcher Chloé , Schott Céline , Chidiac Rony , Bagci Halil , Thibault Marie-Pier , Davidson Dominique , Ferron Mathieu , Veillette André , Daly Roger J. , Gingras Anne-Claude , Gratton Jean-Philippe , Côté Jean-François 
Published: July 2020

AbstractAberrant expression of receptor tyrosine kinase AXL is linked to metastasis. AXL can be activated by its ligand GAS6 or by other kinases, but the signaling pathways conferring its metastatic activity are unknown. Here, we define the AXL-regulated phosphoproteome in breast cancer cells. We reveal that AXL stimulates the phosphorylation of a network of focal adhesion (FA) proteins, culminating in faster FA disassembly. Mechanistically, AXL phosphorylates NEDD9, leading to its binding to CRKII which in turn associates with and orchestrates the phosphorylation of the pseudo-kinase PEAK1. We find that PEAK1 is in complex with the tyrosine kinase CSK to mediate the phosphorylation of PAXILLIN. Uncoupling of PEAK1 from AXL signaling decreases metastasis in vivo, but not tumor growth. Our results uncover a contribution of AXL signaling to FA dynamics, reveal a long sought-after mechanism underlying AXL metastatic activity, and identify PEAK1 as a therapeutic target in AXL positive tumors.
The circadian phase of antenatal glucocorticoid treatment affects the risk of behavioral disorders
Authors: Astiz Mariana , Heyde Isabel , Fortmann Mats Ingmar , Bossung Verena , Roll Claudia , Stein Anja , Grüttner Berthold , Göpel Wolfgang , Härtel Christoph , Obleser Jonas , Oster Henrik 
Published: July 2020

AbstractDuring pregnancy, maternal endocrine signals drive fetal development and program the offspring’s physiology. A disruption of maternal glucocorticoid (GC) homeostasis increases the child’s risk of developing psychiatric disorders later in life. We here show in mice, that the time of day of antenatal GC exposure predicts the behavioral phenotype of the adult offspring. Offspring of mothers receiving GCs out-of-phase compared to their endogenous circadian GC rhythm show elevated anxiety, impaired stress coping, and dysfunctional stress-axis regulation. The fetal circadian clock determines the vulnerability of the stress axis to GC treatment by controlling GC receptor (GR) availability in the hypothalamus. Similarly, a retrospective observational study indicates poorer stress compensatory capacity in 5-year old preterm infants whose mothers received antenatal GCs towards the evening. Our findings offer insights into the circadian physiology of feto-maternal crosstalk and assign a role to the fetal clock as a temporal gatekeeper of GC sensitivity.
CircGRIA1 shows an age-related increase in male macaque brain and regulates synaptic plasticity and synaptogenesis
Authors: Xu Kaiyu , Zhang Ying , Xiong Wandi , Zhang Zhongyu , Wang Zhengbo , Lv Longbao , Liu Chao , Hu Zhengfei , Zheng Yong-Tang , Lu Lin , Hu Xin-Tian , Li Jiali 
Published: July 2020

AbstractCircular RNAs (circRNAs) are abundant in mammalian brain and some show age-dependent expression patterns. Here, we report that circGRIA1, a conserved circRNA isoform derived from the genomic loci of α-mino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor subunit Gria1, shows an age-related and male-specific increase in expression in the rhesus macaque prefrontal cortex and hippocampus. We show circGRIA1 is predominantly localized to the nucleus, and find an age-related increase in its association with the promoter region of Gria1 gene, suggesting it has a regulatory role in Gria1 transcription. In vitro and in vivo manipulation of circGRIA1 negatively regulates Gria1 mRNA and protein levels. Knockdown of circGRIA1 results in an age-related improvement of synaptogenesis, and GluR1 activity-dependent synaptic plasticity in the hippocampal neurons in males. Our findings underscore the importance of circRNA regulation and offer an insight into the biology of brain aging.
Real-time 3D single molecule tracking
Authors: Hou Shangguo , Exell Jack , Welsher Kevin 
Published: July 2020

AbstractTo date, single molecule studies have been reliant on tethering or confinement to achieve long duration and high temporal resolution measurements. Here, we present a 3D single-molecule active real-time tracking method (3D-SMART) which is capable of locking on to single fluorophores in solution for minutes at a time with photon limited temporal resolution. As a demonstration, 3D-SMART is applied to actively track single Atto 647 N fluorophores in 90% glycerol solution with an average duration of ~16 s at count rates of ~10 kHz. Active feedback tracking is further applied to single proteins and nucleic acids, directly measuring the diffusion of various lengths (99 to 1385 bp) of single DNA molecules at rates up to 10 µm2/s. In addition, 3D-SMART is able to quantify the occupancy of single Spinach2 RNA aptamers and capture active transcription on single freely diffusing DNA. 3D-SMART represents a critical step towards the untethering of single molecule spectroscopy.
A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features
Authors: Reis Andre L. M. , Deveson Ira W. , Wong Ted , Madala Bindu Swapna , Barker Chris , Blackburn James , Marcellin Esteban , Mercer Tim R. 
Published: July 2020

AbstractStandard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a next-generation sequencing library. The ladder can be spiked into a DNA sample, and act as an internal scale that measures quantitative genetics features. Unlike previous spike-ins, the ladder is encoded within a single molecule, and can be equivalently and independently synthesized by different laboratories. We show how the ladder can measure diverse quantitative features, including human genetic variation and microbial abundance, and also estimate uncertainty due to technical variation and improve normalization between libraries. This ladder provides an independent quantitative unit that can be used with any organism, application or technology, thereby providing a common metric by which genomes can be measured.
Mapping the oxygen structure of γ-Al2O3 by high-field solid-state NMR spectroscopy
Authors: Wang Qiang , Li Wenzheng , Hung Ivan , Mentink-Vigier Frederic , Wang Xiaoling , Qi Guodong , Wang Xiang , Gan Zhehong , Xu Jun , Deng Feng 
Published: July 2020

Abstractγ-Al2O3 is one of the most widely used catalysts or catalyst supports in numerous industrial catalytic processes. Understanding the structure of γ-Al2O3 is essential to tuning its physicochemical property, which still remains a great challenge. We report a strategy for the observation and determination of oxygen structure of γ-Al2O3 by using two-dimensional (2D) solid-state NMR spectroscopy at high field. 2D 17O double-quantum single-quantum homonuclear correlation NMR experiment is conducted at an ultra-high magnetic field of 35.2 T to reveal the spatial proximities between different oxygen species from the bulk to surface. Furthermore, 2D proton-detected 1H-17O heteronuclear correlation NMR experiments allow for a rapid identification and differentiation of surface hydroxyl groups and (sub-)surface oxygen species. Our experimental results demonstrate a non-random distribution of oxygen species in γ-Al2O3.
An fMRI study of error monitoring in Montessori and traditionally-schooled children
Authors: Denervaud Solange , Fornari Eleonora , Yang Xiao-Fei , Hagmann Patric , Immordino-Yang Mary Helen , Sander David 
Published: July 2020

AbstractThe development of error monitoring is central to learning and academic achievement. However, few studies exist on the neural correlates of children’s error monitoring, and no studies have examined its susceptibility to educational influences. Pedagogical methods differ on how they teach children to learn from errors. Here, 32 students (aged 8–12 years) from high-quality Swiss traditional or Montessori schools performed a math task with feedback during fMRI. Although the groups’ accuracies were similar, Montessori students skipped fewer trials, responded faster and showed more neural activity in right parietal and frontal regions involved in math processing. While traditionally-schooled students showed greater functional connectivity between the ACC, involved in error monitoring, and hippocampus following correct trials, Montessori students showed greater functional connectivity between the ACC and frontal regions following incorrect trials. The findings suggest that pedagogical experience influences the development of error monitoring and its neural correlates, with implications for neurodevelopment and education.
Neurocognitive patterns dissociating semantic processing from executive control are linked to more detailed off-task mental time travel
Authors: Wang Hao-Ting , Ho Nerissa Siu Ping , Bzdok Danilo , Bernhardt Boris C. , Margulies Daniel S. , Jefferies Elizabeth , Smallwood Jonathan 
Published: July 2020

AbstractFeatures of ongoing experience are common across individuals and cultures. However, certain people express specific patterns of thought to a greater extent than others. Contemporary psychological theory assumes that individual differences in thought patterns occur because different types of experience depend on the expression of different neurocognitive processes. Consequently, individual variation in the underlying neurocognitive architecture is hypothesised to determine the ease with which certain thought patterns are generated or maintained. Our study (N = 178) tested this hypothesis using multivariate pattern analysis to infer shared variance among measures of cognitive function and neural organisation and examined whether these latent variables explained reports of the patterns of on-going thoughts people experienced in the lab. We found that relatively better performance on tasks relying primarily on semantic knowledge, rather than executive control, was linked to a neural functional organisation associated, via meta-analysis, with task labels related to semantic associations (sentence processing, reading and verbal semantics). Variability of this functional mode predicted significant individual variation in the types of thoughts that individuals experienced in the laboratory: neurocognitive patterns linked to better performance at tasks that required guidance from semantic representation, rather than those dependent on executive control, were associated with patterns of thought characterised by greater subjective detail and a focus on time periods other than the here and now. These relationships were consistent across different days and did not vary with level of task demands, indicating they are relatively stable features of an individual’s cognitive profile. Together these data confirm that individual variation in aspects of ongoing experience can be inferred from hidden neurocognitive architecture and demonstrate that performance trade-offs between executive control and long-term semantic knowledge are linked to a person’s tendency to imagine situations that transcend the here and now.
Sex differences in visuomotor tracking
Authors: Mathew James , Masson Guillaume S. , Danion Frederic R. 
Published: July 2020

AbstractThere is a growing interest in sex differences in human and animal cognition. However, empirical evidences supporting behavioral and neural sex differences in humans remain sparse. Visuomotor behaviors offer a robust and naturalistic empirical framework to seek for the computational mechanisms underlying sex biases in cognition. In a large group of human participants (N = 127), we investigated sex differences in a visuo-oculo-manual motor task that consists of tracking with the hand a target moving unpredictably. We report a clear male advantage in hand tracking accuracy. We tested whether men and women employ different gaze strategy or hand movement kinematics. Results show no key difference in these distinct visuomotor components. However, highly consistent differences in eye-hand coordination were evidenced by a larger temporal lag between hand motion and target motion in women. This observation echoes with other studies showing a male advantage in manual reaction time to visual stimuli. We propose that the male advantage for visuomotor tracking does not reside in a more reliable gaze strategy, or in more sophisticated hand movements, but rather in a faster decisional process linking visual information about target motion with forthcoming hand, but not eye, actions.
Sirtuin-1 expression and activity is diminished in aged liver grafts
Authors: Scheuermann Uwe , Seyferth Elisabeth R. , Abraham Nader , Kesseli Samuel J. , Halpern Samantha E. , Zhu Minghua , Song Mingqing , Hartwig Matthew G. , Parker William , Kwun Jean , Cherry Anne D. , Lee Jaewoo , Barbas Andrew S. 
Published: July 2020

AbstractThe cellular mechanisms underlying impaired function of aged liver grafts have not been fully elucidated, but mitochondrial dysfunction appears to be contributory. Sirtuin1 has been identified as a key mediator of mitochondrial recovery following ischemia–reperfusion injury. The purpose of this study was to determine whether differences exist in sirtuin-1 expression/activity in old vs. young liver grafts and to determine correlations with mitochondrial function, graft metabolic function, and graft injury. Old and young rat liver grafts (N = 7 per group) were exposed to 12 h of static cold storage (SCS), followed by a 2 h period of graft reperfusion ex vivo. Sirtuin1 expression and activity, mitochondrial function, graft metabolic function, and graft injury were compared. Sirtuin1 expression is upregulated in young, but not old, liver grafts in response to cold storage and reperfusion. This is associated with diminished tissue ATP, antioxidant defense, and graft metabolic function in old liver grafts. There was no evidence of increased inflammation or histologic injury in old grafts. Sirtuin1 expression is diminished in old liver grafts and correlates with mitochondrial and metabolic function. The sirtuin pathway may represent a target for intervention to enhance the function of aged liver grafts.
Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology
Authors: Hylling Ole , Carstens Alexander B. , Kot Witold , Hansen Martin , Neve Horst , Franz Charles M. A. P. , Johansen Anders , Ellegaard-Jensen Lea , Hansen Lars H. 
Published: July 2020

AbstractAlthough bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.