bluuebunny/crossref_metadata_2025_split huggingface dataset:
The concurrence of DNA methylation and demethylation is associated with transcription regulation
Authors: Shi Jiejun , Xu Jianfeng , Chen Yiling Elaine , Li Jason Sheng , Cui Ya , Shen Lanlan , Li Jingyi Jessica , Li Wei 
Published: September 2021

AbstractThe mammalian DNA methylome is formed by two antagonizing processes, methylation by DNA methyltransferases (DNMT) and demethylation by ten-eleven translocation (TET) dioxygenases. Although the dynamics of either methylation or demethylation have been intensively studied in the past decade, the direct effects of their interaction on gene expression remain elusive. Here, we quantify the concurrence of DNA methylation and demethylation by the percentage of unmethylated CpGs within a partially methylated read from bisulfite sequencing. After verifying ‘methylation concurrence’ by its strong association with the co-localization of DNMT and TET enzymes, we observe that methylation concurrence is strongly correlated with gene expression. Notably, elevated methylation concurrence in tumors is associated with the repression of 40~60% of tumor suppressor genes, which cannot be explained by promoter hypermethylation alone. Furthermore, methylation concurrence can be used to stratify large undermethylated regions with negligible differences in average methylation into two subgroups with distinct chromatin accessibility and gene regulation patterns. Together, methylation concurrence represents a unique methylation metric important for transcription regulation and is distinct from conventional metrics, such as average methylation and methylation variation.
Atomistic processes of surface-diffusion-induced abnormal softening in nanoscale metallic crystals
Authors: Wang Xiang , Zheng Sixue , Shinzato Shuhei , Fang Zhengwu , He Yang , Zhong Li , Wang Chongmin , Ogata Shigenobu , Mao Scott X. 
Published: September 2021

AbstractUltrahigh surface-to-volume ratio in nanoscale materials, could dramatically facilitate mass transport, leading to surface-mediated diffusion similar to Coble-type creep in polycrystalline materials. Unfortunately, the Coble creep is just a conceptual model, and the associated physical mechanisms of mass transport have never been revealed at atomic scale. Akin to the ambiguities in Coble creep, atomic surface diffusion in nanoscale crystals remains largely unclear, especially when mediating yielding and plastic flow. Here, by using in situ nanomechanical testing under high-resolution transmission electron microscope, we find that the diffusion-assisted dislocation nucleation induces the transition from a normal to an inverse Hall-Petch-like relation of the strength-size dependence and the surface-creep leads to the abnormal softening in flow stress with the reduction in size of nanoscale silver, contrary to the classical “alternating dislocation starvation” behavior in nanoscale platinum. This work provides insights into the atomic-scale mechanisms of diffusion-mediated deformation in nanoscale materials, and impact on the design for ultrasmall-sized nanomechanical devices.
Quantitative modelling of amino acid transport and homeostasis in mammalian cells
Authors: Gauthier-Coles Gregory , Vennitti Jade , Zhang Zhiduo , Comb William C. , Xing Shuran , Javed Kiran , Bröer Angelika , Bröer Stefan 
Published: September 2021

AbstractHomeostasis is one of the fundamental concepts in physiology. Despite remarkable progress in our molecular understanding of amino acid transport, metabolism and signaling, it remains unclear by what mechanisms cytosolic amino acid concentrations are maintained. We propose that amino acid transporters are the primary determinants of intracellular amino acid levels. We show that a cell’s endowment with amino acid transporters can be deconvoluted experimentally and used this data to computationally simulate amino acid translocation across the plasma membrane. Transport simulation generates cytosolic amino acid concentrations that are close to those observed in vitro. Perturbations of the system are replicated in silico and can be applied to systems where only transcriptomic data are available. This work explains amino acid homeostasis at the systems-level, through a combination of secondary active transporters, functionally acting as loaders, harmonizers and controller transporters to generate a stable equilibrium of all amino acid concentrations.
Hydrogen radical-shuttle (HRS)-enabled photoredox synthesis of indanones via decarboxylative annulation
Authors: Yang Bo , Li Shi-Jun , Wang Yongdong , Lan Yu , Zhu Shifa 
Published: September 2021

AbstractHydrogen atom transfer (HAT) process is a powerful and effective strategy for activating C-H bonds followed by further functionalization. Intramolecular 1,n (n = 5 or 6)-HATs are common and frequently encountered in organic synthesis. However, intramolecular 1,n (n = 2 or 3)-HAT is very challenging due to slow kinetics. Compared to proton-shuttle process, which is well established for organic synthesis, hydrogen radical-shuttle (HRS) is unexplored. In this work, a HRS-enabled decarboxylative annulation of carbonyl compounds via photoredox catalysis for the synthesis of indanones is developed. This protocol features broad substrate scope, excellent functional group tolerance, internal hydrogen radical transfer, atom- and step-economy. Critical to the success of this process is the introduction of water, acting as both HRS and hydrogen source, which was demonstrated by mechanistic experiments and density functional theory (DFT) calculations. Importantly, this mechanistically distinctive HAT provides a complement to that of typical proton-shuttle-promoted, representing a breakthrough in hydrogen radical transfer, especially in the inherently challenging 1,2- or 1,3-HAT.
β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture
Authors: Mahmood Syed Raza , Xie Xin , Hosny El Said Nadine , Venit Tomas , Gunsalus Kristin C. , Percipalle Piergiorgio 
Published: September 2021

Abstractβ-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can induce changes in chromatin structure by affecting the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings reveal that β-actin-dependent chromatin remodeling plays a role in shaping the chromatin landscape and influences the regulation of genes involved in development and differentiation.
Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production
Authors: Saaret Annica , Villiers Benoît , Stricher François , Anissimova Macha , Cadillon Mélodie , Spiess Reynard , Hay Sam , Leys David 
Published: September 2021

AbstractIsobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group.
Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase
Authors: Malär Alexander A. , Wili Nino , Völker Laura A. , Kozlova Maria I. , Cadalbert Riccardo , Däpp Alexander , Weber Marco E. , Zehnder Johannes , Jeschke Gunnar , Eckert Hellmut , Böckmann Anja , Klose Daniel , Mulkidjanian Armen Y. , Meier Beat H. , Wiegand Thomas 
Published: September 2021

AbstractThe ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing
Authors: Briggs Emma M. , Rojas Federico , McCulloch Richard , Matthews Keith R. , Otto Thomas D. 
Published: September 2021

AbstractDevelopmental steps in the trypanosome life-cycle involve transition between replicative and non-replicative forms specialised for survival in, and transmission between, mammalian and tsetse fly hosts. Here, using oligopeptide-induced differentiation in vitro, we model the progressive development of replicative ‘slender’ to transmissible ‘stumpy’ bloodstream form Trypanosoma brucei and capture the transcriptomes of 8,599 parasites using single cell transcriptomics (scRNA-seq). Using this framework, we detail the relative order of biological events during asynchronous development, profile dynamic gene expression patterns and identify putative regulators. We additionally map the cell cycle of proliferating parasites and position stumpy cell-cycle exit at early G1 before progression to a distinct G0 state. A null mutant for one transiently elevated developmental regulator, ZC3H20 is further analysed by scRNA-seq, identifying its point of failure in the developmental atlas. This approach provides a paradigm for the dissection of differentiation events in parasites, relevant to diverse transitions in pathogen biology.
Boron-doped sodium layered oxide for reversible oxygen redox reaction in Na-ion battery cathodes
Authors: Guo Yu-Jie , Wang Peng-Fei , Niu Yu-Bin , Zhang Xu-Dong , Li Qinghao , Yu Xiqian , Fan Min , Chen Wan-Ping , Yu Yang , Liu Xiangfeng , Meng Qinghai , Xin Sen , Yin Ya-Xia , Guo Yu-Guo 
Published: September 2021

AbstractNa-ion cathode materials operating at high voltage with a stable cycling behavior are needed to develop future high-energy Na-ion cells. However, the irreversible oxygen redox reaction at the high-voltage region in sodium layered cathode materials generates structural instability and poor capacity retention upon cycling. Here, we report a doping strategy by incorporating light-weight boron into the cathode active material lattice to decrease the irreversible oxygen oxidation at high voltages (i.e., >4.0 V vs. Na+/Na). The presence of covalent B–O bonds and the negative charges of the oxygen atoms ensures a robust ligand framework for the NaLi1/9Ni2/9Fe2/9Mn4/9O2 cathode material while mitigating the excessive oxidation of oxygen for charge compensation and avoiding irreversible structural changes during cell operation. The B-doped cathode material promotes reversible transition metal redox reaction enabling a room-temperature capacity of 160.5 mAh g−1 at 25 mA g−1 and capacity retention of 82.8% after 200 cycles at 250 mA g−1. A 71.28 mAh single-coated lab-scale Na-ion pouch cell comprising a pre-sodiated hard carbon-based anode and B-doped cathode material is also reported as proof of concept.
Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community
Authors: Canarini Alberto , Schmidt Hannes , Fuchslueger Lucia , Martin Victoria , Herbold Craig W. , Zezula David , Gündler Philipp , Hasibeder Roland , Jecmenica Marina , Bahn Michael , Richter Andreas 
Published: September 2021

AbstractClimate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.
Super fine cerium hydroxide abrasives for SiO2 film chemical mechanical planarization performing scratch free
Authors: Son Young-Hye , Jeong Gi-Ppeum , Kim Pil-Su , Han Man-Hyup , Hong Seong-Wan , Bae Jae-Young , Kim Sung-In , Park Jin-Hyung , Park Jea-Gun 
Published: September 2021

AbstractFace-centered-cubic crystallized super-fine (~ 2 nm in size) wet-ceria-abrasives are synthesized using a novel wet precipitation process that comprises a Ce4+ precursor, C3H4N2 catalyst, and NaOH titrant for a synthesized termination process at temperature of at temperature of 25 °C. This process overcomes the limitations of chemical–mechanical-planarization (CMP)-induced scratches from conventional dry ceria abrasives with irregular surfaces or wet ceria abrasives with crystalline facets in nanoscale semiconductor devices. The chemical composition of super-fine wet ceria abrasives depends on the synthesis termination pH, that is, Ce(OH)4 abrasives at a pH of 4.0–5.0 and a mixture of CeO2 and Ce(OH)4 abrasives at a pH of 5.5–6.5. The Ce(OH)4 abrasives demonstrate better abrasive stability in the SiO2-film CMP slurry than the CeO2 abrasives and produce a minimum abrasive zeta potential (~ 12 mV) and a minimum secondary abrasive size (~ 130 nm) at the synthesis termination pH of 5.0. Additionally, the abrasive stability of the SiO2-film CMP slurry that includes super-fine wet ceria abrasives is notably sensitive to the CMP slurry pH; the best abrasive stability (i.e., a minimum secondary abrasive size of ~ 130 nm) is observed at a specific pH (6.0). As a result, a maximum SiO2-film polishing rate (~ 524 nm/min) is achieved at pH 6.0, and the surface is free of stick-and-slip type scratches.
Discontinuous phase transitions in the q-voter model with generalized anticonformity on random graphs
Authors: Abramiuk-Szurlej Angelika , Lipiecki Arkadiusz , Pawłowski Jakub , Sznajd-Weron Katarzyna 
Published: September 2021

AbstractWe study the binary q-voter model with generalized anticonformity on random Erdős–Rényi graphs. In such a model, two types of social responses, conformity and anticonformity, occur with complementary probabilities and the size of the source of influence $$q_c$$

q
c

in case of conformity is independent from the size of the source of influence $$q_a$$

q
a

in case of anticonformity. For $$q_c=q_a=q$$

q
c

=

q
a

=
q

the model reduces to the original q-voter model with anticonformity. Previously, such a generalized model was studied only on the complete graph, which corresponds to the mean-field approach. It was shown that it can display discontinuous phase transitions for $$q_c \ge q_a + \Delta q$$

q
c

≥

q
a

+
Δ
q

, where $$\Delta q=4$$

Δ
q
=
4

for $$q_a \le 3$$

q
a

≤
3

and $$\Delta q=3$$

Δ
q
=
3

for $$q_a>3$$

q
a

>
3

. In this paper, we pose the question if discontinuous phase transitions survive on random graphs with an average node degree $$\langle k\rangle \le 150$$

⟨
k
⟩
≤
150

observed empirically in social networks. Using the pair approximation, as well as Monte Carlo simulations, we show that discontinuous phase transitions indeed can survive, even for relatively small values of $$\langle k\rangle$$

⟨
k
⟩

. Moreover, we show that for $$q_a < q_c - 1$$

q
a

<

q
c

-
1

pair approximation results overlap the Monte Carlo ones. On the other hand, for $$q_a \ge q_c - 1$$

q
a

≥

q
c

-
1

pair approximation gives qualitatively wrong results indicating discontinuous phase transitions neither observed in the simulations nor within the mean-field approach. Finally, we report an intriguing result showing that the difference between the spinodals obtained within the pair approximation and the mean-field approach follows a power law with respect to $$\langle k\rangle$$

⟨
k
⟩

, as long as the pair approximation indicates correctly the type of the phase transition.
Modified N-linked glycosylation status predicts trafficking defective human Piezo1 channel mutations
Authors: Li Jinyuan Vero , Ng Chai-Ann , Cheng Delfine , Zhou Zijing , Yao Mingxi , Guo Yang , Yu Ze-Yan , Ramaswamy Yogambha , Ju Lining Arnold , Kuchel Philip W. , Feneley Michael P. , Fatkin Diane , Cox Charles D. 
Published: September 2021

AbstractMechanosensitive channels are integral membrane proteins that sense mechanical stimuli. Like most plasma membrane ion channel proteins they must pass through biosynthetic quality control in the endoplasmic reticulum that results in them reaching their destination at the plasma membrane. Here we show that N-linked glycosylation of two highly conserved asparagine residues in the ‘cap’ region of mechanosensitive Piezo1 channels are necessary for the mature protein to reach the plasma membrane. Both mutation of these asparagines (N2294Q/N2331Q) and treatment with an enzyme that hydrolyses N-linked oligosaccharides (PNGaseF) eliminates the fully glycosylated mature Piezo1 protein. The N-glycans in the cap are a pre-requisite for N-glycosylation in the ‘propeller’ regions, which are present in loops that are essential for mechanotransduction. Importantly, trafficking-defective Piezo1 variants linked to generalized lymphatic dysplasia and bicuspid aortic valve display reduced fully N-glycosylated Piezo1 protein. Thus the N-linked glycosylation status in vitro correlates with efficient membrane trafficking and will aid in determining the functional impact of Piezo1 variants of unknown significance.
Generation and characterization of cardiac valve endothelial-like cells from human pluripotent stem cells
Authors: Cheng LinXi , Xie MingHui , Qiao WeiHua , Song Yu , Zhang YanYong , Geng YingChao , Xu WeiLin , Wang Lin , Wang Zheng , Huang Kai , Dong NianGuo , Sun YuHua 
Published: September 2021

AbstractThe cardiac valvular endothelial cells (VECs) are an ideal cell source that could be used for making the valve organoids. However, few studies have been focused on the derivation of this important cell type. Here we describe a two-step chemically defined xeno-free method for generating VEC-like cells from human pluripotent stem cells (hPSCs). HPSCs were specified to KDR+/ISL1+multipotent cardiac progenitors (CPCs), followed by differentiation into valve endothelial-like cells (VELs) via an intermediate endocardial cushion cell (ECC) type. Mechanistically, administration of TGFb1 and BMP4 may specify VEC fate by activating the NOTCH/WNT signaling pathways and previously unidentified targets such as ATF3 and KLF family of transcription factors. When seeded onto the surface of the de-cellularized porcine aortic valve (DCV) matrix scaffolds, hPSC-derived VELs exhibit superior proliferative and clonogenic potential than the primary VECs and human aortic endothelial cells (HAEC). Our results show that hPSC-derived valvular cells could be efficiently generated from hPSCs, which might be used as seed cells for construction of valve organoids or next generation tissue engineered heart valves.
CO2-tuned highly selective reduction of formamides to the corresponding methylamines
Authors: Guo Zhiqiang , Pang Tengfei , Yan Leilei , Wei Xuehong , Chao Jianbin , Xi Chanjuan 
Published: September 2021

An efficient, CO2-tuned and highly selective C–O bond cleavage of N-methylated formanilides with NaBH4 has been achieved. Notably, when using N2 as reaction atmosphere, the reaction gave N-methylaniline as major product via C–N bond hydrogenolysis.
A study on preterm birth predictions using physiological signals, medical health record information and low‐dimensional embedding methods
Authors: Nsugbe Ejay , Samuel Oluwarotimi William , Sanusi Ibrahim , Asogbon Mojisola Grace , Li Guanglin 
Published: September 2021

AbstractPreterm births have been seen to have psychological and financial implications; current surveys suggest that amongst the various methods of preterm prediction, there is yet to exist a reliable and standard means of predicting preterm births. This study investigates the application of electrohysterogram and tocogram signals acquired at various points during the third pregnancy trimester, alongside information from the patients' medical health record regarding the pregnancy, towards preterm prediction and an associated delivery imminency timeline. In addition to this, the impact of both linear and non‐linear dimensional embedding methods towards the preterm prediction is explored. The classification exercises were carried out using a support vector machine and decision tree, both of which have a certain degree of model interpretability and have potential to be introduced into a clinical operating framework.