bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains
Authors: Khoury Amanda , Achinger-Kawecka Joanna , Bert Saul A. , Smith Grady C. , French Hugh J. , Luu Phuc-Loi , Peters Timothy J. , Du Qian , Parry Aled J. , Valdes-Mora Fatima , Taberlay Phillippa C. , Stirzaker Clare , Statham Aaron L. , Clark Susan J. 
Published: January 2020

AbstractThe architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood. Here we perform RNAi knockdown to reduce CTCF levels and reveal a shared subset of CTCF-bound sites are robustly resistant to protein depletion. The ‘persistent’ CTCF sites are enriched at domain boundaries and chromatin loops constitutive to all cell types. CRISPR-Cas9 deletion of 2 persistent CTCF sites at the boundary between a long-range epigenetically active (LREA) and silenced (LRES) region, within the Kallikrein (KLK) locus, results in concordant activation of all 8 KLK genes within the LRES region. CTCF genome-wide depletion results in alteration in Topologically Associating Domain (TAD) structure, including the merging of TADs, whereas TAD boundaries are not altered where persistent sites are maintained. We propose that the subset of essential CTCF sites are involved in cell-type constitutive, higher order chromatin architecture.
Double layer charging driven carbon dioxide adsorption limits the rate of electrochemical carbon dioxide reduction on Gold
Authors: Ringe Stefan , Morales-Guio Carlos G. , Chen Leanne D. , Fields Meredith , Jaramillo Thomas F. , Hahn Christopher , Chan Karen 
Published: January 2020

AbstractElectrochemical CO$$_{2}$$

2

reduction is a potential route to the sustainable production of valuable fuels and chemicals. Here, we perform CO$$_{2}$$

2

reduction experiments on Gold at neutral to acidic pH values to elucidate the long-standing controversy surrounding the rate-limiting step. We find the CO production rate to be invariant with pH on a Standard Hydrogen Electrode scale and conclude that it is limited by the CO$$_{2}$$

2

adsorption step. We present a new multi-scale modeling scheme that integrates ab initio reaction kinetics with mass transport simulations, explicitly considering the charged electric double layer. The model reproduces the experimental CO polarization curve and reveals the rate-limiting step to be *COOH to *CO at low overpotentials, CO$$_{2}$$

2

adsorption at intermediate ones, and CO$$_{2}$$

2

mass transport at high overpotentials. Finally, we show the Tafel slope to arise from the electrostatic interaction between the dipole of *CO$$_{2}$$

2

and the interfacial field. This work highlights the importance of surface charging for electrochemical kinetics and mass transport.
Ratiometric upconversion nanothermometry with dual emission at the same wavelength decoded via a time-resolved technique
Authors: Qiu Xiaochen , Zhou Qianwen , Zhu Xingjun , Wu Zugen , Feng Wei , Li Fuyou 
Published: January 2020

AbstractThe in vivo temperature monitoring of a microenvironment is significant in biology and nanomedicine research. Luminescent nanothermometry provides a noninvasive method of detecting the temperature in vivo with high sensitivity and high response speed. However, absorption and scattering in complex tissues limit the signal penetration depth and cause errors due to variation at different locations in vivo. In order to minimize these errors and monitor temperature in vivo, in the present work, we provided a strategy to fabricate a same-wavelength dual emission ratiometric upconversion luminescence nanothermometer based on a hybrid structure composed of upconversion emissive PbS quantum dots and Tm-doped upconversion nanoparticles. The ratiometric signal composed of two upconversion emissions working at the same wavelength, but different luminescent lifetimes, were decoded via a time-resolved technique. This nanothermometer improved the temperature monitoring ability and a thermal resolution and sensitivity of ~0.5 K and ~5.6% K−1 were obtained in vivo, respectively.
The RepID–CRL4 ubiquitin ligase complex regulates metaphase to anaphase transition via BUB3 degradation
Authors: Jang Sang-Min , Nathans Jenny F. , Fu Haiqing , Redon Christophe E. , Jenkins Lisa M. , Thakur Bhushan L. , Pongor Lőrinc S. , Baris Adrian M. , Gross Jacob M. , OʹNeill Maura J. , Indig Fred E. , Cappell Steven D. , Aladjem Mirit I. 
Published: January 2020

AbstractThe spindle assembly checkpoint (SAC) prevents premature chromosome segregation by inactivating the anaphase promoting complex/cyclosome (APC/C) until all chromosomes are properly attached to mitotic spindles. Here we identify a role for Cullin–RING ubiquitin ligase complex 4 (CRL4), known for modulating DNA replication, as a crucial mitotic regulator that triggers the termination of the SAC and enables chromosome segregation. CRL4 is recruited to chromatin by the replication origin binding protein RepID/DCAF14/PHIP. During mitosis, CRL4 dissociates from RepID and replaces it with RB Binding Protein 7 (RBBP7), which ubiquitinates the SAC mediator BUB3 to enable mitotic exit. During interphase, BUB3 is protected from CRL4-mediated degradation by associating with promyelocytic leukemia (PML) nuclear bodies, ensuring its availability upon mitotic onset. Deficiencies in RepID, CRL4 or RBBP7 delay mitotic exit, increase genomic instability and enhance sensitivity to paclitaxel, a microtubule stabilizer and anti-tumor drug.
A van der Waals antiferromagnetic topological insulator with weak interlayer magnetic coupling
Authors: Hu Chaowei , Gordon Kyle N. , Liu Pengfei , Liu Jinyu , Zhou Xiaoqing , Hao Peipei , Narayan Dushyant , Emmanouilidou Eve , Sun Hongyi , Liu Yuntian , Brawer Harlan , Ramirez Arthur P. , Ding Lei , Cao Huibo , Liu Qihang , Dessau Dan , Ni Ni 
Published: January 2020

AbstractMagnetic topological insulators (TI) provide an important material platform to explore quantum phenomena such as quantized anomalous Hall effect and Majorana modes, etc. Their successful material realization is thus essential for our fundamental understanding and potential technical revolutions. By realizing a bulk van der Waals material MnBi4Te7 with alternating septuple [MnBi2Te4] and quintuple [Bi2Te3] layers, we show that it is ferromagnetic in plane but antiferromagnetic along the c axis with an out-of-plane saturation field of ~0.22 T at 2 K. Our angle-resolved photoemission spectroscopy measurements and first-principles calculations further demonstrate that MnBi4Te7 is a Z2 antiferromagnetic TI with two types of surface states associated with the [MnBi2Te4] or [Bi2Te3] termination, respectively. Additionally, its superlattice nature may make various heterostructures of [MnBi2Te4] and [Bi2Te3] layers possible by exfoliation. Therefore, the low saturation field and the superlattice nature of MnBi4Te7 make it an ideal system to investigate rich emergent phenomena.
Time-dependent solid-state molecular motion and colour tuning of host-guest systems by organic solvents
Authors: Yang Yu-Dong , Ji Xiaofan , Lu Zhi-Hao , Yang Jian , Gao Chao , Zhang Haoke , Tang Ben Zhong , Sessler Jonathan L. , Gong Han-Yuan 
Published: January 2020

AbstractHost-guest complex solid state molecular motion is a critical but underexplored phenomenon. In principle, it can be used to control molecular machines that function in the solid state. Here we describe a solid state system that operates on the basis of complexation between an all-hydrocarbon macrocycle, D4d-CDMB-8, and perylene. Molecular motion in this solid state machine is induced by exposure to organic solvents or grinding and gives rise to different co-crystalline, mixed crystalline, or amorphous forms. Distinct time-dependent emissive responses are seen for different organic solvents as their respective vapours or when the solid forms are subject to grinding. This temporal feature allows the present D4d-CDMB-8⊃perylene-based system to be used as a time-dependent, colour-based 4th dimension response element in pattern-based information codes. This work highlights how dynamic control over solid-state host-guest molecular motion may be used to induce a tuneable temporal response and provide materials with information storage capability.
Ceramic-like stable CsPbBr3 nanocrystals encapsulated in silica derived from molecular sieve templates
Authors: Zhang Qinggang , Wang Bo , Zheng Weilin , Kong Long , Wan Qun , Zhang Congyang , Li Zhichun , Cao Xueyan , Liu Mingming , Li Liang 
Published: January 2020

AbstractAchieving good stability while maintaining excellent properties is one of the main challenges for enhancing the competitiveness of luminescent perovskite CsPbX3 (X=Cl, Br, I) nanocrystals (NCs). Here, we propose a facile strategy to synthesize ceramic-like stable and highly luminescent CsPbBr3 NCs by encapsulating them into silica derived from molecular sieve templates at high temperature (600–900 oC). The obtained CsPbBr3-SiO2 powders not only show high photoluminescence quantum yield (~71%), but also show an exceptional stability comparable to the ceramic Sr2SiO4:Eu2+ green phosphor. They can maintain 100% of their photoluminescence value under illumination on blue light-emitting diodes (LEDs) chips (20 mA, 2.7 V) for 1000 h, and can also survive in a harsh hydrochloric acid aqueous solution (1 M) for 50 days. We believe that the above robust stabilities will significantly enhance the potential of perovskite CsPbX3 NCs to be practically applied in LEDs and backlight displays.
Titania supported synergistic palladium single atoms and nanoparticles for room temperature ketone and aldehydes hydrogenation
Authors: Kuai Long , Chen Zheng , Liu Shoujie , Kan Erjie , Yu Nan , Ren Yiming , Fang Caihong , Li Xingyang , Li Yadong , Geng Baoyou 
Published: January 2020

AbstractSelective reduction of ketone/aldehydes to alcohols is of great importance in green chemistry and chemical engineering. Highly efficient catalysts are still demanded to work under mild conditions, especially at room temperature. Here we present a synergistic function of single-atom palladium (Pd1) and nanoparticles (PdNPs) on TiO2 for highly efficient ketone/aldehydes hydrogenation to alcohols at room temperature. Compared to simple but inferior Pd1/TiO2 and PdNPs/TiO2 catalysts, more than twice activity enhancement is achieved with the Pd1+NPs/TiO2 catalyst that integrates both Pd1 and Pd NPs on mesoporous TiO2 supports, obtained by a simple but large-scaled spray pyrolysis route. The synergistic function of Pd1 and PdNPs is assigned so that the partial Pd1 dispersion contributes enough sites for the activation of C=O group while PdNPs site boosts the dissociation of H2 molecules to H atoms. This work not only contributes a superior catalyst for ketone/aldehydes hydrogenation, but also deepens the knowledge on their hydrogenation mechanism and guides people to engineer the catalytic behaviors as needed.
Pharmacological polyamine catabolism upregulation with methionine salvage pathway inhibition as an effective prostate cancer therapy
Authors: Affronti Hayley C. , Rowsam Aryn M. , Pellerite Anthony J. , Rosario Spencer R. , Long Mark D. , Jacobi Justine J. , Bianchi-Smiraglia Anna , Boerlin Christoph S. , Gillard Bryan M. , Karasik Ellen , Foster Barbara A. , Moser Michael , Wilton John H. , Attwood Kristopher , Nikiforov Mikhail A. , Azabdaftari Gissou , Pili Roberto , Phillips James G. , Casero Robert A. , Smiraglia Dominic J. 
Published: January 2020

AbstractProstatic luminal epithelial cells secrete high levels of acetylated polyamines into the prostatic lumen, sensitizing them to perturbations of connected metabolic pathways. Enhanced flux is driven by spermidine/spermine N1-acetyltransferase (SSAT) activity, which acetylates polyamines leading to their secretion and drives biosynthetic demand. The methionine salvage pathway recycles one-carbon units lost to polyamine biosynthesis to the methionine cycle to overcome stress. Prostate cancer (CaP) relies on methylthioadenosine phosphorylase (MTAP), the rate-limiting enzyme, to relieve strain. Here, we show that inhibition of MTAP alongside SSAT upregulation is synergistic in androgen sensitive and castration recurrent CaP models in vitro and in vivo. The combination treatment increases apoptosis in radical prostatectomy ex vivo explant samples. This unique high metabolic flux through polyamine biosynthesis and connected one carbon metabolism in CaP creates a metabolic dependency. Enhancing this flux while simultaneously targeting this dependency in prostate cancer results in an effective therapeutic approach potentially translatable to the clinic.
Mechanisms of triplet energy transfer across the inorganic nanocrystal/organic molecule interface
Authors: Luo Xiao , Han Yaoyao , Chen Zongwei , Li Yulu , Liang Guijie , Liu Xue , Ding Tao , Nie Chengming , Wang Mei , Castellano Felix N. , Wu Kaifeng 
Published: January 2020

AbstractThe mechanisms of triplet energy transfer across the inorganic nanocrystal/organic molecule interface remain poorly understood. Many seemingly contradictory results have been reported, mainly because of the complicated trap states characteristic of inorganic semiconductors and the ill-defined relative energetics between semiconductors and molecules used in these studies. Here we clarify the transfer mechanisms by performing combined transient absorption and photoluminescence measurements, both with sub-picosecond time resolution, on model systems comprising lead halide perovskite nanocrystals with very low surface trap densities as the triplet donor and polyacenes which either favour or prohibit charge transfer as the triplet acceptors. Hole transfer from nanocrystals to tetracene is energetically favoured, and hence triplet transfer proceeds via a charge separated state. In contrast, charge transfer to naphthalene is energetically unfavourable and spectroscopy shows direct triplet transfer from nanocrystals to naphthalene; nonetheless, this “direct” process could also be mediated by a high-energy, virtual charge-transfer state.
Identification of osteoclast-osteoblast coupling factors in humans reveals links between bone and energy metabolism
Authors: Weivoda Megan M. , Chew Chee Kian , Monroe David G. , Farr Joshua N. , Atkinson Elizabeth J. , Geske Jennifer R. , Eckhardt Brittany , Thicke Brianne , Ruan Ming , Tweed Amanda J. , McCready Louise K. , Rizza Robert A. , Matveyenko Aleksey , Kassem Moustapha , Andersen Thomas Levin , Vella Adrian , Drake Matthew T. , Clarke Bart L. , Oursler Merry Jo , Khosla Sundeep 
Published: January 2020

AbstractBone remodeling consists of resorption by osteoclasts followed by formation by osteoblasts, and osteoclasts are a source of bone formation-stimulating factors. Here we utilize osteoclast ablation by denosumab (DMAb) and RNA-sequencing of bone biopsies from postmenopausal women to identify osteoclast-secreted factors suppressed by DMAb. Based on these analyses,LIF, CREG2, CST3, CCBE1, andDPP4are likely osteoclast-derived coupling factors in humans. Given the role of Dipeptidyl Peptidase-4 (DPP4) in glucose homeostasis, we further demonstrate that DMAb-treated participants have a significant reduction in circulating DPP4 and increase in Glucagon-like peptide (GLP)-1 levels as compared to the placebo-treated group, and also that type 2 diabetic patients treated with DMAb show significant reductions in HbA1c as compared to patients treated either with bisphosphonates or calcium and vitamin D. Thus, our results identify several coupling factors in humans and uncover osteoclast-derived DPP4 as a potential link between bone remodeling and energy metabolism.
Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform
Authors: Munck Christian , Sheth Ravi U. , Freedberg Daniel E. , Wang Harris H. 
Published: January 2020

AbstractThe flow of genetic material between bacteria is central to the adaptation and evolution of bacterial genomes. However, our knowledge about DNA transfer within complex microbiomes is lacking, with most studies of horizontal gene transfer (HGT) relying on bioinformatic analyses of genetic elements maintained on evolutionary timescales or experimental measurements of phenotypically trackable markers. Here, we utilize the CRISPR-Cas spacer acquisition process to detect DNA acquisition events from complex microbiota in real-time and at nucleotide resolution. In this system, an E. coli recording strain is exposed to a microbial sample and spacers are acquired from transferred plasmids and permanently stored in genomic CRISPR arrays. Sequencing and analysis of acquired spacers enables identification of the transferred plasmids. This approach allowed us to identify individual mobile elements without relying on phenotypic markers or post-transfer replication. We found that HGT into the recording strain in human clinical fecal samples can be extensive and is driven by different plasmid types, with the IncX type being the most actively transferred.
Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize
Authors: Li Changsheng , Xiang Xiaoli , Huang Yongcai , Zhou Yong , An Dong , Dong Jiaqiang , Zhao Chenxi , Liu Hongjun , Li Yubin , Wang Qiong , Du Chunguang , Messing Joachim , Larkins Brian A. , Wu Yongrui , Wang Wenqin 
Published: January 2020

AbstractMutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is assembled from single-molecule, real-time shotgun sequencing reads collinear with an optical map. We achieve a N50 contig length of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73 and 1.48 Mb for Mo17. To characterize Mo2s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F2 population derived from crossing K0326Y and W64Ao2. RNA-seq analysis of QPM and o2 endosperms reveals a group of differentially expressed genes that coincide with Mo2 QTLs, suggesting a potential role in vitreous endosperm formation.
Time-delay polaritonics
Authors: Töpfer J. D. , Sigurdsson H. , Pickup L. , Lagoudakis P. G. 
Published: January 2020

AbstractNon-linearity and finite signal propagation speeds are omnipresent in nature, technologies, and real-world problems, where efficient ways of describing and predicting the effects of these elements are in high demand. Advances in engineering condensed matter systems, such as lattices of trapped condensates, have enabled studies on non-linear effects in many-body systems where exchange of particles between lattice nodes is effectively instantaneous. Here, we demonstrate a regime of macroscopic matter-wave systems, in which ballistically expanding condensates of microcavity exciton-polaritons act as picosecond, microscale non-linear oscillators subject to time-delayed interaction. The ease of optical control and readout of polariton condensates enables us to explore the phase space of two interacting condensates up to macroscopic distances highlighting its potential in extended configurations. We demonstrate deterministic tuning of the coupled-condensate system between fixed point and limit cycle regimes, which is fully reproduced by time-delayed coupled equations of motion similar to the Lang-Kobayashi equation.
Longitudinal Growth in Single-Word Intelligibility Among Children With Cerebral Palsy From 24 to 96 Months of Age: Effects of Speech-Language Profile Group Membership on Outcomes
Authors: Hustad Katherine C. , Mahr Tristan J. , Broman Aimee Teo , Rathouz Paul J. 
Published: January 2020

Purpose
We examined whether there were differences among speech-language profile groups of children with cerebral palsy (CP) in age of crossing 25%, 50%, and 75% intelligibility thresholds; age of greatest intelligibility growth; rate of intelligibility growth; maximum attained intelligibility at 8 years; and how well intelligibility at 36 months predicts intelligibility at 96 months when group membership is accounted for. Profile groups were children with no speech motor impairment (NSMI), those with speech motor impairment and language comprehension that is typically developing (SMI-LCT), and those with speech motor impairment and language comprehension impairment (SMI-LCI).

Method

Sixty-eight children with CP were followed longitudinally between 24 and 96 months of age. A total of 564 time points were examined across children (
M
= 8.3 time points per child,
SD
= 2.6). We fitted a nonlinear random effects model for longitudinal observations, allowing for differences between profile groups. We used the fitted model trajectories to generate descriptive analyses of intelligibility growth by group and to generate simulations to analyze how well 36-month intelligibility data predicted 96-month data accounting for profile groups.

Results
Children with CP who have NSMI have different growth and better intelligibility outcomes than those with speech motor impairment. Children with SMI-LCT tend to have better outcomes but similar intelligibility growth as children with SMI-LCI. There may be a subset of children that cut across SMI-LCI and SMI-LCT groups who have severe speech motor involvement and show limited growth in intelligibility.

Conclusions
Intelligibility outcomes for children with CP are affected by profile group membership. Intelligibility growth tends to be delayed in children with speech motor impairment. Intelligibility at 3 years is highly predictive of later outcomes regardless of profile group. Intervention decision making should include consideration of early intelligibility, and treatment directions should include consideration of augmentative and alternative communication.
Predicting Dyslexia in Children With Developmental Language Disorder
Authors: Alonzo Crystle N. , McIlraith Autumn L. , Catts Hugh W. , Hogan Tiffany P. 
Published: January 2020

Purpose
In this study, we examine how well kindergarten letter identification and phonological awareness predict 2nd grade word reading and dyslexia in children with developmental language disorder (DLD) and their age- and grade-matched peers with typical language (TL).

Method
We employ (a) logistic regression to determine how letter identification and phonological awareness predict dyslexia, that is, dichotomous categorization of good or poor word reading, in children with DLD and TL and (b) quantile regression to determine how letter identification and phonological awareness are associated with word reading abilities on a continuum in these groups of children.

Results
Logistic regression revealed that letter identification was the only significant, unique kindergarten predictor of dyslexia in 2nd grade children with DLD, when compared to phonological awareness. In children with TL, both kindergarten letter identification and phonological awareness significantly predicted dyslexia in 2nd grade. Quantile regression revealed that kindergarten letter identification was a stronger predictor of 2nd grade word reading for average and lower achieving word readers with DLD and their peers with TL compared to higher performing readers. Phonological awareness was weakly associated with word reading across the full continuum of word reading abilities in children with DLD.

Conclusion
Letter identification is a more accurate predictor of poor word reading and dyslexia than phonological awareness in kindergarten children with DLD, which has important implications for recent U.S. legislation around early identification of dyslexia in all children.