Spin-mediated shear oscillators in a van der Waals antiferromagnet.

Understanding how microscopic spin configuration gives rise to exotic properties at the macroscopic length scale has long been pursued in magnetic materials1-5. One seminal example is the Einstein-de Haas effect in ferromagnets1,6,7, in which angular momentum of spins can be converted into mechanical rotation of an entire object. However, for antiferromagnets without net magnetic moment, how spin ordering couples to macroscopic movement remains elusive. Here we observed a seesaw-like rotation of reciprocal lattice peaks of an antiferromagnetic nanolayer film, whose gigahertz structural resonance exhibits more than an order-of-magnitude amplification after cooling below the Néel temperature. Using a suite of ultrafast diffraction and microscopy techniques, we directly visualize this spin-driven rotation in reciprocal space at the nanoscale. This motion corresponds to interlayer shear in real space, in which individual micro-patches of the film behave as coherent oscillators that are phase-locked and shear along the same in-plane axis. Using time-resolved optical polarimetry, we further show that the enhanced mechanical response strongly correlates with ultrafast demagnetization, which releases elastic energy stored in local strain gradients to drive the oscillators. Our work not only offers the first microscopic view of spin-mediated mechanical motion of an antiferromagnet but it also identifies a new route towards realizing high-frequency resonators8,9 up to the millimetre band, so the capability of controlling magnetic states on the ultrafast timescale10-13 can be readily transferred to engineering the mechanical properties of nanodevices.

Chiral assemblies of pinwheel superlattices on substrates.

The unique topology and physics of chiral superlattices make their self-assembly from nanoparticles highly sought after yet challenging in regard to (meta)materials1-3. Here we show that tetrahedral gold nanoparticles can transform from a perovskite-like, low-density phase with corner-to-corner connections into pinwheel assemblies with corner-to-edge connections and denser packing. Whereas corner-sharing assemblies are achiral, pinwheel superlattices become strongly mirror asymmetric on solid substrates as demonstrated by chirality measures. Liquid-phase transmission electron microscopy and computational models show that van der Waals and electrostatic interactions between nanoparticles control thermodynamic equilibrium. Variable corner-to-edge connections among tetrahedra enable fine-tuning of chirality. The domains of the bilayer superlattices show strong chiroptical activity as identified by photon-induced near-field electron microscopy and finite-difference time-domain simulations. The simplicity and versatility of substrate-supported chiral superlattices facilitate the manufacture of metastructured coatings with unusual optical, mechanical and electronic characteristics.

Nanosecond Structural Dynamics during Electrical Melting of Charge Density Waves in 1T-TaS_{2}.

Electrical control of charge density waves has been of immense interest, as the strong underlying electron-lattice interactions potentially open new, efficient pathways for manipulating their ordering and, consequently, their electronic properties. However, the transition mechanisms are often unclear as electric field, current, carrier injection, heat, and strain can all contribute and play varying roles across length scales and timescales. Here, we provide insight on how electrical stimulation melts the room temperature charge density wave order in 1T-TaS_{2} by visualizing the atomic and mesoscopic structural dynamics from quasi-static to nanosecond pulsed melting. Using a newly developed ultrafast electron microscope setup with electrical stimulation, we reveal the order and strain dynamics during voltage pulses as short as 20 ns. The order parameter dynamics across a range of pulse amplitudes and durations support a thermally driven mechanism even for fields as high as 19 kV cm^{-1}. In addition, time-resolved imaging reveals a heterogeneous, mesoscopic strain response across the flake, including MHz-scale acoustic resonances that emerge during sufficiently short pulsed excitation which may modulate the order. These results suggest that metallic charge density wave phases like studied here may be more robust to electronic switching pathways than insulating ones, motivating further investigations at higher fields and currents in this and other related systems.

FGF21 overexpression alleviates VSMC senescence in diabetic mice by modulating the SYK-NLRP3 inflammasome-PPARγ-catalase pathway.

Diabetes accelerates vascular senescence, which is the basis for atherosclerosis and stiffness. The activation of the NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome and oxidative stress are closely associated with progressive senescence in vascular smooth muscle cells (VSMCs). The vascular protective effect of FGF21 has gradually gained increasing attention, but its role in diabetes-induced vascular senescence needs further investigation. In this study, diabetic mice and primary VSMCs are transfected with an FGF21 activation plasmid and treated with a peroxisome proliferator-activated receptor γ (PPARγ) agonist (rosiglitazone), an NLRP3 inhibitor (MCC950), and a spleen tyrosine kinase (SYK)-specific inhibitor, R406, to detect senescence-associated markers. We find that FGF21 overexpression significantly restores the level of catalase (CAT), vascular relaxation, inhibits the intensity of ROSgreen fluorescence and p21 immunofluorescence, and reduces the area of SA-ß-gal staining and collagen deposition in the aortas of diabetic mice. FGF21 overexpression restores CAT, inhibits the expression of p21, and limits the area of SA-ß-gal staining in VSMCs under high glucose conditions. Mechanistically, FGF21 inhibits SYK phosphorylation, the production of the NLRP3 dimer, the expression of NLRP3, and the colocalization of NLRP3 with PYCARD (ASC), as well as NLRP3 with caspase-1, to reverse the cleavage of PPARγ, preserve CAT levels, suppress ROSgreen density, and reduce the expression of p21 in VSMCs under high glucose conditions. Our results suggest that FGF21 alleviates vascular senescence by regulating the SYK-NLRP3 inflammasome-PPARγ-catalase pathway in diabetic mice.

Ultrafast Nanoimaging of Spin-Mediated Shear Waves in an Acoustic Cavity.

Strong spin-lattice coupling in van der Waals (vdW) magnets shows potential for innovative magneto-mechanical applications. Here, nanoscale and picosecond imaging by ultrafast electron microscopy reveal heterogeneous spin-mediated coherent acoustic phonon dynamics in a thin-film cavity of the vdW antiferromagnet FePS3. The harmonics of the interlayer shear acoustic modes are observed, in which the even and odd harmonics exhibit distinct nanoscopic dynamics. Corroborated by acoustic wave simulation, the role of defects in forming even harmonics is elucidated. Above the Néel temperature (TN), the interlayer shear acoustic harmonics are suppressed, while the in-plane traveling wave is predominantly excited. The dominant acoustic dynamics shifts from the out-of-plane shear to the in-plane traveling wave across TN, demonstrating that magnetic properties can influence phonon scattering pathways. The spatiotemporally resolved structural characterization provides valuable nanoscopic insights for interlayer-shear-mode-based acoustic cavities, opening up possibilities for magneto-mechanical applications of vdW magnets.

Small extracellular vesicles-transported lncRNA TDRKH-AS1 derived from AOPPs-treated trophoblasts initiates endothelial cells pyroptosis through PDIA4/DDIT4 axis in preeclampsia.

BACKGROUND: Substantial studies have demonstrated that oxidative stress placenta and endothelial injury are considered to inextricably critical events in the pathogenesis of preeclampsia (PE). Systemic inflammatory response and endothelial dysfunction are induced by the circulating factors released from oxidative stress placentae. As a novel biomarker of oxidative stress, advanced oxidation protein products (AOPPs) levels are strongly correlated with PE characteristics. Nevertheless, the molecular mechanism underlying the effect of factors is still largely unknown. METHODS: With the exponential knowledge on the importance of placenta-derived extracellular vesicles (pEVs), we carried out lncRNA transcriptome profiling on small EVs (sEVs) secreted from AOPPs-treated trophoblast cells and identified upregulated lncRNA TDRKH-AS1 as a potentially causative factor for PE. We isolated and characterized sEVs from plasma and trophoblast cells by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA) and western blotting. The expression and correlation of lncRNA TDRKH-AS1 were evaluated using qRT-PCR in plasmatic sEVs and placentae from patients. Pregnant mice injected with TDRKH-AS1-riched trophoblast sEVs was performed to detect the TDRKH-AS1 function in vivo. To investigate the potential effect of sEVs-derived TDRKH-AS1 on endothelial function in vitro, transcriptome sequencing, scanning electron Microscopy (SEM), immunofluorescence, ELISA and western blotting were conducted in HUVECs. RNA pulldown, mass spectrometry, RNA immunoprecipitation (RIP), chromatin isolation by RNA purification (ChIRP) and coimmunoprecipitation (Co-IP) were used to reveal the latent mechanism of TDRKH-AS1 on endothelial injury. RESULTS: The expression level of TDRKH-AS1 was significantly increased in plasmatic sEVs and placentae from patients, and elevated TDRKH-AS1 in plasmatic sEVs was positively correlated with clinical severity of the patients. Moreover, pregnant mice injected with TDRKH-AS1-riched trophoblast sEVs exhibited a hallmark feature of PE with increased blood pressure and systemic inflammatory responses. Pyroptosis, an inflammatory form of programmed cell death, is involved in the development of PE. Indeed, our in vitro study indicated that sEVs-derived TDRKH-AS1 secreted from AOPPs-induced trophoblast elevated DDIT4 expression levels to trigger inflammatory response of pyroptosis in endothelial cells through interacting with PDIA4. CONCLUSIONS: Herein, results in the present study supported that TDRKH-AS1 in sEVs isolated from oxidative stress trophoblast may be implicated in the pathogenesis of PE via inducing pyroptosis and aggravating endothelial dysfunction.

Antioxidant System and Endoplasmic Reticulum Stress in Cataracts.

The primary underlying contributor for cataract, a leading cause of vision impairment and blindness worldwide, is oxidative stress. Oxidative stress triggers protein damage, cell apoptosis, and subsequent cataract formation. The nuclear factor-erythroid 2-related factor 2 (Nrf2) serves as a principal redox transcriptional factor in the lens, offering a line of defense against oxidative stress. In response to oxidative challenges, Nrf2 dissociates from its inhibitor, Kelch-like ECH-associated protein 1 (Keap1), moves to the nucleus, and binds to the antioxidant response element (ARE) to activate the Nrf2-dependent antioxidant system. In parallel, oxidative stress also induces endoplasmic reticulum stress (ERS). Reactive oxygen species (ROS), generated during oxidative stress, can directly damage proteins, causing them to misfold. Initially, the unfolded protein response (UPR) activates to mitigate excessive misfolded proteins. Yet, under persistent or severe stress, the failure to rectify protein misfolding leads to an accumulation of these aberrant proteins, pushing the UPR towards an apoptotic pathway, further contributing to cataractogenesis. Importantly, there is a dynamic interaction between the Nrf2 antioxidant system and the ERS/UPR mechanism in the lens. This interplay, where ERS/UPR can modulate Nrf2 expression and vice versa, holds potential therapeutic implications for cataract prevention and treatment. This review explores the intricate crosstalk between these systems, aiming to illuminate strategies for future advancements in cataract prevention and intervention. The Nrf2-dependent antioxidant system communicates and cross-talks with the ERS/UPR pathway. Both mechanisms are proposed to play pivotal roles in the onset of cataract formation.

Blended learning model via small private online course improves active learning and academic performance of embryology.

While blended learning has been growing in popularity in recent years, the effectiveness of this procedure remains controversial. In this report, we assess the effectiveness of blended learning of embryology within international medical students. The participants were international medical students taking embryology in the Bachelor of Medicine and Bachelor of Surgery program. The blended learning group (BLG) consisted of students (n = 43) in the 2018-2019 academic year, taught with blended learning model via a customized small private online course (SPOC). The control traditional teaching group (TTG) consisted students (n = 48) in the 2017-2018 academic year, taught with traditional teaching model. Academic performance, including mean scores and passing ratios on the final exam of two groups were compared and analyzed with a t-test. In addition, a questionnaire directed toward evaluating student's perceptions with the blended learning was administered to students in BLG. The majority of students in BLG actively participated in online self-study activities and discussion in face-to-face class sessions. The mean score and passing ratio were significantly greater than those of students in TTG (p < 0.01). Results from the questionnaire revealed that the majority of BLG students felt that this method was beneficial for their learning of human embryology. The blended learning model, that integrates SPOC with face-to-face class lectures proved a more effective means for the teaching of embryology than the traditional lecture-based teaching model. This blended learning method may serve as a feasible model that can be readily applied for use in other medical courses.

Visualization of Plasmonic Couplings Using Ultrafast Electron Microscopy.

Hybrids of graphene and metal plasmonic nanostructures are promising building blocks for applications in optoelectronics, surface-enhanced scattering, biosensing, and quantum information. An understanding of the coupling mechanism in these hybrid systems is of vital importance to its applications. Previous efforts in this field mainly focused on spectroscopic studies of strong coupling within the hybrids with no spatial resolution. Here we report direct imaging of the local plasmonic coupling between single Au nanocapsules and graphene step edges at the nanometer scale by photon-induced near-field electron microscopy in an ultrafast electron microscope for the first time. The proximity of a step in the graphene to the nanocapsule causes asymmetric surface charge density at the ends of the nanocapsules. Computational electromagnetic simulations confirm the experimental observations. The results reported here indicate that this hybrid system could be used to manipulate the localized electromagnetic field on the nanoscale, enabling promising future plasmonic devices.

Infrared PINEM developed by diffraction in 4D UEM.

The development of four-dimensional ultrafast electron microscopy (4D UEM) has enabled not only observations of the ultrafast dynamics of photon-matter interactions at the atomic scale with ultrafast resolution in image, diffraction, and energy space, but photon-electron interactions in the field of nanoplasmonics and nanophotonics also have been captured by the related technique of photon-induced near-field electron microscopy (PINEM) in image and energy space. Here we report a further extension in the ongoing development of PINEM using a focused, nanometer-scale, electron beam in diffraction space for measurements of infrared-light-induced PINEM. The energy resolution in diffraction mode is unprecedented, reaching 0.63 eV under the 200-keV electron beam illumination, and separated peaks of the PINEM electron-energy spectrum induced by infrared light of wavelength 1,038 nm (photon energy 1.2 eV) have been well resolved for the first time, to our knowledge. In a comparison with excitation by green (519-nm) pulses, similar first-order PINEM peak amplitudes were obtained for optical fluence differing by a factor of more than 60 at the interface of copper metal and vacuum. Under high fluence, the nonlinear regime of IR PINEM was observed, and its spatial dependence was studied. In combination with PINEM temporal gating and low-fluence infrared excitation, the PINEM diffraction method paves the way for studies of structural dynamics in reciprocal space and energy space with high temporal resolution.

Reporting and Methodological Quality of Systematic Reviews and Meta-Analyses of Nursing Interventions in Patients With Alzheimer's Disease: General Implications of the Findings.

OBJECTIVE: The aim of this study was to evaluate the reporting characteristics as well as the methodological quality of systematic reviews (SRs) and meta-analyses (MAs) of nursing interventions in patients with Alzheimer's disease and determine potential factors for high quality. METHODS: Following the inclusion and exclusion criteria, we searched the databases PubMed, EMBASE, and The Cochrane Library from inception through October 1, 2017. Two reviewers independently selected articles and extracted data. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist and Assessment of Multiple Systematic Reviews (AMSTAR) checklist were adopted to evaluate reporting and methodological quality, respectively. RESULTS: A total of 64 eligible articles, published from 2001 to 2017, were included. The mean PRISMA and AMSTAR scores were 19.310 ± 4.167 and 6.390 ± 2.208, respectively. For the PRISMA checklist, the following characteristics had less than 50% compliance: protocol or registration, full electronic search strategy, summary measures, risk for bias across studies, and synthesis of results. For the AMSTAR checklist, the following characteristics had less than 50% compliance: a priori study design, comprehensive literature search, status of publication used as inclusion criteria, scientific quality, publication bias, and conflicts of interest stated. Logistic regression analyses indicated that systematic reviews including meta-analyses that followed PRISMA guidelines, had a protocol or registration, and had funding support were related to higher reporting quality; systematic reviews including meta-analyses that had a protocol or registration were related to higher methodological quality. CONCLUSIONS: The reporting and methodological quality of systematic reviews and meta-analyses of nursing interventions in patients with Alzheimer's disease were suboptimal, with some areas needing further improvement. More endorsement by journals of the reporting guidelines for SRs and MAs may improve article quality and the dissemination of reliable evidence to nurses. We recommend that authors, readers, reviewers, and editors become better acquainted with and adhere more strictly to the PRISMA and AMSTAR checklists.

The effects of the PRISMA statement to improve the conduct and reporting of systematic reviews and meta-analyses of nursing interventions for patients with heart failure.

AIMS: The study aims to evaluate the reporting and methodological quality of systematic reviews and meta-analyses on nursing interventions in the field of heart failure and investigate whether reporting and methodological quality has been improved after PRISMA statement was published. METHODS: Pubmed, Cochrane Database of Systematic Review, and Embase databases were searched from inception of databases to July 31, 2018. Two authors independently extracted data from October 1, 2018, to October 31, 2018. AMSTAR and PRISMA checklists were used to assessed methodological and reporting quality. RESULTS: The 50 English articles satisfied inclusion criteria and were published from 2001 to 2017. After introduction of PRISMA statement, significant improvement in reporting of the following items was found: title, search, risk of bias in individual studies, summary measures, study selection, synthesis of results, summary of evidence for PRISMA checklists, and scientific quality of included studies provided (item 7) for AMSTAR checklists. CONCLUSION: There were higher methodological and reporting quality after publication of PRISMA. We recommend authors, readers, reviewers, and editors to become more acquainted with and to more strictly adhere to the PRISMA and AMSTAR.

LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals.

MOTIVATION: Genomic imprinting is regulated by lncRNAs and is important for embryogenesis, physiology and behaviour in mammals. Aberrant imprinting causes diseases and disorders. Experimental studies have examined genomic imprinting primarily in humans and mice, thus leaving some fundamental issues poorly addressed. The cost of experimentally examining imprinted genes in many tissues in diverse species makes computational analysis of lncRNAs' DNA binding sites valuable. RESULTS: We performed lncRNA/DNA binding analysis in imprinting clusters from multiple mammalian clades and discovered the following: (i) lncRNAs and imprinting sites show significant losses and gains and distinct lineage-specificity; (ii) binding of lncRNAs to promoters of imprinted genes may occur widely throughout the genome; (iii) a considerable number of imprinting sites occur in only evolutionarily more derived species; and (iv) multiple lncRNAs may bind to the same imprinting sites, and some lncRNAs have multiple DNA binding motifs. These results suggest that the occurrence of abundant lncRNAs in mammalian genomes makes genomic imprinting a mechanism of adaptive evolution at the epigenome level. AVAILABILITY AND IMPLEMENTATION: The data and program are available at the database LongMan at lncRNA.smu.edu.cn. CONTACT: zhuhao@smu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Exploring reporting quality of systematic reviews and Meta-analyses on nursing interventions in patients with Alzheimer's disease before and after PRISMA introduction.

BACKGROUND: Systematic reviews (SRs) and meta-analyses (MAs) are distillation of current best available evidence, but are potentially prone to bias. The bias of SRs and MAs comes from sampling bias, selection bias and within study bias. So, their reporting quality is especially important as it may directly influence their utility for clinicians, nurses, patients and policy makers. The SRs and MAs on nursing interventions in patients with Alzheimer's disease (AD) have been increasingly published over the past decade, but the reporting quality of article has not been evaluated after the introduction of Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) Statement. METHODS: According to the inclusion and exclusion criteria, we searched the databases including PubMed, EMBASE and The Cochrane Library from inception through October 16th 2018. Two reviewers independently selected articles and extracted data. The PRISMA checklist was adopted to evaluate reporting quality. Comparisons were made between studies published before (2001-2009) and after (2011-2018) its introduction. RESULTS: A total of 77 eligible articles, 18 (23.4%) were published before the PRISMA Statement and 59 (76.6%) were published afterwards. There was higher score after publication of the PRISMA Statement than before (20.83 ± 3.78 vs 17.11 ± 4.56, P <  0.05). There was an improvement in the following items after the PRISMA statement was released (P <  0.05): title (item 1, 50.0% vs 74.6%, OR = 3.10, 95CI%: 1.00-9.61), search (item8, 27.8% vs 57.6%,OR = 3.25, 95CI%: 1.14-9.28), study selection (item 9, 44.4% vs 81.4%,OR = 6.28, 95CI%: 1.93-20.37), Data collection process (item 10, 50.0% vs 76.3%,OR = 3.45, 95CI%:1.10-10.84), risk of bias in individual studies (item 12, 50.0% vs 83.1%, OR = 5.78, 95CI%:1.71-19.52), risk of bias across studies (item15, 5.6% vs 28.8%,OR = 3.60, 95CI%:1.04-12.43), study characteristics (item 18, 77.8% vs 98.3%, OR = 28.13, 95CI%:3.35-236.19), risk of bias with studies (item 19, 50.0% vs 83.1%, OR = 5.78, 95CI%:1.71-19.52), results in individual studies (item 20, 72.2% vs 94.9%, OR = 11.09, 95CI%:1.99-61.82), conclusions (item 26, 77.8% vs 98.3%, OR = 28.13, 95CI%:3.35-236.19). After controlling for the confounding factors, there were higher PRISMA score for systematic reviews including meta-analyses, protocol or registration, can't answer of RCT, journal source of SCI (Science Citation Index), manuscript length > 13 page and funding support. CONCLUSION: Since the publication of the PRISMA Statement, there has been an improvement in the quality of reporting of SRs and MAs on nursing interventions in patients with AD. More endorsement by journals of the report guideline for SRs/MAs may improve articles reporting quality, and the dissemination of reliable evidence to nurses. We recommend authors, readers, reviewers, and editors to become more acquainted with and to more strictly adhere to the PRISMA checklist.

Photon gating in four-dimensional ultrafast electron microscopy.

Ultrafast electron microscopy (UEM) is a pivotal tool for imaging of nanoscale structural dynamics with subparticle resolution on the time scale of atomic motion. Photon-induced near-field electron microscopy (PINEM), a key UEM technique, involves the detection of electrons that have gained energy from a femtosecond optical pulse via photon-electron coupling on nanostructures. PINEM has been applied in various fields of study, from materials science to biological imaging, exploiting the unique spatial, energy, and temporal characteristics of the PINEM electrons gained by interaction with a "single" light pulse. The further potential of photon-gated PINEM electrons in probing ultrafast dynamics of matter and the optical gating of electrons by invoking a "second" optical pulse has previously been proposed and examined theoretically in our group. Here, we experimentally demonstrate this photon-gating technique, and, through diffraction, visualize the phase transition dynamics in vanadium dioxide nanoparticles. With optical gating of PINEM electrons, imaging temporal resolution was improved by a factor of 3 or better, being limited only by the optical pulse widths. This work enables the combination of the high spatial resolution of electron microscopy and the ultrafast temporal response of the optical pulses, which provides a promising approach to attain the resolution of few femtoseconds and attoseconds in UEM.

Temporal Doppler Effect and Future Orientation: Adaptive Function and Moderating Conditions.

The objectives of this study were to examine whether the temporal Doppler effect exists in different time intervals and whether certain individual and environmental factors act as moderators of the effect. Using hierarchical linear modeling, we examined the existence of the temporal Doppler effect and the moderating effect of future orientation among 139 university students (Study 1), and then the moderating conditions of the temporal Doppler effect using two independent samples of 143 and 147 university students (Studies 2 and 3). Results indicated that the temporal Doppler effect existed in all of our studies, and that future orientation moderated the temporal Doppler effect. Further, time interval perception mediated the relationship between future orientation and the motivation to cope at long time intervals. Finally, positive affect was found to enhance the temporal Doppler effect, whereas control deprivation did not influence the effect. The temporal Doppler effect is moderated by the personality trait of future orientation and by the situational variable of experimentally manipulated positive affect. We have identified personality and environmental processes that could enhance the temporal Doppler effect, which could be valuable in cases where attention to a future task is necessary.

4D multiple-cathode ultrafast electron microscopy.

Four-dimensional multiple-cathode ultrafast electron microscopy is developed to enable the capture of multiple images at ultrashort time intervals for a single microscopic dynamic process. The dynamic process is initiated in the specimen by one femtosecond light pulse and probed by multiple packets of electrons generated by one UV laser pulse impinging on multiple, spatially distinct, cathode surfaces. Each packet is distinctly recorded, with timing and detector location controlled by the cathode configuration. In the first demonstration, two packets of electrons on each image frame (of the CCD) probe different times, separated by 19 picoseconds, in the evolution of the diffraction of a gold film following femtosecond heating. Future elaborations of this concept to extend its capabilities and expand the range of applications of 4D ultrafast electron microscopy are discussed. The proof-of-principle demonstration reported here provides a path toward the imaging of irreversible ultrafast phenomena of materials, and opens the door to studies involving the single-frame capture of ultrafast dynamics using single-pump/multiple-probe, embedded stroboscopic imaging.

LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis.

MOTIVATION: In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program (LongTarget) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide. AVAILABILITY AND IMPLEMENTATION: Website of LongTarget: lncrna.smu.edu.cn, or contact: hao.zhu@ymail.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

4D imaging and diffraction dynamics of single-particle phase transition in heterogeneous ensembles.

In this Letter, we introduce conical-scanning dark-field imaging in four-dimensional (4D) ultrafast electron microscopy to visualize single-particle dynamics of a polycrystalline ensemble undergoing phase transitions. Specifically, the ultrafast metal-insulator phase transition of vanadium dioxide is induced using laser excitation and followed by taking electron-pulsed, time-resolved images and diffraction patterns. The single-particle selectivity is achieved by identifying the origin of all constituent Bragg spots on Debye-Scherrer rings from the ensemble. Orientation mapping and dynamic scattering simulation of the electron diffraction patterns in the monoclinic and tetragonal phase during the transition confirm the observed behavior of Bragg spots change with time. We found that the threshold temperature for phase recovery increases with increasing particle sizes and we quantified the observation through a theoretical model developed for single-particle phase transitions. The reported methodology of conical scanning, orientation mapping in 4D imaging promises to be powerful for heterogeneous ensemble, as it enables imaging and diffraction at a given time with a full archive of structural information for each particle, for example, size, morphology, and orientation while minimizing radiation damage to the specimen.