Improved detection and consistency of RNA-interacting proteomes using DIA SILAC.

The RNA-interacting proteome is commonly characterized by UV-crosslinking followed by RNA purification, with protein recovery quantified using SILAC labeling followed by data-dependent acquisition (DDA) of proteomic data. However, the low efficiency of UV-crosslinking, combined with limited sensitivity of the DDA approach often restricts detection to relatively abundant proteins, necessitating multiple mass spec injections of fractionated peptides for each biological sample. Here we report an application of data-independent acquisition (DIA) with SILAC in a total RNA-associated protein purification (TRAPP) UV-crosslinking experiment. This gave 15% greater protein detection and lower inter-replicate variation relative to the same biological materials analyzed using DDA, while allowing single-shot analysis of the sample. As proof of concept, we determined the effects of arsenite treatment on the RNA-bound proteome of HEK293T cells. The DIA dataset yielded similar GO term enrichment for RNA-binding proteins involved in cellular stress responses to the DDA dataset while detecting extra proteins unseen by DDA. Overall, the DIA SILAC approach improved detection of proteins over conventional DDA SILAC for generating RNA-interactome datasets, at a lower cost due to reduced machine time. Analyses are described for TRAPP data, but the approach is suitable for proteomic analyses following essentially any RNA-binding protein enrichment technique.

Valley-conserved topological integrated antenna for 100-Gbps THz 6G wireless.

The topological phase revolutionized wave transport, enabling integrated photonic interconnects with sharp light bending on a chip. However, the persistent challenge of momentum mismatch during intermedium topological mode transitions due to material impedance inconsistency remains. We present a 100-Gbps topological wireless communication link using integrated photonic devices that conserve valley momentum. The valley-conserved silicon topological waveguide antenna achieves a 12.2-dBi gain, constant group delay across a 30-GHz bandwidth and enables active beam steering within a 36° angular range. The complementary metal oxide semiconductor-compatible valley-conserved devices represent a major milestone in hybrid electronic-photonic-based topological wireless communications, enabling terabit-per-second backhaul communication, high throughput, and intermedium transport of information carriers, vital for the future of communication from the sixth to X generation.

The minor chicken class I gene BF1 is deleted between short imperfect direct repeats in the B14 and typical B15 major histocompatibility complex (MHC) haplotypes.

The chicken major histocompatibility complex (MHC, also known as the BF-BL region of the B locus) is notably small and simple with few genes, most of which are involved in antigen processing and presentation. There are two classical class I genes, of which only BF2 is well and systemically expressed as the major ligand for cytotoxic T lymphocytes (CTLs). The other class I gene, BF1, is believed to be primarily a natural killer (NK) cell ligand. Among most standard chicken MHC haplotypes examined in detail, BF1 is expressed tenfold less than BF2 at the RNA level due to defects in the promoter or in a splice site. However, in the B14 and typical B15 haplotypes, BF1 RNA was not detected, and here, we show that a deletion between imperfect 32 nucleotide direct repeats has removed the BF1 gene entirely. The phenotypic effects of not having a BF1 gene (particularly on resistance to infectious pathogens) have not been systematically explored, but such deletions between short direct repeats are also found in some BF1 promoters and in the 5' untranslated region (5'UTR) of some BG genes found in the BG region of the B locus. Despite the opposite transcriptional orientation of homologous genes in the chicken MHC, which might prevent the loss of key genes from a minimal essential MHC, it appears that small direct repeats can still lead to deletion.

Brillouin zone folding driven bound states in the continuum.

Non-radiative bound states in the continuum (BICs) allow construction of resonant cavities with confined electromagnetic energy and high-quality (Q) factors. However, the sharp decay of the Q factor in the momentum space limits their usefulness for device applications. Here we demonstrate an approach to achieve sustainable ultrahigh Q factors by engineering Brillouin zone folding-induced BICs (BZF-BICs). All the guided modes are folded into the light cone through periodic perturbation that leads to the emergence of BZF-BICs possessing ultrahigh Q factors throughout the large, tunable momentum space. Unlike conventional BICs, BZF-BICs show perturbation-dependent dramatic enhancement of the Q factor in the entire momentum space and are robust against structural disorders. Our work provides a unique design path for BZF-BIC-based silicon metasurface cavities with extreme robustness against disorder while sustaining ultrahigh Q factors, offering potential applications in terahertz devices, nonlinear optics, quantum computing, and photonic integrated circuits.

EGCG inactivates a pore-forming toxin by promoting its oligomerization and decreasing its solvent-exposed hydrophobicity.

Natural proteinaceous pore-forming agents can bind and permeabilize cell membranes, leading to ion dyshomeostasis and cell death. In the search for antidotes that can protect cells from peptide toxins, we discovered that the polyphenol epigallocatechin gallate (EGCG) interacts directly with melittin from honeybee venom, resulting in the elimination of its binding to the cell membrane and toxicity by markedly lowering the extent of its solvent-exposed hydrophobicity and promoting its oligomerization into larger species. These physicochemical parameters have also been shown to play a key role in the binding to cells of misfolded protein oligomers in a host of neurodegenerative diseases, where oligomer-membrane binding and associated toxicity have been shown to correlate negatively with oligomer size and positively with solvent-exposed hydrophobicity. For melittin, which is not an amyloid-forming protein and has a very distinct mechanism of toxicity compared to misfolded oligomers, we find that the size-hydrophobicity-toxicity relationship also rationalizes the pharmacological attenuation of melittin toxicity by EGCG. These results highlight the importance of the physicochemical properties of pore forming agents in mediating their interactions with cell membranes and suggest a possible therapeutic approach based on compounds with a similar mechanism of action as EGCG.

Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes.

Control of mRNA translation adjusts protein production rapidly and facilitates local cellular responses to environmental conditions. Traditionally initiation of translation is considered to be a major translational control point, however, control of peptide elongation is also important. Here we show that the function of the elongation factor, eIF5a, is regulated dynamically in naïve CD8+ T cells upon activation by post-translational modification, whereupon it facilitates translation of specific subsets of proteins. eIF5a is essential for long-term survival of effector CD8+ T cells and sequencing of nascent polypeptides indicates that the production of proteins which regulate proliferation and key effector functions, particularly the production of IFNγ and less acutely TNF production and cytotoxicity, is dependent on the presence of functional eIF5a. Control of translation in multiple immune cell lineages is required to co-ordinate immune responses and these data illustrate that translational elongation contributes to post-transcriptional regulons important for the control of inflammation.

Self-adaptive deep reinforcement learning for THz beamforming with silicon metasurfaces in 6G communications.

Exponential growth in data rate demands has driven efforts to develop novel beamforming techniques for realizing massive multiple-input and multiple-output (MIMO) systems in sixth-generation (6G) terabits per second wireless communications. Existing beamforming techniques rely on conventional optimization algorithms that are too computationally expensive for real-time applications and require complex digital processing yet to be achieved for phased array antennas at terahertz frequencies. Here, we develop an intelligent and self-adaptive beamforming scheme enabled by deep reinforcement learning, which can predict the spatial phase profiles required to produce arbitrary desired radiation patterns in real-time. Our deep learning model adaptively trains an artificial neural network in real-time by comparing the input and predicted intensity patterns via automatic differentiation of the phase-to-intensity function. As a proof of concept, we experimentally demonstrate two-dimensional beamforming by spatially modulating broadband terahertz waves using silicon metasurfaces designed with the aid of the deep learning model. Our work offers an efficient and robust deep learning model for real-time self-adaptive beamforming to enable multi-user massive MIMO systems for 6G terahertz wireless communications, as well as intelligent metasurfaces for other terahertz applications in imaging and sensing.

Greater individual variability in functional brain activity during working memory performance in Schizophrenia Spectrum Disorders (SSD).

Heterogeneity has been a persistent challenge in understanding Schizophrenia Spectrum Disorders (SSD). Traditional case-control comparisons often show variable results, and may not map well onto individuals. To better understand heterogeneity and group differences in SSD compared to typically developing controls (TDC), we examined variability in functional brain activity during a working memory (WM) task with known deficits in SSD. Neuroimaging and behavioural data were extracted from two datasets collectively providing 34 TDC and 56 individuals with SSD (n = 90). Functional activity in response to an N-Back WM task (3-Back vs 1-Back) was examined between and within groups. Individual variability was calculated via the correlational distance of fMRI activity maps between participants; mean correlational distance from one participant to all others was defined as a 'variability score'. Greater individual variability in functional activity was found in SSD compared to TDC (p = 0.00090). At the group level, a case-control comparison suggested SSD had reduced activity in task positive and task negative networks. However, when SSD were divided into high and low variability subgroups, the low variability groups showed no differences relative to TDC while the high variability group showed little activity at the group level. Our results imply prior case-control differences may be driven by a subgroup of SSD who do not show specific impairments but instead show more 'idiosyncratic' activity patterns. In SSD but not TDC, variability was also related to cognitive performance and age. This novel approach focusing on individual variability has important implications for understanding the neurobiology of SSD.

Active Ultrahigh-Q (0.2 × 106 ) THz Topological Cavities on a Chip.

Rapid scaling of semiconductor devices has led to an increase in the number of processor cores and integrated functionalities onto a single chip to support the growing demands of high-speed and large-volume consumer electronics. To meet this burgeoning demand, an improved interconnect capacity in terms of bandwidth density and active tunability is required for enhanced throughput and energy efficiency. Low-loss terahertz silicon interconnects with larger bandwidth offer a solution for the existing inter-/intrachip bandwidth density and energy-efficiency bottleneck. Here, a low-loss terahertz topological interconnect-cavity system is presented that can actively route signals through sharp bends, by critically coupling to a topological cavity with an ultrahigh-quality (Q) factor of 0.2 × 106 . The topologically protected large Q factor cavity enables energy-efficient optical control showing 60 dB modulation. Dynamic control is further demonstrated of the critical coupling between the topological interconnect-cavity for on-chip active tailoring of the cavity resonance linewidth, frequency, and modulation through complete suppression of the back reflection. The silicon topological cavity is complementary metal-oxide-semiconductor (CMOS)-compatible and highly desirable for hybrid electronic-photonic technologies for sixth (6G) generation terahertz communication devices. Ultrahigh-Q cavity also paves the path for designing ultrasensitive topological sensors, terahertz topological integrated circuits, and nonlinear topological photonic devices.

Visuomotor Activation of Inhibition-Processing in Pediatric Obsessive Compulsive Disorder: A Magnetoencephalography Study.

Background: Response inhibition engages the cortico-striato-thalamo-cortical (CSTC) circuit, which has been implicated in children, and youth with obsessive compulsive disorder (OCD). This study explored whether CSTC engagement during response inhibition, measured using magnetoencephalography (MEG), differed in a sample of medication-naïve youth with OCD, compared to typically developing controls (TDC). Methods: Data was analyzed in 17 medication-naïve children and youth with OCD (11.7 ± 2.2 SD years) and 13 TDC (12.6 ± 2.2 SD years). MEG was used to localize and characterize neural activity during a Go/No-Go task. Task performance on Go/No-Go conditions and regional differences in amplitude of activity during Go and No-Go condition between OCD vs. TDC were examined using two-sample t-tests. Post-hoc analysis with Bayesian t-tests was used to estimate the certainty of outcomes. Results: No differences in Go/No-Go performance were found between OCD and TDC groups. In response to the visual cue presented during the Go condition, participants with OCD showed significantly increased amplitude of activity in the primary motor (MI) cortex compared to TDC. In addition, significantly reduced amplitude of PCu was found following successful stopping to No-Go cues in OCD vs. TDC during No-Go task performance. Bayesian t-tests indicated high probability and large effect sizes for the differences in MI and PCu amplitude found between groups. Conclusion: Our preliminary study in a small medication-naïve sample extends previous work indicating intact response inhibition in pediatric OCD. While altered neural response in the current study was found during response inhibition performance in OCD, differences localized to regions outside of the CSTC. Our findings suggest that additional imaging research in medication-naïve samples is needed to clarify regional differences associated with OCD vs. influenced by medication effects, and suggest that MEG may be sensitive to detecting such differences.

Active Control of Nanodielectric-Induced THz Quasi-BIC in Flexible Metasurfaces: A Platform for Modulation and Sensing.

A bound state in the continuum (BIC) is a nonradiating state of light embedded in the continuum of propagating modes providing drastic enhancement of the electromagnetic field and its localization at micro-nanoscale. However, access to such modes in the far-field requires symmetry breaking. Here, it is demonstrated that a nanometric dielectric or semiconductor layer, 1000 times thinner than the resonant wavelength (λ/1000), induces a dynamically controllable quasi-bound state in the continuum (QBIC) with ultrahigh quality factor in a symmetric metallic metasurface at terahertz frequencies. Photoexcitation of nanostrips of germanium activates ultrafast switching of a QBIC resonance with 200% transmission intensity modulation and complete recovery within 7 ps on a low-loss flexible substrate. The nanostrips also form microchannels that provide an opportunity for BIC-based refractive index sensing. An optimization model is presented for (switchable) QBIC resonances of metamaterial arrays of planar symmetric resonators modified with any (active) dielectric for inverse metamaterial design that can serve as an enabling platform for active micro-nanophotonic devices.

Dental and oral health students' perceptions of loupes.

Objectives. The dental industry has embraced the usage of loupes, with recent literature identifying numerous clinical and ergonomic benefits. Despite the growing usage of loupes among Australian dental professionals and dental students, few data regarding the perceived benefits and limitations of their use in clinical practice are available. The aim of this study was to examine the experiences and opinions of loupe usage among Australian dental and oral health students. Methods. A self-reporting questionnaire was distributed to all dental and oral health students across Australia during 2016. Results. A total of 223 students responded to the questionnaire. Of these responses, 45.7% reported they wear loupes during their clinical training, with the majority (32%) purchasing them due to recommendation by a demonstrator. Primary benefits reported included ergonomics/posture (89%), restoration evaluation/detection (72%) and quality of care/improved patient care (63%). Primary limitations reported included infection control (53%), decreased awareness of patients' non-verbal communications (44%) and vision dependency (30%). Conclusions. Overall, the students in this study identified both benefits and limitations to wearing loupes in clinical practice. Despite this, an overwhelming majority (96%) of those who used loupes would recommend them to other dental and/or oral health students.

Greater Individual Variability in Functional Brain Activity during Working Memory Performance in young people with Autism and Executive Function Impairment.

BACKGROUND: Individuals with autism spectrum disorder (ASD) often present with executive functioning (EF) deficits, including spatial working memory (SWM) impairment, which impedes real-world functioning. The present study examined task-related brain activity, connectivity and individual variability in fMRI-measured neural response during an SWM task in older youth and young adults with autism and clinically significant EF impairment. METHODS: Neuroimaging was analyzed in 29 individuals with ASD without intellectual disability who had clinically significant EF impairment on the Behavior Rating Inventory of Executive Function, and 20 typically developing controls (participant age range=16-34). An SWM N-Back task was performed during fMRI. SWM activity (2-Back vs. 0-Back) and task-related dorsolateral prefrontal cortex (DLPFC) connectivity was examined within and between groups. Variability of neural response during SWM was also examined. RESULTS: During SWM performance both groups activated the expected networks, and no group differences in network activation or task-related DLPFC-connectivity were found. However, greater individual variability in the pattern of SWM activity was found in the ASD versus the typically developing control group. CONCLUSIONS: While there were no group differences in SWM task-evoked activity or connectivity, fronto-parietal network engagement was found to be more variable/idiosyncratic in ASD. Our results suggest that the fronto-parietal network may be shifted or sub-optimally engaged during SWM performance in participants with ASD with clinically significant EF impairment, with implications for developing targeted interventions for this subgroup.

Spinal Extradural Cyst: Case Report and Review of Literature.

BACKGROUND: Spinal extradural cyst (SEDC) accounts for <1% of spinal epidural lesions. It is commonly asymptomatic but can give rise to back pain and compressive neurologic symptoms. CASE DESCRIPTION: We report the case of a 51-year-old male who presented with gait difficulties over 5 months associated with occasional urge incontinence. Clinical examination revealed signs suggestive of thoracic myelopathy with bilateral lower limbs spasticity, decreased proprioception, and pinprick sensation. Magnetic resonance imaging showed a thoracic (T) 7-T9 extradural cystic lesion with an area of flow void on the right side between T8 and T9. A right hemilaminotomy was initially performed, and the dural defect was identified and repaired primarily. Unfortunately, there was a recurrence of the SEDC 2 weeks post operation and a T7-T9 laminoplasty with a complete excision was performed. CONCLUSIONS: Computed tomography myelography or magnetic resonance imaging flow study best visualizes the communication between the epidural cyst and subarachnoid space. The ideal surgical management for SEDC remains controversial. Our case suggests that there may be higher recurrence associated with fenestration of the SEDC and closure of the dural defect, but perhaps higher complications associated with complete excision. We present a case report and literature review of the terminology, presentation, recommended investigations, management, and outcomes of patients with SEDC.

Early Decompressive Hemicraniectomy for Malignant Middle Cerebral Artery Infarction in Asian Patients: A Single-Center Study.

INTRODUCTION: Early decompression craniectomy (within 48 hours of stroke onset) in acute and malignant middle cerebral artery (MCA) ischemic stroke (IS) reduces mortality and increases the proportion of patients with favorable functional outcome. Various cultural and social issues among Asians lead to some differences in clinical practice, especially when surgical interventions are involved. Accordingly, decompressive craniectomy in Asian patients with stroke is often delayed. MATERIALS AND METHODS: Data for all patients with acute IS hospitalized in our center were entered into a prospectively maintained registry. In this retrospective analysis, data for all patients with malignant MCA IS who underwent decompressive craniectomy were extracted. Various demographic, clinical, and neuroimaging factors were analyzed for identifying independent predictors of favorable functional outcome at 6 months, which was defined as modified Rankin Scale score of 0-3 points. RESULTS: From January 2005 to December 2014, a total of 75 patients with acute MCA IS underwent decompressive craniectomy. Median age was 55 years (interquartile range 44-64) with male preponderance (66%) and median National Institute of Health Stroke Scale score 21 points (interquartile range 18-24). A considerable proportion of these patients (38.7%) received intravenous thrombolysis. The majority (70%) of patients suffered right MCA IS, and decompressive surgery was performed within 48 hours of symptom onset in 50 (67%) of the patients. Favorable functional outcome was achieved in 25 (33.3%) patients at 6 months. Right MCA stroke (odds ratio 9.158; 95% confidence interval 1.881-44.596, P = 0.006) and early decompression surgery (odds ratio 4.011; 95% confidence interval 1.058-15.208, P = 0.041) were independent predictors of favorable functional outcome at 6 months. CONCLUSIONS: Early decompression craniectomy, especially in right MCA ischemic stroke, is associated with better favorable functional outcome.

Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells.

Global transcriptomic and proteomic analyses of T cells have been rich sources of unbiased data for understanding T-cell activation. Lack of full concordance of these datasets has illustrated that important facets of T-cell activation are controlled at the level of translation. We undertook translatome analysis of CD8 T-cell activation, combining polysome profiling and microarray analysis. We revealed that altering T-cell receptor stimulation influenced recruitment of mRNAs to heavy polysomes and translation of subsets of genes. A major pathway that was compromised, when TCR signaling was suboptimal, was linked to ribosome biogenesis, a rate-limiting factor in both cell growth and proliferation. Defective TCR signaling affected transcription and processing of ribosomal RNA precursors, as well as the translation of specific ribosomal proteins and translation factors. Mechanistically, IL-2 production was compromised in weakly stimulated T cells, affecting the abundance of Myc protein, a known regulator of ribosome biogenesis. Consequently, weakly activated T cells showed impaired production of ribosomes and a failure to maintain proliferative capacity after stimulation. We demonstrate that primary T cells respond to various environmental cues by regulating ribosome biogenesis and mRNA translation at multiple levels to sustain proliferation and differentiation.

HLA class I downregulation is associated with enhanced NK-cell killing of melanoma cells with acquired drug resistance to BRAF inhibitors.

The frequent development of drug resistance to targeted therapies in cancer patients has stimulated interest in strategies counteracting resistance. Combining immunotherapies with targeted therapies is one such strategy. In this context, we asked whether human NK cells can target melanoma cells that have acquired resistance to selective inhibitors targeting activating mutants of the B-Raf kinase (BRAF inhibitors, BRAFi). We generated drug-resistant cell variants in vitro from human BRAF-mutant melanoma cell lines MEL-HO, COLO-38, SK-MEL-37, 1520 and from primary melanoma cells freshly isolated from two patients. All drug-resistant cell variants remained susceptible to lysis by IL-2-activated NK cells; and two BRAFi-resistant lines (BRAFi-R) became significantly more susceptible to NK-cell lysis than their parental lines. This was associated with significant HLA class I antigen downregulation and PD-L1 upregulation on the drug-resistant lines. Although blocking HLA class I enhanced the extent of lysis of both BRAFi-R and parental cells to NK-cell-mediated lysis, antibody-mediated inhibition of PD1-PD-L1 interactions had no detectable effect. HLA class I antigen expression on BRAFi-R melanoma variants thus appears to play a major role in their susceptibility to NK-cell cytotoxicity. These findings suggest that NK-cell-based immunotherapy may be a viable approach to treat melanoma patients with acquired resistance to BRAF inhibitors.

Telomere maintenance and telomerase activity are differentially regulated in asexual and sexual worms.

In most sexually reproducing animals, replication and maintenance of telomeres occurs in the germ line and during early development in embryogenesis through the use of telomerase. Somatic cells generally do not maintain telomere sequences, and these cells become senescent in adults as telomeres shorten to a critical length. Some animals reproduce clonally and must therefore require adult somatic mechanisms for maintaining their chromosome ends. Here we study the telomere biology of planarian flatworms with apparently limitless regenerative capacity fueled by a population of highly proliferative adult stem cells. We show that somatic telomere maintenance is different in asexual and sexual animals. Asexual animals maintain telomere length somatically during reproduction by fission or when regeneration is induced by amputation, whereas sexual animals only achieve telomere elongation through sexual reproduction. We demonstrate that this difference is reflected in the expression and alternate splicing of the protein subunit of the telomerase enzyme. Asexual adult planarian stem cells appear to maintain telomere length over evolutionary timescales without passage through a germ-line stage. The adaptations we observe demonstrate indefinite somatic telomerase activity in proliferating stem cells during regeneration or reproduction by fission, and establish planarians as a pertinent model for studying telomere structure, function, and maintenance.

Krüppel-like factor 15 activates hepatitis B virus gene expression and replication.

UNLABELLED: Hepatitis B virus (HBV) is a small DNA virus that requires cellular transcription factors for the expression of its genes. To understand the molecular mechanisms that regulate HBV gene expression, we conducted a yeast one-hybrid screen to identify novel cellular transcription factors that may control HBV gene expression. Here, we demonstrate that Krüppel-like factor 15 (KLF15), a liver-enriched transcription factor, can robustly activate HBV surface and core promoters. Mutations in the putative KLF15 binding site in the HBV core promoter abolished the ability of KLF15 to activate the core promoter in luciferase assays. Furthermore, the overexpression of KLF15 stimulated the expression of HBV surface antigen (HBsAg) and the core protein and enhanced viral replication. Conversely, small interfering RNA knockdown of the endogenous KLF15 in Huh7 cells resulted in a reduction in HBV surface- and core-promoter activities. In electrophoretic mobility shift and chromatin immunoprecipitation assays, KLF15 binds to DNA probes derived from the core promoter and the surface promoter. Introduction of an expression vector for KLF15 short hairpin RNA, together with the HBV genome into the mouse liver using hydrodynamic injection, resulted in a significant reduction in viral gene expression and DNA replication. Additionally, mutations in the KLF15 response element in the HBV core promoter significantly reduced viral DNA levels in the mouse serum. CONCLUSION: KLF15 is a novel transcriptional activator for HBV core and surface promoters. It is possible that KLF15 may serve as a potential therapeutic target to reduce HBV gene expression and viral replication.