Significance tests for R2 of out-of-sample prediction using polygenic scores.

The coefficient of determination (R2) is a well-established measure to indicate the predictive ability of polygenic scores (PGSs). However, the sampling variance of R2 is rarely considered so that 95% confidence intervals (CI) are not usually reported. Moreover, when comparisons are made between PGSs based on different discovery samples, the sampling covariance of R2 is required to test the difference between them. Here, we show how to estimate the variance and covariance of R2 values to assess the 95% CI and p value of the R2 difference. We apply this approach to real data calculating PGSs in 28,880 European participants derived from UK Biobank (UKBB) and Biobank Japan (BBJ) GWAS summary statistics for cholesterol and BMI. We quantify the significantly higher predictive ability of UKBB PGSs compared to BBJ PGSs (p value 7.6e-31 for cholesterol and 1.4e-50 for BMI). A joint model of UKBB and BBJ PGSs significantly improves the predictive ability, compared to a model of UKBB PGS only (p value 3.5e-05 for cholesterol and 1.3e-28 for BMI). We also show that the predictive ability of regulatory SNPs is significantly enriched over non-regulatory SNPs for cholesterol (p value 8.9e-26 for UKBB and 3.8e-17 for BBJ). We suggest that the proposed approach (available in R package r2redux) should be used to test the statistical significance of difference between pairs of PGSs, which may help to draw a correct conclusion about the comparative predictive ability of PGSs.

Leucyl-tRNA Synthetase Contributes to Muscle Weakness through Mammalian Target of Rapamycin Complex 1 Activation and Autophagy Suppression in a Mouse Model of Duchenne Muscular Dystrophy.

Duchenne muscular dystrophy (DMD), caused by loss-of-function mutations in the dystrophin gene, results in progressive muscle weakness and early fatality. Impaired autophagy is one of the cellular hallmarks of DMD, contributing to the disease progression. Molecular mechanisms underlying the inhibition of autophagy in DMD are not well understood. In the current study, the DMD mouse model mdx is used for the investigation of signaling pathways leading to suppression of autophagy. Mammalian target of rapamycin complex 1 (mTORC1) is found to be hyperactive in the DMD muscles, accompanying muscle weakness and autophagy impairment. Surprisingly, Akt, a well-known upstream regulator of mTORC1, is not responsible for mTORC1 activation or the dystrophic muscle phenotypes. Instead, leucyl-tRNA synthetase (LeuRS) is found to be overexpressed in mdx muscles compared with the wild type. LeuRS is known to activate mTORC1 in a noncanonical mechanism that involves interaction with RagD, an activator of mTORC1. Disrupting LeuRS interaction with RagD by the small-molecule inhibitor BC-LI-0186 reduces mTORC1 activity, restores autophagy, and ameliorates myofiber damage in the mdx muscles. Furthermore, inhibition of LeuRS by BC-LI-0186 improves dystrophic muscle strength in an autophagy-dependent manner. Taken together, our findings uncover a noncanonical function of the housekeeping protein LeuRS as a potential therapeutic target in the treatment of DMD.

Posteromedial thalamic nucleus activity significantly contributes to perceptual discrimination.

Higher-order sensory thalamic nuclei are densely connected with multiple cortical and subcortical areas, yet the role of these nuclei remains elusive. The posteromedial thalamic nucleus (POm), the higher-order thalamic nucleus in the rodent somatosensory system, is an anatomical hub broadly connected with multiple sensory and motor brain areas yet weakly responds to passive sensory stimulation and whisker movements. To understand the role of POm in sensory perception, we developed a self-initiated, two-alternative forced-choice task in freely moving mice during active sensing. Using optogenetic and chemogenetic manipulation, we show that POm plays a significant role in sensory perception and the projection from the primary somatosensory cortex to POm is critical for the contribution of POm in sensory perception during active sensing.

Dissection of brain-wide resting-state and functional somatosensory circuits by fMRI with optogenetic silencing.

To further advance functional MRI (fMRI)-based brain science, it is critical to dissect fMRI activity at the circuit level. To achieve this goal, we combined brain-wide fMRI with neuronal silencing in well-defined regions. Since focal inactivation suppresses excitatory output to downstream pathways, intact input and suppressed output circuits can be separated. Highly specific cerebral blood volume-weighted fMRI was performed with optogenetic stimulation of local GABAergic neurons in mouse somatosensory regions. Brain-wide spontaneous somatosensory networks were found mostly in ipsilateral cortical and subcortical areas, which differed from the bilateral homotopic connections commonly observed in resting-state fMRI data. The evoked fMRI responses to somatosensory stimulation in regions of the somatosensory network were successfully dissected, allowing the relative contributions of spinothalamic (ST), thalamocortical (TC), corticothalamic (CT), corticocortical (CC) inputs, and local intracortical circuits to be determined. The ventral posterior thalamic nucleus receives ST inputs, while the posterior medial thalamic nucleus receives CT inputs from the primary somatosensory cortex (S1) with TC inputs. The secondary somatosensory cortex (S2) receives mostly direct CC inputs from S1 and a few TC inputs from the ventral posterolateral nucleus. The TC and CC input layers in cortical regions were identified by laminar-specific fMRI responses with a full width at half maximum of <150 µm. Long-range synaptic inputs in cortical areas were amplified approximately twofold by local intracortical circuits, which is consistent with electrophysiological recordings. Overall, whole-brain fMRI with optogenetic inactivation revealed brain-wide, population-based, long-range circuits, which could complement data typically collected in conventional microscopic functional circuit studies.

Combinatorial Effect of Tricomponent Dual-Rim Nanoring Building Blocks: Label-Free SERS Detection of Biomolecules.

Detecting weakly adsorbing molecules via label-free surface-enhanced Raman scattering (SERS) has presented a significant challenge. To address this issue, we propose a novel approach for creating tricomponent SERS substrates using dual-rim nanorings (DRNs) made of Au, Ag, and CuO, each possessing distinct functionalities. Our method involves depositing different metals on Pt nanoring skeletons to obtain each nanoring with varying surface compositions while maintaining a similar size and shape. Next, the mixture of these nanorings is transferred into a monolayer assembly with homogeneous intermixing on a solid substrate. The surface of the CuO DRNs has dangling bonds (Cu2+) that facilitate the strong adsorption of carboxylates through the formation of chelating bonds, while the combination of Au and Ag DRNs significantly enhances the SERS signal intensity through a strong coupling effect. Notably, the tricomponent assemblies enable the successful SERS-based analysis of biomolecules such as amino acids, proteins, nucleobases, and nucleotides.

Plasmonic Annular Nanotrenches with 1 nm Nanogaps for Detection of SARS-CoV-2 Using SERS-Based Immunoassay.

This study represents the synthesis of a novel class of nanoparticles denoted as annular Au nanotrenches (AANTs). AANTs are engineered to possess embedded, narrow circular nanogaps with dimensions of approximately 1 nm, facilitating near-field focusing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via a surface-enhanced Raman scattering (SERS)-based immunoassay. Notably, AANTs exhibited an exceedingly low limit of detection (LOD) of 1 fg/mL for SARS-CoV-2 spike glycoproteins, surpassing the commercially available enzyme-linked immunosorbent assay (ELISA) by 6 orders of magnitude (1 ng/mL from ELISA). To assess the real-world applicability, a study was conducted on 50 clinical samples using an SERS-based immunoassay with AANTs. The results revealed a sensitivity of 96% and a selectivity of 100%, demonstrating the significantly enhanced sensing capabilities of the proposed approach in comparison to ELISA and commercial lateral flow assay kits.

Discovery of Three Bemisia tabaci Effectors and Their Effect on Gene Expression in Planta.

Bemisia tabaci (whitefly) is a polyphagous agroeconomic pest species complex. Two members of this species complex, Mediterranean (MED) and Middle-East-Asia Minor 1 (MEAM1), have a worldwide distribution and have been shown to manipulate plant defenses through effectors. In this study, we used three different strategies to identify three MEAM1 proteins that can act as effectors. Effector B1 was identified using a bioinformatics-driven effector-mining strategy, whereas effectors S1 and P1 were identified in the saliva of whiteflies collected from artificial diet and in phloem exudate of tomato on which nymphs were feeding, respectively. These three effectors were B. tabaci specific and able to increase whitefly fecundity when transiently expressed in tobacco plants (Nicotiana tabacum). Moreover, they reduced growth of Pseudomonas syringae pv. tabaci in Nicotiana benthamiana. All three effectors changed gene expression in planta, and B1 and S1 also changed phytohormone levels. Gene ontology and KEGG pathway enrichment analysis pinpointed plant-pathogen interaction and photosynthesis as the main enriched pathways for all three effectors. Our data thus show the discovery and validation of three new B. tabaci MEAM1 effectors that increase whitefly fecundity and modulate plant immunity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.

Piwi-interacting RNAs (piRNAs) silence transposons and maintain genome integrity during germline development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed to drive a ping-pong amplification cycle catalyzed by proteins that localize to the perinuclear nuage. We show that the HP1 homolog Rhino is required for nuage organization, transposon silencing, and ping-pong amplification of piRNAs. rhi mutations virtually eliminate piRNAs from the dual-strand clusters and block production of putative precursor RNAs from both strands of the major 42AB dual-strand cluster, but not of transcripts or piRNAs from the uni-strand clusters. Furthermore, Rhino protein associates with the 42AB dual-strand cluster,but does not bind to uni-strand cluster 2 or flamenco. Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle.

Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies.

Piwi-interacting RNAs (piRNAs) silence transposons in animal germ cells. piRNAs are thought to derive from long transcripts spanning transposon-rich genomic loci and to direct an autoamplification loop in which an antisense piRNA, bound to Aubergine or Piwi protein, triggers production of a sense piRNA bound to the PIWI protein Argonaute3 (Ago3). In turn, the new piRNA is envisioned to produce a second antisense piRNA. Here, we describe strong loss-of-function mutations in ago3, allowing a direct genetic test of this model. We find that Ago3 acts to amplify piRNA pools and to enforce on them an antisense bias, increasing the number of piRNAs that can act to silence transposons. We also detect a second, Ago3-independent piRNA pathway centered on Piwi. Transposons targeted by this second pathway often reside in the flamenco locus, which is expressed in somatic ovarian follicle cells, suggesting a role for piRNAs beyond the germline.

Segmental dynamics of polystyrene near polymer-polymer interfaces.

This study investigated the segmental dynamics of polymers near polymer-polymer interfaces by probing the rotation of polymer-tethered fluorescent molecules using imaging rotational fluorescence correlation microscopy. Multilayered films were utilized to provide spatial selectivity relative to different polymer-polymer interfaces. In the experimental setup, for the overlayer polymer, polystyrene (PS) was employed and a 15 nm-thick probe-containing layer was placed ≈25 nm apart from different underlayer polymers with glass transition temperatures (Tg) either lower or higher than that of PS. The underlayer of poly-n-butyl methacrylate had 72 K lower Tg than that of PS, whereas polymethyl methacrylate and polysulfone had 22 and 81 K higher Tg, respectively, than that of PS. Two key dynamic features of the glass transition, the non-Arrhenius temperature dependence and stretched relaxation, were examined to study the influence of soft and hard confinements on the segmental dynamics of the overlayer polymer near the polymer-polymer interfaces. Although complications exist in the probing location owing to the diffusion of the polymer-tethered probe during the annealing protocol to consolidate the multilayers, the results suggest that either the segmental dynamics of the polymer near the polymer-polymer interface do not change owing to the soft and hard confinements or the interfacial perturbation is very short ranged.

Plasmonic-Magnetic Active Nanorheology for Intracellular Viscosity.

We demonstrate active plasmonic systems where plasmonic signals are repeatedly modulated by changing the orientation of nanoprobes under an external magnetic field, which is a prerequisite for in situ active nanorheology in intracellular viscosity measurements. Au/Ni/Au nanorods act as "nanotransmitters", which transmit the mechanical motion of nanorods to an electromagnetic radiation signal as a periodic sine function. This fluctuating optical response is transduced to frequency peaks via Fourier transform surface plasmon resonance (FTSPR). As a driving frequency of the external magnetic field applied to the Au/Ni/Au nanorods increases and reaches above a critical threshold, there is a transition from the synchronous motion of nanorods to asynchronous responses, leading to the disappearance of the FTSPR peak, which allows us to measure the local viscosity of the complex fluids. Using this ensemble-based method with plasmonic functional nanomaterials, we measure the intracellular viscosity of cancer cells and normal cells in a reliable and reproducible manner.

The Importance of Accounting for Movement When Relating Neuronal Activity to Sensory and Cognitive Processes.

A surprising finding of recent studies in mouse is the dominance of widespread movement-related activity throughout the brain, including in early sensory areas. In awake subjects, failing to account for movement risks misattributing movement-related activity to other (e.g., sensory or cognitive) processes. In this article, we (1) review task designs for separating task-related and movement-related activity, (2) review three "case studies" in which not considering movement would have resulted in critically different interpretations of neuronal function, and (3) discuss functional couplings that may prevent us from ever fully isolating sensory, motor, and cognitive-related activity. Our main thesis is that neural signals related to movement are ubiquitous, and therefore ought to be considered first and foremost when attempting to correlate neuronal activity with task-related processes.

Au Octahedral Nanosponges: 3D Plasmonic Nanolenses for Near-Field Focusing.

Here, we report the synthesis of three-dimensional plasmonic nanolenses for strong near-field focusing. The nanolens exhibits a distinctive structural arrangement composed of nanoporous sponge-like networks within their interior. We denote these novel nanoparticles as "Au octahedral nanosponges" (Au Oh NSs). Employing a carefully planned multistep synthetic approach with Au octahedra serving as sacrificial templates, we successfully synthesized Au Oh NSs in solution. The porous domains resembling sponges contributed to enhanced scattering and absorption of incident light within metal ligaments. This optical energy was subsequently transferred to the nanospheres at the vertex, where near-field focusing was maximized. We named this observed enhancement a "lightning-sphere effect". Using single particle-by-particle surface-enhanced Raman scattering (SERS), we optimized the morphological dimensions of the spheres and porous domains to achieve the most effective near-field focusing. In the context of bulk SERS measurements targeting weakly adsorbing analytes (2-chloroethyl phenyl sulfide) in the gas phase, we achieved a low detection limit of 10 ppb. For nonadsorbing species (dimethyl methyl phosphonate), utilization of hybrid SERS substrates consisting of Au Oh NSs and metal-organic frameworks as gas-adsorbing intermediate layers was highly effective for successful SERS detection.

A randomized Phase 2 study to compare erlotinib with or without bevacizumab in previously untreated patients with advanced non-small cell lung cancer with EGFR mutation.

BACKGROUND: This study evaluated whether an addition of bevacizumab to erlotinib improves clinical outcomes in patients with advanced EGFR-mutated non-small cell lung cancer (NSCLC). METHODS: This is an open-label, multicenter, randomized Phase 2 study in South Korea. Chemonaïve patients with Stage IIIB/IV NSCLC with EGFR 19 deletion or L858R mutation were eligible. Asymptomatic brain metastasis (BM) was enrolled without local treatment. Patients received either erlotinib plus bevacizumab or erlotinib. RESULTS: Between December 2016 and March 2019, 127 patients were randomly assigned to receive erlotinib plus bevacizumab (n = 64) or erlotinib (n = 63). Fifty-nine (46.5%) patients had baseline BM. Fewer patients in the erlotinib plus bevacizumab arm received radiotherapy for BM than in the erlotinib arm (10.3% vs. 40.0%). A trend toward longer progression-free survival (PFS) was observed in the erlotinib plus bevacizumab arm compared with the erlotinib alone arm; however, it was not statistically significant (median PFS, 17.5 months vs. 12.4 months; hazard ratio [HR], 0.74; 95% CI, 0.51-1.08; p = .119). The unplanned subgroup analysis showed a longer PFS with erlotinib plus bevacizumab in patients with BM (median PFS, 18.6 months vs. 10.3 months; HR, 0.54; 95% CI, 0.31-0.95; p = .032). Grade 3 or worse adverse events occurred in 56.6% of the erlotinib plus bevacizumab arm and 20.6% of the erlotinib arm. CONCLUSIONS: Although it was not statistically significant, a trend to improvement in PFS was observed in patients with erlotinib plus bevacizumab compared to erlotinib alone. PLAIN LANGUAGE SUMMARY: A randomized Phase 2 study compared erlotinib with or without bevacizumab in previously untreated patients with advanced non-small cell lung cancer with EGFR mutation. The erlotinib plus bevacizumab failed to improve median progression-free survival compared with the erlotinib alone. However, the progression-free survival benefit from erlotinib plus bevacizumab was found in patients with brain metastasis with no severe hemorrhagic adverse effects.

Multi-Layered PtAu Nanoframes and Their Light-Enhanced Electrocatalytic Activity via Plasmonic Hot Spots.

Here, the rational design of complex PtAu double nanoframes (DNFs) for plasmon-enhanced electrocatalytic activity toward the methanol oxidation reaction (MOR) is reported. The synthetic strategy for the DNFs consists of on-demand multiple synthetic chemical toolkits, including well-faceted Au growth, rim-on selective Pt deposition, and selective Au etching steps. DNFs are synthesized by utilizing Au truncated octahedrons (TOh) as a starting template. The outer octahedral (Oh) nanoframes (NFs) nest the inner TOh NFs, eventually forming DNFs with a tunable intra-nanogap distance. Residual Au adatoms on Pt skeletons act as light entrappers and produce plasmonic hot spots between inner and outer frames through localized surface plasmon resonance (LSPR) coupling, which promotes enhanced electrocatalytic activity for the MOR. Importantly, the correlation between the gap-induced hot carriers and electrocatalytic activity is evaluated. The highest catalytic activity is achieved when the gap is the narrowest. To further harness their light-trapping capability, hierarchically structured triple NFs (TNFs) are synthesized, wherein three NFs are entangled in a single entity with a high density of hot regions, exhibiting superior electrocatalytic activity toward the MOR with a sixfold larger current density under light irradiation compared to the dark conditions.

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.

SUMMARY: As the amount of 3D chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files. AVAILABILITY AND IMPLEMENTATION: The format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/pairsqc.

Programmable, high-speed, adaptive optics partially confocal multi-spot ophthalmoscope using a digital micromirror device.

A high-speed, adaptive optics partially confocal multi-spot ophthalmoscope (AO-pcMSO) using a digital micromirror device (DMD) in the illumination channel and a fast 2D CMOS camera is described. The camera is synchronized with the DMD allowing projection of multiple, simultaneous AO-corrected spots onto the human retina. Spatial filtering on each raw retinal image before reconstruction works as an array virtual pinholes. A frame acquisition rate of 250 fps is achieved by applying this parallel projection scheme. The contrast improves by 2-3 fold when compared to a standard flood illumination architecture. Partially confocal images of the human retina show cone and rod photoreceptors over a range of retinal eccentricities.

Impact of Chain Conformation on Structural Heterogeneity in Polymer Network.

Polymer networks generally consist of an ensemble of single chains. However, understanding how chain conformation affects the structure and properties of polymer networks remains a challenge for optimizing their functionality. Here, we present the fabrication and comparative study of a polymer network composed of collapsed self-entangled chains (intrachain entangled network) and a standard polymer network in which random-coil chains are entangled with each other (interchain entangled network). For poly(methyl methacrylate) thin films composed of these networks, we coupled solvent vapor swelling and single-molecule tracking techniques to examine the anomalies in the dynamics of a small-molecular probe included in the system. We demonstrate that when compared to the interchain entangled network the intrachain one exhibits a more substantial structural heterogeneity, particularly under highly crowded conditions. This network also exhibits physical compactness, which keeps the heterogeneous network structure frozen over time and impedes network plasticization through solvent uptake by the film.

Ring-in-a-Triangle Nanoframes: Integrating with Intra- and Interhotspots for Highly Amplified Near-Field Focusing.

The development of a stepwise synthetic strategy for Au ring-in-a-triangle nanoframes with a high degree of structural solidity is essential to the advancement of highly amplified near-field focusing. This strategy leads to the formation of an inscribed nanoring in a triangular metal frame with stability to withstand elevated temperatures and an oxidizing environment, which is critical for successful single-particle surface-enhanced Raman scattering (SERS). The existence of inscribed nanorings plays an important role in enhancing the so-called "lightning rod effect," whereby the electromagnetic near-field enhancement occurs on the highly curved curvature of a metallic interface. We evaluated the corresponding single-particle SERS as a function of the thickness of the rims and then constructed two-dimensional (2D) bulk SERS substrates, wherein an ensemble of hotspots exists. The synergic contribution from both inter- and intrahotspots allowed the outstanding linearity of the calibration curve and the lowest limit of detection, ∼10-18 M for the analyte concentration.

All-Hot-Spot Bulk Surface-Enhanced Raman Scattering (SERS) Substrates: Attomolar Detection of Adsorbates with Designer Plasmonic Nanoparticles.

Here we report a synthetic pathway toward Au truncated octahedral dual-rim nanoframes wherein two functional facets are formed including (1) eight hot nanogaps formed by hexagonal nanoframes embracing core circular nanorings for near-field focusing and (2) six flat squares that facilitate the formation of well-ordered arrays of nanoframes through self-assembly. The existence of intra-nanogaps in a single entity enables strong electromagnetic near-field focusing, allowing single-particle surface-enhanced Raman spectroscopy. Then, we built "all-hot-spot bulk SERS substrates" with those entities, wherein the presence of truncated terraces with high homogeneity in size and shape facilitate spontaneous self-assembly into a highly ordered and uniform superlattice, exhibiting a limit of detection of attomolar concentrations toward 2-naphthalenethiol, which is 6 orders lower than that of monorim counterparts. The observed low limit of detection originates from the combined synergic effect from both inter- and intraparticle coupling in a superlattice, which we dubbed "all-hot-spot bulk SERS substrates".