Exploring the impact of awe on the multifaceted construct of empathy

Empathy helps us navigate social interactions and promotes prosocial behaviors like caregiving and helping. Here, we explored whether awe, a key self-transcendent and epistemic emotion, could encourage greater empathy across seven diverse student and community samples collected between 2020 and 2022. Empathy is a multifaceted construct; thus, we assessed performance on a range of empathy measures including perspective taking accuracy (Study 2), empathic accuracy (Study 3; preregistered), emotion contagion and compassion (Study 4). We also directly tested whether awe motivated people to empathize with others (Study 5; preregistered). Although dispositional awe was positively correlated with trait measures of empathy (Study 1), experimental inductions of awe did not improve performance on empathy measures or motivate people to empathize, compared to a control (Studies 2-5). However, a moderation effect emerged in which awe had divergent effects on empathy depending on participants' self-reported dispositional levels of cognitive empathy. Although effects only reached significance in two studies (Studies 3; preregistered and 4), an internal meta-analysis revealed that awe improved empathy for those high in dispositional cognitive empathy, while marginally reducing it among those low in dispositional cognitive empathy, compared to a control. These results suggest that awe may have polarizing effects on empathy depending on one's dispositional level of cognitive empathy and reveal a potentially important role of cognitive processes in linking awe and empathy. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Protein purification via consecutive histidine-polyphosphate interaction

While nickel-nitrilotriacetic acid (Ni-NTA) has greatly advanced recombinant protein purification, its limitations, including nonspecific binding and partial purification for certain proteins, highlight the necessity for additional purification such as size exclusion and ion exchange chromatography. However, specialized equipment such as FPLC is typically needed but not often available in many laboratories. Here, we show a novel method utilizing polyphosphate (polyP) for purifying proteins with histidine repeats via non-covalent interactions. Our study demonstrates that immobilized polyP efficiently binds to histidine-tagged proteins across a pH range of 5.5-7.5, maintaining binding efficacy even in the presence of reducing agent DTT and chelating agent EDTA. We carried out experiments of purifying various proteins from cell lysates and fractions post-Ni-NTA. Our results demonstrate that polyP resin is capable of further purification post-Ni-NTA without the need for specialized equipment and without compromising protein activity. This cost-effective and convenient method offers a viable approach as a complementary approach to Ni-NTA.

Hypothalamic vasopressin sex differentiation is observed by embryonic day 15 in mice and is disrupted by the xenoestrogen bisphenol A

Arginine vasopressin (AVP) neurons of the hypothalamic paraventricular region (AVPPVN) mediate sex-biased social behaviors across most species, including mammals. In mice, neural sex differences are thought to be established during a critical window around birth ( embryonic (E) day 18 to postnatal (P) day 2) whereby circulating testosterone from the fetal testis is converted to estrogen in sex-dimorphic brain regions. Here, we found that AVPPVN neurons are sexually dimorphic by E15.5, prior to this critical window, and that gestational bisphenol A (BPA) exposure permanently masculinized female AVPPVN neuronal numbers, projections, and electrophysiological properties, causing them to display male-like phenotypes into adulthood. Moreover, we showed that nearly twice as many neurons that became AVP+ by P0 were born at E11 in males and BPA-exposed females compared to control females, suggesting that AVPPVN neuronal masculinization occurs between E11 and P0. We further narrowed this sensitive period to around the timing of neurogenesis by demonstrating that exogenous estrogen exposure from E14.5 to E15.5 masculinized female AVPPVN neuronal numbers, whereas a pan-estrogen receptor antagonist exposed from E13.5 to E15.5 blocked masculinization of males. Finally, we showed that restricting BPA exposure to E7.5-E15.5 caused adult females to display increased social dominance over control females, consistent with an acquisition of male-like behaviors. Our study reveals an E11.5 to E15.5 window of estrogen sensitivity impacting AVPPVN sex differentiation, which is impacted by prenatal BPA exposure.

Next Generation Computing and Communication Hub for First Responders in Smart Cities

This paper contributes to the development of a Next Generation First Responder (NGFR) communication platform with the key goal of embedding it into a smart city technology infrastructure. The framework of this approach is a concept known as SmartHub, developed by the US Department of Homeland Security. The proposed embedding methodology complies with the standard categories and indicators of smart city performance. This paper offers two practice-centered extensions of the NGFR hub, which are also the main results: first, a cognitive workload monitoring of first responders as a basis for their performance assessment, monitoring, and improvement; and second, a highly sensitive problem of human society, the emergency assistance tools for individuals with disabilities. Both extensions explore various technological-societal dimensions of smart cities, including interoperability, standardization, and accessibility to assistive technologies for people with disabilities. Regarding cognitive workload monitoring, the core result is a novel AI formalism, an ensemble of machine learning processes aggregated using machine reasoning. This ensemble enables predictive situation assessment and self-aware computing, which is the basis of the digital twin concept. We experimentally demonstrate a specific component of a digital twin of an NGFR, a near-real-time monitoring of the NGFR cognitive workload. Regarding our second result, a problem of emergency assistance for individuals with disabilities that originated as accessibility to assistive technologies to promote disability inclusion, we provide the NGFR specification focusing on interactions based on AI formalism and using a unified hub platform. This paper also discusses a technology roadmap using the notion of the Emergency Management Cycle (EMC), a commonly accepted doctrine for managing disasters through the steps of mitigation, preparedness, response, and recovery. It positions the NGFR hub as a benchmark of the smart city emergency service.

Earliest observation of the tetracycline destructase tet(X3)

Tigecycline is an antibiotic of last resort for infections with carbapenem-resistant Acinetobacter baumannii. Plasmids harboring variants of the tetracycline destructase gene tetX promote rising tigecycline resistance rates. We report the earliest observation of tet(X3) in a clinical strain predating tigecycline's commercialization, suggesting selective pressures other than tigecycline contributed to its emergence.

IMPORTANCE

We present the earliest observation of a tet(X3)-positive bacterial strain, predating by many years the earliest reports of this gene so far. This finding is significant as tigecycline is an antibiotic of last resort for carbapenem-resistant Acinetobacter baumannii (CRAB), which the World Health Organization ranks as one of its top three critical priority pathogens, and tet(X3) variants have become the most prevalent genes responsible for enabling CRAB to become tigecycline resistant. Moreover, the tet(X3)-positive strain we report is the first and only to be found that predates the commercialization of tigecycline, an antibiotic that was thought to have contributed to the emergence of this resistance gene. Understanding the factors contributing to the origin and spread of novel antibiotic resistance genes is crucial to addressing the major global public health issue, which is antimicrobial resistance.

Identifying cognitive profiles in children with neurodevelopmental disorders using online cognitive testing

Children with neurodevelopmental disorders (NDDs) such as autism spectrum disorder (ASD), and attention deficit hyperactivity disorder (ADHD) tend to exhibit similar deficits in attention and memory ability. Early screening of cognitive deficits in children with NDDs, particularly in preschool children, is fundamental to improving cognitive and academic outcomes. In order to determine cognitive profiles in children with ASD and ADHD, we developed accessible audiovisual instructions for an online battery of 13 cognitive tests. Children ages 4-16 who were diagnosed with ADHD (n = 83), or ASD (n = 37), or who were typically developing children (TD) (n = 86) were recruited. Data were analyzed using a stepwise Discriminant Analysis to determine which cognitive tasks were the strongest discriminators between the diagnostic groups. Results revealed four tasks reflective of working memory, reasoning, and attentional processes, which correctly classified approximately 53-60% of each group. The ADHD group had lower scores on attentional tasks compared to TD, while ASD group had lower scores on reasoning tasks compared to the TD children, and made more attempts across all four tasks. The results from this study stress the need for cognitive screening assessments that include domain-specific items to improve the characterization of executive function deficits and promote academic achievement in all children with NDDs.

Porous versus solid shoulder implants in humeri of different bone densities: A finite element analysis

Porous metallic prosthesis components can now be manufactured using additive manufacturing techniques, and may prove beneficial for promoting bony ingrowth, for accommodating drug delivery systems, and for reducing stress shielding. Using finite element modeling techniques, 36 scenarios (three porous stems, three bone densities, and four held arm positions) were analysed to assess the viability of porous humeral stems for use in total shoulder arthroplasty, and their resulting mechanobiological impact on the surrounding humerus bone. All three porous stems were predicted to experience stresses below the yield strength of Ti6Al4V (880 MPa) and to be capable of withstanding more than 10 million cycles of each loading scenario before failure. There was an indication that within an 80 mm region of the proximal humerus, there would be a reduction in bone resorption as stem porosity increased. Overall, this study shows promise that these porous structures are mechanically viable for incorporation into permanent shoulder prostheses to combat orthopedic infections.

Where do the symptoms come from in depression? Topography and dynamics matter

This scientific commentary refers to 'Brain dynamics predictive of response to psilocybin for treatment-resistant depression', by Vohryzek et al. (https://doi.org/10.1093/braincomms/fcae049).

Short-wave Infrared Photoluminescence Lifetime Mapping of Rare-Earth Doped Nanoparticles Using All-Optical Streak Imaging

The short-wave infrared (SWIR) photoluminescence lifetimes of rare-earth doped nanoparticles (RENPs) have found diverse applications in fundamental and applied research. Despite dazzling progress in the novel design and synthesis of RENPs with attractive optical properties, existing optical systems for SWIR photoluminescence lifetime imaging are still considerably restricted by inefficient photon detection, limited imaging speed, and low sensitivity. To overcome these challenges, SWIR photoluminescence lifetime imaging microscopy using an all-optical streak camera (PLIMASC) is developed. Synergizing scanning optics and a high-sensitivity InGaAs CMOS camera, SWIR-PLIMASC has a 1D imaging speed of up to 138.9 kHz in the spectral range of 900-1700 nm, which quantifies the photoluminescence lifetime of RENPs in a single shot. A 2D photoluminescence lifetime map can be acquired by 1D scanning of the sample. To showcase the power of SWIR-PLIMASC, a series of core-shell RENPs with distinct SWIR photoluminescence lifetimes is synthesized. In particular, using Er3+ -doped RENPs, SWIR-PLIMASC enables multiplexed anti-counterfeiting. Leveraging Ho3+ -doped RENPs as temperature indicators, this system is applied to SWIR photoluminescence lifetime-based thermometry. Opening up a new avenue for efficient SWIR photoluminescence lifetime mapping, this work is envisaged to contribute to advanced materials characterization, information science, and biomedicine.

Transcriptomic Analysis of Mineralized Adipose-Derived Stem Cell Tissues for Calcific Valve Disease Modelling

Calcific aortic valve disease (CAVD) is characterized by the fibrosis and mineralization of the aortic valve, which leads to aortic stenosis and heart failure. At the cellular level, this is due to the osteoblastic-like differentiation of valve interstitial cells (VICs), resulting in the calcification of the tissue. Unfortunately, human VICs are not readily available to study CAVD pathogenesis and the implicated mechanisms in vitro; however, adipose-derived stromal/stem cells (ASCs), carrying the patient's specific genomic features, have emerged as a promising cell source to model cardiovascular diseases due to their multipotent nature, availability, and patient-specific characteristics. In this study, we describe a comprehensive transcriptomic analysis of tissue-engineered, scaffold-free, ASC-embedded mineralized tissue sheets using bulk RNA sequencing. Bioinformatic and gene set enrichment analyses revealed the up-regulation of genes associated with the organization of the extracellular matrix (ECM), suggesting that the ECM could play a vital role in the enhanced mineralization observed in these tissue-engineered ASC-embedded sheets. Upon comparison with publicly available gene expression datasets from CAVD patients, striking similarities emerged regarding cardiovascular diseases and ECM functions, suggesting a potential link between ECM gene expression and CAVDs pathogenesis. A matrisome-related sub-analysis revealed the ECM microenvironment promotes the transcriptional activation of the master gene runt-related transcription factor 2 (RUNX2), which is essential in CAVD development. Tissue-engineered ASC-embedded sheets with enhanced mineralization could be a valuable tool for research and a promising avenue for the identification of more effective aortic valve replacement therapies.

rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection

Toward the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole-genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research has revealed the insight into TWAS: the 2 steps in TWAS, building and applying the expression prediction models, are essentially genetic feature selection and aggregations that do not have to involve predictions. Based on this insight disentangling TWAS, rare variants' inability of predicting expression traits is no longer an obstacle. Herein, we developed "rare variant TWAS," or rvTWAS, that first uses a Bayesian model to conduct expression-directed feature selection and then uses a kernel machine to carry out feature aggregation, forming a model leveraging expressions for association mapping including rare variants. We demonstrated the performance of rvTWAS by thorough simulations and real data analysis in 3 psychiatric disorders, namely schizophrenia, bipolar disorder, and autism spectrum disorder. We confirmed that rvTWAS outperforms existing TWAS protocols and revealed additional genes underlying psychiatric disorders. Particularly, we formed a hypothetical mechanism in which zinc finger genes impact all 3 disorders through transcriptional regulations. rvTWAS will open a door for sequence-based association mappings integrating gene expressions.

Modulating Gut Microbiota Prevents Anastomotic Leak to Reduce Local Implantation and Dissemination of Colorectal Cancer Cells after Surgery

PURPOSE

Anastomotic leak (AL) is a major complication in colorectal cancer surgery and consists of the leakage of intestinal content through a poorly healed colonic wound. Colorectal cancer recurrence after surgery is a major determinant of survival. We hypothesize that AL may allow cancer cells to escape the gut and lead to cancer recurrence and that improving anastomotic healing may prevent local implantation and metastatic dissemination of cancer cells.

EXPERIMENTAL DESIGN

We investigated the association between AL and postoperative outcomes in patients with colorectal cancer. Using mouse models of poor anastomotic healing, we assessed the processes of local implantation and dissemination of cancer cells. The effect of dietary supplementation with inulin and 5-aminosalicylate (5-ASA), which activate PPAR-γ in the gut, on local anastomotic tumors was assessed in mice undergoing colonic surgery. Inulin and 5-ASA were also assessed in a mouse model of liver metastasis.

RESULTS

Patients experiencing AL displayed lower overall and oncologic survival than non-AL patients. Poor anastomotic healing in mice led to larger anastomotic and peritoneal tumors. The microbiota of patients with AL displays a lower capacity to activate the antineoplastic PPAR-γ in the gut. Modulation of gut microbiota using dietary inulin and 5-ASA reinforced the gut barrier and prevented anastomotic tumors and metastatic spread in mice.

CONCLUSIONS

Our findings reinforce the hypothesis that preventing AL is paramount to improving oncologic outcomes after colorectal cancer surgery. Furthermore, they pave the way toward dietary targeting of PPAR-γ as a novel way to enhance healing and diminish cancer recurrence.

cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions

Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions, which reflects more biological interactions between variants, in addition to lack of recombination. We derived the theoretical variance of cLD using delta methods to demonstrate its higher stability than LD for rare variants. This property is also verified by bootstrapped simulations using real data. In application, we find cLD reveals an increased genetic association between genes in 3D chromatin interactions, a phenomenon recently reported negatively by calculating standard LD between common variants. Additionally, we show that cLD is higher between gene pairs reported in interaction databases, identifies unreported protein-protein interactions, and reveals interacting genes distinguishing case/control samples in association studies.

Coastal erosion and climate change: A review on coastal-change process and modeling

Coastal erosion is a normal process of nature. However, the rate of coastal erosion, and the frequency and intensity of coastal flooding events, are now on the rise around the world due to the changing climate. Current responses to coastal erosion are primarily determined by site-specific factors, such as coastal elevation, coastal slope, coastal features, and historical coastline change rate, without a systematic understanding of the coastal-change processes in the context of climate change, including spatiotemporal changes in sea level, regional changes in wave climate, and sea ice coverage. In the absence of a clear understanding of the coastal-change processes, most of the current coastal responses have been built upon a risky assumption (i.e., the present-day coastal change will persist) and are not resilient to future climate change. Here, we conduct a literature review to summarize the latest scientific understanding of the coastal-change processes under climate change and the potential research gaps towards the prediction of future coastal erosion. Our review suggests that a coupled coastal simulation system with a nearshore wave model (e.g., SWAN, MIKE21, etc.) can play a critical role in both the short-term and long-term coastal risk assessment and protective measure development.

Bright ferritin for long-term MR imaging of human embryonic stem cells

BACKGROUND

A non-invasive imaging technology that can monitor cell viability, retention, distribution, and interaction with host tissue after transplantation is needed for optimizing and translating stem cell-based therapies. Current cell imaging approaches are limited in sensitivity or specificity, or both, for in vivo cell tracking. The objective of this study was to apply a novel ferritin-based magnetic resonance imaging (MRI) platform to longitudinal tracking of human embryonic stem cells (hESCs) in vivo.

METHODS

Human embryonic stem cells (hESCs) were genetically modified to stably overexpress ferritin using the CRISPR-Cas9 system. Cellular toxicity associated with ferritin overexpression and manganese (Mn) supplementation were assessed based on cell viability, proliferation, and metabolic activity. Ferritin-overexpressing hESCs were characterized based on stem cell pluripotency and cardiac-lineage differentiation capability. Cells were supplemented with Mn and imaged in vitro as cell pellets on a preclinical 3 T MR scanner. T1-weighted images and T1 relaxation times were analyzed to assess contrast. For in vivo study, three million cells were injected into the leg muscle of non-obese diabetic severe combined immunodeficiency (NOD SCID) mice. Mn was administrated subcutaneously. T1-weighted sequences and T1 mapping were used to image the animals for longitudinal in vivo cell tracking. Cell survival, proliferation, and teratoma formation were non-invasively monitored by MRI. Histological analysis was used to validate MRI results.

RESULTS

Ferritin-overexpressing hESCs labeled with 0.1 mM MnCl2 provided significant T1-induced bright contrast on in vitro MRI, with no adverse effect on cell viability, proliferation, pluripotency, and differentiation into cardiomyocytes. Transplanted hESCs displayed significant bright contrast on MRI 24 h after Mn administration, with contrast persisting for 5 days. Bright contrast was recalled at 4-6 weeks with early teratoma outgrowth.

CONCLUSIONS

The bright-ferritin platform provides the first demonstration of longitudinal cell tracking with signal recall, opening a window on the massive cell death that hESCs undergo in the weeks following transplantation before the surviving cell fraction proliferates to form teratomas.

Phloem-Mobile MYB44 Negatively Regulates Expression of PHOSPHATE TRANSPORTER 1 in Arabidopsis Roots

Phosphorus (P) is an essential plant macronutrient; however, its availability is often limited in soils. Plants have evolved complex mechanisms for efficient phosphate (Pi) absorption, which are responsive to changes in external and internal Pi concentration, and orchestrated through local and systemic responses. To explore these systemic Pi responses, here we identified AtMYB44 as a phloem-mobile mRNA, an Arabidopsis homolog of Cucumis sativus MYB44, that is responsive to the Pi-starvation stress. qRT-PCR assays revealed that AtMYB44 was up-regulated and expressed in both shoot and root in response to Pi-starvation stress. The atmyb44 mutant displayed higher shoot and root biomass compared to wild-type plants, under Pi-starvation conditions. Interestingly, the expression of PHOSPHATE TRANSPORTER1;2 (PHT1;2) and PHT1;4 was enhanced in atmyb44 in response to a Pi-starvation treatment. A split-root assay showed that AtMYB44 expression was systemically regulated under Pi-starvation conditions, and in atmyb44, systemic controls on PHT1;2 and PHT1;4 expression were moderately disrupted. Heterografting assays confirmed graft transmission of AtMYB44 transcripts, and PHT1;2 and PHT1;4 expression was decreased in heterografted atmyb44 rootstocks. Taken together, our findings support the hypothesis that mobile AtMYB44 mRNA serves as a long-distance Pi response signal, which negatively regulates Pi transport and utilization in Arabidopsis.

XA4C: eXplainable representation learning via Autoencoders revealing Critical genes

Machine Learning models have been frequently used in transcriptome analyses. Particularly, Representation Learning (RL), e.g., autoencoders, are effective in learning critical representations in noisy data. However, learned representations, e.g., the "latent variables" in an autoencoder, are difficult to interpret, not to mention prioritizing essential genes for functional follow-up. In contrast, in traditional analyses, one may identify important genes such as Differentially Expressed (DiffEx), Differentially Co-Expressed (DiffCoEx), and Hub genes. Intuitively, the complex gene-gene interactions may be beyond the capture of marginal effects (DiffEx) or correlations (DiffCoEx and Hub), indicating the need of powerful RL models. However, the lack of interpretability and individual target genes is an obstacle for RL's broad use in practice. To facilitate interpretable analysis and gene-identification using RL, we propose "Critical genes", defined as genes that contribute highly to learned representations (e.g., latent variables in an autoencoder). As a proof-of-concept, supported by eXplainable Artificial Intelligence (XAI), we implemented eXplainable Autoencoder for Critical genes (XA4C) that quantifies each gene's contribution to latent variables, based on which Critical genes are prioritized. Applying XA4C to gene expression data in six cancers showed that Critical genes capture essential pathways underlying cancers. Remarkably, Critical genes has little overlap with Hub or DiffEx genes, however, has a higher enrichment in a comprehensive disease gene database (DisGeNET) and a cancer-specific database (COSMIC), evidencing its potential to disclose massive unknown biology. As an example, we discovered five Critical genes sitting in the center of Lysine degradation (hsa00310) pathway, displaying distinct interaction patterns in tumor and normal tissues. In conclusion, XA4C facilitates explainable analysis using RL and Critical genes discovered by explainable RL empowers the study of complex interactions.

Materials for Electrochemiluminescence: TADF, Hydrogen-Bonding, and Aggregation- and Crystallization-Induced Emission Luminophores

Electrochemiluminescence (ECL) is a rapidly growing discipline with many analytical applications from immunoassays to single-molecule detection. At the forefront of ECL research is materials chemistry, which looks at engineering new materials and compounds exhibiting enhanced ECL efficiencies compared to conventional fluorescent materials. In this review, we summarize recent molecular design strategies that lead to high efficiency ECL. In particular, we feature recent advances in the use of thermally activated delayed fluorescence (TADF) emitters to produce enhanced electrochemiluminescence. We also document how hydrogen bonding, aggregation, and crystallization can each be recruited in the design of materials showing enhanced electrochemiluminescence.

Mueller matrix polarization parameters correlate with local recurrence in patients with stage III colorectal cancer

The peri-tumoural stroma has been explored as a useful source of prognostic information in colorectal cancer. Using Mueller matrix (MM) polarized light microscopy for quantification of unstained histology slides, the current study assesses the prognostic potential of polarimetric characteristics of peri-tumoural collagenous stroma architecture in 38 human stage III colorectal cancer (CRC) patient samples. Specifically, Mueller matrix transformation and polar decomposition parameters were tested for association with 5-year patient local recurrence outcomes. The results show that some of these polarimetric parameters were significantly different (p value < 0.05) for the recurrence versus the no-recurrence patient cohorts (Mann-Whitney U test). MM parameters may thus be prognostically valuable towards improving clinical management/treatment stratification in CRC patients.

Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids

BACKGROUND

Mitochondrial dysfunction is involved in several diseases ranging from genetic mitochondrial disorders to chronic metabolic diseases. An emerging approach to potentially treat mitochondrial dysfunction is the transplantation of autologous live mitochondria to promote cell regeneration. We tested the differential filtration-based mitochondrial isolation protocol established by the McCully laboratory for use in cellular models but found whole cell contaminants in the mitochondrial isolate.

METHODS

Therefore, we explored alternative types of 5-μm filters (filters A and B) for isolation of mitochondria from multiple cell lines including HEK293 cells and induced pluripotent stem cells (iPSCs). MitoTracker™ staining combined with flow cytometry was used to quantify the concentration of viable mitochondria. A proof-of-principle mitochondrial transplant was performed using mitoDsRed2-tagged mitochondria into a H9-derived cerebral organoid.

RESULTS

We found that filter B provided the highest quality mitochondria as compared to the 5-μm filter used in the original protocol. Using this method, mitochondria were also successfully isolated from induced pluripotent stem cells. To test for viability, mitoDsRed2-tagged mitochondria were isolated and transplanted into H9-derived cerebral organoids and observed that mitochondria were engulfed as indicated by immunofluorescent co-localization of TOMM20 and MAP2.

CONCLUSIONS

Thus, use of filter B in a differential filtration approach is ideal for isolating pure and viable mitochondria from cells, allowing us to begin evaluating long-term integration and safety of mitochondrial transplant using cellular sources.

ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development

ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.

FRET Imaging of Nonuniformly Distributed DNA SAMs on Gold Reveals the Role Played by the Donor/Acceptor Ratio and the Local Environment in Measuring the Rate of Hybridization

Mixed DNA SAMs labeled with a fluorophore (either AlexaFluor488 or AlexaFluor647) were prepared on a single crystal gold bead electrode using potential-assisted thiol exchange and studied using Förster resonance energy transfer (FRET). A measure of the local environment of the DNA SAM (e.g., crowding) was possible using FRET imaging on these surfaces since electrodes prepared this way have a range of surface densities (Γ_DNA). The FRET signal was strongly dependent on Γ_DNA and on the ratio of AlexaFluor488 to AlexaFluor647 used to make the DNA SAM, which were consistent with a model of FRET in 2D systems. FRET was shown to provide a direct measure of the local DNA SAM arrangement on each crystallographic region of interest providing a direct assessment of the probe environment and its influence on the rate of hybridization. The kinetics of duplex formation for these DNA SAMs was also studied using FRET imaging over a range of coverages and DNA SAM compositions. Hybridization of the surface-bound DNA increased the average distance between the fluorophore label and the gold electrode surface and decreased the distance between the donor (D) and acceptor (A), both of which result in an increase in FRET intensity. This increase in FRET was modeled using a second order Langmuir adsorption rate equation, reflecting the fact that both D and A labeled DNA are required to become hybridized to observe a FRET signal. The self-consistent analysis of the hybridization rates on low and high coverage regions on the same electrode showed that the low coverage regions achieved full hybridization 5× faster than the higher coverage regions, approaching rates typically found in solution. The relative increase in FRET intensity from each region of interest was controlled by manipulating the donor to acceptor composition of the DNA SAM without changing the rate of hybridization. The FRET response can be optimized by controlling the coverage and the composition of the DNA SAM sensor surface and could be further improved with the use of a FRET pair with a larger (e.g., > 5 nm) Förster radius.

Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness

The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.

Long-Term Care Resident Health and Quality of Care During the COVID-19 Pandemic: A Synthesis Analysis of Canadian Institute for Health Information Data Tables

Objective

Long-term care (LTC) homes ("nursing homes") were challenged during the first year of the COVID-19 pandemic in Canada. The objective of this study was to measure the impact of the COVID-19 pandemic on resident admission and discharge rates, resident health attributes, treatments, and quality of care.

Design

Synthesis analysis of "Quick Stats" standardized data table reports published yearly by the Canadian Institute for Health Information. These reports are a pan-Canadian scorecard of LTC services rendered, resident health characteristics, and quality indicator performance.

Setting and participants

LTC home residents in Alberta, British Columbia, Manitoba, and Ontario, Canada that were assessed with the interRAI Minimum Data Set 2.0 comprehensive health assessment in fiscal years 2018/2019, 2019/2020 (pre-pandemic period), and 2020/2021 (pandemic period).

Methods

Risk ratio statistics were calculated to compare admission and discharge rates, validated interRAI clinical summary scale scores, medication, therapy and treatment provision, and seventeen risk-adjusted quality indicator rates from the pandemic period relative to prior fiscal years.

Results

Risk of dying in the LTC home was greater in all provinces (risk ratio [RR] range 1.06-1.18) during the pandemic. Quality of care worsened substantially on 6 of 17 quality indicators in British Columbia and Ontario, and 2 quality indicators in Manitoba and Alberta. The only quality indicator where performance worsened during the pandemic in all provinces was the percentage of residents that received antipsychotic medications without a diagnosis of psychosis (RR range 1.01-1.09).

Conclusions and implications

The COVID-19 pandemic has unveiled numerous areas to strengthen LTC and ensure that resident's physical, social, and psychological needs are addressed during public health emergencies. Except an increase in potentially inappropriate antipsychotic use, this provincial-level analysis indicates that most aspects of resident care were maintained during the first year of the COVID-19 pandemic.

Functional neuronal circuits promote disease progression in cancer

The molecular and functional contributions of intratumoral nerves to disease remain largely unknown. We localized synaptic markers within tumors suggesting that these nerves form functional connections. Consistent with this, electrophysiological analysis shows that malignancies harbor significantly higher electrical activity than benign disease or normal tissues. We also demonstrate pharmacologic silencing of tumoral electrical activity. Tumors implanted in transgenic animals lacking nociceptor neurons show reduced electrical activity. These data suggest that intratumoral nerves remain functional at the tumor bed. Immunohistochemical staining demonstrates the presence of the neuropeptide, Substance P (SP), within the tumor space. We show that tumor cells express the SP receptor, NK1R, and that ligand/receptor engagement promotes cellular proliferation and migration. Our findings identify a mechanism whereby intratumoral nerves promote cancer progression.

The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations

BACKGROUND

Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an "ecological scaffold". We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or "scaffold" the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection.

RESULTS

Using computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the "ecological scaffold" onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists.

CONCLUSIONS

The fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient "oligotrophic" environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.

The Unintended Consequences of Information Provision: The World Health Organization and Border Restrictions during COVID-19

Why do some international agreements fail to achieve their goals? Rather than states' engaging in cheap talk, evasion, or shallow commitments, the World Health Organization's (WHO) International Health Regulations (IHR)-the agreement governing states' and WHO's response to global health emergencies-point to the unintended consequences of information provision. The IHR have a dual goal of providing public health protection from health threats while minimizing unnecessary interference in international traffic. As such, during major outbreaks WHO provides information about spread and severity, as well as guidance about how states should respond, primarily regarding border policies. During COVID-19, border restrictions such as entry restrictions, flight suspensions, and border closures have been commonplace even though WHO recommended against such policies when it declared the outbreak a public health emergency in January 2020. Building on findings from the 2014 Ebola outbreak, we argue that without raising the cost of disregarding (or the benefits of following) recommendations against border restrictions, information from WHO about outbreak spread and severity leads states to impose border restrictions inconsistent with WHO's guidance. Using new data from COVID-19, we show that WHO's public health emergency declaration and pandemic announcement are associated with increases in the number of states imposing border restrictions.

Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver

Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (i) coexpression network analyses focusing on correlations between genes and (ii) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: A slight change of parameterization or dataset could lead to marked alterations of outcomes. Here, we propose Stabilized COre gene and Pathway Election (SCOPE), a tool integrating bootstrapped least absolute shrinkage and selection operator and coexpression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD, and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations toward complex interactions using transcriptome data.

Ultrafast response of spontaneous photovoltaic effect in 3R-MoS2-based heterostructures

Rhombohedrally stacked MoS₂ has been shown to exhibit spontaneous polarization down to the bilayer limit and can sustain a strong depolarization field when sandwiched between graphene. Such a field gives rise to a spontaneous photovoltaic effect without needing any p-n junction. In this work, we show that the photovoltaic effect has an external quantum efficiency of 10% for devices with only two atomic layers of MoS₂ at low temperatures, and identify a picosecond-fast photocurrent response, which translates to an intrinsic device bandwidth at ∼100-GHz level. To this end, we have developed a nondegenerate pump-probe photocurrent spectroscopy technique to deconvolute the thermal and charge-transfer processes, thus successfully revealing the multicomponent nature of the photocurrent dynamics. The fast component approaches the limit of the charge-transfer speed at the graphene-MoS₂ interface. The remarkable efficiency and ultrafast photoresponse in the graphene-3R-MoS₂ devices support the use of ferroelectric van der Waals materials for future high-performance optoelectronic applications.

Loading and Release of Quercetin from Contact-Drawn Polyvinyl Alcohol Fiber Scaffolds

Polymeric drug releasing systems have numerous applications for the treatment of chronic diseases and traumatic injuries. In this study, a simple, cost-effective, and scalable method for dry spinning of crosslinked polyvinyl alcohol (PVA) fibers is presented. This method utilizes an entangled solution of PVA to form liquid bridges that are drawn into rapidly drying fibers through extensional flow. The fibers are crosslinked by a one-pot reaction in which glyoxal is introduced to the PVA solution prior to contact drawing. Failure analysis of fiber formation is used to understand the interplay of polymer concentration, glyoxal concentration, and crosslinking time to identify appropriate formulations for the production of glyoxal-crosslinked PVA fibers. The small molecule quercetin (an anti-inflammatory plant flavonoid) can be added to the one-pot reaction and is shown to be incorporated into the fibers in a concentration-dependent manner. Upon rehydration in an aqueous medium, the glyoxal-crosslinked PVA fiber scaffolds retain their morphology and slowly degrade, as measured over the course of 10 days. As the scaffolds degrade, they release the loaded quercetin, reaching a cumulative release of 56 ± 6% of the loaded drug after 10 days. The bioactivity of the released quercetin is verified by combining quercetin-loaded fibers with contact-drawn polyethylene oxide-type I collagen (PEO-Col) fibers and monitoring the growth of PC12 cells on the fibers. PC12 cells readily attach to the PEO-Col fibers and display increased nerve growth factor-induced elongation and neurite formation in the presence of quercetin-loaded PVA fibers relative to substrates formed from only PEO-Col fibers or PEO-Col and PVA fibers without quercetin.

Widespread formation of toxic nitrated bisphenols indoors by heterogeneous reactions with HONO

With numerous structurally diverse indoor contaminants, indoor transformation chemistry has been largely unexplored. Here, by integrating protein affinity purification and nontargeted mass spectrometry analysis (PUCA), we identified a substantial class of previously unrecognized indoor transformation products formed through gas-surface reactions with nitrous acid (HONO). Through the PUCA, we identified a noncommercial compound, nitrated bisphenol A (BPA), from house dust extracts strongly binding to estrogen-related receptor γ. The compound was detected in 28 of 31 house dust samples with comparable concentrations (ND to 0.30 μg/g) to BPA. Via exposing gaseous HONO to surface-bound BPA, we demonstrated it likely forms via a heterogeneous indoor chemical transformation that is highly selective toward bisphenols with electron-rich aromatic rings. We used 15N-nitrite for in situ labeling and found 110 nitration products formed from indoor contaminants with distinct aromatic moieties. This study demonstrates a previously unidentified class of chemical reactions involving indoor HONO, which should be incorporated into the risk evaluation of indoor contaminants, particularly bisphenols.

The ER protein Creld regulates ER-mitochondria contact dynamics and respiratory complex 1 activity

Dynamic contacts are formed between endoplasmic reticulum (ER) and mitochondria that enable the exchange of calcium and phospholipids. Disturbed contacts between ER and mitochondria impair mitochondrial dynamics and are a molecular hallmark of Parkinson's disease, which is also characterized by impaired complex I activity and dopaminergic neuron degeneration. Here, we analyzed the role of cysteine-rich with EGF-like domain (Creld), a poorly characterized risk gene for Parkinson's disease, in the regulation of mitochondrial dynamics and function. We found that loss of Creld leads to mitochondrial hyperfusion and reduced ROS signaling in Drosophila melanogaster, Xenopus tropicalis, and human cells. Creld fly mutants show differences in ER-mitochondria contacts and reduced respiratory complex I activity. The resulting low-hydrogen peroxide levels are linked to disturbed neuronal activity and lead to impaired locomotion, but not neurodegeneration, in Creld mutants. We conclude that Creld regulates ER-mitochondria communication and thereby hydrogen peroxide formation, which is required for normal neuron function.

On-Site Viral Inactivation and RNA Preservation of Gargle and Saliva Samples Combined with Direct Analysis of SARS-CoV-2 RNA on Magnetic Beads

Samples of nasopharyngeal swabs (NPS) are commonly used for the detection of SARS-CoV-2 and diagnosis of COVID-19. As an alternative, self-collection of saliva and gargle samples minimizes transmission to healthcare workers and relieves the pressure of resources and healthcare personnel during the pandemic. This study aimed to develop an enhanced method enabling simultaneous viral inactivation and RNA preservation during on-site self-collection of saliva and gargle samples. Our method involves the addition of saliva or gargle samples to a newly formulated viral inactivation and RNA preservation (VIP) buffer, concentration of the viral RNA on magnetic beads, and detection of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction directly from the magnetic beads. This method has a limit of detection of 25 RNA copies per 200 μL of gargle or saliva sample and 9-111 times higher sensitivity than the viral RNA preparation kit recommended by the United States Centers for Disease Control and Prevention. The integrated method was successfully used to analyze more than 200 gargle and saliva samples, including the detection of SARS-CoV-2 in 123 gargle and saliva samples collected daily from two NPS-confirmed positive SARS-CoV-2 patients throughout the course of their infection and recovery. The VIP buffer is stable at room temperature for at least 6 months. SARS-CoV-2 RNA (65 copies/200 μL sample) is stable in the VIP buffer at room temperature for at least 3 weeks. The on-site inactivation of SARS-CoV-2 and preservation of the viral RNA enables self-collection of samples, reduces risks associated with SARS-CoV-2 transmission, and maintains the stability of the target analyte.

Drug Delivery Systems in the Development of Novel Strategies for Glioblastoma Treatment

Glioblastoma multiforme (GBM) is a grade IV glioma considered the most fatal cancer of the central nervous system (CNS), with less than a 5% survival rate after five years. The tumor heterogeneity, the high infiltrative behavior of its cells, and the blood-brain barrier (BBB) that limits the access of therapeutic drugs to the brain are the main reasons hampering the current standard treatment efficiency. Following the tumor resection, the infiltrative remaining GBM cells, which are resistant to chemotherapy and radiotherapy, can further invade the surrounding brain parenchyma. Consequently, the development of new strategies to treat parenchyma-infiltrating GBM cells, such as vaccines, nanotherapies, and tumor cells traps including drug delivery systems, is required. For example, the chemoattractant CXCL12, by binding to its CXCR4 receptor, activates signaling pathways that play a critical role in tumor progression and invasion, making it an interesting therapeutic target to properly control the direction of GBM cell migration for treatment proposes. Moreover, the interstitial fluid flow (IFF) is also implicated in increasing the GBM cell migration through the activation of the CXCL12-CXCR4 signaling pathway. However, due to its complex and variable nature, the influence of the IFF on the efficiency of drug delivery systems is not well understood yet. Therefore, this review discusses novel drug delivery strategies to overcome the GBM treatment limitations, focusing on chemokines such as CXCL12 as an innovative approach to reverse the migration of infiltrated GBM. Furthermore, recent developments regarding in vitro 3D culture systems aiming to mimic the dynamic peritumoral environment for the optimization of new drug delivery technologies are highlighted.

Microbial Consortium Associated with Crustacean Shells Composting

Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and fungal genera including bacteria Flavobacterium, Clostridium, Pseudomonas, and Sanguibacter and fungi Mortierella, Mycochlamys, and Talaromyces were increased with approximation to the shell surface. Association with the shell triggered significant changes in microbial cooperation that incorporate microorganisms that were previously reported to be involved in chitin degradation as well as ones with no reported chitinolytic activity. Our study indicates that the biodegradation of crab shells in soil incorporates a consortium of microorganisms that might provide a more efficient way for bioconversion.

Predicting hospitalisations related to ambulatory care sensitive conditions with machine learning for population health planning: derivation and validation cohort study

OBJECTIVE

To predict older adults' risk of avoidable hospitalisation related to ambulatory care sensitive conditions (ACSC) using machine learning applied to administrative health data of Ontario, Canada.

DESIGN, SETTING AND PARTICIPANTS

A retrospective cohort study was conducted on a large cohort of all residents covered under a single-payer system in Ontario, Canada over the period of 10 years (2008-2017). The study included 1.85 million Ontario residents between 65 and 74 years old at any time throughout the study period.

DATA SOURCES

Administrative health data from Ontario, Canada obtained from the (ICES formely known as the Institute for Clinical Evaluative Sciences Data Repository.

MAIN OUTCOME MEASURES

Risk of hospitalisations due to ACSCs 1 year after the observation period.

RESULTS

The study used a total of 1 854 116 patients, split into train, validation and test sets. The ACSC incidence rates among the data points were 1.1% for all sets. The final XGBoost model achieved an area under the receiver operating curve of 80.5% and an area under precision-recall curve of 0.093 on the test set, and the predictions were well calibrated, including in key subgroups. When ranking the model predictions, those at the top 5% of risk as predicted by the model captured 37.4% of those presented with an ACSC-related hospitalisation. A variety of features such as the previous number of ambulatory care visits, presence of ACSC-related hospitalisations during the observation window, age, rural residence and prescription of certain medications were contributors to the prediction. Our model was also able to capture the geospatial heterogeneity of ACSC risk in Ontario, and especially the elevated risk in rural and marginalised regions.

CONCLUSIONS

This study aimed to predict the 1-year risk of hospitalisation from ambulatory-care sensitive conditions in seniors aged 65-74 years old with a single, large-scale machine learning model. The model shows the potential to inform population health planning and interventions to reduce the burden of ACSC-related hospitalisations.

The cell biology of fertilization: Gamete attachment and fusion

Fertilization is defined as the union of two gametes. During fertilization, sperm and egg fuse to form a diploid zygote to initiate prenatal development. In mammals, fertilization involves multiple ordered steps, including the acrosome reaction, zona pellucida penetration, sperm-egg attachment, and membrane fusion. Given the success of in vitro fertilization, one would think that the mechanisms of fertilization are understood; however, the precise details for many of the steps in fertilization remain a mystery. Recent studies using genetic knockout mouse models and structural biology are providing valuable insight into the molecular basis of sperm-egg attachment and fusion. Here, we review the cell biology of fertilization, specifically summarizing data from recent structural and functional studies that provide insights into the interactions involved in human gamete attachment and fusion.

Quantification of fast molecular adhesion by fluorescence footprinting

Rolling adhesion is a unique process in which the adhesion events are short-lived and operate under highly nonequilibrium conditions. These characteristics pose a challenge in molecular force quantification, where in situ measurement of these forces cannot be achieved with molecular force sensors that probe near equilibrium. Here, we demonstrated a quantitative adhesion footprint assay combining DNA-based nonequilibrium force probes and modeling to measure the molecular force involved in fast rolling adhesion. We were able to directly profile the ensemble molecular force distribution in our system during rolling adhesion with a dynamic range between 0 and 18 pN. Our results showed that the shear stress driving bead rolling motility directly controls the molecular tension on the probe-conjugated adhesion complex. Furthermore, the shear stress can steer the dissociation bias of components within the molecular force probe complex, favoring either DNA probe dissociation or receptor-ligand dissociation.

Evidence of the effectiveness of travel-related measures during the early phase of the COVID-19 pandemic: a rapid systematic review

OBJECTIVE

To review the effectiveness of travel measures implemented during the early stages of the COVID-19 pandemic to inform changes on how evidence is incorporated in the International Health Regulations (2005) (IHR).

DESIGN

We used an abbreviated Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols to identify studies that investigated the effectiveness of travel-related measures preprinted or published by 1 June 2020.

RESULTS

We identified 29 studies, of which 26 were modelled. Thirteen studies investigated international measures, while 17 investigated domestic measures (one investigated both). There was a high level of agreement that the adoption of travel measures led to important changes in the dynamics of the early phases of the COVID-19 pandemic: the Wuhan measures reduced the number of cases exported internationally by 70%-80% and led to important reductions in transmission within Mainland China. Additional travel measures, including flight restrictions to and from China, may have led to additional reductions in the number of exported cases. Few studies investigated the effectiveness of measures implemented in other contexts. Early implementation was identified as a determinant of effectiveness. Most studies of international travel measures did not account for domestic travel measures thus likely leading to biased estimates.

CONCLUSION

Travel measures played an important role in shaping the early transmission dynamics of the COVID-19 pandemic. There is an urgent need to address important evidence gaps and also a need to review how evidence is incorporated in the IHR in the early phases of a novel infectious disease outbreak.

Power analysis of transcriptome-wide association study: Implications for practical protocol choice

The transcriptome-wide association study (TWAS) has emerged as one of several promising techniques for integrating multi-scale 'omics' data into traditional genome-wide association studies (GWAS). Unlike GWAS, which associates phenotypic variance directly with genetic variants, TWAS uses a reference dataset to train a predictive model for gene expressions, which allows it to associate phenotype with variants through the mediating effect of expressions. Although effective, this core innovation of TWAS is poorly understood, since the predictive accuracy of the genotype-expression model is generally low and further bounded by expression heritability. This raises the question: to what degree does the accuracy of the expression model affect the power of TWAS? Furthermore, would replacing predictions with actual, experimentally determined expressions improve power? To answer these questions, we compared the power of GWAS, TWAS, and a hypothetical protocol utilizing real expression data. We derived non-centrality parameters (NCPs) for linear mixed models (LMMs) to enable closed-form calculations of statistical power that do not rely on specific protocol implementations. We examined two representative scenarios: causality (genotype contributes to phenotype through expression) and pleiotropy (genotype contributes directly to both phenotype and expression), and also tested the effects of various properties including expression heritability. Our analysis reveals two main outcomes: (1) Under pleiotropy, the use of predicted expressions in TWAS is superior to actual expressions. This explains why TWAS can function with weak expression models, and shows that TWAS remains relevant even when real expressions are available. (2) GWAS outperforms TWAS when expression heritability is below a threshold of 0.04 under causality, or 0.06 under pleiotropy. Analysis of existing publications suggests that TWAS has been misapplied in place of GWAS, in situations where expression heritability is low.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.

The role of TDP-43 mislocalization in amyotrophic lateral sclerosis

Since its discovery as a primary component in cytoplasmic aggregates in post-mortem tissue of patients with Amyotrophic Lateral Sclerosis (ALS), TAR DNA Binding Protein 43 kDa (TDP-43) has remained a central focus to understand the disease. TDP-43 links both familial and sporadic forms of ALS as mutations are causative for disease and cytoplasmic aggregates are a hallmark of nearly all cases, regardless of TDP-43 mutational status. Research has focused on the formation and consequences of cytosolic protein aggregates as drivers of ALS pathology through both gain- and loss-of-function mechanisms. Not only does aggregation sequester the normal function of TDP-43, but these aggregates also actively block normal cellular processes inevitably leading to cellular demise in a short time span. Although there may be some benefit to therapeutically targeting TDP-43 aggregation, this step may be too late in disease development to have substantial therapeutic benefit. However, TDP-43 pathology appears to be tightly linked with its mislocalization from the nucleus to the cytoplasm, making it difficult to decouple the consequences of nuclear-to-cytoplasmic mislocalization from protein aggregation. Studies focusing on the effects of TDP-43 mislocalization have demonstrated both gain- and loss-of-function consequences including altered splicing regulation, over responsiveness to cellular stressors, increases in DNA damage, and transcriptome-wide changes. Additionally, mutations in TARDBP confer a baseline increase in cytoplasmic TDP-43 thus suggesting that small changes in the subcellular localization of TDP-43 could in fact drive early pathology. In this review, we bring forth the theme of protein mislocalization as a key mechanism underlying ALS, by highlighting the importance of maintaining subcellular proteostasis along with the gain- and loss-of-functional consequences when TDP-43 localization is dysregulated. Additional research, focusing on early events in TDP-43 pathogenesis (i.e. to the protein mislocalization stage) will provide insight into disease mechanisms, therapeutic targets, and novel biomarkers for ALS.