i-Motif DNA: identification, formation, and cellular functions.

An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.

Topoisomerase 3α Is Required for Decatenation and Segregation of Human mtDNA.

How mtDNA replication is terminated and the newly formed genomes are separated remain unknown. We here demonstrate that the mitochondrial isoform of topoisomerase 3α (Top3α) fulfills this function, acting independently of its nuclear role as a component of the Holliday junction-resolving BLM-Top3α-RMI1-RMI2 (BTR) complex. Our data indicate that mtDNA replication termination occurs via a hemicatenane formed at the origin of H-strand replication and that Top3α is essential for resolving this structure. Decatenation is a prerequisite for separation of the segregating unit of mtDNA, the nucleoid, within the mitochondrial network. The importance of this process is highlighted in a patient with mitochondrial disease caused by biallelic pathogenic variants in TOP3A, characterized by muscle-restricted mtDNA deletions and chronic progressive external ophthalmoplegia (CPEO) plus syndrome. Our work establishes Top3α as an essential component of the mtDNA replication machinery and as the first component of the mtDNA separation machinery.

Normal table of embryonic development in the Anji salamander Hynobius amjiensis (Hynobiidae).

We established a normal embryonic development table for the Anji salamander Hynobius amjiensis, a critically endangered tailed amphibian of the family Hynobiidae with a very limited distribution in East China, following the standards set by the early developmental table of vertebrates. Put together 32 embryonic stages for the Anji salamander was defined. The total embryonic period from oviposition to hatching is approximately 30 days at 9 °C. Stages 1-16 represent early development from cleavage to neurulation. Stages 17-32 represent organogenesis documenting later developmental events such as tail, gill, and limb formation, and hatching (Stage 32). We provided a detailed description of the external morphology and color changes of the head, trunk, limbs, tail, external gills, and balancers at various stages from egg-laying to hatching. We also described several cases of abnormal embryonic development. The establishment of the embryonic development table in H. amjiensis contributes to better understanding of the ontogeny in tailed amphibians, distinguishing closely related species, and identifying abnormal embryonic amphibians.

Distinct roles of the major binding residues in the cation-binding pocket of the melibiose transporter MelB.

Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the major facilitator superfamily (MFS) transporters, which play important roles in human health and diseases. MelBSt catalyzed the symport of galactosides with Na+, Li+, or H+ but prefers the coupling with Na+. Previously, we determined the structures of the inward- and outward-facing conformation of MelBSt and the molecular recognition for galactoside and Na+. However, the molecular mechanisms for H+- and Na+-coupled symport remain poorly understood. In this study, we solved two x-ray crystal structures of MelBSt, the cation-binding site mutants D59C at an unliganded apo-state and D55C at a ligand-bound state, and both structures display the outward-facing conformations virtually identical as published. We determined the energetic contributions of three major Na+-binding residues for the selection of Na+ and H+ by free energy simulations. Transport assays showed that the D55C mutant converted MelBSt to a solely H+-coupled symporter, and together with the free-energy perturbation calculation, Asp59 is affirmed to be the sole protonation site of MelBSt. Unexpectedly, the H+-coupled melibiose transport exhibited poor activities at greater bulky ΔpH and better activities at reversal ΔpH, supporting the novel theory of transmembrane-electrostatically localized protons and the associated membrane potential as the primary driving force for the H+-coupled symport mediated by MelBSt. This integrated study of crystal structure, bioenergetics, and free energy simulations, demonstrated the distinct roles of the major binding residues in the cation-binding pocket of MelBSt.

Multiple imputation of more than one environmental exposure with nondifferential measurement error.

Measurement error is common in environmental epidemiologic studies, but methods for correcting measurement error in regression models with multiple environmental exposures as covariates have not been well investigated. We consider a multiple imputation approach, combining external or internal calibration samples that contain information on both true and error-prone exposures with the main study data of multiple exposures measured with error. We propose a constrained chained equations multiple imputation (CEMI) algorithm that places constraints on the imputation model parameters in the chained equations imputation based on the assumptions of strong nondifferential measurement error. We also extend the constrained CEMI method to accommodate nondetects in the error-prone exposures in the main study data. We estimate the variance of the regression coefficients using the bootstrap with two imputations of each bootstrapped sample. The constrained CEMI method is shown by simulations to outperform existing methods, namely the method that ignores measurement error, classical calibration, and regression prediction, yielding estimated regression coefficients with smaller bias and confidence intervals with coverage close to the nominal level. We apply the proposed method to the Neighborhood Asthma and Allergy Study to investigate the associations between the concentrations of multiple indoor allergens and the fractional exhaled nitric oxide level among asthmatic children in New York City. The constrained CEMI method can be implemented by imposing constraints on the imputation matrix using the mice and bootImpute packages in R.

IK-DDI: a novel framework based on instance position embedding and key external text for DDI extraction.

Determining drug-drug interactions (DDIs) is an important part of pharmacovigilance and has a vital impact on public health. Compared with drug trials, obtaining DDI information from scientific articles is a faster and lower cost but still a highly credible approach. However, current DDI text extraction methods consider the instances generated from articles to be independent and ignore the potential connections between different instances in the same article or sentence. Effective use of external text data could improve prediction accuracy, but existing methods cannot extract key information from external data accurately and reasonably, resulting in low utilization of external data. In this study, we propose a DDI extraction framework, instance position embedding and key external text for DDI (IK-DDI), which adopts instance position embedding and key external text to extract DDI information. The proposed framework integrates the article-level and sentence-level position information of the instances into the model to strengthen the connections between instances generated from the same article or sentence. Moreover, we introduce a comprehensive similarity-matching method that uses string and word sense similarity to improve the matching accuracy between the target drug and external text. Furthermore, the key sentence search method is used to obtain key information from external data. Therefore, IK-DDI can make full use of the connection between instances and the information contained in external text data to improve the efficiency of DDI extraction. Experimental results show that IK-DDI outperforms existing methods on both macro-averaged and micro-averaged metrics, which suggests our method provides complete framework that can be used to extract relationships between biomedical entities and process external text data.

Structural insight and characterization of human Twinkle helicase in mitochondrial disease.

Twinkle is the mammalian helicase vital for replication and integrity of mitochondrial DNA. Over 90 Twinkle helicase disease variants have been linked to progressive external ophthalmoplegia and ataxia neuropathies among other mitochondrial diseases. Despite the biological and clinical importance, Twinkle represents the only remaining component of the human minimal mitochondrial replisome that has yet to be structurally characterized. Here, we present 3-dimensional structures of human Twinkle W315L. Employing cryo-electron microscopy (cryo-EM), we characterize the oligomeric assemblies of human full-length Twinkle W315L, define its multimeric interface, and map clinical variants associated with Twinkle in inherited mitochondrial disease. Cryo-EM, crosslinking-mass spectrometry, and molecular dynamics simulations provide insight into the dynamic movement and molecular consequences of the W315L clinical variant. Collectively, this ensemble of structures outlines a framework for studying Twinkle function in mitochondrial DNA replication and associated disease states.

High-Efficiency and Stable Colloidal One-Dimensional Core/Shell Nanorod Light-Emitting Diodes.

Anisotropic nanocrystals such as nanorods (NRs) display unique linearly polarized emission, which is expected to break the external quantum efficiency (EQE) limit of quantum dot-based light-emitting diodes (LEDs). However, the progress in achieving a higher EQE using NRs encounters several challenges, primarily involving a low photoluminescence quantum yield (PLQY) of NRs and imbalanced charge injection in NR-LEDs. In this work, we investigated NR-LEDs based on CdSe/CdZnS/ZnS rod-in-rod NRs with a high PLQY and higher linear polarization compared to those of dot-in-rod NRs. The balanced charge injection is achieved using ZnMgO nanoparticles as the electron transport layer and poly-TPD {poly[N,N'-bis(4-butylphenyl)-N,N'-bis(phenyl)benzidine]} as the hole transport layer. Therefore, the NR-LEDs exhibit a maximum EQE of 21.5% and a maximum luminance of >120 000 cd/m2 owing to the high level of in-plane transitions with a dipole moment of 90%. The NR-LEDs also have greatly inhibited droop in EQE under a high current density as well as outstanding operation lifetime and cycle stability.

Electronic and Transport Properties of InSe/PtTe2 van der Waals Heterostructure.

Two-dimensional (2D) InSe and PtTe2 have drawn extensive attention due to their intriguing properties. However, the InSe monolayer is an indirect bandgap semiconductor with a low hole mobility. van der Waals (vdW) heterostructures produce interesting electronic and optoelectronic properties beyond the existing 2D materials and endow totally new device functions. Herein, we theoretically investigated the electronic structures, transport behaviors, and electric field tuning effects of the InSe/PtTe2 vdW heterostructures. The calculated results show that the direct bandgap type-II vdW heterostructures can be realized by regulating the stacking configurations of heterostructures. By applying an external electric field, the band alignment and bandgap of the heterostructures can also be flexibly modulated. Particularly, the hole mobility of the heterostructures is improved by 2 orders of magnitude to ∼103 cm2 V-1 s-1, which overcomes the intrinsic disadvantage of the InSe monolayer. The InSe/PtTe2 vdW heterostructures have great potential applications in developing novel optoelectronic devices.

Efficient Carrier Multiplication in Self-Powered Near-Ultraviolet γ-InSe/Graphene Heterostructure Photodetector with External Quantum Efficiency Exceeding 161.

Carrier multiplication (CM) in semiconductors, the process of absorbing a single high-energy photon to form two or more electron-hole pairs, offers great potential for the high-response detection of high-energy photons in the ultraviolet spectrum. However, compared to two-dimensional semiconductors, conventional bulk semiconductors not only face integration and flexibility bottlenecks but also exhibit inferior CM performance. To attain efficient CM for ultraviolet detection, we designed a two-terminal photodetector featuring a unilateral Schottky junction based on a two-dimensional γ-InSe/graphene heterostructure. Benefiting from a strong built-in electric field, the photogenerated high-energy electrons in γ-InSe, an ideal ultraviolet light-absorbing layer, can efficiently transfer to graphene without cooling. It results in efficient CM within the graphene, yielding an ultrahigh responsivity of 468 mA/W and a record-high external quantum efficiency of 161.2% when it is exposed to 360 nm light at zero bias. This work provides valuable insights into developing next-generation ultraviolet photodetectors with high performance and low-power consumption.

Precursor Engineering Induced High-Efficiency Electroluminescence of Quasi-Two-Dimensional Perovskites: A Synergistic Defect Inhibition and Passivation Approach.

Despite light-emitting diodes (LEDs) based on quasi-two-dimensional (Q-2D) perovskites being inexpensive and exhibiting high performance, defects still limit the improvement of electroluminescence efficiency and stability by causing nonradiative recombination. Here, an organic molecule, 1-(o-tolyl) biguanide, is used to simultaneously inhibit and passivate defects of Q-2D perovskites via in situ synchronous crystallization. This molecule not only prevents surface bromine vacancies from forming through hydrogen bonding with the bromine of intermediaries but also passivates surface defects through its interaction with uncoordinated Pb. Via combination of defect inhibition and passivation, the trap density of Q-2D perovskite films can be significantly reduced, and the emission efficiency of the film can be improved. Consequently, the corresponding LED shows an external quantum efficiency of 24.3%, and its operational stability has been increased nearly 15 times.

Embryonic development of the neotropical pit viper Bothrops atrox (Serpentes: Viperidae: Crotalinae), with emphasis on pit organ morphogenesis and its evolution in snakes.

BACKGROUND: Bothrops atrox is a pit viper with a loreal pit organ, and its embryological development remains undescribed. Here, we provide a comprehensive description of the embryology of B. atrox, focusing on the loreal pit organ and cephalic scales. RESULTS: We characterized 13 developmental stages of B. atrox based on external features consistent with the embryogenesis of previously described snake species. The loreal pit organ originates from the circumorbital region and migrates to its final position. In Crotalinae, the pit organ first becomes visible at stage 28, whereas in Pythonidae labial, pit organs appear at Stage 35. Pit organs evolved independently three times in Serpentes, encompassing Boidae, Pythonidae, and Crotalinae. Boidae lacks embryological information for pit organs. Furthermore, we observed that head scalation onset occurs at Stage 33 in B. atrox, with fusion of scales surrounding the loreal pit organ. CONCLUSIONS: The embryology of pit organs in Pythonidae and Boidae species remains poorly understood. Our detailed embryological descriptions are critical for proposing developmental scenarios for pit organs and guiding future research on these structures.

The European Organisation of External Quality Assurance Providers in Laboratory Medicine (EQALM) Statement: guidelines for publishing about interlaboratory comparison studies (PubILC).

Data and results from interlaboratory comparison (ILC) studies, external quality assessment (EQA) and proficiency testing (PT) activities are important and valuable contributions both to the further development of all disciplines of medical laboratory diagnostics, and to the evaluation and comparison of in vitro diagnostic assays. So far, however, there are no recommendations as to which essential items should be addressed in publications on interlaboratory comparisons. The European Organization of External Quality Assurance Providers in Laboratory Medicine (EQALM) recognized the need for such recommendations, and these were developed by a group of experts. The result of this endeavor is the EQALM Statement on items recommended to be addressed in publications on interlaboratory comparison activities (PubILC), in conjunction with a user-friendly checklist. Once adopted by authors and journals, the EQALM Statement will ensure essential information and/or study-related facts are included within publications on EQA/PT activities.

Comparison of unitary synaptic currents generated by indirect and direct pathway neurons of the mouse striatum.

Two subtypes of striatal spiny projection neurons, iSPNs and dSPNs, whose axons form the "indirect" and "direct" pathways of the basal ganglia, respectively, both make synaptic connections in the external globus pallidus (GPe) but are usually found to have different effects on behavior. Activation of the terminal fields of iSPNs or dSPNs generated compound currents in almost all GPe neurons. To determine whether iSPNs and dSPNs have the same or different effects on pallidal neurons, we studied the unitary synaptic currents generated in GPe neurons by action potentials in single striatal neurons. We used optogenetic excitation to elicit repetitive firing in a small number of nearby SPNs, producing sparse barrages of inhibitory postsynaptic currents (IPSCs) in GPe neurons. From these barrages, we isolated sequences of IPSCs with similar time courses and amplitudes, which presumably arose from the same SPN. There was no difference between the amplitudes of unitary IPSCs generated by the indirect and direct pathways. Most unitary IPSCs were small, but a subset from each pathway were much larger. To determine the effects of these unitary synaptic currents on the action potential firing of GPe neurons, we drove SPNs to fire as before and recorded the membrane potential of GPe neurons. Large unitary potentials from iSPNs and dSPNs perturbed the spike timing of GPe neurons in a similar way. Most SPN-GPe neuron pairs are weakly connected, but a subset of pairs in both pathways are strongly connected.NEW & NOTEWORTHY This is the first study to record the synaptic currents generated by single identified direct or indirect pathway striatal neurons on single pallidal neurons. Each GPe neuron receives synaptic inputs from both pathways. Most striatal neurons generate small synaptic currents that become influential when occurring together, but a few are powerful enough to be individually influential.

External segment of the globus pallidus in health and disease: Its interactions with the striatum and subthalamic nucleus.

The external segment of the globus pallidus (GPe) has long been considered a homogeneous structure that receives inputs from the striatum and sends processed information to the subthalamic nucleus, composing a relay nucleus of the indirect pathway that contributes to movement suppression. Recent methodological revolution in rodents led to the identification of two distinct cell types in the GPe with different fiber connections. The GPe may be regarded as a dynamic, complex and influential center within the basal ganglia circuitry, rather than a simple relay nucleus. On the other hand, many studies have so far been performed in monkeys to clarify the functions of the basal ganglia in the healthy and diseased states, but have not paid much attention to such classification and functional differences of GPe neurons. In this minireview, we consider the knowledge on the rodent GPe and discuss its impact on the understanding of the basal ganglia circuitry in monkeys.

Heterogeneous effects of increased availability of alcohol on hospitalisation due to external causes. Quasi-experimental evidence from the introduction of Saturday opening at Swedish alcohol retail stores.

Responses to increased alcohol availability may vary across the population as a function of differential vulnerability. This study therefore aimed to examine the effects of the implementation of Saturday opening at the Swedish alcohol retail monopoly in 2000 on risks of hospitalisation due to external causes (HEC) among different population subgroups. Leveraging the experimental design of the reform, longitudinal difference-in-differences analyses were applied to a register-based cohort of individuals aged 20-40 at the time of implementation. The population was stratified into groups of Swedish, Finnish, and Middle Eastern origin, known to represent different levels of alcohol consumption and rates of alcohol-related morbidity. Results showed a 17.7% increase (p<0.029) in the risk of HEC among individuals of Finnish origin, as jointly caused by both increased prevalence in the experiment area and decreased prevalence in the control area. The increase was primarily driven by younger men with lower levels of education. Those of Swedish origin exhibited largely similar patterns (9.7% increase; p<0.001) while no measurable impact was observed among individuals of Middle Eastern origin (-21.4% decrease; p<0.076). The findings confirm that increasing alcohol availability contributes to the disease burden related to alcohol among population subgroups already susceptible to its effects.

Variable Selection When Estimating Effects in External Target Populations.

External validity is an important part of epidemiologic research. To validly estimate effects in specific external target populations using a chosen effect measure (i.e., "transport"), some methods require that one account for all effect measure modifiers [EMMs]. However, little is known about how including other variables that are not EMMs (i.e., non-EMMs) in adjustment sets impacts estimates. Using simulations, we evaluated how inclusion of non-EMMs affected estimation of the transported risk difference (RD) by assessing impacts of covariates that A) differ (or not) between the trial and the target, B) are associated with the outcome (or not), and C) modify the RD (or not). We assessed variation and bias when covariates with each possible combination of these factors were used to transport RDs using outcome modeling or inverse odds weighting. Including variables that differed in distribution between the populations but were non-EMMs reduced precision, regardless of whether they were associated with the outcome. However, non-EMMs associated with selection did not amplify bias resulting from omitting necessary EMMs. Including all variables associated with the outcome may result in unnecessarily imprecise estimates when estimating treatment effects in external target populations.

Standardizing to specific target populations in distributed networks and multisite pharmacoepidemiologic studies.

Distributed network studies and multisite studies assess drug safety and effectiveness in diverse populations by pooling information. Targeting groups of clinical or policy interest (including specific sites or site combinations) and applying weights based on effect measure modifiers (EMMs) prior to pooling estimates within multisite studies may increase interpretability and improve precision. We simulated a 4-site study, standardized each site using inverse odds weights (IOWs) to resemble the 3 smallest sites or the smallest site, estimated IOW-weighted risk differences (RDs), and combined estimates with inverse variance weights (IVWs). We also created an artificial distributed network in the Clinical Practice Research Datalink (CPRD) Aurum consisting of 1 site for each geographic region. We compared metformin and sulfonylurea initiators with respect to mortality, targeting the smallest region. In the simulation, IOWs reduced differences between estimates and increased precision when targeting the 3 smallest sites or the smallest site. In the CPRD Aurum study, the IOW + IVW estimate was also more precise (smallest region: RD = 5.41% [95% CI, 1.03-9.79]; IOW + IVW estimate: RD = 3.25% [95% CI, 3.07-3.43]). When performing pharmacoepidemiologic research in distributed networks or multisite studies in the presence of EMMs, designation of target populations has the potential to improve estimate precision and interpretability. This article is part of a Special Collection on Pharmacoepidemiology.

Statistical approaches for the integration of external controls in a cystic fibrosis clinical trial: a simulation and an application.

Development of new therapeutics for a rare disease such as cystic fibrosis (CF) is hindered by challenges in accruing enough patients for clinical trials. Using external controls from well-matched historical trials can reduce prospective trial sizes, and this approach has supported regulatory approval of new interventions for other rare diseases. We consider three statistical methods that incorporate external controls into a hypothetical clinical trial of a new treatment to reduce pulmonary exacerbations in CF patients: 1) inverse probability weighting, 2) Bayesian modeling with propensity score-based power priors, and 3) hierarchical Bayesian modeling with commensurate priors. We compare the methods via simulation study and in a real clinical trial data setting. Simulations showed that bias in the treatment effect was <4% using any of the methods, with type 1 error (or in the Bayesian cases, posterior probability of the null hypothesis) usually <5%. Inverse probability weighting was sensitive to similarity in prevalence of the covariates between historical and prospective trial populations. The commensurate prior method performed best with real clinical trial data. Using external controls to reduce trial size in future clinical trials holds promise and can advance the therapeutic pipeline for rare diseases.

Differences in real-world outcomes by risk classification for localized prostate cancer patients after radiation therapy.

BACKGROUND: Limited real-world evidence exists on the long-term clinical outcomes of patients with localized prostate cancer (LPC) who received external beam radiation therapy (EBRT) as the initial treatment. This study evaluated clinical outcomes of US patients with high-risk LPC (HR-LPC) and low/intermediate-risk LPC (LIR-LPC) who received EBRT. METHODS: This retrospective study using Surveillance, Epidemiology, and End Results-Medicare linked data from 2012 to 2019 included patients ≥ 65 years old who received EBRT as initial therapy. Baseline patient characteristics were summarized, metastasis-free survival (MFS), overall survival, and time to initiation of advanced prostate cancer treatment were compared using Kaplan-Meier (KM) and adjusted Cox proportional hazard (PH) models. 5-year survival probabilities stratified by race/ethnicity (non-Hispanic [NH] White, NH Black, NH Asian, and Hispanic) were assessed. RESULTS: Of 11,313 eligible patients, 41% (n = 4600) had HR-LPC and 59% (n = 6713) had LIR-LPC. Patient characteristics for both groups were comparable, with mean age at EBRT initiation > 70 years, 86% white, and mean follow-up time >40 months. More patients in the HR-LPC than LIR-LPC groups (78% vs 34%) had concurrent androgen deprivation therapy use and for a longer duration (median 10.4 months vs. 7.4 months). A higher proportion of HR-LPC patients developed metastasis, died, or received advanced prostate cancer treatment. Adjusted Cox PH survival analyses showed significantly (p < 0.0001) higher risk of mortality (hazard ratios [HR], 1.57 [1.38, 2.34]), metastasis or death (HR, 1.97 [1.78, 2.17]), and advanced prostate cancer therapy use (HR, 2.57 [2.11, 3.14]) for HR-LPC than LIR-LPC patients. Within 5 years after the initial EBRT treatment, 18%-26% of patients with HR-LPC are expected to have died or developed metastasis. The 5-year MFS rate in the HR-LPC group was lower than the LIR-LPC group across all racial/ethnic subgroups. NH Black patients with HR-LPC had the highest all-cause mortality rate and lowest rate of receiving advanced prostate cancer treatment, compared to other racial/ethnic subgroups. CONCLUSIONS: This real-world study of clinical outcomes in patients with LPC treated with EBRT suggests substantial disease burden in patients with HR-LPC and highlights the need for additional treatment strategies to improve clinical outcomes in patients with HR-LPC.