A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.

As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of structural variants (SVs) from long reads. Long reads enable detection of SVs that could not be previously detected from short-read sequencing, but computational methods must adapt to the unique challenges and opportunities presented by long-read sequencing. Here, we summarize over 50 long-read-based methods for SV detection, genotyping and visualization, and discuss how new telomere-to-telomere genome assemblies and pangenome efforts can improve the accuracy and drive the development of SV callers in the future.

Deep learning-driven adaptive optics for single-molecule localization microscopy.

The inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless adaptive optics methods rely on iterative mirror changes and image-quality metrics. However, these metrics result in inconsistent metric responses and thus fundamentally limit their efficacy for aberration correction in tissues. To bypass iterative trial-then-evaluate processes, we developed deep learning-driven adaptive optics for SMLM to allow direct inference of wavefront distortion and near real-time compensation. Our trained deep neural network monitors the individual emission patterns from single-molecule experiments, infers their shared wavefront distortion, feeds the estimates through a dynamic filter and drives a deformable mirror to compensate sample-induced aberrations. We demonstrated that our method simultaneously estimates and compensates 28 wavefront deformation shapes and improves the resolution and fidelity of three-dimensional SMLM through >130-µm-thick brain tissue specimens.

A map of cis-regulatory elements and 3D genome structures in zebrafish.

The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.

Calcium-mediated DAD in membrane potentials and triggered activity in atrial myocytes of ETV1f / fMyHCCre /+ mice.

The E-twenty-six variant 1 (ETV1)-dependent transcriptome plays an important role in atrial electrical and structural remodelling and the occurrence of atrial fibrillation (AF), but the underlying mechanism of ETV1 in AF is unclear. In this study, cardiomyocyte-specific ETV1 knockout (ETV1f/fMyHCCre/+, ETV1-CKO) mice were constructed to observe the susceptibility to AF and the underlying mechanism in AF associated with ETV1-CKO mice. AF susceptibility was examined by intraesophageal burst pacing, induction of AF was increased obviously in ETV1-CKO mice than WT mice. Electrophysiology experiments indicated shortened APD50 and APD90, increased incidence of DADs, decreased density of ICa,L in ETV1-CKO mice. There was no difference in VINACT,1/2 and VACT,1/2, but a significantly longer duration of the recovery time after inactivation in the ETV1-CKO mice. The recording of intracellular Ca2+ showed that there was significantly increased in the frequency of calcium spark, Ca2+ transient amplitude, and proportion of SCaEs in ETV1-CKO mice. Reduction of Cav1.2 rather than NCX1 and SERCA2a, increase RyR2, p-RyR2 and CaMKII was reflected in ETV1-CKO group. This study demonstrates that the increase in calcium spark and SCaEs corresponding to Ca2+ transient amplitude may trigger DAD in membrane potential in ETV1-CKO mice, thereby increasing the risk of AF.

Mycobacterium vaccae alleviates allergic airway inflammation and airway hyper-responsiveness in asthmatic mice by altering intestinal microbiota.

Host immunity can influence the composition of the gut microbiota and consequently affect disease progression. Previously, we reported that a Mycobacterium vaccae vaccine could ameliorate allergic inflammation in asthmatic mice by regulating inflammatory immune processes. Here, we investigated the anti-inflammatory effects of M. vaccae on allergic asthma via gut microbiota modulation. An ovalbumin (OVA)-induced asthmatic murine model was established and treated with M. vaccae. Gut microbiota profiles were determined in 18 BALB/c mice using 16S rDNA gene sequencing and metabolomic profiling was performed using liquid chromatography quadrupole time-of-flight mass spectrometry. Mycobacterium vaccae alleviated airway hyper-reactivity and inflammatory infiltration in mice with OVA-induced allergic asthma. The microbiota of asthmatic mice is disrupted and that this can be reversed with M. vaccae. Additionally, a total of 24 differential metabolites were screened, and the abundance of PI(14:1(9Z)/18:0), a glycerophospholipid, was found to be correlated with macrophage numbers (r = 0.52, p = 0.039). These metabolites may affect chemokine (such as macrophage chemoattractant protein-1) concentrations in the serum, and ultimately affect pulmonary macrophage recruitment. Our data demonstrated that M. vaccae might alleviate airway inflammation and hyper-responsiveness in asthmatic mice by reversing imbalances in gut microbiota. These novel mechanistic insights are expected to pave the way for novel asthma therapeutic strategies.

Disrupting circadian control of autophagy induces podocyte injury and proteinuria.

The circadian clock influences a wide range of biological process and controls numerous aspects of physiology to adapt to the daily environmental changes caused by Earth's rotation. The kidney clock plays an important role in maintaining tubular function, but its effect on podocytes remains unclear. Here, we found that podocytes expressed CLOCK proteins, and that 2666 glomerular gene transcripts (13.4%), including autophagy related genes, had 24-hour circadian rhythms. Deletion of Clock in podocytes resulted in 1666 gene transcripts with the loss of circadian rhythm including autophagy genes. Podocyte-specific Clock knockout mice at age three and eight months showed deficient autophagy, loss of podocytes and increased albuminuria. Chromatin immunoprecipitation (ChIP) sequence analysis indicated autophagy related genes were targets of CLOCK in podocytes. ChIP-PCR further confirmed Clock binding to the promoter regions of Becn1 and Atg12, two autophagy related genes. Furthermore, the association of CLOCK regulated autophagy with chronic sleep fragmentation and diabetic kidney disease was analyzed. Chronic sleep fragmentation resulted in the loss of glomerular Clock rhythm, inhibition of podocyte autophagy, and proteinuria. Rhythmic oscillations of Clock also disappeared in high glucose treated podocytes and in glomeruli from diabetic mice. Finally, circadian differences in podocyte autophagy were also abolished in diabetic mice. Deletion Clock in podocytes aggravated podocyte injury and proteinuria in diabetic mice. Thus, our findings demonstrate that clock-dependent regulation of autophagy may be essential for podocyte survival. Hence. loss of circadian controlled autophagy may play an important role in podocyte injury and proteinuria.

Global risk dynamics of Borrelia miyamotoi in the context of climate change.

The impact of Borrelia miyamotoi on human health, facilitated by the expanding geographical distribution and increasing population of Ixodes ticks, remains obscure in the context of global climate change. We employed multiple models to evaluate the effect of global climate change on the risk of B. miyamotoi worldwide across various scenarios. The habitat suitability index of four primary vector tick species for B. miyamotoi, including Ixodes persulcatus, Ixodes ricinus, Ixodes pacificus and Ixodes scapularis, was projected using a boosted regression tree model, considering multiple shared socio-economic pathway scenarios over various time periods. The modelling analysis reveals that, apart from I. scapularis, future global warming will result in a northward shift in the other three vector tick species and a gradual reduction in suitable habitats. Random forest models indicate consistent changes in B. miyamotoi and its primary tick species, with potential risk areas shrinking and shifting northward, particularly in the eastern USA, northeastern and northern Europe and northeast Asia. These findings highlight the urgent need for enhanced active surveillance of B. miyamotoi infection in primary vector tick species across projected potential risk areas. The effect of climate change on B. miyamotoi distribution might have significant implications for public health decision-making regarding tick-borne pathogens.

Epidemiological characteristics and antibody kinetics of elderly population with booster vaccination following both Omicron BA.5 and XBB waves in China.

After the termination of zero-COVID-19 policy, the populace in China has experienced both Omicron BA.5 and XBB waves. Considering the poor antibody responses and severe outcomes observed among the elderly following infection, we conducted a longitudinal investigation to examine the epidemiological characteristics and antibody kinetics among 107 boosted elderly participants following the Omicron BA.5 and XBB waves. We observed that 96 participants (89.7%) were infected with Omicron BA.5, while 59 (55.1%) participants were infected with Omicron XBB. Notably, 52 participants (48.6%) experienced dual infections of both Omicron BA.5 and XBB. The proportion of symptomatic cases appeared to decrease following the XBB wave (18.6%) compared to that after the BA.5 wave (59.3%). Omicron BA.5 breakthrough infection induced lower neutralizing antibody titers against XBB.1.5, BA.2.86, and JN.1, while reinfection with Omicron XBB broadened the antibody responses against all measured Omicron subvariants and may alleviate the wild type-vaccination induced immune imprinting. Boosted vaccination type and comorbidities were the significant factors associated with antibody responses. Updated vaccines based on emerging severe acute respiratory syndrome coronavirus 2 variants are needed to control the Coronavirus Disease 2019 pandemic in the elderly.

SARS-CoV-2 reinfection broadens the antibody responses and promotes the phenotypic differentiation of virus-specific memory T cells in adolescents.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants raises concerns regarding the effectiveness of immunity acquired from previous Omicron subvariants breakthrough infections (BTIs) or reinfections (RIs) against the current circulating Omicron subvariants. In this study, we prospectively investigate the dynamic changes of virus-specific antibody and T cell responses among 77 adolescents following Omicron BA.2.3 BTI with or without subsequent Omicron BA.5 RI. Notably, the neutralizing antibodies (NAbs) titers against various detected SARS-CoV-2 variants, especially the emerging Omicron CH.1.1, XBB.1.5, XBB.1.16, EG.5.1, and JN.1 subvariants, exhibited a significant decrease along the time. A lower level of IgG and NAbs titers post-BTI was found to be closely associated with subsequent RI. Elevated NAbs levels and shortened antigenic distances were observed following Omicron BA.5 RI. Robust T cell responses against both Omicron BA.2- and CH.1.1-spike peptides were observed at each point visited. The exposure to Omicron BA.5 promoted phenotypic differentiation of virus-specific memory T cells, even among the non-seroconversion adolescents. Therefore, updated vaccines are needed to provide effective protection against newly emerging SARS-CoV-2 variants among adolescents.

Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell-like blasts in KMT2A-rearranged leukemia.

KMT2A-rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single-cell multiomics analyses. We uncovered the following critical new insights: leukemia cells from patients <6 months have significantly increased lineage plasticity. Steroid response pathways are downregulated in the most immature blasts from younger patients. We identify a hematopoietic stem and progenitor-like (HSPC-like) population in the blood of younger patients that contains leukemic blasts and form an immunosuppressive signaling circuit with cytotoxic lymphocytes. These observations offer a compelling explanation for the ability of leukemias in young patients to evade chemotherapy and immune-mediated control. Our analysis also revealed preexisting lymphomyeloid primed progenitors and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in 2 patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank acute myeloid leukemia (AML). These findings provide critical insights into KMT2A-r ALL and have clinical implications for molecularly targeted and immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single-cell multiomics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.

Rotational angle and speed detection via a chip-scale GaN optoelectronic device.

In this paper, a new method for rotational angle and speed measurements is proposed by integrating a GaN optoelectronic chip with a stepped disc. The optoelectronic chip that integrates a light-emitting diode (LED) and a photodiode (PD) is fabricated by wafer-level microfabrication. The disc is designed with a spiral staircase shape, and has increasing thickness distribution along the circumferential direction. The sensing mechanism is that the optoelectronic chip measures angle-dependent intensity change of the light reflected off the stepped disc. Through a series of performance tests, the chip is highly sensitive to a continuous rotation from 0 ∘ to 360 ∘, and produces photocurrent to indicate the rotational angle and speed. A rotational speed up to 5000 rpm is measured with a relative error less than 1.27%. The developed sensing architecture provides an alternative solution for constructing a low-cost, miniaturized, and high-efficiency rotational angle and speed sensing system.

Large-sized light-emitting diode integrated with a thermopile for on-chip temperature and power monitoring.

A large-sized multiple quantum well (MQW) light-emitting diode (LED) integrated with a thermopile for on-chip temperature and power monitoring is presented in this study. Seven thermopile structures, fully compatible with the fabrication of LEDs, are strategically placed at different locations on the LED to monitor its temperature during the operation. Additionally, the thermopile allows for monitoring the power of the LED, as there exists an approximate linear relationship between the light output power and temperature. Compared to traditional methods of measuring LED temperature, the thermopile offers several advantages, including no moving parts, long lifetime, no maintenance, high reliability, and direct conversion without intermediate processes. The results demonstrate that the integration of the thermopiles onto the LED provides superior temperature and power monitoring capabilities. Furthermore, this integrated solution has the potential to enable real-time management and control of LED temperature.

Effect of temperature on GaN-integrated optical transceiver chips.

The gallium nitride (GaN) integrated optical transceiver chip based on multiple quantum wells (MQW) structure exhibits great promise in the fields of communication and sensing. In this Letter, the effect of ambient temperature on the performance of GaN-integrated optical transceiver chips including a blue MQW light-emitting diode (LED) and a MQW photodiode (PD) is comprehensively studied. Temperature-dependent light-emitting and current-voltage characteristics of the blue MQW LEDs are measured with the ambient temperature ranging from -70°C to 120°C. The experimental results reveal a decline in the electroluminescent (EL) intensity and an obvious redshift in the emission peak wavelength of the LED with increasing ambient temperature. The light detection performance of MQW PD under different temperatures is also measured with the illumination of an external blue MQW LED, indicating an enhancement in the PD sensitivity as the temperature rises. Finally, the temperature effect on the MQW PD under the illumination of the MQW LED on the GaN-integrated optical transceiver chip is characterized, and the PD photocurrent increases with higher ambient temperature. Furthermore, the measured temperature characteristics indicate that the GaN-integrated optical transceiver chip offers a promising application potential for optoelectronic temperature sensor.

Collinear optical links based on a GaN-integrated chip for fiber-optic acoustic detection.

This Letter reports a collinear optical interconnect architecture for acoustic sensing via a monolithic integrated GaN optoelectronic chip. The chip is designed with a ring-shaped photodiode (PD) surrounding a light-emitting diode (LED) of a spectral range from 420-530 nm. The axisymmetric structure helps the coaxial propagation of light transmission and reception. By placing this multiple-quantum wells (MQW)-based device and a piece of aluminum-coated polyethylene terephthalate (Al/PET) film on fiber ends, an ultra-compact acoustic sensing system is built. The sound vibrations can be simply detected by direct measurement of the diaphragm deformation-induced power change. An average signal noise ratio (SNR) of 40 dB and a maximum sensitivity of 82 mV/Pa are obtained when the acoustic vibration frequency changes from 400 Hz to 3.2 kHz. This work provides a feasible solution to miniaturize the sensing system footprint and reduce the cost.

Strain-Amplified Exciton Chirality in Organic-Inorganic Hybrid Materials.

Chiral organic-inorganic hybrids combining chirality of organic molecules and semiconducting properties of inorganic frameworks generate chiral excitons without external spin injection, creating the potential for chiroptoelectronics. However, the relationship between molecular chirality and exciton chirality is still unclear. Here we show the strain-amplified exciton chirality in one-dimensional chiral metal halides. Utilizing chirality-induced spin-orbital coupling theory, we quantitatively demonstrate the impact of the strain-engineered molecular assembly of chiral cations on exciton chirality, offering a feasible way to amplify exciton chirality by molecular manipulation.

R2-ISS staging combined with circulating plasma cells improves risk stratification for newly diagnosed multiple myeloma: a single-center real-world study.

We aimed to evaluate if circulating plasma cells (CPC) detected by flow cytometry could add prognostic value of R2-ISS staging. We collected the electronic medical records of 336 newly diagnosed MM patients (NDMM) in our hospital from January 2017 to June 2023. The median overall survival (OS) for patients and R2-ISS stage I-IV were not reached (NR), NR, 58 months and 53 months, respectively. There was no significant difference in OS between patients with stage I and patients with stage II (P = 0.309) or between patients with stage III and patients with stage IV (P = 0.391). All the cases were re-classified according to R2-ISS stage and CPC numbers ≥ 0.05% (CPC high) or<0.05% (CPC low) into four new risk groups: Group 1: R2-ISS stage I + R2-ISS stage II and CPC low, Group 2: R2-ISS stage II and CPC high + R2-ISS stage III and CPC low, Group 3: R2-ISS stage III and CPC high + R2-ISS stage IV and CPC low, Group 4: R2-ISS stage IV and CPC high. The median OS were NR, NR, 57 months and 32 months. OS of Group 1 was significantly longer than that of Group 2 (P = 0.033). OS in Group 2 was significantly longer than that of Group 3 (P = 0.007). OS in Group 3 was significantly longer than that of Group 4 (P = 0.041). R2-ISS staging combined with CPC can improve risk stratification for NDMM patients.

A Type-II BiTeCl/SnSe2 Heterostructure with High Photoelectric Conversion Efficiency and Tunable Optoelectronic Properties for Photovoltaic Applications.

In this study, a Janus BiTeCl/SnSe2 van der Waals (vdW) heterostructure is constructed and systematically investigated for its potential in solar cell applications using first-principles calculations. The heterostructure introduces distinct contact interfaces (Cl-Se and Te-Se), both exhibiting a type-II band alignment. However, the conduction band minimum (CBM) and valence band maximum (VBM) contributions vary, depending on the interface. The Cl-Se interface demonstrates a significantly higher power conversion efficiency (PCE) of 20.11%, attributed to the suitable bandgap of the SnSe2 donor material and a smaller conduction band offset. Both interfaces exhibit enhanced optical properties compared to those of isolated BiTeCl and SnSe2 monolayers. Additionally, the electronic structure of the heterostructure is tunable via biaxial strain and electric fields, enabling further optimization of the PCE. Moreover, optical absorption can be adjusted by biaxial strain and electric fields. These findings position the Janus BiTeCl/SnSe2 heterostructure, particularly the Cl-Se interface, as a promising candidate for next-generation photovoltaic devices, offering both high efficiency and an external tunability.

The optimal ratio of endoscope-sheath diameter with negative-pressure ureteral access sheath: an in vitro research.

PURPOSE: To maintain safe intrarenal pelvic pressure (IPP), the combination of flexible ureteroscope (fURS) and traditional ureteral access sheath (T-UAS) should maintain a basic rule that is the ratio of endoscope-sheath diameter (RESD) ≤ 0.75. However, the negative-pressure ureteral access sheath (NP-UAS) may break the rule of negative pressure suction. This study aimed to examine the effect of NP-UAS on IPP and flow rate (FR) with varying RESD. METHODS: In a 3D-printed renal model, flexible ureteroscopy lithotripsy (fURL) was replicated. Six sizes of fURS paired with 12Fr T-UAS and NP-UAS resulted in six distinct RESDs of 0.63, 0.78, 0.87, 0.89, 0.90, and 0.91. While the irrigation pressure (IRP) was set between 100 and 800 cmH2O and the sucking pressure (SP) was set between 0 and 800 cmH2O, the IPP and FR were measured in each RESD. RESULTS: NP-UASs can reduce the IPP and increase the FR at the same RESD compared to T-UASs. The IPP decreased with increasing SP with NP-UAS. When RESD ≤ 0.78, T-UAS and NP-UAS can maintain IPP < 40 cmH2O in most circumstances. When RESD = 0.87, it is challenging for T-UAS to sustain IPP < 40 cmH2O; however, NP-UAS can do so. When RESD ≥ 0.89, it is difficult to maintain an IPP < 40 cmH2O even with NP-UAS. CONCLUSION: NP-UAS can decrease IPP and increase FR compared with T-UAS. To maintain a safe IPP, it is recommended that RESD < 0.85 when utilizing NP-UAS.

Factors affecting the intraoperative calculi excretion during flexible ureteroscopy lithotripsy: an in vitro analysis.

OBJECTIVE: To explore the parameters influencing intraoperative calculi excretion (ICE) during flexible ureteroscopy lithotripsy (fURL) using in vitro simulation experiments. METHODS: 3D-printed human kidney models were used to simulate the elimination of gravel during fURL. The factors influencing the ICE during fURL were analyzed by comparing the effects of different degrees of hydronephrosis (mild, moderate, and severe), surgical positions (supine and lateral position), ratios of endoscope-sheath diameter (RESD) (0.625, 0.725, and 0.825), gravel sizes (0.50-1.00 mm, 0.25-0.50 mm, and 0.10-0.25 mm), and ureteral access sheaths (UASs) (traditional UAS and negative-pressure UAS) on ICE. RESULTS: The impacts of various UAS, RESD, degree of hydronephrosis, surgical positions, and gravel sizes on ICE were all significant (p < 0.05). We found no evidence of multicollinearity for all the independent variables, and the linear regression equation fitted as ICE ( g / min ) = 0.102 + 0.083 ∗ UAS grade - 0.050 ∗ RESD grade - 0.048 ∗ hydronephrosis grade + 0.065 ∗ position grade - 0.027 ∗ gravel size grade (R2 = 0.569). CONCLUSION: Employing negative-pressure UAS, smaller RESD, milder hydronephrosis, lateral position, and smaller gravel size contribute to improved ICE during fURL. Among them, the adoption of negative-pressure UAS had the most substantial effects.

Integrated microbiome and metabolomic analysis of Spodoptera litura under Metarhizium flavoviride qc1401 stress.

Metarhizium spp. have emerged as an alternative to chemical pesticides for protecting crops from insect pest. Here, we investigated midgut microbial community and metabolites of Spodoptera litura at three different timepoints after infection with Metarhizium flavoviride. The innate immune system of S. litura was activated with levels of polyphenol oxidase, carboxylesterase, multifunctional oxidase, and glutathione S-transferase activity significantly increasing. Exposure to the fungal pathogen also altered bacterial abundance and diversity in host's midgut, and these changes varied depending on the time elapsed since exposure. We identified more operational taxonomic units in the treated samples as compared to the control samples at all tested time points. A total of 372 metabolites were identified, and 88, 149, and 142 differentially accumulated metabolites (DAMs) were identified between the treatment and control groups at 3 timepoints after treatment, respectively. Based on the changes of DAMs in response to M. flavoviride infection at different timepoints and significantly enriched KEGG pathways, we speculated that "tyrosine metabolism," "galactose metabolism," "ATP-binding cassette transporters," "neuroactive ligand-receptor interaction," "purine metabolism," "arginine and proline metabolism," "beta-alanine metabolism," "lysosome," and "carbon metabolism" may participate in the metabolic-level defense response. An integrated pathway-level analysis of the 16S-rDNA and metabolomic data illustrated the connections and interdependencies between the metabolic responses of S. litura and the midgut microorganisms to M. flavoviride infection. This work emphasizes the value of integrated analyses of insect-pathogen interactions, provides a framework for future studies of critical microorganisms and metabolic determinants of these interactions, establishes a theoretical basis for the sustainable use of M. flavoviride.