RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.

SUMMARY: We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation. AVAILABILITY AND IMPLEMENTATION: RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.

RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data.

Assessing the quality of sequencing data plays a crucial role in downstream data analysis. However, existing tools often achieve sub-optimal efficiency, especially when dealing with compressed files or performing complicated quality control operations such as over-representation analysis and error correction. We present RabbitQCPlus, an ultra-efficient quality control tool for modern multi-core systems. RabbitQCPlus uses vectorization, memory copy reduction, parallel (de)compression, and optimized data structures to achieve substantial performance gains. It is 1.1 to 5.4 times faster when performing basic quality control operations compared to state-of-the-art applications yet requires fewer compute resources. Moreover, RabbitQCPlus is at least 4 times faster than other applications when processing gzip-compressed FASTQ files and 1.3 times faster with the error correction module turned on. Furthermore, it takes less than 4 minutes to process 280 GB of plain FASTQ sequencing data, while other applications take at least 22 minutes on a 48-core server when enabling the per-read over-representation analysis. C++ sources are available at https://github.com/RabbitBio/RabbitQCPlus.

Comparison of microbial abundance and diversity in uterine and peritoneal fluid in infertile patients with or without endometriosis.

INTRODUCTION: Endometriosis (EM) is a multifactorial disease that affects 10 - 15% of women of reproductive age. Additionally, 30-50% of women with EM suffer from infertility. The mechanism of infertility caused by EM has not yet been consistently explained. In recent years, studies have shown a link between infertility associated with EM and changes in the reproductive tract microbiota. METHODS: In this study, we involved 26 EM patients (8 cases of stage I-II and 18 cases of stage III-IV) and 31 control subjects who were tubal obstruction-related infertility (TORI). The samples from peritoneal fluid (PF) and uterine fluid (UF) were collected and sequenced by 16 S rRNA amplicon. RESULTS: In the comparison of microbial diversity, we found no significant differences in the microbial diversity of PF and UF between patients with stage I-II EM and those with TORI. However, there was a significant difference in microbial diversity among patients with stage III-IV EM compared to the previous two groups. Lactobacillus decreased in PF of EM compared to the control group, while it increased in UF. In PF, the abundance of Pseudomonas, Enterococcus, Dubosiella and Klebsiella was significantly higher in patients with stage III-IV compared to TORI patients. And in UF, the main differences existed between stage I-II EM compared to the other two groups. The abundance of pontibacter, aquabacterium, Rikenellaceae and so on at the genus level was significantly enriched in the EM patients with stage I-II. In the analysis based on KEGG database, EM may affect the receptivity related pathways of the endometrium by influencing changes in the uterine microbiota. CONCLUSION: Our results indicated that as EM progresses, the microorganisms in UF and PF keep changing. These changes in the microbiota, as well as the resulting alternations in gene functional classification, may play an important role in the infertility associated with EM.

In Situ Albumin-Hitchhiking NIR-II Probes for Accurate Detection of Micrometastases.

Tumor metastasis remains the primary cause of treatment failure in cancer patients, and the high-sensitivity preoperative and intraoperative detection of occult micrometastases continues to pose a notorious challenge. Therefore, we have designed an in situ albumin-hitchhiking near-infrared window II (NIR-II) fluorescence probe, IR1080, for the precise detection of micrometastases and subsequent fluorescence image-guided surgery. IR1080 rapidly covalently conjugates with albumin in plasma, resulting in a stronger fluorescence brightness upon binding. Moreover, the albumin-hitchhiked IR1080 has a high affinity for secreted protein acidic and rich in cysteine (SPARC), an albumin-binding protein that is overexpressed in micrometastases. The interaction between SPARC and IR1080-hitchhiked albumin enhances IR1080's capacity to track and anchor micrometastases, leading to a high detection rate and margin delineation ability, as well as a high tumor-to-normal tissue ratio. Therefore, IR1080 represents a highly efficient strategy for the diagnosis and image-guided resection surgery of micrometastases.

Nanomicellar Electrolyte To Control Release Ions and Reconstruct Hydrogen Bonding Network for Ultrastable High-Energy-Density Zn-Mn Battery.

Zn-Mn batteries with two-electron conversion reactions simultaneously on the cathode and anode harvest a high voltage plateau and high energy density. However, the zinc anode faces dendrite growth and parasitic side reactions while the Mn2+/MnO2 reaction on the cathode involves oxygen evolution and possesses poor reversibility. Herein, a novel nanomicellar electrolyte using methylurea (Mu) has been developed that can encapsulate ions in the nanodomain structure to guide the homogeneous deposition of Zn2+/Mn2+ in the form of controlled release under an external electric field. Consecutive hydrogen bonding network is broken and a favorable local hydrogen bonding system is established, thus inhibiting the water-splitting-derived side reactions. Concomitantly, the solid-electrolyte interface protective layer is in situ generated on the Zn anode, further circumventing the corrosion issue resulting from the penetration of water molecules. The reversibility of the Mn2+/MnO2 conversion reaction is also significantly enhanced by regulating interfacial wettability and improving nucleation kinetics. Accordingly, the modified electrolyte endows the symmetric Zn∥Zn cell with extended cyclic stability of 800 h with suppressed dendrites growth at an areal capacity of 1 mAh cm-2. The assembled Zn-Mn electrolytic battery also demonstrates an exceptional capacity retention of nearly 100% after 800 cycles and a superior energy density of 800 Wh kg-1 at an areal capacity of 0.5 mAh cm-2.

Exosomes from bone marrow-derived mesenchymal stem cells facilitate corneal wound healing via regulating the p44/42 MAPK pathway.

PURPOSE: This study was aimed at exploring the function of Exosomes isolated from bone marrow-derived mesenchymal stem cells (BMSC-Exos) in corneal wound healing and at revealing the underlying mechanisms involving the p44/42 mitogen-activated protein kinase (MAPK) pathway. METHODS: The isolated BMSC-Exos were identified by transmission electron microscopy, Western blot, and nanoparticle tracking analysis. After coculture with BMSC-Exos, the proliferation and migration of human corneal epithelial cells (HCEs) were evaluated. The protein expression of p-MEK/MEK and p44/42 MAPK was detected by Western blot. A mouse model of alkali-burned cornea was established via NaOH exposure. After injection with BMSC-Exos, the pathological changes and expression of α-SMA (a fibrosis marker) and CD31 (a vascularization marker) in corneal tissues were detected. RESULTS: BMSC-Exos enhanced the proliferation and migration of HCEs in a dose-dependent manner. The p44/42 MAPK pathway was activated by the treatment of BMSC-Exos, and its blocking using U0126 partially abrogated the effects of BMSC-Exos on promoting the proliferation and migration of HCEs. In vivo, the injection of BMSC-Exos facilitated the remission of the pathological changes (inflammation) and weakened the upregulation of α-SMA (fibrosis) and CD31 (vascularization) in corneal tissues of mice with alkali-burn injury. CONCLUSION: BMSC-Exos promoted the proliferation and migration of HCEs via activating the p44/42 MAPK pathway in vitro and also inhibited alkali burn-induced inflammation, fibrosis, and vascularization in corneal tissues in vivo. BMSC-Exos may be promising resources for promoting corneal wound healing.

Fast and Selective Degradation of Biomass for Xylose, Glucose and Lignin under Mild Conditions.

The conversion of lignocellulose into valuable chemicals has been recognized as the key technology in green chemistry. However, selective degradation of hemicellulose and cellulose with the production of lignin is still a challenge. Therefore, a two-step process has been developed to degrade corncob into xylose and glucose under mild conditions. At first, the corncob was treated with the lower concentration of zinc chloride aqueous solution (30-55 w%) at 95 °C with a short reaction time (8-12 min) and 30.4 w% (selectivity = 89%) of xylose obtained with a solid residue of the composite of cellulose and lignin. Next, the solid residue was treated with a high concentration of zinc chloride aqueous solution (65-85 w%) at 95 °C for about 10 min, and 29.4 w% (selectivity = 92%) of glucose can be obtained. Combining the two steps, the total yield of xylose is 97%, while glucose is 95%. In addition, high pure lignin can be obtained simultaneously, which was confirmed using HSQC studies. Furthermore, for the solid residue of the first-step reaction, a ternary deep eutectic solvent (DES) (choline chloride/oxalic acid/1,4-butanediol, ChCl/OA/BD) has been used to separate the cellulose and lignin efficiently, and high-quality cellulose (Re-C) and lignin (Re-L) were obtained. Furthermore, it provides a simple method to disassemble the lignocellulose for monosaccharides, lignin, and cellulose.

Deep Eutectic Solvent-Induced Microphase Separation and Entanglement of PVA Chains for Tough and Reprocessable Eutectogels for Sensors.

A high-strength PVA-based eutectogel has been synthesized by a strategy of solvent-induced microphase separation. Here, PVA was dissolved in water, and green solvent DES (choline chloride/glycerol) was introduced to induce PVA to undergo microphase separation, leading to poorly solvated domains and highly solvated domains. In poorly solvated domains, the PVA chains were folded and crystallized, and the formed crystalline domains served as physical cross-linkers. Such cross-linking structures endowed the eutectogels with remarkable mechanical properties, showing strength in tension reaching up to 1.2 MPa and elongation at a break of 405%, with rupture toughness of 3.23 MJ m-3. Meanwhile, the as-obtained eutectogel possessed reprocessability and could be recycled through high-temperature dissolution and recasting. In addition, the eutectogel also exhibited excellent frost resistance, and its ionic conductivity could still reach 0.62 mS cm-1 at -40 °C. In addition, the eutectogel can maintain a stable output signal during a multiple strain cycle, showing the potential application in the flexible sensor. The eutectogel is capable of detecting the bending movement of joints and identifying the different bending angles of fingers, showing a certain applied potential in motion detection of the human body.

The association of demodex infestation with pediatric chalazia.

PURPOSE: This study aimed to investigate the association of Demodex infestation with pediatric chalazia. METHODS: In a prospective study, 446 children with chalazia and 50 children with non-inflammatory eye disease (controls) who underwent surgical treatment were enrolled from December 2018 to December 2019. Patient ages ranged from 7 months to 13 years old. All patients underwent eyelash sampling for light microscope examination, and statistical correlation analysis between Demodex infestation and chalazia, including the occurrence, recurrence, and course of disease, morphological characteristics, and meibomian gland dysfunction (MGD) in chalazia patients was performed. RESULTS: Demodex was found in 236 (52.91%) patients with chalazia and zero control patients. Demodicosis was significantly more prevalent in chalazia patients than the control group (P < 1 × 10- 14). Recurrent chalazia (P = 0.006) and skin surface involvement (P = 0.029) were highly correlated with Demodex infestation. Demodicosis was also associated with multiple chalazia (P = .023) and MGD(P = .024). However, Demodex infestation was comparable in the course of disease (P = 0.15), seasonal change (P = 0.68) and blepharitis subgroups (P = 0.15). Within the group of chalazia patients who underwent surgical removal of cysts, 4 (0.9%) patients with concurrent demodicosis experienced recurrence. CONCLUSIONS: Demodex infestation was more prevalent in pediatric chalazia patients than healthy children, and was associated with recurrent and multiple chalazia. Demodicosis should be considered as a risk factor of chalazia. In children with chalazia, Demodex examination and comprehensive treatment of Demodex mites should be applied to potentially prevent recurrence.

Synthesis of strong electron donating-accepting type organic fluorophore and its polypeptide nanoparticles for NIR-II phototheranostics.

A novel NIR-II small-molecule D-A type organic fluorophore conjugation of triphenylamine, thiophene, and benzo[c,d] indol groups (TPA-Et) with strong electron-donating and accepting groups has been synthesized. The dye shows a significant Stokes shift for efficient fluorescence in the NIR-II region and high photothermal performance. The TPA-Et was then encapsulated by an amphiphilic copolymer P(OEGMA)20-P(Asp)14, and micelles (P@TP) has been prepared with outstanding NIR-II imaging performance, excellent photothermal conversion efficiency (52.5%) under 808 nm laser irradiation, and good photostability. Fluorescence imaging experiments have consistently shown that P@TP can image tiny blood vessels in mice, enrich effectively in the tumor region, and maintain a relatively stable NIR-II fluorescence signal in the tumor area for a long time up to 60 h. In vivo photothermal therapy has a highly significant anticancer effect without tumor recurrence, demonstrating the apparent advantages of P@TP as a NIR nanotheranostic platform in NIR-II imaging-guided photothermal therapy.

Solid-Liquid-Vapor Triphase Gel.

Gels are soft functional materials with solid networks and open pores filled with solvents (for wet gels) or air (for aerogels), displaying broad applications in tissue engineering, catalysis, environmental remediation, energy storage, etc. However, currently known gels feature only a single (either solid-liquid or solid-vapor) interface, largely limiting their application territories. Therefore, it is both fundamentally intriguing and practically significant to develop conceptually new gel materials that possess solid-liquid-vapor multiple interfaces. Herein, we demonstrate a unique solid-liquid-vapor triphase gel, named as aerohydrogel, by gelling of a poly(vinyl alcohol) aqueous solution with glutaraldehyde in the presence of superhydrophobic silica aerogel microparticles. Owing to its continuous solid, liquid, and vapor phases, the resultant aerohydrogel simultaneously displays solid-liquid, solid-vapor, and liquid-vapor interfaces, leading to excellent properties including tunable density (down to 0.43 g·cm-3), considerable hydrophobicity, and excellent elasticity (compressive ratio of up to 80%). As a proof-of-concept application, the aerohydrogel exhibits a higher evaporative cooling efficiency than its hydrogel counterpart and a better cooling capability than the commercial phase change cooling film, respectively, showing promising performance in cooling various devices. Moreover, the resulting aerohydrogel could be facilely tailored with specific (e.g., magnetic) properties for emerging applications such as solar steam generation. This work extends biphase gel (hydrogel or aerogel) to solid-liquid-vapor triphase gel, as well as provides a promising strategy for designing more aerohydrogels serving as soft functional materials for applications in various emerging fields.

Silica Aerogels with Self-Reinforced Microstructure for Bioinspired Hydrogels.

Aerogel is a kind of high-performance lightweight open-porous solids with ultralow density, high specific surface area, and broad application in many emerging fields including biotechnology, energy, environment, aerospace, etc. A giant challenge remains in preventing of the hydrophilic aerogel framework shrinkage when replacing of solvent with air in its extremely abundant nanosized pores during its fabrication process in ambient conditions. In this work, started from a linear polymeric precursor with further condensation reaction, superhydrophilic silica aerogels with self-reinforced microstructure and the least volume shrinkage have been successfully obtained via ambient pressure drying process without use of any additives in the presence of a low surface tension solvent. The resulting superhydrophilic silica aerogels possess specific surface area up to 1065 m2/g, pore volume up to 2.17 cm3/g and density down to 84 mg/cm3, and these values are comparable to those of their counterparts obtained by supercritical CO2 drying process. Moreover, as an application demonstration, the bioinspired hydrogels with desirable mechanical flexibility and adhesive performance at extremely harsh environment (e.g., below -50 °C) have been successfully synthesized by mimicking carrier of a functional bioagent with the resulting superhydrophilic silica aerogel microparticles. Our work has made a significant step forward for future high-performance hydrophilic aerogels with self-enhanced microstructures and the resulting superhydrophilic aerogels have shown great potentials in making functional hydrogels with bionic properties.

Synthesis of Highly Ion-Conductive Lignin Eutectogels in a Ternary Deep Eutectic Solvent and Nitrogen-Doped 3D Hierarchical Porous Carbons for Supercapacitors.

A new strategy has been developed to synthesize deep eutectic solvent (DES)-based lignin eutectogels by the chemical crosslinking of homogeneously dispersed lignin with poly(ethylene glycol)diglycidyl ether (PEGDE) in a ternary DES of choline chloride (ChCl)/urea/glycerol. The as-prepared lignin eutectogels have high ionic conductivity, high strength, and extreme temperature stability, which can be used as sensors for flexible electronics. N-doped hierarchical porous carbons (HPCs) are prepared when the eutectogels were solvent-replaced and sintered in the atmosphere of N2 and CO2, which results in the formation of porous carbon with a sufficient specific surface area and a three-dimensional framework composed of a hierarchical porous structure. They were used as electrodes with excellent capacitance performance attributed to the synergy of reasonable pore size distribution and excellent nitrogen doping efficiency. The electrode displayed a significantly enhanced specific capacitance (270 F g-1 at a current density of 1.0 A g-1 in a three-electrode system and 224 F g-1 at 0.5 A g-1 in a two-electrode system) and high-performance stability (7% capacitance loss over 10,000 cycles at 8 A g-1) as a supercapacitor electrode. It indicates the great promise of the lignin eutectogels for both sensing and energy storage applications.

Ultra-Stretchable, Self-Healing, Conductive, and Transparent PAA/DES Ionic Gel.

A deep eutectic solvent (DES) ionic gel is fabricated rapidly under mild conditions. The acrylic acid monomer is polymerized based on a dual self-catalytic system between Vitamin C (VC) and metal ions, such as Fe3+ in the presence of ammonium persulfate in the DES of betaine and ethylene glycol. The as-obtained PAA/DES ionic gel possesses excellent conductivity between 0.1 and 1.3 S m-1 in a wide range of temperatures from 0 to 90 °C. Moreover, it also shows an ultra-stretchable performance with stretch more than 200 times its original length even under a stretching rate of 100 mm min-1 . Besides, it can operate in harsh conditions because of its anti-freezing and anti-drying properties. The ionic gel is self-healing, and the stretching and conductive performance can be recovered after it is broken. These superior properties of the DES ionic gel provide new insights into the design of novel gels in various applications, such as tissue engineering, sensing, and wearable electronics.

Sharp pH-sensitive amphiphilic polypeptide macrophotosensitizer for near infrared imaging-guided photodynamic therapy.

Tumor environmental sensitive polypeptide integrated photosensitizer is a platform for imaging-guided photodynamic therapy (PDT). However, the photosensitizer leakage during blood circulation, poor accumulation in tumor tissue and inferior quantum yield of singlet oxygen are still challenges. Herein, NHS-active boron-dipyrromethene derivative with bromine substituted NHS-BODIPY-Br2 was first synthesized, which possessed high singlet oxygen generation efficiency and near infrared (NIR) fluorescence, and then it was conjugated to a sharp pH (6.36) sensitive polypeptide to achieve a macrophotosensitizer for NIR imaging-guided PDT. In vitro study showed that the macrophotosensitizer nanoparticles exhibited good cellular uptake and ability to kill cancer cells. Once accumulating in the tumor tissues, the nanoparticles can be demicellized by tumor acidity to promote cellular uptake, which could enlarge fluorescence signal intensity and enhance in vivo PDT therapeutic effect upon NIR laser irradiation. It provides a strategy to design photosensitizer conjugated tumor acidity sensitive polypeptide for NIR imaging-guided photodynamic therapy.

High Singlet Oxygen Yield Photosensitizer Based Polypeptide Nanoparticles for Low-Power Near-Infrared Light Imaging-Guided Photodynamic Therapy.

NIR photosensitizer is attractive for photodynamic therapy (PDT). Low-power light irradiation and imaging-guided PDT makes it possible to increase tissue penetration depth. The pyrrole-substituted iodinated BODIPY (BDPI) molecule was designed and synthesized, and it possesses an intense NIR absorption and emission band, and exhibits a high singlet oxygen quantum yield (ΦΔ = 0.80) which leads remarkable cytotoxicity upon low power illumination (IC50 = 0.60 µg/mL, 6.1 mW/cm2). After being encapsulated with biocompatibility polypeptide PEG-PLys, polymeric micelles nanoparticles (PBDPI NPs) was obtained that are water-dispersed and passively tumor-targetable. Such enhanced accumulation in tumor area makes it easily traced in vivo due to its NIR fluorescence. In addition, such nanoparticles offer an unprecedented photodynamic therapeutic effect by using a low-power irradiation light, which makes it possible to kill cancer cells in deep tissue efficiently.

[a]-Phenanthrene-Fused BF2 Azadipyrromethene (AzaBODIPY) Dyes as Bright Near-Infrared Fluorophores.

A new substitution pattern of BF2 azadipyrromethene (azaBODIPY) dyes was obtained by phenanthrene fusion through a key palladium-catalyzed intramolecular C-H activation reaction. These [a]-phenanthrene-fused azaBODIPYs have a near planar structure of the phenanthrene-fused azadipyrromethene core in the crystalline state. The chromophore absorbs (log ε > 5) and fluoresces (ϕ = 0.32-0.38) strongly above 700 nm with excellent photostability and may be used as an attractive bright NIR bioimaging agent.

Increased incidence of head and neck cancer in liver transplant recipients: a meta-analysis.

BACKGROUND: It is unclear whether liver transplantation is associated with an increased incidence of post-transplant head and neck cancer. This comprehensive meta-analysis evaluated the association between liver transplantation and the risk of head and neck cancer using data from all available studies. METHODS: PubMed and Web of Science were systematically searched to identify all relevant publications up to March 2014. Standardized incidence ratio (SIR) and 95% confidence intervals (CIs) for risk of head and neck cancer in liver transplant recipients were calculated. Tests for heterogeneity, sensitivity, and publishing bias were also performed. RESULT: Of the 964 identified articles, 10 were deemed eligible. These studies included data on 56,507 patients with a total follow-up of 129,448.9 patient-years. SIR for head and neck cancer was 3.836-fold higher (95% CI 2.754-4.918, P = 0.000) in liver transplant recipients than in the general population. No heterogeneity or publication bias was observed. Sensitivity analysis indicated that omission of any of the studies resulted in an SIR for head and neck cancer between 3.488 (95% CI: 2.379-4.598) and 4.306 (95% CI: 3.020-5.592). CONCLUSIONS: Liver transplant recipients are at higher risk of developing head and neck cancer than the general population.

8-Oxoguanine DNA glycosylase 1 (ogg1) maintains the function of cardiac progenitor cells during heart formation in zebrafish.

Genomic damage may devastate the potential of progenitor cells and consequently impair early organogenesis. We found that ogg1, a key enzyme initiating the base-excision repair, was enriched in the embryonic heart in zebrafish. So far, little is known about DNA repair in cardiogenesis. Here, we addressed the critical role of ogg1 in cardiogenesis for the first time. ogg1 mainly expressed in the anterior lateral plate mesoderm (ALPM), the primary heart tube, and subsequently the embryonic myocardium by in situ hybridisation. Loss of ogg1 resulted in severe cardiac morphogenesis and functional abnormalities, including the short heart length, arrhythmia, decreased cardiomyocytes and nkx2.5(+) cardiac progenitor cells. Moreover, the increased apoptosis and repressed proliferation of progenitor cells caused by ogg1 deficiency might contribute to the heart phenotype. The microarray analysis showed that the expression of genes involved in embryonic heart tube morphogenesis and heart structure were significantly changed due to the lack of ogg1. Among those, foxh1 is an important partner of ogg1 in the cardiac development in response to DNA damage. Our work demonstrates the requirement of ogg1 in cardiac progenitors and heart development in zebrafish. These findings may be helpful for understanding the aetiology of congenital cardiac deficits.