PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations.

Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and intricate genomic architectures of phages is essential to study microbial ecosystems and develop phage therapy strategies. However, the existing phage databases are short of meticulous annotations. To this end, we propose PhageScope (https://phagescope.deepomics.org), an online phage database with comprehensive annotations. PhageScope harbors a collection of 873 718 phage sequences from various sources. Applying fifteen state-of-the-art tools to perform systematic annotations and analyses, PhageScope provides annotations on genome completeness, host range, lifestyle information, taxonomy classification, nine types of structural and functional genetic elements, and three types of comparative genomic studies for curated phages. Additionally, PhageScope incorporates automatic analyses and visualizations for curated and customized phages, serving as an efficient platform for phage study.

Contact between water vapor and silicate surface causes abiotic formation of reactive oxygen species in an anoxic atmosphere.

Spontaneous generation of reactive oxygen species (ROS) in aqueous microdroplets or at a water vapor-silicate interface is a new source of redox chemistry. However, such generation occurs with difficulty in liquid water having a large ionic strength. We report that ROS is spontaneously produced when water vapor contacts hydrogen-bonded hydroxyl groups on a silicate surface. The evolution of hydrogen-bonded species such as hydroxyl groups was investigated by using two-dimensional, time-resolved FT-IR spectroscopy. The participation of water vapor in ROS generation is confirmed by investigating the reaction of D2O vapor and hydroxyl groups on a silicate surface. We propose a reaction pathway for ROS generation based on the change of the hydrogen-bonding network and corresponding electron transfer onto the silicate surface in the water vapor-solid contact process. Our observations suggest that ROS production from water vapor-silicate contact electrification could have contributed to oxidation during the Archean Eon before the Great Oxidation Event.

TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization.

Deciphering the cell-type composition in the tumor immune microenvironment (TIME) can significantly increase the efficacy of cancer treatment and improve the prognosis of cancer. Such a task has benefited from microarrays and RNA sequencing technologies, which have been widely adopted in cancer studies, resulting in extensive expression profiles with clinical phenotypes across multiple cancers. Current state-of-the-art tools can infer cell-type composition from bulk expression profiles, providing the possibility of investigating the inter-heterogeneity and intra-heterogeneity of TIME across cancer types. Much can be gained from these tools in conjunction with a well-curated database of TIME cell-type composition data, accompanied by the corresponding clinical information. However, currently available databases fall short in data volume, multi-platform dataset integration, and tool integration. In this work, we introduce TIMEDB (https://timedb.deepomics.org), an online database for human tumor immune microenvironment cell-type composition estimated from bulk expression profiles. TIMEDB stores manually curated expression profiles, cell-type composition profiles, and the corresponding clinical information of a total of 39,706 samples from 546 datasets across 43 cancer types. TIMEDB comes readily equipped with online tools for automatic analysis and interactive visualization, and aims to serve the community as a convenient tool for investigating the human tumor microenvironment.

Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome.

BACKGROUND: Undernutrition (UN) is a critical public health issue that threatens the lives of children under five in developing countries. While evidence indicates the crucial role of the gut microbiome (GM) in UN pathogenesis, the strain-level inspection and bacterial co-occurrence network investigation in the GM of UN children are lacking. RESULTS: This study examines the strain compositions of the GM in 61 undernutrition patients (UN group) and 36 healthy children (HC group) and explores the topological features of GM co-occurrence networks using a complex network strategy. The strain-level annotation reveals that the differentially enriched species between the UN and HC groups are due to discriminated strain compositions. For example, Prevotella copri is mainly composed of P. copri ASM1680343v1 and P. copri ASM345920v1 in the HC group, but it is composed of P. copri ASM346549v1 and P. copri ASM347465v1 in the UN group. In addition, the UN-risk model constructed at the strain level demonstrates higher accuracy (AUC = 0.810) than that at the species level (AUC = 0.743). With complex network analysis, we further discovered that the UN group had a more complex GM co-occurrence network, with more hub bacteria and a higher clustering coefficient but lower information transfer efficiencies. Moreover, the results at the strain level suggested the inaccurate and even false conclusions obtained from species level analysis. CONCLUSIONS: Overall, this study highlights the importance of examining the GM at the strain level and investigating bacterial co-occurrence networks to advance our knowledge of UN pathogenesis.

Genomic profiling informs therapies and prognosis for patients with hepatocellular carcinoma in clinical practice.

Hepatocellular carcinoma (HCC) genomic research has discovered actionable genetic changes that might guide treatment decisions and clinical trials. Nonetheless, due to a lack of large-scale multicenter clinical validation, these putative targets have not been converted into patient survival advantages. So, it's crucial to ascertain whether genetic analysis is clinically feasible, useful, and whether it can be advantageous for patients. We sequenced tumour tissue and blood samples (as normal controls) from 111 Chinese HCC patients at Qingdao University Hospital using the 508-gene panel and the 688-gene panel, respectively. Approximately 95% of patients had gene variations related to targeted treatment, with 50% having clinically actionable mutations that offered significant information for targeted therapy. Immune cell infiltration was enhanced in individuals with TP53 mutations but decreased in patients with CTNNB1 and KMT2D mutations. More notably, we discovered that SPEN, EPPK1, and BRCA2 mutations were related to decreased median overall survival, although MUC16 mutations were not. Furthermore, we found mutant MUC16 as an independent protective factor for the prognosis of HCC patients after curative hepatectomy. In conclusion, this study connects genetic abnormalities to clinical practice and potentially identifies individuals with poor prognoses who may benefit from targeted treatment or immunotherapy.

Significant but Inequitable Cost-Effective Benefits of a Clean Heating Campaign in Northern China.

Residential emissions significantly contribute to air pollution. To address this issue, a clean heating campaign was implemented to replace coal with electricity or natural gas among 13.9 million rural households in northern China. Despite great success, the cost-benefits and environmental equity of this campaign have never been fully investigated. Here, we modeled the environmental and health benefits, as well as the total costs of the campaign, and analyzed the inequality and inequity. We found that even though the campaign decreased only 1.1% of the total energy consumption, PM2.5 emissions and PM2.5 exposure experienced 20% and 36% reduction, respectively, revealing the amplification effects along the causal pathway. Furthermore, the number of premature deaths attributable to residential emissions reduced by 32%, suggesting that the campaign was highly beneficial. Governments and residents shared the cost of 2,520 RMB/household. However, the benefits and the costs were unevenly distributed, as the residents in mountainous areas were not only less benefited from the campaign but also paid more because of the higher costs, resulting in a notably lower cost-effectiveness. Moreover, villages in less developed areas tended to choose natural gas with a lower initial investment but a higher total cost (2,720 RMB/household) over electricity (2,190 RMB/household). With targeted investment and subsidies in less developed areas and the promotion of electricity and other less expensive alternatives, the multidevelopment goals of improved air quality, reduced health impacts, and reduced inequity in future clean heating interventions could be achieved.

Iron and Steel Industry Emissions: A Global Analysis of Trends and Drivers.

The iron and steel industry (ISI) is important for socio-economic progress but emits greenhouse gases and air pollutants detrimental to climate and human health. Understanding its historical emission trends and drivers is crucial for future warming and pollution interventions. Here, we offer an exhaustive analysis of global ISI emissions over the past 60 years, forecasting up to 2050. We evaluate emissions of carbon dioxide and conventional and unconventional air pollutants, including heavy metals and polychlorinated dibenzodioxins and dibenzofurans. Based on this newly established inventory, we dissect the determinants of past emission trends and future trajectories. Results show varied trends for different pollutants. Specifically, PM2.5 emissions decreased consistently during the period 1970 to 2000, attributed to adoption of advanced production technologies. Conversely, NOx and SO2 began declining recently due to stringent controls in major contributors such as China, a trend expected to persist. Currently, end-of-pipe abatement technologies are key to PM2.5 reduction, whereas process modifications are central to CO2 mitigation. Projections suggest that by 2050, developing nations (excluding China) will contribute 52-54% of global ISI PM2.5 emissions, a rise from 29% in 2019. Long-term emission curtailment will necessitate the innovation and widespread adoption of new production and abatement technologies in emerging economies worldwide.

Updated Global Black Carbon Emissions from 1960 to 2017: Improvements, Trends, and Drivers.

Accurate estimation of black carbon (BC) emissions is essential for assessing the health and climate impact of this pollutant. Past emission inventories were associated with high uncertainty due to data limitations, and recent information has provided a unique updating opportunity. Moreover, understanding the drivers that cause temporal emission changes is of research value. Here, we update the global BC emission estimates using new data on the activities and emission factors (EFs). The new inventory covers 73 detailed sources at 0.1° × 0.1° spatial resolution and monthly temporal resolution from 1960 to 2017. The estimated annual emissions were 32% higher than the average of several previous inventories, which was primarily due to field-measured EFs for residential stoves and differentiated EFs for motor vehicles. In addition, the updated emissions show an inverse U-shaped temporal trend, which was mainly driven by the interaction between the positive effects of population growth, per capita energy consumption, and vehicle fleet and the negative effects of residential energy switching, stove upgrading, phasing out of beehive coke ovens, and reduced EFs for vehicles and industrial processes. Urbanization caused a significant increase in urban emissions accompanied by a more significant decline in rural emissions.

Fabricating poly(1,8-octanediol citrate) elastomer based fibrous mats via electrospinning for soft tissue engineering scaffold.

Poly(1,8-octanediol citrate) (POC) is a recently developed biodegradable crosslinked elastomer that possesses good cytocompatibility and matchable mechanical properties to soft tissues. However, the thermosetting characteristic reveals a big challenge to manufacture its porous scaffold. Herein, POC elastomer was electrospun into fiber mat using poly(L-lactic acid) (PLLA) as a spinnable carrier. The obtained POC/PLLA fiber mats were characterized by scanning electron microscopy (SEM), dynamic mechanical analysis (DMA), uniaxial tensile test, static-water-contact-angle, thermal analysis, in vitro degradation and biocompatibility test. It was found that the fibrous structure could be formed so long as the POC pre-polymer's content was no more than 50 wt%. The presence of elastic POC component not only strengthened the fiber mats but also toughened the fiber mats. The hydrophilicity of 50/50 fiber mat significantly improved. In vitro degradation rate of POC based fiber mats was much faster than that of pure PLLA. Cyto- and histo-compatibility tests confirmed that the POC/PLLA fiber mats had good biocompatibility for potential applications in soft tissue engineering.

[Thoracic extramedullary subdural and epidural of inflammatory myofibroblastoma: a case report].

We present here a rare case of thoracic extramedullary subdural and epidural of leisions. The initial diagnosis of preoperation was hypertrophy of ligamentum flavum, however, after excision of the epidural lesions, the symptoms got worse. A second operation found the subdural leisions which were then totally resected. Two pathological examinations confirmed it was inflammatory myofibroblastic tumor (IMT). The incidence of this disease is extremely low. IMT is benign in histology, but it can be aggressive. The exact pathogenesis is still unknown. Tumor resection is the first choice to treat. Long-term follow-up with MRI is required for the patient.

Safety and efficacy of microscope-assisted insertion of screws into fused C1-occipital condyle complex for occipital cervical fixation in atlantal cervical nonsegmentation patients.

OBJECTIVE: To explore the safety and efficacy of the insertion of screws into fused C1-occipital condyle(CC)complex without image guidance in atlantal-cervical nonsegmentation patients. METHODS: The occipital condyle junction was fixed posteriorly in 10 basilar invagination patients with atlantal-cervical nonsegmentation using polyaxial titanium screws(3.5 mm)inserted unicortically into the CC complex and C2 pedicles,followed by fixation to a 3 mm rod. Drilling was guided by anatomic landmarks. The entry point was at the center of posterior surface of the CC complex. The angle of medicalization was 10-15 degrees. In the sagittal plane,the angle for maximal superior screw angulation was also 10-15 degrees. The screw length to obtain unicortical purchase was 16 to 22 mm. CT scans were obtained before and after the surgery. The length,width,and height of CC complex were measured on computed tomography(CT)preoperatively. The position of screws and the condition of fixation were analyzed on postoperative CT scan. Postoperative complications were recorded. The mean follow-up was(30.2±4.38)months(range: 24-36 months). RESULTS: The width,length,height of left side CC complex were(7.96±2.23)mm,(16.06±2.73)mm,and(13.76±2.06)mm,and the width,length,height of right side CC complex were(7.84±1.38)mm,(16.66±2.58)mm,and(12.81±2.62)mm. No fracture was identified. There was no screw malposition or neurovascular complication related to screw insertion. No screw loosening or construct failure was observed during the follow-up. CONCLUSIONS: In patients with atlantal cervical nonsegmentation,the CC complex screws can be safely inserted assisted by microscope without image guidance. Occipital condyle junction fixation using polyaxial CC complex screws is feasible and can be a good alternative where other fixation techniques are not satisfactory.

Antimony isotopic fractionation induced by Sb(V) adsorption on ß-MnO2.

Antimony (Sb) isotopes hold immense promise for unraveling Sb biogeochemical cycling in environmental systems. Mn oxides help control the fate of Sb via adsorption reactions, yet the behavior and mechanisms of Sb isotopic fractionation on Mn oxides are poorly understood. In this study, we examine the Sb isotopic fractionation induced by adsorption on ß-MnO2 in different experiments (kinetic, isothermal, effect of pH). We observe that adsorption on ß-MnO2 surfaces preferentially enriches lighter Sb isotopes through equilibrium fractionation, with Δ123Sbaqueous-adsorbed of 0.55-0.79 ‰. Neither the pH or surface coverage affects the fractionation magnitude. The analysis of extended X-ray absorption fine structure (EXAFS) demonstrates that the enrichment of light isotope results from the adsorption of inner-sphere complexation on solids. Our finding of this study enhances our comprehension of the impact of ß-MnO2 on Sb isotopic fractionation behavior and mechanism and facilitate the applicability of Sb isotopes as effective tracers to elucidate the origins and pathways of Sb contamination in environmental systems, as well as provide a new insight into forecasting the isotopic fractionation of other similar metals adsorbed by manganese oxides.

Health burden from food systems is highly unequal across income groups.

Food consumption contributes to the degradation of air quality in regions where food is produced, creating a contrast between the health burden caused by a specific population through its food consumption and that faced by this same population as a consequence of food production activities. Here we explore this inequality within China's food system by linking air-pollution-related health burden from production to consumption, at high levels of spatial and sectorial granularity. We find that low-income groups bear a 70% higher air-pollution-related health burden from food production than from food consumption, while high-income groups benefit from a 29% lower health burden relative to their food consumption. This discrepancy largely stems from a concentration of low-income residents in food production areas, exposed to higher emissions from agriculture. Comprehensive interventions targeting both production and consumption sides can effectively reduce health damages and concurrently mitigate associated inequalities, while singular interventions exhibit limited efficacy.

Progress on simultaneous photocatalytic degradation of pollutants and production of clean energy: A review.

In the current era of severe energy and environmental crises, the need for efficient and sustainable methods to control pollution and promote resource recycling has become increasingly important. Photocatalytic degradation of pollutants and simultaneous production of clean energy is one such approach that has garnered significant attention in recent years. The principle of photocatalysis involves the development of efficient photocatalysts and the efficient utilization of solar energy. The use of organic contaminants can enhance the photocatalytic reactions, leading to the sustainable generation of clean energy. Herein, we provide a comprehensive review of the latest advances in the application of photocatalytic synergized clean energy production in the environmental field. This review highlights the latest developments and achievements in this field, highlighting the potential for this approach to revolutionize the way we approach environmental pollution control and resource recycling. The review focuses on (1) the mechanism of photocatalytic degradation and synergistic energy production, (2) photocatalysts and synthesis strategies, (3) photocatalytic carbon dioxide reduction, (4) pollutant degradation, and (5) hydrogen and electricity production. In addition, perspectives on key challenges and opportunities in photocatalysis and clean energy for future developments are proposed. This review provides a roadmap for future research directions and innovations of photocatalysis that could contribute to the development of more sustainable and cleaner energy solutions.

P(VDF-TrFE)/BaTiO3 Nanofibrous Membrane with Enhanced Piezoelectricity for High PM0.3 Filtration and Reusable Face Masks.

In the background of air pollution and regular COVID-19 prevention, personal protective masks are necessary for our daily life. However, protective masks with high PM0.3 filtration usually have poor air permeability and are mostly disposable, leading to a heavy burden on the environment. In this work, a reusable membrane based on piezoelectric poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] nanofibers embedded with BaTiO3 nanoparticles (BTO NPs) was developed. The P(VDF-TrFE)/BTO composite nanofibers not only have enhanced piezoelectricity and surface polarity but also have reduced diameters that could be beneficial for electrostatic adhesion, pole-polar interactions, and mechanical sieving to increase the PM0.3 capture capacity. Moreover, the BTO NPs also improved the charge storage capacity of the composite membrane, which could further enhance the PM0.3 filtration efficiency after corona treatment. The piezoelectric mask based on P(VDF-TrFE)/BTO composite nanofibers has high filtration efficiencies of 96% for PM0.3 and 98% for bacteria, while the pressure drop was only 182 Pa, which is lower than the commercial N95 standard of 343.2 Pa. Furthermore, the piezoelectric mask has a long and stable filtration performance after 5 cycles of 75% alcohol disinfection, demonstrating that the P(VDF-TrFE)/BTO composite membrane has a potential application in personal protective masks with comfortable and reusable properties.

Ultrasound-mediated piezoelectric nanoparticle modulation of intrinsic cardiac autonomic nervous system for rate control in atrial fibrillation.

Rate control is a cornerstone of atrial fibrillation treatment. Barium titanate nanoparticles (BTNPs) are piezoelectric nanomaterials that can generate local electromagnetic fields under ultrasound activation, stimulating nearby neuronal tissue. This study aimed to modulate the inferior right ganglionated plexus (IRGP) of the heart and reduce the ventricular rate during rapid atrial pacing (RAP)-induced atrial fibrillation using ultrasound-mediated BTNPs. Adult male beagles were randomly divided into a phosphate-buffered saline (PBS) group (n = 6) and a BTNP group (n = 6). PBS or nanoparticles were injected into the IRGP of both groups before RAP. The biological safety of the material was evaluated according to electrophysiology recordings, thermal effects and level of inflammation. Compared to the PBS group, the BaTiO3 piezoelectric nanoparticle group had reduced ventricular rates in the sinus rhythm and atrial fibrillation models after stimulating the IRGP by applying ultrasound. In addition, transient stimulation by BTNPs did not lead to sustained neuronal excitation in the IRGP. The activation of the BTNPs did not induce inflammation or thermal damage effects in the IRGP. Ultrasound-mediated BTNP neuromodulation can significantly reduce the ventricular rate by stimulating the IRGP. Thus, ultrasound-mediated BTNP neuromodulation is a potential therapy for atrial fibrillation rate control.

Wireless Self-Powered Optogenetic System for Long-Term Cardiac Neuromodulation to Improve Post-MI Cardiac Remodeling and Malignant Arrhythmia.

Autonomic imbalance is an important characteristic of patients after myocardial infarction (MI) and adversely contributes to post-MI cardiac remodeling and ventricular arrhythmias (VAs). A previous study proved that optogenetic modulation could precisely inhibit cardiac sympathetic hyperactivity and prevent acute ischemia-induced VAs. Here, a wireless self-powered optogenetic modulation system is introduced, which achieves long-term precise cardiac neuromodulation in ambulatory canines. The wireless self-powered optical system based on a triboelectric nanogenerator is powered by energy harvested from body motion and realized the effective optical illumination that is required for optogenetic neuromodulation (ON). It is further demonstrated that long-term ON significantly mitigates MI-induced sympathetic remodeling and hyperactivity, and improves a variety of clinically relevant outcomes such as improves ventricular dysfunction, reduces infarct size, increases electrophysiological stability, and reduces susceptibility to VAs. These novel insights suggest that wireless ON holds translational potential for the clinical treatment of arrhythmia and other cardiovascular diseases related to sympathetic hyperactivity. Moreover, this innovative self-powered optical system may provide an opportunity to develop implantable/wearable and self-controllable devices for long-term optogenetic therapy.

Efficient hydrogenation of p-chlorophenol and Cr(VI) driven by hydrogen rich balls over Pd/C catalysts.

Catalytic hydrogenation can selectively destabilize and detoxify specific contaminants in water. Herein, to explore safer and more efficient hydrogen sources, hydrogen rich balls (HRBs) were researched and applied for hydrogenating p-chlorophenol and Cr(VI) over Pd/C catalyst. The results showed that HRBs can realize the sustained release of H2 by replacing the hydrogen in water, and generate the refined (micro/nano-sized) H2 bubble, which effectively improves the adsorption and activation effectively of H2 molecules on Pd/C catalyst, and the hydrogen atoms utilization efficiency during p-chlorophenol hydrodechlorination is as high as 3.5 %. Continuous flow experiments showed that rapid removal of p-chlorophenol with different concentrations could be achieved by adjusting the flow rate. Moreover, the high-toxic Cr(VI) was successfully reduced to the low-toxic Cr(III) in an appropriate pH range. This research is of far-reaching significance for realizing the detoxification of environmental pollutants and promoting the development of hydrogen economy.