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.

Selective O2-to-H2O2 Electrosynthesis by a High-Performance, Single-Pass Electrofiltration System Using Ibuprofen-Laden CNT Membranes.

Producing H2O2 through a selective, two-electron (2e) oxygen reduction reaction (ORR) is challenging, especially when it serves as an advanced oxidation process (AOP) for cost-effective water decontamination. Herein, we attain a 2e-selectivity H2O2 production using a carbon nanotube electrified membrane with ibuprofen (IBU) molecules laden (IBU@CNT-EM) in an ultrafast, single-pass electrofiltration process. The IBU@CNT-EM can generate H2O2 at a rate of 25.62 mol gCNT-1 h-1 L-1 in the permeate with a residence time of 1.81 s. We demonstrated that an interwoven, hydrophilic-hydrophobic membrane nanostructure offers an excellent air-to-water transport platform for ORR acceleration. The electron transfer number of the ORR for IBU@CNT at neutral pH was confirmed as 2.71, elucidating a near-2e selectivity to H2O2. Density functional theory (DFT) studies validated an exceptional charge distribution of the IBU@CNT for the O2 adsorption. The adsorption energies of the O2 and *OOH intermediates are proportional to the H2O2 selectivity (64.39%), higher than that of the CNT (37.81%). With the simple and durable production of H2O2 by IBU@CNT-EM electrofiltration, the permeate can actuate Fenton oxidation to efficiently decompose emerging pollutants and inactivate bacteria. Our study introduces a new paradigm for developing high-performance H2O2-production membranes for water treatment by reusing environmental functional materials.

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.

[Impact of ultra-early enteral nutrition support on the prognosis of young and middle-aged postoperative patients with cerebral hemorrhage].

OBJECTIVE: To investigate the effect of ultra-early enteral nutrition (UEEN) support on the prognosis of young and middle-aged postoperative patients with cerebral hemorrhage. METHODS: The clinical data of young and middle-aged patients (aged 18-59 years) admitted to Tianjin Fifth Central Hospital from January 2020 to June 2023 after surgery for intracerebral hemorrhage were retrospectively analyzed, and the general data, nutritional indexes, gastrointestinal complications, neurological function recovery and long-term prognosis of the patients were recorded. According to the time of initiation of enteral nutrition (EN) support, patients were divided into UEEN group (EN implementation within 12 hour after surgery) and early enteral nutrition (EEN) group (EN implementation within 24 to 48 hour after surgery). The differences of the above indexes between the two groups were analyzed and compared. RESULTS: A total of 64 young and middle-aged postoperative patients with cerebral hemorrhage were enrolled, including 32 cases in the UEEN group and 32 cases in the EEN group. There were no significant differences in gender, age, proportion of hypertension and diabetes, Glasgow coma score (GCS) on admission and surgical methods between the two groups. In terms of nutritional indexes, serum total protein, albumin and hemoglobin levels of patients in both groups on day 7 after admission were lower than those on day 1, and higher than those on day 3, and the above indexes levels in UEEN group were significantly higher than those in EEN group on day 7 [total protein (g/L): 63.05±5.79 vs. 59.02±6.63, albumin (g/L): 40.40±5.26 vs. 37.66±4.63, hemoglobin (g/L): 133.33±12.58 vs. 123.80±22.12, all P < 0.05]. In terms of gastrointestinal complications, the incidence of stress ulcer in the UEEN group within 14 days after admission was significantly lower than that in the EEN group [12.5% (4/32) vs. 31.3% (10/32), P < 0.05], but there was no statistically significant difference in feeding intolerance symptoms between the two groups. In terms of neurological recovery and long-term prognosis, GCS scores and Barthel index scores of 14 days after admission were higher than those of 1 day after admission, but there was no statistical significance between the two groups. Six months after surgery, Glasgow outcome scale (GOS) and Barthel index score of the UEEN group were significantly higher than those of the EEN group (GOS score: 3.81±1.06 vs. 3.18±1.07, Barthel index score: 60.78±7.24 vs. 54.52±5.13, both P < 0.05). CONCLUSIONS: UEEN support can improve the nutritional level of young and middle-aged postoperative patients with cerebral hemorrhage, reduce the occurrence of postoperative gastrointestinal complications, promote the recovery of neurological function, and improve the long-term prognosis.

A clinical randomized trial: Effects of early application of sacubitril/valsartan on ventricular remodeling and prognosis in acute myocardial infarction patients.

Objectives: To explore the effects of early application of sacubitril/valsartan on ventricular remodeling and prognosis in patients with acute myocardial infarction (AMI). Methods: Total of 295 patients with AMI admitted to the hospital were enrolled between August 2019 and August 2021. According to different treatment methods, they were divided into observation group (sacubitril/valsartan sodium tables combined with standard treatment, 132 patients) and control group (benazepril hydrochloride tablets combined with standard treatment, 163 patients). The levels of plasma N-terminal pro-brain natriuretic peptide (NT-proBNP), creatinine (Cr) and serum K+ before and at 6 months after treatment, standard deviation of all normal-to-normal intervals (SDNN), standard deviation of the average all normal-to-normal intervals (SDANN), root mean square of differences between adjacent normal-to-normal intervals/root mean square differences of successive R-R (RMSSD), left ventricular end-diastolic volume (LVEDV), left ventricular ejection fraction (LVEF) and left ventricular end-systolic volume (LVESV) in the two groups were compared. The adverse reactions during treatment and major adverse cardiac events (MACE) during 6 months of follow-up in both groups were statistically analyzed. Results: The levels of NT-proBNP, Cr and K+, LVEDV and LVESV in observation group were significantly lower than those in control group (P < 0.05), while LVEF, SDNN, SDANN and RMSSD were significantly higher than those in control group (P < 0.05). The incidence of MACE in observation group was lower than that in control group during 6 months of follow-up (7.58 % vs 27.61 %, P < 0.05), but there was no significant difference in the incidence of adverse reactions (9.85 % vs 12.88 %, P > 0.05). Conclusion: Early application of sacubitril/valsartan sodium can effectively delay ventricular remodeling, improve cardiac function and heart rate variability indexes, reduce NT-proBNP level and improve prognosis in AMI patients.

Mitigating black carbon emissions: key drivers in residential usage and coke/brick production.

Black carbon (BC) is a crucial air pollutant that contributes to short-lived climate forcing and adverse health impacts. BC emissions have rapidly declined over the past three decades and it is important to uncover the major factors behind this decline. Herein, the temporal trends in BC emissions were compiled from 146 detailed sources from 1960 to 2019. Results revealed that the major emission sources were residential solid fuel usage, coke production and brick production. Furthermore, 96.9% of the emission reduction from 3.03 Tg in 1995 to 1.02 Tg in 2019 was attributed to these three sources. It was determined that the transition in residential energy/stove usage, phasing-out of beehive coke ovens and brick kiln upgrading were the most important drivers leading to this reduction and will continue to play a key role in future emission mitigation. In addition, this study identified the need to address emissions from coal used in vegetable greenhouses and the commercial sector, and diesel consumption in on/off-road vehicles.

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.

Role of primary drivers leading to emission reduction of major air pollutants and CO2 from global power plants.

Electricity production is a significant source of air pollution. Various factors, including electricity demand, generation efficiency, energy mix, and end-of-pipe control measures, are responsible for the emission changes during electricity generation. Although electricity production more than doubled from 1990 to 2017, air pollutant emissions showed a moderate increase or decrease, which was attributed to mitigating drivers such as increased clean energy use, improved power generation efficiency, and widespread installation of end-of-pipe control facilities. The absence of these mitigating drivers would have increased CO2, fine particulate matter (PM2.5), black carbon, SO2, and NOx emissions in 2017 by 165 %, 403 %, 1070 %, 614 %, and 274 % than their actual levels, respectively. The improved electricity generation efficiency reduced potential CO2, PM2.5, SO2, and NOx emissions by 30 %, 295 %, 119 %, and 52 % compared to actual emissions, respectively. Meanwhile, the installation of end-of-pipe facilities reduced potential SO2 and PM2.5 emissions by 34.7 and 4.0 Tg, respectively. Considerable differences in emissions among countries were found to be attributable to their differences in electricity demand and the implementation of local mitigating polices.

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.