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Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.

Abstract In the Gram-positive pathogen Staphylococcus aureus, the membrane-bound ATP-dependent metalloprotease FtsH plays a critical role in resistance to various stressors. However, the molecular mechanism of the FtsH functions is not known. Here, we identified core FtsH target proteins in S. aureus. In the strains Newman and USA300, the abundance of 33 proteins were altered in both strains, of which 11 were identified as core FtsH substrate protein candidates. In the strain Newman and some other S. aureus strains, the sensor histidine kinase SaeS has an L18P (T53C in saeS) substitution, which transformed the protein into an FtsH substrate. Due to the increase of SaeS L18P in the ftsH mutant, Eap, a sae-regulon protein, was also increased in abundance, causing the Newman-specific cell-aggregation phenotype. Regardless of the strain background, however, the ftsH mutants showed lower virulence and survival in a murine infection model. Our study illustrates the elasticity of the bacterial regulatory network, which can be rewired by a single substitution mutation.

Horizontal wells have significant advantages in coal bed methane exploration and development blocks. However, its application in new exploration and development blocks could be challenging. Limited geological data, uncertain geological conditions, and the emergence of micro-faults in pre-drilled target coal seams make it hard to accurately control the well trajectory. The well trajectory prior to drilling needs to be optimized to ensure that the drilling trajectory is within the target coal seam and to prevent any reduction in drilling ratio (defined here as the percentage of the drilling trajectory in the entire horizontal section of the well located in the target coal seam) caused by faults. In this study, the well trajectory optimization is achieved by implementing the following process to drill pilot hole, acquire 2D resonance, and azimuthal gamma logging while drilling. The pilot hole drilling can obtain the characteristic parameters of the target coal seam and the top and bottom rock layers in advance, which can provide judgment values for the landing site design and real-time monitoring of whether the wellbore trajectory extends along the target coal seam; 2D resonance exploration can obtain the construction of set orientation before drilling and the development of small faults and formation fluctuations in the horizontal section, which can optimize the well trajectory in advance; the azimuth gamma logging while drilling technology can monitor the layers drilled by the current drill bit in real time, and can provide timely and accurate well trajectory adjustment methods.The horizontal well-Q in the Block-W of the Qinshui Basin was taken as a case study and underwent technical mechanism research and applicability analysis. The implementation of this new innovative process resulted in a successful drilling of a 711 m horizontal section, with a target coal seam drilling rate of 80%. Compared to previous L-type wells, the drilling rate increased by about 20%, and the drilling cycle shortened by 25%. The technical experience gained from this successful case provides valuable insight for low-cost exploration and development of new coalbed methane blocks., (© 2024. The Author(s).)

Audiovisual difficulty are especially common in older adults. Audiovisual difficulty seriously affect the quality of life of older adults in their later years. It is a top priority to find out the related factors, and to intervene and prevent them. The purpose of this study was to explore the relationship between recreational physical activities and audiovisual difficulty in older adults. We hope that older adults can reduce the risk of hearing and visual difficulty through scientific physical activity. A total of 4,886 people were sampled from the National Health and Nutrition Examination Survey (NHANES) from 2013 to 2018. Recreational physical activity was assessed through the Global Physical Activity Questionnaire (GPAQ); Hearing and visual difficulty were assessed using the Disability Questionnaire (DLQ). Chi-square test was used for categorical variables and rank sum test was used for measurement variables. P < 0.05 was considered statistically significant (bilateral test). After univariate analysis, binary Logistic regression analysis was performed with recreational physical activity as the independent variable, statistically significant demographic variable as the covariate, and hearing and visual difficulty as the dependent variable, respectively. (1) After excluding all confounding variables, recreational physical activity was significantly associated with hearing difficulty (P < 0.001), odds ratio (OR) 0.657 (95% CI 0.5899-0.733); (2) Recreational physical activity was significantly associated with visual difficulty (P < 0.001), OR 0.731 (95% CI 0.630-0.849). (1) Recreational physical activity is the protective factor of hearing difficulty in older adults; (2) Recreational physical activity is a protective factor for visual difficulty in older adults., (© 2024. The Author(s).)

The purpose of this study was to evaluate the association between recent tobacco smoking, household secondhand smoke exposure, confined space secondhand smoke exposure and depressive symptoms in young adults after adjustments for each other. Data from NHANES 2013-2018 were extracted. A total of 4129 young adults age 18-35 years (mean age 26.11 ± 5.39 years, 2021 males and 2108 females) were included. Depressive symptoms were screened by PHQ-9. Recent tobacco smoking was assessed through question "smoked tobacco in the last 5 days?". Household secondhand smoke exposure was assessed through question "living with a smoker who smoked inside the house?". Confined space secondhand smoke exposure was assessed by SSEQ. Binary logistic regression models were performed to analyze the associations. Significant association were observed in recent tobacco smoking (OR = 1.593, 95% CI 1.318-1.926) and confined space secondhand smoke exposure (OR = 1.399, 95% CI 1.185-1.651), but not in household secondhand smoke exposure (P = 0.108). Among the different settings of confined space secondhand smoke exposure, restaurant (OR = 1.732, 95% CI 1.120-2.678) and in-car (OR = 1.350, 95% CI 1.102-1.652) exposure were significantly associated with depressive symptom after after fully adjustments., (© 2024. The Author(s).)

The study aimed to investigate the association between long-term sedentary behavior (LTSB) and depressive symptoms within a representative sample of the U.S. adult population. Data from NHANES 2017-2018 were used, encompassing information on demographics, depressive symptoms, physical activity (PA), and LTSB. Depressive symptoms were identified using the Patient Health Questionnaire (PHQ-9), with "depressive symptoms" defined as a PHQ-9 score of ≥ 5, and "moderate to severe depressive symptoms (MSDS)" defined as a PHQ-9 score of ≥ 10. PA and LTSB were assessed through the Global Physical Activity Questionnaire, where LTSB was interpreted as sedentary time ≥ 600 min. Restricted Cubic Spline (RCS) curves were utilized to observe potential nonlinear relationships. Binary Logistic regressions were conducted to analyze the associations. A total of 4728 participants (mean age 51.00 ± 17.49 years, 2310 males and 2418 females) were included in the study. Among these individuals, 1194 (25.25%) displayed depressive symptoms, with 417 (8.82%) exhibiting MSDS. RCS curves displayed increased risk of depressive symptoms with prolonged sedentary duration. Logistic regression models indicated significant associations between LTSB and depressive symptoms (OR 1.398, 95% CI 1.098-1.780), and LTSB and MSDS (OR 1.567, 95% CI 1.125-2.183), after adjusting for covariates. These findings suggest that LTSB may act as a potential risk factor for both depressive symptoms and MSDS in the studied population., (© 2024. The Author(s).)

Transgenic technology played a crucial role in developing insect-resistant plants resulting in the reduced application of pesticides. This article reports the expression of two cry proteins (Cry3Bb1 and Cry3) in cotton for enhanced resistance against chewing insect pests. The aforementioned genes were synthetically developed and were cloned under appropriate regulatory sequences followed by transformation into Eagle-2 genotype (Gossypium hirsutum) of cotton through shoot apex-cut Agro-infiltration. The transgene integration was validated by polymerase chain reaction using primers flanking the aforementioned cry genes. Transgene expression was assessed by qRT-PCR using GADPH as a reference gene. The relative fold expression analyses revealed the highest expression of the transgene(s) in M1 plants, which is a 4.5-fold expression (Cry3 + Cry3Bb1) followed by M3 (fold expression, 3.0) (Cry3Bb1) and M2 (fold expression, 2.5) (Cry3) transformants of cotton. The confirmed transgenic plants were exposed to insect pests, pink bollworm (Pectinophora gossypiella), and army bollworm (Helicoverpa armigera). Bioassay results revealed that 60% mortality was observed against pink bollworm, and 75% mortality was observed against army bollworm in transgenic plants containing both Cry3Bb1 and Cry3 genes (M1 transgenic plants). In M2 transgenic plants containing only the Cry3Bb1 gene, the mortality was observed to be 40% in the pink bollworm population, whereas 45% mortality was observed in the army bollworm population. In the case of M3 transgenic plants containing single gene-Cry3, the mortality was 20% in the pink bollworm population, whereas 30% mortality was observed in the army bollworm population. Almost no mortality was observed in non-transgenic Eagle-2 control plants. Hence, the developed cotton transformants have improved resistance against chewing insect pests., (© 2022. The Author(s).)

Post-inflammatory hyperpigmentation is a skin discoloration process that occurs following an inflammatory response or wound. As the skin begins to heal, macrophages first exhibit a proinflammatory phenotype (M1) during the early stages of tissue repair and then transition to a pro-healing, anti-inflammatory phenotype (M2) in later stages. During this process, M1 macrophages remove invading bacteria and M2 macrophages remodel surrounding tissue; however, the relationship between macrophages and pigmentation is unclear. In this study, we examined the effect of macrophages on melanin pigmentation using human induced pluripotent stem cells. Functional melanocytes were differentiated from human induced pluripotent stem cells and named as hiMels. The generated hiMels were then individually cocultured with M1 and M2 macrophages. Melanin synthesis decreased in hiMels cocultured with M1 macrophages but significantly increased in hiMels cocultured with M2 macrophages. Moreover, the expression of vascular endothelial growth factor was increased in M2 cocultured media. Our findings suggest that M2 macrophages, and not M1 macrophages, induce hyperpigmentation in scarred areas of the skin during tissue repair., (© 2022. The Author(s).)

Few reports detail the actual outcome of Hepatitis B Surface Antigen-positive patients after kidney transplant. HBsAg-positive patients who underwent kidney transplant between January, 1999, and December, 2018, were reviewed retrospectively. Outcomes including hepatitis B reactivation rate, risk factors for reactivation, and patient and graft survival rates were analyzed. Seventy-seven patients were enrolled (47.1 ± 11.5 years old). Patients received ABO-incompatible (n = 5), crossmatch positive transplant (n = 2), and re-transplant (n = 4). Forty-six patients received prophylactic; 19, medication at least 3 months before the transplant; and 12, did not receive medication. Seventeen out of 76 patients developed reactivation post-transplant. 52.9% of HBV reactivation was accompanied by hepatitis. Inappropriate, other than lifelong prophylactic, antiviral agents (HR = 7.34, 95% CI 1.51-35.69, P = 0.01) and high hepatitis DNA (≥ 1000 IU/ml) pre-transplant (HR = 4.39, 95% CI 1.08-17.81, P = 0.04) increased reactivation risk. There was no significant difference in patient and graft survival between antigen positive patients who received antiviral agent and propensity score matched negative patients. HBsAg positivity in kidney transplant recipients is associated with substantial HBV reactivation rate. Lifelong antiviral therapy is mandatory, and patients with high preop HBV titer should be monitored closely for HBV reactivation.

In this paper, twelve 1,3-dinitrohexahydropyrimidine-based energetic compounds were designed by introducing various explosopheres into hexahydropyrimidine skeleton. Their geometric and electronic structures, heats of formation (HOFs), energetic performance, thermal stability and impact sensitivity were discussed. It is found that the incorporation of electron-withdrawing groups (-NO 2 , -NHNO 2 , -N 3 , -CH(NO 2 ) 2 , -CF(NO 2 ) 2 , -C(NO 2 ) 3 ) improves HOFs of the derivatives and all the substituents contribute to enhancing the densities and detonation properties (D, P) of the title compounds. Therein, the substitution of -C(NO 2 ) 3 features the best energetic performance with detonation velocity of 9.40 km s -1 and detonation pressure of 40.20 GPa. An analysis of the bond dissociation energies suggests that N-NO 2 bond may be the initial site in the thermal decompositions for most of the derivatives. Besides, -ONO 2 and -NF 2 derivatives stand out with lower impact sensitivity. Characters with striking detonation properties (D = 8.62 km s -1 , P = 35.08 GPa; D = 8.81 km s -1 , P = 34.88 GPa), good thermal stability, and acceptable impact sensitivity (characteristic height H 50 over 34 cm) lead novel compounds 5,5-difluoramine-1,3-dinitrohexahydropyrimidine (K) and 5-fluoro-1,3,5-trinitrohexahydropyrimidine (L) to be very promising energetic materials. This work provides the theoretical molecular design and a reasonable synthetic route of L for further experimental synthesis and testing.

Aeration systems consume a large amount of energy in wastewater treatment plants. Fine-pore membrane diffusers are most commonly used in aeration systems. Scaling and fouling on these membrane diffusers will lead to decreased performance in aeration and increase energy consumption. This pilot-scale study focused on the scaling of the three kinds of fine-pore membrane diffusers under different influent hardness conditions. The results showed that the diffusers were mainly polluted by calcium carbonate scaling. Scaling occurred on the outer surface, orifices and inner surface of the membranes. The dynamic wet pressure (DWP) of ethylene-propylenediene monomer (EPDM), silicone and polyurethane (PU) membrane diffusers increased by 126%, 34% and 304%, respectively, within 50 days when the hardness was 400 mg/L (as CaCO 3 ). However, the increase ratio became obviously slow during the subsequent 60-day operation, indicating a scaling rule of membrane diffusers. Considering that the standard aeration efficiency (SAE) acted as a comprehensive index for judging the aeration performance, the silicone diffuser had better performance than the other two diffusers when severe scaling occurred. This research also provides basic support for the design of membrane diffusers to improve their anti-scaling performance.

In this paper, the influences of conductive carbons on the red phosphorus (P) composites in sodium-ion batteries are studied. Electrochemical testing results show that Ketjen Black makes the P composites present much better cycling performances. Electrochemical impedance spectra (EIS) results indicate that when Ketjen Black is used, the total resistance of the electrode can be decreased. Since Ketjen Black is a low-cost and commercially available material, our results suggest that Ketjen Black might be a promising conductor for the alloying anodes such as P in sodium-ion batteries.

Diabetes is a risk factor for osteoporosis. Annatto-extracted tocotrienols (TT) have proven benefits in preserving bone matrix. Here, we evaluated the effects of dietary TT on glucose homeostasis, bone properties, and liver pro-inflammatory mRNA expression in high-fat diet (HFD)-induced type 2 diabetic (T2DM) mice. 58 male C57BL/6 J mice were divided into 5 groups: low-fat diet (LFD), HFD, HFD + 400 mgTT/kg diet (T400), HFD + 1600 mgTT/kg diet (T1600), and HFD + 200 mg metformin/kg (Met) for 14 weeks. Relative to the HFD group, both TT-supplemented groups (1) improved glucose homeostasis by lowering the area under the curve for both glucose tolerance and insulin tolerance tests, (2) increased serum procollagen I intact N-terminal propeptide (bone formation) level, trabecular bone volume/total volume, trabecular number, connectivity density, and cortical thickness, (3) decreased collagen type 1 cross-linked C-telopeptide (bone resorption) levels, trabecular separation, and structure model index, and (4) suppressed liver mRNA levels of inflammation markers including IL-2, IL-23, IFN-γ, MCP-1, TNF-α, ITGAX and F4/80. There were no differences in glucose homeostasis and liver mRNA expression among T400, T1600, and Met. The order of osteo-protective effects was LFD ≥T1600 ≥T400 = Met >HFD. Collectively, these data suggest that TT exerts osteo-protective effects in T2DM mice by regulating glucose homeostasis and suppressing inflammation.

To evaluate the effects of HCV NS5B amino acid substitutions on treatment outcome in Ledipasvir (LDV)/Sofosbuvir (SOF) for Japanese patients with genotype 1b HCV infection, NS5B sequences were examined in i) seven patients experiencing virologic failure after LDV/SOF in real-world practice, ii) 109 SOF-naïve patients, iii) 165 patients enrolled in Phase-3 LDV/SOF trial. A218S and C316N were detected in all patients with viral relapse; the percentages of these substitutions in SOF-naïve patients were 64.2% and 55.0%, respectively. Genotype 1b HCV strains with NS5B-C316N mutation were located in the leaves different from those in which HCV strains without such substitutions were present on the phylogenetic tree. Structural modeling revealed that amino acid 218 was located on the surface of the NTP tunnel. Free energy analysis based on molecular dynamics simulations demonstrated that the free energy required to pass through the tunnel was larger for triphosphate SOF than for UTP in NS5B polymerase carrying A218S, but not in wild-type. However, no susceptibility change was observed for these substitutions to SOF in replicon assay. Furthermore, the SVR rate was 100% in patients enrolled the Phase-3 trial. In conclusion, NS5B A218S and C316N were detected in all patients who relapsed following LDV/SOF in real-world practice. These substitutions did not impact the overall SVR rate after LDV/SOF, however, further studies are needed to elucidate the impact of these substitutions.

Gankyrin is an important oncoprotein that is overexpressed in human hepatocellular carcinoma (HCC). However, the gradual alteration of Gankyrin in successive stages during human HCC development and the mechanism of Gankyrin-mediated hepatocarcinogenesis remain largely unknown. In this study, we evaluated the pattern and level of Gankyrin protein expression using immunohistochemistry in various liver tissues, including normal liver, chronic hepatitis, cirrhosis, adenomatous hyperplasia (AH), and HCC tissues, to analyze its clinicopathological significance. Furthermore, we stably transfected the shRNA-Gan vector, which targets human Gankyrin, into HepG2 cells to assess the role of Gankyrin in cell proliferation and tumorigenicity. The expression level of Gankyrin in the cytoplasm, nucleus, and whole cell was gradually elevated during consecutive stages of hepatocarcinogenesis. The nuclear Gankyrin level in AH was significantly higher than that in normal liver, chronic hepatitis, and cirrhotic tissues. The cytoplasmic, nuclear, and total cellular Gankyrin expression levels in HCC were significantly correlated with capsular invasion and intrahepatic metastasis. Silencing Gankyrin expression using shRNA-Gan repressed tumor cell proliferation, tumorigenicity, migration, and invasion in vitro. Our findings demonstrate that Gankyrin is aberrantly expressed beginning at the initiation stage and plays an important role in the initiation, promotion, and progression of hepatocarcinogenesis.

A photovoltaic reactor was designed for artificial photosynthesis, based on the reactions involved in high energy hydrogen atoms, which were produced from water electrolysis. Water and CO2, under the conditions studied, were converted to oxalate (H2C2O4) and a polymer. This was the first time that the oxalates and oxalate-based polymer were produced from the artificial photosynthesis process.