Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints.

With the exponential growth of digital data, there is a pressing need for innovative storage media and techniques. DNA molecules, due to their stability, storage capacity, and density, offer a promising solution for information storage. However, DNA storage also faces numerous challenges, such as complex biochemical constraints and encoding efficiency. This paper presents Explorer, a high-efficiency DNA coding algorithm based on the De Bruijn graph, which leverages its capability to characterize local sequences. Explorer enables coding under various biochemical constraints, such as homopolymers, GC content, and undesired motifs. This paper also introduces Codeformer, a fast decoding algorithm based on the transformer architecture, to further enhance decoding efficiency. Numerical experiments indicate that, compared with other advanced algorithms, Explorer not only achieves stable encoding and decoding under various biochemical constraints but also increases the encoding efficiency and bit rate by ¿10%. Additionally, Codeformer demonstrates the ability to efficiently decode large quantities of DNA sequences. Under different parameter settings, its decoding efficiency exceeds that of traditional algorithms by more than two-fold. When Codeformer is combined with Reed-Solomon code, its decoding accuracy exceeds 99%, making it a good choice for high-speed decoding applications. These advancements are expected to contribute to the development of DNA-based data storage systems and the broader exploration of DNA as a novel information storage medium.

Fast photocatalytic degradation of rhodamine B using indium-porphyrin based cationic MOF under visible light irradiation.

A broad light-harvesting range and efficient charge separation are two main ways to enhance the visible photocatalytic performance of semiconductors. Herein, an ionic porphyrin MOF [In(TPyP)]·(NO3) (1) (TPyP = 5,10,15,20-tetrakis(4-pyridyl)-21H,23H-porphyrin) was synthesized via in situ metalation. The orderly arranged porphyrin photosensitizer and the internal electric field between the MOF host and NO3- guests enable effective visible light response and electron-hole separation. Consequently, the as-synthesized MOF shows efficient photocatalytic degradation of rhodamine B (RhB), methyl orange (MO) and methylene blue (MB) organic pollutants. It can degrade 99.07% of RhB within only 20 minutes under visible light irradiation (λ > 420 nm) with a high chemical reaction rate constant of 0.2400 min-1. The photocatalytic activity of the title MOF is more efficient than those of other reported MOFs, COFs and even inorganic semiconductors. The reusability, energy level, band gap, charge distribution and main degradation mechanisms of the photocatalyst were well studied.

Standardized lymph node dissection for gallbladder cancer under laparoscopy: en-bloc resection technique.

PURPOSE: Positive lymph node (LN) is a key prognostic factor in radically resected gallbladder cancer (GBCA). However, only a few underwent an adequate lymphadenectomy, and the number and extent of lymph node dissection (LND) have not been standardized. This study aims to develop an en bloc and standardized surgical procedure of LND for GBCA under laparoscopy. METHODS: Data of patients with GBCA underwent laparoscopic radical resection using a standardized and en bloc technique for LND were collected. Perioperative and long-term outcomes were retrospectively analyzed. RESULTS: A total of 39 patients underwent laparoscopic radical resection using standardized and en bloc technique for LND except one case (open conversion rate: 2.6%). Patients with stage T1b had significantly lower LNs involved rate than patients with stage T3 (P = 0.04), whereas median LN count in stage T1b was significantly higher than that in stage T2 (P = 0.04), which was significantly higher than that in stage T3 (P = 0.02). Lymphadenectomy with ≥ 6 LNs accounted for 87.5% in stage T1b, up to 93.3% in T2 and 81.3% in T3, respectively. All the patients in stage T1b were alive without recurrence at this writing. The 2-year recurrence-free survival rate was 80% for T2 and 25% for T3, and the 3-year overall survival rate was 73.3% for T2 and 37.5% for T3. CONCLUSION: The standardized and en bloc LND permits complete and radical removal of lymph stations for patients with GBCA. This technique is safe and feasible with low complication rates and good prognosis. Further studies are required to explore its value and long-term outcomes compared to conventional approaches.

Angle-Dependent Polarized Emission and Photoelectron Performance of Dye-Encapsulated Metal-Organic Framework.

Molecule-based crystalline materials with angle-dependent polarized emission have attracted considerable attention owing to their extensive applications in displays and anticounterfeiting. Herein, one anionic metal-organic framework (MOF) {[Zn2.5(µ3-OH)(NDC)2(HNDC)](HPIM)}n was constructed on the basis of an excellent photoactive ligand naphthalene-1,4-dicarboxylic acid (H2NDC). The protonated 2-propylimidazole (HPIM) guests residing in the nanochannels of MOF can be exchanged by a D-π-A cationic dye. The resulted host-guest system shows a rare example of ratiometric fluorescent polarizations and highly enhanced photoelectron performance in comparison with the pristine MOF.

Processing and characterization of thermoplastic corn starch-based film/paper composites containing microcrystalline cellulose.

BACKGROUND: Different thermoplastic starch (TPS) films were prepared with or without the addition of microcrystalline cellulose (MCC) obtained via the melt-extrusion method, and then the hot-press method was used to produce environmentally friendly TPS-based film/paper composites to replace petroleum-based materials. RESULTS: The paper-plastic composites exhibited good interfacial adhesion from the scannign elctron microscopy images. It was seen that 5 wt.% MCC was added to reinforce the mechanical properties of TPS films, such that it also improved the barrier properties of MCC@TPS/paper composites and extended the path of water vapor through TPS films, which decreased the water vapor transmission rate of MCC@TPS/paper composites. TPS/paper composites and MCC@TPS/paper composites have better physical properties (i.e. smoothness, flexibility and folding resistance) than only paper. In particular, it was found that the water contact angle of MCC@TPS/paper composites and TPS/paper composites were higher than single-layer paper. Furthermore, MCC reinforced paper-plastic composites demonstrated good barrier properties which can meet the requirement of the need for lower water sensitive materials in the food packaging industry. CONCLUSION: Thermoplastic corn starch-based film/paper composites have good application properties as a potential source of bioplastic materials. © 2021 Society of Chemical Industry.

Techno-Economic Analysis of Producing Glacial Acetic Acid from Poplar Biomass via Bioconversion.

Most of the current commercial production of glacial acetic acid (GAA) is by petrochemical routes, primarily methanol carbonylation. GAA is an intermediate in the production of plastics, textiles, dyes, and paints. GAA production from biomass might be an economically viable and sustainable alternative to petroleum-derived routes. Separation of acetic acid from water is a major expense and requires considerable energy. This study evaluates and compares the technical and economic feasibility of GAA production via bioconversion using either ethyl acetate or alamine in diisobutylkerosene (DIBK) as organic solvents for purification. Models of a GAA biorefinery with a production of 120,650 tons/year were simulated in Aspen software. This biorefinery follows the path of pretreatment, enzymatic hydrolysis, acetogen fermentation, and acid purification. Estimated capital costs for different scenarios ranged from USD 186 to 245 million. Recovery of GGA using alamine/DIBK was a more economical process and consumed 64% less energy, due to lower steam demand in the recovery distillation columns. The estimated average minimum selling prices of GGA were USD 756 and 877/ton for alamine/DIBK and ethyl acetate scenarios, respectively. This work establishes a feasible and sustainable approach to produce GGA from poplar biomass via fermentation.

Relationships of LDLR genetic polymorphisms with cerebral infarction: a meta-analysis.

This meta-analysis was undertaken to identify the relationships between genetic polymorphisms in the LDLR gene and the risk of cerebral infarction. The Web of Science (1945-2013), the Cochrane Library Database (Issue 12, 2013), PubMed (1966-2013), EMBASE (1980-2013), CINAHL (1982-2013) and the Chinese Biomedical Database (CBM) (1982-2013) were searched for relevant articles without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Crude odds ratios (OR) with their corresponding 95% confidence interval (CI) were calculated. Eight case-control studies with a total of 4,655 patients with cerebral infarction and 15,920 healthy control subjects were included in our meta-analysis. Five common polymorphisms in the LDLR gene were evaluated, including rs11669576 A > T, rs1433099 C > T, rs5925 C > T, rs688 C > T, rs1122608 T > G in the LDLR gene. The results of this meta-analysis revealed that cerebral infarction patients had a higher frequency of LDLR genetic polymorphisms than that of healthy controls (allele model: OR 1.17, 95% CI 1.05-1.30, P = 0.004; dominant model: OR 1.18, 95% CI 1.05-1.33, P = 0.007; homozygous model: OR 1.50, 95% CI 1.03-2.16, P = 0.032; respectively), especially for the rs11669576 A > T, rs1433099 C > T and rs5925 C > T polymorphisms. Among different ethnic subgroups, the results demonstrated positive correlations between LDLR genetic polymorphisms and an increased risk of cerebral infarction among both Asians and Caucasians under the allele and dominant models (all P < 0.05). Our findings indicate that LDLR genetic polymorphisms may be strongly involved in the pathogenesis of cerebral infarction, especially the rs11669576 A > T, rs1433099 C > T, rs5925 C > T polymorphisms.

Inhalable particulate matter and mitochondrial DNA copy number in highly exposed individuals in Beijing, China: a repeated-measure study.

BACKGROUND: Mitochondria are both a sensitive target and a primary source of oxidative stress, a key pathway of air particulate matter (PM)-associated diseases. Mitochondrial DNA copy number (MtDNAcn) is a marker of mitochondrial damage and malfunctioning. We evaluated whether ambient PM exposure affects MtDNAcn in a highly-exposed population in Beijing, China. METHODS: The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. Personal PM2.5 and elemental carbon (EC, a tracer of traffic particles) were measured during work hours using portable monitors. Post-work blood samples were obtained on two different days. Ambient PM10 was averaged from 27 monitoring stations in Beijing. Blood MtDNAcn was determined by real-time PCR and examined in association with particle levels using mixed-effect models. RESULTS: In all participants combined, MtDNAcn was negatively associated with personal EC level measured during work hours (ß=-0.059, 95% CI: -0.011; -0.0006, p=0.03); and 5-day (ß=-0.017, 95% CI: -0.029;-0.005, p=0.01) and 8-day average ambient PM10 (ß=-0.008, 95% CI: -0.043; -0.008, p=0.004) after adjusting for possible confounding factors, including study groups. MtDNAcn was also negatively associated among office workers with EC (ß=-0.012, 95% CI: -0.022;-0.002, p=0.02) and 8-day average ambient PM10 (ß=-0.030, 95% CI: -0.051;-0.008, p=0.007). CONCLUSIONS: We observed decreased blood MtDNAcn in association with increased exposure to EC during work hours and recent ambient PM10 exposure. Our results suggest that MtDNAcn may be influenced by particle exposures. Further studies are required to determine the roles of MtDNAcn in the etiology of particle-related diseases.

U-type π-conjugated phosphorescent ligand sensitized lanthanide metal-organic frameworks for efficient white-light-emitting diodes.

Lanthanide metal-organic framework (Ln-MOF) based phosphors for light-emitting diodes (LEDs) play an important role in the fields of solid-state lighting and display. The rational design of organic antennae to address the drawback of low extinction coefficients of the lanthanide ions is highly desired. In this work, we provide a new design strategy to achieve an energy transfer molecule with a through-space conjugated folded structure, which can strengthen the skeleton rigidity and facilitate triplet state energy transfer. Consequently, one U-type π-conjugated molecule 2,6-bis(3,5-dicarboxylphenoxy) pyridine (H4L) was selected as a light gatherer to sensitize lanthanide ions for the construction of Ln-MOFs [Ln(HL)(H2O)3]n (Eu-MOF and Tb-MOF), which exhibit a long-lived luminescence lifetime (0.88 ms for Eu-MOF and 1.31 ms for Tb-MOF) and high quantum yields (50.87% for Eu-MOF and 85.64% for Tb-MOF). Furthermore, a white LED device with a colour rendering index (89) was fabricated using the mixture of Ln-MOFs with a commercial blue phosphor.

[Correlations of angio-architectural factors with cerebral arteriovenous malformation hemorrhage].

OBJECTIVE: To explore the relationship between angio-architectures of cerebral arteriovenous malformations (AVM) and hemorrhage. METHODS: A total of 55 consecutive surgical cases of AVM were collected in August 2010 to May 2011 at Beijing Tiantan Hospital. There were 34 males and 21 females with an average age of 32.5 years (range: 3 - 59). The initial symptoms included bleeding (n = 20), epilepsy (n = 21), headache (n = 7), neurological dysfunctions (n = 6) and others (n = 1). The relationship between size, location, type of feeding artery, type of draining vein, complicated venous aneurysm and hemorrhage was analyzed by single factor test. RESULTS: The cases of AVM fed by perforators, located in basal ganglia and post-cranial fossa, with small size, exclusively deep drainage and complicated venous aneurysm were more likely to present with hemorrhage. CONCLUSION: The hemorrhage of AVM is significantly correlated with many factors, such as the type of feeding artery, size and location of AVM, the type of draining vein and complicated venous aneurysm. But the number of draining vein is irrelevant.

Can Information Intervention Enhance Consumers' Purchase Intentions of Organic Agricultural Products? A Choice Experiment Based on Organic Milk.

Despite the current rapid growth of organic agriculture, the problem of low demand for organic agricultural products persists in China, and the consumption space warrants improvement. Exploring consumers' preferences for organic agricultural products and increasing their purchase intentions are of utmost significance to promote organic agricultural production. Thus, this study takes organic milk, which accounts for 58% of China's organic processed agricultural products in sales, as the research object, and uses a choice experiment to investigate the influence of consumers on the purchase intention of organic milk under the intervention of environmental protection information and quality and safety information. The main research results revealed that both environmental protection information and quality and safety information have significantly increased consumers' willingness to purchase and that quality and safety information has increased more than environmental protection information.

Effects of particulate air pollution on blood pressure in a highly exposed population in Beijing, China: a repeated-measure study.

BACKGROUND: Particulate Matter (PM) exposure is critical in Beijing due to high population density and rapid increase in vehicular traffic. PM effects on blood pressure (BP) have been investigated as a mechanism mediating cardiovascular risks, but results are still inconsistent. The purpose of our study is to determine the effects of ambient and personal PM exposure on BP. METHODS: Before the 2008 Olympic Games (June 15-July 27), we examined 60 truck drivers and 60 office workers on two days, 1-2 weeks apart (n = 240). We obtained standardized measures of post-work BP. Exposure assessment included personal PM(2.5) and Elemental Carbon (EC, a tracer of traffic particles) measured using portable monitors during work hours; and ambient PM(10) averaged over 1-8 days pre-examination. We examined associations of exposures (exposure group, personal PM(2.5)/EC, ambient PM(10)) with BP controlling for multiple covariates. RESULTS: Mean personal PM(2.5) was 94.6 µg/m(3) (SD = 64.9) in office workers and 126.8 (SD = 68.8) in truck drivers (p-value < 0.001). In all participants combined, a 10 µg/m(3) increase in 8-day ambient PM(10) was associated with BP increments of 0.98 (95%CI 0.34; 1.61; p-value = 0.003), 0.71 (95%CI 0.18; 1.24; p-value = 0.01), and 0.81 (95%CI 0.31; 1.30; p-value = 0.002) mmHg for systolic, diastolic, and mean BP, respectively. BP was not significantly different between the two groups (p-value > 0.14). Personal PM(2.5) and EC during work hours were not associated with increased BP. CONCLUSIONS: Our results indicate delayed effects of ambient PM(10) on BP. Lack of associations with exposure groups and personal PM(2.5)/EC indicates that PM effects are related to background levels of pollution in Beijing, and not specifically to work-related exposure.

Effect of exposure to high temperatures during early pregnancy on hippocampal-dependent learning and memory integrity in neonatal rats.

To explore the influence of short-term (0, 30 and 60 min) exposure to high temperatures on the integrity of hippocampal-dependent learning and memory in neonatal rats. Confocal laser scanning microscopy (CLSM) was used to observe neuronal apoptosis in the hippocampi of neonatal rats. In situ hybridization was conducted for the detection of hippocampal c-fos messenger RNA (mRNA) expression, and reverse transcription-polymerase chain reaction was performed to test the expression of NR1 (an N-methyl-D-aspartate receptor [NR] subunit) gene in the hippocampus. Finally, the Morris water maze (MWM) was used to evaluate hippocampal-dependent learning and memory. The number of c-fos mRNA-positive cells in the hippocampus was positively correlated with increasing heat exposure times. NR1 mRNA expression in the hippocampal CA1 area was positively correlated with the proportion of dead and apoptotic cells. In addition, neonatal rats exposed to high temperatures had significantly reduced platform crossings in the MWM compared to controls. The duration of heat exposure during early pregnancy was correlated with severe deficits in hippocampal-dependent learning and memory in neonatal rats.

[Metabolism of Rhizopus oryzae with xylose or glucose as carbon resource].

OBJECTIVE: As one of the most abandon and cheapest recyclable bio-resources, cellulosic biomass appear to be the promising new energy if the two major components, glucose and xylose, are efficiently used. METHODS: We compared the metabolism of Rhizopus oryzae growing on glucose or xylose. We measured biomass accumulation, intercellular metabolite contents, and organic acids production. RESULTS: When cultured on xylose, the rate of bio-transformation reached 35.2% compared to 24.3% in the glucose. Intercellular contents accumulated much more by using xylose as sole carbon than using glucose. However, the quantity of organic acid was less with xylose than with glucose. In addition, during the coexistence of both substrates, Rhizopus oryzae utilizes glucose first, and xylose later when the glucose is almost exhausted. CONCLUSION: With our data analysis, both the NADH/NAD + and ATP quantity are differed between the utilization of two carbon resources. In xylose, biological macromolecule and biomass accumulation are in advantage, while in glucose, the inorganic acid production is enhanced.

Analysis of antibiotic usage for viral community-acquired pneumonia in adults.

The rationale for the antibiotic treatment of viral community-acquired pneumonia (CAP) in adults was analyzed to develop a clinical reference standard for this condition. Clinical data from 166 patients diagnosed with viral pneumonia across 14 hospitals in Beijing from November 2010 to December 2017 were collected. The indications for medications were evaluated, and the rationale for the use of antibiotics was analyzed. A total of 163 (98.3%) patients with viral pneumonia were treated with antibiotics. A combination of C-reactive protein (CRP) and procalcitonin (PCT) was used as markers to analyze the possible indications for antibiotic use. With threshold levels set at 0.25 µg/L for PCT and 20 mg/L for CRP, the rate of unreasonable use of antibiotics was 55.2%. By contrast, at a CRP level threshold of 60 mg/L, the rate of antibiotic misuse was 77.3%. A total of 39 of the 163 (23.9%) patients did not meet the guidelines for drug selection for viral CAP in adults. The unreasonable use of antibacterial drugs for the treatment of viral CAP in adults is a serious concern. Clinicians must reduce the unnecessary use of antibiotics.

Transforming biorefinery designs with 'Plug-In Processes of Lignin' to enable economic waste valorization.

Biological lignin valorization has emerged as a major solution for sustainable and cost-effective biorefineries. However, current biorefineries yield lignin with inadequate fractionation for bioconversion, yet substantial changes of these biorefinery designs to focus on lignin could jeopardize carbohydrate efficiency and increase capital costs. We resolve the dilemma by designing 'plug-in processes of lignin' with the integration of leading pretreatment technologies. Substantial improvement of lignin bioconversion and synergistic enhancement of carbohydrate processing are achieved by solubilizing lignin via lowering molecular weight and increasing hydrophilic groups, addressing the dilemma of lignin- or carbohydrate-first scenarios. The plug-in processes of lignin could enable minimum polyhydroxyalkanoate selling price at as low as $6.18/kg. The results highlight the potential to achieve commercial production of polyhydroxyalkanoates as a co-product of cellulosic ethanol. Here, we show that the plug-in processes of lignin could transform biorefinery design toward sustainability by promoting carbon efficiency and optimizing the total capital cost.

Simultaneous transcatheter arterial chemoembolization and portal vein embolization for patients with large hepatocellular carcinoma before major hepatectomy.

BACKGROUND: Sequential transarterial chemoembolization (TACE) and portal vein embolization (PVE) are associated with long time interval that can allow tumor growth and nullify treatments' benefits. AIM: To evaluate the effect of simultaneous TACE and PVE for patients with large hepatocellular carcinoma (HCC) prior to elective major hepatectomy. METHODS: Fifty-one patients with large HCC who underwent PVE combined with or without TACE prior to hepatectomy were included in this study, with 13 patients in the simultaneous TACE + PVE group, 17 patients in the sequential TACE + PVE group, and 21 patients in the PVE-only group. The outcomes of the procedures were compared and analyzed. RESULTS: All patients underwent embolization. The mean interval from embolization to surgery, the kinetic growth rate of the future liver remnant (FLR), the degree of tumor size reduction, and complete tumor necrosis were significantly better in the simultaneous TACE + PVE group than in the other groups. Although the patients in the simultaneous TACE + PVE group had a higher transaminase levels after PVE and TACE, they recovered to comparable levels with the other two groups before surgery. The intraoperative course and the complication and mortality rates were similar among the three groups. The overall survival and disease-free survival were higher in the simultaneous TACE + PVE group than in the other two groups. CONCLUSION: Simultaneous TACE and PVE is a safe and effective approach to increase FLR volume for patients with large HCC before major hepatectomy.

Bridging the gap between feedstock growers and users: the study of a coppice poplar-based biorefinery.

BACKGROUND: In the biofuel industry, land productivity is important to feedstock growers and conversion process product yield is important to the biorefinery. The crop productivity, however, may not positively correlate with bioconversion yield. Therefore, it is important to evaluate sugar yield and biomass productivity. In this study, 2-year-old poplar trees harvested in the first coppice cycle, including one low-productivity hybrid and one high-productivity hybrid, were collected from two poplar tree farms. Through steam pretreatment and enzymatic hydrolysis, the bioconversion yields of low- and high-productivity poplar hybrids were compared for both sites. RESULTS: The low-productivity hybrids had 9-19% higher sugar yields than the high-productivity hybrids, although they have the similar chemical composition. Economic calculations show the impact on the plantation and biorefinery of using the two feedstocks. Growing a high-productivity hybrid means the land owner would use 11-26% less land (which could be used for other crops) or collect $2.53-$3.46 MM/year extra revenue from the surplus feedstock. On the other side, the biorefinery would receive 5-10% additional revenue using the low-productivity hybrid. CONCLUSION: We propose a business model based on the integration of the plantation and the biorefinery. In this model, different feedstocks are assessed using a metric of product tonnage per unit land per year. Use of this new economic metric bridges the gap between feedstock growers and users to maximize the overall production efficiency.

Removal of non-structural components from poplar whole-tree chips to enhance hydrolysis and fermentation performance.

BACKGROUND: Whole-tree chips will be a likely feedstock for future biorefineries because of their low cost. Non-structural components (NSC), however, represent a significant part of whole-tree chips. The NSC can account for more than 10% of whole-tree poplar mass when the trees are grown in short rotation cycles. The influence of NSC, however, on the production of fuels and chemicals is not well known. In this study, we assessed the impact of NSC removal from poplar whole-tree chips on pretreatment and enzymatic hydrolysis yields, overall sugar recovery, and fermentation yield. In addition, we evaluated the economics of preprocessing as a new unit operation in the biorefinery. RESULTS: Poplar whole-tree chips were preprocessed by neutral or acidic washing before steam pretreatment, enzymatic hydrolysis, and fermentation. Preprocessing of poplar reduced ash and extractives content as much as 70 and 50%, respectively. The overall sugar yield after pretreatment and hydrolysis was 18-22% higher when the biomass had been preprocessed, which was explained by higher sugar yields in liquid fraction and more efficient enzymatic hydrolysis of the solid fraction. The liquid fraction ethanol fermentation yield was 36-50% higher for the preprocessed biomass. CONCLUSIONS: It appears that preprocessing reduced the buffering capacity of the biomass due to ash removal, and thereby improved the enzymatic hydrolysis. Removal of extractives during preprocessing improved the fermentation yield. The economic modeling shows that a preprocessing unit could have significant economic benefits in a biorefinery, where poplar whole-tree chips are used as bioconversion feedstock.