The safety and feasibility assessment of overlap esophagojejunostomy with self-pulling and latter transection technique in totally laparoscopic total gastrectomy.

BACKGROUND: This study presented an innovative technique in totally laparoscopic total gastrectomy (TLTG) for overlap esophagojejunostomy (E-J), termed self-pulling and latter transection (SPLT) (overlap SPLT). It evaluated the effectiveness and short-term outcomes of this novel method through a comparative analysis with the established functional end-to-end (FETE) E-J incorporating SPLT. METHODS: From September 2018 to September 2023, this study enrolled 68 patients with gastric cancer who underwent TLTG with overlap SPLT anastomosis and 120 patients who underwent TLTG with FETE SPLT anastomosis. Clinicopathologic characteristics and surgical and postoperative outcomes data for overlap SPLT cases were gathered and retrospectively compared with those from FETE SPLT TLTG to evaluate the effectiveness and clinical safety. RESULTS: The duration of anastomosis for overlap SPLT was 25.3 ± 7.4 minutes, significantly longer than that for the FETE SPLT (18.1 ± 4.0 minutes, P = .031). Perioperatively, 1 anastomosis-related complication occurred in each group, but this did not constitute a statistically significant difference (P = .682). No statistically significant differences were found between the 2 groups in terms of operative time, postoperative hospital stay, operative cost, surgical margins, or number of lymph nodes removed. Postoperative morbidity rates were similar between the groups (4.4% vs 5.8%, P = .676). CONCLUSION: The overlap SPLT technique is regarded as a safe and feasible method for anastomosis. There were no apparent differences in complications between overlap SPLT and FETE SPLT, but overlap SPLT costed 1 additional stapler cartridge and required a longer duration.

Ultrasound-Based Deep Learning Radiomics Nomogram for the Assessment of Lymphovascular Invasion in Invasive Breast Cancer: A Multicenter Study.

RATIONALE AND OBJECTIVES: The aim of this study was to develop a deep learning radiomics nomogram (DLRN) based on B-mode ultrasound (BMUS) and color doppler flow imaging (CDFI) images for preoperative assessment of lymphovascular invasion (LVI) status in invasive breast cancer (IBC). MATERIALS AND METHODS: In this multicenter, retrospective study, 832 pathologically confirmed IBC patients were recruited from eight hospitals. The samples were divided into training, internal test, and external test sets. Deep learning and handcrafted radiomics features reflecting tumor phenotypes on BMUS and CDFI images were extracted. The BMUS score and CDFI score were calculated after radiomics feature selection. Subsequently, a DLRN was developed based on the scores and independent clinic-ultrasonic risk variables. The performance of the DLRN was evaluated for calibration, discrimination, and clinical usefulness. RESULTS: The DLRN predicted the LVI with accuracy, achieving an area under the receiver operating characteristic curve of 0.93 (95% CI 0.90-0.95), 0.91 (95% CI 0.87-0.95), and 0.91 (95% CI 0.86-0.94) in the training, internal test, and external test sets, respectively, with good calibration. The DLRN demonstrated superior performance compared to the clinical model and single scores across all three sets (p < 0.05). Decision curve analysis and clinical impact curve confirmed the clinical utility of the model. Furthermore, significant enhancements in net reclassification improvement (NRI) and integrated discrimination improvement (IDI) indicated that the two scores could serve as highly valuable biomarkers for assessing LVI. CONCLUSION: The DLRN exhibited strong predictive value for LVI in IBC, providing valuable information for individualized treatment decisions.

In vitro inhalation bioaccessibility and health risk assessment of difenoconazole in the atmosphere.

BACKGROUND: Assessment of the risk of pesticide inhalation in populations around farmland is necessary because inhalation is one of the ways in which pesticides can risk human health. This study aimed to identify the inhalation risk of difenoconazole on humans by using dose-response and exposure assessments. RESULTS: In the field simulation application, respiratory exposure in populations around farmland ranged from 71 to 430 ng/m3 . Using response surface methodology, the maximum bioaccessibility of difenoconazole in three simulated lung fluids was 35.33% in Gamble's solution (GS), 34.12% in artificial lysosomal fluid (ALF), and 42.06% in simulated interstitial lung fluid (SLF). Taking the proliferation activity of the A549 cell model as the endpoint, the benchmark dose limit and benchmark dose of difenoconazole on A549 cells were 16.36 and 5.60 mg/kg, respectively. The margin of exposure to difenoconazole in GS, ALF and SLF were, respectively, 8.66 × 105 to 5.28 × 106 , 8.97 × 105 to 5.47 × 106 and 7.28 × 105 to 4.44 × 106 . CONCLUSION: The risk assessment results indicate that under all circumstances, applying difenoconazole is safe for populations around farmland. However, a fan-shaped nozzle, suspension concentrate and greater inhalation height increase the risk of inhalation. © 2023 Society of Chemical Industry.

A comprehensive assessment of external exposure to persistent halogenated organic pollutants for residents in an e-waste recycling site, South China.

Human skin wipes from 30 participants, air, dust, and food items were collected from a former electronic waste site in South China to provide a comprehensive understanding of residents' exposure to halogenated flame retardants (HFRs) and polychlorinated biphenyls (PCBs). The total concentration of halogenated organic pollutants (HOPs) in the dust, air, food and skin wipes ranged 240-25000 ng/g, 130-2500 pg/m3, 0.08-590 ng/g wet weight, and 69-28000 ng/m2, respectively. Wild fish, vegetables, and air were dominated by PCBs, whereas dust, livestock, and poultry were dominated by HFRs. The HOP concentrations were several orders of magnitude higher in local foodstuffs than in market foodstuffs. The chemical composition on the forehead was remarkably different from that on the hand. The importance of different exposure routes depends on the residents' food choices, except decabromodiphenyl ethane (DBDPE). For residents who consumed a 100-foot diet (mainly egg) and local wild fish, diet ingestion overwhelmed other exposure routes, and PCBs were mainly contributed by fish and HFRs by egg. For residents who consumed market food, the dermal absorption of most PCB congeners and dust ingestion of highly brominated flame retardants were relatively prominent. Inhalation was found to be a crucial route for pentabromoethylbenzene (PBEB).

Multi-pathway exposure assessment of organophosphate flame retardants in a southern Chinese population: Main route identification with compound-specificity.

In this study, we conducted comprehensive organophosphorus flame retardant (PFR) exposure assessments of both dietary and non-dietary pathways in a rural population in southern China. Skin wipes were collected from 30 volunteers. Indoor and outdoor air (gas and particles), dust in the houses of these volunteers, and foodstuffs consumed by these volunteers were simultaneously collected. The total PFR concentrations in dust, gas, and PM2.5 varied from 53.8 to 5.14 × 105 ng/g, 0.528 to 4.27 ng/m3, and 0.390 to 16.5 ng/m3, respectively. The forehead (median of 1.36 × 103 ng/m2) and hand (median of 920 ng/m2) exhibited relatively high PFR concentrations, followed by the forearm (median of 440 ng/m2) and upper arm (median of 230 ng/m2). The PFR concentrations in the food samples varied from 0.0700 to 10.9 ng/g wet weight in the order of egg > roast duck/goose and vegetable > pork > chicken > fish. Tris(1-chloro-isopropyl) phosphate (TCPP) was the main PFR in the non-diet samples, whereas the profiles of PFR individuals varied by food type. Among the multiple pathways investigated (inhalation, dermal exposure, dust ingestion, and food ingestion), dermal absorption and dust ingestion were the predominant pathways for tris(2-chloroethyl) phosphate (TCEP) and bisphenol A-bis(diphenyl phosphate) (BDP), respectively, whereas dietary exposure was the most important route for other chemicals.

Healthy life expectancy for 202 countries up to 2030: Projections with a Bayesian model ensemble.

Background: Healthy life expectancy (HLE) projections are required for optimising social and health service management in the future. Existing studies on the topic were usually conducted by selecting a single model for analysis. We thus aimed to use an ensembled model to project the future HLE for 202 countries/region. Methods: We obtained data on age-sex-specific HLE and the sociodemographic index (SDI) level of 202 countries from 1990 to 2019 from the Global Burden of Disease (GBD) database and used a probabilistic Bayesian model comprised of 21 forecasting models to predict their HLE in 2030. Results: In general, HLE is projected to increase in all 202 countries, with the least probability of 82.4% for women and 81.0% for men. Most of the countries with the lowest projected HLE would be located in Africa. Women in Singapore have the highest projected HLE in 2030, with a 94.5% probability of higher than 75.2 years, which is the highest HLE in 2019 across countries. Maldives, Kuwait, and China are projected to have a probability of 49.3%, 41.2% and 31.6% to be the new entries of the top ten countries with the highest HLE for females compared with 2019. Men in Singapore are projected to have the highest HLE at birth in 2030, with a 93.4% probability of higher than 75.2 years. Peru and Maldives have a probability of 48.7% and 35.3% being new top ten countries in male's HLE. The female advantage in HLE will shrink by 2030 in 117 countries, especially in most of the high SDI and European countries. Conclusions: HLE will likely continue to increase in most countries and regions worldwide in the future. More attention needs to be paid to combatting obesity, chronic diseases, and specific infectious diseases, especially in African and some Pacific Island countries. Although gender gaps may not be fully bridged, HLE could partially mitigate and even eliminate them through economic development and improvements in health care.

Low-Cost Full-Range Detection of C-Reactive Protein in Clinical Samples by Aptamer Hairpin Probes and Coprecipitation of Silver Ions and Gold Nanoparticles.

C-reactive protein (CRP) levels can vary widely related to diverse disease contexts. However, expensive antibodies have impeded the clinical utility of antibody-based full-range CRP assays, especially in developing countries. Herein, we established a low-cost, antibody-free, 96-well plate-based full-range CRP detection method by combining gold nanoparticles (AuNPs), silver iodide (AgI), Eosin Y, and the aptamer hairpin probe (AHP) with Ag+-mediated cytosine-cytosine mismatches, that is, the Au@AgI/Eosin Y-AHP method. After binding the target CRP, the AHP released Ag+, which subsequently induced the aggregation of AuNPs on the surface of AgI colloids, resulting in a significant increase in the adsorption of Eosin Y on the surface of AuNPs. The changes in fluorescence intensity (FI) of Eosin Y in the supernate without and with CRP were proportional to the concentration of the CRP in the wide range of 0.01-40 ng/mL (r = 0.9969), and 96 samples can be detected in 96-well plates simultaneously by a microplate reader within 45 min. Remarkably, the CRP levels of 100 clinical samples achieved with the Au@AgI/Eosin Y-AHP had a good correlation with those obtained with the latex-enhanced immune turbidimetry assay (r = 0.986). Furthermore, the kit based on the Au@AgI/Eosin Y-AHP method costs only $8.1 for 100 tests. Therefore, the new method is beneficial for less developed areas where expensive assays are not affordable.

Applicability of LC-QToF and Microscopical Tools in Combating the Sophisticated, Economically Motivated Adulteration of Poppy Seeds.

Morphine and codeine are the two principal opiates found in the opium poppy (Papaver somniferum L.) and are therapeutically used for pain management. Poppy seeds with low opiates are primarily used for culinary purposes due to their nutritional and sensory attributes. Intentional adulteration of poppy seeds is common, often combined with immature, less expensive, exhausted, or substituted with morphologically similar seeds, viz., amaranth, quinoa, and sesame. For a safer food supply chain, preventive measures must be implemented to mitigate contamination or adulteration. Moreover, the simultaneous analysis of P. somniferum and its adulterants is largely unknown. Pre- and post-processing further complicate the alkaloid content and may pose a significant health hazard. To address these issues, two independent methods were investigated with eight botanically verified and fifteen commercial samples. Microscopical features were established for the authenticity of raw poppy seeds. Morphine, codeine, and thebaine quantities ranged from 0.8-223, 0.2-386, and 0.1-176 mg/kg, respectively, using LC-QToF. In most cases, conventional opiates have a higher content than papaverine and noscapine. The analytical methodology provided a chemical profile of 47 compounds that can be effectively applied to distinguish poppy seeds from their adulterants and may serve as an effective tool to combat ongoing adulteration.

A new insight into the emission source of DDT in indoor environment from rural area of South China and comprehensive human health exposure assessment.

Human exposure to dichlorodiphenyltrichloroethanes (DDTs) and the subsequent risk to human health remain an important concern due to the "new" input of DDTs in the environment, especially since exposure to DDTs in indoor microenvironments is often ignored. In this study, we identified a new source of DDT emission in indoor environments and evaluated the health risk from the exposure to DDTs by investigating DDTs in indoor and outdoor dust, air, and coatings of household items in rural areas of Qingyuan, South China. The concentrations of DDTs in house dust and air were < MQL (method quantification limit)-3450 ng/g (median 42.4 ng/g) and 22.7-965 pg/m3 (median 49.5 pg/m3), respectively, which were significantly higher than the outdoor DDT values. Dichlorodiphenyldichloroethylene (DDE) was the main isomer in air samples, while DDT was the dominant isomer in indoor dust. Significant correlations between different DDT isomers were observed in indoor samples but not in outdoor samples. Furniture coating was identified as a source of DDTs in the indoor dust. The total daily exposure dose of DDTs (1.75 × 10-2 ng/kg bw/day for adults and 1.28 × 10-1 ng/kg bw/day for toddlers) through inhalation, dust ingestion, and dermal contact was found unlikely to pose a health risk. Our findings provide new insights into the emission sources and health risks caused by DDT indoors, highlighting the need to further investigate the toxicity mechanisms of parent DDT compound.

Occurrence, spatial distribution, and risk assessment of short- and medium-chain chlorinated paraffins in sediment from black-odorous rivers across China.

Chlorinated paraffins (CPs) were massively produced for varied industrial purposes, of which improper handling and consequent environmental release resulted in worldwide contamination. The present study investigated the occurrence and spatial distribution of short- and medium-chain chlorinated paraffins (SCCP/MCCPs) in 171 sediment samples from black-odorous urban rivers across China. Total SCCP and MCCP concentrations ranged from 8.3 to 9.4 × 104 (median: 1.1 × 103) ng/g dw, and from not-detected-value to 1.0 × 106 (median: 1.3 × 104) ng/g dw, respectively. No clear spatial distribution of SCCPs and MCCPs was observed since black-odorous urban rivers were polluted by point-sources of the SCCP/MCCPs. Significant positive correlations were identified between SCCP/MCCPs and total organic carbon, and between SCCP/MCCPs and other persistent organic matter, including polybrominated diethyl ethers, polychlorinated biphenyls, antibiotics, and plasticizers. The average ratios of MCCPs to SCCPs in most samples were divided into 11 and 16, implying the manufacturing and use of at least two types of CP technical mixtures in China. The composition of SCCP/MCCPs were similar to that in their commercial products. Ecological risk assessments by two approaches, including the Federal Environmental Quality Guidelines and Risk Quotient, both revealed that SCCP/MCCP in surface sediments confer an ecological risk. ENVIRONMENTAL IMPLICATION: SCCPs and MCCPs can be considered "hazardous materials" because of their massive production and their potential persistence, long-distance transfer, bioaccumulation potential, and toxicity. This research conducted a comprehensive study on SCCP/MCCP in black-odorous urban river sediments across China and revealed their environmental risk, which may improve understanding of SCCP/MCCP contamination characteristics.

Exploring the convergence patterns of PM2.5 in Chinese cities.

Economic development and ongoing urbanization are usually accompanied by severe haze pollution. Revealing the spatial and temporal evolution of haze pollution can provide a powerful tool for formulating sustainable development policies. Previous studies mostly discuss the differences in the level of PM2.5 among regions, but have paid little attention to the change rules of such differences and their clustering patterns over long periods. Therefore, from the perspective of club convergence, this study employs the log t regression test and club clustering algorithm proposed by Phillips and Sul (Econometrica 75(6):1771-1855, 2007. 10.1111/j.1468-0262.2007.00811.x) to empirically examine the convergence characteristics of PM2.5 concentrations in Chinese cities from 1998 to 2016. This study found that there was no evidence of full panel convergence, but supported one divergent group and eleven convergence clubs with large differences in mean PM2.5 concentrations and growth rates. The geographical distribution of these clubs showed significant spatial dependence. In addition, certain meteorological and socio-economic factors predominantly determined the convergence club for each city.

Energy efficiency evaluation, changing trends and determinants of energy productivity growth across South Asian countries: SBM-DEA and Malmquist approach.

Energy efficiency is widely regarded as the most efficient means of supplying additional energy to meet the rising demand. However, extensive energy consumption causes greenhouse emissions, environmental destruction, and a decrease in energy efficiency (EE). This study investigates the role of energy efficiency and productivity growth in the ecological improvement of South Asia. Moreover, it evaluates the determinants (efficiency change or technology change) of energy productivity change across different SA (South Asian) countries. To estimate the energy efficiency and productivity change, we employed SBM-DEA and Malmquist Productivity Index methods with three inputs (capital stock, labor, and energy consumption), a single desirable output (gross domestic product) and a single undesirable output (CO2 emissions) on the well-extended dataset (2001-2019) for 6 South Asian countries. Furthermore, to check the impact of energy policy (2010) over the study period, the statistical significance of the change in mean scores for energy efficiency and productivity over two time periods (2001-2010 and 2011-2019) and six countries was examined using the Mann-Whitney U and Kruskal-Wallis tests. Results reveal that the average EE score of all 6 SA countries for the study period is 0.7278. This score shows that SA countries still have the potential of 27.22% to improve their energy efficiency to minimize the inputs to get the optimum output level with the least emissions. The primary determinant of energy productivity growth is technological change instead of efficiency. The average energy efficiency level is significantly different for two time periods, 2001-2010 and 2011-2019. Results conclude that energy efficiency and productivity in SA declined over the period, and potential causes are an inefficiency in the energy conversion process, extensive utilization of inputs, and less output growth.

Risk Assessment for Birth Defects in Offspring of Chinese Pregnant Women.

OBJECTIVE: This study aimed to develop a nomogram for the risk assessment of any type of birth defect in offspring using a large birth-defect database in Northwest China. METHODS: This study was based on a birth-defect survey, which included 29,204 eligible women who were pregnant between 2010 and 2013 in the Shaanxi province of Northwest China. The participants from central Shaanxi province were assigned to the training group, while the subjects from the south and north of Shaanxi province were assigned to the external validation group. The primary outcome was the occurrence of any type of birth defect in the offspring. A multivariate logistic regression model was used to establish a prediction nomogram, while the discrimination and calibration were evaluated by external validation. RESULTS: The multivariate analyses revealed that household registration, history of miscarriages, family history of birth defects, infection, taking medicine, pesticide exposure, folic acid supplementation, and single/twin pregnancy were significant factors in the occurrence of birth defects. The area under the receiver operating characteristic curve (AUC) in the prediction model was 0.682 (95% CI 0.653 to 0.710) in the training set. The validation set showed moderate discrimination, with an AUC of 0.651 (95% CI 0.614 to 0.689). Additionally, the prediction model had a good calibration (HL χ2 = 8.106, p= 0.323). CONCLUSIONS: We developed a nomogram risk model for any type of birth defect in a Chinese population based on important modifying factors in pregnant women. This risk-prediction model could be a tool for clinicians to assess the risk of birth defects and promote health education.

Assessment of the juvenile vulnerability of symbiont-bearing giant clams to ocean acidification.

Ocean acidification (OA) severely affects marine bivalves, especially their calcification processes. However, very little is known about the fate of symbiont-bearing giant clams in the acidified oceans, which hinders our ability to develop strategies to protect this ecologically and economically important group in coral reef ecosystems. Here, we explored the integrated juvenile responses of fluted giant clam Tridacna squamosa (Lamarck, 1819) to acidified seawater at different levels of biological organization. Our results revealed that OA did not cause a significant reduction in survival and shell growth performance, indicating that T. squamosa juveniles are tolerated to moderate acidification. Yet, significantly reduced net calcification rate demonstrated the calcifying physiology sensitivity to OA, in line with significant declines in symbiont photosynthetic yield and zooxanthellae density which in turn lowered the amount of energy supply for energetically expensive calcification processes. Subsequent transcriptome sequencing and comparative analysis of differentially expressed genes revealed that the regulation of calcification processes, such as transport of calcification substrates, acid-base regulation, synthesis of organic matrix in the calcifying fluid, as well as metabolic depression were the major response to OA. Taken together, the integration of physiological and molecular responses can provide a comprehensive understanding of how the early life history stages of giant clams respond to OA and make an important leap forward in assessing their fate under future ocean conditions.

Halogenated flame retardants in wild, prey-sized mud carp from an e-waste recycling site in South China, 2006-2016: Residue dynamics and ecological risk assessment.

The crude e-waste recycling has been regulated in China since the late 2000s; however, information on the recent levels and the ecological risks of e-waste derived contaminants such as halogenated flame retardants (HFRs) in the e-waste sites are limited. We therefore examined the concentrations of several HFRs in wild, prey-sized mud carps collected from a typical e-waste site in 2006, 2011 and 2016, to understand the exposure dynamics and ecological risk of these chemicals. Several ecological and biological parameters including δ15N, δ13C, body size and lipid content of the fish were also examined, to ensure an overall uniformity of the sample set among the sampling years. Among the HFRs measured, polybrominated diphenyl ethers (PBDEs) were detected at the highest concentrations (contributing >90% to ∑HFRs), followed by Dechlorane Plus (DPs), polybrominated biphenyls (PBBs), and alternative brominated flame retardants (ABFRs). The fish concentrations of ∑PBDEs, ∑PBBs and ∑DPs significantly dropped by 65%, 57% and 53% from 2006 to 2011, and 12%, 74% and 51% from 2011 to 2016, respectively; likely reflecting the positive impact of the environmental regulations on crude e-waste recycling. The ∑ABFRs concentrations were also decreased by 80% from 2006 to 2011, but increased by 127% from 2011 to 2016; suggesting possible fresh input of these novel HFRs in recent years. In addition to the changes in the HFR concentrations, contaminant profiles in the fish were also changed, possibly due to environmental degradation of the HFRs. Despite our conservative method of risk assessment, we found that PBDEs posed an important risk both for the mud carp and for piscivorous wildlife that inhabit the e-waste site.

Legacy and alternative plasticizers in surface sediment of black-odorous urban rivers across China: Occurrence, spatial distribution, and ecological risk assessment.

In this study, surface sediment samples from 173 black-odorous urban rivers in 74 cities of China were investigated regarding the occurrence, spatial distribution, and ecological risk of legacy phthalates (LPs) and alternative plasticizers (APs). The total concentrations of Σ7LPs and Σ6APs ranged from 0.0035 to 522 µg/g dw (median: 33 µg/g dw; mean: 60 µg/g dw) and from 0.0015 to 16 µg/g dw (median: 16 µg/g dw; mean: 2.2 µg/g dw), respectively. Di(2-ethylhexyl) phthalate (DEHP), di-n-butyl phthalate (DnBP), and di-iso-butyl phthalate (DiBP) were the dominant LPs, and di-iso-decyl phthalate and di-iso-nonylcyclohexane-1,2-dicarboxylate were the dominant APs. The concentrations and compositions of the LPs and APs varied among different sites and regions, implying location-specific use or production of LPs and APs. The pollutant concentrations in southern and central China were higher than those in northern China. Among the seven regions, Northwest China had the lowest concentrations of LPs and APs. This could be related to industry development level, municipal facilities, and population density. Total organic carbon (TOC) was significantly and positively correlated with the pollutant concentrations, implying that TOC could be an important influencing factor for the distribution of LPs and APs in sediments. The risk quotients of DiBP and DnBP in almost all sediment samples were above 1, indicating the high ecological risks to aquatic organisms. Nevertheless, DEHP, di-methyl phthalate, di-ethyl phthalate, and di-n-octyl phthalate showed low or moderate ecological risks for most sampling sites.

Genetic Diversity Assessment of a Chinese Medicinal Endemic Species, Aspidopterys obcordata var. obcordata, by Combined Molecular Marker Methods (ISSR & SRAP).

Aspidopterys obcordata var. obcordata, a medicinal plant endemic to China, is a narrowly distributed species and wild resources are extremely limited. To evaluate the genetic variability and degree of genetic divergence of A. obcordata var. obcordata, and to make rational scientific decisions on its harvest and germplasm conservation, we collected 122 samples from across nearly all of its distribution area and studied genetic diversity using inter-simple sequence repeats (ISSRs), sequence-related amplified polymorphisms (SRAPs), and a method combining the two techniques. The results revealed the high genetic diversity of A. obcordata var. obcordata, mainly due to its intra-population diversity, and the top two populations with the highest levels of intra-population diversity were ML and DH, individuals of which can serve as excellent germplasm candidates during the processing of germplasm screening and conservation. In general, the combining method was prior to the ISSR analyses and SRAP analyses results, except for a slight difference in the genetic structure of individual populations. Therefore, we suggest that a combination analysis of the two marker methods is ideal for evaluating the genetic diversity and genetic relationships of A. obcordata var. obcordata.

HiSCF: leveraging higher-order structures for clustering analysis in biological networks.

MOTIVATION: Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into the understanding of complex biological systems. Existing clustering techniques make use of lower-order connectivity patterns at the level of individual biological entities and their connections, but few of them can take into account of higher-order connectivity patterns at the level of small network motifs. RESULTS: Here, we present a novel clustering framework, namely HiSCF, to identify functional modules based on the higher-order structure information available in a biological network. Taking advantage of higher-order Markov stochastic process, HiSCF is able to perform the clustering analysis by exploiting a variety of network motifs. When compared with several state-of-the-art clustering models, HiSCF yields the best performance for two practical clustering applications, i.e. protein complex identification and gene co-expression module detection, in terms of accuracy. The promising performance of HiSCF demonstrates that the consideration of higher-order network motifs gains new insight into the analysis of biological networks, such as the identification of overlapping protein complexes and the inference of new signaling pathways, and also reveals the rich higher-order organizational structures presented in biological networks. AVAILABILITY AND IMPLEMENTATION: HiSCF is available at https://github.com/allenv5/HiSCF. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effect of laying sequence and selection of maternal tissues in assessment of maternal transfer of organohalogenated contaminants during chicken egg formation: A pilot study.

Many studies have reported maternal transfer of organic contaminants in oviparous species, with inconsonant results. Egg-laying sequence and selected maternal tissues may impact on assessment of potential maternal transfer of contaminants. Here, this hypothesis was verified by exposing chickens (Gallus domesticus) to polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and dechlorane plus (DPs). Concentrations in eggs laid during exposure exhibited periodic fluctuations (conforming to egg-laying cycles) and a decreasing trend during depuration. Fluctuation patterns of DPs and BDE209 differed from those of other compounds. The PBDE congener profiles in eggs were dominated by BDE209 during exposure and by BDE100 and 153 during depuration. The abundance of PCB congener (CB138) which is recalcitrant to metabolism increased with laying sequence. Maternal transfer potential was negatively correlated (P = 0.0014, R2 = 0.7874) to the log KOW of chemicals (log KOW >7) when the muscle, heart, lung, or stomach was used. No correlations were found when the liver, fat, kidneys, or intestine was used (log KOW >7), although DPs and BDE209 showed the highest maternal transfer potential. Different fluctuation patterns of DPs and BDE209 in eggs and increased abundance of BDE209 in eggs laid in the initial egg-laying period imply that the liver, fat, kidney, or intestinal tissues could be more appropriate in assessing maternal transfer of the target analytes.