Analysis of South American climate and teleconnection indices

Oceanic heat anomalies affect climate in remote regions through the atmospheric cycle. South America (SA) was the first region found associated with EI Niño, which affects the fishery, agriculture, forestry, and livestock industry of SA. As approximately 60% of the total water is used for agriculture, climate changes in SA caused by ocean anomalies have led to the variability of available water, especially for irrigation water. Where the precipitation is low and/or the temperature is high, the availability and quality of water resources are under pressure. For instance, droughts associated with La Niña severely limited water supply and irrigation requirements between 25°S - 40°S in west-central Argentina and central Chile. In order to study the relationship between ocean variability and the climate of SA, 19 teleconnection indices (TI) related to Ocean abnormity are considered. The 19 indices are: the sea surface temperature (SST) and their anomaly in 4 Niño regions (SST1 + 2, SST3, SST3.4, SST4, ANOM1 + 2, ANOM3, ANOM3.4, ANOM4), Southern Oscillation Index (SOI), Oceanic Niño Index (ONI), Outgoing Longwave Radiation (OLR), Arctic Oscillation (AO), North Atlantic Oscillation (NAO), Pacific Decadal Oscillation (PDO), Pacific-North America (PNA), Atlantic Multi-decadal Oscillation (AMO), West and East of Indian Ocean Dipole (IODW, IODE), and the difference between IODW and IODE (IODd). High-resolution gridded climate data (1982-2016) from the Global Precipitation Climatology Centre (GPCC), the Climate Prediction Center (CPC), and the National Centers for Environmental Prediction (NCEP) are applied for correlation analyses. The results show that the 89.4% area of South American climate has a significant correlation with the SST in Niño region 1 + 2, the mean correlation coefficient is 0.55 for NCEP precipitation and 0.54 for CPC temperature. The lag duration for the remote correlation is around 2-3 months. It is the first attempt to analyze the correlation relationship based on 19 TIs, which can provide comprehensive insight into the climate of SA at a high-resolution scale. These findings are helpful for identifying the sensitive factors that affect climate in SA, for projecting the climate variables of SA, and for managing the irrigation water resources of SA.

A Stepwise-Clustered Simulation Approach for Projecting Future Heat Wave Over Guangdong Province

A heat wave is an important meteorological extreme event related to global warming, but little is known about the characteristics of future heat waves in Guangdong. Therefore, a stepwise-clustered simulation approach driven by multiple global climate models (i.e., GCMs) is developed for projecting future heat waves over Guangdong under two representative concentration pathways (RCPs). The temporal-spatial variations of four indicators (i.e., intensity, total intensity, frequency, and the longest duration) of projected heat waves, as well as the potential changes in daily maximum temperature (i.e., Tmax) for future (i.e., 2006–2095) and historical (i.e., 1976–2005) periods, were analyzed over Guangdong. The results indicated that Guangdong would endure a notable increasing annual trend in the projected Tmax (i.e., 0.016–0.03°C per year under RCP4.5 and 0.027–0.057°C per year under RCP8.5). Evaluations of the multiple GCMs and their ensemble suggested that the developed approach performed well, and the model ensemble was superior to any single GCM in capturing the features of heat waves. The spatial patterns and interannual trends displayed that Guangdong would undergo serious heat waves in the future. The variations of intensity, total intensity, frequency, and the longest duration of heat wave are likely to exceed 5.4°C per event, 24°C, 25 days, and 4 days in the 2080s under RCP8.5, respectively. Higher variation of those would concentrate in eastern and southwestern Guangdong. It also presented that severe heat waves with stronger intensity, higher frequency, and longer duration would have significant increasing tendencies over all Guangdong, which are expected to increase at a rate of 0.14, 0.83, and 0.21% per year under RCP8.5, respectively. Over 60% of Guangdong would suffer the moderate variation of heat waves to the end of this century under RCP8.5. The findings can provide decision makers with useful information to help mitigate the potential impacts of heat waves on pivotal regions as well as ecosystems that are sensitive to extreme temperature.

Long-distance communication through systemic macromolecular signaling mediates stress defense responses in plants

Land plants have a unique vascular bundle system that ranges in length from a few centimeters to hundreds of meters. These systems integrate the various organs of the whole plant, perform material exchange between different plant tissues and mediate the transmission of signals between cells or over long distances. Grafting and parasitism can reshape the vascular tissues of different ecotypes or species and represent two important systems for studying plant systemic signaling. In recent years, with the advancement of genomics and sequencing technology, the transportation, identification, and function of systemic plant macromolecules have been extensively studied. Here, we review the current body of knowledge of the transport pathways and regulatory mechanisms of macromolecules in plants and assess systemic, long-distance signal trafficking that mediates stress responses, and plant-environment or plant-insect community interactions. Additionally, we propose several methods for identifying mobile mRNAs and proteins. Finally, we discuss the challenges facing systemic signaling research and put forth the most urgent questions that need to be answered to advance our understanding of plant systemic signaling.

Projections of meteorological drought based on CMIP6 multi-model ensemble: A case study of Henan Province, China

Future changes in drought events are critical for risk assessment and associated policymaking. In this study, the future changes in meteorological droughts in Henan Province, China are explored. Random forests downscaling model is first constructed based on ERA5 reanalysis data and meteorological observations. The model is validated using evaluation indices such as R² and RMSE, and is shown to be able to capture the relationship between large-scale predictors and monthly precipitation. The validated random forests downscaling model is driven by multiple global climate models (GCMs) from the Phase 6 of the Coupled Model Intercomparison Project (CMIP6) under three emission scenarios for projecting three future drought characteristics (duration, frequency, and intensity). Results show that drought frequency decreases in most areas of Henan while drought duration and intensity increase in various degrees. Some differences are also observed among different emission scenarios, especially under SSP2-4.5, where the magnitudes of changes in drought duration and intensity are lower relative to other scenarios. The decrease in drought frequency in most areas is found to be caused by increases in monthly mean precipitation in this study. Changes in drought duration and intensity are related to a combination of increases in precipitation mean and variability.

Identifying optimal virtual water management strategy for Kazakhstan: A factorial ecologically-extended input-output model

Virtual water is an important indicator measuring the amount of water needed from the perspective of consumption, which can help decision makers to identify desired system design and optimal management strategy against water resources shortage. In this study, a novel model named as factorial ecologically-extended input-output model (abbreviated as FEIOM) is developed for virtual water management. FEIOM integrates techniques of input-output model (IOM), ecological network analysis (ENA) and factorial analysis (FA) into a general framework. It is effective to evaluate the virtual water flows, reveal ecological inter-connections in virtual water system (VWS), and identify key water consumption sectors that have significant individual and interactive effects on VWS's performance. FEIOM is then applied to identifying optimal virtual water management strategies for Kazakhstan in Central Asia. The main findings are: (i) Kazakhstan is a net importer of virtual water (reaching up to 46.0 × 10⁹ m³), demonstrating that the national economic structure is reasonable, which can abate the national water scarcity and improve its eco-environmental protection; (ii) the virtual water of agricultural sector is net exporter, where vegetables, fruits and nuts occupy 86% of the total agricultural exports; the massive export of water-intensive products further squeezes the water for other users; (iii) the key factors affecting the national VWS are agriculture > primary manufacturing > advanced manufacturing > services. Therefore, from solving water resources shortage and facilitating sustainable development perspectives, Kazakhstan should stimulate the domestic primary manufacturing productions and improve agriculture and advanced manufacturing water-use efficiencies.

A review on graphitic carbon nitride (g-C3N4) based hybrid membranes for water and wastewater treatment

Graphitic carbon nitride (g-C₃N₄) has gained enormous attention for water and wastewater treatment. Compared with g-C₃N₄ nanopowders, g-C₃N₄ based hybrid membranes have demonstrated great potential for its superior practicability. This review outlines the preparation and characterization of g-C₃N₄ based hybrid membranes and presents their representative applications in water and wastewater treatment (e.g., removal of organic dyes, phenolic compounds, pharmaceuticals, salt ions, heavy metals, and oils). Meanwhile, g-C₃N₄ based films for the removal of contaminants through photocatalytic degradation is also summarized. In addition, the corresponding mechanisms and relevant findings are discussed. Finally, the challenges and research needs in the future and application of g-C₃N₄ based hybrid membranes are highlighted.

Oral oligofructose challenge reduces expression of glucose transport-1 and 5'-adenosine monophosphate-activated protein kinase in lamellar wall of Holstein heifer claw

The laminar tissue of bovine laminitis may undergo energy failure. The expression of glucose transport protein-1 (GLUT-1) and 5'-adenosine monophosphate-activated protein kinase (AMPK) affects the energy metabolism of digital laminar tissue. This study aimed to determine the expression of glucose uptake and AMPK in laminar wall corium of Holstein heifer claw by oral administration of oligofructose. A total of twelve clinically healthy Holstein heifers were selected and divided into two groups, including control (CON, n = 6) and experimental (OF, n = 6) groups. The heifers of OF group were given 17 g/kg BW oligofructose dissolved in water (20 mL/kg BW) and the heifers of CON group were given water only (20 mL/kg BW). The laminar tissues were collected after euthanasia. The amount of protein and transcript expression of AMPK and GLUT-1 were determined by western blot and quantitative reverse transcription-polymerase chain reaction (qRT-PCR), respectively. Expressions of phosphoenolpyruvate carboxy-kinase (PEPCK), receptor-c coactivator1-α (PGC-1α) and peroxisome proliferator-activated receptor-γ (PPAR-γ) were determined by qRT-PCR. The heifers of OF group showed no significant change in the expression and concentration of AMPK. The phosphor-(Thr172) AMPK and GLUT-1 were significantly decreased, while the gene contents of PPAR-γ and PGC-1α were significantly increased. The activation of AMPK and GLUT-1 in digital laminar tissues of heifers was inhibited, which may contribute to digital laminar tissue damage.

miRNATissueAtlas2: an update to the human miRNA tissue atlas

Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).

miRTargetLink 2.0-interactive miRNA target gene and target pathway networks

Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.

Impacts of climate variations on non-stationarity of streamflow over Canada

With climate change, understanding and assessing the impact of climate variations on non-stationary changes of streamflow is of importance in the hydrologic and atmospheric sciences. In this study, tempo-spatial and scaling effects in the impacts of 18 climate variations on nonstationary streamflow for 279 watersheds across Canada are explored. Specifically, the change point and trends of streamflow are examined through Pettitt's test and Mann-Kendall test. Spatial patterns of correlations between the climate variations and flow rates over Canada, especially their non-stationarity, are investigated at seasonal and decadal scales. The patterns are also quantified by seven spatial classification algorithms under method uncertainty. A series of findings regarding the impacts are revealed. For instance, nonstationary changes of streamflow exist for approximately 9% of Canadian watersheds and most of them are located in Prairie Provinces and the eastern coast. The Atlantic Multidecadal Oscillation, Niño 12, Niño 3, Niño 4, and Niño 3.4 pose significant impacts on Canadian streamflow, which vary with watersheds and seasons. The impacts are closely associated with human activities, e.g., significant impacts of climate variations on populated-area streamflow over Canada. Different climatic variations have different time-varying effects on streamflow. All watersheds have obvious clustering characteristics and four spatial patterns are identified, which is insensitive with classification algorithm. These findings are conducive to understanding the hydrological impacts of atmospheric circulation and enhancing the reliability of hydrological prediction.

[Influencing factors on the death of HIV/AIDS patients treated with antiviral treatment in Butuo county, Liangshan Yi Autonomous Prefecture, 2010-2019]

Objective: To understand influencing factors on the deaths of HIV/AIDS patients receiving antireviral treatment in Butuo county of Liangshan Yi Autonomous Prefecture (Liangshan) from 2010 to 2019, to provide data for drug replacement and sustainable antiviral treatment strategy. Methods: A matched case-control study was used to collect basic and follow-up information on AIDS death patients receiving antiviral treatment in Butuo county of Liangshan from 2010 to 2019. The control group was formed by sampling twice the number of cases. The logistic regression model was used to analyze the risk factors affecting mortality. Results: In 3 355 patients of HIV/AIDS treated with antiviral therapy, 1 179 cases in the death group and 2 176 cases in the control group. Including 81.34% were 30-49 years old, 69.09％males, 99.55% Yi nationality, 91.12% were married or cohabitated, 95.77% had junior high school education or below, and 88.41% peasants. Amultivariate logistic stepwise regression model showed that among the death risk factors, age ≥50 years old was 5.08 times (95%CI:3.05-8.48) that of the 18-29, female was 0.70 times (95%CI: 0.52-0.94) than male, the transmission rate of intravenous drug use was 1.43 times (95%CI: 1.06-1.91) that of heterosexual transmission, CD4⁺T lymphocyte (CD4) count ≥350 cells/μl before treatment was 0.38 times (95%CI: 0.30-0.48) that of CD4 <200 cells/μl before treatment, the most recent antiviral treatment regimen containing LPV/r was 0.04 times (95%CI: 0.01-0.18) than that of stavudine (d4T) + lamivudine (3TC) + nevirapine (NVP)/efavirenz (EFV) regimen, drug resistance was 3.40 times (95%CI: 2.13-5.42) of non-drug resistance, non-viral load and non-drug resistance test results were 12.98 times (95%CI: 10.28-16.40) of non-drug resistance. Conclusions: Age, gender, transmission route, CD4 before treatment, the latest antiviral treatment program, and drug resistance test after antiviral therapy were the influencing factors of HIV/AIDS death in Butuo county. It is necessary to expand the coverage of viral load and drug resistance test to change the antiviral therapeutic schedule scientifically and carry out publicity and education on the compliance of patients with antiviral treatment and medical staff training in order to reduce the mortality of patients with antiviral treatment.

Stepwise clustering future meteorological drought projection and multi-level factorial analysis under climate change: A case study of the Pearl River Basin, China

Climate change has significant impacts on the Pearl River Basin, and the regional ecological environment and human production may face severe challenges in the future due to changes in temperature and precipitation, as well as their derivative disasters (e.g., drought). Therefore, a full understanding of the possible impacts of climate change on Pearl River Basin is desired. In this study, the potential changes in temperature, precipitation, and drought conditions were projected through a stepwise clustering projection (SCP) model driven by multiple GCMs under two different RCPs. The developed model could facilitate specifying the inherently complex relationship between predictors and predictands, and its performance was proven to be great by comparing the observations and model simulations. A multi-level factorial analysis was employed to explore the major contributing factors to the variations in projecting drought conditions. The results suggested that the Pearl River Basin would suffer significant increasing trends in T_mean (i.e., 0.25-0.34 °C per decade under RCP4.5 and 0.42-0.60 °C per decade under RCP8.5), and the annual mean precipitation would increase under both RCPs. The drought events lasting for 1-2 months would be decreased by 7.7%, lasting for 3-4 months would be increased by 4.3%, and lasting for more than five months would be increased by 3.4% under RCP4.5, respectively. While they changed to 6.1%, 1.4%, and 4.7% under RCP8.5, respectively. More medium and long-term drought events with higher drought severity would occur. GCM has dominant influences on four different responses of drought duration, accounting for 50.20%, 52.61%, 56.71%, and 56.24% of total variabilities, respectively. Meanwhile, the effects explained by GCM*RCP interactions cannot be neglected, with an average contribution rate of 44.37%, 37.86%, 37.66%, and 35.83%, respectively.

A Real-Time Fluorescent Reverse Transcription Quantitative PCR Assay for Rapid Detection of Genetic Markers' Expression Associated with Fusarium Wilt of Banana Biocontrol Activities in Bacillus

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), especially Tropical Race 4 (TR4), seriously threatens banana production worldwide. There is no single effective control measure, although certain Bacillus strains secrete antibiotics as promising disease-biocontrol agents. This study identified five Bacillus strains displaying strong antibiotic activity against TR4, using a systemic assessment for presence/absence of genetic markers at genome level, and expression profiles at transcriptome level. A conventional PCR with 13 specific primer pairs detected biocontrol-related genes. An accurate, quantitative real-time PCR protocol with novel designed specific primers was developed to characterise strain-specific gene expression, that optimises strain-culturing and RNA-isolation methodologies. Six genes responsible for synthesising non-ribosomal peptide synthetase biocontrol metabolites were detected in all five strains. Three genes were involved in synthesising three Polyketide synthetase metabolites in all five strains, but the macrolactin synthase gene mln was only detected in WBN06 and YN1282-2. All five Bacillus strains have the genes dhb and bioA, essential for synthesising bacillibactin and biotin. However, the gene sboA, involved in subtilisin synthesis, is absent in all five strains. These genes' expression patterns were significantly different among these strains, suggesting different mechanisms involved in TR4 biocontrol. Results will help elucidate functional genes' biocontrol mechanisms.

[The diagnostic performance of galactomannan detection in invasive pulmonary aspergillosis with severe and critically ill influenza]

Objective: To analyze the diagnostic performance of serum and bronchoalveolar lavage fluid (BALF) galactomannan (GM) test in invasive pulmonary aspergillosis(IPA) with severe and critically ill influenza. Methods: A retrospective study was performed for 157 patients with severe and critically ill influenza admitted to the Department of Pulmonary and Critical Care Medicine of the First Affiliated Hospital of Wenzhou Medical University from December 2017 to April 2019.Clinical characteristics and serum and BALF GM values were collected. The patients were divided into an IPA group (n=18) and a non-IPA group (n=139). The definition of IPA modified from AspICU algorithm taken as the gold standard (The corresponding clinical manifestations, imaging manifestations and microbiological diagnostic criteria should be met simultaneously), the performance of serum and BALF GM test and their combination to IPA with influenza were analyzed respectively and receiver operating characteristic curve (ROC) was drawn. Results: A total of 157 cases were enrolled, 95 were critically ill, and the mortality of IPA with influenza was 55.6%(10/18). The APACHE Ⅱ score, PSI score, urea nitrogen, influenza severity (Percentage of critically ill influenza) and invasive ventilator in IPA group were (16±6), (110±31), 10.7 (8.4, 17.8) mmol/L, 88.9% and 66.7%, respectively, which were significantly higher than those in non-IPA group [(10±5), (83±30), 5.2 (3.6, 7.6) mmol/L, 56.8% and 24.5%, P<0.05]. All patients received serum GM test and 32 patients performed BALF GM test at the same time. When the cut-off valve of serum GM test was 0.5 μg/L, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were 66.7% (12/18), 95.0% (132/139), 63.2% (12/19) and 95.7% (132/138) respectively. When the cut-off value of BALF GM test was 1.0 μg/L, the sensitivity, specificity, PPV and NPV were 80%(8/10),86.4%(19/22),72.7%(8/11)and 90.5%(19/21)respectively. The BALF GM cut-off value of 0.88 μg/L showed the highest diagnostic efficacy for IPA, for which the sensitivity and specificity were 90%(9/10) and 86.4%(19/22). The areas under the ROC curve of serum GM, BALF GM, and the combination of them were 0.81, 0.85, and 0.94 respectively. The difference was statistically significant (P<0.05) and the combined diagnosis efficiency was higher. Conclusions: Critically ill influenza patients should be alert for IPA. The sensitivity of serum GM test in the diagnosis of IPA with influenza was low, while the NPV was high. The optimum BALF GM cut-off value was 0.88 μg/L. The combination with BALF and serum GM test can improve the diagnostic performance.

Development of an integrated multivariate trend-frequency analysis method: Spatial-temporal characteristics of climate extremes under global warming for Central Asia

Temperature and precipitation are the two most critical climate variables and their extreme states have more severe impacts than average states on both human society and natural ecosystem. In this study, an integrated multivariate trend-frequency analysis (IMTFA) approach is developed for the risk assessment of climate extremes under the global warming. Through incorporating multiple time series analysis techniques (i.e., M-K test, Sen's slope estimator and Pettitt test) and copula function into a general framework, IMTFA is capable not only of analyzing the temporal trends and change points of extreme temperatures and precipitations, but also of quantifying their univariate and multivariate risks. IMTFA is applied to the Central Asia with considering a long-term (1881-2018) observation data. Our findings are: (i) significant wetting and warming trends were occurred in the Central Asia over past one hundred years, where 42.5%, 59.4% and 79.2% stations have change points for extreme precipitations, maximum and minimum temperatures, respectively; (ii) the occurrences of extreme climate events show obviously spatial heterogeneity, where the highest risks of meteorological drought, flood and frost events are occurred in the southwest, southeast and northeast regions, respectively; (iii) global warming significantly affects the intensities and frequencies of extreme precipitations and temperatures, and their univariate and multivariate risks are intensified in the most regions of Central Asia. The above findings can provide more valuable information for risk assessment and disaster adaptation of climate extremes in Central Asia.

Assessment of the effects of human activity and natural condition on the outflow of Syr Darya River: A stepwise-cluster factorial analysis method

Water scarcity causes a series of eco-environmental problems, such as land salinization, biodiversity reduction and food crisis, which seriously restricts the sustainable development of the Aral Sea basin. In this study, a stepwise-cluster factorial analysis (SCFA) approach is proposed for assessing the effects of natural condition and human activity on the outflow of Syr Darya River (abbreviated as OSR) that has significant effects on the eco-environmental restoration of the Aral Sea. SCFA coupled stepwise cluster analysis and factorial analysis cannot only reflect the variability of outflow, but also identify the driving factors quantitatively. The results disclose that, in 1960-1991, the dominant factors (affecting the OSR) are upstream inflow (25.77%) > agricultural water use of Uzbekistan (7.21%) > industrial water use of Uzbekistan (4.53%) > agricultural water use of Kazakhstan (3.81%) > Precipitation (3.66%); interactions between upstream inflow and agricultural water use of Uzbekistan, Kazakhstan and Tajikistan and interactions between reservoir and evapotranspiration have the significant effects on the OSR. Results also indicate that, in 1992-2015, the dominant factors that affect the OSR are agricultural water use of Uzbekistan (23.31%) > agricultural water use of Kazakhstan (22.15%) > industrial water use of Uzbekistan (8.31%) > domestic water use of Kazakhstan (4.68%) > agricultural water use of Tajikistan (4.54%) > domestic water use of Uzbekistan (4.41%); the interactions between industrial water use and agricultural water use of Uzbekistan, Kazakhstan and Tajikistan and the interactions between reservoir and upstream inflow have the pivotal effects on OSR. In the future, when the agricultural water use of the basin decrease as 4% and the industry water use of Uzbekistan decrease as 2%, the OSR may recover to the middle level of 1970s. The results help identify the major factors affecting the outflow of Syr Darya River as well as seek an effective approach to restore the eco-environment of Aral Sea basin.

Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database

Cultivated strawberry (Fragaria × ananassa) is an important fruit crop species whose fruits are enjoyed by many worldwide. An octoploid of hybrid origin, the complex genome of this species was recently sequenced, serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family. The current annotation of the F. ananassa genome mainly relies on ab initio predictions and, to a lesser extent, transcriptome data. Here, we present the structure and functional reannotation of the F. ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, comprises a total of 108,447 gene models, with 97.85% complete BUSCOs. The models of 19,174 genes were modified, 360 new genes were identified, and 11,044 genes were found to have alternatively spliced isoforms. Additionally, we constructed a strawberry genome database (SGD) for strawberry gene homolog searching and annotation downloading. Finally, the transcriptome of the receptacles and achenes of F. ananassa at four developmental stages were reanalyzed and qualified, and the expression profiles of all the genes in this annotation are also provided. Together, this study provides an updated annotation of the F. ananassa genome, which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.

[A comparative study of breast cancer mass screening and opportunistic screening in Chinese women]

Objective: To compare the population characteristics, the positive rate of screening, the detection rate of breast cancer, early diagnosis rate and the cost between the mass screening group and opportunistic screening group of breast cancer. Methods: This study is a prospective multicenter cohort study conducted from January 1, 2014 to December 31, 2016. The participants were enrolled for mass screening or opportunistic screening of breast cancer. After completing the questionnaire, all the participants received breast physical examination and breast ultrasound examination every year for 3 rounds by year. The participants' characteristics and screening results of the two groups were compared by χ² test, Fisher exact test or Wilcoxon rank-sum test. Results: A total of 20 080 subjects were enrolled. In the mass screening group, 9 434 (100%), 8 111 (85.98%) and 3 940 (41.76%) cases completed the 3 rounds of screening, and 10 646 (100%), 6 209 (58.32%) and 2 988 (28.07%) cases in the opportunistic screening group, respectively. In the opportunistic screening group, the proportions of less than 3 months lactation (1 275/9 796 vs. 1 061/8 860, χ²=4.597, P=0.032), non-fertility (850/10 646 vs. 574/9 434, χ²=27.400, P<0.01), abortion history (6 384/10 646 vs. 5 062/9 434, χ²=81.232, P<0.01), postmenopausal (2 776/10 646 vs. 2 217/9 434, χ²=17.757, P<0.01), long-term oral contraceptives(>6 months) (171/10 646 vs. 77/9 434, χ²=25.593, P<0.01) and family history of breast cancer in first-degree relatives (464/10 646 vs. 236/9 434, χ²=51.257, P<0.01) were significantly higher than those in mass screening group. The positive rate of screening (514/10 646 vs. 128/9 434, χ²=194.736, P<0.01), the detection rate of breast cancer (158/10 646 vs. 13/9 434, χ²=107.374, P<0.01), and positive rate of biopsy (158/452 vs. 13/87, χ²=13.491, P<0.01) in the opportunistic screening group were significantly higher than those of the mass screening group. The early diagnosis rate of the mass screening group was significantly higher than the opportunistic screening group (10/12 vs. 66/141, χ²=5.902, P=0.015). The average cost for detecting each breast cancer case of the mass screening group was 215 038 CNY, which was 13.6 times of the opportunistic screening group (15 799 CNY/case). In the opportunistic screening group, the positive rate of biopsy in primary hospitals was significantly lower than that in large-volume hospitals (79/267 vs. 79/185, χ²=8.267, P=0.004), but there was no significant difference in the mass screening group (6/37 vs. 7/50, χ²=0.082, P=0.774). Conclusions: Breast cancer screening can improve early detection rate. Compared with the mass screening mode, the opportunistic screening mode has the advantages of higher proportion of high-risk factors, higher positive rate of screening, higher detection rate of breast cancer, higher positive rate of biopsy, and lower cost of screening. However, the early diagnosis rate of breast cancer of opportunistic screening is lower than that of mass screening. The positive rate of opportunistic screening in primary hospitals is lower than that of large-volume hospitals. The two screening modes have their own advantages and should be chosen according to local conditions of different regions in China.

A Novel Targeted Therapy System for Cervical Cancer: Co-Delivery System of Antisense LncRNA of MDC1 and Oxaliplatin Magnetic Thermosensitive Cationic Liposome Drug Carrier

BACKGROUND

This study was aimed to prepare a novel magnetic thermosensitive cationic liposome drug carrier for the codelivery of Oxaliplatin (OXA) and antisense lncRNA of MDC1 (MDC1-AS) to Cervical cancer cells and evaluate the efficiency of this drug carrier and its antitumor effects on Cervical cancer.

METHODS

Thermosensitive magnetic cationic liposomes were prepared using thin-film hydration method. The OXA and MDC1-AS vectors were loaded into the codelivery system, and the in vitro OXA thermosensitive release activity, efficiency of MDC1-AS regulating MDC1, in vitro cytotoxicity, and in vivo antitumor activity were determined.

RESULTS

The codelivery system had desirable targeted delivery efficacy, OXA thermosensitive release, and MDC1-AS regulating MDC1. Codelivery of OXA and MDC1-AS enhanced the inhibition of cervical cancer cell growth in vitro and in vivo, compared with single drug delivery.

CONCLUSION

The novel codelivery of OXA and MDC1-AS magnetic thermosensitive cationic liposome drug carrier can be applied in the combined chemotherapy and gene therapy for cervical cancer.

[Expert consensus on the treatment of oral and maxillofacial space infections]

Oral and maxillofacial space infections (OMSI) are common diseases of the facial region involving fascial spaces. Recently, OMSI shows trends of multi drug-resistance, severe symptoms, and increased mortality. OMSI treatment principles need to be updated to improve the cure rate. Based on the clinical experiences of Chinese experts and with the incorporation of international counterparts' expertise, the principles of preoperative checklist, interpretation of examination results, empirical medication principles, surgical treatment principles, postoperative drainage principles, prevention strategies of wisdom teeth pericoronitis-related OMSI, blood glucose management, physiotherapy principles, Ludwig's angina treatment and perioperative care were systematically summarized and an expert consensus on the diagnosis and treatment of OMSI was reached. The consensus aims to provide criteria for the diagnosis and treatment of OMSI in China so as to improve the level of OMSI treatment.

Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions

Selecting suitable internal reference genes is an important prerequisite for the application of quantitative real-time PCR (qRT-PCR). However, no systematic studies have been conducted on reference genes in luffa. In this study, seven reference genes were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H₂O₂, and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated that EF-1α was the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally, UBQ expression was stable following the salt treatment, whereas TUB was identified as a suitable reference gene for H₂O₂ and drought treatments. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase (Cu/Zn-SOD) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. These results will be conducive to more accurate quantification of gene expression levels in luffa.

CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.