bluuebunny/crossref_metadata_2025_split huggingface dataset:
The anti-phytoalexin gene Bx-cathepsin W supports the survival of Bursaphelenchus xylophilus under Pinus massoniana phytoalexin stress
Authors: Wang Feng , Chen Qiaoli , Zhang Ruizhi , Li Danlei , Ling Yaming , Song Ruiqing 
Published: October 2019

AbstractBackgroundPine trees challenged byBursaphelenchus xylophilusinvasion produce phytoalexins to combat this nematode. Nevertheless, the phytoalexins of Asian pine trees are ineffective againstB. xylophilus. The anti-phytoalexin genes ofB. xylophilusdisable almost all Asian pine phytoalexins, which has allowedB. xylophilusto devastate pine forests in eastern Asia over the last four decades. However, to date, the factors that stimulate anti-phytoalexin gene expression and the mechanisms by which these genes act are not well understood.ResultsHere, we described anti-phytoalexin genes inB. xylophilususing transcriptomic and bioinformatics analyses. The genes that were induced by bothPinus massonianaand carvone and had similarly elevated expression trends were considered anti-phytoalexin genes. Altogether, 187 anti-phytoalexin genes were identified, including 4 cathepsin genes. KEGG pathway enrichment indicated that those cathepsins were related to the Lysosome pathway. Since cathepsins help to maintain metabolic homeostasis by participating in the degradation of heterophagic and autophagic material, the lysosomal cathepsin geneBx-cathepsin Wwas cloned and characterized. The results of the RNAi assessment indicated that the knockdown ofBx-cathepsin Wreduced the survival rates ofB. xylophilusunder carvone orP. massonianastress. The correlation betweenBx-cathepsin Wand the susceptibility of pines showed thatBx-cathepsin Wmight help improve the anti-phytotoxin ability ofB. xylophilus.ConclusionsThe results indicated that the anti-phytoalexin geneBx-cathepsin Wsupported the survival ofB. xylophilusunderP. massonianaphytoalexin stress. The cDNA library sequencing, differentially expressed gene identification, and WGCNA algorithm analysis provided insight at a systemic level into the gene regulation ofB. xylophilusin response to the immune reaction ofP. massoniana. These results will lead to a better understanding of the function of nematode defenses in host innate immunity.
Physiological and transcriptome analysis reveal molecular mechanism in Salvia miltiorrhiza leaves of near-isogenic male fertile lines and male sterile lines
Authors: Wang Ruihong , Jiang Han , Zhou Ziyun , Guo Hongbo , Dong Juane 
Published: October 2019

Abstract

Background
Our previous study finds that male sterility in Salvia miltiorrhiza could result in stunted growth and reduced biomass, but their molecular mechanisms have not yet been revealed. In this article, we investigate the underlying mechanism of male sterility and its impact on plant growth and metabolic yield by using physiological analysis and mRNA sequencing (RNA-Seq).

Results
In this study, transcriptomic and physiological analysis were performed to identify the mechanism of male sterility in mutants and its impact on plant growth and metabolic yield. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it is found that the pathways are mainly enriched in processes including organ development, primary metabolic process and secondary metabolic process. Physiological analysis show that the chloroplast structure of male sterile mutants of S. miltiorrhiza is abnormally developed, which could result in decrease in leaf gas exchange (A, E and gs), chlorophyll fluorescence (Fv, Fm and Fv/Fm), and the chlorophyll content. Expression level of 7 differentially expressed genes involved in photosynthesis-related pathways is downregulated in male sterile lines of S. miltiorrhiza, which could explain the corresponding phenotypic changes in chlorophyll fluorescence, chlorophyll content and leaf gas exchange. Transcriptomic analysis establishes the role of disproportionating enzyme 1 (DPE1) as catalyzing the degradation of starch, and the role of sucrose synthase 3 (SUS3) and cytosolic invertase 2 (CINV2) as catalyzing the degradation of sucrose in the S. miltiorrhiza mutants. The results also confirm that phenylalanine ammonialyase (PAL) is involved in the biosynthesis of rosmarinic acid and salvianolic acid B, and flavone synthase (FLS) is an important enzyme catalyzing steps of flavonoid biosynthesis.

Conclusions
Our results from the physiological and transcriptome analysis reveal underlying mechanism of plant growth and metabolic yield in male sterile mutants, and provide insight into the crop yield of S. miltiorrhiza.
Dynamic metabolic modelling of overproduced protein secretion in Streptomyces lividans using adaptive DFBA
Authors: Valverde Jósé R. , Gullón Sonia , García-Herrero Clara A. , Campoy Iván , Mellado Rafael P. 
Published: October 2019

Abstract

Background
Streptomyces lividans is an appealing host for the production of proteins of biotechnological interest due to its relaxed exogenous DNA restriction system and its ability to secrete proteins directly to the medium through the major Sec or the minor Tat routes. Often, protein secretion displays non-uniform time-dependent patterns. Understanding the associated metabolic changes is a crucial step to engineer protein production. Dynamic Flux Balance Analysis (DFBA) allows the study of the interactions between a modelled organism and its environment over time. Existing methods allow the specification of initial model and environment conditions, but do not allow introducing arbitrary modifications in the course of the simulation. Living organisms, however, display unexpected adaptive metabolic behaviours in response to unpredictable changes in their environment. Engineering the secretion of products of biotechnological interest has systematically proven especially difficult to model using DFBA. Accurate time-dependent modelling of complex and/or arbitrary, adaptive metabolic processes demands an extended approach to DFBA.

Results
In this work, we introduce Adaptive DFBA, a novel, versatile simulation approach that permits inclusion of changes in the organism or the environment at any time in the simulation, either arbitrary or interactively responsive to environmental changes. This approach extends traditional DFBA to allow steering arbitrarily complex simulations of metabolic dynamics. When applied to Sec- or Tat-dependent secretion of overproduced proteins in S. lividans, Adaptive DFBA can overcome the limitations of traditional DFBA to reproduce experimental data on plasmid-free, plasmid bearing and secretory protein overproducing S. lividans TK24, and can yield useful insights on the behaviour of systems with limited experimental knowledge such as agarase or amylase overproduction in S. lividans TK21.

Conclusions
Adaptive DFBA has allowed us to overcome DFBA limitations and to generate more accurate models of the metabolism during the overproduction of secretory proteins in S. lividans, improving our understanding of the underlying processes. Adaptive DFBA is versatile enough to permit dynamical metabolic simulations of arbitrarily complex biotechnological processes.
Expression patterns of two pal genes of Pleurotus ostreatus across developmental stages and under heat stress
Authors: Hou Ludan , Wang Lining , Wu Xiangli , Gao Wei , Zhang Jinxia , Huang Chenyang 
Published: October 2019

Abstract

Background
Phenylalanine ammonia-lyase (PAL, EC 4.3.1.24) is the first key enzyme in the phenylpropanoid pathway. The pal gene has been widely studied in plants and participates in plant growth, development and defense systems. However, in Pleurotus ostreatus, the biological functions of pal during organismal development and exposure to abiotic stress have not been reported.

Results
In this study, we cloned and characterized the pal1 (2232 bp) and pal2 (2244 bp) genes from the basidiomycete P. ostreatus CCMSSC 00389. The pal1 and pal2 genes are interrupted by 6 and 10 introns, respectively, and encode proteins of 743 and 747 amino acids, respectively. Furthermore, prokaryotic expression experiments showed that PAL enzymes catalyzed the conversion of L-phenylalanine to trans-cinnamic acid. The function of pal1 and pal2 was determined by constructing overexpression (OE) and RNA interference (RNAi) strains. The results showed that the two pal genes had similar expression patterns during different developmental stages. The expression of pal genes was higher in the reproductive growth stage than in the vegetative growth stage. And the interference of pal1 and pal2 delayed the formation of primordia. The results of heat stress assays showed that the RNAi-pal1 strains had enhanced mycelial tolerance to high temperature, while the RNAi-pal2 strains had enhanced mycelial resistance to H2O2.

Conclusions
These results indicate that two pal genes may play a similar role in the development of P. ostreatus fruiting bodies, but may alleviate stress through different regulatory pathways under heat stress.
Peptide Deformylase (def) is essential in Mycobacterium smegmatis, but the essentiality is compensated by inactivation of methionine formylation
Authors: Naor Noga , Gadot Omer , Meir Michal , Barkan Daniel 
Published: October 2019

AbstractBackgroundCo-translational processes in bacteria are attractive drug targets, but while some processes are essential, others are not. The essentiality of Peptide Deformylase (PDF,def) for vitality of mycobacteria was speculated, but never unequivocally proven.ResultsHere we show by targeted deletion experiments thatdefcan only be deleted fromM. smegmatiswhen an additional copy is present; that prior deletion of tRNAfMet-Formyl Transferase (FMT, encoded byfmt) rendersdefcompletely dispensable; and that re-introduction offmtinto aΔdefmutant is not possible – constituting a definitive proof for the essentiality ofdefin mycobacteria.ConclusionsPeptide deformylase is essential inM. smegmatis, but the fact that inactivation offmtrenders the gene completely dispensable, and thus any inhibitor ofdefuseless, casts doubt on the usefulness of PDF as a drug-target in mycobacteria.
Incorporating repeated measurements into prediction models in the critical care setting: a framework, systematic review and meta-analysis
Authors: Plate Joost D. J. , van de Leur Rutger R. , Leenen Luke P. H. , Hietbrink Falco , Peelen Linda M. , Eijkemans M. J. C. 
Published: October 2019

AbstractBackgroundThe incorporation of repeated measurements into multivariable prediction research may greatly enhance predictive performance. However, the methodological possibilities vary widely and a structured overview of the possible and utilized approaches lacks. Therefore, we [1] propose a structured framework for these approaches, [2] determine what methods are currently used to incorporate repeated measurements in prediction research in the critical care setting and, where possible, [3] assess the added discriminative value of incorporating repeated measurements.MethodsThe proposed framework consists of three domains: the observation window (static or dynamic), the processing of the raw data (raw data modelling, feature extraction and reduction) and the type of modelling. A systematic review was performed to identify studies which incorporate repeated measurements to predict (e.g. mortality) in the critical care setting. The within-study difference in c-statistics between models with versus without repeated measurements were obtained and pooled in a meta-analysis.ResultsFrom the 2618 studies found, 29 studies incorporated multiple repeated measurements. The annual number of studies with repeated measurements increased from 2.8/year (2000–2005) to 16.0/year (2016–2018). The majority of studies that incorporated repeated measurements for prediction research used a dynamic observation window, and extracted features directly from the data. Differences in c statistics ranged from − 0.048 to 0.217 in favour of models that utilize repeated measurements.ConclusionsRepeated measurements are increasingly common to predict events in the critical care domain, but their incorporation is lagging. A framework of possible approaches could aid researchers to optimize future prediction models.
Partial ALPPS versus complete ALPPS for staged hepatectomy
Authors: Wu Xukun , Rao Jiawei , Zhou Xiaozhuan , Deng Ronghai , Ma Yi 
Published: October 2019

Abstract

Background
Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) can induce a stronger regenerative ability than traditional 2-stage hepatectomy (TSH). ALPPS has become popular for achieving fast hypertrophy in patients with an insufficient future liver remnant (FLR). However, ALPPS is associated with high morbidity and mortality. Partial ALPPS is a variation that may decrease the morbidity and mortality. The purpose of this study was to perform a meta-analysis comparing outcomes of ALLPS and partial ALLPS.

Methods
PubMed, Embase, and Cochrane Library databases were searched for studies comparing partial ALPPS and complete ALPPS up to April 2019. Included studies were assessed by the Newcastle-Ottawa Scale (NOS). Weighted mean difference (WMD)/standard mean difference (SMD) and odds ratios (OR) with 95% confidence intervals (CIs) were calculated to compare FLR, time interval between stages, postoperative complications, and mortality between partial and complete ALPPS.

Results
Four studies including 124 patients were included. FLR hypertrophy of partial ALPPS was comparable to complete ALPPS (p = 0.09). The time interval between stages was not different between the 2 procedures (p = 0.57). The postoperative complications rate of partial ALPPS was significantly lower than that of complete ALPPS (OR = 0.38; p = 0.03). The mortality rate of partial ALLPS (4.9%) was lower than that of complete ALLPS (18.9%), but the difference was not significant (OR = 0.37; p = 0.12).

Conclusions
Partial ALLPS is associated with similar FLR hypertrophy and time interval between stages as complete ALLPS, and a lower complication rate. Further studies are needed to examine patient selection and outcomes of the 2 procedures.
Impact of a delirium prevention project among older hospitalized patients who underwent orthopedic surgery: a retrospective cohort study
Authors: Choi Jung-Yeon , Kim Kwang-il , Kang Min-gu , Lee Young-Kyun , Koo Kyung-Hoi , Oh Joo Han , Park Young Ho , Suh Jeewon , Kim Nak-Hyun , Yoo Hyun-Jung , Koo Jahyun , Moon Hyun Mi , Kim Eun Hui , Park Kayoung , Kim Cheol-Ho 
Published: October 2019

AbstractBackgroundPostoperative delirium (POD) is a common clinical syndrome with significant negative outcomes. Thus, we aimed to evaluate the feasibility and effectiveness of a delirium screening tool and multidisciplinary delirium prevention project.MethodsA retrospective cohort study was conducted at a single teaching center in Korea. A cohort of patients who underwent a delirium prevention program using a simple delirium screening tool from December 2018 to February 2019 (intervention group,N = 275) was compared with the cohort from the year before implementation of the delirium prevention program (December 2017 to February 2018) (control group,N = 274). Patients aged ≥65 years who were admitted to orthopedic wards and underwent surgery were included. The incidence rates of delirium before and after implementation of the delirium prevention program, effectiveness of the delirium screening tool, change in the knowledge score of nurses, and length of hospital stay were assessed.ResultsThe sensitivity and specificity of the screening tool for the incidence of POD were 94.1 and 72.7%, respectively. The incidence rates of POD were 10.2% (control group) and 6.2% (intervention group). The odds ratio for the risk reduction effect of the project related to the incidence of POD was 0.316 (95% confidence interval: 0.125–0.800,p = 0.015) after adjustment for possible confounders. The delirium knowledge test score increased from 40.52 to 43.24 out of 49 total points (p < 0.001). The median length of hospital stay in the intervention and control groups was 6.0 (interquartile range, 4–9) and 7.0 (interquartile range, 4–10) days, respectively (p = 0.062).ConclusionThe screening tool successfully identified patients at a high risk of POD at admission. The POD prevention project was feasible to implement, effective in preventing delirium, and improved knowledge regarding delirium among the medical staff.Trial registrationNone.
Case report: whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China
Authors: Luo Lijuan , Chen Xi , Payne Michael , Cao Xiaolong , Wang Yan , Zhang Jie , Deng Jianping , Wang Hong , Zhang Zhengdong , Li Qun , Lan Ruiting , Ye Changyun 
Published: October 2019

Abstract

Background
Neonatal listeriosis is a rare but severe disease manifesting as septicemia and central nervous system (CNS) infections with a high fatality rate of around 20 to 30%. Whole genome sequencing (WGS) is a promising technique for pathogen identification and infection source tracing with its high resolution.

Case presentation
A case of neonatal sepsis with listeriosis was reported with positive blood culture for Listeria monocytogenes. The case was investigated to confirm the vertical transmission of the infection and identify the potential food source of the maternal L. monocytogenes infection using WGS. L. monocytogenes was isolated from the neonate’s blood sample the day after caesarean delivery and from the mother’s genital and pudenda swab samples 5 days and 13 days after caesarean delivery. WGS showed that the isolate from the neonate was identical to the genome type of the isolates from the mother, with only one of the 4 isolates from the mother differing by one single nucleotide polymorphism (SNP). By WGS, one L. monocytogenes isolate from a ready-to-eat (RTE) meat sample in the patients’ community market shared the same sequence type but was ruled out as the cause of infection, with 57 SNP differences to the strain causing the maternal-neonatal infection. The food isolate also carried a novel plasmid pLM1686 that harbored heavy metal resistance genes. After caesarean section, the mother was treated with a third generation cephalosporin which L. monocytogenes is naturally resistant to, which may explain why genital and pudenda swabs were still culture-positive for L. monocytogenes 13 days after delivery.

Conclusions
Genital swab culture for L. monocytogenes had been informative in the diagnosis of maternal listeriosis in this case. The high resolution of WGS confirmed the maternal-neonatal transmission of L. monocytogenes infection and ruled out the L. monocytogenes contaminated RTE meat from the local market as the direct source of the mother’s infection.
Decoding of novel missense TSC2 gene variants using in-silico methods
Authors: Sudarshan Shruthi , Kumar Manoj , Kaur Punit , Kumar Atin , G. Sethuraman , Sapra Savita , Gulati Sheffali , Gupta Neerja , Kabra Madhulika , Roy Chowdhury Madhumita 
Published: October 2019

Abstract

Background
Mutations in TSC1 or TSC2 gene cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the formation of non-malignant hamartomas in multiple vital organs. TSC1 and TSC2 gene products form TSC heterodimer that senses specific cell growth conditions to control mTORC1 signalling.

Methods
In the present study 98 TSC patients were tested for variants in TSC1 and TSC2 genes and 14 novel missense variations were identified. The pathogenecity of these novel variations was determined by applying different bioinformatics tools involving computer aided protein modeling.

Results
Protein modelling could be done only for ten variants which were within the functional part of the protein. Homology modeling is the most reliable method for structure prediction of a protein. Since no sequence homology structure was available for the tuberin protein, three dimensional structure was modeled by a combination of homology modeling and the predictive fold recognition and threading method using Phyre2 threading server. The best template structures for model building of the TSC1 interacting domain, tuberin domain and GAP domain are the crystal structures of clathrin adaptor core protein, Rap1GAP catalytic domain and Ser/Thr kinase Tor protein respectively.

Conclusions
In this study, an attempt has been made to assess the impact of each novel missense variant based on their TSC1-TSC2 hydrophobic interactions and its effect on protein function.
Liddle syndrome due to a novel mutation in the γ subunit of the epithelial sodium channel (ENaC) in family from Russia: a case report
Authors: Kozina Anastasiya A. , Trofimova Tatiana A. , Okuneva Elena G. , Baryshnikova Natalia V. , Obuhova Varvara A. , Krasnenko Anna Yu. , Tsukanov Kirill Yu. , Klimchuk Olesya I. , Surkova Ekaterina I. , Shatalov Peter A. , Ilinsky Valery V. 
Published: October 2019

Abstract

Background
Liddle syndrome is a monogenic disease with autosomal dominant inheritance. Basic characteristics of this disease are hypertension, reduced concentration of aldosterone and renin activity, as well as increased excretion of potassium leading to low level of potassium in serum and metabolic alkalosis. The cause of Liddle syndrome is missense or frameshift mutations in SCNN1A, SCNN1B, or SCNN1G genes that encode epithelial sodium channel subunits.

Case presentation
We describe a family with Liddle syndrome from Russia. 15-year-old proband has arterial hypertension, hypokalemia, hyporeninemia, metabolic alkalosis, but aldosterone level is within the normal range. At 12 years of age, arterial hypertension was noticed for the first time. We identified novel frameshift mutation c.1769delG (p.Gly590Alafs) in SCNN1G, which encodes the γ subunit of ENaC in vertebrates. The father and younger sister also harbor this heterozygous deletion. Treatment with amiloride of proband and his sister did not normalize the blood pressure, but normalized level of plasma renin activity.

Conclusions
Our results expand the mutational spectrum of Liddle syndrome and provide further proof that the conserved PY motif is crucial to control of ENaC activity. Genetic analysis has implications for the management of hypertension, specific treatment with amiloride and counselling in families with Liddle syndrome.
Risk factors and consequences of undiagnosed cesarean scar pregnancy: a cohort study in China
Authors: Xie Ri-hua , Guo Xiaoyan , Li Meng , Liao Yan , Gaudet Laura , Walker Mark , Lei Huizhong , Wen Shi Wu 
Published: October 2019

Abstract

Background
The historically high cesarean section rate and the recent change in second-child policy could increase the risk of cesarean scar pregnancy (CSP) in China. This study aims to assess risk factors and consequences of undiagnosed CSP in China.

Methods
We conducted a retrospective cohort study between January 2013 and December 2017 in Qingyuan, Guangdong, China. Independent risk factors for undiagnosed CSP at the first contact with healthcare providers were assessed by log binomial regression analysis. Occurrence of serious complications was compared between undiagnosed and diagnosed CSP cases.

Results
A total of 195 women with CSP were included in the analysis. Of them, 81 (41.5%) women were undiagnosed at the first contact with healthcare providers. Women initially cared in primary or secondary hospitals were at increased risk for undiagnosed CSP: adjusted relative risks (95% confidence intervals) were 3.28 (2.06, 5.22) and 1.91 (1.16, 3.13), respectively, compared with women initially cared in the tertiary hospital. Undiagnosed CSP cases had higher incidences in serious complications (11 versus 0) and post-surgery anemia (23 (28.4%) versus 8 (7.0%)), stayed longer in hospital, and cost higher than diagnosed CSP cases.

Conclusions
Initial care provided at primary or secondary maternity care facilities is an important risk factor for undiagnosed CSP, with serious consequences to the affected women.