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Advances in Biochemical Engineering/Biotechnology
Eichhornia crassipes is one of the aquatic plants that creates enormous annoyances because of its propensity to completely cover the surface of the water it colonizes, hence its negative impact on navigation, irrigation, fishing and the conservation of biodiversity. The aim of this work is its valorization by producing bioethanol of second generation; it is an optimal valorization for the production of simple fermentable sugars with high added value. In the first process which is chemicaldoi:10.1007/10_2011_131 pmid:22231654 fatcat:ybdqckgblzfwppwtetvpk4czlm
more »... ysis, the biomass was depolymerized by steam treatment. Then a second process which is enzymatic hydrolys is with Aspergillus Niger cellulase. The monitoring of kinetic parameters such as Brix, pH and glucose level showed a considerable evolution of the glucose level from 0.5 to 11.21 mg/ml according to the pretreatment time and from 11.21 to 21.46 mg/mL after the enzymatic hydrolysis according to the type of hydrolysed sample. In conclusion, this work allowed to show the impact of the thermomechanical and biotechnological processes used on the lignocellulosic biomass and to set up a time of pretreatment by steam explosion and an optimal concentration of cellulase applied to Eichhornia crassipes for its bioconversion in ethanol fuel.
Nicotine, the primary psychoactive component in tobacco, can exert a broad impact on both the central and peripheral nervous systems. During the past years, a tremendous amount of efforts has been put to exploring the molecular mechanisms underlying tobacco smoking related behaviors and diseases, and many susceptibility genes have been identified via various genomic approaches. For many human complex diseases, there is a trend towards collecting and integrating the data from genetic studies anddoi:10.1093/database/bax097 fatcat:vla7ie7jeffvnobcmvou6i6nve
more »... the biological information related to them into a comprehensive resource for further investigation, but we have not found such an effort for nicotine addiction or smoking-related phenotypes yet. To collect, curate, and integrate cross-platform genetic data so as to make them interpretable and easily accessible, we developed Genetic Resources Of Nicotine and Smoking (GRONS), a comprehensive database for genes related to biological response to nicotine exposure, tobacco smoking related behaviors or diseases. GRONS deposits genes from nicotine addiction studies in the following four categories, i.e. association study, genome-wide linkage scan, expression analysis on genes/proteins via high-throughput technologies, as well as single gene/protein-based experimental studies via literature search. Moreover, GRONS not only provides tools for data browse, search and graphical presentation of gene prioritization, but also presents the results from comprehensive bioinformatics analyses for the prioritized genes associated with nicotine addiction. With more and more genetic data and analysis tools integrated, GRONS will become a useful resource for studies focusing on nicotine addiction or tobacco smoking.
Cardiophrenic angle lymph node metastases are relatively rare. Surgical resection is the main treatment for cardiophrenic angle lymph node metastasis, but it is not always possible. Case presentation: Here, we report our initial experience with cryoablation of a cardiophrenic angle lymph node metastasis from liver cancer. As the cardiophrenic angle lymph node metastasis was located close to the heart, about 200 mL of 0.9% saline was injected into the pericardium to separate the heart from thedoi:10.1186/s13256-017-1313-4 pmid:28803547 pmcid:PMC5554983 fatcat:taytva5i45ephfnbdpxgzboyfi
more »... rget area. The cardiophrenic angle lymph node metastasis was successfully ablated, without any complications. Conclusions: Cryoablation may be a suitable alternative treatment for cardiophrenic angle lymph node metastasis.
Purpose: To evaluate the performance of PCR-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection. Methods: All the 5 NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing DNA input and library preparation protocol (PCR-based versus PCR-free protocols for library preparation). The DP (depth of coverage) and GQ (genotype quality) of each sample were compared. We developed adoi:10.1101/2020.06.19.160739 fatcat:tpzwaaw6hvfrjohau3bpqsg2l4
more »... tematic WGS pipeline for the analysis of down-sampling samples of the 5 NA12878 samples. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes and CNVs. Results: In general, NA12878-2 (PCR-free WGS) showed better DP and GQ distribution than NA12878-1 (PCR-based WGS). With a mean depth of ~40X, the sensitivity of homozyous and heterozygous SNPs of NA12878-2 showed higher sensitivity (>99.77% and > 99.82%) than NA12878-1, and positive predictive value (PPV) exceeded 99.98% and 99.07%. The sensitivity and PPV of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and CNVs are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. Conclusion: Different experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.
The prevalence of tobacco use in people with schizophrenia is much higher than in general population, which indicates a close relationship between nicotine addiction and schizophrenia. However, the molecular mechanism underlying the high comorbidity of tobacco smoking and schizophrenia remains largely unclear. In this study, we conducted a pathway and network analysis on the genes potentially associated with nicotine addiction or schizophrenia to reveal the functional feature of these genes anddoi:10.1038/s41598-018-21297-x pmid:29440730 pmcid:PMC5811491 fatcat:gcb6kwvtgrbc3dlmghfhja3pma
more »... their interactions. Of the 276 genes associated with nicotine addiction and 331 genes associated with schizophrenia, 52 genes were shared. From these genes, 12 significantly enriched pathways associated with both diseases were identified. These pathways included those related to synapse function and signaling transduction, and drug addiction. Further, we constructed a nicotine addiction-specific and schizophrenia-specific sub-network, identifying 11 novel candidate genes potentially associated with the two diseases. Finally, we built a schematic molecular network for nicotine addiction and schizophrenia based on the results of pathway and network analysis, providing a systematic view to understand the relationship between these two disorders. Our results illustrated that the biological processes underlying the comorbidity of nicotine addiction and schizophrenia was complex, and was likely induced by the dysfunction of multiple molecules and pathways. Schizophrenia is a severe psychiatric disorder with 1% of the life-time prevalence in the general population 1,2 . Patients suffering from schizophrenia may show protean manifestations including auditory hallucinations, weird delusions, significant social withdrawal, difficulty in learning/memory retention, and disorganized speech 3 . Currently, there is still no effective treatment for schizophrenia, and those available largely consist in the using of antipsychotic drugs combined with psychological therapies and other approaches. Thus, developing better approaches for schizophrenia treatment remains a pressing task for public health 1 . Epidemiological studies have shown that individuals with schizophrenia have a higher incidence of substance use as compared to the general population 4-7 . Especially, there is a high prevalence of tobacco smoking among those suffering from the disorder. It has been found that more than 80% of individuals with schizophrenia smoke and are nicotine dependent, compared to the smoking rate of about 25% in the normal individuals 8 . Also, patients suffering from the disorder often smoke high-tar cigarettes and extract more nicotine per cigarette than the common smokers 9 . Moreover, compared to smokers without mental illness, people with schizophrenia face additional challenges, making it more difficult for them to quit smoking 10,11 . Thus, exploring the neurobiological mechanisms that contribute to comorbid nicotine use in schizophrenics is necessary to understand the aetiology and pathogenesis of schizophrenia, and will be helpful for developing more effective therapeutic strategies to prevent and treat the two diseases. From another prospective, the prevalence of smoking among patients with schizophrenia implicates that some shared neurobiological processes may be responsible for the co-occurrence of the two disorders. One hypothesis is that the use of tobacco in schizophrenic is mainly driven by self-medication since some psychiatric symptoms of schizophrenia can be relieved by smoking    . There are two main arguments for this hypothesis, one is Published: xx xx xxxx OPEN www.nature.com/scientificreports/
Leiomyosarcoma with osteoclast-like giant cells (LMS-OGC) has seldom been reported clinically. LMS-OGC of the breast is extremely rare according to the literature. Here, we report a case of LMS-OGC leiomyosarcoma with osteoclast-like giant cells of the breast. A 51-year-old female patient presented with a breast mass which was treated surgically and the pathological examination of the tumor indicated LMS-OGC. Microscopically, the tumor was composed of spindle cells arranged in bundles or spokesdoi:10.1111/1759-7714.13190 pmid:31474003 pmcid:PMC6775023 fatcat:3dynnpofabca7pdy7jcesyhi5u
more »... with giant tumor cells and mitosis. Eosinophilic cytoplasm and morphologically benign osteoclast-like cells were mixed together. Immunohistochemistry examination revealed SMA and desmin were positive with a Ki-67 proliferation index of 40%. However, CK (AE1/AE3), E-cadherin, ER, PR, CD34, S-100 and CD10 were negatively expressed in the tumor tissue. LMS-OGC is a soft tissue malignant tumor which develops extremely rarely in the breast. It should be differentiated and diagnosed according to the history, histological characteristics and immunohistochemical staining.
Evidence has been shown that circular RNAs (circRNAs) play a vital role during the development of ovarian cancer. However, the mechanism by which circEXOC6B regulates tumorigenesis of ovarian cancer remains unknown. Thus, this study aimed to investigate the role of circEXOC6B during the progression of ovarian cancer. The dual-luciferase reporter system assay was used to determine the interaction between circEXOC6B, miR-421 and RUS1 in ovarian cancer, respectively. CCK8 and colony formattingdoi:10.2147/ott.s243040 pmid:32884301 pmcid:PMC7443403 fatcat:jm2sbeir5ndqvaawcylsatts6i
more »... used to evaluate cell proliferation. Meanwhile, the expressions of RSU1, PINCH1 and ILK in SKOV3 cells were detected with Western blot. Downregulation of circEXOC6B markedly promoted the proliferation and invasion in A2780 cells. In contrast, upregulation of circEXOC6B significantly inhibited the proliferation and invasion in SKOV3 cells. Moreover, overexpression of circEXOC6B obviously induced the apoptosis of SKOV3 cells. Furthermore, luciferase reporter assay identified that miR-421 was the potential miRNA binding of circEXOC6B, and RUS1 was the potential binding target of miR-421. Mechanism analysis indicated that upregulation of circEXOC6B increased the level of RUS1 by acting as a competitive "sponge" of miR-421. In this study, we found that circEXOC6B suppressed the growth of ovarian cancer cells through upregulating RSU1 partially via sponging miR-421. Therefore, circEXOC6B might be a potential target for the treatment of ovarian cancer.
Purpose: To explore the safety and efficacy of irreversible electroporation ablation in unresectable fibrous sarcoma with 2 electrodes. Methods: A 74-year-old woman with unresectable retroperitoneal malignant fibrous sarcoma was treated with percutaneous irreversible electroporation. Four ablations were performed on the mass, which measured 7.3 Â 7.0 Â 7.5 cm, with 2 electrodes. Results: A contrast-enhanced computed tomography scan 2 months postoperatively showed that the tumor had reduced todoi:10.1177/1533034617711530 pmid:28558487 pmcid:PMC5762055 fatcat:5c2hcvs5hjclxaype66s33twru
more »... 1 Â 4.0 Â 5.2 cm, without obvious enhancement. Any adverse reactions were evaluated as level 1. Conclusion: In the short term, the treatment with 2 electrodes for fibrous sarcoma appears to be safe and effective.
The Plant Cell
Leaf senescence is a highly coordinated, complicated process involving the integration of numerous internal and environmental signals. Salicylic acid (SA) and reactive oxygen species (ROS) are two well-defined inducers of leaf senescence whose contents progressively and interdependently increase during leaf senescence via an unknown mechanism. Here, we characterized the transcription factor WRKY75 as a positive regulator of leaf senescence in Arabidopsis thaliana. Knockdown or knockout ofdoi:10.1105/tpc.17.00438 pmid:29061866 pmcid:PMC5728132 fatcat:z2tvmne3nfcstle4l5evfpw2u4
more »... delayed age-dependent leaf senescence, while overexpression of WRKY75 accelerated this process. WRKY75 transcription is induced by age, SA, H 2 O 2 , and multiple plant hormones. Meanwhile, WRKY75 promotes SA production by inducing the transcription of SA INDUCTION-DEFICIENT2 (SID2) and suppresses H 2 O 2 scavenging, partly by repressing the transcription of CATALASE2 (CAT2). Genetic analysis revealed that the mutation of SID2 or an increase in catalase activity rescued the precocious leaf senescence phenotype evoked by WRKY75 overexpression. Based on these results, we propose a tripartite amplification loop model in which WRKY75, SA, and ROS undergo a gradual but self-sustained rise driven by three interlinking positive feedback loops. This tripartite amplification loop provides a molecular framework connecting upstream signals, such as age and plant hormones, to the downstream regulatory network executed by SA-and H 2 O 2 -responsive transcription factors during leaf senescence.
Filamentous fungus Penicillium oxalicum produces diverse lignocellulolytic enzymes, which are regulated by the combinations of many transcription factors. Here, a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production. Twenty transcription factors (including ClrB, CreA, XlnR, Ace1, AmyR, and 15 unknown proteins) were identified to play putative roles in the activation or repression of cellulase synthesis. Most of thesedoi:10.1371/journal.pgen.1005509 pmid:26360497 pmcid:PMC4567317 fatcat:li4zeplr2ffexm6donjkdlhnl4
more »... gulators have not been characterized in any fungi before. We identified the ClrB, CreA, XlnR, and AmyR transcription factors as critical dose-dependent regulators of cellulase expression, the core regulons of which were identified by analyzing several transcriptomes and/or secretomes. Synergistic and additive modes of combinatorial control of each cellulase gene by these regulatory factors were achieved, and cellulase expression was fine-tuned in a proper and controlled manner. With one of these targets, the expression of the major intracellular β-glucosidase Bgl2 was found to be dependent on ClrB. The Bgl2-deficient background resulted in a substantial gene activation by ClrB and proved to be closely correlated with the relief of repression mediated by CreA and AmyR during cellulase induction. Our results also signify that probing the synergistic and dose-controlled regulation mechanisms of cellulolytic regulators and using it for reconstruction of expression regulation network (RERN) may be a promising strategy for cellulolytic fungi to develop enzyme hyper-producers. Based on our data, ClrB was identified as focal point for the synergistic activation regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a "seesaw model" in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors. Cellulolytic fungi have evolved into sophisticated lignocellulolytic systems to adapt to their natural habitat. This trait is important for filamentous fungi, which are the main source of cellulases utilized to degrade lignocellulose to fermentable sugars. Penicillium oxalicum, which produces lignocellulolytic enzymes with more diverse components than Trichoderma reesei, has the capacity to secrete large amounts of cellulases. Meanwhile, cellulase expression is regulated by a complex network involved in many transcription factors in this organism. To better understand how cellulase genes are systematically regulated in P. oxalicum, we employed molecular genetics to uncover the cellulolytic transcription factors on a genome-wide scale. We discovered the synergistic and tunable regulation of cellulase expression by integrating cellulolytic regulators and their target genes, which refined our understanding of transcriptional-regulatory network as a "seesaw model" in which the coordinated regulation of cellulolytic genes is established by counteracting activators and repressors. 6 / 45 Fig 2. Regulation of cellulolytic gene expression by ClrB, XlnR and CreA. (A) Northern blot analysis of the transcription of cellulolytic genes in the mutants versus wild-type strain. The strains were pre-cultured on glucose for 22 hours and then were shifted to Vogel's medium without carbon source for starvation cultivation for 2 hours, and then transferred to the same medium containing 2% (w/v) cellulose. 2 μg of total RNA was electrophoresed and blotted onto Hybond N+ nylon membrane. cbh1, eg2 or xyn1 mRNA was probed at different time points after shift to cellulose. (B) Under the same culture condition, gene expression levels of 3 cellobiohydrolase and 15 endoglucanase genes were determined in the mutants versus wild-type strain by q-PCR. All values Regulation of Cellulase Gene Expression PLOS Genetics | DOI:10.1371/journal.pgen.1005509 September 11, 2015 7 / 45 were normalized using the actin gene value/10000. Values reported were means of three biological replicates of each strain. Error bars represent the standard deviation of 3 biological replicates. Fig 3. Defining the categories of genes potentially regulated by ClrB. The ΔclrB mutant and wild-type strains were pre-cultured on glucose for 22 hours and then shifted to Vogel's media with no carbon source for 2 hours, and then transferred to Vogel's medium containing 2% (w/v) cellulose for 4 hours. These differential expression genes were subjected to gene ontology enrichment analysis and percentages of genes varying significantly for ClrB regulon distributed within each functional category. The x-axis represents the percentage of genes in the corresponding GO class.
Irreversible electroporation (IRE) is a new non-thermal ablation therapy that is currently undergoing clinical investigation for treatment of malignant liver and lung tumors; however, there is emerging evidence that is method can interfere with heart function. Here we report the first case of a 61-year-old Malaysian woman who underwent IRE ablation on liver metastases from pancreatic cancer located adjacent to the heart. During IRE ablation, two electrodes were placed on the liver tumor, withdoi:10.4172/2475-3181.1000142 fatcat:y7hykyl5mrf53a56ojf2urj6a4
more »... nimum distances from the heart of 5.7 mm. Despite using a cardiac synchronization device during the IRE ablation, paroxysmal ventricular tachycardia was induced in this patient. Therefore, care must be taken when treating lesions located near the heart with IRE.
A 36-year-old Asian man was referred to our hospital with cardiac metastasis. He had a history of alveolar soft part sarcoma and initially underwent resection in 2005. After exposing the tumor by thoracotomy, cryoablation was performed under ultrasound guidance. This treatment was combined with iodine-125 seed implantation to treat the cardiac metastasis. The patient had an uneventful recovery, and his cardiac function shows no obvious abnormalities. Imaging techniques suggest that cardiacdoi:10.1159/000449403 pmid:31988888 pmcid:PMC6945912 fatcat:dt7ggt4oqrgezaaz4o4oz6q36m
more »... tasis was well controlled, and the patient is still alive 12 months after treatment. Tumor cryoablation, combined with iodine seed implantations, may be regarded as a means of palliative treatment.
AbstractBackgroundWith the reduce of cost and incomparable advantages, WGS is likely to change the way of clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated, especially for CNV detection.MethodsAll the samples underwent WGS using MGISEQ-2000. The performance of NA12878, YH cell line, and the Chinese trios were measured for sensitivity, PPV, depth and breadthdoi:10.1101/2020.04.01.019570 fatcat:bmdd57a25zhlljy3cnxa2e5thu
more »... of coverage. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using family-based trio design in the Chinese trios. We also developed a systematic WGS pipeline for the analysis of 8 clinical cases with known disease-causing variants.ResultsIn general, the sensitivity and PPV for SNV/indel detection increased with mean depth, and reached a plateau at a ~40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozyous and heterozygous SNPs of NA12878 was >99.25% and >99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV is still not 100% even with a mean depth of ~150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size of less than 1kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~40X) is better than WES (~120X). Among the Chinese trios with ~40X mean depth, the sensitivity in the offspring was >99.48% and >96.36% for SNP and indel detection, and PPVs were 99.86% and 97.93%. All the 12 previously validated variants in the 8 clinical cases were successfully detected by our WGS pipeline.ConclusionsThe current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. Clinical scientists should know the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.
Objective: To inform health insurance payment reforms and hospital cost management by investigating the case-mix of viral hepatitis, a common disease, in a Chinese city. Methods: All inpatient medical records of viral hepatitis of selected hospitals in Xiamen from 2008 to 2013 were collected. Both univariate and multivariate analyses were performed to test the association between hospitalization costs and other key variables. The CHAID model was employed to generate the Diagnosis-related Groupsdoi:10.5430/ijh.v2n1p102 fatcat:bdmt7a6sjjfb3ebzqcv2mqz5d4
more »... (DRGS). Evaluation indexes were adopted to evaluate the grouped results. Standard expenditures were estimated for each group. Results: Gender, age, marital status, mode of payment, admission condition, discharged condition and length of stay were found significantly associated with inpatient expenditures, with p values smaller than .001. Eleven diagnosis-related groups were obtained with the CHAID methods and three classification nodes were obtained from the CHAID decision tree, including age, admission status and mode of payment. The analysis revealed a considerable discrepancy in expenditures across groups with similar characteristics. This variance suggests the existence of inflated inpatient costs as well as inefficient use of medical resources. Conclusions: The analysis provided more accurate estimation on case-mix costs for a major disease in China. The standard expenditures are of reference values for the social insurance administration in calibrating reimbursement rates in its move to case-mix payment system and helpful for hospital cost management.
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