bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery
Authors: Mondo Stephen J. , Jiménez Diego Javier , Hector Ronald E. , Lipzen Anna , Yan Mi , LaButti Kurt , Barry Kerrie , van Elsas Jan Dirk , Grigoriev Igor V. , Nichols Nancy N.
Published: September 2019

Background

Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1).

Results

The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source.

Conclusions

We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and “eco-enzymology” of lignocellulolytic Coniochaeta species.
The clinical profile, hematological parameters and liver transaminases of dengue NS1 Ag positive patients admitted to Jaffna Teaching Hospital, Sri Lanka
Authors: Jayadas T. T. P. , Kumanan T. , Arasaratnam V. , Gajapathy K. , Surendran S. N.
Published: September 2019

Objective

Objective of the study is to evaluate the on-admission day symptoms and signs, clinical, hematological parameters and liver transaminases of the dengue NS1 positive patients who got admitted on different clinical phases [Febrile phase (day 1–3) and Critical phase(day 4–5)] of dengue at medical wards of Jaffna Teaching Hospital.

Results

Blood samples were collected from 150 suspected dengue patients from day 1 to 5 of the illness. Seventy-eight patients were positive for dengue NS1, according to the WHO proposed dengue clinical phase framework 37 patients were from febrile phase and 41 patients from critical phase. Patients who admitted on critical phase framework suffered from leukopenia and thrombocytopenia. Nine patients had the evidence of leakage with fever and the leakers had significant rise in hemoglobin, hematocrit and liver transaminase levels which are considered as severe form of the disease.
Factors affecting neonatal mortality in the general population: evidence from the 2016 Ethiopian Demographic and Health Survey (EDHS)—multilevel analysis
Authors: Wolde Haileab Fekadu , Gonete Kedir Abdela , Akalu Temesgen Yihunie , Baraki Adhanom Gebreegziabher , Lakew Ayenew Molla
Published: September 2019

Objective

This study was aimed to identify factors affecting neonatal mortality in Ethiopia.

Results

According to the multilevel multivariable logistic regression analysis, the odds of neonatal mortality was significantly associated with husbands with no education (AOR = 2.30, 95% CI 1.10, 4.83), female birth (AOR = 0.57, 95% CI 0.39, 0.83), twin birth (AOR = 13.62, 95% CI 7.14, 25.99), pre-term birth (AOR = 15.07, 95% CI 7.80, 29.12) and mothers with no antenatal care (ANC) visit during pregnancy (AOR = 1.90 95% CI 1.11, 3.25).
Prevalence and associated factors of bronchial asthma among adult patients in Debre Berhan Referral Hospital, Ethiopia 2018: a cross-sectional study
Authors: Shine Sisay , Muhamud Sindew , Demelash Alebachew
Published: September 2019

Objective

Bronchial asthma is one of the major public health challenges throughout the world that negatively impact patients, families and community. The objective of this study was to assess the prevalence and associated risk factors of bronchial asthma among patients in adult emergency department of Debre Berhan Referral Hospital. A hospital based cross-sectional study design was used among 257 study participants. A systematic sampling technique was used to select the study participants. Data was collected by using pretested and structured questionnaire and analyzed by using SPSS version 20.0. Both bivariate and multivariate logistic regression model was used to identify the predictors of asthma.

Results

Prevalence of bronchial asthma among adult patients was 29.6%. Being an urban resident (AOR: 1.5: 95% CI 1.3–3.9), income of household less than 1000 EBr/month (AOR: 1.7: 95% CI 1.6–4.1), having family history of asthma (AOR: 2.7: 95% CI 1.3–5.8), and presence of vermin in the house (AOR: 2.4: 95% CI 1.2–4.7) were significantly associated with bronchial asthma. The authors concluded that the prevalence of bronchial asthma among adult patients was high. Therefore, educational program about the risk factors and preventive measures of asthma is highly recommended.
Validation of an informatics tool to assess resident’s progress in developing reporting skills
Authors: Diaz Facundo N. , Ulla Marina
Published: September 2019

Background

Diagnostic radiology residency programs pursuits as main objectives of the development of diagnostic capabilities and written communication skills to answer clinicians’ questions of referring clinicians.

There has been also an increasing focus on competencies, rather than just education inputs. Then, to show ongoing professional development is necessary for a system to assess and document resident’s competence in these areas.

Therefore, we propose the implementation of an informatics tool to objectively assess resident’s progress in developing diagnostics and reporting skills. We expect to found decreased preliminary report-final report variability within the course of each year of the residency program.

Results

We analyzed 12,162 evaluations from 32 residents (8 residents per year in a 4-year residency program) in a 7-month period. 73.96% of these evaluations belong to 2nd-year residents.

We chose two indicators to study the evolution of evaluations: the total of discrepancies over the total of preliminary reports (excluding score 0) and the total of likely to be clinically significant discrepancies (scores 2b, 3b, and 4b) over the total of preliminary reports (excluding score 0).

With the analysis of these two indicators over the evaluations of 2nd-year residents, we found a slight decrease in the value of the first indicator and relative stable behavior of the second one.

Conclusions

This tool is useful for objective assessment of reporting skill of radiology residents. It can provide an opportunity for continuing medical education with case-based learning from those cases with clinically significant discrepancies between the preliminary and the final report.
Imaging findings of cesarean delivery complications: cesarean scar disease and much more
Authors: Rosa F. , Perugin G. , Schettini D. , Romano N. , Romeo S. , Podestà R. , Guastavino A. , Casaleggio A. , Gandolfo N.
Published: September 2019

In the last years, there has been a significant increase in the number of cesarean deliveries and, with it, of the number of complications following the procedure. They can be divided into early and late ones. We will illustrate herein the most common complications following cesarean section to help radiologists to recognize them. To familiarize with these various pathologic conditions is crucial to alert referring clinicians for a prompt and appropriate maternal and fetal management. Special attention will be given to the cesarean scar defect (CSD), the most common but also the most unknown of such conditions. Although often asymptomatic, a severe CSD represents a predisposing factor for subsequent complications especially in future pregnancies.
Brain MR findings in patients treated with particle therapy for skull base tumors
Authors: Viselner Gisela , Farina Lisa , Lucev Federica , Turpini Elena , Lungarotti Luca , Bacila Ana , Iannalfi Alberto , D’Ippolito Emma , Vischioni Barbara , Ronchi Sara , Marchioni Enrico , Valvo Francesca , Bastianello Stefano , Preda Lorenzo
Published: September 2019

Nowadays, hadrontherapy is increasingly used for the treatment of various tumors, in particular of those resistant to conventional radiotherapy. Proton and carbon ions are characterized by physical and biological features that allow a high radiation dose to tumors, minimizing irradiation to adjacent normal tissues. For this reason, radioresistant tumors and tumors located near highly radiosensitive critical organs, such as skull base tumors, represent the best target for this kind of therapy. However, also hadrontherapy can be associated with radiation adverse effects, generally referred as acute, early-delayed and late-delayed. Among late-delayed effects, the most severe form of injury is radiation necrosis. There are various underlying mechanisms involved in the development of radiation necrosis, as well as different clinical presentations requiring specific treatments. In most cases, radiation necrosis presents as a single focal lesion, but it can be multifocal and involve a single or multiple lobes simulating brain metastasis, or it can also involve both cerebral hemispheres. In every case, radiation necrosis results always related to the extension of radiation delivery field. Multiple MRI techniques, including diffusion, perfusion imaging, and spectroscopy, are important tools for the radiologist to formulate the correct diagnosis. The aim of this paper is to illustrate the possible different radiologic patterns of radiation necrosis that can be observed in different MRI techniques in patients treated with hadrontherapy for tumors involving the skull base. The images of exemplary cases of radiation necrosis are also presented.
Umbilical cord as a long-term source of activatable mesenchymal stromal cells for immunomodulation
Authors: Selich Anton , Zimmermann Katharina , Tenspolde Michel , Dittrich-Breiholz Oliver , von Kaisenberg Constantin , Schambach Axel , Rothe Michael
Published: September 2019

Background

Mesenchymal stromal cells (MSCs) are used in over 800 clinical trials mainly due to their immune inhibitory activity. Umbilical cord (UC), the second leading source of clinically used MSCs, is usually cut in small tissue pieces. Subsequent cultivation leads to a continuous outgrowth of MSC explant monolayers (MSC-EMs) for months. Currently, the first MSC-EM culture takes approximately 2 weeks to grow out, which is then expanded and applied to patients. The initiating tissue pieces are then discarded. However, when UC pieces are transferred to new culture dishes, MSC-EMs continue to grow out. In case the functional integrity of these cells is maintained, later induced cultures could also be expanded and used for cell therapy. This would drastically increase the number of available cells for each patient. To test the functionality of MSC-EMs from early and late induction time points, we compared the first cultures to those initiated after 2 months by investigating their clonality and immunomodulatory capacity.

Methods

We analyzed the clonal composition of MSC-EM cultures by umbilical cord piece transduction using integrating lentiviral vectors harboring genetic barcodes assessed by high-throughput sequencing. We investigated the transcriptome of these cultures by microarrays. Finally, the secretome was analyzed by multiplexed ELISAs, in vitro assays, and in vivo in mice.

Results

DNA barcode analysis showed polyclonal MSC-EMs even after months of induction cycles. A transcriptome and secretome analyses of early and late MSC cultures showed only minor changes over time. However, upon activation with TNF-α and IFN-γ, cells from both induction time points produced a multitude of immunomodulatory cytokines. Interestingly, the later induced MSC-EMs produced higher amounts of cytokines. To test whether the different cytokine levels were in a therapeutically relevant range, we used conditioned medium (CM) in an in vitro MLR and an in vivo killing assay. CM from late induced MSC-EMs was at least as immune inhibitory as CM from early induced MSC-EMs.

Conclusion

Human umbilical cord maintains a microenvironment for the long-term induction of polyclonal and immune inhibitory active MSCs for months. Thus, our results would offer the possibility to drastically increase the number of therapeutically applicable MSCs for a substantial amount of patients.
miR-106b regulates the proliferation and differentiation of neural stem/progenitor cells through Tp53inp1-Tp53-Cdkn1a axis
Authors: Xia Xiaohuan , Lu Hongfang , Li Chunhong , Huang Yunlong , Wang Yi , Yang Xiaoyu , Zheng Jialin C.
Published: September 2019

Background

Recent studies suggested that miR-17~106 family was involved in the regulation of neural stem/progenitor cells (NPCs). However, distinct function of each family member was reported in regulating stem cells within and without the brain. Hence, to investigate the roles of individual miRNAs in miR-17~106 family and mechanisms underlying their effects on neurogenesis is important to extend our understanding in the CNS development.

Methods

Here, we examined the influence of miR-106a/b on the proliferation, differentiation, and survival of embryonic NPCs using specific mimics and inhibitor. The targets of miR-106a/b were identified from miRNA target prediction database and confirmed by luciferase assay. Specific siRNAs were utilized to erase the effects of miR-106a/b on the expression levels of target genes.

Results

A positive correlation was observed between the temporal reduction of miR-106a/b expression levels and the decline of NPC pools in vivo and in vitro. The perturbation of miR-106’s function approaches revealed that miR-106b, but not miR-106a, facilitated the maintenance of NPCs and repressed the generation of both neuronal and glial cells, without preference to a particular lineage. No effect was observed for miR-106a/b in NPCs’ survival. The influence of miR-106b on NPCs’ proliferation and differentiation is likely achieved by directly inhibiting the expression of Tp53inp1 and Cdkn1a, key components of Tp53inp1-Tp53-Cdkn1a axis.

Conclusion

Our study demonstrated a novel axis, miR-106b-Tp53inp1-Tp53-Cdkn1a, in regulating the proliferation and differentiation of NPCs.
Mechanical process prior to cryopreservation of lipoaspirates maintains extracellular matrix integrity and cell viability: evaluation of the retention and regenerative potential of cryopreserved fat-derived product after fat grafting
Authors: Feng Jingwei , Hu Wansheng , Fanai Mimi Lalrimawii , Zhu Shengqian , Wang Jing , Cai Junrong , Lu Feng
Published: September 2019

Background

Cryopreservation of fat grafts facilitates reinjection for later use. However, low temperature and thawing can disrupt tissues and cause lipid leakage, which raises safety concerns. Here, we compared the cryopreservation potential of stromal vascular fraction (SVF) gel processed from lipoaspirate with that of fat.

Methods

Human SVF gel and fat were cryopreserved at − 20 °C without cryoprotectant for 1 month. Fresh SVF gel and fat were used as controls. Tissue viability, adipose-derived stem cell (ASC) function, and the extracellular content were evaluated. At 3 months after transplanting the specimens to immunocompromised mice subcutaneously, the grafts were examined for retention, tissue engraftment, and inflammatory levels. The regenerative effect of cryopreserved SVF gel was evaluated in a murine ischemic wound healing model.

Results

At 1 month, the cell death rate in the SVF gel group was 36 ± 2%. The survived ASCs not only could be isolated via explant culture but also preserved colony-forming and differentiation. However, prolonged cryopreservation exacerbated apoptosis. Assessment of recovered tissues showed that the morphology, cell viability, and extracellular protein enrichment were better in SVF gel-preserved tissues than in frozen fat. At 3 months after lipotransfer, the retention ability of 1-month cryopreserved fat was 41.1 ± 9% compared to that of 1-month cryopreserved SVF gel. Immunostaining results showed that adipose tissue regeneration and integrity in the 1-month cryopreserved SVF gel group were superior to those of the cryopreserved fat group. The cryopreserved SVF gel also accelerated healing of the ischemic wound, compared with cryopreserved fat.

Conclusion

Cryopreserved SVF gel maintained tissue integrity and cell viability and resulted in a better long-term retention rate than that of cryopreserved fat. Cryopreserved SVF gel also showed superior regenerative potential and improved ischemic wound healing.
iPSC-derived MSC therapy induces immune tolerance and supports long-term graft survival in mouse orthotopic tracheal transplants
Authors: Khan Mohammad Afzal , Alanazi Fatimah , Ahmed Hala Abdalrahman , Shamma Talal , Kelly Kilian , Hammad Mohamed A. , Alawad Abdullah O. , Assiri Abdullah Mohammed , Broering Dieter Clemens
Published: September 2019

Background

Lung transplantation is a life-saving surgical replacement of diseased lungs in patients with end-stage respiratory malfunctions. Despite remarkable short-term recovery, long-term lung survival continues to face several major challenges, including chronic rejection and severe toxic side effects due to global immunosuppression. Stem cell-based immunotherapy has been recognized as a crucial immunoregulatory regimen in various preclinical and clinical studies. Despite initial therapeutic outcomes, conventional stem cells face key limitations. The novel Cymerus™ manufacturing facilitates production of a virtually limitless supply of consistent human induced pluripotent stem cell (iPSC)-derived mesenchymal stem cells, which could play a key role in selective immunosuppression and graft repair during rejection.

Methods

Here, we demonstrated the impact of iPSC-derived human MSCs on the development of immune tolerance and long-term graft survival in mouse orthotopic airway allografts. BALB/c → C57BL/6 allografts were reconstituted with iPSC-derived MSCs (2 million/transplant/at d0), and allografts were examined for regulatory T cells (Tregs), oxygenation, microvascular blood flow, airway epithelium, and collagen deposition during rejection.

Results

We demonstrated that iPSC-derived MSC treatment leads to significant increases in hTSG-6 protein, followed by an upregulation of mouse Tregs and IL-5, IL-10, and IL-15 cytokines, which augments graft microvascular blood flow and oxygenation, and thereby maintained a healthy airway epithelium and prevented the subepithelial deposition of collagen at d90 post transplantation.

Conclusions

Collectively, these data confirmed that iPSC-derived MSC-mediated immunosuppression has potential to establish immune tolerance and rescue allograft from sustained hypoxic/ischemic phase, and subsequently limits long-term airway epithelial injury and collagen progression, which therapeutically warrant a study of Cymerus iPSC-derived MSCs as a potential management option for immunosuppression in transplant recipients.
Haemophilus parasuis VtaA2 is involved in adhesion to extracellular proteins
Authors: Costa-Hurtado Mar , Garcia-Rodriguez Laura , Lopez-Serrano Sergi , Aragon Virginia
Published: September 2019

Haemophilus parasuis is part of the microbiota of the upper respiratory tract in swine. However, virulent strains can cause a systemic disease known as Glässer’s disease. Several virulence factors have been described in H. parasuis including the virulence-associated trimeric autotransporters (VtaAs). VtaA2 is up-regulated during infection and is only found in virulent strains. In order to determine its biological function, the vtaA2 gene was cloned with its native promotor region in pACYC184, and the transformed Escherichia coli was used to perform functional in vitro assays. VtaA2 was found to have a role in attachment to plastic, mucin, BSA, fibronectin and collagen. As other VtaAs from H. parasuis, the passenger domain of VtaA2 contains collagen domains. In order to examine the contribution of the collagen repeats to VtaA2 function, a recombinant vtaA2 without the central collagen domains was obtained and named vtaA2OL. VtaA2OL showed similar capacity than VtaA2 to adhere to plastic, mucin, BSA, fibronectin and plasma but a reduced capacity to adhere to collagen, suggesting that the collagen domains of VtaA2 are involved in collagen attachment. No function in cell adhesion and invasion to epithelial alveolar cell line A549 or unspecific binding to primary alveolar macrophages was found. Likewise VtaA2 had no role in serum or phagocytosis resistance. We propose that VtaA2 mediates adherence to the host by binding to the mucin, found in the upper respiratory tract mucus, and to the extracellular matrix proteins, present in the connective tissue of systemic sites, such as the serosa.
Urothelial carcinoma associated 1 promotes trophoblast invasion by regulating MMP9
Authors: Shao Hongfang , Jin Feng , Hu Jiangshan , Zhu Zhangying , Tian Fuju , Tao Minfang , Teng Yincheng
Published: September 2019

Background

The long non-coding RNA UCA1 is reportedly increased in several human tumors and critical for the cell migration, invasion, or proliferation of several cancer cells. However, the potential roles of UCA1 in trophoblasts at early pregnancy still poorly understood. Here, we sought to unravel the roles of UCA1 in the occurrence of the recurrent miscarriage (RM) disorders.

Results

The knockdown of UCA1 in human HTR-8 trophoblast cell line reduced their cell proliferative and invasive ability. Conversely, the UCA1 overexpression promoted the cell proliferation and invasion of HTR-8 cells. Quantitative RT-PCR screening revealed that UCA1 overexpression significantly enhanced MMP9, but not MMP2, mRNA expression in trophoblast cells. The overexpression of UCA1 also promoted trophoblast invasion by upregulating MMP9 expression and activity both in vitro and ex vivo. Consistently, UCA1 and MMP9 mRNA expression level was notably reduced in placental villi derived from patients with RM diseases.

Conclusion

This study revealed that UCA1 is critical for the regulation of invasive ability in trophoblasts. The abnormal UCA1/MMP9 pathway might result in the impaired trophoblast activities and lead to the development of RM. Our data may also provide a novel angle for the treatment in RM patients.
Nephrotoxic drug burden among 1001 critically ill patients: impact on acute kidney injury
Authors:   Clinical research in intensive care and sepsis-Trial group for global evaluation and research in sepsis (CRICS-TRIGGERSEP network), Ehrmann Stephan , Helms Julie , Joret Aurélie , Martin-Lefevre Laurent , Quenot Jean-Pierre , Herbrecht Jean-Etienne , Benzekri-Lefevre Dalila , Robert René , Desachy Arnaud , Bellec Fréderic , Plantefeve Gaëtan , Bretagnol Anne , Dargent Auguste , Lacherade Jean-Claude , Meziani Ferhat , Giraudeau Bruno , Tavernier Elsa , Dequin Pierre-François
Published: September 2019

Background

Nephrotoxic drug prescription may contribute to acute kidney injury (AKI) occurrence and worsening among critically ill patients and thus to associated morbidity and mortality. The objectives of this study were to describe nephrotoxic drug prescription in a large intensive-care unit cohort and, through a case–control study nested in the prospective cohort, to evaluate the link of nephrotoxic prescription burden with AKI.

Results

Six hundred and seventeen patients (62%) received at least one nephrotoxic drug, among which 303 (30%) received two or more. AKI was observed in 609 patients (61%). A total of 351 patients were considered as cases developing or worsening AKI a given index day during the first week in the intensive-care unit. Three hundred and twenty-seven pairs of cases and controls (patients not developing or worsening AKI during the first week in the intensive-care unit, alive the case index day) matched on age, chronic kidney disease, and simplified acute physiology score 2 were analyzed. The nephrotoxic burden prior to the index day was measured in drug.days: each drug and each day of therapy increasing the burden by 1 drug.day. This represents a semi-quantitative evaluation of drug exposure, potentially easy to implement by clinicians. Nephrotoxic burden was significantly higher among cases than controls: odds ratio 1.20 and 95% confidence interval 1.04–1.38. Sensitivity analysis showed that this association between nephrotoxic drug prescription in the intensive-care unit and AKI was predominant among the patients with lower severity of disease (simplified acute physiology score 2 below 48).

Conclusions

The frequently observed prescription of nephrotoxic drugs to critically ill patients may be evaluated semi-quantitatively through computing drug.day nephrotoxic burden, an index significantly associated with subsequent AKI occurrence, and worsening among patients with lower severity of disease.
A new viscosity-type iteration for a finite family of split variational inclusion and fixed point problems between Hilbert and Banach spaces
Authors: Izuchukwu C. , Isiogugu F. O. , Okeke C. C.
Published: September 2019

In this paper, we introduce a new viscosity-type iteration process for approximating a common solution of a finite family of split variational inclusion problem and fixed point problem. We prove that the proposed algorithm converges strongly to a common solution of a finite family of split variational inclusion problems and fixed point problem for a finite family of type-one demicontractive mappings between a Hilbert space and a Banach space. Furthermore, we applied our results to study a finite family of split convex minimization problems, and also considered a numerical experiment of our results to further illustrate its applicability. Our results extend and improve the results of Byrne et al. (J. Nonlinear Convex Anal. 13:759–775, 2012), Kazmi and Rizvi (Optim. Lett. 8(3):1113–1124, 2014), Moudafi (J. Optim. Theory Appl. 150:275–283, 2011), Shehu and Ogbuisi (Rev. R. Acad. Cienc. Exactas Fís. Nat., Ser. A Mat. 110(2):503–518, 2016), Takahashi and Yao (Fixed Point Theory Appl. 2015:87, 2015), Chidume and Ezeora (Fixed Point Theory Appl. 2014:111, 2014), and a host of other important results in this direction.
Fractional order ecological system for complexities of interacting species with harvesting threshold in imprecise environment
Authors: Khan Najeeb Alam , Razzaq Oyoon Abdul , Mondal Sankar Parsad , Rubbab Qammar
Published: September 2019

The key objective of this paper is to study the imprecise biological complexities in the interaction of two species pertaining to harvesting threshold. It is explained by taking the prey–predator model with imprecise biological parameters and fractional order generalized Hukuhara (fgH) differentiability. In this vain, different possible systems of the model are constructed, according to the increasing and decreasing behavior of population growth. Feasibility and stability analyses of equilibrium points of the stated models are also discussed by means of variational matrix with Routh–Hurwitz conditions. In addition, the numerical elaborations are carried out by taking parametric expansion of fuzzy fractional Laplace transform (FFLT). This significantly helps the researchers in using a novel approach to analyze the constant solutions of the dynamical systems in the presence of fractional index. This would allow the avoidance of any intricacy that occurs while solving fractional order derivatives. Furthermore, this attempt also provides numerical and pictorial results, obtained through some well-known methods, namely fifth-forth Runge–Kutta method (FFRK), Grunwald–Letnikov’s definition (GL) and Adams–Bashforth method (ABM) that are deemed appropriate to scrutinize the dynamics of the system of equations.
Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci
Authors: Janes Victoria A. , Notermans Daan W. , Spijkerman Ingrid J.B. , Visser Caroline E. , Jakobs Marja E. , van Houdt Robin , Willems Rob J.L. , de Jong Menno D. , Schultsz Constance , Matamoros Sébastien
Published: September 2019

Background

Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months.

Methods

Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors.

Results

Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4–5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward.

Conclusion

AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.
Simultaneous determination of various platycosides in Four Platycodon grandiflorum cultivars by UPLC-QTOF/MS
Authors: Lee Dae Young , Choi Bo-Ram , Lee Jae Won , Um Yurry , Yoon Dahye , Kim Hyoung-Geun , Lee Young-Seob , Kim Geum-Soog , Lee Youn-Hyung , Baek Nam-In
Published: September 2019

In Platycodi Radix (root of Platycodon grandiflorum), there are a number of platycosides that consist of a pentacyclic triterpenoid aglycone and two sugar moieties. Due to the pharmacological activities of platycosides, it is critical to assess their contents in PR, and develop an effective method to profile various platycosides is required. In this study, an analytical method based on ultra performance liquid chromatography coupled with quadrupole time-of-flight/mass spectrometry (UPLC-QTOF/MS) with an in-house library was developed and applied to profile various platycosides from four different Platycodi Radix cultivars. As a result, platycosides, including six isomeric pairs, were successfully analyzed in the PRs. In the principal component analysis, several platycosides were represented as main variables to differentiate the four Platycodi Radix cultivars. Their different levels of platycosides were also represented by relative quantification. Finally, this study indicated the proposed method based on the UPLC-QTOF/MS can be an effective tool for identifying the detail characterization of various platycosides in the Platycodi Radix.
Dye- and fluorescence-based assay to characterize symplastic and apoplastic trafficking in soybean (Glycime max L.) endosperm
Authors: Shih Ming-Der , Lin Jian-Shin , Fang Mei-Jane , Tsai Yuan-Ching , Hsing Yue-Ie C.
Published: September 2019

Background

Endosperm is a triploid tissue in seed resulting from a sperm nucleus fused with the binucleate central cell after double fertilization. Endosperm may be involved in metabolite production, solute transport, nutrient storage, and germination. In the legume family (Fabaceae), with the greatest number of domesticated crops, approximately 60% of genera contain well-differentiated endosperm in mature seeds. Soybean seeds, the most important legume crop in the worlds, have endosperm surrounding embryos during all stages of seed development. However, the function of soybean endosperm is still unknown.

Results

Flow cytometry assay confirmed that soybean endosperm was triploid. Cytobiological observation showed that soybean endosperm cells were alive with zigzag-shape cell wall. Soybean endosperm cells allowed fusion proteins (42 kDa) to move from bombarded cells to adjacent unbombarded-cells. Such movement is not simple diffusion because the fusion proteins failed to move into dead cells. We used symplastic tracers to test the transport potential of soybean endosperm. Small organic dye and low-molecular-weight symplastic tracers revealed fast symplastic transport. After a treatment of an inhibitor of ATPase,N,N′-dicyclohexylcarbodiimide (DCCD), symplastic transport was blocked, but all tracers still showed fast apolopastic transport. The transport speed of 8-hydroxypyrene-1,3,6-trisulfonic acid in endosperm was 1.5 to 3 times faster than in cotyledon cells or Arabidopsis embryos.

Conclusions

Soybean endosperm is a membrane-like, semi-transparent, and fully active tissue located between the seed coat and cotyledon. Soybean endosperm cells allowed macromolecules to move fast via plasmodesmata transport. The size exclusion limit is larger for soybean endosperm cells than its cotyledon or even Arabidopsis embryo cells. Soybean endosperm may be involved in fast and horizontal transport during the mid-developmental stage of seeds.
Recent progress in directed evolution of stereoselective monoamine oxidases
Authors: Duan Jiaqi , Li Beibei , Qin Youcai , Dong Yijie , Ren Jie , Li Guangyue
Published: September 2019

Monoamine oxidases (MAOs) use molecular dioxygen as oxidant to catalyze the oxidation of amines to imines. This type of enzyme can be employed for the synthesis of primary, secondary, and tertiary amines by an appropriate deracemization protocol. Consequently, MAOs are an attractive class of enzymes in biocatalysis. However, they also have limitations in enzyme-catalyzed processes due to the often-observed narrow substrate scope, low activity, or poor/wrong stereoselectivity. Therefore, directed evolution was introduced to eliminate these obstacles, which is the subject of this review. The main focus is on recent efforts concerning the directed evolution of four MAOs: monoamine oxidase (MAO-N), cyclohexylamine oxidase (CHAO),D-amino acid oxidase (pkDAO), and 6-hydroxy-D-nicotine oxidase (6-HDNO).
A longitudinal analysis of the U.S. Air Force reserve officers’ training corps physical fitness assessment
Authors: Mackey Cameron S. , DeFreitas Jason M.
Published: September 2019

Background

The U.S. Air Force physical fitness assessment (PFA) is used to determine the overall fitness of their personnel. It is currently unknown to what extent the PFA scores of Reserve Officers’ Training Corps (ROTC) cadets are affected by mandatory physical training. The purpose of this investigation was to longitudinally examine the PFAs of ROTC cadets over a four-year period, evaluate the results across class ranks, and evaluate the sensitivity of the classification of the tests.

Methods

Air Force ROTC cadets performed the PFAs (abdominal circumference, 1-min pushups, 1-min sit-ups, and a 1.5-mile run) in both the spring (n = 26) and fall (n = 22) semesters. PFAs were compiled over a four-year period (Spring 2014 – Fall 2017) and were performed in accordance with Air Force Instruction 36–2905. A one-way repeated measures ANOVA was performed separately for the fall and spring groups for each dependent variable across the 4 years. Additionally, a one-way between groups ANOVA was performed for each dependent variable during the time point (fall 2015; N = 46) with the most recorded cadets for each class rank.

Results

Longitudinal assessments revealed a main effect of time (P = 0.010) on abdominal circumference; cadets had a smaller abdominal circumference in their freshman year than in their senior year. A main effect of time (P = 0.006) was also observed on sit-up quantity; cadets performed more sit-ups in their junior year than in their freshman year. Examining between class ranks during the same year (between-subjects ANOVA) revealed a main effect of class rank on sit-up quantity (P = 0.003); the freshmen completed fewer repetitions than the sophomores (P = 0.018) and the juniors did (P = 0.001).

Conclusion

The results indicated that only the sit-up component showed differences between class ranks. These findings suggest that the Air Force PFA may not be sensitive enough to detect changes in physical fitness or distinguish between class ranks regarding physical performance, even after years of training. This limitation may be in part due to the limited duration of training incorporated by the ROTC program (2 h per week), which provided a maintenance effect rather than improvement in physical performance. We recommend that more attention be directed to the efficacy of physical training, the sensitivity of measures included in the PFA, or both.
Occupational stress and job dissatisfaction with health work
Authors: de Sousa Camila Carvalho , de Araújo Tânia Maria , Lua Iracema , Gomes Mariana Rabelo
Published: September 2019

Objective

The purpose of this study is to evaluate the association between psychosocial aspects at work and dissatisfaction among health workers in five cities in Bahia, Brazil.

Methods

The evaluation was based on different models proposed to measuring occupational stress and possible combinations between them: demand-control model (DCM) and effort-reward imbalance (ERI). We conducted a cross-sectional epidemiological study including 3084 health workers. The analysis considered the association between partial/full/partial (combined) occupational stress models (the variable “exposure”) and job dissatisfaction (the variable “outcome”).

Results

Dissatisfaction rate was 26%. Full DCM and ERI models were better than partial ones to investigate job dissatisfaction. After adjustments, the combined models presented more robust measures of prevalence ratio than models evaluated separately (PR 2.93; CI 2.26–3.80).

Conclusions

The combination of models has shown greater capacity to identify situations of job dissatisfaction and provided more potential information to support actions for workers’ health.
Impact of Health-Related Quality of Life and Prediagnosis Risk of Major Depressive Disorder on Treatment Choice for Stage I Lung Cancer
Authors: van Dams Ritchell , Grogan Tristan , Lee Percy , Punglia Rinaa , Raldow Ann
Published: September 2019

PURPOSE

We hypothesized that prediagnosis depressive symptoms and patient-reported health-related quality of life (HRQOL) would be associated with treatment choice for stage I non–small-cell lung cancer (NSCLC).

METHODS

Using the SEER and Medicare Health Outcomes Survey (SEER-MHOS)–linked data set, we identified patients age 65 years and older with stage I NSCLC diagnosed between 2004 and 2013 who completed the HOS 24 or fewer months before diagnosis. HRQOL was measured by the Physical Component Summary (PCS) and Mental Component Summary (MCS) scores of the Medical Outcomes Study Short Form-36 and the Veterans RAND 12-Item Health Survey instruments. Major depressive disorder (MDD) risk was derived from responses to HOS questions that screen for depressive symptoms. Associations with treatment choice were assessed with multivariable multinomial logistic regression while controlling for prespecified patient characteristics.

RESULTS

We analyzed 515 evaluable patients, of whom 140 (27%) met criteria for risk of MDD. On univariable analysis, a higher proportion of patients who received radiotherapy (RT) versus surgery were at risk for MDD (34% v 22%, respectively; P = .011). On multivariable analysis, higher PCS and MCS scores were associated with a decreased likelihood of receiving RT compared with surgery (adjusted odds ratio per 10-point PCS increase, 0.60 [95% CI, 0.45 to 0.79; P < .001]; adjusted odds ratio per 10-point MCS increase, 0.61 [95% CI 0.46 to 0.80; P < .001]).

CONCLUSION

Among older patients with stage I NSCLC, there was a significant association between those who self-reported lower HRQOL and receipt of RT. There was also a nonsignificant association in MDD risk and increased likelihood of RT receipt. Additional studies are warranted to examine the impact of pretreatment HRQOL and MDD risk on clinical decision making.
Restriction of mitochondrial calcium overload by mcu inactivation renders neuroprotective effect in Zebrafish models of Parkinson's disease
Authors: Soman Smijin K. , Bazała Michal , Keatinge Marcus , Bandmann Oliver , Kuznicki Jacek
Published: September 2019

The loss of dopaminergic neurons (DA) is a pathological hallmark of sporadic and familial forms of Parkinson's Disease (PD). We had previously shown that inhibiting mitochondrial calcium uniporter (mcu) using morpholinos can rescue DA neurons in pink1−/− zebrafish model of PD. In this study, we are showing results from our studies in mcu knockout zebrafish, which was generated using the CRISPR/Cas9 system. Functional assays confirmed impaired mitochondrial calcium influx in mcu−/− zebrafish. We also used in-vivo calcium imaging and fluorescent assays in purified mitochondria to investigate mitochondrial calcium dynamics in a pink1−/− zebrafish model of PD. Mitochondrial morphology was evaluated in DA neurons and muscle fibres using immunolabelling and transgenic lines, respectively. We observed diminished mitochondrial volume in DA neurons of pink1−/− zebrafish, while deletion of mcu restored mitochondrial volume. In contrast, the mitochondrial volume in muscle fibers was not restored after inactivation of mcu in pink1−/− zebrafish. Mitochondrial calcium overload coupled with depolarization of mitochondrial membrane potential leads to mitochondrial dysfunction in pink1−/− zebrafish model of PD. We used in situ hybridisation and immunohistochemical labelling of DA neurons to evaluate the effect of mcu deletion on DA neuronal clusters in the ventral telencephalon of zebrafish brain. We show that DA neurons are rescued after deletion of mcu in pink1−/− and the MPTP zebrafish model of PD. Thus, inactivation of mcu is protective in both genetic and chemical models of PD. Our data reveal that regulating mcu function could be an effective therapeutic target in PD pathology.
Methane emissions in triple rice cropping: patterns and a method for reduction
Authors: Oda Masato , Nguyen Huu Chiem
Published: September 2019

The Mekong Delta paddies are known as hotspots of methane emission, but these emissions are not well studied. We analyzed methane emission patterns based on monitoring data from typical triple rice cropping paddies collected over 5 years. We found that the total emissions in a crop season doubled in the second crop, tripled in the third crop, and reset after the annual natural flood of the Mekong River. The emission peaks occurred around 0 to 3 weeks after starting irrigation, then gradually decreased. This suggests that methane was generated by the soil organic matter, because the small rice plants provide little carbon for methanogenesis. In general, the main source of emitted methane is rice-derived carbon by current-season photosynthates and the emission peaks at the rice heading stage. However, the contribution of the rice-derived carbon is negligible in the hotspot paddies while total emission is high. The increase in emission levels from the first to the third crop can be explained by the accumulation of rice residue from the preceding crops, especially rice straw incorporated into the soil. The reset of emission levels after annual flood means that the rice straw is decomposed without methanogenesis in water with dissolved oxygen. Thus, the annual emission pattern shows that decomposing rice straw in paddy surface-water is an effective method to reduce methane emissions.
Optimized Scheduling Approach for Scientific Applications Based on Clustering in Cloud Computing Environment
Authors: Kadri Walid , Yagoubi Belabbas
Published: September 2019

Cloud Computing refers to the use of the computing capabilities of remote computers, where the user has considerable computing power without having powerful units. Scientific applications, usually represented as Directed Acyclic Graphs (DAGs), are an important class of applications that lead to challenging problems for resource management in distributed computing. With the advent of Cloud Computing, particularly the IaaS offers for on demand virtual machines leasing, multiple jobs execution, consisting of a large number of DAGs, needs an elaborated scheduling and resource provisioning policies, for efficient use of resources. Only few works exists that consider this problem in the context of clouds environment. In goal of optimization and fault tolerance, DAGs applications are generally partitioned into multiple parallel DAGs using clustering algorithm and assigned to VM (Virtual Machine) resources independently. In this work, we investigate through simulation, the impact of clustering for both provisioning and scheduling policies in the total makespan and financial costs for execution of user's application. We implemented four scheduling policies well-known in grid computing systems, and adapted clustering algorithm to our resource management policy that leases and destroys dynamically VMs. We show that dynamic policies can achieve equal or even better performance than static management policies.
Formação de administradores para o terceiro setor no município de Juiz de Fora, MG
Authors: Doro Ana Paula Gonçalves , Oliveira Virgílio Cézar da Silva e , Ferreira Victor Cláudio Paradela
Published: September 2019

Este trabalho buscou compreender práticas (atividades realizadas) e lacunas (atividades não realizadas) de bacharelados presenciais em administração, em Juiz de Fora (MG), no que diz respeito à qualificação de gestores para o terceiro setor. Como fundamentação teórica discutiu-se a formação de administradores no Brasil e as especificidades do terceiro setor. A pesquisa, qualitativa e exploratória, baseou-se na realização de entrevistas. Os resultados revelaram como prática mais comum a inserção assistemática de elementos relativos ao terceiro setor em disciplinas regulares. As lacunas foram diversas. Conclui-se que a pluralização dos conteúdos curriculares e das metodologias de ensino dos cursos é ação necessária.