bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of acyl-CoA binding protein in Neospora caninum
Authors: Zhou Bingxin , Fu Yong , Zhang Heng , Wang Xianmei , Jin Gaowei , Xu Jianhai , Liu Qun , Liu Jing 
Published: February 2020

Abstract
Background
Lipid metabolism is pivotal for the growth of apicomplexan parasites. Lipid synthesis requires bulk carbon skeleton acyl-CoAs, the transport of which depends on the acyl-CoA binding protein (ACBP). In Neospora caninum, the causative agent of neosporosis, the FASII pathway is required for growth and pathogenicity. However, little is known about the fatty acid transport mechanism in N. caninum.

Methods
We have identified a cytosolic acyl-CoA binding protein, with highly conserved amino acid residues and a typical acyl-CoA binding domain in N. caninum. The recombinant NcACBP protein was expressed to verify the binding activities of NcACBP in vitro, and the heterologous expression of NcACBP in Δacbp yeast in vivo. Lipid extraction from ΔNcACBP or the wild-type of N. caninum was analyzed by GC-MS or TLC. Furthermore, transcriptome analysis was performed to compare the gene expression in different strains.

Results
The NcACBP recombinant protein was able to specifically bind acyl-CoA esters in vitro. A yeast complementation assay showed that heterologous expression of NcACBP rescued the phenotypic defects in Δacbp yeast, indicating of the binding activity of NcACBP in vivo. The disruption of NcACBP did not perturb the parasite’s growth but enhanced its pathogenicity in mice. The lipidomic analysis showed that disruption of NcACBP caused no obvious changes in the overall abundance and turnover of fatty acids while knockout resulted in the accumulation of triacylglycerol. Transcriptional analysis of ACBP-deficient parasites revealed differentially expressed genes involved in a wide range of biological processes such as lipid metabolism, posttranslational modification, and membrane biogenesis.

Conclusions
Our study demonstrated that genetic ablation of NcACBP did not impair the survival and growth phenotype of N. caninum but enhanced its pathogenicity in mice. This deletion did not affect the overall fatty acid composition but modified the abundance of TAG. The loss of NcACBP resulted in global changes in the expression of multiple genes. This study provides a foundation for elucidating the molecular mechanism of lipid metabolism in N. caninum.
Evaluation of RNA purification methods by using different blood stabilization tubes: identification of key features for epidemiological studies
Authors: Carrillo-Ávila J. A. , de la Puente R. , Catalina P. , Rejón J. D. , Espín-Vallejo L. , Valdivieso V. , Aguilar-Quesada R. 
Published: February 2020

Abstract
Objective
Peripheral blood is the most promising source of RNA biomarkers for diagnostic and epidemiological studies, because the presence of disease and prognostic information is reflected in the gene expression pattern. Quality RNA is used by a number of different downstream applications, so the selection of the most appropriate RNA stabilization and purification method is important. We have analyzed the RNA purified from 300 blood samples from 25 donors processed by two technicians using three methodologies with Tempus and PaxGene tubes.

Results
The best quality sample results were obtained with the Tempus Spin RNA Isolation Kit and the PaxGene Blood miRNA Kit, although larger amounts of RNA were obtained with the Tempus Spin RNA Isolation Kit. Lower Cq values were observed for RNA and miRNA genes in samples that were tested with PaxGene Blood miRNA Kit and Tempus Spin RNA Isolation Kit respectively. We identify the Tempus Spin RNA Isolation Kit as the most robust methodology, whilst the MagMax for Stabilized Blood Tubes RNA Isolation Kit showed the most instability. For biobanks, which process a large cohort and conduct epidemiological studies, the Tempus Spin RNA Isolation Kit is the most appropriate methodology. The study demonstrates the robustness of real-life procedures.
Prospective isolation of chondroprogenitors from human iPSCs based on cell surface markers identified using a CRISPR-Cas9-generated reporter
Authors: Dicks Amanda , Wu Chia-Lung , Steward Nancy , Adkar Shaunak S. , Gersbach Charles A. , Guilak Farshid 
Published: February 2020

AbstractBackgroundArticular cartilage shows little or no capacity for intrinsic repair, generating a critical need of regenerative therapies for joint injuries and diseases such as osteoarthritis. Human-induced pluripotent stem cells (hiPSCs) offer a promising cell source for cartilage tissue engineering and in vitro human disease modeling; however, off-target differentiation remains a challenge during hiPSC chondrogenesis. Therefore, the objective of this study was to identify cell surface markers that define the true chondroprogenitor population and use these markers to purify iPSCs as a means of improving the homogeneity and efficiency of hiPSC chondrogenic differentiation.MethodsWe used a CRISPR-Cas9-editedCOL2A1-GFPknock-in reporter hiPSC line, coupled with a surface marker screen, to identify a novel chondroprogenitor population. Single-cell RNA sequencing was then used to analyze the distinct clusters within the population. An unpairedttest with Welch’s correction or an unpaired Kolmogorov-Smirnov test was performed with significance reported at a 95% confidence interval.ResultsChondroprogenitors expressing CD146, CD166, and PDGFRβ, but not CD45, made up an average of 16.8% of the total population. Under chondrogenic culture conditions, these triple-positive chondroprogenitor cells demonstrated decreased heterogeneity as measured by single-cell RNA sequencing with fewer clusters (9 clusters in unsorted vs. 6 in sorted populations) closer together. Additionally, there was more robust and homogenous matrix production (unsorted: 1.5 ng/ng vs. sorted: 19.9 ng/ng sGAG/DNA;p < 0.001) with significantly higher chondrogenic gene expression (i.e.,SOX9,COL2A1,ACAN;p < 0.05).ConclusionsOverall, this study has identified a unique hiPSC-derived subpopulation of chondroprogenitors that are CD146+/CD166+/PDGFRβ+/CD45−and exhibit high chondrogenic potential, providing a purified cell source for cartilage tissue engineering or disease modeling studies.
Insights into the roles of sperm in animal cloning
Authors: Qu Pengxiang , Wang Yongsheng , Zhang Chengsheng , Liu Enqi 
Published: February 2020

AbstractSomatic cell nuclear transfer (SCNT) has shown a wide application in the generation of transgenic animals, protection of endangered animals, and therapeutic cloning. However, the efficiency of SCNT remains very low due to some poorly characterized key factors. Compared with fertilized embryos, somatic donor cells lack some important components of sperm, such as sperm small noncoding RNA (sncRNA) and proteins. Loss of these factors is considered an important reason for the abnormal development of SCNT embryo. This study focused on recent advances of SCNT and the roles of sperm in development. Sperm-derived factors play an important role in nucleus reprogramming and cytoskeleton remodeling during SCNT embryo development. Hence, considering the role of sperm may provide a new strategy for improving cloning efficiency.
Role and therapeutic effects of skeletal muscle-derived non-myogenic cells in a rat myocardial infarction model
Authors: Iseoka Hiroko , Miyagawa Shigeru , Saito Atsuhiro , Harada Akima , Sawa Yoshiki 
Published: February 2020

Abstract
Background
Transplantation of skeletal myoblast sheets is a promising strategy for the treatment of heart failure, and its therapeutic effects have already been proven in both animal disease models and clinical trials. Myoblast sheets reportedly demonstrate their therapeutic effects by producing many paracrine factors. Although the quality of processed cells for transplantation can be evaluated by the positive ratio of CD56, a myoblast marker, it is unclear which cell populations from isolated cells produce paracrine factors that have an impact on therapeutic effects, and whether these therapeutic effects are closely correlated with CD56-positive cells isolated from the skeletal muscle is also unclear. Therefore, we hypothesized that CD56-negative cells as well as CD56-positive cells isolated from the skeletal muscle produce paracrine factors and have therapeutic effects in skeletal muscle-derived cell sheet therapy for heart failure.

Methods
Cell surface and intracellular markers of CD56-negative non-myogenic cells (NMCs) and CD56-positive myoblasts were evaluated. We also analyzed cytokine expression, tube formation ability, and stem cell mobilization in both cell populations. Finally, we assessed the therapeutic effects of the cell populations in a rat myocardial infarction model.

Results
Analysis of cell surface and intracellular markers revealed that CD56-negative NMCs expressed fibroblast markers and a higher level of mesenchymal cell markers, such as CD49b and CD140a, than myoblasts. Both NMCs and myoblasts expressed various cytokines in vitro with different expression patterns. In addition, NMCs induced tube formation (control vs. myoblasts vs. NMCs: 100 ± 11.2 vs. 142 ± 8.3 vs. 198 ± 7.4%) and stem cell mobilization (control vs. myoblasts vs. NMCs: 100 ± 6.8 vs. 210 ± 22.9 vs. 351 ± 36.0%) to a higher degree in vitro than did myoblasts. The effect of NMCs and myoblasts on the improvement of cardiac function and suppression of myocardial fibrosis in rat myocardial infarction model was comparable.

Conclusion
These results indicate that NMCs exhibit therapeutic effects in skeletal muscle-derived cell sheet therapy for heart failure. Thus, accurate parameters correlating with therapeutic effects need to be further explored.
A cytokine screen using CRISPR-Cas9 knock-in reporter pig iPS cells reveals that Activin A regulates NANOG
Authors: Xu Junjun , Zheng Zheng , Du Xuguang , Shi Bingbo , Wang Jichang , Gao Dengfeng , Zhu Qianqian , Chen Xinze , Han Jianyong 
Published: February 2020

AbstractBackgroundNANOGfunctions as the gateway for the generation of pluripotent stem cells (PSCs) in mice and humans. NANOG is a transcription factor highly expressed in pig pre-implantation embryos, indicating that it is a conserved pluripotency-associated factor. However, pigNANOGreporter PSCs have yet to be established, and the regulation of pluripotency byNANOGis not fully understood in this animal.MethodsIn this study, pigNANOGtdTomato knock-in reporter positive PC-iPS cells were established using CRISPR/Cas9. The resulting cell line was treated with several cytokines and their corresponding inhibitors to identify pathways that regulateNANOGexpression. The pathways examined were LIF (leukemia inhibitory factor)/IL6 (interleukin 6)-STAT3, FGF (fibroblast growth factor)/ERK, IGF1 (insulin-like growth factor 1)/PIP3 (phosphoinositide 3-kinase)-AKT, Activin A/SMAD, and BMP4 (bone morphogenetic proteins)/SMAD.ResultsOur experiments showed that the Activin A/SMAD pathway is directly associated with activation ofNANOGexpression in the pig, as is also the case in mice and humans. Activin A directly regulates the expression of pigNANOGvia SMAD2/3; inhibition of this pathway by SB431542 resulted in inhibition of NANOG expression.ConclusionsOur results show that Activin A plays an important regulatory role in NANOG-mediated pluripotency in pig iPS cells. Activin A treatment may be therefore an effective method for de novo derivation of authentic embryonic stem cells (ESCs) from pig pre-implantation embryos.
Uncertainty quantification with risk measures in production planning
Authors: Göttlich Simone , Knapp Stephan 
Published: February 2020

AbstractThis paper is concerned with a simulation study for a stochastic production network model, where the capacities of machines may change randomly. We introduce performance measures motivated by risk measures from finance leading to a simulation based optimization framework for the production planning. The same measures are used to investigate the scenario when capacities are related to workers that are randomly not available. This corresponds to the study of a workforce planning problem in an uncertain environment.
Neimark–Sacker bifurcation and the generate cases of Kopel oligopoly model with different adjustment speed
Authors: Li Bo , He Qizhi , Chen Ruoyu 
Published: February 2020

AbstractIn this paper, bifurcations and chaotic behaviours of Kopel oligopoly model with different adjustment speed are discussed. The results imply that the Kopel oligopoly model undergoes flip bifurcation, Neimark–Sacker bifurcation, 1:3 and 1:4 resonances, which could induce complex dynamics, especially global behaviours between different orbits. The conditions for the occurrence of three different kinds of bifurcation are derived. Furthermore, the numerical simulations provide us the case study of theoretical analysis and the corresponding dynamical behaviours, especially the occurrence of global orbits.
Note on the persistence and stability property of a stage-structured prey–predator model with cannibalism and constant attacking rate
Authors: Chen Fengde , Deng Hang , Zhu Zhenliang , Li Zhong 
Published: February 2020

AbstractWe revisit the persistence and stability property of a stage-structured prey–predator model with cannibalism and constant attacking rate. By using the differential inequality theory and Bendixson–Dulac criterion, we show that if the system without cannibalism is permanent, then the system with cannibalism is also permanent. By developing some new analysis technique, we obtain a new set of sufficient conditions which ensure the global asymptotic stability of the nonnegative equilibrium, which means that, under some suitable assumption, prey cannibalism has no influence on the stability property of the predator free equilibrium. Our results essentially improve the corresponding results of Limin Zhang and Chaofeng Zhang.
Effectiveness of a structured, framework-based approach to implementation: the Researching Effective Approaches to Cleaning in Hospitals (REACH) Trial
Authors: Hall Lisa , White Nicole M. , Allen Michelle , Farrington Alison , Mitchell Brett G. , Page Katie , Halton Kate , Riley Thomas V. , Gericke Christian A. , Graves Nicholas , Gardner Anne 
Published: February 2020

Abstract
Background
Implementing sustainable practice change in hospital cleaning has proven to be an ongoing challenge in reducing healthcare associated infections. The purpose of this study was to develop a reliable framework-based approach to implement and quantitatively evaluate the implementation of evidence-based practice change in hospital cleaning.

Design/methods
The Researching Effective Approaches to Cleaning in Hospitals (REACH) trial was a pragmatic, stepped-wedge randomised trial of an environmental cleaning bundle implemented in 11 Australian hospitals from 2016 to 2017. Using a structured multi-step approach, we adapted the integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) framework to support rigorous and tailored implementation of the cleaning bundle intervention in eleven diverse and complex settings. To evaluate the effectiveness of this strategy we examined post-intervention cleaning bundle alignment calculated as a score (an implementation measure) and cleaning performance audit data collected using ultraviolet (UV) gel markers (an outcome measure).

Results
We successfully implemented the bundle and observed improvements in cleaning practice and performance, regardless of hospital size, intervention duration and contextual issues such as staff and organisational readiness at baseline. There was a positive association between bundle alignment scores and cleaning performance at baseline. This diminished over the duration of the intervention, as hospitals with lower baseline scores were able to implement practice change successfully.

Conclusion
Using a structured framework-based approach allows for pragmatic and successful implementation of clinical trials across diverse settings, and assists with quantitative evaluation of practice change.

Trial registration
Australia New Zealand Clinical Trial Registry ACTRN12615000325505, registered on 4 September 2015.
What bereaved parents want health care providers to know when their babies are stillborn: a community-based participatory study
Authors: Farrales Lynn L. , Cacciatore Joanne , Jonas-Simpson Christine , Dharamsi Shafik , Ascher Jaime , Klein Michael C. 
Published: February 2020

Abstract
Background
Bereaved parents experience higher rates of depressive and post-traumatic stress symptoms after the stillbirth of a baby than after live-birth. Yet, these effects remain underreported in the literature and, consequently, insufficiently addressed in health provider education and practice. We conducted a participatory based study to explore the experiences of grieving parents during their interaction with health care providers during and after the stillbirth of a baby.

Methods
This community-based participatory study utilized four focus groups comprised of twenty-seven bereaved parents (44% fathers). Bereaved parents conceptualized the study, participating at all stages of research, analyses, and drafting. Data were reduced into a main theme and subthemes, then broad-based member checked to ensure fidelity and nuances within themes.

Results
The major theme that emerged centered on provider acknowledgement of the baby as an irreplaceable individual. Subthemes reflected 1) acknowledgement of parenthood and grief, 2) recognition of the traumatic nature of stillbirth, and 3) acknowledgement of enduring grief coupled with access to support. It was important that providers realized how grief was experienced within health care and social support systems, concretized by their desire for long-term, specialized support.

Conclusions
Both mothers and fathers feel that acknowledgement of their baby as an individual, their parenthood, and their enduring traumatic grief by healthcare providers are key elements required in the process of initiating immediate and ongoing care after the stillbirth of a baby.
Development of high-resolution melting curve analysis in rapid detection of vanA gene, Enterococcus faecalis, and Enterococcus faecium from clinical isolates
Authors: Dehbashi Sanaz , Tahmasebi Hamed , Sedighi Parinaz , Davarian Faeze , Arabestani Mohammad Reza 
Published: February 2020

Abstract
Background
High-resolution melting analysis (HRMA) is a novel molecular technique based on the real-time PCR that can be used to detect vancomycin resistance Enterococcus (VRE). The purpose of this study was to identify VRE species with HRMA in clinical isolates.

Results
Out of 49 Enterococcus isolates, 11 (22.44%) E. faecium isolates and 19 (38.77%) E. faecalis isolates were detected. Average melting temperatures for divIVA in E.faecalis, alanine racemase in E.faecium, and vanA in VRE strains were obtained as 79.9 ± 0.5 °C, 85.4 ± 0.5 °C, and 82.99 ± 0.5 °C, respectively. Furthermore, the data showed that the HRMA method was sensitive to detect 100 CFU/ml for the divIVA, alanine racemase, and vanA genes. Also, out of 49 Enterococcus spp., which were isolated by HRMA assay, 8 isolates (16.32%) of E. faecium and 18 isolates (36.73%) of E. faecalis were detected. The vanA gene was reported in 2 isolates (25%) of E. faecium and 9 isolates (50%) of E. faecalis.

Conclusions
This study demonstrated that using the HRMA method, we can detect E. faecium, E. faecalis, and the vanA gene with high sensitivity and specificity.
Identification of DNA variation in callus derived from Zingiber officinale and anticoagulation activities of ginger rhizome and callus
Authors: Abd El-Hameid Asmaa R. , Abo El-kheir Zakia A. , Abdel-Hady M. S. , Helmy Wafaa A. 
Published: February 2020

Abstract
Background
The medicinal plants have been used as alternative treatments for many diseases in many countries. Thus, the possibility of the alteration of some naturally relatively cheap sources into highly valuable products for pharmaceutical and biological importance via tissue culture is investigated in this study. Special attention is needed to estimate the molecular genetic variation between the studied plant and the callus.

Results
Ginger (Zingiber officinale Roscoe) rhizome was affected by various concentrations of cytokinin and auxin for the induction of callus. The highest percentage of callus induction and maximal callus fresh weight was achieved when Murashige and Skoog (MS) medium was supplemented with 2 mg/l 2, 4-D + 1mg/l BA. The genetic variations accompanied with in vitro conditions of callus induction was evaluated by four primers of inter-simple sequence repeat (ISSR) that amplified 36 bands. The highest readings for clotting times were found by using the sulfated neutral extract of ginger rhizome at a concentration of 400 μg/ml, and the extract of sulfated alkaline plant callus had an anticoagulation activity at (200 μg/ml) comparable to that of a standard preparation of heparin sodium.

Conclusion
These results showed that ginger (Zingiber officinale Roscoe) rhizome was affected by various concentrations of cytokinin and auxin for induction of callus especially when MS was supplemented with 2 mg/l 2, 4-D + 1 mg/l BA. Also, the results of ISSR markers confirmed the occurrence of genetic variations during callus induction process. The results indicated that the sulfated alkaline of ginger rhizome and sulfated aqueous extracts of ginger rhizome and callus exhibited anticoagulant activity. So, it was clear that the addition of sulfate group into the investigated extracts enhances the anticoagulation activities.
Transcranial pulsed electromagnetic fields for treatment-resistant depression: A multicenter 8-week single-arm cohort study
Authors: Larsen Erik Roj , Licht Rasmus W. , Nielsen René Ernst , Lolk Annette , Borck Bille , Sørensen Claus , Christensen Ellen Margrethe , Bizik Gustav , Ravn Janus , Martiny Klaus , Vinberg Maj , Jankuviené Odeta , Jørgensen Pernille Blenker , Videbech Poul , Bech Per 
Published: February 2020

AbstractBackground.The efficacy of antidepressant treatment is fair, but the efficacy is considerably lower in patients failing two or more trials underscoring the need for new treatment options. Our study evaluated the augmenting antidepressant effect of 8-weeks transcranial pulsed electromagnetic field (T-PEMF) therapy in patients with treatment-resistant depression.Methods.A multicenter 8-week single-arm cohort study conducted by the Danish University Antidepressant Group.Results.In total, 58 participants (20 men and 38 women) with a moderate to severe depression as part of a depressive disorder according to ICD-10 who fulfilled criteria for treatment resistance were included, with 19 participants being nonresponders to electroconvulsive therapy during the current depressive episode. Fifty-two participants completed the study period. Scores on the Hamilton Depression Scale 17-items version (HAM-D17) decreased significantly from baseline (mean = 20.6, SD 4.0) to endpoint (mean = 12.6, SD 7.1;N = 58). At endpoint, utilizing a Last Observation Carried Forward analysis, 49 and 28% of those participants with, respectively, a nonchronic current episode (≤2 years;N = 33) and a chronic current episode (>2 years;N = 25) were responders, that is, achieved a reduction of 50% or more on the HAM-D17scale. At endpoint, respectively, 30 and 16% obtained remission, defined as HAM-D17 ≤ 7. On the Hamilton Scale 6-item version (HAM-D6), respectively, 51 and 16% obtained remission, defined as HAM-D6 ≤ 4.Conclusions.The findings indicate a potential beneficial role of T-PEMF therapy as an augmentation treatment to ongoing pharmacotherapy in treatment-resistant depression.