bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adapting CRISPR/Cas9 System for Targeting Mitochondrial Genome
Authors: Hussain Syed-Rehan A. , Yalvac Mehmet E. , Khoo Bendict , Eckardt Sigrid , McLaughlin K. John 
Published: February 2020

ABSTRACTGene editing of the mitochondrial genome using CRISPR-Cas9 system is highly challenging mainly due to sub-efficient delivery of guide RNA and Cas9 enzyme complexes into mitochondria. In this study, we were able to perform gene editing in the mitochondrial DNA by appending NADH-ubiquinone oxidoreductase chain 4 (ND4) targeting guide RNA to a RNA transport derived stem loop element (RP-loop) and expressing the Cas9 enzyme with preceding mitochondrial localization sequence. Our results showed mitochondrial co-localization of RP-loop gRNA and a marked reduction of ND4 expression in the cells carrying a A11204G variant in their ND4 sequence coincidently decreasing the mtDNA levels. This proof-of-concept study suggests that stem loop element added sgRNA can be transported to the mitochondria and functionally interact with Cas9 to mediate sequence specific mtDNA cleavage. Using this novel approach to target the mtDNA, our results provide further evidence that CRISPR-Cas9 mediated gene editing might potentially be used to treat mtDNA related diseases.
MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas
Authors: Tsugawa Hiroshi , Ikeda Kazutaka , Takahashi Mikiko , Satoh Aya , Mori Yoshifumi , Uchino Haruki , Okahashi Nobuyuki , Yamada Yutaka , Tada Ipputa , Bonini Paolo , Higashi Yasuhiro , Okazaki Yozo , Zhou Zhiwei , Zhu Zheng-Jiang , Koelmel Jeremy , Cajka Tomas , Fiehn Oliver , Saito Kazuki , Arita Masanori , Arita Makoto 
Published: February 2020

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1–2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.
Epidemic size of novel coronavirus-infected pneumonia in the Epicenter Wuhan: using data of five-countries’ evacuation action
Authors: Zhao Hongxin , Man Sailimai , Wang Bo , Ning Yi 
Published: February 2020

AbstractBackgroundSince late December 2019, novel coronavirus–infected pneumonia (NCP) emerged in Wuhan, Hubei province, China. Meanwhile, NCP rapidly spread from China to other countries, and several countries’ government rush to evacuate their citizens from Wuhan. We analyzed the infection rate of the evacuees and extrapolated the results in Wuhan’s NCP incidence estimation.MethodsWe collected the total number and confirmed cases of 2019-nCov infection in the evacuation of Korea, Japan, Germany, Singapore, and France and estimated the infection rate of the 2019 novel coronavirus (2019-nCov) among people who were evacuated from Wuhan with a meta-analysis. NCP incidence of Wuhan was indirectly estimated based on data of evacuation.ResultsFrom Jan 29 to Feb 2, 2020, 1916 people have been evacuated from Wuhan, among them 17 have been confirmed 2019-nCov infected. The infection rate is estimated to be 1.1% (95% CI 0.4%-3.1%) using one group meta-analysis method with random effect model. We then estimated that almost 110,000 (95% CI: 40,000-310,000) people were infected with 2019-nCov in Wuhan around Feb 2, 2020, assuming the infection risk of evacuees is close to Chinese citizens in Wuhan.ConclusionsAt the beginning of the outbreak, incidence of NCP may be vastly underestimated. Our result emphasizes that 2019-nCov has proposed a huge public health threats in Wuhan. We need to respond more rapidly, take large-scale public health interventions and draconian measures to limiting population mobility and control the epidemic.
ACE2 Expression in Kidney and Testis May Cause Kidney and Testis Damage After 2019-nCoV Infection
Authors: Fan Caibin , Li Kai , Ding Yanhong , Lu Wei , Wang Jianqing 
Published: February 2020

AbstractIn December 2019 and January 2020, novel coronavirus (2019-nCoV) - infected pneumonia (NCIP) occurred in Wuhan, and has already posed a serious threat to public health. ACE2 (Angiotensin Converting Enzyme 2) has been shown to be one of the major receptors that mediate the entry of 2019-nCoV into human cells, which also happens in severe acute respiratory syndrome coronavirus (SARS). Several researches have indicated that some patients have abnormal renal function or even kidney damage in addition to injury in respiratory system, and the related mechanism is unknown. This arouses our interest in whether coronavirus infection will affect the urinary and male reproductive systems. Here in this study, we used the online datasets to analyze ACE2 expression in different human organs. The results indicate that ACE2 highly expresses in renal tubular cells, Leydig cells and cells in seminiferous ducts in testis. Therefore, virus might directly bind to such ACE2 positive cells and damage the kidney and testicular tissue of patients. Our results indicate that renal function evaluation and special care should be performed in 2019-nCoV patients during clinical work, because of the kidney damage caused by virus and antiviral drugs with certain renal toxicity. In addition, due to the potential pathogenicity of the virus to testicular tissues, clinicians should pay attention to the risk of testicular lesions in patients during hospitalization and later clinical follow-up, especially the assessment and appropriate intervention in young patients’ fertility.
Host-induced gene silencing involves Arabidopsis ESCRT-III pathway for the transfer of dsRNA-derived siRNA
Authors: Timo Schlemmer , Lisa Weipert , Patrick Barth , Timo Werner Bernhard , Christian Preußer , Martin Hardt , Anna Möbus , Dagmar Biedenkopf , Martina Claar , Lukas Jelonek , Alexander Goesmann , Vannuruswamy Garikapati , Bernhard Spengler , Tobias Busche , Jörn Kalinowski , Aline Koch 
Published: February 2020

AbstractSmall (s)RNAs and their double-stranded (ds)RNA precursors have been adopted to control diseases in crop plants through expression in transgenic plants and targeted gene silencing (host-induced gene silencing, HIGS). While HIGS strategies proved to be effective, the mechanism of RNA transfer at the plant - pathogen interface is widely unknown. Here we show that extracellular vesicles (EVs) purified fromArabidopsis thalianaplants expressing CYP3RNA, a dsRNA originally designed to target the threeCYP51genes of the fungal pathogenFusarium graminearum, contain CYP3RNA-derived small interfering (si)RNAs as shown by RNA sequencing (RNA-seq) analysis. These transgene specific siRNAs had a length of 21 and 22 nucleotides with a bias towards 5’-uracil (U) and 5’-adenine (A). Notably, stringent protease and RNase treated EV fractions contained >70% less CYP3RNA-derived siRNAs, suggesting the presence of co-purified extravesicular nucleoprotein complexes stabilizing siRNAs outside of EVs. In addition, mutants of the ESCRT-III complex showed a loss of HIGS-mediated disease resistance and EVs isolated from these mutants were free of CYP3RNA-derived siRNAs. Together, these findings support the view that endosomal vesicle trafficking is required for HIGS mediating the transfer of transgene-derived siRNAs between donor host cells and recipient fungal cells probably in an EV-independent manner.
Adaptive laboratory evolution and reverse engineering of single-vitamin prototrophies inSaccharomyces cerevisiae
Authors: Perli Thomas , Moonen Dewi P.I. , van den Broek Marcel , Pronk Jack T. , Daran Jean-Marc 
Published: February 2020

AbstractQuantitative physiological studies onSaccharomyces cerevisiaecommonly use synthetic media (SM) that contain a set of water-soluble growth factors that, based on their roles in human nutrition, are referred to as B-vitamins. Previous work demonstrated that, inS. cerevisiaeCEN.PK113-7D, requirements for biotin could be eliminated by laboratory evolution. In the present study, this laboratory strain was shown to exhibit suboptimal specific growth rates when either inositol, nicotinic acid, pyridoxine, pantothenic acid,para-aminobenzoic acid (pABA) or thiamine were omitted from SM. Subsequently, this strain was evolved in parallel serial-transfer experiments for fast aerobic growth on glucose in the absence of individual B-vitamins. In all evolution lines, specific growth rates reached at least 90 % of the growth rate observed in SM supplemented with a complete B-vitamin mixture. Fast growth was already observed after a few transfers on SM withoutmyo-inositol, nicotinic acid orpABA. Reaching similar results in SM lacking thiamine, pyridoxine or pantothenate required over 300 generations of selective growth. The genomes of evolved single-colony isolates were re-sequenced and, for each B-vitamin, a subset of non-synonymous mutations associated with fast vitamin-independent growth were selected. These mutations were introduced in a non-evolved reference strain using CRISPR/Cas9-based genome editing. For each B-vitamin, introduction of a small number of mutations sufficed to achieve substantially a increased specific growth rate in non-supplemented SM that represented at least 87% of the specific growth rate observed in fully supplemented complete SM.ImportanceMany strains ofSaccharomyces cerevisiae, a popular platform organism in industrial biotechnology, carry the genetic information required for synthesis of biotin, thiamine, pyridoxine,para-aminobenzoic acid, pantothenic acid, nicotinic acid and inositol. However, omission of these B-vitamins typically leads to suboptimal growth. This study demonstrates that, for each individual B-vitamin, it is possible to achieve fast vitamin-independent growth by adaptive laboratory evolution (ALE). Identification of mutations responsible for these fast-growing phenotype by whole-genome sequencing and reverse engineering showed that, for each compound, a small number of mutations sufficed to achieve fast growth in its absence. These results form an important first step towards development ofS. cerevisiaestrains that exhibit fast growth on cheap, fully mineral media that only require complementation with a carbon source, thereby reducing costs, complexity and contamination risks in industrial yeast fermentation processes.
Therapeutic Communication Skills Training: An Effective Tool to Improve the Caring Behaviors of ICU Nurses
Authors: Zare Farzane , Farokhzadian Jamileh , Nematollahi Monirsadat , Miri Sakineh , Foroughameri Golnaz 
Published: February 2020

AbstractBackgroundCaring behaviors are crucial in intensive care units (ICU) because patients in these wards require high levels of care. Effective communication with patients is one of the most important factors in caring behaviors of nurses working in ICUs. Therefore, the aim of this study was to evaluate the effect of therapeutic communication skills training on the caring behaviors of ICU nurese.Materials and MethodsThis experimental pre-test/post-test study was carried out on 105 nurses working in ICUs of hospitals affiliated to Yazd University of Medical Sciences in Iran in 2019. Nurses were randomly assigned into control (52 nurses) and intervention (53 nurses) groups. A two-day therapeutic communication training workshop was conducted for the participants. Data were collected using demographic information questionnaire and caring behaviors questionnaire before and one month after the intervention.ResultsThe findings showed no significant difference between the control and intervention groups regarding the nurses’ caring behaviors in the pretest (P = 0.148). However, after implementation of the training program, a significant difference was observed in the mean scores of caring behaviors between the two groups. In the control group, the mean scores of caring behaviors decreased significantly after the intervention (P = 0.001); whereas, the mean scores of intervention group increased significantly after the intervention (P = 0.001).ConclusionAccording to the results, ICU nurses’ training in therapeutic communication skills had a positive effect on their caring behaviors. Therefore, we suggest the authorities prepare and implement educational packages of therapeutic communication skills as a coherent program for other nurses. As a result, the caring behaviors and the quality of cares can be improved for patients.
Genetic conditionality of strength by the ACE gene in women horse riders
Authors: Majchrowicz Lena , Matłosz Piotr , Majchrowicz Rena 
Published: February 2020

ABSTRACTThe sport performance relies on hard work, intensity, duration of workout and undoubtedly on genetic background. These components fold on multicausal character of sport achievements. One of the best known genes associated with sport performance is angiotensin converting enzyme gene (ACE). In this study, we showed ACE distribution in women horse riders and the correlation between physiological and genetic background, that should be taken into account when deciding to train sports discipline. Data from 40 healthy female adults were collected. Participants trained horse-riding for at least 3 years and participated in sport competition at least at national level and control group consist of out of training persons. We analysed BMI, %FAT, cardiorespiratory efficiency (VO2max), Complex Reaction Time, body balance, force and Lower Limbs Explosive Force between both calculated groups. Physiological data was calculated by non-parametric Mann-Whitney test with Dunnett’s post hoc test. The DNA amplification from saliva was performed by PCR method to analyze the ACE genotype distribution. In our study, for the first time we showed that the women training dressage have higher force and complex reaction time than the control group. It was correlated with possession of the D allele in genotype that is associated with muscle strength, efficiency and muscle power. There is no research relating to ACE polymorphism among horse riders. This paper showed angiotensin converting enzyme gene distribution polymorphism in female Polish professional horse riders. This article confirms correlation between genotype, sports results and physiological parameters.
Mitochondria regulateDrosophilaintestinal stem cell differentiation through FOXO
Authors: Zhang Fan , Pirooznia Mehdi , Xu Hong 
Published: February 2020

AbstractStem cells often rely on glycolysis for energy production, and switching to oxidative phosphorylation is believed to be essential for their differentiation. To explore the link between mitochondrial respiration and stem cell differentiation, we genetically disrupted electron transport chain (ETC) complexes in the intestinal stem cells (ISCs) ofDrosophila. We found that ISCs carrying impaired ETC proliferated much more slowly than normal, produced very few intestinal progenitors, or enteroblasts, and failed to differentiate into enterocytes or enteroendocrine cells. One of the main impediments to ISCs’ differentiation appeared to be abnormally elevated forkhead box O (FOXO) signaling in the ETC-deficient ISCs, as genetically suppressing the signaling pathway partially rescued the differentiation defect. Contrary to common belief, neither reactive oxygen species (ROS) accumulation nor adenosine triphosphate (ATP) reduction appeared to mediate the ETC mutant phenotype. Our results demonstrate that ETC is essential forDrosophilaISC proliferation and differentiationin vivo, and acts at least partially by repressing endogenous FOXO signaling. They also raise the possibility that ETC complexes have a role in stem cell differentiation beyond electron transfer and ATP production.
Salamander-like tail regeneration in the West African lungfish
Authors: Verissimo Kellen Matos , Perez Louise Neiva , Dragalzew Aline Cutrim , Senevirathne Gayani , Darnet Sylvain , Mendes Wainna Renata Barroso , dos Santos Neves Ciro Ariel , dos Santos Erika Monteiro , de Sousa Moraes Cassia Nazare , Elewa Ahmed , Shubin Neil , Froebisch Nadia Belinda , de Freitas Sousa Josane , Schneider Igor 
Published: February 2020

AbstractSalamanders, frog tadpoles, and diverse lizards have the remarkable ability to regenerate tails. Paleontological data suggests that this capacity is plesiomorphic, yet when the developmental and genetic architecture of tail regeneration arose is poorly understood. Here we show morphological and molecular hallmarks of tetrapod tail regeneration in the West African lungfishProtopterus annectens, a living representative of the sister group of tetrapods. As in salamanders, lungfish tail regeneration occursviaformation of a proliferative blastema and restores original structures, including muscle, skeleton and spinal cord. In contrast to lizards and similar to salamanders and frogs, lungfish regenerate spinal cord neurons and reconstitute dorsoventral patterning of the tail. Similar to salamander and frog tadpoles,Shhis required for lungfish tail regeneration. Through RNA-seq analysis of uninjured and regenerating tail blastema, we show that the genetic program deployed during lungfish tail regeneration maintains extensive overlap with that of tetrapods, with the upregulation of genes and signaling pathways previously implicated in amphibian and lizard tail regeneration. Furthermore, the lungfish tail blastema showed marked upregulation of genes encoding post-transcriptional RNA processing components and transposon-derived genes. Our results show that developmental processes and genetic program of tetrapod tail regeneration were present at least near the base of the sarcopterygian clade and establish the lungfish as a valuable research system for regenerative biology.
A novel temporal identity window generates alternating cardinal motor neuron subtypes in a single progenitor lineage
Authors: Seroka Austin , Yazejian Rita M , Lai Sen-Lin , Doe Chris Q 
Published: February 2020

AbstractSpatial patterning specifies neural progenitor identity, with further diversity generated by temporal patterning within individual progenitor lineages. These mechanisms generate cardinal classes of motor neurons (sharing a transcription factor identity and common muscle group targets). InDrosophila, two cardinal classes are Even-skipped (Eve)+ motor neurons projecting to dorsal muscles and Nkx6+ motor neurons projecting to ventral muscles. TheDrosophilaneuroblast 7-1 (NB7-1) lineage generates distinct Eve+ motor neurons via the temporal transcription factor (TTF) cascade Hunchback (Hb)-Krüppel (Kr)-Pdm-Castor (Cas). Here we show that a newly discovered Kr/Pdm temporal identity window gives rise to an Nkx6+ Eve-motor neuron projecting to ventral oblique muscles, resulting in alternation of cardinal motor neuron subtypes from a single progenitor (Eve>Nkx6>Eve). We show that co-overexpression of Kr/Pdm generates ectopic VO motor neurons within the NB7-1 lineage and that Kr/Pdm act via Nkx6, which itself is necessary and sufficient for VO motor neuron identity. Lastly, Nkx6 is required for ventral oblique muscle targeting, thereby linking temporal patterning to motor neuron morphology and synaptic target selection. In conclusion, we show that one neuroblast lineage generates interleaved cardinal motor neurons fates; that the Kr/Pdm TTFs form a novel temporal identity window that promotes expression of Nkx6; and that the Kr/Pdm>Nkx6 pathway is necessary and sufficient to specify VO motor neuron identity and morphology.
Optimal energy management of microgrid using advanced multi-objective particle swarm optimization
Authors: Anh Ho Pham Huy , Kien Cao Van 
Published: February 2020

Purpose
The purpose of this paper is to propose an optimal energy management (OEM) method using intelligent optimization techniques applied to implement an optimally hybrid heat and power isolated microgrid. The microgrid investigated combines renewable and conventional power generation.

Design/methodology/approach
Five bio-inspired optimization methods include an advanced proposed multi-objective particle swarm optimization (MOPSO) approach which is comparatively applied for OEM of the implemented microgrid with other bio-inspired optimization approaches via their comparative simulation results.

Findings
Optimal multi-objective solutions through Pareto front demonstrate that the advanced proposed MOPSO method performs quite better in comparison with other meta-heuristic optimization methods. Moreover, the proposed MOPSO is successfully applied to perform 24-h OEM microgrid. The simulation results also display the merits of the real time optimization along with the arbitrary of users’ selection as to satisfy their power requirement.

Originality/value
This paper focuses on the OEM of a designed microgrid using a newly proposed modified MOPSO algorithm. Optimal multi-objective solutions through Pareto front demonstrate that the advanced proposed MOPSO method performs quite better in comparison with other meta-heuristic optimization approaches.
Seismic structural responses reduction of double-layered containment nuclear power plant via BIS-TMD
Authors: Hou Gangling , Liu Yu , Li Meng , Sun Menghan , Sun Feng , Zhu Xiuyun , Pan Rong , Zhang Dongyu 
Published: February 2020

Purpose
In recent years, a new type of double-layered containment structure of nuclear power plant has been built in China, named ACP1000 NNP. This paper aims to propose a new method to mitigate the seismic responses of this type of the structure.

Design/methodology/approach
The new base isolation structure (BIS)- tuned mass damper (TMD) structure was proposed and implemented only by modifying the connection between various components of NPPs, and the application of this concept design in ACP1000 was skillfully realized.

Findings
The new structure adopts the combination of structural form and function, adopts appropriate amplification of the seismic response of the secondary component, possesses advantages in explicit damping mechanism, good damping effect, robustness of seismic structures, simple implementation process, etc., and meets the special seismic safety requirements of the NPPs.

Originality/value
This seismic and hazard mitigation and BIS-TMD structure can avoid the risk of ACP1000 accidents caused by horizontal earthquakes.
The development of entrepreneurial alertness in undergraduate students
Authors: Bueckmann-Diegoli Rafaela , García de los Salmones Sánchez María del Mar , San Martín Gutiérrez Héctor 
Published: February 2020

PurposeThe main goal of this work is to argue the theoretical validity of two competitive models that integrate entrepreneurial alertness in the Theory of Planned Behavior (TPB), and also to propose an explanation for the conceptual approach with a higher explicative ability.Design/Methodology/ApproachA total of 281 undergraduate students participated in the survey, and the data were analyzed using structural equation modeling and competitive models.FindingsThe research shows it is possible to defend and test two competing TPB models with entrepreneurial alertness (EA), which alerts other field researchers to consider more than one possibility. The model showing the impact EA has on attitude toward the behavior (ATB) and perceived behavioral control (PBC), as well as the model showing the impact of ATB and PBC on EA are both valid. The shared characteristic of the sample may explain a higher predictive power in the first model.Research limitations/implicationsThe sample was limited to undergraduate students of one university.Practical implicationsFor educators and policymakers, these results highlight the need to include content related to EA in entrepreneurship education programs since it could trigger the entrepreneurial process.Originality/valueThe paper is the first of its kind to demonstrate competing arguments for the role of EA in TPB.