bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural Family-Free Genomic Distance
Authors: Rubert Diego P. , Martinez Fábio V. , Braga Marília 
Published: February 2021

Abstract
Background: A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome.The traditional approaches in this area are family-based, i.e., require the classification of DNA fragments of both genomes into families. Furthermore, the most elementary family-based models, which are able to compute distances in polynomial time, restrict the families to occur at most once in each genome. In contrast, the distance computation in models that allow multifamilies (i.e., families with multiple occurrences) is NP-hard. Very recently, Bohnenkamper etal. (J. Comput. Biol., 2020) proposed an ILP formulation for computing the genomic distance of genomes with multifamilies, allowing structural rearrangements, represented by the generic double cut and join (DCJ) operation, and content-modifying insertions and deletions of DNA segments. This ILP is very efficient, but must maximize a matching of the genes in each multifamily, in order to prevent the free lunch artifact that would otherwise let empty or almostempty matchings give smaller distances. Results: In this paper, we adopt the alternative family-free setting that, instead of family classification, simply uses the pairwise similarities between DNA fragments of both genomes to compute their rearrangement distance. We adapted the ILP mentioned above and developed a model in which pairwise similarities are used to assign weights to both matched and unmatched genes, so that an optimal solution does not necessarily maximize the matching. Our modelthen results in a natural family-free genomic distance, that takes into consideration all given genes, without prior classification into families, and has a search space composed of matchings of any size. In spite of its bigger searchspace, our ILP seems to be boosted by a reduction of the number of co-optimal solutions due to the weights. Indeed, it converged faster than the original one by Bohnenkamper et al. for instances with the same number of multipleconnections. We can handle not only bacterial genomes, but also fungi and insects, or sets of chromosomes of mammals and plants. In a comparison study of six fruit fly genomes, we obtained accurate results.
How do concerned significant others experience Community Reinforcement and Family Training (CRAFT) – a qualitative study.
Authors: Hellum Rikke , Bilberg Randi , Bischof Gallus , Nielsen Anette Søgaard 
Published: February 2021

Abstract
Introduction: In the last 20 years, there has been growing evidence that heavy drinking causes serious harm, not only to the person who drinks but also to the person’s relations and concerned significant others (CSOs). Several interventions have been developed to help CSOs of persons with substance abuse e.g., Community Reinforcement and Family Training (CRAFT). The aim of this study was to investigate what the CSOs who participated in a CRAFT intervention aimed for, when they sought help, what they found helpful from the intervention, and which elements of the interventions they utilized. Furthermore, we wanted to investigate how the CSOs managed to apply the components to their life.Method: This is a qualitative study is based on data from 11 interviews with help-seeking CSOs of individuals with alcohol problems. The participants were recruited from an RCT study of various formats for delivering CRAFT (by means of group sessions + written material, individual sessions + written material or self-delivered CRAFT with written material only). Semi-structured interviews were conducted, audio-recorded, and transcribed. The analysis was based on the Interpretative Phenomenological Analysis.Results: The results describe how the CSOs experienced the intervention and the format that CRAFT in which was delivered, what they felt they gained, and, lastly, how the CSO experienced that it affected their life after the intervention.Conclusion: CSOs who participated in CRAFT intervention, felt helped by the CRAFT components, regardless of the format through which the intervention was delivered. Written material on CRAFT was considered helpful alongside the interventions and may, even for some, function as a useful intervention, albeit probably not as effective. The “Communication-element” from CRAFT, positive reinforcement, and knowledge about the disorder seemed particularly helpful.
Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato
Authors: Liu Mengyuan , Zhi Xiaona , Wang Yi , Wang Yang 
Published: February 2021

Abstract
Background: Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference of nitrate as inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-Like Proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results: In this study, genome-wide analysis revealed six NLP members in tomato genome. They were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that SlNLP genes had collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in tomato genome. Tissue-specific expression analysis showed that the close homologues of AtNLP6/7, SlNLP3, was strongly expressed in roots during both seedling and flowering stages; SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves; and SlNLP6 were expressed in high levels in fruits. Further, the nitrate uptake in tomato roots and expression patterns of SlNLP genes were measured under nitrogen/phosphate/potassium deficiency and nitrate resupply conditions. The transcript abundance of SlNLP3 decreased to 70% under phosphate/potassium deficiency. Most of SlNLPs were up-regulated after nitrogen starvation. SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions: These results provided significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.
Different sterilization methods used for human tendons – A systematic review
Authors: Farago Denes , Kozma Blanka , Kiss Rita Maria 
Published: February 2021

Abstract
BackgroundIt is important to know the biomechanical properties of an allograft. This is because when looking to do a transplant of a tendon, the tendon must have very similar biomechanical properties to the original tendon. To use tendon allografts, it is critical to properly sterilize the tendon before implantation. In past decades, several sterilization procedures have been used. This study aimed to systematically evaluate the existing literature to compare the values of failure load/ultimate strength and Young’s modulus of elasticity of different sterilization methods on commonly used tendon allografts. Five major scientific literature databases (Web of Science, Science Direct, Scopus, PLOS ONE, Hindawi) and additional sources were used.ResultsStudies used had to show a particular sterilization method. Studies were identified to meet the following inclusion criteria: is a controlled laboratory study, gamma irradiation (dose reported), and other sterilization methods. Search for publications dated between 1991 and March 31st, 2020. A total of 54 articles have been included. Data collected from the full-text assessment included: a) author and date, b) type of tendon, c) type of sterilization, d) sterilization dose, and g) measured and calculated parameters. Different types of sterilization methods used before tendon durability testing have been identified and categorized.ConclusionsIdentified sterilization methods (gamma irradiation, dry ice, supercritical carbon dioxide (SCCO2), BioCleanse, Electron Beam) are offered as a catalog of potential methods.As a result of the broadness of the present research, it provides an overview of sterilization methods. It does not stand for the state-of-the-art of any single process.
Optimal ATN biomarkers and their role in predicting cognitive progress of mild cognitive impairment
Authors: Song Rao , Wu Xiaojia , Liu Huan , Guo Dajing , Tang Lin , Zhang Wei , Feng Junbang , Li Chuanming 
Published: February 2021

Abstract
Background

It is of great significance to investigate the optimal cerebrospinal fluid (CSF) and magnetic resonance image biomarkers of ATN system and clarify their predictive value in cognitive progression of mild cognitive impairment individuals (MCI).
Methods

147 healthy control (HC), 197 patients with MCI, and 128 patients with Alzheimer’ Disease (AD) were included from the ADNI database. All MCI patients were followed up from 6 to 60 months. The amyloid (A) was assessed by CSF Aβ42 or Aβ42/Aβ40. The tau pathology (T) was assessed by CSF p-tau. The neurodegeneration (N) was assessed by radiomics of the whole brain MRI or by CSF t-tau. Biomarkers with larger area under the receiver operating characteristic curve (AUC) in the discrimination of AD and HC were considered to be the optimal biomarkers. The conversion rates of different ATN profiles in MCI subjects during follow-up were analyzed using Kaplan-Meier estimates and compared using the Log-rank test.
Results

The CSF Aβ 42 and the radiomics signature (AUC 0.822 and 0.998, respectively) were identified as the optimal A and N biomarkers, respectively. For MCI patients of the Alzheimer continuum, there was no significant difference in the progression rate of A + T − N− and A − T−N − profiles (p > 0.05). The A + T + N−, A + T − N + profiles had a significant higher progression rate than that of the A + T − N− patients (all p < 0.05). For MCI of the suspected non-AD pathophysiology (SNAP), patients with the A − T−N + profile (p < 0.05) showed significant higher progression rate than A − T−N − profile. There was no significant difference in the progression rate of A − T + N − and A − T−N − profiles (p > 0.05).
Discussion

We proposed a new radiomics method to assess N accurately and ascertained the optimal A/T/N biomarkers for the discrimination of HC and AD. For MCI patients of the Alzheimer continuum, isolated A + was indicator of cognitive stability, while the abnormality of T and N, respectively or simultaneously, indicated the high risk of progression. For MCI patients of SNAP, isolated T + indicated the cognitive stability, while the appearance of N + indicated the high risk of progression.
Transition mechanism of melt depth during Laser Powder Bed Fusion using in-situ X-ray and thermal imaging
Authors: Ogura Tomoya , Wakai Yuki , Nakano Shizuka , Sato Naoko , Kajino Satoshi , Suzuki Shinsuke 
Published: February 2021

Abstract
This research clarified the transition mechanism of melt depth in Ti powder bed during Laser Powder Bed Fusion process using in-situ X-ray and thermal imaging. A fiber laser beam of 150 W was irradiated on a powder bed at a scan speed of 15 mm/s for 3.5 s in a vacuum chamber. The obtained X-ray images showed a keyhole depth Ld increased immediately after laser irradiation, gradually decreased, and became constant. It also showed a keyhole width Lw increased immediately after laser irradiation and decreased afterward, after that, Lw increased again, and became constant. Furthermore, thermal images that measured the temperature on the powder bed showed the high temperature width Lh gradually increased and become constant. The model of the driving force which pushed the molten droplet was examined by analyzing the volume and scattering speed of the molten droplet. The model indicated the recoil pressure caused by the vaporization of powder metal was a driving force for the molten droplet scattering. The transition mechanism of keyhole depth was considered as follows. The increase of Ld at the beginning is due to the increase of the recoil pressure PT. This is because the decrease of Lw and large quantity of vaporization. Next, the decrease of Ld is due to the decrease in PT. This is because the increase of Lw and decrease of quantity of vaporization. At last, the transition to the constant Ld is caused by stabilization of Lw and Lh followed by stabilization of PT.
A Highly Efficient Identification of Mutants Generated by&nbsp;CRISPR/Cas9 Using the&nbsp;Non‑Functional DsRed Assisted Selection in Aspergillus Oryzae
Authors: Fan Junxia , Zhang Huanxin , Li Yuzhen , Chen Ziming , Chen Tianming , Zeng Bin , Zhang Zhe 
Published: February 2021

Abstract
The CRISPR/Cas9 system has become a great tool for target gene knock-out in filamentous fungi. It is laborious and time-consuming that identification mutants from a large number of transformants through PCR or enzyme-cut method. Here, we first developed a CRISPR/Cas9 system in Aspergillus oryzae using AMA1-based autonomously replicating plasmid and Cas9 under the control of the Aspergillus nidulans gpdA promoter. By the genome editing technique, we successfully obtained mutations within each target gene in Aspergillus oryzae. Then, we put the protospacer sequence of a target gene and its protospacer adjacent motif (PAM) behind the start codon “ATG” of DsRed, yielding the non‑functional DsRed (nDsRed) reporter gene, and the nDsRed reporter gene could be rescued after successful targeted editing. Moreover, this method was also applied by targeting the kojic acid synthesis gene kojA, and the transformants with DsRed activity were found to harbor targeted mutations in kojA. These results suggest that the nDsRed can be used as a powerful tool to facilitate the identification of mutants generated by CRISPR/Cas9 in Aspergillus oryzae.
Multi-technique characterization and conservation of an ancient Egyptian fabric from King Khufu first solar ship
Authors: Nabil Eman , Khattab Tawfik A. , kamel samir 
Published: February 2021

Abstract
Textiles are among the most fragile artefacts in the world. They have been difficult to preserve even in the best circumstances. Herein, we studied an artefact fabric of a special nature in terms of usage. Despite the multiple applications of textiles, the piece understudy is one of the unique pieces that the ancient Egyptian used as fenders for King Khufu first solar boat which is the second-largest discovery in Egypt history. The boat was discovered inside a limestone pit. It was disassembled and arranged in several layers. Four pillows of wrapped fabric were found in the first layer, which were used as boat fenders. This use is in itself a great discovery of the role played by textiles in the manufacture of ancient boats. Thus, we conducted tests and analytical studies of those fenders using a scanning electron microscopy (SEM) and an optical microscope to identify the type and nature of fibers, spinning method and aspects of damage. Both energy-dispersive X-ray (EDX) analysis and infrared analysis (FT-IR) were employed to explore the elemental content of the sample and to study the functional groups of the fabric. These analytical processes were useful in carrying out the restoration and preservation work necessary for the artefact under study.
In vivo efficacy of combination therapy with albendazole and atovaquone against primary hydatid cysts in mice
Authors: enkai shigehiro , Kouguchi Hirokazu , Inaoka Daniel Ken , Irie Takao , Yagi Kinpei , Kita Kiyoshi 
Published: February 2021

Abstract
Purpose
Alveolar echinococcosis (AE) is caused by the larval stage of Echinococcus multilocularis. Chemotherapy for AE involves albendazole (ABZ), which has shown insufficient efficacy. More effective chemotherapy for AE is needed. Previously, we have demonstrated that atovaquone (ATV), an anti-malarial, inhibits mitochondrial complex III of E. multilocularis and restricts the development of larval cysts in in vivo experiments. Therefore, in this study, we evaluated the efficacy of ABZ and ATV combination therapy on E. multilocularis in culture and in vivo experiments.
Methods
Protoscoleces were treated with 50 µM ABZ and/or ATV in the medium; the duration of parasite elimination was determined under aerobic and anaerobic culture. In the in vivo experiment, the effects of ABZ and ATV combination treatment in BALB/c mice infected orally with eggs from the feces of an adult-stage E. multilocularis-infected dog were compared with those of standard oral ABZ therapy.
Results
In the culture assay, the duration of elimination associated with ABZ and ATV combination treatment was 1 day shorter than that associated with ATV alone under aerobic conditions. Protoscolex viability progressively reduced owing to the combination treatment under anaerobic conditions; however, either drug used singly did not exhibit antiparasitic effects under hypoxia. Furthermore, compared with ABZ alone, the combination treatment significantly reduced the growth of the primary cyst in the liver of mice infected orally with parasite eggs.
Conclusion
ATV enhanced the effect of ABZ in the treatment of AE in mice.
3D Models Improve Understanding of Congenital Heart Disease
Authors: Awori Jonathan , Friedman Seth , Chan Titus , Howard Christopher , Seslar Stephen , Soriano Brian , Buddhe Sujatha 
Published: February 2021

Abstract
Introduction:Understanding congenital heart disease (CHD) is vital for medical personnel and parents of affected children. While traditional 2D schematics serve as the typical approach used, several studies have shown these models to be limiting in understanding complex structures. Recent world-emphasis has shifted to 3D printed models as a complement to 2D imaging to bridge knowledge and create new opportunities for experiential learning. We sought to systematically compare 3D digital and physical models for medical personnel and parent education compared to traditional methods.Methods:3D printed and digital models were made out of MRI and CT data for 20 common CHD. Fellows and nurse practitioners used these models to explore intra-cardiac pathologies following traditional teaching. The models were also used for parent education in outpatient settings after traditional education. The participants were then asked to fill out a Likert scale questionnaire to assess their understanding and satisfaction with different teaching techniques. These ratings were compared using paired t-tests and Pearson’s correlation. Results:Twenty-five medical personnel (18 fellows; 2 nurses; 4 nurse practitioners and one attending) and twenty parents participated in the study. The diagnosis varied from simple mitral valve pathology to complex single ventricle palliation. Parent and medical personnel understanding with digital models was significantly higher than traditional (p = 0.01). Subjects also felt that physical models were overall more useful than digital ones (p=0.001). Physicians using models for parent education also perceived the models to be useful, not significantly impacting their clinical workflow.Conclusions:3D models, both digital and printed, enhance medical personnel and parental understanding of CHD.
Using Fuzzy Control for Feedrate Scheduling of Computer Numerical Control Machine Tools
Authors: Lin Cheng-Jian , Lin Chun-Hui , Wang Shyh-Hau 
Published: February 2021

Abstract
In industrial processing, workpiece quality and processing time have become important issues lately. Fortunately, dynamic cutting feedrate scheduling has been proposed to improve machining accuracy and decrease cutting time. Studies have shown that the curvature and cutting feedrate significantly influence the machining accuracy. Therefore, the present study proposes a fuzzy control system for feedrate scheduling based on the curvature and curvature variation. The proposed system is implemented in actual cutting, and an optical three-dimensional scanner is performed as a verification to measure the cutting trajectory of the workpiece. Experimental results prove that the proposed fuzzy control system for dynamic cutting feedrate scheduling increases the cutting accuracy by 43% under the same cutting time; moreover, it decreases the cutting time by 49% under the same cutting accuracy.
Wheat (Triticum Aestivum L.) Response to Applied Potassium on Two Contrasting Soil Types (Vertisols and Cambisols) in The Central Highlands of Ethiopia
Authors: Shewangizaw Beza Woldearegay , Assefa Shawl , Kassie Kenzemed , Shegaw Getanh 
Published: February 2021

Abstract
Background: A field experiment was conducted at Basonawerana district, Amhara regional state on two major soil types for three consecutive years to determine the effect of application of potassium fertilizer on yield and yield components of wheat and to verify the soil fertility and fertilizer recommendation Atlas of the study site. Six levels potassium were applied (0, 15, 30, 45, 60 and 75 kg K ha-1). At each potassium levels, a balanced nutrient of 92 kg N, 30 kg P, 30 kg S, 2 kg Zn, 0.5 kg Cu and 0.5 kg B ha-1 were applied. The experiment was laid out in a randomized complete block design with tree replications. Result: The analysis of variance showed that all the measured parameters were Significant influenced by year, soil type and the interaction of year x soil type. The highest grain yield, which was observed from cambisols during the first year was increased grain yield by 176.7 % (3954 kg ha-1) compared with the lowest yield observed from vertisols during the third year. Similar trend was also observed in straw yield and harvest index. On the other hand, all the measured parameters was non-significant influenced by K rate, interaction of K rate x soil type and year x K rate x soil types. Numerically, the highest yield (3878.9 kg ha-1) was observed from the highest K rate. However, the trend was not consistent. Conclusion: application of different rates of potassium fertilizer brings any significant growth and yield response on two soil types of the study sites. So, application of this fertilizer is not recommended for the crop with such high K soil status.
Integrated Biocontrol of Tobacco Bacterial Wilt By Antagonistic&nbsp;Bacteria and Marigold
Authors: Hu Yun , Zhao Wan , Li Yanyan , Feng Ji , Li Chunli , Yang Xiaoqiong , Guo Qingqing , Wang Lin , Chen Shouwen , Li Xihong , Yang Yong 
Published: February 2021

Abstract
Tobacco bacterial wilt (TBW) is seriously damages the growth of tobacco. There is an urgent need to find a safer and more effective measure to control TBW. In this study, B. amyloliquefaciens ZM9 and marigold powder were applied to the tobacco roots alone or in combination, and the potential inhibition of TBW was assessed. On the other hand, the effects of these treatments on soil physicochemical properties, rhizosphere microbial community and soil metabolites were also evaluated. The results showed that the application of B. amyloliquefaciens ZM9 or marigold powder alone significantly reduced the abundance of R. solanacearum in rhizosphere soil, while the integrated treatment showed the strongest inhibitory effect. Moreover, the integrated treatment can inhibit the secretion of chemoattractants, and affect the change of rhizosphere soil microbial composition. In conclusion, the combination of antagonistic bacteria agent B. amyloliquefaciens ZM9 with marigold powder can enhance the suppression of TBW. Furthermore, B. amyloliquefaciens ZM9 and marigold have synergistic effects on suppressing TBW by regulation soil physicochemical properties, soil metabolites and microbial structure. This study provide a promising strategy for TBW control by integrated applying of B. amyloliquefaciens ZM9 and marigold powder.