bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
Authors: Burkhardt Alyssa Kay , Childs Kevin L. , Wang Jie , Ramon Marina L. , Martin Frank N. 
Published: October 2019

Abstract
Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.

Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.

Conclusions: High-quality reference genomes of M. phaseolina have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.
Symbiotic bacteria motivate the foraging decision and promote fecundity and survival of Bactrocera dorsalis (Diptera: Tephritidae)
Authors: Akami Mazarin , Ren Xue-Ming , Qi Xuewei , Mansour Abdelaziz , Gao Bingli , Cao Shuai , Niu Chang-Ying 
Published: October 2019

Abstract
Background The gut bacteria of tephritid fruit flies play prominent roles in nutrition, reproduction, maintenance and ecological adaptations of the host. Here, we adopted an approach based on direct observation of symbiotic or axenic flies feeding on dishes seeded with drops of full diet (containing all amino acids) or full diet supplemented with bacteria at similar concentrations to explore the effects of intestinal bacteria on foraging decision and fitness of Bactrocera dorsalis. Results The results show that intestinal probiotics elicit beneficial foraging decision and enhance the female reproduction fitness and survival of B. dorsalis (symbiotic and axenic), yet preferences for probiotic diets were significantly higher in axenic flies to which they responded faster compared to full diet. Moreover, females fed diet supplemented with Pantoea dispersa and Enterobacter cloacae laid more eggs but had shorter lifespan while female fed Enterococcus faecalis and Klebsiella oxytoca enriched diets lived longer but had lower fecundity compared to the positive control. Conversely, flies fed sugar diet (negative control) were not able to produce eggs, but lived longer than those from the positive control. Conclusions These results suggest that intestinal bacteria can drive the foraging decision in a way which promotes the reproduction and survival of B. dorsalis. Our data highlight the potentials of gut bacterial isolates to control the foraging behavior of the fly and c empower the sterile insect technique (SIT) program through the mass rearing.
Comparison of GeneXpert and Line Probe Assay for Detection of Mycobacterium tuberculosis and Rifampicin-Mono resistance at the National Tuberculosis Reference Laboratory, Kenya
Authors: Aricha S.A. , King'wara Leonard , Mwirigi N.W. , Chaba Linda , Kiptai T. , Wahogo J. , Otwabe J.S , Onyango P.O. , Karanja Muthoni , Ayieko C. , Matu S.W. 
Published: October 2019

Abstract
Background: The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA)
Methods : 329 sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays.
Results: Against culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5%, 64.9%, 59.4 % and 82.2% respectively while LPA had 98.4%, 66.0 %, 65.4% and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa 0.59, P<0.01) (sensitivity 62.50%, specificity 96.50 %) while LPA that had almost perfect agreement (Kappa=0.89, p<0.01) with a (sensitivity 90.0% and specificity 99.1%).
Conclusion : LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF’s mono-resistance.
Keywords : LPA, GeneXpert, Sensitivity, Specificity, Drug-resistant TB
NMAAP1 Maintains M1 Phenotype in Macrophages Through Binding to IP3R and Activating Calcium-related Signaling Pathways
Authors: Liu Qihui , Zhu Pei , Liu Shanshan , Tang Mengyan , Wang Yuanxin , Tian Yuan , Jin Zheng , Li Dong , Yan Dongmei 
Published: October 2019

Background:NMAAP1 plays a role in regulating macrophage differentiation to the M1 type and exerting antitumoral functions. It is not clear what role and mechanism NMAAP1 does play in the reversal of macrophages from M1 to M2.Methods:We detected the typing of macrophages with high or low expression of NMAAP1 by QPCR and ELISA, and detected the colocalization of NMAAP1 and endogenous IP3R by laser confocal microscopy, and detected the protein expression in cells by Western-blotting.Methods:Our study found that knockdown NMAAP1 in RAW264.7 cells induced macrophage polarization to the M2 type and up-regulation of NMAAP1 in RAW264.7 cells maintain M1 Phenotype even in the presence of IL-4, a stronger inducer of the M2 type. Additionally, Coimmunoprecipitation revealed a protein-protein interaction between NMAAP1 and IP3R and then activates key molecules in the PKC-dependent Raf/MEK/ERK and Ca2+/CaM/CaMKII signaling pathways. Activation of PKC (Thr638/641), ERK1/2 (Thr202/Tyr204) and CaMKII (Thr286) is involved in the regulation of cell differentiation.Conclusion:NMAAP1 interacts with IP3R, which in turn activates the PKC-dependent Raf/MEK/ERK and Ca2+/CaM/CaMKII signaling pathways. These results provide a new explanation of the mechanism underlying M1 differentiation.
Identification of Antibacterial Molecule(s) from Animals Living in Polluted Environments
Authors: Winnie Foo Y.M. , Siddiqui Ruqaiyyah , Sagathevan Kuppusamy , Khan Naveed A. 
Published: October 2019

Background:
Snakes feed on germ-infested rodents, while water monitor lizards thrive on
rotten matter in unhygienic conditions. We hypothesize that such creatures survive the assault of superbugs
and are able to fend off disease by producing antimicrobial substances. In this study, we investigated
the potential antibacterial activity of sera/lysates of animals living in polluted environments.

Methods:
Snake (Reticulatus malayanus), rats (Rattus rattus), water monitor lizard (Varanus salvator),
frog (Lithobates catesbeianus), fish (Oreochromis mossambicus), chicken (Gallus gallus domesticus),
and pigeon (Columba livia) were dissected and their organ lysates/sera were collected. Crude extracts
were tested for bactericidal effects against neuropathogenic E. coli K1, methicillin-resistant Staphylococcus
aureus (MRSA), Streptococcus pyogenes, Pseudomonas aeruginosa, Bacillus cereus and
Klebsiella pneumoniae. To determine whether lysates/sera protect human cells against bacterialmediated
damage, cytotoxicity assays were performed by measuring lactate dehydrogenase release as
an indicator of cell death. Lysates/sera were partially characterized using heat-treatment and pronasetreatment
and peptide sequences were determined using the Liquid Chromatography Mass Spectrometry
(LC-MS).

Results:
Snake and water monitor lizard sera exhibited potent broad-spectrum bactericidal effects
against all bacteria tested. Heat inactivation and pronase-treatment inhibited bactericidal effects indicating
that activity is heat-labile and pronase-sensitive suggesting that active molecules are proteinaceous
in nature. LCMS analyses revealed the molecular identities of peptides.

Conclusion:
The results revealed that python that feeds on germ-infested rodents and water monitor
lizards that feed on rotten organic waste possess antibacterial activity in a heat-sensitive manner and
several peptides were identified. We hope that the discovery of antibacterial activity in the sera of animals
living in polluted environments will stimulate research in finding antibacterial agents from unusual
sources as this has the potential for the development of novel strategies in the control of infectious
diseases.
A Review on the Finite Element Modeling of the Particle Reinforced Metal Matrix Composites in Cutting Process
Authors: Qi Xiaole , Li Guohe , Zhang Qi , Sun Fei 
Published: October 2019

Background::
Particle Reinforced Metal Matrix Composites (PRMMCs) are widely used
because of the higher specific strength, better dimensional stability, lower thermal expansion coefficient,
better wear and corrosion resistance. However, the existence of reinforcing particles makes it
hard to machine. The main manifestations are as follows: severe tool wear, easy generation of debris
tumors in processing, and many defects on the machined surface, etc. These seriously limit its wider
application. The Finite Element Method (FEM) has been widely applied in the research of
PRMMCs machining according to recent patents, which can improve the efficiency and reduce the
cost of research. Therefore, it is necessary to carry out a deep research for the processing technology
of PRMMCs.

Methods::
In this paper, the latest research progress of finite element simulation of cutting PRMMCs
was summarized. The key technologies of finite element simulation, including constitutive model,
geometric model, friction model between chip and tool, fracture criterion and mesh generation, are
comprehensively analyzed and summarized. The application in the specific processing methods was
discussed, such as turning, milling, grinding, ultrasonic vibration grinding and drilling. The existing
problems and development direction of the simulation of PRMMCs cutting are also given. Besides,
a lot of patents on finite element simulation for PRMMCs machining were studied.

Results::
Finite element model for the actual composition determines the accuracy of finite element
simulation. Through the secondary development of finite element software, a more realistic finite
element model of Particle reinforced metal matrix composites can be established.

Conclusion::
Finite Element Method (FEM) provides a new approach for the study of mechanism of
Particle reinforced metal matrix composites machining. Quantitative analysis and prediction of micro-
details in cutting can be realized.
Design and Performance Analysis of Distributed Equal Angle Spiral Vertical Axis Wind Turbine
Authors: Zheng Li , Wenda Zhang , Ruihua Han , Yongsheng Tian 
Published: October 2019

Background:
The wind turbine is divided into a horizontal axis and a vertical axis depending
on the relative positions of the rotating shaft and the ground. The advantage of the choke
wind turbine is that the starting torque is large and the starting performance is good. The disadvantage
is that the rotation resistance is large, the rotation speed is low, the asymmetric flow occurs
when the wind wheel rotates, the lateral thrust is generated, and the wind energy utilization rate is
lowered. How to improve the wind energy utilization rate of the resistance wind turbine is an important
issue to be solved by the wind power technology.

Objective:
The nautilus isometric spiral wind turbines studied in this paper have been introduced
and analyzed in detail, preparing for the further flow analysis and layout of wind turbines, improving
the wind energy utilization rate of wind turbines, introducing patents of other structures and output
characteristics of its generator set.

Methods:
Combined with the flow field analysis of ANSYS CFX software, the numerical simulation
of the new wind turbine was carried out, and the aerodynamic performance of the new vertical
axis wind turbine was analyzed. The mathematical model and control model of the generator were
established by the maximum power control method, and the accuracy of the simulation results was
verified by the measured data.

Results:
The basic parameters of the new wind turbine tip speed ratio, torque coefficient and wind
energy utilization coefficient are analyzed. Changes in wind speed, pressure and eddy viscosity were
investigated. Three-dimensional distribution results of wake parameters such as wind speed and
pressure are obtained. By simulating the natural wind speed, the speed and output current of the
generator during normal operation are obtained.

Conclusion:
By analyzing the wind performance and power generation characteristics of the new
wind turbine, the feasibility of the new wind turbine is determined, which provides reference and
reference for the optimal design and development of the wind turbine structure.
DNA Fingerprinting of Resistant Mycobacterium tuberculosis Isolates in Iran by IS6110-RFLP Method
Authors: Farazi Aliasghar , Sofian Masoomeh , Keshavarz Rohollah , Malekmohammadi Shima 
Published: October 2019

The objective of the research was to identify resistant Mycobacterium tuberculosis strains and recognize their molecular epidemiology and how they are disseminated in order to determine the cause and the effect of drug resistance and the process of its development.
Materials and methods. Genomic deoxyribonucleic acid obtained from 37 drug-resistant Mycobacterium tuberculosis isolates were examined and fingerprinted by the IS6110- restriction fragment length polymorphism method. The data obtained were then analyzed using SPSS statistics software.
Results. The mean patients’ age was 51 ± 15.5 years. There were 46% of male patients, 67.6% of the patients from urban areas, 86.5% of Iranians, 21.6% of relapsed cases, 8.1% of human immunodeficiency virus-positive patients, and 10.8% of the patients with a history of contact with tuberculosis patient. Based on IS6110 - restriction fragment length polymorphism, 30 different genetic types were observed which indicated a significant variation of this pathogen in Markazi province, Iran. The number of cluster genotypes was determined by 6 clusters; the number of unique types was 24. There were no relationships between age, gender, nationality, residence, close contact with tuberculosis patients, recurrence of tuberculosis, positive human immunodeficiency virus status and clustered or non-clustered strain genotype.
Conclusions. Considering the high genetic diversity in Mycobacterium tuberculosis strains, it can be concluded that, based on IS6110 - restriction fragment length polymorphism, about 65% of cases occurred due to reactivation, and 35% of the cases were due to recent transmission. The information obtained through the molecular typing method can be very effective in future planning for tuberculosis control in Iran.
Prevalence of Chronic Venous Diseases in Students of Ivano-Frankivsk National Medical University
Authors: Sabadosh Rostyslav , Riziuk Mykola , Ryziuk Nazarii 
Published: October 2019

The Objective of the Research was to increase the frequency of detecting chronic venous disorders in young people by surveing the students using a specially designed questionnaire with an analysis of its results for timely treatment.
Materials and Methods. To detect lower extremity chronic venous disorders, 1,007 students of the Ivano-Frankivsk National Medical University were interviewed using questionnaire that was based on the VEIN-TERM, the Venous Clinical Severity Score, the Chronic Venous Insufficiency Quality of Life Questionnaire. In the surveyed people, there were estimated the following data: age; gender; objective symptoms of chronic venous disorders such as telangiectasia, reticular (spider) veins, varicose veins and leg swelling; 11 most common symptoms of chronic venous disorders; risk factors such as the presence of lower extremity varicose veins in parents, previous childbirth and frequent or rare use of high heels in females.
Results. In 617 (61.3%; 95 CI, 58.2 - 64.3%) respondents, phlebopathy was detected; 63 (6.3%, 95 CI 4.8 - 7.9%) students reported lower extremity telangiectasias; 11 (1.1%; 95 CI 0.5 - 1.9%) students reported reticular veins. Varicose veins were detected in 33 (3.3%; 95 CI 2.3 - 4.6%) cases. Among them, there were 14 (1.4%, 95 CI 0.8 - 2.3%) cases of leg swelling. Only two symptoms, namely calf cramps (p=0.01) and leg pain (p=0.04) turned out to occur significantly more frequent in the respondents with varicose veins. Varicose veins were more often found in the students whose fathers suffered from varicose veins as compared to those whose mothers had varicose veins – 12.1% (95% CI 5.4 - 22.5%) versus 4.2% (95% CI 2.1 - 7.5%), respectively (p=0.008). Among females without lower extremity varicose veins, 34.1% (95% CI 29.7 - 38.3%) of the respondents indicated wearing high heels (above 5 cm) which was approximately 3 times more often as compared to female respondents with varicose veins - 11.2% (95% CI 0.0 - 21.7%) of women (p=0.001).
Conclusions. 1. Leg pain and calf cramps can be considered as the most important subjective symptoms for early diagnosis of lower extremity varicose veins in young people. 2. The presence of lower extremity varicose veins in a father results in higher risk of detecting this pathology in the respondent than the presence of lower extremity varicose veins in a mother: 12.1% (95% CI 5.4-22.5%) versus 4.2% (95% CI 2.1 - 7.5%) (p = 0.008). 3. Early diagnostics of lower extremity varicose veins in young people with the aim of further adequate treatment to prevent their progression and the development of complications can be implemented by questioning students in different educational institutions.
Algorithm for Surgical Treatment of Children with Hirschsprung’s Disease
Authors: Kurtash Oleh 
Published: October 2019

Hirschsprung’s disease requires surgical treatment. Depending on the form of aganglionosis and severity of pathology, open or minimally invasive, one-stage or multi-stage radical surgery may be used.
The objective of the research was to develop an algorithm for surgical treatment of children with Hirschsprung’s disease.
Materials and methods. The analysis of surgical treatment of 1,129 children with different forms of Hirschsprung’s disease aged from birth to 18 years over the period 1980-2018 was conducted. All the patients underwent both traditional and minimally invasive radical surgery.
Results and discussion. The patients were divided into three groups; each group was characterized by modernization of surgical methods, as well as intensification of diagnostics for early detection of such patients. Radical surgery without a protective colostomy was used in 773 (68.46%) cases, while in 356 (31.53%) cases, a protective colostomy was created. Due to the intensification of diagnostics that markedly contributed to early detection of patients with various forms of Hirschsprung’s disease, during each study period, there was observed a dramatic decrease in the number of stoma patients with a significant increase in the number of children diagnosed with Hirschsprung’s disease: from 68.54% (1980-1992) to 37.93% (1993-2010) and 12.00% (2011-2018).
Conclusions. Timely diagnostics contributes to early detection of children with different forms of Hirschsprung’s disease. In uncomplicated forms of Hirschsprung’s disease, it is reasonable to perform one-stage radical surgery, namely the resection of the aganglionic segment and the affected colon segment followed by colorectal anastomosis. In severe Hirschsprung’s disease, two-stage surgery should be used: creation of a protective colostomy (the first stage) and radical surgery (the second stage). In some cases, in colectomy, three-stage surgical approach is needed, namely the creation of a protective colostomy (the first stage), radical surgery (the second stage) and protective colostomy closure (the third stage).
PENTINGNYA KEPUASAN KERJA
Authors: Sunarta Sunarta 
Published: October 2019

Abstrak: Pentingnya Kepuasan Kerja. Upaya meraih kepuasan kerja penting baik bagi individu maupun organisasi. Ditinjau dari individu, kepuasan kerja tidak hanya berkaitan dengan pekerjaan yang menyenangkan, namun juga berhubungan dengan kebahagiaan dan kesehatan. Ditinjau dari organisasi, kepuasan kerja pegawai berhubungan dengan produktivitas, perilaku kerja positif, mengendalikan turn over dan kinerja. Kerja baik dalam pendekatan transaksional maupun relasional melibatkan dua pihak yaitu pegawai dan organisasi, sehingga kepuasan kerja dipengaruhi oleh faktor-faktor dari sisi pegawai dan organisasi. Upaya saling memahami menjadi penting untuk meraih kepuasan kerja yaitu bagaimana organisasi memahami kebutuhan, keinginan dan harapan pegawainya, serta bagaimana pegawai memahami tujuan bersama antara dirinya dengan organisasi. Komunikasi diperlukan sebagai sarana untuk meningkatkan pemahaman antara pegawai dan organisasi. Kata kunci: Kepuasan Kerja, pegawai, organisasi dan produktivitas Abstract: The Importance of Job Satisfaction. Efforts to achieve job satisfaction are important for both individuals and organizations. In terms of individuals, job satisfaction is not only related to pleasant work, but also related to happiness and health. In terms of organization, employee job satisfaction is related to productivity, positive work behavior, controlling turnover and performance. Work in both the transactional and relational approaches involves two parties, namely employees and the organization, so job satisfaction is influenced by factors in terms of employees and the organization. Efforts to understand each other are important for achieving job satisfaction, namely how the organization understands the needs, desires and expectations of its employees, and how employees understand the shared goals between themselves and the organization. Communication is needed as a means to increase understanding between employees and organizations. Keyword: Job Satisfaction, employee, organization and productivity