bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)
Authors: Tao Huan , Wan Weifeng , Huang Jian , Woldegiorgis Samuel Tareke , Xiong Yifan , Wei Xiaoling , Wan Luoyao , Xu Zaiquan , Zhang Lina , Liu Wei , He Huaqin 
Published: January 2020

Abstract
Background：Heat shock transcription factors (Hsfs) take part in many physiological and biochemical pathways in plants by regulating the expression of various stress-responsive genes, such as heat shock proteins (Hsps). With the development of rice genome re-sequencing projects, some researches had been carried out to identify Hsf gene family members in rice at the whole genomic scale. However, Hsfs in cultivated and wild rice genomes has not been fully studied and compared, although genetic diversity in cultivated rice is limited compared to wild rice. Results：In this research work, Hsfs genes were screened and evolutionally compared in the genomes of 6 wild rice and 1 cultivated rice varieties, including O. barthii, O. glumaepatula, O. meridionalis, O. nivara, O. punctate, O. rufipogon and O. sativa & Nipponbare. Total 22, 23, 24, 24, 25, 25 and 25 Hsf genes were identified in the tested 7 rice genomes, respectively. The different number of Hsf genes between wild and cultivated rice genotypes was due to dispersed duplication and whole genome duplication (WGD) events, reversely contributed to different stress-tolerant ability between wild and cultivated rice. The evolutional analysis on the Hsf genes confirmed that O. rufipogon was the immediate ancestral progenitors of O. sativa. The expression profile of Hsf genes in Nipponbare and O. rufipogon under different stage of salinity stress showed that 4 root Hsf genes, including HsfA3a, HsfA4d, HsfC2a and HsfC2b, were simultaneously up-regulated by salinity stress in cultivated rice and its ancestral progenitor, implying that these 4 Hsf genes played conserved roles in rice in response to salinity stress. However, a substantial number of Hsf genes were exclusively regulated only in Oryza rufipogon rice seedling, suggesting that some of genuine salinity stress tolerance genes might be missing in cultivated rice. Conclusion：The results of this study would give insight into the evolution and function of Hsf gene members in rice, and hint to the use of wild relative genes to improve rice performance.
The potential of human skin and plant-based odours combination to attract malaria mosquito, Anopheles gambiae s.s. in Laboratory and Semi field settings.
Authors: KEMIBALA ELISON ELIEZA , Mafra-Neto Agenor , Dekker Teun , Saroli Jesse , Silva Rodrigo , Philbert Anitha , Ng’habi Kija , Mboera Leonard E.G. 
Published: January 2020

Abstract
Background Knowledge on mosquito attraction to various host-mimicking odors provides a potential opportunity for designing effective tools for surveillance and control of potential disease vectors. This study was carried out to explore the potential of combining plant and human mimicking odours to attract Anopheles gambiae s. s . in the laboratory and semi field settings in Tanzania. Methodology Blood fed and unfed female Anopheles gambiae s.s. mosquitoes were offered choices between human skin, plant-based odours or combination thereof in laboratory and semi-field setting. The captured mosquitoes from each source were scored for comparison. Results In laboratory and semi-field trials, the tested attractants combination of plant and human-mimicking odours found to be slightly attractive (approximately 10% higher) than either individual attractant to blood fed female mosquitoes under lab and semi-field settings. The unfed female mosquitoes were more attracted to Vectrax (plant-based materials) by more than 10% in comparison to human skin-based attractant both in lab and semi-field settings. In semi-field settings particularly, more unfed female mosquitoes were attracted to Vectrax than to the combination (p < 0.01). Conclusions The findings that the combination blend (human host and plant based) semiochemical increases mosquito attraction hold the potential to increase efficiency of mosquitoes trapping devices in both indoor and outdoor settings. This may provide valuable tools for mosquito vector management programs. Moreover, these results also suggest the potential of the combination odours to be used in the attract and kill strategies.
Glucose transporter Glut1 influences Plasmodium berghei infection in Anopheles stephensi
Authors: Wang Mengfei , Wang Jingwen 
Published: January 2020

Abstract
Background Sugar feeding provides energy for mosquito. Facilitated glucose transporters (GLUT) are responsible for cellular uptake of glucose. However, the knowledge of GLUT function in Anopheles mosquito is limited. Methods Phylogenetic analysis of GLUTs in Anopheles stephensi (AsteGlut) was performed by the maximum likelihood and Bayesian method. The spatial and temporal expression patterns of three Astegluts were analyzed by qPCR. The function of AsteGlut1 was examined using a dsRNA-mediated RNA interference method. Transcriptome analysis was used to understand the influence of AsteGlut1 on mosquito vector competence. Results We identified 3 glut genes, Asteglut1 , Asteglutx and Asteglut3 in An. stephensi . Asteglut1 and Asteglut3 were mainly localized in the midgut. The expression of all three Astegluts were strongly induced after blood meal. All three genes were knocked down successfully, but only abrogation of Asteglut1 significantly increased the susceptibility of An. stephensi to Plasmodium berghei infection. Our transcriptome analysis revealed that knockdown of Asteglut1 differentially regulated expression of genes associated with the functional clusters including detoxification, serine proteases, and immunity. The dysregulation of multiple pathways might contribute to the increased P. berghei infection. Conclusions Our study shows that Asteglut1 plays a role in defense against P. berghei in An. stephensi . The regulation of Asteglut1 on vector competence might through modulating multiple biological processes, including detoxification and immunity.
New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi
Authors: De Joshua Ang Xin , Kadir Khamisah Abdul , Mohamad Dayang Shuaisah Awang , Matusop Asmad , Divis Paul Cliff Simon , Yaman Khatijah , Singh Balbir 
Published: January 2020

Abstract
BackgroundThe vectors for Plasmodium knowlesi, a significant cause of human malaria in Southeast Asia, identified previously in nature all belong to the Anopheles Leucosphyrus Group. Only one study has been previously undertaken in Sarawak, Malaysian Borneo, to identify vectors of P. knowlesi, where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak. MethodsMosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of anophelines were subjected to nested PCR malaria-detection assays. The small sub-unit ribosomal RNA (SSUrRNA) genes of Plasmodium, and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences of the mosquitoes were derived from the Plasmodium-positive samples for phylogenetic analyses. ResultsA total of 65 anophelines and 127 culicines were collected. By PCR, six An. balabacensis and five An. barbirostris were found to have single P. knowlesi infecions while three other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Phylogenetic analyses of the Plasmodium SSUrRNA genes confirmed 3 An. barbirostris and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and possibly novel species of Plasmodium. Phylogenies inferred from the ITS2 and CO1 sequences of An. balabacensis and An. barbirostris indicate that the former is genetically indistinguishable from An. balabacensis in Borneo while the latter is a novel sibling species belonging to the Anopheles Barbirostris Subgroup. ConclusionsNew vectors for P. knowlesi in Sarawak were identified, including An. barbirostris, which is a species that does not belong to the Anopheles Leucosphyrus Group.
Emodin alleviates LPS-induced inflammatory response in lung injury mice by affecting the function of neutrophils
Authors: Mei Hongxia , Tao Ying , Zhang Tianhao , Qi Feng 
Published: January 2020

Abstract
Background: This study aims to investigate the role of Emodin(Emo) on the pulmonary inflammatory response and the neutrophil function in a murine model of lipopolysaccharide (LPS)-induced ALI. The mouse model of lipopolysaccharide (LPS)-induced ALI was produced by acute lung injury of injecting 20 mg/kg LPS via the caudal vein.The right lower lung lobes were harvested, fixed,embedded and stained with hematoxylin and eosin (H&E) for light microscopy analysis to evaluate lung injury. TNF-αand IL-1 ELISA kits were used to detect the levels of TNF-α and IL-1 in the right lung homogenate of rats. The primary rat neutrophils were separated and treated with LPS to mimic a ALI cellular model. The expression of Respiratory burst and Neutrophil NETs Production was examined using spectrophotometer.The Elastase release was detected using Elastase Activity Assay kit.The ROS Production was measured by Luminometer.the phagocytosis of Neutrophils and the rate of apoptotic Neutrophils were measured by flow cytometry. Results: This study demonstrates that Emo alleviates lung injury and reduces the release of inflammatory cytokines. Moreover, Emo also downregulated neutrophil respiratory burst and the production of ROS in the LPS-stimulated neutrophils, thus reducing the damage of neutrophils to the surrounding tissues. Emo can also up-regulate the ability of neutrophils to phagocytize bacteria and generate NETs, thereby enhancing the bactericidal ability of neutrophils. In addition, Emo can promote the apoptosis of neutrophils and accelerate the resolution of inflammation. Conclusion: Emo has a protection effect on LPS-induced acute lung injury mice. It can alleviate lung injury and reduces the release of inflammatory cytokines, perhaps by affecting the various function of neutrophils in a dose-dependent manner.
Correlates of pregnancy among Female Sex Workers (FSWs) in semi urban Blantyre, Malawi
Authors: Twizelimana Donatien , Muula Adamson S 
Published: January 2020

Abstract
Background Little is known about female sex workers’ (FSWs) reproductive health apart from their being at higher than usual risk of sexually transmitted infections (STIs), including HIV. The problem addressed in this study was: “what are the correlates of pregnancy among FSWs in semi – urban Blantyre in Malawi?”.Methods We used systematic sampling to recruit a total of 200 FSWs in four different study sites in Blantyre. Data were collected through questionnaire interviews. We calculated the mean and standard deviation for continuous covariates and proportions for categorical variables to describe the data. Logistic regression analysis was used to examine the correlates between the outcome variable (pregnancy) and independent variables.Results Ninety one (45, 5%) FSWs were between 18 and 24 years. The prevalence of pregnancy was 61% for FSWs born in rural place as compared to 37% for those who were born in town. In multivariate analysis FSWs who reported to value being respected as mothers had 12 times the risk of pregnancy comparing to the ones who did not (AOR: 11.8, 95% CI: [4.56, 30.72] p -value <0.001). FSWs who reported using condoms inconsistently had five times the risk of pregnancy compared to the ones who did not, (AOR: 5.26, 95% CI: [2.29, 12.081], p -value <0.001). FSWs who had a request to bear children from steady partners had 5 times the risk of pregnancy comparing to the ones who did not (AOR: 5.07, 95% CI: [2.14, 11.99]). FSWs who reported forgetfulness of contraceptives’ use had 3 times more risk of pregnancy comparing to the ones who did not (A0R: 3.49 CI: [1.29, 9.37], p- value < 0.013).Conclusion The study documents a wide range of correlates of pregnancies among FSWs in the study sites. It is important to recognize the child bearing desires and circumstances of FSWs in order to inform health programs responsive to their needs.
Development and comparison of RNA-Sequencing pipelines for more accurate SNP identification: Practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle.
Authors: Lam S. , Zeidan J. , Miglior F. , Suárez-Vega A. , Gómez-Redondo I. , Fonseca P. A. S. , Guan L. L. , Waters S. , Cánovas A. 
Published: January 2020

Abstract
Optimization of an RNA-Sequencing (RNA-Seq) pipeline can maximize power and accuracy for identifying genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study determined an optimized pipeline for variant detection using a dataset with multiple samples and tissues. The RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n=6 low-RFI, n=6 high-RFI) were used. Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by group for low-RFI and for high-RFI for each tissue, iii) merged samples by group and tissue for low- and high-RFI for both tissues. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Approaches were compared by comparing read depth, overlap of SNP detection results, and following SNP annotation for positional candidate genes. On average, total reads detected for Approach i) individual liver and muscle samples were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), total reads detected for each merged group of samples was 162,030,705, and for Approach iii) was 324,061,410, revealing the highest read depth. Additionally, Approach iii) encompassed the majority of localized positional genes detected by each approach, suggesting Approach iii) be applied to maximize detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive rate. Approach iii) was used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Annotation of moderate to high functional impact SNPs revealed co-localized positional candidate genes for each RFI group (2,886 for low-RFI, 3,075 for high-RFI), which were significantly (P<0.05) associated with immune and metabolism pathways. The most optimized RNA-Seq pipeline allowed for more accurate identification of SNP, associated positional candidate genes, and associated metabolic pathways in muscle and liver tissues, providing insight on the genetic architecture of feed efficiency in beef cattle.
Research on Improved Adaptive ViBe Algorithm For Vehicle Detection
Authors: Jiang Kun , Wang Jianguo 
Published: January 2020

Abstract
Vehicle detection is an important step in vehicle tracking and recognition in video environment. Vibe algorithm is a moving target detection algorithm based on background difference method. Based on the traditional ViBe algorithm, this paper introduces three-frame difference method combined with ViBe algorithm to speed up the elimination of ghosts, and proposes an adaptive Vibe algorithm, which defines two kinds of vehicle detection errors and their corresponding error functions. Then, according to the range of these two errors, a set of reasonable judgment methods are determined to adjust the unreasonable threshold, which ensures the adaptive updating of the background model. It improves the environmental adaptability of vehicle detection and ensures higher accuracy of vehicle detection under complex illumination conditions.
Detection of Blink State Based on Fatigued Driving
Authors: Chao Lei , Changyuan Wang , Guang Li , Lu Shi 
Published: January 2020

Abstract
In recent years, with the improvement of the national economy, the penetration rate of automobiles has been increasing, and traffic accidents have also increased. Fatigue driving is the main factor in many traffic accidents. Fatigue driving can cause the driver’s inattention, slow response, and make wrong decisions on danger signals, which affect the driver’s personal safety. In modern development, driving safety is developing towards intelligence and safety. Therefore, the detection of driver fatigue has become a generally accepted demand. This paper proposes a method to calculate the threshold of blinking, which can detect the blinking state of the driver in real time through video. During the driving process, when the driver is in the closed eye state for a long time, an early warning is issued to avoid the accident. This paper uses Python language to achieve the first, through the digital image technology call Dlib open source library to detect 68 feature points of the face, and then measure the aspect ratio between the length and width of the human eye, and finally through the Kmeans clustering algorithm to collect the ratio The analysis yields the blink threshold. The experimental results show that the recognition rate is 92.5% when the video frame rate is 30, and the recognition accuracy is 92.5%. The experimental results show that the method designed in this paper can quickly detect the fatigue characteristics of the human eye, has a higher recognition rate and accuracy for fatigue driving, and helps reduce the occurrence of traffic accidents.
Modeling and experimental validation of the hysteretic dynamics of shape memory alloy springs
Authors: Abubakar R. A. , Hu Yutian , Wang Fan , Wang Linxiang 
Published: January 2020

Abstract
In this work, the hysteretic dynamics of a pseudoelastic shape memory alloy (SMA) spring is modeled and tested. A constitutive model of SMA spring is constructed by combining the theory of mechanical spring and the derived SMA constitutive relation. The SMA spring recovery force is modeled by employing the Euler–Lagrange equation based on a non-convex potential function. A macroscopic differential model is formulated to describe the hysteretic dynamics and the pseudoelasticity of the SMA spring. A theoretical method for estimating the equivalent stretch ratio at a specific temperature of SMA spring is given. Numerical simulations were presented in studying the influence of the stretch ratio at a temperature of 50, 70, and 90°C. The experimental tests are performed and presented together with their numerical counterparts. The comparison is made between numerical and experimental results to validate the proposed model for SMA spring.
Options for surgical treatment of cicatrical stenosis of the middle (folded) larynx
Authors: Nazhmudinov I. I. , Vavin V. V. , Davudov Kh. Sh. , Garashchenko T. I. , Davudova B. Kh. , Magomedova K. M. , Khoranova M. Yu. 
Published: January 2020

Aim of the study: to develop a tactic of surgical treatment of cicatrical lesion of the middle larynx depending on the localization and length of stenosis.Materials and methods: from 2014 to 2019, 43 patients with cicatrical stenosis of the folded larynx underwent surgery. The average age of the patients was 39 years and ranged from 18 to 78 years. Depending on the clinical situation, patients were divided into 4 groups, in which different methods of surgical treatment were applied – removal of scars of the middle larynx using CO2-laser and additional application of keel-shaped implant (n = 21), microflaps in the area of commissure (n = 10) and intraretynoid region (n = 4), endoprosthesis covered with xenopericord (n = 8).Results: in the postoperative period endoscopic examination of the larynx was carried out in dynamics during the period up to 1 year. Patients were examined daily while in hospital, then monthly. In addition to endoscopic examination, the study of voice function was carried out by the method of determining the time of maximum fonation. The estimation of respiratory and voice rehabilitation was carried out and stable positive effect was received in 90% in the first group, 70% - in the second, 75% - in the third, 75% – in the fourth. The obtained data allow to develop an individual approach to surgical treatment of cicatrical stenosis of the larynx depending on the localization and extent of cicatrical lesion.Discussion: the optimal method of treating cicatrical lesion of the middle larynx is to create conditions that prevent the contact of wound surfaces and their separation. For this purpose, methods that are individually addressed to the main clinical situations in this problem have been developed. In addition, the use of CO2-laser in the surgical treatment of cicatrical lesions of the middle larynx significantly expands operational capabilities due to high accuracy and low level of damage to surrounding tissues.Conclusions: in case of cicatrical lesion of the middle larynx up to 4 mm in length, in the absence of a tracheostoma an effective method of restoration of respiratory and vocal function of the larynx is the use of microflaps formed by microsurgery with th e help of CO2-laser; stenoses in the area of middle larynx commissure of more than 4 mm require additional stenting for the period of epithelization of the wound surface and remodeling of the scar, which is 3–4 weeks. In the presence of a tracheostoma in patients with prolonged stenosis of the middle laryngeal commissiure, an implant coated with xenopericardium and chlorhexidine ionic-covalent immobilization, which helps to avoid inflammatory changes during the period of stenting, has proved to be a good choice.
Looking deeper – exploring hidden patterns in reactor data of N-removal systems through clustering analysis
Authors: Alejo Luz , Atkinson John , Lackner Susanne 
Published: January 2020

Abstract
In this work, clustering analysis of two partial nitritation–anammox (PN-A) moving bed biofilm reactors (MBBR) containing different types of carrier material was explored for the identification of patterns and operational conditions that may benefit process performance. The systems ran for two years under fluctuations of temperature and organic matter. Ex situ batch activity tests were performed every other week during the operation of these reactors. These datasets and the parameters, which were monitored online and in the laboratory, were combined and analyzed applying clustering analysis to identify non-obvious information regarding the performance of the systems. The initial results were consistent with the literature and from an operational perspective, which allowed the parameters to be explored further. The new information revealed that the oxidation reduction potential (ORP) and the anaerobic ammonium oxidizing bacteria (AnAOB) activity correlated well. ORP also dropped when the reactors were exposed to real wastewater (presence of organic matter). Moreover, operating conditions during nitrite accumulation were identified through clustering, and also revealed inhibition of anammox bacteria already at low nitrite concentrations.