bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of malaria transmission dynamics under varying assumptions about the spatial scale of transmission: a modelling study in three elimination settings
Authors: Routledge Isobel , Bhatt Samir 
Published: November 2020

Abstract
BackgroundIndividual-level geographic information about malaria cases, such as the GPS coordinates of residence or health facility, is often collected as part of surveillance in near-elimination settings, but could be more effectively utilised to infer transmission dynamics, in conjunction with additional information such as symptom onset time and genetic distance. However, in the absence of data about the flow of parasites between populations, the spatial scale of malaria transmission is often not clear. As a result, it is important to understand the impact of varying assumptions about the spatial scale of transmission on key metrics of malaria transmission, such as reproduction numbers. MethodsWe developed a method which allows the flexible integration of distance metrics (such as Euclidian distance, genetic distance or accessibility matrices) with temporal information into a single inference framework to infer malaria reproduction numbers. Twelve scenarios were defined, representing different assumptions about the likelihood of transmission occurring over different geographic distances and likelihood of missing infections (as well as high and low amounts of uncertainty in this estimate). These scenarios were applied to four individual level datasets from malaria eliminating contexts to estimate individual reproduction numbers and how they varied over space and time.Results Model comparison suggested that including spatial information improved models as measured by ΔAICc, compared to time only results. Across scenarios and across datasets, including spatial information tended to increase the seasonality of temporal patterns in reproduction numbers and reduced noise in the temporal distribution of reproduction numbers. The best performing parameterisations assumed long-range transmission (>200km) was possible.ConclusionsOur approach is flexible and provides the potential to incorporate other sources of information which can be converted into distance or adjacency matrices such as travel times or molecular markers.
Effect of Dark Septate Endophytes on Plant Performance of Artemisia Ordosica and Associated Soil Microbial Community Under Salt Stress
Authors: Hou Lifeng , Li Xia , He Xueli , Zuo Yiling , Zhang Dongdong , Zhao Lili 
Published: November 2020

Abstract
Background: Fungal endophytes can improve plant tolerance to abiotic stress, however, the role of these plant–fungal interactions in desert species ecology and their management implications remain unclear. This study aimed to assess whether dark septate endophytes (DSE) can shift the performance of Artemisia ordosica and associated soil microbial community under salt stress.Methods: We investigated the effects of three DSE (Alternaria chlamydosporigena [AC], Paraphoma chrysanthemicola [PC] and Bipolaris sorokiniana [BS]) isolated from desert habitats on plant morphology, physiology and rhizosphere soil microhabitat of Artemisia ordosica seedlings under different NaCl concentrations (0 %, 0.1 %, 0.2 %, and 0.3 %) in a growth chamber. Results: Three DSE strains could colonize the roots of A. ordosica, and the symbiotic response with host plants depended on DSE species and NaCl concentration. The greatest benefits associated with DSE occurred under 0.1 % NaCl. Specifically, AC improved root morphology, and increased total biomass and superoxide dismutase (SOD) activity; PC increased root morphology, root biomass, and glutathione (GSH) and indoleacetic acid (IAA) contents; and BS promoted SOD activity and GSH and IAA contents. DSE reduced the root Na+ content. Interestingly, BS promoted gram-positive (G +) and gram-negative (G −) bacteria under 0.1 % NaCl and the abundance of AM fungi under 0.2 % and 0.3 % NaCl. PC positively affected fungi, AM fungi, G − bacteria and actinomycetes under 0.2 % and 0.3 % NaCl, while AC increased the abundance of all examined microbes under 0.3 % NaCl. A structural equation modeling (SEM) demonstrated that DSE not only positively affects A. ordosica performance but also directly or indirectly impacts soil microbes by regulating the soil organic carbon (SOC), available phosphorus (AP), and alkaline nitrogen (AN) content.Conclusions: DSE isolated from A. ordosica enhanced the root development of host plants and altered the soil nutrient content and soil microbiota under different NaCl concentrations, possibly contributing to plant growth and ecological adaptability under saline environment. These results contribute to the understanding of the ecological function of DSE in desert ecosystems and may be used to promote vegetation restoration in salinized desert areas.
R2R3-MYB Transcription Factor MdMYB73 Confers Increased Resistance to the Fungal Pathogen Botryosphaeria Dothidea via the Salicylic acid Pathway in Apple
Authors: Gu Kai-Di , Zhang Quan-Yan , Yu Jian-Qiang , Wang Jia-Hui , Zhang Fu-Jun , Wang Chu-Kun , Zhao Yu-Wen , Sun Cui-Hui , You Chun-Xiang , Hu Da-Gang , Hao Yu-Jin 
Published: November 2020

Abstract
Background: The MYB transcription factor (TF) family is involved in many biological processes. However, the molecular mechanism of the MYB family in the resistance to apple ring rot remains poorly understood. Results: Here, the R2R3-MYB subfamily member MdMYB73 was cloned from “Royal Gala,” and its function was characterized by a positive regulator in controlling defense against Botryosphaeria dothidea. qRT-PCR and GUS staining analysis demonstrated that the expression of MdMYB73 was notably induced in apple fruits and transgenic calli after inoculation with B. dothidea. Overexpression of MdMYB73 enhanced resistance, while suppressing MdMYB73 expression weakened resistance to B. dothidea in apple calli and fruits. The increased resistance to B. dothidea was also observed in MdMYB73-expressing Arabidopsis thaliana. Interestingly, we found that MdMYB73 improved resistance against B. dothidea, possibly by the salicylic acid (SA) pathway, since SA content and expression of SA synthesis- and signaling-associated genes were higher in MdMYB73 overexpression plant materials compared with wild-type controls after inoculation. In addition, we discovered that MdMYB73 interacts with the B. dothidea positive regulator MdWRKY31 and together enhance the resistance to B. dothidea in apple. Conclusions: Overall, these findings shed light on the mechanism by which MdMYB73 enhances the resistance to B. dothidea, possibly by regulating the SA pathway.
Comparison of The 7th and 8th Editions of The Union for International Cancer Control /American Joint Committee on Cancer Staging System for Nonmetastatic Nasopharyngeal Carcinoma in The Intensity-Modulated Radiotherapy Era
Authors: He Tao , Yan Ruo-Nan , Chen Hua-Ying , Zeng Yuan-Yuan , Xiang Zhong-Zheng , Liu Fang , Shao Bian-Fei , Ma Jia-Chun , Wang Xi-Ran , Liu Lei 
Published: November 2020

Abstract
Background: To compare the prognostic value of 7th and 8th editions of the Union for International Cancer Control /American Joint Committee on Cancer (AJCC) staging system for patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with intensity-modulated radiotherapy and simultaneous integrated boost– intensity-modulated radiation therapy (SIB-IMRT).Methods: Patients with NPC (n = 300) who received SIB-IMRT were included. Survival by T-classification, N-classification, and stage group of each staging system was assessed.Results: For T-classification, nonsignificant difference was observed between T1 and T2 and between T2 and T3 disease (P = 0.066 and 0.106, respectively) for overall survival (OS) in the 7th staging system, whereas all these differences were significant in the 8th staging system (all P < 0.05). The survival curves for disease-free survival (DFS) and LRFS in both staging systems were similar, except for the comparison of T2 and T4 disease for LRFS (P = 0.07 for 7th edition; P = 0.011 for 8th edition). For N-classification, significant differences were observed between N2 and N3 diseases after revision (P = 0.046 and P = 0.043 for OS and DFS, respectively). For staging system, no significant difference was observed between IVA and IVB of 7th edition.Conclusion: The 8th AJCC staging system appeared to have superior prognosis value in the SIB-IMRT era compared with the 7th edition.
Modeling and Simulation of Knowledge Innovation Diffusion in Weighted Scale-free Industry-University-Research Cooperative Innovation Network
Authors: Cao Xia , Li Chuanyun , Li Jinqiu , Li Yunchang 
Published: November 2020

Abstract
With the weighted scale-free cooperative innovation network of industry-university-research established by the weighted evolutionary BBV model as the research object, based on the interaction between knowledge innovation diffusion and network structure, a corresponding model of knowledge innovation diffusion is constructed. By using complex network theory and simulation analysis methods, the evolution law of knowledge innovation diffusion in the industry-university-research cooperative innovation network is analyzed. The results show that the overall knowledge level of the industry-university-research cooperative innovation network shows a rapid growth trend, and the growth rate of knowledge shows a changing trend of slowing first and then increasing abruptly; the greater the degree of the innovator, the higher its knowledge level; the more stable the cooperative relationships between innovator, and the stronger its knowledge diffusion ability; the knowledge diffusion mode and network structure are the reasons for the emergence of sudden changes in the network; the knowledge diffusion constraints and network structure are the keys to knowledge innovation and diffusion; with the passage of time, the knowledge level differentiation among innovators gradually increases, and the role of hub institutions in knowledge innovation diffusion becomes increasingly prominent.
Comparative proteomic profiling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease
Authors: Dhufaigh Kerrie Ní , Dillon Eugene , Botwright Natasha , Talbot Anita , O'Connor Ian , MacCarthy Eugene , Slattery Orla 
Published: November 2020

Abstract
The causative agent of amoebic gill disease, Neoparamoeba perurans is reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from three isolates: a newly acquired, virulent and attenuated N. perurans culture. Proteins were analysed using two-dimensional electrophoresis coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). The challenge trial using naïve smolts confirmed a loss in virulence in the attenuated N. perurans culture. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate in contrast to a reduction in microbial community richness in the attenuated microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins differentially expressed between the three cultures. The present LC-MS/MS results indicate protein synthesis, oxidative stress and immunomodulation are upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifications for therapeutic purposes in infected farmed fish.
Enhanced Interactions of Kuroshio Extension With Tropical Pacific in a Changing Climate&nbsp;
Authors: Joh Youngji , Lorenzo Emanuele Di , Siqueira Leo , Kirtman Benjamin 
Published: November 2020

Abstract
Quasi-decadal climate of the Kuroshio Extension (KE) is pivotal to understanding the North Pacific coupled ocean-atmosphere dynamics and their predictability. Recent observational studies suggest that extratropical-tropical coupling between the KE and the central tropical Pacific El Niño Southern Oscillation (CP-ENSO) leads to the observed preferred decadal time-scale of Pacific climate variability. By combining reanalysis data with numerical simulations from a high-resolution climate model and a linear inverse model (LIM), we confirm that KE and CP-ENSO dynamics are linked through extratropical-tropical teleconnections. Specifically, the atmospheric response to the KE excites Meridional Modes that energize the CP-ENSO (extratropics→tropics), and in turn, CP-ENSO teleconnections energize the extratropical atmospheric forcing of the KE (tropics→extratropics). However, both observations and the model show that the KE/CP-ENSO coupling is non-stationary and has intensified in recent decades after the mid-1980. Given the short length of the observational and climate model record, it is difficult to attribute this shift to anthropogenic forcing. However, using a large-ensemble of the LIM we show that the intensification in the KE/CP-ENSO coupling after the mid-1980 is significant and linked to changes in the KE atmospheric downstream response, which exhibit a stronger imprint on the subtropical winds that excite the Pacific Meridional modes and CP-ENSO.
A Longitudinal and Geospatial Analysis of COVID-19 Tweets During the Early Outbreak Period in the United States
Authors: Cuomo Raphael , Purushothaman Vidya , Li Jiawei , Cai Mingxiang , Mackey Timothy 
Published: November 2020

Abstract
Introduction: Local rates of COVID-19 cases and deaths may not accurately convey the variability in community-level concern about COVID-19 during the early outbreak period in the United States. Social media interaction may elucidate communication about COVID-19 in this critical period, during which communities may have formulated initial conceptions pertaining to the perceived gravity of the disease and potential behavioral strategies for prevention.Methods: Scripts were written to obtain tweets related to COVID-19 from Twitter. Using manually-annotated tweets about symptom-related concerns from a prior study, a machine learning classifier was applied to obtain a subset of tweets about concerns relating to COVID-19. The longitudinal relationship between these social media posts and active COVID-19 cases was assessed using linear and exponential regression. Changes in the geospatial clustering of tweets was assessed for the top five most populous cities in the United States.Results: Social media posts relating to COVID-19 concerns appeared more predictive of active COVID-19 cases as temporal distance increased. The distribution of tweets in New York City and Phoenix appeared concentrated in city centers, whereas tweets from other cities were more residential. Tweets from New York City became more highly concentrated, but the opposite trend was observed in tweets from Los Angeles.Conclusion: Clustering of social media posts about COVID-19 revealed discrepancies across major US cities. General concern about the COVID-19 pandemic may moderate the relationship between behavioral/environmental factors and COVID-19 transmission. The degree and modality of this moderating effect may differ across US areas.
Zircon Record of Supercontinent Amalgamation in Back-arc Volcanic Rocks
Authors: Zeng Zhigang , Chen Zuxing , Zhang Yuxiang 
Published: November 2020

Abstract
Episodic supercontinental amalgamation has profoundly influenced the evolution of the geosphere, hydrosphere, atmosphere and biosphere. However, the timing of supercontinent formation has mainly been constrained by the global age spectra of detrital zircon. Here, we show that the zircons in back-arc volcanic rocks not only reflect the evolution of local magmatism but also contain a record of global continental amalgamation events. We found that the young (<100 ka) zircons in volcanic rocks from the Okinawa Trough have old (108 Ma to 2.7 Ga) inherited zircon, which were captured as the magma ascended through the rifting continental crust. Moreover, the ages of the inherited zircons correspond to five supercontinent amalgamation events. Specifically, the Archaean inherited zircons, which have positive ɛHf(t) and low δ18O values, correspond to the formation of juvenile global continental crust. In contrast, the negative ɛHf(t) and high δ18O values of post-Archaean inherited zircons indicate that their parental magma contained recycled, old crust due to the enhanced crustal thickening and crust-mantle interactions during supercontinent assembly. Therefore, inherited zircons in back-arc volcanic rocks not only reflect the evolution of local magmatism but also contain a record of global supercontinental amalgamation events.
Surgeon Dominated Design Can Improve the Accuracy of Patient-specific Instruments in Kinematically Aligned TKA
Authors: Wang Zhiwei , Wen Liang , Zhang Liang , Ma Desi , Dong Xiang , Qu Tiebing 
Published: November 2020

Abstract
Precise bone resection is mandatory for kinematically aligned total knee arthroplasty（KA-TKA). Patient-specific instrumentation (PSI) has been applied to improve the accuracy of bone resection in TKA for many years. The purpose of this study was to investigate whether surgeons’ domination in PSI design can improve accuracy in KA-TKA. A total of 24 patients (24 knees) who underwent KA-TKA in our institution were assigned into engineer designed PSI group (10 knees) and surgeon designed PSI group (14 knees). The bone resection discrepancies of every key facets were used to evaluate the accuracy of PSI in bone resection, while the absolute differences of joint line orientation before and after surgery were used to evaluate the accuracy of PSI in joint line restoration. The overall discrepancy of bone resection was reduced by surgeon designed PSI compared to engineer designed PSI by 0.33mm (P<0.001). Surgeon designed PSI could reduce the outliers in terms of relative discrepancies in bone resection as well. Moreover, surgeon designed PSI could significantly improve the accuracy of PSI in the restoration of the joint line (p=0.01). This study indicate that the dominance of surgeons in both PSI design and subsequent surgical operation should be emphasized in efforts to improve the accuracy of PSI.
Feasibility and Safety of Laparoscopic Transperitoneal Adrenalectomy in Large Adrenal Tumor From 20 Years Single-center Experiences- A Retrospective Cohort Study
Authors: Prakobpon Thanasit , Santi-ngamkun Apirak , Usawachintachit Manint , Ratchanon Supoj , Sowanthip Dutsadee , Panumatrassamee Kamol 
Published: November 2020

Abstract
Background: The role of laparoscopic adrenalectomy (LA) in a large adrenal tumor is controversial due to the risk of malignancy and technical difficulty. In this study, we compared the perioperative outcomes and complications of LA on large (≥ 6 cm) and (< 6 cm) adrenal tumors.Methods: We retrospectively reviewed all clinical data of patients who underwent unilateral LA in our institution between April 2000 and June 2019. Patients were classified by tumor size into 2 groups. Patients in group 1 had tumor size < 6 cm (n=408) and patient in group 2 had tumor size ≥ 6 cm (n=48). Demographic data, perioperative outcomes, complications, and pathologic reports were compared between groups.Results: Patients in group 2 were significant older (p=0.04), thinner (p=0.001) and had lower incident of hypertension (p=0.001), with a significantly higher median operative time (75 vs 120 min), estimated blood loss (20 vs 100 ml), transfusion rate (0 vs 20.8%), conversion rate (0.25 vs 14.6%) and length of stays (6 vs 9 days) than in group 2 (all p<0.001). Group 2 patients also had significantly higher frequency of intraoperative complication (4.7 vs 31.3%; adjust Odds Ratio [OR] =7.73 (95% CI 3.35-17.84), p-value < 0.001) and postoperative complication (5.4 vs 31.3%; adjust OR=6.06, 95% CI 2.84-13.73, p-value < 0.001). Only eight (1.8%) major complications occurred in this study. The most common pathology in group 2 patient was pheochromocytoma and metastasis. Conclusions: Laparoscopic transperitoneal adrenalectomy in large adrenal tumor ≥ 6 cm is feasible but associated with significantly worse intraoperative complications, postoperative complications and recovery. However, most of the complications were minor and could be managed conservatively. Careful patient selection with the expertise surgeon in adrenal surgery are the key factors for successful laparoscopic surgery in a large adrenal tumor. Trial registration: This study was retrospectively registered in the Thai Clinical Trials Registry on 02/03/2020. The registration number was TCTR20200312004.
An Exploratory Qualitative Study of the Prevention of Road Traffic Collisions and Neurotrauma in India: Perspectives From Key Informants in an Indian Industrial City (Visakhapatnam)
Authors: Selveindran Santhani M , Samarutilake Gurusinghe , Rao K Madhu Narayana , Patisappu Jogi , Hill Christine , Kolias Angelos , Pathi Rajesh , Hutchinson Peter , Vijayasekhar N 
Published: November 2020

Abstract
Background: Despite current preventative strategies, road traffic collisions (RTCs) and resultant neurotrauma remain a major problem in India. This study seeks to explore local perspectives in the context within which RTCs take place and identify potential suggestions for improving the current status.Methods: Ten semi-structured interviews were carried out with purposively selected key informants from the city of Visakhapatnam, Andhra Pradesh. Participants were from one of the following categories: commissioning stakeholders; service providers; community or local patient group/advocacy group representatives. Transcripts from these interviews were analysed qualitatively using the Framework Method.Results: Participants felt RTCs are a serious problem in India and a leading cause of neurotrauma. Major risk factors identified related to user behaviour such as speeding and not using personal safety equipment, and the user state, namely drink driving and underage driving. Other reported risk factors included poor infrastructure, moving obstacles on the road, overloaded vehicles and substandard safety equipment. Participants discussed how RTCs affect not only the health of the victim, but are also a burden to the healthcare system, families, and the national economy. Although there are ongoing preventative strategies being carried out by both the government and the community, challenges to successful prevention emerged from the interviews which included resource deficiencies, inconsistent implementation, lack of appropriate action, poor governance, lack of knowledge and the mindset of the community and entities involved in prevention. Recommendations were given on how prevention of RTCs and neurotrauma might be improved, addressing the areas of education and awareness, research, the pre-hospital and trauma systems, enforcement and legislation, and road engineering, in addition to building collaborations and changing mindsets.Conclusions: RTCs remain a major problem in India and a significant cause of neurotrauma. Addressing the identified gaps and shortfalls in current approaches and reinforcing collective responsibility towards road safety would be the way forward in improving prevention and reducing the burden.