bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resident bacterial populations mediating biogeochemical dynamics in a Uranium roll front deposit
Authors: Jrou Fadwa , Descostes Michael , Povedano-Priego Cristina , Sanchez-Castro Iván , Suvannagan Vitthavat , Grizard Pierre , Merroun Mohamed L. 
Published: November 2019

Abstract
Background Uranium-mineralized sandy aquifer, planned for a mining by in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding the Uranium roll front deposits. Since microorganisms are likely to play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was made on the characterization of the resident microbiome of an aquifer surrounding uranium roll-front deposit that is part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the aquifer, including the native mineralized orebody, and both the upstream and downstream compartments.Results An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed in all water samples. High-throughput sequencing showed that the bacterial community structure was shaped by the redox gradient and the oxygen availability. Several interesting bacteria were observed including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans) iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may be also involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). The taxa residing in each aquifer compartment followed a strong redox zonation differentiation, although as a whole the population of each water section seems to define an ecologically functional ecosystem containing suitable microorganisms that are probably prone to promote the remediation of the acidified aquifer by natural attenuation. Co-occurrence patterns confirmed a strong correlations among the bacterial genera suggesting either a shared and preferred environmental conditions or the performance of functions similar or complementary to each other.Conclusions Assessing the composition, and structure of the resident bacterial communities is a prerequisite for understanding the natural attenuation and predicting bacterial input in the improvement of ISR efficiency.
Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses.
Authors: Dupont S. , Lokmer A. , Corre E. , Auguet J.-C. , Petton B. , Toulza E. , Montagnani C. , Tanguy G. , Pecqueur D. , Salmeron C. , Guillou L. , Desnues C. , Scola B. La , Khalil J. Bou , de Lorgeril J. , Mitta G. , Gueguen Y. , Escoubas Jean-Michel 
Published: November 2019

Abstract
Background: The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results: We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease . To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 µVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion: Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment
Authors: Liu Qianshuo , Zhu Lu , Liu Xiaobai , Zheng Jian , Liu Yunhui , Ruan Xuelei , Cao Shuo , Cai Heng , Li Zhen , Xue Yixue 
Published: November 2019

Abstract
The blood-brain barrier (BBB) plays a pivotal role in maintenance and regulation of the neural microenvironment. The occurrence of BBB disruption is the pathological change of early Alzheimer’s disease (AD). RNA-binding proteins and long non-coding RNAs are involved in the regulation of BBB permeability. Our study was performed to demonstrate TRA2A/LINC00662/ELK4 axis in regulating BBB permeability in AD microenvironment. In Aβ1-42-incubated microvascular endothelial cells (ECs) of BBB model in vitro, TRA2A and LINC00662 were enriched. TRA2A increased the stability of LINC00662 by binding with it. The knockdown of either TRA2A or LINC00662 decreased the BBB permeability via upregulating the expressions of tight junction-related proteins. ELK4 was lower expressed in BBB model in vitro in AD microenvironment. LINC00662 mediated the degradation of ELK4 mRNA by SMD pathway. The downregulated ELK4 increased the permeability of BTB by increasing the tight junction-related proteins expressions. TRA2A/LINC00662/ELK4 axis plays a crucial role in the regulation of BBB permeability in AD microenvironment, which may provide a novel target for the therapy of AD.
Indoor residual spraying for malaria control in Sub-Saharan Africa 1997 to 2017; an adjusted retrospective analysis
Authors: Tangena Julie-Anne , Hendriks Chantal M.J. , Devine Maria , Tammaro Meghan , Trett Anna E. , Williams Ignatius , DePina Adilson José , Sisay Achamylesh , Herizo Ramandimbiarijaona , Kafy Hmooda Toto , Chizema Elizabeth , Were Allan , Rozier Jennifer , Coleman Michael , Moyes Catherine L. 
Published: November 2019

Abstract
Background: Indoor residual spraying (IRS) is a key tool for controlling and eliminating malaria by targeting vectors. To support the development of effective intervention strategies it is important to understand the impact of vector control tools on malaria incidence and on the spread of insecticide resistance. In 2006, the World Health Organization (WHO) stated that countries should report on coverage and impact of IRS, yet IRS coverage data are still sparse and unspecific. Here we estimated the subnational coverage of IRS across sub-Saharan Africa for the four main insecticide classes from 1997 to 2017. Methods: Data on IRS deployment were collated from a variety of sources, including the President’s Malaria Initiative spray reports and National Malaria Control program reports, for all 46 malaria-endemic countries in Sub-Saharan Africa from 1997 to 2017. The data were mapped to the applicable administrative divisions and the proportion of households sprayed for each of the four main insecticide classes; carbamates, organochlorines, organophosphates and pyrethroids was calculated. Results: We found that the number of countries implementing IRS increased considerably over time, although the focal nature of deployment means the number of people protected remains low. From 1997 to 2010, DDT and pyrethroids were commonly used, then partly replaced by carbamates from 2011 and by organophosphates from 2013. IRS deployment since the publication of resistance management guidelines has typically avoided overlap between pyrethroid IRS and ITN use. However, annual rotations of insecticide classes with differing modes of action are not routinely used. Conclusion: This study highlights the gaps between policy and practice, emphasizing the continuing potential of IRS to drive resistance. The data presented here can improve studies on the impact of IRS on malaria incidence and help to guide future malaria control efforts.
First evidence of the deletion in the Pfhrp2 and Pfhrp3 genes in P. falciparum from Equatorial Guinea
Authors: Berzosa Pedro , González V , Taravillo L , Mayor A , Romay-Barja M , Garcia L , Ncogo P , Riloha M , Benito A 
Published: November 2019

Abstract
Background: WHO recommends RDTs as a good alternative malaria-diagnosis method in remote parts of sub-Saharan Africa. The majority of commercial RDTs currently available detect the P. falciparum protein histidine-rich protein 2 (PfHRP2). There have also been recent reports of Pfhrp2 deletions being found in parasites collected from several African countries. WHO has concluded that the lacking the Pfhrp2 gene must be monitored in Africa. The purpose of the study was to analyze why the samples that were positive by PCR were negative by RDTs; and, therefore, to determine whether there have been deletions in the Pfhrp2 and/or Pfhrp3 genes. Methods: Malaria NM-PCR was carried out to all the samples collected in the field. A group of 128 samples was positive by PCR but negatives by RDT, these samples were classified as RDT false-negatives. It was carried out a PCR for exon2 of Pfhrp2 and Pfhrp3 genes to detect the presence or absence of these two genes. Frequencies with 95% confidence intervals (CIs) were used for categorical variables. Associations were assessed by the chi-square test or Fisher´s exact test. The level of significance was set at p ≤ 0.05. Statistical analyses were performed using the software package SPSSv.15.0. Sensitivity and specificity calculations were performed using Epidat 3.1 software. Results: After the PCR, 81 samples were identified (4.7%, 95%CI: 3.8-5.8) which had deletion in both genes, Pfhrp2 and Pfhrp3. Overall, however, 11 samples (0.6%, 95%CI: 0.36-1.14) had deletion only in Pfhrp2 but not in Pfhrp3, and 15 (0.9%, 95%CI: 0.6-1.5) presented with deletion only in Pfhrp3 but not in Pfhrp2. Considering the Pfhrp2 gene separately, within the total of 1,724 samples, 92 (5.3%, 95%CI: 4.37-6.5) had evidence of deletion. Conclusion: The present study provides the first evidence of deletion in the Pfhrp2 and Pfhrp3 genes in P. falciparum isolates from Equatorial Guinea. However, larger studies across different regions within the country and across different seasonal profiles are needed to determine the full extent of Pfhrp2- and Pfhrp3-deletion. it would be strongly recommendable to implement an active surveillance program in order to detect any increases in Pfhrp2- and Pfhrp3-deletion frequencies.
Construction of High-quality Linkage Maps in Populus with RADseq Data and their Application in QTL Mapping and Genome Assembly
Authors: Tong Chunfa , Yao Dan , Wu Hainan , Chen Yuhua , Yang Wenguo , Zhao Wei , Gao Hua 
Published: November 2019

Abstract
Background: Although great efforts have been made to construct genetic linkage maps in Populus using traditional molecular markers, these maps are typically sparse, and the number of linkage groups does not match the karyotype of Populus . With the advances in high-throughput sequencing technologies and new software packages available for extracting single nucleotide polymorphisms (SNPs) across a mapping population, it is possible to construct high-quality, high-density genetic linkage maps with thousands of SNPs in such outbred species. Results: Two parent-specific linkage maps were constructed with restriction site-associated DNA sequencing (RADseq) data from an F 1 hybrid population from Populus de l toides and Populus simonii and were applied to identify growth trait loci and facilitate genome assembly. The female Populus deltoides map contained 4,018 SNPs, which were divided into 19 linkage groups under a wide range of LOD thresholds from 7 to 55, perfectly matching the karyotype of Populus . The male Populus simonii map showed similar characteristics, consisting of 2,097 SNPs, which also belonged to 19 linkage groups under LOD thresholds of 7 to 29. The SNP genotype data for linkage analysis were confirmed to be of high quality. The SNP order of each linkage group was optimal among different ordering results from several available software platforms. Moreover, the linkage maps allowed the detection of 39 QTLs underlying tree height and 47 for diameter at breast height, some of which were strongly associated with QTLs identified in previous studies. In addition, the linkage maps enabled the anchoring of 671 contigs of a draft genome assembly of Populus simonii to chromosomes, corresponding to approximately 83.6% of the genome and showing a high level of collinearity with the genetic maps. Conclusions: The two parental genetic maps of Populus are of high quality, especially in terms of SNP data quality, the SNP order within linkage groups, and the perfect match between the number of linkage groups and the karyotype of Populus as well as performance in QTL mapping and genome assembly. The adopted approaches for both extracting and ordering SNPs could be applied to other species to construct high-density, high-quality genetic maps.
How and why do medical students choose the specialty of Infectious and Tropical Diseases? A national cross-sectional study
Authors: Peiffer-Smadja Nathan , Ardellier François-Daniel , Thill Pauline , Beaumont Anne-Lise , Catho Gaud , Osei Lindsay , Dubée Vincent , Bleibtreu Alexandre , Lemaignen Adrien , Thy Michaël 
Published: November 2019

Abstract
Background Infectious diseases (ID) physicians are more needed than ever to tackle existing and emerging global threats. However, in the US approximately one quarter of the ID fellowship programs are unfilled every year. The creation of the ID residency in 2017 in France offers the opportunity to know how and why the specialty is chosen by medical students. Methods We first analyzed the choice of specialty of all French medical students in 2017 and 2018 according to their rank at the national exam that ends medical studies. A web questionnaire was then sent on January 2019 to all ID residents in France (n=100) to assess their professional project and the factors influencing their choice of specialty. Results We analyzed the choice of 17,087 medical students. ID was the first-chosen specialty with a median national rank of 526/8539, followed by plastic surgery and ophthalmology. The questionnaire was completed by 90% of the French ID residents. The most encouraging factors to choose ID were the multi-system approach of the specialty, the importance of diagnostic medicine and having done an internship in ID during medical school. The most dissuading factors were the work-life balance, the workload and the salary. Conclusions The recent recognition of ID as a qualifying specialty in France can be considered a success insofar as the specialty is the most popular among all medical and surgical specialties. Individuals who choose ID are attracted by the intellectual simulation of the specialty but express concerns about the working conditions and salaries.
Differential blood miRNA expression in brain amyloid imaging defined Alzheimer's disease and controls.
Authors: Wu Helen Zong Ying , Thalamuthu Anbupalam , Cheng Lesley , Fowler Christopher , Masters Colin L , Sachdev Perminder , Mather Karen A. 
Published: November 2019

Abstract
Background: Peripheral blood microRNAs (miRNA) have been identified as potential biomarkers for Alzheimer’s disease (AD). Study results have generally been inconsistent and limited by sample heterogeneity. The aim of this study is to establish candidate blood miRNA biomarkers for AD by comparing differences in miRNA expression between participants with brain amyloid imaging defined AD and normal cognition. Methods: Blood RNA was extracted from a subset of participants from the Australian Imaging Biomarkers Lifestyle Study of Ageing cohort (AIBL) with brain amyloid imaging results. MiRNA profiling was performed using small RNA sequencing on 71 participants, comprising 40 AD with high brain amyloid burden on imaging (amyloid positive) and 31 cognitively normal controls with low brain amyloid burden (amyloid negative). Cross-sectional comparisons were made between groups to examine differential miRNA expression levels using Fisher’s exact tests. Replication of results was undertaken using a publicly available dataset of blood miRNA data of AD and controls. In silico analysis of downstream messenger RNA targets of candidate miRNAs was performed to elucidate potential biological function. Results: After quality control, 816 miRNAs were available for analysis. There were 71 significantly differentially expressed miRNAs between the AD and control groups (p<0.05). Two of these miRNAs, miR-146b-5p and miR-15b-5p, were also significant in the replication cohort. Pathways analysis showed these miRNAs to be involved in innate immune system and regulation of the cell cycle respectively, both of which have relevance to AD pathogenesis. Conclusion: Blood miR-146b-5p and miR15b-5p showed consistent differential expression in AD compared to controls. Further replication and translational studies in strictly phenotyped cohorts are needed to establish their role as biomarkers for AD to have clinical utility.
Developmental loss of oligodendrocytes exacerbates adult CNS demyelination
Authors: Pajoohesh-Ganji Ahdeah , Karl Molly , Garrison Eric , Clarkson-Paredes Cheryl , Ahn Julie , Miller Robert H. 
Published: November 2019

Abstract
Background
Multiple sclerosis (MS), a neurodegenerative autoimmune disease characterized by loss of oligodendrocytes and myelin in the brain and spinal cord, results in localized functional deficits. Several risk factors have been associated with MS, however none can fully explain an enhanced susceptibility. Epidemiological data, based on geographical prevalence studies suggest susceptibility is established early in life and frequently long before disease diagnosis implicating developmental events influence adult disease progression. Here we test the hypothesis that loss of mature oligodendrocytes during postnatal development results in enhanced susceptibility to an adult demyelinating insult.
Methods
A transgenic mouse model was utilized to specifically induce apoptosis in a subset of mature oligodendrocytes (MBP-iCP9) during the first 2 postnatal weeks followed by either a local LPC spinal cord injection or the induction of EAE in the adult. Immunostaining, immunoblotting, behavioral testing, and electron microscopy were utilized to examine the differences between groups.
Results
We show that during development, oligodendrocyte apoptosis results in transient reductions in myelination and functional deficits that recover after 10-14 days. Compared to animals in which oligodendrocyte development was unperturbed, animals subjected to postnatal oligodendrocyte ablation showed delayed recovery from an LPC lesion. Unexpectedly, the induction and severity of EAE was not significantly altered in animals following oligodendrocyte ablation even though there was a substantial increase in spinal cord tissue damage and CNS inflammation. It is currently unclear why these changes are not reflected in enhanced functional deficits.
Conclusions
These observations suggest that developmental loss of oligodendrocytes results in long lasting tissue changes that alter its capacity for repair in the adult.
Low ambulance availability at health facilities and disparity across regions in Ethiopia: a cross-sectional health facility level assessment
Authors: Defar Atkure , Getachew Theodros , Gonfa Geremew , Bekele Abebe , Molla Million , Alemu Kassahun 
Published: November 2019

Abstract
Background: Lack of well-functioning referral and quality of the service are challenges for many of the developing countries health care system. This study evaluated the referral transport services for maternal and newborn care in Ethiopian health facilities. Methods: The study used 2016 Ethiopian Emergency Obstetric and Newborn care assessment data. All public and private health facilities that provided maternal and newborn health services were included in the study. The data analysis was done on a total of 3,804 facilities. Results: Overall, in this study only 17% (95% CI: 16-18) of health facilities had their dedicated functioning ambulance (motor vehicle, motorcycle, or tricycle ambulance). Among these, reports of using the ambulance for non-emergency transport were common. Use of the ambulance for transporting client’s home was reported by 48% (95% CI: 44-52) of facilities. A total of 62% health facilities provided by district health offices. Hospitals/MCH centres had almost 5 times (95% CI: 3.16, 7.12) more likely to have ambulance on-site compared with health centres/speciality clinics. The urban-based health facilities were three times (aOR =2.86, 95% CI: 2.29, 3.58) more likely to have ambulance onsite than their counter. Availability of ambulance on-site in public facilities was found to be 80% and 63% less to that of private owned and private-for-profit health facilities. Facilities that didn’t provide onsite obstetric surgery were also less likely to have an ambulance on-site. There was no significant difference in ambulance availability for the facilities that have referred in/out and in the provision of 24/7 service for emergency obstetric and newborn care. There is no relation between institutional delivery and availability of ambulance on-site (ρ=0.14). Conclusions: In this study, low ambulance availability for emergency referral for maternal and newborn cases in Ethiopian facilitates was observed. There is a disparity in the availability of Ambulance onsite by regions facility location and type of health facility. No effect of referral transport service on-site availability on institutional deliveries was noted. An ambulance is mandatory for interconnected health centers to hospital referrals. However, this needs to be backed up with an adequate supply of basic and emergency obstetric care at all facilities.