bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence ofSchistosoma mansoniinfection in Ethiopia: A systematic review and meta-analysis
Authors: Hussen Siraj , Assegu Demissie , Shimelis Techalew 
Published: April 2019

AbstractBackgroundSchistosomiasis is the most predominant helminthic infection in tropics and subtropics mainly in sub-Saharan African countries including Ethiopia.S. mansoniinfection is still becoming a public health problem since the risk of reinfection and recurrent disease remain, even in areas with high treatment coverage. There is no summarized data regarding prevalence ofS. mansoniinfection in Ethiopia. Therefore, this review was done to determine the pooled prevalence ofS. mansoniinfection in Ethiopia.MethodsThe PRISMA guidelines protocol was followed to perform the systematic review and meta-analysis. Published studies from January 1999 to September 1 2018 were searched in Medline, PubMed, Google scholar, HINARI and Cochrane Library. The study search terms were: “prevalence”, “incidence”, “schistosomiasis” “Bilharziasis”, “Ethiopia”. The heterogeneity of studies was assessed using Cochran’s Q test and I2test statistics. Publication bias was assessed by Egger’s test.ResultsEighty four studies were included in this review and meta–analysis. The pooled prevalence ofS. mansoniamong Ethiopian population was 18.7% (95%CI: 14.7-23.5). Southern regions of Ethiopia had a higherS.mansoniprevalence of 33.6% 995% CI: 20.2-50.4).S.mansoniwas higher in rural areas and among males with a pooled prevalence, 20.8% (95% CI: 14.2-29.4) and 29.4% (95%CI: 23.2-36.6), respectively. Similarly, the prevalence ofS.mansonihave been increased over the past 15 years.ConclusionThe review showed a moderate prevalence ofS.mansoniinfection in Ethiopia and disease is still a major health problem. Therefore, integrated control approach could be implemented to reduce the burden of this parasite in Ethiopia. Interventions leading to reduction of open water sources exposure to reduce schistosomiasis transmission, strengthen of deworming program, giving appropriate health education on the risk of schistosomal infection and transmission should be applied.Author SummaryUnderstanding summarized data regarding prevalence ofS. mansoniinfection in Ethiopia is essential to inform decisions on appropriate control strategies for schistosomiasis. We searched Published studies from January 1999 to September 1 2018 from Medline, PubMed, Google scholar, HINARI and Cochrane Library. Eighty four studies were included in this review and meta–analysis. The limit of language was English and the limit of study group was human. The pooled prevalence ofS. mansoniamong Ethiopian population was 18.7%. Southern regions of Ethiopia had a higherS.mansoniprevalence and the parasite was higher in rural areas and among males. The prevalence ofS.mansonihave been increased over the past 15 years. Our review showed a moderate prevalence ofS.mansoniinfection in Ethiopia and disease is still a major health problem. Therefore, appropriate controlling approach could be implemented. Interventions leading to reduction of open water sources, strengthen of deworming program, and giving appropriate health education should be applied.
Ifit1 regulates norovirus infection and enhances the interferon response in murine macrophage-like cells
Authors: Mears Harriet V. , Emmott Edward , Chaudhry Yasmin , Hosmillo Myra , Goodfellow Ian G. , Sweeney Trevor R. 
Published: April 2019

AbstractBackgroundNorovirus, also known as the winter vomiting bug, is the predominant cause of non-bacterial gastroenteritis worldwide. Disease control is predicated on a robust innate immune response during the early stages of infection. Double-stranded RNA intermediates generated during viral genome replication are recognised by host innate immune sensors in the cytoplasm, activating the strongly antiviral interferon gene programme. Ifit proteins, which are highly expressed during the interferon response, have been shown to directly inhibit viral protein synthesis as well as regulate innate immune signalling pathways. Ifit1 is well-characterised to inhibit viral translation by sequestration of eukaryotic initiation factors or by directly binding to the 5’ terminus of foreign RNA, particularly those with non-self cap structures. However, noroviruses have a viral protein, VPg, covalently linked to the 5’ end of the genomic RNA, which acts as a cap substitute to recruit the translation initiation machinery.MethodsIfit1 knockout RAW264.7 murine macrophage-like cells were generated using CRISPR-Cas9 gene editing. These cells were analysed for their ability to support murine norovirus infection, determined by virus yield, and respond to different immune stimuli, assayed by quantitative PCR. The effect of Ifit proteins on norovirus translation was also tested in vitro.ResultsHere, we show that VPg-dependent translation is completely refractory Ifit1-mediated translation inhibition in vitro and Ifit1 cannot bind the 5’ end of VPg-linked RNA. Nevertheless, knockout of Ifit1 promoted viral replication in murine norovirus infected cells. We then demonstrate that Ifit1 promoted interferon-beta expression following transfection of synthetic double-stranded RNA but had little effect on toll-like receptor 3 and 4 signalling.ConclusionsIfit1 is an antiviral factor during norovirus infection but cannot directly inhibit viral translation. Instead, Ifit1 stimulates the antiviral state following cytoplasmic RNA sensing, contributing to restriction of norovirus replication.
Induction of Chk2 signaling in the germarium is sufficient to cause oogenesis arrest inDrosophila
Authors: Durdevic Zeljko , Ephrussi Anne 
Published: April 2019

AbstractThe conserved RNA helicase Vasa is required for germ cell development in many organisms. It is established that inDrosophilaloss of piRNA pathway components, including Vasa, causes Chk2-dependent oogenesis arrest, however the stage at which Chk2-signaling is triggered was unknown. We found that absence of Vasa during the germarial stages arrests oogenesis due to Chk2 activation. Importantly, once induced in the germarium, Chk2-mediated arrest of oogenesis cannot be overcome by restoration of Vasa to the arrested egg-chambers. We conclude that Vasa activity specifically in the germarium is essential for germ cell lineage development.
A highly responsive pyruvate sensor reveals pathway-regulatory role of the mitochondrial pyruvate carrier MPC
Authors: Arce-Molina R , Cortés-Molina F , Sandoval PY , Galaz A , Alegría K , Schirmeier S , Barros LF , San Martín A 
Published: April 2019

AbstractMitochondria generate ATP and building blocks for cell growth and regeneration, using pyruvate as the main substrate. Here we introduce PyronicSF, a user-friendly GFP-based sensor of improved dynamic range that enables real-time subcellular quantitation of mitochondrial pyruvate transport, concentration and flux. We report that cultured mouse astrocytes maintain mitochondrial pyruvate in the low micromolar range, below cytosolic pyruvate, which means that the mitochondrial pyruvate carrier MPC controls the decision between respiration and anaplerosis/gluconeogenesis in an ultrasensitive fashion. The functionality of the sensor in living tissue is demonstrated in the brain ofDrosophila melanogasterlarvae. Mitochondrial subpopulations are known to coexist within a given cell, which differ in their morphology, mobility, membrane potential, and vicinity to other organelles. The present tool can be used to investigate how mitochondrial diversity relates to metabolism, to study the role of MPC in disease, and to screen for small-molecule MPC modulators.
Reference plasmid pHXB2_D is an HIV-1 molecular clone that exhibits identical LTRs and a single integration site indicative of an HIV provirus
Authors: Gener Alejandro R. , Zou Wei , Foley Brian T. , Hyink Deborah P. , Klotman Paul E. 
Published: April 2019

AbstractObjectiveTo compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D.DesignWe sequenced pHXB2_D and a control plasmid pNL4-3_gag-pol(Δ1443-4553)_EGFP with long- and short-read DNA-seq, evaluating sample variability with resequencing (sequencing and mapping to reference HXB2) and de novo viral genome assembly.MethodsWe prepared pHXB2_D and pNL4-3_gag-pol(Δ1443-4553)_EGFP for long-read nanopore DNA-seq, varying DNA polymerases Taq (Sigma-Aldrich) and Long Amplicon (LA) Taq (Takara). Nanopore basecallers were compared. After aligning reads to the reference HXB2 to evaluate sample coverage, we looked for variants. We next assembled reads into contigs, followed by finishing and polishing. We hired an external core to sequence-verify pHXB2_D and pNL4-3_gag-pol(Δ1443-4553)_EGFP with single-end 150 base-long Illumina reads, after masking sample identity.ResultsWe achieved full-coverage (100%) of HXB2 HIV-1 from 5’ to 3’ long terminal repeats (LTRs), with median per-base coverage of over 9000x in one experiment on a single MinION flow cell. The longest HIV-spanning read to-date was generated, at a length of 11,487 bases, which included full-length HIV-1 and plasmid backbone with flanking host sequences supporting a single HXB2 integration event. We discovered 20 single nucleotide variants in pHXB2_D compared to reference, verified by short-read DNA sequencing. There were no variants detected in the HIV-1 segments of pNL4-3_gag-pol(Δ1443-4553)_EGFP.ConclusionsNanopore sequencing performed as-expected, phasing LTRs, and even covering full-length HIV. The discovery of variants in a reference plasmid demonstrates the need for sequence verification moving forward, in line with calls from funding agencies for reagent verification. These results illustrate the utility of long-read DNA-seq to advance the study of HIV at single integration site resolution.
Osteocytes remodel bone by TGF-β-induced YAP/TAZ signaling
Authors: Kegelman Christopher D. , Coulombe Jennifer C. , Jordan Kelsey M. , Horan Daniel J. , Qin Ling , Robling Alexander G. , Ferguson Virginia. L , Bellido Teresita M. , Boerckel Joel D. 
Published: April 2019

ABSTRACTOsteocytes are bone matrix-entombed cells that form an interconnected network of processes called the lacunar/canalicular system, which enables osteocytes to coordinate bone formation and resorption. Osteocytes indirectly regulate osteoblast and osteoclast activity on bone surfaces but also directly resorb and deposit their surrounding bone matrix through perilacunar/canalicular remodeling. However, the molecular mechanisms by which osteocytes control bone remodeling remain unclear. We previously reported that the transcriptional regulators Yes-associated protein (YAP) and Transcriptional co-activator with PDZ-motif (TAZ) promote bone acquisition in osteoblast-lineage cells. Here, we tested the hypothesis that YAP and TAZ regulate osteocyte-mediated bone remodeling by conditional ablation of both YAP and TAZ from mouse osteocytes using 8kb-DMP1-Cre. Osteocyte conditional YAP/TAZ deletion reduced bone mass and dysregulated matrix collagen content and organization, which together impaired bone mechanical properties. YAP/TAZ deletion reduced osteoblast number and activity and increased osteoclast activity. In addition, YAP/TAZ deletion directly impaired osteocyte lacunar/canalicular network remodeling, reducing canalicular density, length, and branching, but did not alter lacunar size or shape. Further, consistent with recent studies identifying TGF-β signaling as a key inducer of perilacunar/canalicular remodeling through expression of matrix-remodeling enzymes, YAP/TAZ deletion in vivo decreased osteocyte expression of matrix proteases Mmp13, Mmp14, and Cathepsin K. In vitro, pharmacologic inhibition of YAP/TAZ transcriptional activity in osteocyte-like cells abrogated TGF-β-induced protease gene expression. Together, these data show that YAP and TAZ act downstream of TGF-β in osteocytes to control bone matrix accrual, organization, and mechanical properties indirectly by coordinating osteoblast/osteoclast activity and directly by regulating perilacunar/canalicular remodeling.
Molecular Diversity and Network Complexity in Growing Protocells
Authors: Kamimura Atsushi , Kaneko Kunihiko 
Published: April 2019

AbstractA great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources are limited, it is shown that diversity in intracellular components is increased to allow the use of diverse resources for cellular growth. Scaling relation is demonstrated between resource abundances and molecular diversity. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. Later, the species turn to be host species that support the replication of other species. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell.
The feasibility of atrial and ventricular arrhythmias recognition using metrics of signal complexity for heartbeat intervals
Authors: Huang Ming , Kido Koshiro , Ono Naoaki , Altaf-UI-Amin  , Tamura Toshiyo , Kanaya Shigehiko 
Published: April 2019

AbstractIt is well known that the cardiac system is controlled by the complex nonlinear self-regulation and the heartbeat variability (HRV) is an independent indicator of the autonomic regulation. With the assumption that intrinsic differences of atrial fibrillation (A) and ventricular ectopic arrhythmias (V) can be unveiled by a proper approach based on of signal complexity, we examine the feasibility of detecting these arrhythmias of different pathological origins using metrics of complexity for heartbeat intervals (HRI). Specifically, the normal sinus rhythm (N), the A type and the V type are used as the targeted types of heartbeat. By extracting the entropy-based features from HRI of different lengths, i.e., from 300 heartbeats to 1000 heartbeats, we examined the distinguishability of these 3 types of heartbeat. By applying the features to the random forest model, the HRI signal of 600-heartbeat-length can be used to detect the A and V completely, i.e., with 100% of type-wise recall and precision. What is more, this approach is sensitive to the existence of the corresponding arrhythmias. The results substantiate our assumption about the intrinsic difference of the A and V type. A further investigation applying this approach to a wider spectrum and a finer stratification of arrhythmias/ cardiac diseases and may lead to the systematic understanding in the context of complexity and better insight for its practical use for wearable/unconstrained monitors.
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index
Authors: Liu Bo , Liu Yadong , Li Junyi , Guo Hongzhe , Zang Tianyi , Wang Yadong 
Published: April 2019

AbstractLong-read RNA sequencing (RNA-seq) is promising to transcriptomics studies, however, the alignment of long RNA-seq reads is still non-trivial due to high sequencing errors and complicated gene structures. Herein, we propose deSALT, a tailored two-pass alignment approach, which constructs graph-based alignment skeletons to infer exons and uses them to generate spliced reference sequences to produce refined alignments. deSALT addresses several difficult technical issues, such as small exons and sequencing errors, which breakthroughs the bottlenecks of long RNA-seq read alignment. Benchmarks demonstrate that deSALT has a greater ability to produce accurate and homogeneous full-length alignments. deSALT is available at: https://github.com/hitbc/deSALT.
Cell type-specific genetic regulation of expression in the granule cell layer of the human dentate gyrus
Authors: Jaffe AE , Hoeppner DJ , Saito T , Blanpain L , Ukaigwe J , Burke EE , Tao R , Tajinda K , Deep-Soboslay A , Shin JH , Kleinman JE , Weinberger DR , Matsumoto M , Hyde TM 
Published: April 2019

AbstractLaser capture microdissection followed by RNA-seq (LCM-seq) was used to profile the transcriptional landscape of the granule cell layer of the dentate gyrus (DG-GCL) in human hippocampus, and contrasted to homogenate tissue. We identified widespread cell type-specific aging and genetic effects in the DG-GCL that were either missing or directionally discordant in corresponding bulk hippocampus RNA-seq data from largely the same subjects. Of the ∼9 million eQTLs in the DG-GCL, 15% were not in bulk hippocampus, including 15 schizophrenia genome-wide association study (GWAS) risk variants. We then created custom transcriptome-wide association study (TWAS) genetic weights from the DG-GCL which identified many novel schizophrenia-associated genetic signals not found in TWAS from bulk hippocampus, including GRM3 and CACNA1C. These results highlight the biological resolution of cell type-specific expression profiling using targeted sampling strategies like LCM, and complement homogenate and single nuclei approaches in human brain.
Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats
Authors: Tikhonenkov Denis V. , Jhin Soo Hwan , Eglit Yana , Miller Kai , Plotnikov Andrey , Simpson Alastair G.B. , Park Jong Soo 
Published: April 2019

AbstractThe heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide that range from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rDNA divergences (up to 42.4%). Some strains grew best at salinities from 75 to 125‰ and represent halophiles. All but one of these belonged to two geographically heterogeneous clusters that formed a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rDNA phylogenies, unlike most previous analyses based on two sequences.
The first Miocene fossils of Lacerta cf.trilineata(Squamata, Lacertidae) with a comparative study of the main cranial osteological differences in green lizards and their relatives
Authors: Čerňanský Andrej , Syromyatnikova Elena V. 
Published: April 2019

AbstractWe here describe the first fossil remains of a green lizardof theLacertagroup from the late Miocene (MN 13) of the Solnechnodolsk locality in southern European Russia. This region of Europe is crucial for our understanding of the paleobiogeography and evolution of these middle-sized lizards. Although this clade has a broad geographical distribution across the continent today, its presence in the fossil record has only rarely been reported. In contrast to that, the material described here is abundant, consists of a premaxilla, maxillae, frontals, parietals, jugals, quadrate, pterygoids, dentaries and vertebrae. The comparison of these elements to all extant green lizard species shows that these fossils are indistinguishable fromLacerta trilineata. Thus, they form the first potential evidence of the occurrence of this species in the Miocene. This may be also used as a potential calibration point for further studies. Together with other lizard fossils, Solnechnodolsk shows an interesting combination of survivors and the dawn of modern species. This locality provides important evidence for the transition of an archaic Miocene world to the modern diversity of lizards in Europe. In addition, this article represents a contribution to the knowledge of the comparative osteological anatomy of the selected cranial elements in lacertid. This study gives special emphasis to the green lizards, but new data are also presented for related taxa, e.g.,Timon lepidus, Podarcis muralisorZootoca vivipara. Although the green lizards include several cryptic species for which determination based on isolated osteological material would be expected to be difficult, our comparisons show several important morphological differences.
DefiningEscherichia colias a health-promoting microbe against intestinalPseudomonas aeruginosa
Authors: Christofi Theodoulakis , Panayidou Stavria , Dieronitou Irini , Michael Christina , Apidianakis Yiorgos 
Published: April 2019

AbstractGut microbiota acts as a barrier against intestinal pathogens, but species-specific protection of the host from infection remains relatively unexplored. Taking a Koch’s postulates approach in reverse to define health-promoting microbes we find thatEscherichia colinaturally colonizes the gut of healthy mice, but it is depleted from the gut of antibiotic-treated mice, which become susceptible to intestinal colonization byPseudomonas aeruginosaand concomitant mortality. Reintroduction of fecal bacteria andE. coliestablishes a high titer ofE. coliin the host intestine and increases defence againstP. aeruginosacolonization and mortality. Moreover, diet is relevant in this process because high sugars or dietary fat favoursE. colifermentation to lactic acid andP. aeruginosagrowth inhibition. To the contrary, low sugars allowP. aeruginosato produce the oxidative agent pyocyanin that inhibitsE. coligrowth. Our results provide an explanation as to whyP. aeruginosadoesn’t commonly infect the human gut, despite being a formidable microbe in lung and wound infections.Author SummaryHere we interrogate the conundrum as to whyPseudomonas aeruginosais not a clinical problem in the intestine as opposed to other tissues.P. aeruginosainteracts with Neisseria, Streptococcus, Staphylococcus and Actinomyces species found in the human lung. These are predominantly gram-positive bacteria that induceP. aeruginosavirulence. Moreover, peptidoglycan, which is abundant in gram-positive bacteria, can directly trigger the virulence ofP. aeriginosa. We reasoned thatP. aeruginosamight be benign in the human gut due to the inhibitory action of benign gram-negative intestinal bacteria, such asEscherichia coli. Therefore, we dissected the antagonism betweenE. coliandP. aeruginosaand the effect of a conventional, a fat-, a carbohydrate-and a protein-based diet in intestinal dysbiosis. Our findings support the notion that an unbalanced diet or antibiotics induces gut dysbiosis by the elimination of commensalE. coli, in addition to lactic acid bacteria, imposing a gut environment conducive toP. aeruginosainfection. Moreover, commensalE. coliprovides an explanation as to whyP. aeruginosadoesn’t commonly infect the human gut, despite being a formidable microbe in lung and wound infections.