bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques
Authors: Theis Kevin R. , Romero Roberto , Winters Andrew D. , Jobe Alan H. , Gomez-Lopez Nardhy 
Published: March 2020

ABSTRACTThe prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony ofCutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of thein uterocolonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.
Model-based ordination of pin-point cover data: effect of management on dry heathland
Authors: Damgaard Christian , Hansen Rikke Reisner , Hui Francis K. C. 
Published: March 2020

AbstractRecently, there has been an increasing interest in model-based approaches for the statistical modelling of the joint distribution of multi-species abundances. The Dirichlet-multinomial distribution has been proposed as a suitable candidate distribution for the joint species distribution of pin-point plant cover data and is here applied in a model-based ordination framework. Unlike most model-based ordination methods, both fixed and random effects are in our proposed model structured asp-dimensional vectors and added to the latent variables before the inner product with the species-specific coefficients. This changes the interpretation of the parameters, so that the fixed and random effects now measure the relative displacement of the vegetation by the fixed and random factors in thep-dimensional latent variable space. This parameterization allows statistical inference of the effect of fixed and random factors in vector space, and makes it easier for practitioners to perform inferences on species composition in a multivariate setting. The method was applied on plant pin-point cover data from dry heathlands that had received different management treatments (burned, grazed, harvested, unmanaged), and it was found that treatment have a significant effect on heathland vegetation both when considering plant functional groups or when the taxonomic resolution was at the species level.
Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods
Authors: Nasheri Neda , Harlow Jennifer , Chen Angela , Dussault Forest , Corneau Nathalie , Bidawid Sabah 
Published: March 2020

AbstractEnteric viruses, such as human norovirus (NoV) and hepatitis A virus (HAV), are the major causes of foodborne illnesses worldwide. These viruses are shed in high numbers, have low infectious dose, and may remain infectious for weeks in the environment and food. While numerous viral survival studies have been conducted in fresh fruits and produce, limited information is available regarding viral survival and transmission in low moisture foods (LMF). LMFs are generally considered as ready-to-eat products, which undergo no or minimal pathogen reduction steps. However, numerous foodborne outbreaks associated with LMFs have been reported in recent years. The objective of this study was to examine the survival of foodborne viruses in LMFs during long-term storage at ambient temperature and to evaluate the efficacy of advanced oxidative process (AOP) treatment in the inactivation of these viruses. For this purpose, select LMFs such as pistachios, chocolate, and cereal were inoculated with HAV and the norovirus surrogates, murine norovirus (MNV) and feline calicivirus (FCV), then viral survival on these food matrices was measured over a four-week incubation at ambient temperature, by both plaque assay and droplet-digital RT-PCR (ddRT-PCR). We observed an approximately 0.5 log reduction in viral genome copies, and 1 log reduction in viral infectivity for all three tested viruses following storage of select inoculated LMFs for 4 weeks. Therefore, the present study shows that foodborne viruses can persist for long-time in LMFs. Next, we examined the inactivation efficacy of AOP treatment, which combines UV-C, ozone, and hydrogen peroxide vapor, and observed that while approximately 100% inactivation can be achieved for FCV, MNV, and HAV in chocolate, the inactivation efficiency diminishes to approximately 90% in pistachios and 70% in cereal. AOP treatment could therefore be a good candidate for the elimination of foodborne viruses from certain LMFs depending on the food matrix and surface of treatment.ImportanceLow moisture foods have been increasingly recognized as important vehicles of foodborne pathogens. In the present study, we demonstrated that foodborne viruses remain infectious during long-term storage on select low moisture foods. In addition, we evaluated the efficacy of an advanced oxidative process in the inactivation of foodborne viruses in low moisture foods. This research will help increase the safety of low moisture foods and reduce the number of foodborne illnesses due to contaminated products.
A bivariate zero-inflated negative binomial model and its applications to biomedical settings
Authors: Cho Hunyong , Liu Chuwen , Preisser John S. , Wu Di 
Published: March 2020

SummaryThe zero-inflated negative binomial (ZINB) distribution has been widely used for count data analyses in various biomedical settings due to its capacity of modeling excess zeros and overdispersion. When there are correlated count variables, a bivariate model is essential for understanding their full distributional features. For this purpose, we develop a Bivariate Zero-Inflated Negative Binomial (BZINB) model that has a simple latent variable framework and parameters with intuitive interpretations. Using this model, we examine two biomedical data examples where the counts are zero-inflated—single cell RNA sequencing (scRNA-seq) data and dental caries count indices. In scRNA-seq data example, a correlation between a pair of genes is estimated after adjusting for the effects of dropout events represented by excess zeros. In the dental caries data, we analyze how the treatment with Xylitol mints affects the marginal mean and other patterns of response manifested in the two dental caries traits. AnRpackage ‘bzinb’ is available on CRAN.
Circ_0005962 functions as an oncogene to aggravate non-small cell lung cancer progression via circ_0005962/miR-382-5p/PDK4 regulatory network
Authors: Zhang Zhihong , Shan Zhenxiu , Chen Rubin , Peng Xiaorong , Xu Bin , Xiao Liang , Zhang Guofei 
Published: March 2020

AbstractNon-small cell lung cancer (NSCLC) is a leading threat to human lives with high incidence and mortality. Circular RNAs (circRNAs) were reported to play important roles in human cancers. The purpose of this study was to investigate the role of circ_0005962 and explore the underlying functional mechanisms. The expression of circ_0005962, miR-382-5p and pyruvate dehydrogenase kinase 4 (PDK4) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation and cell apoptosis were assessed by cell counting kit-8 (CCK-8) assay and flow cytometry assay, respectively. The protein levels of Beclin 1, light chain3 (LC3-II/LC3-I), PDK4, Cleaved Caspase 3 (C-caspase 3) and proliferating cell nuclear antigen (PCNA) were examined using western blot analysis. Glycolysis was determined according to the levels of glucose consumption and lactate production. The interaction between miR-382-5p and circ_0005962 or PDK4 was predicted by the online tool CircInteractome or starbase and verified by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Xenograft model was constructed to investigate the role of circ_0005962in vivo. circ_0005962 expressed with a high level in NSCLC tissues and cells. Circ_0005962 knockdown inhibited proliferation, autophagy, and glycolysis but promoted apoptosis in NSCLC cells. MiR-382-5p was targeted by circ_0005962, and its inhibition reversed the role of circ_0005962 knockdown. Besides, PDK4, a target of miR-382-5p, was regulated by circ_0005962 through miR-382-5p, and its overexpression abolished the effects of miR-382-5p reintroduction. Circ_0005962 knockdown suppressed tumor growthin vivo. Circ_0005962 knockdown restrained cell proliferation, autophagy, and glycolysis but stimulated apoptosis through modulating the circ_0005962/miR-382-5p/PDK4 axis. Our study broadened the insights into understanding the mechanism of NSCLC progression.
Identification and characterization of long noncoding RNAs and their association with acquisition of blood meal inCulex quinquefasciatus
Authors: Azlan Azali , Halim Mardani Abdul , Mohamad Faisal , Azzam Ghows 
Published: March 2020

AbstractThe Southern house mosquito,Culex quinquefasciatus(Cx. quinquefasciatus) is an important vector that transmit multiple diseases including West Nile encephalitis, Japanese encephalitis, St. Louis encephalitis and lymphatic filariasis. Long noncoding RNAs (lncRNAs) involve in many biological processes such development, infection, and virus-host interaction. However, there is no systematic identification and characterization of lncRNAs inCx. quinquefasciatus. Here, we report the first ever lncRNA identification inCx. quinquefasciatus. By using 31 public RNA-seq datasets, a total of 4,763 novel lncRNA transcripts were identified, of which 3,591, 569, and 603 were intergenic, intronic, and antisense respectively. Examination of genomic features revealed thatCx. quinquefasciatusshared similar characteristics with other species such as short in length, low GC content, low sequence conservation, and low coding potential. Furthermore, compared to protein-coding genes,Cx. quinquefasciatuslncRNAs had lower expression values, and tended to be expressed in temporally-specific fashion. In addition, weighted correlation network and functional annotation analyses showed that lncRNAs may have roles in blood meal acquisition of adult femaleCx. quinquefasciatusmosquitoes. This study presents the first systematic identification and analysis ofCx. quinquefasciatuslncRNAs and their association with blood feeding. Results generated from this study will facilitate future investigation on the function ofCx. quinquefasciatuslncRNAs.
A bHLH transcription factor (VfTT8) underlieszt2, the locus determining zero tannin content in faba bean (Vicia faba L.)
Authors: Gutierrez Natalia , Avila Carmen M. , Torres Ana M. 
Published: March 2020

AbstractFaba bean (Vicia fabaL.) is an important protein-rich fodder crop widely cultivated in temperate areas. However, antinutritional compounds such as condensed tannins, limit the use of this protein source in monogastric feed formulations. Previous studies demonstrated that two recessive and complementary genes,zt1andzt2, control the absence of tannin and the white flower colour in faba bean. An ortholog of theMedicagoWD40 transcription factor, (TTG1) was reported to encode the zt1 phenotypes but the responsible gene for zt2 is still unknown. A candidate gene approach combined with linkage mapping, comparative genomics and gene expression has been used in this study to fine map thezt2genomic region and to identify the regulatory gene controlling both traits. Seventy-two genes, including 23 regulatory genes (MYB and bHLH) predicted to be associated with anthocyanin expression together with WRKY proteins were screened and genotyped in three mapping populations. The linkage groups constructed identified the regulatory gene,TRANSPARENT TESTA8(TT8), encoding a basic helix-loop-helix transcription factor (bHLH), as the best candidate forzt2. This finding was supported by qPCR analyses and further validated in different genetic backgrounds. Accordingly, VfTT8 was down-regulated in white flowered types, in contrast to the levels of expression in wild genotypes. Our results provide new insights on the regulatory mechanisms for tannin biosynthesis in faba bean and will favour the development of an ultimate zt2 diagnostic marker for the fast generation of new value-added cultivars free of tannins and improved nutritional value.
Reactive oxygen species as important regulators of cell division
Authors: Qi Weiliang , Ma Li , Wang Fei , Wang Ping , Wu Junyan , Jin Jiaojiao , Liu Songqing , Sun Wancang 
Published: March 2020

AbstractCurrently, the role of reactive oxygen species (ROS) in plant growth is a topic of interest. In this study, we discuss the role of ROS in cell division. We analyzed ROS’ impact on the stiffness of plant cell walls and whether ROS play an important role inBrassica napus’ ability to adapt to cold stress. Cultivated sterile seedlings and calli of cold-tolerant cultivar 16NTS309 were subjected to cold stress at 25°C and 4°C, respectively. Under normal conditions, O2.−mainly accumulated in the leaf edges, shoot apical meristem, leaf primordia, root tips, lateral root primordia, calli of meristematic nodular tissues, cambia, vascular bundles and root primordia, which are characterized by high division rates. After exposure to cold stress, the malondialdehyde and ROS (O2.−) contents in roots, stems and leaves of cultivar 16NTS309 were significantly higher than under non-cold conditions (P< 0.05). ROS (O2.−) were not only distributed in these zones, but also in other cells, at higher levels than under normal conditions. A strong ROS-based staining appeared in the cell wall. The results support a dual role for apoplastic ROS, in which they have direct effects on the stiffness of the cell wall, because ROS cleave cell-wall, and act as wall loosening agents, thereby either promoting or restricting cellular division. This promotes the appearance of new shoots and a strong root system, allowing plants to adapt to cold stress.
Are dogs with congenital hearing and/or vision impairments so different from sensory normal dogs? A survey of demographics, morphology, health, behaviour, communication, and activities
Authors: Savel Sophie , Sombé Patty 
Published: March 2020

AbstractThe births of domestic dogs with pigment deletion and associated congenital hearing and/or vision impairments are increasing, as a result of mutations of certain genes expressing popular coat colour patterns (Merle, piebald, Irish spotting). The future of these dogs is often pessimistic (early euthanasia or placement in rescues/fosters, lack of interactions and activities for adults). These pessimistic scenarios result from popular assumptions predicting that dogs with congenital hearing/vision impairments exhibit severe Merle-related health troubles (cardiac, skeletal, neurological), impairment-related behavioural troubles (aggressiveness, anxiety), and poor capacities to communicate, to be trained, and to be engaged in leisure or work activities. However, there is no direct scientific testing, and hence no evidence or refutation, of these assumptions. We therefore addressed an online questionnaire to owners of 223 congenitally sensory impaired (23 vision impaired, 63 hearing impaired, 137 hearing and vision impaired) and 217 sensory normal dogs from various countries. The sensory normal cohort was matched in age, lifetime with owner, breed and sex with the sensory impaired cohort, and was used as a baseline. The questionnaire assessed demographics, morphology, sensory impairments, health and behavioural troubles, activities, and dog-owner communication. Most hearing and vision impaired dogs exhibited abnormal pigment deletion in their coat and irises. Vision impaired dogs additionally exhibited ophthalmic abnormalities related to Merle. The results refute all above-listed assumptions, except for neurological troubles. We however suggest that reports of neurological troubles could be partially accounted for by lacks of diagnosis of breed-related drug sensitivity and impairment-related compulsive behaviours. Results about communication and activities are particularly optimistic. The need for future studies of numerous dogs from various breeds tested for Merle, piebald and medical-drug-resistance genes, and the beneficial effects that present and future research may have on the future of sensory impaired dogs, are discussed.
Specialised functions of two common plasmid mediated toxin-antitoxin systems,ccdABandpemIK, inEnterobacteriaceae
Authors: Wu Alma Y. , Kamruzzaman Muhammad , Iredell Jonathan R. 
Published: March 2020

AbstractToxin-antitoxin systems (TAS) are commonly found on bacterial plasmids and are involved in plasmid maintenance. Even though the same TAS are present in a variety of plasmid types and bacterial species, differences in their sequences, expression and functions are not well defined. Here, we aimed to identify commonly occurring plasmid TAS inEscherichia coliandKlebsiella pneumoniaeand compare the sequence, expression and plasmid stability function of their variants. 27 putative type II TAS were identified from 1063 plasmids ofKlebsiella pneumoniaein GenBank. Among these,ccdABandpemIKwere found to be most common, also occurring in plasmids ofE. coli. Comparisons ofccdABvariants, taken fromE. coliandK. pneumoniae, revealed sequence differences, whilepemIKvariants from IncF and IncL/M plasmids were almost identical. Similarly, the expression and plasmid stability functions ofccdABvariants varied according to the host strain and species, whereas the expression and functions ofpemIKvariants were consistent among host strains. The specialised functions of some TAS may determine the host specificity and epidemiology of major antibiotic resistance plasmids.
The Role of Potassium and Host Calcium Signaling inToxoplasma gondiiegress
Authors: Vella Stephen A. , Moore Christina A. , Li Zhu-Hong , Hortua Triana Miryam A. , Potapenko Evgeniy , Moreno Silvia N J 
Published: March 2020

AbstractToxoplasma gondii, an obligate intracellular parasite, is capable of invading virtually any nucleated cell. Ca2+signaling is universal and bothT. gondiiand its mammalian host cell will utilize Ca2+signaling to stimulate diverse cellular functions. Egress ofT. gondiifrom the host cell is an essential step for the infection cycle ofT. gondiiand a cytosolic Ca2+increase initiates the Ca2+signaling cascade that culminates in stimulation of motility and egress. In this work we demonstrate that intracellularT. gondiiis capable of taking up Ca2+from the host cytoplasm when this concentration is increased during host signaling events. Both intracellular and extracellular Ca2+sources are important to reach a threshold of cytosolic Ca2+needed for a successful egress. Two peaks of Ca2+were observed in single parasites that egressed with the second peak resulting from Ca2+influx. We patched infected host cells to allow a precise delivery of exact concentrations of Ca2+for stimulating motility and egress. Using this approach, we found that low potassium concentration modulates but do not trigger host cell egress. This is the first study using whole-cell patches to study the role of ions such as K+and Ca2+inT. gondiiegress.
Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize
Authors: Aguirre-Liguori Jonás A. , Luna-Sánchez Javier A. , Gasca-Pineda Jaime , Eguiarte Luis E. 
Published: March 2020

ABSTRACTMassive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS,FIS,FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics.FISwas particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.