bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic Changes in Fecal Bacterial Microbiota of Dairy Cattle across the Production Line
Authors: Zhao Lei , Li Xunde , Atwill Edward R. , Aly Sharif , Williams Deniece R. , Rossitto Paul , Su Zhengchang 
Published: February 2020

ABSTRACTBacteria play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy are still lacking. In this study, we used 16S rRNA sequencing to evaluate the fecal bacterial communities of 90 dairy cattle raised and housed in 12 clearly defined management units on a modern dairy farm. We found that α-diversity differed between several pairs of management units, especially between the hutch calves (management unit 1) and the other units except post weaned heifers (management unit 2). Although β-diversity revealed that most of the samples did not cluster according to their management unit membership except management unit 1, in which the samples grouped and separated from others, we observed three major clusters. Besides the hutch calves (management unit 1), most samples from the other 11 units formed two distinct clusters and the relative abundance of Patescibacteria might be the reason for the separation. Moreover, we identified 212 amplicon sequence variants (ASVs) with relative abundances > 0.1% in more than 10% of the total samples that had significantly different abundances in these units. Furthermore, we found that, as the calves aged, 19 ASVs that were exclusively detected in unit 1, gradually degraded and never reoccurred in other management units. Lastly, we recognized 181 pairs of interactions between 61 ASVs with possibly strong synergistic or antagonistic relationships. These results suggest the enteric microbial communities of dairy cattle housed in different management units are quite dynamic.IMPORTANCEBacterial communities of GIT are crucial for ruminants, such as dairy cattle since they contribute to not only the cattle’s physiology and health but also milk production and food safety that are closely related to human health. Both scientifically and agriculturally, it is necessary to have deep insights into the composition and changes of the bacteria on modern dairy farms. In this study, we provided the profiles of fecal bacterial communities of dairy cattle in each management unit on a modern dairy and described how the enteric microbial communities changed across these management units. The findings have implications for improving animal health, dairy production, farm management, and food safety.
Adult mouse retina explants: an ex vivo window to explore central nervous system diseases
Authors: Schaeffer Julia , Tardy Celine , Albert Floriane , Belin Stephane , Nawabi Homaira 
Published: February 2020

ABSTRACTWhen the developing central nervous system (CNS) becomes mature, it loses its ability to regenerate. Therefore, any insult to adult CNS leads to a permanent and irreversible loss of motor and cognitive functions. For a long time, much effort has been deployed to uncover mechanisms of axon regeneration in the CNS. It is now well understood that neurons themselves lose axon regeneration capabilities during development, and also after a lesion or in pathological conditions. Since then, many molecular pathways such as mTOR and JAK/STAT have been associated with axon regeneration. However, no functional recovery has been achieved yet. Today, there is a need not only to identify new molecules implicated in adult CNS axon regeneration, but also to decipher the fine molecular mechanisms associated with regeneration failure. This is critical to make progress in our understanding of neuroprotection and neuroregeneration and for the development of new therapeutic strategies. In this context, it remains particularly challenging to address molecular mechanisms in in vivo models of CNS regeneration. The extensive use of embryonic neurons as in vitro model is a source of bias, as they have the intrinsic competence to grow their axon upon injury, unlike mature neurons. In addition, this type of dissociated neuronal cultures lack a tissue environment to recapitulate properly molecular and cellular events in vitro. Here, we propose to use cultures of adult retina explants to fill this gap. The visual system - which includes the retina and optic nerve - is a gold-standard model to study axon regeneration and degeneration in the mature CNS. Cultures of adult retina explants combine two advantages: they have the simplicity of embryonic neurons cultures and they recapitulate all the aspects of in vivo features in the tissue. Importantly, it is the most appropriate tool to date to isolate molecular and cellular events of axon regeneration and degeneration of the adult CNS in a dish. This ex vivo system allows to set up a large range of experiments to decipher the fine molecular and cellular regulations underlying mature CNS axon growth.
A Pumpless Microfluidic Neonatal Lung Assist Device for Support of Preterm Neonates in Respiratory Distress
Authors: Dabaghi Mohammadhossein , Rochow Niels , Saraei Neda , Fusch Gerhard , Monkman Shelley , Da Kevin , Shahin-Shamsabadi Alireza , Brash John L. , Predescu Dragos , Delaney Kathleen , Fusch Christoph , Selvaganapathy P. Ravi 
Published: February 2020

AbstractPremature neonates suffer from respiratory morbidity as their lungs are immature and current supportive treatment such as mechanical ventilation or extracorporeal membrane oxygenation (ECMO) cause iatrogenic injuries. A non-invasive and biomimetic concept known as the “artificial placenta” would be beneficial to overcome complications associated with the current respiratory support of preterm infants. Here, a pumpless oxygenator connected to the systemic circulation supports the lung function to relieve respiratory distress. In this paper, we demonstrate the first successful operation of a microfluidic, artificial placenta type neonatal lung assist device (LAD) on a newborn piglet model which is the closest representation of preterm human infants. This LAD has high oxygenation capability in both pure oxygen and room air as the sweep gas. It was able to relieve the respiratory distress that the newborn piglet was put under during experimentation, repeatedly and over significant duration of time. These findings indicate that this LAD has potential application as a biomimetic artificial placenta to support respiratory needs of preterm neonates.
Anopheles stephensias an emerging malaria vector in the Horn of Africa with high susceptibility to EthiopianPlasmodium vivaxandPlasmodium falciparumisolates
Authors: Ashine Temesgen , Teka Hiwot , Esayas Endashaw , Messenger Louisa A. , Chali Wakweya , Meerstein-Kessel Lisette , Walker Thomas , Behaksra Sinknesh Wolde , Lanke Kjerstin , Heutink Roel , Jeffries Claire L. , Mekonnen Daniel Abebe , Hailemeskel Elifaged , Tebeje Surafel K , Tafesse Temesgen , Gashaw Abrham , Tsegaye Tizita , Emiru Tadele , Simon Kigozi , Bogale Eyuel Asemahegn , Yohannes Gedeon , Kedir Soriya , Shumie Girma , Sabir Senya Asfer , Mumba Peter , Dengela Dereje , Kolaczinski Jan H , Wilson Anne , Churcher Thomas S , Chibsa Sheleme , Murphy Matthew , Balkew Meshesha , Irish Seth , Drakeley Chris , Gadisa Endalamaw , Bousema Teun , Tadesse Fitsum G 
Published: February 2020

AbstractAnopheles stephensi, an efficient Asian malaria vector, recently spread into the Horn of Africa and may increase malaria receptivity in African urban areas. We assessed occurrence, genetic complexity, blood meal source and infection status ofAn. stephensiin Awash Sebat Kilo town, Ethiopia. We used membrane feeding assays to assess competence of localAn. stephensitoP. vivaxandP. falciparumisolates from clinical patients. 75.3% of the examined waterbodies were infested withAn. stephensidevelopmental stages that were genetically closely related to isolates from Djibouti and Pakistan. BothP. vivaxandP. falciparumwere detected in wild-caught adultAn. stephensi. LocalAn. stephensiwas more receptive toP. vivaxcompared to a colony ofAn. arabiensis. We conclude thatAn. stephensiis an established vector in this part of Ethiopia, highly permissive for localP. vivaxandP. falciparumisolates and presents an important new challenge for malaria control.Summary of the articleAn. stephensi, a metropolitan malaria vector that recently expanded to the Horn of African, was highly susceptible to localP. falciparumandP. vivaxisolates from Ethiopia and may increase malariogenic potential of rapidly expanding urban settings in Africa.
Untargeted Metabolomics Shows Alterations in Homocysteine, Lipids and Fatty Acids predicting Memory Decline in Healthy Middle-Aged Individuals
Authors: Hajjar Ihab , Cai Qingpo , Yu Tianwei , Jones Dean P. 
Published: February 2020

AbstractINTRODUCTIONSome aspects of memory start declining in the fifth decade which may be related to systemic metabolic changes. These changes have not been fully identified. This is the first Metabolome-Wide Association Study of the human plasma for the longitudinal change in memory in healthy adults.METHODSUltra-high resolution mass spectrometry with liquid chromatography was performed on 207 University employees’ plasma.RESULTSFrom 10,201 measured metabolic features, 558 differed between those experiencing change vs no change in memory (False Discovery Rate, FDR< 0.2). Differentially abundant metabolites were observed in lipid and fatty acid metabolism pathways: glycerophospholipid (p=0.0003), fatty acid (p=0.0003) and linoleate (p=0.0003) pathways. Within these pathways, higher homocysteine (OR for memory decline=1.09, FDR=0.19) and lower arachidonic acid (OR=0.97, FDR=0.19), sterol (OR=0.92, FDR=0.02), acetylcholine (OR=0.78, FDR=0.19), carnitine (OR=0.75, FDR=0.19) and linoleic acid (OR=0.74, FDR=0.19) were associated memory decline.DISCUSSIONAltered systemic lipid and fatty acid are linked with early memory decline in middle-aged individuals.
Post-copulatory behavior of olive baboons (Papio anubis) infected byTreponema pallidum
Authors: Paciência Filipa M. D. , Chuma Idrissa S. , Lipende Iddi F. , Knauf Sascha , Zinner Dietmar 
Published: February 2020

AbstractIn nonhuman primates pathogens are known to exert a profound and pervasive cost on various aspects of their sociality and reproduction. In olive baboons (Papio anubis) at Lake Manyara National Park, genital skin ulcers caused byTreponema pallidumsubsp.pertenuelead to mating avoidance in females and altered mating patterns at a pre-copulatory and copulatory level. Beyond this level, sexual behavior comprises also post-copulatory interactions among the sexual partners. To investigate whether the presence of genital skin ulcers has an impact at the post-copulatory level, we analyzed 517 copulation events of 32 cycling females and 29 males. The occurrence of post-copulatory behaviors (i.e., copulation calls, darting [female rapid withdraw from the male] and post-copulatory grooming) was not altered by the presence of genital skin ulcerations. Similarly to other baboon populations, females of our group were more likely to utter copulation calls after ejaculatory copulation. The likelihood of darting was higher after ejaculatory copulations and with the presence of copulation calls. Post-copulatory grooming was rarely observed but when it occurred, males groomed females for longer periods when females uttered copulation calls during, or preceding mating. Our results indicate that despite the presence of conspicuous genital skin ulcers, the post-copulatory behavior was not affected by the genital health status of the dyad. This suggests that infection cues play a major role before and during mating but do not affect post-copulatory behavior.
Staphylococcal DNA repair is required for infection
Authors: Ha Kam Pou , Clarke Rebecca S. , Kim Gyu-Lee , Brittan Jane L. , Rowley Jessica E. , Mavridou Despoina A. I. , Parker Dane , Clarke Thomas B. , Nobbs Angela H. , Edwards Andrew M. 
Published: February 2020

AbstractThe repair of DNA damage is essential for bacterial viability and contributes to adaptation via increased rates of mutation and recombination. However, the mechanisms by which DNA is damaged and repaired during infection are poorly understood. Using a panel of transposon mutants, we identified therexBAoperon as important for the survival ofStaphylococcus aureusin whole human blood. Mutants lackingrexBwere also attenuated for virulence in murine models of both systemic and skin infections. We then demonstrated that RexAB is a member of the AddAB family of helicase/nuclease complexes responsible for initiating the repair of DNA double strand breaks. Using a fluorescent reporter system, we were able to show that neutrophils cause staphylococcal DNA double strand breaks via the oxidative burst, which are repaired by RexAB, leading to induction of the mutagenic SOS response. We found that RexAB homologues inEnterococcus faecalisandStreptococcus gordoniialso promoted survival of these pathogens in human blood, suggesting that DNA double strand break repair is required for Gram-positive bacteria to survive in host tissues. Together, these data demonstrate that DNA is a target of host immune cells, leading to double-strand breaks, and that repair of this damage by an AddAB-family enzyme enables the survival of Gram-positive pathogens during infection.
The strength and form of natural selection on transcript abundance in the wild
Authors: Ahmad Freed , Debes Paul V. , Nousiainen Ilkka , Kahar Siim , Pukk Lilian , Gross Riho , Ozerov Mikhail , Vasemägi Anti 
Published: February 2020

AbstractGene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. We estimated selection on transcript abundance in cohort of a wild salmonid fish (Salmo trutta) affected by a myxozoan parasite through mark-recapture field sampling and the integration of RNA-seq with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) and subsequent host survival is linked to the upregulation of mitotic cell cycle genes. We also detect a widespread signal of disruptive selection; intermediate transcription levels were frequently associated with reduced host survival. Our results provide insights how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary natural selection driven by climate change and emerging anthropogenic threats.
Plastid gene expression is required for singlet oxygen-induced chloroplast degradation and cell death
Authors: Alamdari Kamran , Fisher Karen E. , Sinson Andrew B. , Chory Joanne , Woodson Jesse D. 
Published: February 2020

SummaryChloroplasts constantly experience photo-oxidative stress while performing photosynthesis. This is particularly true under abiotic stresses that lead to the accumulation of reactive oxygen species (ROS). While ROS leads to the oxidation of DNA, proteins, and lipids, it can also act as a signal to induce acclimation through chloroplast degradation, cell death, and nuclear gene expression. Although the mechanisms behind ROS signaling from chloroplasts remain mostly unknown, several genetic systems have been devised in the model plantArabidopsisto understand their signaling properties. One system uses theplastid ferrochelatase two(fc2) mutant that conditionally accumulates the ROS singlet oxygen (1O2) leading to chloroplast degradation and eventually cell death. Here we have mapped three mutations that suppress chloroplast degradation in thefc2mutant and demonstrate that they affect two independent loci (PPR30andmTERF9) encoding chloroplast proteins predicted to be involved in post-transcriptional gene expression. Mutations in either gene were shown to lead to broadly reduced chloroplast gene expression, impaired chloroplast development, and reduced chloroplast stress signaling. In these mutants, however,1O2levels were uncoupled to chloroplast degradation suggesting that PPR30 and mTERF9 are involved in ROS signaling pathways. In the wild type background,ppr30andmTERF9mutants were also observed to be less susceptible to cell death induced by excess light stress. Together these results suggest that plastid gene expression (or the expression of specific plastid genes) is a necessary prerequisite for chloroplasts to activate1O2signaling pathways to induce chloroplast degradation and/or cell death.Significance summaryReactive oxygen species accumulate in the chloroplast (photosynthetic plastids) and signal for stress acclimation by inducing chloroplast degradation, cell death, and changes in nuclear gene expression. We have identified two chloroplast-localized proteins involved in gene regulation that are required to transmit these signals, suggesting that proper plastid gene expression and chloroplast development is necessary to activate chloroplast controlled cellular degradation and nuclear gene expression pathways.
HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
Authors: Dimmick Michael C. , Lee Leo J. , Frey Brendan J. 
Published: February 2020

AbstractMotivationHi-C data has enabled the genome-wide study of chromatin folding and architecture, and has led to important discoveries in the structure and function of chromatin conformation. Here, high resolution data plays a particularly important role as many chromatin substructures such as Topologically Associating Domains (TADs) and chromatin loops cannot be adequately studied with low resolution contact maps. However, the high sequencing costs associated with the generation of high resolution Hi-C data has become an experimental barrier. Data driven machine learning models, which allow low resolution Hi-C data to be computationally enhanced, offer a promising avenue to address this challenge.ResultsBy carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. This was achieved using a novel loss function tailored to the Hi-C enhancement problem which optimizes for an adversarial loss from a Generative Adversarial Network (GAN), a feature reconstruction loss derived from the latent representation of a denoising autoencoder, and a pixel-wise loss. Not only can the resulting framework generate enhanced Hi-C maps more visually similar to the original high resolution maps, it also excels on a suite of reproducibility metrics produced by members of the ENCODE Consortium compared to existing approaches, including HiCPlus, HiCNN, hicGAN and DeepHiC. Finally, we demonstrate that HiCSR is capable of enhancing Hi-C data across sequencing depth, cell types, and species, recovering biologically significant contact domain boundaries.AvailabilityWe make our implementation available for download at:https://github.com/PSI-Lab/HiCSRContactljlee@psi.toronto.eduSupplementary informationAvailable Online
Tumour gene expression signature in primary melanoma predicts long-term outcomes: A prospective multicentre study
Authors: Garg Manik , Couturier Dominique-Laurent , Nsengimana Jérémie , Fonseca Nuno A. , Wongchenko Matthew , Yan Yibing , Lauss Martin , Jönsson Göran B , Newton-Bishop Julia , Parkinson Christine , Middleton Mark R. , Bishop Tim , Corrie Pippa , Adams David J. , Brazma Alvis , Rabbie Roy 
Published: February 2020

AbstractPurposePredicting outcomes after resection of primary melanoma remains crude, primarily based on tumour thickness. We explored gene expression signatures for their ability to better predict outcomes.MethodsDifferential expression analysis of 194 primary melanomas resected from patients who either developed distant metastasis (n=89) or did not (n=105) was performed. We identified 121 metastasis-associated genes that were included in our prognostic signature, “Cam_121”. Several machine learning classification models were trained using nested leave- one-out cross validation (LOOCV) to test the signature’s capacity to predict metastases, as well as regression models to predict survival. The prognostic accuracy was externally validated in two independent datasets.ResultsCam_121 performed significantly better in predicting distant metastases than any of the models trained with the clinical covariates alone (pAccuracy=4.92×10−3), as well as those trained with two published prognostic signatures. Cam_121 expression score was strongly associated with progression-free survival (HR=1.7, p=3.44×10−6), overall survival (HR=1.73, p=7.71×10−6) and melanoma-specific survival (HR=1.59, p=0.02). Cam_121 expression score also negatively correlated with measures of immune cell infiltration (ρ=−0.73, p<2.2×10−16), with a higher score representing reduced tumour lymphocytic infiltration and a higher absolute 5-year risk of death in stage II melanoma.ConclusionsThe Cam_121 primary melanoma gene expression signature outperformed currently available alternatives in predicting the risk of distant recurrence. The signature confirmed (using unbiased approaches) the central prognostic importance of immune cell infiltration in long-term patient outcomes and could be used to identify stage II melanoma patients at highest risk of metastases and poor survival who might benefit most from adjuvant therapies.Translational relevancePredicting outcomes after resection of primary melanoma is currently based on traditional histopathological staging, however survival outcomes within these disease stages varies markedly. Since adjuvant systemic therapies are now being used routinely, accurate prognostic information is needed to better risk stratify patients and avoid unnecessary use of high cost, potentially harmful drugs, as well as to inform future adjuvant strategies. The Cam_121 gene expression signature appears to have this capability and warrants evaluation in prospective clinical trials.