bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced risk of new onset stroke after kidney transplantation in Asian dialysis patients: a propensity score-matched, competing risk study in Taiwan
Authors: Weng S -F , Shen Y -C , Wang J -J , Tien K -J 
Published: February 2019

Abstract

Background
Kidney transplantation (KT) has been found to reduce cardiovascular events and mortality in chronic dialysis patients. There is little data, however, regarding the risk reduction of cerebrovascular events after KT in Asian populations. This study evaluates the risk of cerebrovascular events after KT in Taiwan.

Methods
Tapping Taiwan’s National Health Insurance claims data of patients with a diagnosis of end-stage renal disease (ESRD), we enrolled all KT recipients from 1999 to 2011 (n = 2908). For each KT patient, four controls (patients also diagnosed with ESRD) without KT were propensity matched by birth date, sex, selected comorbidities and duration of dialysis. All subjects were followed to the end of 2011.

Results
The incidence rate for stroke in the KT recipients and comparison group were 52.63 and 137.26 per 10 000 person-years, respectively. After adjustment for age, gender and comorbidities with competing mortality, KT recipients had 60% reduction in all kinds of stroke, compared to those who did not receive procedure. They were found to have a 48 and 74% reduction in ischemic and hemorrhagic stroke risk, respectively. Subgroup analyses also showed similar trends in the improvement of stroke after KT. While elderly patients, men, and those with diabetes, hypertension and coronary artery disease are at increased risk for stroke, our log-rank test revealed those that received KT had significantly lower cumulative incidence rates of stroke than those that did not (P < 0.001).

Conclusions
KT was associated with reduced risk of new onset stroke in chronic dialysis patients in Taiwan.
New approaches to political economy
Authors: Amable Bruno , Regan Aidan , Avdagic Sabina , Baccaro Lucio , Pontusson Jonas , Van der Zwan Natascha 
Published: February 2019

Abstract
The discussion on ‘New Approaches to Political Economy (PE)’ gives us a state-of-the-art overview of the main theoretical and conceptual developments within the concept of political economy. Thereby, it invites us to broaden our knowledge regarding manifold novel approaches, which make use of more complex methods to study the less stable, less predictable, but faster changing realities of smaller or bigger geographical regions. In this discussion forum, Amable takes a closer look on the nature of ‘conflict’ as well as the relationship between conflict and institutional change or stability. After stressing the relevance of comparative capitalism in general, Regan also zooms in on the political conflicts in comparative political economy from three different perspectives (electoral politics, organized interest groups and business-state elites), where he finds new avenues, tensions and research agendas are opening up. From a different perspective, Avdagic reviews the broad developments in the field of political economy with respect to the supply and demand side of redistributive policy. Thereafter, Baccaro and Pontusson sketch an alternative ‘growth model perspective’, which puts demand and distribution at the center of the analysis. Finally, Van der Zwan analyses the usefulness of financialization studies for the study of (comparative) political economy.
How does water flow from vessel to vessel? Further investigation of the tracheid bridge concept
Authors: Pan Ruihua , Tyree Melvin T 
Published: February 2019

AbstractHydraulic safety and efficiency have become the central concept of the interpretation of the structure and function of vessels and their interconnections. Plants form an appropriate xylem network structure to maintain a balance of hydraulic safety vs efficiency. The term ‘tracheid bridge’ is used to describe a possible pathway of water transport between neighboring vessels via tracheids, and this pathway could also provide increased safety against embolisms. However, the only physiological study of such a structure thus far has been in Hippophae rhamnoides Linn. To test the function of tracheid bridges, this research examined four species that have relatively long and solitary vessels, which are two of the criteria for efficient tracheid bridges. Tracheids contributed less than 2.2% of the total conductance of the vessels in these species, but in theory, tracheids could serve as very efficient transport connector pathways that may or may not make direct vessel-to-vessel contact via pit fields between adjacent vessels. In some species, tracheid bridges may represent the dominant pathway for water flow between vessels, whereas in other species, tracheid bridges may be sub-dominant or virtually nil. Broader searches of woody taxa are needed to reveal the functional importance of tracheid bridges in vascular plants.
From prevalence to incidence - a new approach in the hospital setting
Authors: Willrich Niklas , Haller Sebastian , Eckmanns Tim , Zacher Benedikt , Kärki Tommi , Plachouras Diamantis , Cassini Alessandro , Suetens Carl , Behnke Michael , Gastmeier Petra , Walter Jan 
Published: February 2019

AbstractPoint-prevalence surveys (PPSs) are often used to estimate the prevalence of healthcare-associated infections (HAIs). Methods for estimating incidence of HAIs from prevalence have been developed, but application of these methods is often difficult because key quantities, like the average length of infection, cannot be derived directly from the data available in a PPS. We propose a new theory-based method to estimate incidence from prevalence data dealing with these limitations and compare it to other estimation methods in a simulation study. In contrast to previous methods, our method does not depend on any assumptions on the underlying distributions of length of infection and length of stay. As a basis for the simulation study we use data from the second study of nosocomial infections in Germany (Nosokomiale Infektionen in Deutschland, Erfassung und Prävention - NIDEP2) and the European surveillance of HAIs in intensive care units (HAI-Net ICU). The new method compares favourably with the other estimation methods and has the advantage of being consistent in its behaviour across the different setups. It is implemented in an R-package prevtoinc which will be freely available on CRAN (http://cran.r-project.org/).
Highly sensitive and multiplexed in situ protein profiling with cleavable fluorescent streptavidin
Authors: Liao Renjie , Mastroeni Diego , Coleman Paul D. , Guo Jia 
Published: February 2019

AbstractThe ability to perform highly sensitive and multiplexed in situ protein analysis is crucial to advance our understanding of normal physiology and disease pathogenesis. To achieve this goal, here we develop an approach using cleavable biotin conjugated antibodies and cleavable fluorescent streptavidin (CFS). In this approach, protein targets are first recognized by the cleavable biotin labeled antibodies. Subsequently, CFS is applied to stain the protein targets. Though layer-by-layer signal amplification using cleavable biotin conjugated orthogonal antibodies and CSF, the protein detection sensitivity can be enhanced by at least 10 fold, compared with the existing methods. After imaging, the fluorophores and the biotins unbound to streptavidin are removed by chemical cleavage. The leftover streptavidin is blocked by biotin. Upon reiterative analysis cycles, a large number of different proteins with a wide range of expression levels can be unambiguously detected in individual cell in situ.
Optical flow analysis reveals that Kinesin-mediated advection impacts on the orientation of microtubules in theDrosophilaoocyte
Authors: Drechsler Maik , Lang Lukas F. , Al-Khatib Layla , Dirks Hendrik , Burger Martin , Schönlieb Carola-Bibiane , Palacios Isabel M. 
Published: February 2019

ABSTRACTThe orientation of microtubule networks is exploited by motors to deliver cargoes to specific intracellular destinations, and is thus essential for cell polarity and function. Reconstitutedin vitrosystems have largely contributed to understanding the molecular framework regulating the behavior of microtubule filaments. In cells however, microtubules are exposed to various biomechanical forces that might impact on their orientation, but little is known about it. Oocytes, which display forceful cytoplasmic streaming, are excellent model systems to study the impact of motion forces on cytoskeletonsin vivo. Here we implement variational optical flow analysis as a new approach to analyze the polarity of microtubules in theDrosophilaoocyte, a cell that displays distinct Kinesin-dependent streaming. After validating the method as robust for describing microtubule orientation from confocal movies, we find that increasing the speed of flows results in aberrant plus end growth direction. Furthermore, we find that in oocytes where Kinesin is unable to induce cytoplasmic streaming, the growth direction of microtubule plus ends is also altered. These findings lead us to propose that cytoplasmic streaming - and thus motion by advection – contributes to the correct orientation of MTsin vivo. Finally, we propose a possible mechanism for a specialised cytoplasmic actin network (the actin mesh) to act as a regulator of flow speeds; to counteract the recruitment of Kinesin to microtubules.HIGHLIGHT SUMMARYCytoskeletal networks do not exist in isolation, but experience crowded and dynamic intracellular environments. However, microtubule-environment interactions are not well understood, and such system-environment interactions are an unresolved question in biology that demands bridging across disciplines. Here we introduce an optical flow motion estimation approach to study microtubule orientation in theDrosophilaoocyte, a cell displaying substantial cytoplasmic streaming. We show that microtubule polarity is affected by the regime of these flows, and furthermore, that the presence of flows is necessary for MTs to adopt their proper polarity. With these findings we are contributing to further understanding how microtubules organize in their impacting natural environment.
Unbiased estimation of linkage disequilibrium from unphased data
Authors: Ragsdale Aaron P. , Gravel Simon 
Published: February 2019

AbstractLinkage disequilibrium is used to infer evolutionary history and to identify regions under selection or associated with a given trait. In each case, we require accurate estimates of linkage disequilibrium from sequencing data. Unphased data presents a challenge because the co-occurrence of alleles at different loci is ambiguous. Commonly used estimators for the common statisticsr2andD2exhibit large and variable upward biases that complicate interpretation and comparison across cohorts. Here, we show how to find unbiased estimators for a wide range of two-locus statistics, includingD2, for both single and multiple randomly mating populations. These provide accurate estimates over three orders of magnitude in LD. We also use these estimators to construct an estimator forr2that is less biased than commonly used estimators, but nevertheless argue for usingrather thanr2for population size estimates.
Gut Microbiome Analysis In Adult Tropical Gars (Atractosteus tropicus)
Authors: Méndez-Pérez Roberto , García-López Rodrigo , Bautista-López J. Santiago , Vázquez-Castellanos Jorge F. , Peña-Marín Emyr S. , Martínez-García Rafael , Domínguez-Rodríguez Verónica I. , Adams-Schroeder Randy H. , Baltierra-Trejo Eduardo , Valdés Carolina Melgar , Moya Andrés , Alvarez-González Carlos A. , Gómez-Cruz Rodolfo 
Published: February 2019

AbstractTropical gar (Atractosteus tropicus), is freshwater and estuarine fish that has inhabited the Earth since the Mesozoic era, undergoing limited physiological variation ever since. This omnivorous fish is endemic to southern Mexico and part of Central America. Besides its recognized cultural and scientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. Previous studies have highlighted the role of microbial communities in fish, particularly those in the gut microbiome, in maintaining their host homeostasis or disease. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents of adults’A. tropicus, by sex (female/male) and origin (wild/cultivated). Using culture-independent techniques, we extracted metagenomic DNA that was used for high throughput 16S rDNA profiling by amplifying the V4 – V5 hypervariable regions of the bacterial gene. A total of 364,735 total paired-end reads were obtained on an Illumina MiSeq sequencing platform, belonging to 508 identified genera, with the most and least abundant areCetobacterium, Edwardsiella, Serratia, Clostridium sensu stricto, PaludibacterandCampylobacter, Snodgrassella, Albirhodobacter, Lentilitoribacter, respectively. We detected that, by sex and origin, Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes phyla are the core gut microbiome of the adults’A. tropicus. We discover the Deinococcus-Thermus phylum sequence, wildtype males only, with extremophile capacity in another freshwater fish. We also identified the speciesLactococcus lactisstrains CAU929 and CAU6600, Cp6 and CAU9951,Cetobacteriumstrain H69,Aeromonas hydrophilastrains P5 and WR-5-3-2,Aeromonas sobriastrain CP DC28 andAeromonas hydrophilawith probiotic potential in aquaculture within the three dominant phyla, especially in wild-type organisms.
The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis inCaulobacter
Authors: Woldemeskel Selamawit Abi , Alvarez Laura , Daitch Allison K. , Zeinert Rilee , Bhargava Anant , Gonzalez Diego , Collier Justine , Chien Peter , Cava Felipe , Goley Erin D. 
Published: February 2019

AbstractBacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show thatCaulobacter crescentuscells lacking CdnL have severe morphological and growth defects. Specifically,ΔcdnLcells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes. Notably, we find thatΔcdnLcells are severely limited in glutamate synthesis, rendering them auxotrophic for that amino acid. Moreover,ΔcdnLcells produce low amounts of the cell wall precursor lipid II, andΔcdnLis synthetic lethal with other genetic perturbations that limit lipid II production.ΔcdnLcells also have aberrant localization of MreB and CtpS, cytoskeletal proteins required for maintaining proper cell width and curvature. Interestingly, the localization of CtpS is dependent on availability of CTP, which is predicted to be low inΔcdnLcells. Our findings implicate CdnL as a global regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and through metabolite-mediated changes in localization of cytoskeletal regulators of cell shape.
Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies
Authors: Ubbens Jordan , Cieslak Mikolaj , Prusinkiewicz Przemyslaw , Stavness Ian 
Published: February 2019

AbstractAssociation mapping studies have enabled researchers to identify candidate loci for many important environmental resistance factors, including agronomically relevant resistance traits in plants. However, traditional genome-by-environment studies such as these require a phenotyping pipeline which is capable of accurately and consistently measuring stress responses, typically in an automated high-throughput context using image processing. In this work, we present Latent Space Phenotyping (LSP), a novel phenotyping method which is able to automatically detect and quantify response to treatment directly from images. Using two synthetically generated image datasets, we first show that LSP is able to successfully recover the simulated QTL in both simple and complex synthetic imagery. We then demonstrate an example application of an interspecific cross of the model C4grassSetaria. We propose LSP as an alternative to traditional image analysis methods for phenotyping, enabling association mapping studies without the need for engineering complex image processing pipelines.
Glutarate metabolism in Pseudomonas putida is regulated by two distinct glutarate sensing transcription factors
Authors: Thompson Mitchell G. , Cruz-Morales Pablo , Krishna Rohith N. , Blake-Hedges Jacquelyn M. , Incha Matthew R. , Keasling Jay D. 
Published: February 2019

ABSTRACTTranscription factor based biosensors can be leveraged to screen thousands of genetics designs for optimal production in engineered microbes. In this study we characterize two glutarate sensing transcription factors (CsiR and GcdR) from Pseudomonas putida. The genomic contexts of CsiR homologs were analyzed and DNA binding sites were bioinformatically predicted. Both CsiR and GcdR were purified and shown to bind upstream of their coding sequencing in vitro. CsiR was shown to dissociate from DNA in vitro when exogenous glutarate was added confirming it acts as a genetic repressor. Both transcription factors were then engineered into plasmid based biosensors and their respective sensing performance features calculated. Both sensor plasmids were then reintroduced into P. putida and were evaluated for their ability to sense flux through glutarate when grown on various lysine metabolites as sole carbon sources. These findings provide information describing glutarate flux in P. putida, and potentially useful tools for future metabolic engineering and synthetic biology efforts.
Pathogen-encoded evasion of CXCL10 and T cell responses
Authors: Antonia Alejandro L. , Alvarez Monica I. , Trahair Esme , Gibbs Kyle D. , Pittman Kelly J. , Barnes Alyson B. , Smith Jeffrey S. , Rajagopal Sudarshan , Thompson J. Will , Reinhardt R. Lee , Ko Dennis C. 
Published: February 2019

AbstractClearance of intracellular pathogens, such asLeishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor.L. majorsuppresses CXCL10 through the virulence factor and protease, glycoprotein-63(gp63).GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxisin vitro.GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWTmice. Correspondingly, in C57BL/6JWTmice,gp63deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3−/−mice revealed the delay to lesion development required CXCR3 signaling. Finally,Salmonella entericaandChlamydia trachomatisinfection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens.Author SummaryLeishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the host’s attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasiteLeishmania (L.) majoremploys to disrupt the immune response by interfering with chemokine signaling. By this strategy,L. majoruses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show thatL. majorcleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, includingChlamydia trachomatisandSalmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.
ANME-2d anaerobic methanotrophic archaea differ from other ANME archaea in lipid composition and carbon source
Authors: Kurth Julia M. , Smit Nadine T. , Berger Stefanie , Schouten Stefan , Jetten Mike S.M. , Welte Cornelia U. 
Published: February 2019

AbstractThe anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast,Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments not much is known about their lipid composition or carbon sources. To close this gap, we analyzed the lipid composition of ANME-2d archaea and found that they mainly synthesize archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup which is rare among microorganisms. Batch incubations with13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea which primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterization and analysis of the carbon source ofCa.Methanoperedens facilitates distinction between ANME-2d and other ANMEs.