bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Donor Age on Outcome of Lung Transplantation Stratified by Recipient Diagnosis: A Nordic Multicenter Study
Authors: Auråen Henrik , Durheim Michael Thomas , Dellgren Göran , Hämmäinen Pekka , Larsson Hillevi , Geiran Odd , Schultz Hans Henrik Lawaetz , Leuckfeld Inga , Iversen Martin , Fiane Arnt , Holm Are Martin 
Published: August 2018

Background.
Organs from older donors are increasingly used in lung transplantation, and studies have demonstrated that this could be safe in selected recipients. However, which recipient groups that have the largest benefit of older organs are unclear. This multicenter study reviews all bilateral lung transplantations (BLTx) from donors 55 years or older stratified by recipient diagnosis and compares outcomes with transplantations from younger donors.

Methods.
All BLTx recipients (excluding retransplantation) at 5 Scandiatransplant centers between 2000 and 2013 were included (n = 913). Recipients were stratified to diagnosis groups including cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), and “other.” Intensive care unit (ICU) length of stay (LOS) and survival were assessed.

Results.
Overall, there was no difference in survival among patients transplanted from donors 55 years or older compared with younger donors. However, in CF recipients, donor age 55 years or older was associated with inferior survival (P = 0.014), and this remained significant in a multivariate model (hazard ratio, 5.0; 95% confidence interval, 1.8–14.1; P = 0.002). There was no significant effect of donor age on survival in recipients with COPD, ILD, or in the “other” group in multivariate models. Utilization of older donors was associated with increased ICU LOS for recipients with CF and ILD, but not in the COPD or “other” group.

Conclusions.
The BLTx recipients with CF had inferior survival and longer ICU LOS when receiving organs from donors 55 years or older. Recipients with COPD, ILD, or in the “other” group did not have inferior survival in multivariate models.
Polyhexanide Versus Metronidazole for Odor Management in Malignant (Fungating) Wounds
Authors: Villela-Castro Diana Lima , Santos Vera Lucia Conceição de Gouveia , Woo Kevin 
Published: August 2018

PURPOSE:The aim of this study was to compare the effects of 0.2% polyhexamethylene biguanide (PHMB) to 0.8% metronidazole on malignant wound (MW) odor, health-related quality of life (HRQOL), and pain upon application.DESIGN:A double-blinded, randomized, clinical trial.SUBJECTS AND SETTING:Twenty-four patients with malodorous MWs hospitalized in a referral cancer center in Sao Paulo, Brazil, participated in the trial.METHODS:Participants were randomly allocated to treatment with 0.8% metronidazole solution (control group) or 0.2% PHMB (experimental group). Study outcomes were measured at baseline (day 0), 4 days, and 8 days. The primary end point was the odor that was measured in terms of its intensity, quality, and impact on participants during the study period. Health-related quality of life was measured with the Ferrans and Powers Quality of Life Index–Wounds Version (FPQLI-WV) on day 0 and on the day when odor was completely eliminated as per evaluation by the investigators. Pain intensity related to application of the control and experimental solutions was measured as a secondary outcome using a scale of 0 to 10.RESULTS:Twenty patients (83.3%) were classified as having “no wound odor” at 4 days, and 100% achieved no wound odor by day 8 (P< .001). Odor control in patients with MW significantly influenced their general HRQOL (P= .002). We found no difference in odor elimination, or HRQOL, when patients managed with PHMB were compared to those managed with metronidazole. There were no statistically significant differences over time in pain measurement between the 2 groups.CONCLUSIONS:Both PHMB and metronidazole significantly reduced odor in malodorous MWs within 4 days. Neither solution was found to be more effective than the other in the magnitude of odor reduction or its effect on condition-specific HRQOL.
One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence inHaemonchus contortus
Authors: Wintersinger Jeff A. , Mariene Grace M. , Wasmuth James D. 
Published: August 2018

AbstractBackgroundNumerous quality issues may compromise genomic data’s representation of its underlying organism. In this study, we compared two genomes published by different research groups for the parasitic nematodeHaemonchus contortus, corresponding to divergent isolates. We analyzed differences between the genomes, attempting to ascertain which were attributable to legitimate biological differences, and which to technical error in one or both genomes.ResultsWe found discrepancies between theH. contortusgenomes in both assembly and annotation. The genomes differed in representation of genes that are highly conserved across eukaryotes, with clear evidence of misassembly underlying conserved genes missing from one genome or the other. Only 45% of genes in one genome were orthologous to genes in the other genome, with one genome exhibiting almost as much orthology toC. elegansas its counterpartH. contortusstrain. The two genomes differed substantially in probable causes underlying this unexpectedly low orthology. One genome included many more inparalogues than the other, and more frequently assembled inparalogues together on the same portions of contiguous sequence. It also exhibited cases of better-conserved gene position relative toC. elegans.ConclusionThe discrepancies between the two genomes far exceeded those expected as a consequence of biological differences between the twoH. contortusisolates. This implies substantial quality issues in one or both genomes, suggesting that researchers must exercise caution when using genomic data for newly sequenced species.
Two-step concentration of complex water samples for the detection of viruses
Authors: Farkas Kata , McDonald James E. , Malham Shelagh K. , Jones Davey L. 
Published: August 2018

AbstractThe accurate detection and quantification of pathogenic viruses in water is essential to understand and reduce the risk of human infection. This paper describes a two-step method suitable for the concentration of viruses in water and wastewater samples. The method involves a tangential flow ultrafiltration step that reduces the sample volume of 1-10 l to approx. 50 ml, followed by secondary precipitation using polyethylene glycol 6000 that reduces the volume to 1-4 ml. For method validation, water samples were spiked with different concentrations of enteric viruses and viral recoveries in the concentrates exceeded 10% in all experiments. The method is suitable for water samples with high and low salinity and turbidity, allowing the accurate comparison of viral titers in a diverse range of water types. Furthermore, the method has the potential to concentrate other pathogens, e.g. bacteria or protozoa. Hence, the use of this method can improve the holistic assessment of risks associated with wastewater-contaminated environments.
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
Authors: Lees John A. , Ferwerda Bart , Kremer Philip H. C. , Wheeler Nicole E. , Valls Serón Mercedes , Croucher Nicholas J. , Gladstone Rebecca A. , Bootsma Hester J. , Rots Nynke , Wijmega-Monsuur Alienke J. , Sanders Elisabeth A. M. , Trzciński Krzysztof , Wyllie Anne L. , Zwinderman Aeilko H. , den Berg Leonard H. van , Rheenen Wouter van , H. Veldink Jan , Harboe Zitta B. , Lundbo Lene F. , Groot Lisette C. P. G. M. de , Schoor Natasja M. van , Velde Nathalie van der , Ängquist Lars H. , Sørensen Thorkild I.A. , Nohr Ellen A. , Mentzer Alexander J. , C. Mills Tara , Knight Julian C. , du Plessis Mignon , Nzenze Susan , N. Weiser Jeffrey , Parkhill Julian , Madhi Shabir , Benfield Thomas , von Gottberg Anne , Ende Arie van der , Brouwer Matthijs C. , Barrett Jeffrey C. , Bentley Stephen D. , de Beek Diederik van 
Published: August 2018

AbstractStreptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, and identified variants in CCDC33 associated with susceptibility. Pneumococcal variation explained a large amount of invasive potential, but serotype explained only half of this variation. Newly developed methods identified pneumococcal genes involved in invasiveness including pspC and zmpD, and allowed a human-bacteria interaction analysis, finding associations between pneumococcal lineage and STK32C.
Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility
Authors: Amin Sara A. , Gopinarayanan Venkatesh Endalur , Nair Nikhil U. , Hassoun Soha 
Published: August 2018

AbstractCurrent pathway synthesis tools identify possible pathways that can be added to a host to produce a desired target molecule through the exploration of abstract metabolic and reaction network space. However, not many of these tools do explore gene-level information required to physically realize the identified synthesis pathways, and none explore enzyme-host compatibility. Developing tools that address this disconnect between abstract reactions/metabolic design space and physical genetic sequence design space will enable expedited experimental efforts that avoid exploring unprofitable synthesis pathways. This work describes a workflow, termed Probabilistic Pathway Assembly with Solubility Scores (ProPASS), which links synthesis pathway construction with the exploration of the physical design space as imposed by the availability of enzymes with characterized activities within the host. Predicted protein solubility propensity scores are used as a confidence level to quantify the compatibility of each pathway enzyme with the host (E. coli). This work also presents a database, termed Protein Solubility Database (ProSol DB), which provides solubility confidence scores inE. colifor 240,016 characterized enzymes obtained fromUniProtKB/Swiss-Prot. The utility ofProPASSis demonstrated by generating genetic implementations of heterologous synthesis pathways inE. colithat target several commercially useful biomolecules.AvailabilityProSol DBdata and code forProPASSare available for download fromhttps://github.com/HassounLab/
An Evolutionarily Conserved piRNA-producing Locus Required for Male Mouse Fertility
Authors: Wu Pei-Hsuan , Fu Yu , Cecchini Katharine , Özata Deniz M. , Arif Amena , Yu Tianxiong , Colpan Cansu , Gainetdinov Ildar , Weng Zhiping , Zamore Phillip D. 
Published: August 2018

SUMMARYPachytene piRNAs, which comprise >80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like miRNAs, cleave targets like siRNAs, or lack biological function altogether. Although piRNA pathway protein mutants are male sterile, no biological function has been identified for any mammalian piRNA-producing locus. Here, we report that males lacking piRNAs from a conserved mouse pachytene piRNA locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. Moreover, heterozygous embryos sired bypi6−/−fathers show reduced viability in utero. Molecular analyses suggest thatpi6piRNAs repress gene expression by cleaving mRNAs encoding proteins required for sperm function.pi6also participates in a network of piRNA-piRNA precursor interactions that initiate piRNA production from a second piRNA locus on chromosome 10 as well aspi6itself. Our data establish a direct role for pachytene piRNAs in spermiogenesis and embryo viability.HighlightsNormal male mouse fertility and spermiogenesis require piRNAs from thepi6locusSperm capacitation and binding to the zona pellucida of the egg requirepi6piRNAsHeterozygous embryos sired bypi6−/−fathers show reduced viability in uteroDefects inpi6mutant sperm reflect changes in the abundance of specific mRNAs.
iProteinDB: an integrative database of Drosophila post-translational modifications
Authors: Hu Yanhui , Sopko Richelle , Chung Verena , Studer Romain A. , Landry Sean D. , Liu Daniel , Rabinow Leonard , Gnad Florian , Beltrao Pedro , Perrimon Norbert 
Published: August 2018

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.
Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea
Authors: Jaffe Alexander L. , Castelle Cindy J. , Dupont Christopher L. , Banfield Jillian F. 
Published: August 2018

SUMMARYRibulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for catalytic activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a nucleotide-based, CO2-incorporating pathway. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham Cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.
Locomotion-dependent remapping of distributed cortical networks
Authors: Clancy Kelly B. , Orsolic Ivana , Mrsic-Flogel Thomas D. 
Published: August 2018

AbstractThe interactions between areas of the neocortex are fluid and state-dependent, but how individual neurons couple to cortex-wide network dynamics remains poorly understood. We correlated the spiking of individual neurons in primary visual (V1) and retrosplenial (RSP) cortex to activity across dorsal cortex, recorded simultaneously by calcium imaging. Individual neurons were correlated with distinct and reproducible patterns of activity across the cortical surface; while some fired predominantly with their local area, others coupled to activity in subsets of distal areas. The extent of distal coupling was predicted by how strongly neurons correlated with the local network. Changes in brain state triggered by locomotion re-structured how neurons couple to cortical activity patterns: running strengthened affiliations of V1 neurons with visual areas, while strengthening distal affiliations of RSP neurons with sensory cortices. Thus, individual neurons within a cortical area can independently engage in different cortical networks depending on the animal's behavioral state.
Can patients with cerebellar disease switch learning mechanisms to reduce their adaptation deficits?
Authors: Wong Aaron L. , Marvel Cherie L. , Taylor Jordan A. , Krakauer John W. 
Published: August 2018

ABSTRACTSystematic perturbations in motor adaptation tasks are primarily countered by learning from sensory-prediction errors, with secondary contributions from other learning processes. Despite the availability of these additional processes, particularly the use of explicit re-aiming to counteract observed target errors, patients with cerebellar degeneration are surprisingly unable to compensate for their sensory-prediction-error deficits by spontaneously switching to another learning mechanism. We hypothesized that if the nature of the task was changed – by allowing vision of the hand, which eliminates sensory-prediction errors – patients could be induced to preferentially adopt aiming strategies to solve visuomotor rotations. To test this, we first developed a novel visuomotor rotation paradigm that provides participants with vision of their hand in addition to the cursor, effectively setting the sensory-prediction-error signal to zero. We demonstrated in younger healthy controls that this promotes a switch to strategic re-aiming based on target errors. We then showed that with vision of the hand, patients with spinocerebellar ataxia could also switch to an aiming strategy in response to visuomotor rotations, performing similarly to age-matched participants (older controls). Moreover, patients could retrieve their learned aiming solution after vision of the hand was removed, and retain it for at least one year. Both patients and older controls, however, exhibited impaired overall adaptation performance compared to younger healthy controls (age, 18-33), likely due to age-related reductions in spatial and working memory. Moreover, patients failed to generalize, i.e., they were unable to adopt analogous aiming strategies in response to novel rotations, nor could they further improve their performance without vision of the hand. Hence, there appears to be an inescapable obligatory dependence on sensory-prediction-error-based learning – even when this system is impaired in patients with cerebellar degeneration. The persistence of sensory-prediction-error-based learning effectively suppresses a switch to target-error-based learning, which perhaps explains the unexpectedly poor performance by patients with spinocerebellar ataxia in visuomotor adaptation tasks.
Transcriptional regulation of voltage-gated sodium channels contributes to GM-CSF induced pain
Authors: Zhang Fan , Wang Yiying , Zhang Dandan , Fan Xizhenzi , Han Hao , Du Xiaona , Gamper Nikita , Zhang Hailin 
Published: August 2018

AbstractGranolocyte-macrophage colony stimulating factor (GM-CSF) induces production of granulocyte and macrophage populations from the hematopoietic progenitor cells; it is one of the most common growth factors in the blood. GM-CSF is also involved in bone cancer pain development by regulating tumor-nerve interactions, remodeling of peripheral nerves and sensitization of damage-sensing (nociceptive) nerves. However, the precise mechanism for GM-CSF-dependent pain is unclear. In this study, we found that GM-CSF is highly expressed in human malignant osteosarcoma. Rats implanted with bone cancer cells develop mechanical and thermal hyperalgesia but antagonizing GM-CSF in these animals significantly reduced such hypersensitivity. Nociceptor-specific voltage gated Na+channels Nav1.7, Nav1.8 and Nav1.9 were found to be selectively up-regulated in rat DRG neurons treated with GM-CSF, which resulted in enhanced excitability. GM-CSF activated the Jak2 and Stat3 signaling pathway which promoted the transcription of Nav1.7-1.9 in DRG neurons. Accordingly targeted knocking down either Nav1.7-1.9 or Jak2/Stat3 in DRG neurons alleviated the hyperalgesia in rats. Our findings describe a new bone cancer pain mechanism and provide a new insight into the physiological and pathological functions of GM-CSF.
Familiarity increases aggressiveness among clonal fish
Authors: Doran Carolina , Bierbach David , Laskowski Kate L. 
Published: August 2018

AbstractUnderstanding how animal groups form and function is a major goal in behavioural ecology. Both genetic relatedness and familiarity among group mates have been shown to be key mediators of group composition. However, disentangling the two in most species is challenging as the most familiar individuals are often the most related, and vice versa. In order to gain a complete understanding of how individual interactions shape group behaviour it is crucial to understand the role each of this social relationship factors plays individually. To this end, we manipulated the level of familiarity among groups of the naturally clonal, and genetically identical fish, the Amazon molly (Poecilia formosa) and monitored group behaviour in an open-field and when given the opportunity to forage. Contrary to our predictions, fish that were the most familiar with each other showed the highest levels of aggression. Additionally, fish that were less familiar with each other exhibited the highest group cohesion and took the longest to begin feeding, compared to the more familiar fish. These results suggest that familiarity may socially buffer individuals from the perception of risk in novel environments, such as is common in most behavioural tests designed to test group behaviour. Increases in aggression that are associated with increasing familiarity as shown here might be a mechanism by which fish maintain a fission-fusion society with important consequences for the patterns of associations in group living animals.