bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Preoperative Oropharyngeal Microflora on the Occurrence of Postoperative Pneumonia and Survival in Patients Undergoing Esophagectomy for Esophageal Cancer
Authors: Yuda Masami , Yamashita Kotaro , Okamura Akihiko , Hayami Masaru , Fukudome Ian , Toihata Tasuku , Imamura Yu , Mine Shinji , Ishizuka Naoki , Watanabe Masayuki 
Published: April 2019

Objective:The aim of this study was to clarify the correlation between oropharyngeal microflora and postoperative complications as well as long-term survival after esophagectomy.Background:Although the oral cavity is known to be a potential reservoir for pathogens, the influence of abnormal oropharyngeal microflora on the outcomes of patients undergoing esophagectomy remains unknown.Methods:This study included 675 patients who underwent esophagectomy between 2007 and 2014. Saliva samples from the oropharynx were collected 2 days before the operation. There were 442 patients with indigenous flora (Ind group) and 233 with allopatric flora. Among the patients with allopatric flora, 140 had antibiotic-sensitive microbes only (Allo-S group) while 93 had different types of antibiotic-resistant microbes (Allo-R group). We investigated the correlation between the types of oropharyngeal microflora and the incidence of postoperative complications as well as long-term outcomes.Results:Sixteen microbes could be cultivated from the saliva samples. The incidence of postoperative pneumonia in the Allo-S and Allo-R groups was significantly higher than in the Ind group (P< 0.001). In addition, acute respiratory distress syndrome was more often observed in the Allo-R group than in the other groups (P= 0.002). A significantly higher rate of antibiotic use and longer hospital stays were observed in the Allo-R group compared with the Ind group. Multivariate logistic regression analysis revealed that the presence of allopatric antibiotic-resistant microbes in the oropharynx was an independent risk factor for postoperative pneumonia (odds ratio, 3.93; 95% confidence interval, 2.41–6.42). The overall survival was significantly poorer in the Allo-R group than in the other groups.Conclusions:Preoperative oropharyngeal culture is a simple and low-cost method that can predict both the occurrence of postoperative pneumonia and poor prognosis after esophagectomy.
Facilitation of Surgical Innovation
Authors: Marcus Rebecca K. , Lillemoe Heather A. , Caudle Abigail S. , Weinberg Jeffrey S. , Gidley Paul W. , Skibber John M. , Levenback Charles F. , Swisher Stephen G. , Aloia Thomas A. 
Published: April 2019

Objective:
To review efficiency metrics and patient safety data before and after implementation of a structured review process for surgical innovations.

Summary Background Data:
Surgical innovation ranges from minor incremental improvement to radical experimentation. Although innovation paradigms have been described, these are not widely adopted or enforced in the surgical community.

Methods:
A Continuous Quality Improvement Team (CQIT) of surgical quality officers and perioperative nurses was organized to perform structured reviews of proposed new surgical devices and procedures at a large quaternary cancer care center. The CQIT process was placed to precede an established Value Analysis Team business evaluation. Pre- and post-CQIT implementation metrics of approval process efficiency and patient safety data were compared. Seven novel procedures were also vetted by the CQIT.

Results:
Forty-six product requests were evaluated after CQIT implementation. Compared with 34 products evaluated prior to CQIT establishment, the total mean evaluation time decreased from 124 to 51 days (P
= 0.007). For new devices requiring intraoperative trial, the time between product proposal and trial decreased from a mean of 260 to 99 days (P
= 0.014). The rate of device-related complications in the pre-CQIT group was 10% compared with 0% post-CQIT. Two devices, which administratively bypassed CQIT review, had both minor and major complications, including a mortality. Five novel procedures approved by CQIT with simulation were performed without complications.

Conclusions:
Using novel algorithms, the addition of a dedicated team of surgical quality officers to the surgical innovation evaluation process improved both the efficiency and the safety associated with introducing new devices and procedures into practice.
Endovascular Aneurysm Repair With Inferior Mesenteric Artery Embolization for Preventing Type II Endoleak
Authors: Samura Makoto , Morikage Noriyasu , Otsuka Ryo , Mizoguchi Takahiro , Takeuchi Yuriko , Nagase Takashi , Harada Takasuke , Yamashita Osamu , Suehiro Kotaro , Hamano Kimikazu 
Published: April 2019

Objective:
This study aimed to evaluate the effect of inferior mesenteric artery (IMA) embolization during endovascular aneurysm repair (EVAR) in patients at high risk of type II endoleak (T2EL) in randomized controlled trial (RCT).

Summary Background Data:
Several studies have demonstrated a reduction of T2EL by IMA embolization before EVAR. However, there have been no RCT confirming the efficacy of IMA embolization.

Methods:
Patients scheduled for elective EVAR between April 2014 and March 2018 were eligible. Patients at high risk of T2EL (IMA patency with IMA ≥3 mm, LAs ≥2 mm, or an aortoiliac-type aneurysm) were prospectively randomized to receive EVAR with or without IMA embolization. The primary endpoint was occurrence of T2EL during follow-up. Secondary endpoints included aneurysmal sac changes, adverse events from IMA embolization, and reintervention rate due to T2EL. This trial is registered with the University Hospital Medical Information Network, number UMIN000022147.

Results:
One hundred thirteen patients had high risk and 106 were randomized. In the intention-to-treat analysis, the incidence of T2EL was significantly lower in the embolization group [24.5% vs 49.1%; P = 0.009, absolute risk reduction = 24.5%; 95% confidence interval (CI), 6.2–40.5, number needed to treat = 4.1; 95% CI, 2.5–16.1]. The aneurysmal sac shrunk significantly more in the embolization group (−5.7 ± 7.3 mm vs −2.8 ± 6.6 mm; P = 0.037), and the incidence of aneurysmal sac growth related to T2EL was significantly lower in the embolization group (3.8% vs 17.0%; P = 0.030). There were no complications related to IMA embolization or reinterventions associated with T2EL.

Conclusions:
Our results demonstrated the effectiveness of IMA embolization during EVAR in high-risk patients for the prevention of T2EL, which is suggested for avoiding aneurysmal sac enlargement related to T2EL.
Growth Patterns After Kidney Transplantation in European Children Over the Past 25 Years: An ESPN/ERA-EDTA Registry Study
Authors: Bonthuis Marjolein , Groothoff Jaap W. , Ariceta Gema , Baiko Sergey , Battelino Nina , Bjerre Anna , Cransberg Karlien , Kolvek Gabriel , Maxwell Heather , Miteva Polina , Molchanova Maria S. , Neuhaus Thomas J. , Pape Lars , Reusz Gyorgy , Rousset-Rouviere Caroline , Sandes Ana Rita , Topaloglu Rezan , Van Dyck Maria , Ylinen Elisa , Zagozdzon Ilona , Jager Kitty J. , Harambat Jérôme 
Published: April 2019

Background.
Improved management of growth impairment might have resulted in less growth retardation after pediatric kidney transplantation (KT) over time. We aimed to analyze recent longitudinal growth data after KT in comparison to previous eras, its determinants, and the association with transplant outcome in a large cohort of transplanted children using data from the European Society for Paediatric Nephrology/European Renal Association and European Dialysis and Transplant Association Registry.

Methods.
A total of 3492 patients transplanted before 18 years from 1990 to 2012 were included. Height SD scores (SDS) were calculated using recent national or European growth charts. We used generalized equation models to estimate the prevalence of growth deficit and linear mixed models to calculate adjusted mean height SDS.

Results.
Mean adjusted height post-KT was −1.77 SDS. Height SDS was within normal range in 55%, whereas 28% showed moderate, and 17% severe growth deficit. Girls were significantly shorter than boys, but catch-up growth by 5 years post-KT was observed in both boys and girls. Children <6 years were shortest at KT and showed the greatest increase in height, whereas there was no catch-up growth in children transplanted >12.

Conclusions.
Catch-up growth post-KT remains limited, height SDS did not improve over time, resulting in short stature in nearly half of transplanted children in Europe.
Enhanced Advocacy and Health Systems Training Through Patient Navigation Increases Access to Living-donor Kidney Transplantation
Authors: Locke Jayme E. , Reed Rhiannon D. , Kumar Vineeta , Berry Beverly , Hendricks Daagye , Carter Alexis , Shelton Brittany A. , Mustian Margaux N. , MacLennan Paul A. , Qu Haiyan , Hannon Lonnie , Yates Clayton , Hanaway Michael J. 
Published: April 2019

Background.
To date, no living donation program has simultaneously addressed the needs of both transplant candidates and living donors by separating the advocacy role from the candidate and improving potential donor comfort with the evaluation process. We hypothesized that the development of a novel program designed to promote both advocacy and systems training among transplant candidates and their potential living kidney donors would result in sustained increases in living-donor kidney transplantation (LDKT). To this end, we developed and implemented a Living Donor Navigator (LDN) Program at the University of Alabama at Birmingham.

Methods.
We included adult patients awaiting kidney-only transplant in a retrospective cohort analysis. Using time-varying Cox proportional hazards regression, we explored likelihood of living donor screening and approval by participation in the LDN program.

Results.
There were 56 LDN participants and 1948 nonparticipants (standard of care). LDN was associated with a 9-fold increased likelihood of living donor screenings (adjusted hazard ratio, 9.27; 95% confidence interval, 5.97-14.41, P < 0.001) and a 7-fold increased likelihood of having an approved living donor (adjusted hazard ratio, 7.74; 95% confidence interval, 3.54-16.93; P < 0.001) compared with the standard of care. Analyses by participant race demonstrated higher likelihood of screened donors and a similar likelihood of having an approved donor among African Americans compared with Caucasians.

Conclusions.
These data suggest that both advocacy and systems training are needed to increase actual LDKT rates, and that LDN programs may mitigate existing racial disparities in access to LDKT.
Leptindeficient rats develop nonalcoholic steatohepatitis with unique disease progression
Authors: Lu Ping , Yang Guang , He Wen , Wu Wanwan , Qi Lingbin , Shen Shijun , Rao Junhua , Fan Guoping , Xue Zhigang , Zhang Peng , Jiang Cizhong , Zhu Xianmin 
Published: April 2019

AbstractNonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlikeob/obmice,Lep∆I14/∆I14rats develop unique NASH phenotype with steatosis, lymphocyte infiltration and ballooning after postnatal week 16. UsingLep∆I14/∆I14rats as NASH model, we studied the natural history of NASH progression by performing an integrated analysis of hepatic transcriptome from postnatal week 4 to 48.Leptindeficiency results in a robust increase in expression of genes encoding 9 rate-limiting enzymes in lipid metabolism such as ACC and FASN. However, genes in positive regulation of inflammatory response are highly expressed at week 16 and then remain the steady elevated expression till week 48. The high expression of cytokines and chemokines including CCL2, TNFα, IL6 and IL1β is correlated with the phosphorylation of several key molecules in pathways such as JNK and NF-κB. Meanwhile, we observed cell infiltration of MPO+neutrophils, CD8+T cells, CD68+hepatic macrophages and CCR2+inflammatory monocyte-derived macrophages, together with macrophage polarization from M2 to M1. Importantly,Lep∆I14/∆I14rats share more homologous genes with NASH patients than previously established mouse models and crab eating monkeys with spontaneous hepatic steatosis. Transcriptomic analysis showed that many drug targets in clinical trials can be evaluated inLep∆I14/∆I14rats.ConclusionWe characterizeLep∆I14/∆I14rats as a unique NASH model by performing a long-term (i.e., 4 to 48 postnatal weeks) integrated transcriptomic analysis. This work reveal the temporal dynamics of hepatic gene expression in lipid metabolism and inflammation, and shed light on understanding the natural history of NASH in human beings.
Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
Authors: Starr Evan P. , Nuccio Erin E. , Pett-Ridge Jennifer , Banfield Jillian F. , Firestone Mary K. 
Published: April 2019

AbstractViruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil. Here, we assembled 48 individual metatranscriptomes from four habitats within a soil sampled over a 22-day time series: rhizosphere alone, detritosphere alone, a combination of the two, and unamended soil (four time points and three biological replicates per time point). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker gene content. Based on viral phylogeny, much of the diversity wasNarnaviridaethat parasitize fungi orLeviviridaethat infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral communities were structured based on the presence of litter, while putative hosts appeared to be impacted by both the presence of litter and roots. A clear time signature fromLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant and active in soil. Their replication causes host cell death, mobilizing carbon in a process that represents a largely overlooked component of carbon cycling in soil.
Rapid, ultra-local adaptation facilitated by phenotypic plasticity
Authors: Sun Syuan-Jyun , Catherall Andrew M. , Pascoal Sonia , Jarrett Benjamin J. M. , Miller Sara E. , Sheehan Michael J. , Kilner Rebecca M. 
Published: April 2019

AbstractModels of ‘plasticity-first’ evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can still facilitate rapid evolution when diverging populations are connected by gene flow. Here we show how plasticity has generated adaptive divergence in fecundity in wild populations of burying beetlesNicrophorus vespilloides, which are still connected by gene flow, which occupy distinct Cambridgeshire woodlands that are just 2.5km apart and which diverged from a common ancestral population c. 1000-4000 years ago. We show that adaptive divergence is duetothe coupling of an evolved increase in the elevation of the reaction norm linking clutch size to carrion size (i.e. genetic accommodation) with plastic secondary elimination of surplus offspring. Working in combination, these two processes have facilitated rapid adaptation to fine-scale environmental differences, despite ongoing gene flow.
A comparative analysis of histone methyltransferases and demethylases in insect genome: A meta-analysis
Authors: Gulati Parul , Kohli Surbhi , Narang Ankita , Brahmachari Vani 
Published: April 2019

AbstractBackgroundThe epigenetic regulation through post-translational modification of histones, especially methylation is well conserved, while DNA methylation is variable, being very low or absent in Drosophila melanogaster. Though there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have compared the histone methyltransferases and the demethylases in the genome of Drosophila melanogaster, Aedes aegypti (Diptera), the pea aphid Acyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera), the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum (Coleoptera).ResultsWe identified 38 clusters consisting of arginine, lysine methyltransferases and demethylases using OrthoFinder. To eliminate false positives, we designed a method based on identifying highly conserved domain within each class designated as the high priority domain. Out of the 9 arginine methyltransferases, Art2, Art6 and Art9 are identified in D.melanogaster only. We observe copy number variation between the genomes; A.pisum has nine copies of eggless gene (H3K9me3 methyltransferase), which can be correlated with the switch between parthenogenesis and sexual reproduction. Other than the high-priority domains, these proteins contain shared and unique domains that can mediate protein-protein interaction. Phylogenetic analysis indicates that the there is a broad conservation within the members of a class while duplication and divergence is observed in LSD1.ConclusionThis meta-analysis provides a method for reliable identification of epigenetic modifiers of histones in newly sequenced insect genomes. Similar approach can be taken for other classes of genes.
Renewal theory provides a universal quantitative framework to characterise the continuous regeneration of rotational events in cardiac fibrillation
Authors: Dharmaprani Dhani , Schopp Madeline , Kuklik Pawel , Chapman Darius , Lahiri Anandaroop , Dykes Lukah , Xiong Feng , Aguilar Martin , Strauss Benjamin , Mitchell Lewis , Pope Kenneth , Meyer Christian , Willems Stephan , Akar Fadi G. , Nattel Stanley , McGavigan Andrew D , Ganesan Anand N. 
Published: April 2019

ABSTRACTBackgroundCardiac fibrillation is thought to be maintained by rotational activity, with pivoting regions called phase singularities (PSs). Despite a century of research, no clear quantitative framework exists to model the fundamental processes responsible for the continuous formation and destruction of rotors in fibrillation.ObjectiveWe conducted a multi-modality, multi-species study of AF/VF under the hypothesis that PS formation/destruction in fibrillation can be modelled as self-regenerating renewal processes, producing exponential distributions of inter-event times governed by constant rate-parameters defined by the prevailing properties of the system.MethodsPS formation/destruction was studied and cross-validated in 5 models, using basket recordings and optical mapping from: i) human persistent AF (n = 20), ii) tachypaced sheep AF (n = 5), iii) rat AF (n = 4), iv) rat VF (n = 11) and v) computer simulated AF (SIM). Hilbert phase maps were constructed. PS lifetime data were fitted by exponential probability distribution functions (PDFs) computed using maximum entropy theory, and the rate parameter (λ) determined. A systematic review was conducted to cross-validate with source data from literature.ResultsPS destruction/formation distributions showed good fits to an exponential in all systems (R2≥ 0.90). In humans,λ= 4.6%/ms (95%CI,4.3,4.9)), sheep 4.4%/ms (95%CI,4.1,4.7)), rat AF 38%/ms (95%CI,22,55), rat VF 46%/ms (95%CI,31.2,60.2) and SIM 5.4%/ms (95%CI,4.1,6.7). All PS distributions identified through systematic review were exponential with λ comparable to experimental data.ConclusionThese results provide a universal quantitative framework to explain rotor formation and destruction in AF/VF, and a platform for therapeutic advances in cardiac fibrillation.
Pan-Cancer Exploration of mRNA Mediated Dysregulated Pathways in the Cancer Genomics Cloud
Authors: Linan Margaret , Wang Junwen , Dinu Valentin 
Published: April 2019

AbstractWe performed a comprehensive pan-cancer analysis in the Cancer Genomics Cloud of HTSeq-FPKM normalized protein coding mRNA data from 17 cancer projects in the Cancer Genome Atlas, these are Adrenal Gland, Bile Duct, Bladder, Brain, Breast, Cervix, Colorectal, Esophagus, Head and Neck, Kidney, Liver, Lung, Pancreas, Prostate, Stomach, Thyroid and Uterus. The PoTRA algorithm was applied to the normalized mRNA protein coding data and detected dysregulated pathways that can be implicated in the pathogenesis of these cancers. Then the PageRank algorithm was applied to the PoTRA results to find the most influential dysregulated pathways among all 17 cancer types. Pathways in cancer is the most common dysregulated pathway, and the MAPK signaling pathway is the most influential (PageRank score = 0.2034) while the purine metabolism pathway is the most significantly dysregulated metabolic pathway.
Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome
Authors: Schostag Morten Dencker , Anwar Muhammad Zohaib , Jacobsen Carsten Suhr , Larose Catherine , Vogel Timothy M. , Maccario Lorrie , Jacquiod Samuel , Faucherre Samuel , Priemé Anders 
Published: April 2019

AbstractBackgroundArctic surface soils experience pronounced seasonal changes in temperature and chemistry. However, it is unclear how these changes affect microbial degradation of organic matter, nitrogen cycling and microbial stress responses. We combined measurements of microbiome transcriptional activity, CO2production, and pools of carbon and nitrogen to investigate the microbial response to warming in the laboratory, from −10 °C to 2 °C, and subsequent cooling, from 2 °C to −10 °C, of a high Arctic tundra soil from Svalbard, Norway.ResultsGene expression was unaffected by warming from −10 °C to −2 °C and by cooling from −2 °C to −10 °C, while upon freezing (2 °C to −2 °C) a defense response against oxidative stress was observed. Following modest transcriptional changes one day after soil thaw, a more pronounced response was observed after 17 days, involving numerous functions dominated by an upregulation of genes involved in transcription, translation and chaperone activity. Transcripts related to carbohydrate metabolism and degradation of complex polymers (e.g. cellulose, hemicellulose and chitin) were also enhanced following 17 days of soil thaw, which was accompanied by a four-fold increase in CO2production. In addition, anaerobic ammonium oxidation and turnover of organic nitrogen were upregulated. In contrast, nitrification, denitrification and assimilatory nitrate reduction were downregulated leading to an increase in the concentration of soil inorganic nitrogen.Conclusionthe microorganisms showed negligible response to changes in sub-zero temperatures and a delayed response to thaw, which after 17 days led to upregulation of soil organic matter degradation and enhanced CO2production, as well as downregulation of key pathways in nitrogen cycling and a concomitant accumulation of inorganic nitrogen available for plants.