bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insurance Type and Major Complications After Hysterectomy
Authors: Swenson Carolyn Weaver , Kamdar Neil S. , Levy Helen , Campbell Darrell A. , Morgan Daniel M. 
Published: September 2016

Objectives
The aim of this study was to investigate the relationship between primary insurance type and major complications after hysterectomy.

Methods
A retrospective analysis was performed on women with Medicaid, Medicare, and private insurance who underwent hysterectomy from January 1, 2012, to July 1, 2014, and were included in the Michigan Surgical Quality Collaborative. Major complications within 30 days of surgery included the following: deep/organ space surgical site infection, deep venous and pulmonary thromboembolism, myocardial infarction or stroke, pneumonia or sepsis, blood transfusion, readmission, and death. Multivariable logistic regression was used to identify factors associated with major complications and characteristics associated with the Medicaid and Medicare groups.

Results
A total of 1577 women had Medicaid, 2103 had Medicare, and 11,611 had private insurance. The Medicaid and Medicare groups had a similar rate of major complications, nearly double that of the private insurance group (6.85% vs 7.85% vs 3.79%; P < .001). Compared with private insurance, women with Medicaid and Medicare had increased odds of major complications (Medicaid: odds ratio [OR], 1.60; 95% confidence interval [CI], 1.26–2.04; P < .001; Medicare: OR, 1.34; 95% CI, 1.04–1.73; P = .03). Women with Medicaid were more likely to be nonwhite, have a higher body mass index (BMI), report tobacco use in the last year and undergo an abdominal hysterectomy. Those with Medicare were more likely to be white, to have gynecologic cancer, and to be functionally dependent. Both groups had increased odds of American Society of Anesthesiology class 3 or higher and decreased odds of undergoing hysterectomy at large hospitals (≥500 beds).

Conclusions
Women with Medicaid and Medicare insurance have increased odds of major complications after hysterectomy. Abdominal hysterectomy, BMI, and smoking are potentially modifiable risk factors for women with Medicaid.
Effect of a New Risk Calculator on Patient Satisfaction With the Decision for Concomitant Midurethral Sling During Prolapse Surgery: A Randomized Controlled Trial
Authors: Miranne Jeannine Marie , Gutman Robert Eric , Sokol Andrew Ian , Park Amy Josephine , Iglesia Cheryl Bernadette 
Published: September 2016

Objective
To determine whether use of a new personalized risk calculator increases patient satisfaction with the decision whether or not to have a prophylactic midurethral sling (MUS) during pelvic organ prolapse (POP) surgery.

Methods
We performed a randomized controlled trial involving English-speaking women without symptoms of stress urinary incontinence (SUI) with ≥ stage 2 POP who planned to undergo POP surgery with 1 of 4 fellowship-trained urogynecologists at a single academic center. Women with a history of prior POP or incontinence surgery, or who were pregnant, or unable to complete study forms were excluded. Participants were randomly assigned to standard preoperative counseling or preoperative counseling with the use of a validated, online risk calculator for de novo SUI after POP surgery. The primary outcome was patient satisfaction with the decision for prophylactic MUS placement during POP surgery at 3 months postoperative assessed using the Satisfaction with Decision Scale for Pelvic Floor Disorders.

Results
Sixty-three women were approached for participation. Forty-two agreed to participate, 41 underwent randomization, and 33 had POP surgery and completed 3-month follow-up. Of these 33, 17 were randomized to the risk calculator and 16 to standard counseling. The mean age was 61.2 ± 9.1 years, and 41% (14/33) had a prophylactic MUS. At 3 months postoperative, there was no difference in Satisfaction with Decision Scale for Pelvic Floor Disorders scores between groups (4.67 ± 0.46 [intervention] vs 4.78 ± 0.34 [control]; P = 0.61).

Conclusions
Use of the de novo SUI risk calculator did not increase patient satisfaction with the decision regarding MUS placement during POP surgery.
Voiding Function After Midurethral Slings With and Without Local Anesthetic: Randomized Controlled Trial
Authors: Dueñas-Garcia Omar Felipe , Patterson Danielle , De la Luz Nieto Maria , Leung Katherine , Flynn Michael Kevin 
Published: September 2016

Objectives
This study aimed to compare the effect of periurethral infiltration of bupivacaine versus normal saline on postoperative voiding function and pain in patients undergoing retropubic midurethral sling

Methods
A randomized double-blind placebo-controlled study was performed at the University of Massachusetts from March 2012 to June 2015. Ninety patients were randomized to receive 0.5% bupivacaine with epinephrine or normal saline with epinephrine solution for periurethral hydrodissection. Postoperative pain was assessed at 2 to 3 and 6 to 7 hours using a visual analog scale. Voiding function was determined by the proportion of subjects passing or failing a voiding trial. Descriptive statistics and percentages were used to compare the rate of voiding dysfunction. A logistic regression analysis was performed adjusting for possible covariates.

Results
Ninety subjects enrolled and 45 were randomized to each group. Thirty-nine subjects received the normal saline and 41 received bupivacaine. The remaining 10 withdrew before the procedure. Pain scores at 2 to 3 hours did not differ between the groups (P = 0.837), but at 6 to 7 hours, patients who received bupivacaine had less pain (P = 0.028). There was no difference in voiding dysfunction between the study and placebo groups (17.9% and 24.4%, respectively; P = 0.481). Because of the unavailability of indigo carmine midway through the study, 36 of 80 subjects received preoperative phenazopyridine for the assessment of ureteral patency. Three (8%) of these subjects failed their voiding trial compared with 19 (30%) of the patients who did not receive phenazopyridine (P = 0.010).

Conclusions
The use of bupivacaine did not affect postoperative voiding function but had lower pain scores at 6 to 7 hours postoperatively. Preoperative phenazopyridine may reduce postoperative urinary retention.
From homeostasis to pathology: decrypting microbe–host symbiotic signals in the intestinal crypt
Authors: Pédron Thierry , Nigro Giulia , Sansonetti Philippe J. 
Published: September 2016

Metagenomic analysis of the human intestinal microbiome has provided a wealth of information that allowed an exceptionally detailed description of its microbial content and physiological potential. It also set the basis for studies allowing correlation of alterations in the balance of this microbiota and the occurrence of a certain number of emerging diseases, such as inflammatory bowel diseases, obesity and diabetes, and possibly colorectal cancer. The time has come to give the intestinal microbiota in symbiosis with its host an experimental dimension. This brief review summarizes our attempt at developing a cellular microbiology of the mutualistic symbiosis established between the gut microbiota and the host intestinal surface. Particular attention is paid to the intestinal crypt, due to its role in epithelial regeneration.
This article is part of the themed issue ‘The new bacteriology’.
Identification of a novel sequence type of Escherichia coli as the causative agent of pyelonephritis and bloodstream infection
Authors: Mac Aogáin Micheál , Miajlovic Helen , Moloney Geraldine , Chotirmall Sanjay H. , Rogers Thomas R. , Smith Stephen G. J. 
Published: September 2016

Introduction:
Globally, extra-intestinal pathogenic Escherichia coli are one of the predominant causative agents of bacteraemia.

Case presentation:
This case report outlines a presentation of community-acquired pyelonephritis and secondary bloodstream infection in an 81-year-old man. Laboratory investigations revealed that the causative isolate was a multi-drug-resistant E. coli of a novel multi-locus sequence type. This sequence type (ST) was designated ST-458 and was most closely related to the globally prevalent ST-131 lineage.

Conclusion:
This is the first report of a novel E. coli ST, ST-458, which caused pyelonephritis and bacteraemia.
Co-estimation of Phylogeny-aware Alignment and Phylogenetic Tree
Authors: Li Chunxiang , Medlar Alan , Löytynoja Ari 
Published: September 2016

AbstractThe phylogeny-aware alignment algorithm implemented in both PRANK and PAGAN has been found to produce highly accurate alignments for comparative sequence analysis. However, the algorithm’s reliance on a guide tree during the alignment process can bias the resulting alignment rendering it unsuitable for phylogenetic inference. To overcome these issues, we have developed a new tool, Canopy, for parallelized iterative search of optimal alignment. Using Canopy, we studied the impact of the guide tree as well as the number and relative divergence of sequences on the accuracy of the alignment and inferred phylogeny. We find that PAGAN is the more robust of the two phylogeny-aware alignment methods to errors in the guide tree, but Canopy largely resolves the guide tree-related biases in PRANK. We demonstrate that, for all experimental settings tested, Canopy produces the most accurate sequence alignments and, further, that the inferred phylogenetic trees are of comparable accuracy to those obtained with the leading alternative method, SATé. Our analyses also show that, unlike traditional alignment algorithms, the phylogeny-aware algorithm effectively uses the information from denser sequence sampling and produces more accurate alignments when additional closely-related sequences are included. All methods are available for download athttp://wasabiapp.org/software.
Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis
Authors: Medlar Alan , Laakso Laura , Miraldo Andreia , Löytynoja Ari 
Published: September 2016

AbstractHigh-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to bede novoassembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available fromhttp://wasabiapp.org/software/glutton/and is licensed under the GPLv3.
Nuclear and structural dynamics during the establishment of a specialized effector-secreting cell byMagnaporthe oryzaein living rice cells
Authors: Shipman Emma N. , Jones Kiersun , Jenkinson Cory B. , Kim Dong Won , Zhu Jie , Khang Chang Hyun 
Published: September 2016

AbstractBackgroundTo cause an economically important blast disease on rice, the filamentous fungusMagnaporthe oryzaeforms a specialized infection structure, called an appressorium, to penetrate host cells. Once inside host cells, the fungus produces a filamentous primary hypha that differentiates into multicellular bulbous invasive hyphae (IH), which are surrounded by a host-derived membrane. These hyphae secrete cytoplasmic effectors that enter host cells presumably via the biotrophic interfacial complex (BIC). The first IH cell, also known as the side BIC-associated cell, is a specialized effector-secreting cell essential for a successful infection. This study aims to determine cellular processes that lead to the development of this effector-secreting first IH cell inside susceptible rice cells.ResultsUsing live-cell confocal imaging, we determined a series of cellular events by which the appressorium gives rise to the first IH cell in live rice cells. The filamentous primary hypha extended from the appressorium and underwent asymmetric swelling at its apex. The single nucleus in the appressorium divided, and then one nucleus migrated into the swollen apex. Septation occurred in the filamentous region of the primary hypha, establishing the first IH cell. The tip BIC that was initially associated with the primary hypha becomes the side BIC on the swollen apex prior to nuclear division in the appressorium. The average distance between the early side BIC and the nearest nucleus in the appressorium was estimated to be more than 32 µm. These results suggest an unknown mechanism by which effectors that are expressed in the appressorium are transported through the primary hypha for their secretion to the distantly located BIC. WhenM. oryzaewas inoculated on heat-killed rice cells, penetration proceeded as normal, but there was no differentiation of a bulbous IH cell, suggesting its specialization for establishment of biotrophic infection.ConclusionsOur studies reveal cellular dynamics associated with the development of the effector-secreting first IH cell. Our data raise new mechanistic questions concerning hyphal differentiation in response to host environmental cues and effector trafficking from the appressorium to the BIC.
Directed dispersal by an abiotic vector: wetland plants disperse their seeds selectively to suitable sites along the hydrological gradient via water
Authors: Soons Merel B. , de Groot G. Arjen , Cuesta Ramirez M. Teresa , Fraaije Rob G. A. , Verhoeven Jos T. A. , de Jager Monique 
Published: September 2016

Summary

Plant species around the world invest in seed dispersal by producing large numbers of seeds, with a wide range of morphological adaptations that facilitate dispersal. Not all dispersed seeds reach suitable sites, however, and plants can significantly improve their fitness by increasing the proportion of seeds arriving at suitable sites for germination and establishment. Disproportionate dispersal to suitable sites is known as ‘directed dispersal’. Yet, mechanisms of directed dispersal are only known for a limited number of animal‐dispersed plant species.

We tested the hypothesis that directed dispersal can also be driven by abiotic vectors, such as water or wind. We used a tiered approach, combining analyses of experimental, field and literature data on wetland plant species and evaluating the potential for evolution of directed dispersal with a spatially explicit individual‐based model.

The data collected demonstrate that wetland plants produce seeds with adaptations to promote transportation and deposition by water towards microsites along the hydrological gradient where they germinate and establish best. Aquatic species produce seeds that sink and are transported by water as bed load towards inundated sites. In contrast, shoreline species produce seeds that float for very long periods of time so that they are eventually entrapped by shoreline vegetation or deposited at the waterline. Our model simulations confirm that the patterns we observed in nature can evolve under natural selection through adaptations in seed buoyancy.

For wind dispersal, the situation is more complex. Wind does not provide directed dispersal in the strictest sense but, rather, simply appears to be the best available dispersal vector for more terrestrial wetland plant species to reach drier areas in a wet environment.

Synthesis. We show that directed dispersal towards specific, suitable microsites is not exclusive to animal‐dispersed plant species, but may be far more common in plants – also in species dispersed by abiotic vectors, in particular water. As water and wind are very common dispersal vectors throughout the plant kingdom, directed dispersal (and not just dispersal distance) seems to be of general importance for the ecology of plants.

A lay summary is available for this article.
Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses
Authors: Sheil Douglas , Eastaugh Chris S. , Vlam Mart , Zuidema Pieter A. , Groenendijk Peter , van der Sleen Peter , Jay Alex , Vanclay Jerome 
Published: September 2016

SummaryThe long‐standing view that biomass growth in trees typically follows a rise‐and‐fall unimodal pattern has been challenged by studies concluding that biomass growth increases with size even among the largest stems in both closed forests and in open competition‐free environments. We highlight challenges and pitfalls that influence such interpretations.The ability to observe and calibrate biomass change in large stems requires adequate data regarding these specific stems.Data checking and control procedures can bias estimates of biomass growth and generate false increases with stem size.It is important to distinguish aggregate and individual‐level trends: a failure to do so results in flawed interpretations.Our assessment of biomass growth in 706 tropical forest stems indicates that individual biomass growth patterns often plateau for extended periods, with no significant difference in the number of stems indicating positive and negative trends in all but one of the 14 species. Nonetheless, when comparing aggregate growth during the most recent five years, 13 out of our 14 species indicate that biomass growth increases with size even among the largest sizes. Thus, individual and aggregate patterns of biomass growth with size are distinct.Claims concerning general biomass growth patterns for large trees remain unconvincing. We suggest how future studies can improve our knowledge of growth patterns in and among large trees.Alay summaryis available for this article.
Longing: A Patient and Caregiver Focused Clinical Diagnostic Validity (CDV) Study
Authors: Pehler Shelley‐Rae 
Published: September 2016

PURPOSETo gather data from patients and caregivers about their personal experiences with longing.METHODSUsing Fehring's Clinical Diagnostic Validity model, patients and caregivers were surveyed for their experiences with longing. The survey was developed based on two previous research projects (a content analysis and survey of expert nurses). Approval for the study was received from the University of Wisconsin‐Eau Claire Institutional Review Board.FINDINGSNone of the 84 attributes met major criteria (weighted ratios ≥ 0.8), but 19 met minor (weighted ratios of 0.60–0.79) across patients, caregivers, and combined scores. The proposed definition was supported by the respondents.CONCLUSIONSThe phenomenon of longing may exist.IMPLICATIONS FOR NURSING PRACTICEThere is evidence justifying the submission to NANDA‐I for a new nursing diagnosis for longing.
Energy Drink Use Patterns Among Young Adults: Associations with Drunk Driving
Authors: Arria Amelia M. , Caldeira Kimberly M. , Bugbee Brittany A. , Vincent Kathryn B. , O'Grady Kevin E. 
Published: September 2016

BackgroundHighly caffeinated “energy drinks” (ED) are commonly consumed and sometimes mixed with alcohol. Associations between ED consumption, risk‐taking, and alcohol‐related problems have been observed. This study examines the relationship between ED consumption—both with and without alcohol—and drunk driving.MethodsData were derived from a longitudinal study of college students assessed annually via personal interviews. In Year 6 (modal age 23; n = 1,000), participants self‐reported their past‐year frequency of drunk driving, ED consumption patterns (frequency of drinking alcohol mixed with energy drinks [AmED] and drinking energy drinks without alcohol [ED]), alcohol use (frequency, quantity), and other caffeine consumption. Earlier assessments captured suspected risk factors for drunk driving. Structural equation modeling was used to develop an explanatory model for the association between ED consumption patterns and drunk driving frequency while accounting for other suspected risk factors.ResultsMore than half (57%) consumed ED at least once during the past year. Among ED consumers, 71% drank AmED and 85% drank ED alone; many (56%) engaged in both styles of ED consumption while others specialized in one or the other (29% drank ED alone exclusively, while, 15% drank AmED exclusively). After accounting for other risk factors, ED consumption was associated with drunk driving frequency in 2 ways. First, a direct path existed from ED frequency (without alcohol) to drunk driving frequency. Second, an indirect path existed from AmED frequency through alcohol quantity to drunk driving frequency.ConclusionsAmong this sample, ED consumption with and without alcohol was common, and both styles of ED consumption contributed independently to drunk driving frequency. Results call for increased attention to the impact of different patterns of ED consumption on alcohol‐related consequences, such as drunk driving.
Alcohol Involvement in Homicide Victimization in the United States
Authors: Naimi Timothy S. , Xuan Ziming , Cooper Susanna E. , Coleman Sharon M. , Hadland Scott E. , Swahn Monica H. , Heeren Timothy C. 
Published: September 2016

BackgroundAlthough the association between alcohol and homicide is well documented, there has been no recent study of alcohol involvement in homicide victimization in U.S. states. The objective of this article was to determine the prevalence of alcohol involvement in homicide victimization and to identify socio demographic and other factors associated with alcohol involvement in homicide victimization.MethodsData from homicide victims with a reported blood alcohol content (BAC) level were analyzed from 17 states from 2010 to 2012 using the National Violent Death Reporting System. Logistic regression was used to investigate factors associated with the odds of homicide victims having a BAC ≥ 0.08%.ResultsAmong all homicide victims, 39.9% had a positive BAC including 13.7% with a BAC between 0.01% and 0.79% and 26.2% of victims with a BAC ≥ 0.08%. Males were twice as likely as females to have a BAC ≥ 0.08% (29.1% vs. 15.2%; p < 0.001). Characteristics that were independent predictors of homicide victims having a BAC ≥ 0.08 included male sex, American Indian/Alaska Native race, Hispanic ethnicity, history of intimate partner violence, and nonfirearm homicides.ConclusionsAlcohol is present in a substantial proportion of homicide victims in the United States, with substantial variation by state, demographic, and circumstantial characteristics. Future studies should explore the relationships between state‐level alcohol policies and alcohol involvement among perpetrators and victims of homicide.