bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Composition of Largemouth Bass in Puerto Rico Reservoirs
Authors: Peterson Nick R. , Lutz-Carrillo Dijar , Neal J. Wesley 
Published: October 2017

Abstract
The Largemouth Bass Micropterus salmoides includes two recognized subspecies, the Northern Largemouth Bass (NLMB; M. salmoides salmoides) and the Florida Largemouth Bass (FLMB; M. salmoides floridanus), which can hybridize to produce introgressed Largemouth Bass (ILMB; NLMB × FLMB). Largemouth Bass were introduced into Puerto Rico by using source populations from unknown origins (1915), a natural intergrade zone (1946 and 1947; ILMB), and peninsular Florida (1957; FLMB). All subsequent supplemental stocking efforts used broodstock collected from reservoirs in Puerto Rico with an effort to preferentially propagate non-introgressed FLMB. Here, we document contemporary FLMB-specific alleles and genotypes, changes in allele frequencies over the last decade, and differences in size structure between genotypes of the FLMB and its hybrids (ILMB) in Puerto Rico. Among 12 island reservoirs, FLMB alleles were prevalent at rates similar to estimates from a decade earlier, and the proportion of FLMB alleles (0.77–0.85) was less than that of the hatchery broodstock. No NLMB genotypes were resolved, and the proportion of FLMB genotypes ranged from 0.03 to 0.64. Length frequency distributions differed between the FLMB and ILMB types (Kolmogorov D-statistic = 0.172, P = 0.026), with FLMB observed more frequently in larger size-classes. Given their greater sizes and potentially greater longevity, we suggest that FLMB should be used exclusively for future stocking efforts in Puerto Rico.
Received January 25, 2017; accepted July 3, 2017 Published online October 11, 2017
Detection Efficiency of a Portable PIT Antenna for Two Small-Bodied Fishes in a Piedmont Stream
Authors: Kelly Brett B. , Cary Joshua B. , Smith Alisha D. , Pregler Kasey C. , Kim Seoghyun , Kanno Yoichiro 
Published: October 2017

Abstract
Passive integrated transponder (PIT) tags have been used to infer demography and behavior of lotic fishes, but their application has mostly been limited to salmonids. We studied the efficiency of a portable PIT antenna in a small Piedmont stream (mean width = 2.4 m) in South Carolina by comparing two tag sizes (8- and 12-mm full-duplex tags) applied to two nongame species (Mottled Sculpin Cottus bairdii and Creek Chub Semotilus atromaculatus). A 285-m stream reach was blocked off under base flow conditions in September 2016, and 8- or 12-mm PIT tags were implanted in 67 Creek Chub (62–138 mm TL) and 65 Mottled Sculpin (60–88 mm TL). Starting at 1 d after tagging, the study reach was sampled with the portable PIT antenna twice daily for five consecutive days, during which apparent survival of tagged fish was assumed. Generalized linear mixed-effects models with a logistic link identified that detection efficiency depended on species, tag size, body length, and the species × body length interaction. Mottled Sculpin had detection rates of 56% (8-mm tags) and 79% (12-mm tags), with 67% of detections occurring in riffle-dominated sections, whereas Creek Chub had 3% (8-mm tags) and 16% (12-mm tags) detection rates, with 62% of detections occurring in pool-dominated sections. Detection efficiency decreased with body size in Creek Chub but not in Mottled Sculpin; the observed decrease for Creek Chub was most likely attributable to an ontogenetic habitat shift. The reasonably high detection efficiency of Mottled Sculpin, even with 8-mm tags, suggested that the portable PIT antenna can be a viable option for some species in small streams, allowing individual-based approaches to studying small-bodied species or earlier life stages without the need for repeated physical capture and handling.
Received May 13, 2017; accepted October 2, 2017Published online November 10, 2017
Helminthosporic acid functions as an agonist for gibberellin receptor
Authors: Miyazaki Sho , Jiang Kai , Kobayashi Masatomo , Asami Tadao , Nakajima Masatoshi 
Published: October 2017

Abstract
Helminthosporol was isolated from a fungus, Helminthosporium sativum, as a natural plant growth regulator in 1963. It showed gibberellin-like bioactivity that stimulated the growth of the second leaf sheath of rice. After studying the structure–activity relationship between the compound and some synthesized analogs, it was found that helminthosporic acid (H-acid) has higher gibberellin-like activity and chemical stability than helminthosporol. In this study, we showed that (1) H-acid displays gibberellin-like activities not only in rice but also in Arabidopsis, (2) it regulates the expression of gibberellin-related genes, (3) it induces DELLA degradation through binding with a gibberellin receptor (GID1), and (4) it forms the GID1-(H-acid)-DELLA complex to transduce the gibberellin signal in the same manner as gibberellin. This work shows that the H-acid mode of action acts as an agonist for gibberellin receptor.
An enzymatic method for the production of 6-oxohexanoic acid from 6-aminohexanoic acid by an enzyme oxidizing ω-amino compounds from Phialemonium sp. AIU 274
Authors: Yamada Miwa , Ooe Mitsuaki , Sasaki Tomoko , Miyazaki Masao , Isobe Kimiyasu 
Published: October 2017

Abstract
An enzymatic method for 6-oxohexanoic acid production was developed using 6-aminohexanoic acid and an ω-amino group-oxidizing enzyme (ω-AOX) from Phialemonium sp. AIU 274. 6-Oxohexanoic acid was produced from 6-aminohexanoic acid with 100% yield by incubation with 0.3 U of the ω-AOX and 20 U of catalase at 30 °C for 30 h in 0.1 M potassium phosphate buffer (pH 7.0).
A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects
Authors: Mayer Gerhard , Quast Christian , Felden Janine , Lange Matthias , Prinz Manuel , Pühler Alfred , Lawerenz Chris , Scholz Uwe , Glöckner Frank Oliver , Müller Wolfgang , Marcus Katrin , Eisenacher Martin 
Published: October 2017

Abstract
Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific ‘service provision units’ is introduced together with the factors influencing them and the main underlying assumptions for these ‘value influencing factors’. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared.
An omnibus test for differential distribution analysis of microbiome sequencing data
Authors: Chen Jun , King Emily , Deek Rebecca , Wei Zhi , Yu Yue , Grill Diane , Ballman Karla 
Published: October 2017

AbstractMotivationOne objective of human microbiome studies is to identify differentially abundant microbes across biological conditions. Previous statistical methods focus on detecting the shift in the abundance and/or prevalence of the microbes and treat the dispersion (spread of the data) as a nuisance. These methods also assume that the dispersion is the same across conditions, an assumption which may not hold in presence of sample heterogeneity. Moreover, the widespread outliers in the microbiome sequencing data make existing parametric models not overly robust. Therefore, a robust and powerful method that allows covariate-dependent dispersion and addresses outliers is still needed for differential abundance analysis.ResultsWe introduce a novel test for differential distribution analysis of microbiome sequencing data by jointly testing the abundance, prevalence and dispersion. The test is built on a zero-inflated negative binomial regression model and winsorized count data to account for zero-inflation and outliers. Using simulated data and real microbiome sequencing datasets, we show that our test is robust across various biological conditions and overall more powerful than previous methods.Availability and implementationR package is available at https://github.com/jchen1981/MicrobiomeDDA.Supplementary informationSupplementary data are available at Bioinformatics online.
Quantification of Propionic Acid in the Bovine Spinal Disk After Infection of the Tissue With Propionibacteria acnes Bacteria
Authors: Magnitsky Sergey , Dudli Stefan , Tang Xinyan , Kaur Jaskanwaljeet , Diaz Joycelyn , Miller Steve , Lotz Jeffrey C. 
Published: October 2017

Study Design.
Research.

Objective.
The goal of this study was to investigate whether Propionibacteria acnes infection of the intervertebral disc can be detected noninvasively by nuclear magnetic resonance (NMR) spectroscopy.

Summary of Background Data.
Microbiological studies of surgical samples suggest that a significant subpopulation of back pain patients may have occult disc infection with P. acnes bacteria. This hypothesis is further supported by a double-blind clinical trial showing that back pain patients with Modic type 1 changes may respond to antibiotic treatment. Because significant side effects are associated with antibiotic treatment, there is a need for a noninvasive method to detect whether specific discs in back pain patients are infected with P acnes bacteria.

Methods.

P. acnes bacteria were obtained from human patients. NMR detection of a propionic acid (PA) in the bacteria extracts was conducted on 500 MHz high-resolution spectrometer, whereas in vivo NMR spectroscopy of an isolated bovine disk tissue infected with P. acnes was conducted on 7 T magnetic resonance imaging scanner.

Results.
NMR spectra of P. acnes metabolites revealed a distinct NMR signal with identical chemical shits (1.05 and 2.18 ppm) as PA (a primary P. acne metabolite). The 1.05 ppm signal does not overlap with other bacteria metabolites, and its intensity increases linearly with P. acnes concentration. Bovine disks injected with P. acnes bacteria revealed a very distinct NMR signal at 1.05 ppm, which linearly increased with P. acnes concentration.

Conclusion.
The 1.05 ppm NMR signal from PA can be used as a marker of P. acnes infection of discs. This signal does not overlap with other disc metabolites and linearly depends on P. acnes concentration. Consequently, NMR spectroscopy may provide a noninvasive method to detect disc infection in the clinical setting.

Level of Evidence: N/A
Outcomes of ICU Patients With a Discharge Diagnosis of Critical Illness Polyneuromyopathy: A Propensity-Matched Analysis
Authors: Kelmenson Daniel A. , Held Natalie , Allen Richard R. , Quan Dianna , Burnham Ellen L. , Clark Brendan J. , Ho P. Michael , Kiser Tyree H. , Vandivier R. William , Moss Marc 
Published: October 2017

Objectives:
To assess the impact of a discharge diagnosis of critical illness polyneuromyopathy on health-related outcomes in a large cohort of patients requiring ICU admission.

Design:
Retrospective cohort with propensity score–matched analysis.

Setting:
Analysis of a large multihospital database.

Patients:
Adult ICU patients without preexisting neuromuscular abnormalities and a discharge diagnosis of critical illness polyneuropathy and/or myopathy along with adult ICU propensity-matched control patients.

Interventions:
None.

Measurements and Main Results:
Of 3,567 ICU patients with a discharge diagnosis of critical illness polyneuropathy and/or myopathy, we matched 3,436 of these patients to 3,436 ICU patients who did not have a discharge diagnosis of critical illness polyneuropathy and/or myopathy. After propensity matching and adjusting for unbalanced covariates, we used conditional logistic regression and a repeated measures model to compare patient outcomes. Compared to patients without a discharge diagnosis of critical illness polyneuropathy and/or myopathy, patients with a discharge diagnosis of critical illness polyneuropathy and/or myopathy had fewer 28-day hospital-free days (6 [0.1] vs 7.4 [0.1] d; p < 0.0001), had fewer 28-day ventilator-free days (15.7 [0.2] vs 17.5 [0.2] d; p < 0.0001), had higher hospitalization charges (313,508 [4,853] vs 256,288 [4,470] dollars; p < 0.0001), and were less likely to be discharged home (15.3% vs 32.8%; p < 0.0001) but had lower in-hospital mortality (13.7% vs 18.3%; p < 0.0001).

Conclusions:
In a propensity-matched analysis of a large national database, a discharge diagnosis of critical illness polyneuropathy and/or myopathy is strongly associated with deleterious outcomes including fewer hospital-free days, fewer ventilator-free days, higher hospital charges, and reduced discharge home but also an unexpectedly lower in-hospital mortality. This study demonstrates the clinical importance of a discharge diagnosis of critical illness polyneuropathy and/or myopathy and the need for effective preventive interventions.
Dysphagia in Mechanically Ventilated ICU Patients (DYnAMICS): A Prospective Observational Trial
Authors: Schefold Joerg C. , Berger David , Zürcher Patrick , Lensch Michael , Perren Andrea , Jakob Stephan M. , Parviainen Ilkka , Takala Jukka 
Published: October 2017

Objectives:
Swallowing disorders may be associated with adverse clinical outcomes in patients following invasive mechanical ventilation. We investigated the incidence of dysphagia, its time course, and association with clinically relevant outcomes in extubated critically ill patients.

Design:
Prospective observational trial with systematic dysphagia screening and follow-up until 90 days or death.

Settings:
ICU of a tertiary care academic center.

Patients:
One thousand three-hundred four admissions of mixed adult ICU patients (median age, 66.0 yr [interquartile range, 54.0–74.0]; Acute Physiology and Chronic Health Evaluation-II score, 19.0 [interquartile range, 14.0–24.0]) were screened for postextubation dysphagia. Primary ICU admissions (n = 933) were analyzed and followed up until 90 days or death. Patients from an independent academic center served as confirmatory cohort (n = 220).

Interventions:
Bedside screening for dysphagia was performed within 3 hours after extubation by trained ICU nurses. Positive screening triggered confirmatory specialist bedside swallowing examinations and follow-up until hospital discharge.

Measurements and Main Results:
Dysphagia screening was positive in 12.4% (n = 116/933) after extubation (18.3% of emergency and 4.9% of elective patients) and confirmed by specialists within 24 hours from positive screening in 87.3% (n = 96/110, n = 6 missing data). The dysphagia incidence at ICU discharge was 10.3% (n = 96/933) of which 60.4% (n = 58/96) remained positive until hospital discharge. Days on feeding tube, length of mechanical ventilation and ICU/hospital stay, and hospital mortality were higher in patients with dysphagia (all p < 0.001). The univariate hazard ratio for 90-day mortality for dysphagia was 3.74 (95% CI, 2.01–6.95; p < 0.001). After adjustment for disease severity and length of mechanical ventilation, dysphagia remained an independent predictor for 28-day and 90-day mortality (excess 90-d mortality 9.2%).

Conclusions:
Dysphagia after extubation was common in ICU patients, sustained until hospital discharge in the majority of affected patients, and was an independent predictor of death. Dysphagia after mechanical ventilation may be an overlooked problem. Studies on underlying causes and therapeutic interventions seem warranted.
Personal and Professional Characteristics of U.S. Dual-Boarded Critical Care Cardiologists in 2015
Authors: Blumenthal Daniel M. , Mikhael Bassem , Lawler Patrick R. , Yeh Robert W. , Metlay Joshua P. , Dudzinski David M. 
Published: October 2017

Objectives:
Evaluate the characteristics of U.S. physicians who are board certified in cardiology and critical care medicine (“dual-boarded cardiologists”).

Design:
Retrospective cross-sectional study using a comprehensive database of licensed U.S. physicians linked to Medicare claims.

Setting:
The United States.

Subjects:
Dual-boarded cardiologists.

Measurements and Main Results:
We used a comprehensive physician database to identify all physicians who were board certified in cardiology and critical care medicine before July 2015. We assessed physicians’ characteristics and compared dual-boarded cardiologists with and without active board certification in critical care medicine and estimated the maximum proportion of 2014 Medicare Cardiac ICU admissions treated by dual-boarded cardiologists. Among 473 dual-boarded cardiologists, 16 (3.4%) were women; 468 (99%) and 85 (18%) maintained active board certification in cardiology and critical care medicine, respectively. Overall, 98 dual-boarded cardiologists (21%) submitted 1,215 total claims for critical care services in 2014. Compared to dual-boarded cardiologists without active board certification in critical care medicine, those with active certification had more publications (median publications: 6.5 vs 3.0; p = 0.002), were more likely to be professors (22.3% vs 9.5%; p = 0.003), and were more likely to bill Medicare for critical care services (29% vs 17.8%; p = 0.002). We estimated that no more than 0.47% of all 2014 Medicare Cardiac ICU admissions were treated by a dual-boarded cardiologist.

Conclusions:
Dual-boarded cardiologists appear to deliver a small proportion of all Cardiac ICU services received by Medicare beneficiaries. Optimizing the modern Cardiac ICU workforce will require greater efforts to promote and support the training of dual-boarded cardiologists.
Novel Sternal Protection Device for Cardiac Surgery via Median Sternotomy Incision
Authors: Marasco Silvana F. , McGiffin David C. , Zimmet Adam D. , Soils Pablo C. , Bingham Judy M. , Moshinsky Randall A. 
Published: October 2017

Objective Sternal bleeding during cardiac surgery is currently controlled using bone wax or other chemical substances that may result in adverse effects and affect wound healing and recovery. The purpose of this study was to identify a safe, cost-effective, and easy-to-use technique to reduce sternal bleeding and sternal trauma during cardiac surgery. Methods After sternotomy, a sternal protection device was placed over each hemisternal section before insertion of the retractor and remained in situ until the end of surgery. Sternal bleeding and ease of use were assessed and recorded during surgery. Sternal trauma was assessed and recorded within 5 minutes of removal of the device, and overall satisfaction (Global Impression) and any intraoperative adverse events or device malfunction were reported at surgery completion. Patients were followed up 24 hours and 4 weeks after surgery. Results Twelve patients completed the study. Adverse events reported were not considered related to the device. No sternal trauma was identified in any patient. In 9 of 11 patients, sternal bleeding was reduced after insertion of the device. The device was generally considered easy to use, although some difficulty was encountered when used with the Internal Mammary Artery retractor. Conclusions Our data suggest that the device is safe and able to reduce sternal bleeding during surgery using sternal retractors. We recommend further studies in a larger population of patients with a control group to evaluate the device's ability to reduce the morbidity associated with sternal bleeding and sternal trauma.
Renal dysfunction and cirrhosis
Authors: Durand François , Olson Jody C. , Nadim Mitra K. 
Published: October 2017

Purpose of review
Hepatorenal syndrome (HRS) does not represent the predominant phenotype of acute kidney injury (AKI) in cirrhosis. Early recognition of HRS helps initiate appropriate therapy. The aims of this review are to present redefinition of AKI, to list new biomarkers, to report recent data on vasopressors in HRS and to propose criteria for simultaneous liver and kidney transplantation (SLKT).

Recent findings
Urine output, which was not part of the definition of AKI might be reconsidered as it has an independent prognostic value. Biomarkers (NGAL and IL-18) could help identify ATN. However, cut-off values have to be clarified. Vasopressors with albumin represent first option in HRS. Continuous infusion of terlipressin has a better safety profile than intravenous boluses. SLKT should be considered whenever native kidney recovery is unlikely [i.e. prolonged renal replacement therapy (RRT) and/or GFR less than 25 ml/min for 6 weeks prior to transplantation].

Summary
New definitions and recent biomarkers may help differentiate HRS from ATN at an earlier stage. Urine output should be reconsidered in the definitions. Even in patients who are not candidates for transplantation, a short trial of RRT is justified whenever needed. SLKT should be considered whenever posttransplant renal recovery is unlikely.
Favorable liver cancer mortality-to-incidence ratios of countries with high health expenditure
Authors: Wang Chi-Chih , Tsai Ming-Chang , Peng Cheng-Ming , Lee Hsiang-Lin , Chen Hsuan-Yi , Yang Tzu-Wei , Sung Wen-Wei , Lin Chun-Che 
Published: October 2017

Objective
Health expenditure is a marker associated with an advanced healthcare system, which contributes toward the good prognosis of patients. Mortality-to-incidence ratios (MIRs) are one of the predictors that reflect the prognosis of cancer patients. There remains some uncertainty on the correlation of MIRs of liver cancer with the health expenditure of countries.

Methods
We therefore analyzed the correlation of MIRs from the GLOBOCAN 2012 database with the WHO rankings and the total expenditures on health/gross domestic product from WHO by linear regression analyses. A total of 29 countries were selected in this study according to the data quality and the incidence number.

Results
The results showed high rates of incidence/mortality and MIRs in less developed regions (0.92 vs. 0.96 for more vs. less developed regions). Among the continents, Asia has the highest incidence/mortality in case number, crude rate, and age-standardized rate. In terms of the MIR, Northern America has the lowest MIR and Latin America and the Caribbean have the highest MIRs (0.82 and 1.04, respectively). Finally, favorable MIRs are associated significantly with good WHO ranking and high expenditures on gross domestic product (P=0.048 and 0.025, respectively).

Conclusion
The MIR variation for liver cancer is thus found to be associated with the health expenditure and WHO ranking.