bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haemodialysis: hospital or home?
Authors: Power Albert , Ashby Damien 
Published: November 2013

Abstract
Healthcare costs associated with the provision of dialysis therapy are escalating globally as the number of patients developing end-stage renal disease increases. In this setting, there has been heightened interest in the application and potential benefit of home haemodialysis therapies compared with the conventional approach of thrice weekly, incentre treatments. Increasingly, national healthcare systems are financially incentivising the expansion of home haemodialysis programmes with observational studies demonstrating better patient survival, superior control of circulating volume and blood pressure, greater patient satisfaction and lower running costs compared with incentre dialysis. Nonetheless, increasing the prevalence of home haemodialysis is challenged by the technological complexity of conventional dialysis systems, the need for significant adaptations to the home as well as suboptimal clinician and patient education about the feasibility and availability of this modality. In addition, enthusiasm about frequent as well as nocturnal (extended-hours) haemodialysis has been tempered by results from the recent Frequent Haemodialysis Network randomised controlled trials comparing these schedules with a conventional incentre regime. An increasing emphasis on empowering patient choice and promoting self-management of chronic illness is a powerful driver for the expansion of home haemodialysis programmes in the UK and internationally.
Serum Levels of Cytokines and Biomarkers for Inflammation and Immune Activation, and HIV-Associated Non-Hodgkin B-Cell Lymphoma Risk
Authors: Vendrame Elena , Hussain Shehnaz K. , Breen Elizabeth Crabb , Magpantay Larry I. , Widney Daniel P. , Jacobson Lisa P. , Variakojis Daina , Knowlton Emilee R. , Bream Jay H. , Ambinder Richard F. , Detels Roger , Martínez-Maza Otoniel 
Published: November 2013

AbstractBackground: HIV infection is associated with a marked increase in risk for non-Hodgkin lymphoma (AIDS-NHL). However, the mechanisms that promote the development of AIDS-NHL are not fully understood.Methods: In this study, serum levels of several cytokines and other molecules associated with immune activation were measured in specimens collected longitudinally during 1 to 5 years preceding AIDS-NHL diagnosis, in 176 AIDS-NHL cases and 176 HIV+ controls from the Multicenter AIDS Cohort Study (MACS).Results: Multivariate analyses revealed that serum levels of immunoglobulin free light chains (FLC), interleukin (IL)-6, IL-10, IP-10/CXCL10, neopterin, and TNF-α were elevated in those HIV+ individuals who went on to develop AIDS-NHL. In addition, the fraction of specimens with detectable IL-2 was increased and the fraction with detectable IL-4 was decreased in these subjects.Conclusions: These results suggest that long-term, chronic immune activation, possibly driven by macrophage-produced cytokines, precedes development of NHL in HIV+ individuals.Impact: FLC, IL-6, IL-10, IP-10/CXCL10, neopterin, and TNF-α may serve as biomarkers for AIDS-NHL. Cancer Epidemiol Biomarkers Prev; 23(2); 343–9. ©2013 AACR.
Plasma Alkylresorcinol Metabolites as Biomarkers for Whole-Grain Intake and Their Association with Prostate Cancer: A Swedish Nested Case–Control Study
Authors: Drake Isabel , Sonestedt Emily , Gullberg Bo , Bjartell Anders , Olsson Håkan , Adlercreutz Herman , Tikkanen Matti J. , Wirfält Elisabet , Wallström Peter 
Published: November 2013

Abstract
Background: Observational studies have mostly found no association between self-reported whole-grain intake and prostate cancer. Plasma alkylresorcinol metabolites have been suggested as biomarkers for whole-grain intake in free-living populations.
Methods: We investigated the major dietary and lifestyle determinants of plasma alkylresorcinol metabolites in a nested case–control study (1,016 cases and 1,817 controls) in the Malmö Diet and Cancer Study. Multivariate adjusted ORs and 95% confidence intervals (95% CI) were estimated to assess the association between plasma alkylresorcinol metabolites and prostate cancer using logistic regression.
Results: Whole-grain intake, waist circumference, educational level, and smoking status were the main determinants of alkylresorcinol metabolites. We observed significant correlations between alkylresorcinol metabolites and whole-grain (r = 0.31) and fiber (r = 0.27) intake. Metabolite concentration was positively associated with prostate cancer risk (Poverall effect = 0.0004) but the association was not linear (P = 0.04). The lowest risk was seen among men with moderate plasma concentrations. The OR for high compared with moderate plasma alkylresorcinol metabolites was 1.41 (95% CI, 1.10–1.80) for prostate cancer.
Conclusions: Results suggest that plasma alkylresorcinol metabolites are mainly determined by whole-grain intake in this nested case–control study of Swedish men. The increased risk of prostate cancer seen among men with high plasma alkylresorcinol metabolites requires further study, but residual confounding, detection bias, or competing risks of nonprostate cancer–related deaths are plausible explanations that could not be ruled out.
Impact: We found no evidence of a protective effect of whole grains on incident prostate cancer. Further validation of alkylresorcinol metabolites as a biomarker for whole-grain intake is needed. Cancer Epidemiol Biomarkers Prev; 23(1); 73–83. ©2013 AACR.
Aortic Annular Sizing Using a Novel 3-Dimensional Echocardiographic Method
Authors: Khalique Omar K. , Kodali Susheel K. , Paradis Jean-Michel , Nazif Tamim M. , Williams Mathew R. , Einstein Andrew J. , Pearson Gregory D. , Harjai Kishore , Grubb Kendra , George Isaac , Leon Martin B. , Hahn Rebecca T. 
Published: November 2013

Background—
Previous studies have shown cross-sectional 3-dimensional (3D) transesophageal echocardiographic (TEE) measurements to severely underestimate multidetector row computed tomographic (MDCT) measurements for the assessment of aortic annulus before transcatheter aortic valve replacement. This study compares annulus measurements from 3D-TEE using off-label use of commercially available software with MDCT measurements and assesses their ability to predict paravalvular regurgitation.

Methods and Results—

One hundred patients with severe, symptomatic aortic stenosis who had both contrast MDCT and 3D-TEE for annulus assessment before balloon-expandable transcatheter aortic valve replacement were analyzed. Annulus area, perimeter, and orthogonal maximum and minimum diameters were measured. Receiver operating characteristic analysis was performed with mild or greater paravalvular regurgitation as the classification variable. Three-dimensional TEE and MDCT cross-sectional perimeter and area measurements were strongly correlated (
r
=0.93–0.94;
P
<0.0001); however, the small differences (≤1%) were statistically significant (
P
=0.0002 and 0.0074, respectively). Discriminatory ability for ≥ mild paravalvular regurgitation was good for both MDCT (area under the curve for perimeter and area cover index=0.715 and 0.709, respectively) and 3D-TEE (area under the curve for perimeter and area cover index=0.709 and 0.694, respectively). Differences in receiver operating characteristic analysis between MDCT and 3D-TEE perimeter and area cover indexes were not statistically significant (
P
=0.15 and 0.35, respectively).

Conclusions—
Annulus measurements using a new method for analyzing 3D-TEE images closely approximate those of MDCT. Annulus measurements from both modalities predict mild or greater paravalvular regurgitation with equivalent accuracy.
Association Between a Hospital’s Quality Performance for In-Hospital Cardiac Arrest and Common Medical Conditions
Authors: Chen Lena M. , Nallamothu Brahmajee K. , Krumholz Harlan M. , Spertus John A. , Tang Fengming , Chan Paul S. 
Published: November 2013

Background—
Public reporting on hospital quality has been widely adopted for common medical conditions. Adding a measure of inpatient survival after cardiac arrest is being considered. It is unknown whether this measure would be redundant, given evidence that hospital organization and culture can have hospital-wide effects on quality. Therefore, we sought to evaluate the correlation between inpatient survival after cardiac arrest and 30-day risk-standardized mortality rates for common medical conditions.

Methods and Results—

Using data between 2007 and 2010 from a national in-hospital cardiac arrest registry, we calculated risk-standardized in-hospital survival rates for cardiac arrest at each hospital. We obtained risk-standardized 30-day mortality rates for acute myocardial infarction, heart failure, and pneumonia from Hospital Compare for the same period. The relationship between a hospital’s performance on cardiac arrest and these other medical conditions was assessed using weighted Pearson correlation coefficients. Among 26 270 patients with in-hospital cardiac arrest at 130 hospitals, survival rates varied across hospitals, with a median risk-standardized hospital survival rate of 22.1% and an interquartile range of 19.7% to 24.2%. There were no significant correlations between a hospital’s outcomes for its cardiac arrest patients and its patients admitted for acute myocardial infarction (correlation, −0.12;
P
=0.16), heart failure (correlation, −0.05;
P
=0.57), or pneumonia (correlation, −0.15;
P
=0.10).

Conclusions—
Hospitals that performed better on publicly reported outcomes for 3 common medical conditions did not necessarily have better cardiac arrest survival rates. Public reporting on cardiac arrest outcomes could provide new information about hospital quality.
Ankle Brachial Index Values, Leg Symptoms, and Functional Performance Among Community‐Dwelling Older Men and Women in the Lifestyle Interventions and Independence for Elders Study
Authors: McDermott Mary M. , Applegate William B. , Bonds Denise E. , Buford Thomas W. , Church Timothy , Espeland Mark A. , Gill Thomas M. , Guralnik Jack M. , Haskell William , Lovato Laura C. , Pahor Marco , Pepine Carl J. , Reid Kieran F. , Newman Anne 
Published: November 2013

Background

The prevalence and significance of low normal and abnormal ankle brachial index (
ABI
) values in a community‐dwelling population of sedentary, older individuals is unknown. We describe the prevalence of categories of definite peripheral artery disease (
PAD
), borderline
ABI
, low normal
ABI,
and no
PAD
and their association with lower‐extremity functional performance in the
LIFE
Study population.

Methods and Results

Participants age 70 to 89 in the
LIFE
Study underwent baseline measurement of the
ABI
, 400‐m walk, and 4‐m walking velocity. Participants were classified as follows: definite
PAD
(
ABI
<0.90), borderline
PAD
(
ABI
0.90 to 0.99), low normal
ABI
(
ABI
1.00 to 1.09), and no
PAD
(
ABI
1.10 to 1.40). Of 1566 participants, 220 (14%) had definite
PAD
, 250 (16%) had borderline
PAD
, 509 (33%) had low normal
ABI
, and 587 (37%) had no
PAD
. Among those with definite
PAD
, 65% were asymptomatic. Adjusting for age, sex, race, body mass index, smoking, and comorbidities, lower
ABI
was associated with longer mean 400‐m walk time: (definite
PAD
=533 seconds; borderline
PAD
=514 seconds; low normal
ABI
=503 seconds; and no
PAD
=498 seconds [
P
<0.001]). Among asymptomatic participants with and without
PAD
, lower
ABI
values were also associated with longer 400‐m walk time (
P
<0.001) and slower walking velocity (
P
=0.042).

Conclusion

Among older community‐dwelling men and women, 14% had
PAD
and 49% had borderline or low normal
ABI
values. Lower
ABI
values were associated with greater functional impairment, suggesting that lower extremity atherosclerosis may be a common preventable cause of functional limitations in older people.

Clinical Trial Registration

URL:
http://clinicaltrials.gov/
Unique identifier: NCT01072500.
Regional Climate Modeling over the Maritime Continent. Part I: New Parameterization for Convective Cloud Fraction
Authors: Gianotti Rebecca L. , Eltahir Elfatih A. B. 
Published: November 2013

Abstract
This paper describes a new method for parameterizing convective cloud fraction that can be used within large-scale climate models, and evaluates the new method using the Regional Climate Model, version 3 (RegCM3), coupled to the land surface scheme Integrated Biosphere Simulator (IBIS). The horizontal extent of convective cloud cover is calculated by utilizing a relationship between the simulated amount of convective cloud water and typical observations of convective cloud water density. This formulation not only provides a physically meaningful basis for the simulation of convective cloud cover, but it is also spatially and temporally variable and independent of model resolution, rendering it generally applicable for large-scale climate models. Simulations over the Maritime Continent show that the new method allows for simulation of an essential convective–radiative feedback, which was absent in the existing version of RegCM3–IBIS, such that moist convection not only responds to diurnal variability at the earth’s surface but also impacts the solar radiation received at the surface via cumulus cloud production. The impact on model performance was mixed, but it is considered that appropriate representation of the convective–radiative feedback and improved physical realism resulting from the new cloud fraction parameterization will likely have positive benefits elsewhere. The role of convective rainfall production in the convective–radiative feedback and a new parameterization for convective autoconversion are addressed in Part II of this paper series.
A New Method for Tracking Meddies by Satellite Altimetry
Authors: Ienna Federico , Jo Young-Heon , Yan Xiao-Hai 
Published: November 2013

Abstract
Subsurface coherent vortices in the North Atlantic, whose saline water originates from the Mediterranean Sea and which are known as Mediterranean eddies (meddies), have been of particular interest to physical oceanographers since their discovery, especially for their salt and heat transport properties into the North Atlantic Ocean. Many studies in the past have been successful in observing and studying the typical properties of meddies by probing them with in situ techniques. The use of remote sensing techniques would offer a much cheaper and easier alternative for studying these phenomena, but only a few past studies have been able to study meddies by remote sensing, and a reliable method for observing them remotely remains elusive. This research presents a new way of locating and tracking meddies in the North Atlantic Ocean using satellite altimeter data. The method presented in this research makes use of ensemble empirical mode decomposition (EEMD) as a means to isolate the surface expressions of meddies on the ocean surface and separates them from any other surface constituents, allowing robust meddies to be consistently tracked by satellite. One such meddy is successfully tracked over a 6-month time period (2 November 2005 to 17 May 2006). Results of the satellite tracking method are verified using expendable bathythermographs (XBT).
ANRIL/CDKN2B-AS shows two-stage clade-specific evolution and becomes conserved after transposon insertions in simians
Authors: He Sha , Gu Weiling , Li Yize , Zhu Hao 
Published: November 2013

Abstract

Background
Many long non-coding RNA (lncRNA) genes identified in mammals have multiple exons and functional domains, allowing them to bind to polycomb proteins, DNA methyltransferases, and specific DNA sequences to regulate genome methylation. Little is known about the origin and evolution of lncRNAs. ANRIL/CDKN2B-AS consists of 19 exons on human chromosome 9p21 and regulates the expression of three cyclin-dependent kinase inhibitors (CDKN2A/ARF/CDKN2B).

Results
ANRIL/CDKN2B-AS originated in placental mammals, obtained additional exons during mammalian evolution but gradually lost them during rodent evolution, and reached 19 exons only in simians. ANRIL lacks splicing signals in mammals. In simians, multiple transposons were inserted and transformed into exons of the ANRIL gene, after which ANRIL became highly conserved. A further survey reveals that multiple transposons exist in many lncRNAs.

Conclusions
ANRIL shows a two-stage, clade-specific evolutionary process and is fully developed only in simians. The domestication of multiple transposons indicates an impressive pattern of “evolutionary tinkering” and is likely to be important for ANRIL’s structure and function. The evolution of lncRNAs and that of transposons may be highly co-opted in primates. Many lncRNAs may be functional only in simians.
Metabolic engineering of Escherichia coli to optimize melanin synthesis from glucose
Authors: Chávez-Béjar María I , Balderas-Hernandez Victor E , Gutiérrez-Alejandre Aída , Martinez Alfredo , Bolívar Francisco , Gosset Guillermo 
Published: November 2013

Abstract

Background
Natural aromatic polymers, mainly melanins, have potential and current applications in the cosmetic, pharmaceutical and chemical industries. The biotechnological production of this class of compounds is based on tyrosinase-dependent conversion of L-tyrosine and other aromatic substrates into melanins. The purpose of this work was to apply metabolic engineering for generating Escherichia coli strains with the capacity to synthesize an aromatic polymer from a simple carbon source.

Results
The strategy was based on the expression in E. coli of the MutmelA gene from Rhizobium etli, encoding an improved mutant tyrosinase. To direct the carbon flow from central metabolism into the common aromatic and the L-tyrosine biosynthetic pathways, feedback inhibition resistant versions of key enzymes were expressed in strains lacking the sugar phosphotransferase system and TyrR repressor. The expressed tyrosinase consumed intracellular L-tyrosine, thus causing growth impairment in the engineered strains. To avoid this issue, a two phase production process was devised, where tyrosinase activity was controlled by the delayed addition of the cofactor Cu. Following this procedure, 3.22 g/L of melanin were produced in 120 h with glucose as carbon source. Analysis of produced melanin by Fourier transform infrared spectroscopy revealed similar characteristics to a pure eumelanin standard.

Conclusions
This is the first report of a process for producing melanin from a simple carbon source at grams level, having the potential for reducing production cost when compared to technologies employing L-tyrosine as raw material.
sybil – Efficient constraint-based modelling in R
Authors: Gelius-Dietrich Gabriel , Desouki Abdelmoneim Amer , Fritzemeier Claus Jonathan , Lercher Martin J 
Published: November 2013

Abstract

Background
Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users.

Results
Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model.

Conclusions
Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).
The neuropeptide Y Y1 receptor knockdown modulates activator protein 1-involved feeding behavior in amphetamine-treated rats
Authors: Hsieh Yih-Shou , Chen Pei-Ni , Yu Ching-Han , Liao Jiuan-Miaw , Kuo Dong-Yih 
Published: November 2013

Abstract

Background
Hypothalamic neuropeptide Y (NPY) and two immediate early genes, c-fos and c-jun, have been found to be involved in regulating the appetite-suppressing effect of amphetamine (AMPH). The present study investigated whether cerebral catecholamine (CA) might regulate NPY and POMC expression and whether NPY Y1 receptor (Y1R) participated in activator protein-1 (AP-1)–mediated feeding.

Methods
Rats were given AMPH daily for 4 days. Changes in the expression of NPY, Y1R, c-Fos, c-Jun, and AP-1 were assessed and compared.

Results
Decreased CA could modulate NPY and melanocortin receptor 4 (MC4R) expressions. NPY and food intake decreased the most on Day 2, but Y1R, c-Fos, and c-Jun increased by approximately 350%, 280%, and 300%, respectively, on Day 2. Similarly, AP-1/DNA binding activity was increased by about 180% on Day 2. The expression patterns in Y1R, c-Fos, c-Jun, and AP-1/DNA binding were opposite to those in NPY during AMPH treatment. Y1R knockdown was found to modulate the opposite regulation between NPY and AP-1, revealing an involvement of Y1R in regulating NPY/AP-1–mediated feeding.

Conclusions
These results point to a molecular mechanism of CA/NPY/Y1R/AP-1 signaling in the control of AMPH-mediated anorexia and may advance the medical research of anorectic and anti-obesity drugs.
Histologic Findings and Clinical Characteristics in Acutely Symptomatic Ulcerative Colitis Patients With Superimposed Clostridium difficile Infection
Authors: Wang Tao , Matukas Larissa , Streutker Catherine J. 
Published: November 2013

Abstract

Objectives
To examine biopsy specimens for histologic features suggestive of Clostridium difficile infection in patients with ulcerative colitis (UC).

Methods
Nine patients with UC had colonic biopsy specimens taken during a symptomatic flare that coincided with positive C difficile (C difficile+) tests. Twenty-eight controls were biopsied during a UC flare but tested negative for C difficile. We reviewed the slides for evidence of pseudomembranes, ischemic-like changes, degree of colitis, and lamina propria hemorrhage.

Results
In C difficile+ patients, 4 (44.4%) of 9 had microscopic pseudomembranes compared with 11% in controls (P &lt; .05). Other histologic/clinical features were not predictive.

Conclusions
Although the presence of microscopic pseudomembranes suggests C difficile infection in patients with UC, sensitivity and specificity are poor; biopsy findings do not reliably detect this infection in patients with UC.