bluuebunny/crossref_metadata_2025_split huggingface dataset:
VALUE OF FRACTAL ANALYSIS OF OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY IN VARIOUS STAGES OF DIABETIC RETINOPATHY
Authors: Bhardwaj Suruchi , Tsui Edmund , Zahid Sarwar , Young Emma , Mehta Nitish , Agemy Steven , Garcia Patricia , Rosen Richard B. , Young Joshua A. 
Published: July 2017

Purpose:
To use fractal dimensional analysis to investigate retinal vascular disease patterns in patients with diabetic retinopathy using spectral domain optical coherence tomography angiography.

Methods:
A retrospective study was conducted which included 49 eyes from 26 control subjects and 58 eyes from 35 patients known to have diabetic retinopathy. Of the 58 eyes with known retinopathy, 31 were categorized as nonproliferative diabetic retinopathy (13 mild, 9 moderate, and 9 severe) and 27 were categorized as proliferative diabetic retinopathy. Optical coherence tomography angiography images were acquired using the RTVue XR Avanti (Optovue, Inc). Automated segmentation was obtained through both the superficial and deep capillary plexuses for each eye. Grayscale optical coherence tomography angiography images were standardized and binarized using ImageJ (National Institutes of Health). Fractal box-counting analyses were conducted using Fractalyse (ThéMA). Fractal dimensions (FDs) and correlation coefficient of the superficial and deep capillary plexuses were compared between control eyes and those in various stages of diabetic retinopathy.

Results:
The superficial and deep capillary plexuses from diabetic and control eyes were analyzed. The average FD for diabetic eyes was significantly lower than in control eyes in the superficial plexus (P = 2.4 × 10−6) and in the deep capillary plexus (P = 1.87 × 10 −12) with a more statistically significant difference noted in the deep capillary plexus. When analyzing diabetic patients without edema noted on optical coherence tomography, the FD was significantly reduced in the superficial (P = 0.001) and deep (P = 1.49 × 10−6) plexuses. When analyzing diabetic patients with edema noted on optical coherence tomography, the FD was significantly reduced in the superficial (P = 2.0 × 10−5) and deep (P = 1.85 × 10−9) plexuses.

Conclusion:
The optical coherence tomography angiography FD is significantly lower in both superficial and deep capillary plexuses in eyes with all stages studied of diabetic retinopathy. The results were more often significant for the deep capillary plexus. The use of fractal analysis provides an objective criterion to assess microvascular disease burden in diabetic retinopathy.
Prevalence of Persistent Renal Dysfunction in Perinatally HIV-infected Thai Adolescents
Authors: Bunupuradah Torsak , Phupitakphol Tanit , Sophonphan Jiratchaya , Prasitsuebsai Wasana , Anugulruengkitt Suvaporn , Jantarabenjakul Watsamon , Sopa Bunruan , Ruxrungtham Kiat , Chanakul Ankanee , Puthanakit Thanyawee 
Published: July 2017

Background:
Persistent renal dysfunction (PRD) has been reported in up to 22% of perinatally HIV-infected adolescents (PHAs) in the United States and Europe. There are limited data available on PRD among PHAs in resource-limited settings regarding access to antiretroviral therapy (ART) at more advanced HIV stages.

Methods:
We retrospectively described the prevalence of PRD and associated factors in a Thai PHA cohort. Inclusion criteria were current age ≥10 years old and at least 2 serum creatinine (Cr) measurements after ART initiation. Cr and urine examination were performed every 6–12 months. PRD was defined as having ≥2 measurements of low estimated glomerular filtration rate (eGFR); either <60 mL/min/1.73 m2 or elevated Cr for age and eGFR 60–89 mL/min/1.73 m2, or proteinuria (dipstick proteinuria ≥1+). Factors associated with PRD were analyzed using a multivariate logistic regression analysis.

Results:
This study included 255 PHAs with median (interquartile range) age of 16.7 (14.5–18.8) and ART duration of 10.3 (7.1–12.4) years. Fifty-six percentage used boosted protease inhibitor (bPI)–based regimens, and 63% used tenofovir disoproxil fumarate (TDF). The overall PRD prevalence was 14.1% [95% confidence interval (CI): 10.1–19.0]; low eGFR 6.7%, proteinuria 3.5% and both 3.9%. Among 109 users of TDF with bPI, 22.9% had PRD and 2.8% discontinued/adjusted dosing of TDF because of nephrotoxicity. Factors associated with PRD were age 10–15 years old (adjusted odd ratio (aOR): 10.1, 95% CI: 4.1–25.2), male (aOR: 3.2, 95% CI: 1.4–7.7), CD4 nadir <150 cells/mm3 (aOR: 2.6, 95% CI: 1.1–6.1) and use of TDF with bPI (aOR: 9.6, 95% CI: 3.2–28.9).

Conclusions:
PRD is common among PHAs. Almost one-fifth of adolescents using TDF with bPI had PRD. These adolescents should be a priority group for renal monitoring.
A Retrospective Cohort Study of the Incidence, Health Care Resource Utilization and Costs of International Classification of Diseases, Clinical Modification, 9th Revision Diagnosed Influenza and Related Complications in US Children
Authors: Buck Philip O. , Smith David M. , Shenolikar Rahul , Irwin Debra E. 
Published: July 2017

Background:
There is a paucity of data on the clinical and economic impact of seasonal influenza in children. This study estimated the incidence of diagnosed influenza and related complications and associated health care resource utilization and costs in US children.

Methods:
Children ≥6 months and <18 years old diagnosed with influenza using International Classification of Diseases, Clinical Modification, 9th revision codes and enrolled in a health plan during at least one influenza season between 2010 and 2014 were matched to similar patients without diagnosed influenza (GSK study identifier: HO-15-15728). Outcomes included incidence of influenza and complications, health care resource utilization frequency and health care costs during 21 days of follow-up. Adjusted costs were estimated using generalized linear models.

Results:
Incidence (per 1000) of influenza was 20.3 (commercially insured) and 32.6 (Medicaid), with the highest incidence among 6–35 months old (Commercial: 26.8; Medicaid: 47.9). Approximately 12%–17% of influenza patients experienced complications, with the 6–35 months group having the highest percentage (25%–30%). The 6–35-month-old influenza patients with complications had the highest proportion with hospitalizations (5%–6%) and emergency room visits (Commercial: 19%; Medicaid: 36%). Influenza patients with (vs. without) complications had greater adjusted mean influenza-specific costs (Commercial: $1161 vs. $337; Medicaid: $1199 vs. $354; P<0.05), and influenza cases (vs. controls) had greater adjusted mean all-cause costs (Commercial: $688 vs. $470; Medicaid: $818 vs. $453; P < 0.05).

Conclusions:
Pediatric patients with influenza incurred higher health care costs compared with matched controls, and influenza-specific costs were greater among those with complications.
Four-year Outcomes After Cessation of Tenofovir in Immune-tolerant Chronic Hepatitis B Patients
Authors: Wong Vincent Wai-Sun , Hui Aric J. , Wong Grace Lai-Hung , Chan Rosita Suk-Yi , Chim Angel Mei-Ling , Lo Angeline Oi-Shan , Chan Henry Lik-Yuen 
Published: July 2017

Goals:
To study the long-term outcome after cessation of antiviral therapy in immune-tolerant patients.

Background:
Experience in the treatment of immune-tolerant chronic hepatitis B is scanty. Some immune-tolerant patients may receive temporary antiviral therapy, such as for prevention of vertical transmission at pregnancy or prophylaxis for chemotherapy.

Study:
This was a follow-up study of a phase 2 trial at 2 centers. Immune-tolerant patients received tenofovir disoproxil fumarate and/or emtricitabine for 4 years and were followed for another 4 years after treatment cessation. Virological relapse was defined as hepatitis B virus (HBV) DNA>2000 IU/mL; clinical relapse was defined as HBV DNA>2000 IU/mL; and alanine aminotransferase (ALT)>2 times the upper limit of normal.

Results:
In total, 20 patients stopped treatment and were followed up for 206±14 weeks. All patients developed virological relapse at posttreatment week 4 (HBV DNA, 7.07±1.45 log IU/mL). A total of 10 (50%) patients developed clinical relapse at 15±11 weeks (highest ALT, 1149 U/L). In total, 11 (55%) patients were restarted on antiviral therapy; 4 achieved complete HBV DNA suppression and 1 achieved hepatitis B e antigen (HBeAg) seroconversion. Among the 9 patients not restarted on therapy, 2 patients had HBeAg seroconversion with normal ALT and HBV DNA of 7.12 and 1.62 IU/mL, respectively. The remaining 7 untreated patients continued to have positive HBeAg, high HBV DNA, and normal ALT.

Conclusions:
Rapid virological relapse is universal and clinical relapse is common after stopping antiviral therapy in patients with immune-tolerant chronic hepatitis B. HBeAg seroconversion is rare regardless of treatment reinitiation.
Medicaid and Uninsured Hepatocellular Carcinoma Patients Have More Advanced Tumor Stage and Are Less Likely to Receive Treatment
Authors: Wang Jennifer , Ha John , Lopez Aristeo , Bhuket Taft , Liu Benny , Wong Robert J. 
Published: July 2017

Goals:
To evaluate the impact of insurance status on tumor stage at diagnosis, treatment received, and overall survival among adults with hepatocellular carcinoma (HCC).

Background:
Insurance status affects access to care, which impacts timely access to cancer screening for early detection and treatment.

Study:
Using the 2007 to 2012 Surveillance, Epidemiology, and End Results (SEER) database, we retrospectively evaluated US adults with HCC. Insurance status included Medicare/commercial insurance (MC), Medicaid (MA), and no insurance (NI). HCC tumor stage was evaluated using SEER staging system and Milan criteria. HCC treatment and survival were evaluated using multivariate logistic regression and Cox proportional hazards models.

Results:
Among 32,388 HCC patients (71.2% MC, 23.9% MA, and 4.9% NI), patients with MA or NI were significantly less likely to have localized tumor stage at time of diagnosis compared with MC [NI vs. MC; odds ratio, 0.41; 95% confidence interval (CI), 0.78-0.92; P<0.001]. MA and NI patients were less likely to receive treatment, and specifically less likely to receive surgical resection or liver transplantation compared with MC patients, even after correcting for tumor stage at diagnosis (odds of surgical resection or liver transplant in NI vs. MC: odds ratio, 0.26; 95% CI, 0.21-0.33; P<0.001). NI patients (hazard ratio, 1.39; 95% CI, 1.29-1.50; P<0.001) had significantly lower survival compared with MC patients.

Conclusions:
Among US adults with HCC, MA, or NI patients had more advanced tumor stage at diagnosis, lower rates treatment, and significantly lower overall survival. Ensuring equal insurance coverage may improve access to care and mitigate some disparities in HCC outcomes.
Management of chest pain in the French emergency healthcare system: the prospective observational EPIDOULTHO study
Authors: Charpentier Sandrine , Beaune Sebastien , Joly Luc Marie , Khoury Abdo , Duchateau François-Xavier , Briot Raphael , Renaud Bertrand , Ageron François-Xavier 
Published: July 2017

Objective
The aim of this paper was to describe the epidemiology, and diagnostic and therapeutic strategies that emergency physicians use to manage patients presenting with chest pain at all three levels of the French emergency medical system – that is, dispatch centres (SAMUs: the medical emergency system), which operate the mobile intensive care units (MICUs), and hospitals’ emergency departments (EDs), with a focus on acute coronary syndrome (ACS).

Patients and methods
All patients with chest pain who contacted a SAMU and/or were managed by a MICU and/or were admitted into an ED were included in a 1-day multicentre prospective study carried out in January 2013. Data on diagnostic and therapeutic management and disposition were collected. An in-hospital follow-up was performed.

Results
In total, 1339 patients were included: 537 from SAMU, 187 attended by a MICU and 615 in EDs. Diagnosing ACS was the main diagnostic strategy of the French emergency care system, diagnosed in 16% of SAMU patients, 25% of MICU patients and 10% of ED patients. Among patients calling the SAMU, 76 (14%) received only medical advice, 15 (8%) patients remained at home after being seen by a MICU and 454 (74%) were discharged from an ED.

Conclusion
Management of chest pain at the three levels of the French medical emergency system is mainly oriented towards ruling out ACS. The strategy of diagnostic management is based on minimizing missed diagnoses of ACS.
Pediatric mitochondrial diseases and the heart
Authors: Enns Gregory M. 
Published: July 2017

Purpose of review
Mitochondrial disorders are an increasingly recognized cause of heart dysfunction, with the primary manifestations being cardiomyopathy and conduction defects. This review focuses on the complex genetics of mitochondrial disease and recently discovered conditions that affect mitochondrial function.

Recent findings
Next-generation sequencing techniques, especially whole-exome sequencing, have led to the discovery of a number of conditions that cause mitochondrial dysfunction and subsequent cardiac abnormalities. Nuclear DNA defects are the main cause of mitochondrial disease in children, with disease pathogenesis being related to either abnormalities in specific mitochondrial electron transport chain subunits or in proteins related to subunit or mitochondrial DNA maintenance, mitochondrial protein translation, lipid bilayer structure, or other aspects of mitochondrial function.

Summary
Currently, symptomatic therapy using standard medications targeting relief of complications is the primary approach to treatment. There are no US Food and Drug Administration-approved therapies for the specific treatment of mitochondrial disease. However, on the basis of recent advances in understanding of the pathophysiology of these complex disorders, various novel approaches are either in clinical trials or in development.
Critical Evaluation of Metallization in Electric Injury
Authors: Laima Sigitas , Bytautaite Jana , Chmieliauskas Sigitas , Fomin Dmitrij , Jasulaitis Algimantas , Jukna Arturas , Mazeikiene Sandra , Stasiuniene Jurgita 
Published: July 2017

Abstract
The article presents 3 forensic medicine cases in the field of electric injury. In addition to traditional findings in electric injury (electric mark and histological findings), the forensic medicine experts in Lithuania also perform an atomic absorption spectrometry analysis. This method confirms the effects of electric current to the body through the electric conductor. Typical macroscopic finding in the skin is electric mark. Histologically, the damaged skin possesses characteristic features of thermal burns. The atomic absorption spectroscopy analysis identifies traces of metal particles devolved from the electrical conductor, which confirms a premortal contact with it. In one of our presented cases, the metallization was negative, although there were obvious data of electric current effect. This shows that it is not always worth to rely on the method of atomic absorption spectrometry analysis recognized worldwide in forensic medicine. The determination of electrical injury diagnosis requires a critical and comprehensive assessment of all the available data and laboratory tests.
Somatotopic Fascicular Lesions of the Brachial Plexus Demonstrated by High-Resolution Magnetic Resonance Neurography
Authors: Hilgenfeld Tim , Jende Johann , Schwarz Daniel , Bäumer Philipp , Kollmer Jennifer , Heiland Sabine , Bendszus Martin , Pham Mirko 
Published: July 2017

Objectives
The aim of this study was to evaluate whether high-resolution brachial plexus (BP) magnetic resonance neurography (MRN) is capable of (1) distinguishing patients with compressive neuropathy or noncompressive plexopathy from age- and sex-matched controls, (2) discriminating between patients with compressive neuropathy and noncompressive plexopathy, and (3) detecting spatial lesion patterns suggesting somatotopic organization of the BP.

Materials and Methods
Thirty-six patients (50.9 ± 12.7 years) with clinical symptoms, nerve conduction studies, and needle electromyography findings suggestive of brachial plexopathy and 36 control subjects matched for age and sex (50.8 ± 12.6 years) underwent high-resolution MRN of the BP. Lesion determination and localization was performed by 2 blinded neuroradiologists at the anatomical levels of the plexus trunks and cords.

Results
By applying defined criteria of structural plexus lesions on high-resolution MRN, all patients were correctly rated as affected, whereas 34 of 36 controls were correctly rated as unaffected by independent and blinded reading from 2 neuroradiologists with overall good to excellent interrater reliability. In all cases, plexopathies with a compressive etiology (n = 12) were correctly distinguished from noncompressive plexopathies with inflammatory origin (n = 24). Pathoanatomical contiguity of lesion from trunk into cord level allowed recognition of distinct somatotopical patterns of fascicular involvement, which correlated closely with the spatial distribution of clinical symptoms and electrophysiological data.

Conclusions
Brachial plexus MRN is highly accurate for differentiating patients with symptomatic plexopathy from healthy controls and for distinguishing patients with compressive neuropathy and noncompressive plexopathy. Furthermore, BP MRN revealed evidence for somatotopic organization of the BP. Therefore, as an addition to functional information of electrodiagnostic studies, anatomical information gained by BP MRN may help to improve the efficiency and accuracy of patient care.
The role of intraspecific variation in the ecological and evolutionary success of diatoms in changing environments
Authors: Godhe Anna , Rynearson Tatiana 
Published: July 2017

Intraspecific variation in diatoms has been shown to play a key role in species' responses to several important environmental factors such as light, salinity, temperature and nutrients. Furthermore, modelling efforts indicate that this variation within species extends bloom periods, and likely provides sufficient variability in competitive interactions between species under hydrographically variable conditions. The intraspecific variation most likely corresponds to optimal fitness in temporary microhabitats and may help to explain the paradox of the plankton. Here, we examine the implications of intraspecific variation for the ecology and success of diatoms in general and emphasize the potential implications for our understanding of carbon metabolism in these important organisms. Additionally, data from palaeoecological studies have the potential for evaluating genetic variation through past climate changes, going thousands of years back in time. We suggest pathways for future research including the adoption of multiple strains of individual species into studies of diatom carbon metabolism, to refine our understanding of the variation within and between species, and the inclusion of experimental evolution as a tool for understanding potential evolutionary responses of diatom carbon metabolism to climate change.This article is part of the themed issue ‘The peculiar carbon metabolism in diatoms’.
The effects of phosphorus limitation on carbon metabolism in diatoms
Authors: Brembu Tore , Mühlroth Alice , Alipanah Leila , Bones Atle M. 
Published: July 2017

Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms. Two transcriptome studies are analysed in detail, supplemented by other transcriptome, proteome and metabolite data, to gain an overview of different pathways and their responses. Phosphorus, nitrogen and silicon limitation responses are compared, and similarities and differences discussed. We use the current knowledge to propose a suggestive model for the carbon flow in phosphorus-replete and phosphorus-limited diatom cells.
This article is part of the themed issue ‘The peculiar carbon metabolism in diatoms’.
pyABC: distributed, likelihood-free inference
Authors: Klinger Emmanuel , Rickert Dennis , Hasenauer Jan 
Published: July 2017

SummaryLikelihood-free methods are often required for inference in systems biology. While Approximate Bayesian Computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements computation-minimizing and scalable, runtime-minimizing parallelization strategies for multi-core and distributed environments scaling to thousands of cores. The framework is accessible to non-expert users and also enables advanced users to experiment with and to custom implement many options of ABC-SMC schemes, such as acceptance threshold schedules, transition kernels and distance functions without alteration of pyABC’s source code. pyABC includes a web interface to visualize ongoing and 1nished ABC-SMC runs and exposes an API for data querying and post-processing.Availability and ImplementationpyABC is written in Python 3 and is released under the GPLv3 license. The source code is hosted onhttps://github.com/neuralyzer/pyabcand the documentation onhttp://pyabc.readthedocs.io. It can be installed from the Python Package Index (PyPI).
Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs
Authors: Liu Wan-Hsin , Tsai Zing Tsung-Yeh , Tsai Huai-Kuang 
Published: July 2017

AbstractBackgroundThe regulatory roles of long intergenic noncoding RNAs (lincRNAs) in humans have been revealed through the use of advanced sequencing technology. Recently, three possible scenarios of lincRNA origin have been proposed:de novoorigination from intergenic regions, duplication from long noncoding RNA, and pseudogenization from protein. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudo genized protein-coding sequence to lincRNA. Due to the non-mutually exclusive nature that these three scenarios have, accompanied by the need of systematic investigation of lincRNA origination, we conduct a comparative genomics study to investigate the evolution of human lincRNAs.ResultsCombining with syntenic analysis and stringent Blastne-value cutoff, we found that the majority of lincRNAs are aligned to the intergenic regions of other species. Interestingly, 193 human lincRNAs could have protein-coding orthologs in at least two of nine vertebrates. Transposable elements in these conserved regions in human genome are much less than expectation. Moreover, 19% of these lincRNAs have overlaps with or are close to pseudogenes in the human genome.ConclusionsWe suggest that a notable portion of lincRNAs could be derived from pseudogenized protein-coding genes. Furthermore, based on our computational analysis, we hypothesize that a subset of these lincRNAs could have potential to regulate their paralogs by functioning as competing endogenous RNAs. Our results provide evolutionary evidence of the relationship between human lincRNAs and protein-coding genes.