bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regression Analysis of Optical Coherence Tomography Disc Variables for Glaucoma Diagnosis
Authors: Richter Grace M. , Zhang Xinbo , Tan Ou , Francis Brian A. , Chopra Vikas , Greenfield David S. , Varma Rohit , Schuman Joel S. , Huang David 
Published: February 2016

Purpose:
To report diagnostic accuracy of optical coherence tomography (OCT) disc variables using both time-domain (TD) and Fourier-domain (FD) OCT, and to improve the use of OCT disc variable measurements for glaucoma diagnosis through regression analyses that adjust for optic disc size and axial length–based magnification error.

Design:
Observational, cross-sectional.

Participants:
In total, 180 normal eyes of 112 participants and 180 eyes of 138 participants with perimetric glaucoma from the Advanced Imaging for Glaucoma Study.

Methods:
Diagnostic variables evaluated from TD-OCT and FD-OCT were: disc area, rim area, rim volume, optic nerve head volume, vertical cup-to-disc ratio (CDR), and horizontal CDR. These were compared with overall retinal nerve fiber layer thickness and ganglion cell complex. Regression analyses were performed that corrected for optic disc size and axial length. Area-under-receiver-operating curves (AUROC) were used to assess diagnostic accuracy before and after the adjustments. An index based on multiple logistic regression that combined optic disc variables with axial length was also explored with the aim of improving diagnostic accuracy of disc variables.

Main Outcome Measure:
Comparison of diagnostic accuracy of disc variables, as measured by AUROC.

Results:
The unadjusted disc variables with the highest diagnostic accuracies were: rim volume for TD-OCT (AUROC=0.864) and vertical CDR (AUROC=0.874) for FD-OCT. Magnification correction significantly worsened diagnostic accuracy for rim variables, and while optic disc size adjustments partially restored diagnostic accuracy, the adjusted AUROCs were still lower. Axial length adjustments to disc variables in the form of multiple logistic regression indices led to a slight but insignificant improvement in diagnostic accuracy.

Conclusions:
Our various regression approaches were not able to significantly improve disc-based OCT glaucoma diagnosis. However, disc rim area and vertical CDR had very high diagnostic accuracy, and these disc variables can serve to complement additional OCT measurements for diagnosis of glaucoma.
Raised Intraocular Pressure in Nonjuvenile Idiopathic Arthritis-Uveitis Children: Risk Factors and Effect on Retinal Nerve Fiber Layer
Authors: Md Din Norshamsiah , Tomkins-Netzer Oren , Talat Lazha , Taylor Simon R.J. , Isa Hazlita , Bar Asaf , Lightman Sue 
Published: February 2016

Purpose:
To determine risk factors for intraocular pressure (IOP) elevation and glaucoma in children with nonjuvenile idiopathic arthritis–related uveitis and any IOP-related changes in the retinal nerve fiber layer (RNFL) thickness.

Patients and Methods:
Clinical data were collected from children attending a tertiary referral uveitis clinic between May 2010 and October 2012. We assigned 206 eyes of 103 children into 32 normal eyes, 108 normotensive uveitics (NU), 41 hypertensive uveitics (HU: raised IOP without glaucomatous disc), and 25 glaucomatous uveitics (GU: raised IOP with glaucomatous disc). Risk factors for raised IOP, glaucoma and steroid response (SR) were evaluated and RNFL thickness across groups was compared with determine changes related to raised IOP.

Results:
IOP elevation occurred in 40 patients (38.8%) or 66/174 eyes with uveitis (37.9%); and SR occurred in 35.1% of all corticosteroid-treated eyes. Chronic uveitis was a significant risk factor for raised IOP [odds ratio (OR)=9.28, P=0.001], glaucoma, and SR (OR=8.4, P<0.001). Higher peak IOP was also a risk factor for glaucoma (OR=1.4, P=0.003). About 70% of SR eyes were high responders (IOP increase >15 mm Hg from baseline), associated with younger age and corticosteroid injections. Although no significant RNFL thinning was detected between HU and NU eyes, significant thinning was detected in the inferior quadrant of GU (121.3±28.9 μm) compared with NU eyes (142.1±32.0 μm, P=0.043).

Conclusions:
Children with chronic uveitis are at higher risk of raised IOP and glaucoma. Thinning of the inferior RNFL quadrant may suggest glaucomatous changes in uveitic children with raised IOP.
Evaluation of Nonmydriatic Hand-held Optic Disc Photography Grading in the Philadelphia Glaucoma Detection and Treatment Project
Authors: Waisbourd Michael , Bond Emily A. , Sullivan Timothy , Hu Wanda D. , Shah Sonya B. , Molineaux Jeanne , Sembhi Harjeet , Spaeth George L. , Myers Jonathan S. , Hark Lisa A. , Katz L. Jay 
Published: February 2016

Purpose:
To determine the reproducibility of optic disc photograph grading obtained by a hand-held fundus camera and to determine the diagnostic value of these photographs in detecting patients with glaucoma in a community-based glaucoma-detection program.

Materials and Methods:
Patients underwent slit-lamp examination by an ophthalmologist who graded each patient’s optic discs using 2 methods: cup-to-disc ratio (CDR) and disc damage likelihood scale (DDLS). After a comprehensive glaucoma evaluation, patients were diagnosed as having “glaucoma,” “glaucoma suspect,” or “no glaucoma.” Nonmydriatic, monoscopic optic disc photographs were then taken with a portable digital imaging device. On a different day, the same examiner and a second observer graded the disc photographs in a masked manner and determined a diagnostic impression based only on the disc photographs.

Results:
Of the 1649 patients examined, 119 subjects were randomly selected according to 3 groups of diagnoses: “glaucoma” (n=36), “glaucoma suspect” (n=50), and “no glaucoma” (n=33). For CDR, the intraobserver agreement was 0.71 and the interobserver agreement was 0.69. For disc DDLS, the intraobserver agreement was 0.65 and the interobserver agreement was 0.67. The area under the receiver-operating characteristic distinguishing between normal and glaucoma was 0.88 and 0.86 for CDR and disc DDLS, respectively.

Conclusions:
Nonmydriatic, monoscopic disc photographs obtained by a hand-held camera had only moderate disc grading reproducibility. This could be due to a reduced quality of images, making interpretation more challenging, due to taking photographs through small pupils by a hand-held camera and the high percentage of patients with significant cataracts.
Outcomes of Trabeculectomy With Mitomycin-C in Uveitis Associated With Vogt-Koyanagi-Harada Disease
Authors: Almobarak Faisal A. , Alharbi Ali H. , Morales Jose , Aljadaan Ibrahim 
Published: February 2016

Objectives:
To evaluate the outcomes of trabeculectomy with mitomycin-C (MMC) in uveitis associated with Vogt-Koyanagi-Harada disease (VKH).

Methods:
Retrospective cohort study included 27 eyes of 15 patients with uveitic glaucoma associated with VKH disease who underwent trabeculectomy with MMC as a first glaucoma procedure at King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia between 1992 and 2011. The main outcome measures were: the intraocular pressure (IOP), the number of antiglaucoma medications, the presence of visually threatening complications, and the need for further surgeries to control the IOP.

Results:
The mean follow-up was 78.19 months. The IOP decreased significantly from a mean of 40.15±7.0 to 13.12±6.9 mm Hg on the last follow-up (P<0.01) as well as during the whole follow-up period. The number of medications needed to control the IOP also decreased significantly from 3.89±0.6 to 1.04±1.3. The cumulative probabilities of success were 77.8%, 74.1%, 63.0%, and 51.9% at 12, 24, 36, and 48 months postoperatively, respectively. The most common complications were cataract development and progression (53.8%), hypotony (IOP≤5 mm Hg) (33.3%), choroidal effusion (7.4%), and decompressive retinopathy (7.4%). Eight eyes (29.6%) needed a second procedure to control the IOP.

Conclusions:
Trabeculectomy with MMC offers an acceptable intermediate term success and IOP control in uveitic glaucoma associated with VKH. However, significant number of eyes needed further procedures to control the pressure. Therefore, continuous monitoring of the pressure is important.
A Systematic Review of End-of-Life Visual Impairment in Open-Angle Glaucoma: An Epidemiological Autopsy
Authors: Mokhles Palwasha , Schouten Jan S. A. G. , Beckers Henny J. M. , Azuara-Blanco Augusto , Tuulonen Anja , Webers Carroll A. B. 
Published: February 2016

Purpose:
Glaucoma patients are still at risk of becoming blind. It is of clinical significance to determine the risk of blindness and its causes to prevent its occurrence. This systematic review estimates the number of treated glaucoma patients with end-of-life visual impairment (VI) and blindness and the factors that are associated with this.

Methods:
A systematic literature search in relevant databases was conducted in August 2014 on end-of-life VI. A total of 2574 articles were identified, of which 5 on end-of-life VI. Several data items were extracted from the reports and presented in tables.

Results:
All studies had a retrospective design. A considerable number of glaucoma patients were found to be blind at the end of their life; with up to 24% unilateral and 10% bilateral blindness. The following factors were associated with blindness: (1) baseline severity of visual field loss: advanced stage of glaucoma or substantial visual field loss at the initial visit; (2) factors influencing progression: fluctuation of intraocular pressure (IOP) during treatment, presence of pseudoexfoliation, poor patient compliance, higher IOP; (3) longer time period: longer duration of disease and older age at death because of a longer life expectancy; and (4) coexistence of other ocular pathology.

Conclusions:
Further prevention of blindness in glaucoma patients is needed. To reach this goal, it is important to address the risk factors for blindness identified in this review, especially those that can be modified, such as advanced disease at diagnosis, high and fluctuating IOP, and poor compliance.
Single-chromosome aneuploidy commonly functions as a tumor suppressor
Authors: Sheltzer Jason M. , Ko Julie H. , Habibe Burgos Nicole C. , Chung Erica S. , Meehl Colleen M. , Passerini Verena , Storchova Zuzana , Amon Angelika 
Published: February 2016

SummaryWhole-chromosome aneuploidy is a hallmark of human malignancies. The prevalence of chromosome segregation errors in cancer – first noted more than 100 years ago – has led to the widespread belief that aneuploidy plays a crucial role in tumor development. Here, we set out to test this hypothesis. We transduced congenic euploid and trisomic fibroblasts with 14 different oncogenes or oncogene combinations, thereby creating genetically-matched cancer cell lines that differ only in karyotype. Surprisingly, nearly all aneuploid cell lines divided slowlyin vitro, formed few colonies in soft agar, and grew poorly as xenografts, relative to matched euploid lines. Similar results were obtained when comparing a near-diploid human colorectal cancer cell line with derivatives of that line that harbored extra chromosomes. Only a few aneuploid lines grew at close to wild-type levels, and no aneuploid line exhibited greater tumorigenic capabilities than its euploid counterpart. These results demonstrate that rather than promoting tumorigenesis, aneuploidy, particularly single chromosome gains, can very often function as a tumor suppressor. Moreover, our results suggest one potential way that cancers can overcome the tumor suppressive effects of aneuploidy: rapidly-growing aneuploid cell lines that had evolvedin vitroorin vivodemonstrated recurrent karyotype changes that were absent from their euploid counterparts. Thus, the genome-destabilizing effects of single-chromosome aneuploidy may facilitate the development of balanced, high-complexity karyotypes that are frequently found in advanced malignancies.
Reconstruction of ancestral genomes in presence of gene gain and loss
Authors: Avdeyev Pavel , Jiang Shuai , Aganezov Sergey , Hu Fei , Alekseyev Max A. 
Published: February 2016

AbstractSince most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the “simplest” case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes.One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets.We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genomes reconstruction tools. The MGRA2 tool is distributed as an open-source software and can be downloaded from GitHub repositoryhttp://github.com/ablab/mgra/. It is also available in the form of a web-server athttp://mgra.cblab.org, which makes it readily accessible for inexperienced users.
Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability
Authors: Magnabosco C. , Timmers P.H.A. , Lau M.C.Y. , Borgonie G. , Linage-Alvarez B. , Kuloyo O. , Alleva R. , Kieft T.L. , Slater G.F. , van Heerden E. , Sherwood Lollar B. , Onstott T.C. 
Published: February 2016

AbstractThe concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static—generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1,339 meters-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of13C-CH4laboratory incubation experiments, highlighting a connection between composition of subsurface CH4oxidizing communities and electron acceptor availability.
StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees
Authors: Roosaare Märt , Vaher Mihkel , Kaplinski Lauris , Möls Märt , Andreson Reidar , Lepamets Maarja , Kõressaar Triinu , Naaber Paul , Kõljalg Siiri , Remm Maido 
Published: February 2016

AbstractBackgroundFast, accurate and high-throughput detection of bacteria is in great demand. The present work was conducted to investigate the possibility of identifying both known and unknown bacterial strains from unassembled next-generation sequencing reads using custom-made guide trees.ResultsA program named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes within minutes. StrainSeeker has been tested and shown to successfully identifyEscherichia colistrains from mixed samples in less than 5 minutes. StrainSeeker can also identify bacterial strains from highly diverse metagenomics samples. StrainSeeker is available athttp://bioinfo.ut.ee/strainseeker.ConclusionsOur novel approach can be useful for both clinical diagnostics and research laboratories because novel bacterial strains are constantly emerging and their fast and accurate detection is very important.
ZIKA - How Fast Does This Virus Mutate?
Authors: Logan Ian 
Published: February 2016

ABSTRACTThe World Health Organisation has declared the present epidemic of infection with the Zika virus to be a ‘Public Health Emergency of International Concern’. The virus appears to have spread from Thailand to French Polynesia in 2013, and has since infected over a million people in the countries of South and Central America. In most cases the infection is mild and transient, but the virus does appear to be strongly neurotropic and the presumptive cause of both birth defects in foetuses and Guillain-Barré syndrome in some adults.In this paper the techniques and utilities developed in the study of mitochondrial DNA are applied to the Zika virus. As a result it is possible to show in a simple manner how a phylogenetic tree may be constructed and how the mutation rate of the virus can be measured.The study shows the mutation rate to vary between 12 and 25 bases a year, in a viral genome of 10,272 bases. This rapid mutation rate will enable the geographic spread of the epidemic to be monitored easily and may also prove useful in assisting the identification of preventative measures that are working, and those which are not.
Micro- and macroevolutionary trade-offs in plant-feeding insects
Authors: Peterson Daniel A. , Hardy Nate B. , Normark Benjamin B. 
Published: February 2016

AbstractA long-standing hypothesis asserts that plant-feeding insects specialize on particular host plants because of negative interactions (trade-offs) between adaptations to alternative hosts, yet empirical evidence for such trade-offs is scarce. Most studies have looked for microevolutionary performance trade-offs within insect species, but host-use could also be constrained by macroevolutionary trade-offs caused by epistasis and historical contingency. On the other hand, evolutionary interactions between adaptations to diverse hosts could be neutral or positive rather than negative. Here we used a phylogenetic approach to estimate the micro-and macroevolutionary correlations between use of alternative host plants within two major orders of plant-feeding insects: Lepidoptera (caterpillars) and Hemiptera (true bugs). Across 1604 caterpillar species, we found both positive and negative pairwise correlations between use of diverse host taxa, with overall network patterns suggesting that different host-use constraints act over micro-and macroevolutionary timescales. In contrast, host-use patterns of 955 true bug species revealed uniformly positive correlations between presence on the same host taxa over both timescales. The lack of consistent patterns across timescales and insect orders indicates that host-use trade-offs are historically contingent rather than universal constraints. Moreover, we observed few negative correlations overall despite the wide taxonomic and ecological diversity of the focal host taxa, suggesting that positive interactions between host-use adaptations, not trade-offs, dominate the long-term evolution of host use in plant-feeding insects.
Do persistent rare species experience stronger negative frequency dependence than common species?
Authors: Yenni Glenda , Adler Peter B. , Ernest S. K. Morgan 
Published: February 2016

AbstractUnderstanding why so many species are rare yet persistent remains a significant challenge for both theoretical and empirical ecologists. Yenni, Adler, and Ernest (2012) proposed that strong negative frequency dependence causes species to be rare while simultaneously buffering them against extinction. This hypothesis predicts that, on average, rare species should experience stronger negative frequency dependence than common species. However, it is unknown if ecological communities generally show this theoretical pattern, or if rarity is primarily determined by other processes that overwhelm the effects of strong negative frequency dependence. We discuss the implications of this mechanism for natural communities, and develop a method to test for a non-random relationship between negative frequency dependence and relative abundance, using species abundance data from 90 communities across a broad range of environments and taxonomic groups. To account for biases introduced by measurement error, we compared the observed correlation between species relative abundance and the strength of frequency dependence against expectations from a randomization procedure. In approximately half of the analyzed communities, rare species showed disproportionately strong negative frequency dependence compared to common species. Specifically, we found a pattern of increasingly strong negative frequency dependence with decreasing relative abundance. Our results suggest that strong negative frequency dependence is a signature of both rarity and persistence for many species in many communities.
An ecological assessment of the pandemic threat of Zika virus
Authors: Carlson Colin J. , Dougherty Eric R. , Getz Wayne 
Published: February 2016

SummaryThe current outbreak of Zika virus poses a threat of unknown magnitude to human health1. While the range of the virus has been cataloged growing slowly over the last 50 years, the recent explosive expansion in the Americas indicates that the full potential distribution of Zika remains uncertain2-4. Moreover, most current epidemiology relies on its similarities to dengue fever, a phylogenetically closely related disease of unknown similarity in spatial range or ecological niche5,6. Here we compile the first spatially explicit global occurrence dataset from Zika viral surveillance and serological surveys, and construct ecological niche models to test basic hypotheses about its spread and potential establishment. The hypothesis that the outbreak of cases in Mexico and North America are anomalous and outside the ecological niche of the disease, and may be linked to El Nino or similar climatic events, remains plausible at this time7. Comparison of the Zika niche against the known distribution of dengue fever suggests that Zika is more constrained by the seasonality of precipitation and diurnal temperature fluctuations, likely confining the disease to the tropics outside of pandemic scenarios. Projecting the range of the diseases in conjunction with vector species (Aedes africanus,Ae. aegypti, andAe. albopictus) that transmit the pathogens, under climate change, suggests that Zika has potential for northward expansion; but, based on current knowledge, Zika is unlikely to fill the full range its vectors occupy. With recent sexual transmission of the virus known to have occurred in the United States, we caution that our results only apply to the vector-borne aspect of the disease, and while the threat of a mosquito-carried Zika pandemic may be overstated in the media, other transmission modes of the virus may emerge and facilitate naturalization worldwide.