bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term Surgical Outcomes of 180-Degree Suture Trabeculotomy in Korean Patients With Primary Congenital Glaucoma
Authors: Park Ji-Hye , Yoo Chungkwon , Yoo Eunjoo , Kim Yong Yeon 
Published: November 2015

Purpose:
To investigate the surgical outcomes of 180-degree suture trabeculotomy in Korean patients with primary congenital glaucoma (PCG).

Patients and Methods:
This retrospective study included 21 eyes of 17 children with PCG who underwent 180-degree suture trabeculotomy as a first surgical procedure. Surgical success was defined as (1) an intraocular pressure (IOP)<22 mm Hg with or without medication; (2) no additional intraocular surgery; and (3) no evidence of progressive optic disc cupping. The main outcome measure was the success rate of 180-degree suture trabeculotomy. Secondary outcome measures were IOP, number of glaucoma medications, and occurrence of complications.

Results:
Of the 21 eyes included, 18 (85.7%) were classified as having achieved success at the final visit (mean last follow-up or failure time, 54.91±45.68 mo). Median age at surgery was 11.97 months with mean IOP 29.8±9.6 mm Hg, on average of 1.52 medications. The mean IOP at the final visit was 16.9±5.6 mm Hg on an average of 0.38 medications. The surgical success rate of 180-degree suture trabeculotomy at 1, 3, and 5 years was 95.0%, 87.7%, and 78.9%, respectively (Kaplan-Meier analysis). Three eyes underwent second operations and the mean time to failure was 29.39±19.75 months. Hyphema was observed in 10 eyes, but it cleared up within 7.6 days.

Conclusion:
The 180-degree suture trabeculotomy performed for PCG had a significant IOP-lowering effect and caused no remarkable complications.
Management of Elevated Intraocular Pressure Associated With Subluxated/Dislocated Lenses by Combining Trabeculectomy With Adjunctive Mitomycin C With Lensectomy, Vitrectomy, and Scleral Fixation of Intraocular Lens
Authors: David Rathini L. , Balekudaru Shantha , George Ronnie J. , Sen Parveen , Lingam Vijaya 
Published: November 2015

Aim:
To evaluate the short-term outcomes of lensectomy, combined with vitrectomy, scleral-fixated intraocular lens (SFIOL), and trabeculectomy with adjunctive mitomycin C (MMC) in patients with subluxated/dislocated crystalline lenses with associated elevated intraocular pressure (IOP).

Materials and Methods:
This retrospective case series included 51 eyes of 51 patients who underwent lensectomy, vitrectomy, and SFIOL combined with trabeculectomy with MMC between 2003 and 2012. The main outcome measures assessed were IOP, change in visual acuity, IOP-lowering medications, and the complications and reoperation rates.

Results:
The most common etiology observed was blunt trauma in 35 eyes (68.6%). Glaucomatous optic neuropathy was detected in 13 eyes (25.49%) preoperatively. The IOP reduced significantly from a preoperative mean of 26.3±11.5 mm Hg to 13±4.6 mm Hg (P<0.001) at the final visit. The mean preoperative number of IOP-lowering medications of 2.9±0.8 reduced to 0.3±0.7 at last follow-up (P<0.001). The best-corrected visual acuity (Snellens) improved significantly from 20/600 to 20/60 (P<0.001). Complete success defined as IOP≤21 mm Hg without medications was achieved in 93%±5% and 80%±13% at 1 and 2 years, respectively. Major postoperative complications included retinal detachment in one eye and SFIOL dislocation in another.

Conclusions:
The technique of combining SFIOLs with trabeculectomy with adjunctive MMC in the management of subluxated/dislocated lenses resulted in good IOP control and improvement in visual acuity.
The Effects of an Empowerment Intervention on Renal Transplant Recipients
Authors: Hsiao Chiu-Yueh , Lin Li-Wei , Su Yu-Wen , Yeh Shu-Hui , Lee Li-Na , Tsai Fu-Mian 
Published: November 2015

ABSTRACT

Background:
Renal transplantation is a vital treatment for end-stage renal disease. To help improve quality of life after renal transplant surgery, interventions are needed to strengthen the coping skills and self-care behaviors of patients. However, most research studies on self-care after renal transplantation have addressed related factors. Few studies have examined the effects of interventions on renal transplant recipients.

Purpose:
This study investigated the effects of an empowerment support group on the empowerment levels and self-care behaviors of renal transplant recipients.

Methods:
This study was a randomized controlled trial. Eligible participants were individuals who had undergone a renal transplant within the past 20 years, were 18 years old or older, were able to read and write in Chinese, and were willing to participate. We recruited 122 renal transplant recipients from two medical centers in southern Taiwan. The renal transplant outpatients were randomly assigned into empowerment support (n = 56) and comparison (n = 66) groups. The developed measures as well as the content, protocols, and the two groups were assessed for reliability and validity. The intervention involved one 2-hour meeting every 2 weeks for a total of six meetings. The topics included goal setting, problem solving, coping with daily stress, seeking social support, and staying motivated. The sessions consisted of introductions that highlighted the topic, group discussions, identifying areas of difficulty with self-care behaviors after renal transplant, and developing a set of goals and strategies to overcome these problems.

Results:
The empowerment group reported significant increases both in terms of level of empowerment (F = 5.29, p = .023) based on age and time interaction (F = 9.86, p < .001) and in terms of self-care behaviors (F = 7.15, p = .009). Moreover, these increases were significantly larger than the increases recorded by the comparison group. In addition, these increases were particularly large in the older empowerment-group participants with lower pretest scores for empowerment.

Conclusions:
Empowerment support may be critical to improve the empowerment and self-care behaviors of renal transplant patients. The results of this study may be applied to improve patient education and empowerment programs for renal transplant patients. Furthermore, these programs may be adjusted to take into consideration the learning preferences or needs of different age groups.
What’s in my pot? Real-time species identification on the MinION™
Authors: Juul Sissel , Izquierdo Fernando , Hurst Adam , Dai Xiaoguang , Wright Amber , Kulesha Eugene , Pettett Roger , Turner Daniel J. 
Published: November 2015

AbstractWhole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows. This limits the utility of the approach in settings where rapid species identification is crucial, such as in the quality control of food-chain components, or in during an outbreak of an infectious disease. Here we present What’s in my Pot? (WIMP), a laboratory and analysis workflow in which, starting with an unprocessed sample, sequence data is generated and bacteria, viruses and fungi present in the sample are classified to subspecies and strain level in a quantitative manner, without prior knowledge of the sample composition, in approximately 3.5 hours. This workflow relies on the combination of Oxford Nanopore Technologies’ MinION™ sensing device with a real-time species identification bioinformatics application.
Patterns of transcriptional response to 1,25-dihydroxyvitamin D3 and bacterial lipopolysaccharide in primary human monocytes
Authors: Kariuki Silvia N. , Blischak John D. , Nakagome Shigeki , Witonsky David B. , Di Rienzo Anna 
Published: November 2015

AbstractThe active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25D), plays an important immunomodulatory role, regulating transcription of genes in the innate and adaptive immune system. The present study examines patterns of transcriptome-wide response to 1,25D and the bacterial lipopolysaccharide (LPS) in primary human monocytes, to elucidate pathways underlying the effects of 1,25D on the immune system. Monocytes obtained from healthy individuals of African-African and European-American ancestry were treated with 1,25D alone or in the presence of LPS, which induced significant up-regulation of genes in the antimicrobial and autophagy pathways, while pro-inflammatory response genes were significantly down-regulated. A joint Bayesian analysis enabled clustering of genes into patterns of shared transcriptional response across treatments. The biological pathways enriched within these expression patterns highlighted several mechanisms through which 1,25D could exert its immunomodulatory role. Pathways such as mTOR signaling, EIF2 signaling, IL-8 signaling and Tec Kinase signaling were enriched among genes with opposite transcriptional responses to 1,25D and LPS, respectively, highlighting the important roles of these pathways in mediating the immunomodulatory activity of 1,25D. Furthermore, a subset of genes with evidence of inter-ethnic differences in transcriptional response was also identified, suggesting that in addition to the well-established inter-ethnic variation in circulating levels of vitamin D, the intensity of transcriptional response to 1,25D and LPS also varies between ethnic groups. We propose that dysregulation of the pathways identified in this study could contribute to immune-mediated disease risk.
Convergent patterns of sex chromosome dosage compensation between lepidopteran species (WZ/ZZ) and eutherian mammals (XX/XY): insights from a moth neo-Z chromosome
Authors: Gu Liuqi , Walters James R. , Knipple Douglas C. 
Published: November 2015

AbstractIn contrast to XX/XY species, Z-linked expression is overall reduced in female WZ/ZZ species compared to males or the autosomal expression. This pattern (Z<ZZ≈AA) has been consistently reported in all the WZ/ZZ taxa examined so far, with the singular exception of the insect order of Lepidoptera (moths and butterflies). However, conflicting results linger in this taxon due to discrepancies in data analyses and tissues sampled. To address this issue, we analyzed dosage compensation in the codling mothCydia pomonella(Tortricidae) using tissues that represent different levels of sexual divergence.C. pomonellais the most basal lepidopteran species yet examined for dosage compensation and has a neo-Z chromosome resulting from an ancient Z:autosome translocation. We based our analyses on RNAseq andde novotranscriptome data fromC. pomonella,as well as scrutiny into investigations of other lepidopteran species. Our evidence supports that the lepidopterans share a pattern (Z ≈ ZZ < AA) of dosage compensation that mirrors the eutherian mammals (X ≈ XX < AA). In particular, reproductive tissues appear to be exempt from dosage compensation, which helps explain the incongruence in prior reports. Furthermore,C. pomonellaancestral-Z segment exhibited a greater expression reduction than genes on the neo-Z segment, which intriguingly also reflects the differential up-regulation between the ancestral and newly-acquired X-linked genes in mammals. The insect order of Lepidoptera challenges both the classic theories regarding evolution of sex chromosome dosage compensation and the emerging view on dosage compensation’s association with sexual heterogamety.
Simulating serial-target antibacterial drug synergies using flux balance analysis
Authors: Krueger Andrew S. , Munck Christian , Dantas Gautam , Church George M. , Galagan James , Lehár Joseph , Sommer Morten O.A. 
Published: November 2015

AbstractFlux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts can not predict drug combination synergies observed between serial metabolic targets, even though such synergies give rise to some of the most widely used antibiotic treatments. Here we extend FBA modeling to simulate responses to chemical inhibitors at varying concentrations, by diverting enzymatic flux to a waste reaction. This flux diversion yields very similar qualitative predictions to prior methods for single target activity. However, we find very different predictions for combinations, where flux diversion, which mimics the kinetics of competitive metabolic inhibitors, can explain serial target synergies between metabolic enzyme inhibitors that we confirmed inEscherichia colicultures. FBA flux diversion opens the possibility for more accurate genome-scale predictions of drug synergies, which can be used to suggest treatments for infections and other diseases.
chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts
Authors: Kehr Birte , Melsted Páll 
Published: November 2015

AbstractSummaryAdvances in sequencing capacity have lead to the generation of unprecedented amounts of genomic data. The processing of this data frequently leads to I/O bottlenecks, e. g. when analyzing a small genomic region across a large number of samples. The largest I/O burden is, however, often not imposed by the amount of data needed for the analysis but rather by index files that help retrieving this data. We have developed chopBAI, a program that can chop a BAM index (BAI) file into small pieces. The program outputs a list of BAI files each indexing a specified genomic interval. The output files are much smaller in size but maintain compatibility with existing software tools. We show how preprocessing BAI files with chopBAI can lead to a reduction of I/O by more than 95% during the analysis of 10 Kbp genomic regions, eventually enabling the joint analysis of more than 10,000 individuals.Availability and ImplementationThe software is implemented in C++, GPL licensed and available athttp://github.com/DecodeGenetics/chopBAI
Spaces of Extraction, Metropolitan Explosions: Planetary Urbanization and the Commodity Boom in Latin America
Authors: Arboleda Martín 
Published: November 2015

AbstractThrough an exploration of the political economy of the current commodity boom in Latin America, and on the basis of recent appropriations of Henri Lefebvre's notion of planetary urbanization, this article proposes viewing spaces of resource extraction resulting from an escalating international demand for raw materials as particular morphological expressions of market‐driven processes of urbanization. Furthermore, the article draws on Lefebvre to argue that such burgeoning spaces of urbanization are the result of a contradictory tension between spatial homogenization—in the form of multiscalar governance frameworks and infrastructural programs—and territorial fragmentation—in the form of fixed capital allocations and state‐led spatial segregation. When considered jointly, these contradictory movements allow us to grasp fully the extent of the problematic explosion of spaces that, according to Lefebvre, characterizes capitalist urbanization. The article concludes by reflecting on the emancipatory promise that underlies the planetary extension of the urban form because, with the projection of material infrastructures required for resource extraction—especially information technologies—across the rural realm, local communities have been able to shed their isolated state and emerge as fully fledged political actors.
Role of vision loss, functional limitations and the supporting network in depression in a general population
Authors: van Nispen Ruth M. A. , Vreeken Hilde L. , Comijs Hannie C. , Deeg Dorly J. H. , van Rens Ger H. M. B. 
Published: November 2015

AbstractPurposeAlthough the prevalence of depression in visually impaired older persons is high, the association between vision loss and depression seems to be influenced by factors other than visual impairment. In this study, the role of vision loss, functional limitations and social network characteristics in relation to depressive symptoms was investigated.MethodsCross‐sectional data (N = 1237) from the Longitudinal Aging Study Amsterdam were used to investigate the prevalence of depression (Center of Epidemiological Studies‐Depression scale) within subgroups with increasing vision loss. In linear regression models, functional limitations and social network characteristics were examined as possible mediators in the association between vision loss and depression. Having a partner was considered to be a potential moderator.ResultsAlthough a significant linear trend was found in the presence of depressive symptoms with 14% in normally sighted, 23% in mild and 37% in severe vision loss (χ2(1) = 14.9; p < 0.001), vision loss was not an independent determinant of depression. Mediators were functional limitations (p < 0.001) and social network size (p = 0.009). No interaction with partner status was found.ConclusionIn the presence of depression, a trend was found with increasing severity of vision loss, indicating the need for more attention in (mental) health care and low‐vision rehabilitation. In the general older population, vision loss was not an independent determinant of depression but was mediated by functional limitations and social network size. Rather than receiving actual social support, the idea of having a social network to rely on when needed seemed to be associated with lower levels of depression.
Bone fractures and lumbar mineral density after renal transplantation. A long‐term cross‐sectional study
Authors: Jiménez Sara , Marcén Roberto , Vaamonde Carlos , Caballero Carmen , Fernández‐Rodríguez Ana , Villafruela Juan José , Galeano Cristina , Teruel José Luis , Quereda Carlos 
Published: November 2015

AbstractBackgroundThe purpose of this work was to investigate the association of vertebral and peripheral fractures 10 yr after grafting with bone metabolic markers and body mass density (BMD).Patients and methodsOne hundred thirty‐eight recipients with stable graft function were included in a cross‐sectional study. Graft function, biochemical mineral metabolism markers and body mass density (DEXA) were measured. Vertebral fractures were assessed by a semiquantitative analysis of lateral spine X‐ray exam.ResultsAt the time of the study, intact parathyroid hormone levels were 127.5 ± 78.4 pg/mL and serum calcidiol 20.4 ± 9.3 ng/mL. DEXA showed osteopenia in 47% and osteoporosis in 23% at lumbar spine, 51% and 14% at femoral neck, and 53% and 8% at trochanter. Eighty‐five recipients presented vertebral fractures, 69 mild and 16 moderate/severe fractures. In the multivariate analysis, vertebral fractures were associated with older age (p = 0.010), length of follow‐up (p = 0.022) and trochanter T‐score (p = 0.038). Twenty‐three patients presented peripheral fractures and 19 of them also had vertebral fractures. Patients with peripheral fractures were younger, mostly women and had lower BMD.ConclusionsVertebral fractures were associated with lower BMD at trochanter. Most fractures were mild and were several times more frequent than in general population. Their clinical significance needs to be determined.
Global environmental change effects on ecosystems: the importance of land‐use legacies
Authors: Perring Michael P. , De Frenne Pieter , Baeten Lander , Maes Sybryn L. , Depauw Leen , Blondeel Haben , Carón María M. , Verheyen Kris 
Published: November 2015

AbstractOne of the major challenges in ecology is to predict how multiple global environmental changes will affect future ecosystem patterns (e.g. plant community composition) and processes (e.g. nutrient cycling). Here, we highlight arguments for the necessary inclusion of land‐use legacies in this endeavour. Alterations in resources and conditions engendered by previous land use, together with influences on plant community processes such as dispersal, selection, drift and speciation, have steered communities and ecosystem functions onto trajectories of change. These trajectories may be modulated by contemporary environmental changes such as climate warming and nitrogen deposition. We performed a literature review which suggests that these potential interactions have rarely been investigated. This crucial oversight is potentially due to an assumption that knowledge of the contemporary state allows accurate projection into the future. Lessons from other complex dynamic systems, and the recent recognition of the importance of previous conditions in explaining contemporary and future ecosystem properties, demand the testing of this assumption. Vegetation resurvey databases across gradients of land use and environmental change, complemented by rigorous experiments, offer a means to test for interactions between land‐use legacies and multiple environmental changes. Implementing these tests in the context of a trait‐based framework will allow biologists to synthesize compositional and functional ecosystem responses. This will further our understanding of the importance of land‐use legacies in determining future ecosystem properties, and soundly inform conservation and restoration management actions.
Elevated carbon dioxide increases soil nitrogen and phosphorus availability in a phosphorus‐limited Eucalyptus woodland
Authors: Hasegawa Shun , Macdonald Catriona A. , Power Sally A. 
Published: November 2015

AbstractFree‐air CO2 enrichment (FACE) experiments have demonstrated increased plant productivity in response to elevated (e)CO2, with the magnitude of responses related to soil nutrient status. Whilst understanding nutrient constraints on productivity responses to eCO2 is crucial for predicting carbon uptake and storage, very little is known about how eCO2 affects nutrient cycling in phosphorus (P)‐limited ecosystems. Our study investigates eCO2 effects on soil N and P dynamics at the EucFACE experiment in Western Sydney over an 18‐month period. Three ambient and three eCO2 (+150 ppm) FACE rings were installed in a P‐limited, mature Cumberland Plain Eucalyptus woodland. Levels of plant accessible nutrients, evaluated using ion exchange resins, were increased under eCO2, compared to ambient, for nitrate (+93%), ammonium (+12%) and phosphate (+54%). There was a strong seasonality to responses, particularly for phosphate, resulting in a relatively greater stimulation in available P, compared to N, under eCO2 in spring and summer. eCO2 was also associated with faster nutrient turnover rates in the first six months of the experiment, with higher N (+175%) and P (+211%) mineralization rates compared to ambient rings, although this difference did not persist. Seasonally dependant effects of eCO2 were seen for concentrations of dissolved organic carbon in soil solution (+31%), and there was also a reduction in bulk soil pH (‐0.18 units) observed under eCO2. These results demonstrate that CO2 fertilization increases nutrient availability – particularly for phosphate – in P‐limited soils, likely via increased plant belowground investment in labile carbon and associated enhancement of microbial turnover of organic matter and mobilization of chemically bound P. Early evidence suggests that there is the potential for the observed increases in P availability to support increased ecosystem C‐accumulation under future predicted CO2 concentrations.