bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recruitment of Young Bull Trout into the Metolius River and Lake Billy Chinook, Oregon
Authors: Ratliff Don , Spateholts Robert , Hill Megan , Schulz Eric 
Published: November 2015

Abstract
The abundance of Bull Trout Salvelinus confluentus in the Metolius River and Lake Billy Chinook, a hydroelectric reservoir, increased dramatically from 1998 to 2004, following implementation of restrictive fishery regulations. However, both adult Bull Trout and kokanee Oncorhynchus nerka (prey) populations have declined in more recent years. We investigated the relationships between Bull Trout spawner densities, emerging fry densities, and numbers of juveniles migrating into the reservoir to determine the potential role of juvenile production in this decline. We hypothesized that age-1 and older juvenile production is now limited by natal habitat capacity and that excess fry production is lost to density-dependent mortality. Bull trout redd densities in surveyed spawning reaches ranged from 14 to 39 redds/km during recent years. The estimated abundance of emerging Bull Trout fry in monitored spawning reaches has varied from about 1.0–2.5 million annually since 2005, while mean estimated densities of newly emerged fry varied from over 35/m2 in Roaring Creek during 2005 to less than 1/m2 in Jefferson Creek during 2009. Fry capture numbers from high versus low escapement broods at the Metolius River downstream trap varied by a factor of four, but capture of age-1 and age-2 juveniles did not differ substantially. These findings indicate natal Bull Trout habitats are seeded at spawner densities of 14 redds/km and higher. Fry in excess of natal habitat capacity are probably lost to density-dependent mortality factors. We estimate natural recruitment of age-1 and older Bull Trout into Lake Billy Chinook of at least 9 individuals/ha annually since 2001. Recent population bottlenecks limiting adult Bull Trout abundance occurred after juvenile recruits entered the lake and are probably related to prey availability.
Received February 23, 2015; accepted July 8, 2015
Enteric lactoferrin attenuates the development of high-fat and high-cholesterol diet-induced hypercholesterolemia and atherosclerosis in Microminipigs
Authors: Morishita Satoru , Kawaguchi Hiroaki , Ono Tomoji , Miura Naoki , Murakoshi Michiaki , Sugiyama Keikichi , Kato Hisanori , Tanimoto Akihide , Nishino Hoyoku 
Published: November 2015

Abstract
Previously, we found that enteric lactoferrin (eLF) could reduce the visceral fat accumulation known to associate strongly with metabolic syndrome symptoms and consequently with an increased risk of atherosclerosis. In this study, the atherosclerosis-preventive potential of LF was assessed in a high-fat and high-cholesterol diet (HFCD)-induced hypercholesterolemia and atherosclerosis model using Microminipig™. Eight-week orally administered eLF remarkably reduced the HFCD-induced serum total and low-density lipoprotein cholesterol levels but not high-density lipoprotein cholesterol levels. A histological analysis of 15 arteries revealed that eLF systemically inhibited the development of atherosclerotic lesions. Pathway analysis using identified genes that characterized eLF administration in liver revealed significant changes in the steroid biosynthesis pathway (ssc00100) and all affected genes in this pathway were upregulated, suggesting that cholesterol synthesis inhibited by HFCD was recovered by eLF. In summary, eLF could potentially prevent the hypercholesterolemia and atherosclerosis through protecting homeostasis from HFCD-induced dysfunction of cholesterol metabolism.
Development of suitable hydroponics system for phytoremediation of arsenic-contaminated water using an arsenic hyperaccumulator plant Pteris vittata
Authors: Huang Yi , Miyauchi Keisuke , Inoue Chihiro , Endo Ginro 
Published: November 2015

Abstract
In this study, we found that high-performance hydroponics of arsenic hyperaccumulator fern Pteris vittata is possible without any mechanical aeration system, if rhizomes of the ferns are kept over the water surface level. It was also found that very low-nutrition condition is better for root elongation of P. vittata that is an important factor of the arsenic removal from contaminated water. By the non-aeration and low-nutrition hydroponics for four months, roots of P. vittata were elongated more than 500 mm. The results of arsenate phytofiltration experiments showed that arsenic concentrations in water declined from the initial concentrations (50 μg/L, 500 μg/L, and 1000 μg/L) to lower than the detection limit (0.1 μg/L) and about 80% of arsenic removed was accumulated in the fern fronds. The improved hydroponics method for P. vittata developed in this study enables low-cost phytoremediation of arsenic-contaminated water and high-affinity removal of arsenic from water.
Probabilistic models of genetic variation in structured populations applied to global human studies
Authors: Hao Wei , Song Minsun , Storey John D. 
Published: November 2015

AbstractMotivation: Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important problem is how to formulate and estimate probabilistic models of observed genotypes that account for complex population structure. The most prominent work on this problem has focused on estimating a model of admixture proportions of ancestral populations for each individual. Here, we instead focus on modeling variation of the genotypes without requiring a higher-level admixture interpretation.Results: We formulate two general probabilistic models, and we propose computationally efficient algorithms to estimate them. First, we show how principal component analysis can be utilized to estimate a general model that includes the well-known Pritchard–Stephens–Donnelly admixture model as a special case. Noting some drawbacks of this approach, we introduce a new ‘logistic factor analysis’ framework that seeks to directly model the logit transformation of probabilities underlying observed genotypes in terms of latent variables that capture population structure. We demonstrate these advances on data from the Human Genome Diversity Panel and 1000 Genomes Project, where we are able to identify SNPs that are highly differentiated with respect to structure while making minimal modeling assumptions.Availability and Implementation: A Bioconductor R package called lfa is available at http://www.bioconductor.org/packages/release/bioc/html/lfa.html.Contact: jstorey@princeton.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Evaluation of hierarchical models for integrative genomic analyses
Authors: Denis Marie , Tadesse Mahlet G. 
Published: November 2015

AbstractMotivation: Advances in high-throughput technologies have led to the acquisition of various types of -omic data on the same biological samples. Each data type gives independent and complementary information that can explain the biological mechanisms of interest. While several studies performing independent analyses of each dataset have led to significant results, a better understanding of complex biological mechanisms requires an integrative analysis of different sources of data.Results: Flexible modeling approaches, based on penalized likelihood methods and expectation-maximization (EM) algorithms, are studied and tested under various biological relationship scenarios between the different molecular features and their effects on a clinical outcome. The models are applied to genomic datasets from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serous cystadenocarcinoma. The integrative models lead to improved model fit and predictive performance. They also provide a better understanding of the biological mechanisms underlying patients’ survival.Availability and implementation: Source code implementing the integrative models is freely available at https://github.com/mgt000/IntegrativeAnalysis along with example datasets and sample R script applying the models to these data. The TCGA datasets used for analysis are publicly available at https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp.Contact: marie.denis@cirad.fr or mgt26@georgetown.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Chemical evolution of the HC3N and N2H+ molecules in dense cores of the Vela C giant molecular cloud complex
Authors: Ohashi Satoshi , Tatematsu Ken'ichi , Fujii Kosuke , Sanhueza Patricio , Nguyen Luong Quang , Choi Minho , Hirota Tomoya , Mizuno Norikazu 
Published: November 2015

Abstract
We have observed the HC3N(J = 10–9) and N2H+ (J = 1–0) lines toward the Vela C molecular clouds with the Mopra 22 m telescope to study the chemical characteristics of dense cores. The intensity distributions of these molecules are similar to each other at an angular resolution of 53″, corresponding to 0.19 pc, suggesting that these molecules trace the same dense cores. We identified 25 local peaks in the velocity-integrated intensity maps of the HC3N and/or N2H+ emission. Assuming local thermodynamic equilibrium conditions, we calculated the column densities of these molecules and found a tendency for the N2H+/HC3N abundance ratio to be low in starless regions while it seems to be high in star-forming regions, similar to the tendencies in the NH3/CCS, NH3/HC3N, and N2H+/CCS abundance ratios found in previous studies of dark clouds and the Orion A giant molecular cloud (GMC). We suggest that carbon chain molecules, including HC3N, may trace chemically young molecular gas, and that N-bearing molecules, such as N2H+, may trace later stages of chemical evolution in the Vela C molecular clouds. It may be possible that the N2H+/HC3N abundance ratio of ∼1.4 divides the star-forming and starless peaks in Vela C, although it is not as clear as those in NH3/CCS, NH3/HC3N, and N2H+/CCS for the Orion A GMC. This less clear separation may be caused by our lower spatial resolution or the misclassification of star-forming and starless peaks due to the larger distance of Vela C. It might also be possible that the HC3N (J = 10–9) transition is not a good chemical evolution tracer compared with CCS (J = 4–3 and 7–6) transitions.
Muscle Triggers as a Possible Source of Pain in a Subgroup of Tension-type Headache Patients?
Authors: Arendt-Nielsen Lars , Castaldo Matteo , Mechelli Filippo , Fernández-de-las-Peñas César 
Published: November 2015

Objectives:
Tension-type headache (TTH) is a common condition but the underlying etiology is not understood. Episodic TTH may develop into chronic TTH, and some possible triggers may be involved in generation and maintenance. Nociceptive generators and hyperexcitable spots in neck and shoulder regions may to some degree contribute to TTH. The current paper highlights some of the possible triggers and associated pain mechanisms involved in TTH and discusses whether inhibition of these possible triggers may provide new treatment options.

Results:
This paper presents possible pathophysiological factors in TTH, the role of muscle pain, and how referred pain from triggers can contribute to development, maintenance of sensitization, or both. Referred pain patterns from trigger points and associated muscle hyperalgesia seem to be clinically important factors. Damping the nociceptive peripheral drive may not only reduce the number of TTH attacks but may also prevent, delay the transition from episodic into more chronic TTH, or both. The role of muscle triggers in driving TTH is debated as the pathogenesis of such triggers is not fully understood. Furthermore, inhibiting the drive from the triggers does not consistently modulate TTH.

Discussion:
Understanding the possible triggers in TTH, muscle hyperalgesia, and widespread pain sensitization, may help to develop better management regimes and possibly prevent TTH from developing into more chronic conditions. Currently, there is a striking difference between the clinical observational studies favoring the role of muscle triggers in TTH and the intervention studies generally not supporting the role of muscle triggers in TTH.
Involvement of CCL3/CCR5 Signaling in Dorsal Root Ganglion in Remifentanil-induced Hyperalgesia in Rats
Authors: Li Nan , Zhang Linlin , Shu Ruichen , Ding Ling , Wang Zhifen , Wang Haiyun , Yu Yonghao , Wang Guolin 
Published: November 2015

Background:
Several mechanisms of remifentanil-induced hyperalgesia in spinal cord mainly have been explained such as N-methyl-d-aspartate receptors activation, but the mechanism in dorsal root ganglion (DRG) is poorly understood. It has been reported that CCL3 may be a regulator in both inflammatory pain and hyperalgesia. In this paper we explored whether CCL3 and CCR5, the mainly receptor of CCL3, play a role in the remifentanil-induced hyperalgesia in DRG by using a rat model with remifentanil administration.

Materials and Methods:
The von Frey test and hot plate test were performed to measure the different threshold to evaluate mechanical and thermal hyperalgesia. Real-time polymerase chain reaction and Western blot analysis were used to evaluate time course of CCL3 and CCR5 expression in DRG after remifentanil infusion. The changes of glial cells and the expression of CCL3 and CCR5 were detected by immunofluorescence assay. Finally, intrathecal injection of CCL3-neutralizing antibody and maraviroc, the CCR5 antagonists, were used sevoflurane to confirm the role of CCL3/CCR5 signaling in the rat model of remifentanil-induced hyperalgesia.

Results:
Remifentanil infusion profoundly increased thermal and mechanical hyperalgesia from 2 to 48 hours according to paw withdrawal latency (PWL) and paw withdrawal thresholds (PWT) (mean±SD, hyperalgesia vs. control, 17.4±0.91 vs. 8.5±1.46 s; 20.1±0.32 vs. 9.6±0.5 g, n=8). Moreover, the expression of mRNAs and proteins of CCL3 and its receptor CCR5 in DRG were dramatically increased after remifentanil infusion as compared with the normal saline group. We also found that CCL3 and CCR5 were colocalized with glial cells or neurons. Furthermore, intrathecal injection of CCL3-neutralizing antibody (mean±SD, hyperalgesia vs. control, 17.4±0.91 vs. 8.5±1.46 s; 20.1±0.32 vs. 9.6±0.5 g, n=5) and maraviroc(mean±SD, hyperalgesia vs. control, 17.4±0.91 vs. 8.5±1.46 s; 20.1±0.32 vs. 9.6±0.5 g, n=5) were able to suppress remifentanil-related thermal and mechanical hyperalgesia according to behavioral test.

Conclusions:
The results highlighted the fact that CCL3 and its receptor CCR5 in DRG might contribute to remifentanil-induced hyperalgesia. Thus CCL3/CCR5 signaling may be further considered in the development of new therapeutic strategies.
Body Awareness as an Important Target in Multidisciplinary Chronic Pain Treatment
Authors: van der Maas Lia C.C. , Köke Albère , Bosscher Ruud J. , Twisk Jos W.R. , Janssen Thomas W.J. , Peters Madelon 
Published: November 2015

Background:
The results of a recently performed randomized clinical trial showed that the effect of a multidisciplinary treatment of chronic pain patients on body awareness (BA), catastrophizing, and depression was improved by adding psychomotor therapy (PMT), an intervention targeting BA. No significant effects were found on quality of life and disability. The present follow-up study aimed to explore the relationship between improvements in BA and multidisciplinary chronic pain rehabilitation treatment outcome across treatment conditions and the possible mediating effect of BA between treatment conditions. Furthermore, the hypothesis that patients with low BA benefit more from PMT was investigated.

Methods:
In total, 94 patients with chronic pain participated in a randomized clinical trial comparing multidisciplinary treatment as usual (TAU) with TAU plus PMT. Outcome variables were health-related quality of life, disability, and depression. Self-efficacy and catastrophizing were the process variables of treatment and the potential mediating factors in the relationship between BA and the outcome variables. The data were analyzed by linear mixed-model analysis.

Results:
Improvements in BA were related to improvements in all outcome variables across treatment conditions. The relationships were partly mediated by self-efficacy, catastrophizing, or both. In the regression model with depression as the outcome variable, the regression coefficient of treatment (ie, PMT vs. TAU) decreased by 34% and became nonsignificant when BA was added as a potential mediator. Patients with low BA seemed to benefit more from PMT than patients with high BA, especially on depression, BA, and catastrophizing.

Conclusions:
BA might be an important target of treatment to improve the multidisciplinary treatment outcome in chronic pain patients. Furthermore, PMT is an intervention that seems to provide its benefits through improving BA and may be especially beneficial for patients with low BA.
Effect of Axial Length on Macular Ganglion Cell Complex Thickness and on Early Glaucoma Diagnosis by Spectral-Domain Optical Coherence Tomography
Authors: Nakanishi Hideo , Akagi Tadamichi , Hangai Masanori , Kimura Yugo , Suda Kenji , Hasegawa Tomoko , Yamada Hiroshi , Yoshikawa Munemitsu , Morooka Satoshi , Ikeda Hanako Ohashi , Yoshimura Nagahisa 
Published: November 2015

Purpose:
To investigate the effects of the axial length (AL)-related ocular magnification on the thickness of the macular ganglion cell complex (mGCC), and the diagnostic accuracy of the built-in normative database of the spectral-domain optical coherence tomographic (SD-OCT) instrument for early glaucoma detection.

Methods:
This retrospective study included 41 eyes with early primary open-angle glaucoma and 36 normal eyes. The mGCC thickness within a 20-degree circle, equivalent to a 6 mm diameter in the Gullstrand model eye, was measured in the SD-OCT images. The magnification effect was corrected using Bennett formula, and the mGCC thickness within the actual 6 mm diameter circle was determined.

Results:
In normal eyes, the inferior corrected mGCC was significantly correlated with the AL (β=−0.40, P=0.028), but correction for the magnification reduced the correlation. In 38 nonhighly myopic eyes, the sensitivity and specificity of the SD-OCT’s significance maps for distinguishing early glaucoma were 95.0% and 94.4% when using either the uncorrected or the corrected mGCC. In 39 highly myopic eyes, the diagnostic accuracy was lower when using the uncorrected mGCC thickness (sensitivity was 95.2% and specificity was 44.4%), and was not improved when using the corrected mGCC (81.0% and 61.1%, respectively).

Conclusions:
The inferior mGCC was thinner in eyes with longer AL. The accuracy of the diagnosis with the SD-OCT built-in normative database for early glaucoma was not improved significantly by the correction of the AL-associated magnification in highly myopic eyes. Evaluation of highly myopic eyes with the nonhighly myopic normative database can lead to misdiagnosis.
Assessing the Role of the Family/Support System Perspective in Patients With Glaucoma
Authors: Shtein Roni M. , Newman-Casey Paula A. , Herndon Leon , Coleman Anne L. , Lee Paul P. 
Published: November 2015

Purpose:
To investigate the role of the family/friends support system for patients with glaucoma and their perspective on barriers to effective glaucoma management.

Methods:
Six focus groups were conducted in 3 geographically and ethnically diverse areas of the United States (Los Angeles, CA; Rochester, MN; Durham, NC) that included 31 participants; 68% (21/31) were family members and friends of glaucoma patients with poor vision and 32% (10/31) were support system individuals of patients with good vision. Content analysis was used to identify important themes. Semiquantitative analysis was used to measure the frequency of each theme.

Results:
A total of 134 relevant comments were made in the 6 focus groups and 72% of relevant comments were made by individuals providing support for patients with poor vision. Family members and friends mentioned the following areas of concern regarding patients’ glaucoma care: patient education (19.4%), doctor-patient relationship (17.9%), their own lack of involvement in the patient’s medical care (17.2%), frustration with glaucoma and with the patient (14.9%), patient dependency on caregivers (14.9%), patient frustration with the disease (10.4%), and sex differences in coping mechanisms (5.2%).

Conclusions:
Support system individuals tend to be minimally involved in the patient’s glaucoma status and care. This is especially true for support system members of patients with glaucoma who maintain good vision and those who do not have any other personal experiences with difficulties from glaucoma. Many of these family members express an interest in acquiring more education about glaucoma and becoming more involved in the patient’s glaucoma care.
Outcomes of Nd:YAG Goniopuncture After Viscocanalostomy/Phacoviscocanalostomy
Authors: Mathews Divya , Shirodkar Amy-lee , Ahnood Dana , Garrick Adesuwa 
Published: November 2015

Purpose:
The aim of this study is to evaluate the safety and efficacy of laser goniopuncture (LGP) to lower intraocular pressure (IOP) post-viscocanalostomy (VC)/phacoviscocanalostomy (PVC). Outcomes include: IOP reduction from pre-LGP levels and the need for further topical antiglaucomatous medication or surgery.

Patients and Methods:
A total of 541 eyes that underwent VC/PVC between 2009 and 2012, at the Stanley eye unit in Abergele were included in the study.

Inclusion criteria:
All patients who had LGP at any timepoint after VC/PVC when target IOP was not achieved +/− progression in visual field with at least 6 months of follow-up data.
Statistical analysis was performed on IOP values pre- and post-LGP, involving χ2, Fischer exact, Mann-Whitney U, and Wilcoxon tests. A P-value of <0.05 was accepted as the level of significance.

Results:
Of the 515 included eyes, 136 (26%) required LGP after a mean of 15.11±9.73 months after surgery (95% confidence interval, 13.46-16.76 mo), ranging from 1 to 42 months. LGP reduced IOP significantly from a mean of 22.92±5.80 to 17.08±5.30 mm Hg immediately for all eyes, a reduction of 5.84 mm Hg (or a 25% reduction) (P<0.0001). IOP significantly reduced in the VC group with a mean reduction of 7.60 mm Hg compared with 4.85 mm Hg in the PVC group immediately after the procedure (P=0.0038). LGP was required sooner in the VC group compared with PVC, 11.35 and 14.57 months, respectively (P=0.0393). A total of 69 (62%) eyes were commenced on topical IOP-lowering medications, mean 7.26±6.41 months after LGP.

Conclusions:
This study supports previous evidence that LGP enhances the IOP-lowering success of VC/PVC. The advantages of LGP are that it is a minimally invasive clinic-based procedure with a low complication rate.