bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Evaluation of Supplementation Assisted American Shad Restoration in the James River, Virginia
Authors: Aunins Aaron W. , Epifanio John M. , Brown Bonnie L. 
Published: June 2014

Abstract
Hatchery supplementation programs have been implemented for several populations of American Shad Alosa sapidissima, which are declining across the species' native range due to disrupted access to spawning grounds, habitat degradation, and overfishing. The genetic impacts of stocking Pamunkey River origin larvae into the James River American Shad population since 1994 were investigated, and the effects were considered within a regional context by including American Shad populations from other Chesapeake Bay tributaries that also received interbasin stockings from various rivers over the same period. Levels of genetic diversity for microsatellite markers were high in all populations except the Susquehanna River population, which showed a significant decline in diversity between the 1990s and 2007. Before supplementation of James River American Shad, the James and Pamunkey River populations exhibited subtle standardized differentiation among groups (F′CT = 0.012), whereas differentiation was reduced after supplementation (F′CT = 0.007), indicating that supplementation contributed to homogenization of population structure within the two rivers. Chesapeake Bay tributaries also displayed higher levels of differentiation in the 1990s (F′CT = 0.063) than in contemporary, supplemented samples (F′CT = 0.004). Bayesian analyses of population structure among 1990s Chesapeake Bay samples only identified the Susquehanna River as having a distinguishable population, and no population structure was detected among samples collected in the late 2000s. In light of the fact that Chesapeake Bay American Shad populations are not rebounding in response to supplementation, our observation of reduced genetic differentiation among populations is a likely signal of substitution by hatchery origin fish rather than increasing natural recruitment. As such, spawning habitat improvement in conjunction with continued baywide fishing regulation may be a more beneficial strategy for restoring viable American Shad populations than continued reliance on supplementation.
Received June 5, 2013; accepted February 3, 2014
Annular itineraries for entire functions
Authors: Rippon P. , Stallard G. 
Published: June 2014

In order to analyse the way in which the size of the iterates of a transcendental entire function

f
f

can behave, we introduce the concept of the annular itinerary of a point

z
z

. This is the sequence of non-negative integers

s
0

s
1

…

s_0s_1\ldots

defined by
\[

f
n

(
z
)
∈

A

s
n

(
R
)
,

for
n
≥
0
,

f^n(z)\in A_{s_n}(R),\;\;\text {for }n\ge 0,

\]
where

A
0

(
R
)
=
{
z
:

|

z

|

>
R
}

A_0(R)=\{z:|z|>R\}

and
\[

A
n

(
R
)
=
{
z
:

M

n
−
1

(
R
)
≤

|

z

|

>

M
n

(
R
)
}
,

n
≥
1.

A_n(R)=\{z:M^{n-1}(R)\le |z|>M^n(R)\},\;\;n\ge 1.

\]
Here

M
(
r
)

M(r)

is the maximum modulus of

f
f

on

{
z
:

|

z

|

=
r
}

\{z:|z|=r\}

and

R
>
0

R>0

is so large that

M
(
r
)
>
r

M(r)>r

, for

r
≥
R

r\ge R

.

We consider the different types of annular itineraries that can occur for any transcendental entire function

f
f

and show that it is always possible to find points with various types of prescribed annular itineraries. The proofs use two new annuli covering results that are of wider interest.
CNV-guided multi-read allocation for ChIP-seq
Authors: Zhang Qi , Keleş Sündüz 
Published: June 2014

Abstract
Motivation: In chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and other short-read sequencing experiments, a considerable fraction of the short reads align to multiple locations on the reference genome (multi-reads). Inferring the origin of multi-reads is critical for accurately mapping reads to repetitive regions. Current state-of-the-art multi-read allocation algorithms rely on the read counts in the local neighborhood of the alignment locations and ignore the variation in the copy numbers of these regions. Copy-number variation (CNV) can directly affect the read densities and, therefore, bias allocation of multi-reads.
Results: We propose cnvCSEM (CNV-guided ChIP-Seq by expectation-maximization algorithm), a flexible framework that incorporates CNV in multi-read allocation. cnvCSEM eliminates the CNV bias in multi-read allocation by initializing the read allocation algorithm with CNV-aware initial values. Our data-driven simulations illustrate that cnvCSEM leads to higher read coverage with satisfactory accuracy and lower loss in read-depth recovery (estimation). We evaluate the biological relevance of the cnvCSEM-allocated reads and the resultant peaks with the analysis of several ENCODE ChIP-seq datasets.
Availability and implementation : Available at http://www.stat.wisc.edu/∼qizhang/
Contact : qizhang@stat.wisc.edu or keles@stat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Leptin deficiency in vivo enhances the ability of splenic dendritic cells to activate T cells
Authors: Ramirez Oscar , Garza Kristine M. 
Published: June 2014

Abstract
Leptin is a pleiotropic adipokine that is critical for regulating food intake and energy expenditure and also participates in functions of the immune system, including those of antigen-presenting cells. Here, we assess the effect of leptin deficiency on the function splenic dendritic cells (sDC). sDC from leptin-deficient mice (Lepob) were evaluated ex vivo for phenotype, ability to respond to inflammatory stimuli, to acquire and process antigens and to activate T cells. The data show that Lepob sDC express activation markers similar to controls and respond similarly to LPS activation or anti-CD40 cross-linking. In addition, antigen acquisition and processing by Lepob sDC was similar to controls. However, Lepob sDC elicited higher production of IFN-γ in mixed lymphocyte reactions and increased production of IL-2 by antigen-specific T-cell hybridoma relative to controls. To assess Lepob sDC activation of T cells in vivo, Lepob and control mice were infected systemically with Mycobacterium avium. Lepob mice were significantly better at neutralizing the infection as measured by splenic bacterial load over time. This was mirrored with an increased percentage of activated T cells in M. avium-infected Lepob mice. Thus, although no changes were detected in sDC phenotype, activation, antigen processing or presentation, these DC surprisingly presented an enhanced ability to activate T cells ex vivo and in vivo. These data demonstrate that leptin can modulate DC function and suggest that leptin may dampen T-cell responsiveness in the physiological setting.
Culturally and linguistically diverse patient participation in glioma research
Authors: Lwin Zarnie , Broom Alexander , Cosman Rasha , Livingstone Ann , Sawkins Kate , Good Phillip , Kirby Emma , Koh Eng-Siew , Hovey Elizabeth ,   on behalf of the COGNO CALD working group
Published: June 2014

Abstract
Marginal communities, such as culturally and linguistically diverse (CALD) patients, have significantly lower rates of recruitment, accrual, and retention in cancer clinical trials. A combination of language and cultural barriers means that trial participation from CALD communities remains at suboptimal levels, which in turn favors research findings that are biased towards therapeutic effects or toxicities within the context of non-CALD populations. Here we outline some key challenges and implications for CALD patient participation in glioma research in countries such as Australia, where English is the language of governance and health services implementation. We highlight multistakeholder interventions to improve both investigator recruitment and participation of CALD communities in future glioma research, particularly in this era when global migration has come of age. Enhancing research participation of CALD communities ensures not only wider understanding of genetic heterogeneity to improve glioma outcomes but also equity in access to care.
The β-relaxation in metallic glasses
Authors: Yu Hai Bin , Wang Wei Hua , Bai Hai Yang , Samwer Konrad 
Published: June 2014

Abstract
Focusing on metallic glasses as model systems, we review the features and mechanisms of the β-relaxations, which are intrinsic and universal to supercooled liquids and glasses, and demonstrate their importance in understanding many crucial unresolved issues in glassy physics and materials science, including glass transition phenomena, mechanical properties, shear-banding dynamics and deformation mechanisms, diffusion and the breakdown of the Stokes–Einstein relation as well as crystallization and stability of glasses. We illustrate that it is an attractive prospect to incorporate these insights into the design of new glassy materials with extraordinary properties. We also outline important questions regarding the nature of β-relaxations and highlight some emerging research directions in this still-evolving field.
Amantadine Alleviates Postoperative Cognitive Dysfunction Possibly by Increasing Glial Cell Line-derived Neurotrophic Factor in Rats
Authors: Zhang Junfeng , Tan Hongying , Jiang Wei , Zuo Zhiyi 
Published: June 2014

Abstract

Background:
Postoperative cognitive dysfunction is a clinical entity that is associated with poor outcome. We determined the effectiveness of amantadine in reducing surgery-induced cognitive impairment and the role of glial cell line-derived neurotrophic factor (GDNF) in this effect.

Methods:
Four-month old male Fischer 344 rats were subjected to right carotid exposure under intravenous anesthesia. Some rats received intraperitoneal injection of 25 mg/kg/day amantadine for 3 days with the first dose at 15 min before the surgery or intracerebroventricular injection of GDNF or an anti-GDNF antibody at the end of surgery. One week later, rats were started to be tested by Barnes maze and fear conditioning. Hippocampus was harvested at 6 h, 24 h or 10 days after the surgery for biochemical analysis. C8-B4 cells, a microglial cell line, were pretreated with 1 ng/ml GDNF for 30 min before being exposed to 5 ng/ml lipopolysaccharide for 2 h.

Results:
Surgery increased the time to identify the target box in the Barnes maze when tested 1 day [22 (median) (11–66) (interquartile range) of control group vs. 158 (29–180) of surgery group, n = 15, P = 0.022) or 8 days after the training sessions and reduced context-related freezing behavior in the fear conditioning test. These effects were attenuated by amantadine (25 (14–90), n = 15, P = 0.029 compared with surgery group at 1 day after the training sessions in Barnes maze) and intracerebroventricular GDNF. Amantadine increased GDNF that was co-localized with glial fibrillary acidic protein, an astrocytic marker, in the hippocampus. Intracerebroventricular injection of an anti-GDNF antibody but not the denatured antibody blocked the effects of amantadine on cognition. Surgery induced neuroinflammation that was inhibited by amantadine. Lipopolysaccharide increased interleukin 1β production from C8-B4 cells. This effect was inhibited by GDNF.

Conclusions:
Our results suggest that amantadine attenuated surgery-induced learning and memory impairment. This effect may be mediated by GDNF via inhibition of neuroinflammation.
Overcoming the Challenges of Unstructured Data in Multisite, Electronic Medical Record-based Abstraction
Authors: Polnaszek Brock , Gilmore-Bykovskyi Andrea , Hovanes Melissa , Roiland Rachel , Ferguson Patrick , Brown Roger , Kind Amy J.H. 
Published: June 2014

Background:
Unstructured data encountered during retrospective electronic medical record (EMR) abstraction has routinely been identified as challenging to reliably abstract, as these data are often recorded as free text, without limitations to format or structure. There is increased interest in reliably abstracting this type of data given its prominent role in care coordination and communication, yet limited methodological guidance exists.

Objectives:
As standard abstraction approaches resulted in substandard data reliability for unstructured data elements collected as part of a multisite, retrospective EMR study of hospital discharge communication quality, our goal was to develop, apply and examine the utility of a phase-based approach to reliably abstract unstructured data. This approach is examined using the specific example of discharge communication for warfarin management.

Research Design:
We adopted a “fit-for-use” framework to guide the development and evaluation of abstraction methods using a 4-step, phase-based approach including (1) team building; (2) identification of challenges; (3) adaptation of abstraction methods; and (4) systematic data quality monitoring.

Measures:
Unstructured data elements were the focus of this study, including elements communicating steps in warfarin management (eg, warfarin initiation) and medical follow-up (eg, timeframe for follow-up).

Results:
After implementation of the phase-based approach, interrater reliability for all unstructured data elements demonstrated κ’s of ≥0.89—an average increase of +0.25 for each unstructured data element.

Conclusions:
As compared with standard abstraction methodologies, this phase-based approach was more time intensive, but did markedly increase abstraction reliability for unstructured data elements within multisite EMR documentation.
National Trends and Outcomes of Pediatric Gastrostomy Tube Placement
Authors: Fox David , Campagna Elizabeth J. , Friedlander Joel , Partrick David A. , Rees Daniel I. , Kempe Allison 
Published: June 2014

ABSTRACTObjectives:National outcomes data regarding surgical gastrostomy tube (G‐tube) and percutaneous endoscopic gastrostomy (PEG) tube procedures are lacking. Our objectives were to describe trends in G‐tube and PEG procedures, examine regional variation, and compare outcomes.Methods:This was a retrospective study using pediatric admissions during 1997, 2000, 2003, 2006, and 2009 from the Kids' Inpatient Database. Length of stay and cost were adjusted for demographics, complexity, setting, year, and infection or surgical complication.Results:G‐tubes were placed during 64,412 admissions, increasing from 16.6 procedures/100,000 US children in 1997 to 18.5 in 2009. Surgical gastrostomy rates increased by 19% (0.17 procedures/100,000/year, P < 0.002) and, among children <1 year, they increased by 32% (2.56 procedures/100,000/year, P < 0.01). PEG rates did not increase (0.02 procedures/100,000/year, P = 0.47) in the study years. The West had an 18% higher rate than the national average for surgical G‐tubes and a 10% higher rate for PEGs. When the sole procedure during the admission was gastrostomy, the G‐tube was associated with a 19% (confidence interval 9.7–57.5) longer length of stay, and a 25% higher cost (confidence interval 16.4–34.5) compared with PEG.Conclusions:Surgical gastrostomy insertion rates have increased whereas PEG rates have not, despite evidence of better severity‐adjusted outcome measures for PEG tubes. Surgical gastrostomy insertion in children <1 year of age yielded the greatest increase, which may relate to a changing patient population; however, regional variation suggests that provider preference also plays a role. Our data underline the need for more robust collection and analysis of surgical outcomes to guide decision making.
svaseq: removing batch effects and other unwanted noise from sequencing data
Authors: Leek Jeffrey T. 
Published: June 2014

AbstractIt is now well known that unwanted noise and unmodeled artifacts such as batch effects can dramatically reduce the accuracy of statistical inference in genomic experiments. We introduced surrogate variable analysis for estimating these artifacts by (1) identifying the part of the genomic data only affected by artifacts and (2) estimating the artifacts with principal components or singular vectors of the subset of the data matrix. The resulting estimates of artifacts can be used in subsequent analyses as adjustment factors. Here I describe an update to the sva approach that can be applied to analyze count data or FPKMs from sequencing experiments. I also describe the addition of supervised sva (ssva) for using control probes to identify the part of the genomic data only affected by artifacts. These updates are available through the surrogate variable analysis (sva) Bioconductor package.
Volatility in Cereal Prices: Intra‐ Versus Inter‐annual Volatility
Authors: Ott Herve 
Published: June 2014

AbstractIntra‐annual (within crop year) price volatility and inter‐annual (between crop years) price volatility are measured for wheat, maize, rice, barley, oats and rye. A set of explanatory variables is used in a pooled regression to explain variations in these price volatilities. With low cereal stocks, supply (yield) shocks (defined here as volatilities, as for the price volatilities) mostly influence inter‐annual volatility while other influential factors are the crude oil price and exchange rate. Cereal demand and interest rate shocks combined with low stocks affect intra‐annual volatility, while other explanatory factors include exchange rate and crude oil price shocks. The derivatives market activity appears to have no significant effect on either intra‐ or inter‐annual volatility. In contrast, large cereal stocks and a well‐functioning international cereal market reduce the effects of shocks in the explanatory variables on both intra‐ and inter‐annual volatilities.
Impaired hepatic Gd‐EOB‐DTPA enhancement after radioembolisation of liver malignancies
Authors: Powerski Maciej Janusz , Scheurig‐Münkler Christian , Hamm Bernd , Gebauer Bernhard 
Published: June 2014

AbstractIntroductionTo evaluate the uptake of the liver‐specific magnetic resonance imaging (MRI) contrast agent gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid (Gd‐EOB‐DTPA) by functional liver parenchyma after radioembolisation (RE) of hepatic malignancies.MethodsUptake of Gd‐EOB‐DTPA prior to RE versus 60+/−24d and 126+/−32d after RE was compared in a group of 33 patients with primary or secondary hepatic malignancies. In patients who underwent single‐lobe treatment, left and right lobes were compared 59+/−24 days after RE. Gd‐EOB‐DTPA uptake was determined as follows: ratio of mean signal intensity in liver parenchyma to muscle in Gd‐EOB‐DTPA‐enhanced T1‐weighted MRI was subtracted from ratio of mean intensity in liver parenchyma to muscle in unenhanced T1‐weighted MRI.ResultsGd‐EOB‐DTPA uptake in liver parenchyma was 0.845+/−0.29 before RE, 0.615+/−0.38 (P = 0.0022) at day 60+/−24, and 0.739+/−0.30 at day 126+/−32 after RE. In cases of single‐lobe treatment, Gd‐EOB‐DTPA uptake was 0.581+/−0.256 for treated and 0.828+/−0.32 (P = 0.0164) for untreated hepatic lobes.ConclusionsUptake of Gd‐EOB‐DTPA by liver parenchyma is impaired after RE, indicating dysfunction of the local hepatic system. These findings suggest that Gd‐EOB‐DTPA‐enhanced MRI has the potential to be used for monitoring liver damage after RE.
Childhood onset systemic lupus erythematosus: how is it different from adult SLE?
Authors: Aggarwal Amita , Srivastava Puja 
Published: June 2014

AbstractAbout 20% of systemic lupus erythematosus (SLE) starts in childhood and children have less gender bias in favor of females as compared to adults. Systemic manifestations, nephritis, neuro‐psychiatric disease and cytopenias are more common in children at presentation than adults. Since most children develop lupus in their early adolescence, dealing with the diagnosis of an unpredictable lifelong disease during this phase of life is challenging. Physicians must recognise specific medical and social needs of this age group, for optimal long‐term outcome. Steroids and immunosuppressive drugs are the cornerstone for treatment in children as with adults with lupus. The outcome has improved considerably with these drugs and 10‐year survival is nearly 90%. Due to longer life spans more damage accrues in children as compared to adults. Most of the drugs are associated with significant toxicity and the goal of having a drug which reduces disease activity and damage without hampering normal growth, development and fertility is still an elusive one. The current review focuses on clinical and immunological aspects of childhood SLE and how it differs from adulthood SLE.
Contextualising pollination benefits: effect of insecticide and fungicide use on fruit set and weight from bee pollination in lowbush blueberry
Authors: Melathopoulos A.P. , Tyedmers P. , Cutler G.C. 
Published: June 2014

AbstractCurrent approaches to determining the value of insect pollinators to crop yield assume that plants are primarily pollen limited. This is particularly relevant in a crop such as lowbush blueberry, Vaccinium angustifolium, where no fruit will set without insect‐mediated cross‐pollination. However, such valuations usually ignore other factors that are necessary to maximise crop yields. We conducted an experiment to test whether yields of lowbush blueberry attributed to pollinator activity increased independently of pest management. The experiment was a 2 × 2 factorial design, incorporating two intensities of pollination (25% or 100% of flowers), and two levels of insect and disease management with recommended fungicide and insecticide sprays (‘full inputs’ or ‘no inputs’). We demonstrated an interaction between these two factors, such that increased fruit set at harvest was only possible if 100% pollination was combined with the ‘full input’ treatment. Furthermore, increases in fruit weight among the remaining treatments were only realised in the ‘full input’ plots. These results suggest that the value accorded to pollinator activity in blueberries is strongly dependent upon pest and disease management of the crop.
Primary immune‐mediated thrombocytopenia and immune‐mediated neutropenia suspected in a 21‐week‐old Maine Coon cat
Authors: Best MP , Fry DR 
Published: June 2014

Case reportA 21‐week‐old Maine Coon cat presented with an acute‐onset coagulopathy. Severe concurrent thrombocytopenia and neutropenia were identified on peripheral blood smears and bone marrow cytology supported a peripheral consumptive process. Other than mild superficial haemorrhage, the cat was clinically well and screening for retroviral diseases, abdominal ultrasound examination, thoracic radiography, haematology and biochemistry panels did not identify an underlying disease. There was no historical pharmaceutical or toxicological trigger noted and the cat was from an area without endemic Ehrlichia spp. There was a rapid resolution of both cytopenias following treatment with immunosuppressive doses of prednisolone, though a mild relapse occurred during gradual prednisolone withdrawal and was responsive to a dose increase.ConclusionsThis report describes this combination of diseases for the first time in a cat and presents a younger patient than previously described with feline primary immune‐mediated haematological disease.