bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactive Effects of Stocking Density and Algal Feed Ration on Growth, Survival, and Ingestion Rate of Larval Geoduck Clams
Authors: Marshall Robert , Pearce Christopher M , McKinley R Scott
Published: June 2014

The combined effects of initial stocking density (2, 5, 10 individuals [inds]/mL) and feed ration (5×103, 20×103, 40×103, 100×103 cells·ind−1·d−1) on growth, survival, and ingestion rate of larval geoduck clams Panopea generosa fed Isochrysis sp. (Tahitian strain, TISO clone) were assessed. All three measurements were significantly affected by stocking density, ration, and their interaction. Growth rate ranged from 2.15 to 3.85 μm/d in the various treatments. It increased with stocking density at 5×103 cells·ind−1·d−1, was significantly higher at 5 than at 2 inds/mL at 20×103 cells·ind−1·d−1, and was significantly higher at 2 and 5 than at 10 inds/mL at 40×103 and 100×103 cells·ind−1·d−1. Growth rate increased with increasing ration up to 40×103 cells·ind−1·d−1 at 2 and 5 inds/mL, but decreased with increasing ration at 10 inds/mL. Percent survival over the experiment duration (23 d) ranged from 7% to 56% in the various treatments and generally decreased with increasing stocking density. There was no significant effect of ration on percent survival at 2 and 5 inds/mL, but survival decreased with increasing ration at 10 inds/mL. Ingestion rate ranged from 2×103 to 29×103 cells·ind−1·d−1 in the various treatments. It was not significantly affected by stocking density at 5×103 and 20×103 cells·ind−1·d−1, but larvae held at 2 and 5 inds/mL had significantly higher ingestion rates than those stocked at 10 inds/mL at 40×103 and 100×103 cells·ind−1·d−1. Ingestion rate increased with ration at 2 and 5 inds/mL but was not significantly affected by ration at 10 inds/mL. Due to the significant interaction of the treatment factors, stocking density-specific ration levels must be selected in order to maximize growth and survival.
More Judicious Use of Fish Oil in Cobia Feeds: II. Effects of Graded Fish Oil Sparing and Finishing
Authors: Woitel Franklin R , Trushenski Jesse T , Schwarz Michael H , Jahncke Michael L
Published: June 2014

Replacement of long-chain (LC) polyunsaturated fatty acid (PUFA)-rich fish oil with alternative lipids in aquafeeds typically reduces the LC-PUFA content and associated nutritional value of farmed fish even if production performance is unaffected. Finishing can be used to augment tissue LC-PUFA levels prior to harvest; however, the effectiveness of this strategy for use with the Cobia Rachycentron canadum is relatively unknown. For 8 weeks, Cobias (initial weight [mean ± SE] = 59.8 ± 0.2 g) were fed diets in which the supplemental lipid consisted of 100% fish oil; 100% beef tallow; a blend of 33% beef tallow and 67% fish oil; or a blend of 67% beef tallow and 33% fish oil. After the 8-week grow-out period, all treatment groups received the 100% fish oil feed for 6 weeks to simulate finishing. Differences in production performance were observed, but growth and growth efficiency were not reduced by inclusion of beef tallow in the grow-out feeds. Prior to the finishing period, fatty acid profiles of fillet, liver, eye, and brain tissues varied considerably among treatments. As finishing progressed, tissue profiles converged on the profiles of fish that were fed the 100% fish oil diet exclusively. Specifically, saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) declined, whereas LC-PUFA levels varied relatively little during the trial. Results indicate that SFA- and MUFA-rich alternative lipids like beef tallow minimize LC-PUFA loss during grow-out and that finishing feeds can be used to modify Cobia tissue profiles prior to harvest.
Evaluation of a Gonadotropin Releasing Hormone Analog of cGnRH II as a Spawning Aid for Channel Catfish Versus Analogs of mGnRH I and sGnRH III
Authors: Quiniou Sylvie M A , Bosworth Brian , Chatakondi Nagaraj , Oberle Danny
Published: June 2014

The effectiveness of three different analogs of gonadotropin-releasing hormone (GnRH) to induce spawning in female Channel Catfish Ictalurus punctatus were evaluated concurrently in a blind study. Two of those analogs are currently used under Investigative New Animal Drug by the catfish industry, mGnRH Ia (D-Ala6, Pro9-NHet) and sGnRH IIIa (D-Arg6, Trp7, Leu8, Pro9-NHet). A third analog, cGnRH IIa (D-Arg6, Pro9-NHet) derived from a different type of GnRH (i.e., type II), previously thought to have only secondary roles in reproduction compared to type I and III, was also evaluated. The study was divided into four independent, weekly trials over the course of the spawning season, and 78 females were tested for each of the three hormone treatments. Each female received one type of hormone (type I, II, or III) in two doses, one for priming and one for induction: mGnRH Ia or cGnRH IIa at 20 μg/kg of body weight (priming) and 80 μg/kg (induction) or sGnRH IIIa at 2 μg/kg and 8 μg/kg. Treatment had a significant effect on the mean percent ovulation, cGnRH IIa producing the highest ovulation rate (90.2%), followed by mGnRH Ia (64.9%) and then sGnRH IIIa (44.3%). For females that ovulated, there were no significant treatment differences for number of eggs or viable fry per kilogram of body weight. Therefore, the treatment differences for total egg and fry production reflect hormone effects on ovulation rate while egg quality for females that ovulated was not different among treatments. These results indicate that cGnRH IIa shows great potential as a spawning aid for channel catfish, outperforming mGnRH Ia and sGnRH IIIa.
Short and Long-Term Preservation of Sablefish Sperm from Baja California, Mexico
Authors: Sanchez-Serrano Samuel , Paniagua-Chavez Carmen Guadalupe , Segovia Manuel , Weirich Charles R
Published: June 2014

Sablefish Anoplopoma fimbria is a species with high potential for aquaculture in Mexico. The development of protocols for short- and long-term preservation of Sablefish sperm becomes necessary to store viable sperm that can be used as needed. In October and November of 2011 and 2012, Sablefish broodstock (mean weight, 3.5 kg; SD, 0.02) were captured using deepwater longlines in an area localized between the cities of Tijuana and Ensenada, Baja California, Mexico. The sperm concentration was evaluated by spectrophotometry. We determined the efficiency of two extender solutions in the short-term storage of Sablefish sperm and evaluated three cryoprotectants (DMSO, methanol, and glycerol) and three cryopreservation protocols. Significant differences in sperm concentration between years and months were found. No differences were found in sperm activation time between both extender solutions. Significant differences were found among storage time, extender, month, year, and sperm motility or membrane integrity. A significant correlation between sperm motility and membrane integrity was found for both extenders in November. Significant differences were found among type and concentration of cryoprotectant, incubation time, and motility. Significant differences among cryopreservation protocols, cryoprotectant, and sperm motility and membrane integrity were registered. Glycerol (10%) registered the best motility (78%) and membrane integrity using the third cryopreservation protocol when samples were placed 5 cm above the liquid nitrogen for 9 min before being plunged in liquid nitrogen. These results will allow us to establish a reproduction program for Sablefish that will be used as a tool to advance the culture of this species in Mexico.
Growth Response of Juvenile Walleyes after Cold Banking
Authors: Harder Thomas M , Gotsch Gordon G , Summerfelt Robert C
Published: June 2014

The natural geographical range of Walleye Sander vitreus extends to northern latitudes where lakes are often ice covered for 8 months. Their adaptation to long intervals at low temperature provides aquaculturists the opportunity to purposefully maintain Walleyes in confinement for several months at low temperatures with minimal feeding, i.e., a protocol termed cold banking (CB). To be successful, CB should not result in substantial mortality or loss of body condition, and after CB interval, fish should show a strong positive growth response. The objective of this study was to determine the growth response and condition of fingerling Walleyes cold banked, for 125 d at mean temperature of 6.9°C, in a 76-d post-CB (PCB) interval. Survival in the CB interval was 99%, and means of initial and final length, weight (4.5% loss), and relative weight (Wr) were not significantly different. After a 4-d transition from 5.1°C to 19.2°C, some CB Walleyes were cultured in a water reuse aquaculture system at mean temperature of 22.6°C for 76 d. In the PCB interval, fish length increased 31%, and weight 170%, and Wr was 99.8. This study demonstrates that CB did not result in substantial mortality or weight loss, and Walleyes show a strong PCB growth response after cold banking.
Production and Enrichment of Chironomid Larva with Different Levels of Vitamin C and Effects on Performance of Persian Sturgeon Larvae
Authors: Hamidoghli Ali , Falahatkar Bahram , Khoshkholgh Majidreza , Sahragard Ahad
Published: June 2014

Chironomid larvae have a high reproduction capacity. Because of their excellent nutritional quality, they have great potential in larval fish nutrition, specially bottom feeders like sturgeons. In this study, indoor production of Chironomus riparius was performed by controlling the physicochemical factors and developing an appropriate condition for this insect to complete the life cycle. Enrichment of lava was conducted by adding 0 (C0), 100 (C100), or 1000 (C1000) mg of ascorbic acid to 1 kg of chicken manure (as substrate). Ascorbic acid analysis of chironomid larva showed significant differences among the groups: 74.2 μg/g for C0, 325.0 μg/g for C100, and 779.9 for C1000. In the second experiment, enriched chironomids were fed to larval Persian Sturgeon Acipenser persicus and were compared with sturgeons fed live cladocerans, Daphnia, which are regulary used in hatcheries. Length and weight measurements after 14 d of the experimental period showed no significant differences in growth performance. Analysis of ascorbic acid in Persian Sturgeon viscera also showed no significant differences between the groups. In conclusion, chironomids could be cultured indoors and can be enriched to meet the nutritional requirements of fish. We found ascorbic acid did not have a signifucant effect on Persian Sturgeon larval feeding, but longer feeding periods and implication of unfavorable physicochemical conditions or causing stress tests might demonstrate the beneficial effects of this vitamin.
Growth and Feed Conversion Ratio of Pond-Raised Hybrid Catfish Harvested at Different Sizes
Authors: Li Menghe H , Robinson Edwin H , Bosworth Brian G , Torrans Eugene L
Published: June 2014

A study was conducted to examine growth and feed conversion ratios (FCRs) of pond-raised hybrid catfish (Channel Catfish Ictalurus punctatus×Blue Catfish I. furcatus) harvested at different sizes. Fingerling hybrid catfish (initial weight per fish, mean±SD = 62±2.0 g) were stocked into 25 earthen ponds (0.04 ha each) at a density of 14,826 fish/ha. Fish were fed daily to apparent satiation with a commercial 28% protein feed. When fish reached a predetermined weight (0.454, 0.680, 0.907, 1.361, or 1.814 kg/fish), they were harvested. Fish grown to 0.46 kg and 0.70 kg during the first season had FCRs of 1.61 and 1.59, respectively. Fish carried over for a second season of growth were harvested at mean weights of 0.85, 1.43, and 2.01 kg/fish, respectively. The FCRs of these fish, 1.97, 2.10, and 1.93, respectively, were significantly higher than those of fish harvested in first season. These results suggest it is generally more cost effective to harvest food-size hybrid catfish after one season because of their increased FCR the following year. However, if fish are raised to be marketed for large fillets, hybrid catfish appear to be a good choice because they continue to grow and utilize feed relatively well in a second season.
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

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
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper A Subscript n Baseline left-parenthesis upper R right-parenthesis equals StartSet z colon upper M Superscript n minus 1 Baseline left-parenthesis upper R right-parenthesis less-than-or-equal-to StartAbsoluteValue z EndAbsoluteValue greater-than upper M Superscript n Baseline left-parenthesis upper R right-parenthesis EndSet comma n greater-than-or-equal-to 1 period">

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.
The XMAP215 family drives microtubule polymerization using a structurally diverse TOG array
Authors: Fox Jaime C. , Howard Amy E. , Currie Joshua D. , Rogers Stephen L. , Slep Kevin C.
Published: June 2014

XMAP215 family members are potent microtubule (MT) polymerases, with mutants displaying reduced MT growth rates and aberrant spindle morphologies. XMAP215 proteins contain arrayed tumor overexpressed gene (TOG) domains that bind tubulin. Whether these TOG domains are architecturally equivalent is unknown. Here we present crystal structures of TOG4 from Drosophila Msps and human ch-TOG. These TOG4 structures architecturally depart from the structures of TOG domains 1 and 2, revealing a conserved domain bend that predicts a novel engagement with α-tubulin. In vitro assays show differential tubulin-binding affinities across the TOG array, as well as differential effects on MT polymerization. We used Drosophila S2 cells depleted of endogenous Msps to assess the importance of individual TOG domains. Whereas a TOG1-4 array largely rescues MT polymerization rates, mutating tubulin-binding determinants in any single TOG domain dramatically reduces rescue activity. Our work highlights the structurally diverse yet positionally conserved TOG array that drives MT polymerization.
ROCC, a conserved region in cohesin's Mcd1 subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation
Authors: Eng Thomas , Guacci Vincent , Koshland Doug
Published: June 2014

Cohesin helps orchestrate higher-order chromosome structure, thereby promoting sister chromatid cohesion, chromosome condensation, DNA repair, and transcriptional regulation. To elucidate how cohesin facilitates these diverse processes, we mutagenized Mcd1p, the kleisin regulatory subunit of budding yeast cohesin. In the linker region of Mcd1p, we identified a novel evolutionarily conserved 10–amino acid cluster, termed the regulation of cohesion and condensation (ROCC) box. We show that ROCC promotes cohesion maintenance by protecting a second activity of cohesin that is distinct from its stable binding to chromosomes. The existence of this second activity is incompatible with the simple embrace mechanism of cohesion. In addition, we show that the ROCC box is required for the establishment of condensation. We provide evidence that ROCC controls cohesion maintenance and condensation establishment through differential functional interactions with Pds5p and Wpl1p.
CNV-guided multi-read allocation for ChIP-seq
Authors: Zhang Qi , Keleş Sündüz
Published: June 2014

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

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

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

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

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

Objectives:

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.
The evolution of respiratory O
2
/NO reductases: an out-of-the-phylogenetic-box perspective
Authors: Ducluzeau Anne-Lise , Schoepp-Cothenet Barbara , van Lis Robert , Baymann Frauke , Russell Michael J. , Nitschke Wolfgang
Published: June 2014

Complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. However, the history of O
2
-levels in the atmosphere is complex and prior to the Great Oxidation Event some 2.3 billion years ago, the amount of O
2
in the biosphere is considered to have been extremely low as compared with present-day values. Therefore the evolutionary histories of life and of O
2
-levels are likely intricately intertwined. The obvious biological proxy for inferring the impact of changing O
2
-levels on life is the evolutionary history of the enzyme allowing organisms to tap into the redox power of molecular oxygen, i.e. the bioenergetic O
2
reductases,
alias
the cytochrome and quinol oxidases. Consequently, molecular phylogenies reconstructed for this enzyme superfamily have been exploited over the last two decades in attempts to elucidate the interlocking between O
2
levels in the environment and the evolution of respiratory bioenergetic processes. Although based on strictly identical datasets, these phylogenetic approaches have led to diametrically opposite scenarios with respect to the history of both the enzyme superfamily and molecular oxygen on the Earth. In an effort to overcome the deadlock of molecular phylogeny, we here review presently available structural, functional, palaeogeochemical and thermodynamic information pertinent to the evolution of the superfamily (which notably also encompasses the subfamily of nitric oxide reductases). The scenario which, in our eyes, most closely fits the ensemble of these non-phylogenetic data, sees the low O
2
-affinity SoxM- (or A-) type enzymes as the most recent evolutionary innovation and the high-affinity O
2
reductases (SoxB or B and
cbb
3
or C) as arising independently from NO-reducing precursor enzymes.
svaseq: removing batch effects and other unwanted noise from sequencing data
Authors: Leek Jeffrey T.
Published: June 2014

It 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.
Crystal structures of (μ2-η2,η2-4-hydroxybut-2-yn-1-yl 2-bromo-2-methylpropanoate-κ4C2,C3:C2,C3)bis[tricarbonylcobalt(II)](Co—Co) and [μ2-η2,η2-but-2-yne-1,4-diyl bis(2-bromo-2-methylpropanoate)-κ4C2,C3:C2,C3]bis[tricarbonylcobalt(II)](Co—Co)
Authors: McAdam C. John , Moratti Stephen C. , Robinson Brian H. , Simpson Jim , Stanley Roderick G.
Published: June 2014

The title compounds, [Co2(C8H11BrO3)(CO)6], (1), and [Co2(C12H16Br2O4)(CO)6], (2), result from the replacement of two carbonyl ligands from dicobalt octacarbonyl by the alkynes 4-hydroxybut-2-ynyl 2-bromo-2-methylpropanoate and but-2-yne-1,4-diyl bis(2-bromo-2-methylpropanoate), respectively. Both molecules have classic tetrahedral C2Co2cluster cores with the CoIIatoms in a highly distorted octahedral coordination geometry. The alkyne ligands both adopt acis-bent conformation on coordination. In the crystal structure of (1), classical O—H...O and non-classical C—H...O contacts form inversion dimers. These combine with weak O...O and Br...O contacts to stack the molecules into interconnected columns along theb-axis direction. C—H...O and C—H...Br contacts stabilize the packing for (2), and a weak Br...O contact is also observed. Interconnected columns of molecules again form along theb-axis direction.
Crystal structure of ammonium divanadium(IV,V) tellurium(IV) heptaoxide
Authors: Harrison William T. A. , Johnston Magnus G.
Published: June 2014

The polyhedral building blocks of the layered inorganic network in the mixed-valence title compound, (NH4)(VIVO2)(VVO2)(TeO3), are vertex-sharing VVO4tetrahedra, distorted VIVO6octahedra and TeO3pyramids, which are linked by V—O—V and V—O—Te bonds, forming double layers lying parallel to (100). The presumed TeIVlone-pairs of electrons appear to be directed inwards into cavities in the double layers. The charge-balancing ammonium cations lie between the layers and probably interact with themviaN—H...O hydrogen bonds.
Crystal structure of poly[[(acetato-κO){μ3-N-[(pyridin-4-yl)methyl]pyrazine-2-carboxamidato-κ4N:N1,N2:N4]copper(II)] dihydrate]: a metal–organic framework (MOF)
Authors: Cati Dilovan S. , Stoeckli-Evans Helen
Published: June 2014

The title compound, [Cu(C11H9N4O)(CH3CO2)]·2H2O (CuL), is a hydrated copper acetate complex of the ligandN-[(pyridin-4-yl)methyl]pyrazine-2-carboxamide (HL). Complex CuLhas a metal–organic framework (MOF) structure with a 10 (3) network topology. The ligand coordinates in a bidentate and a bis-monodentate manner, bridging three equivalent CuIIatomsviathe pyridine N atom and the second pyrazine N atom. The CuIIatom has a fivefold coordination sphere, CuN4O, being coordinated to three N atoms of the ligand and the acetate O atom in the equatorial plane and to the second pyrazine atom in the apical position. This gives rise to a fairly regular square-pyramidal geometry. In the crystal, the water molecules are linked to each other and to the three-dimensional frameworkviaO—H...O hydrogen bonds. There are also a number of C—H...O hydrogen bonds present within the framework.
Crystal structures of 1,4-diazabicyclo[2.2.2]octan-1-ium 4-nitrobenzoate dihydrate and 1,4-diazabicyclo[2.2.2]octane-1,4-diium bis(4-nitrobenzoate): the influence of solvent upon the stoichiometry of the formed salt
Authors: Akhmad Aznan Aina Mardia , Abdullah Zanariah , Tiekink Edward R. T.
Published: June 2014

The 1:1 co-crystallization of 1,4-diazabicyclo[2.2.2]octane (DABCO) with 4-nitrobenzoic acid in ethanol–water (3/1) gave the salt dihydrate C6H13N2+·C7H4NO4−·2H2O, (1), whereas from methanol, the salt C6H14N22+·2C7H4NO4−, (2), was isolated. In (1), the cation and anion are linked by a strong N—H...O hydrogen bond, and the carboxylate anion is close to planar [dihedral angle between terminal residues = 6.83 (9)°]. In (2), a three-ion aggregate is assembled by two N—H...O hydrogen bonds, and the carboxylate anions are again close to planar [dihedral angles between terminal residues = 1.7 (3) and 5.9 (3)°]. Through the intervention of solvent water molecules, which self-assemble into helical supramolecular chains along thebaxis, the three-dimensional architecture in (1) is stabilized by water–DABCO O—H...N and water–carboxylate O—H...O hydrogen bonds, with additional stability afforded by C—H...O interactions. The global crystal structure comprises alternating layers of water molecules and ion pairs stacked along thecaxis. In the crystal of (2), the three-ion aggregates are assembled into a three-dimensional architecture by a large number of methylene–carboxylate/nitro C—H...O interactions as well as π–π contacts between inversion-related benzene rings [inter-centroid distances = 3.5644 (16) and 3.6527 (16) Å]. The cations and anions assemble into alternating layers along thecaxis.
Crystal structure of chlorido(piperidine-κN)(quinoline-2-carboxylato-κ2N,O)platinum(II)
Authors: Nguyen Thi Thanh Chi , Nguyen Bich Ngan , Van Meervelt Luc
Published: June 2014

The title compound, [Pt(C10H6NO2)Cl(C5H11N)], crystallizes with one molecule in the asymmetric unit. The PtIIcation has a slightly distorted square-planar coordination environment defined by a chloride anion, the quinoline N atom and a carboxylate O atom of the bidentate quinaldate ligand and a piperidine N atom. An intramolecular C—H...Cl hydrogen bond occurs. In the crystal, molecules are stacked into columns along thecaxis by the formation of N—H...Cl and C—H...O hydrogen bonds.
Crystal structures of 2,5-diazido-1,4-phenylene diacetate and 2,5-diazido-1,4-phenylene dibutyrate
Authors: Glöcklhofer Florian , Fröhlich Johannes , Stöger Berthold , Weil Matthias
Published: June 2014

The asymmetric units of the title compounds, C10H8N6O4, (I), and C14H16N6O4, (II), each contain half of the respective molecule which is completed by inversion symmetry. The two molecules differ in the ester moiety (acetateversusbutyrate) and the crystal symmetry is different,i.e.triclinic for (I) and monoclinic for (II). The diazidophenylene moieties are essentially planar [maximum deviation of 0.0216 (7) Å for (I) and 0.0330 (14) Å for (II)], and the ester functionalities are almost perpendicular to these planes, making dihedral angles of 79.93 (3)° for (I) and 79.42 (6)° for (II). In the crystals of both (I) and (II), there are no significant intermolecular interactions present.
Crystallization screening: the influence of history on current practice
Authors: Luft Joseph R. , Newman Janet , Snell Edward H.
Published: June 2014

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.
Volatility in Cereal Prices: Intra‐ Versus Inter‐annual Volatility
Authors: Ott Herve
Published: June 2014

Intra‐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.
At the Crossroads: Putin's Third Presidential Term and Russia's Institutions
Authors: Rochlitz Michael
Published: June 2014

In 2013, Russia's economy entered a phase of stagnation, with a rate of gross domestic product (GDP) growth much lower than that of other emerging economies. This article argues that economic stagnation is linked to the dysfunctional system of informal institutions that permeates every level of political decision making in the country. By discussing four recent books on the topic, the article shows the negative effect of Russia's informal institutions on economic development, as well as how their emergence and persistence is linked to the political system built by Vladimir Putin. The article then outlines different scenarios of institutional reform to show how Russia stands very much at a crossroads between different paths of political, economic and institutional development.
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

Introduction

To 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.

Methods

Uptake 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.

Results

Gd‐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.

Conclusions

Uptake 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

About 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

Current 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 report

A 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.

Conclusions

This 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.