bluuebunny/crossref_metadata_2025_split huggingface dataset:
TfR1 interacts with the IKK complex and is involved in IKK–NF-κB signalling
Authors: Kenneth Niall S. , Mudie Sharon , Naron Sanne , Rocha Sonia 
Published: October 2012

The IKK [inhibitor of NF-κB (nuclear factor κB) kinase] complex has an essential role in the activation of the family of NF-κB transcription factors in response to a variety of stimuli. To identify novel IKK-interacting proteins, we performed an unbiased proteomics screen where we identified TfR1 (transferrin receptor 1). TfR1 is required for transferrin binding and internalization and ultimately for iron homoeostasis. TfR1 depletion does not lead to changes in IKK subunit protein levels; however, it does reduce the formation of the IKK complex, and inhibits TNFα (tumour necrosis factor α)-induced NF-κB-dependent transcription. We find that, in the absence of TfR1, NF-κB does not translocate to the nucleus efficiently, and there is a reduction in the binding to target gene promoters and consequentially less target gene activation. Significantly, depletion of TfR1 results in an increase in apoptosis in response to TNFα treatment, which is rescued by elevating the levels of RelA/NF-κB. Taken together, these results indicate a new function for TfR1 in the control of IKK and NF-κB. Our data indicate that IKK–NF-κB responds to changes in iron within the cell.
Toward a Quantitative Basis for Assessment and Diagnosis of Apraxia of Speech
Authors: Haley Katarina L. , Jacks Adam , de Riesthal Michael , Abou-Khalil Rima , Roth Heidi L. 
Published: October 2012

Purpose
We explored the reliability and validity of 2 quantitative approaches to document presence and severity of speech properties associated with apraxia of speech (AOS).

Method
A motor speech evaluation was administered to 39 individuals with aphasia. Audio-recordings of the evaluation were presented to 3 experienced clinicians to determine AOS diagnosis and to rate severity of 11 speech dimensions. Additionally, research assistants coded 11 operationalized metrics of articulation, fluency, and prosody in the same speech samples and in recordings from 20 neurologically healthy participants.

Results
Agreement among the 3 clinicians was limited for both AOS diagnosis and perceptual scaling, but inter-observer reliability for the operationalized metrics was strong. The relationships between most operationalized metrics and mean severity ratings for corresponding perceptual dimensions were moderately strong and statistically significant. Both perceptual scaling and operationalized quantification approaches were sensitive to the presence or absence of AOS.

Conclusions
Perceptual scaling and operationalized metrics are promising quantification techniques that can help establish diagnostic transparency for AOS. However, because satisfactory reliability cannot be assumed for scaling techniques, effective training and calibration procedures should be implemented. Operationalized metrics show strong potential for enhancing diagnostic objectivity and sensitivity.
An Individual‐Based Model of Ontogenetic Migration in Reef Fish Using a Biased Random Walk
Authors: Saul Steven , Die David , Brooks Elizabeth N. , Burns Karen 
Published: October 2012

AbstractMigration is an important component of the life history and ontogeny of reef fish. On the west coast of Florida, the interaction between ontogenetically migrating reef fish and fishing effort is an important contributor to the pattern of fishing mortality. A biased random walk model was developed to represent the movement of red grouper Epinephelus morio from the inshore nursery habitat occupied by juveniles to the offshore reef habitat inhabited by adults on the West Florida Shelf. A simulated tagging study was conducted to develop distributions of movement speed. Time at large, release location, and input movement speed from conventional tagging data were used to parameterize the simulation. Maturity at age, determined when fish began moving, and directional movement behavior were modeled as functions of preferential habitat. The results suggest that the general movement of tagged fish can be represented using simple assumptions. Comparison of the tagging study and the tagging simulation showed no statistical differences between these two in terms of movement speed, distance traveled, mean size of fish at release, and mean size of fish at recapture. Furthermore, the age distribution of the fish arriving at the reef in the model matched the observed age distribution in the commercial catch.
Empirical Evidence of Fall Spawning by Atlantic Sturgeon in the James River, Virginia
Authors: Balazik Matthew T. , Garman Greg C. , Van Eenennaam Joel P. , Mohler Jerre , Woods L. Curry 
Published: October 2012

AbstractDue to overfishing and habitat alteration, the anadromous Atlantic sturgeon Acipenser oxyrinchus oxyrinchus is severely depleted across its historic range. The James and York rivers in Virginia are the two rivers comprising the Chesapeake Bay distinct population segment, where Atlantic sturgeon reproduction has been confirmed. It is widely recognized that Atlantic sturgeon spawn in the spring throughout their range; however, there is debate over whether they also spawn in the fall. To determine if Atlantic sturgeon spawn in the fall, independent of the spring spawn, large‐mesh gill netting in the freshwater portion of the James River (above river kilometer 108) was conducted in the spring (April–June) and fall (August–October) for 3 years (2009–2011), resulting in the capture of 125 adult Atlantic sturgeon (three were recaptures) during the fall sampling, but none were captured during the spring. Field examination for sex and stage of maturity identified 106 mature males and one postspawned female. Sex was not determined for four fish, and due to time constraints, 11 were not examined. Forty mature males were externally tagged with Vemco© ultrasonic passives tags and movements were monitored with a Vemco© VR2W passive receiver array. Collection and tracking data showed that mature Atlantic sturgeon aggregate in the freshwater portion of the James River during the fall season, entering during August and out‐migrating by the end of November. No tagged fish were detected in the freshwater area of the river during the subsequent spring months. Though James River Atlantic sturgeon may spawn in the spring, we suggest there is strong evidence for an independent fall spawn, which should be considered in future management and recovery actions.
Short-Term Retention Rates of Passive Integrated Transponders Surgically Implanted in Burbot and the Effects on Survival
Authors: Gardunio E. I. , Myrick C. A. 
Published: October 2012

Abstract
Passive integrated transponder tags are commonly used in fisheries science to individually identify fish in studies that assume high fish survival and tag retention rates, and have recently been used in studies on burbot Lota lota, although information on retention and survival rates is unavailable. Burbot (310–676-mm TL) surgically implanted with 23-mm PIT tags had 93% survival and 100% retention over 60 d; the survival of these burbot was not significantly different from that of a control group. This suggests that this marking method is a viable means of individually identifying burbot for short-term studies.
Received January 21, 2012; accepted July 4, 2012
Spatial and Temporal Variation of Whirling Disease Risk in Montana Spring Creeks and Rivers
Authors: Neudecker Ryen A. , McMahon Thomas E. , Vincent E. Richard 
Published: October 2012

Abstract
Spring creeks are important spawning and rearing areas for wild trout, but the stable flows, cool temperatures, and high nutrient levels that characterize these unique habitats may also make them highly susceptible to establishment and proliferation of the whirling disease pathogen Myxobolus cerebralis. We evaluated the spatial and temporal dynamics in whirling disease risk by using sentinel rainbow trout Oncorhynchus mykiss fry in nine different spring creeks and their conjoining rivers or reservoirs in Montana over a 20-month period. Whirling disease risk was high in five of the seven pathogen-positive spring creek study sites; at these sites, prevalence levels exceeded 90% and over 50% of sentinel fry had moderate to high infection severity scores. Spring creeks generally had higher disease prevalence and severity than paired river or reservoir sites. Fine sediment levels varied widely among springs creeks with high and low whirling disease risk, and we found no significant association between fine sediment level and infection severity. The low risk measured for some spring creeks was likely attributable to the pathogen invasion being in its early stages rather than to environmental characteristics limiting the severity of infection. High whirling disease risk occurred over a wide range of temperatures at spring creek sites (4.5–13°C) and river sites (1.7–12.5°C). There was an unusual seasonal cycle of infection in spring creeks, with peak infection levels occurring from late fall to early spring and declining to near zero in late spring to early fall. The low infection risk during spring suggests that spring-spawning trout would be at a low risk of infection, even in spring creeks with otherwise high disease severity. In contrast, fry of fall-spawning trout may be much more susceptible to infection in spring creek environments.
Received November 22, 2011; accepted May 7, 2012
Effect of Dietary Supplementation with Achyranthes aspera Seed on Larval Rohu Labeo rohita Challenged with Aeromonas hydrophila
Authors: Chakrabarti R. , Srivastava P. K. 
Published: October 2012

Abstract
Larval rohu Labeo rohita were fed four different diets: three of the diets contained Achyranthes aspera (prickly chaff-flower) seeds at 0.10% (D1), 0.25% (D2), or 0.50% (D3); the fourth diet was a control diet (D4; no A. aspera supplementation). After 70 d, the rohu were injected intraperitoneally with live Aeromonas hydrophila. Mortality of fish was recorded for 7 d. In the D4 group, the first mortality was observed within 12 h of exposure, whereas in the D1–D3 treatment groups, mortality was first observed at 24 h postexposure. In the D4 group, 50% of fish died within 72 h of exposure, whereas in the D3 group, 10–15% mortality occurred between 72 and 84 h. The cumulative mortality rate was 50% for D4, 40% for D1, 35% for D2, and 15% for D3. Total tissue protein level in the larvae was higher for the D2 and D3 groups than for the other groups. Glutamic oxaloacetic transaminase, glutamate pyruvate transaminase, and thiobarbituric acid reactive substance levels were significantly lower in D3 larvae than in the other groups, whereas lysozyme and nitric oxide synthase levels were significantly higher in D3 larvae compared with the other groups. Dietary supplementation with A. aspera seeds at the 0.50% level provided protection against oxidative stress, prevented tissue damage, and enhanced disease resistance in rohu larvae.
Received December 26, 2011; accepted May 7, 2012
Can Copper-Based Substrates Be Used to Protect Hatcheries from Invasion by the New Zealand Mudsnail?
Authors: Hoyer S A , Myrick C A 
Published: October 2012

Abstract
Copper sheet (abbreviated SC), copper mesh (MC), copper-based ablative antifouling paint (AP), and copper-based nonablative antifouling paint (NP) were tested to determine each material's ability to serve as contact deterrents to the invasive New Zealand mudsnail Potamopyrgus antipodarum. Mudsnail responses to each surface treatment was measured across a range of water temperatures (8, 12, 18, and 24°C), hardness levels (75, 125, 175, and 300 mg/L as CaCO3), pH values (6, 7, and 8.5), water velocities (0, 9, and 33 cm/s), and levels of surface fouling (0, 6, and 10 weeks of exposure). Mean crawling distances (MCD) by the mudsnails in the temperature, hardness, and pH experiments were significantly lower on the SC and MC surface treatment than the NP treatment. In the velocity experiment, static, nonflowing conditions produced the lowest MCD, whereas increasing water velocity from 9 cm/s to 33 cm/s did not produce a significant change in MCD on either the SC or MC surfaces. Finally, MCD did increase significantly on the AP surface treatment after exposure to surface fouling; fouling had no significant effect on MCD on the MC or SC surface. Overall, MC and SC were determined to be the most effective surfaces in limiting the locomotor activity of the mudsnail. By lining the inside surface of effluent pipes with either material, hatcheries may be able to eliminate a potential invasion pathway for this organism. Based on the maximum observed crawling distance observed throughout these experiments, we recommend that barriers constructed of MC or SC be a minimum length of 250 cm to provide a satisfactory level of protection against mudsnail invasion. Additional considerations include design and integration with other types of barriers.
Using Golf Balls to Keep Screens Clean in Circular Rearing Tanks
Authors: Irvine James R , Gaetz Harley 
Published: October 2012

Abstract
Screens on bottom-draining circular tanks typically require daily cleaning with a brush. The addition of three golf balls to 9,000-L tanks virtually eliminated the need for cleaning, saving money and potentially reducing the risk of damage to fish during cleaning. Circular moving water kept the golf balls in perpetual motion on top of the screens, crushing entrained feces and waste food, which then exited the tanks. Golf balls typically require replacement after 6 months.
HiCNorm: removing biases in Hi-C data via Poisson regression
Authors: Hu Ming , Deng Ke , Selvaraj Siddarth , Qin Zhaohui , Ren Bing , Liu Jun S. 
Published: October 2012

Abstract
Summary: We propose a parametric model, HiCNorm, to remove systematic biases in the raw Hi-C contact maps, resulting in a simple, fast, yet accurate normalization procedure. Compared with the existing Hi-C normalization method developed by Yaffe and Tanay, HiCNorm has fewer parameters, runs &gt;1000 times faster and achieves higher reproducibility.
Availability: Freely available on the web at: http://www.people.fas.harvard.edu/∼junliu/HiCNorm/.
Contact: jliu@stat.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Advanced Complex Trait Analysis
Authors: Gray A. , Stewart I. , Tenesa A. 
Published: October 2012

Abstract
Motivation: The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance.
Results: We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279 435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min.
Availability and implementation: The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta.
Contact: a.gray@ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
The ortho : para ratio of H
3
+
in laboratory and astrophysical plasmas
Authors: Crabtree Kyle N. , McCall Benjamin J. 
Published: October 2012

In diffuse molecular clouds, the nuclear spin temperature of

(approx. 30 K) is much lower than the cloud kinetic temperature (approx. 70 K). To understand this temperature discrepancy, we have measured the ratio of the hop to exchange pathways (
α
) in the

reaction (which interconverts ortho- and para-

) using high-resolution spectroscopy of the
ν
2
fundamental band of

in a hydrogenic plasma. We find that
α
decreases from 1.6±0.1 at 350 K to its statistical value of 0.5±0.1 at 135 K. We use this result to model the steady-state chemistry of diffuse molecular clouds, finding good agreement with astronomical data provided the dissociative recombination rates of ortho- and para-

are equal and the identity branching fraction for the

reaction is large. Our results highlight the need for further studies of the

reaction as well as state-selective measurements of

dissociative recombination.
Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
Authors: Windram Oliver , Madhou Priyadharshini , McHattie Stuart , Hill Claire , Hickman Richard , Cooke Emma , Jenkins Dafyd J. , Penfold Christopher A. , Baxter Laura , Breeze Emily , Kiddle Steven J. , Rhodes Johanna , Atwell Susanna , Kliebenstein Daniel J. , Kim Youn-sung , Stegle Oliver , Borgwardt Karsten , Zhang Cunjin , Tabrett Alex , Legaie Roxane , Moore Jonathan , Finkenstadt Bärbel , Wild David L. , Mead Andrew , Rand David , Beynon Jim , Ott Sascha , Buchanan-Wollaston Vicky , Denby Katherine J. 
Published: October 2012

Abstract
Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. We generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions, and testing of one such prediction identified a role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.
Uncontrolled allergic rhinitis and chronic rhinosinusitis: where do we stand today?
Authors: Hellings P. W. , Fokkens W. J. , Akdis C. , Bachert C. , Cingi C. , Dietz de Loos D. , Gevaert P. , Hox V. , Kalogjera L. , Lund V. , Mullol J. , Papadopoulos N. G. , Passalacqua G. , Rondón C. , Scadding G. , Timmermans M. , Toskala E. , Zhang N. , Bousquet J. 
Published: October 2012

AbstractState‐of‐the‐art documents like ARIA and EPOS provide clinicians with evidence‐based treatment algorithms for allergic rhinitis (AR) and chronic rhinosinusitis (CRS), respectively. The currently available medications can alleviate symptoms associated with AR and RS. In real life, a significant percentage of patients with AR and CRS continue to experience bothersome symptoms despite adequate treatment. This group with so‐called severe chronic upper airway disease (SCUAD) represents a therapeutic challenge. The concept of control of disease has only recently been introduced in the field of AR and CRS. In case of poor control of symptoms despite guideline‐directed pharmacotherapy, one needs to consider the presence of SCUAD but also treatment‐related, diagnosis‐related and/or patient‐related factors. Treatment‐related issues of uncontrolled upper airway disease are linked with the correct choice of treatment and route of administration, symptom‐oriented treatment and the evaluation of the need for immunotherapy in allergic patients. The diagnosis of AR and CRS should be reconsidered in case of uncontrolled disease, excluding concomitant anatomic nasal deformities, global airway dysfunction and systemic diseases. Patient‐related issues responsible for the lack of control in chronic upper airway inflammation are often but not always linked with adherence to the prescribed medication and education. This review is an initiative taken by the ENT section of the EAACI in conjunction with ARIA and EPOS experts who felt the need to provide a comprehensive overview of the current state of the art of control in upper airway inflammation and stressing the unmet needs in this domain.
Weight misperception and its barriers to keep health weight in Chinese children
Authors: Zhao Min , Zhang Min , Zhou Xiaoqi , Yang Hongying , Yang Yanhong , Yang Nianhong 
Published: October 2012

AbstractAims:  To examine the prevalence rate of misperception, assess the relationship between weight perception and weight‐related behaviors in Chinese children.Methods:  A total of 2708 children aged 7–12 years from five public primary schools and their parents completed questionnaires assessing social demographic background, dietary and activity related factors. Weight and height were measured by trained investigators. The prevalence of misperception was defined by comparing calculated BMI and their perceived weight status. Log‐binomial model yielded adjusted prevalence ratios (PRs) for each behavior by weight misperception in boys and girls separately.Results:  Misperception was more prevalent in normal weight children 33.3% for girls and 40.5% for boys and boys were more likely to underestimate their weight status than girls. Associations were observed between misperceived thinness and eating before bed, want to eat seeing others eating, eating sugar and snacks frequently, monophagia and choosy in food both in girls and boys. And associations between misperceived fatness and depression and want to eat seeing others eating were found only in girls.Conclusions:  Our findings underscore the importance of weight perception in shaping realistic body image among normal weight children. Education must be introduced to help children accurately look on their body shape.
Molecular determinants of platelet delta storage pool deficiencies: an update
Authors: Masliah‐Planchon Julien , Darnige Luc , Bellucci Sylvia 
Published: October 2012

SummaryDelta storage pool deficiency (δ‐SPD) is a rare heterogeneous group of platelet disorders characterized by a reduction in the number or content of dense granules. δ‐SPD causes a mild to moderate bleeding diathesis characterized mainly by mucocutaneous bleeding. Currently, no specific treatment is available and the therapeutic approach is based on prevention of excessive bleeding. However, during the last few years, important insights into the pathophysiology of δ‐SPD have been achieved using mouse models and dense granule deficiency‐associated congenital diseases, such as Hermansky–Pudlak syndrome and Chediak–Higashi syndrome. It thus appears that δ‐SPD represents a genetically heterogeneous group of intracellular vesicle biogenesis and/or trafficking disorders. This review summarizes recent data regarding the molecular mechanisms together with clinical features of the different types of δ‐SPD. Although the molecular basis of isolated inherited δ‐SPD remains currently unknown, next‐generation sequencing strategies should enable researchers to identify the causative genes. Identification of those genes should contribute to our understanding of the pathophysiology, represent useful tools for genetic diagnosis, and eventually lead to new specific therapeutic approaches.