bluuebunny/crossref_metadata_2025_split huggingface dataset:
Passage of Spawning Alabama Shad at Jim Woodruff Lock and Dam, Apalachicola River, Florida
Authors: Young Shawn P. , Ingram Travis R. , Tannehill Josh E. , Isely J. Jeffery 
Published: June 2012

AbstractIn 2005, a pilot study was initiated to evaluate the potential use of the navigation lock at Jim Woodruff Lock and Dam (JWLD), Florida, as a means for fish passage. The focal species was the Alabama shad Alosa alabamae. The Apalachicola River population is one of the last‐remaining, extant self‐sustaining populations, estimated adult spawning returns ranging from lows of 5,211 to 14,674 individuals in 2007 to highs of 51,417 to 127,251 individuals in 2010. We estimated the passage of migrating Alabama shad during spawning migrations during March–May 2005, 2007, 2010, and 2011. During 2005, 23 of 36 Alabama shad that were implanted with transmitters successfully passed from the lock into the reservoir 1–7 d after release, for a passage rate of 64% (95% CI = 48–80%). Advancing on the promising results from 2005, voluntary passage was evaluated during spring 2007, 2010, and 2011. During these years, 63–100% of implanted shad were relocated at the lock at least once, and voluntary passage ranged from 33% to 45%. Voluntary passage occurred 3–39 d postimplanting, most shad passing < 28 d after initial capture. Implanted Alabama shad were subsequently relocated upstream in both the Flint and Chattahoochee rivers. Based on these results, the navigation lock at JWLD was an effective means to pass migrating Alabama shad. Increased passage could be achieved by maximizing attraction flow near the lock entrance and increasing the time the upper gates are open during an afternoon locking cycle. By coupling passage and population estimates, the total number of shad that migrated through JWLD ranged from 2,137 in 2007 to 57,262 in 2010.
Emulating Riverine Landscape Controls of Beaver in Stream Restoration
Authors: DeVries Paul , Fetherston Kevin L , Vitale Angelo , Madsen Sue 
Published: June 2012

ABSTRACT
Stream and floodplain restoration at the reach scale has ranged from expensive, heavy-handed modification of the channel and floodplain to simple, longer-term revegetation efforts. We have developed and implemented a simple approach that emulates the ecosystem engineering effects of beaver. This approach is less expensive and disruptive than typical large-scale engineering efforts and has the potential to restore both fish habitat and floodplain vegetation more rapidly than simply revegetating and waiting for the riparian zone to mature. The approach involves constructing log flow-choke structures that mimic the hydraulic function of a natural beaver dam during flooding. By placing these structures throughout a naturally entrenched stream reach at locations promoting increased frequency of flood connection with floodplain swales and relict channels, we set the stage to restore the riparian corridor and floodplain more quickly than could be achieved through revegetation alone. Monitoring shows that within just one to two years of implementation, beaver are building more persistent dams in close proximity to our structures, and we are seeing increased hydraulic connectivity with the floodplain. Our technique may therefore provide a cost-effective, natural process-based restoration tool with potential large-scale benefits.
RESUMEN
El gradiente de restauración ribereña y de planicies de inundación puede ir desde una importante modificación artificial de canales y llanuras inundables, hasta esfuerzos de reforestación a largo plazo. En este estudio se desarrolló e implementó un enfoque que emula los efectos a nivel de ecosistema que tienen las construcciones hechas por los castores. Este enfoque es menos costoso e invasivo que los típicos esfuerzos de ingeniería a gran escala, y tiene el potencial de poder restaurar tanto el hábitat de los peces como la vegetación de las planicies de inundación más rápidamente que la práctica de sólo reforestar y esperar a que el área ribereña madure por sí misma. Este enfoque consiste en la construcción de estructuras hechas a base de troncos que controlan el flujo de agua, emulando la función hidráulica de las presas construidas por los castores. La colocación de dichas estructuras en lugares donde el agua se confina de forma natural a lo largo de sitios que promueven la comunicación con canales tributarios y llanuras de inundación, representa la infraestructura que sirve para restaurar el corredor ribereño y las planicies de inundación más rápidamente que lo que pudiera lograrse sólo mediante la reforestación. Un seguimiento muestra que tras dos años de la implementación del enfoque, los castores están edificando presas más resistentes en sitios próximos a las estructuras, y se aprecia un incremento en la conectividad hidráulica con las llanuras de inundación. Esta técnica, por lo tanto, representa una herramienta de restauración de bajo costo y basada en un proceso natural con beneficios potenciales observables a gran escala.
Nutritional Composition and Use of Common Carp Muscle in Yellow Perch Diets
Authors: Schaeffer Travis W , Hennen Matthew J , Brown Michael L , Rosentrater Kurt A 
Published: June 2012

Abstract
High market demand for marine fish meals coupled with increasing costs and questionable sustainability of wild stocks have led researchers to investigate a variety of alternative plant and animal protein sources for aquaculture feeds. Our objective was to evaluate the use of common carp Cyprinus carpio, a locally abundant, nonnative fish species, to offset the cost of marine fish meal in fish feed. We completed analyses of common carp whole muscle, formulated diets containing combinations of carp and Gulf menhaden Brevoortia patronus fish meal, and then evaluated test diets in a feeding trial with yellow perch Perca flavescens. Composition (dry matter basis [dmb]) of common carp flesh (crude protein [CP] = 73.4%, crude lipid [CL] = 25.7%) slightly differed from menhaden fish meal (MFM; CP = 71.0%, CL = 11.7%, dmb). Three experimental diets were formulated to include percentage ratios of 50:0, 25:25, or 0:50 of common carp muscle meal (CCMM) to MFM to obtain similar crude protein (29.7 ± 0.9% [mean ± SD]), crude lipid (15.0 ± 3.7%), and digestible energy (14.2 ± 0.3 kJ/g) levels. Juvenile yellow perch (initial weight = 18.1 ± 3.3 g) were randomly stocked (n = 7) in twelve 37-L tanks resulting in four replicate tanks per treatment. Fish fed 25% CCMM : 25% MFM had significantly higher weight gain, while fish fed 50% CCMM : 0% MFM had significantly higher food conversion ratios and lower visceral somatic indices. No statistically significant differences were observed for protein efficiency ratios, Fulton condition factors, hepatosomatic indices, or feed intake of fish fed the different diets. These results indicate that CCMM can be used to partially offset the use of MFM in yellow perch diets.
The Effect of Calcium Hardness on Hatching Success of Channel Catfish × Blue Catfish Hybrid Catfish Eggs
Authors: Chatakondi Nagaraj G , Torrans Eugene L 
Published: June 2012

Abstract
The present study was designed to determine the optimal level of calcium hardness in hatching waters to incubate channel catfish Ictalurus punctatus × blue catfish I. furcatus hybrid catfish eggs. Hatching success of hybrid catfish eggs was higher (P &lt; 0.05) at a calcium hardness (CaCO3) of 75 mg/L in hatching waters than at a calcium hardness of 25 or 50 mg/L; however, further increases in calcium concentration did not improve hatching success. A minimum water hardness of CaCO3 at 75 mg/L is recommended for incubating hybrid catfish eggs.
Baffled and Standard Raceways: A Comparison of Juvenile Spring Chinook Salmon Performance and Smolt-to-Adult Survival
Authors: Brignon William R , Olson Douglas E , Peters Mary H , Gutenberger Susan K 
Published: June 2012

Abstract
We compared on-station mortality, growth (mm), feed conversion, health parameters, and smolt-to-adult survival rate of spring Chinook salmon Oncorhynchus tshawytscha reared in baffled and standard (unbaffled) raceways. Fish reared in baffled raceways survived from release to adulthood at a rate 0.85 times that of fish reared in unbaffled raceways. There was no difference in percent on-station mortality (range, 0.00–0.001), health, or average length gained (1–12 mm) between fish reared in baffled and unbaffled raceways. Average feed conversion was constant (1.20–2.25) throughout the period of juvenile rearing and was similar between fish reared in baffled and unbaffled raceways, a finding supported by adiposomatic and hepatosomatic indices. Overall, we found similar on-station performance between fish reared in baffled and unbaffled raceways. The difference between SARs of fish reared in baffled versus unbaffled raceways was not statistically significant (P = 0.08). However, it is suggestive of a biological difference between the two treatments. The self-cleaning characteristics of baffled raceways free up a substantial amount of hatchery personnel time to attend to other duties, which ultimately reduces the annual operation budget for any facility. In the end, the self-cleaning feature of baffled raceways needs to be weighed against any advantage in adult survival of fish reared in unbaffled raceways.
SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides
Authors: Zhang Lida , Huang Yuyi , Zou Zehong , He Ying , Chen Ximo , Tao Ailin 
Published: June 2012

Abstract
Summary: SORTALLER is an online allergen classifier based on allergen family featured peptide (AFFP) dataset and normalized BLAST E-values, which establish the featured vectors for support vector machine (SVM). AFFPs are allergen-specific peptides panned from irredundant allergens and harbor perfect information with noise fragments eliminated because of their similarity to non-allergens. SORTALLER performed significantly better than other existing software and reached a perfect balance with high specificity (98.4%) and sensitivity (98.6%) for discriminating allergenic proteins from several independent datasets of protein sequences of diverse sources, also highlighting with the Matthews correlation coefficient (MCC) as high as 0.970, fast running speed and rapidly predicting a batch of amino acid sequences with a single click.
Availability and implementation: http://sortaller.gzhmc.edu.cn/.
Contact: taoailin@gzhmc.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
mcaGUI: microbial community analysis R-Graphical User Interface (GUI)
Authors: Copeland Wade K. , Krishnan Vandhana , Beck Daniel , Settles Matt , Foster James A. , Cho Kyu-Chul , Day Mitch , Hickey Roxana , Schütte Ursel M.E. , Zhou Xia , Williams Christopher J. , Forney Larry J. , Abdo Zaid 
Published: June 2012

Abstract
Summary: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future.
Availability: The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html
Contact: wade@kingcopeland.com; zabdo@uidaho.edu
Supplementary Information: Supplementary data and figures are available at Bioinformatics online.
Postoperative QT Interval Prolongation in Patients Undergoing Noncardiac Surgery under General Anesthesia
Authors: Nagele Peter , Pal Swatilika , Brown Frank , Blood Jane , Miller J. Philipp , Johnston Joshua 
Published: June 2012

Background
Abnormal cardiac repolarization, indicated by a prolongation of the QT interval, increases the risk for torsades de pointes, a potentially life-threatening arrhythmia. Many perioperatively administered drugs and conditions prolong the QT interval. Despite several reports of perioperative torsades de pointes, systematic evidence regarding perioperative QT interval prolongation is limited.

Methods
Serial postoperative 12-lead electrocardiograms were obtained from 469 adult patients undergoing major noncardiac surgery under general anesthesia. Heart rate corrected QT-interval duration (Fridericia formula) was the primary outcome. All perioperatively administered drugs were recorded. Emphasis was placed on absolute QTc prolongation greater than 500 ms and relative increases of 30 and 60 ms.

Results
At the end of surgery, 80% of the patients (345 of 429) experienced a significant QTc interval prolongation (ΔQTc 23 ± 26 ms (mean and SD), 95% CI 20-25 ms, P less than 0.001). Approximately 51% (219 of 429) had a QTc greater than 440 ms, and 4% (16 of 429) a QTc greater than 500 ms. In 39% (166 of 429), the ΔQTc was greater than 30 ms, in 8% (34 of 429) >60 ms, and in greater than 0.5% (2 of 429) >100 ms. No changes in ΔQTc occurred at subsequent time points. One patient developed torsades de pointes with a ΔQTc: 29 ms (0.4% incidence rate). Several drugs had a large effect on ΔQTc: isoflurane, methadone, ketorolac, cefoxitin, zosyn, unasyn, epinephrine, ephedrine, and calcium. Postoperative body temperature had a weak negative correlation with ΔQTc (r = -0.15, P = 0.02); serum magnesium, potassium, and calcium concentrations were not correlated.

Conclusion
Postoperative QT-interval prolongation is common. Several perioperatively administered drugs are associated with a substantial QT-interval prolongation. The exact cause and its clinical relevance are, however, unclear. Nevertheless, an association between postoperative QT prolongation and risk for torsades de pointes is likely.
QTL region–specific microarrays reveal differential expression of positional candidate genes of signaling pathways associated with the liability for the inverted teat defect
Authors: Chomwisarutkun K. , Murani E. , Brunner R. , Ponsuksili S. , Wimmers K. 
Published: June 2012

SummaryThe inverted teat defect is the most common disorder of the mammary complex in pigs. It is characterized by the failure of teats to protrude from the udder surface, preventing normal milk flow and thus limiting the rearing capacity and increasing the risk of mastitis. The inverted teat defect is a liability trait with a complex mode of inheritance. We previously identified QTL for inverted teats. As a complementary approach that integrates map‐based efforts to identify candidate genes for the inverted teat defect with function‐driven expression analysis, application‐specific microarrays were constructed that cover 1525 transcripts mapping in QTL regions on pig chromosomes 2, 3, 4, 6 and 11. About 950 transcripts were expressed in epithelial and mesenchymal teat tissue. The expression of three categories of teats was compared: normal teats of both non‐affected and affected animals and inverted teats of affected animals. In epithelium and mesenchyme, 62 and 24 genes respectively were significantly differentially expressed (DE). The majority of biofunctions to which a significant number of DE genes were assigned are related to the following: (1) cell maintenance, proliferation, differentiation and replacement; (2) organismal, organ and tissue development; or (3) genetic information and nucleic acid processing. Moreover, the DE genes belong almost exclusively to canonical pathways related to signaling rather than metabolic pathways. This is in line with findings obtained by genome‐wide catalogue microarrays. This study adds another piece to the puzzle of the etiology of inverted teats by indicating that causal genetic variation leading to the disorder is likely among the genes encoding for members of the signaling cascades of growth factors.
Genetic variants in a lipid regulatory pathway as potential tools for improving the nutritional quality of grass‐fed beef
Authors: Baeza M. C. , Corva P. M. , Soria L. A. , Pavan E. , Rincon G. , Medrano J. F. 
Published: June 2012

SummaryThe aim of this study was to evaluate the effect of genetic variants on candidate genes corresponding to the sterol recognition element–binding protein‐1 (SREBP‐1) signaling pathway and stearoyl‐CoA desaturases (SCD1andSCD5) on muscle fatty acid (FA) composition of Brangus steers fattened on grass.FAprofiles were measured on Longissimus lumborum muscle samples using a gas chromatography–flame ionization detection technique. A total of 43 tag single‐nucleotide polymorphisms on theSCD1,SCD5,SREBP‐1,SCAP,INSIG1,INSIG2,MBTPS1,MBTPS2,andSRPRgenes were genotyped on 246 steers to perform a marker–trait association study. To evaluate the influence of the Indicine breed in the composite breed, additional groups of 48 Angus, 18 Hereford, 75 Hereford x Angus, and 36 Limousin x Hereford–Angus steers were also genotyped. To perform the association analysis,FAdata were grouped according to the number of carbon atoms and/or number of double bonds (i.e.SFA,MUFA,PUFA, etc.). In addition, different indexes that reflect the activity ofFAdesaturase and elongase enzymes were calculated.SCD1markers significantly affected C14:1/(C14:0 + C14:1) and C18:1/(C18:0 + C18:1) indexes, whereas oneSNPinSCD5was correlated with the C16:1/(C16:0 + C16:1) index. Polymorphisms in thesignal recognition particle receptor(SRPR) gene were associated with all the estimated desaturase indexes. Because the evaluated markers showed no effect on total lipid content of beef, this work supports the potential utilization of these markers for the improvement of grass‐fed beef without undesirable side effects.
Phosphorylated 4E‐binding protein 1 (p‐4E‐BP1): a novel prognostic marker in human astrocytomas
Authors: Korkolopoulou Penelope , Levidou Georgia , El‐Habr Elias A , Piperi Christina , Adamopoulos Christos , Samaras Vassilis , Boviatsis Efstathios , Thymara Irene , Trigka Eleni‐Andriana , Sakellariou Stratigoula , Kavantzas Nikolaos , Patsouris Efstratios , Saetta Angelica A 
Published: June 2012

Korkolopoulou P, Levidou G, El‐Habr E A, Piperi C, Adamopoulos C, Samaras V, Boviatsis E, Thymara I, Trigka E‐A, Sakellariou S, Kavantzas N, Patsouris E & Saetta A A  (2012) Histopathology 61, 293–305Phosphorylated 4E‐binding protein 1 (p‐4E‐BP1): a novel prognostic marker in human astrocytomasAims:  To investigate the significance of the mammalian target of rapamycin (mTOR) pathway in astrocytic tumours, published information in this context being limited, especially regarding phosphorylated 4E‐binding protein (p‐4E‐BP) 1.Methods and results:  Paraffin‐embedded tissue from 111 patients with astroglial tumours (grades II–IV) was investigated for the association of phosphorylated mTOR (p‐mTOR) signalling components with phosphorylated extracellular signal‐related kinase 1/2 (p‐ERK1/2) and phosphorylated AKT (p‐AKT) expression, clinicopathological features, angiogenesis, isocitrate dehydrogenase 1 (IDH1)‐R132H, and survival. Expression was also quantified by western blot analysis in 12 cases and in three primary glioma cell cultures following rapamycin treatment. p‐mTOR expression correlated with p‐4E‐BP1 expression and marginally with p‐p70S6K expression. p‐4E‐BP1 expression increased with tumour grade. Rapamycin induced a decline in phosphorylation levels of all three proteins. Nuclear p‐AKT and cytoplasmic p‐ERK1/2 immunoexpression correlated with p‐4E‐BP1 expression, whereas cytoplasmic p‐AKT expression correlated with p‐p70S6K expression. All three proteins were associated with increased angiogenesis but not with IDH1‐R132H expression status. p‐mTOR adversely affected overall and disease‐free survival in univariate analysis. In multivariate survival analysis, the presence of p‐4E‐BP1 predicted shortened overall survival in the entire cohort and glioblastomas.Conclusions:  mTOR signalling components are differentially involved in the acquisition of a more aggressive and angiogenic phenotype in astrocytic tumours. Moreover, p‐4E‐BP1 emerges as a novel prognostic marker, which might aid in the selection of patients who are more likely to benefit from therapy with mTOR inhibitors.
RUNX‐1 and CD44 as markers of resident stem cell derivation in undifferentiated intimal sarcoma of pulmonary artery
Authors: Vasuri Francesco , Resta Leonardo , Fittipaldi Silvia , Malvi Deborah , Pasquinelli Gianandrea 
Published: June 2012

Vasuri F, Resta L, Fittipaldi S, Malvi D & Pasquinelli G  (2012) Histopathology 61, 737–743RUNX‐1 and CD44 as markers of resident stem cell derivation in undifferentiated intimal sarcoma of pulmonary arteryAims:  To report a rare case of undifferentiated intimal sarcoma (UIS) of the pulmonary artery in a 44‐year‐old woman, and to study it by electron microscopy and a novel immunohistochemical (IHC) panel that recognizes markers of endothelial and haematopoietic stemness, in order to extend current knowledge about the histogenesis of this rare neoplasm.Methods and results:  Immunohistochemical reactions for CD31, CD34, α‐smooth muscle actin (α‐SMA), caldesmon, calponin, actin, desmin, epithelial membrane antigen, WT1, CD117, Ki67, nestin, RUNX‐1, platelet‐derived growth factor, NG2, CD44, CD90 and CD105 were performed manually or automatically. Neoplastic cells were negative for CD31 and CD34, but positive for calponin, nestin, WT1, CD44, and RUNX‐1. Electron microscopy was performed after osmium tetroxide fixation and staining with lead citrate and uranyl acetate. Ultrastructurally, tumour cells had slightly irregular nuclei, cisternae of rough endoplasmic reticulum, and punctate intercellular junctions.Conclusions:  We report a case of pulmonary artery UIS expressing previously unreported markers, i.e. RUNX‐1, nestin, WT1, and CD44, that are commonly seen in different stages of the vascular differentiation hierarchy. These findings, together with the negativity for mature endothelial and smooth muscle markers, raise the question of whether this neoplasm may derive from a vessel wall‐resident stem cell, such as the haemangioblast or an embryonic‐like stem cell.
Differential expression of microRNAs miR‐21, miR‐31, miR‐203, miR‐125a‐5p and miR‐125b and proteins PTEN and p63 in verrucous carcinoma of the head and neck
Authors: Odar Katarina , Boštjančič Emanuela , Gale Nina , Glavač Damjan , Zidar Nina 
Published: June 2012

Odar K, Boštjančič E, Gale N, Glavač D & Zidar N  (2012) Histopathology 61, 257–265Differential expression of microRNAs miR‐21, miR‐31, miR‐203, miR‐125a‐5p and miR‐125b and proteins PTEN and p63 in verrucous carcinoma of the head and neckAims:  To investigate the expression of microRNAs miR‐21, miR‐31, miR‐203, miR‐125a‐5p and miR‐125b and proteins phosphatase and tensin homologue (PTEN) and p63 in verrucous carcinoma (VC) of the head and neck.Methods and results:  Thirty cases of VC, 50 cases of conventional squamous cell carcinoma (SCC) and 30 samples of normal epithelium of the head and neck were included. Real‐time polymerase chain reaction and immunohistochemistry were used to analyse the expression of microRNAs and proteins, respectively. In comparison to normal epithelium, miR‐21 was overexpressed in both VC and SCC and miR‐31 was overexpressed in VC and in well‐ and moderately differentiated SCC. Levels of miR‐203 were elevated in VC but unaltered or reduced in SCC, and levels of miR‐125a‐5p and miR‐125b were reduced in VC but unaltered in SCC. PTEN was down‐regulated in both VC and SCC, whereas p63 was down‐regulated in VC but up‐regulated in SCC. Differential expression of p63 in VC correlated inversely with the expression of miR‐21 and miR‐203.Conclusions:  Differences between VC, SCC and normal epithelium in expression profiles of investigated molecules indicate their association with the pathogenesis and clinicopathological characteristics of VC. Our results suggest that some microRNAs and proteins, particularly miR‐125b, miR‐203 and p63, might be useful in the diagnosis of VC.