bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantitative analysis of branching, growth cone turning, and directed growth in zebrafish retinotectal axon guidance
Authors: Simpson Hugh D. , Kita Elizabeth M. , Scott Ethan K. , Goodhill Geoffrey J. 
Published: November 2012

AbstractThe topographic projection from the eye to the tectum (amphibians and fish)/superior colliculus (birds and mammals) is a paradigm model system for studying mechanisms of neural wiring development. It has previously been proposed that retinal ganglion cell axons use distinct guidance strategies in fish vs. mammals, with direct guidance to the tectal target zone in the former and overshoot followed by biased branching toward the target zone in the latter. Here we visualized individual retinal ganglion cell axons as they grew over the tectum in zebrafish for periods of 10‐21 hours and analyzed these results using an array of quantitative measures. We found that, although axons were generally guided directly toward their targets, this occurred without growth cone turning. Instead, axons branched dynamically and profusely throughout pathfinding, and successive branches oriented growth cone extension toward a target zone in a stepwise manner. These data suggest that the guidance strategies used between fish and mammals may be less distinct than previously thought. J. Comp. Neurol., 521:1409–1429, 2013. © 2012 Wiley Periodicals, Inc.
Cortical projections to the superior colliculus in tree shrews (Tupaia belangeri)
Authors: Baldwin Mary K.L. , Wei Haiyang , Reed Jamie L. , Bickford Martha E. , Petry Heywood M. , Kaas Jon H. 
Published: November 2012

AbstractThe visuomotor functions of the superior colliculus depend not only on direct inputs from the retina, but also on inputs from neocortex. As mammals vary in the areal organization of neocortex, and in the organization of the number of visual and visuomotor areas, patterns of corticotectal projections vary. Primates in particular have a large number of visual areas projecting to the superior colliculus. As tree shrews are close relatives of primates, and they are also highly visual, we studied the distribution of cortical neurons projecting to the superior colliculus by injecting anatomical tracers into the colliculus. Since projections from visuotopically organized visual areas are expected to match the visuotopy of the superior colliculus, injections at different retinotopic locations in the superior colliculus provide information about the locations and organization of topographic areas in extrastriate cortex. Small injections in the superior colliculus labeled neurons in locations within areas 17 (V1) and 18 (V2) that are consistent with the known topography of these areas and the superior colliculus. In addition, the separate locations of clusters of labeled cells in temporal visual cortex provide evidence for five or more topographically organized areas. Injections that included deeper layers of the superior colliculus also labeled neurons in medial frontal cortex, likely in premotor cortex. Only occasional labeled neurons were observed in somatosensory or auditory cortex. Regardless of tracer injection location, we found that, unlike primates, a substantial projection to the superior colliculus from posterior parietal cortex is not a characteristic of tree shrews. J. Comp. Neurol. 521:1614–1632, 2013. © 2012 Wiley Periodicals, Inc.
Projections of the superior colliculus to the pulvinar in prosimian galagos (Otolemur garnettii) and VGLUT2 staining of the visual pulvinar
Authors: Baldwin Mary K.L. , Balaram Pooja , Kaas Jon H. 
Published: November 2012

AbstractAn understanding of the organization of the pulvinar complex in prosimian primates has been somewhat elusive due to the lack of clear architectonic divisions. In the current study we reveal features of the organization of the pulvinar complex in galagos by examining superior colliculus (SC) projections to this structure and comparing them with staining patterns of the vesicular glutamate transporter, VGLUT2. Cholera toxin subunit β (CTB), Fluoro‐ruby (FR), and wheat germ agglutinin conjugated with horseradish peroxidase (WGA‐HRP) were placed in topographically different locations within the SC. Our results showed multiple topographically organized patterns of projections from the SC to several divisions of the pulvinar complex. At least two topographically distributed projections were found within the lateral region of the pulvinar complex, and two less obvious topographical projection patterns were found within the caudomedial region, in zones that stain darkly for VGLUT2. The results, considered in relation to recent observations in tree shrews and squirrels, suggest that parts of the organizational scheme of the pulvinar complex in primates are present in rodents and other mammals. J. Comp. Neurol. 521:1664–1682, 2013. © 2012 Wiley Periodicals, Inc.
Laminar segregation of GABAergic neurons in the avian nucleus isthmi pars magnocellularis: A retrograde tracer and comparative study
Authors: Faunes Macarena , Fernández Sara , Gutiérrez‐Ibáñez Cristián , Iwaniuk Andrew N. , Wylie Douglas R. , Mpodozis Jorge , Karten Harvey J. , Marín Gonzalo 
Published: November 2012

AbstractThe isthmic complex is part of a visual midbrain circuit thought to be involved in stimulus selection and spatial attention. In birds, this circuit is composed of the nuclei isthmi pars magnocellularis (Imc), pars parvocellularis (Ipc), and pars semilunaris (SLu), all of them reciprocally connected to the ipsilateral optic tectum (TeO). The Imc conveys heterotopic inhibition to the TeO, Ipc, and SLu via widespread γ‐aminobutyric acid (GABA)ergic axons that allow global competitive interactions among simultaneous sensory inputs. Anatomical studies in the chick have described a cytoarchitectonically uniform Imc nucleus containing two intermingled cell types: one projecting to the Ipc and SLu and the other to the TeO. Here we report that in passerine species, the Imc is segregated into an internal division displaying larger, sparsely distributed cells, and an external division displaying smaller, more densely packed cells. In vivo and in vitro injections of neural tracers in the TeO and the Ipc of the zebra finch demonstrated that neurons from the external and internal subdivisions project to the Ipc and the TeO, respectively, indicating that each Imc subdivision contains one of the two cell types hodologically defined in the chick. In an extensive survey across avian orders, we found that, in addition to passerines, only species of Piciformes and Rallidae exhibited a segregated Imc, whereas all other groups exhibited a uniform Imc. These results offer a comparative basis to investigate the functional role played by each Imc neural type in the competitive interactions mediated by this nucleus. J. Comp. Neurol. 521:1727–1742, 2013. © 2012 Wiley Periodicals, Inc.
Commissural axons of the mouse cochlear nucleus
Authors: Brown M. Christian , Drottar Marie , Benson Thane E. , Darrow Keith 
Published: November 2012

AbstractThe axons of commissural neurons that project from one cochlear nucleus to the other were studied after labeling with anterograde tracer. Injections were made into the dorsal subdivision of the cochlear nucleus in order to restrict labeling only to the group of commissural neurons that gave off collaterals to, or were located in, this subdivision. The number of labeled commissural axons in each injection was correlated with the number of labeled radiate multipolar neurons, suggesting radiate neurons as the predominant origin of the axons. The radiate commissural axons are thick and myelinated, and they exit the dorsal acoustic stria of the injected cochlear nucleus to cross the brainstem in the dorsal half, near the crossing position of the olivocochlear bundle. They enter the opposite cochlear nucleus via the dorsal and ventral acoustic stria and at its medial border. Reconstructions of single axons demonstrate that terminations are mostly in the core and typically within a single subdivision of the cochlear nucleus. Extents of termination range from narrow to broad along both the dorsoventral (i.e., tonotopic) and the rostrocaudal dimensions. In the electron microscope, labeled swellings form synapses that are symmetric (in that there is little postsynaptic density), a characteristic of inhibitory synapses. Our labeled axons do not appear to include excitatory commissural axons that end in edge regions of the nucleus. Radiate commissural axons could mediate the broadband inhibition observed in responses to contralateral sound, and they may balance input from the two ears with a quick time course. J. Comp. Neurol. 521:1683–1696, 2013. © 2012 Wiley Periodicals, Inc.
Lipid oxidation products of heated soybeans as a possible cause of protection from ruminal biohydrogenation
Authors: Kaleem Muhammad , Farizon Yves , Enjalbert Francis , Troegeler‐Meynadier Annabelle 
Published: November 2012

AbstractHeating oilseeds has been shown to improve the milk fatty acid profile when given to dairy cows, compared to raw oilseeds. However, results from published studies are conflicting. The conditions of heating and storage of the oilseeds could be responsible for these differences, probably partly through their effects on lipid oxidation, the products of which could act on ruminal biohydrogenation (BH). Thus, 15 different treatments were applied to ground soybeans: three levels of heating (no heating, 30 min at 110 or 150°C) × 5 ambient storage durations (0, 1, 2, 4, or 6 months). Soybeans were incubated in vitro with ruminal fluid for 6 h. Triacylglycerol (TAG) polymers, hydroperoxides and hydroxyacids (HOA), aldehydes, and fatty acids were assayed in soybeans and ruminal culture. No TAG polymer was detected in any treatment. Soybeans stored for a long time had a high content of HOA, whereas those heated at 150°C, whatever the storage duration, had high aldehyde contents. The percentage disappearance of cis‐9,cis‐12 18:2 and cis‐9,cis‐12,cis‐15 18:3 in incubates decreased significantly in cultures with heated soybeans, especially at 150°C, suggesting that this partial protection of polyunsaturated fatty acids (PUFA) from BH was at least in part linked to the aldehyde content of the heated soybeans.Practical applications: Oilseeds given to ruminants are often heated, and heat treatment is known to generate oxidation products. Knowing what oxidation products influence ruminal biohydrogenation of unsaturated fatty acids could result in technological processes allowing a better transfer of unsaturated fatty acids from oilseeds to ruminant products.
Bedforms: views and new perspectives from the third international workshop on Marine and River Dune Dynamics (MARID3)
Authors: Parsons Daniel R. , Best Jim 
Published: November 2012

ABSTRACTThis Commentary introduces a Special Issue of Earth Surface Processes and Landforms dedicated to the memory of Stephen Coleman (1966–2012) who sadly passed away on July 23, 2012. Stephen was an incredible enthusiast for the study of bedforms and made seminal contributions to our knowledge and understanding of flow, sediment transport and bedform dynamics. Stephen presented a keynote address at MARID 3, which has led to this Special Issue (see Coleman SE, Nikora VI. 2011. Fluvial dunes: initiation, characterization, flow structure. Earth Surface Processes and Landforms 36: 39–57. DOI. 10.1002/esp.2096) and was always keen to discuss research, from theory to techniques to experiments. He was always generous with his time and touched many with the influence of his thoughts and intellect. Our community has lost an outstanding scientist and Stephen will be greatly missed by us all. Copyright © 2012 John Wiley & Sons, Ltd.
PPARα activation in portal hypertension
Authors: Liu Hongqun , Lee Samuel S. , Groszmann Roberto J. , Iwakiri Yasuko , Taddei Tamar H. 
Published: November 2012

Abstract

Peroxisome proliferator-activated receptor α (PPARα) is a transcription factor activated by ligands that regulates genes related to vascular tone, oxidative stress, and fibrogenesis, pathways implicated in the development of cirrhosis and portal hypertension. This study aims at evaluating the effects of PPARα activation with fenofibrate on hepatic and systemic hemodynamics, hepatic endothelial dysfunction, and hepatic fibrosis in CCl(4)-cirrhotic rats. Mean arterial pressure (MAP), portal pressure (PP), and portal blood flow (PBF) were measured in cirrhotic rats treated with oral fenofibrate (25mg/kg/day, n=10) or its vehicle (n=12) for 7 days. The liver was then perfused and dose-relaxation curves to acetylcholine (Ach) were performed. We also evaluated Sirius Red staining of liver sections, collagen-I mRNA expression, and smooth muscle actin (α-SMA) protein expression, cyclo-oxygenase-1 (COX-1) protein expression, and cGMP levels in liver homogenates, and TXB(2) production in perfusates. Nitric oxide (NO) bioavailability and eNOS activation were measured in hepatic endothelial cells (HEC) isolated from cirrhotic rat livers. CCl(4) cirrhotic rats treated with fenofibrate had a significantly lower PP (-29%) and higher MAP than those treated with vehicle. These effects were associated with a significant reduction in hepatic fibrosis and improved vasodilatory response to acetylcholine. Moreover, a reduction in COX-1 expression and TXB(2) production in rats receiving fenofibrate and a significant increase in NO bioavailability in HEC with fenofibrate were observed. PPARα activation markedly reduced PP and liver fibrosis and improved hepatic endothelial dysfunction in cirrhotic rats, suggesting it may represent a new therapeutic strategy for portal hypertension in cirrhosis.
Will catchment characteristics moderate the projected effects of climate change on flow regimes in the Scottish Highlands?
Authors: Capell R. , Tetzlaff D. , Soulsby C. 
Published: November 2012

AbstractRegional climate models were used with the UKCP09 weather generator to downscale outputs from the HadCM3 General Circulation Model, to project climate change by 2050 in the Scottish Highlands. The resulting hydroclimatic data were used to drive a tracer‐aided hydrological model to assess likely changes in flow regimes in three experimental catchments. These are located along a hydroclimatic transect from the wet, mild western Highlands (Strontian), through the colder, more continental central Highlands (Allt a' Mharcaidh), to the drier eastern Highlands (Girnock). At all sites, temperatures are projected to increase by around 2 °C, with associated increases in potential evapotranspiration. Precipitation is expected to increase by around 10–15% at Strontian but remains slightly changed at the Allt a' Mharcaidh and Girnock. However, the seasonal distribution of precipitation is projected to change, increasing in winter and decreasing in summer. Cautious interpretation of model outputs indicates that flows are likely to change accordingly at all sites, though the characteristics of each catchment result in some subtle differences. At Strontian, marked increases in winter high flows are expected, at the Allt a' Mharcaidh, reduction in winter snowfall and reduced snowpack will increase winter high flows and moderate the influence of spring melts. In the Girnock, decreasing summer low flows are the most notable element of change. These subtle differences in response to climatic drivers are consistent with the distinct storage characteristics of the catchments which in turn reflect their landscape evolution histories. Copyright © 2012 John Wiley & Sons, Ltd.
On the testing of fully integrated surface–subsurface hydrological models
Authors: Sebben Megan L. , Werner Adrian D. , Liggett Jessica E. , Partington Daniel , Simmons Craig T. 
Published: November 2012

AbstractStudies employing integrated surface–subsurface hydrological models (ISSHMs) have utilized a variety of test cases to demonstrate model accuracy and consistency between codes. Here, we review the current state of ISSHM testing and evaluate the most popular ISSHM test cases by comparing the hydrodynamic processes simulated in each case to the processes found in well‐characterized, real‐world catchments and by comparing their general attributes to those of successful benchmark problems from other fields of hydrogeology. The review reveals that (1) ISSHM testing and intercode comparison have not adopted specific test cases consistently; (2) despite the wide range of ISSHM metrics available for model testing, only two model performance diagnostics are typically adopted: the catchment outflow hydrograph and the catchment water balance; (3) in intercode comparisons, model performance is usually judged by evaluating only one performance diagnostic: the catchment outflow hydrograph; and (4) ISSHM test cases evaluate a small number of hydrodynamic processes that are largely uniform across the model domain, representing a limited selection of the processes of interest in well‐characterized, real‐world catchments. ISSHM testing would benefit from more intercode comparisons using a consistent set of test cases, aimed at evaluating more catchment processes (e.g. flooding) and using a wider range of simulation diagnostics (e.g. pressure head distributions). To achieve this, a suite of test case variations is required to capture the relevant catchment processes. Finally, there is a need for additional ISSHM test problems that compare model predictions with hydrological observations from intensively monitored field sites and controlled laboratory experiments. Copyright © 2012 John Wiley & Sons, Ltd.
Recombinant anti‐podoplanin (NZ‐1) immunotoxin for the treatment of malignant brain tumors
Authors: Chandramohan Vidyalakshmi , Bao Xuhui , Kato Kaneko Mika , Kato Yukinari , Keir Stephen T. , Szafranski Scott E. , Kuan Chien‐Tsun , Pastan Ira H. , Bigner Darell D. 
Published: November 2012

AbstractOur study demonstrates the glioma tumor antigen podoplanin to be present at very high levels (>90%) in both glioblastoma (D2159MG, D08‐0308MG and D08‐0493MG) and medulloblastoma (D283MED, D425MED and DAOY) xenografts and cell line. We constructed a novel recombinant single‐chain antibody variable region fragment (scFv), NZ‐1, specific for podoplanin from the NZ‐1 hybridoma. NZ‐1‐scFv was then fused to Pseudomonas exotoxin A, carrying a C‐terminal KDEL peptide (NZ‐1‐PE38KDEL). The immunotoxin (IT) was further stabilized by a disulfide (ds) bond between the heavy‐chain and light‐chain variable regions as the construct NZ‐1‐(scdsFv)‐PE38KDEL. NZ‐1‐(scdsFv)‐PE38KDEL exhibited significant reactivity to glioblastoma and medulloblastoma cells. The affinity of NZ‐1‐(scdsFv), NZ‐1‐(scdsFv)‐PE38KDEL and NZ‐1 antibody for podoplanin peptide was 2.1 × 10−8 M, 8.0 × 10−8 M and 3.9 × 10−10 M, respectively. In a protein stability assay, NZ‐1‐(scdsFv)‐PE38KDEL retained 33–98% of its activity, whereas that of NZ‐1‐PE38KDEL declined to 13% of its initial levels after incubation at 37°C for 3 days. In vitro cytotoxicity of the NZ‐1‐(scdsFv)‐PE38KDEL was measured in cells isolated from glioblastoma xenografts, D2159MG, D08‐0308MG and D08‐0493MG, and in the medulloblastoma D283MED, D425MED and DOAY xenografts and cell line. The NZ‐1‐(scdsFv)‐PE38KDEL IT was highly cytotoxic, with an 50% inhibitory concentration in the range of 1.6–29 ng/ml. Significantly, NZ‐1‐(scdsFv)‐PE38KDEL demonstrated tumor growth delay, averaging 24 days (p < 0.001) and 21 days (p < 0.001) in D2159MG and D283MED in vivo tumor models, respectively. Crucially, in the D425MED intracranial tumor model, NZ‐1‐(scdsFv)‐PE38KDEL caused a 41% increase in survival (p ≤ 0.001). In preclinical studies, NZ‐1‐(scdsFv)‐PE38KDEL exhibited significant potential as a targeting agent for malignant brain tumors.
Known glioma risk loci are associated with glioma with a family history of brain tumours—A case–control gene association study
Authors: Melin Beatrice , Dahlin Anna M. , Andersson Ulrika , Wang Zhaoming , Henriksson Roger , Hallmans Göran , Bondy Melissa L. , Johansen Christoffer , Feychting Maria , Ahlbom Anders , Kitahara Cari M. , Wang Sophia S. , Ruder Avima M. , Carreón Tania , Butler Mary Ann , Inskip Peter D. , Purdue Mark , Hsing Ann W. , Mechanic Leah , Gillanders Elizabeth , Yeager Meredith , Linet Martha , Chanock Stephen J. , Hartge Patricia , Rajaraman Preetha 
Published: November 2012

AbstractFamilial cancer can be used to leverage genetic association studies. Recent genome‐wide association studies have reported independent associations between seven single nucleotide polymorphisms (SNPs) and risk of glioma. The aim of this study was to investigate whether glioma cases with a positive family history of brain tumours, defined as having at least one first‐ or second‐degree relative with a history of brain tumour, are associated with known glioma risk loci. One thousand four hundred and thirty‐one glioma cases and 2,868 cancer‐free controls were identified from four case–control studies and two prospective cohorts from USA, Sweden and Denmark and genotyped for seven SNPs previously reported to be associated with glioma risk in case–control designed studies. Odds ratios were calculated by unconditional logistic regression. In analyses including glioma cases with a family history of brain tumours (n = 104) and control subjects free of glioma at baseline, three of seven SNPs were associated with glioma risk: rs2736100 (5p15.33, TERT), rs4977756 (9p21.3, CDKN2A‐CDKN2B) and rs6010620 (20q13.33, RTEL1). After Bonferroni correction for multiple comparisons, only one marker was statistically significantly associated with glioma risk, rs6010620 (ORtrend for the minor (A) allele, 0.39; 95% CI: 0.25–0.61; Bonferroni adjusted ptrend, 1.7 × 10−4). In conclusion, as previously shown for glioma regardless of family history of brain tumours, rs6010620 (RTEL1) was associated with an increased risk of glioma when restricting to cases with family history of brain tumours. These findings require confirmation in further studies with a larger number of glioma cases with a family history of brain tumours.
A Novel Noniterative Metal Artifact Reduction Method Using Coherence Transport with Fast Marching in Computed Tomography
Authors: Zhang Yi , Pu Yi‐Fei , Zhang Wei‐Hua , Hu Jin‐Rong , Wang Han , Lei Yin‐Jie , Zhou Ji‐Liu 
Published: November 2012

ABSTRACTMetal artifact reduction (MAR) is still a challenging problem in current computed tomography reconstruction. Traditional methods usually use the unaffected projection data in the same degree to interpolate contaminated positions in the bins. The continuality and smoothness features become hard to fulfill. In this article, we propose a novel noniterative MAR method that uses coherence transport with fast marching. Two‐dimensional information, including the neighboring bins, is used to inpaint the uncorrected sinogram with a special form of weighted average according to a sequence calculated by the fast marching method. The results of the experiments and the quantitative analysis demonstrate that the proposed method can effectively suppress the artifacts caused by metal with a high‐attenuation coefficient. Compared with linear interpolation, the proposed method can introduce less streak artifacts and obtain more accurate structure information of organs.
Three‐Dimensional Shape Reconstruction System Based on Fiber‐Optic Interference Fringe Imaging
Authors: Duan Xiaojie , Duan Fajie , Lv Changrong 
Published: November 2012

ABSTRACTIn this article, we describe a three‐dimensional shape reconstruction system based on the Mach–Zehnder interferometer structure and Young's double pinhole interference principle, while utilizing Fresnel reflection on fiber end face and interference at the fourth port of 3‐dB coupler to achieve closed‐loop precise control of fringe phase. A root‐mean‐square phase stability of 4 mrad is measured with the system. The shape of the object is determined by analyzing the fringe pattern. A new algorithm called rotating rectangular window autoselection is used as the band‐pass filter. The measuring time of the whole system is less than 200 ms, and the error of system is 0.27 mm. Meanwhile, the overall complexity of the measuring algorithm is O(n log n).