bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunostaining of Whole-Mount and Sectioned Lamprey Embryos
Authors: Nikitina Natalya , Bronner-Fraser Marianne , Sauka-Spengler Tatjana 
Published: January 2009

INTRODUCTIONLampreys are one of the most basal animals in which many of the true vertebrate characteristics (e.g., neural crest, placodes, segmented brain, skull, paired sensory organs, pharyngeal skeleton) are present. Studying the molecular and developmental mechanisms responsible for the formation of these structures in lamprey and higher vertebrates can provide insight into how these vertebrate characteristics evolved. The relative ease of obtaining mature adults and embryos makes this animal an ideal model for investigations into early vertebrate evolution. In addition, studies of features that are unique to lampreys can provide insights into mechanisms of parallel evolution. This protocol describes how to immunostain whole-mount or sectioned lamprey embryos using an antibody raised against the protein of interest and detected with a horseradish peroxidase (HRP)-conjugated secondary antibody.
Fixation and Dissection of Parhyale hawaiensis Embryos
Authors: Rehm E. Jay , Hannibal Roberta L. , Chaw R. Crystal , Vargas-Vila Mario A. , Patel Nipam H. 
Published: January 2009

INTRODUCTIONThe great diversity of arthropod body plans, together with our detailed understanding of fruit fly development, makes arthropods a premier taxon for examining the evolutionary diversification of developmental patterns and hence the diversity of extant life. Crustaceans, in particular, show a remarkable range of morphologies and provide a useful outgroup to the insects. The amphipod crustacean Parhyale hawaiensis is becoming established as a model organism for developmental studies within the arthropods. This protocol describes the dissection and fixation of P. hawaiensis embryos. Embryonic tissue fixed in the following manner is suitable for in situ hybridization experiments to study mRNA expression or for immunocytochemistry to study protein localization.
Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene
Authors: Kelly Christopher M. R. , Barker Nigel P. , Villet Martin H. , Broadley Donald G. 
Published: January 2009

AbstractThe snake superfamily Elapoidea presents one of the most intransigent problems in systematics of the Caenophidia. Its monophyly is undisputed and several cohesive constituent lineages have been identified (including the diverse and clinically important family Elapidae), but its basal phylogenetic structure is obscure. We investigate phylogenetic relationships and spatial and temporal history of the Elapoidea using 94 caenophidian species and approximately 2300–4300 bases of DNA sequence from one nuclear and four mitochondrial genes. Phylogenetic reconstruction was conducted in a parametric framework using complex models of sequence evolution. We employed Bayesian relaxed clocks and Penalized Likelihood with rate smoothing to date the phylogeny, in conjunction with seven fossil calibration constraints. Elapoid biogeography was investigated using maximum likelihood and maximum parsimony methods. Resolution was poor for early relationships in the Elapoidea and in Elapidae and our results imply rapid basal diversification in both clades, in the late Eocene of Africa (Elapoidea) and the mid‐Oligocene of the Oriental region (Elapidae). We identify the major elapoid and elapid lineages, present a phylogenetic classification system for the superfamily (excluding Elapidae), and combine our phylogenetic, temporal and biogeographic results to provide an account of elapoid evolution in light of current palaeontological data and palaeogeographic models.© The Willi Hennig Society 2009.
Sulphur cycling in organic‐rich marine sediments from a Scottish fjord
Authors: BOTTRELL SIMON H. , MORTIMER ROBERT J.G. , DAVIES IAN M. , MARTYN HARVEY S. , KROM MICHAEL D. 
Published: January 2009

AbstractIn this study, the biogeochemical transformations of sulphur in organic‐rich marine sediments in a Scottish fjord are investigated by a combination of pore water and sediment geochemistry with sulphide diffusive gradient thin‐film probes and sulphate isotopic data (δ34S and δ18O). Particular attention is paid to sulphur cycling in the upper sediment profile where sulphate reduction occurs but free sulphide is below the detection limits of conventional pore water geochemical analysis but quantifiable by sulphide diffusive gradient thin film. In the uppermost part of the sediment core, δ18O sulphate decreased from near‐sea water values to +7‰, indicating that anoxic sulphide oxidation dominated during this interval. Sulphate δ34S remained unchanged as there was no net sulphate reduction (i.e. reduction was balanced by re‐oxidation). Below 4 cm depth, there was a slight increase in sulphate δ34S from 20‰ to 23‰ associated with minor accumulation of iron sulphide. The δ18O of the sulphate also increased, to around +10‰ at 10 cm depth, as a result of the isotopic exchange of sulphate–oxygen with pore water and/or sulphur disproportionation reactions mediated during sulphur cycling. These processes continued to increase the δ18O of the sulphate to 14‰ at 20 cm depth with no further change in the δ34S of the sulphate. Below 20 cm depth, free sulphide is detectable in pore waters and both the δ34S of the sulphate and sulphide increase with depth with an offset controlled by kinetic fractionation during bacterial sulphate reduction. The δ34S of the sedimentary organic fraction shifted towards lower, more bacteriogenic, values with depth in the profile, without any increase in the size of this sulphur pool. Thus, the organic sulphur fraction was open to interaction with bacteriogenic sulphide without the occurrence of net addition. Therefore, caution should be exercised when using sulphur isotopic compositions to infer simple net addition of bacteriogenic sulphide to the organic sulphur fraction.
Flow patterns, sedimentation and deposit architecture under a hydraulic jump on a non‐eroding bed: defining hydraulic‐jump unit bars
Authors: MACDONALD ROBERT G. , ALEXANDER JAN , BACON JOHN C. , COOKER MARK J. 
Published: January 2009

AbstractThis paper presents results from two flume runs of an ongoing series examining flow structure, sediment transport and deposition in hydraulic jumps. It concludes in the presentation of a model for the development of sedimentary architecture, considered characteristic of a hydraulic jump over a non‐eroding bed. In Run 1, a hydraulic jump was formed in sediment‐free water over the solid plane sloping flume floor. Ultrasonic Doppler velocity profilers recorded the flow structure within the hydraulic jump in fine detail. Run 2 had identical initial flow conditions and a near‐steady addition of sand, which formed beds with two distinct characteristics: a laterally extensive, basal, wedge‐shaped massive sand bed overlain by cross‐laminated sand beds. Each cross‐laminated bed recorded the initiation and growth of a single surface feature, here defined as a hydraulic‐jump unit bar. A small massive sand mound formed on the flume floor and grew upstream and downstream without migrating to form a unit bar. In the upstream portion of the unit bar, sand finer than the bulk load formed a set of laminae dipping upstream. This set passed downstream through the small volume of massive sand into a foreset, which was initially relatively coarse‐grained and became finer‐grained downstream. This downstream‐fining coincided with cessation of the growth of the upstream‐dipping cross‐set. At intervals, a new bed feature developed above and upstream of the preceding hydraulic‐jump unit bar and grew in the same way, with the foreset climbing the older unit bar. The composite architecture of the superimposed unit bars formed a fanning, climbing coset above the massive wedge, defined as one unit: a hydraulic‐jump bar complex.
Bromide distribution characteristics of different Zechstein 2 rock salt sequences of the Southern Permian Basin: a comparison between bedded and domal salts
Authors: KÜSTER YVONNE , SCHRAMM MICHAEL , BORNEMANN OTTO , LEISS BERND 
Published: January 2009

AbstractThe bromide profile of the bedded Zechstein 2 rock salts in the Southern Permian Basin is characterized by a continuous increase in the bromide contents from base to top, indicating progressive evaporation of sea water. Former studies have suggested that the bromide distribution in domal salts is more irregular, raising such questions as whether there is a causal relationship between bromide distribution and deformation‐related processes or whether various halite types with different primary bromide contents account for such irregularities. In this study, the bromide distribution of a defined stratigraphic section (Hauptsalz) of the Zechstein 2 was investigated in three salt deposits, with bedded salt (Teutschenthal) compared with domal salts (Morsleben and Gorleben). Furthermore, two different halite types (Kristallbrocken, matrix) were distinguished during sampling. Comparison between the locations reveals that: (i) the characteristic trend of the bromide profile was generally preserved in both the bedded and the more intensely deformed domal salts; (ii) the dispersion of bromide contents along the running average curve is lower in domal salt, especially in the lower half of the Hauptsalz; and (iii) the Kristallbrocken are absent in the lower half of the Hauptsalz of Morsleben and Gorleben. The absence of the Kristallbrocken and the lower dispersion of the bromide contents in the domal salts are clear indications for the influence of salt migration‐related processes on the bromide distribution characteristics. It shows that these processes are associated with a redistribution of bromide, which eventually results in a homogenization of the originally varying bromide contents. On the other hand, preservation of the characteristic trend in the bromide profiles indicates that large‐scale brecciation, folding processes or circulating bromide‐rich fluids played only a minor role during the formation of the salt domes. Selective sampling of the Kristallbrocken and matrix halite displays a disparity in bromide content that is not consistent between the studied locations. These specific phenomena might be related to different depositional locations in the Zechstein Basin or to post‐depositional processes.
Salt shield: intracellular salts provide cellular protection against ionizing radiation in the halophilic archaeon, Halobacterium salinarum NRC‐1
Authors: Kish A. , Kirkali G. , Robinson C. , Rosenblatt R. , Jaruga P. , Dizdaroglu M. , DiRuggiero J. 
Published: January 2009

SummaryThe halophilic archaeon Halobacterium salinarum NRC‐1 was used as a model system to investigate cellular damage induced by exposure to high doses of ionizing radiation (IR). Oxidative damages are the main lesions from IR and result from free radicals production via radiolysis of water. This is the first study to quantify DNA base modification in a prokaryote, revealing a direct relationship between yield of DNA lesions and IR dose. Most importantly, our data demonstrate the significance of DNA radiation damage other than strand breaks on cell survival. We also report the first in vivo evidence of reactive oxygen species scavenging by intracellular halides in H. salinarum NRC‐1, resulting in increased protection against nucleotide modification and carbonylation of protein residues. Bromide ions, which are highly reactive with hydroxyl radicals, provided the greatest protection to cellular macromolecules. Modified DNA bases were repaired in 2 h post irradiation, indicating effective DNA repair systems. In addition, measurements of H. salinarum NRC‐1 cell interior revealed a high Mn/Fe ratio similar to that of Deinococcus radiodurans and other radiation‐resistant microorganisms, which has been shown to provide a measure of protection for proteins against oxidative damage. The work presented here supports previous studies showing that radiation resistance is the product of mechanisms for cellular protection and detoxification, as well as for the repair of oxidative damage to cellular macromolecules. The finding that not only Mn/Fe but also the presence of halides can decrease the oxidative damage to DNA and proteins emphasizes the significance of the intracellular milieu in determining microbial radiation resistance.
Relationship between post‐occlusive forearm skin reactive hyperaemia and vascular disease in patients with Type 2 diabetes—a novel index for detecting micro‐ and macrovascular dysfunction using laser Doppler flowmetry
Authors: Yamamoto‐Suganuma R. , Aso Y. 
Published: January 2009

AbstractAims  To investigate the relationship between the novel post‐occlusive forearm skin reactive hyperaemia (PORH) index and macro‐ and microangiopathy by comparing it with traditional indices and a morphological analysis of skin blood flow after ischaemia.Methods  We studied 20 control subjects and 104 patients with Type 2 diabetes. Cutaneous blood flow (flux) in response to 5‐min arterial occlusion in the forearm was measured using laser Doppler flowmetry. We defined the PORH index as the ratio of the area under the curve (AUC) 1 min after the release of the cuff relative to the AUC of a 1‐min period before cuff inflation. The flux in response to arterial occlusion was divided morphologically into three patterns. Brachial‐ankle pulse wave velocity (baPWV) was measured.Results  The PORH index was markedly lower in patients with diabetes than in control subjects. The PORH index correlated negatively with urinary albumin, peroneal motor nerve conduction velocity, and baPWV in the patients with diabetes. The PORH index, but not the morphological analysis, was an independent determinant of cardiovascular disease in patients with diabetes.Conclusions  The PORH index may be the most sensitive indicator of micro‐ and macrovascular disease of the various measures of PORH in patients with Type 2 diabetes.
Haemodialysis is associated with changes in cutaneous microcirculation in diabetes mellitus
Authors: Beckert S. , Sundermann K. , Wolf S. , Königsrainer A. , Coerper S. 
Published: January 2009

AbstractAims  To examine the cutaneous microcirculation on the dorsum of the foot before, during and after haemodialysis in diabetic and non‐diabetic patients.Methods  Fourteen age‐matched patients (seven diabetic, seven non‐diabetic) without active foot ulceration were studied. Cutaneous microcirculation was assessed using a micro‐lightguide spectrophotometer to measure venous oxygen saturation and relative blood flow determined at two tissue depths: 2 and 6 mm. Cumulative relative changes of each parameter during haemodialysis were calculated as area under the curve. Differences between and within the groups were calculated by Mann–Whitney U‐test and anova following post hoc testing, respectively.Results  At baseline, relative blood flow at 6 mm tissue depth was significantly greater in diabetic patients (P = 0.048). Thirty minutes after the end of dialysis, relative blood flow at 2 and 6 mm tissue depth was significantly higher in non‐diabetic patients (P = 0.048 and P = 0.001). Mean cumulative relative changes in venous oxygen saturation and relative blood flow at 2 mm as well as 6 mm tissue depth were positive for non‐diabetic subjects and negative for diabetic patients.Conclusions  Haemodialysis is associated with changes in cutaneous microcirculation, which differ between people with and without diabetes. In those without diabetes, we found an increase in blood flow during haemodialysis, whereas blood flow was reduced in diabetic patients. This may be the result of abnormal vasomotor regulation due to distal neuropathy.
Shrinkage Inverse Regression Estimation for Model-Free Variable Selection
Authors: Bondell Howard D. , Li Lexin 
Published: January 2009

SummaryThe family of inverse regression estimators that was recently proposed by Cook and Ni has proven effective in dimension reduction by transforming the high dimensional predictor vector to its low dimensional projections. We propose a general shrinkage estimation strategy for the entire inverse regression estimation family that is capable of simultaneous dimension reduction and variable selection. We demonstrate that the new estimators achieve consistency in variable selection without requiring any traditional model, meanwhile retaining the root n estimation consistency of the dimension reduction basis. We also show the effectiveness of the new estimators through both simulation and real data analysis.
Impact of a modified directly administered antiretroviral treatment intervention on virological outcome in HIV‐infected patients treated in Burkina Faso and Mali
Authors: Pirkle CM , Boileau C , Nguyen V‐K , Machouf N , Ag‐Aboubacrine S , Niamba PA , Drabo J , Koala S , Tremblay C , Rashed S 
Published: January 2009

ObjectiveThis study explores whether viral load measurements can be used in resource‐limited settings to target those in need of adherence assistance. It was hypothesized that high plasma viral loads (pVLs) (≥500 HIV‐1 RNA copies/mL) were the result of poor antiretroviral therapy adherence and amenable to improvement with adherence assistance.DesignA single‐arm, multicentre pilot study was conducted from November 2003 to March 2004 on 606 treatment‐experienced patients who had initiated an antiretroviral regimen in Mali and Burkina Faso ≥6 months before study enrolment. In these patients, those whose pVL was ≥500 copies/mL were offered 1 month of modified directly administered antiretroviral treatment (mDAART) with weekly follow‐up visits from pharmacists or adherence counsellors.MethodsAn adherence questionnaire was given to all cohort patients and viral load was used to screen for patients with ≥500 copies/mL. mDAART participants included cohort patients with ≥500 copies/mL, who completed the adherence questionnaire. Genotypic analyses were conducted on samples taken prior to and after the intervention. The intervention was considered effective when there was a decrease of ≥1 log10 in pVL.ResultsmDAART was effective in over one‐third of the intervention participants, while in two‐thirds no decrease in pVL was observed. The majority of mDAART participants had major resistance mutations.ConclusionspVL measurement was useful to identify patients who needed adherence assistance. However, because it was performed ≥6 months after starting treatment, mDAART came too late for most participants, as they had already developed important resistance mutations that might have been avoided with better laboratory monitoring.
Superficial basal cell carcinoma treated with imiquimod 5% topical cream for a 4‐week period: a case series
Authors: Ruiz‐Villaverde R , Sánchez‐Cano D , Burkhardt‐Pérez P 
Published: January 2009

AbstractBasal cell carcinoma (BCC) is a malignant cutaneous neoplasm with a tendency to spread locally and with several clinical and histological subsets. We studied 82 patients with a clinical diagnosis of superficial BCC on different anatomical locations, to whom imiquimod 5% cream was administered on a low‐frequency regime (three times a week for 4 weeks), and who were followed up 2 years after completion of treatment. Clinical clearance rate at 1 and 2 years were 89% and 85%, respectively. We conclude that imiquimod seems to be an appropriate therapeutic alternative for the treatment of superficial BCC in patients with associated comorbidities.Conflicts of interestNone declared
Shared and disorder‐specific prefrontal abnormalities in boys with pure attention‐deficit/hyperactivity disorder compared to boys with pure CD during interference inhibition and attention allocation
Authors: Rubia Katya , Halari Rozmin , Smith Anna B. , Mohammad Majeed , Scott Stephen , Brammer Michael J. 
Published: January 2009

Background:  Inhibitory and attention deficits have been suggested to be shared problems of disruptive behaviour disorders. Patients with attention deficit hyperactivity disorder (ADHD) and patients with conduct disorder (CD) show deficits in tasks of attention allocation and interference inhibition. However, functional magnetic resonance imaging (fMRI) of inhibitory and attention control has only been investigated in patients with ADHD, including comorbidity with CD, finding fronto‐striatal and temporo‐parietal dysfunction. This study investigates differences and commonalities in functional neural networks mediating interference inhibition and attention allocation between medication‐naïve children and adolescents with pure CD and those with pure ADHD.Methods:  Event‐related fMRI was used to compare brain activation of 13 boys with non‐comorbid CD, 20 boys with non‐comorbid ADHD and 20 healthy comparison boys during a Simon task that measures interference inhibition and controls for attention allocation, thus tapping into interference inhibition and selective attention networks.Results:  During interference inhibition, both patient groups shared reduced activation compared to controls in right superior temporal lobe and in predominantly right precuneus. During the oddball condition, both patient groups showed reduced activation compared to healthy control children in right medial prefrontal lobe. However, only ADHD patients showed a disorder‐specific under‐activation compared to the other two groups in an extensive activation cluster in left inferior prefrontal cortex.Conclusions:  This study shows shared dysfunction in both patients groups in right hemispheric temporal and parietal brain regions during interference inhibition and in right dorsolateral prefrontal cortex during attention allocation. Ventrolateral prefrontal dysfunction, however, was specific to ADHD and not observed in patients with CD in the context of attention allocation. The findings suggest that the typically reduced functional activation in patients with ADHD in ventrolateral prefrontal cortex may be specific to the disorder, at least when compared to patients with CD.
The Inefficiencies of Regionalised Milk Quota Trade
Authors: Hennessy Thia , Shrestha Shailesh , Shalloo Laurence , Wallace Michael 
Published: January 2009

Abstract This paper estimates the inefficiencies associated with the regionalisation of the milk quota trade. An optimisation model is developed to estimate the economic value of quota. Quota values are aggregated to derive quota sale and purchase curves under two scenarios: first, where quotas can be traded nationally and second, where the trade of quota is regionally restricted. Quota trade is simulated and the consequent effects on supplier structure estimated. Through the derivation of sectoral cumulative cost curves it is possible to estimate the impact of regionalising quota trade on sector efficiency. The model is solved using National Farm Survey data from Ireland and the inefficiencies of regionalised quota trade in Ireland are estimated at €27 million. The paper concludes by discussing the implications of restricted quota trade, especially in the context of eventual quota removal.