bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroglobin is up‐regulated in the cerebellum of pups exposed to maternal epileptic seizures
Authors: Lima Daiana Correia , Cossa Ana Carolina , Perosa Sandra Regina , de Oliveira Elaine Menezes , da Silva José Antonio , da Silva Fernandes Maria José , da Silva Iara Ribeiro , Higa Elisa Mieko Suemitsu , da Graça Naffah‐Mazzacoratti Maria , Cavalheiro Esper Abrão , Amado Débora 
Published: July 2011

AbstractTo evaluate a potential insult in the cerebellum of pups exposed to maternal epileptic seizures during intrauterine life, female rats were subjected to pilocarpine‐induced epilepsy. Pups from different litters were sacrificed at 1, 3, 7 and 14 post‐natal days (PN) and neuroglobin (Ngb) and gliosis were analyzed in the cerebellum by Western blotting (WB) and RT‐PCR. 14C‐l‐leucine‐[14C‐Leu] incorporation was used to analyze protein synthesis at PN1. Nitric Oxide (NO) and thiobarbituric acid‐reactive substances (TBARS) levels were also measured. Pups from naive mothers were used as controls. The mRNA level of Ngb was increased in experimental animals at PN1 (**p ≤ 0.001) and PN3 (**p ≤ 0.001), at PN7 (***p ≤ 0.0001) and at PN14 (**p ≤ 0.001) compared to the respective controls. The protein level of Ngb increased significantly in the experimental pups at PN1 (*p ≤ 0.05) and at PN3 (**p ≤ 0.001), when compared to the control pups at PN1 and PN3. At PN7 and PN14 no difference was found. The mRNA level of GFAP increased significantly about two times at PN3 (*p ≤ 0.05) and PN7 (*p ≤ 0.05) in the experimental pups when compared to the respective controls, but was unchanged in the other studied ages. Data showed that experimental pups at PN1 exhibited reduced (about 2 times, *p ≤ 0.05) total protein synthesis in the cerebellum when compared to control. No differences were found in the NO and TBARS levels. Our data support the hypothesis that an up‐regulation of Ngb could be a compensatory mechanism in response to the hypoxic–ischemic insults caused by seizures in pups during intrauterine life.
WEAKLY UNIFORM RANK TWO VECTOR BUNDLES ON MULTIPROJECTIVE SPACES
Authors: BALLICO EDOARDO , MALASPINA FRANCESCO 
Published: July 2011

AbstractHere we classify the weakly uniform rank two vector bundles on multiprojective spaces. Moreover, we show that every rank r>2 weakly uniform vector bundle with splitting type a1,1=⋯=ar,s=0 is trivial and every rank r>2 uniform vector bundle with splitting type a1>⋯>ar splits.
COHOMOLOGICAL CHARACTERIZATIONS OF CHARACTER PSEUDO-AMENABLE BANACH ALGEBRAS
Authors: NASR-ISFAHANI RASOUL , NEMATI MEHDI 
Published: July 2011

AbstractFor a Banach algebra 𝒜 and a character ϕ on 𝒜, we have recently introduced and studied the notion of ϕ-pseudo-amenability of 𝒜. Here, we give some characterizations of this notion in terms of derivations from 𝒜 into various Banach 𝒜-bimodules.
A PSEUDOCOMPACT TYCHONOFF SPACE THAT IS NOT STAR LINDELÖF
Authors: SONG YANKUI 
Published: July 2011

AbstractLet P be a topological property. A space X is said to be star P if whenever 𝒰 is an open cover of X, there exists a subspace A⊆X with property P such that X=St(A,𝒰), where St(A,𝒰)=⋃ {U∈𝒰:U∩A≠0̸}. In this paper we construct an example of a pseudocompact Tychonoff space that is not star Lindelöf, which gives a negative answer to Alas et al. [‘Countability and star covering properties’, Topology Appl.158 (2011), 620–626, Question 3].
CHARACTERIZATIONS OF JORDAN DERIVATIONS ON STRONGLY DOUBLE TRIANGLE SUBSPACE LATTICE ALGEBRAS
Authors: CHEN YUN-HE , LI JIAN-KUI 
Published: July 2011

AbstractLet 𝒟 be a strongly double triangle subspace lattice on a nonzero complex reflexive Banach space X and let δ:Alg 𝒟→Alg 𝒟 be a linear mapping. We show that δ is Jordan derivable at zero, that is, δ(AB+BA)=δ(A)B+Aδ(B)+δ(B)A+Bδ(A) whenever AB+BA=0 if and only if δ has the form δ(A)=τ(A)+λA for some derivation τ and some scalar λ. We also show that if the dimension of X is greater than 2, then δ satisfies δ(AB+BA)=δ(A)B+Aδ(B)+δ(B)A+Bδ(A) whenever AB=0 if and only if δ is a derivation.
A NOTE ON DERIVATIONS OF LIE ALGEBRAS
Authors: SHAHRYARI M. 
Published: July 2011

AbstractIn this note, we will prove that a finite-dimensional Lie algebra L over a field of characteristic zero, admitting an abelian algebra of derivations D≤Der(L), with the property for some n>1, is necessarily solvable. As a result, we show that if L has a derivation d:L→L such that Ln⊆d(L), for some n>1, then L is solvable.
The Road to Democracy: The Political Legacy of “1968”
Authors: Maeckelbergh Marianne 
Published: July 2011

SummaryOver the past forty years, the social struggles of the “long 1960s” have been continuously reinterpreted, each interpretation allocating a new mix of relevance and irrelevance to the brief global uprising. This article is a contribution to one such interpretation: the small but growing body of literature on the central importance of experiments with democracy within movements of the 1960s. Rather than examining the transformative effect of 1960s movements on institutional politics or popular culture, this article examines the lasting transformation 1960s movements had on social-movement praxis. Based on seven years of ethnography within contemporary global movement networks, I argue that when viewed from within social-movement networks, we see that thepoliticallegacy of the 1960s lies in the lasting significance of movement experiments with democracy as part of a prefigurative strategy for social change that is still relevant today because it is still in practice today.
Ectopic, submandibular thyroid causing hyperthyroidism
Authors: Eli S U , Marnane C , Peter R , Winter S 
Published: July 2011

AbstractBackground:Ectopic thyroid tissue in the submandibular region is exceptionally rare. Nevertheless, the treating physician should consider this condition within the differential diagnosis of a submandibular mass.Method:Case report of ectopic thyroid tissue presenting as a submandibular mass in a patient with hyperthyroidism, together with a review of the English-literature concerning ectopic thyroid tissue.Conclusion:To our knowledge, this is the first report of ectopic thyroid tissue presenting as a submandibular mass and causing hyperthyroidism. Removal of the submandibular mass resulted in normalisation of thyroid function, and subsequent reduction in the patient's antithyroid medication dosage. Ectopic thyroid tissue should be suspected in any patient with a submandibular mass. Prior to resection of such a lesion, it is essential to ensure that normal, functioning thyroid tissue is present elsewhere. Ectopic thyroid tissue can also present with pathology similar to that affecting the normal thyroid gland.
Is undergraduate medical education working for ENT surgery? A survey of UK medical school graduates
Authors: Powell J , Cooles F A H , Carrie S , Paleri V 
Published: July 2011

AbstractBackground:Despite the patient numbers and scope of ENT surgery, it is under-represented in most undergraduate medical curricula.Method:An online questionnaire was e-mailed, at National Health Service trust level, to 3544 newly qualified doctors from 30 UK medical schools. Undergraduate ENT exposure, confidence and educational value were measured on a Likert scale.Results:We received 444 eligible responses. The mean undergraduate ENT exposure was 3.4 days of pre-clinical teaching plus 5.0 days of ENT departmental experience. However, 15.8 per cent of respondents reported no formal departmental ENT experience, and 65.8 per cent would have liked further undergraduate experience. Teaching modalities with a lower perceived educational value were generally offered more frequently than those with a higher perceived educational value. Graduates felt significantly less confident with ENT history-taking, examination and management, compared with their cardiology clinical competencies (p < 0.001).Conclusion:These results highlight the lack of UK ENT undergraduate education, and the significant effect this has on junior doctors’ clinical confidence. In addition, commonly used teaching methods may not be optimally effective.
Selected plasma fatty acid levels in subsistence fed sled dogs along the Yukon River: a pilot study for biomonitoring
Authors: Dunlap Kriya L. , Reynolds Arleigh J. , Duffy Lawrence K. , Gerlach S. Craig , Loring Philip A. , Cleroux Marilyn , Godin Jean Philippe 
Published: July 2011

ABSTRACTThe introduction of the ‘western diet’ marked a decline in omega–3 fatty acids rich foods and a concurrent increase in saturated and omega–6 fatty acids that persists today. Historically, circumpolar people have had a low incidence of obesity, diabetes and cardiovascular disease and this has been largely attributed to polyphenolic compounds and omega–3 fatty acids offered from subsistence foods. In this report, we studied sled dogs as an Arctic sentinel species for monitoring the effect of a changing diet on lipid profiles along the Yukon River. Subsistence fed village sled dogs along the Yukon River, maintained largely on salmon were compared with a control kennel maintained on commercial food. Profiles showed higher levels for long chain omega–3 fatty acids in village subsistence fed dogs compared to control dogs and an opposite trend for omega–6 fatty acids, establishing baseline levels for follow up studies. A comparison with data for previously published mercury levels from the same cohort of dogs revealed a positive correlation with alpha–linolenic fatty acid and a negative correlation with linoleic fatty acid. Food and nutritional security is a concern in the Arctic as the impacts of climate change and transport of contaminants become obvious. This study supports not only the nutritional value of a subsistence diet but also the utility of sled dogs as a sentinel for human dietary change.
Gerard Manley Hopkins' sprung rhythm: corpus study and stochastic grammar
Authors: Hayes Bruce , Moore-Cantwell Claire 
Published: July 2011

AbstractSprung rhythm is a complex poetic metre invented and used by Gerard Manley Hopkins. We re-examine and amplify a seminal analysis of this metre by Kiparsky (1989). We coded the sprung rhythm corpus for stress, weight and phrasing, then used a computer program to locate every scansion compatible with Kiparsky's analysis. The analysis appears to be nearly exceptionless. However, it is incomplete in that it permits dozens or even hundreds of scansions for certain lines. We propose a Parsability Principle for metrics mandating that ambiguity of scansion be minimised, and suggest that under this proposal, the Kiparskyan system is not a possible metre. Our own revised analysis adds ten new constraints and is cast in the form of a stochastic maxent grammar. It produces an acceptably low level of ambiguity in metrical parsing, and is supported by a good match to the diacritics Hopkins employed to mark his intended scansion.
Chronic hypobaric hypoxia, patent arterial duct and a new interventional technique to close it
Authors: Freudenthal Franz P. , Heath Alexandra , Villanueva Jorge , Mendes Janne , Vicente Ximena , von Alvensleben Inge , Echazú Gabriel , Navarro Joaquin , Lang Nora , Kozlik-Feldmann Rainer 
Published: July 2011

AbstractBackgroundInterventional closure of patent arterial duct has become an accepted alternative to surgical closure. Clinical trial with “Nit-Occlud®PDA-R”.Methods and resultsTo assess the safety and efficacy of the device, we performed a prospective clinical study between June, 2009 and December, 2010 in La Paz, Bolivia. In all, 29 – 22 female patients and 7 male patients – out of 59 patients were selected on the basis of inclusion criteria. The procedures were performed under sedation at an age and weight of 5.7 years and 22.7 kilograms, respectively, with 4–6 French arterial sheaths and 5–7 French venous sheaths. The minimal diameter of the duct was 3.5 millimetres. The procedure, fluoroscopy, and hospitalisation times were 96.4 minutes (55 to 145), 13.1 minutes (3 to 25.2), and 24 hours, respectively. The “Nit-Occlud®PDA-R” was successfully deployed in all patients. Immediate, 24-hour, 1-, 3-, and 6-month closure rates were 65.5%, 79.3%, 96.5%, and 100%, respectively. The systolic pulmonary pressure diminished from 37 millimetres of mercury (21 to 57) before the intervention to 31 millimetres of mercury (21 to 45) after the intervention. No early or late embolisation, haemolysis, left pulmonary artery, or descending aorta obstruction occurred.ConclusionsWe conclude that the “Nit-Occlud®PDA-R” device is safe and effective in closing patent arterial duct up to a diameter of 8 millimetres.
Prenatal complex congenital heart disease with Loeys–Dietz syndrome
Authors: Kawazu Yukiko , Inamura Noboru , Kayatani Futoshi , Okamoto Nobuhiko , Morisaki Hiroko 
Published: July 2011

AbstractWe report an infantile case of Loeys–Dietz syndrome prenatally diagnosed with congenital complex heart disease – double outlet right ventricle and interruption of the aortic arch. The patient also showed prominent dilatation of the main pulmonary artery. Emergency bilateral pulmonary artery banding was performed on the 9th day. However, on the 21st day, the patient died of massive bleeding due to rupture of the right pulmonary artery. Subsequently, a mutation of the TGFBR1 gene was detected. As cardiovascular lesions of Loeys–Dietz syndrome appear early and progress rapidly, the prognosis is generally poor. Patients require periodic examination and early intervention with medical therapy such as Losartan administration and surgical therapy. Early genetic screening is thought to be useful for the prediction of complications as well as vascular disease.
Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus
Authors: Holmes Dawn E , Risso Carla , Smith Jessica A , Lovley Derek R 
Published: July 2011

Abstract
Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (&gt;80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.
Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system
Authors: Feike Janie , Jürgens Klaus , Hollibaugh James T , Krüger Siegfried , Jost Günter , Labrenz Matthias 
Published: July 2011

Abstract
An analysis of the microbial metabolism is fundamental to understanding globally important element transformations. One culture-independent approach to deduce those prokaryotic metabolic functions is to analyze metatranscriptomes. Unfortunately, since mRNA is extremely labile, it is unclear whether the abundance patterns detected in nature are vulnerable to considerable modification in situ simply due to sampling procedures. Exemplified on comparisons of metatranscriptomes retrieved from pelagic suboxic zones of the central Baltic Sea (70–120 m depth), earlier identified as areas of high aerobic ammonium oxidation activity, and quantification of specific transcripts in them, we show that different sampling techniques significantly influence the relative abundance of transcripts presumably diagnostic of the habitat. In situ fixation using our newly developed automatic flow injection sampler resulted in an abundance of thaumarchaeal ammonia monooxygenase transcripts that was up to 30-fold higher than that detected in samples obtained using standard oceanographic sampling systems. By contrast, the abundance of transcripts indicative of cellular stress was significantly greater in non-fixed samples. Thus, the importance of in situ fixation in the reliable evaluation of distinct microbial activities in the ecosystem based on metatranscriptomics is obvious. In consequence, our data indicate that the significance of thaumarchaeota to aerobic ammonium oxidation could yet have been considerably underestimated. Taken these results, this could in general also be the case in attempts aimed at an unbiased gene expression analysis of areas below the epipelagic zone, which cover 90% of the world's oceans.
A ‘universal’ type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities
Authors: Chaban Bonnie , Hill Janet E 
Published: July 2011

Abstract
Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust ‘universal’ PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, ‘universal’ PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or ‘cocktail’ of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. ‘Universal’ thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a ‘universal’ thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.
Novel magnetite-producing magnetotactic bacteria belonging to the Gammaproteobacteria
Authors: Lefèvre Christopher T , Viloria Nathan , Schmidt Marian L , Pósfai Mihály , Frankel Richard B , Bazylinski Dennis A 
Published: July 2011

Abstract
Two novel magnetotactic bacteria (MTB) were isolated from sediment and water collected from the Badwater Basin, Death Valley National Park and southeastern shore of the Salton Sea, respectively, and were designated as strains BW-2 and SS-5, respectively. Both organisms are rod-shaped, biomineralize magnetite, and are motile by means of flagella. The strains grow chemolithoautotrophically oxidizing thiosulfate and sulfide microaerobically as electron donors, with thiosulfate oxidized stoichiometrically to sulfate. They appear to utilize the Calvin–Benson–Bassham cycle for autotrophy based on ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity and the presence of partial sequences of RubisCO genes. Strains BW-2 and SS-5 biomineralize chains of octahedral magnetite crystals, although the crystals of SS-5 are elongated. Based on 16S rRNA gene sequences, both strains are phylogenetically affiliated with the Gammaproteobacteria class. Strain SS-5 belongs to the order Chromatiales; the cultured bacterium with the highest 16S rRNA gene sequence identity to SS-5 is Thiohalocapsa marina (93.0%). Strain BW-2 clearly belongs to the Thiotrichales; interestingly, the organism with the highest 16S rRNA gene sequence identity to this strain is Thiohalospira alkaliphila (90.2%), which belongs to the Chromatiales. Each strain represents a new genus. This is the first report of magnetite-producing MTB phylogenetically associated with the Gammaproteobacteria. This finding is important in that it significantly expands the phylogenetic diversity of the MTB. Physiology of these strains is similar to other MTB and continues to demonstrate their potential in nitrogen, iron, carbon and sulfur cycling in natural environments.
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
Authors: Xu Mengyuan , Weinberg Clarice R. , Umbach David M. , Li Leping 
Published: July 2011

Abstract
Motivation: ChIP-seq data are enriched in binding sites for the protein immunoprecipitated. Some sequences may also contain binding sites for a coregulator. Biologists are interested in knowing which coregulatory factor motifs may be present in the sequences bound by the protein ChIP'ed.
Results: We present a finite mixture framework with an expectation–maximization algorithm that considers two motifs jointly and simultaneously determines which sequences contain both motifs, either one or neither of them. Tested on 10 simulated ChIP-seq datasets, our method performed better than repeated application of MEME in predicting sequences containing both motifs. When applied to a mouse liver Foxa2 ChIP-seq dataset involving ~ 12 000 400-bp sequences, coMOTIF identified co-occurrence of Foxa2 with Hnf4a, Cebpa, E-box, Ap1/Maf or Sp1 motifs in ~6–33% of these sequences. These motifs are either known as liver-specific transcription factors or have an important role in liver function.
Availability: Freely available at http://www.niehs.nih.gov/research/resources/software/comotif/.
Contact: li3@niehs.nih.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.
Making whole genome multiple alignments usable for biologists
Authors: Blankenberg Daniel , Taylor James , Nekrutenko Anton ,   The Galaxy Team
Published: July 2011

Abstract
Summary: Here we describe a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface.
Availability and Implementation: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Additional help is available as a live supplement from http://usegalaxy.org/u/dan/p/maf.
Contact: james.taylor@emory.edu; anton@bx.psu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.