bluuebunny/crossref_metadata_2025_split huggingface dataset:
Animal Cap Isolation from Xenopus laevis: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONThis protocol presents a method for isolating Xenopus laevis animal cap cells, which are cells situated around the animal (pigmented) pole of a blastula or very early gastrula-stage embryo. This tissue is fated to become cement gland/neurectoderm on the dorsal side of the embryo and epidermis on the ventral side. Animal caps are composed of pluripotent cells that can be induced to form endodermal, mesodermal, or ectodermal cell types, and can therefore serve as a useful substrate to assess the activity of various inducing factors. Caps from embryos that have been injected with expression constructs can also be removed and analyzed to assess the activity of various genes. In addition, caps can be used in conjugation (induction) assays.
Xenopus laevis Keller Explants: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONThe basic Keller explant is a rectangle of dorsal mesendoderm and ectoderm from an early-gastrula-stage Xenopus laevis embryo. It is ~60° to 90° wide, extending from the bottle cells to the animal pole. This protocol describes how to dissect, assemble, and cultivate Keller explants. The purpose of Keller explants was initially to allow observation of gastrulation movements, particularly convergent extension, in culture. This is difficult to do when explants curl up, but in Keller sandwiches, the explants are cultured flat, either as a single sheet (open-face explant) or more frequently as two sheets sandwiched together with their inner surfaces apposed (closed sandwich). Explants are cultured beneath a coverslip fragment or a glass bridge resting on silicone vacuum grease until the desired stage, usually during or after neurulation. Instead of involuting beneath the ectoderm, mesoderm elongates in a plane with adjacent ectoderm. Explants are made at the onset of gastrulation before significant vertical juxtaposition of ectoderm and mesoderm has occurred.
Dissection of Tightly Adhering Xenopus laevis Tissues by Trypsin Treatment
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M. 
Published: June 2007

INTRODUCTIONIn older Xenopus laevis embryos (late gastrula and beyond), tissues begin to stick to one another and cannot be peeled apart. For assays requiring isolated tissues, it is necessary to separate such tissues enzymatically, which can be readily accomplished by mild trypsin treatment. Embryos are treated singly, or in small numbers, to avoid possible toxic effects of excessive trypsin digestion. This protocol describes a method for the separation of neural tissue from a neural-plate-stage embryo, although the technique can be adapted to many different tissue types. Enzymatically dissected tissue can be used in quantitative gene expression assays or in specification or induction assays.
Chromatin Immunoprecipitation (ChIP) on Unfixed Chromatin from Cells and Tissues to Analyze Histone Modifications
Authors: Wagschal Alexandre , Delaval Katia , Pannetier Maëlle , Arnaud Philippe , Feil Robert 
Published: June 2007

INTRODUCTIONIn cells and tissues, the histone proteins that constitute the nucleosomes can present multiple post-translational modifications, such as lysine acetylation, lysine and arginine methylation, serine phosphorylation, and lysine ubiquitination. On their own, or in combination, these covalent modifications on the core histones are thought to play essential roles in chromatin organization and gene expression in eukaryotes. Importantly, patterns of histone modifications may be somatically conserved and can, thereby, maintain locus-specific repression/activity in defined lineages, or throughout development. Indirect immunofluorescence studies on cultured cells have been pivotal in unraveling the roles of histone modifications. However, to address in detail what happens at specific sites in vivo, chromatin immunoprecipitation (ChIP) is the method of choice. Here, we describe how ChIP can be performed on non-fixed chromatin from animal cells or tissues (fresh or frozen) to analyze histone modifications at specific chromosomal sites. These protocols are suitable only for analyzing histones and their modifications. For other applications, chromatin immunoprecipitation should be performed on cross-linked chromatin.
A Behavioral Stress Assay in Drosophila Larvae: Figure 1.
Authors: Daubert Elizabeth A. , Condron Barry G. 
Published: June 2007

INTRODUCTIONThis protocol describes a simple behavioral assay designed to test the response of Drosophila larvae to a homeostatic insult: bright light. Treating normally photophobic larvae with bright light before placing them near a target food source reveals a greater latency to reach the target when compared to controls not receiving light treatment. This effect is reversible given a recovery period after light treatment, and it may reveal a method by which to measure behavioral plasticity and stress responses in fruit fly larvae.
TheArabidopsisATNRT2.7 Nitrate Transporter Controls Nitrate Content in Seeds
Authors: Chopin Franck , Orsel Mathilde , Dorbe Marie-France , Chardon Fabien , Truong Hoai-Nam , Miller Anthony J. , Krapp Anne , Daniel-Vedele Françoise 
Published: June 2007

AbstractIn higher plants, nitrate is taken up by root cells where Arabidopsis thaliana NITRATE TRANSPORTER2.1 (ATNRT2.1) chiefly acts as the high-affinity nitrate uptake system. Nitrate taken up by the roots can then be translocated from the root to the leaves and the seeds. In this work, the function of the ATNRT2.7 gene, one of the seven members of the NRT2 family in Arabidopsis, was investigated. High expression of the gene was detected in reproductive organs and peaked in dry seeds. β-Glucuronidase or green fluorescent protein reporter gene expression driven by the ATNRT2.7 promoter confirmed this organ specificity. We assessed the capacity of ATNRT2.7 to transport nitrate in Xenopus laevis oocytes or when it is expressed ectopically in mutant plants deficient in nitrate transport. We measured the impact of an ATNRT2.7 mutation and found no difference from the wild type during vegetative development. By contrast, seed nitrate content was affected by overexpression of ATNRT2.7 or a mutation in the gene. Finally, we showed that this nitrate transporter protein was localized to the vacuolar membrane. Our results demonstrate that ATNRT2.7 plays a specific role in nitrate accumulation in the seed.
Glucocorticoid receptor gene polymorphisms and susceptibility to rheumatoid arthritis
Authors: Donn Rachelle , Payne Debbie , Ray David 
Published: May 2007

SummaryBackground  A defect in hypothalamic–pituitary–adrenal (HPA) axis function has been suggested to contribute to susceptibility to rheumatoid arthritis (RA).Objective  To investigate polymorphisms of the glucocorticoid receptor (GR) gene and determine any associations with RA.Methods  Three GR polymorphisms that tag 95% of all haplotypes across the GR gene were genotyped. These are an intron B Bcl1 polymorphism, a ttg insertion/deletion within intron F (rs2307674) and the single nucleotide polymorphism (SNP) lying in the 3′ untranslated region of exon 9b (rs6198). The dye terminator‐based SNaPshot method or size resolution by capillary electrophoresis was performed. The study population comprised 198 UK Caucasian RA cases and 393 ethnically matched controls.Results  No significant single point or haplotypic associations were found for GR polymorphisms with RA susceptibility. Furthermore, no evidence for GR polymorphisms with aspects of RA severity was seen.Conclusion  In this study of the most comprehensive coverage of GR polymorphisms with RA, no significant contributing role for GR polymorphisms with RA was found.
Congenital hypothyroidism with goitre caused by new mutations in the thyroglobulin gene
Authors: Caputo Mariela , Rivolta Carina M. , Esperante Sebastían A. , Gruñeiro‐Papendieck Laura , Chiesa Ana , Pellizas Claudia G. , González‐Sarmiento Rogelio , Targovnik Héctor M. 
Published: May 2007

SummaryContext  Thyroid dyshormonogenesis is associated with mutations in the thyroglobulin (TG) gene and characterized by normal organification of iodide and low serum TG. These mutations give rise to congenital goitrous hypothyroidism, transmitted in an autosomal recessive mode.Objectives  The aim of this study was to identify new mutations in the TG gene in an attempt to increase the understanding of the molecular basis of this disorder. Three unrelated patients with marked impairment of TG synthesis were studied.Methods  The promoter and the complete coding regions of the TG gene, along with the flanking intronic regions, were analysed by direct DNA sequencing.Results  Four different inactivating TG mutations, three novel mutations (c.548G>A, p.C164Y; c.759–760insA, p.L234fsX237; c.6701C>A, p.A2215D) and one previously identified mutation (c.886C>T, p.R277X) were identified. Multiple sequence alignment study revealed that the wild‐type cysteine residue at position 164 is strictly conserved in the TG of all the species analysed, whereas the wild‐type alanine residue at position 2215 is well conserved in the TG and acetylcholinesterase (AChE) of all the species analysed except in rabbit AChE, in which it is substituted by glutamic acid.Conclusions  We report three patients with congenital hypothyroidism with goitre caused by two compound heterozygous mutations, p.C164Y/p.L234fsX237 and p.R277X/p.A2215D, and one homozygous mutation, p.R277X, in the TG gene. To our knowledge this is the first report of the presence of a nucleotide insertion mutation in the TG gene.
Uterine leiomyosarcomas are characterized by high p16, p53 and MIB1 expression in comparison with usual leiomyomas, leiomyoma variants and smooth muscle tumours of uncertain malignant potential
Authors: O'Neill C J , McBride H A , Connolly L E , McCluggage W G 
Published: June 2007

Aims:  It has been suggested that p16 is overexpressed in uterine leiomyosarcomas in comparison with leiomyomas. In this study, p16 immunohistochemical expression was assessed in a variety of uterine smooth muscle tumours, including usual leiomyomas, leiomyoma variants, smooth muscle tumours of uncertain malignant potential (STUMPs) and leiomyosarcomas. The aim was to ascertain whether there are differences in p16 expression between these groups and whether p16 is of potential value in the assessment of problematic uterine smooth muscle neoplasms. p16 expression was also compared with that of p53 and MIB1.Methods and results:  Cases of usual leiomyoma (n = 10), leiomyoma variants (n = 27), STUMP (n = 4) and leiomyosarcoma (n = 22) were subject to p16, p53 and MIB1 immunohistochemistry. For p16, cases were evaluated with respect to both staining distribution and intensity. There was a statistically significant difference in p16 distribution (P < 0.001) and intensity (P = 0.001) between leiomyosarcomas and the other groups. There was no difference in p16 expression between usual leiomyomas, leiomyoma variants and STUMPs. There were also statistically significant differences in p53 (P = 0.014) and MIB1 (P < 0.001) immunoreactivity between leiomyosarcomas and the other groups.Conclusions:  p16 is overexpressed in uterine leiomyosarcomas compared with leiomyomas, benign leiomyoma variants and STUMPs, suggesting that p16 may be implicated in the pathogenesis of malignant uterine smooth muscle neoplasms. p16, in combination with p53 and MIB1, may be of value as an adjunct to morphological examination in the assessment of problematic uterine smooth muscle tumours, although further large‐scale studies with follow‐up are necessary to confirm this.
Reactive astrocytes and activated microglial cells express EAAT1, but not EAAT2, reflecting a neuroprotective potential following ischaemia
Authors: Beschorner R , Simon P , Schauer N , Mittelbronn M , Schluesener H J , Trautmann K , Dietz K , Meyermann R 
Published: June 2007

Aims: Glutamate receptor antagonists have failed clinical stroke trials and it has been proposed that the action of N‐methyld‐aspartate receptors is necessary for neuronal survival. Thus, excitatory amino acid transporters (EAATs) might be a promising therapeutic target. The aim of this study was to investigate glial expression of EAATs following ischaemia.Methods and results: Expression of EAAT1 (GLAST) and EAAT2 (Glt‐1) in 24 cases of ischaemia was examined by immunohistochemistry. Cortical expression of both EAATs in the lesion decreased within 24 h (P < 0.01, each). Whereas EAAT1+ white matter cells increased 18‐fold (P < 0.05) within 24 h in the lesion and remained elevated for months in adjacent (469‐fold,P < 0.01) and remote areas (20‐fold,P < 0.05), EAAT2+ white matter cells were equivalent in ischaemia and controls. In the first week after stroke mainly activated (ramified and amoeboid) microglia expressed EAAT1, whereas monocytic cells in perivascular spaces and foamy macrophages lacked EAAT1. After more than 1 week, predominantly reactive astrocytes expressed EAAT1.Conclusions: Microglial EAAT1 expression is restricted to the early/intermediate stage of activation and blood‐derived (perivascular) monocytes do not contribute to EAAT1+ cells following ischaemia. Whether a pharmacological increase in glial EAAT expression may compensate for loss of cortical EAAT expression and reduce neuronal damage following stroke requires investigation by further functional studies.
Sleep habits and circadian preference in Italian children and adolescents
Authors: RUSSO PAOLO M. , BRUNI OLIVIERO , LUCIDI FABIO , FERRI RAFFAELE , VIOLANI CRISTIANO 
Published: June 2007

SummarySleep habits and circadian preference (morningness/eveningness, M/E) have been extensively analyzed in adolescents and young adults, while few studies were conducted on children and early adolescents. Aim of the present study was to investigate the developmental changes of circadian preference and to analyze its relationship with sleep habits, sleep problems and circadian preference in a large sample by means of a school‐based survey. One thousand seventy‐three participants (50.8% boys and 49.2% girls; mean age = 10.6; range = 8–14 years), recruited from four schools randomly extracted within the district of Rome, completed a modified version of School Sleep Habits Survey developed by Carskadon et al. The questionnaire included items about sleep habits during schooldays and weekends; a Sleepiness Scale; a Sleep–Wake Problems Behaviour Scale; a Morningness/Eveningness scale. The results show a consistent age‐related change in sleep habits, particularly in the weekends. The difference in sleep duration between schooldays and weekends increases linearly with age. No gender difference was observed in morningness/eveningness, while a significant linear increase in evening preference was found with increasing ages. M/E total scores correlated significantly with both self‐reported sleep/wake problems and daytime sleepiness indicating a higher prevalence of sleep complaints in evening‐type subjects. Overall, the present results support the existence of consistent age‐related changes in sleep habits and M/E dimension in the 8‐ to 14‐year age range.
Alcohol‐induced sleepwalking or confusional arousal as a defense to criminal behavior: a review of scientific evidence, methods and forensic considerations
Authors: PRESSMAN MARK R. , MAHOWALD MARK W. , SCHENCK CARLOS H. , BORNEMANN MICHEL CRAMER 
Published: June 2007

SummaryAn increasing number of criminal cases have claimed the defendant to be in a state of sleepwalking or related disorders induced by high quantities of alcohol. Sleepwalkers who commit violent acts, sexual assaults and other criminal acts are thought to be in a state of automatism, lacking conscious awareness and criminal intent. They may be acquitted in criminal trials. On the other hand, criminal acts performed as the result of voluntary alcohol intoxication alone cannot be used as a complete defense. The alcohol‐induced sleepwalking criminal defense is most often based on past clinical or legal reports that ingestion of alcohol directly ‘triggers’ sleepwalking or increased the risk of sleepwalking by increasing the quantity of slow wave sleep (SWS). A review of the sleep medicine literature found no sleep laboratory studies of the effects of alcohol on the sleep of clinically diagnosed sleepwalkers. However, 19 sleep laboratory studies of the effects of alcohol on the sleep of healthy non‐drinkers or social drinkers were identified with none reporting a change in SWS as a percentage of total sleep time. However, in six of 19 studies, a modest but statistically significant increase in SWS was found in the first 2–4 h. Among studies of sleep in alcohol abusers and abstinent abusers, the quantity and percentage of SWS was most often reduced and sometimes absent. Claims that direct alcohol provocation tests can assist in the forensic assessment of these cases found no support of any kind in the medical literature with not a single report of testing in normative or patient groups and no reports of validation testing of any sort. There is no direct experimental evidence that alcohol predisposes or triggers sleepwalking or related disorders. A legal defense of sleepwalking resulting from voluntarily ingested alcohol should be consistent with the current state of art sleep science and meet generally accepted requirements for the diagnosis of sleepwalking and other parasomnias.
The association between children’s sleep disruption and salivary interleukin‐6
Authors: EL‐SHEIKH MONA , BUCKHALT JOSEPH A. , GRANGER DOUGLAS A. , ERATH STEPHEN A. , ACEBO CHRISTINE 
Published: June 2007

SummaryWe explored relations between children’s sleep and levels of salivary interleukin‐6 (IL‐6). Children were healthy boys (n = 28) and girls (n = 36) who ranged in age between 8 and 9 years. Through actigraphy, the amount and quality of children’s sleep was examined objectively in their homes for 1 week. Children also rated their Morningness/Eveningness predisposition and subjective sleepiness, and parents reported on their children’s Sleep Disordered Breathing and Sleepiness. Children provided saliva samples before and after a series of cognitive/social tasks (an intelligence test, listening to a marital argument, and performing a star‐tracing task), which were later assayed for IL‐6. Children with higher salivary IL‐6 levels reported increased Eveningness predispositions and their parents reported higher levels of Sleep Disordered Breathing. Furthermore, lower levels of sleepiness, longer sleep amount, and better quality sleep in children were each predictive of increased IL‐6 reactivity from pre‐ to post‐task conditions. The findings illustrate (for the first time to our knowledge) that sleep disruptions in otherwise healthy and normally developing children may be associated with individual differences in levels of IL‐6 in saliva.
Trait interindividual differences in the sleep physiology of healthy young adults
Authors: TUCKER ADRIENNE M. , DINGES DAVID F. , VAN DONGEN HANS P. A. 
Published: June 2007

SummaryDespite decades of sleep research by means of polysomnography (PSG), systematic interindividual differences in PSG‐assessed sleep parameters have been scarcely investigated. The present study is the first to quantify interindividual variability in standard PSG‐assessed variables of sleep structure in terms of stability and robustness as well as magnitude. Twenty‐one carefully screened healthy young adults were studied continuously in a strictly controlled laboratory environment, where their PSGs were recorded for eight nights interspersed with three separate 36 h sleep deprivation periods. All PSG records were scored blind to subject and condition, using conventional criteria, and delta power in the non‐REM sleep EEG was computed for four electrode derivations. Interindividual differences in sleep variables were examined for stability and robustness, respectively, by comparing results across equivalent nights (e.g. baseline nights) and across experimentally differentiated nights (baseline nights versus recovery nights following sleep deprivation). Among 18 sleep variables analyzed, all except slow‐wave sleep (SWS) latency were found to exhibit significantly stable and robust – i.e. trait‐like – interindividual differences. This was quantified by means of intraclass correlation coefficients (ICCs), which ranged from 36% to 89% across physiologic variables, and were highest for SWS (73%) and delta power in the non‐REM sleep EEG (78–89%). The magnitude of the trait interindividual differences was considerable, consistently exceeding the magnitude of the group‐average effect on sleep structure of 36 h total sleep deprivation. Notably, for non‐REM delta power – a putative marker of sleep homeostasis – the interindividual differences were from 9.9 to 12.8 times greater than the group‐average increase following sleep deprivation relative to baseline. Physiologic sleep variables did not vary among subjects in a completely independent manner – 61.1% of their combined variance clustered in three trait dimensions, which appeared to represent sleep duration, sleep intensity, and sleep discontinuity. Any independent functional significance of these sleep physiologic phenotypes remains to be determined.
Is the circumferential resection margin a predictor of local recurrence after preoperative radiotherapy and optimal surgery for rectal carcinoma?
Authors: Khani M. Hosseinali , Smedh K. , Kraaz W. 
Published: May 2007

AbstractObjective  Circumferential resection margin (CRM) involvement has been correlated with a high risk of developing local recurrence. The aim of this study was to examine the prognostic significance of the CRM involvement after curative resection of rectal cancer in patients treated with preoperative radiotherapy and postoperative chemotherapy where indicated.Method  All patients with rectal cancer treated in a regional central unit from 1996 to 2004 were identified. A surgical resection was performed on 257 patients, and in 229 of these this was assessed as potentially curative. The CRM was examined in all patients. A CRM of ≤1 mm was considered positive.Results  A positive margin was seen in 19 (8%) patients. At a median follow up of 40 months, only four (1.7%) patients had developed local recurrence, one of whom had a positive CRM. In the four patients the tumour was 5 cm or less from the anal verge. There were no significant differences regarding local recurrence and survival between CRM positive and negative tumours.Conclusion  Rectal cancer managed by combined radiochemotherapy and surgery resulted in a low positive CRM rate and a low local recurrence rate. An involved CRM was not a predictor of local recurrence.
On Elder‐Vass: Refining a Refinement
Authors: PORPORA DOUGLAS 
Published: June 2007

ABSTRACTThis paper responds to Dave Elder‐Vass's generally sympathetic critique of Margaret Archer's position on structure and emergence. Elder‐Vass does helpfully emphasize the synchronic effects of structure. Yet, it is argued here, in his treatment of structure, Elder‐Vass tends to concede too much to methodological individualism and to overemphasize social rules at the expense of social relations. Finally, a question is raised about how both Archer and Elder‐Vass and Critical Realism in general speak of emergence.
Why I am not an Individualist
Authors: KING ANTHONY 
Published: June 2007

ABSTRACTIn his defence of emergence, David Elder‐Vass assumes that my hermeneutic position represents a form of individualism. Although a common reading of my position, the claim that I am in individualist is incorrect; I, too, recognize the centrality of collective phenomena to social reality. In fact, there is a close convergence between emergence and the hermeneutic sociology I advocate. However, there also remains an important divide between us. Despite his care to avoid reification, Edler‐Vass descends into ontological dualism, conceptualizing society in terms of structure and agency.