bluuebunny/crossref_metadata_2025 huggingface dataset:
GASSST: global alignment short sequence search tool
Authors: Rizk Guillaume , Lavenier Dominique
Published: August 2010

Motivation: The rapid development of next-generation sequencing technologies able to produce huge amounts of sequence data is leading to a wide range of new applications. This triggers the need for fast and accurate alignment software. Common techniques often restrict indels in the alignment to improve speed, whereas more flexible aligners are too slow for large-scale applications. Moreover, many current aligners are becoming inefficient as generated reads grow ever larger. Our goal with our new aligner GASSST (Global Alignment Short Sequence Search Tool) is thus 2-fold—achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads.

Results: We propose a new efficient filtering step that discards most alignments coming from the seed phase before they are checked by the costly dynamic programming algorithm. We use a carefully designed series of filters of increasing complexity and efficiency to quickly eliminate most candidate alignments in a wide range of configurations. The main filter uses a precomputed table containing the alignment score of short four base words aligned against each other. This table is reused several times by a new algorithm designed to approximate the score of the full dynamic programming algorithm. We compare the performance of GASSST against BWA, BFAST, SSAHA2 and PASS. We found that GASSST achieves high sensitivity in a wide range of configurations and faster overall execution time than other state-of-the-art aligners.

Availability: GASSST is distributed under the CeCILL software license at http://www.irisa.fr/symbiose/projects/gassst/

Contact:  guillaume.rizk@irisa.fr; dominique.lavenier@irisa.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Population Structure and Resistance to Mefenoxam of Phytophthora capsici in New York State
Authors: Dunn A. R. , Milgroom M. G. , Meitz J. C. , McLeod A. , Fry W. E. , McGrath M. T. , Dillard H. R. , Smart C. D.
Published: August 2010

In 2006, 2007, and 2008, we sampled 257 isolates of Phytophthora capsici from vegetables at 22 sites in four regions of New York, to determine variation in mefenoxam resistance and population genetic structure. Isolates were assayed for mefenoxam resistance and genotyped for mating type and five microsatellite loci. We found mefenoxam-resistant isolates at a high frequency in the Capital District and Long Island, but none were found in western New York or central New York. Both A1 and A2 mating types were found at 12 of the 22 sites, and we detected 126 distinct multilocus genotypes, only nine of which were found at more than one site. Significant differentiation (FST) was found in more than 98% of the pairwise comparisons between sites; approximately 24 and 16% of the variation in the population was attributed to differences among regions and sites, respectively. These results indicate that P. capsici in New York is highly diverse, but gene flow among regions and fields is restricted. Therefore, each field needs to be considered an independent population, and efforts to prevent movement of inoculum among fields need to be further emphasized to prevent the spread of this pathogen.
A Minimally Invasive Cox-Maze Procedure Operative Technique and Results
Authors: Lee Anson M. , Clark Kal , Bailey Marci S. , Aziz Abdulhameed , Schuessler Richard B. , Damiano Ralph J.
Published: August 2010

Objective

The Cox-Maze procedure (CMP) for the surgical treatment of atrial fibrillation (AF) traditionally has required a median sternotomy and cardiopulmonary bypass. This study describes a method using ablation technologies to create the full Cox-Maze lesion set through a 5- to 6-cm right minithoracotomy.

Methods

Twenty-two consecutive patients underwent a CMP through a right mini-thoracotomy and cardiopulmonary bypass. All patients were followed prospectively with electrocardiogram and 24-hour Holter monitoring at 3, 6, and 12 months. The CMP lesion set was created using bipolar radiofrequency energy and cryotherapy.

Results

There was no operative mortality or major complications. Two patients required a permanent pacemaker. Five patients (23%) had early atrial tachyarrhythmias. At last follow-up (mean, 18 ± 12 months), all the patients (n = 22) were free from atrial dysrhythmias. At 3 months (n = 19), 84% of patients were off antiarrhythmic drugs. At 6 months (n = 18), 94% of patients were free from AF and off antiarrhythmic medications. At 12 months (n = 16), 81% of patients were free from AF and off antiarrhythmic drugs and three patients remained on warfarin for a mechanical mitral valve.

Conclusions

A full CMP can be performed through a right mini-thoracotomy with outstanding short-term results. This less invasive procedure can be offered to patients without compromising efficacy.
Neochordae Implantation Made Easy with an Adjustable Device Early Report of Acute and Chronic Animal Experiments
Authors: Maisano Francesco , Denti Paolo , Vanermen Hugo K. , Seeburger Joerg , Falk Volkmar , Mohr Friedrich Wilhelm , Mack Michael J. , Alfieri Ottavio R.
Published: August 2010

Objective

Neochordae implantation is a well-established surgical solution for the treatment of mitral valve prolapse. The main limitation to wide usage of the technique has been the difficulty associated with accurate determination of neochordal length. We describe a system specifically designed to facilitate rapid, uncomplicated implantation and off-pump, beating heart adjustment of neochordae.

Methods

Five swine underwent implantation of the adjustable neochordal system (V-Chordal; Valtech Cardio LTD, Israel) while on cardiopulmonary bypass after cutting native chordae to create a significant lesion. Neochordae length was adjusted with millimeter-level resolution, off-pump after discontinuation from bypass.

Results

In all animals, the implant was successful. Under echocardiographic monitoring, flail lesions were corrected in all cases, using the anatomic landmarks or the degree of mitral regurgitation for real-time guidance. At postmortem gross examination, the implant and the neochordae were completely healed with evidence of tissue ingrowth.

Conclusions

Preliminary animal experience suggests that the V-Chordal-adjustable neochordae system can be safely and effectively implanted, with accurate and precise adjustment of chordal length. The design of the device is suitable for a minimally invasive environment because of the long, flexible shafted design of the delivery system.
Endoscopic Radial Artery Harvest Produces Equivalent and Excellent Midterm Patency Compared with Open Harvest
Authors: Dimitrova Kamellia R. , Hoffman Darryl M. , Geller Charles M. , DeCastro Helbert , Dienstag Bill , Tranbaugh Robert F.
Published: August 2010

Objective

A recent multicenter study reported reduced patency of aortocoronary bypass grafts when the saphenous vein was harvested by endoscopic technique compared with patency of vein grafted after harvest by the traditional “open” approach. Our aim was to compare the patency rates of radial artery graft (RAG) harvested endoscopically with those harvested using an open technique.

Methods

Two cohorts were identified: from January 1995 to January 2000, 724 consecutive patients had one or both radial arteries harvested through an open technique, and from February 2000 to January 2008, 727 consecutive patients had endoscopic radial artery (RA) harvest. All patients who underwent symptom-indicated angiography in our institution at any time after coronary artery bypass grafting (CABG) surgery were identified.

Results

Two hundred two patients had angiograms for symptoms: 90 of these patients (119 RAG) had open RA harvest and were studied 78.3 ± 40 months (range, 1–156 months) after CABG. The other 112 patients (148 RAG) had endoscopic RA harvest and underwent angiography 36 ± 24 months (range, 1–96 months) after CABG. The two groups had identical demographics and risk profiles. Overall patency of the “open” RAG was 78.9% versus 83.7% for the endoscopic group (P = 0.3). Patency increased to 90% in both groups when the RAG was anastomosed to a native coronary vessel with stenosis >80%.

Conclusions

Endoscopic and open RA harvesting techniques have equivalent and excellent midterm and long-term patency rates in CABG patients studied by angiography for recurrent symptoms of myocardial ischemia. The degree of stenosis of the target vessel strongly influences the patency rate independent of the harvesting technique.
Infant anticipatory stress
Authors: Haley David W. , Cordick Jennifer , Mackrell Sarah , Antony Immaculate , Ryan-Harrison Maireanne
Published: August 2010

In humans, anticipatory stress involves activation of the limbic–hypothalamic–pituitary–adrenal axis, which releases stress hormones such as cortisol in response to an impending stressor. Conditioning of the stress response to anticipate and prepare for future challenges is a hallmark of adaptation. It is unknown whether human infants in the first year of life have developed the neural circuitry to support the anticipation of stressful events in an attachment context. Here, we show that human infants at six months of age produce an anticipatory stress response, as indicated by the release of stress hormones, when re-exposed after 24 h to a context in which they demonstrated a stress response to a disruption in the parent–infant relationship. Although infant stress response (cortisol elevation) was greater to the stressful event (parent unresponsiveness) than to the second exposure to the stress context (room, chair, presence of parent and experimenter, etc.), it was greater in the stress group than in the control group on both days. Results suggest that human infants have the capacity to produce an anticipatory stress response that is based on expectations about how their parents will treat them in a specific context.
Macromolecular dynamics in red blood cells investigated using neutron spectroscopy
Authors: Stadler Andreas Maximilian , van Eijck Lambert , Demmel Franz , Artmann Gerhard
Published: August 2010

We present neutron scattering measurements on the dynamics of haemoglobin (Hb) in human red blood cells (RBCs)
in vivo
. Global and internal Hb dynamics were measured in the ps to ns time and Å length scales using quasi-elastic neutron backscattering spectroscopy. We observed the cross over from global Hb short-time to long-time self-diffusion. Both short- and long-time diffusion coefficients agree quantitatively with predicted values from the hydrodynamic theory of non-charged hard-sphere suspensions when a bound water fraction of around 0.23 gram H
2
O per gram Hb is taken into account. The higher amount of water in the cells facilitates internal protein fluctuations in the ps time scale when compared with fully hydrated Hb powder. Slower internal dynamics of Hb in RBCs in the ns time range were found to be rather similar to results obtained with fully hydrated protein powders, solutions and
Escherichia coli
cells.
On the coevolution of social responsiveness and behavioural consistency
Authors: Wolf Max , Van Doorn G. Sander , Weissing Franz J.
Published: August 2010

Recent research focuses on animal personalities, that is individual differences in behaviour that are consistent across contexts and over time. From an adaptive perspective, such limited behavioural plasticity is surprising, since a more flexible structure of behaviour should provide a selective advantage. Here, we argue that consistency can be advantageous because it makes individuals predictable. Predictability, however, can only be advantageous if at least some individuals in the population respond to individual differences. Consequently, the evolution of consistency and responsiveness are mutually dependent. We present a general analysis of this coevolutionary feedback for scenarios that can be represented as matrix games with two pure strategies (e.g. hawk-dove game, snowdrift game). We first show that responsive strategies are favoured whenever some individual differences are present in the population (e.g. due to mutation and drift). We then show that the presence of responsive individuals can trigger a coevolutionary process between responsiveness and consistency that gives rise to populations in which responsive individuals coexist with unresponsive individuals who show high levels of adaptive consistency in their behaviour. Next to providing an adaptive explanation for consistency, our results also link two key features associated with personalities, individual differences in responsiveness and behavioural consistency.
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake
Authors: Manichanh Chaysavanh , Reeder Jens , Gibert Prudence , Varela Encarna , Llopis Marta , Antolin Maria , Guigo Roderic , Knight Rob , Guarner Francisco
Published: August 2010

The intestinal microbiota consists of over 1000 species, which play key roles in gut physiology and homeostasis. Imbalances in the composition of this bacterial community can lead to transient intestinal dysfunctions and chronic disease states. Understanding how to manipulate this ecosystem is thus essential for treating many disorders. In this study, we took advantage of recently developed tools for deep sequencing and phylogenetic clustering to examine the long-term effects of exogenous microbiota transplantation combined with and without an antibiotic pretreatment. In our rat model, deep sequencing revealed an intestinal bacterial diversity exceeding that of the human gut by a factor of two to three. The transplantation produced a marked increase in the microbial diversity of the recipients, which stemmed from both capture of new phylotypes and increase in abundance of others. However, when transplantation was performed after antibiotic intake, the resulting state simply combined the reshaping effects of the individual treatments (including the reduced diversity from antibiotic treatment alone). Therefore, lowering the recipient bacterial load by antibiotic intake prior to transplantation did not increase establishment of the donor phylotypes, although some dominant lineages still transferred successfully. Remarkably, all of these effects were observed after 1 mo of treatment and persisted after 3 mo. Overall, our results indicate that the indigenous gut microbial composition is more plastic that previously anticipated. However, since antibiotic pretreatment counterintuitively interferes with the establishment of an exogenous community, such plasticity is likely conditioned more by the altered microbiome gut homeostasis caused by antibiotics than by the primary bacterial loss.
Canadian cities as regional engines of growth: agglomeration and amenities
Authors: Partridge Mark , Olfert M. Rose , Alasia Alessandro
Published: August 2010

Abstract.  Canadian regional population growth is less understood than that of the United States. In both countries, certain regions have persistent population growth. Yet, unlike U.S. trends of amenity‐driven migration away from historic urban centres, Canadian growth is more urban centric. This study assesses whether agglomeration economies in the few major Canadian metropolitan areas lead to population growth in or near these cities rather than the more‐dispersed U.S. patterns. The results suggest that disparities such as the concentration of Canadians along its southern border may explain migration patterns, indicating that key differences in initial conditions may produce different outcomes between the two countries.
Technical compatibility and the mode of foreign entry with network externalities
Authors: Klimenko Mikhail , Saggi Kamal
Published: August 2010

Abstract.  We examine the preferences of a foreign firm and a local government over two modes of foreign direct investment: de novo entry and acquisition of the domestic incumbent. Two crucial features of the model are network externalities and partial incompatibility between the domestic and the foreign technology. The relative welfare impact of the two entry modes depends on the degree of market competition and the strength of the network externality. The clash between the foreign firm's choice and the local government's ranking of the two entry modes can motivate limits on the degree of foreign ownership of the local firm.
Retailers and consumers in sequential auctions of collectibles
Authors: Vincent Lyk‐Jensen Stéphanie , Chanel Olivier
Published: August 2010

Abstract.  We analyse an independent private‐value model, where heterogeneous bidders compete for objects sold in sequential second‐price auctions. In this heterogeneous game, bidders may have differently distributed valuations, and some have multi‐unit demand with decreasing marginal values (retailers); others have a specific single‐unit demand (consumers). By examining equilibrium bidding strategies and price sequences, we show that the presence of consumers leads to more aggressive bidding from the retailers on average and heterogeneous bidders is a plausible explanation of the price decline effect. The study of the expected revenue of the seller confirms the interest of auctioneers in inviting different types of bidders.
Do border crossings contribute to underage motor‐vehicle fatalities? An analysis of Michigan border crossings
Authors: Kreft Steven F. , Epling Nancy M.
Published: August 2010

Abstract. Currently, Michigan residents can avoid the national drinking age of 21 by crossing into Ontario, where the drinking age is 19. This paper explores the impact that border crossings, connecting areas with different minimum legal drinking ages (MLDA), have on motor‐vehicle fatalities. We analyse border crossings connecting Michigan to Ontario as well as to its surrounding states in the period in which Michigan's MLDA was raised to 21. Using a ‘differences‐in‐differences‐in‐differences’ approach, we find that the MLDA change did not contribute to increased underage fatalities in border‐crossing counties.
Tariff reduction and employment in Canadian manufacturing
Authors: LaRochelle‐Côté Sébastien
Published: August 2010

Abstract.  This paper uses firm‐level tax data to investigate whether the link between tariff changes and manufacturing employment differed across firms with various productivity and leverage characteristics over the period 1988–94. The results suggest that the effect of domestic tariff reductions on employment was typically small, but that losses were significantly larger for less productive firms. For instance, firms with average productivity in 1988 responded to domestic tariff changes by cutting employment by 11.3% over the period 1988–94, while lower‐productivity firms typically shed 20.8% of their workforce over the same period. This paper also indicates that firms with unhealthy balance sheets – those with relatively too much equity or too much leverage – downsized more in the face of declining domestic tariffs, suggesting that financial constraints became more binding when tariff cuts were implemented. These results suggest that firms with high productivity and better financial health were better positioned to face the challenge of trade liberalization.
Innis Lecture: Hedonic equilibrium
Authors: Peters Michael
Published: August 2010

Abstract.  This paper describes hedonic equilibrium and shows how and why the concept has to be modified when characteristics of traders on both sides of the market are endogenous.
Technology, agglomeration, and regional competition for investment
Authors: Blonigen Bruce A. , Kolpin Van
Published: August 2010

Abstract.  Competition for firms by region has a long‐standing history, and the academic literature has debated whether such competition is efficient. We develop a model that explores technology development by firms facing regional competition for their investment and examine the endogenous determination of region policy, firm technology, and agglomeration externalities. We find a new source of inefficiency – regional competition leads firms to inefficiently distort their development and selection of production technology to improve their standing in the regional competition for their investment. We show that these inefficient firm decisions on technology and location can also weaken agglomeration externalities.
Bilateral war in a multilateral world: carrots and sticks for conflict resolution
Authors: Becsi and Sajal Lahiri Zsolt
Published: August 2010

Abstract.  This paper constructs a three‐country, specific‐factor, trade‐theoretic model in which two of the countries are in conflict and where war effort is determined endogenously in a Nash equilibrium. The third country does not take part in the war, but trades with the warring countries. In the framework, we examine, inter alia, how war and welfare are affected by globalization and by two instruments available to the third country – one carrot and one stick. Our overall conclusion is that the third parties do have the incentives for, and can play an effective role in, conflict resolution. JEL classification: F02, F11, H56, H77
Raising taxes through equalization
Authors: Smart Michael
Published: August 2010

Abstract. A simple theory suggests that a common form of federal horizontal equalization grants should cause subnational governments to levy higher tax rates, distorting local tax bases and so increasing federal transfers. To test this, I examine Canadian provincial tax policies in the 1972–2002 period. Consistent with the theory, provinces respond to expansions of equalization transfers by increasing their own tax rates. I estimate that on average tax rates in grant‐receiving provinces were substantially and significantly higher as a consequence of the transfer formula. JEL classification: H21
Crises and human capital accumulation
Authors: Heylen Freddy , Pozzi Lorenzo
Published: August 2010

Abstract.  This paper studies the effects of crises on human capital formation. Theoretically, a crisis undermines total factor productivity, which reduces the return to working and to accumulating physical capital. If the crisis is temporary, young agents will study now and work later. Human capital rises. To test our model we rely on inflation crises as our main empirical proxy. Using GMM panel procedures, our analysis for 86 countries in 1970–2000 confirms the positive effects of crises on human capital. Our main findings survive several robustness tests. JEL classification: E31, D90
Biochemical composition of ovine follicular fluid in relation to follicle size
Authors: Nandi S. , Kumar V. Girish , Manjunatha B. M. , Gupta P. S. P.
Published: August 2010

The aim of this study was to biochemically characterize ovine follicular fluid and to relate possible changes in composition to follicular size. Ovaries were collected from adult and cycling non‐pregnant slaughtered sheep (Ovis aries) during breeding season. A total of 104 pairs of ovaries were investigated and these data were then compared. Follicular fluid was aspirated from small (< 2 mm), medium (2–4 mm) and large (> 4 mm) nonatretic ovarian follicles. The follicular fluid was centrifuged at 4°C and 5000 g for 30 min to remove any cells and stored at −80°C prior to assay. Follicular fluid samples were analyzed for glucose, total protein, cholesterol, triglycerides, lactate, urea, creatinine, sodium, potassium, chloride, calcium, phosphorus, magnesium, acid phosphatase, alkaline phosphatase, and lactate dehydrogenase. Data were analyzed by the linear regression model. As follicles became larger, the concentrations of glucose and cholesterol significantly (P < 0.05) increased while those of triglycerides, lactate, alkaline phosphatase and lactate dehydrogenase significantly (P < 0.05) decreased.
Expression of matrix metalloproteinase genes in regressing or remodeling organs during amphibian metamorphosis
Authors: Fujimoto Kenta , Nakajima Keisuke , Yaoita Yoshio
Published: August 2010

Several matrix metalloproteinases (MMP) are induced by thyroid hormone (TH) during the climax of amphibian metamorphosis and play a pivotal role in the remodeling of the intestine and the regressing tail and gills by degrading the extracellular matrix (ECM). We compared MMP gene expression levels precisely by quantitative real‐time reverse transcription‐polymerase chain reaction. The expression of MMP genes increases prominently at Nieuwkoop and Faber (NF) stages 60, 60–61 and 62 in the intestine, gills and tail, respectively, when the drastic morphological changes start in each organ. Gene expression analysis in the TH‐treated tadpoles and cell line revealed that MMP mRNAs are upregulated in response to TH quickly within several hours to low levels and then increase in a day to high levels. All TH‐induced MMP genes have TH response elements (TREs). The presence of high affinity TREs in MMP genes correlates with early TH‐induction. Based on these results, we propose that TH stimulates the transcription of MMP genes through TREs within several hours to low levels and then brings about the main increase of mRNAs by TH‐induced transcriptional factors, including TH receptor β, in a cell type‐specific transcriptional environment.
Unifying principles of regeneration I: Epimorphosis versus morphallaxis
Authors: Agata Kiyokazu , Saito Yumi , Nakajima Elizabeth
Published: August 2010

Because research on regeneration has a long history, some classic definitions and concepts about regeneration which were established in earlier times have been retained without reconsideration for a long time, even though many relevant new findings have accumulated. To clarify the points on which research should be focused on for elucidating the mechanisms of regeneration, we should reconsider such classical definitions and principles of regeneration at the cellular and molecular level. Here, we consider two differing principles of regeneration which have been classically defined as ‘epimorphosis’ and ‘morphallaxis’, and propose the abandonment of these classical categories and their replacement by a new unifying principle in order to facilitate regeneration studies.
Inheritance of two M type mitochondrial DNA from sperm and unfertilized eggs to offspring in Mytilus galloprovincialis
Authors: Obata Mayu , Sano Natsumi , Kawamura Kouichi , Komaru Akira
Published: August 2010

In Mytilus mussels, paternal mitochondrial DNA (mtDNA) from sperm is known to be transmitted to offspring. This phenomenon is called doubly uniparental inheritance (DUI). Under DUI, sperm mtDNA (M type) is inherited only by males. Female mussels receive maternal mtDNA (F type). However, in our previous study, we showed female and unfertilized eggs have both F and M types. We hypothesized that the two M types both from sperm and unfertilized eggs were transmitted to offspring. To test the hypothesis, we examined the number of M type haplotypes in mature M. galloprovincialis. The M type in larvae was compared with those of the parents. Cross experiments were carried out to test the inheritance of M type. In six of 20 mature mussels, two M types were detected by sequence analysis and polymerase chain reaction‐restriction fragment length polymorphism. In cross experiments of larval samples from five of 12 crosses, double peak wave was observed by single nucleotide polymorphisms analysis. In these larval samples, the higher peak wave was identical to the parental M type. Larvae received much more paternal M type than the maternal ones. We demonstrated that two M types from sperm and unfertilized eggs were transmitted to offspring in M. galloprovincialis.
Bone morphogenetic protein is required for dorso‐ventral patterning in the planarian Dugesia japonica
Authors: Orii Hidefumi , Watanabe Kenji
Published: August 2010

In order to clarify the function of the Djbmp (Dugesia japonica bone morphogenetic protein) gene in planarian body patterning, we carried out knockdown of this gene by RNA interference. When the planarians were treated with double‐stranded RNA of Djbmp, a bulge formed on the dorsal side, with a dent in the middle of the bulge, and the body surface inside the dent was smoothened and less pigmented. In situ hybridization of the DjIFb gene, which is expressed in the body margin, revealed that the additional body margin was formed ectopically at the region surrounding the dent. The Djbmp‐knockdown planarians often had a pair of incomplete nerve cords in the dorsal side, in addition to the original pair of ventral nerve cords. Taken together, we concluded that the Djbmp‐knockdown induced formation of an ectopic ventral side, suggesting that Djbmp is required for the dorso‐ventral body patterning in the planarian.
Regional specification of the endoderm in the early chick embryo
Authors: Kimura Wataru , Yasugi Sadao , Fukuda Kimiko
Published: August 2010

In the avian embryo, the endoderm, which forms a simple flat‐sheet structure after gastrulation, is regionally specified in a gradual manner along the antero‐posterior and dorso‐ventral axes, and eventually differentiates into specific organs with defined morphologies and gene expression profiles. In our study, we carried out transplantation experiments using early chick embryos to elucidate the timing of fate establishment in the endoderm. We showed that at stage 5, posteriorly grafted presumptive foregut endoderm expressed CdxA, a posterior endoderm marker, but not cSox2, an anterior endoderm marker. Conversely, anteriorly grafted presumptive mid‐hindgut endoderm expressed cSox2 but not CdxA. At stage 8, posteriorly grafted presumptive foregut endoderm also expressed CdxA and not cSox2, but anteriorly grafted presumptive mid‐hindgut endoderm showed no changes in its posterior‐specific gene expression pattern. At stage 10, both posteriorly grafted foregut endoderm and anteriorly grafted mid‐hindgut endoderm maintain their original gene expression patterns. These results suggest that the regional specification of the endoderm occurs between stages 8 and 10 in the foregut, and between stages 5 and 8 in the mid‐hindgut.
Right‐elevated expression of charon is regulated by fluid flow in medaka Kupffer's vesicle
Authors: Hojo Motoki , Takashima Shigeo , Kobayashi Daisuke , Sumeragi Akira , Shimada Atsuko , Tsukahara Tatsuya , Yokoi Hayato , Narita Takanori , Jindo Tomoko , Kage Takahiro , Kitagawa Tadao , Kimura Tetsuaki , Sekimizu Koshin , Miyake Akimitsu , Setiamarga Davin , Murakami Ryohei , Tsuda Sachiko , Ooki Shinya , Kakihara Ken , Naruse Kiyoshi , Takeda Hiroyuki
Published: August 2010

Recent studies have revealed that a cilium‐generated liquid flow in the node has a crucial role in the establishment of the left‐right (LR) axis in the mouse. In fish, Kupffer's vesicle (KV), a teleost‐specific spherical organ attached to the tail region, is known to have an equivalent role to the mouse node during LR axis formation. However, at present, there has been no report of an asymmetric gene expressed in KV under the control of fluid flow. Here we report the earliest asymmetric gene in teleost KV, medaka charon, and its regulation. Charon is a member of the Cerberus/DAN family of proteins, first identified in zebrafish. Although zebrafish charon was reported to be symmetrically expressed in KV, medaka charon displays asymmetric expression with more intense expression on the right side. This asymmetric expression was found to be regulated by KV flow because symmetric and up‐regulated charon expression was observed in flow‐defective embryos with immotile cilia or disrupted KV. Taken together, medaka charon is a reliable gene marker for LR asymmetry in KV and thus, will be useful for the analysis of the early steps downstream of the fluid flow.
Busulfan‐induced central polydactyly, syndactyly and cleft hand or foot: A common mechanism of disruption leads to divergent phenotypes
Authors: Naruse Takuji , Takahara Masatoshi , Takagi Michiaki , Oberg Kerby C. , Ogino Toshihiko
Published: August 2010

The prevalence of clinical phenotypes that exhibit combinations of central polydactyly, syndactyly, or cleft hand or foot is higher than would be expected for random independent mutations. We have previously demonstrated that maternal ingestion of a chemotherapeutic agent, busulfan, at embryonic day 11 (E11) induces these defects in various combinations in rat embryo limbs. In an effort to determine the mechanism by which busulfan disrupts digital development, we examined cell death by Nile Blue staining and TdT‐mediated dUTP nick end labeling (TUNEL) assays; we also carried out whole mount in situ hybridization for fibroblast growth factor‐8 (Fgf8), bone morphogenetic protein‐4 (Bmp4), and sonic hedgehog (Shh) to examine developmental pathways linked to these defects. In busulfan‐treated embryos, diffuse cell death was evident in both ectoderm and mesoderm, peaking at E13. The increased cell death leads to regression of Fgf8 in the apical ectodermal ridge (AER) and Bmp4 and Shh in the underlying mesoderm. The subsequent pattern of interdigital apoptosis and cartilage condensation was variably disrupted. These results suggest that busulfan manifests its teratogenic effects by inducing cell death of both ectoderm and mesoderm, with an associated reduction in tissue and a disruption in the generation of patterning molecules during critical periods of digit specification.
Analysis of terminal sugar moieties and species‐specificities of acrosome reaction‐inducing substance in Xenopus (ARISX)
Authors: Ueda Yasushi , Imaizumi Chisato , Kubo Hideo , Sato Ken‐ichi , Fukami Yasuo , Iwao Yasuhiro
Published: August 2010

The acrosome reaction of Xenopus sperm is triggered by the acrosome reaction‐inducing substance in Xenopus (ARISX), an oviductal pars recta‐derived, sugar‐rich substance decorated on the entire surface of the vitelline envelope (VE) during ovulation. Here we addressed the functional importance of the sugar moiety in ARISX. Among various lectins examined, soybean agglutinin and Dolichos biflorus agglutinin were shown to abolish the acrosome reaction‐inducing activity of ARISX present in pars recta extract or on the VE, indicating the importance of the terminal α‐N‐acetylgalactosamine residue for the function of ARISX. Consistently, the acrosome reaction‐inducing activity was not affected by proteinase K digestion, in spite of the simultaneous shift of ARISX to a smaller molecular weight. Indirect immunofluorescence microscopic examinations showed that ARISX was distributed as two types of structures on VE; thick fiber‐like materials and thin filamentous materials, and that a new structure appeared on the fertilization envelope instead of the thin filamentous materials. Sperm from several amphibian species were subjected to an in vitro assay during induction of the acrosome reaction with ARISX. The resulting limited population of sperm from a non‐Xenopus species underwent acrosome reaction, implying a weak species‐specificity of ARISX.
Comparative genomics identifies a cis‐regulatory module that activates transcription in specific subsets of neurons in Ciona intestinalis larvae
Authors: Yoshida Reiko , Horie Takeo , Tsuda Motoyuki , Kusakabe Takehiro G.
Published: August 2010

The larval nervous system of the ascidian Ciona intestinalis exhibits an abstract form of the vertebrate nervous system. The Ci‐Gαi1 gene, which encodes a G‐protein α subunit, is specifically expressed in distinct sets of neurons in C. intestinalis larvae, including papillar neurons of the adhesive organ, ocellus photoreceptor cells, and cholinergic and GABAergic neurons in the central nervous system (CNS). A GFP reporter gene driven by the 4.2‐kb 5′ flanking region of Ci‐Gαi1 recapitulated the endogenous gene expression patterns. Comparative genomic analysis of the Gαi1 gene between C. intestinalis and Ciona savignyi identified an 87‐bp highly conserved non‐coding sequence located between –3176 and –3090 bp upstream of the gene. Deletion of this conserved upstream sequence resulted in the complete loss of reporter expression in the central nervous system, while reporter expression in the adhesive organ and mesenchyme cells remained unaffected. The conserved upstream sequence can activate gene expression from basal promoters in the brain vesicle, although it requires additional cis‐regulatory sequences to fully activate the CNS‐specific gene expression. These results suggest that different types of central neurons share a common transcriptional activation mechanism that is different from that of papillar neurons.
Women and Class – A Problematic Relationship?
Authors: Charles Nicola
Published: August 2010

The relationship between gender and class is important and controversial within sociology and has significant theoretical and political dimensions. But how do women experience class? Is it a meaningful dimension of everyday life The experiential aspects of class were explored with two hundred women, A third of them perceived social class m terms perceived of income. Others perceived it in terms of occupation their parents. their partner's or their own type of housing or the need to work to earn a living These different perceptions relate to women's own occupational class and educational background more closely than they relate to the occupational class of their partners. Women occupied full-time as housewives did not appear to differ from those m full or part-time paid employment m terms of their perceptions of class, nor did they experience their situation as marginal to the class structure of society. Although women's class does count there arc problems with assigning individual women to classes solely on the basis of their current position in the occupational hierarchy.
Professions and Powerlessness: Female Marginality in the Learned Occupations
Authors: Atkinson Paul , Delamont Sara
Published: August 2010

This paper argues that the existing sociological literature on the learned professions and on scientific occupations has developed in ways that are now theoretically unproductive. One sympton of this dead-end is the failure of sociologists of the professions to include research on scientists in their discussions and vice versa. A second symptom is the lack of attention to the implications of the work of Jamous, Peloille. and Bourdieu in both the sociology of scientists and of professions. The third symptom of the malaise is the failure to generate sociologically plausible explanations for the marginalisation of female entrants to science and the professions. The paper argues that a novel direction for sociological argument can be derived by remedying the three symptoms simultaneously.
Female Marital Mobility within Northern Ireland and the Republic of Ireland: A Log-Linear Analysis
Authors: Miller Robert L. , Hayes Bernadette C.
Published: August 2010

A series of log-linear models predicting the exchange marital experiences of Irish wives are prevented for the Irish Republic. The best explanatory model is one in which the relationship between a husband's occupational status and that of his father-in-law remains homogeneous across age levels, Women show a marked propensity to marry husbands at a similar occupational status as that of their fathers and long-range upward or downward mobility across the manual/nonmanual divide is unlikely. This tendency towards endogamy is particularly pronounced within the two upper non-manual categories and the manual strata generally the same general model of homogeneous association holds for Northern Ireland across age levels and religious affiliation. In the North, however, more short-range mobility occurs, particularly between the two upper non-manual groups. Despite this the norm for both the Irish Republic and Northern Ireland is marital immobility rather than marital mobility with no evidence of a fundamental trend towards increased marital mobility. Furthermore. The mobility through marriage that did occur does not result in an overall net advantage for women.
Divorce, Remarriage and Family Obligations
Authors: Finch Janet , Mason Jennifer
Published: August 2010

This article is concerned with relationships between adult kin following divorce, and especially those relationships between former in-laws. Questions are raised about the circumstances under which these continue, the extent to which they provide the basis for practical assistance, and how far the continuation of such relationships after divorce is seen as normatively appropriate. Data from a study of family obligations are used to discuss these questions. The authors conclude that the continuation of close supportive relationships can happen, but that this is both rare and unpredictable. Where it does occur, it is as much a product of the history of the relationships between the individuals concerned, as of their genealogical locations in relation to each other. Therefore it cannot be assumed that ex in-law relationships could represent a reliable basis for practical support. However, where supportive relationships do continue they are welcomed by the participants and the situation is widely approved of at a normative level.
The Adult Mother/Daughter Relationship: A Uniquely and Universally Close Relationship?
Authors: O'Connor Pat
Published: August 2010

Despite developments in the sociology of welfare and in feminism, the examination of young adult mother/daughter relationships has been relatively neglected. Such relationships are still popularly seen as ‘very close’, although studies such as Brannen and Collard's (1982) have shown that they are not intimate. In this paper the content and quality of such mother/daughter relationships is examined using a small scale intensive study of sixty married or cohabiting women randomly selected from medical records in north London. Their relationships with their mothers were typically characterised by high levels of visual contact, felt attachment and identity enhancement. The majority of the women did not see their relationships with their mother as very close. Furthermore, even those who did see them in this way, did not have relationships characterised by high levels of practical help, dependency or intimacy. In arguing that mother/daughter relationships are neither universally nor uniquely close, such relationships are juxtaposed with relationships with sisters who were identified as very close. Finally it is argued that the continued popular perception of mother/daughter relationships as very close reflects current definitions of feminity; the idealization of the mother role and an equation between closeness and tending.
Industrial Injuries in British Manufacturing Industry
Authors: Tombs Steve
Published: August 2010

This paper begins by considering the effects of the business cycle upon the incidence of industrial accidents in British manufacturing industries, arguing that a generalized discussion of such cycles obscures important aspects of the political economy within individual cycles. In particular, the strength of the labour movement is related to the incidence of accidents at work. Since the trade unions are only one part of the tripartite system of the legal regulation of safety in British manufacturing industries, the paper goes on to consider the effects of recent material and ideological initiatives on the part of both the government and employers upon the ability of the Health and Safety Executive in general and the Factory Inspectorate in particular, to fulfil their role in this tripartite system of self-regulation. As a result of weakened trade unions and emasculated regulatory agencies, it is argued that there has been a virtual demise of this system of self-regulation. While the analysis outlined does not suggest that this demise is causal of the decline in safety performance across much of British manufacturing industry in the present decade, the paper does argue that the role of the law and its (non) implementation is not an insignificant factor in explaining this decline.
Culture and Community: Drink and Soft Drugs in Hebridean Youth Culture
Authors: Dean Alan
Published: August 2010

This paper discusses the way in which ideas about deviance and thus moral judgements are ultimately grounded within native culture. Through focusing on underage drinking and soft drug use in the Western Isles of Scotland an analysis is presented which seeks to unfold the relationship between tradition, morality and belonging.
Factors in the Length of Stay of Homeless Families in Temporary Accommodation
Authors: Kelly Elinor , Mitchell J. Clyde , Smith Susan J.
Published: August 2010

Data relating to 526 homeless families in temporary accommodation were collected in a study directed mainly to the examination of support networks of a sample of these families. The data, however, have allowed the authors to examine the effects of certain characteristics of these families on the average length of stay in temporary accommodation before they were housed permanently. Log-linear analysis was used to establish the independent effect of various attributes available from the data. In general the feature which seemed to influence the length of stay most was the time of the year when the family was admitted into temporary accommodation followed by the sort of reason the families gave for being homeless at the time of admission. Those who had been illegally evicted tended to take longer to be rehoused whilst those with rental or tenant difficulties took less time to be rehoused. The authors are then able to produce profiles based on this analysis of those families which are likely to stay longest in temporary accommodation as against those likely to stay the shortest time.
The Road to Functional Flexibility: White Collar Work and Employment Relations in a Privatised Public Utility
Authors: Davidson Julia O'Connell
Published: August 2010

This paper is concerned with the changing nature of office work in one region of a privatised public utility, which will be referred to as National Utility (NU). It describes how clerical work at NU, traditionally characterised by a detailed division of labour and functional specialism, is being transformed by the introduction of on-line processing and multi-functional team-working. At the same time, NU management is seeking to change the nature and pattern of clerical employment. The intention is to increase the ratio of part time to full time staff, to increase the ‘personal accountability’ of staff, and to move towards a performance-based, rather than a seniority-based, pay and promotion structure.

These changes are of some broader theoretical significance. As Batstone et al. (1987) note, much industrial sociology literature has focused on job content as the primary determinant of a number of features of work and employment, including worker autonomy, supervisory styles, and management control strategies. Indeed, much recent industrial sociology, management and institutional economics literature has tended to link employment patterns and conditions, as a whole, with job content, in a direct and unproblematic fashion. In particular, it is often assumed that in order to secure multiple skills, high quality work and the innovative capacities of labour, employers will have to offer not only better pay, but also a better package of conditions, job security, fringe benefits and training and promotion opportunities. Developments at National Utility suggest that the link between job content and employment relations may be weaker than has sometimes been implied, and cast doubt on the theoretical basis for ‘post-Fordist’ confidence in the emergence of a new deal for labour as a result of flexible methods of work organisation.